Energy Technology Data Exchange (ETDEWEB)
Alam, T.M.
1998-09-01
The influence of changes in the contracted Gaussian basis set used for ab initio calculations of nuclear magnetic resonance (NMR) phosphorous chemical shift anisotropy (CSA) tensors was investigated. The isotropic chemical shitl and chemical shift anisotropy were found to converge with increasing complexity of the basis set at the Hartree-Fock @IF) level. The addition of d polarization function on the phosphorous nucIei was found to have a major impact of the calculated chemical shi~ but diminished with increasing number of polarization fimctions. At least 2 d polarization fimctions are required for accurate calculations of the isotropic phosphorous chemical shift. The introduction of density fictional theory (DFT) techniques through tie use of hybrid B3LYP methods for the calculation of the phosphorous chemical shift tensor resulted in a poorer estimation of the NMR values, even though DFT techniques result in improved energy and force constant calculations. The convergence of the W parametem with increasing basis set complexity was also observed for the DFT calculations, but produced results with consistent large deviations from experiment. The use of a HF 6-31 l++G(242p) basis set represents a good compromise between accuracy of the simulation and the complexity of the calculation for future ab initio calculations of 31P NMR parameters in larger complexes.
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
Sijens, P. E.; Heesters, Martinus; Enting, Roeline; van der Graaf, W. T. A.; Potze, J. H.; Irwan, Roy; Meiners, L. C.; Oudkerk, M.
2007-01-01
Diffusion tensor imaging and multiple voxel magnetic resonance spectroscopy were performed in the MRI follow-up of a patient with a glioma treated with temozolomide chemotherapy. Tumor shrinkage was paralleled by reductions in choline level and by increases in apparent diffusion coefficient indicati
Sijens, P E; Heesters, M A A M; Enting, R H; van der Graaf, W T A; Potze, J H; Irwan, R; Meiners, L C; Oudkerk, M
2007-12-01
Diffusion tensor imaging and multiple voxel magnetic resonance spectroscopy were performed in the MRI follow-up of a patient with a glioma treated with temozolomide chemotherapy. Tumor shrinkage was paralleled by reductions in choline level and by increases in apparent diffusion coefficient indicating decreased cellularity. Within the tumor, choline level and apparent diffusion coefficient showed a significant inverse correlation (P < 0.01). Fractional anisotropy distribution in the tumor correlated positively with N-acetyl aspartate level (P < 0.001), indicating that these parameters reflect (remaining) axonal structure. Tumor lactate level, also found to decrease under therapy, did not correlate with any other parameter.
Energy Technology Data Exchange (ETDEWEB)
Xia Zhicheng; Nguyen, Bao D.; La Mar, Gerd N. [University of California, Department of Chemistry (United States)
2000-06-15
The use of dipolar shifts as important constraints in refining molecular structure of paramagnetic metalloproteins by solution NMR is now well established. A crucial initial step in this procedure is the determination of the orientation of the anisotropic paramagnetic susceptibility tensor in the molecular frame which is generated interactively with the structure refinement. The use of dipolar shifts as constraints demands knowledge of the diamagnetic shift, which, however, is very often not directly and easily accessible. We demonstrate that temperature gradients of dipolar shifts can serve as alternative constraints for determining the orientation of the magnetic axes, thereby eliminating the need to estimate the diamagnetic shifts. This approach is tested on low-spin, ferric sperm whale cyanometmyoglobin by determining the orientation, anisotropies and anisotropy temperature gradients by the alternate routes of using dipolar shifts and dipolar shift gradients as constraints. The alternate routes ultimately lead to very similar orientation of the magnetic axes, magnetic anisotropies and magnetic anisotropy temperature gradients which, by inference, would lead to an equally valid description of the molecular structure. It is expected that the use of the dipolar shift temperature gradients, rather than the dipolar shifts directly, as constraints will provide an accurate shortcut in a solution structure determination of a paramagnetic metalloprotein.
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...
Quantum-Chemical Insights from Deep Tensor Neural Networks
Schütt, Kristof T; Chmiela, Stefan; Müller, Klaus R; Tkatchenko, Alexandre
2016-01-01
Learning from data has led to paradigm shifts in a multitude of disciplines, including web, text, and image search, speech recognition, as well as bioinformatics. Can machine learning enable similar breakthroughs in understanding quantum many-body systems? Here we develop an efficient deep learning approach that enables spatially and chemically resolved insights into quantum-mechanical observables of molecular systems. We unify concepts from many-body Hamiltonians with purpose-designed deep tensor neural networks (DTNN), which leads to size-extensive and uniformly accurate (1 kcal/mol) predictions in compositional and configurational chemical space for molecules of intermediate size. As an example of chemical relevance, the DTNN model reveals a classification of aromatic rings with respect to their stability -- a useful property that is not contained as such in the training dataset. Further applications of DTNN for predicting atomic energies and local chemical potentials in molecules, reliable isomer energies...
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.
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…
Effects of structural differences on the NMR chemical shifts in isostructural dipeptides.
Altheimer, Benjamin D; Mehta, Manish A
2014-04-10
Porous crystalline dipeptides have gained recent attention for their potential as gas-storage materials. Within this large class is a group of dipeptides containing alanine, valine, and isoleucine with very similar crystal structures. We report the (13)C (carbonyl and Cα) and (15)N (amine and amide) solid-state NMR isotropic chemical shifts in a series of seven such isostructural porous dipeptides as well as shift tensor data for the carbonyl and amide sites. Using their known crystal structures and aided by ab initio quantum chemical calculations for the resonance assignments, we elucidate trends relating local structure, hydrogen-bonding patterns, and chemical shift. We find good correlation between the backbone dihedral angles and the Cα1 and Cα2 shifts. For the C1 shift tensor, the δ11 value shifts downfield as the hydrogen-bond distance increases, δ22 shifts upfield, and δ33 shows little variation. The C2 shift tensor shows no appreciable correlation with structural parameters. For the N2 tensor, δ11 shows little dependence on the hydrogen-bond length, whereas δ22 and δ33 both show a decrease in shielding as the hydrogen bond shortens. Our analysis teases apart some, but not all, structural contributors to the observed differences the solid-state NMR chemical shifts.
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...... chemical shifts. The method is benchmarked on folding simulations of five small proteins. In four cases the resulting structures are in excellent agreement with experimental data, the fifth case fail likely due to inaccuracies in the energy function. For the Chymotrypsin Inhibitor protein, a structure...
Chemical shift prediction for denatured proteins
Energy Technology Data Exchange (ETDEWEB)
Prestegard, James H., E-mail: jpresteg@ccrc.uga.edu; Sahu, Sarata C.; Nkari, Wendy K.; Morris, Laura C.; Live, David; Gruta, Christian
2013-02-15
While chemical shift prediction has played an important role in aspects of protein NMR that include identification of secondary structure, generation of torsion angle constraints for structure determination, and assignment of resonances in spectra of intrinsically disordered proteins, interest has arisen more recently in using it in alternate assignment strategies for crosspeaks in {sup 1}H-{sup 15}N HSQC spectra of sparsely labeled proteins. One such approach involves correlation of crosspeaks in the spectrum of the native protein with those observed in the spectrum of the denatured protein, followed by assignment of the peaks in the latter spectrum. As in the case of disordered proteins, predicted chemical shifts can aid in these assignments. Some previously developed empirical formulas for chemical shift prediction have depended on basis data sets of 20 pentapeptides. In each case the central residue was varied among the 20 amino common acids, with the flanking residues held constant throughout the given series. However, previous choices of solvent conditions and flanking residues make the parameters in these formulas less than ideal for general application to denatured proteins. Here, we report {sup 1}H and {sup 15}N shifts for a set of alanine based pentapeptides under the low pH urea denaturing conditions that are more appropriate for sparse label assignments. New parameters have been derived and a Perl script was created to facilitate comparison with other parameter sets. A small, but significant, improvement in shift predictions for denatured ubiquitin is demonstrated.
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
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......, which allows the accurate random coil chemical shifts to be obtained at any pH. By correcting the random coil chemical shifts for the effects of temperature and pH, systematic biases of the secondary chemical shifts are minimized, which will improve the reliability of detection of transient secondary...
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...
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 (δ(iso)) 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 δ(iso). 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 σ(MC) and π*(MC) orbitals under the action of the magnetic field, is analogous to that resulting from coupling σ(CC) 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 δ(iso) in alkylidene complexes relative to ethylene is thus due to the smaller energy gap between σ(MC) and π*(MC) vs this between σ(CC) and π*(CC) in ethylene. This effect also explains why the highest value of δ(iso) 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 π(MX)) 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 δ(iso). PMID:26787258
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 (δ(iso)) 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 δ(iso). 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 σ(MC) and π*(MC) orbitals under the action of the magnetic field, is analogous to that resulting from coupling σ(CC) 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 δ(iso) in alkylidene complexes relative to ethylene is thus due to the smaller energy gap between σ(MC) and π*(MC) vs this between σ(CC) and π*(CC) in ethylene. This effect also explains why the highest value of δ(iso) 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 π(MX)) 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 δ(iso).
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)
Energy Technology Data Exchange (ETDEWEB)
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)
Hartman, Joshua D; Beran, Gregory J O
2014-11-11
First-principles chemical shielding tensor predictions play a critical role in studying molecular crystal structures using nuclear magnetic resonance. Fragment-based electronic structure methods have dramatically improved the ability to model molecular crystal structures and energetics using high-level electronic structure methods. Here, a many-body expansion fragment approach is applied to the calculation of chemical shielding tensors in molecular crystals. First, the impact of truncating the many-body expansion at different orders and the role of electrostatic embedding are examined on a series of molecular clusters extracted from molecular crystals. Second, the ability of these techniques to assign three polymorphic forms of the drug sulfanilamide to the corresponding experimental (13)C spectra is assessed. This challenging example requires discriminating among spectra whose (13)C chemical shifts differ by only a few parts per million (ppm) across the different polymorphs. Fragment-based PBE0/6-311+G(2d,p) level chemical shielding predictions correctly assign these three polymorphs and reproduce the sulfanilamide experimental (13)C chemical shifts with 1 ppm accuracy. The results demonstrate that fragment approaches are competitive with the widely used gauge-invariant projector augmented wave (GIPAW) periodic density functional theory calculations. PMID:26584373
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
Improved chemical shift prediction by Rosetta conformational sampling
Energy Technology Data Exchange (ETDEWEB)
Tian Ye [Sanford Burnham Medical Research Institute (United States); Opella, Stanley J. [University of California San Diego, Department of Chemistry and Biochemistry (United States); Marassi, Francesca M., E-mail: fmarassi@sbmri.org [Sanford Burnham Medical Research Institute (United States)
2012-11-15
Chemical shift frequencies represent a time-average of all the conformational states populated by a protein. Thus, chemical shift prediction programs based on sequence and database analysis yield higher accuracy for rigid rather than flexible protein segments. Here we show that the prediction accuracy can be significantly improved by averaging over an ensemble of structures, predicted solely from amino acid sequence with the Rosetta program. This approach to chemical shift and structure prediction has the potential to be useful for guiding resonance assignments, especially in solid-state NMR structural studies of membrane proteins in proteoliposomes.
Calculations of proton chemical shifts in olefins and aromatics
Escrihuela, M C
2000-01-01
induced reagents on alpha,beta unsaturated ketones has also been investigated in order to deduce molecular structures and to obtain the assignment of the spectra of these molecules. A semi-empirical calculation of the partial atomic charges in organic compounds based on molecular dipole moments (CHARGE3) was developed into a model capable of predicting proton chemical shifts in a wide variety of organic compounds to a reasonable degree of accuracy. The model has been modified to include condensed aromatic hydrocarbons and substituted benzenes, alkenes, halo-monosubstituted benzenes and halo-alkenes. Within the aromatic compounds the influence of the pi electron densities and the ring current have been investigated, along with the alpha, beta and gamma effects. The model gives the first accurate calculation of the proton chemical shifts of condensed aromatic compounds and the proton substituent chemical shifts (SCS) in the benzene ring. For the data set of 55 proton chemical shifts spanning 3 ppm the rms error...
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
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
Direct solution of the Chemical Master Equation using quantized tensor trains.
Directory of Open Access Journals (Sweden)
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
Bayesian inference of protein structure from chemical shift data
DEFF Research Database (Denmark)
Bratholm, Lars Andersen; Christensen, Anders Steen; Hamelryck, Thomas Wim;
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......, 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...
Ab Initio Prediction of 29Si-NMR Chemical Shifts
Institute of Scientific and Technical Information of China (English)
CHU Shidong; LI Yingxia; SONG Ni; GUAN Huashi
2002-01-01
The ability of several ab initio models to predict experimental 29Si-NMR chemical shift is examined. The shielding values of trimethylsilyl chloride (A), t-butyldimethylsilyl chloride (B) and allyltrimethylsilane (C) are calculated by GIAO, CSGT and IGAIM methods, using HF/6-31G*, B3LYP/6-31G*, HF/6-311+G**, B3LYP/6-311+G** and MPWlPW91/6-311+G** models respectively. The 29Si chemical shifts calculated by GIAO method using HF/6-311+G**model are highly in agreement with those obtained experimentally. All of the models above reproduce the trends of chemical shifts in all cases studied, suggesting that the models are of practical value.
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...
Black hole hair formation in shift-symmetric generalised scalar-tensor gravity
Benkel, Robert; Witek, Helvi
2016-01-01
A linear coupling between a scalar field and the Gauss-Bonnet invariant is the only known interaction term between a scalar and the metric that: respects shift symmetry; does not lead to higher order equations; inevitably introduces black hole hair in asymptotically flat, 4-dimensional spacetimes. Here we focus on the simplest theory that includes such a term and we explore the dynamical formation of scalar hair. In particular, we work in the decoupling limit that neglects the backreaction of the scalar onto the metric and evolve the scalar configuration numerically in the background of a Schwarzschild black hole or a collapsing dust star described by the Oppenheimer-Snyder solution. For all types of initial data that we consider, the scalar relaxes at late times to the known, static, analytic configuration that is associated with a hairy, spherically symmetric black hole. This suggests that the corresponding black hole solutions are indeed endpoints of collapse.
Basse, Kristoffer; Shankar, Ravi; Bjerring, Morten; Vosegaard, Thomas; Nielsen, Niels Chr.; Nielsen, Anders B.
2016-09-01
We present a theoretical analysis of the influence of chemical shifts on amplitude-modulated heteronuclear dipolar recoupling experiments in solid-state NMR spectroscopy. The method is demonstrated using the Rotor Echo Short Pulse IRrAdiaTION mediated Cross-Polarization (RESPIRATIONCP) experiment as an example. By going into the pulse sequence rf interaction frame and employing a quintuple-mode operator-based Floquet approach, we describe how chemical shift offset and anisotropic chemical shift affect the efficiency of heteronuclear polarization transfer. In this description, it becomes transparent that the main attribute leading to non-ideal performance is a fictitious field along the rf field axis, which is generated from second-order cross terms arising mainly between chemical shift tensors and themselves. This insight is useful for the development of improved recoupling experiments. We discuss the validity of this approach and present quaternion calculations to determine the effective resonance conditions in a combined rf field and chemical shift offset interaction frame transformation. Based on this, we derive a broad-banded version of the RESPIRATIONCP experiment. The new sequence is experimentally verified using SNNFGAILSS amyloid fibrils where simultaneous 15N → 13CO and 15N → 13Cα coherence transfer is demonstrated on high-field NMR instrumentation, requiring great offset stability.
Correction for Eddy Current-Induced Echo-Shifting Effect in Partial-Fourier Diffusion Tensor Imaging
Directory of Open Access Journals (Sweden)
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.
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
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.
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.
Toušek, Jaromír; Straka, Michal; Sklenář, Vladimír; Marek, Radek
2013-01-24
The interpretation of nuclear magnetic resonance (NMR) parameters is essential to understanding experimental observations at the molecular and supramolecular levels and to designing new and more efficient molecular probes. In many aromatic natural compounds, unusual (13)C NMR chemical shifts have been reported for out-of-plane methoxy groups bonded to the aromatic ring (~62 ppm as compared to the typical value of ~56 ppm for an aromatic methoxy group). Here, we analyzed this phenomenon for a series of aromatic natural compounds using Density Functional Theory (DFT) calculations. First, we checked the methodology used to optimize the structure and calculate the NMR chemical shifts in aromatic compounds. The conformational effects of the methoxy group on the (13)C NMR chemical shift then were interpreted by the Natural Bond Orbital (NBO) and Natural Chemical Shift (NCS) approaches, and by excitation analysis of the chemical shifts, breaking down the total nuclear shielding tensor into the contributions from the different occupied orbitals and their magnetic interactions with virtual orbitals. We discovered that the atypical (13)C NMR chemical shifts observed are not directly related to a different conjugation of the lone pair of electrons of the methoxy oxygen with the aromatic ring, as has been suggested. Our analysis indicates that rotation of the methoxy group induces changes in the virtual molecular orbital space, which, in turn, correlate with the predominant part of the contribution of the paramagnetic deshielding connected with the magnetic interactions of the BD(CMet-H)→BD*(CMet-OMet) orbitals, resulting in the experimentally observed deshielding of the (13)C NMR resonance of the out-of-plane methoxy group.
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...
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...... anisotropy (CSA). (71)Ga quadrupole coupling and CSA parameters for the two (tetrahedrally and octahedrally coordinated) gallium sites with axial symmetry in YGG (Ga(IV), C(Q) = 13.1 +/- 0.2 MHz and delta(sigma) = 54 +/- 50 ppm; Ga(VI), C(Q) = 4.10 +/- 0.06 MHz and delta(sigma) = 24 +/- 3 ppm) are fully...... consistent with its cubic crystal structure which supports the reliability of the experimental data. In addition, the (71)Ga and (27)Al isotropic chemical shifts for YGG and YAG give further support to the linear correlation observed earlier between (71)Ga and (27)Al isotropic chemical shifts....
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 ...
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.
Pitfalls of adrenal imaging with chemical shift MRI
International Nuclear Information System (INIS)
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
Applications of Chemical Shift Imaging to Marine Sciences
Directory of Open Access Journals (Sweden)
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.
Diagnostic value of chemical shift artifact in distinguishing benign lymphadenopathy
International Nuclear Information System (INIS)
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.
DEFF Research Database (Denmark)
Nevald, Rolf; Hansen, P. E.
1978-01-01
contributions of comparable sizes. The transferred hyperfine interactions turn out to be almost isotropic and exhibiting no temperature or field dependence. In LiHoF4 the line shifts are detectable within the entire temperature range. In LiTbF4 the fluorine and lithium lines broaden to such an extent......The fluorine and lithium NMR line shifts have been followed in temperature from 300 to 1.3 K and in fields up to 40 kG for LiTbF4 and LiHoF4. The Tb3+ and Ho3+ ionic moments cause these shifts. The Li shifts are dominated by dipole interactions, whereas the F shifts also have transferred hyperfine...
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...
