Anisotropy of the fluorine chemical shift tensor in UF6
International Nuclear Information System (INIS)
An 19F magnetic resonance study of polycrystalline UF6 is presented. The low temperature complex line can be analyzed as the superposition of two distinct lines, which is attributed to a distortion of the UF6 octahedron in the solid. The shape of the two components is studied. Their width is much larger than the theoretical dipolar width, and must be explained by large anisotropies of the fluorine chemical shift tensors. The resulting shape functions of the powder spectra are determined. The values of the parameters of the chemical shift tensors yield estimates of the characters of the U-F bonds, and this gives some information on the ground state electronic wave function of the UF6 molecule in the solid. (author)
Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy
Energy Technology Data Exchange (ETDEWEB)
Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy, E-mail: ramamoor@umich.edu [Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055 (United States)
2015-10-14
Proton NMR spectroscopy in the solid state has recently attracted much attention owing to the significant enhancement in spectral resolution afforded by the remarkable advances in ultrafast magic angle spinning (MAS) capabilities. In particular, proton chemical shift anisotropy (CSA) has become an important tool for obtaining specific insights into inter/intra-molecular hydrogen bonding. However, even at the highest currently feasible spinning frequencies (110–120 kHz), {sup 1}H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong {sup 1}H–{sup 1}H homonuclear dipolar couplings and narrow {sup 1}H chemical shift (CS) ranges, which render it difficult to determine the CSA of specific proton sites in the standard CSA/single-quantum (SQ) chemical shift correlation experiment. Herein, we propose a three-dimensional (3D) {sup 1}H double-quantum (DQ) chemical shift/CSA/SQ chemical shift correlation experiment to extract the CS tensors of proton sites whose signals are not well resolved along the single-quantum chemical shift dimension. As extracted from the 3D spectrum, the F1/F3 (DQ/SQ) projection provides valuable information about {sup 1}H–{sup 1}H proximities, which might also reveal the hydrogen-bonding connectivities. In addition, the F2/F3 (CSA/SQ) correlation spectrum, which is similar to the regular 2D CSA/SQ correlation experiment, yields chemical shift anisotropic line shapes at different isotropic chemical shifts. More importantly, since the F2/F1 (CSA/DQ) spectrum correlates the CSA with the DQ signal induced by two neighboring proton sites, the CSA spectrum sliced at a specific DQ chemical shift position contains the CSA information of two neighboring spins indicated by the DQ chemical shift. If these two spins have different CS tensors, both tensors can be extracted by numerical fitting. We believe that this robust and elegant single-channel proton-based 3D experiment provides useful atomistic
Alkan, Fahri; Dybowski, C
2015-10-14
Cluster models are used in calculation of (207)Pb NMR magnetic-shielding parameters of α-PbO, β-PbO, Pb3O4, Pb2SnO4, PbF2, PbCl2, PbBr2, PbClOH, PbBrOH, PbIOH, PbSiO3, and Pb3(PO4)2. We examine the effects of cluster size, method of termination of the cluster, charge on the cluster, introduction of exact exchange, and relativistic effects on calculation of magnetic-shielding tensors with density functional theory. Proper termination of the cluster for a network solid, including approximations such as compensation of charge by the bond-valence (BV) method, is essential to provide results that agree with experiment. The inclusion of relativistic effects at the spin-orbit level for such heavy nuclei is an essential factor in achieving agreement with experiment. PMID:26345261
International Nuclear Information System (INIS)
R. Blinc et al. have made an initial study of polycrystalline uranium hexafluoride using the magnetic resonance of fluorine at 40 Mc/s. The low-temperattire spectrum (t 6 octahedron has one long axis and two short axes, the fluorine atoms are divided among two different types of site. The change in the spectrum with temperature (coalescence of the two lines) suggests movement of the fluorine atoms between the two types of site. By repeating these experiments at 56.4 Mc/s and 94 Mc/s, we have been able to demonstrate the existence of considerable axial anisotropy of the chemical shift tensor (about 650 ppm). The absorption line obtained for a powder in these conditions is complex, and to study it we must envisage a line-shape function f(h), which is the probability that a grain of powder is so orientated that it resonates for the value h of the field. In the absence of movement (low-temperature spectrum) the line-shape function for each of the two lines (corresponding to the two types of site) is of the form obtained for equivalent atoms. It is known that the parameters of chemical shift tensors give information on chemical bond character. We are thus led, for example, to attribute a considerable ionic character (I ≃ 1/2) to the bonds between the uranium and the two most distant fluorine atoms. In the presence of movement the line-shape function is very different, and depends on the type of movement. For UF6, study of the shape of the single line (t > 20°C) in cases where we have anisotropy, shows that the fluorine atoms of the same molecule interchange with each other, each atom remaining in each of the positions for about 5 μsec at 30°C, with an activation energy of about 0.5 eV. (author)
Protein Chemical Shift Prediction
Larsen, Anders S
2014-01-01
The protein chemical shifts holds a large amount of information about the 3-dimensional structure of the protein. A number of chemical shift predictors based on the relationship between structures resolved with X-ray crystallography and the corresponding experimental chemical shifts have been developed. These empirical predictors are very accurate on X-ray structures but tends to be insensitive to small structural changes. To overcome this limitation it has been suggested to make chemical shift predictors based on quantum mechanical(QM) calculations. In this thesis the development of the QM derived chemical shift predictor Procs14 is presented. Procs14 is based on 2.35 million density functional theory(DFT) calculations on tripeptides and contains corrections for hydrogen bonding, ring current and the effect of the previous and following residue. Procs14 is capable at performing predictions for the 13CA, 13CB, 13CO, 15NH, 1HN and 1HA backbone atoms. In order to benchmark Procs14, a number of QM NMR calculatio...
Monitoring the refinement of crystal structures with 15N solid-state NMR shift tensor data
International Nuclear Information System (INIS)
The 15N chemical shift tensor is shown to be extremely sensitive to lattice structure and a powerful metric for monitoring density functional theory refinements of crystal structures. These refinements include lattice effects and are applied here to five crystal structures. All structures improve based on a better agreement between experimental and calculated 15N tensors, with an average improvement of 47.0 ppm. Structural improvement is further indicated by a decrease in forces on the atoms by 2–3 orders of magnitude and a greater similarity in atom positions to neutron diffraction structures. These refinements change bond lengths by more than the diffraction errors including adjustments to X–Y and X–H bonds (X, Y = C, N, and O) of 0.028 ± 0.002 Å and 0.144 ± 0.036 Å, respectively. The acquisition of 15N tensors at natural abundance is challenging and this limitation is overcome by improved 1H decoupling in the FIREMAT method. This decoupling dramatically narrows linewidths, improves signal-to-noise by up to 317%, and significantly improves the accuracy of measured tensors. A total of 39 tensors are measured with shifts distributed over a range of more than 400 ppm. Overall, experimental 15N tensors are at least 5 times more sensitive to crystal structure than 13C tensors due to nitrogen’s greater polarizability and larger range of chemical shifts
Energy Technology Data Exchange (ETDEWEB)
Walder, Brennan J.; Davis, Michael C.; Grandinetti, Philip J. [Department of Chemistry, Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210 (United States); Dey, Krishna K. [Department of Physics, Dr. H. S. Gour University, Sagar, Madhya Pradesh 470003 (India); Baltisberger, Jay H. [Division of Natural Science, Mathematics, and Nursing, Berea College, Berea, Kentucky 40403 (United States)
2015-01-07
A new two-dimensional Nuclear Magnetic Resonance (NMR) experiment to separate and correlate the first-order quadrupolar and chemical/paramagnetic shift interactions is described. This experiment, which we call the shifting-d echo experiment, allows a more precise determination of tensor principal components values and their relative orientation. It is designed using the recently introduced symmetry pathway concept. A comparison of the shifting-d experiment with earlier proposed methods is presented and experimentally illustrated in the case of {sup 2}H (I = 1) paramagnetic shift and quadrupolar tensors of CuCl{sub 2}⋅2D{sub 2}O. The benefits of the shifting-d echo experiment over other methods are a factor of two improvement in sensitivity and the suppression of major artifacts. From the 2D lineshape analysis of the shifting-d spectrum, the {sup 2}H quadrupolar coupling parameters are 〈C{sub q}〉 = 118.1 kHz and 〈η{sub q}〉 = 0.88, and the {sup 2}H paramagnetic shift tensor anisotropy parameters are 〈ζ{sub P}〉 = − 152.5 ppm and 〈η{sub P}〉 = 0.91. The orientation of the quadrupolar coupling principal axis system (PAS) relative to the paramagnetic shift anisotropy principal axis system is given by (α,β,γ)=((π)/2 ,(π)/2 ,0). Using a simple ligand hopping model, the tensor parameters in the absence of exchange are estimated. On the basis of this analysis, the instantaneous principal components and orientation of the quadrupolar coupling are found to be in excellent agreement with previous measurements. A new point dipole model for predicting the paramagnetic shift tensor is proposed yielding significantly better agreement than previously used models. In the new model, the dipoles are displaced from nuclei at positions associated with high electron density in the singly occupied molecular orbital predicted from ligand field theory.
Effects of tensors coupling to Dirac equation with shifted Hulthen potential via SUSYQM
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Akpan N. Ikot
2015-10-01
Full Text Available The Dirac equation with shifted Hulthen potential in the presence of the Yukawa-like tensor (YLT and generalized tensor (GLT interactions using supersymmetric quantum mechanics (SUSYQM is presented. The bound state energy spectra and the radial wave functions have been approximately obtained in the case of spin and pseudospin symmetries. We have also reported some numerical results and figures to show the effect of the tensor interactions. Furthermore, scattering state solution under the generalized tensor (GLT interaction is reported.
International Nuclear Information System (INIS)
The authors present calculations of NMR chemical shifts in crystalline phases of some representative amino acids such as glycine, alanine, and alanyl-alanine. To get an insight on how different environments affect the chemical shifts, they study the transition from the crystalline phase to completely isolated molecules of glycine. In the crystalline limit, the shifts are dominated by intermolecular hydrogen-bonds. In the molecular limit, however, dipole electric field effects dominate the behavior of the chemical shifts. They show that it is necessary to average the chemical shifts in glycine over geometries. Tensor components are analyzed to get the angle dependent proton chemical shifts, which is a more refined characterization method
A Short History of Three Chemical Shifts
Nagaoka, Shin-ichi
2007-01-01
A short history of chemical shifts in nuclear magnetic resonance (NMR), electron spectroscopy for chemical analysis (ESCA) and Mossbauer spectroscopy, which are useful for chemical studies, is described. The term chemical shift is shown to have originated in the mistaken assumption that nuclei of a given element would all undergo resonance at the…
Geometric effects on carbon-13 chemical shifts
International Nuclear Information System (INIS)
In the course of our investigations on carbon-13 chemical shifts of tetracyclic dodecanes, we managed to show that a large number of chemical shift differences between members of the series and models provided by bicyclic analogs could be attributed to steric effects. There are examples, however, where this is clearly not the case. In order to investigate apparent anomalies we calculated structures of interest and looked into the relationships between molecular geometry and chemical shifts. As the assignment of some of the key structures in these analysis were made by comparison with model compounds and crucial experiments that could remove ambiguities were missing, we prepared and interpreted two spectra which are presented
MR chemical shift imaging of human atheroma
International Nuclear Information System (INIS)
The lipid content of atheromatous plaques has been measured with chemical shift MR imaging by taking advantage of the different resonance frequencies of protons in lipid and water. Fifteen postmortem aortic specimens of the human descending aorta and the aortae of seven patients with documented peripheral vascular disease were studied at 0.5 T. Spin-echo images were used to localize the lesions before acquisition of the chemical shift images. The specimens were examined histologically, and the lipid distribution in the plaque showed good correlation with the chemical shift data. Validation in vivo and clinical applications remain to be established
Pulse NMR in solids: chemical shift, lead fluoride, and thorium hydride
International Nuclear Information System (INIS)
The fluorine chemical shift of a single crystal CaF2 was measured up to 4 kilobar at room temperature using multiple pulse NMR. The pressure dependence of the shift is found to be --1.7 +- 1 ppM/kbar, while an overlap model predicts a shift of --0.46 ppM/kbar.The chemical shift tensor is separated into ''geometrical'' and ''chemical'' contributions, and comparison of the proposed model calculations with recent data on hydroxyl proton chemical shift tensors shows that the geometrical portion accounts for the qualitative features of the measured tensors. A study of fluoride ion motion in β-PbF2 doped with NaF was conducted by measurement of the 19F transverse relaxation time (T2), spin lattice relaxation time (T1) and the spin lattice relaxation time in the rotating frame (T/sub 1r). Two samples of Th4H15, prepared under different conditions but both having the proper ratio of H/Th (to within 1 percent), were studied. The structure of the Th4H15 suggested by x-ray measurements is confirmed through a moment analysis of the rigid lattice line shape
Accessible surface area from NMR chemical shifts
Energy Technology Data Exchange (ETDEWEB)
Hafsa, Noor E.; Arndt, David; Wishart, David S., E-mail: david.wishart@ualberta.ca [University of Alberta, Department of Computing Science (Canada)
2015-07-15
Accessible surface area (ASA) is the surface area of an atom, amino acid or biomolecule that is exposed to solvent. The calculation of a molecule’s ASA requires three-dimensional coordinate data and the use of a “rolling ball” algorithm to both define and calculate the ASA. For polymers such as proteins, the ASA for individual amino acids is closely related to the hydrophobicity of the amino acid as well as its local secondary and tertiary structure. For proteins, ASA is a structural descriptor that can often be as informative as secondary structure. Consequently there has been considerable effort over the past two decades to try to predict ASA from protein sequence data and to use ASA information (derived from chemical modification studies) as a structure constraint. Recently it has become evident that protein chemical shifts are also sensitive to ASA. Given the potential utility of ASA estimates as structural constraints for NMR we decided to explore this relationship further. Using machine learning techniques (specifically a boosted tree regression model) we developed an algorithm called “ShiftASA” that combines chemical-shift and sequence derived features to accurately estimate per-residue fractional ASA values of water-soluble proteins. This method showed a correlation coefficient between predicted and experimental values of 0.79 when evaluated on a set of 65 independent test proteins, which was an 8.2 % improvement over the next best performing (sequence-only) method. On a separate test set of 92 proteins, ShiftASA reported a mean correlation coefficient of 0.82, which was 12.3 % better than the next best performing method. ShiftASA is available as a web server ( http://shiftasa.wishartlab.com http://shiftasa.wishartlab.com ) for submitting input queries for fractional ASA calculation.
Accessible surface area from NMR chemical shifts
International Nuclear Information System (INIS)
Accessible surface area (ASA) is the surface area of an atom, amino acid or biomolecule that is exposed to solvent. The calculation of a molecule’s ASA requires three-dimensional coordinate data and the use of a “rolling ball” algorithm to both define and calculate the ASA. For polymers such as proteins, the ASA for individual amino acids is closely related to the hydrophobicity of the amino acid as well as its local secondary and tertiary structure. For proteins, ASA is a structural descriptor that can often be as informative as secondary structure. Consequently there has been considerable effort over the past two decades to try to predict ASA from protein sequence data and to use ASA information (derived from chemical modification studies) as a structure constraint. Recently it has become evident that protein chemical shifts are also sensitive to ASA. Given the potential utility of ASA estimates as structural constraints for NMR we decided to explore this relationship further. Using machine learning techniques (specifically a boosted tree regression model) we developed an algorithm called “ShiftASA” that combines chemical-shift and sequence derived features to accurately estimate per-residue fractional ASA values of water-soluble proteins. This method showed a correlation coefficient between predicted and experimental values of 0.79 when evaluated on a set of 65 independent test proteins, which was an 8.2 % improvement over the next best performing (sequence-only) method. On a separate test set of 92 proteins, ShiftASA reported a mean correlation coefficient of 0.82, which was 12.3 % better than the next best performing method. ShiftASA is available as a web server ( http://shiftasa.wishartlab.com http://shiftasa.wishartlab.com ) for submitting input queries for fractional ASA calculation
Random coil chemical shift for intrinsically disordered proteins
DEFF Research Database (Denmark)
Kjærgaard, Magnus; Brander, Søren; Poulsen, Flemming Martin
2011-01-01
Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins. The quality of the secondary chemical shifts is dependent on an appropriate choice of random coil chemical shifts. We report random coil chemical....... Temperature has a non-negligible effect on the (13)C random coil chemical shifts, so temperature coefficients are reported for the random coil chemical shifts to allow extrapolation to other temperatures. The pH dependence of the histidine random coil chemical shifts is investigated in a titration series...
Protein Structure Determination Using Chemical Shifts
DEFF Research Database (Denmark)
Christensen, Anders Steen
In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes che...... residues. For Rhodopsin (225 residues) a structure is found at 2.5 Å CA-RMSD from the experimental X-ray structure, and a structure is determined for the Savinase protein (269 residues) with 2.9 Å CA-RMSD from the experimental X-ray structure....
Mai, W.; Hu, W; Wang, C; Cross, T A
1993-01-01
Chemical shifts observed from samples that are uniformly aligned with respect to the magnetic field can be used as very high-resolution structural constraints. This constraint takes the form of an orientational constraint rather than the more familiar distance constraint. The accuracy of these constraints is dependent upon the quality of the tensor characterization. Both tensor element magnitudes and tensor orientations with respect to the molecular frame need to be considered. Here these con...
Chemical shift MR imaging of the skin
International Nuclear Information System (INIS)
MR imaging with conventional spin-echo pulse sequences has not found wide application in the evaluation of skin pathology. This paper reports that this study was designed to determine the value of chemical shift imaging (CSI) compared with conventional pulse sequences for the noninvasive evaluation of connective tissue and neoplastic disease of the skin and underlying fascia. The studies were acquired in patients and volunteers on a whole-body system at 1.5 T and small surface coils. Comparisons were made between T1- and T2-weighted gradient-echo, spin-echo, and hybrid lipid and water-suppressed CSI series (Chopper-Dixon combined with frequency-selective pulse). CSI improves detail in the hypodermis by eliminating unwanted (lipid) signal and chemical shift misregistration artifact. The detail of water-based signal is improved in the deeper layers of the skin by improved tissue contrast and elimination of the disturbing adjacent dominant fat-based signal. MR imaging has the potential to provide information that can complement skin biopsy. A more optimal choice of pulse sequences can improve the sensitivity of MR imaging to water-based pathology and allow noninvasive visualization of deep layers. The CSI sequences may be useful in the evaluation of infiltrative and neoplastic disease of the skin, particularly as they are adapted into microimaging methods with local gradient coils
Halbert, Stéphanie; Copéret, Christophe; Raynaud, Christophe; Eisenstein, Odile
2016-02-24
The nucleophilic carbon of d(0) Schrock alkylidene metathesis catalysts, [M] = CHR, display surprisingly low downfield chemical shift (δiso) and large chemical shift anisotropy. State-of-the-art four-component relativistic calculations of the chemical shift tensors combined with a two-component analysis in terms of localized orbitals allow a molecular-level understanding of their orientations, the magnitude of their principal components (δ11 > δ22 > δ33) and associated δiso. This analysis reveals the dominating influence of the paramagnetic contribution yielding a highly deshielded alkylidene carbon. The largest paramagnetic contribution, which originates from the coupling of alkylidene σMC and π*MC orbitals under the action of the magnetic field, is analogous to that resulting from coupling σCC and π*CC in ethylene; thus, δ11 is in the MCH plane and is perpendicular to the MC internuclear direction. The higher value of carbon-13 δiso in alkylidene complexes relative to ethylene is thus due to the smaller energy gap between σMC and π*MC vs this between σCC and π*CC in ethylene. This effect also explains why the highest value of δiso is observed for Mo and the lowest for Ta, the values for W and Re being in between. In the presence of agostic interaction, the chemical shift tensor principal components orientation (δ22 or δ33 parallel or perpendicular to πMX) is influenced by the MCH angle because it determines the orientation of the alkylidene CHR fragment relative to the MC internuclear axis. The orbital analysis shows how the paramagnetic terms, understood with a localized bond model, determine the chemical shift tensor and thereby δiso. PMID:26787258
Costanzo, G. A.; Micalizio, S.; Godone, A.; Camparo, J. C.; Levi, F.
2016-06-01
The ac Stark shift, or light shift, is a physical phenomenon that plays a fundamental role in many applications ranging from basic atomic physics to applied quantum electronics. Here, we discuss experiments testing light-shift theory in a cold-atom cesium fountain clock for the Cs D2 transition (i.e., 6 2S1 /2→6 2P3 /2 at 852 nm). Cold-atom fountains represent a nearly ideal system for the study of light shifts: (1) The atoms can be perturbed by a field of arbitrary character (e.g., coherent field or nonclassical field); (2) there are no trapping fields to complicate data interpretation; (3) the probed atoms are essentially motionless in their center-of-mass reference frame, T ˜ 1 μK; and (4) the atoms are in an essentially collisionless environment. Moreover, in the present work the resolution of the Cs excited-state hyperfine splittings implies that the D2 ac Stark shift contains a nonzero tensor polarizability contribution, which does not appear in vapor phase experiments due to Doppler broadening. Here, we test the linearity of the ac Stark shift with field intensity, and measure the light shift as a function of field frequency, generating a "light-shift curve." We have improved on the previous best test of theory by a factor of 2, and after subtracting the theoretical scalar light shift from the experimental light-shift curves, we have isolated and tested the tensor light shift for an alkali D2 transition.
Further conventions for NMR shielding and chemical shifts (IUPAC Recommendations 2008)
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Harris, R.K. [University of Durham, Durham (United Kingdom). Dept. of Chemistry; Becker, E.D. [National Institutes of Health, Bethesda, MD (United States); Menezes, S.M. Cabral de [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas (CENPES); Granger, P. [University Louis Pasteur, Strasbourg (France). Inst. of Chemistry; Hoffman, R.E. [The Hebrew University of Jerusalem, Safra Campus, Jerusalem (Israel). Dept. of Organic Chemistry; Zilm, K.W., E-mail: r.k.harris@durham.ac.uk [Yale University, New Haven, CT (United States). Dept. of Chemistry
2008-07-01
IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem. 73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the {sup 1}H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3- (trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a part per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating {sup 13}C NMR chemical shifts in solids to the scales used for high resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids are reviewed in some detail, and recommendations are given for best practice. (author)
Further conventions for NMR shielding and chemical shifts (IUPAC Recommendations 2008)
International Nuclear Information System (INIS)
IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem. 73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the 1H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3- (trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a part per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating 13C NMR chemical shifts in solids to the scales used for high resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids are reviewed in some detail, and recommendations are given for best practice. (author)
International Nuclear Information System (INIS)
We describe a probabilistic model for deriving, from the database of assigned chemical shifts, a set of random coil chemical shift values that are 'unbiased' insofar as contributions from detectable secondary structure have been minimized (RCCSu). We have used this approach to derive a set of RCCSu values for 13Cα and 13Cβ for 17 of the 20 standard amino acid residue types by taking advantage of the known opposite conformational dependence of these parameters. We present a second probabilistic approach that utilizes the maximum entropy principle to analyze the database of 13Cα and 13Cβ chemical shifts considered separately; this approach yielded a second set of random coil chemical shifts (RCCSmax-ent). Both new approaches analyze the chemical shift database without reference to known structure. Prior approaches have used either the chemical shifts of small peptides assumed to model the random coil state (RCCSpeptide) or statistical analysis of chemical shifts associated with structure not in helical or strand conformation (RCCSstruct-stat). We show that the RCCSmax-ent values are strikingly similar to published RCCSpeptide and RCCSstruct-stat values. By contrast, the RCCSu values differ significantly from both published types of random coil chemical shift values. The differences (RCCSpeptide-RCCSu) for individual residue types show a correlation with known intrinsic conformational propensities. These results suggest that random coil chemical shift values from both prior approaches are biased by conformational preferences. RCCSu values appear to be consistent with the current concept of the 'random coil' as the state in which the geometry of the polypeptide ensemble samples the allowed region of (φ,ψ)-space in the absence of any dominant stabilizing interactions and thus represent an improved basis for the detection of secondary structure. Coupled with the growing database of chemical shifts, this probabilistic approach makes it possible to refine
Probabilistic validation of protein NMR chemical shift assignments
International Nuclear Information System (INIS)
Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data. ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/ http://areca.nmrfam.wisc.edu/
Probabilistic validation of protein NMR chemical shift assignments
Energy Technology Data Exchange (ETDEWEB)
Dashti, Hesam [University of Wisconsin-Madison, Graduate Program in Biophysics, Biochemistry Department (United States); Tonelli, Marco; Lee, Woonghee; Westler, William M.; Cornilescu, Gabriel [University of Wisconsin-Madison, Biochemistry Department, National Magnetic Resonance Facility at Madison (United States); Ulrich, Eldon L. [University of Wisconsin-Madison, BioMagResBank, Biochemistry Department (United States); Markley, John L., E-mail: markley@nmrfam.wisc.edu, E-mail: jmarkley@wisc.edu [University of Wisconsin-Madison, Biochemistry Department, National Magnetic Resonance Facility at Madison (United States)
2016-01-15
Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data. ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/ http://areca.nmrfam.wisc.edu/.
Conformational propensities of intrinsically disordered proteins from NMR chemical shifts
International Nuclear Information System (INIS)
The realization that a protein can be fully functional even in the absence of a stable three-dimensional structure has motivated a large number of studies describing the conformational behaviour of these proteins at atomic resolution. Here, we review recent advances in the determination of local structural propensities of intrinsically disordered proteins (IDPs) from experimental NMR chemical shifts. A mapping of the local structure in IDPs is of paramount importance in order to understand the molecular details of complex formation, in particular, for IDPs that fold upon binding or undergo structural transitions to pathological forms of the same protein. We discuss experimental strategies for the spectral assignment of IDPs, chemical shift prediction algorithms and the generation of representative structural ensembles of IDPs on the basis of chemical shifts. Additionally, we highlight the inherent degeneracies associated with the determination of IDP sub-state populations from NMR chemical shifts alone. (authors)
Phase-shift analysis of NN scattering below 160 MeV: Indication for a strong tensor force
International Nuclear Information System (INIS)
A new phase-shift analysis of NN scattering in the energy range 15--160 MeV is presented. The analysis is based on the carefully reviewed world pp+np data, including recent results for higher-order spin observables in n-p scattering. The latter are essential to determine the mixing parameter var-epsilon 1 which is directly related to the isoscalar tensor force. var-epsilon 1 displays a high trend, in agreement with recent analyses above 140 MeV, and is only reproduced by potential models with a strong tensor force. The prediction of the full Bonn potential is too low by 20% for energies above 40 MeV. All other I=0 phase shifts show agreement with potential models; in particular, the notorious problem with 1P1 around 50 MeV has disappeared. Around 25 MeV a ten parameter fit based purely on np data agrees with the corresponding fit to the pp data and reveals no indication of anomalous charge independence breaking
Energy Technology Data Exchange (ETDEWEB)
Mielke, S.P.; Krishnan, V.V. [Biophysics Graduate Group, University of California, Davis (United States)], E-mail: krish@llnl.gov
2004-10-15
Random coil chemical shifts are commonly used to detect protein secondary structural elements in chemical shift index (CSI) calculations. Though this technique is widely used and seems reliable for folded proteins, the choice of reference random coil chemical shift values can significantly alter the outcome of secondary structure estimation. In order to evaluate these effects, we present a comparison of secondary structure content calculated using CSI, based on five different reference random coil chemical shift value sets, to that derived from three-dimensional structures. Our results show that none of the reference random coil data sets chosen for evaluation fully reproduces the actual secondary structures. Among the reference values generally available to date, most tend to be good estimators only of helices. Based on our evaluation, we recommend the experimental values measured by Schwarzinger et al. (2000), and statistical values obtained by Lukin et al. (1997), as good estimators of both helical and sheet content.
Bayesian inference of protein structure from chemical shift data
DEFF Research Database (Denmark)
Bratholm, Lars Andersen; Christensen, Anders Steen; Hamelryck, Thomas Wim; Jensen, Jan Halborg
2015-01-01
Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model...... chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the......, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction....
Bayesian inference of protein structure from chemical shift data
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Lars A. Bratholm
2015-03-01
Full Text Available Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model, and a bias is introduced which might result in incorrect structures. In the inferential structure determination framework, both the unknown structure and the disagreement between experimental and back-calculated data are formulated as a joint probability distribution, thus utilizing the full information content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the simulations suggests that sampling both the structure and the uncertainties in chemical shift prediction leads more accurate structures compared to conventional methods using empirical determined weights. The Cauchy distribution, using either sampled uncertainties or predetermined weights, did, however, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction.
Counterion influence on chemical shifts in strychnine salts
Energy Technology Data Exchange (ETDEWEB)
Metaxas, Athena E.; Cort, John R.
2013-05-01
The highly toxic plant alkaloid strychnine is often isolated in the form of the anion salt of its protonated tertiary amine. Here we characterize the relative influence of different counterions on 1H and 13C chemical shifts in several strychnine salts in D2O, methanol-d4 (CD3OD) and chloroform-d (CDCl3) solvents. In organic solvents, but not in water, substantial variation in chemical shifts of protons near the tertiary amine was observed among different salts. These secondary shifts reveal differences in the way each anion influences electronic structure within the protonated amine. The distributions of secondary shifts allow salts to be easily distinguished from each other as well as from the free base form. The observed effects are much greater in organic solvents than in water. Slight concentration-dependence in chemical shifts of some protons near the amine was observed for two salts in CDCl3, but this effect is small compared to the influence of the counterion. Distinct chemical shifts in different salt forms of the same compound may be useful as chemical forensic signatures for source attribution and sample matching of alkaloids such as strychnine and possibly other organic acid and base salts.
Counterion influence on chemical shifts in strychnine salts.
Metaxas, Athena E; Cort, John R
2013-05-01
The highly toxic plant alkaloid strychnine is often isolated in the form of the anion salt of its protonated tertiary amine. Here, we characterize the relative influence of different counterions on (1)H and (13)C chemical shifts in several strychnine salts in D2O, methanol-d4 (CD3OD), and chloroform-d (CDCl3) solvents. In organic solvents but not in water, substantial variation in chemical shifts of protons near the tertiary amine was observed among different salts. These secondary shifts reveal differences in the way each anion influences electronic structure within the protonated amine. The distributions of secondary shifts allow salts to be easily distinguished from each other as well as from the free base form. Slight concentration dependence in chemical shifts of some protons near the amine was observed for two salts in CDCl3, but this effect is small compared with the influence of the counterion. Distinct chemical shifts in different salt forms of the same compound may be useful as chemical forensic signatures for source attribution and sample matching of alkaloids such as strychnine and possibly other organic acid and base salts. PMID:23495106
Benchmarks for the 13C NMR chemical shielding tensors in peptides in the solid state
Czernek, Jiří; Pawlak, Tomasz; Potrzebowski, Marek J.
2012-02-01
The benchmark set is proposed, which comprises 126 principal elements of chemical shielding tensors, and the respective isotropic chemical shielding values, of all 42 13C nuclei in crystalline Tyr-D-Ala-Phe and Tyr-Ala-Phe tripeptides with known, but highly dissimilar structures. These data are obtained by both the NMR measurements and the density functional theory in the pseudopotential plane-wave scheme. Using the CASTEP program, several computational strategies are employed, for which the level of agreement between calculations and experiment is established. This set is mainly intended for the validation of methods capable of predicting the 13C NMR parameters in solid-state systems.
Data requirements for reliable chemical shift assignments in deuterated proteins
International Nuclear Information System (INIS)
The information required for chemical shift assignments in large deuterated proteins was investigated using a Monte Carlo approach (Hitchens et al., 2002). In particular, the consequences of missing amide resonances on the reliability of assignments derived from Cα and CO or from Cα and Cβ chemical shifts was investigated. Missing amide resonances reduce both the number of correct assignments as well as the confidence in these assignments. More significantly, a number of undetectable errors can arise when as few as 9% of the amide resonances are missing from the spectra. However, the use of information from residue specific labeling as well as local and long-range distance constraints improves the reliability and extent of assignment. It is also shown that missing residues have only a minor effect on the assignment of protein-ligand complexes using Cα and CO chemical shifts and Cα inter-residue connectivity, provided that the known chemical shifts of the unliganded protein are utilized in the assignment process
Direct solution of the Chemical Master Equation using quantized tensor trains.
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Vladimir Kazeev
2014-03-01
Full Text Available The Chemical Master Equation (CME is a cornerstone of stochastic analysis and simulation of models of biochemical reaction networks. Yet direct solutions of the CME have remained elusive. Although several approaches overcome the infinite dimensional nature of the CME through projections or other means, a common feature of proposed approaches is their susceptibility to the curse of dimensionality, i.e. the exponential growth in memory and computational requirements in the number of problem dimensions. We present a novel approach that has the potential to "lift" this curse of dimensionality. The approach is based on the use of the recently proposed Quantized Tensor Train (QTT formatted numerical linear algebra for the low parametric, numerical representation of tensors. The QTT decomposition admits both, algorithms for basic tensor arithmetics with complexity scaling linearly in the dimension (number of species and sub-linearly in the mode size (maximum copy number, and a numerical tensor rounding procedure which is stable and quasi-optimal. We show how the CME can be represented in QTT format, then use the exponentially-converging hp-discontinuous Galerkin discretization in time to reduce the CME evolution problem to a set of QTT-structured linear equations to be solved at each time step using an algorithm based on Density Matrix Renormalization Group (DMRG methods from quantum chemistry. Our method automatically adapts the "basis" of the solution at every time step guaranteeing that it is large enough to capture the dynamics of interest but no larger than necessary, as this would increase the computational complexity. Our approach is demonstrated by applying it to three different examples from systems biology: independent birth-death process, an example of enzymatic futile cycle, and a stochastic switch model. The numerical results on these examples demonstrate that the proposed QTT method achieves dramatic speedups and several orders of
Direct solution of the Chemical Master Equation using quantized tensor trains.
Kazeev, Vladimir; Khammash, Mustafa; Nip, Michael; Schwab, Christoph
2014-03-01
The Chemical Master Equation (CME) is a cornerstone of stochastic analysis and simulation of models of biochemical reaction networks. Yet direct solutions of the CME have remained elusive. Although several approaches overcome the infinite dimensional nature of the CME through projections or other means, a common feature of proposed approaches is their susceptibility to the curse of dimensionality, i.e. the exponential growth in memory and computational requirements in the number of problem dimensions. We present a novel approach that has the potential to "lift" this curse of dimensionality. The approach is based on the use of the recently proposed Quantized Tensor Train (QTT) formatted numerical linear algebra for the low parametric, numerical representation of tensors. The QTT decomposition admits both, algorithms for basic tensor arithmetics with complexity scaling linearly in the dimension (number of species) and sub-linearly in the mode size (maximum copy number), and a numerical tensor rounding procedure which is stable and quasi-optimal. We show how the CME can be represented in QTT format, then use the exponentially-converging hp-discontinuous Galerkin discretization in time to reduce the CME evolution problem to a set of QTT-structured linear equations to be solved at each time step using an algorithm based on Density Matrix Renormalization Group (DMRG) methods from quantum chemistry. Our method automatically adapts the "basis" of the solution at every time step guaranteeing that it is large enough to capture the dynamics of interest but no larger than necessary, as this would increase the computational complexity. Our approach is demonstrated by applying it to three different examples from systems biology: independent birth-death process, an example of enzymatic futile cycle, and a stochastic switch model. The numerical results on these examples demonstrate that the proposed QTT method achieves dramatic speedups and several orders of magnitude storage
Freedman, Daniel A.; Roundy, D.; Arias, T. A.
2008-01-01
We present a study of the local strain effects associated with vacancy defects in strontium titanate and report the first calculations of elastic dipole tensors and chemical strains for point defects in perovskites. The combination of local and long-range results will enable determination of x-ray scattering signatures that can be compared with experiments. We find that the oxygen vacancy possesses a special property -- a highly anisotropic elastic dipole tensor which almost vanishes upon ave...
Hartman, Joshua D; Monaco, Stephen; Schatschneider, Bohdan; Beran, Gregory J O
2015-09-14
We assess the quality of fragment-based ab initio isotropic (13)C chemical shift predictions for a collection of 25 molecular crystals with eight different density functionals. We explore the relative performance of cluster, two-body fragment, combined cluster/fragment, and the planewave gauge-including projector augmented wave (GIPAW) models relative to experiment. When electrostatic embedding is employed to capture many-body polarization effects, the simple and computationally inexpensive two-body fragment model predicts both isotropic (13)C chemical shifts and the chemical shielding tensors as well as both cluster models and the GIPAW approach. Unlike the GIPAW approach, hybrid density functionals can be used readily in a fragment model, and all four hybrid functionals tested here (PBE0, B3LYP, B3PW91, and B97-2) predict chemical shifts in noticeably better agreement with experiment than the four generalized gradient approximation (GGA) functionals considered (PBE, OPBE, BLYP, and BP86). A set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided based on these benchmark calculations. Statistical cross-validation procedures are used to demonstrate the robustness of these fits. PMID:26374002
International Nuclear Information System (INIS)
We assess the quality of fragment-based ab initio isotropic 13C chemical shift predictions for a collection of 25 molecular crystals with eight different density functionals. We explore the relative performance of cluster, two-body fragment, combined cluster/fragment, and the planewave gauge-including projector augmented wave (GIPAW) models relative to experiment. When electrostatic embedding is employed to capture many-body polarization effects, the simple and computationally inexpensive two-body fragment model predicts both isotropic 13C chemical shifts and the chemical shielding tensors as well as both cluster models and the GIPAW approach. Unlike the GIPAW approach, hybrid density functionals can be used readily in a fragment model, and all four hybrid functionals tested here (PBE0, B3LYP, B3PW91, and B97-2) predict chemical shifts in noticeably better agreement with experiment than the four generalized gradient approximation (GGA) functionals considered (PBE, OPBE, BLYP, and BP86). A set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided based on these benchmark calculations. Statistical cross-validation procedures are used to demonstrate the robustness of these fits
Improving 3D structure prediction from chemical shift data
International Nuclear Information System (INIS)
We report advances in the calculation of protein structures from chemical shift nuclear magnetic resonance data alone. Our previously developed method, CS-Rosetta, assembles structures from a library of short protein fragments picked from a large library of protein structures using chemical shifts and sequence information. Here we demonstrate that combination of a new and improved fragment picker and the iterative sampling algorithm RASREC yield significant improvements in convergence and accuracy. Moreover, we introduce improved criteria for assessing the accuracy of the models produced by the method. The method was tested on 39 proteins in the 50–100 residue size range and yields reliable structures in 70 % of the cases. All structures that passed the reliability filter were accurate (<2 Å RMSD from the reference)
Calculations of NMR chemical shifts with APW-based methods
Laskowski, Robert; Blaha, Peter
2012-01-01
We present a full potential, all electron augmented plane wave (APW) implementation of first-principles calculations of NMR chemical shifts. In order to obtain the induced current we follow a perturbation approach [Pickard and Mauri, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.63.245101 63, 245101 (2001)] and extended the common APW + local orbital (LO) basis by several LOs at higher energies. The calculated all-electron current is represented in traditional APW manner as Fourier series in the interstitial region and with a spherical harmonics representation inside the nonoverlapping atomic spheres. The current is integrated using a “pseudocharge” technique. The implementation is validated by comparison of the computed chemical shifts with some “exact” results for spherical atoms and for a set of solids and molecules with available published data.
Improving 3D structure prediction from chemical shift data
Energy Technology Data Exchange (ETDEWEB)
Schot, Gijs van der [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Zhang, Zaiyong [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany); Vernon, Robert [University of Washington, Department of Biochemistry (United States); Shen, Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vranken, Wim F. [VIB, Department of Structural Biology (Belgium); Baker, David [University of Washington, Department of Biochemistry (United States); Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Lange, Oliver F., E-mail: oliver.lange@tum.de [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany)
2013-09-15
We report advances in the calculation of protein structures from chemical shift nuclear magnetic resonance data alone. Our previously developed method, CS-Rosetta, assembles structures from a library of short protein fragments picked from a large library of protein structures using chemical shifts and sequence information. Here we demonstrate that combination of a new and improved fragment picker and the iterative sampling algorithm RASREC yield significant improvements in convergence and accuracy. Moreover, we introduce improved criteria for assessing the accuracy of the models produced by the method. The method was tested on 39 proteins in the 50-100 residue size range and yields reliable structures in 70 % of the cases. All structures that passed the reliability filter were accurate (<2 A RMSD from the reference)
Magnetic shift of the chemical freezeout and electric charge fluctuations
Fukushima, Kenji
2016-01-01
We discuss the effect of a strong magnetic field on the chemical freezeout points in the ultra-relativistic heavy-ion collision. As a result of the inverse magnetic catalysis or the magnetic inhibition, the crossover onset to hot and dense matter out of quarks and gluons should be shifted to a lower temperature. To quantify this shift we employ the hadron resonance gas model and an empirical condition for the chemical freezeout. We point out that the charged particle abundances are significantly affected by the magnetic field so that the electric charge fluctuation is largely enhanced especially at high baryon density. The charge conservation partially cancels the enhancement but our calculation shows that the electric charge fluctuation could serve as a magnetometer.
Correction for Eddy Current-Induced Echo-Shifting Effect in Partial-Fourier Diffusion Tensor Imaging
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Trong-Kha Truong
2015-01-01
Full Text Available In most diffusion tensor imaging (DTI studies, images are acquired with either a partial-Fourier or a parallel partial-Fourier echo-planar imaging (EPI sequence, in order to shorten the echo time and increase the signal-to-noise ratio (SNR. However, eddy currents induced by the diffusion-sensitizing gradients can often lead to a shift of the echo in k-space, resulting in three distinct types of artifacts in partial-Fourier DTI. Here, we present an improved DTI acquisition and reconstruction scheme, capable of generating high-quality and high-SNR DTI data without eddy current-induced artifacts. This new scheme consists of three components, respectively, addressing the three distinct types of artifacts. First, a k-space energy-anchored DTI sequence is designed to recover eddy current-induced signal loss (i.e., Type 1 artifact. Second, a multischeme partial-Fourier reconstruction is used to eliminate artificial signal elevation (i.e., Type 2 artifact associated with the conventional partial-Fourier reconstruction. Third, a signal intensity correction is applied to remove artificial signal modulations due to eddy current-induced erroneous T2*-weighting (i.e., Type 3 artifact. These systematic improvements will greatly increase the consistency and accuracy of DTI measurements, expanding the utility of DTI in translational applications where quantitative robustness is much needed.
Estimation of optical chemical shift in nuclear spin optical rotation
International Nuclear Information System (INIS)
Highlights: • Analytical theory of nuclear spin optical rotation (NSOR) is further developed. • Derive formula of NSOR ratio R between different nuclei in a same molecule. • Calculated results of R agree with the experiments. • Analyze influence factors on R and chemical distinction by NSOR. - Abstract: A recently proposed optical chemical shift in nuclear spin optical rotation (NSOR) is studied by theoretical comparison of NSOR magnitude between chemically non-equivalent or different element nuclei in the same molecule. Theoretical expressions of the ratio R between their NSOR magnitudes are derived by using a known semi-empirical formula of NSOR. Taking methanol, tri-ethyl-phosphite and 2-methyl-benzothiazole as examples, the ratios R are calculated and the results approximately agree with the experiments. Based on those, the important influence factors on R and chemical distinction by NSOR are discussed
Chemical-shift MRI of exogenous lipoid pneumonia
Energy Technology Data Exchange (ETDEWEB)
Cox, J.E.; Choplin, R.H.; Chiles, C. [Wake Forest Univ., Winston-Salem, NC (United States)
1996-05-01
Exogenous lipoid pneumonia results from the aspiration or inhalation of fatty substances, such as mineral oil found in laxatives or nasal medications containing liquid paraffin. We present standard and lipid-sensitive (chemical-shift) MR findings in a patient with histologically confirmed lipoid pneumonia. The loss of signal intensity in an area of airspace disease on opposed-phase imaging was considered specific for the presence of lipid. 14 refs., 3 figs.
Substituent effects on 61Ni NMR chemical shifts
Bühl, Michael; Peters, Dietmund; Herges, Rainer
2009-01-01
Ni-61 chemical shifts of Ni(all-trans-cdt) L (cdt = cyclododecatriene, L = none, CO, PMe3), Ni(CO)(4), Ni(C2H4)(2)(PMe3), Ni(cod)(2) (cod = cyclooctadiene) and Ni(PX3)(4) (X = Me, F, Cl) are computed at the GIAO (gauge-including atomic orbitals), BPW91, B3LYP and BHandHLYP levels, using BP86-optimised geometries and an indirect referencing scheme. For this set of compounds, substituent effects on delta(Ni-61) are better described with hybrid functionals than with the pure BPW91 functional. On...
Computational Assignment of Chemical Shifts for Protein Residues
Bratholm, Lars A
2013-01-01
Fast and accurate protein structure prediction is one of the major challenges in structural biology, biotechnology and molecular biomedicine. These fields require 3D protein structures for rational design of proteins with improved or novel properties. X-ray crystallography is the most common approach even with its low success rate, but lately NMR based approaches have gained popularity. The general approach involves a set of distance restraints used to guide a structure prediction, but simple NMR triple-resonance experiments often provide enough structural information to predict the structure of small proteins. Previous protein folding simulations that have utilised experimental data have weighted the experimental data and physical force field terms more or less arbitrarily, and the method is thus not generally applicable to new proteins. Furthermore a complete and near error-free assignment of chemical shifts obtained by the NMR experiments is needed, due to the static, or deterministic, assignment. In this ...
Accurate calculation of (31)P NMR chemical shifts in polyoxometalates.
Pascual-Borràs, Magda; López, Xavier; Poblet, Josep M
2015-04-14
We search for the best density functional theory strategy for the determination of (31)P nuclear magnetic resonance (NMR) chemical shifts, δ((31)P), in polyoxometalates. Among the variables governing the quality of the quantum modelling, we tackle herein the influence of the functional and the basis set. The spin-orbit and solvent effects were routinely included. To do so we analysed the family of structures α-[P2W18-xMxO62](n-) with M = Mo(VI), V(V) or Nb(V); [P2W17O62(M'R)](n-) with M' = Sn(IV), Ge(IV) and Ru(II) and [PW12-xMxO40](n-) with M = Pd(IV), Nb(V) and Ti(IV). The main results suggest that, to date, the best procedure for the accurate calculation of δ((31)P) in polyoxometalates is the combination of TZP/PBE//TZ2P/OPBE (for NMR//optimization step). The hybrid functionals (PBE0, B3LYP) tested herein were applied to the NMR step, besides being more CPU-consuming, do not outperform pure GGA functionals. Although previous studies on (183)W NMR suggested that the use of very large basis sets like QZ4P were needed for geometry optimization, the present results indicate that TZ2P suffices if the functional is optimal. Moreover, scaling corrections were applied to the results providing low mean absolute errors below 1 ppm for δ((31)P), which is a step forward in order to confirm or predict chemical shifts in polyoxometalates. Finally, via a simplified molecular model, we establish how the small variations in δ((31)P) arise from energy changes in the occupied and virtual orbitals of the PO4 group. PMID:25738630
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We apply the Grassmann tensor renormalization group (GTRG) to the one-flavor lattice Gross–Neveu model in the presence of a chemical potential. We compute the fermion number density and its susceptibility and confirm the validity of GTRG for the finite-density system. We introduce a method analogous to the reweighting method for the Monte Carlo method and test it for some parameters
Random coil chemical shifts in acidic 8 M urea: Implementation of random coil shift data in NMRView
International Nuclear Information System (INIS)
Studies of proteins unfolded in acid or chemical denaturant can help in unraveling events during the earliest phases of protein folding. In order for meaningful comparisons to be made of residual structure in unfolded states, it is necessary to use random coil chemical shifts that are valid for the experimental system under study. We present a set of random coil chemical shifts obtained for model peptides under experimental conditions used in studies of denatured proteins. This new set, together with previously published data sets, has been incorporated into a software interface for NMRView, allowing selection of the random coil data set that fits the experimental conditions best
Pitfalls of adrenal imaging with chemical shift MRI
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Chemical shift (CS) MRI of the adrenal glands exploits the different precessional frequencies of fat and water protons to differentiate the intracytoplasmic lipid-containing adrenal adenoma from other adrenal lesions. The purpose of this review is to illustrate both technical and interpretive pitfalls of adrenal imaging with CS MRI and emphasize the importance of adherence to strict technical specifications and errors that may occur when other imaging features and clinical factors are not incorporated into the diagnosis. When performed properly, the specificity of CS MRI for the diagnosis of adrenal adenoma is over 90%. Sampling the in-phase and opposed-phase echoes in the correct order and during the same breath-hold are essential requirements, and using the first echo pair is preferred, if possible. CS MRI characterizes more adrenal adenomas then unenhanced CT but may be non-diagnostic in a proportion of lipid-poor adenomas; CT washout studies may be able to diagnose these lipid-poor adenomas. Other primary and secondary adrenal tumours and supra-renal disease entities may contain lipid or gross fat and mimic adenoma or myelolipoma. Heterogeneity within an adrenal lesion that contains intracytoplasmic lipid could be due to myelolipoma, lipomatous metaplasia of adenoma, or collision tumour. Correlation with previous imaging, other imaging features, clinical history, and laboratory investigations can minimize interpretive errors
Diagnostic value of chemical shift artifact in distinguishing benign lymphadenopathy
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Purpose: Today, distinguishing metastatic lymph nodes from secondary benign inflammatory ones via using non-invasive methods is increasingly favorable. In this study, the diagnostic value of chemical shift artifact (CSA) in magnetic resonance imaging (MRI) was evaluated to distinguish benign lymphadenopathy. Subjects and methods: A prospective intraindividual internal review board-approved study was carried out on 15 men and 15 women having lymphadenopathic lesions in different locations of the body who underwent contrast-enhanced dynamic MR imaging at 1.5 T. Then, the imaging findings were compared with pathology reports, using the statistics analyses. Results: Due to the findings of the CSA existence in MRI, a total of 56.7% of the studied lesions (17 of 30) were identified as benign lesions and the rest were malignant, whereas the pathology reports distinguished twelve malignant and eighteen benign cases. Furthermore, the CSA findings comparing the pathology reports indicated that CSA, with confidence of 79.5%, has a significant diagnostic value to differentiate benign lesions from malignant ones. Conclusion: Our study demonstrated that CSA in MR imaging has a suitable diagnostic potential nearing readiness for clinical trials. Furthermore, CSA seems to be a feasible tool to differentiate benign lymph nodes from malignant ones; however, further studies including larger numbers of patients are required to confirm our results.
Applications of Chemical Shift Imaging to Marine Sciences
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Haakil Lee
2010-08-01
Full Text Available The successful applications of magnetic resonance imaging (MRI in medicine are mostly due to the non-invasive and non-destructive nature of MRI techniques. Longitudinal studies of humans and animals are easily accomplished, taking advantage of the fact that MRI does not use harmful radiation that would be needed for plain film radiographic, computerized tomography (CT or positron emission (PET scans. Routine anatomic and functional studies using the strong signal from the most abundant magnetic nucleus, the proton, can also provide metabolic information when combined with in vivo magnetic resonance spectroscopy (MRS. MRS can be performed using either protons or hetero-nuclei (meaning any magnetic nuclei other than protons or 1H including carbon (13C or phosphorus (31P. In vivo MR spectra can be obtained from single region ofinterest (ROI or voxel or multiple ROIs simultaneously using the technique typically called chemical shift imaging (CSI. Here we report applications of CSI to marine samples and describe a technique to study in vivo glycine metabolism in oysters using 13C MRS 12 h after immersion in a sea water chamber dosed with [2-13C]-glycine. This is the first report of 13C CSI in a marine organism.
19-Fluorine nuclear magnetic resonance chemical shift variability in trifluoroacetyl species
Sloop, Joseph
2013-01-01
Joseph C SloopSchool of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA, USAAbstract: This review examines the variability of chemical shifts observed in 19-fluorine (19F) nuclear magnetic resonance spectra for the trifluoroacetyl (TFA) functional group. The range of 19F chemical shifts reported spectra for the TFA group varies generally from −85 to −67 ppm relative to CFCl3. The literature revealed several factors that impact chemical shifts of the TFA...
International Nuclear Information System (INIS)
We introduce a Python-based program that utilizes the large database of 13C and 15N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D 13C–13C, 15N–13C, or 3D 15N–13C–13C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D 13C–13C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40–60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO–Cα–Cβ or N–Cα–Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.
Chemical structure and intra-molecular effects on NMR-NQR tensors of harmine and harmaline alkaloids
Ahmadinejad, Neda; Tahan, Arezoo; Talebi Tari, Mostafa
2016-02-01
Density functional theory (DFT) methods were used to analyze the effects of molecular structure and ring currents on the NMR chemical shielding tensors and NQR frequencies of harmine and harmaline alkaloids in the gas phase. The results demonstrated that NMR tensors and NQR frequencies of 15N nuclei in these compounds depend on chemical environment and resonance interactions. Hence, their values are obviously different in the mentioned structures. The interpretation of natural bond orbital (NBO) data suggests that in harmine structure, the lone pair participation of N9 in π-system electron clouds causes to development of aromaticity nature in pyrrole ring. However, the chemical shielding around N9 atom in harmine structure is higher than in harmaline, while in harmaline structure, lone pair participation of N2 in π-system electron clouds causes to development of aromaticity nature in pyridine ring. Hence, chemical shielding around N2 atom in harmaline structure is higher than in harmine. It can be deduced that by increasing lone pair electrons contribution of nitrogen atoms in ring resonance interactions and aromaticity development, the values of NMR chemical shielding around them increase, while χ and q zz values of these nuclei decrease.
A procedure to validate and correct the 13C chemical shift calibration of RNA datasets
International Nuclear Information System (INIS)
Chemical shifts reflect the structural environment of a certain nucleus and can be used to extract structural and dynamic information. Proper calibration is indispensable to extract such information from chemical shifts. Whereas a variety of procedures exist to verify the chemical shift calibration for proteins, no such procedure is available for RNAs to date. We present here a procedure to analyze and correct the calibration of 13C NMR data of RNAs. Our procedure uses five 13C chemical shifts as a reference, each of them found in a narrow shift range in most datasets deposited in the Biological Magnetic Resonance Bank. In 49 datasets we could evaluate the 13C calibration and detect errors or inconsistencies in RNA 13C chemical shifts based on these chemical shift reference values. More than half of the datasets (27 out of those 49) were found to be improperly referenced or contained inconsistencies. This large inconsistency rate possibly explains that no clear structure–13C chemical shift relationship has emerged for RNA so far. We were able to recalibrate or correct 17 datasets resulting in 39 usable 13C datasets. 6 new datasets from our lab were used to verify our method increasing the database to 45 usable datasets. We can now search for structure–chemical shift relationships with this improved list of 13C chemical shift data. This is demonstrated by a clear relationship between ribose 13C shifts and the sugar pucker, which can be used to predict a C2′- or C3′-endo conformation of the ribose with high accuracy. The improved quality of the chemical shift data allows statistical analysis with the potential to facilitate assignment procedures, and the extraction of restraints for structure calculations of RNA.
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The natural abundance carbon-13 nuclear magnetic resonance spectra of various clinically used furocoumarins and furochromones have been studied. The assignments of carbon chemical shift values were based on the theory of chemical shift, additivity rules, SFORD spectra and model compounds. (author)
Method of evaluating chemical shifts of X-ray emission lines in molecules and solids
Lomachuk, Yuriy V.; Titov, Anatoly V.
2013-01-01
Method of evaluating chemical shifts of X-ray emission lines for sufficiently heavy atoms (beginning from period 4 elements) in chemical compounds is developed. This method is based on the pseudopotential model and one-center restoration method (to reconstruct the proper electronic structure in heavy-atom cores). The approximations of instantaneous transition and frozen inner core spinors of the atom are used for derivation of an expression for chemical shift as a difference between mean valu...
Christensen, Anders S
2015-01-01
This report covers the development of a new, fast method for calculating the backbone amide proton chemical shifts in proteins. Through quantum chemical calculations, structure-based forudsiglese the chemical shift for amidprotonen in protein has been parameterized. The parameters are then implemented in a computer program called Padawan. The program has since been implemented in protein folding program Phaistos, wherein the method andvendes to de novo folding of the protein structures and to refine the existing protein structures.
International Nuclear Information System (INIS)
There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder
A robust algorithm for optimizing protein structures with NMR chemical shifts
Energy Technology Data Exchange (ETDEWEB)
Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S., E-mail: david.wishart@ualberta.ca [University of Alberta, Department of Computing Science (Canada)
2015-11-15
Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and “PDB worthy”. The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca http://www.gamdy.ca.
A robust algorithm for optimizing protein structures with NMR chemical shifts
International Nuclear Information System (INIS)
Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and “PDB worthy”. The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca http://www.gamdy.ca
DEFF Research Database (Denmark)
Vosegaard, Thomas; Massiot, Dominique; Gautier, Nathalie;
1997-01-01
A single-crystal (71)Ga NMR study of the garnet Y(3)Ga(5)O(12) (YGG) has resulted in the determination of the first chemical shielding tensors reported for the (71)Ga quadrupole. The single-crystal spectra are analyzed in terms of the combined effect of quadrupole coupling and chemical shielding ...
International Nuclear Information System (INIS)
The variety of coordination numbers, symmetries, distortions and ligand environments in thermally-stable iron-bearing minerals provide wide ranges of chemical shift (δ) and quadrupole splitting (Δ) parameters, which serve to characterize the crystal chemistries and site occupancies of Fe2+ and Fe3+ ions in minerals of terrestrial and extraterrestrial origins. Correlations between ferrous and ferric chemical shifts enable thermally-induced electron delocalization behavior in mixed-valence Fe2+-Fe3+ minerals to be identified, while chemical shift versus quadrupole splitting correlations serve to identify nanophase ferric oxides and oxyhydroxides in oxidized minerals and in meteorites subjected to aqueous oxidation before and after they arrived on Earth. (orig.)
DEFF Research Database (Denmark)
Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael;
2013-01-01
We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...... QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift...
Truflandier, Lionel A; Autschbach, Jochen
2010-03-17
Ab initio molecular dynamics (aiMD) simulations based on density functional theory (DFT) were performed on a set of five anionic platinum complexes in aqueous solution. (195)Pt nuclear magnetic shielding constants were computed with DFT as averages over the aiMD trajectories, using the two-component relativistic zeroth-order regular approximation (ZORA) in order to treat relativistic effects on the Pt shielding tensors. The chemical shifts obtained from the aiMD averages are in good agreement with experimental data. For Pt(II) and Pt(IV) halide complexes we found an intermediate solvent shell interacting with the complexes that causes pronounced solvent effects on the Pt chemical shifts. For these complexes, the magnitude of solvent effects on the Pt shielding constant can be correlated with the surface charge density. For square-planar Pt complexes the aiMD simulations also clearly demonstrate the influence of closely coordinated non-equatorial water molecules on the Pt chemical shift, relating the structure of the solution around the complex to the solvent effects on the metal NMR chemical shift. For the complex [Pt(CN)(4)](2-), the solvent effects on the Pt shielding constant are surprisingly small. PMID:20166712
Prediction of proton chemical shifts in RNA - Their use in structure refinement and validation
International Nuclear Information System (INIS)
An analysis is presented of experimental versus calculated chemical shifts of the non-exchangeable protons for 28 RNA structures deposited in the Protein Data Bank, covering a wide range of structural building blocks. We have used existing models for ring-current and magnetic-anisotropy contributions to calculate the proton chemical shifts from the structures. Two different parameter sets were tried: (i) parameters derived by Ribas-Prado and Giessner-Prettre (GP set) [(1981) J. Mol. Struct.,76, 81-92.]; (ii) parameters derived by Case [(1995) J. Biomol. NMR, 6, 341-346]. Both sets lead to similar results. The detailed analysis was carried using the GP set. The root-mean-square-deviation between the predicted and observed chemical shifts of the complete database is 0.16 ppm with a Pearson correlation coefficient of 0.79. For protons in the usually well-defined A-helix environment these numbers are, 0.08 ppm and 0.96, respectively. As a result of this good correspondence, a reliable analysis could be made of the structural dependencies of the 1H chemical shifts revealing their physical origin. For example, a down-field shift of either H2' or H3' or both indicates a high-syn/syn χ-angle. In an A-helix it is essentially the 5'-neighbor that affects the chemical shifts of H5, H6 and H8 protons. The H5, H6 and H8 resonances can therefore be assigned in an A-helix on the basis of their observed chemical shifts. In general, the chemical shifts were found to be quite sensitive to structural changes. We therefore propose that a comparison between calculated and observed 1H chemical shifts is a good tool for validation and refinement of structures derived from NOEs and J-couplings
Struppe, Jochem; Zhang, Yong; Rozovsky, Sharon
2015-01-01
The genetically encoded amino acid selenocysteine and its dimeric form, selenocystine, are both utilized by nature. They are found in active sites of selenoproteins, enzymes that facilitate a diverse range of reactions, including the detoxification of reactive oxygen species and regulation of redox pathways. Due to selenocysteine and selenocystine’s specialized biological roles, it is of interest to examine their 77Se NMR properties and how those can in turn be employed to study biological sy...
Combined Effects of Noise and Shift Work on Workers’ Physiological Parameters in a Chemical Industry
M. Motamedzade; S. Ghazaiee
2003-01-01
This study was conducted to determine the combined effects of noise and shift work on physiological parameters including body temperature, heart rate and blood pressure. This study was performed in a chemical industry in Tehran in 1993. The workers’ physiological parameters was recorded at the beginning and at the end of all work shifts. Groups under study included : day workers (n=115) , day workers with continuous noise exposure (n=44) , two-shift workers without...
PPM-One: a static protein structure based chemical shift predictor
Energy Technology Data Exchange (ETDEWEB)
Li, Dawei; Brüschweiler, Rafael, E-mail: bruschweiler.1@osu.edu [The Ohio State University, Campus Chemical Instrument Center (United States)
2015-07-15
We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM-One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain protons and it is found that the prediction accuracy is at a level allowing an independent assessment of stereospecific assignments. For a previously established set of test proteins some overall improvement was achieved over current top-performing chemical shift prediction programs.
Chemical shifts and coupling constants of C8H10N4O2
Jain, M.
This document is part of Subvolume D3 `Chemical Shifts and Coupling Constants for Carbon-13: Heterocycles' of Volume 35 `Nuclear Magnetic Resonance (NMR) Data' of Landolt-Börnstein Group III `Condensed Matter'
Directory of Open Access Journals (Sweden)
Dalia Z. Zidan
2014-09-01
Conclusion: Quantitative chemical shift MR imaging could be a valuable addition to standard MR imaging techniques and represent a rapid problem solving tool in differentiating benign from malignant vertebral compression, especially in patients with known primary malignancies.
PPM-One: a static protein structure based chemical shift predictor
International Nuclear Information System (INIS)
We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM-One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain protons and it is found that the prediction accuracy is at a level allowing an independent assessment of stereospecific assignments. For a previously established set of test proteins some overall improvement was achieved over current top-performing chemical shift prediction programs
DEFF Research Database (Denmark)
Beeren, Sophie; Meier, Sebastian
2015-01-01
We introduce the concept of supramolecular chemical shift reagents as a tool to improve signal resolution for the NMR analysis of homooligomers. Non-covalent interactions with the shift reagent can constrain otherwise flexible analytes inducing a conformational transition that results in signal...
International Nuclear Information System (INIS)
We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poisson–Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation shell around the solute; the latter substantially improves the accuracy of chemical shift prediction of protons involved in hydrogen bonding with solvent. We also compare the performance of AF-QM/MM on proteins and nucleic acids with two leading empirical chemical shift prediction programs SHIFTS and SHIFTX2. Although the empirical programs outperform AF-QM/MM in predicting chemical shifts, the differences are in some cases small, and the latter can be applied to chemical shifts on biomolecules which are outside the training set employed by the empirical programs, such as structures containing ligands, metal centers, and non-standard residues. The AF-QM/MM described here is implemented in version 5 of the SHIFTS software, and is fully automated, so that only a structure in PDB format is required as input
International Nuclear Information System (INIS)
The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the 1H NMR and 13C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and 1H and 13C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA 1H and 13C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides
Brown, Joshua D; Summers, Michael F; Johnson, Bruce A
2015-09-01
The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the (1)H NMR and (13)C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and (1)H and (13)C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA (1)H and (13)C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides. PMID:26141454
Energy Technology Data Exchange (ETDEWEB)
Brown, Joshua D.; Summers, Michael F. [University of Maryland Baltimore County, Howard Hughes Medical Institute (United States); Johnson, Bruce A., E-mail: bruce.johnson@asrc.cuny.edu [University of Maryland Baltimore County, Department of Chemistry and Biochemistry (United States)
2015-09-15
The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the {sup 1}H NMR and {sup 13}C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and {sup 1}H and {sup 13}C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA {sup 1}H and {sup 13}C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides.
Energy Technology Data Exchange (ETDEWEB)
Swails, Jason [Rutgers University, Department of Chemistry and Chemical Biology and BioMaPS Institute (United States); Zhu, Tong; He, Xiao, E-mail: xiaohe@phy.ecnu.edu.cn [East China Normal University, State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science (China); Case, David A., E-mail: case@biomaps.rutgers.edu [Rutgers University, Department of Chemistry and Chemical Biology and BioMaPS Institute (United States)
2015-10-15
We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poisson–Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation shell around the solute; the latter substantially improves the accuracy of chemical shift prediction of protons involved in hydrogen bonding with solvent. We also compare the performance of AF-QM/MM on proteins and nucleic acids with two leading empirical chemical shift prediction programs SHIFTS and SHIFTX2. Although the empirical programs outperform AF-QM/MM in predicting chemical shifts, the differences are in some cases small, and the latter can be applied to chemical shifts on biomolecules which are outside the training set employed by the empirical programs, such as structures containing ligands, metal centers, and non-standard residues. The AF-QM/MM described here is implemented in version 5 of the SHIFTS software, and is fully automated, so that only a structure in PDB format is required as input.
Chemical shift MRI can aid in the diagnosis of indeterminate skeletal lesions of the spine
Energy Technology Data Exchange (ETDEWEB)
Douis, H. [University Hospital Birmingham, Department of Radiology, Birmingham (United Kingdom); Royal Orthopaedic Hospital, Department of Radiology, Birmingham (United Kingdom); Davies, A.M. [Royal Orthopaedic Hospital, Department of Radiology, Birmingham (United Kingdom); Jeys, L. [Royal Orthopaedic Hospital, Department of Orthopaedic Oncology, Birmingham (United Kingdom); Sian, P. [Royal Orthopaedic Hospital, Department of Spinal Surgery and Spinal Oncology, Birmingham (United Kingdom)
2016-04-15
To evaluate the role of chemical shift MRI in the characterisation of indeterminate skeletal lesions of the spine as benign or malignant. Fifty-five patients (mean age 54.7 years) with 57 indeterminate skeletal lesions of the spine were included in this retrospective study. In addition to conventional MRI at 3 T which included at least sagittal T1WI and T2WI/STIR sequences, patients underwent chemical shift MRI. A cut-off value with a signal drop-out of 20 % was used to differentiate benign lesions from malignant lesions (signal drop-out <20 % being malignant). There were 45 benign lesions and 12 malignant lesions. Chemical shift imaging correctly diagnosed 33 of 45 lesions as benign and 11 of 12 lesions as malignant. In contrast, there were 12 false positive cases and 1 false negative case based on chemical shift MRI. This yielded a sensitivity of 91.7 %, a specificity of 73.3 %, a negative predictive value of 97.1 %, a positive predictive value of 47.8 % and a diagnostic accuracy of 82.5 %. Chemical shift MRI can aid in the characterisation of indeterminate skeletal lesions of the spine in view of its high sensitivity in diagnosing malignant lesions. Chemical shift MRI can potentially avoid biopsy in a considerable percentage of patients with benign skeletal lesions of the spine. (orig.)
Chemical shift MRI can aid in the diagnosis of indeterminate skeletal lesions of the spine
International Nuclear Information System (INIS)
To evaluate the role of chemical shift MRI in the characterisation of indeterminate skeletal lesions of the spine as benign or malignant. Fifty-five patients (mean age 54.7 years) with 57 indeterminate skeletal lesions of the spine were included in this retrospective study. In addition to conventional MRI at 3 T which included at least sagittal T1WI and T2WI/STIR sequences, patients underwent chemical shift MRI. A cut-off value with a signal drop-out of 20 % was used to differentiate benign lesions from malignant lesions (signal drop-out <20 % being malignant). There were 45 benign lesions and 12 malignant lesions. Chemical shift imaging correctly diagnosed 33 of 45 lesions as benign and 11 of 12 lesions as malignant. In contrast, there were 12 false positive cases and 1 false negative case based on chemical shift MRI. This yielded a sensitivity of 91.7 %, a specificity of 73.3 %, a negative predictive value of 97.1 %, a positive predictive value of 47.8 % and a diagnostic accuracy of 82.5 %. Chemical shift MRI can aid in the characterisation of indeterminate skeletal lesions of the spine in view of its high sensitivity in diagnosing malignant lesions. Chemical shift MRI can potentially avoid biopsy in a considerable percentage of patients with benign skeletal lesions of the spine. (orig.)
International Nuclear Information System (INIS)
An approach to automatic prediction of the amino acid type from NMR chemical shift values of its nuclei is presented here, in the frame of a model to calculate the probability of an amino acid type given the set of chemical shifts. The method relies on systematic use of all chemical shift values contained in the BioMagResBank (BMRB). Two programs were designed, one (BMRB stats) for extracting statistical chemical shift parameters from the BMRB and another one (RESCUE2) for computing the probabilities of each amino acid type, given a set of chemical shifts. The Bayesian prediction scheme presented here is compared to other methods already proposed: PROTYP (Grzesiek and Bax, J. Biomol. NMR, 3, 185-204, 1993) RESCUE (Pons and Delsuc, J. Biomol. NMR, 15, 15-26, 1999) and PLATON (Labudde et al., J. Biomol. NMR, 25, 41-53, 2003) and is found to be more sensitive and more specific. Using this scheme, we tested various sets of nuclei. The two nuclei carrying the most information are Cβ and Hβ, in agreement with observations made in Grzesiek and Bax, 1993. Based on four nuclei: Hβ, Cβ, Cα and C', it is possible to increase correct predictions to a rate of more than 75%. Taking into account the correlations between the nuclei chemical shifts has only a slight impact on the percentage of correct predictions: indeed, the largest correlation coefficients display similar features on all amino acids
Enhanced conformational space sampling improves the prediction of chemical shifts in proteins.
Markwick, Phineus R L; Cervantes, Carla F; Abel, Barrett L; Komives, Elizabeth A; Blackledge, Martin; McCammon, J Andrew
2010-02-01
A biased-potential molecular dynamics simulation method, accelerated molecular dynamics (AMD), was combined with the chemical shift prediction algorithm SHIFTX to calculate (1)H(N), (15)N, (13)Calpha, (13)Cbeta, and (13)C' chemical shifts of the ankyrin repeat protein IkappaBalpha (residues 67-206), the primary inhibitor of nuclear factor kappa-B (NF-kappaB). Free-energy-weighted molecular ensembles were generated over a range of acceleration levels, affording systematic enhancement of the conformational space sampling of the protein. We have found that the predicted chemical shifts, particularly for the (15)N, (13)Calpha, and (13)Cbeta nuclei, improve substantially with enhanced conformational space sampling up to an optimal acceleration level. Significant improvement in the predicted chemical shift data coincides with those regions of the protein that exhibit backbone dynamics on longer time scales. Interestingly, the optimal acceleration level for reproduction of the chemical shift data has previously been shown to best reproduce the experimental residual dipolar coupling (RDC) data for this system, as both chemical shift data and RDCs report on an ensemble and time average in the millisecond range. PMID:20063881
Directory of Open Access Journals (Sweden)
Anthony J. SAVIOLA, David CHISZAR, Stephen P. MACKESSY
2012-08-01
Full Text Available Snakes often have specialized diets that undergo a shift from one prey type to another depending on the life stage of the snake. Crotalus viridis viridis (prairie rattlesnake takes different prey at different life stages, and neonates typically prey on ectotherms, while adults feed almost entirely on small endotherms. We hypothesized that elevated rates of tongue flicking to chemical stimuli should correlate with particular prey consumed, and that this response shifts from one prey type to another as individuals age. To examine if an ontogenetic shift in response to chemical cues occurred, we recorded the rate of tongue flicking for 25 neonate, 20 subadult, and 20 adult (average SVL = 280.9, 552, 789.5 mm, respectively wild-caught C. v. viridis to chemical stimuli presented on a cotton-tipped applicator; water-soluble cues from two ectotherms (prairie lizard, Sceloporus undulatus, and house gecko, Hemidactylus frenatus, two endotherms (deer mouse, Peromyscus maniculatus and lab mouse, Mus musculus, and water controls were used. Neonates tongue flicked significantly more to chemical cues of their common prey, S. undulatus, than to all other chemical cues; however, the response to this lizard’s chemical cues decreased in adult rattlesnakes. Subadults tongue flicked with a higher rate of tongue flicking to both S. undulatus and P. maniculatus than to all other treatments, and adults tongue flicked significantly more to P. maniculatus than to all other chemical cues. In addition, all three sub-classes demonstrated a greater response for natural prey chemical cues over chemical stimuli of prey not encountered in the wild (M. musculus and H. frenatus. This shift in chemosensory response correlated with the previously described ontogenetic shifts in C. v. viridis diet. Because many vipers show a similar ontogenetic shift in diet and venom composition, we suggest that this shift in prey cue discrimination is likely a general phenomenon among viperid
International Nuclear Information System (INIS)
Pseudo contact shifts (PCSs) induced by paramagnetic lanthanide ions fixed in a protein frame provide long-range distance and angular information, and are valuable for the structure determination of protein–protein and protein–ligand complexes. We have been developing a lanthanide-binding peptide tag (hereafter LBT) anchored at two points via a peptide bond and a disulfide bond to the target proteins. However, the magnetic susceptibility tensor displays symmetry, which can cause multiple degenerated solutions in a structure calculation based solely on PCSs. Here we show a convenient method for resolving this degeneracy by changing the spacer length between the LBT and target protein. We applied this approach to PCS-based rigid body docking between the FKBP12-rapamycin complex and the mTOR FRB domain, and demonstrated that degeneracy could be resolved using the PCS restraints obtained from two-point anchored LBT with two different spacer lengths. The present strategy will markedly increase the usefulness of two-point anchored LBT for protein complex structure determination.
Energy Technology Data Exchange (ETDEWEB)
Kobashigawa, Yoshihiro; Saio, Tomohide [Hokkaido University, Department of Structural Biology, Faculty of Advanced Life Science (Japan); Ushio, Masahiro [Hokkaido University, Graduate School of Life Science (Japan); Sekiguchi, Mitsuhiro [Astellas Pharma Inc., Analysis and Pharmacokinetics Research Labs, Department of Drug Discovery (Japan); Yokochi, Masashi; Ogura, Kenji; Inagaki, Fuyuhiko, E-mail: finagaki@pharm.hokudai.ac.jp [Hokkaido University, Department of Structural Biology, Faculty of Advanced Life Science (Japan)
2012-05-15
Pseudo contact shifts (PCSs) induced by paramagnetic lanthanide ions fixed in a protein frame provide long-range distance and angular information, and are valuable for the structure determination of protein-protein and protein-ligand complexes. We have been developing a lanthanide-binding peptide tag (hereafter LBT) anchored at two points via a peptide bond and a disulfide bond to the target proteins. However, the magnetic susceptibility tensor displays symmetry, which can cause multiple degenerated solutions in a structure calculation based solely on PCSs. Here we show a convenient method for resolving this degeneracy by changing the spacer length between the LBT and target protein. We applied this approach to PCS-based rigid body docking between the FKBP12-rapamycin complex and the mTOR FRB domain, and demonstrated that degeneracy could be resolved using the PCS restraints obtained from two-point anchored LBT with two different spacer lengths. The present strategy will markedly increase the usefulness of two-point anchored LBT for protein complex structure determination.
Institute of Scientific and Technical Information of China (English)
Khandakar Showkat Osman; M. Jashimuddin; S. M. Sirajul Haque; Sohag Miah
2013-01-01
This study reports the effects of shifting cultivation at slashing stage on soil physicochemical properties at Bandarban Sadar Upazila in Chittagong Hill Tracts of Bangladesh. At this initial stage of shifting cultivation no general trend was found for moisture content, maximum water holding capacity, field capacity, dry and moist bulk density, parti-cle density for some chemical properties between shifting cultivated land and forest having similar soil texture. Organic matter was significantly (p≤0.05) lower in 1-year and 3-year shifting cultivated lands and higher in 2-year shifting cultivation than in adjacent natural forest. Significant differences were also found for total N, exchangeable Ca, Mg and K and in CEC as well as for available P. Slashed area showed higher soil pH. Deterioration in land quality starts from burning of slashing materials and continues through subsequent stages of shifting cultivation.
Method for evaluating chemical shifts of x-ray emission lines in molecules and solids
Lomachuk, Yuriy V.; Titov, Anatoly V.
2013-12-01
A method of evaluating chemical shifts of x-ray emission lines for period four and heavier elements is developed. This method is based on the relativistic pseudopotential model and one-center restoration approach [Int. J. Quantum Chem.IJQCB20020-760810.1002/qua.20418 104, 223 (2005)] to recover a proper electronic structure in heavy-atom cores after the pseudopotential simulation of chemical compounds. The approximations of instantaneous transition and frozen core are presently applied to derive an expression for chemical shift as a difference between mean values of certain effective operator. The method allows one to avoid evaluation of small quantities (chemical shifts ˜0.01-1 eV) as differences of very large values (transition energies ˜1-100 keV in various compounds). The results of our calculations of chemical shifts for the Kα1, Kα2, and L transitions of group-14 metal cations with respect to neutral atoms are presented. Calculations of Kα1-line chemical shifts for the Pb core transitions in PbO and PbF2 with respect to those in the Pb atom are also performed and discussed. The accuracy of approximations used is estimated and the quality of the calculations is analyzed.
Method of evaluating chemical shifts of X-ray emission lines in molecules and solids
Lomachuk, Yuriy V
2013-01-01
Method of evaluating chemical shifts of X-ray emission lines for sufficiently heavy atoms (beginning from period 4 elements) in chemical compounds is developed. This method is based on the pseudopotential model and one-center restoration method (to reconstruct the proper electronic structure in heavy-atom cores). The approximations of instantaneous transition and frozen inner core spinors of the atom are used for derivation of an expression for chemical shift as a difference between mean values of some effective operator. The method allows one to avoid evaluating small values (chemical shifts ~ 0.01{\\div}1 eV) as differences of very large values (transition energies ~ 1{\\div}100 keV in various compounds). The results of our calculations of chemical shifts for the K_{\\alpha1,2} and L transitions of the group 14 metal cations with respect to neutral atoms are presented. The calculations of chemical shift of K_{\\alpha1}-line in the Pb-core transition within PbO and PbF_2 with respect to the neutral Pb are also p...
International Nuclear Information System (INIS)
Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in φ/ψ/χ1 torsion angles and sequence similarity to the query triplet of interest. The database contains 15N, 1HN, 1Hα, 13Cα, 13Cβ and 13C' chemical shifts for 200 proteins for which a high resolution X-ray (≤2.4 A) structure is available. The relative importance of the weighting factors for the φ/ψ/χ1 angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for 15N, 1HN, 1Hα, 13Cα, 13Cβ and 13C', respectively, including outliers
RefDB: A database of uniformly referenced protein chemical shifts
International Nuclear Information System (INIS)
RefDB is a secondary database of reference-corrected protein chemical shifts derived from the BioMagResBank (BMRB). The database was assembled by using a recently developed program (SHIFTX) to predict protein 1H, 13C and 15N chemical shifts from X-ray or NMR coordinate data of previously assigned proteins. The predicted shifts were then compared with the corresponding observed shifts and a variety of statistical evaluations performed. In this way, potential mis-assignments, typographical errors and chemical referencing errors could be identified and, in many cases, corrected. This approach allows for an unbiased, instrument-independent solution to the problem of retrospectively re-referencing published protein chemical shifts. Results from this study indicate that nearly 25% of BMRB entries with 13C protein assignments and 27% of BMRB entries with 15N protein assignments required significant chemical shift reference readjustments. Additionally, nearly 40% of protein entries deposited in the BioMagResBank appear to have at least one assignment error. From this study it evident that protein NMR spectroscopists are increasingly adhering to recommended IUPAC 13C and 15N chemical shift referencing conventions, however, approximately 20% of newly deposited protein entries in the BMRB are still being incorrectly referenced. This is cause for some concern. However, the utilization of RefDB and its companion programs may help mitigate this ongoing problem. RefDB is updated weekly and the database, along with its associated software, is freely available at http://redpoll.pharmacy.ualberta.ca and the BMRB website
International Nuclear Information System (INIS)
Chemical shift MRI is widely used for identifying adenomas, but it is not a perfect method. We determined whether combined dynamic MRI methods can lead to improved diagnostic accuracy. Fifty-seven adrenal masses were examined by chemical shift and dynamic MR imaging using 2 MR systems. The masses included 38 adenomas and 19 non-adenomas. In chemical shift MRI studies, the signal intensity index (SI) was calculated, and the lesions classified into 5 types in the dynamic MRI studies. Of the 38 adenomas studied, 37 had an SI greater than 0. In the dynamic MRI, 34 of 38 adenomas showed a benign pattern (type 1). If the SI for the adenomas in the chemical shift MRI was considered to be greater than 0, the positive predictive value was 0.9, and the negative predictive value was 0.94 and κ=0.79. If type 1 was considered to indicate adenomas in the dynamic MRI, the corresponding values were 0.94, 0.81 and κ=0.77 respectively. The results obtained when the 2 methods were combined were 1, 0.95 and κ=0.96 respectively. The chemical shift MRI was found to be useful for identifying adenomas in most cases. If the adrenal mass had a low SI (0< SI<5), dynamic MRI was also found to be helpful for making a differential diagnosis. (author)
Energy Technology Data Exchange (ETDEWEB)
Labudde, D.; Leitner, D.; Krueger, M.; Oschkinat, H. [Forschungsinstitut fuer Molekulare Pharmakologie (Germany)], E-mail: oschkinat@fmp-berlin.de
2003-01-15
The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the {alpha}-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely {alpha}-helix, {beta}-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time.
Directory of Open Access Journals (Sweden)
Anders S Christensen
Full Text Available We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts--sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94. ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond ((h3J(NC' spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding.
Christensen, Anders S; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H
2013-01-01
We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to refine protein structures to this...
International Nuclear Information System (INIS)
The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the α-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely α-helix, β-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time
Isotope effects on chemical shifts in the study of intramolecular hydrogen bonds
DEFF Research Database (Denmark)
Hansen, Poul Erik
2015-01-01
The paper deals with the use of isotope effects on chemical shifts in characterizing intramolecular hydrogen bonds. Both so-called resonance-assisted (RAHB) and non-RAHB systems are treated. The importance of RAHB will be discussed. Another very important issue is the borderline between “static......” and tautomeric systems. Isotope effects on chemical shifts are particularly useful in such studies. All kinds of intramolecular hydrogen bonded systems will be treated, typical hydrogen bond donors: OH, NH, SH and NH+, typical acceptors C=O, C=N, C=S C=N−. The paper will be deal with both secondary...... and primary isotope effects on chemical shifts. These two types of isotope effects monitor the same hydrogen bond, but from different angles...
DEFF Research Database (Denmark)
Modig, K.; Jürgensen, Vibeke Würtz; Lindorff-Larsen, K.;
2007-01-01
A simple alternative method for obtaining "random coil" chemical shifts by intrinsic referencing using the protein's own peptide sequence is presented. These intrinsic random coil backbone shifts were then used to calculate secondary chemical shifts, that provide important information on the resi...
What can we learn by computing 13Cα chemical shifts for X-ray protein models?
International Nuclear Information System (INIS)
The room-temperature X-ray structures of two proteins, solved at 1.8 and 1.9 Å resolution, are used to investigate whether a set of conformations, rather than a single X-ray structure, provides better agreement with both the X-ray data and the observed 13Cα chemical shifts in solution. The room-temperature X-ray structures of ubiquitin and of the RNA-binding domain of nonstructural protein 1 of influenza A virus solved at 1.8 and 1.9 Å resolution, respectively, were used to investigate whether a set of conformations rather than a single X-ray structure provides better agreement with both the X-ray data and the observed 13Cα chemical shifts in solution. For this purpose, a set of new conformations for each of these proteins was generated by fitting them to the experimental X-ray data deposited in the PDB. For each of the generated structures, which show R and Rfree factors similar to those of the deposited X-ray structure, the 13Cα chemical shifts of all residues in the sequence were computed at the DFT level of theory. The sets of conformations were then evaluated by their ability to reproduce the observed 13Cα chemical shifts by using the conformational average root-mean-square-deviation (ca-r.m.s.d.). For ubiquitin, the computed set of conformations is a better representation of the observed 13Cα chemical shifts in terms of the ca-r.m.s.d. than a single X-ray-derived structure. However, for the RNA-binding domain of nonstructural protein 1 of influenza A virus, consideration of an ensemble of conformations does not improve the agreement with the observed 13Cα chemical shifts. Whether an ensemble of conformations rather than any single structure is a more accurate representation of a protein structure in the crystal as well as of the observed 13Cα chemical shifts is determined by the dispersion of coordinates, in terms of the all-atom r.m.s.d. among the generated models; these generated models satisfy the experimental X-ray data with accuracy as good as
Proton Magnetic Resonance and Human Thyroid Neoplasia III. Ex VivoChemical-Shift Microimaging
Rutter, Allison; Künnecke, Basil; Dowd, Susan; Russell, Peter; Delbridge, Leigh; Mountford, Carolyn E.
1996-03-01
Magnetic-resonance chemical-shift microimaging, with a spatial resolution of 40 × 40 μm, is a modality which can detect alterations to cellular chemistry and hence markers of pathological processes in human tissueex vivo.This technique was used as a chemical microscope to assess follicular thyroid neoplasms, lesions which are unsatisfactorily investigated using standard histopathological techiques or water-based magnetic-resonance imaging. The chemical-shift images at the methyl frequency (0.9 ppm) identify chemical heterogeneity in follicular tumors which are histologically homogeneous. The observed changes to cellular chemistry, detectable in foci of approximately 100 cells or less, support the existence of a preinvasive state hitherto unidentified by current pathological techniques.
DEFF Research Database (Denmark)
Kjærgaard, Magnus; Poulsen, Flemming Martin
2011-01-01
this study, we use random coil peptides containing glutamine instead of glycine to determine the random coil chemical shifts and the neighbor correction factors. The resulting correction factors correlate to changes in the populations of the major wells in the Ramachandran plot, which demonstrates that...... changes in the conformational ensemble are an important source of neighbor effects in disordered proteins. Glutamine derived random coil chemical shifts and correction factors modestly improve our ability to predict (13)C chemical shifts of intrinsically disordered proteins compared to existing datasets......Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues...
Parameter-free calculation of K alpha chemical shifts for Al, Si, and Ge oxides
DEFF Research Database (Denmark)
Lægsgaard, Jesper
2001-01-01
The chemical shifts of the K alpha radiation line from Al, Si, and Ge ions between their elemental and oxide forms are calculated within the framework of density functional theory using ultrasoft pseudopotentials. It is demonstrated that this theoretical approach yields quantitatively accurate re...... implanted in silica are found to be in excellent agreement with experimental data, providing support for the proposed atomic geometry....
Database proton NMR chemical shifts for RNA signal assignment and validation
International Nuclear Information System (INIS)
The Biological Magnetic Resonance Data Bank contains NMR chemical shift depositions for 132 RNAs and RNA-containing complexes. We have analyzed the 1H NMR chemical shifts reported for non-exchangeable protons of residues that reside within A-form helical regions of these RNAs. The analysis focused on the central base pair within a stretch of three adjacent base pairs (BP triplets), and included both Watson–Crick (WC; G:C, A:U) and G:U wobble pairs. Chemical shift values were included for all 43 possible WC-BP triplets, as well as 137 additional triplets that contain one or more G:U wobbles. Sequence-dependent chemical shift correlations were identified, including correlations involving terminating base pairs within the triplets and canonical and non-canonical structures adjacent to the BP triplets (i.e. bulges, loops, WC and non-WC BPs), despite the fact that the NMR data were obtained under different conditions of pH, buffer, ionic strength, and temperature. A computer program (RNAShifts) was developed that enables convenient comparison of RNA 1H NMR assignments with database predictions, which should facilitate future signal assignment/validation efforts and enable rapid identification of non-canonical RNA structures and RNA-ligand/protein interaction sites.
Payne, R.; Magee, R. J.; Liesegang, J.
1982-11-01
Measurements of the IR stretching frequencies of the NC and MS bonds in transition-metal (M) dithiocarbamates show significant correlation with measurement of core level XPS chemical shifts. This is believed to be the first demonstration of such a correlation for a series of solid-phase compounds.
Automated assignment of NMR chemical shifts based on a known structure and 4D spectra.
Trautwein, Matthias; Fredriksson, Kai; Möller, Heiko M; Exner, Thomas E
2016-08-01
Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [(1)H,(15)N]-HSQC-NOESY-[(1)H,(15)N]-HSQC spectra which is able to assign a large percentage of chemical shifts (73-82 %) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95 % of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzyme I. The program including source code is available at https://github.com/thomasexner/4Dassign . PMID:27484442
Ab Initio Calculations of Deuterium Isotope Effects on Chemical Shifts of Salt-Bridged Lysines
DEFF Research Database (Denmark)
Ullah, Saif; Ishimoto, Takayoshi; Williamson, Mike P.;
2011-01-01
Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation. This me...
Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins
Tamiola, Kamil; Mulder, Frans A. A.
2012-01-01
NMR spectroscopy offers the unique possibility to relate the structural propensities of disordered proteins and loop segments of folded peptides to biological function and aggregation behaviour. Backbone chemical shifts are ideally suited for this task, provided that appropriate reference data are a
Identification of helix capping and {beta}-turn motifs from NMR chemical shifts
Energy Technology Data Exchange (ETDEWEB)
Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)
2012-03-15
We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and {sup 13}C{sup {beta}} chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of {beta}-turns: I, II, I Prime , II Prime and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and {beta}-turn motifs are used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. The trained neural networks, contained in the MICS (motif identification from chemical shifts) program, also provide a confidence level for each of their predictions, and values ranging from ca 0.7-0.9 for the Matthews correlation coefficient of its predictions far exceed those attainable by sequence analysis. MICS is anticipated to be useful both in the conventional NMR structure determination process and for enhancing on-going efforts to determine protein structures solely on the basis of chemical shift information, where it can aid in identifying protein database fragments suitable for use in building such structures.
Noninvasive Temperature Mapping With MRI Using Chemical Shift Water-Fat Separation
Soher, Brian J.; Wyatt, Cory; Reeder, Scott B.; MacFall, James R.
2010-01-01
Tissues containing both water and lipids, e.g., breast, confound standard MR proton reference frequency-shift methods for mapping temperatures due to the lack of temperature-induced frequency shift in lipid protons. Generalized Dixon chemical shift–based water-fat separation methods, such as GE’s iterative decomposition of water and fat with echo asymmetry and least-squares estimation method, can result in complex water and fat images. Once separated, the phase change over time of the water s...
International Nuclear Information System (INIS)
NMR-monitored chemical shift titrations for the study of weak protein–ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (KD) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the KD value of a 1:1 protein–ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125–138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of 1H–15N 2D HSQC NMR spectra acquired using precise protein–ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (koff). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, koff ∼ 3,000 s−1 in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for koff from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise koff values over a wide range, from 100 to 15,000 s−1. The validity of line shape analysis for koff values approaching intermediate exchange (∼100 s−1), may be facilitated by more accurate KD measurements from NMR-monitored chemical shift
PACSY, a relational database management system for protein structure and chemical shift analysis
International Nuclear Information System (INIS)
PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.eduhttp://pacsy.nmrfam.wisc.edu.
Directory of Open Access Journals (Sweden)
Karl-Heinz Böhm
2014-04-01
Full Text Available We present ab-initio calculations of secondary isotope effects on NMR chemical shieldings. The change of the NMR chemical shift of a certain nucleus that is observed if another nucleus is replaced by a different isotope can be calculated by computing vibrational corrections on the NMR parameters using electronic structure methods. We demonstrate that the accuracy of the computational results is sufficient to even distinguish different conformers. For this purpose, benchmark calculations for fluoro(2-2Hethane in gauche and antiperiplanar conformation are carried out at the HF, MP2 and CCSD(T level of theory using basis sets ranging from double- to quadruple-zeta quality. The methodology is applied to the secondary isotope shifts for 2-fluoronorbornane in order to resolve an ambiguity in the literature on the assignment of endo- and exo-2-fluoronorbornanes with deuterium substituents in endo-3 and exo-3 positions, also yielding insight into mechanistic details of the corresponding synthesis.
Substituent Chemical Shifts of (E)-1-Aryl-3-thienylpropen-1-ones
International Nuclear Information System (INIS)
Substituent chemical shifts were examined for the 2- and 3-thiophene derivatives of chalcone and compared to the thiophene series of derivatives with the phenyl series. The chemical shift values for the α-carbons of the enones showed and inverse correlation with the Hammett σ values, but the correlation coefficients were moderate (r = 0.836 - 0.878). On the other hand, the β-carbons showed a normal correlation with excellent correlation coefficients (r = 0.994). The absolute magnitude of the ρ values for the α-carbon are about half of those of the β-carbon. The observation may be the result of a through-space transition of the electronic effect of the substituents in addition to the through bond transition
1H chemical shift imaging characterization of human brain tumor and edema
International Nuclear Information System (INIS)
Longitudinal (T1) and transverse (T2) relaxation times of metabolites in human brain tumor, peritumoral edema, and unaffected brain tissue were assessed from point resolved spectroscopy (PRESS) 1H chemical shift imaging results at different repetition times (TR=1500 and 5000 ms; T1: n=19) and echo times (TE=135 and 270 ms; T2: n=7). Metabolite T1 and T2 relaxation times in unaffected brain tissue corresponded with those published for healthy volunteers. T2 relaxation times were reduced in tumor (choline, N-acetyl aspartate) and edema (choline, creatine) compared with unaffected brain tissue (p1H chemical shift imaging is most suited in the use of choline elevation as tumor marker. (orig.)
Casella, Girolamo; Bagno, Alessandro; Komorovsky, Stanislav; Repisky, Michal; Saielli, Giacomo
2015-12-14
We have calculated the (13)C NMR chemical shifts of a large ensemble of halogenated organic molecules (81 molecules for a total of 250 experimental (13)C NMR data at four different levels of theory), ranging from small rigid organic compounds, used to benchmark the performance of various levels of theory, to natural substances of marine origin with conformational degrees of freedom. Carbon atoms bonded to heavy halogen atoms, particularly bromine and iodine, are known to be rather challenging when it comes to the prediction of their chemical shifts by quantum methods, due to relativistic effects. In this paper, we have applied the state-of-the-art four-component relativistic density functional theory for the prediction of such NMR properties and compared the performance with two-component and nonrelativistic methods. Our results highlight the necessity to include relativistic corrections within a four-component description for the most accurate prediction of the NMR properties of halogenated organic substances. PMID:26541625
International Nuclear Information System (INIS)
A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ≥90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (φ, ψ) torsion angles of ca 12º. TALOS-N also reports sidechain χ1 rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts
Energy Technology Data Exchange (ETDEWEB)
Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)
2013-07-15
A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, {>=}90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed ({phi}, {psi}) torsion angles of ca 12 Masculine-Ordinal-Indicator . TALOS-N also reports sidechain {chi}{sup 1} rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts.
Using Neural Networks for 13C NMR Chemical Shift Prediction-Comparison with Traditional Methods
Meiler, Jens; Maier, Walter; Will, Martin; Meusinger, Reinhard
2002-08-01
Interpretation of 13C chemical shifts is essential for structure elucidation of organic molecules by NMR. In this article, we present an improved neural network approach and compare its performance to that of commonly used approaches. Specifically, our recently proposed neural network ( J. Chem. Inf. Comput. Sci. 2000, 40, 1169-1176) is improved by introducing an extended hybrid numerical description of the carbon atom environment, resulting in a standard deviation (std. dev.) of 2.4 ppm for an independent test data set of ˜42,500 carbons. Thus, this neural network allows fast and accurate 13C NMR chemical shift prediction without the necessity of access to molecule or fragment databases. For an unbiased test dataset containing 100 organic structures the accuracy of the improved neural network was compared to that of a prediction method based on the HOSE code ( hierarchically ordered spherical description of environment) using S PECI NFO. The results show the neural network predictions to be of quality (std. dev.=2.7 ppm) comparable to that of the HOSE code prediction (std. dev.=2.6 ppm). Further we compare the neural network predictions to those of a wide variety of other 13C chemical shift prediction tools including incremental methods (C HEMD RAW, S PECT OOL), quantum chemical calculation (G AUSSIAN, C OSMOS), and HOSE code fragment-based prediction (S PECI NFO, ACD/CNMR, P REDICTI T NMR) for the 47 13C-NMR shifts of Taxol, a natural product including many structural features of organic substances. The smallest standard deviations were achieved here with the neural network (1.3 ppm) and S PECI NFO (1.0 ppm).
Relationship between electrophilicity index, Hammett constant and nucleus-independent chemical shift
Indian Academy of Sciences (India)
M Elango; R Parthasarathi; G Karthik Narayanan; A Md Sabeelullah; U Sarkar; N S Venkatasubramaniyan; V Subramanian; P K Chattaraj
2005-01-01
Inter-relationships between the electrophilicity index (), Hammett constant (ó) and nucleusindependent chemical shift (NICS (1) - NICS value one å ngstrom above the ring centre) have been investigated for a series of meta- and para-substituted benzoic acids. Good linear relationships between Hammett constant vs electrophilicity and Hammett constant vs NICS (1) values have been observed. However, the variation of NICS (1) against shows only a low correlation coefficient.
Chemical shifts and EXAFS in some rare-earth metals and compounds
International Nuclear Information System (INIS)
The positions of the Lsub(111) absorption edge and accompanying Kossel and EXAFS oscillations of terbium, dysprosium and holmium in metals and compounds (acetate, carbonate, chloride, fluoride, nitrate, oxalate, oxide, phosphate and sulphate) have been measured. The chemical shifts of the main edge range from about 1 eV to about 10 eV and the EXAFS are observed up to about 150 eV. (author)
On the bathochromic shift of the absorption by astaxanthin in crustacyanin: a quantum chemical study
Durbeej, Bo; Eriksson, Leif A.
2003-06-01
The structural origin of the bathochromic shift assumed by the electronic absorption spectrum of protein-bound astaxanthin, the carotenoid that upon binding to crustacyanin is responsible for the blue colouration of lobster shell, is investigated by means of quantum chemical methods. The calculations suggest that the bathochromic shift is largely due to one of the astaxanthin C4 keto groups being hydrogen-bonded to a histidine residue of the surrounding protein, and that the effect of this histidine is directly dependent on its protonation state. Out of the different methodologies (CIS, TD-DFT, and ZINDO/S) employed to calculate wavelengths of maximum absorption, the best agreement with experimental data is obtained using the semiempirical ZINDO/S method.
Energy Technology Data Exchange (ETDEWEB)
Fritzsching, Keith J., E-mail: kfritzsc@brandeis.edu [Brandeis University, Department of Chemistry (United States); Hong, Mei [Massachusetts Institute of Technology, Department of Chemistry (United States); Schmidt-Rohr, Klaus, E-mail: srohr@brandeis.edu [Brandeis University, Department of Chemistry (United States)
2016-02-15
We have determined refined multidimensional chemical shift ranges for intra-residue correlations ({sup 13}C–{sup 13}C, {sup 15}N–{sup 13}C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 {sup 13}C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited “hand-picked” data sets, we show that ∼94 % of the {sup 13}C NMR data and almost all {sup 15}N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6 % of the {sup 13}C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. −2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra
International Nuclear Information System (INIS)
We have determined refined multidimensional chemical shift ranges for intra-residue correlations (13C–13C, 15N–13C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 13C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited “hand-picked” data sets, we show that ∼94 % of the 13C NMR data and almost all 15N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6 % of the 13C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. −2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra-residue cross peaks by inspection or by using a provided
Fritzsching, Keith J; Hong, Mei; Schmidt-Rohr, Klaus
2016-02-01
We have determined refined multidimensional chemical shift ranges for intra-residue correlations ((13)C-(13)C, (15)N-(13)C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 (13)C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited "hand-picked" data sets, we show that ~94% of the (13)C NMR data and almost all (15)N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6% of the (13)C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. -2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra-residue cross peaks by inspection or by using a provided
Energy Technology Data Exchange (ETDEWEB)
Shen Yang; Bax, Ad, E-mail: bax@nih.go [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)
2010-09-15
NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and {sup 13}C{sup {beta}} chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and {sup 13}C{sup {beta}} atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for {delta}{sup 15}N, {delta}{sup 13}C', {delta}{sup 13}C{sup {alpha}}, {delta}{sup 13}C{sup {beta}}, {delta}{sup 1}H{sup {alpha}} and {delta}{sup 1}H{sup N}, respectively, between the SPARTA+ predicted and experimental shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2-10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chemical shifts.
International Nuclear Information System (INIS)
NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and 13Cβ chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and 13Cβ atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for δ15N, δ13C', δ13Cα, δ13Cβ, δ1Hα and δ1HN, respectively, between the SPARTA+ predicted and experimental shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2-10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chemical shifts.
Simulations of Xe-129 NMR chemical shift of atomic xenon dissolved in liquid benzene
Czech Academy of Sciences Publication Activity Database
Standara, Stanislav; Kulhánek, P.; Marek, R.; Horníček, Jan; Bouř, Petr; Straka, Michal
2011-01-01
Roč. 129, 3/5 (2011), s. 677-684. ISSN 1432-881X R&D Projects: GA ČR GA203/09/2037; GA ČR GAP208/11/0105 Grant ostatní: AV ČR(CZ) M200550902; European Reintegration Grant(XE) 230955; European Community(XE) 205872 Institutional research plan: CEZ:AV0Z40550506 Keywords : Xe-129 NMR chemical shift * dynamical averaging * density functional theory * Breit-Pauli perturbation theory * relativistic effects Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.162, year: 2011
Grodzka, P.; Facemire, B.
1977-01-01
Three investigations conducted aboard Skylab IV and Apollo-Soyuz involved phenomena that are of interest to the biochemistry community. The formaldehyde clock reaction and the equilibrium shift reaction experiments conducted aboard Apollo Soyuz demonstrate the effect of low-g foams or air/liquid dispersions on reaction rate and chemical equilibrium. The electrodeposition reaction experiment conducted aboard Skylab IV demonstrate the effect of a low-g environment on an electrochemical displacement reaction. The implications of the three space experiments for various applications are considered.
Calculation of NMR chemical shifts. 7. Gauge-invariant INDO method
Fukui, H.; Miura, K.; Hirai, A.
A gauge-invariant INDO method based on the coupled Hartree-Fuck perturbation theory is presented and applied to the calculation of 1H and 13C chemical shifts of hydrocarbons including ring compounds. Invariance of the diamagnetic and paramagnetic shieldings with respect to displacement of the coordinate origin is discussed. Comparison between calculated and experimental results exhibits fairly good agreement, provided that the INDO parameters of Ellis et al. (J. Am. Chem. Soc.94, 4069 (1972)) are used with the inclusion of all multicenter one-electron integrals.
International Nuclear Information System (INIS)
An analysis is presented of the influences of High-Temperature Reactor on probable location shifting of big chemical plants, in the future. This is done by a spatial location model, that includes an investigation on 116 industrial locations within the first six countries of Common Market. The results of a computerized program show differences in location qualities when furnished either with traditional or with nuclear energy systems. In addition to location factor energy some other important factors, as subventions, taxes, labour, and transport costs are analysed, and their influence on industrial location is quantified. (orig.)
NMR Chemical Shift Ranges of Urine Metabolites in Various Organic Solvents.
Görling, Benjamin; Bräse, Stefan; Luy, Burkhard
2016-01-01
Signal stability is essential for reliable multivariate data analysis. Urine samples show strong variance in signal positions due to inter patient differences. Here we study the exchange of the solvent of a defined urine matrix and how it affects signal and integral stability of the urinary metabolites by NMR spectroscopy. The exchange solvents were methanol, acetonitrile, dimethyl sulfoxide, chloroform, acetone, dichloromethane, and dimethyl formamide. Some of these solvents showed promising results with a single batch of urine. To evaluate further differences between urine samples, various acid, base, and salt solutions were added in a defined way mimicking to some extent inter human differences. Corresponding chemical shift changes were monitored. PMID:27598217
DEFF Research Database (Denmark)
Hanson, Lars Peter Grüner; Adalsteinsson, E; Pfefferbaum, A;
2000-01-01
Quantification of gray and white matter levels of spectroscopically visible metabolites can provide important insights into brain development and pathological conditions. Chemical shift imaging offers a gain in efficiency for estimation of global gray and white matter metabolite concentrations co...
Qualitative Study of Substituent Effects on NMR 15N and 17O Chemical Shifts
Contreras, Rubén H.; Llorente, Tomás; Pagola, Gabriel I.; Bustamante, Manuel G.; Pasqualini, Enrique E.; Melo, Juan I.; Tormena, Cláudio F.
2009-08-01
A qualitative approach to analyze the electronic origin of substituent effects on the paramagnetic part of chemical shifts is described and applied to few model systems, where its potentiality can be appreciated. The formulation of this approach is based on the following grounds. The influence of different inter- or intramolecular interactions on a second-order property can be qualitatively predicted if it can be known how they affect the main virtual excitations entering into that second-order property. A set of consistent approximations are introduced in order to analyze the behavior of occupied and virtual orbitals that define some experimental trends of magnetic shielding constants. This approach is applied first to study the electronic origin of methyl-β substituent effects on both 15N and 17O chemical shifts, and afterward it is applied to a couple of examples of long-range substituent effects originated in charge transfer interactions such as the conjugative effect in aromatic compounds and σ-hyperconjugative interactions in saturated multicyclic compounds.
Qualitative study of substituent effects on NMR (15)N and (17)O chemical shifts.
Contreras, Rubén H; Llorente, Tomás; Pagola, Gabriel I; Bustamante, Manuel G; Pasqualini, Enrique E; Melo, Juan I; Tormena, Cláudio F
2009-09-10
A qualitative approach to analyze the electronic origin of substituent effects on the paramagnetic part of chemical shifts is described and applied to few model systems, where its potentiality can be appreciated. The formulation of this approach is based on the following grounds. The influence of different inter- or intramolecular interactions on a second-order property can be qualitatively predicted if it can be known how they affect the main virtual excitations entering into that second-order property. A set of consistent approximations are introduced in order to analyze the behavior of occupied and virtual orbitals that define some experimental trends of magnetic shielding constants. This approach is applied first to study the electronic origin of methyl-beta substituent effects on both (15)N and (17)O chemical shifts, and afterward it is applied to a couple of examples of long-range substituent effects originated in charge transfer interactions such as the conjugative effect in aromatic compounds and sigma-hyperconjugative interactions in saturated multicyclic compounds. PMID:19685922
Stereoelectronic effects on 1H nuclear magnetic resonance chemical shifts in methoxybenzenes
DEFF Research Database (Denmark)
Lambert, Maja; Olsen, Lars; Jaroszewski, Jerzy W
2006-01-01
differences are due to different conformational behavior of the OH and OCH3 groups; while the ortho-disubstituted OH group remains planar in polyphenols due to hydrogen bonding and conjugative stabilization, the steric congestion in ortho-disubstituted anisoles outweighs the conjugative effects and forces the......Investigation of all O-methyl ethers of 1,2,3-benzenetriol and 4-methyl-1,2,3-benzenetriol (3-16) by 1H NMR spectroscopy and density-functional calculations disclosed practically useful conformational effects on 1H NMR chemical shifts in the aromatic ring. While the conversion of phenol (2) to...... Ar-OCH3 torsion out of the ring plane, resulting in large stereoelectronic effects on the chemical shift of Hpara. Conformational searches and geometry optimizations for 3-16 at the B3LYP/6-31G** level, followed by B3LYP/6-311++G(2d,2p) calculations for all low-energy conformers, gave excellent...
Water-fat imaging and general chemical shift imaging with spectrum modeling
An, Li
Water-fat chemical shift imaging (CSI) has been an active research area in magnetic resonance imaging (MRI) since the early 1980's. There are two main reasons for water- fat imaging. First, water-fat imaging can serve as a fat- suppression method. Removing the usually bright fatty signals not only extends the useful dynamic range of an image, but also allows better visualization of lesions or injected contrast, and removes chemical shift artifacts, which may contribute to improved diagnosis. Second, quantification of water and fat provides useful chemical information for characterizing tissues such as bone marrow, liver, and adrenal masses. A milestone in water- fat imaging is the Dixon method that can produce separate water and fat images with only two data acquisitions. In practice, however, the Dixon method is not always successful due to field inhomogeneity problems. In recent years, many variations of the Dixon method have been proposed to overcome the field inhomogeneity problem. In general, these methods can at best separate water and fat without identifying the two because the water and fat magnetization vectors are sampled symmetrically, only parallel and anti-parallel. Furthermore, these methods usually depend on two-dimensional phase unwrapping which itself is sensitive to noise and artifacts, and becomes unreliable when the images have disconnected tissues in the field-of-view (FOV). We will first introduce the basic principles of nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) in chapter 1, and briefly review the existing water-fat imaging techniques in chapter 2. In chapter 3, we will introduce a new method for water-fat imaging. With three image acquisitions, a general direct phase encoding (DPE) of the chemical shift information is achieved, which allows an unambiguous determination of water and fat on a pixel by pixel basis. Details of specific implementations and noise performance will be discussed. Representative results
Nagamura, Naoka; Kitada, Yuta; Tsurumi, Junto; Matsui, Hiroyuki; Horiba, Koji; Honma, Itaru; Takeya, Jun; Oshima, Masaharu
2015-06-01
A chemical potential shift in an organic field effect transistor (OFET) during operation has been revealed by soft X-ray operando nano-spectroscopy analysis performed using a three-dimensional nanoscale electron-spectroscopy chemical analysis system. OFETs were fabricated using ultrathin (3 ML or 12 nm) single-crystalline C10-DNBDT-NW films on SiO2 (200 nm)/Si substrates with a backgate electrode and top source/drain Au electrodes, and C 1s line profiles under biasing at the backgate and drain electrodes were measured. When applying -30 V to the backgate, there is C 1s core level shift of 0.1 eV; this shift can be attributed to a chemical potential shift corresponding to band bending by the field effect, resulting in p-type doping.