NMR chemical shift as analytical derivative of the Helmholtz free energy
Heuvel, Willem Van den
2012-01-01
We present a theory for the temperature-dependent nuclear magnetic shielding tensor of molecules with arbitrary electronic structure. The theory is a generalization of Ramsey's theory for closed-shell molecules. The shielding tensor is defined as a second derivative of the Helmholtz free energy of the electron system in equilibrium with the applied magnetic field and the nuclear magnetic moments. This derivative is analytically evaluated and expressed as a sum over states formula. Special consideration is given to a system with an isolated degenerate ground state for which the size of the degeneracy and the composition of the wave functions are arbitrary. In this case the paramagnetic part of the shielding tensor is expressed in terms of the $g$ and $A$ tensors of the EPR spin Hamiltonian of the degenerate state. As an illustration of the proposed theory, we provide an explicit formula for the paramagnetic shift of the central lanthanide ion in endofullerenes Ln@C$_{60}$, with Ln=Ce$^{3+}$, Nd$^{3+}$, Sm$^{3+...
Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts
DEFF Research Database (Denmark)
Boomsma, Wouter; Tian, Pengfei; Frellsen, J.;
2014-01-01
Significance Chemical shifts are the most fundamental parameters measured in nuclear magnetic resonance spectroscopy. Since these parameters are exquisitely sensitive to the local atomic environment, they can provide detailed information about the three-dimensional structures of proteins. It has...... their thermal fluctuations, thereby broadening the scope of chemical shifts in structural biology....
International Nuclear Information System (INIS)
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)
Deuterium isotope effects on 13C chemical shifts of 10-Hydroxybenzo[h]quinolines
DEFF Research Database (Denmark)
Hansen, Poul Erik; Kamounah, Fadhil S.; Gryko, Daniel T.
2013-01-01
Deuterium isotope effects on 13C-NMR chemical shifts are investigated in a series of 10-hydroxybenzo[h]quinolines (HBQ’s) The OH proton is deuteriated. The isotope effects on 13C chemical shifts in these hydrogen bonded systems are rather unusual. The formal four-bond effects are found...... to be negative, indicating transmission via the hydrogen bond. In addition unusual long-range effects are seen. Structures, NMR chemical shifts and changes in nuclear shieldings upon deuteriation are calculated using DFT methods. Two-bond deuterium isotope effects on 13C chemical shifts are correlated...... with calculated OH stretching frequencies. Isotope effects on chemical shifts are calculated for systems with OH exchanged by OD. Hydrogen bond potentials are discussed. New and more soluble nitro derivatives are synthesized....
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.
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...
Energy Technology Data Exchange (ETDEWEB)
Karp, Jerome M.; Erylimaz, Ertan; Cowburn, David, E-mail: cowburn@cowburnlab.org, E-mail: David.cowburn@einstein.yu.edu [Albert Einstein College of Medicine of Yeshiva University, Department of Biochemistry (United States)
2015-01-15
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.
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
A robust algorithm for optimizing protein structures with NMR chemical shifts.
Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S
2015-11-01
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.
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.
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.)
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.
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)
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)
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
Pandey, Manoj Kumar; Yarava, Jayasubba Reddy; Zhang, Rongchun; Ramamoorthy, Ayyalusamy; Nishiyama, Yusuke
2016-01-01
Chemical shift anisotropy (CSA) tensors offer a wealth of information for structural and dynamics studies of a variety of chemical and biological systems. In particular, CSA of amide protons can provide piercing insights into hydrogen-bonding interactions that vary with the backbone conformation of a protein and dynamics. However, the narrow span of amide proton resonances makes it very difficult to measure (1)H CSAs of proteins even by using the recently proposed 2D (1)H/(1)H anisotropic/isotropic chemical shift (CSA/CS) correlation technique. Such difficulties due to overlapping proton resonances can in general be overcome by utilizing the broad span of isotropic chemical shifts of low-gamma nuclei like (15)N. In this context, we demonstrate a proton-detected 3D (15)N/(1)H/(1)H CS/CSA/CS correlation experiment at fast MAS frequency (70kHz) to measure (1)H CSA values of unresolved amide protons of N-acetyl-(15)N-l-valyl-(15)N-l-leucine (NAVL).
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...
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.
Theoretical Modeling of (99)Tc NMR Chemical Shifts.
Hall, Gabriel B; Andersen, Amity; Washton, Nancy M; Chatterjee, Sayandev; Levitskaia, Tatiana G
2016-09-01
Technetium-99 (Tc) displays a rich chemistry due to its wide range of accessible oxidation states (from -I to +VII) and ability to form coordination compounds. Determination of Tc speciation in complex mixtures is a major challenge, and (99)Tc nuclear magnetic resonance (NMR) spectroscopy is widely used to probe chemical environments of Tc in odd oxidation states. However, interpretation of (99)Tc NMR data is hindered by the lack of reference compounds. Density functional theory (DFT) calculations can help to fill this gap, but to date few computational studies have focused on (99)Tc NMR of compounds and complexes. This work evaluates the effectiveness of both pure generalized gradient approximation and their corresponding hybrid functionals, both with and without the inclusion of scalar relativistic effects, to model the (99)Tc NMR spectra of Tc(I) carbonyl compounds. With the exception of BLYP, which performed exceptionally well overall, hybrid functionals with inclusion of scalar relativistic effects are found to be necessary to accurately calculate (99)Tc NMR spectra. The computational method developed was used to tentatively assign an experimentally observed (99)Tc NMR peak at -1204 ppm to fac-Tc(CO)3(OH)3(2-). This study examines the effectiveness of DFT computations for interpretation of the (99)Tc NMR spectra of Tc(I) coordination compounds in high salt alkaline solutions. PMID:27518482
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......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 residual secondary structure elements in the acid-denatured state of an acylcoenzyme A binding protein. This method reveals a clear correlation between the carbon secondary chemical shifts and the amide secondary chemical shifts 3-5 residues away in the primary sequence. These findings strongly suggest...... transient formation of short helix-like segments, and identify unique sequence segments important for protein folding....
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
Stereoelectronic effects on 1H nuclear magnetic resonance chemical shifts in methoxybenzenes.
Lambert, Maja; Olsen, Lars; Jaroszewski, Jerzy W
2006-12-01
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 anisole (1) causes only small positive changes of 1H NMR chemical shifts (Delta delta Hmeta > Hpara, the experimental O-methylation induced shifts in ortho-disubstituted phenols are largest for Hpara, Delta delta equals; 0.19 +/- 0.02 ppm (n = 11). The 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 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 correlation between computed and observed 1H NMR chemical shifts, including agreement between computed and observed chemical shift changes caused by O-methylation. The observed regularities can aid structure elucidation of partly O-methylated polyphenols, including many natural products and drugs, and are useful in connection with chemical shift predictions by desktop computer programs. PMID:17137372
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
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...
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...
Deuterium isotope effects on 13C chemical shifts of negatively charged NH.N systems
DEFF Research Database (Denmark)
Hansen, Poul Erik; Pietrzak, Mariusz; Grech, Eugeniusz;
2013-01-01
” and equilibrium cases. NMR assignments of the former have been revised. The NH proton is deuteriated. The isotope effects on 13C chemical shifts are rather unusual in these strongly hydrogen bonded systems between a NH and a negatively charged nitrogen atom. The formal four-bond effects are found to be negative...... indicating transmission via the hydrogen bond. In addition, unusual long range effects are seen. Structures, 1H and 13C NMR chemical shifts and changes in nuclear shieldings upon deuteriation are calculated using density functional theory methods......Deuterium isotope effects on 13C chemical shifts are investigated in anions of 1,8-bis(4-toluenesulphonamido)naphthalenes together with N,N-(naphthalene-1,8-diyl)bis(2,2,2-trifluoracetamide) all with bis(1,8-dimethylamino)napthaleneH+ as counter ion. These compounds represent both “static...
Energy Technology Data Exchange (ETDEWEB)
Marin, Antoine; Malliavin, Therese E. [Institut de Biologie Physico-Chimique, Laboratoire de Biochimie Theorique, CNRS UPR 9080 (France)], E-mail: therese.malliavin@ibpc.fr; Nicolas, Pierre; Delsuc, Marc-Andre [INRA - Domaine de Vilvert, Unite Mathematique Informatique et Genome (France)
2004-09-15
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 C{sub {beta}} and H{sub {beta}}, in agreement with observations made in Grzesiek and Bax, 1993. Based on four nuclei: H{sub {beta}}, C{sub {beta}}, C{sub {alpha}} 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.
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......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...
Institute of Scientific and Technical Information of China (English)
Anthony J.SAVIOLA; David CHISZAR; Stephen P.MACKESSY
2012-01-01
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,Hemidactylusfrenatus),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 snakes.
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
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...... 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, and may thus improve...
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
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
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 an...
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.
Pritchard, Benjamin P.; Simpson, Scott; Zurek, Eva; Autschbach, Jochen
2014-01-01
A computational experiment investigating the [superscript 1]H and [superscript 13]C nuclear magnetic resonance (NMR) chemical shifts of molecules with unpaired electrons has been developed and implemented. This experiment is appropriate for an upper-level undergraduate laboratory course in computational, physical, or inorganic chemistry. The…
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...
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.
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.
Lof, R.W.; Schropp, R.E.I.
2010-01-01
The behavior of the electrical conductivity in hydrogenated microcrystalline silicon (μ c-Si:H) that is frequently observed is explained by considering the statistical shift in the chemical potential as a function of the crystalline fraction (Xc), the dangling bond density (N db), and the doping den
Magnetic Shift of the Chemical Freeze-out and Electric Charge Fluctuations
Fukushima, Kenji; Hidaka, Yoshimasa
2016-09-01
We discuss the effect of a strong magnetic field on the chemical freeze-out points in ultrarelativistic heavy-ion collisions. As a result of inverse magnetic catalysis or 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 freeze-out. 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. We find that the fluctuation exhibits a crossover behavior rapidly increased for e B ≳(0.4 GeV )2, while the charge chemical potential has smoother behavior with an increasing magnetic field.
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...
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.
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.
First-principles calculation of core-level binding energy shift in surface chemical processes
Institute of Scientific and Technical Information of China (English)
无
2010-01-01
Combined with third generation synchrotron radiation light sources, X-ray photoelectron spectroscopy (XPS) with higher energy resolution, brilliance, enhanced surface sensitivity and photoemission cross section in real time found extensive applications in solid-gas interface chemistry. This paper reports the calculation of the core-level binding energy shifts (CLS) using the first-principles density functional theory. The interplay between the CLS calculations and XPS measurements to uncover the structures, adsorption sites and chemical reactions in complex surface chemical processes are highlight. Its application on clean low index (111) and vicinal transition metal surfaces, molecular adsorption in terms of sites and configuration, and reaction kinetics are domonstrated.
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.
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).
Substituent effects in the 13C NMR chemical shifts of alpha-mono-substituted acetonitriles.
Reis, Adriana K C A; Rittner, Roberto
2007-03-01
13C chemical shifts empirical calculations, through a very simple additivity relationship, for the alpha-methylene carbon of some alpha-mono-substituted acetonitriles, Y-CH(2)-CN (Y=H, F, Cl, Br, I, OMe, OEt, SMe, SEt, NMe(2), NEt(2), Me and Et), lead to similar, or even better, results in comparison to the reported values obtained through Quantum Mechanics methods. The observed deviations, for some substituents, are very similar for both approaches. This divergence between experimental and calculated, either empirically or theoretically, values are smaller than for the corresponding acetones, amides, acetic acids and methyl esters, which had been named non-additivity effects (or intramolecular interaction chemical shifts, ICS) and attributed to some orbital interactions. Here, these orbital interactions do not seem to be the main reason for the non-additivity effects in the empirical calculations, which must be due solely to the magnetic anisotropy of the heavy atom present in the substituent. These deviations, which were also observed in the theoretical calculations, were attributed in that case to the non-inclusion of relativistic effects and spin-orbit coupling in the Hamiltonian. Some divergence is also observed for the cyano carbon chemical shifts, probably due to the same reasons.
DFT calculations of 1H and 13C NMR chemical shifts in transition metal hydrides.
del Rosal, I; Maron, L; Poteau, R; Jolibois, F
2008-08-14
Transition metal hydrides are of great interest in chemistry because of their reactivity and their potential use as catalysts for hydrogenation. Among other available techniques, structural properties in transition metal (TM) complexes are often probed by NMR spectroscopy. In this paper we will show that it is possible to establish a viable methodological strategy in the context of density functional theory, that allows the determination of 1H NMR chemical shifts of hydride ligands attached to transition metal atoms in mononuclear systems and clusters with good accuracy with respect to experiment. 13C chemical shifts have also been considered in some cases. We have studied mononuclear ruthenium complexes such as Ru(L)(H)(dppm)2 with L = H or Cl, cationic complex [Ru(H)(H2O)(dppm)2]+ and Ru(H)2(dppm)(PPh3)2, in which hydride ligands are characterized by a negative 1H NMR chemical shift. For these complexes all calculations are in relatively good agreement compared to experimental data with errors not exceeding 20% except for the hydrogen atom in Ru(H)2(dppm)(PPh3)2. For this last complex, the relative error increases to 30%, probably owing to the necessity to take into account dynamical effects of phenyl groups. Carbonyl ligands are often encountered in coordination chemistry. Specific issues arise when calculating 1H or 13C NMR chemical shifts in TM carbonyl complexes. Indeed, while errors of 10 to 20% with respect to experiment are often considered good in the framework of density functional theory, this difference in the case of mononuclear carbonyl complexes culminates to 80%: results obtained with all-electron calculations are overall in very satisfactory agreement with experiment, the error in this case does not exceed 11% contrary to effective core potentials (ECPs) calculations which yield errors always larger than 20%. We conclude that for carbonyl groups the use of ECPs is not recommended, although their use could save time for very large systems, for
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
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)
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
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.
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
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...... results fur the systems investigated, provided that relaxations of the valence electrons upon the core-hole transition are properly accounted for. Therefore, such calculations provide a powerful tool for identification of impurity states based on x-ray fluorescence data. Results for an Al impurity...
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.)
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.
NMR Chemical Shift Ranges of Urine Metabolites in Various Organic Solvents
Directory of Open Access Journals (Sweden)
Benjamin Görling
2016-09-01
Full Text Available 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.
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
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.
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
Predicting Pt-195 NMR chemical shift using new relativistic all-electron basis set.
Paschoal, D; Guerra, C Fonseca; de Oliveira, M A L; Ramalho, T C; Dos Santos, H F
2016-10-01
Predicting NMR properties is a valuable tool to assist the experimentalists in the characterization of molecular structure. For heavy metals, such as Pt-195, only a few computational protocols are available. In the present contribution, all-electron Gaussian basis sets, suitable to calculate the Pt-195 NMR chemical shift, are presented for Pt and all elements commonly found as Pt-ligands. The new basis sets identified as NMR-DKH were partially contracted as a triple-zeta doubly polarized scheme with all coefficients obtained from a Douglas-Kroll-Hess (DKH) second-order scalar relativistic calculation. The Pt-195 chemical shift was predicted through empirical models fitted to reproduce experimental data for a set of 183 Pt(II) complexes which NMR sign ranges from -1000 to -6000 ppm. Furthermore, the models were validated using a new set of 75 Pt(II) complexes, not included in the descriptive set. The models were constructed using non-relativistic Hamiltonian at density functional theory (DFT-PBEPBE) level with NMR-DKH basis set for all atoms. For the best model, the mean absolute deviation (MAD) and the mean relative deviation (MRD) were 150 ppm and 6%, respectively, for the validation set (75 Pt-complexes) and 168 ppm (MAD) and 5% (MRD) for all 258 Pt(II) complexes. These results were comparable with relativistic DFT calculation, 200 ppm (MAD) and 6% (MRD). © 2016 Wiley Periodicals, Inc.
DEFF Research Database (Denmark)
Kjærgaard, Magnus; Iesmantavicius, Vytautas; Poulsen, Flemming M
2011-01-01
of ¿-gauche effect. To overcome this, we reference the chemical shifts to those in a more disordered state resulting in residue specific random coil chemical shifts. The (13)C secondary chemical shifts of the methyl groups of valine, leucine, and isoleucine show sequence specific effects, which allow...
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…
Wang, Ching-Cheng; Lai, Wen-Chung; Chuang, Woei-Jer
2016-09-01
A tool for predicting the redox state and secondary structure of cysteine residues using multi-dimensional analyses of different combinations of nuclear magnetic resonance (NMR) chemical shifts has been developed. A data set of cysteine [Formula: see text], (13)C(α), (13)C(β), (1)H(α), (1)H(N), and (15)N(H) chemical shifts was created, classified according to redox state and secondary structure, using a library of 540 re-referenced BioMagResBank (BMRB) entries. Multi-dimensional analyses of three, four, five, and six chemical shifts were used to derive rules for predicting the structural states of cysteine residues. The results from 60 BMRB entries containing 122 cysteines showed that four-dimensional analysis of the C(α), C(β), H(α), and N(H) chemical shifts had the highest prediction accuracy of 100 and 95.9 % for the redox state and secondary structure, respectively. The prediction of secondary structure using 3D, 5D, and 6D analyses had the accuracy of ~90 %, suggesting that H(N) and [Formula: see text] chemical shifts may be noisy and made the discrimination worse. A web server (6DCSi) was established to enable users to submit NMR chemical shifts, either in BMRB or key-in formats, for prediction. 6DCSi displays predictions using sets of 3, 4, 5, and 6 chemical shifts, which shows their consistency and allows users to draw their own conclusions. This web-based tool can be used to rapidly obtain structural information regarding cysteine residues directly from experimental NMR data.
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
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
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
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...
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.
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.
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
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.
Regional Differences in Muscle Energy Metabolism in Human Muscle by 31P-Chemical Shift Imaging.
Kime, Ryotaro; Kaneko, Yasuhisa; Hongo, Yoshinori; Ohno, Yusuke; Sakamoto, Ayumi; Katsumura, Toshihito
2016-01-01
Previous studies have reported significant region-dependent differences in the fiber-type composition of human skeletal muscle. It is therefore hypothesized that there is a difference between the deep and superficial parts of muscle energy metabolism during exercise. We hypothesized that the inorganic phosphate (Pi)/phosphocreatine (PCr) ratio of the superficial parts would be higher, compared with the deep parts, as the work rate increases, because the muscle fiber-type composition of the fast-type may be greater in the superficial parts compared with the deep parts. This study used two-dimensional 31Phosphorus Chemical Shift Imaging (31P-CSI) to detect differences between the deep and superficial parts of the human leg muscles during dynamic knee extension exercise. Six healthy men participated in this study (age 27±1 year, height 169.4±4.1 cm, weight 65.9±8.4 kg). The experiments were carried out with a 1.5-T superconducting magnet with a 5-in. diameter circular surface coil. The subjects performed dynamic one-legged knee extension exercise in the prone position, with the transmit-receive coil placed under the right quadriceps muscles in the magnet. The subjects pulled down an elastic rubber band attached to the ankle at a frequency of 0.25, 0.5 and 1 Hz for 320 s each. The intracellular pH (pHi) was calculated from the median chemical shift of the Pi peak relative to PCr. No significant difference in Pi/PCr was observed between the deep and the superficial parts of the quadriceps muscles at rest. The Pi/PCr of the superficial parts was not significantly increased with increasing work rate. Compared with the superficial areas, the Pi/PCr of the deep parts was significantly higher (p<0.05) at 1 Hz. The pHi showed no significant difference between the two parts. These results suggest that muscle oxidative metabolism is different between deep and superficial parts of quadriceps muscles during dynamic exercise. PMID:26782194
Regional Differences in Muscle Energy Metabolism in Human Muscle by 31P-Chemical Shift Imaging.