International Nuclear Information System (INIS)
A chemical potential shift in an organic field effect transistor (OFET) during operation has been revealed by soft X-ray operando nano-spectroscopy analysis performed using a three-dimensional nanoscale electron-spectroscopy chemical analysis system. OFETs were fabricated using ultrathin (3 ML or 12 nm) single-crystalline C10-DNBDT-NW films on SiO2 (200 nm)/Si substrates with a backgate electrode and top source/drain Au electrodes, and C 1s line profiles under biasing at the backgate and drain electrodes were measured. When applying −30 V to the backgate, there is C 1s core level shift of 0.1 eV; this shift can be attributed to a chemical potential shift corresponding to band bending by the field effect, resulting in p-type doping
Energy Technology Data Exchange (ETDEWEB)
Nagamura, Naoka, E-mail: NAGAMURA.Naoka@nims.go.jp; Kitada, Yuta; Honma, Itaru [Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Tsurumi, Junto; Matsui, Hiroyuki; Takeya, Jun [Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561 (Japan); Horiba, Koji [Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Oshima, Masaharu [Synchrotron Radiation Research Organization, The University of Tokyo, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan)
2015-06-22
A chemical potential shift in an organic field effect transistor (OFET) during operation has been revealed by soft X-ray operando nano-spectroscopy analysis performed using a three-dimensional nanoscale electron-spectroscopy chemical analysis system. OFETs were fabricated using ultrathin (3 ML or 12 nm) single-crystalline C10-DNBDT-NW films on SiO{sub 2} (200 nm)/Si substrates with a backgate electrode and top source/drain Au electrodes, and C 1s line profiles under biasing at the backgate and drain electrodes were measured. When applying −30 V to the backgate, there is C 1s core level shift of 0.1 eV; this shift can be attributed to a chemical potential shift corresponding to band bending by the field effect, resulting in p-type doping.
Palazzo, Teresa A.; Truong, Tiana T.; Wong, Shirley M. T.; Mack, Emma T.; Lodewyk, Michael W.; Harrison, Jason G.; Gamage, R. Alan; Siegel, Justin B.; Kurth, Mark J.; Tantillo, Dean J.
2015-01-01
An applied computational chemistry laboratory exercise is described in which students use modern quantum chemical calculations of chemical shifts to assign the structure of a recently isolated natural product. A pre/post assessment was used to measure student learning gains and verify that students demonstrated proficiency of key learning…
Energy Technology Data Exchange (ETDEWEB)
Bermel, Wolfgang [Bruker BioSpin GmbH (Germany); Bruix, Marta [Consejo Superior de Investigaciones Cientificas, Instituto de Quimica Fisica ' ' Rocasolano' ' (Spain); Felli, Isabella C., E-mail: felli@cerm.unifi.it [University of Florence, Department of Chemistry ' Ugo Shiff' (Italy); Kumar, M.V. Vasantha [University of Florence, Magnetic Resonance Center (Italy); Pierattelli, Roberta, E-mail: pierattelli@cerm.unifi.it [University of Florence, Department of Chemistry ' Ugo Shiff' (Italy); Serrano, Soraya [Consejo Superior de Investigaciones Cientificas, Instituto de Quimica Fisica ' ' Rocasolano' ' (Spain)
2013-03-15
Intrinsically disordered proteins (IDPs) have recently attracted the attention of the scientific community challenging the well accepted structure-function paradigm. In the characterization of the dynamic features of proteins nuclear magnetic resonance spectroscopy (NMR) is a strategic tool of investigation. However the peculiar properties of IDPs, with the lack of a unique 3D structure and their high flexibility, have a strong impact on NMR observables (low chemical shift dispersion, efficient solvent exchange broadening) and thus on the quality of NMR spectra. Key aspects to be considered in the design of new NMR experiments optimized for the study of IDPs are discussed. A new experiment, based on direct detection of {sup 13}C{sup {alpha}}, is proposed.
Study of wavelength-shifting chemicals for use in large-scale water Cherenkov detectors
Energy Technology Data Exchange (ETDEWEB)
Sweany, M; Bernstein, A; Dazeley, S; Dunmore, J; Felde, J; Svoboda, R; Tripathi, S M
2011-09-21
Cherenkov detectors employ various methods to maximize light collection at the photomultiplier tubes (PMTs). These generally involve the use of highly reflective materials lining the interior of the detector, reflective materials around the PMTs, or wavelength-shifting sheets around the PMTs. Recently, the use of water-soluble wavelength-shifters has been explored to increase the measurable light yield of Cherenkov radiation in water. These wave-shifting chemicals are capable of absorbing light in the ultravoilet and re-emitting the light in a range detectable by PMTs. Using a 250 L water Cherenkov detector, we have characterized the increase in light yield from three compounds in water: 4-Methylumbelliferone, Carbostyril-124, and Amino-G Salt. We report the gain in PMT response at a concentration of 1 ppm as: 1.88 {+-} 0.02 for 4-Methylumbelliferone, stable to within 0.5% over 50 days, 1.37 {+-} 0.03 for Carbostyril-124, and 1.20 {+-} 0.02 for Amino-G Salt. The response of 4-Methylumbelliferone was modeled, resulting in a simulated gain within 9% of the experimental gain at 1 ppm concentration. Finally, we report an increase in neutron detection performance of a large-scale (3.5 kL) gadolinium-doped water Cherenkov detector at a 4-Methylumbelliferone concentration of 1 ppm.
Study of wavelength-shifting chemicals for use in large-scale water Cherenkov detectors
International Nuclear Information System (INIS)
Cherenkov detectors employ various methods to maximize light collection at the photomultiplier tubes (PMTs). These generally involve the use of highly reflective materials lining the interior of the detector, reflective materials around the PMTs, or wavelength-shifting sheets around the PMTs. Recently, the use of water-soluble wavelength-shifters has been explored to increase the measurable light yield of Cherenkov radiation in water. These wave-shifting chemicals are capable of absorbing light in the ultraviolet and re-emitting the light in a range detectable by PMTs. Using a 250 L water Cherenkov detector, we have characterized the increase in light yield from three compounds in water: 4-Methylumbelliferone, Carbostyril-124, and Amino-G Salt. We report the gain in PMT response at a concentration of 1 ppm as 1.88±0.02 for 4-Methylumbelliferone, stable within 0.5% over 50 days, 1.37±0.03 for Carbostyril-124, and 1.20±0.02 for Amino-G Salt. The response of 4-Methylumbelliferone was modeled, resulting in a simulated gain within 9% of the experimental gain at 1 ppm concentration. Finally, we report an increase in neutron detection performance of a large-scale (3.5 kL) gadolinium-doped water Cherenkov detector at a 4-Methylumbelliferone concentration of 1 ppm.
Study of wavelength-shifting chemicals for use in large-scale water Cherenkov detectors
Sweany, M; Dazeley, S; Dunmore, J; Felde, J; Svoboda, R; Tripathi, M
2011-01-01
Cherenkov detectors employ various methods to maximize light collection at the photomultiplier tubes (PMTs). These generally involve the use of highly reflective materials lining the interior of the detector, reflective materials around the PMTs, or wavelength-shifting sheets around the PMTs. Recently, the use of water-soluble wavelength-shifters has been explored to increase the measurable light yield of Cherenkov radiation in water. These wave-shifting chemicals are capable of absorbing light in the ultravoilet and re-emitting the light in a range detectable by PMTs. Using a 250 L water Cherenkov detector, we have characterized the increase in light yield from three compounds in water: 4-Methylumbelliferone, Carbostyril-124, and Amino-G Salt. We report the gain in PMT response at a concentration of 1 ppm as: 1.88 $\\pm$ 0.02 for 4-Methylumbelliferone, stable to within 0.5% over 50 days, 1.37 $\\pm$ 0.03 for Carbostyril-124, and 1.20 $\\pm$ 0.02 for Amino-G Salt. The response of 4-Methylumbelliferone was modele...
Clinical application of 1H-chemical-shift imaging (CSI) to brain diseases
International Nuclear Information System (INIS)
An H-1 chemical shift imaging (CSI) was developed as part of the clinical MRI system, by which magnetic resonance spectra (MRS) can be obtained from multiple small voxels and metabolite distribution in the brain can be visualized. The present study was to determine the feasibility and clinical potential of using an H-1 CSI. The device used was a Magnetom H 15 apparatus. The study population was comprised of 25 healthy subjects, 20 patients with brain tumor, 4 with ischemic disease, and 6 with miscellaneous degenerative disease. The H-1 CSI was obtained by the 3-dimensional Fourier transformation. After suppressing the lipid signal by the inversion-recovery method and the water signal by the chemical-shift selective pulse with a following dephasing gradient, 2-directional 16 x 16 phase encodings were applied to the 16 x 16∼18 x 18 cm field of view, in which a 8 x 8 x 2∼10 x 10 x 2 cm area was selected by the stimulated echo or spin-echo method. The metabolite mapping and its contour mapping were created by using the curve-fitted area, with interpolation to the 256 x 256 matrix. In the healthy group, high resolution spectra for N-acetyl aspartate (NAA), creatine, choline (Cho), and glutamine/glutamate were obtained from each voxel; and metabolite mapping and contour mapping also clearly showed metabolite distribution in the brain. In the group of brain tumor, an increased Cho and lactate and loss of NAA were observed, along with heterogeneity within the tumor and changes in the surrounding tissue; and there was a good correlation between lactate peak and tumor malignancy. The group of ischemic and degenerative disease had a decreased NAA and increased lactate on both spectra and metabolite mapping, depending on disease stage. These findings indicated that H-1 CSI is helpful for detecting spectra over the whole brain, as well as for determining metabolite distribution. (N.K.)
Shaghaghi, Hoora; Ebrahimi, Hossein Pasha; Fathi, Fariba; Bahrami Panah, Niloufar; Jalali-Heravi, Mehdi; Tafazzoli, Mohsen
2016-05-30
The dependency of amino acid chemical shifts on φ and ψ torsion angle is, independently, studied using a five-residue fragment of ubiquitin and ONIOM(DFT:HF) approach. The variation of absolute deviation of (13) C(α) chemical shifts relative to φ dihedral angle is specifically dependent on secondary structure of protein not on amino acid type and fragment sequence. This dependency is observed neither on any of (13) C(β) , and (1) H(α) chemical shifts nor on the variation of absolute deviation of (13) C(α) chemical shifts relative to ψ dihedral angle. The (13) C(α) absolute deviation chemical shifts (ADCC) plots are found as a suitable and simple tool to predict secondary structure of protein with no requirement of highly accurate calculations, priori knowledge of protein structure and structural refinement. Comparison of Full-DFT and ONIOM(DFT:HF) approaches illustrates that the trend of (13) C(α) ADCC plots are independent of computational method but not of basis set valence shell type. © 2016 Wiley Periodicals, Inc. PMID:26940760
Chemical shifts of the X-ray L3 absorption edge of europium in its trivalent halides
International Nuclear Information System (INIS)
Position of the Eu-L3 absorption edge has been studied in pure metal and in its trivalent halides, EuF3, EuCl3, EuBr3, and EuI3, employing a simple X-ray spectrometer with an LiF single crystal as the analyser. A linear relationship was established between the chemical shift and the effective charge on the absorbing rare earth atom. The chemical shifts have also been correlated to Moessbauer isomer shifts. The results have been discussed in terms of nature of chemical bonding, effective atomic charge on the absorbing atom and some other parameters relevant to the immediate local environment of the absorbing atom. (author)
Ota, Y; Ohba, I; Yoshida, N; Mikami, Shuji; Ohba, Ichiro; Ota, Yukihiro; Yoshida, Noriyuki
2006-01-01
Recently, Yu, Brown, and Chuang [Phys. Rev. A {\\bf 71}, 032341 (2005)] investigated the entanglement attainable from unitary transformed thermal states in liquid-state nuclear magnetic resonance (NMR). Their research gave an insight into the role of the entanglement in a liquid-state NMR quantum computer. Moreover, they attempted to reveal the role of mixed-state entanglement in quantum computing. However, they assumed that the Zeeman energy of each nuclear spin which corresponds to a qubit takes a common value for all; there is no chemical shift. In this paper, we research a model with the chemical shifts and analytically derive the physical parameter region where unitary transformed thermal states are entangled, by the positive partial transposition (PPT) criterion with respect to any bipartition. We examine the effect of the chemical shifts on the boundary between the separability and the nonseparability, and find it is negligible.
Soubias, O.; Jolibois, F.; Massou, S.; Milon, A.; Réat, V.
2005-01-01
A new strategy was established to determine the average orientation and dynamics of ergosterol in dimyristoylphosphatidylcholine model membranes. It is based on the analysis of chemical shift anisotropies (CSAs) averaged by the molecular dynamics. Static 13C CSA tensors were computed by quantum chemistry, using the gauge-including atomic-orbital approach within Hartree-Fock theory. Uniformly 13C-labeled ergosterol was purified from Pichia pastoris cells grown on labeled methanol. After reconstitution into dimyristoylphosphatidylcholine lipids, the complete 1H and 13C assignment of ergosterol's resonances was performed using a combination of magic-angle spinning two-dimensional experiments. Dynamically averaged CSAs were determined by standard side-band intensity analysis for isolated 13C resonances (C3 and ethylenic carbons) and by off-magic-angle spinning experiments for other carbons. A set of 18 constraints was thus obtained, from which the sterol's molecular order parameter and average orientation could be precisely defined. The validity of using computed CSAs in this strategy was verified on cholesterol model systems. This new method allowed us to quantify ergosterol's dynamics at three molar ratios: 16 mol % (Ld phase), 30 mol % (Lo phase), and 23 mol % (mixed phases). Contrary to cholesterol, ergosterol's molecular diffusion axis makes an important angle (14°) with the inertial axis of the rigid four-ring system. PMID:15923221
Pandey, Manoj Kumar; Nishiyama, Yusuke
2015-12-01
The extraction of chemical shift anisotropy (CSA) tensors of protons either directly bonded to 14N nuclei (I = 1) or lying in their vicinity using rotor-synchronous recoupling pulse sequence is always fraught with difficulty due to simultaneous recoupling of 14N-1H heteronuclear dipolar couplings and the lack of methods to efficiently decouple these interactions. This difficulty mainly arises from the presence of large 14N quadrupolar interactions in comparison to the rf field that can practically be achieved. In the present work it is demonstrated that the application of on-resonance 14N-1H decoupling with rf field strength ∼30 times weaker than the 14N quadrupolar coupling during 1H CSA recoupling under ultrafast MAS (90 kHz) results in CSA lineshapes that are free from any distortions from recoupled 14N-1H interactions. With the use of extensive numerical simulations we have shown the applicability of our proposed method on a naturally abundant L-Histidine HCl·H2O sample.
Webster, Nicole S; Xavier, Joana R; Freckelton, Marnie; Motti, Cherie A; Cobb, Rose
2008-12-01
The microbial community composition in affected and unaffected portions of diseased sponges and healthy control sponges of Aplysina aerophoba was assessed to ascertain the role of microbes in the disease process. Sponge secondary metabolites were also examined to assess chemical shifts in response to infection. The microbial profile and aplysinimine levels in unaffected tissue near the lesions closely reflected those of healthy sponge tissue, indicating a highly localized disease process. DGGE detected multiple sequences that were exclusively present in diseased sponges. Most notably, a Deltaproteobacteria sequence with high homology to a coral black band disease strain was detected in all sponge lesions and was absent from all healthy and unaffected regions of diseased sponges. Other potential pathogens identified by DGGE include an environmental Cytophaga strain and a novel Epsilonproteobacteria strain with no known close relatives. The disease process also caused a major shift in prokaryote community structure at a very high taxonomic level. Using 16S rRNA gene sequence analysis, only the diseased sponges were found to contain sequences belonging to the Epsilonproteobacteria and Firmicutes, and there was a much greater number of Bacteroidetes sequences within the diseased sponges. In contrast, only the healthy sponges contained sequences corresponding to the cyanobacteria and 'OP1' candidate division, and the healthy sponges were dominated by Chloroflexi and Gammaproteobacteria sequences. Overall bacterial diversity was found to be considerably higher in diseased sponges than in healthy sponges. These results provide a platform for future cultivation-based experiments to isolate the putative pathogens from A. aerophoba and perform re-infection trials to define the disease aetiology. PMID:18783385
Arcisauskaite, Vaida; Melo, Juan I; Hemmingsen, Lars; Sauer, Stephan P A
2011-07-28
We investigate the importance of relativistic effects on NMR shielding constants and chemical shifts of linear HgL(2) (L = Cl, Br, I, CH(3)) compounds using three different relativistic methods: the fully relativistic four-component approach and the two-component approximations, linear response elimination of small component (LR-ESC) and zeroth-order regular approximation (ZORA). LR-ESC reproduces successfully the four-component results for the C shielding constant in Hg(CH(3))(2) within 6 ppm, but fails to reproduce the Hg shielding constants and chemical shifts. The latter is mainly due to an underestimation of the change in spin-orbit contribution. Even though ZORA underestimates the absolute Hg NMR shielding constants by ∼2100 ppm, the differences between Hg chemical shift values obtained using ZORA and the four-component approach without spin-density contribution to the exchange-correlation (XC) kernel are less than 60 ppm for all compounds using three different functionals, BP86, B3LYP, and PBE0. However, larger deviations (up to 366 ppm) occur for Hg chemical shifts in HgBr(2) and HgI(2) when ZORA results are compared with four-component calculations with non-collinear spin-density contribution to the XC kernel. For the ZORA calculations it is necessary to use large basis sets (QZ4P) and the TZ2P basis set may give errors of ∼500 ppm for the Hg chemical shifts, despite deceivingly good agreement with experimental data. A Gaussian nucleus model for the Coulomb potential reduces the Hg shielding constants by ∼100-500 ppm and the Hg chemical shifts by 1-143 ppm compared to the point nucleus model depending on the atomic number Z of the coordinating atom and the level of theory. The effect on the shielding constants of the lighter nuclei (C, Cl, Br, I) is, however, negligible. PMID:21806118
International Nuclear Information System (INIS)
Background: Computed tomography (CT) histogram analysis and chemical-shift magnetic resonance imaging (MRI) are currently used modalities for adrenal mass characterization. However, it is not yet clear which modality can be regarded as most sensitive in terms of adrenal mass characterization. Purpose: To prospectively compare CT histogram analysis and chemical-shift MRI in the characterization of adrenal masses. Material and Methods: Between May 2007 and November 2008, 93 patients (45 males, 48 females; mean age 56.7 years, range 22-85 years) with 109 adrenal masses prospectively underwent both unenhanced CT and chemical-shift MRI examinations. These masses consisted of 67 adenomas and 42 metastases. Histogram analysis was applied with a circular region of interest (ROI) that recorded mean attenuation, total number of pixels, number of negative pixels, and the percentage of negative pixels on unenhanced CT images for each adrenal mass. In the CT histogram analysis, a 10% negative pixel threshold for unenhanced CT was calculated. In chemical-shift MRI, signal intensity drop between in-phase and opposed-phase images was quantitatively calculated so that adrenal-to-spleen chemical-shift ratios and adrenal signal intensity indexes were determined for each of the adrenal masses. A mass was regarded as an adenoma if it contained more than 10% negative pixels by CT histogram analysis, showed an adrenal-to-spleen chemical-shift ratio of less than 0.71, and had an adrenal signal intensity index of more than 16.5% by chemical-shift MRI. The results were compared to reveal which method was most sensitive in the diagnosis of adrenal masses and whether or not a correlation exists between these two modalities. Final diagnoses were based on imaging follow-up of minimum 6 months, biopsy, surgery, and adrenal washout study. Results: On unenhanced CT examinations, all of the 67 adenomas and 21 out of 42 metastases exhibited negative pixels. None of the metastases showed more than 10
Energy Technology Data Exchange (ETDEWEB)
Halefoglu, A.M.; Yasar, A.; Bas, N.; Ozel, A.; Erturk, S.M.; Basak, M. (Dept. of Radiology, Sisli Etfal Training and Research Hospital, Sisli, Istanbul (Turkey))
2009-11-15
Background: Computed tomography (CT) histogram analysis and chemical-shift magnetic resonance imaging (MRI) are currently used modalities for adrenal mass characterization. However, it is not yet clear which modality can be regarded as most sensitive in terms of adrenal mass characterization. Purpose: To prospectively compare CT histogram analysis and chemical-shift MRI in the characterization of adrenal masses. Material and Methods: Between May 2007 and November 2008, 93 patients (45 males, 48 females; mean age 56.7 years, range 22-85 years) with 109 adrenal masses prospectively underwent both unenhanced CT and chemical-shift MRI examinations. These masses consisted of 67 adenomas and 42 metastases. Histogram analysis was applied with a circular region of interest (ROI) that recorded mean attenuation, total number of pixels, number of negative pixels, and the percentage of negative pixels on unenhanced CT images for each adrenal mass. In the CT histogram analysis, a 10% negative pixel threshold for unenhanced CT was calculated. In chemical-shift MRI, signal intensity drop between in-phase and opposed-phase images was quantitatively calculated so that adrenal-to-spleen chemical-shift ratios and adrenal signal intensity indexes were determined for each of the adrenal masses. A mass was regarded as an adenoma if it contained more than 10% negative pixels by CT histogram analysis, showed an adrenal-to-spleen chemical-shift ratio of less than 0.71, and had an adrenal signal intensity index of more than 16.5% by chemical-shift MRI. The results were compared to reveal which method was most sensitive in the diagnosis of adrenal masses and whether or not a correlation exists between these two modalities. Final diagnoses were based on imaging follow-up of minimum 6 months, biopsy, surgery, and adrenal washout study. Results: On unenhanced CT examinations, all of the 67 adenomas and 21 out of 42 metastases exhibited negative pixels. None of the metastases showed more than 10
International Nuclear Information System (INIS)
Diagnosis of brain lesions after birth anoxia-ischemia is essential for appropriate management. Clinical evaluation is not sufficient. MRI has been proven to provide useful information. To compare abnormalities observed with MRI, including diffusion-weighted imaging (DWI), localised magnetic resonance spectroscopy (MRS) and chemical shift imaging (CSI) and correlate these findings with the clinical outcome. Fourteen full-term neonates with birth asphyxia were studied. MRI, MRS and CSI were performed within the first 4 days of life. Lesions observed with DWI were correlated with outcome, but the apparent diffusion coefficient (ADC) did improve diagnostic confidence. The mean value of Lac/Cr for the neonates with a favourable outcome was statically lower than for those who died (0.22 vs 1.04; P = 0.01). The same results were observed for the Lac/NAA ratio (0.21 vs 1.23; P = 0.01). Data obtained with localised MRS and CSI were correlated for the ratio N-acetyl-aspartate/choline, but not for the other metabolites. No correlation was found between the ADC values and the metabolite ratios. Combination of these techniques could be helpful in our understanding of the physiopathological events occurring in neonates with asphyxia. (orig.)
Repeatability of long and short echo-time in vivo proton chemical-shift imaging
International Nuclear Information System (INIS)
We carried out long (145 ms) and short (25 ms) echo time spectroscopic imaging of the brain (chemical-shift imaging, CSI) on two occasions 1 week apart on 15 healthy individuals. We found coefficients of variation (CVs) generally in the range 10-25% for long and 15-30% for short echo-time measurements. The CVs of metabolite ratios were higher by about 5-10%. Limits of agreement (defined as mean±2 SD of the week 1-week 2 differences) were wider at the shorter echo time. The modest repeatability may be due in part to the difficulty of repositioning spectroscopic voxels at a scale of 1 mm. The generally higher CVs and wider limits of agreement at TE25 ms suggest that the increased spectral complexity more than offsets the theoretical advantage of increased signal at short echo-times. Analysis of variance general linear modelling of metabolites and metabolite ratios showed that, in general, the subject, region of the brain and hemisphere were more important than the occasion in explaining the variability of results. Unless information on short-T2 metabolites is specifically required, better results can probably be achieved with longer echo-times. The magnitude of the CVs needs to be taken into account in the calculation of sample size for cross-sectional or linear studies. (orig.)
International Nuclear Information System (INIS)
Cerebral energy metabolism was evaluated by means of 31P chemical shift imaging (CSI) using the 2.0 T whole-body MRIS system. 31P CSI was carried out by means of Spectroscopic Imaging by Dephasing Amplitude Changing method, four-dimensional CSI, and three-dimensional CSI. Twenty three patients with cerebral infarction and 21 patients with hypertensive intracerebral hemorrhage were examined. In cerebral infarction, an acute infarction was seen as a low-signal area in the PCr and ATP images and as a high-signal area in the Pi image. A subacute and chronic infarction was seen as a low-signal area in all the images -- 31P, PCr, ATP, Pi, PDE and PME. Intracellular acidosis was noticed within 2 days after onset. The intracellular pH became alkaline at the subacute and chronic stages of infarction. The chronological changes in the phosphorus metabolites were evaluated by means of these methods. In hypertensive intracerebral hemorrhage, hematoma and perifocal edema in the acute stage were seen as low-signal areas in the 31P, PCr, and ATP images, and as high-signal areas in the Pi image. In the chronic stage, a hematoma was seen as a low-signal area in all the images -- 31P, PCr, ATP and Pi. 31P CSI is thus a practical tool for studying phosphate metabolites clinically. Changes in the phosphorus metabolism relative to the anatomy of interest were detected by the use of these methods. (author)
Institute of Scientific and Technical Information of China (English)
许波; 李浩然; 王从敏; 许映杰; 韩世钧
2005-01-01
1H NMR chemical shifts of binary aqueous mixtures of acylamide, alcohol, dimethyl sulphoxide (DMSO), and acetone are correlated by statistical associating fluid theory (SAFT) association model. The comparison between SAFT association model and Wilson equation shows that the former is better for dealing with aqueous solutions. Finally, the specialties of both models are discussed.
DEFF Research Database (Denmark)
Hanson, Lars Peter Grüner; Adalsteinsson, E; Pfefferbaum, A; Spielman, D.M.
2000-01-01
Quantification of gray and white matter levels of spectroscopically visible metabolites can provide important insights into brain development and pathological conditions. Chemical shift imaging offers a gain in efficiency for estimation of global gray and white matter metabolite concentrations co...... concentration error (<15%). Magn Reson Med 44:10-18, 2000....
Ichikawa, Kazuhide; Wagatsuma, Ayumu; Kurokawa, Yusaku I.; Sakaki, Shigeyoshi; Tachibana, Akitomo
2011-01-01
We study the electronic structure of two types of transition metal complexes, the inverted-sandwich-type and open-lantern-type, by the electronic stress tensor. In particular, the bond order b_e measured by the energy density which is defined from the electronic stress tensor is studied and compared with the conventional MO based bond order. We also examine the patterns found in the largest eigenvalue of the stress tensor and corresponding eigenvector field, the "spindle structure" and "pseud...
Energy Technology Data Exchange (ETDEWEB)
Ye, Libin; Larda, Sacha Thierry; Frank Li, Yi Feng [University of Toronto, UTM, Department of Chemistry (Canada); Manglik, Aashish [Stanford University School of Medicine, Department of Molecular and Cellular Physiology (United States); Prosser, R. Scott, E-mail: scott.prosser@utoronto.ca [University of Toronto, UTM, Department of Chemistry (Canada)
2015-05-15
The elucidation of distinct protein conformers or states by fluorine ({sup 19}F) NMR requires fluorinated moieties whose chemical shifts are most sensitive to subtle changes in the local dielectric and magnetic shielding environment. In this study we evaluate the effective chemical shift dispersion of a number of thiol-reactive trifluoromethyl probes [i.e. 2-bromo-N-(4-(trifluoromethyl)phenyl)acetamide (BTFMA), N-(4-bromo-3-(trifluoromethyl)phenyl)acetamide (3-BTFMA), 3-bromo-1,1,1-trifluoropropan-2-ol (BTFP), 1-bromo-3,3,4,4,4-pentafluorobutan-2-one (BPFB), 3-bromo-1,1,1-trifluoropropan-2-one (BTFA), and 2,2,2-trifluoroethyl-1-thiol (TFET)] under conditions of varying polarity. In considering the sensitivity of the {sup 19}F NMR chemical shift to the local environment, a series of methanol/water mixtures were prepared, ranging from relatively non-polar (MeOH:H{sub 2}O = 4) to polar (MeOH:H{sub 2}O = 0.25). {sup 19}F NMR spectra of the tripeptide, glutathione ((2S)-2-amino-4-{[(1R)-1-[(carboxymethyl)carbamoyl] -2-sulfanylethyl]carbamoyl}butanoic acid), conjugated to each of the above trifluoromethyl probes, revealed that the BTFMA tag exhibited a significantly greater range of chemical shift as a function of solvent polarity than did either BTFA or TFET. DFT calculations using the B3LYP hybrid functional and the 6-31G(d,p) basis set, confirmed the observed trend in chemical shift dispersion with solvent polarity.
Energy Technology Data Exchange (ETDEWEB)
Sijens, Paul E.; Oudkerk, Matthijs [University Hospital Groningen, Department of Radiology, Hanzeplein 1, P.O. Box 30001, Groningen (Netherlands); Reijngoud, Dirk-Jan; Spronsen, Francjan J. van [University Hospital Groningen, Department of Pediatrics, Groningen (Netherlands); Leenders, Klaas L. [University Hospital Groningen, Department of Neurology, Groningen (Netherlands); Valk, Harold W. de [University Medical Centre of Utrecht, Department of Internal Medicine, Utrecht (Netherlands)
2004-10-01
Short echo time single voxel methods were used in previous MR spectroscopy studies of phenylalanine (Phe) levels in phenylketonuria (PKU) patients. In this study, apparent T{sub 2} relaxation time of the 7.3-ppm Phe multiplet signal in the brain of PKU patients was assessed in order to establish which echo time would be optimal. {sup 1}H chemical shift imaging (CSI) examinations of a transverse plain above the ventricles of the brain were performed in 10 PKU patients and 11 persons not suffering from PKU at 1.5 T, using four echo times (TE 20, 40, 135 and 270 ms). Phe was detectable only when the signals from all CSI voxels were summarized. In patients suffering from PKU the T{sub 2} relaxation times of choline, creatine and N-acetyl aspartate (NAA) were similar to those previously reported for healthy volunteers (between 200 and 325 ms). The T{sub 2} of Phe in brain tissue was 215{+-}120 ms (standard deviation). In the PKU patients the brain tissue Phe concentrations were 141{+-}69 {mu}M as opposed to 58{+-}23 {mu}M in the persons not suffering from PKU. In the detection of Phe, MR spectroscopy performed at TE 135 or 270 ms is not inferior to that performed at TE 20 or 40 ms (all previous studies). Best results were obtained at TE=135 ms, relating to the fact that at that particular TE, the visibility of a compound with a T{sub 2} of 215 ms still is good, while interfering signals from short-TE compounds are negligible. (orig.)
Quantification of fat using chemical shift imaging and 1H-MR spectroscopy in phantom model
International Nuclear Information System (INIS)
Objective: To evaluate the accuracy of chemical shift imaging (CSI) and MR spectroscopy (MRS) for fat quantification in phantom model. Methods: Eleven phantoms were made according to the volume percentage of fat ranging from 0 to 100% with an interval of 10%. The fat concentration in the phantoms were measured respectively by CSI and MRS and compared using one-sample t test. The correlation between the two methods was also analyzed. The concentration of saturated fatty acids (FS), unsaturated fatty acids (FU) and the poly, unsaturation degree (PUD) were calculated by using MRS. Results: The fat concentration was (48.0±1.0)%, (57.0±0.5)%, (67.3±0.6)%, (77.3± 0.6)%, (83.3±0.6)% and (91.0±1.0)% respectively with fat volume of 50% to 100% by CSI. The fat concentration was (8.3±0.6)%, (16.3±0.7)%, (27.7±0.6)%, (36.0±1.0)%, (43.5± 0.6)% and (56.5±1.0)% respectively with fat volume of 10% to 60% by MRS, the fat concentration were underestimated by CSI and MRS (P<0.05), and had high linear correlation with the real concentration in phantoms (CSI: r=0.998, MRS: r=0.996, P<0.01). There was also a linear correlation between two methods (r=0.992, P<0.01) but no statistically significant difference (paired- samples t test, t=-0.125, P=0.903). By using MRS, the relative ratio of FS and FU in fat were 0. 15 and 0.85, the PUD was 0.0325, respectively, and highly consistent with these in phantoms. Conclusion: Both CSI and MRS are efficient and accurate methods in fat quantification at 7.0 T MR. (authors)
Female sea lamprey shift orientation toward a conspecific chemical cue to escape a sensory trap
Brant, Cory O.; Johnson, Nicholas; Li, Ke; Buchinger, Tyler J.; Li, Weiming
2016-01-01
The sensory trap model of signal evolution hypothesizes that signalers adapt to exploit a cue used by the receiver in another context. Although exploitation of receiver biases can result in conflict between the sexes, deceptive signaling systems that are mutually beneficial drive the evolution of stable communication systems. However, female responses in the nonsexual and sexual contexts may become uncoupled if costs are associated with exhibiting a similar response to a trait in both contexts. Male sea lamprey (Petromyzon marinus) signal with a mating pheromone, 3-keto petromyzonol sulfate (3kPZS), which may be a match to a juvenile cue used by females during migration. Upstream movement of migratory lampreys is partially guided by 3kPZS, but females only move toward 3kPZS with proximal accuracy during spawning. Here, we use in-stream behavioral assays paired with gonad histology to document the transition of female preference for juvenile- and male-released 3kPZS that coincides with the functional shift of 3kPZS as a migratory cue to a mating pheromone. Females became increasingly biased toward the source of synthesized 3kPZS as their maturation progressed into the reproductive phase, at which point, a preference for juvenile odor (also containing 3kPZS naturally) ceased to exist. Uncoupling of female responses during migration and spawning makes the 3kPZS communication system a reliable means of synchronizing mate search. The present study offers a rare example of a transition in female responses to a chemical cue between nonsexual and sexual contexts, provides insights into the origins of stable communication signaling systems.
Strictly nonnegative tensors and nonnegative tensor partition
Institute of Scientific and Technical Information of China (English)
HU ShengLong; HUANG ZhengHai; QI LiQun
2014-01-01
We introduce a new class of nonnegative tensors—strictly nonnegative tensors.A weakly irreducible nonnegative tensor is a strictly nonnegative tensor but not vice versa.We show that the spectral radius of a strictly nonnegative tensor is always positive.We give some necessary and su？cient conditions for the six wellconditional classes of nonnegative tensors,introduced in the literature,and a full relationship picture about strictly nonnegative tensors with these six classes of nonnegative tensors.We then establish global R-linear convergence of a power method for finding the spectral radius of a nonnegative tensor under the condition of weak irreducibility.We show that for a nonnegative tensor T,there always exists a partition of the index set such that every tensor induced by the partition is weakly irreducible;and the spectral radius of T can be obtained from those spectral radii of the induced tensors.In this way,we develop a convergent algorithm for finding the spectral radius of a general nonnegative tensor without any additional assumption.Some preliminary numerical results show the feasibility and effectiveness of the algorithm.
International Nuclear Information System (INIS)
Highlights: • Ag 3d5/2 binding energy for Ag(II)SO4 is as large as 370.1 eV. • This is the largest value ever measured for a silver (II) compound. • Large shift is connected with the extreme oxidizing nature of Ag(II) species. • Ag(I)2S2O7 exhibits both positive and negative shifts with respect to metallic Ag. • Two distinct Ag(I) sites are responsible for large BE difference of 3.6 eV. - Abstract: Anomalous chemical shifts, i.e. cases when binding energy decreases with the increase of the oxidation state, have been well-documented for selected compounds of silver, and well understood based on analysis of initial- and final-state effects in the XPS spectra. Here we report two examples of even more exotic behaviour of chemical shifts for two silver compounds. The first one is Ag2S2O7 which exhibits both positive and negative substantial shifts with respect to metallic Ag for two distinct Ag(I) sites in its crystal structure, which differ by as much as 3.6 eV. Another is AgSO4, a rare example of oxo silver (II) salt, which exhibits “normal” chemical shift but the Ag 3d5/2 binding energy takes the largest value measured for a silver (II) compound (370.1 eV). This property is connected predominantly with the extremely strongly oxidizing nature of Ag(II) species
Energy Technology Data Exchange (ETDEWEB)
Grzelak, A. [Faculty of Chemistry, University of Warsaw, Pasteur 1, 02093 Warsaw (Poland); Jaroń, T. [Centre of New Technologies, University of Warsaw, Żwirki i Wigury 93, 02089 Warsaw (Poland); Mazej, Z. [Department of Inorganic Chemistry and Technology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia); Michałowski, T. [Faculty of Chemistry, University of Warsaw, Pasteur 1, 02093 Warsaw (Poland); Centre of New Technologies, University of Warsaw, Żwirki i Wigury 93, 02089 Warsaw (Poland); Szarek, P. [Centre of New Technologies, University of Warsaw, Żwirki i Wigury 93, 02089 Warsaw (Poland); Grochala, W., E-mail: w.grochala@cent.uw.edu.pl [Faculty of Chemistry, University of Warsaw, Pasteur 1, 02093 Warsaw (Poland); Centre of New Technologies, University of Warsaw, Żwirki i Wigury 93, 02089 Warsaw (Poland)
2015-07-15
Highlights: • Ag 3d{sub 5/2} binding energy for Ag(II)SO{sub 4} is as large as 370.1 eV. • This is the largest value ever measured for a silver (II) compound. • Large shift is connected with the extreme oxidizing nature of Ag(II) species. • Ag(I){sub 2}S{sub 2}O{sub 7} exhibits both positive and negative shifts with respect to metallic Ag. • Two distinct Ag(I) sites are responsible for large BE difference of 3.6 eV. - Abstract: Anomalous chemical shifts, i.e. cases when binding energy decreases with the increase of the oxidation state, have been well-documented for selected compounds of silver, and well understood based on analysis of initial- and final-state effects in the XPS spectra. Here we report two examples of even more exotic behaviour of chemical shifts for two silver compounds. The first one is Ag{sub 2}S{sub 2}O{sub 7} which exhibits both positive and negative substantial shifts with respect to metallic Ag for two distinct Ag(I) sites in its crystal structure, which differ by as much as 3.6 eV. Another is AgSO{sub 4}, a rare example of oxo silver (II) salt, which exhibits “normal” chemical shift but the Ag 3d{sub 5/2} binding energy takes the largest value measured for a silver (II) compound (370.1 eV). This property is connected predominantly with the extremely strongly oxidizing nature of Ag(II) species.
Directory of Open Access Journals (Sweden)
Roghieh Tarlani Bashiz
2015-12-01
Full Text Available Density functional theory calculations (DFT, as well as hybrid methods (B3LYP and HF method for CNT-Calixarene complexes have been carried out to study structural stability. The geometry of the Calixarene has been optimized at DFT methods such as M062x B3LYP and HF methods with 6-31G, 6-31G*and 6-31G** basis sets. According to GIAO method, NMR parameters have been evaluated. The Gaussian quantum chemical package is used for all calculations. The gauge including atomic orbital (GIAO approach was applied for chemical shielding calculations for an isolated calix aren and a complex of Calix-SWCNTs.
Evaluation of vertebral bone marrow fat content by chemical-shift MRI in osteoporosis
International Nuclear Information System (INIS)
To quantitatively evaluate vertebral bone marrow fat content and investigate its association with osteoporosis with chemical-shift magnetic resonance imaging (CS-MRI). Fifty-six female patients (age range 50-65 years) with varying bone mineral densities as documented with dual x-ray absorptiometry (DXA) were prospectively included in the study. According to the DXA results, the patients were grouped as normal bone density, osteopenic, or osteoporotic. In order to calculate fat content, the lumbar region was visualized in the sagittal plane by CS-MRI sequence. ''Region of interest'' (ROI)s were placed within L3 vertebral bodies and air (our reference point) at different time points by different radiologists. Fat content was calculated through ''signal intensity (SI) suppression rate'' and ''SI Index''. The quantitative values were compared statistically with those obtained from DXA examinations. Kruskal-Wallis, and Mann-Whitney U tests were used for comparisons between groups. The reliability of the measurements performed by two radiologists was evaluated with the ''intraclass correlation coefficient''. This study was approved by an institutional review board and all participants provided informed consent to participate in the study. Eighteen subjects with normal bone density (mean T score, 0.39 ± 1.3 [standard deviation]), 20 subjects with osteopenia (mean T score, -1.79 ± 0.38), and 18 subjects with osteoporosis (mean T score, -3 ± 0.5) were determined according to DXA results. The median age was 55.9 (age range 50-64 years) in the normal group, 55.5 (age range 50-64 years) in the osteopenic group, and 55.1 (age range 50-65 years) in the osteoporotic group (p = 0.872). In the CS-MRI examination, the values of ''SI suppression ratio'' and ''SI Index'' (median [min:max]) were calculated by the first and second reader, independently. There was no statistically significant difference between the groups with regard to vertebral bone marrow fat content (p > 0
Gravitational Superenergy Tensor
Mashhoon, Bahram; McClune, James C.; Quevedo, Hernando
1996-01-01
We provide a physical basis for the local gravitational superenergy tensor. Furthermore, our gravitoelectromagnetic deduction of the Bel-Debever-Robinson superenergy tensor permits the identification of the gravitational stress-energy tensor. This {\\it local} gravitational analog of the Maxwell stress-energy tensor is illustrated for a plane gravitational wave.
International Nuclear Information System (INIS)
Empirical shielding surfaces are most commonly used to predict chemical shifts in proteins from known backbone torsion angles, φ and ψ. However, the prediction of 15N chemical shifts using this technique is significantly poorer, compared to that for the other nuclei such as 1Hα, 13Cα, and 13Cβ. In this study, we investigated the effects from the preceding residue and the side-chain geometry, χ1, on 15N chemical shifts by statistical methods. For an amino acid sequence XY, the 15N chemical shift of Y is expressed as a function of the amino acid types of X and Y, as well as the backbone torsion angles, φ and ψi-1. Accordingly, 380 empirical 'Preceding Residue Specific Individual (PRSI)' 15N chemical shift shielding surfaces, representing all the combinations of X and Y (except for Y=Pro), were built and used to predict 15N chemical shift from φ and ψi-1. We further investigated the χ1 effects, which were found to account for differences in 15N chemical shifts by ∼5 ppm for amino acids Val, Ile, Thr, Phe, His, Tyr, and Trp. Taking the χ1 effects into account, the χ1-calibrated PRSI shielding surfaces (XPRSI) were built and used to predict 15N chemical shifts for these amino acids. We demonstrated that 15N chemical shift predictions are significantly improved by incorporating the preceding residue and χ1 effects. The present PRSI and XPRSI shielding surfaces were extensively compared with three recently published programs, SHIFTX (Neal et al., 2003), SHIFTS (Xu and Case, 2001 and 2002), and PROSHIFT (Meiler, 2003) on a set of ten randomly selected proteins. A set of Java programs using XPRSI shielding surfaces to predict 15N chemical shifts in proteins were developed and are freely available for academic users at http://www.pronmr.com or by sending email to one of the authors Yunjun Wang
Hess, Siegfried
2015-01-01
This book presents the science of tensors in a didactic way. The various types and ranks of tensors and the physical basis is presented. Cartesian Tensors are needed for the description of directional phenomena in many branches of physics and for the characterization the anisotropy of material properties. The first sections of the book provide an introduction to the vector and tensor algebra and analysis, with applications to physics, at undergraduate level. Second rank tensors, in particular their symmetries, are discussed in detail. Differentiation and integration of fields, including generalizations of the Stokes law and the Gauss theorem, are treated. The physics relevant for the applications in mechanics, quantum mechanics, electrodynamics and hydrodynamics is presented. The second part of the book is devoted to tensors of any rank, at graduate level. Special topics are irreducible, i.e. symmetric traceless tensors, isotropic tensors, multipole potential tensors, spin tensors, integration and spin-...
Wassenhove, Luk; Lebreton, Baptiste; Letizia, Paolo
2007-01-01
textabstractWith the attention of the chemical industry focused on exploiting the low cost feedstocks in the Middle East and the growth markets of Brazil, Russia, India, China and South East Asia, this report provides a timely reminder to policy makers, chemical companies and logistics service providers of the significant opportunities for improving business potential in Europe’s chemical clusters. Europe is still the largest, most sophisticated global market for chemical products, with a wel...
Fenzke, Dieter; Hunger, Michael; Pfeifer, Harry
A procedure is described which allows a separate determination of the proton-aluminum distance and of the chemical-shift anisotropy for the bridging OH groups of crystalline molecular sieves from their 'H MAS NMR sideband patterns. For the bridging OH groups which point into the 6-rings of the framework (line "c"), the 1H- 27Al distance could be determined to be 0.237 ± 0.004 and 0.234 ± 0.004 nm for molecular sieves of type H-Y and SAPO-5, respectively. In contrast, for the bridging OH groups of the 12-rings (line "b"), the corresponding distances are equal and distinctly larger, 0.248 ± 0.004 nm. Within the limits of error, the values of the chemical-shift anisotropy are equal (about 19 ± 2 ppm) except for line b of SAPO-5, which exhibits a much smaller value of 14.5 ± 2 ppm.
Brox, Thomas; Weickert, Joachim; Burgeth, Bernhard; Mrázek, Pavel
2004-01-01
In this article we introduce nonlinear versions of the popular structure tensor, also known as second moment matrix. These nonlinear structure tensors replace the Gaussian smoothing of the classical structure tensor by discontinuity-preserving nonlinear diffusions. While nonlinear diffusion is a well-established tool for scalar and vector-valued data, it has not often been used for tensor images so far. Two types of nonlinear diffusion processes for tensor data are studied: an isotropic one w...
International Nuclear Information System (INIS)
We present a case in which multiple pancreatic tumours were diagnosed as metastatic clear cell renal carcinomas with chemical shift MRI (CSI) before surgery. Radiologists may be unable to recognize the loss of intensity on CSI macroscopically. We believe that it is useful to make subtraction images and calculate signal intensity on CSI, even if the lesions are multiple metastatic tumours Copyright (2005) Blackwell Publishing Asia Pty Ltd
Kumar, Arun V; Ali, Rehana F M; Cao, Yu; Krishnan, V V
2015-10-01
The number of protein sequences deriving from genome sequencing projects is outpacing our knowledge about the function of these proteins. With the gap between experimentally characterized and uncharacterized proteins continuing to widen, it is necessary to develop new computational methods and tools for protein structural information that is directly related to function. Nuclear magnetic resonance (NMR) provides powerful means to determine three-dimensional structures of proteins in the solution state. However, translation of the NMR spectral parameters to even low-resolution structural information such as protein class requires multiple time consuming steps. In this paper, we present an unorthodox method to predict the protein structural class directly by using the residue's averaged chemical shifts (ACS) based on machine learning algorithms. Experimental chemical shift information from 1491 proteins obtained from Biological Magnetic Resonance Bank (BMRB) and their respective protein structural classes derived from structural classification of proteins (SCOP) were used to construct a data set with 119 attributes and 5 different classes. Twenty four different classification schemes were evaluated using several performance measures. Overall the residue based ACS values can predict the protein structural classes with 80% accuracy measured by Matthew correlation coefficient. Specifically protein classes defined by mixed αβ or small proteins are classified with >90% correlation. Our results indicate that this NMR-based method can be utilized as a low-resolution tool for protein structural class identification without any prior chemical shift assignments. PMID:25758094
Directory of Open Access Journals (Sweden)
Ricardo Infante-Castillo
2012-01-01
Full Text Available This work presents a new quantitative model to predict the heat of explosion of nitroaromatic compounds using the natural bond orbital (NBO charge and 15N NMR chemical shifts of the nitro groups (15NNitro as structural parameters. The values of the heat of explosion predicted for 21 nitroaromatic compounds using the model described here were compared with experimental data. The prediction ability of the model was assessed by the leave-one-out cross-validation method. The cross-validation results show that the model is significant and stable and that the predicted accuracy is within 0.146 MJ kg−1, with an overall root mean squared error of prediction (RMSEP below 0.183 MJ kg−1. Strong correlations were observed between the heat of explosion and the charges (R2 = 0.9533 and 15N NMR chemical shifts (R2 = 0.9531 of the studied compounds. In addition, the dependence of the heat of explosion on the presence of activating or deactivating groups of nitroaromatic explosives was analyzed. All calculations, including optimizations, NBO charges, and 15NNitro NMR chemical shifts analyses, were performed using density functional theory (DFT and a 6-311+G(2d,p basis set. Based on these results, this practical quantitative model can be used as a tool in the design and development of highly energetic materials (HEM based on nitroaromatic compounds.
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Ishijima Hideyuki; Ishizaka Hiroshi; Inoue Tomio [Gunma University Hospital, Gunma (Japan). Depts. of Diagnostic Radiaology and Nuclear Medicine
1996-02-01
The purpose of this study was to evaluate the efficacy of chemical shift gradient echo magnetic resonance imaging (MRI) in distinguishing between cystic teratomas and endometriomas of the ovary, using a 1.5 T magnet. The study included 22 patients with 31 ovarian lesions (15 cystic teratomas and 16 endometriomas), which showed high signal intensity on T1-weighted spin echo images. Chemical shift gradient echo images with three different echo times (TE = 2.5, 4.5 and 6.5 ms) were obtained in all cases. Indices were calculated on the basis of the signal intensities of lesions on the chemical shift gradient echo images. All endometriomas had signal intensity indices of less than 2.1, while all cystic teratomas had signal intensity indices of 18.1 or greater. It was concluded that the method used in this study presents the following advantages: the acquisition time is short; it needs no special software; and it does not depend on magnetic field homogeneity. 11 refs., 4 figs.
Chemical shift of Mn and Cr K-edges in X-ray absorption spectroscopy with synchrotron radiation
Indian Academy of Sciences (India)
D Joseph; A K Yadav; S N Jha; D Bhattacharyya
2013-11-01
Mn and Cr K X-ray absorption edges were measured in various compounds containing Mn in Mn2+, Mn3+ and Mn4+ oxidation states and Cr in Cr3+ and Cr6+ oxidation states. Few compounds possess tetrahedral coordination in the 1st shell surrounding the cation while others possess octahedral coordination. Measurements have been carried out at the energy dispersive EXAFS beamline at INDUS-2 Synchrotron Radiation Source at Raja Ramanna Centre for Advanced Technology, Indore. Energy shifts of ∼8–16 eV were observed for Mn K edge in the Mn-compounds while a shift of 13–20 eV was observed for Cr K edge in Cr-compounds compared to values in elementalMn and Cr, respectively. The different chemical shifts observed for compounds having the same oxidation state of the cation but different anions or ligands show the effect of different chemical environments surrounding the cations in determining their X-ray absorption edges in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on Mn and Cr cations in the above compounds.
DYADIC METHOD FOR TENSOR FUNCTIONS
Institute of Scientific and Technical Information of China (English)
黄永念; 鲁昊
2002-01-01
In this paper, we discuss tensor functions by dyadic representation of tensor. Two different cases of scalar invariants and two different cases of tensor invariants are calculated. It is concluded that there are six independent scale invariants for a symmetrical tensor and an antisymmetrical tensor, and there are twelve invariants for two symmetrical tensors and an antisymmetrical tensor. And we present a new list of tensor invariants for the tensor-valued isotropic function.
Directory of Open Access Journals (Sweden)
Chunmei eLi
2015-10-01
Full Text Available Parkinson’s disease (PD is a neurodegenerative disorder characterized by nigrostriatal cell loss. To date the diagnosis of PD is still based primarily on the clinical manifestations which may be typical and obvious only in advanced-stage PD. Thus, it is crucial to find a reliable marker for the diagnosis of PD. We conducted this study to assess the diagnostic efficiency of chemical-exchange-saturation-transfer (CEST imaging and diffusion-tensor imaging (DTI in PD at 3 Tesla by evaluating changes on substantia nigra and striatum. Twenty-three PD patients and twenty-three age-matched normal controls were recruited. All patients and controls were imaged on a 3 Tesla MR system, using an 8-channel head coil. CEST imaging was acquired in two transverse slices of the head, including substantia nigra and striatum. The magnetization-transfer-ratio asymmetry at 3.5 ppm, MTRasym(3.5ppm, and the total CEST signal intensity between 0 and 4 ppm were calculated. Multi-slice DTI was acquired for all the patients and normal controls. Quantitative analysis was performed on the substantia nigra, globus pallidus, putamen and caudate. The MTRasym(3.5ppm value, the total CEST signal intensity and fractional anisotropy (FA value of the substantia nigra were all significantly lower in PD patients than in normal controls (P = 0.003, P = 0.004 and P < 0.001, respectively. The MTRasym(3.5ppm values of the putamen and the caudate were significantly higher in PD patients than in normal controls (P = 0.010 and P = 0.009, respectively. There were no significant differences for the mean diffusivity (MD in these four regions between PD patients and normal controls. In conclusion, CEST MR imaging provided multiple CEST image contrasts in the substantia nigra and the striatum in PD and may be superior to DTI in the diagnosis of PD.
Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH2.
Erlach, Markus Beck; Koehler, Joerg; Crusca, Edson; Kremer, Werner; Munte, Claudia E; Kalbitzer, Hans Robert
2016-06-01
For a better understanding of nuclear magnetic resonance (NMR) detected pressure responses of folded as well as unstructured proteins the availability of data from well-defined model systems are indispensable. In this work we report the pressure dependence of chemical shifts of the backbone atoms (1)H(α), (13)C(α) and (13)C' in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of these nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The polynomial pressure coefficients B 1 and B 2 are dependent on the type of amino acid studied. The coefficients of a given nucleus show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure are also weakly correlated. PMID:27335085
Introduction to Tensor Calculus
Sochi, Taha
2016-01-01
These are general notes on tensor calculus which can be used as a reference for an introductory course on tensor algebra and calculus. A basic knowledge of calculus and linear algebra with some commonly used mathematical terminology is presumed.
International Nuclear Information System (INIS)
The dependence of the inversion barriers (ΔG) of phosphorus compounds directly on a parameter of the inversion center, i.e., the chemical shift of the nucleus (delta31 P) were studied. The possibility of such an approach was justified by the correlation both of ΔG, and of delta31 P for phosphorus compounds with one and the same characteristics (the bond angles and electronegativities of the substituent). The acylphosphines (I-IX) were investigated in the range of variation of ΔG, accessible to dynamic NMR and in a fairly wide range of delta31 P
Gradient-echo in-phase and opposed-phase chemical shift imaging: Role in evaluating bone marrow
International Nuclear Information System (INIS)
Chemical shift imaging (CSI) provides valuable information for assessing the bone marrow, while adding little to total examination time. In this article, we review the uses of CSI for evaluating bone marrow abnormalities. CSI can be used for differentiating marrow-replacing lesions from a range of non-marrow-replacing processes, although the sequence is associated with technical limitations and pitfalls. Particularly at 3 T, susceptibility artefacts are prevalent, and optimal technical parameters must be implemented with appropriate choices for echo times
Renormalizable Tensor Field Theories
Geloun, Joseph Ben
2016-01-01
Extending tensor models at the field theoretical level, tensor field theories are nonlocal quantum field theories with Feynman graphs identified with simplicial complexes. They become relevant for addressing quantum topology and geometry in any dimension and therefore form an interesting class of models for studying quantum gravity. We review the class of perturbatively renormalizable tensor field theories and some of their features.
Applications of tensor analysis
McConnell, A J
2011-01-01
Standard work applies tensorial methods to subjects within realm of advanced college mathematics. Text explains fundamental ideas and notation of tensor theory; covers geometrical treatment of tensor algebra; introduces theory of differentiation of tensors; and applies mathematics to dynamics, electricity, elasticity and hydrodynamics. 685 exercises, most with answers.
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The 'out-and-back' 3D HCP experiment, using gradient- and sensitivity-enhanced detection, provides a convenient method for assignment of the 31P NMR spectra and accurate measurement of the 31P chemical shifts of ribonucleic acids. The 13C resolution in such spectra can be doubled, at the cost of a 50% reduction in sensitivity, by combining 13C evolution during the 13C-31P de- and rephasing periods. The multiple connectivities observable for a given 31P, including correlations to the intranucleotide C5'H2 and C4'H groups, and the C2'H, C3'H and C4'H groups of the preceding nucleotide, permit independent measurements of the 31P shift. The 13C spectrum of these groups is typically crowded for an RNA molecule in isotropic solution and overlap becomes more problematic in media used to achieve partial alignment. However, many of these correlations are resolvable in the combined-evolution HCP spectrum. The difference in 31P chemical shift between isotropic solution and a medium containing liquid crystalline Pf1 provides information on the orientation of phosphate groups. The intensities measured in the 3D HCP spectrum, obtained for an isotropic sample, yield values for the 3JC2'P and 3JC4'P couplings, thereby providing important restraints for the backbone torsion angles ε and β. The experiments are illustrated for a uniformly 13C-enriched, 24-residue stem-loop RNA sequence, and results for the helical stem region show close agreement between observed Δδ(31P) values and those predicted for a model A-form RNA helix when using a uniform 31P CSA tensor. This confirms that Δδ(31P) values can be used directly as restraints in refining nucleic acid structures
Chikayama, Eisuke; Shimbo, Yudai; Komatsu, Keiko; Kikuchi, Jun
2016-04-14
NMR spectroscopy is a powerful method for analyzing metabolic mixtures. The information obtained from an NMR spectrum is in the form of physical parameters, such as chemical shifts, and construction of databases for many metabolites will be useful for data interpretation. To increase the accuracy of theoretical chemical shifts for development of a database for a variety of metabolites, the effects of sets of conformations (structural ensembles) and the levels of theory on computations of theoretical chemical shifts were systematically investigated for a set of 29 small molecules in the present study. For each of the 29 compounds, 101 structures were generated by classical molecular dynamics at 298.15 K, and then theoretical chemical shifts for 164 (1)H and 123 (13)C atoms were calculated by ab initio quantum chemical methods. Six levels of theory were used by pairing Hartree-Fock, B3LYP (density functional theory), or second order Møller-Plesset perturbation with 6-31G or aug-cc-pVDZ basis set. The six average fluctuations in the (1)H chemical shift were ±0.63, ± 0.59, ± 0.70, ± 0.62, ± 0.75, and ±0.66 ppm for the structural ensembles, and the six average errors were ±0.34, ± 0.27, ± 0.32, ± 0.25, ± 0.32, and ±0.25 ppm. The results showed that chemical shift fluctuations with changes in the conformation because of molecular motion were larger than the differences between computed and experimental chemical shifts for all six levels of theory. In conclusion, selection of an appropriate structural ensemble should be performed before theoretical chemical shift calculations for development of an accurate database for a variety of metabolites. PMID:26963288
Rivasseau, Vincent
2016-01-01
This note is a sequel to the previous series "Tensor Track I-III". Assuming some familiarity with the tensor track approach to quantum gravity, we provide a brief introduction to the developments of the last two years and to their corresponding bibliography. They center around understanding the interface between random matrices and random tensors through the intermediate field representation, finding new types of $1/N$ expansions by enhancing sub-leading tensor interactions, exploring the renormalization group flows in the tensor theory space, and developing the constructive aspects of the theory.
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Satkunasingham, Janakan; Besa, Cecilia [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Bane, Octavia [Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Shah, Ami [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Oliveira, André de; Gilson, Wesley D.; Kannengiesser, Stephan [Siemens AG, Healthcare Sector, Erlangen (Germany); Taouli, Bachir, E-mail: bachir.taouli@mountsinai.org [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States)
2015-08-15
Highlights: • We present a large cohort of patients who underwent dual and triple echo chemical shift imaging against multi-echo T{sub 2} corrected MR spectroscopy (MRS) for liver fat quantification. • Our data suggests that a triple-echo sequence is highly accurate for detection of liver fat, even in the presence of T{sub 2}{sup *} shortening, with minor discrepancies when compared with the advanced fat quantification method. - Abstract: Purpose: To assess the diagnostic value of MRI using dual-echo (2PD) and triple-echo (3PD) chemical shift imaging for liver fat quantification against multi-echo T{sub 2} corrected MR spectroscopy (MRS) used as the reference standard, and examine the effect of T{sub 2}{sup *} imaging on accuracy of MRI for fat quantification. Materials and methods: Patients who underwent 1.5 T liver MRI that incorporated 2PD, 3PD, multi-echo T{sub 2}{sup *} and MRS were included in this IRB approved prospective study. Regions of interest were placed in the liver to measure fat fraction (FF) with 2PD and 3PD and compared with MRS-FF. A random subset of 25 patients with a wide range of MRS-FF was analyzed with an advanced FF calculation method, to prove concordance with the 3PD. The statistical analysis included correlation stratified according to T{sub 2}{sup *}, Bland-Altman analysis, and calculation of diagnostic accuracy for detection of MRS-FF > 6.25%. Results: 220 MRI studies were identified in 217 patients (mean BMI 28.0 ± 5.6). 57/217 (26.2%) patients demonstrated liver steatosis (MRS-FF > 6.25%). Bland-Altman analysis revealed strong agreement between 3PD and MRS (mean ± 1.96 SD: −0.5% ± 4.6%) and weaker agreement between 2PD and MRS (4.7% ± 16.0%). Sensitivity of 3PD for diagnosing FF> 6.25% was higher than that of 2PD. 3PD-FF showed minor discrepancies (coefficient of variation <10%) from FF measured with the advanced method. Conclusion: Our large series study validates the use of 3PD chemical shift sequence for detection of
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Highlights: • We present a large cohort of patients who underwent dual and triple echo chemical shift imaging against multi-echo T2 corrected MR spectroscopy (MRS) for liver fat quantification. • Our data suggests that a triple-echo sequence is highly accurate for detection of liver fat, even in the presence of T2* shortening, with minor discrepancies when compared with the advanced fat quantification method. - Abstract: Purpose: To assess the diagnostic value of MRI using dual-echo (2PD) and triple-echo (3PD) chemical shift imaging for liver fat quantification against multi-echo T2 corrected MR spectroscopy (MRS) used as the reference standard, and examine the effect of T2* imaging on accuracy of MRI for fat quantification. Materials and methods: Patients who underwent 1.5 T liver MRI that incorporated 2PD, 3PD, multi-echo T2* and MRS were included in this IRB approved prospective study. Regions of interest were placed in the liver to measure fat fraction (FF) with 2PD and 3PD and compared with MRS-FF. A random subset of 25 patients with a wide range of MRS-FF was analyzed with an advanced FF calculation method, to prove concordance with the 3PD. The statistical analysis included correlation stratified according to T2*, Bland-Altman analysis, and calculation of diagnostic accuracy for detection of MRS-FF > 6.25%. Results: 220 MRI studies were identified in 217 patients (mean BMI 28.0 ± 5.6). 57/217 (26.2%) patients demonstrated liver steatosis (MRS-FF > 6.25%). Bland-Altman analysis revealed strong agreement between 3PD and MRS (mean ± 1.96 SD: −0.5% ± 4.6%) and weaker agreement between 2PD and MRS (4.7% ± 16.0%). Sensitivity of 3PD for diagnosing FF> 6.25% was higher than that of 2PD. 3PD-FF showed minor discrepancies (coefficient of variation <10%) from FF measured with the advanced method. Conclusion: Our large series study validates the use of 3PD chemical shift sequence for detection of liver fat in the clinical environment, even in the presence of
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We have studied the assessment of chemical composition changes in III-V heterostructured semiconductor nanowires (NWs) with nanometric spatial resolution using transmission electron microscopy methods. These materials represent a challenge for conventional spectroscopy techniques due to their high sensitivity to electron beam irradiation. Radiation damage strongly limits the exposure time to a few (5-10) s, which reduces the sensitivity of the traditionally used x-ray spectroscopy. The rather low counting statistics results in significant errors bars for EDS chemical quantification (5-10%) and interface width determination (few nanometers). Plasmon chemical shift is ideal in this situation, as its measurement requires very short exposure times (∼100 ms) and the plasmon peak energy can be measured with high precision (∼20 meV in this work). This high sensitivity allows the detection of subtle changes (1-2%) in composition or even the detection of a small plasmon energy (33 ± 7) meV change along usually assumed pure and homogeneous InAs segments. We have applied this approach to measure interface widths in heterostructure InAs/InP NWs grown using metal catalysts and also to determine the timescale (∼10 s) in which beam irradiation induces material damage in these wires. In particular, we have detected small As concentrations (4.4 ± 0.5)% in the final InP segment close to the Au catalyst, which leads to the conclusion that As diffuses through the metal nanoparticle during growth.
Wang, Tao; Wu, Yi fang; Wang, Xue liang
2014-01-01
We report here theoretical and experimental studies on the molecular structure and vibrational and NMR spectra of both natural enmein type diterpenoids molecule (6, 7-seco-ent-kaurenes enmein type), isolated from the leaves of Isodon japonica (Burm.f.) Hara var. galaucocalyx (maxin) Hara. The optimized geometry, total energy, NMR chemical shifts and vibrational wavenumbers of epinodosinol and epinodosin have been determined using B3LYP method with 6-311G (d,p) basis set. A complete vibrational assignment is provided for the observed IR spectra of studied compounds. The calculated wavenumbers and 13C c.s. are in an excellent agreement with the experimental values. Quantum chemical calculations at the B3LYP/6-311G (d,p) level of theory have been carried out on studied compounds to obtain a set of molecular electronic properties (MEP,HOMO, LUMO and gap energies ΔEg). Electrostatic potential surfaces have been mapped over the electron density isosurfaces to obtain information about the size, shape, charge density distribution and chemical reactivity of the molecules.
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The kinetic and chemical mechanisms of AChE-catalyzed hydrolysis of short-chain thiocholine esters are relatively well documented. Up to propanoylthiocholine (PrTCh) the chemical mechanism is general acid-base catalysis by the active site catalytic triad. The chemical mechanism for the enzyme-catalyzed butyrylthio-choline(BuTCh) hydrolysis shifts to a parallel mechanism in which general base catalysis by E199 of direct water attack to the carbonyl carbon of the substrate. (Selwood, T., et al. J. Am. Chem. Soc. 1993, 115, 10477-10482) The long chain thiocholine esters such as hexanoylthiocholine (HexTCh), heptanoylthiocholine (HepTCh), and octanoylthiocholine (OcTCh) are hydrolyzed by electric eel acetylcholinesterase (AChE). The kinetic parameters are determined to show that these compounds have a lower Michaelis constant than BuTCh and the pH-Rate profile showed that the mechanism is similar to that of BuTCh hydrolysis. The solvent isotope effect and proton inventory of AChE-catalyzed hydrolysis of HexTCh showed that one proton transfer is involved in the transition state of the acylation stage. The relationship between the dipole moment and the Michaelis constant of the long chain thiocholine esters showed that the dipole moment is the most important factor for the binding of a substrate to the enzyme active site
Energy Technology Data Exchange (ETDEWEB)
Jung, Dai Il; Shin, Young Ju [Donga Univ., Busan (Korea, Republic of); Lee, Eun Seok; Lee, Bong Ho [Hanbat National Univ., Daejon (Korea, Republic of); Moon, Tae Sung; Yoon, Chang No [Korea Institute of Science and Technology, Seoul (Korea, Republic of)
2003-01-01
The kinetic and chemical mechanisms of AChE-catalyzed hydrolysis of short-chain thiocholine esters are relatively well documented. Up to propanoylthiocholine (PrTCh) the chemical mechanism is general acid-base catalysis by the active site catalytic triad. The chemical mechanism for the enzyme-catalyzed butyrylthio-choline(BuTCh) hydrolysis shifts to a parallel mechanism in which general base catalysis by E199 of direct water attack to the carbonyl carbon of the substrate. (Selwood, T., et al. J. Am. Chem. Soc. 1993, 115, 10477-10482) The long chain thiocholine esters such as hexanoylthiocholine (HexTCh), heptanoylthiocholine (HepTCh), and octanoylthiocholine (OcTCh) are hydrolyzed by electric eel acetylcholinesterase (AChE). The kinetic parameters are determined to show that these compounds have a lower Michaelis constant than BuTCh and the pH-Rate profile showed that the mechanism is similar to that of BuTCh hydrolysis. The solvent isotope effect and proton inventory of AChE-catalyzed hydrolysis of HexTCh showed that one proton transfer is involved in the transition state of the acylation stage. The relationship between the dipole moment and the Michaelis constant of the long chain thiocholine esters showed that the dipole moment is the most important factor for the binding of a substrate to the enzyme active site.
Koichi, Shungo; Arisaka, Masaki; Koshino, Hiroyuki; Aoki, Atsushi; Iwata, Satoru; Uno, Takeaki; Satoh, Hiroko
2014-04-28
Computer-assisted chemical structure elucidation has been intensively studied since the first use of computers in chemistry in the 1960s. Most of the existing elucidators use a structure-spectrum database to obtain clues about the correct structure. Such a structure-spectrum database is expected to grow on a daily basis. Hence, the necessity to develop an efficient structure elucidation system that can adapt to the growth of a database has been also growing. Therefore, we have developed a new elucidator using practically efficient graph algorithms, including the convex bipartite matching, weighted bipartite matching, and Bron-Kerbosch maximal clique algorithms. The utilization of the two matching algorithms especially is a novel point of our elucidator. Because of these sophisticated algorithms, the elucidator exactly produces a correct structure if all of the fragments are included in the database. Even if not all of the fragments are in the database, the elucidator proposes relevant substructures that can help chemists to identify the actual chemical structures. The elucidator, called the CAST/CNMR Structure Elucidator, plays a complementary role to the CAST/CNMR Chemical Shift Predictor, and together these two functions can be used to analyze the structures of organic compounds. PMID:24655374
Decoupling braided tensor factors
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It is shown that the braided tensor product algebra of two module algebras A1, A2 of a quasitriangular Hopf algebra is equal to the ordinary tensor product algebra of A1 with a subalgebra isomorphic to A2 and commuting with A1. As applications of the theorem the braided tensor product algebras of two or more quantum group covariant quantum space or deformed Heisenberg algebras are considered
Miura, Yoshinori
2016-05-01
It is known that melittin in an aqueous solution undergoes a conformational transition between the monomer and tetramer by variation in temperature. The transition correlates closely with isomers of the proline residue; monomeric melittin including a trans proline peptide bond (trans-monomer) is involved directly in the transition, whereas monomeric melittin having a cis proline peptide bond (cis-monomer) is virtually not. The transition has been explored by using nuclear magnetic resonance spectroscopy in order to clarify the stability of the tetrameric conformation and the cooperativity of the transition. In the light of temperature dependence of chemical shifts of resonances from the isomeric monomers, we qualitatively estimate the temperature-, salt-, and concentration-dependence of the relative equilibrium populations of the trans-monomer and tetramer, and show that the tetramer has a maximum conformational stability at 30-45 °C and that the transition cooperativity is very low. PMID:26658745
Sharma, Rakhi; Sahu, Bhubanananda; Ray, Malay K; Deshmukh, Mandar V
2015-04-01
Carbon catabolite repression (CCR) allows bacteria to selectively assimilate a preferred compound among a mixture of several potential carbon sources, thus boosting growth and economizing the cost of adaptability to variable nutrients in the environment. The RNA-binding catabolite repression control (Crc) protein acts as a global post-transcriptional regulator of CCR in Pseudomonas species. Crc triggers repression by inhibiting the expression of genes involved in transport and catabolism of non-preferred substrates, thus indirectly favoring assimilation of preferred one. We report here a nearly complete backbone and stereospecific (13)C methyl side-chain chemical shift assignments of Ile (δ1), Leu and Val of Crc (~ 31 kDa) from Pseudomonas syringae Lz4W. PMID:24496608
Institute of Scientific and Technical Information of China (English)
无
2010-01-01
The relative chemical shifts (△δ) △δwere put forward to investigate the microscopic structure of 1-ethyl-3-methyl-imidazolium tetrafluoroborate (EmimBF4) during the dilution process with water.The concentration-dependent △δ(C2)H-(C4)H,△δ(C2)H-(C5)H and △δ(C4)H-(C5)H were analyzed.The results reveal that the variations of the microscopic structures of three aromatic protons are inconsistent.The strength of the H-bond between water and three aromatic protons follows the order:(C2)H···O > (C4)H···O > (C5)H···O.The concentration-dependent △δ(C6)H-(C7)H and △δ(C6)H-(C8)H indicate the formation of the H-bonds of (Calkyl)H···O is impossible,and more water is located around (C6)H than around (C7)H or (C8)H.The concentration-dependent △δ(C2)H-(C4)H and △δ(C2)H-(C5)H both increase rapidly when xwater > 0.9 or so,suggesting the ionic pairs of EmimBF4 are dissociated rapidly.The turning points of concentration-dependent △δ(C2)H-(C4)H and △δ(C2)H-(C5)H indicate that some physical properties of the EmimBF4/water mixtures also change at the corresponding concentration point.The microscopic structures of EmimBF4 in water could be clearly detected by the relative chemical shifts.
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Aim: To investigate the feasibility of assessing vertebral marrow adipose tissue using a magnetic resonance imaging (MRI) chemical shift-based water–fat separation technique at 3 T. Material and methods: A modified Dixon technique was performed to obtain the vertebral marrow fat fraction (FF) in a study of 58 postmenopausal females (age range 49.2–77.4 years), including 24 normal bone density, 19 osteopaenia, and 15 osteoporosis as documented with dual-energy X-ray absorptiometry. The reliability of FF measurements performed by two radiologists independently was evaluated with the intraclass correlation coefficient (ICC). Ten participants were scanned twice to assess the reproducibility of FF measurements. FF values were compared between each vertebral level and between groups. Results: The mean coefficient of variation of FF measurements was 2.1%. According to the ICC, the measurements were reliable (ICC = 0.900 for normal bone density, ICC = 0.937 for osteopaenia and ICC = 0.909 for osteoporosis, p < 0.001 for all). There was an inverse association between mean FF at L1–L4 vertebrae and lumbar spine BMD (r = −0.459, p = 0.006), which remained significant even after controlling for confounders (age, height, and body weight). FF values at different vertebral levels were significantly correlated to each other (r = 0.703–0.921, p < 0.05 for all). There was a general trend toward increased marrow adiposity for more inferior vertebral bodies. Patients with osteopaenia and osteoporosis had a higher marrow fat content compared with normal bone mass after adjusting for confounders, although no significant differences in each vertebral level and average marrow fat content were found between the osteopaenia and osteoporosis groups. Conclusion: Chemical shift-based water–fat separation enables the quantitation of vertebral marrow adiposity with excellent reproducibility, which appears to be a useful method to provide complementary information to osteoporosis
Thickness-Dependent Binding Energy Shift in Few-Layer MoS2 Grown by Chemical Vapor Deposition.
Lin, Yu-Kai; Chen, Ruei-San; Chou, Tsu-Chin; Lee, Yi-Hsin; Chen, Yang-Fang; Chen, Kuei-Hsien; Chen, Li-Chyong
2016-08-31
The thickness-dependent surface states of MoS2 thin films grown by the chemical vapor deposition process on the SiO2-Si substrates are investigated by X-ray photoelectron spectroscopy. Raman and high-resolution transmission electron microscopy suggest the thicknesses of MoS2 films to be ranging from 3 to 10 layers. Both the core levels and valence band edges of MoS2 shift downward ∼0.2 eV as the film thickness increases, which can be ascribed to the Fermi level variations resulting from the surface states and bulk defects. Grainy features observed from the atomic force microscopy topographies, and sulfur-vacancy-induced defect states illustrated at the valence band spectra imply the generation of surface states that causes the downward band bending at the n-type MoS2 surface. Bulk defects in thick MoS2 may also influence the Fermi level oppositely compared to the surface states. When Au contacts with our MoS2 thin films, the Fermi level downshifts and the binding energy reduces due to the hole-doping characteristics of Au and easy charge transfer from the surface defect sites of MoS2. The shift of the onset potentials in hydrogen evolution reaction and the evolution of charge-transfer resistances extracted from the impedance measurement also indicate the Fermi level varies with MoS2 film thickness. The tunable Fermi level and the high chemical stability make our MoS2 a potential catalyst. The observed thickness-dependent properties can also be applied to other transition-metal dichalcogenides (TMDs), and facilitates the development in the low-dimensional electronic devices and catalysts. PMID:27488185
Cartesian tensors an introduction
Temple, G
2004-01-01
This undergraduate text provides an introduction to the theory of Cartesian tensors, defining tensors as multilinear functions of direction, and simplifying many theorems in a manner that lends unity to the subject. The author notes the importance of the analysis of the structure of tensors in terms of spectral sets of projection operators as part of the very substance of quantum theory. He therefore provides an elementary discussion of the subject, in addition to a view of isotropic tensors and spinor analysis within the confines of Euclidean space. The text concludes with an examination of t
Ichikawa, Kazuhide; Kurokawa, Yusaku I; Sakaki, Shigeyoshi; Tachibana, Akitomo
2011-01-01
We study the electronic structure of two types of transition metal complexes, the inverted-sandwich-type and open-lantern-type, by the electronic stress tensor. In particular, the bond order b_e measured by the energy density which is defined from the electronic stress tensor is studied and compared with the conventional MO based bond order. We also examine the patterns found in the largest eigenvalue of the stress tensor and corresponding eigenvector field, the "spindle structure" and "pseudo-spindle structure". As for the inverted-sandwich-type complex, our bond order b_e calculation shows that relative strength of the metal-benzene bond among V, Cr and Mn complexes is V > Cr > Mn which is consistent with the MO based bond order. As for the open-lantern-type complex, we find that our energy density based bond order can properly describe the relative strength of Cr--Cr and Mo--Mo bonds by the surface integration of the energy density over the "Lagrange surface" which can take into account the spatial extent ...
Chemical shift measurements of chlorine K X-ray spectra using a high-resolution PIXE system
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A high-efficiency high-resolution wavelength-dispersive spectrograph with a von-Hamos configuration was developed for chemical state identification of elements in environmental samples using PIXE analysis. To evaluate the performance of this system, chlorine K X-ray spectra for NaCl, NH4Cl and polyvinylchloride (PVC) targets were measured and compared. Also, to study the applicability to environmental mixed samples, mixtures of NaCl and NH4Cl with different mixing ratios were measured. Through observation of Cl Kα1 X-ray from NaCl, the energy resolution of the system was determined to be 1.1 eV. For the NaCl sample, a Kβx line was observed at an energy, which is higher than that of the Kβ main peak by 2 eV, whereas no Kβx emission was observed for the NH4Cl sample. The chemical shift of the Kβ main peak for PVC relative to that for NaCl was about 1.2 eV. For NaCl-NH4Cl mixture targets, the relative intensity of Kβx satellite to the Kβ main line provided an indication of mixing ratio. Energies and relative intensity of Cl Kβ X-ray satellites for NaCl and NH4Cl samples calculated by a simple molecular-orbital method agreed only qualitatively with the experimental results
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α-Lytic protease, a bacterial serine protease of 198 aminoacids (19800 Da), has been used as a model system for studies of catalytic mechanism, structure-function relationships, and more recently for studies of pro region-assisted protein folding. We have assigned the backbones of the enzyme alone, and of its complex with the tetrahedral transition state mimic N-tert-butyloxycarbonyl-Ala-Pro-boroVal, using double- and triple-resonance 3D NMR spectroscopy on uniformly15N- and 13C/15N-labeled protein.Changes in backbone chemical shifts between the uncomplexed and inhibited form of the protein are correlated with distance from the inhibitor, the displacement of backbone nitrogens, and change in hydrogen bond strength upon inhibitor binding (derived from previously solved crystal structures).A comparison of the solution secondary structure of the uninhibited enzyme with that of the X-ray structure reveals no significant differences.Significant line broadening, indicating intermediate chemical exchange, was observed in many of the active site amides (including three broadened to invisibility), and in a majority of cases the broadening was reversed upon addition of the inhibitor. Implications and possible mechanisms of this line broadening are discussed
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We have developed the multicomponent hybrid density functional theory [MC-(HF+DFT)] method with polarizable continuum model (PCM) for the analysis of molecular properties including both nuclear quantum effect and solvent effect. The chemical shifts and H/D isotope shifts of the picolinic acid N-oxide (PANO) molecule in chloroform and acetonitrile solvents are applied by B3LYP electron exchange-correlation functional for our MC-(HF+DFT) method with PCM (MC-B3LYP/PCM). Our MC-B3LYP/PCM results for PANO are in reasonable agreement with the corresponding experimental chemical shifts and isotope shifts. We further investigated the applicability of our method for acetylacetone in several solvents
Xiao, Chaoni; Hao, Fuhua; Qin, Xiaorong; Wang, Yulan; Tang, Huiru
2009-05-01
NMR-based metabonomics has been widely employed to understand the stressor-induced perturbations to mammalian metabolism. However, inter-sample chemical shift variations for metabolites remain an outstanding problem for effective data mining. In this work, we systematically investigated the effects of pH and ionic strength on the chemical shifts for a mixture of 9 urinary metabolites. We found that the chemical shifts were decreased with the rise of pH but increased with the increase of ionic strength, which probably resulted from the pH- and ionic strength-induced alteration to the ionization equilibrium for the function groups. We also found that the chemical shift variations for most metabolites were reduced to less than 0.004 ppm when the pH was 7.1-7.7 and the salt concentration was less than 0.15 M. Based on subsequent optimization to minimize chemical shift variation, sample dilution and maximize the signal-to-noise ratio, we proposed a new buffer system consisting of K(2)HPO(4) and NaH(2)PO(4) (pH 7.4, 1.5 M) with buffer-urine volume ratio of 1 : 10 for human urinary metabonomic studies; we suggest that the chemical shifts for the proton signals of citrate and aromatic signals of histidine be corrected prior to multivariate data analysis especially when high resolution data were employed. Based on these, an optimized sample preparation method has been developed for NMR-based urinary metabonomic studies. PMID:19381385
Hoffman, Roy E; Darmon, Eliezer; Aserin, Abraham; Garti, Nissim
2016-02-01
In microemulsions, changes in droplet size and shape and possible transformations occur under various conditions. They are difficult to characterize by most analytical tools because of their nano-sized structure and dynamic nature. Several methods are usually combined to obtain reliable information, guiding the scientist in understanding their physical behavior. We felt that there is a need for a technique that complements those in use today in order to provide more information on the microemulsion behavior, mainly as a function of dilution with water. The improvement of NMR chemical shift measurements independent of bulk magnetization effects makes it possible to study the very weak intermolecular chemical shift effects. In the present study, we used NMR high resolution magic angle spinning to measure the chemical shift very accurately, free of bulk magnetization effects. The chemical shift of microemulsion components is measured as a function of the water content in order to validate the method in an interesting and promising, U-type dilutable microemulsion, which had been previously studied by a variety of techniques. Phase transition points of the microemulsion (O/W, bicontinuous, W/O) and changes in droplet shape were successfully detected using high-accuracy chemical shift measurements. We analyzed the results and found them to be compatible with the previous studies, paving the way for high-accuracy chemical shifts to be used for the study of other microemulsion systems. We detected two transition points along the water dilution line of the concentrate (reverse micelles) corresponding to the transition from swollen W/O nano-droplets to bicontinuous to the O/W droplets along with the changes in the droplets' sizes and shapes. The method seems to be in excellent agreement with other previously studied techniques and shows the advantage of this easy and valid technique. PMID:25113928
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The effects of heteroatoms Eh(Eh=O, S, Se, Te) on 13C chemical shifts in eleven isological series of R1-Eh-R2 unsaturated compounds are compared. A linear relation between 13C nuclei screening and tEh electronegativity is observed. An assumption is suggested that both likeness of the effects of 6A and 7A group elements on 13C chemical shifts of R1 and R2 substituents and their difference for elements of the 4A group are caused by unbonded interactions of the substituents with unshared electron pairs of heteroatoms
Senovilla, J M M
2000-01-01
A purely algebraic construction of super-energy tensors for arbitrary fields is presented in any dimensions. These tensors have good mathematical and physical properties, and they can be used in any theory having as basic arena an n-dimensional manifold with a metric of Lorentzian signature. In general, the completely timelike component of these s-e tensors has the mathematical features of an energy density: they are positive definite and satisfy the dominant property. Similarly, the super-momentum vectors have mathematical properties of s-e flux vectors. The classical Bel-Robinson tensor is included in our general definition. The energy-momentum and super-energy tensors of physical fields are also obtained, and the procedure is illustrated by writing down these tensors explicitly for the cases of scalar, electromagnetic, and Proca fields. Moreover, `(super)$^k$-energy' tensors are defined and shown to be meaningful and in agreement for the different physical fields. In flat spacetimes, they provide infinitel...
Nelson, Sarah J.; Webster, Katherine E.; Loftin, Cynthia S.; Weathers, Kathleen C.
2013-01-01
Major ion and mercury (Hg) inputs to terrestrial ecosystems include both wet and dry deposition (total deposition). Estimating total deposition to sensitive receptor sites is hampered by limited information regarding its spatial heterogeneity and seasonality. We used measurements of throughfall flux, which includes atmospheric inputs to forests and the net effects of canopy leaching or uptake, for ten major ions and Hg collected during 35 time periods in 1999–2005 at over 70 sites within Acadia National Park, Maine to (1) quantify coherence in temporal dynamics of seasonal throughfall deposition and (2) examine controls on these patterns at multiple scales. We quantified temporal coherence as the correlation between all possible site pairs for each solute on a seasonal basis. In the summer growing season and autumn, coherence among pairs of sites with similar vegetation was stronger than for site-pairs that differed in vegetation suggesting that interaction with the canopy and leaching of solutes differed in coniferous, deciduous, mixed, and shrub or open canopy sites. The spatial pattern in throughfall hydrologic inputs across Acadia National Park was more variable during the winter snow season, suggesting that snow re-distribution affects net hydrologic input, which consequently affects chemical flux. Sea-salt corrected calcium concentrations identified a shift in air mass sources from maritime in winter to the continental industrial corridor in summer. Our results suggest that the spatial pattern of throughfall hydrologic flux, dominant seasonal air mass source, and relationship with vegetation in winter differ from the spatial pattern of throughfall flux in these solutes in summer and autumn. The coherence approach applied here made clear the strong influence of spatial heterogeneity in throughfall hydrologic inputs and a maritime air mass source on winter patterns of throughfall flux. By contrast, vegetation type was the most important influence on
Tensor Network Skeletonization
Ying, Lexing
2016-01-01
We introduce a new coarse-graining algorithm, tensor network skeletonization, for the numerical computation of tensor networks. This approach utilizes a structure-preserving skeletonization procedure to remove short-range correlations effectively at every scale. This approach is first presented in the setting of 2D statistical Ising model and is then extended to higher dimensional tensor networks and disordered systems. When applied to the Euclidean path integral formulation, this approach also gives rise to new efficient representations of the ground states for 1D and 2D quantum Ising models.
Mizyuk, Volodymyr; Shibanov, Volodymyr
2011-01-01
The concept of "compatible" and "incompatible" CMR spectra has been introduced. Application of compatibility increments (IC) allows to calculate the chemical shifts of C and C3 atoms of pentyloxyl fragment in 1-pentylbenzoylformate with a sufficiently good accuracy. Введено поняття "сумісних " і "несумісних " ЯМР спектрів. Застосування "інкрементів узгодження " дало можливість з достатньою точністю розрахувати хімічні зсуви атомів С2 і С пентилоксильного фрагменту в 1-пентилбензоїлформіаті....
International Nuclear Information System (INIS)
We investigated whether cytoplasmic fat in clear cell renal cell carcinoma (CCC) can be identified by chemical shift gradient-echo magnetic resonance imaging (CSI). CSI was performed for 22 cases of CCC and 30 cases of other renal tumors (including 16 cases of non-CCC), all of which were surgically proven. Signal reduction in out-of-phase images of these tumors was retrospectively evaluated and compared. The signal loss ratio (SLR) was defined and calculated. Fat staining of specimens from 16 tumors was performed and correlated with SLR. SLR was found to be significantly higher in CCC than in non-CCC (p<0.002). There was a significant correlation between the degree of fat staining positively of the specimens and SLR (p<0.01). When signal reduction in out-of-phase images suggested a diagnosis of CCC, a correct diagnosis of this entity was made in the resected renal tumors with a sensitivity, specificity, and accuracy of 82%, 93%, and 88%, respectively. CSI can demonstrate cytoplasmic fat in CCC, which helps to differentiate this entity from other renal tumors. (author)
International Nuclear Information System (INIS)
The objective of our study was to evaluate diagnostic ability and features of quantitative indices of three modalities: uptake rate on norcholesterol scintigraphy, computed tomography (CT) attenuation value, and fat suppression on chemical-shift magnetic resonance imaging (MRI) for characterizing adrenal adenomas. Image findings of norcholesterol scintigraphy, CT, and MRI were reviewed for 78 patients with functioning (n=48) or nonfunctioning (n=30) adrenal masses. The norcholesterol uptake rate, attenuation value on unenhanced CT, and suppression on in-phase to opposed-phase MRI were measured for adrenal masses. The norcholesterol uptake rate, CT attenuation value, and MR suppression index showed the sensitivity of 60%, 82%, and 100%, respectively, for functioning adenomas of <2.0 cm, and 96%, 79%, and 67%, respectively, for those of ≥2.0 cm. A statistically significant correlation was observed between size and norcholesterol uptake, and between CT attenuation value and MR suppression index. Regarding norcholesterol uptake, the adenoma-to-contralateral gland ratio was significantly higher in cortisol releasing than in aldosterone-releasing adenomas. The norcholesterol uptake rate was reliable for characterization of adenomas among adrenal masses of ≥2.0 cm. CT attenuation value and MR suppression index were well correlated with each other, and were useful regardless of mass size. (author)
International Nuclear Information System (INIS)
Objective: To investigate the value of different proton MR spectroscopy techniques including single-voxel spectroscopy (SVS) and chemical shift imaging (CSI) in diagnosing patients with temporal lobe epilepsy. Methods: Sixty cases (40 normal, 20 temporal lobe epilepsy) experienced SVS and CSI. The volume of interest (VOI) of SVS was placed over the anterior hippocampus formation (HF) region, including part of the head and body of the HF. The VOI of CSI encompassed bilateral HF and the head, body and tail of HF. The VOI was divided into 5 voxels from anterior to posterior. The metabolite data of both SVS and CSI were obtained and the ratios of NAA/Cr and NAA/(Cho+Cr) were recorded or calculated. Results: The ipsilateral hippocampus to the seizure of TLE patients had lower ratios of NAA/(Cho+Cr) and NAA/Cr, and the differences compared with those of the normal group and contralateral subgroup were statistically significant (F=41.958, P1HMRS study improved the diagnostic yield of MR evaluation in TLE patients. There was a correlation between the ratio of NAA/(Cho+Cr) and the location of HF. Regional variation must be considered when interpreting proton spectra of the HF. (author)
Ivanir, Hadar; Goldbourt, Amir
2014-07-01
Magic-angle spinning solid-state NMR has been applied to study CBM3b-Cbh9A (CBM3b), a cellulose binding module protein belonging to family 3b. It is a 146-residue protein having a unique nine-stranded β-sandwich fold, in which 35% of the structure is in a β-sheet conformation and the remainder of the protein is composed of loops and unstructured regions. Yet, the protein can be crystalized and it forms elongated needles. Close to complete chemical shift assignment of the protein was obtained by combining two- and three-dimensional experiments using a fully labeled sample and a glycerol-labeled sample. The use of an optimized protocol for glycerol-based sparse labeling reduces sample preparation costs and facilitates the assignment of the large number of aromatic signals in this protein. Conformational analysis shows good correlation between the NMR-predicted secondary structure and the reported X-ray crystal structure, in particular in the structured regions. Residues which show high B-factor values are situated mainly in unstructured regions, and are missing in our spectra indicating conformational flexibility rather than heterogeneity. Interestingly, long-range contacts, which could be clearly detected for tyrosine residues, could not be observed for aromatic phenylalanine residues pointing into the hydrophobic core, suggesting possible high ring mobility. These studies will allow us to further investigate the cellulose-bound form of CBM proteins. PMID:24824437
Toy, Mehmet; Tanak, Hasan
2016-01-01
In the present work, a combined experimental and theoretical study on ground state molecular structure, spectroscopic and nonlinear optical properties of azo compound 3‧-chloro-4-dimethlamino azobenzene are reported. The molecular geometry, vibrational wavenumbers and the first order hyperpolarizability of the title compound were calculated with the help of density functional theory computations. The optimized geometric parameters obtained by using DFT (B3LYP/6-311++G(d,p)) show good agreement with the experimental data. The vibrational transitions were identified based on the recorded FT-IR spectra in the range of 4000-400 cm-1 for solid state. The 1H isotropic chemical shifts with respect to TMS were also calculated using the gauge independent atomic orbital (GIAO) method and compared with the experimental data. Using the TD-DFT method, electronic absorption spectra of the title compound have been predicted, and good agreement is determined with the experimental ones. To investigate the NLO properties of the title compound, the polarizability and the first hyperpolarizability were calculated using the density functional B3LYP method with the 6-311++G(d,p) basis set. According to results, the title compound exhibits non-zero first hyperpolarizability value revealing second order NLO behavior. In addition, DFT calculations of the title compound, molecular electrostatic potential and frontier molecular orbitals were also performed at 6-311++G(d,p) level of theory.
Shell-structure fingerprints of tensor interaction
Zalewski, M; Dobaczewski, J; Olbratowski, P; Rafalski, M; Werner, T R; Wyss, R A
2008-01-01
We address consequences of strong tensor and weak spin-orbit terms in the local energy density functional, resulting from fits to the $f_{5/2} - f_{7/2}$ splittings in $^{40}$Ca, $^{48}$Ca, and $^{56}$Ni. In this study, we focus on nuclear binding energies. In particular, we show that the tensor contribution to the binding energies exhibits interesting topological features closely resembling that of the shell-correction. We demonstrate that in the extreme single-particle scenario at spherical shape, the tensor contribution shows tensorial magic numbers equal to $N(Z)$=14, 32, 56, and 90, and that this structure is smeared out due to configuration mixing caused by pairing correlations and migration of proton/neutron sub-shells with neutron/proton shell filling. Based on a specific Skyrme-type functional SLy4$_T$, we show that the proton tensorial magic numbers shift with increasing neutron excess to $Z$=14, 28, and 50.
Preservation of tensor sum and tensor product continuous functions
Directory of Open Access Journals (Sweden)
C. S. Kubrusly
2011-02-01
Full Text Available This note deals with preservation of tensor sum and tensor product of Hilbert space operators. Basic operations with tensor sum are presented. The main result addresses to the problem of transferring properties from a pair of operators to their tensor sum and to their tensor product. Sufficient conditions are given to ensure that properties preserved by ordinary sum and ordinary product are preserved by tensor sum and tensor product, which are equally relevant for both finite-dimensional and infinite-dimensional spaces.
Symmetric Tensor Decomposition
DEFF Research Database (Denmark)
Brachat, Jerome; Comon, Pierre; Mourrain, Bernard;
2010-01-01
We present an algorithm for decomposing a symmetric tensor, of dimension n and order d, as a sum of rank-1 symmetric tensors, extending the algorithm of Sylvester devised in 1886 for binary forms. We recall the correspondence between the decomposition of a homogeneous polynomial in n variables of...... polynomial equations of small degree in non-generic cases. We propose a new algorithm for symmetric tensor decomposition, based on this characterization and on linear algebra computations with Hankel matrices. The impact of this contribution is two-fold. First it permits an efficient computation of the...... decomposition of any tensor of sub-generic rank, as opposed to widely used iterative algorithms with unproved global convergence (e.g. Alternate Least Squares or gradient descents). Second, it gives tools for understanding uniqueness conditions and for detecting the rank....
Chung, Daniel J H
2016-01-01
We reformulate gauge theories in analogy with the vierbein formalism of general relativity. More specifically, we reformulate gauge theories such that their gauge dynamical degrees of freedom are local fields that transform linearly under the dual representation of the charged matter field. These local fields, which naively have the interpretation of non-local operators similar to Wilson lines, satisfy constraint equations. A set of basis tensor fields are used to solve these constraint equations, and their field theory is constructed. A new local symmetry in terms of the basis tensor fields is used to make this field theory local and maintain a Hamiltonian that is bounded from below. The field theory of the basis tensor fields is what we call the basis tensor gauge theory.
Energy Technology Data Exchange (ETDEWEB)
Ragab, Yasser [Radiology Department, Faculty of Medicine, Cairo University (Egypt); Radiology Department, Dr Erfan and Bagedo General Hospital (Saudi Arabia)], E-mail: yragab61@hotmail.com; Emad, Yasser [Rheumatology and Rehabilitation Department, Faculty of Medicine, Cairo University (Egypt); Rheumatology and Rehabilitation Department, Dr Erfan and Bagedo General Hospital (Saudi Arabia)], E-mail: yasseremad68@yahoo.com; Gheita, Tamer [Rheumatology and Rehabilitation Department, Faculty of Medicine, Cairo University (Egypt)], E-mail: gheitamer@yahoo.com; Mansour, Maged [Oncology Department, Faculty of Medicine, Cairo University (Egypt); Oncology Department, Dr Erfan and Bagedo General Hospital (Saudi Arabia)], E-mail: magedmansour@yahoo.com; Abou-Zeid, A. [Public Health Department, Faculty of Medicine, Cairo University, Cairo (Egypt)], E-mail: alaabouzeid@yahoo.com; Ferrari, Serge [Division of Bone Diseases, Department of Rehabilitation and Geriatrics, and WHO, Collaborating Center for Osteoporosis Prevention, Geneva University Hospital (Switzerland)], E-mail: serge.ferrari@medecine.unige.ch; Rasker, Johannes J. [Rheumatologist University of Twente, Enschede (Netherlands)], E-mail: j.j.rasker@utwente.nl
2009-10-15
Objective: The objective of this study was to establish the cut-off value of the signal intensity drop on chemical shift magnetic resonance imaging (MRI) with appropriate sensitivity and specificity to differentiate osteoporotic from neoplastic wedging of the spine. Patients and methods: All patients with wedging of vertebral bodies were included consecutively between February 2006 and January 2007. A chemical shift MRI was performed and signal intensity after (in-phase and out-phase) images were obtained. A DXA was performed in all. Results: A total of 40 patients were included, 20 with osteoporotic wedging (group 1) and 20 neoplastic (group 2). They were 21 males and 19 females. Acute vertebral collapse was observed in 15 patients in group 1 and subacute collapse in another 5 patients, while in group 2, 11 patients showed acute collapse and 9 patients (45%) showed subacute vertebral collapse. On the chemical shift MRI a substantial reduction in signal intensity was found in all lesions in both groups. The proportional changes observed in signal intensity of bone marrow lesions on in-phase compared with out-of-phase images showed significant differences in both groups (P < 0.05). At a cut-off value of 35%, the observed sensitivity of out-of-phase images was 95%, specificity was 100%, positive predictive value was 100% and negative predictive value was 95.2%. Conclusion: A chemical shift MRI is useful in order to differentiate patients with vertebral collapse due to underlying osteoporosis or neoplastic process.
Czech Academy of Sciences Publication Activity Database
Přecechtělová, J.; Munzarová, M. L.; Vaara, J.; Novák, P.; Dračínský, Martin; Sklenář, V.
Ireland : University College Dublin, 2012. s. 72-72. [EUROMAR 2012. Magnetic Resonance Conference. 01.07.2012-05.07.2012, Dublin] Institutional research plan: CEZ:AV0Z40550506 Keywords : NMR spectroscopy * phosphorus chemical shift * DFT calculations Subject RIV: CC - Organic Chemistry
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Kohl, Chad A. [Mayo Clinic, Department of Radiology, Phoenix, AZ (United States); Radiology Ltd., Tucson, AZ (United States); Chivers, F.S.; Lorans, Roxanne; Roberts, Catherine C.; Kransdorf, Mark J. [Mayo Clinic, Department of Radiology, Phoenix, AZ (United States)
2014-08-15
To re-assess the accuracy of chemical shift imaging in diagnosing indeterminate bone marrow lesions as benign or malignant. We retrospectively reviewed our experience with MR imaging of the pelvis to assess the accuracy of chemical shift imaging in distinguishing benign from malignant bone lesions. Two musculoskeletal radiologists retrospectively reviewed all osseous lesions biopsied since 2006, when chemical shift imaging was added to our routine pelvic imaging protocol. Study inclusion criteria required (1) MR imaging of an indeterminate bone marrow lesion about the pelvis and (2) subsequent histologic confirmation. The study group included 50 patients (29 male, 21 female) with an average age of 67 years (range, 41-89 years). MR imaging results were evaluated using biopsy results as the ''gold standard.'' There were 27 malignant and 23 benign lesions. Chemical shift imaging using an opposed-phase signal loss criteria of less than 20 % to indicate a malignant lesion, correctly diagnosed 27/27 malignant lesions and 14/23 benign lesions, yielding a 100 % sensitivity, 61 % specificity, 75 % PPV, 100 % NPV, and 82 % accuracy. The area under the receiver operator characteristic (ROC) curve was 0.88. The inter-rater and intra-rater agreement K values were both 1.0. Chemical shift imaging is a useful adjunct MR technique to characterize focal and diffuse marrow abnormalities on routine non-contrast pelvic imaging. It is highly sensitive in identifying malignant disease. Despite its lower specificity, the need for biopsy could be eliminated in more than 60 % of patients with benign disease. (orig.)
International Nuclear Information System (INIS)
Aim: To assess the value of section-selection gradient reversal (SSGR) in liver diffusion-weighted imaging (DWI) by comparing it to conventional DWI with an emphasis on chemical shift artefacts and lesion conspicuity. Materials and methods: Forty-eight patients (29 men and 19 women; age range 33–80 years) with 48 liver lesions underwent two DWI examinations using spectral presaturation with inversion recovery fat suppression with and without SSGR at 3 T. Two reviewers evaluated each DWI (b = 100 and b = 800 image) with respect to chemical shift artefacts and liver lesion conspicuity using five-point scales and performed pairwise comparisons between the two DWIs. The signal-to-noise ratio (SNR) of the liver and the lesion and the lesion–liver contrast-to-noise ratio (CNR) were also calculated. Results: SSGR-DWI was significantly better than conventional DWI with respect to chemical shift artefacts and lesion conspicuity in both separate reviews and pairwise comparisons (p < 0.05). There were significant differences in the SNR of the liver (b = 100 and b = 800 images) and lesion (b = 800) between SSGR-DWI and conventional DWI (p < 0.05). Conclusion: Applying the SSGR method to DWI using SPIR fat suppression at 3 T could significantly reduce chemical shift artefacts without incurring additional acquisition time or SNR penalties, which leads to increased conspicuity of focal liver lesions. - Highlights: • Chemical shift artefact in liver DWI is markedly decreased by applying SSGR. • Liver lesion conspicuity is improved by applying SSGR to DWI. • In SNR of the liver, SSGR-DWI is better than conventional DWI
International Nuclear Information System (INIS)
To re-assess the accuracy of chemical shift imaging in diagnosing indeterminate bone marrow lesions as benign or malignant. We retrospectively reviewed our experience with MR imaging of the pelvis to assess the accuracy of chemical shift imaging in distinguishing benign from malignant bone lesions. Two musculoskeletal radiologists retrospectively reviewed all osseous lesions biopsied since 2006, when chemical shift imaging was added to our routine pelvic imaging protocol. Study inclusion criteria required (1) MR imaging of an indeterminate bone marrow lesion about the pelvis and (2) subsequent histologic confirmation. The study group included 50 patients (29 male, 21 female) with an average age of 67 years (range, 41-89 years). MR imaging results were evaluated using biopsy results as the ''gold standard.'' There were 27 malignant and 23 benign lesions. Chemical shift imaging using an opposed-phase signal loss criteria of less than 20 % to indicate a malignant lesion, correctly diagnosed 27/27 malignant lesions and 14/23 benign lesions, yielding a 100 % sensitivity, 61 % specificity, 75 % PPV, 100 % NPV, and 82 % accuracy. The area under the receiver operator characteristic (ROC) curve was 0.88. The inter-rater and intra-rater agreement K values were both 1.0. Chemical shift imaging is a useful adjunct MR technique to characterize focal and diffuse marrow abnormalities on routine non-contrast pelvic imaging. It is highly sensitive in identifying malignant disease. Despite its lower specificity, the need for biopsy could be eliminated in more than 60 % of patients with benign disease. (orig.)
International Nuclear Information System (INIS)
Objective: To study the reproducibility of relative quantification of phosphorus metabolites in human liver with two-dimensional chemical shift imaging(2D CSI). Methods: Using 2D CSI with FOV 200 mm and average times 40, 500 ml phosphate (NaH2PO4) solution phantom with 0.05 mol/L concentration was scanned 6 times, changing FOV to 280 mm, five healthy volunteers were scanned 6 times under respiration gating. The relative quantification of metabolites was derived from the integral values of peaks on the spectra, and then the errors of metabolite detection were obtained through data analysis. Results: (1) With FOV 200 mm and average times 40, phosphate solution phantom had a good reproducibility with the error less than 5.38%. Under respiration gating, the largest detection error of metabolites within five volunteers was phosphomonoesters (PME) 39.5%, inorganic phosphate (Pi) 40.4%, phosphodiesters (PDE) 23.2%, adenosine triphosphate; γ-ATP 24.3%, α-ATP 20.1%, β-ATP 24.9%, respectively. (2) The baseline of spectra was smoother and the error was less with respiration gating than that without respiration gating. (3) During the phantom test, with average times 40, change FOV to 280 mm and 400 mm, the detection errors were 4.96% and 4.47%. With FOV 200 mm and average times 20, 40, 80, the detection errors were 8.86%, 5.38% and 4.40%, corresponding acquisition time were 1.27 min, 2.53 min and 5.06 min. Conclusion: Detection of phosphorus metabolites in human liver with 2D CSI is a stable and useful technique. Scan parameters should be carefully selected, and other influencing factors of detection must be also noticed during examination. (authors)
Jang, Richard
2011-01-01
Chemical shift mapping is an important technique in NMRbased drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically. However, automated methods are necessary for high-throughput drug screening. We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C- labeling, to resolve the ambiguities for a one-toone mapping. On the three proteins, it achieves an average accuracy of 94% or better. Copyright © 2011 ACM.
Indian Academy of Sciences (India)
D Joseph; C Nayak; P Venu Babu; S N Jha; D Bhattacharyya
2014-05-01
Uranium L3 X-ray absorption edge was measured in various compounds containing uranium in U4+, U5+ and U6+ oxidation states. The measurements have been carried out at the Energy Dispersive EXAFS beamline (BL-08) at INDUS-2 synchrotron radiation source at RRCAT, Indore. Energy shifts of ∼ 2–3 eV were observed for U L3 edge in the U-compounds compared to their value in elemental U. The different chemical shifts observed for the compounds having the same oxidation state of the cation but different anions or ligands show the effect of different chemical environments surrounding the cations in determining their X-ray absorption edges in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on U cation in the above compounds.
International Nuclear Information System (INIS)
The temperature dependence to the 31P NMR spectra of poly[d(GC)]-poly[d(GC)], d(GC)4, phenylalanine tRNA (yeast) and mixtures of poly(A) + oligo(U) is presented. The 31P NMR spectra of mixtures of complementary RNA and of the poly d(GC) self-complementary DNA provide torsional information on the phosphate ester conformation in the double, triple, and ''Z'' helix. The increasing downfield shift with temperature for the single-strand nucleic acids provides a measure of the change in the phosphate ester conformation in the single helix to coil conversion. A seperate upfield peak (20-26% of the total phosphates) is observed at lower temperatures in the oligo(U)-poly(A) mixtures which is assigned to the double helix/triple helix. Proton NMR and UV spectra confirm the presence of the multistrand forms. The 31P chemical shift for the double helix/triple helix is 0.2-0.5 ppm upfield from the chemical shift for the single helix which in turn is 1.0 ppm upfield from the chemical shift for the random coil conformation
International Nuclear Information System (INIS)
A database of peptide chemical shifts, computed at the density functional level, has been used to develop an algorithm for prediction of 15N and 13C shifts in proteins from their structure; the method is incorporated into a program called SHIFTS (version 4.0). The database was built from the calculated chemical shift patterns of 1335 peptides whose backbone torsion angles are limited to areas of the Ramachandran map around helical and sheet configurations. For each tripeptide in these regions of regular secondary structure (which constitute about 40% of residues in globular proteins) SHIFTS also consults the database for information about sidechain torsion angle effects for the residue of interest and for the preceding residue, and estimates hydrogen bonding effects through an empirical formula that is also based on density functional calculations on peptides. The program optionally searches for alternate side-chain torsion angles that could significantly improve agreement between calculated and observed shifts. The application of the program on 20 proteins shows good consistency with experimental data, with correlation coefficients of 0.92, 0.98, 0.99 and 0.90 and r.m.s. deviations of 1.94, 0.97, 1.05, and 1.08 ppm for 15N, 13Cα, 13Cβ and 13C', respectively. Reference shifts fit to protein data are in good agreement with 'random-coil' values derived from experimental measurements on peptides. This prediction algorithm should be helpful in NMR assignment, crystal and solution structure comparison, and structure refinement
Wu, Chong-Rong; Chang, Xiang-Rui; Chang, Shu-Wei; Chang, Chung-En; Wu, Chao-Hsin; Lin, Shih-Yen
2015-11-01
We show that multilayer molybdenum disulfide (MoS2) grown with the chemical vapor deposition (CVD) may exhibit quite distinct behaviors of Raman shifts from those of exfoliated ones. The anomalous Raman shifts depend on CVD growth modes and are attributed to the modified dielectric screening and interlayer coupling of MoS2 in various growth conditions. With repeated CVD growths, we demonstrated the precise control over the layer number of MoS2. A decently large drain current, high ON/OFF ratio of 105, and enhanced field-effect mobility can be achieved in transistors fabricated on the six-layer MoS2.
Tensors, relativity, and cosmology
Dalarsson, Mirjana
2015-01-01
Tensors, Relativity, and Cosmology, Second Edition, combines relativity, astrophysics, and cosmology in a single volume, providing a simplified introduction to each subject that is followed by detailed mathematical derivations. The book includes a section on general relativity that gives the case for a curved space-time, presents the mathematical background (tensor calculus, Riemannian geometry), discusses the Einstein equation and its solutions (including black holes and Penrose processes), and considers the energy-momentum tensor for various solutions. In addition, a section on relativistic astrophysics discusses stellar contraction and collapse, neutron stars and their equations of state, black holes, and accretion onto collapsed objects, with a final section on cosmology discussing cosmological models, observational tests, and scenarios for the early universe. This fully revised and updated second edition includes new material on relativistic effects, such as the behavior of clocks and measuring rods in m...
Relativistic segnificance of curvature tensors
Directory of Open Access Journals (Sweden)
G. P. Pokhariyal
1982-01-01
Full Text Available In thi paper new curvature tensors have been defined on the lines of Weyl's projective curvature tensor and it has been shown that the distribution (order in which the vectors in question are arranged before being acted upon by the tensor in question of vector field over the metric potentials and matter tensors plays an important role in shaping the various physical and geometrical properties of a tensor viz the formulation of gravitational waves, reduction of electromagnetic field to a purely electric field, vanishing of the contracted tensor in an Einstein Space and the cyclic property.