Kime, Ryotaro; Kaneko, Yasuhisa; Hongo, Yoshinori; Ohno, Yusuke; Sakamoto, Ayumi; Katsumura, Toshihito
2016-01-01
Previous studies have reported significant region-dependent differences in the fiber-type composition of human skeletal muscle. It is therefore hypothesized that there is a difference between the deep and superficial parts of muscle energy metabolism during exercise. We hypothesized that the inorganic phosphate (Pi)/phosphocreatine (PCr) ratio of the superficial parts would be higher, compared with the deep parts, as the work rate increases, because the muscle fiber-type composition of the fast-type may be greater in the superficial parts compared with the deep parts. This study used two-dimensional 31Phosphorus Chemical Shift Imaging (31P-CSI) to detect differences between the deep and superficial parts of the human leg muscles during dynamic knee extension exercise. Six healthy men participated in this study (age 27±1 year, height 169.4±4.1 cm, weight 65.9±8.4 kg). The experiments were carried out with a 1.5-T superconducting magnet with a 5-in. diameter circular surface coil. The subjects performed dynamic one-legged knee extension exercise in the prone position, with the transmit-receive coil placed under the right quadriceps muscles in the magnet. The subjects pulled down an elastic rubber band attached to the ankle at a frequency of 0.25, 0.5 and 1 Hz for 320 s each. The intracellular pH (pHi) was calculated from the median chemical shift of the Pi peak relative to PCr. No significant difference in Pi/PCr was observed between the deep and the superficial parts of the quadriceps muscles at rest. The Pi/PCr of the superficial parts was not significantly increased with increasing work rate. Compared with the superficial areas, the Pi/PCr of the deep parts was significantly higher (p<0.05) at 1 Hz. The pHi showed no significant difference between the two parts. These results suggest that muscle oxidative metabolism is different between deep and superficial parts of quadriceps muscles during dynamic exercise.
SUBSTITUENT CHEMICAL SHIFT (SCS) AND THE SEQUENCE STRUCTURE OF ETHYLENE-VINYL ALCOHOL COPOLYMERS
Institute of Scientific and Technical Information of China (English)
ZHOU Zinan; TIAN Wenjing; WU Shengrong; DAI Yingkun; FENG Zhiliu; SHEN Lianfang; YUAN Hanzhen
1992-01-01
Three ethylene-vinyl alcohol copolymers were studied by means of the substituent chemical shift(SCS) method. The SCS parameters of hydroxy (-OH)in two different solvents were obtained: in deuterium oxide/phenol (20/80 W/W ) the parameters are S1 = 42.77 ± 0.08ppm, S2 = 7.15 ±0.06 ppm,S3(s )=-4.08±0.02ppm, S3(t)=-3.09±0.20ppm,S4=0.48±0.03ppm, S5 =0.26±0.05ppm. In o-dichlorobenzen-d4 S1(s)=44.79±0.61ppm, S2=7.40±0.00ppm, S3 (s)=-4.51±0.17ppm, S3 (t)= -3.13± 0.00 ppm, S4 =0 . 63±0.04ppm, S5=0.36±0.00ppm. Simultaneously the 13CNMR spectra of EVA copolymers were assigned by using the SCS parameters obtained.
Chemical shift assignment of the alternative scaffold protein IscA.
Popovic, Matija; Pastore, Annalisa
2016-04-01
The IscA protein (11.5 kDa) is an essential component of the iron sulphur cluster biogenesis machine. In bacteria, the machine components are clustered in operons, amongst which the most important is the isc operon. Bacterial IscA has direct homologues also in eukaryotes. Like the protein IscU, IscA is thought to assist cluster formation as an alternative scaffold protein which receives the cluster before transferring it further to the final acceptors. Several crystal structures have been published. They all report an IscA dimeric form, although the packing of the protomers in the dimers differs amongst structures. No solution studies have currently been reported. Here we report the (1)H, (13)C and (15)N backbone and side-chain chemical shift assignments of the cluster-free E. coli IscA as a starting point for further studies of the structure and functions of this still poorly characterized protein. We show that IscA exists in solution as an equilibrium between different species. Spectrum assignment was thus challenging given the heterogeneous nature of the sample but doable through judicious choice of selective labelling and concentration dependent studies.
Gurau, Razvan
2017-01-01
Written by the creator of the modern theory of random tensors, this book is the first self-contained introductory text to this rapidly developing theory. Starting from notions familiar to the average researcher or PhD student in mathematical or theoretical physics, the book presents in detail the theory and its applications to physics. The recent detections of the Higgs boson at the LHC and gravitational waves at LIGO mark new milestones in Physics confirming long standing predictions of Quantum Field Theory and General Relativity. These two experimental results only reinforce today the need to find an underlying common framework of the two: the elusive theory of Quantum Gravity. Over the past thirty years, several alternatives have been proposed as theories of Quantum Gravity, chief among them String Theory. While these theories are yet to be tested experimentally, key lessons have already been learned. Whatever the theory of Quantum Gravity may be, it must incorporate random geometry in one form or another....
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.
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.
Sahakyan, Aleksandr B; Vendruscolo, Michele
2013-02-21
Ring current and electric field effects can considerably influence NMR chemical shifts in biomolecules. Understanding such effects is particularly important for the development of accurate mappings between chemical shifts and the structures of nucleic acids. In this work, we first analyzed the Pople and the Haigh-Mallion models in terms of their ability to describe nitrogen base conjugated ring effects. We then created a database (DiBaseRNA) of three-dimensional arrangements of RNA base pairs from X-ray structures, calculated the corresponding chemical shifts via a hybrid density functional theory approach and used the results to parametrize the ring current and electric field effects in RNA bases. Next, we studied the coupling of the electric field and ring current effects for different inter-ring arrangements found in RNA bases using linear model fitting, with joint electric field and ring current, as well as only electric field and only ring current approximations. Taken together, our results provide a characterization of the interdependence of ring current and electric field geometric factors, which is shown to be especially important for the chemical shifts of non-hydrogen atoms in RNA bases.
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-...
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...
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.
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.
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)
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
Halogen effect on structure and 13C NMR chemical shift of 3,6-disubstituted-N-alkyl carbazoles
DEFF Research Database (Denmark)
Radula-Janik, Klaudia; Kupka, Teobald; Ejsmont, Krzysztof;
2013-01-01
). The decreasing electronegativity of the halogen substituent (F, Cl, Br and I) was reflected in both nonrelativistic and relativistic NMR results as decreased values of chemical shifts of carbon atoms attached to halogen (C3 and C6) leading to a strong sensitivity to halogen atom type at 3 and 6 positions....... 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 unaffected...
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)
Chen eSong
2015-07-01
Full Text Available Phytochromes are dimeric biliprotein photoreceptors exhibiting characteristic red/far-red photocycles. Full-length cyanobacterial phytochrome Cph1 from Synechocystis 6803 is soluble initially but tends to aggregate in a concentration-dependent manner, hampering attempts to solve the structure using NMR and crystallization methods. Otherwise, the Cph1 sensory module (Cph1Δ2, photochemically indistinguishable from the native protein and used extensively in structural and other studies, can be purified to homogeneity in >10 mg amounts at mM concentrations quite easily. Bulk precipitation of full-length Cph1 by ammonium sulfate (AmS was expected to allow us to produce samples for solid-state magic-angle spinning (MAS NMR from dilute solutions before significant aggregation began. It was not clear, however, what effects the process of partial dehydration might have on the molecular structure. Here we test this by running solid-state MAS NMR experiments on AmS-precipitated Cph1Δ2 in its red-absorbing Pr state carrying uniformly 13C/15N-labeled phycocyanobilin (PCB chromophore. 2D 13C–13C correlation experiments allowed a complete assignment of 13C responses of the chromophore. Upon precipitation, 13C chemical shifts for most of PCB carbons move upfield, in which we found major changes for C4 and C6 atoms associated with the A-ring positioning. Further, the broad spectral lines seen in the AmS 13C spectrum reflect primarily the extensive homogeneous broadening presumably due to an increase in the distribution of conformational states in the protein, in which less free water is available to partake in the hydration shells. Our data suggest that dehydration indeed leads to motional and electronic structural changes of the bilin chromophore and its binding pocket and is not restricted to the protein surface. The extent of the changes induced differs from the freezing process of the solution samples routinely used in previous MAS NMR and
Song, Chen; Lang, Christina; Kopycki, Jakub; Hughes, Jon; Matysik, Jörg
2015-01-01
Phytochromes are dimeric biliprotein photoreceptors exhibiting characteristic red/far-red photocycles. Full-length cyanobacterial phytochrome Cph1 from Synechocystis 6803 is soluble initially but tends to aggregate in a concentration-dependent manner, hampering attempts to solve the structure using NMR and crystallization methods. Otherwise, the Cph1 sensory module (Cph1Δ2), photochemically indistinguishable from the native protein and used extensively in structural and other studies, can be purified to homogeneity in >10 mg amounts at mM concentrations quite easily. Bulk precipitation of full-length Cph1 by ammonium sulfate (AmS) was expected to allow us to produce samples for solid-state magic-angle spinning (MAS) NMR from dilute solutions before significant aggregation began. It was not clear, however, what effects the process of partial dehydration might have on the molecular structure. Here we test this by running solid-state MAS NMR experiments on AmS-precipitated Cph1Δ2 in its red-absorbing Pr state carrying uniformly (13)C/(15)N-labeled phycocyanobilin (PCB) chromophore. 2D (13)C-(13)C correlation experiments allowed a complete assignment of (13)C responses of the chromophore. Upon precipitation, (13)C chemical shifts for most of PCB carbons move upfield, in which we found major changes for C4 and C6 atoms associated with the A-ring positioning. Further, the broad spectral lines seen in the AmS (13)C spectrum reflect primarily the extensive inhomogeneous broadening presumably due to an increase in the distribution of conformational states in the protein, in which less free water is available to partake in the hydration shells. Our data suggest that the effect of dehydration process indeed leads to changes of electronic structure of the bilin chromophore and a decrease in its mobility within the binding pocket, but not restricted to the protein surface. The extent of the changes induced differs from the freezing process of the solution samples routinely
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
Buellesbach, J.; Gadau, J.; Beukeboom, L. W.; Echinger, F.; Raychoudhury, R.; Werren, J. H.; Schmitt, T.
2013-01-01
The evolution and maintenance of intraspecific communication channels constitute a key feature of chemical signalling and sexual communication. However, how divergent chemical communication channels evolve while maintaining their integrity for both sender and receiver is poorly understood. In this s
Tugarinov, Vitali; Venditti, Vincenzo; Marius Clore, G
2014-01-01
A methyl-detected 'out-and-back' NMR experiment for obtaining simultaneous correlations of methyl resonances of valine and isoleucine/leucine residues with backbone carbonyl chemical shifts, SIM-HMCM(CGCBCA)CO, is described. The developed pulse-scheme serves the purpose of convenience in recording a single data set for all Ile(δ1), Leu(δ) and Val(γ) (ILV) methyl positions instead of acquiring two separate spectra selective for valine or leucine/isoleucine residues. The SIM-HMCM(CGCBCA)CO experiment can be used for ILV methyl assignments in moderately sized protein systems (up to ~100 kDa) where the backbone chemical shifts of (13)C(α), (13)Cβ and (13)CO are known from prior NMR studies and where some losses in sensitivity can be tolerated for the sake of an overall reduction in NMR acquisition time.
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.
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.
Directory of Open Access Journals (Sweden)
Elliott J Stollar
Full Text Available There is increasing evidence for the functional importance of multiple dynamically populated states within single proteins. However, peptide binding by protein-protein interaction domains, such as the SH3 domain, has generally been considered to involve the full engagement of peptide to the binding surface with minimal dynamics and simple methods to determine dynamics at the binding surface for multiple related complexes have not been described. We have used NMR spectroscopy combined with isothermal titration calorimetry to comprehensively examine the extent of engagement to the yeast Abp1p SH3 domain for 24 different peptides. Over one quarter of the domain residues display co-linear chemical shift perturbation (CCSP behavior, in which the position of a given chemical shift in a complex is co-linear with the same chemical shift in the other complexes, providing evidence that each complex exists as a unique dynamic rapidly inter-converting ensemble. The extent the specificity determining sub-surface of AbpSH3 is engaged as judged by CCSP analysis correlates with structural and thermodynamic measurements as well as with functional data, revealing the basis for significant structural and functional diversity amongst the related complexes. Thus, CCSP analysis can distinguish peptide complexes that may appear identical in terms of general structure and percent peptide occupancy but have significant local binding differences across the interface, affecting their ability to transmit conformational change across the domain and resulting in functional differences.
Energy Technology Data Exchange (ETDEWEB)
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.
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.
Identification of zinc-ligated cysteine residues based on 13Calpha and 13Cbeta chemical shift data.
Kornhaber, Gregory J; Snyder, David; Moseley, Hunter N B; Montelione, Gaetano T
2006-04-01
Although a significant number of proteins include bound metals as part of their structure, the identification of amino acid residues coordinated to non-paramagnetic metals by NMR remains a challenge. Metal ligands can stabilize the native structure and/or play critical catalytic roles in the underlying biochemistry. An atom's chemical shift is exquisitely sensitive to its electronic environment. Chemical shift data can provide valuable insights into structural features, including metal ligation. In this study, we demonstrate that overlapped 13Cbeta chemical shift distributions of Zn-ligated and non-metal-ligated cysteine residues are largely resolved by the inclusion of the corresponding 13Calpha chemical shift information, together with secondary structural information. We demonstrate this with a bivariate distribution plot, and statistically with a multivariate analysis of variance (MANOVA) and hierarchical logistic regression analysis. Using 287 13Calpha/13Cbeta shift pairs from 79 proteins with known three-dimensional structures, including 86 13Calpha and 13Cbeta shifts for 43 Zn-ligated cysteine residues, along with corresponding oxidation state and secondary structure information, we have built a logistic regression model that distinguishes between oxidized cystines, reduced (non-metal ligated) cysteines, and Zn-ligated cysteines. Classifying cysteines/cystines with a statistical model incorporating all three phenomena resulted in a predictor of Zn ligation with a recall, precision and F-measure of 83.7%, and an accuracy of 95.1%. This model was applied in the analysis of Bacillus subtilis IscU, a protein involved in iron-sulfur cluster assembly. The model predicts that all three cysteines of IscU are metal ligands. We confirmed these results by (i) examining the effect of metal chelation on the NMR spectrum of IscU, and (ii) inductively coupled plasma mass spectrometry analysis. To gain further insight into the frequency of occurrence of non-cysteine Zn
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.
Bonding and chemical shifts in aluminosilicate glasses: importance of Madelung effects
Cruguel, H; Kerjan, O; Bart, F; Gautier-Soyer, M
2003-01-01
A detailed study of the XPS binding energy shifts of Si 2p, O 1s and Zr 3d in a series of aluminosilicate glasses (a three oxide glass: SiO sub 2 -Al sub 2 O sub 3 -CaO, three four-oxide glasses: SiO sub 2 -Al sub 2 O sub 3 -CaO-TiO sub 2 , ZrO sub 2 or CeO sub 2 , along with a six-oxide glass SiO sub 2 -Al sub 2 O sub 3 -CaO-TiO sub 2 -ZrO sub 2 -CeO sub 2) is presented. Their composition is such that these glasses have the same mean electronegativity, so that no changes in the atomic charges is expected. The binding energy shifts are interpreted in terms of initial and final state effects, and the balance of charge transfer contribution and electrostatic effects is discussed. Referred to the ternary glass, the binding energy shifts of the Si 2p, O 1s and Zr 3d lines in the complex glasses are due to an initial state effect, as the extraatomic relaxation is similar along the glass series. These shifts originate from electrostatic Madelung effects, likely coming from a structural change induced by the presenc...
Institute of Scientific and Technical Information of China (English)
LIU, Shu-Shea; XIA, Zhi-Ning; CAI, Shao-Xi; LIU, Yan
2000-01-01
A novel atomic electronegative distance vector (AEDV) has been developed to express the chemical environment of various chemically equivalent carbon atoms in alcohols and alkanes.Combining AEDV and γ parameter, four five-parameter Iinear relationship equations of chemical shift for four types of carbon atoms are created by using multiple linear regression.Correlation coefficients are R = 0.9887, 0.9972, 0.9978 and 0.9968 and roots of mean square error are RMS = 0.906, 0.821, 1.091and 1.091of four types of carbons, i.e., type1,2, 3, and 4 for primary, secondary, tertiary, and quaternary carbons, respectively. The stability and prediction capacity for external samples of four models have been tested by cross- validation.
Dracínský, Martin; Pohl, Radek; Slavetínská, Lenka; Budesínský, Milos
2010-09-01
A series of model sulfides was oxidized in the NMR sample tube to sulfoxides and sulfones by the stepwise addition of meta-chloroperbenzoic acid in deuterochloroform. Various methods of quantum chemical calculations have been tested to reproduce the observed (1)H and (13)C chemical shifts of the starting sulfides and their oxidation products. It has been shown that the determination of the energy-minimized conformation is a very important condition for obtaining realistic data in the subsequent calculation of the NMR chemical shifts. The correlation between calculated and observed chemical shifts is very good for carbon atoms (even for the 'cheap' DFT B3LYP/6-31G* method) and somewhat less satisfactory for hydrogen atoms. The calculated chemical shifts induced by oxidation (the Delta delta values) agree even better with the experimental values and can also be used to determine the oxidation state of the sulfur atom (-S-, -SO-, -SO(2)-).
Isley, William C; Zarra, Salvatore; Carlson, Rebecca K; Bilbeisi, Rana A; Ronson, Tanya K; Nitschke, Jonathan R; Gagliardi, Laura; Cramer, Christopher J
2014-06-14
The behaviour of metal-organic cages upon guest encapsulation can be difficult to elucidate in solution. Paramagnetic metal centres introduce additional dispersion of signals that is useful for characterisation of host-guest complexes in solution using nuclear magnetic resonance (NMR). However, paramagnetic centres also complicate spectral assignment due to line broadening, signal integration error, and large changes in chemical shifts, which can be difficult to assign even for known compounds. Quantum chemical predictions can provide information that greatly facilitates the assignment of NMR signals and identification of species present. Here we explore how the prediction of paramagnetic NMR spectra may be used to gain insight into the spin crossover (SCO) properties of iron(II)-based metal organic coordination cages, specifically examining how the structure of the local metal coordination environment affects SCO. To represent the tetrahedral metal-organic cage, a model system is generated by considering an isolated metal-ion vertex: fac-ML3(2+) (M = Fe(II), Co(II); L = N-phenyl-2-pyridinaldimine). The sensitivity of the (1)H paramagnetic chemical shifts to local coordination environments is assessed and utilised to shed light on spin crossover behaviour in iron complexes. Our data indicate that expansion of the metal coordination sphere must precede any thermal SCO. An attempt to correlate experimental enthalpies of SCO with static properties of bound guests shows that no simple relationship exists, and that effects are likely due to nuanced dynamic response to encapsulation. PMID:24752730
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
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.