Killing tensors and conformal Killing tensors from conformal Killing vectors
International Nuclear Information System (INIS)
Koutras has proposed some methods to construct reducible proper conformal Killing tensors and Killing tensors (which are, in general, irreducible) when a pair of orthogonal conformal Killing vectors exist in a given space. We give the completely general result demonstrating that this severe restriction of orthogonality is unnecessary. In addition, we correct and extend some results concerning Killing tensors constructed from a single conformal Killing vector. A number of examples demonstrate that it is possible to construct a much larger class of reducible proper conformal Killing tensors and Killing tensors than permitted by the Koutras algorithms. In particular, by showing that all conformal Killing tensors are reducible in conformally flat spaces, we have a method of constructing all conformal Killing tensors, and hence all the Killing tensors (which will in general be irreducible) of conformally flat spaces using their conformal Killing vectors
Physical components of tensors
Altman, Wolf
2014-01-01
""This book provides a clear explanation of the mathematical properties of tensors, from a physical perspective. The book is rigorous and concise, yet easy to read and very accessible. The reader will enjoy the wide variety of examples and exercises with solution, which make the book very pedagogical. I believe this can be a very useful book for anyone interested in learning about the mathematics of tensors, no matter the field of study or research. I would definitely like to have this book on my shelf, and use it as a reference in my own lectures."" -Román Orús, Institut für Physik, Jo
Czech Academy of Sciences Publication Activity Database
Phan, A. H.; Tichavský, Petr; Cichocki, A.
Piscataway: IEEE Computer Society, 2015, s. 2169-2173. ISBN 978-1-4673-6997-8. ISSN 1520-6149. [2015 IEEE International Conference on Acoustics, Speech, and Signal Processing ICASSP 2015. Brisbane (AU), 19.04.2015-24.04.2015] R&D Projects: GA ČR(CZ) GA14-13713S Institutional support: RVO:67985556 Keywords : tensor decomposition * CANDECOMP/PARAFAC * tensor deconvolution Subject RIV: BB - Applied Statistics, Operational Research http://library.utia.cas.cz/separaty/2015/SI/tichavsky-0443717.pdf
International Nuclear Information System (INIS)
Spectral features, chemical shifts, and absolute thresholds of electron energy loss near-edge structure (ELNES) and x-ray absorption near-edge structure (XANES) for selected compounds, i.e. TiO2 (rutile), TiO2 (anatase), SrTiO3, Ti2O3, Al2O3, AlN and β-Ga2O3, were calculated by a plane wave pseudopotential method. Experimental ELNES/XANES of those compounds were well reproduced when an excited pseudopotential, which includes a core hole, was used. In addition to the spectral features, it was found that chemical shifts among different compounds were also reproduced by correcting the contribution of the excited pseudopotentials to the energy of the core orbital.
Lande, Dipali N; Rao, Soniya S; Gejji, Shridhar P
2016-07-18
Binding of novel biphene[n]arene hosts to antiaromatic 7,7,8,8-tetracyanoquinodimethane (TCNQ) are investigated by DFT. Biphene[4]arene favors the inclusion complex through noncovalent interactions, such as hydrogen bonding, π-π stacking, C-H⋅⋅⋅π, and C-H⋅⋅⋅H-C dihydrogen bonding. Donor-acceptor complexation renders aromatic character to the guest through charge transfer. The formation of TCNQ anionic radicals through supramolecular π stacking significantly influences its chemical and photophysical behavior. Electron density reorganization consequent to encapsulation of TCNQ reflects in the shift of characteristic vibrations in the IR spectra. The accompanying aromaticities arising from the induced ring currents are analyzed by employing nucleus-independent chemical shifts based profiles. PMID:27028656
Flores, Mario E.; Shibue, Toshimichi; Sugimura, Natsuhiko; Nishide, Hiroyuki; Moreno-Villoslada, Ignacio
2016-01-01
Association of n-hexanol molecules in cyclohexane forming clusters is studied by DFT and 1H NMR. Geometry optimization, corrected binding energies, charge distributions, charge transfer energies, and 1H NMR chemical shifts have been obtained. The calculated chemical shifts of hydroxyl protons have been correlated to experimental data obtained in the range of n-hexanol molar fraction between 0.002 and 0.2, showing that n-hexanol molecules at a molar fraction around 0.1, where well-structured hydrogen bond networks are observed, tend to form linear pentamers and hexamers. The experimental data are consistent with the continuous linear association thermodynamic model, showing a dimensionless association constant of 284.
Energy Technology Data Exchange (ETDEWEB)
Bellstedt, Peter [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany); Herbst, Christian [Ubon Ratchathani University, Department of Physics, Faculty of Science (Thailand); Haefner, Sabine; Leppert, Joerg; Goerlach, Matthias; Ramachandran, Ramadurai, E-mail: raman@fli-leibniz.de [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany)
2012-12-15
We have carried out chemical shift correlation experiments with symmetry-based mixing sequences at high MAS frequencies and examined different strategies to simultaneously acquire 3D correlation spectra that are commonly required in the structural studies of proteins. The potential of numerically optimised symmetry-based mixing sequences and the simultaneous recording of chemical shift correlation spectra such as: 3D NCAC and 3D NHH with dual receivers, 3D NC Prime C and 3D C Prime NCA with sequential {sup 13}C acquisitions, 3D NHH and 3D NC Prime H with sequential {sup 1}H acquisitions and 3D CANH and 3D C'NH with broadband {sup 13}C-{sup 15}N mixing are demonstrated using microcrystalline samples of the {beta}1 immunoglobulin binding domain of protein G (GB1) and the chicken {alpha}-spectrin SH3 domain.
Czech Academy of Sciences Publication Activity Database
Vícha, J.; Novotný, J.; Straka, Michal; Repisky, M.; Ruud, K.; Komorovsky, S.; Marek, R.
2015-01-01
Roč. 17, č. 38 (2015), s. 24944-24955. ISSN 1463-9076 R&D Projects: GA ČR(CZ) GA14-03564S Institutional support: RVO:61388963 Keywords : NMR chemical shifts * transition metal complexes * relativistic effects * method calibration Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.493, year: 2014 http://pubs.rsc.org/en/content/articlepdf/2015/cp/c5cp04214c
Killing tensors and canonical geometry
International Nuclear Information System (INIS)
The systematic derivation of constants of the motion, based on Killing tensors and the gauge covariant approach, is outlined. Quantum dots are shown to support second-, third- and fourth-rank Killing tensors. (paper)
DEFF Research Database (Denmark)
Ziegel, Johanna; Nyengaard, Jens Randel; Jensen, Eva B. Vedel
In the present paper, statistical procedures for estimating shape and orientation of arbitrary three-dimensional particles are developed. The focus of this work is on the case where the particles cannot be observed directly, but only via sections. Volume tensors are used for describing particle s...
International Nuclear Information System (INIS)
We present a unified framework to describe lattice gauge theories by means of tensor networks: this framework is efficient as it exploits the high local symmetry content native to these systems by describing only the gauge invariant subspace. Compared to a standard tensor network description, the gauge invariant model allows one to increase real and imaginary time evolution up to a factor that is square of the dimension of the link variable. The gauge invariant tensor network description is based on the quantum link formulation, a compact and intuitive formulation for gauge theories on the lattice, which is alternative to and can be combined with the global symmetric tensor network description. We present some paradigmatic examples that show how this architecture might be used to describe the physics of condensed matter and high-energy physics systems. Finally, we present a cellular automata analysis which estimates the gauge invariant Hilbert space dimension as a function of the number of lattice sites that might guide the search for effective simplified models of complex theories. (paper)
Simplifying Tensor Polynomials with Indices
Balfagón, A
1998-01-01
We are presenting an algorithm capable of simplifying tensor polynomials with indices when the building tensors have index symmetry properties. These properties include simple symmetry, cyclicity and those due to the presence of partial and covariant derivatives. We are also including some examples using the Riemann tensor as a paradigm. The algorithm is part of a Mathematica package called Tools of Tensor Calculus (TTC) [web address: http//baldufa.upc.es/ttc
International Nuclear Information System (INIS)
Objective: To investigate the reproducibility and influencing factors of relative quantification of phosphorus metabolites with two-dimensional chemical shift imaging (2D CSI) in rabbit liver. Methods: Using 2D CSI MRS, 500 ml phosphate (NaH2PO4) solution phantom with 0.05 mol/L concentration and one healthy rabbit were scanned 30 times respectively in one day and rescanned 30 times in the next day, and the stability of MR scanner and reproducibility of within-run and between-days in the same individual were analyzed. Each of thirty rabbits was scanned and rescanned one time respectively in different days, and the reproducibility of between-days in one group was analyzed. The data were statistically analyzed with t tests. Results: (1) Phosphate solution phantom had a good reproducibility of within-run with the coefficient variation (CV) of 4.92% and 5.12% respectively in different two days. No significant change of phosphorus metabolites was detected in between-days, which was 16.68±0.82 and 16.56± 0.85 respectively (t=0.665, P>0.05). (2) The CV of metabolites in one healthy rabbit ranged from 8.04% to 34.13%. Among the metabolites, β-ATP had the best reproducibility with the CV less than 10%. PME was 0.88±0.28 and 0.88±0.30, PDE was 4.35±0.66 and 4.35±0.66, Pi was 0.95±0.30 and 0.97±0.28, α-ATP was 5.58±0.60 and 5.61±0.61, β-ATP was 2.70±0.22 and 2.71± 0.22, γ-ATP was 2.20±0.63 and 2.18±0.44 respectively, no significant changes of metabolites were detected in between-days (P>0.05). (3) The CV of metabolites in 30 healthy rabbits ranged from 8.48% to 36.21%. Among the metabolites, β-ATP had the best reproducibility with CV less than 10%. PME was 0.84±0.30 and 0.79±0.28, PDE was 4.29±0.72 and 3.94±0.84, Pi was 0.91±0.28 and 0.92± 0.31, α-ATP was 5.65±0.66 and 5.36±0.60, β-ATP was 2.71±0.23 and 2.66±0.25, γ-ATP was 2.07±0.29 and 1.99±0.37 respectively, no significant changes of metabolites were detected in between-days (P>0
Evaluation of Bayesian tensor estimation using tensor coherence
Energy Technology Data Exchange (ETDEWEB)
Kim, Dae-Jin; Park, Hae-Jeong [Laboratory of Molecular Neuroimaging Technology, Brain Korea 21 Project for Medical Science, Yonsei University, College of Medicine, Seoul (Korea, Republic of); Kim, In-Young [Department of Biomedical Engineering, Hanyang University, Seoul (Korea, Republic of); Jeong, Seok-Oh [Department of Statistics, Hankuk University of Foreign Studies, Yongin (Korea, Republic of)], E-mail: parkhj@yuhs.ac
2009-06-21
Fiber tractography, a unique and non-invasive method to estimate axonal fibers within white matter, constructs the putative streamlines from diffusion tensor MRI by interconnecting voxels according to the propagation direction defined by the diffusion tensor. This direction has uncertainties due to the properties of underlying fiber bundles, neighboring structures and image noise. Therefore, robust estimation of the diffusion direction is essential to reconstruct reliable fiber pathways. For this purpose, we propose a tensor estimation method using a Bayesian framework, which includes an a priori probability distribution based on tensor coherence indices, to utilize both the neighborhood direction information and the inertia moment as regularization terms. The reliability of the proposed tensor estimation was evaluated using Monte Carlo simulations in terms of accuracy and precision with four synthetic tensor fields at various SNRs and in vivo human data of brain and calf muscle. Proposed Bayesian estimation demonstrated the relative robustness to noise and the higher reliability compared to the simple tensor regression.
Moment Tensor Analysis of Shallow Sources
Chiang, A.; Dreger, D. S.; Ford, S. R.; Walter, W. R.; Yoo, S.
2013-12-01
For the nuclear explosion source-type identification problem the uncertainty in a solution is as important as the best fitting parameters. A potential issue for shallow seismic sources that are effectively at the free-surface between the ground and air is that the vanishing traction at the free-surface can cause the associated vertical dip-slip (DS) Green's functions to have vanishing amplitudes (Julian et al., 1998), which in turn results in the indeterminacy of the Mxz and Myz components of the moment tensor and bias in the moment tensor solution. The effects of the free-surface on the stability of the moment tensor method becomes important as we continue to investigate and improve the capabilities of regional full moment tensor inversion for source-type identification and discrimination. It is important to understand its effects for discriminating shallow explosive sources in nuclear monitoring, but could also be important in natural systems that have shallow seismicity such as volcanoes and geothermal systems. The HUMMING ALBATROSS quarry blast is an excellent dataset in terms of understanding the effects of free-surface vanishing traction with real data. These chemical explosions are approximately 10 m depth and are recorded at up to several km distances. Therefore the data represents a rather severe source-station geometry in terms of vanishing traction issues. It is possible to obtain a robust full moment tensor solution that is comprised dominantly by an isotropic or explosive component, however the data provide the opportunity to evaluate capabilities of moment tensor inversion as a function of frequency.
Brown, Eric
2008-10-01
Some of the most beautiful and complex theories in physics are formulated in the language of tensors. While powerful, these methods are sometimes daunting to the uninitiated. I will introduce the use of Clifford Algebra as a practical alternative to the use of tensors. Many physical quantities can be represented in an indexless form. The boundary between the classical and the quantum worlds becomes a little more transparent. I will review some key concepts, and then talk about some of the things that I am doing with this interesting and powerful tool. Of note to some will be the development of rigid body dynamics for a game engine. Others may be interested in expressing the connection on a spin bundle. My intent is to prove to the audience that there exists an accessible mathematical tool that can be employed to probe the most difficult of topics in physics.
Rosner, D. E.; Nagarajan, R.
1985-01-01
Partial heterogeneous condensation phenomena in multicomponent reacting systems are analyzed taking into consideration the chemical element transport phenomena. It is demonstrated that the dew-point surface temperature in chemically reactive systems is not a purely thermodynamic quantity, but is influenced by the multicomponent diffusion and Soret-mass diffusion phenomena. Several distinct dew-points are shown to exist in such systems and, as a result of transport constraints, the 'sharp' locus between two chemically distinct condensates is systematically moved to a difference mainstream composition.
Electronic stress tensor analysis of hydrogenated palladium clusters
Ichikawa, Kazuhide; Szarek, Pawel; Zhou, Chenggang; Cheng, Hansong; Tachibana, Akitomo
2011-01-01
We study the chemical bonds of small palladium clusters Pd_n (n=2-9) saturated by hydrogen atoms using electronic stress tensor. Our calculation includes bond orders which are recently proposed based on the stress tensor. It is shown that our bond orders can classify the different types of chemical bonds in those clusters. In particular, we discuss Pd-H bonds associated with the H atoms with high coordination numbers and the difference of H-H bonds in the different Pd clusters from viewpoint of the electronic stress tensor. The notion of "pseudo-spindle structure" is proposed as the region between two atoms where the largest eigenvalue of the electronic stress tensor is negative and corresponding eigenvectors forming a pattern which connects them.
Energy Technology Data Exchange (ETDEWEB)
Min, Ji Hye [Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of); Kim, Young Kon, E-mail: jmyr@dreamwiz.com [Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of); Lim, Sanghyeok [Department of Radiology, Guri Hospital, Hanyang University College of Medicine, Guri (Korea, Republic of); Jeong, Woo Kyoung; Choi, Dongil; Lee, Won Jae [Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of)
2015-06-15
Highlights: • Intra-tumoral fat detected with MR imaging may suggest lower risk for MVI of HCC. • Alfa-fetoprotein, tumor size, and fat component were associated with MVI of HCC. • Chemical shift MRI should be considered for the evaluation of HCC. - Abstract: Purpose: To investigate the impact of intra-tumoral fat detected by chemical-shift MR imaging in predicting the MVI of HCC. Materials and methods: Gadoxetic acid-enhanced MR imaging of 365 surgically proven HCCs from 365 patients (306 men, 59 women; mean age, 55.6 years) were evaluated. HCCs were classified into two groups, fat-containing and non-fat-containing, based on the presence of fat on chemical-shift images. Fat-containing HCCs were subdivided into diffuse or focal fatty change groups. Logistic regression analyses were used to identify clinical and MR findings associated with MVI. Results: Based on MR imaging, 66 tumors were classified as fat-containing HCCs and 299 as non-fat-containing HCCs. Among the 66 fat-containing HCCs, 38 (57.6%) showed diffuse fatty changes and 28 (42.4%) showed focal fatty changes. MVI was present in 18 (27.3%) fat-containing HCCs and in 117 (39.1%) non-fat-containing HCCs (P = 0.07). Univariate analysis revealed that serum alpha-fetoprotein (AFP) and tumor size were significantly associated with MVI (P < 0.001). A multiple logistic regression analysis showed that log AFP (odds ratio 1.178, P = 0.0016), tumor size (odds ratio 1.809, P < 0.001), and intra-tumoral fat (odds ratio 0.515, P = 0.0387) were independent variables associated with MVI. Conclusion: Intra-tumoral fat detected with MR imaging may suggest lower risk for MVI of HCC and, therefore, a possibly more favorable prognosis, but the clinical value of this finding is uncertain.
International Nuclear Information System (INIS)
Magic-angle-spinning solid-state 13C NMR spectroscopy is useful for structural analysis of non-crystalline proteins. However, the signal assignments and structural analysis are often hampered by the signal overlaps primarily due to minor structural heterogeneities, especially for uniformly-13C,15N labeled samples. To overcome this problem, we present a method for assigning 13C chemical shifts and secondary structures from unresolved two-dimensional 13C–13C MAS NMR spectra by spectral fitting, named reconstruction of spectra using protein local structures (RESPLS). The spectral fitting was conducted using databases of protein fragmented structures related to 13Cα, 13Cβ, and 13C′ chemical shifts and cross-peak intensities. The experimental 13C–13C inter- and intra-residue correlation spectra of uniformly isotope-labeled ubiquitin in the lyophilized state had a few broad peaks. The fitting analysis for these spectra provided sequence-specific Cα, Cβ, and C′ chemical shifts with an accuracy of about 1.5 ppm, which enabled the assignment of the secondary structures with an accuracy of 79 %. The structural heterogeneity of the lyophilized ubiquitin is revealed from the results. Test of RESPLS analysis for simulated spectra of five different types of proteins indicated that the method allowed the secondary structure determination with accuracy of about 80 % for the 50–200 residue proteins. These results demonstrate that the RESPLS approach expands the applicability of the NMR to non-crystalline proteins exhibiting unresolved 13C NMR spectra, such as lyophilized proteins, amyloids, membrane proteins and proteins in living cells.
International Nuclear Information System (INIS)
Highlights: • Intra-tumoral fat detected with MR imaging may suggest lower risk for MVI of HCC. • Alfa-fetoprotein, tumor size, and fat component were associated with MVI of HCC. • Chemical shift MRI should be considered for the evaluation of HCC. - Abstract: Purpose: To investigate the impact of intra-tumoral fat detected by chemical-shift MR imaging in predicting the MVI of HCC. Materials and methods: Gadoxetic acid-enhanced MR imaging of 365 surgically proven HCCs from 365 patients (306 men, 59 women; mean age, 55.6 years) were evaluated. HCCs were classified into two groups, fat-containing and non-fat-containing, based on the presence of fat on chemical-shift images. Fat-containing HCCs were subdivided into diffuse or focal fatty change groups. Logistic regression analyses were used to identify clinical and MR findings associated with MVI. Results: Based on MR imaging, 66 tumors were classified as fat-containing HCCs and 299 as non-fat-containing HCCs. Among the 66 fat-containing HCCs, 38 (57.6%) showed diffuse fatty changes and 28 (42.4%) showed focal fatty changes. MVI was present in 18 (27.3%) fat-containing HCCs and in 117 (39.1%) non-fat-containing HCCs (P = 0.07). Univariate analysis revealed that serum alpha-fetoprotein (AFP) and tumor size were significantly associated with MVI (P < 0.001). A multiple logistic regression analysis showed that log AFP (odds ratio 1.178, P = 0.0016), tumor size (odds ratio 1.809, P < 0.001), and intra-tumoral fat (odds ratio 0.515, P = 0.0387) were independent variables associated with MVI. Conclusion: Intra-tumoral fat detected with MR imaging may suggest lower risk for MVI of HCC and, therefore, a possibly more favorable prognosis, but the clinical value of this finding is uncertain
E6Tensors: A Mathematica Package for E6 Tensors
Deppisch, Thomas
2016-01-01
We present the Mathematica package E6Tensors, a tool for explicit tensor calculations in E6 gauge theories. In addition to matrix expressions for the group generators of E6, it provides structure constants, various higher rank tensors and expressions for the representations 27, 78, 351 and 351'. This paper comes along with a short manual including physically relevant examples. I further give a complete list of gauge invariant, renormalisable terms for superpotentials and Lagrangians.
Energy Technology Data Exchange (ETDEWEB)
Araujo, Marcelo F. de; Vieira, Ivo J. Curcino [Universidade Federal Rural do Rio de Janeiro, Seropedica, RJ (Brazil). Dept. de Quimica; Braz-Filho, Raimundo [Universidade Estadual do Norte Fluminense (UENF), Campos dos Goytacases, RJ (Brazil). Centro de Ciencias Tecnologicas. Lab. de Ciencias Quimicas; Carvalho, Mario G. de, E-mail: mgeraldo@ufrrj.br [Universidade Federal do Rio de Janeiro (NPPN/UFRJ), RJ (Brazil). Centro de Ciencias da Saude. Nucleo de Pesquisa em Produtos Naturais
2012-07-01
A new triterpene, 1-epi-castanopsol, besides eleven known compounds: sitosterol, stigmasterol, campesterol, lupeol, lupenone, simirane B, syringaresinol, scopoletin, isofraxidin, 6,7,8-trimethoxycoumarin and harman, were isolated from the wood of Simira glaziovii. The structures of the known compounds were defined by 1D, 2D {sup 1}H, {sup 13}C NMR spectra data analyses and comparison with literature data. The detailed spectral data analyses allowed the definition of the structure of the new 1-epi isomer of castanopsol and performance of {sup 1}H and {sup 13}C NMR chemical shift assignments. (author)
Lim, Sunghyuk; Yu, Qinhong; Rockwell, Nathan C; Martin, Shelley S; Lagarias, J Clark; Ames, James B
2016-04-01
Cyanobacteriochromes (CBCRs) are cyanobacterial photosensory proteins with a tetrapyrrole (bilin) chromophore that belong to the phytochrome superfamily. Like phytochromes, CBCRs photoconvert between two photostates with distinct spectral properties. NpR6012g4 from Nostoc punctiforme is a model system for widespread CBCRs with conserved red/green photocycles. Atomic-level structural information for the photoproduct state in this subfamily is not known. Here, we report NMR backbone chemical shift assignments of the light-activated state of NpR6012g4 (BMRB no. 26577) as a first step toward determining its atomic resolution structure. PMID:26537963
International Nuclear Information System (INIS)
A new triterpene, 1-epi-castanopsol, besides eleven known compounds: sitosterol, stigmasterol, campesterol, lupeol, lupenone, simirane B, syringaresinol, scopoletin, isofraxidin, 6,7,8-trimethoxycoumarin and harman, were isolated from the wood of Simira glaziovii. The structures of the known compounds were defined by 1D, 2D 1H, 13C NMR spectra data analyses and comparison with literature data. The detailed spectral data analyses allowed the definition of the structure of the new 1-epi isomer of castanopsol and performance of 1H and 13C NMR chemical shift assignments. (author)
International Nuclear Information System (INIS)
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.
International Nuclear Information System (INIS)
The chemical shift δS of xenon adsorbed on zeolite and extrapolated to zero concentration depends only on the internal void space of the solid. The smaller the channels or cavities, or the more restricted the diffusion, the greater δS becomes. We have calculated the theoretical values of the mean free path l-bar of xenon adsorbed in various zeolites. We deduce from them the dependence of the δS on l-bar. It is now possible to determine the dimensions of any void space in which xenon can be adsorbed. 4 refs.; 2 figs.; 3 tabs
Tensor Permutation Matrices in Finite Dimensions
Christian, Rakotonirina
2005-01-01
We have generalised the properties with the tensor product, of one 4x4 matrix which is a permutation matrix, and we call a tensor commutation matrix. Tensor commutation matrices can be constructed with or without calculus. A formula allows us to construct a tensor permutation matrix, which is a generalisation of tensor commutation matrix, has been established. The expression of an element of a tensor commutation matrix has been generalised in the case of any element of a tensor permutation ma...
13C-NMR chemical shift databases as a quick tool to evaluate structural models of humic substances
DEFF Research Database (Denmark)
Nyrop Albers, Christian; Hansen, Poul Erik
2010-01-01
Models for humic and fulvic acids are discussed based on 13C liquid state NMR spectra combined with results from elemental analysis and titration studies. The analysis of NMR spectra is based on a full reconstruction of the NMR spectrum done with help of 13C-NMR data bases by adding up chemical s...
Tensor Networks for Entanglement Evolution
Meznaric, Sebastian
2012-01-01
The intuitiveness of the tensor network graphical language is becoming well known through its use in numerical simulations using methods from tensor network algorithms. Recent times have also seen rapid progress in developing equations of motion to predict the time evolution of quantum entanglement [Nature Physics, 4(\\textbf{4}):99, 2008]. Here we cast these recent results into a tensor network framework and in doing so, construct a theory which exposes the topological equivalence of the evolution of a family of entanglement monotones in arbitrary dimensions. This unification was accomplished by tailoring a form of channel state duality through the interpretation of graphical tensor network rewrite rules. The introduction of tensor network methods to the theory of entanglement evolution opens the door to apply methods from the rapidly evolving area known as tensor network states.
Institute of Scientific and Technical Information of China (English)
WANG Zhen; ZHANG Jing
2011-01-01
Quantum chemical calculations on some possible equilibrium geometries of C2402 isomers derived from C24 (D6) and C240 have been performed using density functional theory (DFT) method. The geometric and electronic structures as well as the relative energies and thermal stabilities of various C2402 isomers at the ground state have been calculated at the B3LYP/6-31G(d) level of theory. And the 1,4,2,5-C2402 isomer was found to be the most stable geometry where two oxygen atoms were added to the longest carbon-carbon bonds in the same pentagon from a thermodynamic point of view. Based on the optimized neutral geometries, the vertical ionization potential and vertical electron affinity have been obtained. Meanwhile, the vibrational frequencies,IR spectrum, and 13C chemical shifts of various C2402 isomers have been calculated and analyzed.
Wiggins, Natasha L; Forrister, Dale L; Endara, María-José; Coley, Phyllis D; Kursar, Thomas A
2016-01-01
Selective pressures imposed by herbivores are often positively correlated with investments that plants make in defense. Research based on the framework of an evolutionary arms race has improved our understanding of why the amount and types of defenses differ between plant species. However, plant species are exposed to different selective pressures during the life of a leaf, such that expanding leaves suffer more damage from herbivores and pathogens than mature leaves. We hypothesize that this differential selective pressure may result in contrasting quantitative and qualitative defense investment in plants exposed to natural selective pressures in the field. To characterize shifts in chemical defenses, we chose six species of Inga, a speciose Neotropical tree genus. Focal species represent diverse chemical, morphological, and developmental defense traits and were collected from a single site in the Amazonian rainforest. Chemical defenses were measured gravimetrically and by characterizing the metabolome of expanding and mature leaves. Quantitative investment in phenolics plus saponins, the major classes of chemical defenses identified in Inga, was greater for expanding than mature leaves (46% and 24% of dry weight, respectively). This supports the theory that, because expanding leaves are under greater selective pressure from herbivores, they rely more upon chemical defense as an antiherbivore strategy than do mature leaves. Qualitatively, mature and expanding leaves were distinct and mature leaves contained more total and unique metabolites. Intraspecific variation was greater for mature leaves than expanding leaves, suggesting that leaf development is canalized. This study provides a snapshot of chemical defense investment in a speciose genus of tropical trees during the short, few-week period of leaf development. Exploring the metabolome through quantitative and qualitative profiling enables a more comprehensive examination of foliar chemical defense investment
Hackbusch Conjecture on tensor formats
Buczyńska, Weronika; Buczyński, Jarosław; Michałek, Mateusz
2015-01-01
We prove a conjecture of W. Hackbusch about tensor network states related to a perfect binary tree and train track tree. Tensor network states are used to present seemingly complicated tensors in a relatively simple and efficient manner. Each such presentation is described by a binary tree and a collection of vector spaces, one for each vertex of the tree. A problem suggested by Wolfgang Hackbusch and Joseph Landsberg is to compare the complexities of encodings, if one presents the same tenso...
Gruver, C; Kelly, P F; Gruver, Charro; Hammond, Richard
2001-01-01
A theory of gravity with torsion is examined in which the torsion tensor is constructed from the exterior derivative of an antisymmetric rank two potential plus the dual of the gradient of a scalar field. Field equations for the theory are derived by demanding that the action be stationary under variations with respect to the metric, the antisymmetric potential, and the scalar field. A material action is introduced and the equations of motion are derived. The correct conservation law for rotational angular momentum plus spin is observed to hold in this theory.
Notes on Super Killing Tensors
Howe, P S
2015-01-01
The notion of a Killing tensor is generalised to a superspace setting. Conserved quantities associated with these are defined for superparticles and Poisson brackets are used to define a supersymmetric version of the Schouten-Nijenhuis bracket. Superconformal Killing tensors in flat superspaces are studied for spacetime dimensions 3,4,5,6 and 10. These tensors are also presented in analytic superspaces and super-twistor spaces for 3,4 and 6 dimensions. Algebraic structures associated with superconformal Killing tensors are also briefly discussed
Tensor norms and operator ideals
Defant, A
1992-01-01
The three chapters of this book are entitled Basic Concepts, Tensor Norms, and Special Topics. The first may serve as part of an introductory course in Functional Analysis since it shows the powerful use of the projective and injective tensor norms, as well as the basics of the theory of operator ideals. The second chapter is the main part of the book: it presents the theory of tensor norms as designed by Grothendieck in the Resumé and deals with the relation between tensor norms and operator ideals. The last chapter deals with special questions. Each section is accompanied by a series of exercises.
Notes on super Killing tensors
Howe, P. S.; Lindström, U.
2016-03-01
The notion of a Killing tensor is generalised to a superspace setting. Conserved quantities associated with these are defined for superparticles and Poisson brackets are used to define a supersymmetric version of the even Schouten-Nijenhuis bracket. Superconformal Killing tensors in flat superspaces are studied for spacetime dimensions 3,4,5,6 and 10. These tensors are also presented in analytic superspaces and super-twistor spaces for 3,4 and 6 dimensions. Algebraic structures associated with superconformal Killing tensors are also briefly discussed.
Energy Technology Data Exchange (ETDEWEB)
Smith, Kenneth F.
2006-07-26
The project employed new processes to make emulsion polymers from reduced levels of petroleum-derived chemical feedstocks. Most waterborne paints contain spherical, emulsion polymer particles that serve as the film-forming binder phase. Our goal was to make emulsion polymer particles containing 30 percent feedstock that would function as effectively as commercial emulsions made from higher level feedstock. The processes developed yielded particles maintained their film formation capability and binding capacity while preserving the structural integrity of the particles after film formation. Rohm and Haas Company (ROH) and Archer Daniels Midland Company (ADM) worked together to employ novel polymer binders (ROH) and new, non-volatile, biomass-derived coalescing agents (ADM). The University of Minnesota Department of Chemical Engineering and Material Science utilized its unique microscopy capabilities to characterize films made from the New Emulsion Polymers (NEP).
Rofouie, M K; Salahinejad, M; Ghasemi, J B; Aghaei, A
2013-05-01
Comparative molecular field analysis (CoMFA), comparative molecular field analysis region focusing (CoMFA-RF) for optimizing the region for the final partial least square analysis, and comparative molecular similarity indices analysis (CoMSIA) methods were employed to develop three-dimensional quantitative structure-activity relationship (3D-QSAR) models of (1)H NMR chemical shift of NH proton of diaryl triazene derivatives. The best orientation was searched by all-orientation search (AOS) strategy to minimize the effect of the initial orientation of the structures. The predictive abilities of CoMFA-RF and CoMSIA models were determined using a test set of ten compounds affording predictive correlation coefficients of 0.721 and 0.754, respectively, indicating good predictive power. For further model validation, cross validation (leave one out), progressive scrambling, and bootstrapping were also applied. The accuracy and speed of obtained 3D-QSAR models for the prediction of (1)H NMR chemical shifts of NH group of diaryl triazene derivatives were greater compared to some computational well-known procedures. PMID:23456682
Energy Technology Data Exchange (ETDEWEB)
Ahlner, Alexandra; Andresen, Cecilia; Khan, Shahid N. [Linköping University, Division of Chemistry, Department of Physics, Chemistry and Biology (Sweden); Kay, Lewis E. [The University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry, One King’s College Circle (Canada); Lundström, Patrik, E-mail: patlu@ifm.liu.se [Linköping University, Division of Chemistry, Department of Physics, Chemistry and Biology (Sweden)
2015-07-15
A selective isotope labeling scheme based on the utilization of [2-{sup 13}C]-glycerol as the carbon source during protein overexpression has been evaluated for the measurement of excited state {sup 13}Cα chemical shifts using Carr–Purcell–Meiboom–Gill (CPMG) relaxation dispersion (RD) experiments. As expected, the fractional incorporation of label at the Cα positions is increased two-fold relative to labeling schemes based on [2-{sup 13}C]-glucose, effectively doubling the sensitivity of NMR experiments. Applications to a binding reaction involving an SH3 domain from the protein Abp1p and a peptide from the protein Ark1p establish that accurate excited state {sup 13}Cα chemical shifts can be obtained from RD experiments, with errors on the order of 0.06 ppm for exchange rates ranging from 100 to 1000 s{sup −1}, despite the small fraction of {sup 13}Cα–{sup 13}Cβ spin-pairs that are present for many residue types. The labeling approach described here should thus be attractive for studies of exchanging systems using {sup 13}Cα spin probes.
A strain tensor that couples to the Madelung stress tensor
Delphenich, D H
2013-01-01
Ordinarily, the stress tensor that one derives for a Madelung fluid is not regarded as being coupled to a strain tensor, which is consistent with the fluid hypothesis. However, based upon earlier work regarding the geometric nature of the quantum potential, one can, in fact, define a strain tensor, which is not, however, due to a deformation of a spatial region, but to a deformation of a frame field on that region. When one expresses the Madelung stress tensor as a function of the strain tensor and its derivatives, one then defines a constitutive law for the Madelung medium that might lead to a more detailed picture of its elementary structure. It is pointed out that the resulting constitutive law is strongly analogous to laws that were presented by Kelvin and Tait for the bending and torsion of elastic wires and plates, as well as the Einstein equations for gravitation if one takes the viewpoint of metric elasticity.
Brain temperature and pH measured by 1H chemical shift imaging of a thulium agent
Coman, Daniel; Trubel, Hubert K.; Rycyna, Robert E.; Hyder, Fahmeed
2009-01-01
Temperature and pH are two of the most important physiological parameters and are believed to be tightly regulated because they are intricately related to energy metabolism in living organisms. Temperature and/or pH data in mammalian brain are scarce, however, mainly due to lack of precise and non-invasive methods. At 11.7T, we demonstrate that a thulium-based macrocyclic complex infused through the blood stream can be used to obtain temperature and pH maps of rat brain in vivo by 1H chemical...
The geomagnetic field gradient tensor
DEFF Research Database (Denmark)
Kotsiaros, Stavros; Olsen, Nils
2012-01-01
We develop the general mathematical basis for space magnetic gradiometry in spherical coordinates. The magnetic gradient tensor is a second rank tensor consisting of 3 × 3 = 9 spatial derivatives. Since the geomagnetic field vector B is always solenoidal (∇ · B = 0) there are only eight independent...
Beam-induced tensor pressure tokamak equilibria
International Nuclear Information System (INIS)
D-shaped tensor pressure tokamak equilibria induced by neutral-beam injection are computed. The beam pressure components are evaluated from the moments of a distribution function that is a solution of the Fokker-Planck equation in which the pitch-angle scattering operator is ignored. The level-psub(perpendicular) contours undergo a significant shift away from the outer edge of the device with respect to the flux surfaces for perpendicular beam injection into broad-pressure-profile equilibria. The psub(parallel) contours undergo a somewhat smaller inward shift with respect to the flux surfaces for both parallel and perpendicular injection into broad-pressure-profile equilibria. For peaked-pressure-profile equilibria, the level pressure contours nearly co-incide with the flux surfaces. (author)
Energy Technology Data Exchange (ETDEWEB)
Herbst, Christian
2010-04-27
The basic aim of the thesis was the development and improvement of homo- and heteronuclear feedback sequences for the generation of correlation spectra of the chemical shift. In a first step the possibility of the acquisition of {sup 13}C-{sup 13} correlation spectra of the chemical shift by means of inversion pulses with low RF power factor was studied. Furthermore it was shown that broad-band phase-modulated inversion and universal rotational pulses can be constructed by means of global optimization procedures like the genetic algorithms under regardment of the available RF field strength. By inversion, universal rotational, and 360 pulses as starting values of the optimization efficient homonuclear CN{sub n}{sup {nu}} and RN{sub n}{sup {nu}} mixing sequences as well as heteronuclear RN{sub n}{sup {nu}{sub s},{nu}{sub k}} feedback sequences were generated. The satisfactory power of the numerically optimized sequences was shown by means of the simulation as well by means of correlation experiments of the chemical shift of L-histidine, L-arginine, and the (CUG){sub 97}-RNA. This thesis deals furthermore with the possibility to acquire simultaneously different signals with several receivers. By means of numerically optimized RN{sub n}{sup {nu}{sub s},{nu}{sub k}} pulse sequences both {sup 15}N-{sup 13}C and {sup 13}C-{sup 15}N correlation spectra were simultaneously generated. Furthermore it could be shown that the simultaneous acquisition of 3D-{sup 15}N-{sup 13}C-{sup 13}C and {sup 13}C-{sup 15}N-({sup 1}H)-{sup 1}H correlation spectra is possible. By this in only one measurement process resonance assignments can be met and studies of the global folding performed. A further application of several receivers is the simultaneous acquisition of CHHC, NHHN, NHHC, as well as CHHN spectra. By such experiments it is possible to characterize the hydrogen-bonding pattern and the glycosidic torsion angle {sup {chi}} in RNA. This was demonstrated by means of the (CUG){sub 97
Killing-Yano tensors and Nambu mechanics
International Nuclear Information System (INIS)
Killing-Yano tensors were introduced in 1952 by Kentaro-Yano from mathematical point of view. The physical interpretation of Killing-Yano tensors of rank higher than two was unclear. We found that all Killing-Yano tensors ηi1i2...in with covariant derivative zero are Nambu tensors. We found that in the case of flat space case all Killing-Yano tensors are Nambu tensors. In the case of Taub-NUT and Kerr-Newmann metric Killing-Yano tensors of order two generate Nambu tensors of rank 3
DEFF Research Database (Denmark)
Jankowska, Marzena; Kupka, Teobald; Stobiński, Leszek;
2016-01-01
Hartree-Fock and density functional theory with the hybrid B3LYP and general gradient KT2 exchange-correlation functionals were used for non-relativistic and relativistic nuclear magnetic shielding calculations of helium, neon, argon, krypton and xenon dimers and free atoms. Relativistic...... corrections were calculated with the scalar and spin-orbit zeroth-order regular approximation Hamiltonian in combination with the large Slater-type basis set QZ4P as well as with the 4-component Dirac-Coulomb Hamiltonian using Dyall’s acv4z basis sets. The relativistic corrections to the nuclear magnetic...... shieldings and chemical shifts are combined with non-relativistic CCSD(T) calculations using the very large polarization-consistent basis sets aug-pcSseg-4 for He, Ne and Ar, aug-pcSseg-3 for Kr and the AQZP basis set for Xe. For the dimers also zero-point vibrational corrections obtained at the CCSD...
DEFF Research Database (Denmark)
Kjærgaard, Magnus; Iesmantavicius, Vytautas; Poulsen, Flemming M
2011-01-01
shifts can in principle report the conformations of aliphatic side chains in disordered proteins and in order to examine this two model systems were chosen: the acid denatured state of acyl-CoA binding protein (ACBP) and the intrinsically disordered activation domain of the activator for thyroid hormone...... allow a quantitative analysis of the ensemble of ¿(2)-angles of especially leucine residues in disordered proteins. The changes in the rotamer distributions upon denaturation correlate to the changes upon helix induction by the co-solvent trifluoroethanol, suggesting that the side chain conformers are......The peptide backbones of disordered proteins are routinely characterized by NMR with respect to transient structure and dynamics. Little experimental information is, however, available about the side chain conformations and how structure in the backbone affects the side chains. Methyl chemical...
International Nuclear Information System (INIS)
MR spectroscopy results in a mild case of guanidinoacetate methyltransferase (GAMT) deficiency are presented. The approach differs from previous MRS studies in the acquisition of a chemical shift imaging spectral map showing gray and white matter with the corresponding spectra in one overview. MR spectroscopy revealed guanidinoacetate (GAA) in the absence of creatine. New is that GAA signals are more prominent in gray matter than in white. In the prevailing view, that enzyme deficiency is localized in liver and pancreas and that all GAA is transported into the brain from the blood and the cerebrospinal fluid, this would be compatible with a more limited uptake and/or better clearance of GAA from the white matter compared to the grey matter. (orig.)
Chemical shifts of 17O, 183W NMR and state of [ZW10O36]n-heteropolyanions in aqueous solutions
International Nuclear Information System (INIS)
By 17O, 183W NMR aqueous solutions of Na- and K-salts of heteropolyanions (HPA) [ZW10O36]n-, where Z = La3+-Er3+, Ce3+, Th4+, U4+, have been studied. HPA in aqueous solution exist as inert in the NMR time scale (1-100 ms) complexes, moreover, coordination sphere of Z is filled with O atoms of oxotungstate ligands, as in crystal state. The character of paramagnetic shifts (LIS) of all HPA atoms has been defined - in O and W atoms nearest to Z in LIS contact contribution prevails, for W-O-W bridge atoms and internal O atom dipole contribution prevails, for the rest atoms the dipole and contact contributions are comparable. The change in chemical shifts in lanthanide series depends not only on magnetic properties of element, but also on structural change in HPA. The width of 17O NMR lines for HPA studied (except HPA containing gadolinium) is determined by quadrupole mechanism of nuclear magnetic relaxation. 24 refs., 2 figs., 3 tabs
Marekha, Bogdan A; Kalugin, Oleg N; Bria, Marc; Idrissi, Abdenacer
2015-09-21
Mixtures of ionic liquids (ILs) with polar aprotic solvents in different combinations and under different conditions (concentration, temperature etc.) are used widely in electrochemistry. However, little is known about the key intermolecular interactions in such mixtures depending on the nature of the constituents and mixture composition. In order to systematically address the intermolecular interactions, the chemical shift variation of (1)H and (13)C nuclei has been followed in mixtures of imidazolium ILs 1-n-butyl-3-methylimidazolium tetrafluoroborate (BmimBF4), 1-n-butyl-3-methylimidazolium hexafluorophosphate (BmimPF6), 1-n-butyl-3-methylimidazolium trifluoromethanesulfonate (BmimTfO) and 1-n-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BmimTFSI) with molecular solvent acetonitrile (AN) over the entire composition range at 300 K. The concept of relative chemical shift variation is proposed to assess the observed effects on a unified and unbiased scale. We have found that hydrogen bonds between the imidazolium ring hydrogen atoms and electronegative atoms of anions are stronger in BmimBF4 and BmimTfO ILs than those in BmimTFSI and BmimPF6. Hydrogen atom at position 2 of the imidazolium ring is substantially more sensitive to interionic hydrogen bonding than those at positions 4-5 in the case of BmimTfO and BmimTFSI ILs. These hydrogen bonds are disrupted upon dilution in AN due to ion dissociation which is more pronounced at high dilutions. Specific solvation interactions between AN molecules and IL cations are poorly manifested. PMID:26278514
International Nuclear Information System (INIS)
Aim: Aim of this study was to show whether or not acquisition-weighted chemical shift imaging (AW-CSI) allows the determination of PCr and ATP in the lateral and posterior wall of the human heart at 1.5 T. Methods: 12 healthy volunteers were examined using a conventional chemical shift imaging (CSI) and an AW-CSI. The sequences differed only in the number of repetitions for each point in k space. A hanning function was used as filter function leading to 7 repetitions in the center of the k space and 0 in the corners. Thus, AW-CSI had the same resolution as the CSI sequence. The results for both sequences were analyzed using identically positioned voxels in the septal, anterior, lateral and posterior wall. Results: The determined averaged AW-CSI signal to noise ratios were higher for PCr by a factor of 1.3 and for ATP by 1.4 than those of CSI. The PCr/ATP ratios were higher by a factor of 1.2 - 1.3 and showed a smaller standard deviation in all locations for AW-CSI. The mean PCr/ATP ratios determined by AW-CSI of septal, lateral and posterior wall were almost identical (1.72 - 1.76), while it was higher in the anterior wall (1.9). Conclusions: The reduced contamination in AW-CSI improves the signal to noise ratio and the determination of the PCr/ATP ratio in cardiac 31P spectroscopy compared to CSI with the same resolution. The results in volunteers indicate that AW-CSI renders 31P spectroscopy of the lateral and posterior wall of the human heart feasible for patient studies at 1.5 T. (orig.)
Tensor Network Contractions for #SAT
Biamonte, Jacob D.; Morton, Jason; Turner, Jacob
2015-09-01
The computational cost of counting the number of solutions satisfying a Boolean formula, which is a problem instance of #SAT, has proven subtle to quantify. Even when finding individual satisfying solutions is computationally easy (e.g. 2-SAT, which is in ), determining the number of solutions can be #-hard. Recently, computational methods simulating quantum systems experienced advancements due to the development of tensor network algorithms and associated quantum physics-inspired techniques. By these methods, we give an algorithm using an axiomatic tensor contraction language for n-variable #SAT instances with complexity where c is the number of COPY-tensors, g is the number of gates, and d is the maximal degree of any COPY-tensor. Thus, n-variable counting problems can be solved efficiently when their tensor network expression has at most COPY-tensors and polynomial fan-out. This framework also admits an intuitive proof of a variant of the Tovey conjecture (the r,1-SAT instance of the Dubois-Tovey theorem). This study increases the theory, expressiveness and application of tensor based algorithmic tools and provides an alternative insight on these problems which have a long history in statistical physics and computer science.
MATLAB tensor classes for fast algorithm prototyping.
Energy Technology Data Exchange (ETDEWEB)
Bader, Brett William; Kolda, Tamara Gibson (Sandia National Laboratories, Livermore, CA)
2004-10-01
Tensors (also known as mutidimensional arrays or N-way arrays) are used in a variety of applications ranging from chemometrics to psychometrics. We describe four MATLAB classes for tensor manipulations that can be used for fast algorithm prototyping. The tensor class extends the functionality of MATLAB's multidimensional arrays by supporting additional operations such as tensor multiplication. The tensor as matrix class supports the 'matricization' of a tensor, i.e., the conversion of a tensor to a matrix (and vice versa), a commonly used operation in many algorithms. Two additional classes represent tensors stored in decomposed formats: cp tensor and tucker tensor. We descibe all of these classes and then demonstrate their use by showing how to implement several tensor algorithms that have appeared in the literature.
Solving Tensor Structured Problems with Computational Tensor Algebra
Morozov, Oleksii
2010-01-01
Since its introduction by Gauss, Matrix Algebra has facilitated understanding of scientific problems, hiding distracting details and finding more elegant and efficient ways of computational solving. Today's largest problems, which often originate from multidimensional data, might profit from even higher levels of abstraction. We developed a framework for solving tensor structured problems with tensor algebra that unifies concepts from tensor analysis, multilinear algebra and multidimensional signal processing. In contrast to the conventional matrix approach, it allows the formulation of multidimensional problems, in a multidimensional way, preserving structure and data coherence; and the implementation of automated optimizations of solving algorithms, based on the commutativity of all tensor operations. Its ability to handle large scientific tasks is showcased by a real-world, 4D medical imaging problem, with more than 30 million unknown parameters solved on a current, inexpensive hardware. This significantly...
Calculating contracted tensor Feynman integrals
International Nuclear Information System (INIS)
A recently derived approach to the tensor reduction of 5-point one-loop Feynman integrals expresses the tensor coefficients by scalar 1-point to 4-point Feynman integrals completely algebraically. In this Letter we derive extremely compact algebraic expressions for the contractions of the tensor integrals with external momenta. This is based on sums over signed minors weighted with scalar products of the external momenta. With these contractions one can construct the invariant amplitudes of the matrix elements under consideration, and the evaluation of one-loop contributions to massless and massive multi-particle production at high energy colliders like LHC and ILC is expected to be performed very efficiently.
International Nuclear Information System (INIS)
Biomolecular NMR chemical shift data are key information for the functional analysis of biomolecules and the development of new techniques for NMR studies utilizing chemical shift statistical information. Structural genomics projects are major contributors to the accumulation of protein chemical shift information. The management of the large quantities of NMR data generated by each project in a local database and the transfer of the data to the public databases are still formidable tasks because of the complicated nature of NMR data. Here we report an automated and efficient system developed for the deposition and annotation of a large number of data sets including 1H, 13C and 15N resonance assignments used for the structure determination of proteins. We have demonstrated the feasibility of our system by applying it to over 600 entries from the internal database generated by the RIKEN Structural Genomics/Proteomics Initiative (RSGI) to the public database, BioMagResBank (BMRB). We have assessed the quality of the deposited chemical shifts by comparing them with those predicted from the PDB coordinate entry for the corresponding protein. The same comparison for other matched BMRB/PDB entries deposited from 2001–2011 has been carried out and the results suggest that the RSGI entries greatly improved the quality of the BMRB database. Since the entries include chemical shifts acquired under strikingly similar experimental conditions, these NMR data can be expected to be a promising resource to improve current technologies as well as to develop new NMR methods for protein studies.
Institute of Scientific and Technical Information of China (English)
YAN Ting; YAN Wei; SHEN Cheng-wu; LI Zhi-da
2007-01-01
There are many forms of tensor theory which are quite different. Discussions are put forward and their relationships are found. The differences between them depend on whether there is metric on the space and the basis is orthonormal.
Energy Technology Data Exchange (ETDEWEB)
Zhang, Rongchun; Ramamoorthy, Ayyalusamy, E-mail: ramamoor@umich.edu [Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055 (United States)
2015-05-28
Dynamics plays important roles in determining the physical, chemical, and functional properties of a variety of chemical and biological materials. However, a material (such as a polymer) generally has mobile and rigid regions in order to have high strength and toughness at the same time. Therefore, it is difficult to measure the role of mobile phase without being affected by the rigid components. Herein, we propose a highly sensitive solid-state NMR approach that utilizes a dipolar-coupling based filter (composed of 12 equally spaced 90° RF pulses) to selectively measure the correlation of {sup 1}H chemical shifts from the mobile regions of a material. It is interesting to find that the rotor-synchronized dipolar filter strength decreases with increasing inter-pulse delay between the 90° pulses, whereas the dipolar filter strength increases with increasing inter-pulse delay under static conditions. In this study, we also demonstrate the unique advantages of proton-detection under ultrafast magic-angle-spinning conditions to enhance the spectral resolution and sensitivity for studies on small molecules as well as multi-phase polymers. Our results further demonstrate the use of finite-pulse radio-frequency driven recoupling pulse sequence to efficiently recouple weak proton-proton dipolar couplings in the dynamic regions of a molecule and to facilitate the fast acquisition of {sup 1}H/{sup 1}H correlation spectrum compared to the traditional 2D NOESY (Nuclear Overhauser effect spectroscopy) experiment. We believe that the proposed approach is beneficial to study mobile components in multi-phase systems, such as block copolymers, polymer blends, nanocomposites, heterogeneous amyloid mixture of oligomers and fibers, and other materials.
Tensor 2-sums and entanglement
Klavzar, Sandi
2009-01-01
To define a minimal mathematical framework for isolating some of the characteristic properties of quantum entanglement, we introduce a generalization of the tensor product of graphs. Inspired by the notion of a density matrix, the generalization is a simple one: every graph can be obtained by addiction modulo two, possibly with many summands, of tensor products of adjacency matrices. In this picture, we are still able to prove a combinatorial analogue of the Peres-Horodecki criterion for testing separability.
Tensor Product of Massey Products
Institute of Scientific and Technical Information of China (English)
Qi Bing ZHENG
2006-01-01
In this paper, we interpret Massey products in terms of realizations (twitsting cochains)of certain differential graded coalgebras with values in differential graded algebras. In the case where the target algebra is the cobar construction of a differential graded commutative Hopf algebra, we construct the tensor product of realizations and show that the tensor product is strictly associative,and commutative up to homotopy.
Random Tensors and Quantum Gravity
Rivasseau, Vincent
2016-01-01
We provide an informal introduction to tensor field theories and to their associated renormalization group. We focus more on the general motivations coming from quantum gravity than on the technical details. In particular we discuss how asymptotic freedom of such tensor field theories gives a concrete example of a natural "quantum relativity" postulate: physics in the deep ultraviolet regime becomes asymptotically more and more independent of any particular choice of Hilbert basis in the spac...
Rivasseau, Vincent
2012-01-01
The tensor track approach to quantum gravity is based on a new class of quantum field theories, called tensor group field theories (TGFTs). We provide a brief review of recent progress and list some desirable properties of TGFTs. In order to narrow the search for interesting models, we also propose a set of guidelines for TGFT's loosely inspired by the Osterwalder-Schrader axioms of ordinary Euclidean QFT.
Westphal, Alexander; Pedro, Francisco
2013-01-01
We attempt an estimate for the distribution of the tensor-to-scalar ratio $r$ (the relative power of primordial gravitational waves from inflation) over the landscape of vacua in string theory. The dynamics of eternal inflation and quantum tunneling lead to a kind of democracy on the landscape, providing no bias towards large-field or small-field inflation regardless of the class of measure. The tensor mode fraction $r$ then follows the number frequency distributions of inflationary mechanism...
NCON: A tensor network contractor for MATLAB
Pfeifer, Robert N C; Singh, Sukhwinder; Vidal, Guifre
2014-01-01
A fundamental process in the implementation of any numerical tensor network algorithm is that of contracting a tensor network. In this process, a network made up of multiple tensors connected by summed indices is reduced to a single tensor or a number by evaluating the index sums. This article presents a MATLAB function ncon(), or "Network CONtractor", which accepts as its input a tensor network and a contraction sequence describing how this network may be reduced to a single tensor or number. As its output it returns that single tensor or number. The function ncon() may be obtained by downloading the source of this preprint.
Diffusion tensor image registration using tensor geometry and orientation features.
Yang, Jinzhong; Shen, Dinggang; Davatzikos, Christos; Verma, Ragini
2008-01-01
This paper presents a method for deformable registration of diffusion tensor (DT) images that integrates geometry and orientation features into a hierarchical matching framework. The geometric feature is derived from the structural geometry of diffusion and characterizes the shape of the tensor in terms of prolateness, oblateness, and sphericity of the tensor. Local spatial distributions of the prolate, oblate, and spherical geometry are used to create an attribute vector of geometric feature for matching. The orientation feature improves the matching of the WM fiber tracts by taking into account the statistical information of underlying fiber orientations. These features are incorporated into a hierarchical deformable registration framework to develop a diffusion tensor image registration algorithm. Extensive experiments on simulated and real brain DT data establish the superiority of this algorithm for deformable matching of diffusion tensors, thereby aiding in atlas creation. The robustness of the method makes it potentially useful for group-based analysis of DT images acquired in large studies to identify disease-induced and developmental changes. PMID:18982691
Rao, Madhwesha; Stewart, Neil J.; Norquay, Graham; Griffiths, Paul D.