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
Burum, D. P.; Elleman, D. D.; Rhim, W.-K.
1978-01-01
A simple multiple-pulse 'zero crossing technique' for accurately determining the first moment of a solid-state NMR spectrum is introduced. This technique was applied to obtain the F-19 chemical shift versus pressure curves up to 5 kbar for single crystals of CaF2 (0.29 + or - 0.02 ppm/kbar) and BaF2 (0.62 + or - 0.05 ppm/kbar). Results at ambient temperature and pressure are also reported for a number of other fluorine compounds. Because of its high data rate, this technique is potentially several orders of magnitude more sensitive than similar CW methods.
Carlisle, Elizabeth A; Holder, Jessica L; Maranda, Abby M; de Alwis, Adamberage R; Selkie, Ellen L; McKay, Sonya L
2007-01-01
Accurate random coil alpha-proton chemical shift values are essential for precise protein structure analysis using chemical shift index (CSI) calculations. The current study determines the chemical shift effects of pH, urea, peptide length and neighboring amino acids on the alpha-proton of Ala using model peptides of the general sequence GnXaaAYaaGn, where Xaa and Yaa are Leu, Val, Phe, Tyr, His, Trp or Pro, and n = 1-3. Changes in pH (2-6), urea (0-1M), and peptide length (n = 1-3) had no effect on Ala alpha-proton chemical shifts. Denaturing concentrations of urea (8M) caused significant downfield shifts (0.10 +/- 0.01 ppm) relative to an external DSS reference. Neighboring aliphatic residues (Leu, Val) had no effect, whereas aromatic amino acids (Phe, Tyr, His and Trp) and Pro caused significant shifts in the alanine alpha-proton, with the extent of the shifts dependent on the nature and position of the amino acid. Smaller aromatic residues (Phe, Tyr, His) caused larger shift effects when present in the C-terminal position (approximately 0.10 vs. 0.05 ppm N-terminal), and the larger aromatic tryptophan caused greater effects in the N-terminal position (0.15 ppm vs. 0.10 C-terminal). Proline affected both significant upfield (0.06 ppm, N-terminal) and downfield (0.25 ppm, C-terminal) chemical shifts. These new Ala correction factors detail the magnitude and range of variation in environmental chemical shift effects, in addition to providing insight into the molecular level interactions that govern protein folding.
Decoupling braided tensor factors
International Nuclear Information System (INIS)
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
Gurau, Razvan
2016-01-01
Preface to the SIGMA special issue "Tensor Models, Formalism and Applications." The SIGMA special issue "Tensor Models, Formalism and Applications" is a collection of eight excellent, up to date reviews \\cite{Ryan:2016sundry,Bonzom:2016dwy,Rivasseau:2016zco,Carrozza:2016vsq,Krajewski:2016svb,Rivasseau:2016rgt,Tanasa:2015uhr,Gielen:2016dss} on random tensor models. The reviews combine pedagogical introductions meant for a general audience with presentations of the most recent developments in the field. This preface aims to give a condensed panoramic overview of random tensors as the natural generalization of random matrices to higher dimensions.
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
Chen, Jonathan L; Bellaousov, Stanislav; Tubbs, Jason D; Kennedy, Scott D; Lopez, Michael J; Mathews, David H; Turner, Douglas H
2015-11-17
Knowledge of RNA structure is necessary to determine structure-function relationships and to facilitate design of potential therapeutics. RNA secondary structure prediction can be improved by applying constraints from nuclear magnetic resonance (NMR) experiments to a dynamic programming algorithm. Imino proton walks from NOESY spectra reveal double-stranded regions. Chemical shifts of protons in GH1, UH3, and UH5 of GU pairs, UH3, UH5, and AH2 of AU pairs, and GH1 of GC pairs were analyzed to identify constraints for the 5' to 3' directionality of base pairs in helices. The 5' to 3' directionality constraints were incorporated into an NMR-assisted prediction of secondary structure (NAPSS-CS) program. When it was tested on 18 structures, including nine pseudoknots, the sensitivity and positive predictive value were improved relative to those of three unrestrained programs. The prediction accuracy for the pseudoknots improved the most. The program also facilitates assignment of chemical shifts to individual nucleotides, a necessary step for determining three-dimensional structure.
Garkani-Nejad, Zahra; Poshteh-Shirani, Marziyeh
2010-11-15
A new implemented QSPR method, whose descriptors achieved from bidimensional images, was applied for predicting (13)C NMR chemical shifts of 25 mono substituted naphthalenes. The resulted descriptors were subjected to principal component analysis (PCA) and the most significant principal components (PCs) were extracted. MIA-QSPR (multivariate image analysis applied to quantitative structure-property relationship) modeling was done by means of principal component regression (PCR) and principal component-artificial neural network (PC-ANN) methods. Eigen value ranking (EV) and correlation ranking (CR) were used here to select the most relevant set of PCs as inputs for PCR and PC-ANN modeling methods. The results supported that the correlation ranking-principal component-artificial neural network (CR-PC-ANN) model could predict the (13)C NMR chemical shifts of all 10 carbon atoms in mono substituted naphthalenes with R(2) ≥ 0.922 for training set, R(2) ≥ 0.963 for validation set and R(2) ≥ 0.936 for the test set. Comparison of the results with other existing factor selection method revealed that less accurate results were obtained by the eigen value ranking procedure. PMID:21035668
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 ...
Energy Technology Data Exchange (ETDEWEB)
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
International Nuclear Information System (INIS)
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
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.
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
Li, Da-Wei; Meng, Dan; Brüschweiler, Rafael
2015-05-01
A robust NMR resonance assignment method is introduced for proteins whose 3D structure has previously been determined by X-ray crystallography. The goal of the method is to obtain a subset of correct assignments from a parsimonious set of 3D NMR experiments of 15N, 13C labeled proteins. Chemical shifts of sequential residue pairs are predicted from static protein structures using PPM_One, which are then compared with the corresponding experimental shifts. Globally optimized weighted matching identifies the assignments that are robust with respect to small changes in NMR cross-peak positions. The method, termed PASSPORT, is demonstrated for 4 proteins with 100-250 amino acids using 3D NHCA and a 3D CBCA(CO)NH experiments as input producing correct assignments with high reliability for 22% of the residues. The method, which works best for Gly, Ala, Ser, and Thr residues, provides assignments that serve as anchor points for additional assignments by both manual and semi-automated methods or they can be directly used for further studies, e.g. on ligand binding, protein dynamics, or post-translational modification, such as phosphorylation.
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
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.
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.
Zero discharge tanning: a shift from chemical to biocatalytic leather processing.
Thanikaivelan, Palanisamy; Rao, Jonnalagadda Raghava; Nair, Balachandran Unni; Ramasami, Thirumalachari
2002-10-01
Beam house processes (Beam house processes generally mean liming-reliming processes, which employ beam.) contribute more than 60% of the total pollution from leather processing. The use of lime and sodium sulfide is of environmental concern (1, 2). Recently, the authors have developed an enzyme-based dehairing assisted with a very low amount of sodium sulfide, which completely avoids the use of lime. However, the dehaired pelt requires opening up of fiber bundles for further processing, where lime is employed to achieve this through osmotic swelling. Huge amounts of lime sludge and total solids are the main drawbacks of lime. An alternative bioprocess, based on alpha-amylase for fiber opening, has been attempted after enzymatic unhairing. This totally eliminates the use of lime in leather processing. This method enables subsequent processes and operations in leather making feasible without a deliming process. A control experiment was run in parallel using conventional liming-reliming processes. It has been found that the extent of opening up of fiber bundles using alpha-amylase is comparable to that of the control. This has been substantiated through scanning electron microscopic, stratigraphic chrome distribution analysis, and softness measurements. Performance of the leathers is shown to be on a par with leathers produced by the conventional process through physical and hand evaluation. Importantly, softness of the leathers is numerically proven to be comparable with that of control. The process also demonstrates reduction in chemical oxygen demand load by 45% and total solids load by 20% compared to the conventional process. The total dry sludge from the beam house processes is brought down from 152 to 8 kg for processing 1 ton of raw hides.
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...
Pierens, Gregory K; Venkatachalam, T K; Reutens, David C
2016-04-01
A comparative study of experimental and calculated NMR chemical shifts of six compounds comprising 2-amino and 2-hydroxy phenyl benzoxazoles/benzothiazoles/benzimidazoles in four solvents is reported. The benzimidazoles showed interesting spectral characteristics, which are discussed. The proton and carbon chemical shifts were similar for all solvents. The largest chemical shift deviations were observed in benzene. The chemical shifts were calculated with density functional theory using a suite of four functionals and basis set combinations. The calculated chemical shifts revealed a good match to the experimentally observed values in most of the solvents. The mean absolute error was used as the primary metric. The use of an additional metric is suggested, which is based on the order of chemical shifts. The DP4 probability measures were also used to compare the experimental and calculated chemical shifts for each compound in the four solvents. Copyright © 2015 John Wiley & Sons, Ltd.
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.
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.
Chemical shift measurements of chlorine K X-ray spectra using a high-resolution PIXE system
International Nuclear Information System (INIS)
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
Liu, Zizhong; Goddard, John D
2009-12-17
Perfluorinated carboxylic acids (PFCAs) are a class of persistent environmental pollutants. Commercially available PFCAs are mixtures of linear and branched isomers, possibly with impurities. Different isomers have different physical and chemical properties and toxicities. However, little is known about the properties and the finer details of the structures of the individual branched isomers. Full geometry optimizations for the linear n-alkane (C(6)-C(27)) PFCAs indicated that all have helical structures. The helical angle increases slightly with increasing chain length, from 16.3 degrees in C(6)F(13)COOH to 17.0 degrees in C(27)F(55)COOH. This study predicts (19)F NMR parameters for 69 linear and branched isomers of the perfluoro carboxylic acids C(6)F(13)COOH, C(7)F(15)COOH, and C(8)F(17)COOH. B3LYP-GIAO/6-31++G(d,p)//B3LYP/6-31G(d,p) was used for the NMR calculations with analysis of the chemical shifts by the natural bond orbital method. The predictions of the (19)F chemical shifts revealed the differences among the CF(3), CF(2), and CF groups. In general, the absolute values for the chemical shifts for the CF(3) group are smaller than 90 ppm, for the CF larger than 160 ppm, and for the CF(2) between 110 and 130 ppm. The chemical shifts of the branched isomers are smaller in magnitude than the linear ones. The decrease is correlated with the steric hindrance of the CF(3) groups, the more hindered the CF(3), the greater the decrease in the (19)F chemical shifts. The predicted (19)F chemical shifts are similar to those for analogous perfluoro compounds with other terminal functional groups such as -SO(3)H or -SO(3)NH(2)CH(2)CH(3).
Tensors and their applications
Islam, Nazrul
2006-01-01
About the Book: The book is written is in easy-to-read style with corresponding examples. The main aim of this book is to precisely explain the fundamentals of Tensors and their applications to Mechanics, Elasticity, Theory of Relativity, Electromagnetic, Riemannian Geometry and many other disciplines of science and engineering, in a lucid manner. The text has been explained section wise, every concept has been narrated in the form of definition, examples and questions related to the concept taught. The overall package of the book is highly useful and interesting for the people associated with the field. Contents: Preliminaries Tensor Algebra Metric Tensor and Riemannian Metric Christoffel`s Symbols and Covariant Differentiation Riemann-Christoffel Tensor The e-Systems and the Generalized Krönecker Deltas Geometry Analytical Mechanics Curvature of a Curve, Geodesic Parallelism of Vectors Ricci`s Coefficients of Rotation and Congruence Hyper Surfaces
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.
Tensor Network Renormalization.
Evenbly, G; Vidal, G
2015-10-30
We introduce a coarse-graining transformation for tensor networks that can be applied to study both the partition function of a classical statistical system and the Euclidean path integral of a quantum many-body system. The scheme is based upon the insertion of optimized unitary and isometric tensors (disentanglers and isometries) into the tensor network and has, as its key feature, the ability to remove short-range entanglement or correlations at each coarse-graining step. Removal of short-range entanglement results in scale invariance being explicitly recovered at criticality. In this way we obtain a proper renormalization group flow (in the space of tensors), one that in particular (i) is computationally sustainable, even for critical systems, and (ii) has the correct structure of fixed points, both at criticality and away from it. We demonstrate the proposed approach in the context of the 2D classical Ising model.
Tensor scale-based image registration
Saha, Punam K.; Zhang, Hui; Udupa, Jayaram K.; Gee, James C.
2003-05-01
Tangible solutions to image registration are paramount in longitudinal as well as multi-modal medical imaging studies. In this paper, we introduce tensor scale - a recently developed local morphometric parameter - in rigid image registration. A tensor scale-based registration method incorporates local structure size, orientation and anisotropy into the matching criterion, and therefore, allows efficient multi-modal image registration and holds potential to overcome the effects of intensity inhomogeneity in MRI. Two classes of two-dimensional image registration methods are proposed - (1) that computes angular shift between two images by correlating their tensor scale orientation histogram, and (2) that registers two images by maximizing the similarity of tensor scale features. Results of applications of the proposed methods on proton density and T2-weighted MR brain images of (1) the same slice of the same subject, and (2) different slices of the same subject are presented. The basic superiority of tensor scale-based registration over intensity-based registration is that it may allow the use of local Gestalts formed by the intensity patterns over the image instead of simply considering intensities as isolated events at the pixel level. This would be helpful in dealing with the effects of intensity inhomogeneity and noise in MRI.
Tensor-tensor theory of gravitation
Gogberashvili, Merab
1996-01-01
We consider the standard gauge theory of Poincar\\'{e} group, realizing as a subgroup of GL(5. R). The main problem of this theory was appearing of the fields connected with non-Lorentz symmetries, whose physical sense was unclear. In this paper we treat the gravitation as a Higgs-Goldstone field, and the translation gauge field as a new tensor field. The effective metric tensor in this case is hybrid of two tensor fields. In the linear approximation the massive translation gauge field can give the Yukava type correction to the Newtons potential. Also outer potentials of a sphere and ball of the same mass are different in this case. Corrections to the standard Einshtein post Newtonian formulas of the light deflection and radar echo delay is obtained. The string like solution of the nonlinear equations of the translation gauge fields is found. This objects can results a Aharonov-Bohm type effect even for the spinless particles. They can provide density fluctuations in the early universe, necessary for galaxy fo...
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.
A recursive approach to the reduction of tensor Feynman integrals
Diakonidis, Theodoros; Riemann, Tord; Tausk, Bas
2010-01-01
We describe a new, convenient, recursive tensor integral reduction scheme for one-loop $n$-point Feynman integrals. The reduction is based on the algebraic Davydychev-Tarasov formalism where the tensors are represented by scalars with shifted dimensions and indices, and then expressed by conventional scalars with generalized recurrence relations. The scheme is worked out explicitly for up to $n=6$ external legs and for tensor ranks $R\\leq n$. The tensors are represented by scalar one- to four-point functions in $d$ dimensions. For the evaluation of them, the Fortran code for the tensor reductions has to be linked with a package like QCDloop or LoopTools/FF. Typical numerical results are presented.
Tayler, Alexander B; Benning, Martin; Sederman, Andrew J; Holland, Daniel J; Gladden, Lynn F
2014-06-01
We present simultaneous measurement of dispersed and continuous phase flow fields for liquid-liquid systems obtained using ultrafast magnetic resonance imaging. Chemical-shift artifacts, which are otherwise highly problematic for this type of measurement, are overcome using a compressed sensing based image reconstruction algorithm that accounts for off-resonant signal components. This scheme is combined with high-temporal-resolution spiral imaging (188 frames per second), which is noted for its robustness to flow. It is demonstrated that both quantitative signal intensity and phase preconditioning are preserved throughout the image reconstruction algorithm. Measurements are acquired of oil droplets of varying viscosity rising through stagnant water. From these data it is apparent that the internal droplet flow fields are heavily influenced by the droplet shape oscillations, and that the accurate modeling of droplet shape is of critical importance in the modeling of droplet-side hydrodynamics. The application of the technique to three-component systems is also demonstrated, as is the measurement of local concentration maps of a mutually soluble species (acetone in polydimethylsiloxane-water).
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)
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)
Loth, Karine; Landon, Céline; Paquet, Françoise
2015-04-01
MC1 is the most abundant architectural protein present in Methanosarcina thermophila CHTI55 in laboratory growth conditions and is structurally unrelated to other DNA-binding proteins. MC1 functions are to shape and to protect DNA against thermal denaturation by binding to it. Therefore, MC1 has a strong affinity for any double-stranded DNA. However, it recognizes and preferentially binds to bent DNA, such as four-way junctions and negatively supercoiled DNA minicircles. Combining NMR data, electron microscopy data, biochemistry, molecular modelisation and docking approaches, we proposed recently a new type of DNA/protein complex, in which the monomeric protein MC1 binds on the concave side of a strongly bent 15 base pairs DNA. We present here the NMR chemical shifts assignments of each partner in the complex, (1)H (15)N MC1 protein and (1)H (13)C (15)N bent duplex DNA, as first step towards the first experimental 3D structure of this new type of DNA/protein complex.
Energy Technology Data Exchange (ETDEWEB)
Foster, Mark P.; Wuttke, Deborah S.; Clemens, Karen R.; Jahnke, Wolfgang; Radhakrishnan, Ishwar; Tennant, Linda; Reymond, Martine; Chung, John; Wright, Peter E. [Scripps Research Institute, Department of Molecular Biology and Skaggs Institute for Chemical Biology (United States)
1998-07-15
We report the NMR resonance assignments for a macromolecular protein/DNA complex containing the three amino-terminal zinc fingers (92 amino acid residues) of Xenopus laevis TFIIIA (termed zf1-3) bound to the physiological DNA target (15 base pairs), and for the free DNA. Comparisons are made of the chemical shifts of protein backbone{sup 1} H{sup N}, {sup 15}N,{sup 13} C{sup {alpha}} and{sup 13} C{sup {beta}} and DNA base and sugar protons of the free and bound species. Chemical shift changes are analyzed in the context of the structures of the zf1-3/DNA complex to assess the utility of chemical shift change as a probe of molecular interfaces. Chemical shift perturbations that occur upon binding in the zf1-3/DNA complex do not correspond directly to the structural interface, but rather arise from a number of direct and indirect structural and dynamic effects.
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.
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...
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
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.)
Energy Technology Data Exchange (ETDEWEB)
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.)
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.
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...
Symmetric Tensor Decomposition
DEFF Research Database (Denmark)
Brachat, Jerome; Comon, Pierre; Mourrain, Bernard;
2010-01-01
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...
Energy Technology Data Exchange (ETDEWEB)
Palmkvist, Jakob, E-mail: palmkvist@ihes.fr [Institut des Hautes Etudes Scientifiques, 35 Route de Chartres, FR-91440 Bures-sur-Yvette (France)
2014-01-15
We introduce an infinite-dimensional Lie superalgebra which is an extension of the U-duality Lie algebra of maximal supergravity in D dimensions, for 3 ⩽ D ⩽ 7. The level decomposition with respect to the U-duality Lie algebra gives exactly the tensor hierarchy of representations that arises in gauge deformations of the theory described by an embedding tensor, for all positive levels p. We prove that these representations are always contained in those coming from the associated Borcherds-Kac-Moody superalgebra, and we explain why some of the latter representations are not included in the tensor hierarchy. The most remarkable feature of our Lie superalgebra is that it does not admit a triangular decomposition like a (Borcherds-)Kac-Moody (super)algebra. Instead the Hodge duality relations between level p and D − 2 − p extend to negative p, relating the representations at the first two negative levels to the supersymmetry and closure constraints of the embedding tensor.
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.
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.
Energy Technology Data Exchange (ETDEWEB)
Joseph, D., E-mail: djoseph@barc.gov.in [Nuclear Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Basu, S.; Jha, S.N.; Bhattacharyya, D. [Applied Spectroscopy Division, Bhabha Atomic Research Centre, Mumbai 400085 (India)
2012-03-01
Cu K X-ray absorption edges were measured in compounds such as CuO, Cu(CH{sub 3}CO{sub 2}){sub 2}, Cu(CO{sub 3}){sub 2}, and CuSO{sub 4} where Cu is present in oxidation state of 2+, using the energy dispersive EXAFS beamline at INDUS-2 Synchrotron radiation source at RRCAT, Indore. Energy shifts of {approx}4-7 eV were observed for Cu K X-ray absorption edge in the above compounds compared to its value in elemental copper. The difference in the Cu K edge energy shifts in the different compounds having same oxidation state of Cu shows the effect of different chemical environments surrounding the cation in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on Cu cations in the above compounds.
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.
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
Energy Technology Data Exchange (ETDEWEB)
Taylor, J.S.; Vigneron, D.B.; Murphy-Boesch, J.; Nelson, S.J.; Kessler, H.B.; Coia, L.; Curran, W.; Brown, T.R. (Fox Chase Cancer Center, Philadelphia, PA (United States))
1991-08-01
The authors have studied a series of normal subjects and patients with brain tumors, by using {sup 31}P three-dimensional chemical shift imaging to obtain localized {sup 31}P spectra of the brain. A significant proportion of brain cytosolic ATP in normal brain is not complexed to Mg{sup 2+}, as indicated by the chemical shift {delta} of the {beta}-P resonance of ATP. The ATP {beta}P resonance position in brain thus is sensitive to changes in intracellular free Mg{sup 2+} concentration and in the proportion of ATP complexed with Mg because this shift lies on the rising portion of the {delta} vs. Mg{sup 2+} titration curve for ATP. They have measured the ATP {beta}-P shift and compared intracellular free Mg{sup 2+} concentration and fractions of free ATP for normal individuals and a limited series of patients with brain tumors. In four of the five spectra obtained from brain tissue containing a substantial proportion of tumor, intracellular free Mg{sup 2+} was increased, and the fraction of free ATP was decreased, compared with normal brain.
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.
Thurber, Kent R.; Tycko, Robert
2008-01-01
Accurate determination of sample temperatures in solid state nuclear magnetic resonance (NMR) with magic-angle spinning (MAS) can be problematic, particularly because frictional heating and heating by radio-frequency irradiation can make the internal sample temperature significantly different from the temperature outside the MAS rotor. This paper demonstrates the use of 79Br chemical shifts and spin-lattice relaxation rates in KBr powder as temperature-dependent parameters for the determinati...
Institute of Scientific and Technical Information of China (English)
ZHANG Rong; LUO San-Lai; WU Wen-Juan
2008-01-01
All-atom molecular dynamics(MD)simulation combined with chemical shifts was performed to investigate the interactions over the entire concentration range of the ethanol(EtOH)-water system.The results of the simulation were adopted to explain the NMR experiments by hydrogen bonding analysis.The strong hydrogen bonds and weak C-H…O contacts coexist in the mixtures through the analysis of the radial distribution functions.And the liquid structures in the whole concentration of EtOH-water mixtures can be classified into three regions by the statistic analysis of the hydrogen-bonding network in the MD simulations.Moreover,the chemical shifts of the hydrogen atom are in agreement witb the statistical results of the average number hydrogen bonds in the MD simulations.Interestingly,the excess relative extent Eηrel calculated by the MD simulations and chemical shifts in the EtOH aqueous solutions shows the largest deviation at XEtOH≈0.18.The excess properties present good agreement with the excess enthalpy in the concentration dependence.
Hafsa, Noor E; Arndt, David; Wishart, David S
2015-07-01
The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0.
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.
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.
Shundalau, M. B.; Minko, A. A.
2016-01-01
The influence of the energy denominator shift (EDS) parameter and the quantitative and qualitative compositions of electronic states included in CASSCF(2,14)/XMCQDPT2 ab initio calculations of the ground state equilibrium internuclear distance and dissociation energy of polar KRb was determined.
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.
Matsueda, Hiroaki; Hashizume, Yoichiro
2012-01-01
A tensor network formalism of thermofield dynamics is introduced. The formalism relates the original Hilbert space with its tilde space by a product of two copies of a tensor network. Then, their interface becomes an event horizon, and the logarithm of the tensor rank corresponds to the black hole entropy. Eventually, multiscale entanglement renormalization anzats (MERA) reproduces an AdS black hole at finite temperature. Our finding shows rich functionalities of MERA as efficient graphical representation of AdS/CFT correspondence.
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.
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.
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.
Spichty, Martin; Taly, Antoine; Hagn, Franz; Kessler, Horst; Barluenga, Sofia; Winssinger, Nicolas; Karplus, Martin
2009-01-01
We determine the binding mode of a macrocyclic radicicol-like oxime to yeast HSP90 by combining computer simulations and experimental measurements. We sample the macrocyclic scaffold of the unbound ligand by parallel tempering simulations and dock the most populated conformations to yeast HSP90. Docking poses are then evaluated by the use of binding free energy estimations with the linear interaction energy method. Comparison of QM/MM-calculated NMR chemical shifts with experimental shift data for a selective subset of back-bone 15N provides an additional evaluation criteria. As a last test we check the binding modes against available structure-activity-relationships. We find that the most likely binding mode of the oxime to yeast HSP90 is very similar to the known structure of the radicicol-HSP90 complex. PMID:19482409
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.
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.
Mittal, Puneet; Gupta, Ranjana; Mittal, Amit; Joshi, Sandeep
2016-01-01
Introduction: Magnetic resonance imaging (MRI) is the modality of the first choice for evaluation of vertebral compression/collapse. Many MRI qualitative features help to differentiate benign from malignant collapse. We conducted this study to look for a quantitative difference in chemical shift values in benign and malignant collapse using dual-echo gradient echo in-phase/out-phase imaging. Materials and Methods: MRI examinations of a total of 38 patients were retrospectively included in the study who had vertebral compression/collapse with marrow edema in which final diagnosis was available at the time of imaging/follow-up. Signal intensity value in the region of abnormal marrow signal and adjacent normal vertebra was measured on in phase/out phase images. Signal intensity ratio (SIR) was measured by dividing signal intensity value on opposite phase images to that on in phase images. SIR was compared in normal vertebrae and benign and malignant vertebral collapse. Results: There were 21 males and 17 females with mean age of 52.4 years (range 28–76 years). Out of total 38 patients, 18 were of benign vertebral collapse and 20 of malignant vertebral collapse. SIR in normal vertebrae was 0.30 ± 0.14, 0.67 ± 0.18 in benign vertebral collapse, and 1.20 ± 0.27 in malignant vertebral collapse with significant difference in SIR of normal vertebrae versus benign collapse (P < 0.01) and in benign collapse versus malignant collapse (P < 0.01). Assuming a cutoff of <0.95 for benign collapse and ≥0.95 for malignant collapse, chemical shift imaging had a sensitivity of 90% and specificity of 94.4%. Conclusion: Chemical shift imaging is a rapid and useful sequence in differentiating benign from malignant vertebral collapse with good specificity and sensitivity.
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.
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)
Folini, Laura; Veronelli, Annamaria; Benetti, Alberto; Pozzato, Carlo; Cappelletti, Marco; Masci, Enzo; Micheletto, Giancarlo; Pontiroli, Antonio E
2014-01-01
The aim of this study was to evaluate in morbid obesity clinical and metabolic effects related to weight loss on liver steatosis (LS), measured through chemical-shift magnetic resonance imaging (MRI) and liver enzymes. Forty obese subjects (8 M/32 W; BMI 42.8 ± 7.12 kg/m(2), mean ± SD) were evaluated for LS through ultrasound (US-LS), chemical-shift MRI (MRI-LS), liver enzymes [aspartate aminotransferase (AST), alanine aminotransferase (ALT), γ-glutamyltransferase (GGT), alkaline phosphatase (ALP)], anthropometric parameters [weight, BMI, waist circumference (WC)], lipids, insulin, insulin resistance (HOMA-IR), glycated hemoglobin (HbA1c), oral glucose tolerance test, and body composition [fat mass (FM) and fat-free mass (FFM) at bio-impedance analysis (BIA)]. Anthropometric measures, MRI-LS, BIA, and biochemical parameters were reevaluated 6 months later in 18 subjects undergoing restrictive bariatric approach, i.e., intragastric balloon (BIB, n = 13) or gastric banding (LAGB, n = 5), and in 13 subjects receiving hypocaloric diet. At baseline, US-LS correlates only with MRI-LS, and the latter correlates with ALT, AST, and GGT. After 6 months, subjects undergoing BIB or LAGB had significant changes of BMI, weight, WC, ALT, AST, GGT, ALP, HbA1c, insulin, HOMA-IR, FM, FFM, and MRI-LS. Diet-treated obese subjects had no significant change of any parameter under study; change of BMI, fat mass, and fat-free mass was significantly greater in LAGB/BIB subjects than in diet-treated subjects. Change of MRI-LS showed a significant correlation with changes in weight, BMI, WC, GGT, ALP, and basal MRI-LS. Significant weight loss after BIB or LAGB is associated with decrease in chemical-shift MRI-LS and with reduction in liver enzymes; chemical-shift MRI and liver enzymes allow monitoring of LS in follow-up studies.
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
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 independe...... of the small-scale structure of the Earth’s lithospheric field....
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)
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...
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.
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.
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).
Torii, Hajime
2016-09-15
Understanding on the spectroscopic properties of a functional group is essential to use it to detect changes in the structural and/or dynamical properties through the situations of intermolecular interactions. The present study is devoted to elucidating the factors that control the solvation-induced changes in the C≡N stretching frequency and the (13)C and (15)N NMR chemical shifts of the nitrile group. It is shown that the nonelectrostatic contribution of the hydration-induced changes in the C≡N stretching frequency as previously thought, as well as the specific effect of hydrogen bonding on the (13)C and (15)N chemical shifts, actually originate from the spatially inhomogeneous nature of the electrostatic situation generated by the hydrogen-bond donating water molecule, especially by the OH bond dipole. On this basis, a unified electrostatic interaction model that encompasses the cases of both hydration and dipolar solvation is constructed. The responses of electrons in these two cases are also discussed. PMID:27547990
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.
Goudarzi, Nasser
2016-04-01
In this work, two new and powerful chemometrics methods are applied for the modeling and prediction of the 19F chemical shift values of some fluorinated organic compounds. The radial basis function-partial least square (RBF-PLS) and random forest (RF) are employed to construct the models to predict the 19F chemical shifts. In this study, we didn't used from any variable selection method and RF method can be used as variable selection and modeling technique. Effects of the important parameters affecting the ability of the RF prediction power such as the number of trees (nt) and the number of randomly selected variables to split each node (m) were investigated. The root-mean-square errors of prediction (RMSEP) for the training set and the prediction set for the RBF-PLS and RF models were 44.70, 23.86, 29.77, and 23.69, respectively. Also, the correlation coefficients of the prediction set for the RBF-PLS and RF models were 0.8684 and 0.9313, respectively. The results obtained reveal that the RF model can be used as a powerful chemometrics tool for the quantitative structure-property relationship (QSPR) studies.
Mori, Mirko; Kateb, Fatiha; Bodenhausen, Geoffrey; Piccioli, Mario; Abergel, Daniel
2010-03-17
Multiple quantum relaxation in proteins reveals unexpected relationships between correlated or anti-correlated conformational backbone dynamics in alpha-helices or beta-sheets. The contributions of conformational exchange to the relaxation rates of C'N coherences (i.e., double- and zero-quantum coherences involving backbone carbonyl (13)C' and neighboring amide (15)N nuclei) depend on the kinetics of slow exchange processes, as well as on the populations of the conformations and chemical shift differences of (13)C' and (15)N nuclei. The relaxation rates of C'N coherences, which reflect concerted fluctuations due to slow chemical shift modulations (CSMs), were determined by direct (13)C detection in diamagnetic and paramagnetic proteins. In well-folded proteins such as lanthanide-substituted calbindin (CaLnCb), copper,zinc superoxide dismutase (Cu,Zn SOD), and matrix metalloproteinase (MMP12), slow conformational exchange occurs along the entire backbone. Our observations demonstrate that relaxation rates of C'N coherences arising from slow backbone dynamics have positive signs (characteristic of correlated fluctuations) in beta-sheets and negative signs (characteristic of anti-correlated fluctuations) in alpha-helices. This extends the prospects of structure-dynamics relationships to slow time scales that are relevant for protein function and enzymatic activity.
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...
Block Tensor Decomposition for Source Apportionment of Air Pollution
Hopke, Philip K; Li, Na; Navasca, Carmeliza
2011-01-01
The ambient particulate chemical composition data with three particle diameter sizes (2.5mm
Correlation of proton MR spectroscopy and diffusion tensor imaging.
Irwan, Roy; Sijens, Paul E; Potze, Jan-Hendrik; Oudkerk, Matthijs
2005-10-01
Proton magnetic resonance spectroscopy ((1)H-MRS) provides indices of neuronal damage. Diffusion tensor imaging (DTI) relates to water diffusivity and fiber tract orientation. A method to compare (1)H-MRS and DTI findings was developed, tested on phantom and applied on normal brain. Point-resolved spectroscopy (T(R)/T(E)=1500/135) was used for chemical shift imaging of a supraventricular volume of interest of 8 x 8 x 2 cm(3) (64 voxels). In DTI, a segmental spin-echo sequence (T(R)/T(E)=5500/91) was used and slices were stacked to reproduce the slab used in MRS. The spatial distributions of choline and N-acetylaspartate (NAA) correlated to mean fractional anisotropy and apparent diffusion coefficient (ADC) for the inner 6 x 6=36 voxels defined in MRS, most notably NAA and ADC value (r=-.70, P<.00001; correlation across four subjects, 144 data pairs). This is the first association of neuron metabolite contents in volunteers with structure as indicated by DTI.
Kerler, T
1994-01-01
We investigate invertible elements and gradings in braided tensor categories. This leads us to the definition of theta-, product-, subgrading and orbitcategories in order to construct new families of BTC's from given ones. We use the representation theory of Hecke algebras in order to relate the fusionring of a BTC generated by an object $X$ with a two component decomposition of its tensorsquare to the fusionring of quantum groups of type $A$ at roots of unity. We find the condition of "local isomorphie" on a special fusionring morphism implying that a BTC is obtained from the above constructions applied to the semisimplified representation category of a quantum group. This family of BTC's contains new series of twisted categories that do not stem from known Hopf algebras. Using the language of incidence graphs and the balancing structure on a BTC we also find strong constraints on the fusionring morphism. For Temperley Lieb type categories these are sufficient to show local isomorphie. Thus we obtain a class...
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.
Colored Tensor Models - a Review
Directory of Open Access Journals (Sweden)
Razvan Gurau
2012-04-01
Full Text Available Colored tensor models have recently burst onto the scene as a promising conceptual and computational tool in the investigation of problems of random geometry in dimension three and higher. We present a snapshot of the cutting edge in this rapidly expanding research field. Colored tensor models have been shown to share many of the properties of their direct ancestor, matrix models, which encode a theory of fluctuating two-dimensional surfaces. These features include the possession of Feynman graphs encoding topological spaces, a 1/N expansion of graph amplitudes, embedded matrix models inside the tensor structure, a resumable leading order with critical behavior and a continuum large volume limit, Schwinger-Dyson equations satisfying a Lie algebra (akin to the Virasoro algebra in two dimensions, non-trivial classical solutions and so on. In this review, we give a detailed introduction of colored tensor models and pointers to current and future research directions.
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
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.
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...
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...
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.
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.
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.
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.)
Safari, Mohammad Reza; Rowe, Philip; Buis, Arjan
2013-01-01
The quality of lower-limb prosthetic socket fit is influenced by shape and volume consistency during the residual limb shape-capturing process (i.e., casting). Casting can be quantified with magnetic resonance imaging (MRI) technology. However, chemical shift artifact and image distortion may influence the accuracy of MRI when common socket/casting materials are used. We used a purpose-designed rig to examine seven different materials commonly used in socket fabrication during exposure to MRI. The rig incorporated glass marker tubes filled with water doped with 1 g/L copper sulfate (CS) and 9 plastic sample vials (film containers) to hold the specific material specimens. The specimens were scanned 9 times in different configurations. The absolute mean difference of the glass marker tube length was 1.39 mm (2.98%) (minimum = 0.13 mm [0.30%], maximum = 5.47 mm [14.03%], standard deviation = 0.89 mm). The absolute shift for all materials was <1.7 mm. This was less than the measurement tolerance of +/-2.18 mm based on voxel (three-dimensional pixel) dimensions. The results show that MRI is an accurate and repeatable method for dimensional measurement when using matter containing water. Additionally, silicone and plaster of paris plus 1 g/L CS do not show a significant shape distortion nor do they interfere with the MRI image of the residual limb.
Directory of Open Access Journals (Sweden)
Mohammad Reza Safari, PhD
2013-02-01
Full Text Available The quality of lower-limb prosthetic socket fit is influenced by shape and volume consistency during the residual limb shape-capturing process (i.e., casting. Casting can be quantified with magnetic resonance imaging (MRI technology. However, chemical shift artifact and image distortion may influence the accuracy of MRI when common socket/casting materials are used. We used a purpose-designed rig to examine seven different materials commonly used in socket fabrication during exposure to MRI. The rig incorporated glass marker tubes filled with water doped with 1 g/L copper sulfate (CS and 9 plastic sample vials (film containers to hold the specific material specimens. The specimens were scanned 9 times in different configurations. The absolute mean difference of the glass marker tube length was 1.39 mm (2.98% (minimum = 0.13 mm [0.30%], maximum = 5.47 mm [14.03%], standard deviation = 0.89 mm. The absolute shift for all materials was <1.7 mm. This was less than the measurement tolerance of +/–2.18 mm based on voxel (three-dimensional pixel dimensions. The results show that MRI is an accurate and repeatable method for dimensional measurement when using matter containing water. Additionally, silicone and plaster of paris plus 1 g/L CS do not show a significant shape distortion nor do they interfere with the MRI image of the residual limb.