2016-01-01
Purpose Upon inhalation, xenon diffuses into the bloodstream and is transported to the brain, where it dissolves in various compartments of the brain. Although up to five chemically distinct peaks have been previously observed in 129Xe rat head spectra, to date only three peaks have been reported in the human head. This study demonstrates high resolution spectroscopy and chemical shift imaging (CSI) of 129Xe dissolved in the human head at 1.5 Tesla. Methods A 129Xe radiofrequency coil was built in‐house and 129Xe gas was polarized using spin‐exchange optical pumping. Following the inhalation of 129Xe gas, NMR spectroscopy was performed with spectral resolution of 0.033 ppm. Two‐dimensional CSI in all three anatomical planes was performed with spectral resolution of 2.1 ppm and voxel size 20 mm × 20 mm. Results Spectra of hyperpolarized 129Xe dissolved in the human head showed five distinct peaks at 188 ppm, 192 ppm, 196 ppm, 200 ppm, and 217 ppm. Assignment of these peaks was consistent with earlier studies. Conclusion High resolution spectroscopy and CSI of hyperpolarized 129Xe dissolved in the human head has been demonstrated. For the first time, five distinct NMR peaks have been observed in 129Xe spectra from the human head in vivo. Magn Reson Med 75:2227–2234, 2016. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. PMID:27080441
Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika Agnieszka; Szeleszczuk, Łukasz; Wawer, Iwona
2016-04-15
Solid-state NMR is an excellent and useful method for analyzing solid-state forms of drugs. In the (13)C CP/MAS NMR spectra of the solid dosage forms many of the signals originate from the excipients and should be distinguished from those of active pharmaceutical ingredient (API). In this work the most common pharmaceutical excipients used in the solid drug formulations: anhydrous α-lactose, α-lactose monohydrate, mannitol, sucrose, sorbitol, sodium starch glycolate type A and B, starch of different origin, microcrystalline cellulose, hypromellose, ethylcellulose, methylcellulose, hydroxyethylcellulose, sodium alginate, magnesium stearate, sodium laurilsulfate and Kollidon(®) were analyzed. Their (13)C CP/MAS NMR spectra were recorded and the signals were assigned, employing the results (R(2): 0.948-0.998) of GIPAW calculations and theoretical chemical shifts. The (13)C ssNMR spectra for some of the studied excipients have not been published before while for the other signals in the spectra they were not properly assigned or the assignments were not correct. The results summarize and complement the data on the (13)C ssNMR analysis of the most common pharmaceutical excipients and are essential for further NMR studies of API-excipient interactions in the pharmaceutical formulations. PMID:26845204
Komatsu, Takanori; Kikuchi, Jun
2013-09-17
A multidimensional solution NMR method has been developed using various pulse programs including HCCH-COSY and (13)C-HSQC-NOESY for the structural characterization of commercially available (13)C labeled lignocellulose from potatoes (Solanum tuberosum L.), chicory (Cichorium intybus), and corn (Zea mays). This new method allowed for 119 of the signals in the (13)C-HSQC spectrum of lignocelluloses to be assigned and was successfully used to characterize the structures of lignocellulose samples from three plants in terms of their xylan and xyloglucan structures, which are the major hemicelluloses in angiosperm. Furthermore, this new method provided greater insight into fine structures of lignin by providing a high resolution to the aromatic signals of the β-aryl ether and resinol moieties, as well as the diastereomeric signals of the β-aryl ether. Finally, the (13)C chemical shifts assigned in this study were compared with those from solid-state NMR and indicated the presence of heterogeneous dynamics in the polysaccharides where rigid cellulose and mobile hemicelluloses moieties existed together. PMID:24010724
Energy Technology Data Exchange (ETDEWEB)
Koelblinger, Claus, E-mail: claus.koelblinger@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Krssak, Martin, E-mail: martin.krssak@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Maresch, Judith, E-mail: judith.maresch@meduniwien.ac.at [Department of Pathology, Medical University of Vienna (Austria); Wrba, Fritz, E-mail: fritz.wrba@meduniwien.ac.at [Department of Pathology, Medical University of Vienna (Austria); Kaczirek, Klaus, E-mail: klaus.kaczirek@meduniwien.ac.at [Department of Surgery, Medical University of Vienna (Austria); Gruenberger, Thomas, E-mail: thomas.gruenberger@meduniwien.ac.at [Department of Surgery, Medical University of Vienna (Austria); Tamandl, Dietmar, E-mail: dietmar.tamandl@meduniwien.ac.at [Department of Surgery, Medical University of Vienna (Austria); Ba-Ssalamah, Ahmed, E-mail: ahmed.ba-ssalamah@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Berger-Kulemann, Vanessa, E-mail: vanessa.berger-kulemann@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Weber, Michael, E-mail: michael.weber@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Schima, Wolfgang, E-mail: wolfgang.schima@khgh.at [Department of Radiology, KH Goettlicher Heiland and Herz-Jesu Krankenhaus, Dornbacher Strasse 20-28, 1170 Vienna (Austria)
2012-11-15
Purpose: To compare the accuracy of liver fat quantification using chemical shift imaging (CSI) and H1 MR-spectroscopy (MRS) at 3.0 T in patients undergoing liver resection. Methods: Totally 35 patients were included in this prospective IRB approved study. The histopathologically assessed liver fat was compared to the hepatic fat fractions calculated with CSI (with and without spleen correction) and MRS. Spearman's rank correlation and Fisher z-test were used for correlation analysis. Sensitivity and specificity regarding the detection of marked steatosis were calculated for the different modalities and compared using the McNemar test. Results: MRS (r = .85) and CSI with spleen correction (r = .85) showed a significantly better correlation (p = .03) with histology compared to CSI without spleen correction (r = .67). Sensitivity and specificity for the detection of marked steatosis was 100% (12/12) and 87% (20/23) for MRS and 92% (11/12) and 83% (19/23) for CSI with spleen correction (p > .12). Conclusion: For the assessment of hepatic steatosis both CSI with spleen correction and MRS at 3.0 T, show a good correlation with histology. CSI without spleen correction should not be used. Sensitivity and specificity for the detection of marked steatosis are high with both modalities. However, results that are scattered around the cut-off values are not reliable enough for clinical decisions.
International Nuclear Information System (INIS)
To investigate the diagnostic performance of 15-min delayed contrast-enhanced computed tomography (15-DECT) compared with that of chemical shift magnetic resonance (CSMR) imaging in differentiating hyperattenuating adrenal masses and to perform subgroup analysis in underlying malignancy and non-malignancy. This study included 478 adrenal masses in 453 patients examined with 15-DECT and 235 masses in 217 patients examined with CSMR. Relative percentage washout (RPW) and absolute percentage washout (APW) on 15-DECT, and signal intensity index (SII) and adrenal-to-spleen ratio (ASR) on CSMR were measured. Sensitivity, specificity and accuracy of 15-DECT and CSMR were analysed for characterisation of adrenal adenoma. Subgroup analyses were performed in patients with and without underlying malignancy. Attenuation and size of the masses on unenhanced CT correlated with the risk of non-adenoma. RPW calculated from 15-DECT showed the highest diagnostic performance for characterising hyperattenuating adrenal masses regardless of underlying malignancy, and the sensitivity, specificity and accuracy were 91.7 %, 74.8 % and 88.1 %, respectively in all patients. The risk of non-adenoma increased approximately threefold as mass size increased 1 cm or as its attenuation value increased by 10 Hounsfield units. 15-DECT was more accurate than CSMR in characterising hyperattenuating adrenal masses regardless of underlying malignancy. (orig.)
Energy Technology Data Exchange (ETDEWEB)
Weingaertner, Sebastian; Konstandin, Simon; Schad, Lothar R. [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Wetterling, Friedrich [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Dublin Univ. (Ireland) Trinity Inst. of Neuroscience; Fatar, Marc [Heidelberg Univ., Mannheim (Germany). Dept. of Neurology; Neumaier-Probst, Eva [Heidelberg Univ., Mannheim (Germany). Dept. of Neuroradiology
2015-07-01
To evaluate potential scan time reduction in {sup 23}Na-Magnetic Resonance Imaging with the chemical shift imaging sequence (CSI) using undersampled data of high-quality datasets, reconstructed with an iterative constrained reconstruction, compared to reduced resolution or reduced signal-to-noise ratio. CSI {sup 23}Na-images were retrospectively undersampled and reconstructed with a constrained reconstruction scheme. The results were compared to conventional methods of scan time reduction. The constrained reconstruction scheme used a phase constraint and a finite object support, which was extracted from a spatially registered {sup 1}H-image acquired with a double-tuned coil. The methods were evaluated using numerical simulations, phantom images and in-vivo images of a healthy volunteer and a patient who suffered from cerebral ischemic stroke. The constrained reconstruction scheme showed improved image quality compared to a decreased number of averages, images with decreased resolution or circular undersampling with weighted averaging for any undersampling factor. Brain images of a stroke patient, which were reconstructed from three-fold undersampled k-space data, resulted in only minor differences from the original image (normalized root means square error < 12%) and an almost identical delineation of the stroke region (mismatch < 6%). The acquisition of undersampled {sup 23}Na-CSI images enables up to three-fold scan time reduction with improved image quality compared to conventional methods of scan time saving.
Energy Technology Data Exchange (ETDEWEB)
Koo, Hyun Jung; Choi, Hyuck Jae; Cho, Kyoung-Sik [Asan Medical Center, University of Ulsan College of Medicine, Department of Radiology and Research Institute of Radiology, Seoul (Korea, Republic of); Kim, Hwa Jung; Kim, Sun-Ok [Asan Medical Center, University of Ulsan College of Medicine, Cancer Center, Department of Clinical Epidemiology and Biostatistics, Seoul (Korea, Republic of)
2014-06-15
To investigate the diagnostic performance of 15-min delayed contrast-enhanced computed tomography (15-DECT) compared with that of chemical shift magnetic resonance (CSMR) imaging in differentiating hyperattenuating adrenal masses and to perform subgroup analysis in underlying malignancy and non-malignancy. This study included 478 adrenal masses in 453 patients examined with 15-DECT and 235 masses in 217 patients examined with CSMR. Relative percentage washout (RPW) and absolute percentage washout (APW) on 15-DECT, and signal intensity index (SII) and adrenal-to-spleen ratio (ASR) on CSMR were measured. Sensitivity, specificity and accuracy of 15-DECT and CSMR were analysed for characterisation of adrenal adenoma. Subgroup analyses were performed in patients with and without underlying malignancy. Attenuation and size of the masses on unenhanced CT correlated with the risk of non-adenoma. RPW calculated from 15-DECT showed the highest diagnostic performance for characterising hyperattenuating adrenal masses regardless of underlying malignancy, and the sensitivity, specificity and accuracy were 91.7 %, 74.8 % and 88.1 %, respectively in all patients. The risk of non-adenoma increased approximately threefold as mass size increased 1 cm or as its attenuation value increased by 10 Hounsfield units. 15-DECT was more accurate than CSMR in characterising hyperattenuating adrenal masses regardless of underlying malignancy. (orig.)
Tensor Target Polarization at TRIUMF
Energy Technology Data Exchange (ETDEWEB)
Smith, G
2014-10-27
The first measurements of tensor observables in $\\pi \\vec{d}$ scattering experiments were performed in the mid-80's at TRIUMF, and later at SIN/PSI. The full suite of tensor observables accessible in $\\pi \\vec{d}$ elastic scattering were measured: $T_{20}$, $T_{21}$, and $T_{22}$. The vector analyzing power $iT_{11}$ was also measured. These results led to a better understanding of the three-body theory used to describe this reaction. %Some measurements were also made in the absorption and breakup channels. A direct measurement of the target tensor polarization was also made independent of the usual NMR techniques by exploiting the (nearly) model-independent result for the tensor analyzing power at 90$^\\circ _{cm}$ in the $\\pi \\vec{d} \\rightarrow 2p$ reaction. This method was also used to check efforts to enhance the tensor polarization by RF burning of the NMR spectrum. A brief description of the methods developed to measure and analyze these experiments is provided.
Understanding the Magnetic Polarizability Tensor
Ledger, P D
2015-01-01
The aim of this paper is provide new insights into the properties of the rank 2 polarizability tensor $\\check{\\check{\\mathcal M}}$ proposed in (P.D. Ledger and W.R.B. Lionheart Characterising the shape and material properties of hidden targets from magnetic induction data, IMA Journal of Applied Mathematics, doi: 10.1093/imamat/hxv015) for describing the perturbation in the magnetic field caused by the presence of a conducting object in the eddy current regime. In particular, we explore its connection with the magnetic polarizability tensor and the P\\'olya-Szeg\\"o tensor and how, by introducing new splittings of $\\check{\\check{\\mathcal M}}$, they form a family of rank 2 tensors for describing the response from different categories of conducting (permeable) objects. We include new bounds on the invariants of the P\\'olya-Szeg\\"o tensor and expressions for the low frequency and high conductivity limiting coefficients of $\\check{\\check{\\mathcal M}}$. We show, for the high conductivity case (and for frequencies at...
Ingram, Jenni
2014-01-01
This article examines the shifts in attention and focus as one teacher introduces and explains an image that represents the processes involved in a numeric problem that his students have been working on. This paper takes a micro-analytic approach to examine how the focus of attention shifts through what the teacher and students do and say in the…
Hypersurfaces with Isotropic Para-Blaschke Tensor
Institute of Scientific and Technical Information of China (English)
Jian Bo FANG; Kun ZHANG
2014-01-01
Let Mn be an n-dimensional submanifold without umbilical points in the (n+1)-dimen-sional unit sphere Sn+1. Four basic invariants of Mn under the Moebius transformation group of Sn+1 are a1-form Φ called moebius form, a symmetric (0, 2) tensor A called Blaschke tensor, a symmetric (0, 2) tensor B called Moebius second fundamental form and a positive definite (0, 2) tensor g called Moebius metric. A symmetric (0, 2) tensor D = A+μB called para-Blaschke tensor, where μ is constant, is also an Moebius invariant. We call the para-Blaschke tensor is isotropic if there exists a function λ such that D = λg. One of the basic questions in Moebius geometry is to classify the hypersurfaces with isotropic para-Blaschke tensor. When λ is not constant, all hypersurfaces with isotropic para-Blaschke tensor are explicitly expressed in this paper.
Gravitational wave asteroseismology in scalar-tensor theory of gravity
International Nuclear Information System (INIS)
We study perturbations of relativistic stars in scalar-tensor theory of gravity and examine the effects of the scalar field on the corresponding oscillation spectrum. We show that the frequency of the emitted gravitational waves is shifted proportionally to the scalar field strength. Scalar waves which might be produced from such oscillations can be a unique probe for the theory, but their detectability is questionable if the radiated energy is small. However we show that there is no need for a direct observation of scalar waves: the shift in the gravitational wave spectrum could unambiguously signal the presence of a scalar field. (authors) Keywords: gravitational waves, neutron stars, alternative theories
Distributors on a tensor category
TAMBARA, D.
2006-01-01
Let $\\cA$ be a tensor category and let $\\cV$ denote the category of vector spaces. A distributor on $\\cA$ is a functor $\\cA^{\\op}\\times \\cA\\to \\cV$. We are concerned with distributors with two-sided $\\cA$-action. Those distributors form a tensor category, which we denoted by ${}_{\\cA}\\bD(\\cA,\\cA)_{\\cA}$. The functor category $\\Hom(\\cA^{\\op},\\cV)$ is also a tensor category and has the center $\\bZ(\\Hom(\\cA^{\\op},\\cV))$. We show that if $\\cA$ is rigid, then ${}_{\\cA}\\bD(\\cA,\\cA)_{\\cA}$ and $\\...
Link prediction via generalized coupled tensor factorisation
DEFF Research Database (Denmark)
Ermiş, Beyza; Evrim, Acar Ataman; Taylan Cemgil, A.
2012-01-01
and higher-order tensors. We propose to use an approach based on probabilistic interpretation of tensor factorisation models, i.e., Generalised Coupled Tensor Factorisation, which can simultaneously fit a large class of tensor models to higher-order tensors/matrices with com- mon latent factors using...... different loss functions. Numerical experiments demonstrate that joint analysis of data from multiple sources via coupled factorisation improves the link prediction performance and the selection of right loss function and tensor model is crucial for accurately predicting missing links....
Spacetimes with Semisymmetric Energy-Momentum Tensor
De, U. C.; Velimirović, Ljubica
2015-06-01
The object of the present paper is to introduce spacetimes with semisymmetric energy-momentum tensor. At first we consider the relation R( X, Y)ṡ T=0, that is, the energy-momentum tensor T of type (0,2) is semisymmetric. It is shown that in a general relativistic spacetime if the energy-momentum tensor is semisymmetric, then the spacetime is also Ricci semisymmetric and the converse is also true. Next we characterize the perfect fluid spacetime with semisymmetric energy-momentum tensor. Then, we consider conformally flat spacetime with semisymmetric energy-momentum tensor. Finally, we cited some examples of spacetimes admitting semisymmetric energy-momentum tensor.
Institute of Scientific and Technical Information of China (English)
许波; 李浩然; 王从敏; 许映杰; 韩世钧
2005-01-01
1H NMR chemical shifts of binary aqueous mixtures of acylamide, alcohol, dimethyl sulphoxide (DMSO), and acetone are correlated by statistical associating fluid theory (SAFT) association model. The comparison between SAFT association model and Wilson equation shows that the former is better for dealing with aqueous solutions. Finally, the specialties of both models are discussed.
DEFF Research Database (Denmark)
Hansen, Poul Erik; Borisov, Eugeny V.; Lindon, John C.
2015-01-01
The tautomeric equilibria for 2-pyridoyl-, 3-pyridoyl-, and 4-pyridoyl-benzoyl methane have been investigated using deuterium isotope effects on 1H and 13C chemical shifts both in the liquid and the solid state. Equilibria are established both in the liquid and the solid state. In addition, in th...
Energy Technology Data Exchange (ETDEWEB)
Costa, S.; Marti-Bonmati, L.; Delgado, F.; Ripolles, T. [Hospital Universitario Doctor Peset. Valencia (Spain)
2000-07-01
Lipomatous tumors of the myometrium are rare lesions composed of varying amounts of mature fatty tissue. Our objective was to assess the computed tomography (CT) and magnetic resonance MR findings associated with these tumors and determine the utility of the chemical shift imaging technique in the detection of fact within these focal uterine masses. Lipomatous focal uterine lesions were detected in three women by means of ultrasound. The patients underwent CT and MR using the chemical shift imaging technique and in-phase and opposed phase T1-weighted gradient-echo images. Qualitative and quantitative analyses of the results were carried out, based on the attenuations and relations of signal intensity. The tumors were hypoattenuated in CT seans and hyperintense in T1-weighted images, showing a decreased signal in opposed phase T1-weighted images when compared with in-phase images. The percentage change (between 2% and 3%) is probably proportional to the differing proportions of fact and muscle elements present in these lipoleiomyomas. Lipomatous tumors of the myometrium are uterine lesions with a varying proportion of fact. Their fat composition can be detected by CT and MR. The chemical shift imaging technique reveals the variations in the proportions of fat in these tumors. Since the presence of fat within uterine lesions is virtually diagnostic of the myometrial lipomatous tumor, the chemical shift imaging technique contributes to the characterization of these lesions. (Author) 11 refs.
Conformal Tensors via Lovelock Gravity
Kastor, David
2013-01-01
Constructs from conformal geometry are important in low dimensional gravity models, while in higher dimensions the higher curvature interactions of Lovelock gravity are similarly prominent. Considering conformal invariance in the context of Lovelock gravity leads to natural, higher-curvature generalizations of the Weyl, Schouten, Cotton and Bach tensors, with properties that straightforwardly extend those of their familiar counterparts. As a first application, we introduce a new set of conformally invariant gravity theories in D=4k dimensions, based on the squares of the higher curvature Weyl tensors.
Unique Tensor Factorization of Algebras
Nüsken, Michael
1998-01-01
Tensor product decomposition of algebras is known to be non-unique in many cases. But, as will be shown here, an additively indecomposable, finite-dimensional C-algebra A has an essentially unique tensor factorization A=A1x...xAr into non-trivial, x-indecomposable factors Ai. Thus the semiring of isomorphism classes of finite-dimensional C-algebras is a polynomial semiring N[X]. Moreover, the field C of complex numbers can be replaced by an arbitrary field of characteristic zero if one restr...
The proton nuclear magnetic shielding tensors in biphenyl: experiment and theory.
Schönborn, Frank; Schmitt, Heike; Zimmermann, Herbert; Haeberlen, Ulrich; Corminboeuf, Clémence; Grossmann, Gisbert; Heine, Thomas
2005-07-01
Line-narrowing multiple pulse techniques are applied to a spherical sample crystal of biphenyl. The 10 different proton shielding tensors in this compound are determined. The accuracy level for the tensor components is 0.3 ppm. The assignment of the measured tensors to the corresponding proton sites is given careful attention. Intermolecular shielding contributions are calculated by the induced magnetic point dipole model with empirical atom and bond susceptibilities (distant neighbours) and by a new quantum chemical method (near neighbours). Subtracting the intermolecular contributions from the (correctly assigned) measured shielding tensors leads to isolated-molecule shielding tensors for which there are symmetry relations. Compliance to these relations is the criterion for the correct assignment. The success of this program indicates that intermolecular proton shielding contributions can be calculated to better than 0.5 ppm. The isolated-molecule shielding tensors obtained from experiment and calculated intermolecular contributions are compared with isolated-molecule quantum chemical results. Expressed in the icosahedral tensor representation, the rms differences of the respective tensor components are below 0.5 ppm for all proton sites in biphenyl. In the isolated molecule, the least shielded direction of all protons is the perpendicular to the molecular plane. For the para proton, the intermediate principal direction is along the C-H bond. It is argued that these relations also hold for the protons in the isolated benzene molecule. PMID:15949748
International Nuclear Information System (INIS)
13C isotropic chemical shifts and chemical shift anisotropy parameters have been determined for a number of inorganic carbonates relevant in cement chemistry from slow-speed 13C MAS or 13C(1H) CP/MAS NMR spectra (9.4 T or 14.1 T) for 13C in natural abundance. The variation in the 13C chemical shift parameters is relatively small, raising some doubts that different carbonate species in Portland cement-based materials may not be sufficiently resolved in 13C MAS NMR spectra. However, it is shown that by combining 13C MAS and 13C(1H) CP/MAS NMR carbonate anions in anhydrous and hydrated phases can be distinguished, thereby providing valuable information about the reactivity of limestone in cement blends. This is illustrated for three cement pastes prepared from an ordinary Portland cement, including 0, 16, and 25 wt.% limestone, and following the hydration for up to one year. For these blends 29Si MAS NMR reveals that the limestone filler accelerates the hydration for alite and also results in a smaller fraction of tetrahedrally coordinated Al incorporated in the C-S-H phase. The latter result is more clearly observed in 27Al MAS NMR spectra of the cement–limestone blends and suggests that dissolved aluminate species in the cement–limestone blends readily react with carbonate ions from the limestone filler, forming calcium monocarboaluminate hydrate. -- Highlights: •13C chemical shift anisotropies for inorganic carbonates from 13C MAS NMR. •Narrow 13C NMR chemical shift range (163–171 ppm) for inorganic carbonates. •Anhydrous and hydrated carbonate species by 13C MAS and 13C(1H) CP/MAS NMR. •Limestone accelerates the hydration for alite in Portland – limestone cements. •Limestone reduces the amount of aluminium incorporated in the C-S-H phase
Energy Technology Data Exchange (ETDEWEB)
Koestler, H.; Beer, M.; Buchner, S.; Sandstede, J.; Pabst, T.; Kenn, W.; Hahn, D. [Wuerzburg Univ. (Germany). Abt. fuer Roentgendiagnostik; Landschuetz, W.; Kienlin, M. von [Wuerzburg Univ. (Germany). Physikalisches Inst.; Neubauer, S. [Dept. of Cardiovascular Medicine, John Radcliffe Hospital, Oxford (United Kingdom)
2001-12-01
Aim: Aim of this study was to show whether or not acquisition-weighted chemical shift imaging (AW-CSI) allows the determination of PCr and ATP in the lateral and posterior wall of the human heart at 1.5 T. Methods: 12 healthy volunteers were examined using a conventional chemical shift imaging (CSI) and an AW-CSI. The sequences differed only in the number of repetitions for each point in k space. A hanning function was used as filter function leading to 7 repetitions in the center of the k space and 0 in the corners. Thus, AW-CSI had the same resolution as the CSI sequence. The results for both sequences were analyzed using identically positioned voxels in the septal, anterior, lateral and posterior wall. Results: The determined averaged AW-CSI signal to noise ratios were higher for PCr by a factor of 1.3 and for ATP by 1.4 than those of CSI. The PCr/ATP ratios were higher by a factor of 1.2 - 1.3 and showed a smaller standard deviation in all locations for AW-CSI. The mean PCr/ATP ratios determined by AW-CSI of septal, lateral and posterior wall were almost identical (1.72 - 1.76), while it was higher in the anterior wall (1.9). Conclusions: The reduced contamination in AW-CSI improves the signal to noise ratio and the determination of the PCr/ATP ratio in cardiac {sup 31}P spectroscopy compared to CSI with the same resolution. The results in volunteers indicate that AW-CSI renders {sup 31}P spectroscopy of the lateral and posterior wall of the human heart feasible for patient studies at 1.5 T. (orig.) [German] Ziel: Ziel der Arbeit war es zu untersuchen, ob die akquisitionsgewichtete Chemical-shift-Bildgebung (AW-CSI) die Bestimmung von PCr und ATP in der Seiten- und Hinterwand des menschlichen Herzens an einem klinischen 1,5 T MR-Tomographen erlaubt. Methoden: 12 gesunde Probanden wurden jeweils mit einer chemical shift imaging (CSI) und einer AW-CSI-Sequenz untersucht. Die Sequenzen unterschieden sich lediglich in der Anzahl der Wiederholungen der einzelnen
International Nuclear Information System (INIS)
The solution structure of d(CGCGAATTCGCG)2 has been determined on the basis of an exceptionally large set of residual dipolar couplings. In addition to the heteronuclear 13C-1H and 15N-1H and qualitative homonuclear 1H-1H dipolar couplings, previously measured in bicelle medium, more than 300 quantitative 1H-1H and 22 31P-1H dipolar restraints were obtained in liquid crystalline Pf1 medium, and 22 31P chemical shift anisotropy restraints. High quality DNA structures can be obtained solely on the basis of these new restraints, and these structures are in close agreement with those calculated previously on the basis of 13C-1H and 15N-1H dipolar couplings. In the newly calculated structures, 31P-1H dipolar and 3JsubH3'Psub couplings and 31P CSA data restrain the phosphodiester backbone torsion angles. The final structure represents a quite regular B-form helix with a modest bending of ∼10 deg., which is essentially independent of whether or not electrostatic terms are used in the calculation. Combined, the number of homo- and heteronuclear dipolar couplings significantly exceeds the number of degrees of freedom in the system. Results indicate that the dipolar coupling data cannot be fit by a single structure, but are compatible with the presence of rapid equilibria between C2'-endo and C3'-endo deoxyribose puckers (sugar switching). The C2'-H2'/H2'' dipolar couplings in B-form DNA are particularly sensitive to sugar pucker and yield the largest discrepancies when fit to a single structure. To resolve these discrepancies, we suggest a simplified dipolar coupling analysis that yields N/S equilibria for the ribose sugar puckers, which are in good agreement with previous analyses of NMR JHH couplings, with a population of the minor C3'-endo form higher for pyrimidines than for purines
Tensor calculus for physics a concise guide
Neuenschwander, Dwight E
2015-01-01
Understanding tensors is essential for any physics student dealing with phenomena where causes and effects have different directions. A horizontal electric field producing vertical polarization in dielectrics; an unbalanced car wheel wobbling in the vertical plane while spinning about a horizontal axis; an electrostatic field on Earth observed to be a magnetic field by orbiting astronauts—these are some situations where physicists employ tensors. But the true beauty of tensors lies in this fact: When coordinates are transformed from one system to another, tensors change according to the same rules as the coordinates. Tensors, therefore, allow for the convenience of coordinates while also transcending them. This makes tensors the gold standard for expressing physical relationships in physics and geometry. Undergraduate physics majors are typically introduced to tensors in special-case applications. For example, in a classical mechanics course, they meet the "inertia tensor," and in electricity and magnetism...
Energy momentum tensor in the nonsymmetric gravity
Gisin, Boris V
2016-01-01
General relativity is the theory with unclear energy momentum tensor. An approach is considered, allowing to construct the energy momentum tensor for relativity with nonsymmetric metric. A consequence of the approach is confirmed in the nuclear physics.
Anyon condensation and tensor categories
Energy Technology Data Exchange (ETDEWEB)
Kong, Liang, E-mail: kong.fan.liang@gmail.com [Institute for Advanced Study (Science Hall), Tsinghua University, Beijing 100084 (China); Department of Mathematics and Statistics, University of New Hampshire, Durham, NH 03824 (United States)
2014-09-15
Instead of studying anyon condensation in various concrete models, we take a bootstrap approach by considering an abstract situation, in which an anyon condensation happens in a 2-d topological phase with anyonic excitations given by a modular tensor category C; and the anyons in the condensed phase are given by another modular tensor category D. By a bootstrap analysis, we derive a relation between anyons in D-phase and anyons in C-phase from natural physical requirements. It turns out that the vacuum (or the tensor unit) A in D-phase is necessary to be a connected commutative separable algebra in C, and the category D is equivalent to the category of local A-modules as modular tensor categories. This condensation also produces a gapped domain wall with wall excitations given by the category of A-modules in C. A more general situation is also studied in this paper. We will also show how to determine such algebra A from the initial and final data. Multi-condensations and 1-d condensations will also be briefly discussed. Examples will be given in the toric code model, Kitaev quantum double models, Levin–Wen types of lattice models and some chiral topological phases.
Anyon condensation and tensor categories
Directory of Open Access Journals (Sweden)
Liang Kong
2014-09-01
Full Text Available Instead of studying anyon condensation in various concrete models, we take a bootstrap approach by considering an abstract situation, in which an anyon condensation happens in a 2-d topological phase with anyonic excitations given by a modular tensor category C; and the anyons in the condensed phase are given by another modular tensor category D. By a bootstrap analysis, we derive a relation between anyons in D-phase and anyons in C-phase from natural physical requirements. It turns out that the vacuum (or the tensor unit A in D-phase is necessary to be a connected commutative separable algebra in C, and the category D is equivalent to the category of local A-modules as modular tensor categories. This condensation also produces a gapped domain wall with wall excitations given by the category of A-modules in C. A more general situation is also studied in this paper. We will also show how to determine such algebra A from the initial and final data. Multi-condensations and 1-d condensations will also be briefly discussed. Examples will be given in the toric code model, Kitaev quantum double models, Levin–Wen types of lattice models and some chiral topological phases.
ANISOTROPIC POLARIZATION TENSORS FOR ELLIPSES AND ELLIPSOIDS
Institute of Scientific and Technical Information of China (English)
Hyeonbae Kang; Kyoungsun Kim
2007-01-01
In this paper we present a systematic way of computing the polarization tensors,anisotropic as well as isotropic, based on the boundary integral method. We then use this method to compute the anisotropic polarization tensor for ellipses and ellipsoids. The computation reveals the pair of anisotropy and ellipses which produce the same polarization tensors.
Nondimensional Simplification of Tensor Polynomials with Indices
Jaén, X
1999-01-01
We are presenting an algorithm capable of simplifying tensor polynomials withindices when the building tensors have index symmetry properties. Theseproperties include simple symmetry, cyclicity and those due to the presence ofcovariant derivatives. The algorithm is part of a Mathematica package calledTools of Tensor Calculus (TTC) [web address: http://baldufa.upc.es/ttc
Vector and tensor analysis with applications
Borisenko, A I; Silverman, Richard A
1979-01-01
Concise and readable, this text ranges from definition of vectors and discussion of algebraic operations on vectors to the concept of tensor and algebraic operations on tensors. It also includes a systematic study of the differential and integral calculus of vector and tensor functions of space and time. Worked-out problems and solutions. 1968 edition.
Energy Technology Data Exchange (ETDEWEB)
Martin, J.; Falco, J.; Puig, J.; Donoso, L. [Unidad de Diagnostico por Imagen de Alta Tecnologia (UDIAT). Sabadell (Spain)
1999-07-01
To determine the utility of the chemical shift technique in magnetic resonance imaging (MRI) to confirm small amounts of fat in extrahepatic intraabdominal tumours. 7 extrahepatic abdominal tumours that are suspected to have fat as seen in the axial computed tomography (TC) are analysed retrospectively. In order to confirm the fat content, the chemical displacement technique with gradient echo sequences (GE) in phase (P) and in opposite phase (OP) was used with MRI 1 T equipment. The tumours corresponded to renal angiomyolipoma (AML) (n=4), intraperitoneal liposarcoma (n=1), retroperitoneal liposarcoma (n=1) and intraabdominal extramedular hematopoiesis (n=1). To confirm the existence of fat in the tumours, we used a quantitative percentage variation parameter of the intensity of the signals (VIS) between the images in P and OP, according to the formula: IS{sub (}p)-IS({sub o}p)x100/IS{sub (}op), where IS is the intensity of the signal. The chemical shift technique showed fat in the seven tumours. Upon visual inspection, all the tumoral areas that were suspected to have fat showed a notable difference in the signal intensity, being hypointense in OP and hyperintense in P. In these areas the average VIS percentage was 170% while in the rest of the tumour the average VIS percentage was 3%. The chemical shift technique with RG sequences can be easily used in MRI equipment and allows us to confirm if a specific abdominal tumour has fat, even if there is only a small quantity. (Author) 13 refs.
International Nuclear Information System (INIS)
Highlights: •Diagnosis of AMLs with minimal fat (mfAMLs) is still challenging with MRI. •Drop of signal on opposed-phase MR imaging is not specific of mfAMLs. •Double-echo gradient-echo sequences cannot accurately differentiate renal mfAMLs from other renal tumors. -- Abstract: Objectives: The purpose of this retrospective study was to evaluate the diagnostic performance of double-echo gradient chemical shift (GRE) magnetic resonance (MR) imaging for the differentiation of angiomyolipomas with minimal fat (mfAML) from other homogeneous solid renal tumors. Methods: Between 2005 and 2010 in two institutions, all histologically proven homogenous solid renal tumors imaged with computed tomography and MR imaging, including GRE sequences, have been retrospectively selected. A total of 118 patients (mean age: 61 years; range: 20–87) with 119 tumors were included. Two readers measured independently the signal intensity (SI) on GRE images and calculated SI index (SII) and tumor-to-spleen ratio (TSR) on in-phase and opposed-phase images. Intra- and interreader agreement was obtained. Cut-off values were derived from the receiver operating characteristic (ROC) curve analysis. Results: Twelve mfAMLs in 11 patients were identified (mean size: 2.8 cm; range: 1.2–3.5), and 107 non-AML tumors (3.2 cm; 1–7.8) in 107 patients. The intraobserver reproducibility of SII and TSR was excellent with an intraclass correlation coefficient equal to 0.99 [0.98–0.99]. The coefficient of correlation between the readers was 0.99. The mean values of TSR for mfAMLs and non-mfAMLs were −7.0 ± 22.8 versus −8.2 ± 21.2 for reader 1 and −6.7 ± 22.8 versus −8.4 ± 20.9 for reader 2 respectively. No significant difference was noticed between the two groups for SII (p = 0.98) and TSR (p = 0.86). Only 1 out of 12 mfAMLs and 11 of 107 non-AML tumors presented with a TSR inferior to −30% (p = 0.83). Conclusion: In a routine practice, GRE sequences cannot be a confident tool to
Energy Technology Data Exchange (ETDEWEB)
Ferré, R., E-mail: kn638@yahoo.fr [Department of Radiology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France); Cornelis, F. [Department of Radiology, Pellegrin Hospital, Place Amélie Raba Léon, 33076 Bordeaux (France); Verkarre, V. [Department of Pathology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France); Eiss, D.; Correas, J.M. [Department of Radiology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France); Grenier, N. [Department of Radiology, Pellegrin Hospital, Place Amélie Raba Léon, 33076 Bordeaux (France); Hélénon, O. [Department of Radiology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France)
2015-03-15
Highlights: •Diagnosis of AMLs with minimal fat (mfAMLs) is still challenging with MRI. •Drop of signal on opposed-phase MR imaging is not specific of mfAMLs. •Double-echo gradient-echo sequences cannot accurately differentiate renal mfAMLs from other renal tumors. -- Abstract: Objectives: The purpose of this retrospective study was to evaluate the diagnostic performance of double-echo gradient chemical shift (GRE) magnetic resonance (MR) imaging for the differentiation of angiomyolipomas with minimal fat (mfAML) from other homogeneous solid renal tumors. Methods: Between 2005 and 2010 in two institutions, all histologically proven homogenous solid renal tumors imaged with computed tomography and MR imaging, including GRE sequences, have been retrospectively selected. A total of 118 patients (mean age: 61 years; range: 20–87) with 119 tumors were included. Two readers measured independently the signal intensity (SI) on GRE images and calculated SI index (SII) and tumor-to-spleen ratio (TSR) on in-phase and opposed-phase images. Intra- and interreader agreement was obtained. Cut-off values were derived from the receiver operating characteristic (ROC) curve analysis. Results: Twelve mfAMLs in 11 patients were identified (mean size: 2.8 cm; range: 1.2–3.5), and 107 non-AML tumors (3.2 cm; 1–7.8) in 107 patients. The intraobserver reproducibility of SII and TSR was excellent with an intraclass correlation coefficient equal to 0.99 [0.98–0.99]. The coefficient of correlation between the readers was 0.99. The mean values of TSR for mfAMLs and non-mfAMLs were −7.0 ± 22.8 versus −8.2 ± 21.2 for reader 1 and −6.7 ± 22.8 versus −8.4 ± 20.9 for reader 2 respectively. No significant difference was noticed between the two groups for SII (p = 0.98) and TSR (p = 0.86). Only 1 out of 12 mfAMLs and 11 of 107 non-AML tumors presented with a TSR inferior to −30% (p = 0.83). Conclusion: In a routine practice, GRE sequences cannot be a confident tool to
DEFF Research Database (Denmark)
Brewer, Robert S.; Verdezoto, Nervo; Holst, Thomas;
2015-01-01
people to change their behavior at home. Leveraging prior research on encouraging reductions in residential energy use through game play, we introduce ShareBuddy: a casual mobile game intended to encourage players not only to reduce, but also to shift their electricity use. We conducted two field studies...... integrating real-world resource use into a game....
Stenger, M.; Hargens, A.; Dulchavsky, S.; Ebert, D.; Lee, S.; Lauriie, S.; Garcia, K.; Sargsyan, A.; Martin, D.; Ribeiro, L.; Lui, J.; Macias, B.; Arbeille, P.; Danielson, R.; Chang, D.; Johnston, S.; Ploutz-Snyder, R.; Smith, S.
2016-01-01
NASA is focusing on long-duration missions on the International Space Station (ISS) and future exploration-class missions beyond low-Earth orbit. Visual acuity changes observed after short-duration missions were largely transient, but more than 50% of ISS astronauts experienced more profound, chronic changes with objective structural and functional findings such as papilledema and choroidal folds. Globe flattening, optic nerve sheath dilation, and optic nerve tortuosity also are apparent. This pattern is referred to as the visual impairment and intracranial pressure (VIIP) syndrome. VIIP signs and symptoms, as well as postflight lumbar puncture data, suggest that elevated intracranial pressure (ICP) may be associated with the spaceflight-induced cephalad fluid shifts, but this hypothesis has not been tested. The purpose of this study is to characterize fluid distribution and compartmentalization associated with long-duration spaceflight, and to correlate these findings with vision changes and other elements of the VIIP syndrome. We also seek to determine whether the magnitude of fluid shifts during spaceflight, as well as the VIIP-related effects of those shifts, is predicted by the crewmember's preflight conditions and responses to acute hemodynamic manipulations (such as head-down tilt). Lastly, we will evaluate the patterns of fluid distribution in ISS astronauts during acute reversal of fluid shifts through application of lower body negative pressure (LBNP) interventions to characterize and explain general and individual responses. METHODS: We will examine a variety of physiologic variables in 10 long-duration ISS crewmembers using the test conditions and timeline presented in the Figure below. Measures include: (1) fluid compartmentalization (total body water by D2O, extracellular fluid by NaBr, intracellular fluid by calculation, plasma volume by CO rebreathe, interstitial fluid by calculation); (2) forehead/eyelids, tibia, calcaneus tissue thickness (by
Wormholes, the weak energy condition and scalar-tensor gravity
Shaikh, Rajibul
2016-01-01
We obtain a large class of Lorentzian wormhole spacetimes in scalar-tensor gravity, for which the matter stress energy does satisfy the weak energy condition. Our constructions have zero Ricci scalar and an everywhere finite, non-zero scalar field profile. Interpreting the scalar-tensor gravity as an effective on-brane theory resulting from a two-brane Randall--Sundrum model of warped extra dimensions, it is possible to link wormhole existence with that of extra dimensions. We study the geometry, matter content and gravitational red-shift in such wormholes and argue that our examples are perhaps among those which may have any observational relevance in astrophysics in future.
A uniform parametrization of moment tensors
Tape, Walter; Tape, Carl
2015-09-01
A moment tensor is a 3 × 3 symmetric matrix that expresses an earthquake source. We construct a parametrization of the 5-D space of all moment tensors of unit norm. The coordinates associated with the parametrization are closely related to moment tensor orientations and source types. The parametrization is uniform, in the sense that equal volumes in the coordinate domain of the parametrization correspond to equal volumes of moment tensors. Uniformly distributed points in the coordinate domain therefore give uniformly distributed moment tensors. A cartesian grid in the coordinate domain can be used to search efficiently over moment tensors. We find that uniformly distributed moment tensors have uniformly distributed orientations (eigenframes), but that their source types (eigenvalue triples) are distributed so as to favour double couples.
Killing(-Yano) Tensors in String Theory
Chervonyi, Yuri
2015-01-01
We construct the Killing(-Yano) tensors for a large class of charged black holes in higher dimensions and study general properties of such tensors, in particular, their behavior under string dualities. Killing(-Yano) tensors encode the symmetries beyond isometries, which lead to insights into dynamics of particles and fields on a given geometry by providing a set of conserved quantities. By analyzing the eigenvalues of the Killing tensor, we provide a prescription for constructing several conserved quantities starting from a single object, and we demonstrate that Killing tensors in higher dimensions are always associated with ellipsoidal coordinates. We also determine the transformations of the Killing(-Yano) tensors under string dualities, and find the unique modification of the Killing-Yano equation consistent with these symmetries. These results are used to construct the explicit form of the Killing(-Yano) tensors for the Myers-Perry black hole in arbitrary number of dimensions and for its charged version.
Conformal correlators of mixed-symmetry tensors
Costa, Miguel S
2015-01-01
We generalize the embedding formalism for conformal field theories to the case of general operators with mixed symmetry. The index-free notation encoding symmetric tensors as polynomials in an auxiliary polarization vector is extended to mixed-symmetry tensors by introducing a new commuting or anticommuting polarization vector for each row or column in the Young diagram that describes the index symmetries of the tensor. We determine the tensor structures that are allowed in n-point conformal correlation functions and give an algorithm for counting them in terms of tensor product coefficients. We show, with an example, how the new formalism can be used to compute conformal blocks of arbitrary external fields for the exchange of any conformal primary and its descendants. The matching between the number of tensor structures in conformal field theory correlators of operators in d dimensions and massive scattering amplitudes in d+1 dimensions is also seen to carry over to mixed-symmetry tensors.
Extended vector-tensor theories
Kimura, Rampei; Yoshida, Daisuke
2016-01-01
Recently, several extensions of massive vector theory in curved space-time have been proposed in many literatures. In this paper, we consider the most general vector-tensor theories that contain up to two derivatives with respect to metric and vector field. By imposing a degeneracy condition of the Lagrangian in the context of ADM decomposition of space-time to eliminate an unwanted mode, we construct a new class of massive vector theories where five degrees of freedom can propagate, corresponding to three for massive vector modes and two for massless tensor modes. We find that the generalized Proca and the beyond generalized Proca theories up to the quartic Lagrangian, which should be included in this formulation, are degenerate theories even in curved space-time. Finally, introducing new metric and vector field transformations, we investigate the properties of thus obtained theories under such transformations.
Scalar-tensor cosmological simulations
Rodriguez-Meza, M A
2008-01-01
We present $N$-body cosmlogical simulations in the framework of the Newtonian limit of scalar-tensor theories of gravity. The scalar field is described by a modified Helmholtz equation with a source that is coupled to the standard Poisson equation of Newtonian gravity. The effective gravitational force is given by two contributions: the standard Newtonian potential plus a Yukawa potential stemming from massive scalar fields. In particular, we consider simulations of $\\Lambda$CDM models and co...
Local virial and tensor theorems.
Cohen, Leon
2011-11-17
We show that for any wave function and potential the local virial theorem can always be satisfied 2K(r) = r·ΔV by choosing a particular expression for the local kinetic energy. In addition, we show that for each choice of local kinetic energy there are an infinite number of quasi-probability distributions which will generate the same expression. We also consider the local tensor virial theorem. PMID:21863837
Exact discretization of harmonic tensors
Chumley, Tim; Feres, Renato; Wallace, Matt
2016-01-01
Lyons and Sullivan have shown how to discretize harmonic functions on a Riemannian manifold $M$ whose Brownian motion satisfies a certain recurrence property called $\\ast$-recurrence. We study analogues of this discretization for tensor fields which are harmonic in the sense of the covariant Laplacian. We show that, under certain restrictions on the holonomy of the connection, the lifted diffusion on the orthonormal frame bundle has the same $\\ast$-recurrence property as the original Brownian...
International Nuclear Information System (INIS)
Hydrolysis products of niobium, tantalum, antimony and arsenic pentafluorides in acetonitrile solution were studied by the methods of 17O and 19F NMR. In 17O NMR spectra of niobium and tantalum pentafluorides hydrolysis products resonance signals of oxo-, hydroxo- and aquafluorocomplexes were defined. Considerable shift of 17O NMR resonance signals towards weak field making up about 300 m.p., may indicate a higher covalency (Π-character) of Nb-O bond compared to Ta-O one. Symbasis in the change of chemical shifts in 17O NMR and 19F NMR of the relevant hexafluorides and hydrolysis products was detected implying similarity of chemical bond nature in oxygen and fluorine
Transformation Electromagnetics Devices Based on Printed-Circuit Tensor Impedance Surfaces
Patel, Amit M
2013-01-01
A method for designing transformation electromagnetics devices using tensor impedance surfaces (TISs) is presented. The method is first applied to idealized tensor impedance boundary conditions (TIBCs), and later to printed-circuit tensor impedance surfaces (PCTISs). A PCTIS is a practical realization of a TIBC. It consists of a tensor impedance sheet, which models a subwavelength patterned metallic cladding, over a grounded dielectric substrate. The method outlined in this paper allows anisotropic TIBCs and PCTISs to be designed that support tangential wave vector distributions and power flow directions specified by a coordinate transformation. As an example, beamshifting devices are designed, using TIBCs and PCTISs, that allow a surface wave to be shifted laterally. The designs are verified with a commercial full-wave electromagnetic solver. This work opens new opportunities for the design and implementation of anisotropic and inhomogeneous printed-circuit or graphene based surfaces that can guide or radiat...
Random Tensors and Planted Cliques
Brubaker, S. Charles; Vempala, Santosh S.
The r-parity tensor of a graph is a generalization of the adjacency matrix, where the tensor’s entries denote the parity of the number of edges in subgraphs induced by r distinct vertices. For r = 2, it is the adjacency matrix with 1’s for edges and - 1’s for nonedges. It is well-known that the 2-norm of the adjacency matrix of a random graph is O(sqrt{n}). Here we show that the 2-norm of the r-parity tensor is at most f(r)sqrt{n}log^{O(r)}n, answering a question of Frieze and Kannan [1] who proved this for r = 3. As a consequence, we get a tight connection between the planted clique problem and the problem of finding a vector that approximates the 2-norm of the r-parity tensor of a random graph. Our proof method is based on an inductive application of concentration of measure.
Tensor Interaction Effect in Dibaryon
Institute of Scientific and Technical Information of China (English)
CHEN Ling-Zhi; PANG Hou-Rong; PING Jia-Lun; WANG Fan
2005-01-01
The gluon and Goldstone boson induced tensor interaction effect on the dibaryon mass and the D-wave decay width has been studied in the quark delocalization, color screening model. The effective S-D wave transition interactions induced by gluon and Goldstone boson exchanges decrease quickly as the increasing of the channel strangeness. The K and η meson tensor contribution is negligible in this model. No six-quark state in the light flavor world can become a bound one by the help of these tensor interactions except the deuteron. The partial D-wave decay width of Ijp = 1/2 2+NΩ state to spin 0, 1 ∧([1]) final state is 20.7 keV and 63.1 keV respectively. It is a very narrow dibaryon resonance and might be detected in the relativistic heavy ion reaction by the existing RHIC detectors through the reconstruction of the ∧([1]) vertex mass and the future COMPAS detector at CERN and FAIR project in Germany.
Generalised tensor fluctuations and inflation
International Nuclear Information System (INIS)
Using an effective field theory approach to inflation, we examine novel properties of the spectrum of inflationary tensor fluctuations, that arise when breaking some of the symmetries or requirements usually imposed on the dynamics of perturbations. During single-clock inflation, time-reparameterization invariance is broken by a time-dependent cosmological background. In order to explore more general scenarios, we consider the possibility that spatial diffeomorphism invariance is also broken by effective mass terms or by derivative operators for the metric fluctuations in the Lagrangian. We investigate the cosmological consequences of the breaking of spatial diffeomorphisms, focussing on operators that affect the power spectrum of fluctuations. We identify the operators for tensor fluctuations that can provide a blue spectrum without violating the null energy condition, and operators for scalar fluctuations that lead to non-conservation of the comoving curvature perturbation on superhorizon scales even in single-clock inflation. In the last part of our work, we also examine the consequences of operators containing more than two spatial derivatives, discussing how they affect the sound speed of tensor fluctuations, and showing that they can mimic some of the interesting effects of symmetry breaking operators, even in scenarios that preserve spatial diffeomorphism invariance
Springuel-Huet, M. A.; Fraissard, J.
1989-01-01
The form of the 129Xe NMR signal of xenon adsorbed at low concentration on the molecular sieves SAPO-11 and AlPO 4-11 corresponds to a highly anisotropic chemical shift which expresses the asymmetry of the channels in which the xenon is located. To the asymmetry of the xenon-wall interaction is added that of the xenon-xenon interaction when the channels are largely filled.
Medical Service
2002-01-01
It is reminded that all persons who use chemicals must inform CERN's Chemistry Service (TIS-GS-GC) and the CERN Medical Service (TIS-ME). Information concerning their toxicity or other hazards as well as the necessary individual and collective protection measures will be provided by these two services. Users must be in possession of a material safety data sheet (MSDS) for each chemical used. These can be obtained by one of several means : the manufacturer of the chemical (legally obliged to supply an MSDS for each chemical delivered) ; CERN's Chemistry Service of the General Safety Group of TIS ; for chemicals and gases available in the CERN Stores the MSDS has been made available via EDH either in pdf format or else via a link to the supplier's web site. Training courses in chemical safety are available for registration via HR-TD. CERN Medical Service : TIS-ME :73186 or service.medical@cern.ch Chemistry Service : TIS-GS-GC : 78546
Sieh, Daniel; Kubiak, Clifford P
2016-07-18
A set of pyridine monoimine (PMI) rhenium(I) tricarbonyl chlorido complexes with substituents of different steric and electronic properties was synthesized and fully characterized. Spectroscopic (NMR and IR) and single-crystal X-ray diffraction analyses of these complexes showed that the redox-active PMI ligands are neutral and that the overall electronic structure is little affected by the choices of the substituent at the ligand backbone. One- and two-electron reduction products were prepared from selected starting compounds and could also be characterized by multiple spectroscopic methods and X-ray diffraction. The final product of a one-electron reduction in THF is a diamagnetic metal-metal-bonded dimer after loss of the chlorido ligand. Bond lengths in and NMR chemical shifts of the PMI ligand backbone indicate partial electron transfer to the ligand. Two-electron reduction in THF also leads to the loss of the chlorido ligand and a pentacoordinate complex is obtained. The comparison with reported bond lengths and (13) C NMR chemical shifts of doubly reduced free pyridine monoaldimine ligands indicates that both redox equivalents in the doubly reduced rhenium complex investigated here are located in the PMI ligand. With diamagnetic complexes varying over three formal reduction stages at the PMI ligand we were, for the first time, able to establish correlations of the (13) C NMR chemical shifts with the relevant bond lengths in redox-active ligands over a full redox series. PMID:27319753
Energy Technology Data Exchange (ETDEWEB)
Yoshimura, Yuichi; Kulminskaya, Natalia V.; Mulder, Frans A. A., E-mail: fmulder@chem.au.dk [Aarhus University, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO) (Denmark)
2015-02-15
Sequential resonance assignment strategies are typically based on matching one or two chemical shifts of adjacent residues. However, resonance overlap often leads to ambiguity in resonance assignments in particular for intrinsically disordered proteins. We investigated the potential of establishing connectivity through the three-bond couplings between sequentially adjoining backbone carbonyl carbon nuclei, combined with semi-constant time chemical shift evolution, for resonance assignments of small folded and larger unfolded proteins. Extended sequential connectivity strongly lifts chemical shift degeneracy of the backbone nuclei in disordered proteins. We show here that 3D (H)N(COCO)NH and (HN)CO(CO)NH experiments with relaxation-optimized multiple pulse mixing correlate up to seven adjacent backbone amide nitrogen or carbonyl carbon nuclei, respectively, and connections across proline residues are also obtained straightforwardly. Multiple, recurrent long-range correlations with ultra-high resolution allow backbone {sup 1}H{sup N}, {sup 15}N{sup H}, and {sup 13}C′ resonance assignments to be completed from a single pair of 3D experiments.
Tensor SOM and tensor GTM: Nonlinear tensor analysis by topographic mappings.
Iwasaki, Tohru; Furukawa, Tetsuo
2016-05-01
In this paper, we propose nonlinear tensor analysis methods: the tensor self-organizing map (TSOM) and the tensor generative topographic mapping (TGTM). TSOM is a straightforward extension of the self-organizing map from high-dimensional data to tensorial data, and TGTM is an extension of the generative topographic map, which provides a theoretical background for TSOM using a probabilistic generative model. These methods are useful tools for analyzing and visualizing tensorial data, especially multimodal relational data. For given n-mode relational data, TSOM and TGTM can simultaneously organize a set of n-topographic maps. Furthermore, they can be used to explore the tensorial data space by interactively visualizing the relationships between modes. We present the TSOM algorithm and a theoretical description from the viewpoint of TGTM. Various TSOM variations and visualization techniques are also described, along with some applications to real relational datasets. Additionally, we attempt to build a comprehensive description of the TSOM family by adapting various data structures. PMID:26991392
Mille, Matthieu
2000-01-01
In this paper, the author adopt a time-geography approach to examine the temporal variation of urban density by analysing spatial load changes at different times of the day at the communal and community level. The evolution of means of transport coupled with the abandon of the notion of direct proximity to the urban dwelling place provide the basis for this new approach to the study of urban densities. The shift towards spatial specialisation within cities has lead to radical changes in the f...
The Cotton tensor in Riemannian spacetimes
García, A; Heinicke, C; Macías, A
2004-01-01
Recently, the study of three-dimensional spaces is becoming of great interest. In these dimensions the Cotton tensor is prominent as the substitute for the Weyl tensor. It is conformally invariant and its vanishing is equivalent to conformal flatness. However, the Cotton tensor arises in the context of the Bianchi identities and is present in any dimension. We present a systematic derivation of the Cotton tensor. We perform its irreducible decomposition and determine its number of independent components for the first time. Subsequently, we exhibit its characteristic properties and perform a classification of the Cotton tensor in three dimensions. We investigate some solutions of Einstein's field equations in three dimensions and of the topologically massive gravity model of Deser, Jackiw, and Templeton. For each class examples are given. Finally we investigate the relation between the Cotton tensor and the energy-momentum in Einstein's theory and derive a conformally flat perfect fluid solution of Einstein's ...
Reconstruction of convex bodies from surface tensors
DEFF Research Database (Denmark)
Kousholt, Astrid; Kiderlen, Markus
The set of all surface tensors of a convex body K (Minkowski tensors derived from the surface area measure of K) determine K up to translation, and hereby, the surface tensors of K contain all information on the shape of K. Here, shape means the equivalence class of all convex bodies that are...... translates of each other. An algorithm for reconstructing an unknown convex body in R 2 from its surface tensors up to a certain rank is presented. Using the reconstruction algorithm, the shape of an unknown convex body can be approximated when only a finite number s of surface tensors are available. The...... output of the reconstruction algorithm is a polytope P, where the surface tensors of P and K are identical up to rank s. We establish a stability result based on a generalization of Wirtinger’s inequality that shows that for large s, two convex bodies are close in shape when they have identical surface...
Seamless warping of diffusion tensor fields
DEFF Research Database (Denmark)
Xu, Dongrong; Hao, Xuejun; Bansal, Ravi;
2008-01-01
To warp diffusion tensor fields accurately, tensors must be reoriented in the space to which the tensors are warped based on both the local deformation field and the orientation of the underlying fibers in the original image. Existing algorithms for warping tensors typically use forward mapping...... of seams, including voxels in which the deformation is extensive. Backward mapping, however, cannot reorient tensors in the template space because information about the directional orientation of fiber tracts is contained in the original, unwarped imaging space only, and backward mapping alone cannot...... transfer that information to the template space. To combine the advantages of forward and backward mapping, we propose a novel method for the spatial normalization of diffusion tensor (DT) fields that uses a bijection (a bidirectional mapping with one-to-one correspondences between image spaces) to warp DT...
Derivatives on the isotropic tensor functions
Institute of Scientific and Technical Information of China (English)
DUI Guansuo; WANG Zhengdao; JIN Ming
2006-01-01
The derivative of the isotropic tensor function plays an important part in continuum mechanics and computational mechanics, and also it is still an opening problem. By means of a scalar response function and solving a tensor equation, this problem is well studied. A compact explicit expression for the derivative of the isotropic tensor function is presented, which is valid for both distinct and repeated eigenvalue cases. Throughout the analysis, the formulation holds for general isotropic tensor functions without need to solve eigenvector problems or determine coefficients. On the theoretical side, a very simple solution of a tensor equation is obtained. As an application to continuum mechanics, a base-free expression for the Hill's strain rate is given, which is more compact than the existent results. Finally, with an example we compute the derivative of an exponent tensor function. And the efficiency of the present formulations is demonstrated.
Bayes method for low rank tensor estimation
Suzuki, Taiji; Kanagawa, Heishiro
2016-03-01
We investigate the statistical convergence rate of a Bayesian low-rank tensor estimator, and construct a Bayesian nonlinear tensor estimator. The problem setting is the regression problem where the regression coefficient forms a tensor structure. This problem setting occurs in many practical applications, such as collaborative filtering, multi-task learning, and spatio-temporal data analysis. The convergence rate of the Bayes tensor estimator is analyzed in terms of both in-sample and out-of-sample predictive accuracies. It is shown that a fast learning rate is achieved without any strong convexity of the observation. Moreover, we extend the tensor estimator to a nonlinear function estimator so that we estimate a function that is a tensor product of several functions.
Empirical Evaluation of Four Tensor Decomposition Algorithms
Turney, Peter D
2007-01-01
Higher-order tensor decompositions are analogous to the familiar Singular Value Decomposition (SVD), but they transcend the limitations of matrices (second-order tensors). SVD is a powerful tool that has achieved impressive results in information retrieval, collaborative filtering, computational linguistics, computational vision, and other fields. However, SVD is limited to two-dimensional arrays of data (two modes), and many potential applications have three or more modes, which require higher-order tensor decompositions. This paper evaluates four algorithms for higher-order tensor decomposition: Higher-Order Singular Value Decomposition (HO-SVD), Higher-Order Orthogonal Iteration (HOOI), Slice Projection (SP), and Multislice Projection (MP). We measure the time (elapsed run time), space (RAM and disk space requirements), and fit (tensor reconstruction accuracy) of the four algorithms, under a variety of conditions. We find that standard implementations of HO-SVD and HOOI do not scale up to larger tensors, d...
Dark matter dispersion tensor in perturbation theory
Aviles, Alejandro
2016-03-01
We compute the dark matter velocity dispersion tensor up to third order in perturbation theory using the Lagrangian formalism, revealing growing solutions at the third and higher orders. Our results are general and can be used for any other perturbative formalism. As an application, corrections to the matter power spectrum are calculated, and we find that some of them have the same structure as those in the effective field theory of large-scale structure, with "EFT-like" coefficients that grow quadratically with the linear growth function and are further suppressed by powers of the logarithmic linear growth factor f ; other corrections present additional k dependence. Due to the velocity dispersions, there exists a free-streaming scale that suppresses the whole 1-loop power spectrum. Furthermore, we find that as a consequence of the nonlinear evolution, the free-streaming length is shifted towards larger scales, wiping out more structure than that expected in linear theory. Therefore, we argue that the formalism developed here is better suited for a perturbation treatment of warm dark matter or neutrino clustering, where the velocity dispersion effects are well known to be important. We discuss implications related to the nature of dark matter.
Shell evolution of atomic nuclei due to the tensor force
International Nuclear Information System (INIS)
Magic numbers and shell structure are extremely important for the study of atomic nuclei, as they determine the mass, the shape of surface, and the limit of the existence of nuclei, and have been considered to be universal over all nuclei, since Mayer and Jensen (1949). However, recent studies on exotic nuclei with large variations of proton or neutron numbers indicate that the changes of magic numbers and shell structure, i.e, shell evolution, arise due to nuclear forces, in particular the tensor force, demolishing this universality. We shall present an overview of such a paradigm shift emerging in exotic nuclei. (author)
Stress Tensors of Multiparticle Collision Dynamics Fluids
Winkler, Roland G.; Huang, Chien-Cheng
2008-01-01
Stress tensors are derived for the multiparticle collision dynamics algorithm, a particle-based mesoscale simulation method for fluctuating fluids, resembling those of atomistic or molecular systems. Systems with periodic boundary conditions as well as fluids confined in a slit are considered. For every case, two equivalent expressions for the tensor are provided, the internal stress tensor, which involves all degrees of freedom of a system, and the external stress, which only includes the in...
Tensor theta norms and low rank recovery
Rauhut, Holger; Stojanac, Željka
2015-01-01
We study extensions of compressive sensing and low rank matrix recovery to the recovery of tensors of low rank from incomplete linear information. While the reconstruction of low rank matrices via nuclear norm minimization is rather well-understand by now, almost no theory is available so far for the extension to higher order tensors due to various theoretical and computational difficulties arising for tensor decompositions. In fact, nuclear norm minimization for matrix recovery is a tractabl...
Visualization of Tensor Fields Using Superquadric Glyphs
Ennis, Daniel B.; Kindlman, Gordon; Rodriguez, Ignacio; Helm, Patrick A.; Mcveigh, Elliot R.
2005-01-01
The spatially varying tensor fields that arise in magnetic resonance imaging are difficult to visualize due to the multivariate nature of the data. To improve the understanding of myocardial structure and function a family of objects called glyphs, derived from superquadric parametric functions, are used to create informative and intuitive visualizations of the tensor fields. The superquadric glyphs are used to visualize both diffusion and strain tensors obtained in canine myocardium. The eig...
Gravitational scalar-tensor theory
Naruko, Atsushi; Mukohyama, Shinji
2015-01-01
We consider a new form of theories of gravity in which the action is written in terms of the Ricci scalar and its first and second derivatives. Despite the higher derivative nature of the action, the theory is free from ghost under an appropriate choice of the functional form of the Lagrangian. This model possesses $2+2$ physical degrees of freedom, namely $2$ scalar degrees and $2$ tensor degrees. We exhaust all such theories with the Lagrangian of the form $f(R, (\
Reconstruction of convex bodies from surface tensors
DEFF Research Database (Denmark)
Kousholt, Astrid; Kiderlen, Markus
2016-01-01
We present two algorithms for reconstruction of the shape of convex bodies in the two-dimensional Euclidean space. The first reconstruction algorithm requires knowledge of the exact surface tensors of a convex body up to rank s for some natural number s. When only measurements subject to noise of...... surface tensors are available for reconstruction, we recommend to use certain values of the surface tensors, namely harmonic intrinsic volumes instead of the surface tensors evaluated at the standard basis. The second algorithm we present is based on harmonic intrinsic volumes and allows for noisy...
Bayesian regularization of diffusion tensor images
DEFF Research Database (Denmark)
Frandsen, Jesper; Hobolth, Asger; Østergaard, Leif;
2007-01-01
Diffusion tensor imaging (DTI) is a powerful tool in the study of the course of nerve fibre bundles in the human brain. Using DTI, the local fibre orientation in each image voxel can be described by a diffusion tensor which is constructed from local measurements of diffusion coefficients along...... several directions. The measured diffusion coefficients and thereby the diffusion tensors are subject to noise, leading to possibly flawed representations of the three dimensional fibre bundles. In this paper we develop a Bayesian procedure for regularizing the diffusion tensor field, fully utilizing the...
A uniform parameterization of moment tensors
Tape, C.; Tape, W.
2015-12-01
A moment tensor is a 3 x 3 symmetric matrix that expresses an earthquake source. We construct a parameterization of the five-dimensional space of all moment tensors of unit norm. The coordinates associated with the parameterization are closely related to moment tensor orientations and source types. The parameterization is uniform, in the sense that equal volumes in the coordinate domain of the parameterization correspond to equal volumes of moment tensors. Uniformly distributed points in the coordinate domain therefore give uniformly distributed moment tensors. A cartesian grid in the coordinate domain can be used to search efficiently over moment tensors. We find that uniformly distributed moment tensors have uniformly distributed orientations (eigenframes), but that their source types (eigenvalue triples) are distributed so as to favor double couples. An appropriate choice of a priori moment tensor probability is a prerequisite for parameter estimation. As a seemingly sensible choice, we consider the homogeneous probability, in which equal volumes of moment tensors are equally likely. We believe that it will lead to improved characterization of source processes.
Aspects of tensor permeability in reservoir simulation
Energy Technology Data Exchange (ETDEWEB)
Rogers, C.F.
2002-04-01
A number of simulation grids relevant to reservoir engineering practice are studied. The impact of neglecting correct local flux and pressure continuity at the grid cell interfaces is assessed. It is shown that the correct local interface conditions with increased discretisation support lead to improved solutions on non-orthogonal grids with the generation of a full permeability tensor. A full tensor permeability arises even when the permeability is non-isotropic on orthogonal grids. The approach described efficiently includes the permeability tensor contributions from the geometric grid structure, but also implies the importance of modelling the full permeability tensor pressure equation in the reservoir simulation up-scaling process. (orig.)
Regional Moment Tensor Inversion for Source Type Identification
Dreger, D. S.; Ford, S. R.; Walter, W. R.
2008-12-01
With Green's functions from calibrated seismic velocity models it is possible to use regional distance moment tensor inversion for source-type identification. The deviatoric and isotropic source components for 17 explosions at the Nevada Test Site, as well as 12 earthquakes and 3 collapses in the surrounding region of the western US, are calculated using a regional time-domain full waveform inversion for the complete moment tensor. The events separate into specific populations according to their deviation from a pure double-couple and ratio of isotropic to deviatoric energy. The separation allows for anomalous event identification and discrimination between explosions, earthquakes, and collapses. Confidence regions of the model parameters are estimated from the data misfit by assuming normally distributed parameter values. We investigate the sensitivity of the resolved parameters of an explosion to imperfect Earth models, inaccurate event depths, and data with a low signal-to-noise ratio (SNR) assuming a reasonable azimuthal distribution of stations. In the band of interest (0.02-0.10 Hz) the source-type calculated from complete moment tensor inversion is insensitive to velocity models perturbations that cause less than a half-cycle shift (Korea test.
Pulse EPR-enabled interpretation of scarce pseudocontact shifts induced by lanthanide binding tags
Energy Technology Data Exchange (ETDEWEB)
Abdelkader, Elwy H.; Yao, Xuejun [Australian National University, Research School of Chemistry (Australia); Feintuch, Akiva [Weizmann Institute of Science, Department of Chemical Physics (Israel); Adams, Luke A.; Aurelio, Luigi; Graham, Bim [Monash University, Monash Institute of Pharmaceutical Sciences (Australia); Goldfarb, Daniella [Weizmann Institute of Science, Department of Chemical Physics (Israel); Otting, Gottfried, E-mail: gottfried.otting@anu.edu.au [Australian National University, Research School of Chemistry (Australia)
2016-01-15
Pseudocontact shifts (PCS) induced by tags loaded with paramagnetic lanthanide ions provide powerful long-range structure information, provided the location of the metal ion relative to the target protein is known. Usually, the metal position is determined by fitting the magnetic susceptibility anisotropy (Δχ) tensor to the 3D structure of the protein in an 8-parameter fit, which requires a large set of PCSs to be reliable. In an alternative approach, we used multiple Gd{sup 3+}-Gd{sup 3+} distances measured by double electron–electron resonance (DEER) experiments to define the metal position, allowing Δχ-tensor determinations from more robust 5-parameter fits that can be performed with a relatively sparse set of PCSs. Using this approach with the 32 kDa E. coli aspartate/glutamate binding protein (DEBP), we demonstrate a structural transition between substrate-bound and substrate-free DEBP, supported by PCSs generated by C3-Tm{sup 3+} and C3-Tb{sup 3+} tags attached to a genetically encoded p-azidophenylalanine residue. The significance of small PCSs was magnified by considering the difference between the chemical shifts measured with Tb{sup 3+} and Tm{sup 3+} rather than involving a diamagnetic reference. The integrative sparse data approach developed in this work makes poorly soluble proteins of limited stability amenable to structural studies in solution, without having to rely on cysteine mutations for tag attachment.
Some advances in tensor analysis and polynomial optimization
Li, Zhening; Ling, Chen; Wang, Yiju; Yang, Qingzhi
2014-01-01
Tensor analysis (also called as numerical multilinear algebra) mainly includes tensor decomposition, tensor eigenvalue theory and relevant algorithms. Polynomial optimization mainly includes theory and algorithms for solving optimization problems with polynomial objects functions under polynomial constrains. This survey covers the most of recent advances in these two fields. For tensor analysis, we introduce some properties and algorithms concerning the spectral radius of nonnegative tensors'...
Data fusion in metabolomics using coupled matrix and tensor factorizations
DEFF Research Database (Denmark)
Evrim, Acar Ataman; Bro, Rasmus; Smilde, Age Klaas
2015-01-01
With a goal of identifying biomarkers/patterns related to certain conditions or diseases, metabolomics focuses on the detection of chemical substances in biological samples such as urine and blood using a number of analytical techniques, including nuclear magnetic resonance (NMR) spectroscopy...... vast amounts of data using different analytical methods, data fusion remains a challenging task, in particular, when the goal is to capture the underlying factors and use them for interpretation, e.g., for biomarker identification. Furthermore, many data fusion applications require joint analysis...... of heterogeneous (i.e., in the form of higher order tensors and matrices) data sets with shared/unshared factors. In order to jointly analyze such heterogeneous data sets, we formulate data fusion as a coupled matrix and tensor factorization (CMTF) problem, which has already proved useful in many data mining...
3D reconstruction of tensors and vectors
Energy Technology Data Exchange (ETDEWEB)
Defrise, Michel; Gullberg, Grant T.
2005-02-17
Here we have developed formulations for the reconstruction of 3D tensor fields from planar (Radon) and line-integral (X-ray) projections of 3D vector and tensor fields. Much of the motivation for this work is the potential application of MRI to perform diffusion tensor tomography. The goal is to develop a theory for the reconstruction of both Radon planar and X-ray or line-integral projections because of the flexibility of MRI to obtain both of these type of projections in 3D. The development presented here for the linear tensor tomography problem provides insight into the structure of the nonlinear MRI diffusion tensor inverse problem. A particular application of tensor imaging in MRI is the potential application of cardiac diffusion tensor tomography for determining in vivo cardiac fiber structure. One difficulty in the cardiac application is the motion of the heart. This presents a need for developing future theory for tensor tomography in a motion field. This means developing a better understanding of the MRI signal for diffusion processes in a deforming media. The techniques developed may allow the application of MRI tensor tomography for the study of structure of fiber tracts in the brain, atherosclerotic plaque, and spine in addition to fiber structure in the heart. However, the relations presented are also applicable to other fields in medical imaging such as diffraction tomography using ultrasound. The mathematics presented can also be extended to exponential Radon transform of tensor fields and to other geometric acquisitions such as cone beam tomography of tensor fields.
Tensor decomposition in post-Hartree–Fock methods. II. CCD implementation
International Nuclear Information System (INIS)
In a previous publication, we have discussed the usage of tensor decomposition in the canonical polyadic (CP) tensor format for electronic structure methods. There, we focused on two-electron integrals and second order Møller-Plesset perturbation theory (MP2). In this work, we discuss the CP format for Coupled Cluster (CC) theory and present a pilot implementation for the Coupled Cluster Doubles method. We discuss the iterative solution of the CC amplitude equations using tensors in CP representation and present a tensor contraction scheme that minimizes the effort necessary for the rank reductions during the iterations. Furthermore, several details concerning the reduction of complexity of the algorithm, convergence of the CC iterations, truncation errors, and the choice of threshold for chemical accuracy are discussed
Tensor decomposition in post-Hartree–Fock methods. II. CCD implementation
Energy Technology Data Exchange (ETDEWEB)
Benedikt, Udo; Böhm, Karl-Heinz; Auer, Alexander A., E-mail: alexander.auer@cec.mpg.de [Max-Planck-Institute for Chemical Energy Conversion, Stiftstraße 34 - 36, D-45470 Mülheim an der Ruhr (Germany)
2013-12-14
In a previous publication, we have discussed the usage of tensor decomposition in the canonical polyadic (CP) tensor format for electronic structure methods. There, we focused on two-electron integrals and second order Møller-Plesset perturbation theory (MP2). In this work, we discuss the CP format for Coupled Cluster (CC) theory and present a pilot implementation for the Coupled Cluster Doubles method. We discuss the iterative solution of the CC amplitude equations using tensors in CP representation and present a tensor contraction scheme that minimizes the effort necessary for the rank reductions during the iterations. Furthermore, several details concerning the reduction of complexity of the algorithm, convergence of the CC iterations, truncation errors, and the choice of threshold for chemical accuracy are discussed.
Improving Tensor Based Recommenders with Clustering
DEFF Research Database (Denmark)
Leginus, Martin; Dolog, Peter; Zemaitis, Valdas
2012-01-01
Social tagging systems (STS) model three types of entities (i.e. tag-user-item) and relationships between them are encoded into a 3-order tensor. Latent relationships and patterns can be discovered by applying tensor factorization techniques like Higher Order Singular Value Decomposition (HOSVD...
Tensor product in symmetric function spaces
Astashkin, S. V.
1998-01-01
A concept of multiplicator of symmetric function space concerning to projective tensor product is introduced and studied. This allows to obtain some concrete results. In particular, the well-known theorem of R. O'Neil about the boundedness of tensor product in the Lorentz spaces L_{p,q} is discussed.
Extended Nonnegative Tensor Factorisation Models for Musical Sound Source Separation
Directory of Open Access Journals (Sweden)
Derry FitzGerald
2008-01-01
Full Text Available Recently, shift-invariant tensor factorisation algorithms have been proposed for the purposes of sound source separation of pitched musical instruments. However, in practice, existing algorithms require the use of log-frequency spectrograms to allow shift invariance in frequency which causes problems when attempting to resynthesise the separated sources. Further, it is difficult to impose harmonicity constraints on the recovered basis functions. This paper proposes a new additive synthesis-based approach which allows the use of linear-frequency spectrograms as well as imposing strict harmonic constraints, resulting in an improved model. Further, these additional constraints allow the addition of a source filter model to the factorisation framework, and an extended model which is capable of separating mixtures of pitched and percussive instruments simultaneously.
Preservation of Linear Constraints in Approximation of Tensors
Institute of Scientific and Technical Information of China (English)
Eugene Tyrtyshnikov
2009-01-01
For an arbitrary tensor (multi-index array) with linear constraints at each direction, it is proved that the factors of any minimal canonical tensor approximation to this tensor satisfy the same linear constraints for the corresponding directions.
Halogen effect on structure and ^{13}C NMR chemical shift of 3,6-disubstituted-N-alkyl carbazoles
DEFF Research Database (Denmark)
Radula-Janik, Klaudia; Kupka, Teobald; Ejsmont, Krzysztof; Daszkiewicz, Zdzislaw; Sauer, Stephan P. A.
2013-01-01
Structures of selected 3,6-dihalogeno-N-alkyl carbazole derivatives were calculated at the B3LYP/6-311++G(3df,2pd) level of theory and their 13C NMR isotropic nuclear shieldings were predicted using density functional theory (DFT). The model compounds contained 9H-, N-methyl and N-ethyl derivatives....... The relativistic effect of Br and I atoms on nuclear shieldings was modeled using the spin-orbit ZORA method. Significant heavy atom shielding effects for the carbon atom directly bonded with bromine and iodine were observed (~ -10 and ~ -30 ppm while the other carbon shifts were practically...
Identifying Isotropic Events Using a Regional Moment Tensor Inversion
Energy Technology Data Exchange (ETDEWEB)
Ford, S R; Dreger, D S; Walter, W R
2008-11-04
We calculate the deviatoric and isotropic source components for 17 explosions at the Nevada Test Site, as well as 12 earthquakes and 3 collapses in the surrounding region of the western US, using a regional time-domain full waveform inversion for the complete moment tensor. The events separate into specific populations according to their deviation from a pure double-couple and ratio of isotropic to deviatoric energy. The separation allows for anomalous event identification and discrimination between explosions, earthquakes, and collapses. Confidence regions of the model parameters are estimated from the data misfit by assuming normally distributed parameter values. We investigate the sensitivity of the resolved parameters of an explosion to imperfect Earth models, inaccurate event depths, and data with low signal-to-noise ratio (SNR) assuming a reasonable azimuthal distribution of stations. In the band of interest (0.02-0.10 Hz) the source-type calculated from complete moment tensor inversion is insensitive to velocity models perturbations that cause less than a half-cycle shift (<5 sec) in arrival time error if shifting of the waveforms is allowed. The explosion source-type is insensitive to an incorrect depth assumption (for a true depth of 1 km), and the goodness-of-fit of the inversion result cannot be used to resolve the true depth of the explosion. Noise degrades the explosive character of the result, and a good fit and accurate result are obtained when the signal-to-noise ratio (SNR) is greater than 5. We assess the depth and frequency dependence upon the resolved explosive moment. As the depth decreases from 1 km to 200 m, the isotropic moment is no longer accurately resolved and is in error between 50-200%. However, even at the most shallow depth the resultant moment tensor is dominated by the explosive component when the data have a good SNR.
Inflation and alternatives with blue tensor spectra
International Nuclear Information System (INIS)
We study the tilt of the primordial gravitational waves spectrum. A hint of blue tilt is shown from analyzing the BICEP2 and POLARBEAR data. Motivated by this, we explore the possibilities of blue tensor spectra from the very early universe cosmology models, including null energy condition violating inflation, inflation with general initial conditions, and string gas cosmology, etc. For the simplest G-inflation, blue tensor spectrum also implies blue scalar spectrum. In general, the inflation models with blue tensor spectra indicate large non-Gaussianities. On the other hand, string gas cosmology predicts blue tensor spectrum with highly Gaussian fluctuations. If further experiments do confirm the blue tensor spectrum, non-Gaussianity becomes a distinguishing test between inflation and alternatives
Stress tensors of multiparticle collision dynamics fluids.
Winkler, Roland G; Huang, Chien-Cheng
2009-02-21
Stress tensors are derived for the multiparticle collision dynamics algorithm, a particle-based mesoscale simulation method for fluctuating fluids, resembling those of atomistic or molecular systems. Systems with periodic boundary conditions as well as fluids confined in a slit are considered. For every case, two equivalent expressions for the tensor are provided, the internal stress tensor, which involves all degrees of freedom of a system, and the external stress, which only includes the interactions with the confining surfaces. In addition, stress tensors for a system with embedded particles are determined. Based on the derived stress tensors, analytical expressions are calculated for the shear viscosity. Simulations illustrate the difference in fluctuations between the various derived expressions and yield very good agreement between the numerical results and the analytically derived expression for the viscosity. PMID:19239316
On Lovelock analogs of the Riemann tensor
Energy Technology Data Exchange (ETDEWEB)
Camanho, Xian O. [Albert-Einstein-Institut, Max-Planck-Institut fuer Gravitationsphysik, Golm (Germany); Dadhich, Naresh [Jamia Millia Islamia, Centre for Theoretical Physics, New Delhi (India); Inter-University Centre for Astronomy and Astrophysics, Pune (India)
2016-03-15
It is possible to define an analog of the Riemann tensor for Nth order Lovelock gravity, its characterizing property being that the trace of its Bianchi derivative yields the corresponding analog of the Einstein tensor. Interestingly there exist two parallel but distinct such analogs and the main purpose of this note is to reconcile both formulations. In addition we will introduce a simple tensor identity and use it to show that any pure Lovelock vacuum in odd d = 2N + 1 dimensions is Lovelock flat, i.e. any vacuum solution of the theory has vanishing Lovelock-Riemann tensor. Further, in the presence of cosmological constant it is the Lovelock-Weyl tensor that vanishes. (orig.)
International Nuclear Information System (INIS)
A t20 tensor polarimeter using the 3He(d,p)4He reaction as analyzer has been designed and constructed. Upon its calibration, with a deuteron beam of known polarization, it has been used for measurements of the recoil deuteron polarization from πd elastic scattering. The polarimeter was designed such that the cylindrical symmetry required for the polarimeter could be constructed for any given incident deuteron beam geometry, and was aligned independently on such experimental parameters as the position of the beam centroid, beam intensity distribution, etc. There are contributions from it11 and t22, and therefore most likely from t21 as well, is such symmetry is not maintained. It was found that if the incident deuteron intensity distribution is cylindrically symmetric, then contributions from these components can be neglected on average, provided the polarimeter face is larger than the beam size and the beam centroid is placed on the symmetry axis
Theory of Antisymmetric Tensor Fields
Dvoeglazov, V V
2003-01-01
It has long been claimed that the antisymmetric tensor field of the second rank is pure longitudinal after quantization. In my opinion, such a situation is quite unacceptable. I repeat the well-known procedure of the derivation of the set of Proca equations. It is shown that it can be written in various forms. Furthermore, on the basis of the Lagrangian formalism I calculate dynamical invariants (including the Pauli-Lubanski vector of relativistic spin for this field). Even at the classical level the Pauli-Lubanski vector can be equal to zero after applications of well-known constraints. The importance of the normalization is pointed out for the problem of the description of quantized fields of maximal spin 1. The correct quantization procedure permits us to propose a solution of this puzzle in the modern field theory. Finally, the discussion of the connection of the Ogievetskii-Polubarinov-Kalb-Ramond field and the electrodynamic gauge is presented.
Directory of Open Access Journals (Sweden)
Simone Di Micco
2013-12-01
Full Text Available In this paper the stereostructural investigation of two new oxygenated polyketides, plakilactones G and H, isolated from the marine sponge Plakinastrella mamillaris collected at Fiji Islands, is reported. The stereostructural studies began on plakilactone H by applying an integrated approach of the NOE-based protocol and quantum mechanical calculations of 13C chemical shifts. In particular, plakilactone H was used as a template to extend the application of NMR-derived interproton distances to a highly flexible molecular system with simultaneous assignment of four non-contiguous stereocenters. Chemical derivatization and quantum mechanical calculations of 13C on plakilactone G along with a plausible biogenetic interconversion between plakilactone G and plakilactone H allowed us to determine the absolute configuration in this two new oxygenated polyketides.
Institute of Scientific and Technical Information of China (English)
G. Apaydma, V. Ayhkg; Z. Biyiklioglu; E. Tirasoglu; H. Kantekin
2008-01-01
Chemical effects on the Kβ/Kα intensity ratios and ΔE energy differences for Co, Ni, Cu, and Zn complexes were investigated. The samples were excited by 59.5 keV γ-rays from a 241 Am annular radioactive source. K X-rays emitted by samples were counted by an Ultra-LEGe detector with a resolution of 150 eV at 5.9 keV. We observed the effects of different ligands on the Kβ/Kα intensity ratios and ΔE energy differences for Co, Ni, Cu, and Zn complexes. We tried to investigate chemical effects on central atoms using the behaviors of different ligands in these complexes. The experimental values of Kβ/Kα were compared with the theoretical and other experimental values of pure Co, Ni, Cu, and Zn.
Conformal field theories and tensor categories. Proceedings
International Nuclear Information System (INIS)
First book devoted completely to the mathematics of conformal field theories, tensor categories and their applications. Contributors include both mathematicians and physicists. Some long expository articles are especially suitable for beginners. The present volume is a collection of seven papers that are either based on the talks presented at the workshop ''Conformal field theories and tensor categories'' held June 13 to June 17, 2011 at the Beijing International Center for Mathematical Research, Peking University, or are extensions of the material presented in the talks at the workshop. These papers present new developments beyond rational conformal field theories and modular tensor categories and new applications in mathematics and physics. The topics covered include tensor categories from representation categories of Hopf algebras, applications of conformal field theories and tensor categories to topological phases and gapped systems, logarithmic conformal field theories and the corresponding non-semisimple tensor categories, and new developments in the representation theory of vertex operator algebras. Some of the papers contain detailed introductory material that is helpful for graduate students and researchers looking for an introduction to these research directions. The papers also discuss exciting recent developments in the area of conformal field theories, tensor categories and their applications and will be extremely useful for researchers working in these areas.
Conformal field theories and tensor categories. Proceedings
Energy Technology Data Exchange (ETDEWEB)
Bai, Chengming [Nankai Univ., Tianjin (China). Chern Institute of Mathematics; Fuchs, Juergen [Karlstad Univ. (Sweden). Theoretical Physics; Huang, Yi-Zhi [Rutgers Univ., Piscataway, NJ (United States). Dept. of Mathematics; Kong, Liang [Tsinghua Univ., Beijing (China). Inst. for Advanced Study; Runkel, Ingo; Schweigert, Christoph (eds.) [Hamburg Univ. (Germany). Dept. of Mathematics
2014-08-01
First book devoted completely to the mathematics of conformal field theories, tensor categories and their applications. Contributors include both mathematicians and physicists. Some long expository articles are especially suitable for beginners. The present volume is a collection of seven papers that are either based on the talks presented at the workshop ''Conformal field theories and tensor categories'' held June 13 to June 17, 2011 at the Beijing International Center for Mathematical Research, Peking University, or are extensions of the material presented in the talks at the workshop. These papers present new developments beyond rational conformal field theories and modular tensor categories and new applications in mathematics and physics. The topics covered include tensor categories from representation categories of Hopf algebras, applications of conformal field theories and tensor categories to topological phases and gapped systems, logarithmic conformal field theories and the corresponding non-semisimple tensor categories, and new developments in the representation theory of vertex operator algebras. Some of the papers contain detailed introductory material that is helpful for graduate students and researchers looking for an introduction to these research directions. The papers also discuss exciting recent developments in the area of conformal field theories, tensor categories and their applications and will be extremely useful for researchers working in these areas.
Czech Academy of Sciences Publication Activity Database
Buděšínský, Miloš; Vaněk, Václav; Dračínský, Martin; Pohl, Radek; Poštová Slavětínská, Lenka; Sychrovský, Vladimír; Pícha, Jan; Císařová, I.
2014-01-01
Roč. 70, č. 25 (2014), s. 3871-3886. ISSN 0040-4020 R&D Projects: GA ČR GA203/09/1919; GA ČR GA13-24880S Institutional support: RVO:61388963 Keywords : six-membered saturated heterocycles (N, P, S, Se) * oxidation products * configuration * NMR * quantum chemical calculations * X-ray structures Subject RIV: CC - Organic Chemistry Impact factor: 2.641, year: 2014
Hash: a program to accurately predict protein H{sup {alpha}} shifts from neighboring backbone shifts
Energy Technology Data Exchange (ETDEWEB)
Zeng Jianyang, E-mail: zengjy@gmail.com [Tsinghua University, Institute for Interdisciplinary Information Sciences (China); Zhou Pei [Duke University Medical Center, Department of Biochemistry (United States); Donald, Bruce Randall [Duke University, Department of Computer Science (United States)
2013-01-15
Chemical shifts provide not only peak identities for analyzing nuclear magnetic resonance (NMR) data, but also an important source of conformational information for studying protein structures. Current structural studies requiring H{sup {alpha}} chemical shifts suffer from the following limitations. (1) For large proteins, the H{sup {alpha}} chemical shifts can be difficult to assign using conventional NMR triple-resonance experiments, mainly due to the fast transverse relaxation rate of C{sup {alpha}} that restricts the signal sensitivity. (2) Previous chemical shift prediction approaches either require homologous models with high sequence similarity or rely heavily on accurate backbone and side-chain structural coordinates. When neither sequence homologues nor structural coordinates are available, we must resort to other information to predict H{sup {alpha}} chemical shifts. Predicting accurate H{sup {alpha}} chemical shifts using other obtainable information, such as the chemical shifts of nearby backbone atoms (i.e., adjacent atoms in the sequence), can remedy the above dilemmas, and hence advance NMR-based structural studies of proteins. By specifically exploiting the dependencies on chemical shifts of nearby backbone atoms, we propose a novel machine learning algorithm, called Hash, to predict H{sup {alpha}} chemical shifts. Hash combines a new fragment-based chemical shift search approach with a non-parametric regression model, called the generalized additive model, to effectively solve the prediction problem. We demonstrate that the chemical shifts of nearby backbone atoms provide a reliable source of information for predicting accurate H{sup {alpha}} chemical shifts. Our testing results on different possible combinations of input data indicate that Hash has a wide rage of potential NMR applications in structural and biological studies of proteins.
True energy-momentum tensors are unique. Electrodynamics spin tensor is not zero
Khrapko, R I
2001-01-01
From our point of view, classical electrodynamics is not complete. The task is to discover a nonzero spin tensor of electromagnetic field. The variational principle results in a pair of the canonical tensors: the energy-momentum tensor and the spin tensor. But they contradict experience. The attempt to correct the tensors by subtraction the Rosenfeld's pair of tensors from the canonical pair does not lead to the Minkowski energy-momentum tensor, eliminates electrodynamics spin tensor and is inadmissible on principle because an addition of any construction to an energy-momentum tensor of concrete matter corresponds to a local change of matter. And what is more, the addition can change the total 4-momentum and angular 4-momentum of a system. The elimination of spin tensor leads to a strange opinion that a circularly polarized plane wave with infinite extent can have no angular momentum, that only a quasiplane wave of finite transverse extend carries an angular momentum which is provided by an outer region of th...
Global nuclear structure aspects of tensor interaction
International Nuclear Information System (INIS)
A direct fit of the isoscalar spin-orbit and both isoscalar and isovector tensor coupling constants to the f5/2 - f7/2 SO splittings in 40Ca, 56Ni, and 48Ca requires (i) a significant reduction of the standard isoscalar spin-orbit strength and (ii) strong attractive tensor coupling constants. The aim of this paper is to address the consequences of these strong attractive tensor and weak spin-orbit fields on total binding energies, two-neutron separation energies and nuclear deformability. (author)
The balanced tensor product of module categories
Douglas, Christopher L.; Schommer-Pries, Christopher; Snyder, Noah
2014-01-01
The balanced tensor product M (x)_A N of two modules over an algebra A is the vector space corepresenting A-balanced bilinear maps out of the product M x N. The balanced tensor product M [x]_C N of two module categories over a monoidal linear category C is the linear category corepresenting C-balanced right-exact bilinear functors out of the product category M x N. We show that the balanced tensor product can be realized as a category of bimodule objects in C, provided the monoidal linear cat...
Scalable tensor factorizations for incomplete data
DEFF Research Database (Denmark)
Acar, Evrim; Dunlavy, Daniel M.; KOlda, Tamara G.;
2011-01-01
factorize data sets with missing values with the goal of capturing the underlying latent structure of the data and possibly reconstructing missing values (i.e., tensor completion). We focus on one of the most well-known tensor factorizations that captures multi-linear structure, CANDECOMP/PARAFAC (CP). In...... numerical experiments, our algorithm is shown to successfully factorize tensors with noise and up to 99% missing data. A unique aspect of our approach is that it scales to sparse large-scale data, e.g., 1000 × 1000 × 1000 with five million known entries (0.5% dense). We further demonstrate the usefulness of...
Surface tensor estimation from linear sections
DEFF Research Database (Denmark)
Kousholt, Astrid; Kiderlen, Markus; Hug, Daniel
2015-01-01
From Crofton’s formula for Minkowski tensors we derive stereological estimators of translation invariant surface tensors of convex bodies in the n-dimensional Euclidean space. The estimators are based on one-dimensional linear sections. In a design based setting we suggest three types of estimators....... These are based on isotropic uniform random lines, vertical sections, and non-isotropic random lines, respectively. Further, we derive estimators of the specific surface tensors associated with a stationary process of convex particles in the model based setting....
Surface tensor estimation from linear sections
DEFF Research Database (Denmark)
Kousholt, Astrid; Kiderlen, Markus; Hug, Daniel
From Crofton's formula for Minkowski tensors we derive stereological estimators of translation invariant surface tensors of convex bodies in the n-dimensional Euclidean space. The estimators are based on one-dimensional linear sections. In a design based setting we suggest three types of estimators....... These are based on isotropic uniform random lines, vertical sections, and non-isotropic random lines, respectively. Further, we derive estimators of the specific surface tensors associated with a stationary process of convex particles in the model based setting....
Local Tensor Radiation Conditions For Elastic Waves
DEFF Research Database (Denmark)
Krenk, S.; Kirkegaard, Poul Henning
2001-01-01
A local boundary condition is formulated, representing radiation of elastic waves from an arbitrary point source. The boundary condition takes the form of a tensor relation between the stress at a point on an arbitrarily oriented section and the velocity and displacement vectors at the point....... The tensor relation generalizes the traditional normal incidence impedance condition by accounting for the angle between wave propagation and the surface normal and by including a generalized stiffness term due to spreading of the waves. The effectiveness of the local tensor radiation condition...
Why are tensor field theories asymptotically free?
Rivasseau, Vincent
2015-01-01
In this pedagogic letter we explain the combinatorics underlying the generic asymptotic freedom of tensor field theories. We focus on simple combinatorial models with a $1/p^2$ propagator and quartic interactions and on the comparison between the intermediate field representations of the vector, matrix and tensor cases. The transition from asymptotic freedom (tensor case) to asymptotic safety (matrix case) is related to the crossing symmetry of the matrix vertex whereas in the vector case, the lack of asymptotic freedom ("Landau ghost"), as in the ordinary scalar case, is simply due to the absence of any wave function renormalization at one loop.
Gravitational interaction of fermion antisymmetric tensor fields
International Nuclear Information System (INIS)
The coupling is investigated of classical and quantum antisymmetric tensor fields describing fermions with the gauge gravitational field. It is shown that within the framework of the classical Einstein-Cartan theory the new generalized nonlinear fermion theory can be formulated, which turns out to be the correct microscopic description of the Weyssenhoff spinning fluid. The one-loop gravitational counterterms and the conformal stress tensor and the axial vector current anomalies are obtained. The differences between the antisymmetric tensor fermions and the usual Dirac spinor fields are discussed. (author)
Łączkowski, Krzysztof Z.; Motylewska, Katarzyna; Baranowska-Łączkowska, Angelika; Biernasiuk, Anna; Misiura, Konrad; Malm, Anna; Fernández, Berta
2016-03-01
Synthesis and investigation of antimicrobial activities of novel thiazoles and selenazoles is presented. Their structures were determined using NMR, FAB(+)-MS, HRMS and elemental analyses. To support the experiment, theoretical calculations of the 1H NMR shifts were carried out for representative systems within the DFT B3LYP/6-311++G** approximation which additionally confirmed the structure of investigated compounds. Among the derivatives, compounds 4b, 4h, 4j and 4l had very strong activity against reference strains of Candida albicans ATCC and Candida parapsilosis ATCC 22019 with MIC = 0.49-7.81 μg/ml. In the case of compounds 4b, 4c, 4h - 4j and 4l, the activity was very strong against of Candida spp. isolated from clinical materials, i.e. C. albicans, Candida krusei, Candida inconspicua, Candida famata, Candida lusitaniae, Candida sake, C. parapsilosis and Candida dubliniensis with MIC = 0.24-15.62 μg/ml. The activity of several of these was similar to the activity of commonly used antifungal agent fluconazole. Additionally, compounds 4m - 4s were found to be active against Gram-positive bacteria, both pathogenic staphylococci Staphylococcus aureus ATCC with MIC = 31.25-125 μg/ml and opportunistic bacteria, such as Staphylococcus epidermidis ATCC 12228 and Micrococcus luteus ATCC 10240 with MIC = 7.81-31.25 μg/ml.
Tucker-tensor algorithm for large-scale Kohn-Sham density functional theory calculations
Motamarri, Phani; Gavini, Vikram; Blesgen, Thomas
2016-03-01
In this work, we propose a systematic way of computing a low-rank globally adapted localized Tucker-tensor basis for solving the Kohn-Sham density functional theory (DFT) problem. In every iteration of the self-consistent field procedure of the Kohn-Sham DFT problem, we construct an additive separable approximation of the Kohn-Sham Hamiltonian. The Tucker-tensor basis is chosen such as to span the tensor product of the one-dimensional eigenspaces corresponding to each of the spatially separable Hamiltonians, and the localized Tucker-tensor basis is constructed from localized representations of these one-dimensional eigenspaces. This Tucker-tensor basis forms a complete basis, and is naturally adapted to the Kohn-Sham Hamiltonian. Further, the locality of this basis in real-space allows us to exploit reduced-order scaling algorithms for the solution of the discrete Kohn-Sham eigenvalue problem. In particular, we use Chebyshev filtering to compute the eigenspace of the Kohn-Sham Hamiltonian, and evaluate nonorthogonal localized wave functions spanning the Chebyshev filtered space, all represented in the Tucker-tensor basis. We thereby compute the electron-density and other quantities of interest, using a Fermi-operator expansion of the Hamiltonian projected onto the subspace spanned by the nonorthogonal localized wave functions. Numerical results on benchmark examples involving pseudopotential calculations suggest an exponential convergence of the ground-state energy with the Tucker rank. Interestingly, the rank of the Tucker-tensor basis required to obtain chemical accuracy is found to be only weakly dependent on the system size, which results in close to linear-scaling complexity for Kohn-Sham DFT calculations for both insulating and metallic systems. A comparative study has revealed significant computational efficiencies afforded by the proposed Tucker-tensor approach in comparison to a plane-wave basis.
Diffusion Tensor Imaging of Pedophilia.
Cantor, James M; Lafaille, Sophie; Soh, Debra W; Moayedi, Massieh; Mikulis, David J; Girard, Todd A
2015-11-01
Pedophilia is a principal motivator of child molestation, incurring great emotional and financial burdens on victims and society. Even among pedophiles who never commit any offense,the condition requires lifelong suppression and control. Previous comparison using voxel-based morphometry (VBM)of MR images from a large sample of pedophiles and controls revealed group differences in white matter. The present study therefore sought to verify and characterize white matter involvement using diffusion tensor imaging (DTI), which better captures the microstructure of white matter than does VBM. Pedophilics ex offenders (n=24) were compared with healthy, age-matched controls with no criminal record and no indication of pedophilia (n=32). White matter microstructure was analyzed with Tract-Based Spatial Statistics, and the trajectories of implicated fiber bundles were identified by probabilistic tractography. Groups showed significant, highly focused differences in DTI parameters which related to participants’ genital responses to sexual depictions of children, but not to measures of psychopathy or to childhood histories of physical abuse, sexual abuse, or neglect. Some previously reported gray matter differences were suggested under highly liberal statistical conditions (p(uncorrected)<.005), but did not survive ordinary statistical correction (whole brain per voxel false discovery rate of 5%). These results confirm that pedophilia is characterized by neuroanatomical differences in white matter microstructure, over and above any neural characteristics attributable to psychopathy and childhood adversity, which show neuroanatomic footprints of their own. Although some gray matter structures were implicated previously, only few have emerged reliably. PMID:26494360
Adaptive Multilinear Tensor Product Wavelets.
Weiss, Kenneth; Lindstrom, Peter
2016-01-01
Many foundational visualization techniques including isosurfacing, direct volume rendering and texture mapping rely on piecewise multilinear interpolation over the cells of a mesh. However, there has not been much focus within the visualization community on techniques that efficiently generate and encode globally continuous functions defined by the union of multilinear cells. Wavelets provide a rich context for analyzing and processing complicated datasets. In this paper, we exploit adaptive regular refinement as a means of representing and evaluating functions described by a subset of their nonzero wavelet coefficients. We analyze the dependencies involved in the wavelet transform and describe how to generate and represent the coarsest adaptive mesh with nodal function values such that the inverse wavelet transform is exactly reproduced via simple interpolation (subdivision) over the mesh elements. This allows for an adaptive, sparse representation of the function with on-demand evaluation at any point in the domain. We focus on the popular wavelets formed by tensor products of linear B-splines, resulting in an adaptive, nonconforming but crack-free quadtree (2D) or octree (3D) mesh that allows reproducing globally continuous functions via multilinear interpolation over its cells. PMID:26529742
International Nuclear Information System (INIS)
The graphic technique of 'trees' developed in the previous paper is used for the construction of the q-analogue of the tensor operator algebra. The adjoint action of the suq(2) generator on tensor operators is discussed and adjoint R-matrix is introduced. A set of formulae for the calculation of the matrix elements of tensor operators and their combinations is derived. As an application, the recurrent relations for the suq(2) Clebsh-Gordan and Racah coefficients are obtained
Primordial tensor modes of the early Universe
Martínez, Florencia Benítez
2016-01-01
We study cosmological tensor perturbations on a quantized background within the hybrid quantization approach. In particular, we consider a flat, homogeneous and isotropic spacetime and small tensor inhomogeneities on it. We truncate the action to second order in the perturbations. The dynamics is ruled by a homogeneous scalar constraint. We carry out a canonical transformation in the system where the Hamiltonian for the tensor perturbations takes a canonical form. The new tensor modes now admit a standard Fock quantization with a unitary dynamics. We then combine this representation with a generic quantum scheme for the homogeneous sector. We adopt a Born-Oppenheimer ansatz for the solutions to the constraint operator, previously employed to study the dynamics of scalar inhomogeneities. We analyze the approximations that allow us to recover, on the one hand, a Schr\\"odinger equation similar to the one emerging in the dressed metric approach, and, on the other hand, the ones necessary for the effective evoluti...
Entangled Scalar and Tensor Fluctuations during Inflation
Collins, Hael
2016-01-01
We show how the choice of an inflationary state that entangles scalar and tensor fluctuations affects the angular two-point correlation functions of the $T$, $E$, and $B$ modes of the cosmic microwave background. The propagators for a state starting with some general quadratic entanglement are solved exactly, leading to predictions for the primordial scalar-scalar, tensor-tensor, and scalar-tensor power spectra. These power spectra are expressed in terms of general functions that describe the entangling structure of the initial state relative to the standard Bunch-Davies vacuum. We illustrate how such a state would modify the angular correlations in the CMB with a simple example where the initial state is a small perturbation away from the Bunch-Davies state. Because the state breaks some of the rotational symmetries, the angular power spectra no longer need be strictly diagonal.
Multipartite Entanglement in Stabilizer Tensor Networks
Nezami, Sepehr
2016-01-01
Tensor network models reproduce important structural features of holography, including the Ryu-Takayanagi formula for the entanglement entropy and quantum error correction in the entanglement wedge. In contrast, only little is known about their multipartite entanglement structure, which has been of considerable recent interest. In this work, we study random stabilizer tensor networks and show that here the tripartite entanglement question has a sharp answer: The average number of GHZ triples that can be extracted from a stabilizer tensor network is small, implying that the entanglement is predominantly bipartite. As a consequence, we obtain a new operational interpretation of the monogamy of the Ryu-Takayanagi mutual information and an entropic diagnostic for higher-partite entanglement. Our technical contributions include a spin model for evaluating the average GHZ content of stabilizer tensor networks and a novel formula for the third moment of random stabilizer states.
Damping of tensor modes in inflation
Ng, Kin-Wang
2011-01-01
We discuss the damping of tensor modes due to anisotropic stress in inflation. The effect is negligible in standard inflation and may be significantly large in inflation models that involve drastic production of free-streaming particles.
Seamless warping of diffusion tensor fields
DEFF Research Database (Denmark)
Xu, Dongrong; Hao, Xuejun; Bansal, Ravi;
2008-01-01
To warp diffusion tensor fields accurately, tensors must be reoriented in the space to which the tensors are warped based on both the local deformation field and the orientation of the underlying fibers in the original image. Existing algorithms for warping tensors typically use forward mapping...... deformations in an attempt to ensure that the local deformations in the warped image remains true to the orientation of the underlying fibers; forward mapping, however, can also create "seams" or gaps and consequently artifacts in the warped image by failing to define accurately the voxels in the template...... space where the magnitude of the deformation is large (e.g., |Jacobian| > 1). Backward mapping, in contrast, defines voxels in the template space by mapping them back to locations in the original imaging space. Backward mapping allows every voxel in the template space to be defined without the creation...
Symbolic Tensor Calculus -- Functional and Dynamic Approach
Woszczyna, A; Czaja, W; Golda, Z A
2016-01-01
In this paper, we briefly discuss the dynamic and functional approach to computer symbolic tensor analysis. The ccgrg package for Wolfram Language/Mathematica is used to illustrate this approach. Some examples of applications are attached.
Potentials for transverse trace-free tensors
International Nuclear Information System (INIS)
In constructing and understanding initial conditions in the 3 + 1 formalism for numerical relativity, the transverse and trace-free (TT) part of the extrinsic curvature plays a key role. We know that TT tensors possess two degrees of freedom per space point. However, finding an expression for a TT tensor depending on only two scalar functions is a non-trivial task. Assuming either axial or translational symmetry, expressions depending on two scalar potentials alone are derived here for all TT tensors in flat 3-space. In a more general spatial slice, only one of these potentials is found, the same potential given in (Baker and Puzio 1999 Phys. Rev. D 59 044030) and (Dain 2001 Phys. Rev. D 64 124002), with the remaining equations reduced to a partial differential equation, depending on boundary conditions for a solution. As an exercise, we also derive the potentials which give the Bowen-York curvature tensor in flat space. (paper)
Calculus of tensors and differential forms
Sinha, Rajnikant
2014-01-01
Calculus of tensors and differential forms is an introductory-level textbook. Through this book, students will familiarize themselves with tools they need in order to use for further study on general relativity and research, such as affine tensors, tensor calculus on manifolds, relative tensors, Lie derivatives, wedge products, differential forms, and Stokes' theorem. The treatment is concrete and in detail, so that abstract concepts do not deter even physics and engineering students. This self contained book requires undergraduate-level calculus of several variables and linear algebra as prerequisite. Fubini's theorem in real analysis, to be used in Stokes' theorem, has been proved earlier than Stokes' theorem so that students don't have to search elsewhere.
Analysis of the tensor-tensor type scalar tetraquark states with QCD sum rules
Wang, Zhi-Gang
2016-01-01
In this article, we study the ground states and the first radial excited states of the tensor-tensor type scalar hidden-charm tetraquark states with the QCD sum rules. We separate the ground state contributions from the first radial excited state contributions unambiguously, and obtain the QCD sum rules for the ground states and the first radial excited states, respectively. Then we search for the Borel parameters and continuum threshold parameters according to four criteria and obtain the masses of the tensor-tensor type scalar hidden-charm tetraquark states, which can be confronted to the experimental data in the future.
The Energy-Momentum Tensor(s) in Classical Gauge Theories
Blaschke, Daniel N; Gieres, Francois; Reboud, Meril; Schweda, Manfred
2016-01-01
We give an introduction to, and review of, the energy-momentum tensors in classical gauge field theories in Minkowski space, and to some extent also in curved space-time. For the canonical energy-momentum tensor of non-Abelian gauge fields and of matter fields coupled to such fields, we present a new and simple improvement procedure based on gauge invariance for constructing a gauge invariant, symmetric energy-momentum tensor. The relationship with the Einstein-Hilbert tensor following from t...
Renormalization procedure for random tensor networks and the canonical tensor model
International Nuclear Information System (INIS)
We discuss a renormalization procedure for random tensor networks, and show that the corresponding renormalization-group flow is given by the Hamiltonian vector flow of the canonical tensor model, which is a discretized model of quantum gravity. The result is a generalization of the previous one concerning the relation between the Ising model on random networks and the canonical tensor model with N=2. We also prove a general theorem that relates discontinuity of the renormalization-group flow and the phase transitions of random tensor networks
The Energy-Momentum Tensor(s) in Classical Gauge Theories
Blaschke, Daniel N; Reboud, Meril; Schweda, Manfred
2016-01-01
We give an introduction to, and review of, the energy-momentum tensors in classical gauge field theories in Minkowski space, and to some extent also in curved space-time. For the canonical energy-momentum tensor of non-Abelian gauge fields and of matter fields coupled to such fields, we present a new and simple improvement procedure based on gauge invariance for constructing a gauge invariant, symmetric energy-momentum tensor. The relationship with the Einstein-Hilbert tensor following from the coupling to a gravitational field is also discussed.
Novel Physics with Tensor Polarized Deuteron Targets
Energy Technology Data Exchange (ETDEWEB)
Slifer, Karl J. [UNH; Long, Elena A. [UNH
2013-09-01
Development of solid spin-1 polarized targets will open the study of tensor structure functions to precise measurement, and holds the promise to enable a new generation of polarized scattering experiments. In this talk we will discuss a measurement of the leading twist tensor structure function b1, along with prospects for future experiments with a solid tensor polarized target. The recently approved JLab experiment E12-13-011 will measure the lead- ing twist tensor structure function b1, which provides a unique tool to study partonic effects, while also being sensitive to coherent nuclear properties in the simplest nuclear system. At low x, shadowing effects are expected to dominate b1, while at larger values, b1 provides a clean probe of exotic QCD effects, such as hidden color due to 6-quark configuration. Since the deuteron wave function is relatively well known, any non-standard effects are expected to be readily observable. All available models predict a small or vanishing value of b1 at moderate x. However, the first pioneer measurement of b1 at HERMES revealed a crossover to an anomalously large negative value in the region 0.2 < x < 0.5, albeit with relatively large experimental uncertainty. E12-13-011 will perform an inclusive measurement of the deuteron tensor asymmetry in the region 0.16 < x < 0.49, for 0.8 < Q2 < 5.0 GeV2. The UVa solid polarized ND3 target will be used, along with the Hall C spectrometers, and an unpolarized 115 nA beam. This measurement will provide access to the tensor quark polarization, and allow a test of the Close-Kumano sum rule, which vanishes in the absence of tensor polarization in the quark sea. Until now, tensor structure has been largely unexplored, so the study of these quantities holds the potential of initiating a new field of spin physics at Jefferson Lab.