DEFF Research Database (Denmark)
Hass, M. A. S.; Thuesen, Marianne Hallberg; Christensen, Hans Erik Mølager;
2004-01-01
An approach is presented that allows a detailed, quantitative characterization of conformational exchange processes in proteins on the mus-ms time scale. The approach relies on a combined analysis of NMR relaxation rates and chemical shift changes and requires that the chemical shift...... variabilis (A.v. PCu) (Ma, L.; Hass, M. A. S.; Vierick, N.; Kristensen, S. M.; Ulstrup, J.; Led, J. J. Biochemistry 2003, 42, 320-330). The R-1 and R-2 relaxation rates of the backbone N-15 nuclei were measured at a series of pH and temperatures on an 15N labeled sample of A.v. PCu, and the 15 N chemical...... quantitatively by the correlation between the R-ex terms and the corresponding chemical shift differences of the exchanging species. By this approach, the R-ex terms of N-15 nuclei belonging to contiguous regions in the protein could be assigned to the same exchange process. Furthermore, the analysis...
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.)
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
Renormalization of the energy-momentum tensor on the lattice
Pepe, Michele
2015-01-01
We present the calculation of the non-perturbative renormalization constants of the energy-momentum tensor in the SU(3) Yang-Mills theory. That computation is carried out in the framework of shifted boundary conditions, where a thermal quantum field theory is formulated in a moving reference frame. The non-perturbative renormalization factors are then used to measure the Equation of State of the SU(3) Yang-Mills theory. Preliminary numerical results are presented and discussed.
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.
Compressive sensing of sparse tensors.
Friedland, Shmuel; Li, Qun; Schonfeld, Dan
2014-10-01
Compressive sensing (CS) has triggered an enormous research activity since its first appearance. CS exploits the signal's sparsity or compressibility in a particular domain and integrates data compression and acquisition, thus allowing exact reconstruction through relatively few nonadaptive linear measurements. While conventional CS theory relies on data representation in the form of vectors, many data types in various applications, such as color imaging, video sequences, and multisensor networks, are intrinsically represented by higher order tensors. Application of CS to higher order data representation is typically performed by conversion of the data to very long vectors that must be measured using very large sampling matrices, thus imposing a huge computational and memory burden. In this paper, we propose generalized tensor compressive sensing (GTCS)-a unified framework for CS of higher order tensors, which preserves the intrinsic structure of tensor data with reduced computational complexity at reconstruction. GTCS offers an efficient means for representation of multidimensional data by providing simultaneous acquisition and compression from all tensor modes. In addition, we propound two reconstruction procedures, a serial method and a parallelizable method. We then compare the performance of the proposed method with Kronecker compressive sensing (KCS) and multiway compressive sensing (MWCS). We demonstrate experimentally that GTCS outperforms KCS and MWCS in terms of both reconstruction accuracy (within a range of compression ratios) and processing speed. The major disadvantage of our methods (and of MWCS as well) is that the compression ratios may be worse than that offered by KCS.
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...
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.
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 $\\...
Carrozza, Sylvain; Tanasa, Adrian
2016-11-01
We define in this paper a class of three-index tensor models, endowed with {O(N)^{⊗ 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.
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.
Phase Transition in Tensor Models
Delepouve, Thibault
2015-01-01
Generalizing matrix models, tensor models generate dynamical triangulations in any dimension and support a $1/N$ expansion. Using the intermediate field representation we explicitly rewrite a quartic tensor model as a field theory for a fluctuation field around a vacuum state corresponding to the resummation of the entire leading order in $1/N$ (a resummation of the melonic family). We then prove that the critical regime in which the continuum limit in the sense of dynamical triangulations is reached is precisely a phase transition in the field theory sense for the fluctuation field.
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
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.
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...
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
Weesie, R J; Jansen, F J; Merlin, J C; Lugtenburg, J; Britton, G; de Groot, H J
1997-06-17
Selective isotope enrichment, 13C magic angle spinning (MAS) NMR, and semiempirical quantum chemical modeling, have been used to analyze ligand-protein interactions associated with the bathochromic shift of astaxanthin in alpha-crustacyanin, the blue carotenoprotein complex from the carapace of the lobster Homarus gammarus. Spectra of alpha-crustacyanin were obtained after reconstitution with astaxanthins labeled with 13C at positions 4,4', 12,12', 13,13', or 20,20'. The data reveal substantial downfield shifts of 4.9 and 7.0 ppm at positions 12 and 12' in the complex, respectively. In contrast, at the 13 and 13' positions, small upfield shifts of 1.9 ppm were observed upon binding to the protein. These data are in line with previously obtained results for positions 14,14' (3.9 and 6.8 ppm downfield) and 15,15' (0.6 ppm upfield) and confirm the unequal perturbation of both halves after binding of the chromophore. However, these results also show that the main perturbation is of symmetrical origin, since the chemical shift differences exhibit a similar pattern in both halves of the astaxanthin molecule. A small downfield shift of 2.4 ppm was detected for the 4 and 4' positions. Finally, the 20,20' methyl groups are shifted 0.4 ppm upfield by the protein. The full data set provides convincing evidence that charge polarization is of importance for the bathochromic shift. The NMR shifts are compared with calculated charge densities for astaxanthin subjected to variations in protonation states of the ring-functional groups, as models of ligand-protein interactions. Taking into account the color shift and other available optical data, the current model for the mechanisms of interaction with the protein was refined. The results point toward a mechanism in which the astaxanthin is charged and subject to strong electrostatic polarizations originating from both keto groups, most likely a double protonation. PMID:9200677
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
Thurber, Kent R.; Tycko, Robert
2009-01-01
Accurate determination of sample temperatures in solid state nuclear magnetic resonance (NMR) with magic-angle spinning (MAS) can be problematic, particularly because frictional heating and heating by radio-frequency irradiation can make the internal sample temperature significantly different from the temperature outside the MAS rotor. This paper demonstrates the use of 79Br chemical shifts and spin-lattice relaxation rates in KBr powder as temperature-dependent parameters for the determination of internal sample temperatures. Advantages of this method include high signal-to-noise, proximity of the 79Br NMR frequency to that of 13C, applicability from 20 K to 320 K or higher, and simultaneity with adjustment of the MAS axis direction. We show that spin-lattice relaxation in KBr is driven by a quadrupolar mechanism. We demonstrate a simple approach to including KBr powder in hydrated samples, such as biological membrane samples, hydrated amyloid fibrils, and hydrated microcrystalline proteins, that allows direct assessment of the effects of frictional and radio-frequency heating under experimentally relevant conditions. PMID:18930418
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
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.
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.)
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.
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.
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.
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…
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...
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.
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.
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.
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.
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.
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
Scalar-tensor linear inflation
Artymowski, Michal
2016-01-01
We investigate two approaches to non minimally coupled gravity theories which present linear inflation as attractor solution: a) the scalar-tensor theory approach, where we look for a scalar-tensor theory that would restore results of linear inflation in the strong coupling limit for any form of the non-minimal coupling to gravity of the form of $f(\\varphi)R/2$; b) the particle physics approach, where we motivate the form of the Jordan frame potential by the loop corrections to the inflaton field. In both cases the Jordan frame potentials are modifications of the induced inflation, but instead of the Starobinsky attractor they lead to the linear inflation in the strong coupling limit.
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.
Causality and Primordial Tensor Modes
Baumann, Daniel
2009-01-01
We introduce the real space correlation function of $B$-mode polarization of the cosmic microwave background (CMB) as a probe of superhorizon tensor perturbations created by inflation. By causality, any non-inflationary mechanism for gravitational wave production after reheating, like global phase transitions or cosmic strings, must have vanishing correlations for angular separations greater than the angle subtended by the particle horizon at recombination, i.e. $\\theta \\gtrsim 2^\\circ$. Since ordinary $B$-modes are defined non-locally in terms of the Stokes parameters $Q$ and $U$ and therefore don't have to respect causality, special care is taken to define `causal $\\tilde B$-modes' for the analysis. We compute the real space $\\tilde B$-mode correlation function for inflation and discuss its detectability on superhorizon scales where it provides an unambiguous test of inflationary gravitational waves. The correct identification of inflationary tensor modes is crucial since it relates directly to the energy s...
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
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.
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...
Energy Technology Data Exchange (ETDEWEB)
Saur, R. [Sektion fuer Experimentelle Kernspinresonanz des ZNS, Abt. Neuroradiologie, Universitaetsklinikum Tuebingen (Germany); Augenklinik des Universitaetsklinikums Tuebingen (Germany); Klinik fuer Psychiatrie und Psychotherapie des Universitaetsklinikums Tuebingen (Germany); Gharabaghi, A. [Klinik fuer Neurochirurgie des Universitaetsklinikums Tuebingen (Germany); Erb, M. [Sektion fuer Experimentelle Kernspinresonanz des ZNS, Abt. Neuroradiologie, Universitaetsklinikum Tuebingen (Germany)
2007-07-01
Knowledge about integrity and location of fibre tracts arising from eloquent cortical areas is important to plan neurosurgical interventions and to allow maximization of resection of pathological tissue while preserving vital white matter tracts. Diffusion Tensor Imaging (DTI) is so far the only method to get preoperatively an impression of the individual complexity of nerve bundles. Thereby nerve fibres are not mapped directly. They are derived indirectly by analysis of the directional distribution of diffusion of water molecules which is influenced mainly by large fibre tracts. From acquisition to reconstruction and visualisation of the fibre tracts many representational stages and working steps have to be passed. Exact knowledge about problems of Diffusion Imaging is important for interpretation of the results. Particularly, brain tumor edema, intraoperative brain shift, MR-artefacts and limitations of the mathematical models and algorithms challenge DTI-developers and applicants. (orig.)
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.
de Vries, AH; Hozoi, L; Broer, R; Broer-Braam, H.B.
2003-01-01
The absorption edge in Mn K-edge X-ray absorption spectra of manganese oxide compounds shows a shift of several electronvolts in going from MnO through LaMnO3 to CaMnO3. On the other hand, in X-ray photoelectron spectra much smaller shifts are observed. To identify the mechanisms that cause the obse
Directory of Open Access Journals (Sweden)
Regina Esterhammer
Full Text Available Recently published studies have elucidated alterations of mitochondrial oxidative metabolism during ageing. The intention of the present study was to evaluate the impact of ageing on cardiac high-energy phosphate metabolism and cardiac function in healthy humans. 31-phosphorus 2-dimensional chemical shift imaging (31P 2D CSI and echocardiography were performed in 196 healthy male volunteers divided into groups of 20 to 40 years (I, n = 43, 40 to 60 years (II, n = 123 and >60 years (III, n = 27 of age. Left ventricular PCr/β-ATP ratio, myocardial mass (MM, ejection fraction and E/A ratio were assessed. Mean PCr/β-ATP ratios were significantly different among the three groups of volunteers (I, 2.10 ± 0.37; II, 1.77 ± 0.37; III, 1.45 ± 0.28; all p<0.001. PCr/β-ATP ratios were inversely related to age (r(2 = -0.25; p<0.001 with a decrease from 2.65 by 0.02 per year of ageing. PCr/β-ATP ratios further correlated with MM (r = -0.371; p<0.001 and E/A ratios (r = 0.213; p<0.02. Moreover, E/A ratios (r = -0.502, p<0.001, MM (r = 0.304, p<0.001, glucose-levels (r = 0.157, p<0.05 and systolic blood pressure (r = 0.224, p<0.005 showed significant correlations with age. The ejection fraction did not significantly differ between the groups. This study shows that cardiac PCr/β-ATP ratios decrease moderately with age indicating an impairment of mitochondrial oxidative metabolism due to age. Furthermore, MM increases, and E/A ratio decreases with age. Both correlate with left-ventricular PCr/β-ATP ratios. The findings of the present study confirm numerous experimental studies showing an impairment of cardiac mitochondrial function with age.
Esterhammer, Regina; Klug, Gert; Wolf, Christian; Mayr, Agnes; Reinstadler, Sebastian; Feistritzer, Hans-Josef; Metzler, Bernhard; Schocke, Michael F H
2014-01-01
Recently published studies have elucidated alterations of mitochondrial oxidative metabolism during ageing. The intention of the present study was to evaluate the impact of ageing on cardiac high-energy phosphate metabolism and cardiac function in healthy humans. 31-phosphorus 2-dimensional chemical shift imaging (31P 2D CSI) and echocardiography were performed in 196 healthy male volunteers divided into groups of 20 to 40 years (I, n = 43), 40 to 60 years (II, n = 123) and >60 years (III, n = 27) of age. Left ventricular PCr/β-ATP ratio, myocardial mass (MM), ejection fraction and E/A ratio were assessed. Mean PCr/β-ATP ratios were significantly different among the three groups of volunteers (I, 2.10 ± 0.37; II, 1.77 ± 0.37; III, 1.45 ± 0.28; all p<0.001). PCr/β-ATP ratios were inversely related to age (r(2) = -0.25; p<0.001) with a decrease from 2.65 by 0.02 per year of ageing. PCr/β-ATP ratios further correlated with MM (r = -0.371; p<0.001) and E/A ratios (r = 0.213; p<0.02). Moreover, E/A ratios (r = -0.502, p<0.001), MM (r = 0.304, p<0.001), glucose-levels (r = 0.157, p<0.05) and systolic blood pressure (r = 0.224, p<0.005) showed significant correlations with age. The ejection fraction did not significantly differ between the groups. This study shows that cardiac PCr/β-ATP ratios decrease moderately with age indicating an impairment of mitochondrial oxidative metabolism due to age. Furthermore, MM increases, and E/A ratio decreases with age. Both correlate with left-ventricular PCr/β-ATP ratios. The findings of the present study confirm numerous experimental studies showing an impairment of cardiac mitochondrial function with age. PMID:24940736
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
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...
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.
Tensor coupling effect on relativistic symmetries
Chen, ShouWan; Li, DongPeng; Guo, JianYou
2016-08-01
The similarity renormalization group is used to transform the Dirac Hamiltonian with tensor coupling into a diagonal form. The upper (lower) diagonal element becomes a Schr¨odinger-like operator with the tensor component separated from the original Hamiltonian. Based on the operator, the tensor effect of the relativistic symmetries is explored with a focus on the single-particle energy contributed by the tensor coupling. The results show that the tensor coupling destroying (improving) the spin (pseudospin) symmetry is mainly attributed to the coupling of the spin-orbit and the tensor term, which plays an opposite role in the single-particle energy for the (pseudo-) spin-aligned and spin-unaligned states and has an important influence on the shell structure and its evolution.
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.
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 ...
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...
Hard Exclusive Production of Tensor Mesons
Braun, V M
2001-01-01
We point out that hard exclusive production of tensor mesons $f_2(1270)$ with helicity $\\lambda=\\pm 2$ is dominated by the gluon component in the meson wave function and can be used to determine gluon admixture in tensor mesons in a theoretically clean manner. We present a detailed analysis of the tensor meson distribution amplitudes and calculate the transition form factor $\\gamma+\\gamma^*\\to f_2(1270)$ for one real and one virtual photon.
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...
The Topology of Symmetric Tensor Fields
Levin, Yingmei; Batra, Rajesh; Hesselink, Lambertus; Levy, Yuval
1997-01-01
Combinatorial topology, also known as "rubber sheet geometry", has extensive applications in geometry and analysis, many of which result from connections with the theory of differential equations. A link between topology and differential equations is vector fields. Recent developments in scientific visualization have shown that vector fields also play an important role in the analysis of second-order tensor fields. A second-order tensor field can be transformed into its eigensystem, namely, eigenvalues and their associated eigenvectors without loss of information content. Eigenvectors behave in a similar fashion to ordinary vectors with even simpler topological structures due to their sign indeterminacy. Incorporating information about eigenvectors and eigenvalues in a display technique known as hyperstreamlines reveals the structure of a tensor field. The simplify and often complex tensor field and to capture its important features, the tensor is decomposed into an isotopic tensor and a deviator. A tensor field and its deviator share the same set of eigenvectors, and therefore they have a similar topological structure. A a deviator determines the properties of a tensor field, while the isotopic part provides a uniform bias. Degenerate points are basic constituents of tensor fields. In 2-D tensor fields, there are only two types of degenerate points; while in 3-D, the degenerate points can be characterized in a Q'-R' plane. Compressible and incompressible flows share similar topological feature due to the similarity of their deviators. In the case of the deformation tensor, the singularities of its deviator represent the area of vortex core in the field. In turbulent flows, the similarities and differences of the topology of the deformation and the Reynolds stress tensors reveal that the basic addie-viscosity assuptions have their validity in turbulence modeling under certain conditions.
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...... real-world resource use into a game....
Institute of Scientific and Technical Information of China (English)
无
2008-01-01
@@ "We are entering a new era of world history: the end of Western domination and the arrival of the Asian century. The question is: will Washington wake up to this reality?" This is the central premise of Kishore Mahbubani's provocative new book The New Asian Hemisphere: The Irresistible Shift of Global Power to the East.
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.
Dirac tensor with heavy photon
Energy Technology Data Exchange (ETDEWEB)
Bytev, V.V.; Kuraev, E.A. [Joint Institute of Nuclear Research, Moscow (Russian Federation). Bogoliubov Lab. of Theoretical Physics; Scherbakova, E.S. [Hamburg Univ. (Germany). 1. Inst. fuer Theoretische Physik
2012-01-15
For the large-angles hard photon emission by initial leptons in process of high energy annihilation of e{sup +}e{sup -} {yields} to hadrons the Dirac tensor is obtained, taking into account the lowest order radiative corrections. The case of large-angles emission of two hard photons by initial leptons is considered. This result is being completed by the kinematics case of collinear hard photons emission as well as soft virtual and real photons and can be used for construction of Monte-Carlo generators. (orig.)
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, (\
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.
Tensor power spectrum and disformal transformations
Fumagalli, Jacopo; Postma, Marieke
2016-01-01
In a general effective theory description of inflation a disformal transformation can be used to set the tensor sound speed to one. After the transformation, the tensor power spectrum then automatically only depends on the Hubble parameter. We show that this disformal transformation, however, is nothing else than a change of units. It is a very useful tool for simplifying and interpreting computations, but it cannot change any physics. While the apparent parametrical dependence of the tensor power spectrum does change under a disformal transformation, the physics described is frame invariant. We further illustrate the frame invariance of the tensor power spectrum by writing it exclusively in terms of separately invariant quantities.
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
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
Energy Technology Data Exchange (ETDEWEB)
Hong Jingbo; Jing Qingqing; Yao Lishan, E-mail: yaols@qibebt.ac.cn [Chinese Academy of Sciences, Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology (China)
2013-01-15
The protein amide {sup 1}H{sup N} chemical shift temperature coefficient can be determined with high accuracy by recording spectra at different temperatures, but the physical mechanism responsible for this temperature dependence is not well understood. In this work, we find that this coefficient strongly correlates with the temperature coefficient of the through-hydrogen-bond coupling, {sup 3h}J{sub NC Prime }, based on NMR measurements of protein GB3. Parallel tempering molecular dynamics simulation suggests that the hydrogen bond distance variation at different temperatures/replicas is largely responsible for the {sup 1}H{sup N} chemical shift temperature dependence, from which an empirical equation is proposed to predict the hydrogen bond thermal expansion coefficient, revealing responses of individual hydrogen bonds to temperature changes. Different expansion patterns have been observed for various networks formed by {beta} strands.
Lipton, Andrew S.; Mason, Scott S.; Myers, Sheila M.; Reger, Daniel L.; Ellis, Paul D.