Lagrangian Evolution of the Weyl Tensor
Bertschinger, Edmund; Hamilton, A. J. S.
1994-01-01
We derive the evolution equations for the electric and magnetic parts of the Weyl tensor for cold dust from both general relativity and Newtonian gravity. In a locally inertial frame at rest in the fluid frame, the Newtonian equations agree with those of general relativity. We give explicit expressions for the electric and magnetic parts of the Weyl tensor in the Newtonian limit. In general, the magnetic part does not vanish, implying that the Lagrangian evolution of the fluid is not purely l...
Newtonian Evolution of the Weyl Tensor
Ellis, G. F. R.; Dunsby, P. K. S.
1994-01-01
In an interesting recent paper on the growth of inhomogeneity through the effect of gravity [1], Bertschinger and Hamilton derive equations for the electric and magnetic parts of the Weyl tensor for cold dust for both General Relativity and Newtonian theory. Their conclusion is that both in General Relativity and in Newtonian theory, in general the magnetic part of the Weyl tensor does not vanish, implying that the Lagrangian evolution of the fluid is not local. We show here that the `Newtoni...
Lagrangian evolution of the Weyl tensor
Bertschinger, E; Bertschinger, Edmund
1994-01-01
We derive the evolution equations for the electric and magnetic parts of the Weyl tensor for cold dust from both general relativity and Newtonian gravity. In a locally inertial frame at rest in the fluid frame, the Newtonian equations agree with those of general relativity. We give explicit expressions for the electric and magnetic parts of the Weyl tensor in the Newtonian limit. In general, the magnetic part does not vanish, implying that the Lagrangian evolution of the fluid is not purely local.
Higher-Order Tensors in Diffusion Imaging
Schultz, Thomas; Fuster, Andrea; Ghosh, Aurobrata; Deriche, Rachid; Florack, Luc; Lek-Heng, Lim
2013-01-01
International audience Diffusion imaging is a noninvasive tool for probing the microstructure of fibrous nerve and muscle tissue. Higher-order tensors provide a powerful mathematical language to model and analyze the large and complex data that is generated by its modern variants such as High Angular Resolution Diffusion Imaging (HARDI) or Diffusional Kurtosis Imaging. This survey gives a careful introduction to the foundations of higher-order tensor algebra, and explains how some concepts...
Superconformal tensor calculus in five dimensions
International Nuclear Information System (INIS)
We present a full superconformal tensor calculus in five spacetime dimensions in which the Weyl multiplet has 32 Bose plus 32 Fermi degrees of freedom. It is derived using dimensional reduction from the 6D superconformal tensor calculus. We present two types of 32+32 Weyl multiplets, a vector multiplet, linear multiplet, hypermultiplet and nonlinear multiplet. Their superconformal transformation laws and the embedding and invariant action formulas are given. (author)
Superconformal Tensor Calculus in Five Dimensions
Fujita, Tomoyuki; Ohashi, Keisuke
2001-01-01
We present a full superconformal tensor calculus in five spacetime dimensions in which the Weyl multiplet has 32 Bose plus 32 Fermi degrees of freedom. It is derived by the dimensional reduction from the 6D superconformal tensor calculus. We present two types of 32+32 Weyl multiplets, vector multiplet, linear multiplet, hypermultiplet and nonlinear multiplet. Their superconformal transformation laws and the embedding and invariant action formulas are given.
Involutions on tensor products of quaternion algebras
Barry, Demba
2015-01-01
We study possible decompositions of totally decomposable algebras with involution, that is, tensor products of quaternion algebras with involution. In particular, we are interested in decompositions in which one or several factors are the split quaternion algebra $M_2(F)$, endowed with an orthogonal involution. Using the theory of gauges, developed by Tignol-Wadsworth, we construct examples of algebras isomorphic to a tensor product of quaternion algebras with $k$ split factors, endowed with ...
Electronic stress tensor analysis of molecules in gas phase of CVD process for GeSbTe alloy
Nozaki, Hiroo; Ichikawa, Kazuhide; Tachibana, Akitomo
2015-01-01
We analyze the electronic structure of molecules which may exist in gas phase of chemical vapor deposition process for GeSbTe alloy using the electronic stress tensor, with special focus on the chemical bonds between Ge, Sb and Te atoms. We find that, from the viewpoint of the electronic stress tensor, they have intermediate properties between alkali metals and hydrocarbon molecules. We also study the correlation between the bond order which is defined based on the electronic stress tensor, and energy-related quantities. We find that the correlation with the bond dissociation energy is not so strong while one with the force constant is very strong. We interpret these results in terms of the energy density on the "Lagrange surface", which is considered to define the boundary surface of atoms in a molecule in the framework of the electronic stress tensor analysis.
The Cotton tensor in Riemannian spacetimes
Energy Technology Data Exchange (ETDEWEB)
GarcIa, Alberto A [Departamento de FIsica, CINVESTAV-IPN, Apartado Postal 14-740, CP 07000, Mexico, DF (Mexico); Hehl, Friedrich W [Institute for Theoretical Physics, University of Cologne, D-50923 Cologne (Germany); Heinicke, Christian [Institute for Theoretical Physics, University of Cologne, D-50923 Cologne (Germany); MacIas, Alfredo [Departamento de FIsica, Universidad Autonoma Metropolitana-Iztapalapa, Apartado Postal 55-534, CP 09340, Mexico, DF (Mexico)
2004-02-21
Recently, the study of three-dimensional spaces is becoming of great interest. In these dimensions the Cotton tensor is prominent as the substitute for the Weyl tensor. It is conformally invariant and its vanishing is equivalent to conformal flatness. However, the Cotton tensor arises in the context of the Bianchi identities and is present in any dimension n. We present a systematic derivation of the Cotton tensor. We perform its irreducible decomposition and determine its number of independent components as n(n{sup 2} - 4)/3 for the first time. Subsequently, we show its characteristic properties and perform a classification of the Cotton tensor in three dimensions. We investigate some solutions of Einstein's field equations in three dimensions and of the topologically massive gravity model of Deser, Jackiw and Templeton. For each class examples are given. Finally, we investigate the relation between the Cotton tensor and the energy-momentum in Einstein's theory and derive a conformally flat perfect fluid solution of Einstein's field equations in three dimensions.
TWIN SUPPORT TENSOR MACHINES FOR MCS DETECTION
Institute of Scientific and Technical Information of China (English)
Zhang Xinsheng; Gao Xinbo; Wang Ying
2009-01-01
Tensor representation is useful to reduce the overfitting problem in vector-based learning algorithm in pattern recognition.This is mainly because the structure information of objects in pattern analysis is a reasonable constraint to reduce the number of unknown parameters used to model a classifier.In this paper,we generalize the vector-based learning algorithm TWin Support Vector Machine (TWSVM)to the tensor-based method TWin Support Tensor Machines(TWSTM),which accepts general tensors as input.To examine the effectiveness of TWSTM,we implement the TWSTM method for Microcalcification Clusters (MCs) detection.In the tensor subspace domain,the MCs detection procedure is formulated as a supervised learning and classification problem.and TWSTM is used as a classifier to make decision for the presence of MCs or not.A large number of experiments were carried out to evaluate and compare the performance of the proposed MCs detection algorithm.By comparison with TWSVM,the tensor version reduces the overfitting problem.
Visualization of tensor fields using superquadric glyphs.
Ennis, Daniel B; Kindlman, Gordon; Rodriguez, Ignacio; Helm, Patrick A; McVeigh, Elliot R
2005-01-01
The spatially varying tensor fields that arise in magnetic resonance imaging are difficult to visualize due to the multivariate nature of the data. To improve the understanding of myocardial structure and function a family of objects called glyphs, derived from superquadric parametric functions, are used to create informative and intuitive visualizations of the tensor fields. The superquadric glyphs are used to visualize both diffusion and strain tensors obtained in canine myocardium. The eigensystem of each tensor defines the glyph shape and orientation. Superquadric functions provide a continuum of shapes across four distinct eigensystems (lambda(i), sorted eigenvalues), lambda(1) = lambda(2) = lambda(3) (spherical), lambda(1) lambda(2) = lambda(3) (prolate), and lambda(1) > lambda(2) > lambda(3) (cuboid). The superquadric glyphs are especially useful for identifying regions of anisotropic structure and function. Diffusion tensor renderings exhibit fiber angle trends and orthotropy (three distinct eigenvalues). Visualization of strain tensors with superquadric glyphs compactly exhibits radial thickening gradients, circumferential and longitudinal shortening, and torsion combined. The orthotropic nature of many biologic tissues and their DTMRI and strain data require visualization strategies that clearly exhibit the anisotropy of the data if it is to be interpreted properly. Superquadric glyphs improve the ability to distinguish fiber orientation and tissue orthotropy compared to ellipsoids. PMID:15690516
C%2B%2B tensor toolbox user manual.
Energy Technology Data Exchange (ETDEWEB)
Plantenga, Todd D.; Kolda, Tamara Gibson
2012-04-01
The C++ Tensor Toolbox is a software package for computing tensor decompositions. It is based on the Matlab Tensor Toolbox, and is particularly optimized for sparse data sets. This user manual briefly overviews tensor decomposition mathematics, software capabilities, and installation of the package. Tensors (also known as multidimensional arrays or N-way arrays) are used in a variety of applications ranging from chemometrics to network analysis. The Tensor Toolbox provides classes for manipulating dense, sparse, and structured tensors in C++. The Toolbox compiles into libraries and is intended for use with custom applications written by users.
(Ln-bar, g)-spaces. Special tensor fields
International Nuclear Information System (INIS)
The Kronecker tensor field, the contraction tensor field, as well as the multi-Kronecker and multi-contraction tensor fields are determined and the action of the covariant differential operator, the Lie differential operator, the curvature operator, and the deviation operator on these tensor fields is established. The commutation relations between the operators Sym and Asym and the covariant and Lie differential operators are considered acting on symmetric and antisymmetric tensor fields over (Ln bar, g)-spaces
International Nuclear Information System (INIS)
The 1H, 13C, and 15N NMR spectra of 15N-enriched 5-substituted furfural oximes were investigated. It was shown that the chemical shifts of the ring atoms and the oxime group correlate satisfactorily with the F and R substituent constants, whereas their sensitivity to the effect of the substituents is lower than in monosubstituted furan derivatives. The constants of spin-spin coupling between the ring protons and the oxime group were determined. An analysis of the 1H-1H spin-spin coupling constants (SSCC) on the basis of their stereospecificity indicates that the E isomers have primarily an s-trans conformation in polar dimethyl sulfoxide, whereas the Z isomers, on the other hand, have an s-cis conformation. The signs of the direct and geminal 13C-15N SSCC were determined for 5-trimethylsilylfurfural oxime
Energy Technology Data Exchange (ETDEWEB)
Santos, Allana Kellen L.; Magalhaes, Ticiane S.; Monte, Francisco Jose Q.; Mattos, Marcos Carlos de; Oliveira, Maria Conceicao F. de; Almeida, Maria Mozarina B.; Lemos, Telma L.G.; Braz-Filho, Raimundo [Universidade Federal do Ceara (UFC), Fortaleza, CE (Brazil). Dept. de Quimica Organica e Inorganica], e-mail: tlemos@dqoi.ufc.br
2009-07-01
Six known alkaloids iboga type and the triterpene {alpha}- and {beta}-amyrin acetate were isolated from the roots and stems of Peschiera affinis. Their structures were characterized on the basis of spectral data mainly NMR and mass spectra. 1D and 2D NMR spectra were also used to unequivocal {sup 1}H and {sup 13}C chemical shift assignments of alkaloids. The ethanolic extract of roots, alkaloidic and no-alkaloidic fractions and iso-voacristine hydroxyindolenine and voacangine were evaluated for their antioxidative properties using an autographic assay based on {beta}-carotene bleaching on TLC plates, and also spectrophotometric detection by reduction of the stable DPPH (2,2-diphenyl-1-picrylhydrazyl) free radical. (author)
Thermal field theories and shifted boundary conditions
Giusti, Leonardo
2013-01-01
The analytic continuation to an imaginary velocity of the canonical partition function of a thermal system expressed in a moving frame has a natural implementation in the Euclidean path-integral formulation in terms of shifted boundary conditions. The Poincare' invariance underlying a relativistic theory implies a dependence of the free-energy on the compact length L_0 and the shift xi only through the combination beta=L_0(1+xi^2)^(1/2). This in turn implies that the energy and the momentum distributions of the thermal theory are related, a fact which is encoded in a set of Ward identities among the correlators of the energy-momentum tensor. The latter have interesting applications in lattice field theory: they offer novel ways to compute thermodynamic potentials, and a set of identities to renormalize non-perturbatively the energy-momentum tensor. At fixed bare parameters the shifted boundary conditions also provide a simple method to vary the temperature in much smaller steps than with the standard procedur...
International Nuclear Information System (INIS)
Highlights: • Electronic structure of non-conducting glass studied by hard X-ray photoelectron spectroscopy. • A thin film of Cr was deposited on the vitreous SiO2 glass to overcome the sample charging. • Excellent O 1s and Si 1s linewidths were obtained, matching those reported using the laboratory based Kratos Axis Ultra spectrometer equipped with a magnetic compensation system. • The bulk and interface states of non-conducting samples are studied as a function of photon energy. - Abstract: Hard X-ray photoelectron spectra (2200 eV to 5000 eV photon energies) have been obtained for the first time on a bulk non-conductor, vitreous SiO2, on a high resolution (E/ΔE of 10,000) synchrotron beamline at the Canadian Light Source (CLS). To minimize charging and differential charging, the SiO2 was coated with very thin layers (0.5 to 1.5 nm) of Cr metal. The O 1s linewidth obtained at 2500 eV photon energy was 1.26 eV—the minimum linewidth for SiO2—and in good agreement with that obtained at 1486 eV on a Kratos Axis Ultra spectrometer equipped with a magnetic charge compensation system. The Si 1s linewidth of 1.5 eV, somewhat broader than that previously obtained at 1486 eV on the Si 2p3/2 line of 1.16 eV, is mainly due to the much larger inherent Si 1s linewidth (0.5 eV) compared to the inherent Si 2p linewidth (<0.1 eV). Both linewidths are dominated by the large final state vibrational broadening previously described. The Cr coating produces surface monolayers of interfacial Cr “suboxide” (Cr-subox), Cr metal, and a surface Cr oxide (Cr-surfox). Cr-subox (Si−O−Cr) gives rise to the weak near-surface Si 1s peak, while both oxides give rise to both the weak surface O 1s peak and the Cr 2p oxide peak. Both the O 1s and Si 1s surface peaks are shifted by ∼2 eV relative to the large bulk Si 1s and O 1s peaks. The weak Si 1s and O 1s surface peaks along with the Cr 2p oxide peak decrease in intensity greatly as the photon energy increases, due to an
Knöös, Patrik; Topgaard, Daniel; Wahlgren, Marie; Ulvenlund, Stefan; Piculell, Lennart
2013-11-12
A new technique has been developed using NMR chemical shift imaging (CSI) to monitor water penetration and molecular transport in initially dry polymer tablets that also contain small low-molecular weight compounds to be released from the tablets. Concentration profiles of components contained in the swelling tablets could be extracted via the intensities and chemical shift changes of peaks corresponding to protons of the components. The studied tablets contained hydrophobically modified poly(acrylic acid) (HMPAA) as the polymer component and griseofulvin and ethanol as hydrophobic and hydrophilic, respectively, low-molecular weight model compounds. The water solubility of HMPAA could be altered by titration with NaOH. In the pure acid form, HMPAA tablets only underwent a finite swelling until the maximum water content of the polymer-rich phase, as confirmed by independent phase studies, had been reached. By contrast, after partial neutralization with NaOH, the polyacid became fully miscible with water. The solubility of the polymer affected the water penetration, the polymer release, and the releases of both ethanol and griseofulvin. The detailed NMR CSI concentration profiles obtained highlighted the clear differences in the disintegration/dissolution/release behavior for the two types of tablet and provided insights into their molecular origin. The study illustrates the potential of the NMR CSI technique to give information of importance for the development of pharmaceutical tablets and, more broadly, for the general understanding of any operation that involves the immersion and ultimate disintegration of a dry polymer matrix in a solvent. PMID:24106807
The Weyl curvature tensor, the Cotton-York tensor and gravitational waves
Osano, Bob
2013-01-01
We re-examine the link between the Weyl tensor and gravitational waves, and between the Cotton- York tensor and gravitational waves. Our study is carried out in the language of the congruence approach pioneered by Hawking and Ellis. We find that there is a lack of clarity concerning the conditions that guarantee the existences of cosmological gravitational waves.
The dark matter dispersion tensor in perturbation theory
Aviles, Alejandro
2015-01-01
We compute the dark matter velocity dispersion tensor up to third order in perturbation theory using the Lagrangian formalism, revealing growing solutions at the third and higher orders. Our results are general and can be used for any other perturbative formalism. As an application, corrections to the matter power spectrum are calculated, we find that some of them have the same structure as those in the effective field theory of large-scale structure, with "EFT-like" coefficients that grows quadratically with the linear growth function and are further suppressed by powers of the logarithmic linear growth factor $f$; other corrections present additional $k$ dependences. Due to the velocity dispersions, there exist a free-streaming scale that suppresses the whole 1-loop power spectrum. Furthermore, we find that as a consequence of the nonlinear evolution, the free-streaming length is shifted towards larger scales, wiping out more structure than the expected in linear theory. Therefore, we argue that the formali...
Primordial tensor modes of the early Universe
Martínez, Florencia Benítez; Olmedo, Javier
2016-06-01
We study cosmological tensor perturbations on a quantized background within the hybrid quantization approach. In particular, we consider a flat, homogeneous and isotropic spacetime and small tensor inhomogeneities on it. We truncate the action to second order in the perturbations. The dynamics is ruled by a homogeneous scalar constraint. We carry out a canonical transformation in the system where the Hamiltonian for the tensor perturbations takes a canonical form. The new tensor modes now admit a standard Fock quantization with a unitary dynamics. We then combine this representation with a generic quantum scheme for the homogeneous sector. We adopt a Born-Oppenheimer ansatz for the solutions to the constraint operator, previously employed to study the dynamics of scalar inhomogeneities. We analyze the approximations that allow us to recover, on the one hand, a Schrödinger equation similar to the one emerging in the dressed metric approach and, on the other hand, the ones necessary for the effective evolution equations of these primordial tensor modes within the hybrid approach to be valid. Finally, we consider loop quantum cosmology as an example where these quantization techniques can be applied and compare with other approaches.
Particle creation from the quantum stress tensor
Firouzjaee, Javad T
2015-01-01
Among the different methods to derive particle creation, finding the quantum stress tensor expectation value gives a covariant quantity which can be used for examining the back-reaction issue. However this tensor also includes vacuum polarization in a way that depends on the vacuum chosen. Here we review different aspects of particle creation by looking at energy conservation and at the quantum stress tensor. It will be shown that in the case of general spherically symmetric black holes that have a \\emph{dynamical horizon}, as occurs in a cosmological context, one cannot have pair creation on the horizon because this violates energy conservation. This confirms the results obtained in other ways in a previous paper [25]. Looking at the expectation value of the quantum stress tensor with three different definitions of the vacuum state, we study the nature of particle creation and vacuum polarization in black hole and cosmological models, and the associated stress energy tensors. We show that the thermal tempera...
Estimates of the Nucleon Tensor Charge
Gamberg, L P; Gamberg, Leonard; Goldstein, Gary R.
2001-01-01
Like the axial vector charges, defined from the forward nucleon matrix element of the axial vector current on the light cone, the nucleon tensor charge, defined from the corresponding matrix element of the tensor current, is essential for characterizing the momentum and spin structure of the nucleon. Because there must be a helicity flip of the struck quark in order to probe the transverse spin polarization of the nucleon, the transversity distribution (and thus the tensor charge) decouples at leading twist in deep inelastic scattering, although no such suppression appears in Drell-Yan processes. This makes the tensor charge difficult to measure and its non-conservation makes its prediction model dependent. We present a different approach. Exploiting an approximate SU(6)xO(3) symmetric mass degeneracy of the light axial vector mesons (a1(1260), b1(1235) and h1(1170)) and using pole dominance, we calculate the tensor charge. The result is simple in form and depends on the decay constants of the axial vector me...
Off-shell N = 2 tensor supermultiplets
International Nuclear Information System (INIS)
A multiplet calculus is presented for an arbitrary number n of N = 2 tensor supermultiplets. For rigid supersymmetry the known couplings are reproduced. In the superconformal case the target spaces parametrized by the scalar fields are cones over (3n-1)-dimensional spaces encoded in homogeneous SU(2) invariant potentials, subject to certain constraints. The coupling to conformal supergravity enables the derivation of a large class of supergravity Lagrangians with vector and tensor multiplets and hypermultiplets. Dualizing the tensor fields into scalars leads to hypermultiplets with hyperkaehler or quaternion-Kaehler target spaces with at least n abelian isometries. It is demonstrated how to use the calculus for the construction of Lagrangians containing higher-derivative couplings of tensor multiplets. For the application of the c-map between vector and tensor supermultiplets to Lagrangians with higher-order derivatives, an off-shell version of this map is proposed. Various other implications of the results are discussed. As an example an elegant derivation of the classification of 4-dimensional quaternion-Kaehler manifolds with two commuting isometries is given
Ghavami, Raouf; Sadeghi, Faridoon; Rasouli, Zolikha; Djannati, Farhad
2012-12-01
Experimental values for the 13C NMR chemical shifts (ppm, TMS = 0) at 300 K ranging from 96.28 ppm (C4' of indole derivative 17) to 159.93 ppm (C4' of indole derivative 23) relative to deuteride chloroform (CDCl3, 77.0 ppm) or dimethylsulfoxide (DMSO, 39.50 ppm) as internal reference in CDCl3 or DMSO-d6 solutions have been collected from literature for thirty 2-functionalized 5-(methylsulfonyl)-1-phenyl-1H-indole derivatives containing different substituted groups. An effective quantitative structure-property relationship (QSPR) models were built using hybrid method combining genetic algorithm (GA) based on stepwise selection multiple linear regression (SWS-MLR) as feature-selection tools and correlation models between each carbon atom of indole derivative and calculated descriptors. Each compound was depicted by molecular structural descriptors that encode constitutional, topological, geometrical, electrostatic, and quantum chemical features. The accuracy of all developed models were confirmed using different types of internal and external procedures and various statistical tests. Furthermore, the domain of applicability for each model which indicates the area of reliable predictions was defined.
Identifying isotropic events using a regional moment tensor inversion
Energy Technology Data Exchange (ETDEWEB)
Ford, S R; Dreger, D S; Walter, W R
2008-07-16
The deviatoric and isotropic source components for 17 explosions at the Nevada Test Site, as well as 12 earthquakes and 3 collapses in the surrounding region of the western US, are calculated using a regional time-domain full waveform inversion for the complete moment tensor. The events separate into specific populations according to their deviation from a pure double-couple and ratio of isotropic to deviatoric energy. The separation allows for anomalous event identification and discrimination between explosions, earthquakes, and collapses. Confidence regions of the model parameters are estimated from the data misfit by assuming normally distributed parameter values. We investigate the sensitivity of the resolved parameters of an explosion to imperfect Earth models, inaccurate event depths, and data with a low signal-to-noise ratio (SNR) assuming a reasonable azimuthal distribution of stations. In the band of interest (0.02-0.10 Hz) the source-type calculated from complete moment tensor inversion is insensitive to velocity models perturbations that cause less than a half-cycle shift (<5 sec) in arrival time error if shifting of the waveforms is allowed. The explosion source-type is insensitive to an incorrect depth assumption (for a true depth of 1 km), but the goodness-of-fit of the inversion result cannot be used to resolve the true depth of the explosion. Noise degrades the explosive character of the result, and a good fit and accurate result are obtained when the signal-to-noise ratio (SNR) is greater than 5. We assess the depth and frequency dependence upon the resolved explosive moment. As the depth decreases from 1 km to 200 m, the isotropic moment is no longer accurately resolved and is in error between 50-200%. However, even at the most shallow depth the resultant moment tensor is dominated by the explosive component when the data has a good SNR. The sensitivity investigation is extended via the introduction of the network sensitivity solution, which takes
Newtonian evolution of the Weyl tensor
Ellis, G F R; Ellis, G F R; Dunsby, P K S
1994-01-01
In an interesting recent paper on the growth of inhomogeneity through the effect of gravity [1], Bertschinger and Hamilton derive equations for the electric and magnetic parts of the Weyl tensor for cold dust for both General Relativity and Newtonian theory. Their conclusion is that both in General Relativity and in Newtonian theory, in general the magnetic part of the Weyl tensor does not vanish, implying that the Lagrangian evolution of the fluid is not local. We show here that the `Newtonian' theory discussed by them is in fact not Newtonian theory {\\it per se}, but rather a plausible relativistic generalisation of Newtonian theory. Newtonian cosmology itself is highly non-local irrespective of the behaviour of the magnetic part of the Weyl tensor; in this respect the Bertschinger-Hamilton generalisation is a better theory.
Carrozza, Sylvain
2015-01-01
We define in this paper a class of three indices tensor models, endowed with $O(N)^{\\otimes 3}$ invariance ($N$ being the size of the tensor). This allows to generate, via the usual QFT perturbative expansion, a class of Feynman tensor graphs which is strictly larger than the class of Feynman graphs of both the multi-orientable model (and hence of the colored model) and the $U(N)$ invariant models. We first exhibit the existence of a large $N$ expansion for such a model with general interactions. We then focus on the quartic model and we identify the leading and next-to-leading order (NLO) graphs of the large $N$ expansion. Finally, we prove the existence of a critical regime and we compute the critical exponents, both at leading order and at NLO. This is achieved through the use of various analytic combinatorics techniques.
Holographic duality from random tensor networks
Hayden, Patrick; Qi, Xiao-Liang; Thomas, Nathaniel; Walter, Michael; Yang, Zhao
2016-01-01
Tensor networks provide a natural framework for exploring holographic duality because they obey entanglement area laws. They have been used to construct explicit simple models realizing many of the interesting structural features of the AdS/CFT correspondence, including the non-uniqueness of bulk operator reconstruction in the boundary theory. In this article, we explore the holographic properties of networks of random tensors. We find that our models obey the Ryu-Takayanagi entropy formula for all boundary regions, whether connected or not, a fact closely related to known properties of the multipartite entanglement of assistance. Moreover, we find that all boundary regions faithfully encode the physics of their entire bulk entanglement wedges, not just their smaller causal wedges. Our method is to interpret the average over random tensors as the partition function of a classical ferromagnetic Ising model, so that the minimal surfaces of Ryu-Takayanagi appear as domain walls. Upon including the analog of a bu...
Friction tensor concept for textured surfaces
Indian Academy of Sciences (India)
K R Y Simha; Anirudhan Pottirayil; Pradeep L Menezes; Satish V Kailas
2008-06-01
Directionality of grinding marks inﬂuences the coefﬁcient of friction during sliding. Depending on the sliding direction the coefﬁcient of friction varies between maximum and minimum for textured surfaces. For random surfaces without any texture the friction coefﬁcient becomes independent of the sliding direction. This paper proposes the concept of a friction tensor analogous to the heat conduction tensor in anisotropic media. This implies that there exists two principal friction coefﬁcients $\\mu_{1,2}$ analogous to the principal conductivities $k_{1,2}$. For symmetrically textured surfaces the principal directions are orthogonal with atleast one plane of symmetry. However, in the case of polished single crystalline solids in relative sliding motion, crystallographic texture controls the friction tensor.
Permittivity and permeability tensors for cloaking applications
Choudhury, Balamati; Jha, Rakesh Mohan
2016-01-01
This book is focused on derivations of analytical expressions for stealth and cloaking applications. An optimal version of electromagnetic (EM) stealth is the design of invisibility cloak of arbitrary shapes in which the EM waves can be controlled within the cloaking shell by introducing a prescribed spatial variation in the constitutive parameters. The promising challenge in design of invisibility cloaks lies in the determination of permittivity and permeability tensors for all the layers. This book provides the detailed derivation of analytical expressions of the permittivity and permeability tensors for various quadric surfaces within the eleven Eisenhart co-ordinate systems. These include the cylinders and the surfaces of revolutions. The analytical modeling and spatial metric for each of these surfaces are provided along with their tensors. This mathematical formulation will help the EM designers to analyze and design of various quadratics and their hybrids, which can eventually lead to design of cloakin...
Tensor calculus for engineers and physicists
de Souza Sánchez Filho, Emil
2016-01-01
This textbook provides a rigorous approach to tensor manifolds in several aspects relevant for Engineers and Physicists working in industry or academia. With a thorough, comprehensive, and unified presentation, this book offers insights into several topics of tensor analysis, which covers all aspects of N dimensional spaces. The main purpose of this book is to give a self-contained yet simple, correct and comprehensive mathematical explanation of tensor calculus for undergraduate and graduate students and for professionals. In addition to many worked problems, this book features a selection of examples, solved step by step. Although no emphasis is placed on special and particular problems of Engineering or Physics, the text covers the fundamentals of these fields of science. The book makes a brief introduction into the basic concept of the tensorial formalism so as to allow the reader to make a quick and easy review of the essential topics that enable having the grounds for the subsequent themes, without need...
General Expression of Elastic Tensor for Anisotropic Materials
Institute of Scientific and Technical Information of China (English)
HUANG Bo
2005-01-01
In order to formulate a general expression of elastic tensor for anisotropic materials, a method of tensor derivative is used for determining relationship between fourth-order elastic tensor and second-order structure tensor that has satisfied material symmetrical conditions. From this general expression of elastic tensor, specific expressions of elastic tensor for different anisotropic materials, such as isotropic materials, transverse isotropic materials and orthogonal-anisotropic materials, can be deduced. This expression underlies the scalar description of anisotropic factors, which are used for classifying and analyzing anisotropic materials. Cubic crystals are analyzed macroscopically by means of the general expression and anisotropic factor.
(Ln-bar, g)-spaces. Ordinary and tensor differentials
International Nuclear Information System (INIS)
Different types of differentials as special cases of differential operators acting on tensor fields over (Ln bar, g)-spaces are considered. The ordinary differential, the covariant differential as a special case of the covariant differential operator, and the Lie differential as a special case of the Lie differential operator are investigated. The tensor differential and its special types (Covariant tensor differential, and Lie tensor differential) are determined and their properties are discussed. Covariant symmetric and antisymmetric (external) tensor differentials, Lie symmetric, and Lie antisymmetric (external) tensor differentials are determined and considered over (Ln bar, g)-spaces
Tensor representation techniques in post-Hartree-Fock methods: matrix product state tensor format
Benedikt, Udo; Auer, Henry; Espig, Mike; Hackbusch, Wolfgang; Auer, Alexander A.
2013-09-01
In this proof-of-principle study, we discuss the application of various tensor representation formats and their implications on memory requirements and computational effort for tensor manipulations as they occur in typical post-Hartree-Fock (post-HF) methods. A successive tensor decomposition/rank reduction scheme in the matrix product state (MPS) format for the two-electron integrals in the AO and MO bases and an estimate of the t 2 amplitudes as obtained from second-order many-body perturbation theory (MP2) are described. Furthermore, the AO-MO integral transformation, the calculation of the MP2 energy and the potential usage of tensors in low-rank MPS representation for the tensor contractions in coupled cluster theory are discussed in detail. We are able to show that the overall scaling of the memory requirements is reduced from the conventional N 4 scaling to approximately N 3 and the scaling of computational effort for tensor contractions in post-HF methods can be reduced to roughly N 4 while the decomposition itself scales as N 5. While efficient algorithms with low prefactor for the tensor decomposition have yet to be devised, this ansatz offers the possibility to find a robust approximation with low-scaling behaviour with system and basis-set size for post-HF ab initio methods.
Reconstruction of convex bodies from surface tensors
DEFF Research Database (Denmark)
Kousholt, Astrid; Kiderlen, Markus
We present two algorithms for reconstruction of the shape of convex bodies in the two-dimensional Euclidean space. The first reconstruction algorithm requires knowledge of the exact surface tensors of a convex body up to rank s for some natural number s. The second algorithm uses harmonic intrinsic...... volumes which are certain values of the surface tensors and allows for noisy measurements. From a generalized version of Wirtinger's inequality, we derive stability results that are utilized to ensure consistency of both reconstruction procedures. Consistency of the reconstruction procedure based on...
Tensor Completion Through Multiple Kronecker Product Decomposition
Czech Academy of Sciences Publication Activity Database
Phan, A. H.; Cichocki, A.; Tichavský, Petr; Luta, G.; Brockmeier, A.
Vancouver: IEEE, 2013, s. 3233-3237. ISBN 978-1-4799-0355-9. [IEEE International Conference on Acoustics, Speech, and Signal Processing ICASSP 2013. Vancouver (CA), 27.05.2013-31.05.2013] R&D Projects: GA ČR GA102/09/1278 Institutional support: RVO:67985556 Keywords : tensor factorization * Kronecker product * image completion Subject RIV: BB - Applied Statistics, Operational Research http://library.utia.cas.cz/separaty/2013/SI/tichavsky-tensor completion through multiple kronecker product decomposition.pdf
Introduction to tensor calculus, relativity and cosmology
Lawden, Derek F
2002-01-01
This elementary introduction pays special attention to aspects of tensor calculus and relativity that students tend to find most difficult. Its use of relatively unsophisticated mathematics in the early chapters allows readers to develop their confidence within the framework of Cartesian coordinates before undertaking the theory of tensors in curved spaces and its application to general relativity theory. Additional topics include black holes, gravitational waves, and a sound background in applying the principles of general relativity to cosmology. Numerous exercises advance the theoretical developments of the main text, thus enhancing this volume's appeal to students of applied mathematics and physics at both undergraduate and postgraduate levels.
Conjugation properties of tensor product multiplicities
Coquereaux, Robert
2014-01-01
It was recently proven that the total multiplicity in the decomposition into irreducibles of the tensor product lambda x mu of two irreducible representations of a simple Lie algebra is invariant under conjugation of one of them; at a given level, this also applies to the fusion multiplicities of affine algebras. Here, we show that, in the case of SU(3), the lists of multiplicities, in the tensor products lambda x mu and lambda x bar{mu}, are identical up to permutations. This latter property does not hold in general for other Lie algebras.
On the calculation of Mossbauer isomer shift
Filatov, Michael
2007-01-01
A quantum chemical computational scheme for the calculation of isomer shift in Mossbauer spectroscopy is suggested. Within the described scheme, the isomer shift is treated as a derivative of the total electronic energy with respect to the radius of a finite nucleus. The explicit use of a finite nuc
Institute of Scientific and Technical Information of China (English)
TIAN Dongyan; JIN Ming; DUI Guansuo
2006-01-01
A new approach for the derivation of the principal invariants of the stretch tensor with respect to the right Cauchy Green tensor is presented in this paper. According to the definition of the derivation of tensor function, the three first-order derivatives for the principal invariants of the stretch tensor are obtained through derivation directly to the right Cauchy-Green tensor by incremental method. Then the three second-order derivatives are yielded by the derivation to the right Cauchy-Green strain tensor directly. Furthermore, an explicit expression of the tangent modulus of the general Varga material is given as an example.
The turbulence velocity gradient tensor formed additively by normal and non-normal tensors
Keylock, Christopher J
2016-01-01
We decompose the velocity gradient tensor for turbulence into normal and non-normal parts, and condition our analysis on the strain eigenvector alignments between these tensors. We identify states that always enhance, and always counteract the axisymmetric expansion state, and give a rationale for decomposing the production balance term into its constituents: complex behavior arises when the dominant strain alignments involve the non-normal tensor. Finally, we develop a topological analysis framework where mathematical bounds on two of the three variables leads to an analysis in two planes.
Source-Type Identification Analysis Using Regional Seismic Moment Tensors
Chiang, A.; Dreger, D. S.; Ford, S. R.; Walter, W. R.
2012-12-01
Waveform inversion to determine the seismic moment tensor is a standard approach in determining the source mechanism of natural and manmade seismicity, and may be used to identify, or discriminate different types of seismic sources. The successful applications of the regional moment tensor method at the Nevada Test Site (NTS) and the 2006 and 2009 North Korean nuclear tests (Ford et al., 2009a, 2009b, 2010) show that the method is robust and capable for source-type discrimination at regional distances. The well-separated populations of explosions, earthquakes and collapses on a Hudson et al., (1989) source-type diagram enables source-type discrimination; however the question remains whether or not the separation of events is universal in other regions, where we have limited station coverage and knowledge of Earth structure. Ford et al., (2012) have shown that combining regional waveform data and P-wave first motions removes the CLVD-isotropic tradeoff and uniquely discriminating the 2009 North Korean test as an explosion. Therefore, including additional constraints from regional and teleseismic P-wave first motions enables source-type discrimination at regions with limited station coverage. We present moment tensor analysis of earthquakes and explosions (M6) from Lop Nor and Semipalatinsk test sites for station paths crossing Kazakhstan and Western China. We also present analyses of smaller events from industrial sites. In these sparse coverage situations we combine regional long-period waveforms, and high-frequency P-wave polarity from the same stations, as well as from teleseismic arrays to constrain the source type. Discrimination capability with respect to velocity model and station coverage is examined, and additionally we investigate the velocity model dependence of vanishing free-surface traction effects on seismic moment tensor inversion of shallow sources and recovery of explosive scalar moment. Our synthetic data tests indicate that biases in scalar
The gravitoelectromagnetic stress-energy tensor
Mashhoon, B.; McClune, J. C.; Quevedo, H.(Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, AP 70543, 04510, México, DF, Mexico)
1998-01-01
We study the pseudo-local gravitoelectromagnetic stress-energy tensor for an arbitrary gravitational field within the framework of general relativity. It is shown that there exists a current of gravitational energy around a rotating mass. This gravitational analog of the Poynting flux is evaluated for certain classes of observers in the Kerr field.
Primordial tensor modes from quantum corrected inflation
DEFF Research Database (Denmark)
Joergensen, Jakob; Sannino, Francesco; Svendsen, Ole
2014-01-01
. Finally we confront these theories with the Planck and BICEP2 data. We demonstrate that the discovery of primordial tensor modes by BICEP2 require the presence of sizable quantum departures from the $\\phi^4$-Inflaton model for the non-minimally coupled scenario which we parametrize and quantify. We...
Lax pair tensors in arbitrary dimensions
Goliath, M; Rosquist, K; Goliath, Martin; Karlovini, Max; Rosquist, Kjell
1999-01-01
A recipe is presented for obtaining Lax tensors for any n-dimensional Hamiltonian system admitting a Lax representation of dimension n. Our approach is to use the Jacobi geometry and coupling-constant metamorphosis to obtain a geometric Lax formulation. We also exploit the results to construct integrable spacetimes, satisfying the weak energy condition.
Tensor Fields in Relativistic Quantum Mechanics
Dvoeglazov, Valeriy V
2015-01-01
We re-examine the theory of antisymmetric tensor fields and 4-vector potentials. We discuss corresponding massless limits. We analize the quantum field theory taking into account the mass dimensions of the notoph and the photon. Next, we deduced the gravitational field equations from relativistic quantum mechanics.
Tensors in image processing and computer vision
De Luis García, Rodrigo; Tao, Dacheng; Li, Xuelong
2009-01-01
Tensor signal processing is an emerging field with important applications to computer vision and image processing. This book presents the developments in this branch of signal processing, offering research and discussions by experts in the area. It is suitable for advanced students working in the area of computer vision and image processing.
Dielectric tensor of strongly coupled plasmas
International Nuclear Information System (INIS)
Complex conductivity and dielectric permeability tensors of strongly coupled plasmas are studied and constructed on the basis of exact relations and sum rules. Both Coulomb and magnetic correlation are taken into account. The electromagnetic mode dispersion law is studied. The magnetostatic properties of a system of charged particles are investigated in detail. 26 refs
Dark energy in scalar-tensor theories
International Nuclear Information System (INIS)
We investigate several aspects of dynamical dark energy in the framework of scalar-tensor theories of gravity. We provide a classification of scalar-tensor coupling functions admitting cosmological scaling solutions. In particular, we recover that Brans-Dicke theory with inverse power-law potential allows for a sequence of background dominated scaling regime and scalar field dominated, accelerated expansion. Furthermore, we compare minimally and non-minimally coupled models, with respect to the small redshift evolution of the dark energy equation of state. We discuss the possibility to discriminate between different models by a reconstruction of the equation-of-state parameter from available observational data. The non-minimal coupling characterizing scalar-tensor models can - in specific cases - alleviate fine tuning problems, which appear if (minimally coupled) quintessence is required to mimic a cosmological constant. Finally, we perform a phase-space analysis of a family of biscalar-tensor models characterized by a specific type of σ-model metric, including two examples from recent literature. In particular, we generalize an axion-dilaton model of Sonner and Townsend, incorporating a perfect fluid background consisting of (dark) matter and radiation. (orig.)
Positivity of linear maps under tensor powers
International Nuclear Information System (INIS)
We investigate linear maps between matrix algebras that remain positive under tensor powers, i.e., under tensoring with n copies of themselves. Completely positive and completely co-positive maps are trivial examples of this kind. We show that for every n ∈ ℕ, there exist non-trivial maps with this property and that for two-dimensional Hilbert spaces there is no non-trivial map for which this holds for all n. For higher dimensions, we reduce the existence question of such non-trivial “tensor-stable positive maps” to a one-parameter family of maps and show that an affirmative answer would imply the existence of non-positive partial transpose bound entanglement. As an application, we show that any tensor-stable positive map that is not completely positive yields an upper bound on the quantum channel capacity, which for the transposition map gives the well-known cb-norm bound. We, furthermore, show that the latter is an upper bound even for the local operations and classical communications-assisted quantum capacity, and that moreover it is a strong converse rate for this task
Pomeron as a Reggeized Tensor Glueball
Institute of Scientific and Technical Information of China (English)
MA Wei-Xing; A.W.Thomas; SHEN Peng-Nian; ZHOU Li-Juan
2001-01-01
We study gluonic content of the pomeron and propose that the pomeron could be a reggeized tensor glueball ζ(2230) with quantum numbers IG JPc = 0+2++.This conjecture is examined in high energy proton-proton elastic scattering,and the calculations lend a favorable support to our physical idea.``
Visualization and processing of tensor fields
Weickert, Joachim
2007-01-01
Presents information on the visualization and processing of tensor fields. This book serves as an overview for the inquiring scientist, as a basic foundation for developers and practitioners, and as a textbook for specialized classes and seminars for graduate and doctoral students.
Weinberg's Approach and Antisymmetric Tensor Fields
Dvoeglazov, V V
2002-01-01
We extend the previous series of articles \\cite{HPA} devoted to finding mappings between the Weinberg-Tucker-Hammer formalism and antisymmetric tensor fields. Now we take into account solutions of different parities of the Weinberg-like equations. Thus, the Proca, Duffin-Kemmer and Bargmann-Wigner formalisms are generalized.
Tensor network methods for invariant theory
International Nuclear Information System (INIS)
Invariant theory is concerned with functions that do not change under the action of a given group. Here we communicate an approach based on tensor networks to represent polynomial local unitary invariants of quantum states. This graphical approach provides an alternative to the polynomial equations that describe invariants, which often contain a large number of terms with coefficients raised to high powers. This approach also enables one to use known methods from tensor network theory (such as the matrix product state (MPS) factorization) when studying polynomial invariants. As our main example, we consider invariants of MPSs. We generate a family of tensor contractions resulting in a complete set of local unitary invariants that can be used to express the Rényi entropies. We find that the graphical approach to representing invariants can provide structural insight into the invariants being contracted, as well as an alternative, and sometimes much simpler, means to study polynomial invariants of quantum states. In addition, many tensor network methods, such as MPSs, contain excellent tools that can be applied in the study of invariants. (paper)
Magnetic hydrodynamics with asymmetric stress tensor
Billig, Yuly
2004-01-01
In this paper we study equations of magnetic hydrodynamics with a stress tensor. We interpret this system as the generalized Euler equation associated with an abelian extension of the Lie algebra of vector fields with a non-trivial 2-cocycle. We use the Lie algebra approach to prove the energy conservation law and the conservation of cross-helicity.
Positivity of linear maps under tensor powers
Energy Technology Data Exchange (ETDEWEB)
Müller-Hermes, Alexander, E-mail: muellerh@ma.tum.de; Wolf, Michael M., E-mail: m.wolf@tum.de [Zentrum Mathematik, Technische Universität München, 85748 Garching (Germany); Reeb, David, E-mail: reeb.qit@gmail.com [Zentrum Mathematik, Technische Universität München, 85748 Garching (Germany); Institute for Theoretical Physics, Leibniz Universität Hannover, 30167 Hannover (Germany)
2016-01-15
We investigate linear maps between matrix algebras that remain positive under tensor powers, i.e., under tensoring with n copies of themselves. Completely positive and completely co-positive maps are trivial examples of this kind. We show that for every n ∈ ℕ, there exist non-trivial maps with this property and that for two-dimensional Hilbert spaces there is no non-trivial map for which this holds for all n. For higher dimensions, we reduce the existence question of such non-trivial “tensor-stable positive maps” to a one-parameter family of maps and show that an affirmative answer would imply the existence of non-positive partial transpose bound entanglement. As an application, we show that any tensor-stable positive map that is not completely positive yields an upper bound on the quantum channel capacity, which for the transposition map gives the well-known cb-norm bound. We, furthermore, show that the latter is an upper bound even for the local operations and classical communications-assisted quantum capacity, and that moreover it is a strong converse rate for this task.
Tensor Squeezed Limits and the Higuchi Bound
Bordin, Lorenzo; Mirbabayi, Mehrdad; Noreña, Jorge
2016-01-01
We point out that tensor consistency relations-i.e. the behavior of primordial correlation functions in the limit a tensor mode has a small momentum-are more universal than scalar consistency relations. They hold in the presence of multiple scalar fields and as long as anisotropies are diluted exponentially fast. When de Sitter isometries are approximately respected during inflation this is guaranteed by the Higuchi bound, which forbids the existence of light particles with spin: De Sitter space can support scalar hair but no curly hair. We discuss two indirect ways to look for the violation of tensor con- sistency relations in observations, as a signature of models in which inflation is not a strong isotropic attractor, such as solid inflation: (a) Graviton exchange contribution to the scalar four-point function; (b) Quadrupolar anisotropy of the scalar power spectrum due to super-horizon tensor modes. This anisotropy has a well-defined statistics which can be distinguished from cases in which the background...
Introduction to vector and tensor analysis
Wrede, Robert C
1972-01-01
A broad introductory treatment, this volume examines general Cartesian coordinates, the cross product, Einstein's special theory of relativity, bases in general coordinate systems, maxima and minima of functions of two variables, line integrals, integral theorems, fundamental notions in n-space, Riemannian geometry, algebraic properties of the curvature tensor, and more. 1963 edition.
A Wilsonian Energy-Momentum Tensor
Rosten, Oliver J
2016-01-01
For local conformal field theories, it is shown how to construct an expression for the energy-momentum tensor in terms of a Wilsonian effective Lagrangian. Tracelessness implies a single, unintegrated equation which enforces both the Exact Renormalization Group equation and its partner encoding invariance under special conformal transformations.
Dark energy in scalar-tensor theories
Energy Technology Data Exchange (ETDEWEB)
Moeller, J.
2007-12-15
We investigate several aspects of dynamical dark energy in the framework of scalar-tensor theories of gravity. We provide a classification of scalar-tensor coupling functions admitting cosmological scaling solutions. In particular, we recover that Brans-Dicke theory with inverse power-law potential allows for a sequence of background dominated scaling regime and scalar field dominated, accelerated expansion. Furthermore, we compare minimally and non-minimally coupled models, with respect to the small redshift evolution of the dark energy equation of state. We discuss the possibility to discriminate between different models by a reconstruction of the equation-of-state parameter from available observational data. The non-minimal coupling characterizing scalar-tensor models can - in specific cases - alleviate fine tuning problems, which appear if (minimally coupled) quintessence is required to mimic a cosmological constant. Finally, we perform a phase-space analysis of a family of biscalar-tensor models characterized by a specific type of {sigma}-model metric, including two examples from recent literature. In particular, we generalize an axion-dilaton model of Sonner and Townsend, incorporating a perfect fluid background consisting of (dark) matter and radiation. (orig.)
Khoromskaia, Venera; Khoromskij, Boris N.
2014-12-01
Our recent method for low-rank tensor representation of sums of the arbitrarily positioned electrostatic potentials discretized on a 3D Cartesian grid reduces the 3D tensor summation to operations involving only 1D vectors however retaining the linear complexity scaling in the number of potentials. Here, we introduce and study a novel tensor approach for fast and accurate assembled summation of a large number of lattice-allocated potentials represented on 3D N×N×N grid with the computational requirements only weakly dependent on the number of summed potentials. It is based on the assembled low-rank canonical tensor representations of the collected potentials using pointwise sums of shifted canonical vectors representing the single generating function, say the Newton kernel. For a sum of electrostatic potentials over L×L×L lattice embedded in a box the required storage scales linearly in the 1D grid-size, O(N), while the numerical cost is estimated by O(NL). For periodic boundary conditions, the storage demand remains proportional to the 1D grid-size of a unit cell, n=N/L, while the numerical cost reduces to O(N), that outperforms the FFT-based Ewald-type summation algorithms of complexity O(N3logN). The complexity in the grid parameter N can be reduced even to the logarithmic scale O(logN) by using data-sparse representation of canonical N-vectors via the quantics tensor approximation. For justification, we prove an upper bound on the quantics ranks for the canonical vectors in the overall lattice sum. The presented approach is beneficial in applications which require further functional calculus with the lattice potential, say, scalar product with a function, integration or differentiation, which can be performed easily in tensor arithmetics on large 3D grids with 1D cost. Numerical tests illustrate the performance of the tensor summation method and confirm the estimated bounds on the tensor ranks.
Operator Norm Inequalities between Tensor Unfoldings on the Partition Lattice
Wang, Miaoyan; Duc, Khanh Dao; Fischer, Jonathan; Song, Yun S.
2016-01-01
Interest in higher-order tensors has recently surged in data-intensive fields, with a wide range of applications including image processing, blind source separation, community detection, and feature extraction. A common paradigm in tensor-related algorithms advocates unfolding (or flattening) the tensor into a matrix and applying classical methods developed for matrices. Despite the popularity of such techniques, how the functional properties of a tensor changes upon unfolding is currently no...
Exploring the Tensor Networks/AdS Correspondence
Bhattacharyya, Arpan; Gao, Zhe-Shen; Hung, Ling-Yan; Liu, Si-Nong
2016-01-01
In this paper we study the recently proposed tensor networks/AdS correspondence. We found that the Coxeter group is a useful tool to describe tensor networks in a negatively curved space. Study- ing generic tensor network populated by perfect tensors, we find that the physical wave function generically do not admit any connected correlation functions of local operators. To remedy the problem, we assume that wavefunctions admitting such semi-classical gravitational interpretation are composed ...
Detection of point landmarks in multidimensional tensor data☆
Ruiz-Alzola, J.; Kikinis, R.; Westin, C.-F.
2001-01-01
This paper describes a unified approach to the detection of point landmarks—whose neighborhoods convey discriminant information—including multidimensional scalar, vector, and higher-order tensor data. The method is based on the interpretation of generalized correlation matrices derived from the gradient of tensor functions, a probabilistic interpretation of point landmarks, and the application of tensor algebra. Results on both synthetic and real tensor data are presented.
Automatic Deformable Diffusion Tensor Registration for Fiber Population Analysis
Irfanoglu, M.O.; Machiraju, R.; Sammet, S.; Pierpaoli, C.; Knopp, M.V.
2008-01-01
In this work, we propose a novel method for deformable tensor–to–tensor registration of Diffusion Tensor Images. Our registration method models the distances in between the tensors with Geode-sic–Loxodromes and employs a version of Multi-Dimensional Scaling (MDS) algorithm to unfold the manifold described with this metric. Defining the same shape properties as tensors, the vector images obtained through MDS are fed into a multi–step vector–image registration scheme and the resulting deformati...
Skyrme tensor force in heavy ion collisions
Stevenson, P. D.; Suckling, E. B.; Fracasso, S.; Barton, M. C.; Umar, A. S.
2016-05-01
Background: It is generally acknowledged that the time-dependent Hartree-Fock (TDHF) method provides a useful foundation for a fully microscopic many-body theory of low-energy heavy ion reactions. The TDHF method is also known in nuclear physics in the small-amplitude domain, where it provides a useful description of collective states, and is based on the mean-field formalism, which has been a relatively successful approximation to the nuclear many-body problem. Currently, the TDHF theory is being widely used in the study of fusion excitation functions, fission, and deep-inelastic scattering of heavy mass systems, while providing a natural foundation for many other studies. Purpose: With the advancement of computational power it is now possible to undertake TDHF calculations without any symmetry assumptions and incorporate the major strides made by the nuclear structure community in improving the energy density functionals used in these calculations. In particular, time-odd and tensor terms in these functionals are naturally present during the dynamical evolution, while being absent or minimally important for most static calculations. The parameters of these terms are determined by the requirement of Galilean invariance or local gauge invariance but their significance for the reaction dynamics have not been fully studied. This work addresses this question with emphasis on the tensor force. Method: The full version of the Skyrme force, including terms arising only from the Skyrme tensor force, is applied to the study of collisions within a completely symmetry-unrestricted TDHF implementation. Results: We examine the effect on upper fusion thresholds with and without the tensor force terms and find an effect on the fusion threshold energy of the order several MeV. Details of the distribution of the energy within terms in the energy density functional are also discussed. Conclusions: Terms in the energy density functional linked to the tensor force can play a non
Rank-one tensor injection: A novel method for canonical polyadic tensor decomposition
Czech Academy of Sciences Publication Activity Database
Phan, A. H.; Tichavský, Petr; Cichocki, A.
Piscataway: IEEE, 2016, s. 2549-2553. ISBN 978-1-4799-9987-3. [IEEE International Conference on Acoustics, Speech, and Signal Processing 2016 (ICASSP2016). Shanghai (CN), 20.03.2016-25.03.2016] R&D Projects: GA ČR(CZ) GA14-13713S Institutional support: RVO:67985556 Keywords : CANDECOMP/PARAFAC * tensor decomposition * tensor deflation Subject RIV: BB - Applied Statistics, Operational Research http://library.utia.cas.cz/separaty/2016/SI/tichavsky-0458487.pdf
Tensor based structure estimation in multi-channel images
DEFF Research Database (Denmark)
Schou, Jesper; Dierking, Wolfgang; Skriver, Henning
2000-01-01
second part tensors are used for representing the structure information. This approach has the advantage, that tensors can be averaged either spatially or by applying several images, and the resulting tensor provides information of the average strength as well as orientation of the structure. The...
Conformal operators from spinor fields - I: Symmetric tensor case
International Nuclear Information System (INIS)
The full system of conformal symmetric traceless tensor operators with minimal twist constructed from generalized free massless spinor fields is given. A series of symmetric tensor operators with higher twist and the simplest antisymmetric tensor operators are given as examples for further study. (author)
The Picard crossed module of a braided tensor category
Davydov, Alexei; Nikshych, Dmitri
2012-01-01
For a finite braided tensor category we introduce its Picard crossed module consisting of the group of invertible module categories and the group of braided tensor autoequivalences. We describe the Picard crossed module in terms of braided autoequivalences of the Drinfeld center of the braided tensor category. As an illustration, we compute the Picard crossed module of a braided pointed fusion category.