1996-11-20
The principal elements of the (113)Cd shielding tensor for a set of five- coordinate compounds having mixed donor atoms coordinating to the cadmium were determined via CP/MAS NMR experiments. The first complex, [HB(3,5-Me(2)pz)(3)]CdBH(4) (where pz = pyrazolyl), has a CdN(3)H(2) inner coordination sphere. The isotropic chemical shift in the solid state is 355.1 ppm, and its chemical shift anisotropy (CSA, Deltasigma) is -596 ppm with an asymmetry parameter (eta) of 0.64. The second complex, [HB(3,5-Me(2)pz)(3)]Cd[H(2)B(pz)(2)], has five nitrogen donor atoms bonded to the cadmium. This N(5) or N(3)N(2) compound was the only material of this study to manifest dipolar splitting of the cadmium resonance from the quadrupolar (14)N. The isotropic chemical shift, CSA, and the value of eta for this material were therefore determined at higher field where the dipolar splitting was less than the linewidth, yielding values of 226.6 ppm, -247 ppm, and 0.32, respectively. A second N(5) material, [HB(3-Phpz)(3)]Cd[H(2)B(3,5-Me(2)pz)(2)], was also investigated and has an isotropic shift of 190.2 ppm, a CSA of 254 ppm, and an eta of 0.86. Also studied was [HB(3-Phpz)(3)]Cd[(Bu(t)CO)(2)CH], which has an CdN(3)O(2) inner core. The isotropic chemical shift of this complex is 173.6 ppm, and the values of Deltasigma and eta were determined to be -258 ppm and 0.38, respectively. The final compound, [HB(3,5-Me(2)pz)(3)]Cd[S(2)CNEt(2)], with N(3)S(2) donor atoms, has an isotropic shift of 275.8 ppm, an eta of 0.51, and a CSA of +375 ppm. Utilizing previous assignments, the most shielded tensor element was determined to be oriented normal to the plane of the tridentate ligand. The shielding tensor information is used to speculate on the coordination geometry of the CdN(3)O(2) inner core complex. PMID:11666894
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'...
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.
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.
Shifting entanglement from states to observables
Energy Technology Data Exchange (ETDEWEB)
Ranade, Kedar [Institut fuer Quantenphysik, Universitaet Ulm, 89069 Ulm (Germany); Harshman, Nathan [Department of Physics, American University, Washington DC (United States); Institut fuer Quantenphysik, Universitaet Ulm, 89069 Ulm (Germany)
2011-07-01
We illustrate that for any pure state on a finite-dimensional Hilbert space we can construct observables that induce a tensor product structure such that the amount of entanglement of the state may take arbitrary values. In particular, we provide an example of how to construct observables on a d-dimensional system such that an arbitrary known pure state can be treated as maximally entangled. In effect, we show how entanglement properties can be shifted from states to observables.
Bayesian regularization of diffusion tensor images
DEFF Research Database (Denmark)
Frandsen, Jesper; Hobolth, Asger; Østergaard, Leif;
2007-01-01
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...
Tensor Products of Random Unitary Matrices
Tkocz, Tomasz; Kus, Marek; Zeitouni, Ofer; Zyczkowski, Karol
2012-01-01
Tensor products of M random unitary matrices of size N from the circular unitary ensemble are investigated. We show that the spectral statistics of the tensor product of random matrices becomes Poissonian if M=2, N become large or M become large and N=2.
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.
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.
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.
Tsipis, Athanassios C; Karapetsas, Ioannis N
2016-08-01
(195) Pt NMR chemical shifts of octahedral Pt(IV) complexes with general formula [Pt(NO3 )n (OH)6 - n ](2-) , [Pt(NO3 )n (OH2 )6 - n ](4 - n) (n = 1-6), and [Pt(NO3 )6 - n - m (OH)m (OH2 )n ](-2 + n - m) formed by dissolution of platinic acid, H2 [Pt(OH)6 ], in aqueous nitric acid solutions are calculated employing density functional theory methods. Particularly, the gauge-including atomic orbitals (GIAO)-PBE0/segmented all-electron relativistically contracted-zeroth-order regular approximation (SARC-ZORA)(Pt) ∪ 6-31G(d,p)(E)/Polarizable Continuum Model computational protocol performs the best. Excellent second-order polynomial plots of δcalcd ((195) Pt) versus δexptl ((195) Pt) chemical shifts and δcalcd ((195) Pt) versus the natural atomic charge QPt are obtained. Despite of neglecting relativistic and spin orbit effects the good agreement of the calculated δ (195) Pt chemical shifts with experimental values is probably because of the fact that the contribution of relativistic and spin orbit effects to computed σ(iso) (195) Pt magnetic shielding of Pt(IV) coordination compounds is effectively cancelled in the computed δ (195) Pt chemical shifts, because the relativistic corrections are expected to be similar in the complexes and the proper reference standard used. To probe the counter-ion effects on the (195) Pt NMR chemical shifts of the anionic [Pt(NO3 )n (OH)6 - n ](2-) and cationic [Pt(NO3 )n (OH2 )6 - n ](4 - n) (n = 0-3) complexes we calculated the (195) Pt NMR chemical shifts of the neutral (PyH)2 [Pt(NO3 )n (OH)6 - n ] (n = 1-6; PyH = pyridinium cation, C5 H5 NH(+) ) and [Pt(NO3 )n (H2 O)6 - n ](NO3 )4 - n (n = 0-3) complexes. Counter-anion effects are very important for the accurate prediction of the (195) Pt NMR chemical shifts of the cationic [Pt(NO3 )n (OH2 )6 - n ](4 - n) complexes, while counter-cation effects are less important for the anionic [Pt(NO3 )n (OH)6
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.)
Algebraically contractible topological tensor network states
Denny, S J; Jaksch, D; Clark, S R
2011-01-01
We adapt the bialgebra and Hopf relations to expose internal structure in the ground state of a Hamiltonian with $Z_2$ topological order. Its tensor network description allows for exact contraction through simple diagrammatic rewrite rules. The contraction property does not depend on specifics such as geometry, but rather originates from the non-trivial algebraic properties of the constituent tensors. We then generalise the resulting tensor network from a spin-half lattice to a class of exactly contractible states on spin-S degrees of freedom, yielding the most efficient tensor network description of finite Abelian lattice gauge theories. We gain a new perspective on these states as examples of two-dimensional quantum states with algebraically contractible tensor network representations. The introduction of local perturbations to the network is shown to reduce the von Neumann entropy of string-like regions, creating an unentangled sub-system within the bulk in a certain limit. We also show how perturbations l...
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
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.
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...
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.
Energy Technology Data Exchange (ETDEWEB)
Shi, Pan [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Xi, Zhaoyong; Wang, Hu [School of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026 (China); Shi, Chaowei [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Xiong, Ying, E-mail: yxiong73@ustc.edu.cn [School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Tian, Changlin, E-mail: cltian@ustc.edu.cn [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China)
2010-11-19
Research highlights: {yields} Chemical synthesis of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine. {yields} Site-specific incorporation of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine to SH3. {yields} Site-specific backbone and side chain chemical shift and relaxation analysis. {yields} Different internal motions at different sites of SH3 domain upon ligand binding. -- Abstract: SH3 is a ubiquitous domain mediating protein-protein interactions. Recent solution NMR structural studies have shown that a proline-rich peptide is capable of binding to the human vinexin SH3 domain. Here, an orthogonal amber tRNA/tRNA synthetase pair for {sup 15}N/{sup 19}F-trifluoromethyl-phenylalanine ({sup 15}N/{sup 19}F-tfmF) has been applied to achieve site-specific labeling of SH3 at three different sites. One-dimensional solution NMR spectra of backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F were obtained for SH3 with three different site-specific labels. Site-specific backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F chemical shift and relaxation analysis of SH3 in the absence or presence of a peptide ligand demonstrated different internal motions upon ligand binding at the three different sites. This site-specific NMR analysis might be very useful for studying large-sized proteins or protein complexes.
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....
Tensor methods for large, sparse unconstrained optimization
Energy Technology Data Exchange (ETDEWEB)
Bouaricha, A.
1996-11-01
Tensor methods for unconstrained optimization were first introduced by Schnabel and Chow [SIAM J. Optimization, 1 (1991), pp. 293-315], who describe these methods for small to moderate size problems. This paper extends these methods to large, sparse unconstrained optimization problems. This requires an entirely new way of solving the tensor model that makes the methods suitable for solving large, sparse optimization problems efficiently. We present test results for sets of problems where the Hessian at the minimizer is nonsingular and where it is singular. These results show that tensor methods are significantly more efficient and more reliable than standard methods based on Newton`s method.
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.
Tensor network and a black hole
Matsueda, Hiroaki; Ishihara, Masafumi; Hashizume, Yoichiro
2013-03-01
A tensor-network variational formalism of thermofield dynamics is introduced. The formalism relates the original Hilbert space with its tilde space by a product of two copies of a tensor network. Then, their interface becomes an event horizon, and the logarithm of the tensor rank corresponds to the black hole entropy. Eventually, a multiscale entanglement renormalization ansatz reproduces an anti-de Sitter black hole at finite temperature. Our finding shows rich functionalities of multiscale entanglement renormalization ansatz as efficient graphical representation of AdS/CFT correspondence.
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
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
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...
Unsupervised Tensor Mining for Big Data Practitioners.
Papalexakis, Evangelos E; Faloutsos, Christos
2016-09-01
Multiaspect data are ubiquitous in modern Big Data applications. For instance, different aspects of a social network are the different types of communication between people, the time stamp of each interaction, and the location associated to each individual. How can we jointly model all those aspects and leverage the additional information that they introduce to our analysis? Tensors, which are multidimensional extensions of matrices, are a principled and mathematically sound way of modeling such multiaspect data. In this article, our goal is to popularize tensors and tensor decompositions to Big Data practitioners by demonstrating their effectiveness, outlining challenges that pertain to their application in Big Data scenarios, and presenting our recent work that tackles those challenges. We view this work as a step toward a fully automated, unsupervised tensor mining tool that can be easily and broadly adopted by practitioners in academia and industry.
The Weyl tensor correlator in cosmological spacetimes
Fröb, Markus B
2014-01-01
We give a general expression for the Weyl tensor two-point function in a general Friedmann-Lema\\^itre-Robertson-Walker spacetime. We work in reduced phase space for the perturbations, i.e., quantize only the dynamical degrees of freedom without adding any gauge-fixing term. The general formula is illustrated by a calculation in slow-roll single-field inflation to first order in the slow-roll parameters $\\epsilon$ and $\\delta$, and the result is shown to have the correct de Sitter limit as $\\epsilon, \\delta \\to 0$. Furthermore, it is seen that the Weyl tensor correlation function does not suffer from infrared divergences, unlike the two-point functions of the metric and scalar field perturbations. Lastly, we show how to recover the usual tensor power spectrum from the Weyl tensor correlation function.
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...
The Weyl tensor correlator in cosmological spacetimes
Energy Technology Data Exchange (ETDEWEB)
Fröb, Markus B. [Departament de Física Fonamental, Institut de Ciències del Cosmos (ICC), Universitat de Barcelona (UB), C/ Martí i Franquès 1, 08028 Barcelona (Spain); Institut für Theoretische Physik, Universität Leipzig, Brüderstraße 16, 04103 Leipzig (Germany)
2014-12-05
We give a general expression for the Weyl tensor two-point function in a general Friedmann-Lemaître-Robertson-Walker spacetime. We work in reduced phase space for the perturbations, i.e., quantize only the dynamical degrees of freedom without adding any gauge-fixing term. The general formula is illustrated by a calculation in slow-roll single-field inflation to first order in the slow-roll parameters ϵ and δ, and the result is shown to have the correct de Sitter limit as ϵ,δ→0. Furthermore, it is seen that the Weyl tensor correlation function in slow-roll does not suffer from infrared divergences, unlike the two-point functions of the metric and scalar field perturbations. Lastly, we show how to recover the usual tensor power spectrum from the Weyl tensor correlation function.
The Weyl tensor correlator in cosmological spacetimes
Energy Technology Data Exchange (ETDEWEB)
Fröb, Markus B., E-mail: mfroeb@itp.uni-leipzig.de [Departament de Física Fonamental, Institut de Ciències del Cosmos (ICC), Universitat de Barcelona (UB), C/ Martí i Franquès 1, 08028 Barcelona (Spain)
2014-12-01
We give a general expression for the Weyl tensor two-point function in a general Friedmann-Lemaître-Robertson-Walker spacetime. We work in reduced phase space for the perturbations, i.e., quantize only the dynamical degrees of freedom without adding any gauge-fixing term. The general formula is illustrated by a calculation in slow-roll single-field inflation to first order in the slow-roll parameters ε and δ, and the result is shown to have the correct de Sitter limit as ε, δ → 0. Furthermore, it is seen that the Weyl tensor correlation function in slow-roll does not suffer from infrared divergences, unlike the two-point functions of the metric and scalar field perturbations. Lastly, we show how to recover the usual tensor power spectrum from the Weyl tensor correlation function.
Kinetic-energy-momentum tensor in electrodynamics
Sheppard, Cheyenne J.; Kemp, Brandon A.
2016-01-01
We show that the Einstein-Laub formulation of electrodynamics is invalid since it yields a stress-energy-momentum (SEM) tensor that is not frame invariant. Two leading hypotheses for the kinetic formulation of electrodynamics (Chu and Einstein-Laub) are studied by use of the relativistic principle of virtual power, mathematical modeling, Lagrangian methods, and SEM transformations. The relativistic principle of virtual power is used to demonstrate the field dynamics associated with energy relations within a relativistic framework. Lorentz transformations of the respective SEM tensors demonstrate the relativistic frameworks for each studied formulation. Mathematical modeling of stationary and moving media is used to illustrate the differences and discrepancies of specific proposed kinetic formulations, where energy relations and conservation theorems are employed. Lagrangian methods are utilized to derive the field kinetic Maxwell's equations, which are studied with respect to SEM tensor transforms. Within each analysis, the Einstein-Laub formulation violates special relativity, which invalidates the Einstein-Laub SEM tensor.
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.
Unsupervised Tensor Mining for Big Data Practitioners.
Papalexakis, Evangelos E; Faloutsos, Christos
2016-09-01
Multiaspect data are ubiquitous in modern Big Data applications. For instance, different aspects of a social network are the different types of communication between people, the time stamp of each interaction, and the location associated to each individual. How can we jointly model all those aspects and leverage the additional information that they introduce to our analysis? Tensors, which are multidimensional extensions of matrices, are a principled and mathematically sound way of modeling such multiaspect data. In this article, our goal is to popularize tensors and tensor decompositions to Big Data practitioners by demonstrating their effectiveness, outlining challenges that pertain to their application in Big Data scenarios, and presenting our recent work that tackles those challenges. We view this work as a step toward a fully automated, unsupervised tensor mining tool that can be easily and broadly adopted by practitioners in academia and industry. PMID:27642720
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.
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.
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.
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.
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.
Renormalization procedure for random tensor networks and the canonical tensor model
Sasakura, Naoki
2015-01-01
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 the 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 which relates discontinuity of the renormalization-group flow and the phase transitions of random tensor networks.
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.
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.
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.
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.
Algebraically contractible topological tensor network states
Energy Technology Data Exchange (ETDEWEB)
Denny, S J; Jaksch, D; Clark, S R [Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU (United Kingdom); Biamonte, J D, E-mail: s.denny1@physics.ox.ac.uk [Centre for Quantum Technologies, National University of Singapore, 3 Science Drive 2, Singapore 117543 (Singapore)
2012-01-13
We adapt the bialgebra and Hopf relations to expose internal structure in the ground state of a Hamiltonian with Z{sub 2} topological order. Its tensor network description allows for exact contraction through simple diagrammatic rewrite rules. The contraction property does not depend on specifics such as geometry, but rather originates from the non-trivial algebraic properties of the constituent tensors. We then generalise the resulting tensor network from a spin-1/2 lattice to a class of exactly contractible states on spin-S degrees of freedom, yielding the most efficient tensor network description of finite Abelian lattice gauge theories. We gain a new perspective on these states as examples of two-dimensional quantum states with algebraically contractible tensor network representations. The introduction of local perturbations to the network is shown to reduce the von Neumann entropy of string-like regions, creating an unentangled sub-system within the bulk in a certain limit. We also show how local perturbations induce finite-range correlations in this system. This class of tensor networks is readily translated onto any lattice, and we differentiate between the physical consequences of bipartite and non-bipartite lattices on the properties of the corresponding quantum states. We explicitly show this on the hexagonal, square, kagome and triangular lattices. (paper)
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
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.
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.
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.
Energy Technology Data Exchange (ETDEWEB)
Novacek, Jiri [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic); Haba, Noam Y.; Chill, Jordan H. [Bar Ilan University, Department of Chemistry (Israel); Zidek, Lukas, E-mail: lzidek@chemi.muni.cz; Sklenar, Vladimir [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic)
2012-06-15
A pair of 4D NMR experiments for the backbone assignment of disordered proteins is presented. The experiments exploit {sup 13}C direct detection and non-uniform sampling of the indirectly detected dimensions, and provide correlations of the aliphatic proton (H{sup {alpha}}, and H{sup {beta}}) and carbon (C{sup {alpha}}, C{sup {beta}}) resonance frequencies to the protein backbone. Thus, all the chemical shifts regularly used to map the transient secondary structure motifs in the intrinsically disordered proteins (H{sup {alpha}}, C{sup {alpha}}, C{sup {beta}}, C Prime , and N) can be extracted from each spectrum. Compared to the commonly used assignment strategy based on matching the C{sup {alpha}} and C{sup {beta}} chemical shifts, inclusion of the H{sup {alpha}} and H{sup {beta}} provides up to three extra resonance frequencies that decrease the chance of ambiguous assignment. The experiments were successfully applied to the original assignment of a 12.8 kDa intrinsically disordered protein having a high content of proline residues (26 %) in the sequence.
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.
Moment tensors of a dislocation in a porous medium
Wang, Zhi; Hu, Hengshan
2016-06-01
A dislocation can be represented by a moment tensor for calculating seismic waves. However, the moment tensor expression was derived in an elastic medium and cannot completely describe a dislocation in a porous medium. In this paper, effective moment tensors of a dislocation in a porous medium are derived. It is found that the dislocation is equivalent to two independent moment tensors, i.e., the bulk moment tensor acting on the bulk of the porous medium and the isotropic fluid moment tensor acting on the pore fluid. Both of them are caused by the solid dislocation as well as the fluid-solid relative motion corresponding to fluid injection towards the surrounding rocks (or fluid outflow) through the fault plane. For a shear dislocation, the fluid moment tensor is zero, and the dislocation is equivalent to a double couple acting on the bulk; for an opening dislocation or fluid injection, the two moment tensors are needed to describe the source. The fluid moment tensor only affects the radiated compressional waves. By calculating the ratio of the radiation fields generated by unit fluid moment tensor and bulk moment tensor, it is found that the fast compressional wave radiated by the bulk moment tensor is much stronger than that radiated by the fluid moment tensor, while the slow compressional wave radiated by the fluid moment tensor is several times stronger than that radiated by the bulk moment tensor.
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.
Viesser, Renan V; Ducati, Lucas C; Autschbach, Jochen; Tormena, Cláudio F
2015-07-15
In this study, stereoelectronic interactions were considered to explain the experimental difference in the magnitude of the known heavy-atom effect on the (13)C NMR chemical shifts in cis- and trans-1,2-dihaloethene isomers (halo = F, Cl, Br or I). The experimental values were compared to the calculated values with various DFT functionals using both the nonrelativistic approach (NR) and the relativistic approximations SR-ZORA (SR) and SO-ZORA (SO). NBO and NLMO contributions to the (13)C NMR shielding tensors were determined to assess which stereoelectronic interactions have a more important effect on the shielding tensor in each principal axis system (PAS) coordinate. These analyses associated with the orbital rotation model and the HOMO-LUMO energy gap enable rationalization of trends between cis and trans isomers from fluorine to iodine derivatives. Both paramagnetic and SO shielding terms were responsible for the observed trends. It was possible to conclude that the steric interactions between the two iodine atoms and the hyperconjugative interactions involving the halogen lone pairs (LP(X)) and πC[double bond, length as m-dash]C*, σC[double bond, length as m-dash]C* and σC-X* antibonding orbitals are responsible for the lower (13)C NMR shielding for the cis isomers of the bromine and the iodine compounds than that of the trans isomers.
Tensor network algorithm by coarse-graining tensor renormalization on finite periodic lattices
Zhao, Hui-Hai; Xie, Zhi-Yuan; Xiang, Tao; Imada, Masatoshi
2016-03-01
We develop coarse-graining tensor renormalization group algorithms to compute physical properties of two-dimensional lattice models on finite periodic lattices. Two different coarse-graining strategies, one based on the tensor renormalization group and the other based on the higher-order tensor renormalization group, are introduced. In order to optimize the tensor network model globally, a sweeping scheme is proposed to account for the renormalization effect from the environment tensors under the framework of second renormalization group. We demonstrate the algorithms by the classical Ising model on the square lattice and the Kitaev model on the honeycomb lattice, and show that the finite-size algorithms achieve substantially more accurate results than the corresponding infinite-size ones.
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.
Robust Face Clustering Via Tensor Decomposition.
Cao, Xiaochun; Wei, Xingxing; Han, Yahong; Lin, Dongdai
2015-11-01
Face clustering is a key component either in image managements or video analysis. Wild human faces vary with the poses, expressions, and illumination changes. All kinds of noises, like block occlusions, random pixel corruptions, and various disguises may also destroy the consistency of faces referring to the same person. This motivates us to develop a robust face clustering algorithm that is less sensitive to these noises. To retain the underlying structured information within facial images, we use tensors to represent faces, and then accomplish the clustering task based on the tensor data. The proposed algorithm is called robust tensor clustering (RTC), which firstly finds a lower-rank approximation of the original tensor data using a L1 norm optimization function. Because L1 norm does not exaggerate the effect of noises compared with L2 norm, the minimization of the L1 norm approximation function makes RTC robust. Then, we compute high-order singular value decomposition of this approximate tensor to obtain the final clustering results. Different from traditional algorithms solving the approximation function with a greedy strategy, we utilize a nongreedy strategy to obtain a better solution. Experiments conducted on the benchmark facial datasets and gait sequences demonstrate that RTC has better performance than the state-of-the-art clustering algorithms and is more robust to noises. PMID:25546869
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...
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...
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
Entanglement, tensor networks and black hole horizons
Molina-Vilaplana, J.; Prior, J.
2014-11-01
We elaborate on a previous proposal by Hartman and Maldacena on a tensor network which accounts for the scaling of the entanglement entropy in a system at a finite temperature. In this construction, the ordinary entanglement renormalization flow given by the class of tensor networks known as the Multi Scale Entanglement Renormalization Ansatz (MERA), is supplemented by an additional entanglement structure at the length scale fixed by the temperature. The network comprises two copies of a MERA circuit with a fixed number of layers and a pure matrix product state which joins both copies by entangling the infrared degrees of freedom of both MERA networks. The entanglement distribution within this bridge state defines reduced density operators on both sides which cause analogous effects to the presence of a black hole horizon when computing the entanglement entropy at finite temperature in the AdS/CFT correspondence. The entanglement and correlations during the thermalization process of a system after a quantum quench are also analyzed. To this end, a full tensor network representation of the action of local unitary operations on the bridge state is proposed. This amounts to a tensor network which grows in size by adding succesive layers of bridge states. Finally, we discuss on the holographic interpretation of the tensor network through a notion of distance within the network which emerges from its entanglement distribution.
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...
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.
Geodesic-loxodromes for diffusion tensor interpolation and difference measurement.
Kindlmann, Gordon; Estépar, Raúl San José; Niethammer, Marc; Haker, Steven; Westin, Carl-Fredrik
2007-01-01
In algorithms for processing diffusion tensor images, two common ingredients are interpolating tensors, and measuring the distance between them. We propose a new class of interpolation paths for tensors, termed geodesic-loxodromes, which explicitly preserve clinically important tensor attributes, such as mean diffusivity or fractional anisotropy, while using basic differential geometry to interpolate tensor orientation. This contrasts with previous Riemannian and Log-Euclidean methods that preserve the determinant. Path integrals of tangents of geodesic-loxodromes generate novel measures of over-all difference between two tensors, and of difference in shape and in orientation. PMID:18051037
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.
Inflatonic baryogenesis with large tensor mode
Directory of Open Access Journals (Sweden)
Naoyuki Takeda
2015-06-01
Full Text Available We consider a complex inflaton field with a CP asymmetric term for its potential. This CP asymmetric term produces the global charge of the inflaton after inflation. With the assignment of the baryon number to the inflaton, the baryon asymmetry of the universe is produced by inflaton's decay. In addition to this, the U(1 breaking term modulates the curvature of the inflaton radial direction depending on its phase, which affects the tensor-to-scalar ratio. In this paper, we have studied the relation between the baryon asymmetry and the tensor-to-scalar ratio, then verified that the future CMB observation could test this baryogenesis scenario with large tensor modes.
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...
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.
Carrozza, Sylvain; Tanasa, Adrian
2016-08-01
We define in this paper a class of three-index tensor models, endowed with {O(N)^{⊗ 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.
Spectral analysis of the full gravity tensor
Rummel, R.; van Gelderen, M.
1992-10-01
It is shown that, when the five independent components of the gravity tensor are grouped into (Gamma-zz), (Gamma-xz, Gamma-yz), and (Gamma-xx - Gamma-yy, 2Gamma-xy) sets and expanded into an infinite series of pure-spin spherical harmonic tensors, it is possible to derive simple eigenvalue connections between these three sets and the spherical harmonic expansion of the gravity potential. The three eigenvalues are (n + 1)(n + 2), -(n + 2) sq rt of n(n + 1), and sq rt of (n - 1)n(n + 1)(n + 2). The joint ESA and NASA Aristoteles mission is designed to measure with high precision the tensor components Gamma-zz, Gamma-yz, and Gamma-yy, which will make it possible to determine the global gravity field in six months time with a high precision.
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.
Quantum Fluctuations Of The Stress Tensor
Wu, C
2002-01-01
Quantum fluctuations of the stress tensor are important in many branches of physics, including the study of the validity of semiclassical gravity and the backreaction problem in stochastic semiclassical gravity. The geometry fluctuations induced by stress tensor fluctuations are important to understand quantum gravity and the problem of lightcone fluctuations. Stress tensor fluctuations also hold the key to understand fundamental physical effects like quantum fluctuations of radiation pressure, and that is crucial to the sensitivity of interferometers and the limitations on the detection of gravitational waves. Even the wave-particle duality of light can be better understood by the study of quantum fluctuations of thermal radiation. It is well known in quantum field theory that the expectation value of the energy density, which contains quadratic field operators (e.g. E2 and B2 in the electromagnatic field case), is divergent and can be renormalized simply by normal ordering, which is subtracting out the vac...
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...
Scalable tensor factorizations for incomplete data
DEFF Research Database (Denmark)
Acar, Evrim; Dunlavy, Daniel M.; KOlda, Tamara G.;
2011-01-01
The problem of incomplete data—i.e., data with missing or unknown values—in multi-way arrays is ubiquitous in biomedical signal processing, network traffic analysis, bibliometrics, social network analysis, chemometrics, computer vision, communication networks, etc. We consider the problem of how...... to 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...... 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 CP...
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...
Scalable Tensor Factorizations with Missing Data
DEFF Research Database (Denmark)
Acar, Evrim; Dunlavy, Daniel M.; Kolda, Tamara G.;
2010-01-01
The problem of missing data is ubiquitous in domains such as biomedical signal processing, network trac analysis, bibliometrics, social network analysis, chemometrics, computer vision, and communication networks|all domains in which data collection is subject to occasional errors. Moreover...... of missing data, many important data sets will be discarded or improperly analyzed. Therefore, we need a robust and scalable approach for factorizing multi-way arrays (i.e., tensors) in the presence of missing data. We focus on one of the most well-known tensor factorizations, CANDECOMP/PARAFAC (CP...... is shown to successfully factor tensors with noise and up to 70% missing data. Moreover, our approach is significantly faster than the leading alternative and scales to larger problems. To show the real-world usefulness of CP-WOPT, we illustrate its applicability on a novel EEG (electroencephalogram...
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...... of the recommendations and execution time are improved and memory requirements are decreased. The clustering is motivated by the fact that many tags in a tag space are semantically similar thus the tags can be grouped. Finally, promising experimental results are presented...
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)
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.
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 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.
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.
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.``
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.
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.)
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.
Quantum tensor product structures are observable induced.
Zanardi, Paolo; Lidar, Daniel A; Lloyd, Seth
2004-02-13
It is argued that the partition of a quantum system into subsystems is dictated by the set of operationally accessible interactions and measurements. The emergence of a multipartite tensor product structure of the state space and the associated notion of quantum entanglement are then relative and observable induced. We develop a general algebraic framework aimed to formalize this concept.
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.)
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 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...
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.
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...
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 ...
Tensor correlations in nuclei and exlusive electron scattering
Ryckebusch, J; Van Nespen, W; Debruyne, D
2000-01-01
The effect of tensor nucleon-nucleon correlations upon exclusive and semi-exclusive electronuclear reactions is studied. Differential cross sections for the semi-exclusive ^{16}O(e,e'p) and exclusive ^{16}O(e,e'pn) processes are computed by explicitly evaluating the dynamical electromagnetic coupling to a tensor correlated nucleon pair. In both reaction channels the tensor correlations contribute in a very substantial way. Tensor correlations are found to generate more electronuclear strength than central Jastrow correlations do.
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...
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.
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.
Hermitian Tensor Product Approximation of Complex Matrices and Separability
Fei, S M; Sun, B Z; Fei, Shao-Ming; Jing, Naihuan; Sun, Bao-Zhi
2006-01-01
The approximation of matrices to the sum of tensor products of Hermitian matrices is studied. A minimum decomposition of matrices on tensor space $H_1\\otimes H_2$ in terms of the sum of tensor products of Hermitian matrices on $H_1$ and $H_2$ is presented. From this construction the separability of quantum states is discussed.
Efficient MATLAB computations with sparse and factored tensors.
Energy Technology Data Exchange (ETDEWEB)
Bader, Brett William; Kolda, Tamara Gibson (Sandia National Lab, Livermore, CA)
2006-12-01
In this paper, the term tensor refers simply to a multidimensional or N-way array, and we consider how specially structured tensors allow for efficient storage and computation. First, we study sparse tensors, which have the property that the vast majority of the elements are zero. We propose storing sparse tensors using coordinate format and describe the computational efficiency of this scheme for various mathematical operations, including those typical to tensor decomposition algorithms. Second, we study factored tensors, which have the property that they can be assembled from more basic components. We consider two specific types: a Tucker tensor can be expressed as the product of a core tensor (which itself may be dense, sparse, or factored) and a matrix along each mode, and a Kruskal tensor can be expressed as the sum of rank-1 tensors. We are interested in the case where the storage of the components is less than the storage of the full tensor, and we demonstrate that many elementary operations can be computed using only the components. All of the efficiencies described in this paper are implemented in the Tensor Toolbox for MATLAB.
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
A New Class of Structured Tensors-SB-tensor%一类新的结构张量-SB－张量
Institute of Scientific and Technical Information of China (English)
郑苍松; 马瑞丹; 李耀堂
2016-01-01
A new class of structured tensors,SB-tensor,is proposed,and some properties of SB-tensor are given.The relationship with some existing structured tensors,B-tensors,DB-tensors and MB-tensors,is discussed and the positive definite of even order real symmetric SB-tensors is obtained.%引入了一类新的结构张量—SB－张量，研究了其性质，并讨论它与几类已有的结构张量—B－张量、DB－张量和MB－张量等的关系，由此得到偶数阶实对称SB－张量的正定性。
A preliminary report on the development of MATLAB tensor classes for fast algorithm prototyping.
Energy Technology Data Exchange (ETDEWEB)
Bader, Brett William; Kolda, Tamara Gibson (Sandia National Laboratories, Livermore, CA)
2004-07-01
We describe three MATLAB classes for manipulating tensors in order to allow fast algorithm prototyping. A tensor is a multidimensional or N-way array. We present a tensor class for manipulating tensors which allows for tensor multiplication and 'matricization.' We have further added two classes for representing tensors in decomposed format: cp{_}tensor and tucker{_}tensor. We demonstrate the use of these classes by implementing several algorithms that have appeared in the literature.
Xue, Zhong; Li, Hai; Guo, Lei; Wong, Stephen T.C.
2010-01-01
It is a key step to spatially align diffusion tensor images (DTI) to quantitatively compare neural images obtained from different subjects or the same subject at different timepoints. Different from traditional scalar or multi-channel image registration methods, tensor orientation should be considered in DTI registration. Recently, several DTI registration methods have been proposed in the literature, but deformation fields are purely dependent on the tensor features not the whole tensor info...
On some properties of nonnegative weakly irreducible tensors
Yang, Yuning
2011-01-01
In this paper, we mainly focus on how to generalize some conclusions from \\emph{nonnegative irreducible tensors} to \\emph{nonnegative weakly irreducible tensors}. To do so, a basic lemma as Lemma 3.1 of \\cite{s11} is proven using new tools. First, we define the stochastic tensor. Then we show that every nonnegative weakly irreducible tensor with spectral radius be 1 is diagonally similar to a unique weakly irreducible stochastic tensor. Based on it, we prove some important lemmas, which help us to generalize the results.
Asymptotic expansion of the multi-orientable random tensor model
Fusy, Eric
2014-01-01
Three-dimensional random tensor models are a natural generalization of the celebrated matrix models. The associated tensor graphs, or 3D maps, can be classified with respect to a particular integer or half-integer, the degree of the respective graph. In this paper we analyze the general term of the asymptotic expansion in N, the size of the tensor, of a particular random tensor model, the multi-orientable tensor model. We perform their enumeration and we establish which are the dominant configurations of a given degree.
The physical property tensors of one-dimensional quasicrystals
Institute of Scientific and Technical Information of China (English)
Li Cui-Lian; Liu You-Yan
2004-01-01
According to the group representation theory, we derive the character formulae of representation-matrices of the physical property tensors for the one-dimensional (1D) quasicrystals. Based on this, we have calculated the numbers of independent components of representation-matrices for thermal expansion coefficient tensors, piezoelectric coefficient tensors and elastic constant tensors under 31 point-groups for the 1D quasicrystals. Moreover, we have deduced the particular matrix forms of these tensors under the 31 point-groups. This is an important complement of quasicrystal physical property.
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
Tensor renormalization group methods for spin and gauge models
Zou, Haiyuan
The analysis of the error of perturbative series by comparing it to the exact solution is an important tool to understand the non-perturbative physics of statistical models. For some toy models, a new method can be used to calculate higher order weak coupling expansion and modified perturbation theory can be constructed. However, it is nontrivial to generalize the new method to understand the critical behavior of high dimensional spin and gauge models. Actually, it is a big challenge in both high energy physics and condensed matter physics to develop accurate and efficient numerical algorithms to solve these problems. In this thesis, one systematic way named tensor renormalization group method is discussed. The applications of the method to several spin and gauge models on a lattice are investigated. theoretically, the new method allows one to write an exact representation of the partition function of models with local interactions. E.g. O(N) models, Z2 gauge models and U(1) gauge models. Practically, by using controllable approximations, results in both finite volume and the thermodynamic limit can be obtained. Another advantage of the new method is that it is insensitive to sign problems for models with complex coupling and chemical potential. Through the new approach, the Fisher's zeros of the 2D O(2) model in the complex coupling plane can be calculated and the finite size scaling of the results agrees well with the Kosterlitz-Thouless assumption. Applying the method to the O(2) model with a chemical potential, new phase diagram of the models can be obtained. The structure of the tensor language may provide a new tool to understand phase transition properties in general.
Exploring the Tensor Networks/AdS Correspondence
Bhattacharyya, Arpan; 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 of tensors close to, but not exactly perfect tensors. Computing corrections to the connected two point correlation functions, the leading contribution is given by structures related to geodesics connecting the operators inserted at the boundary physical dofs. Such considerations admits generalizations at least to three point functions. This is highly suggestive of the emergence of the analogues of Witten diagrams in the tensor network. The perturbations alone however do not give the right entanglement spectrum. Using the ...
A gravito-electromagnetic analogy based on tidal tensors
Costa, L F; Herdeiro, Carlos A. R.
2006-01-01
We propose a new approach to a physical analogy between General Relativity and Electromagnetism, based on comparing tidal tensors of both theories. Using this approach we write a covariant form for the gravitational analogues of the Maxwell equations, from which the regime of validity of the analogy becomes manifest. Two explicit realisations of the analogy are given. The first one matches linearised gravitational tidal tensors to exact electromagnetic tidal tensors in Minkwoski spacetime. The second one matches exact magnetic gravitational tidal tensors for ultra-stationary metrics to exact magnetic tidal tensors of electromagnetism in curved spaces. We then establish a new proof for a class of tensor identities that define invariants of the type $\\vec{E}^2-\\vec{B}^2$ and $\\vec{E}\\cdot\\vec{B}$, and we exhibit the invariants built from tidal tensors in both gravity and electromagnetism. We contrast our approach with the two gravito-electromagnetic analogies commonly found in the literature, which are reviewed...
Algebraic and computational aspects of real tensor ranks
Sakata, Toshio; Miyazaki, Mitsuhiro
2016-01-01
This book provides comprehensive summaries of theoretical (algebraic) and computational aspects of tensor ranks, maximal ranks, and typical ranks, over the real number field. Although tensor ranks have been often argued in the complex number field, it should be emphasized that this book treats real tensor ranks, which have direct applications in statistics. The book provides several interesting ideas, including determinant polynomials, determinantal ideals, absolutely nonsingular tensors, absolutely full column rank tensors, and their connection to bilinear maps and Hurwitz-Radon numbers. In addition to reviews of methods to determine real tensor ranks in details, global theories such as the Jacobian method are also reviewed in details. The book includes as well an accessible and comprehensive introduction of mathematical backgrounds, with basics of positive polynomials and calculations by using the Groebner basis. Furthermore, this book provides insights into numerical methods of finding tensor ranks through...
Gamow-Teller resonances and a separable approximation for Skyrme tensor interactions
Directory of Open Access Journals (Sweden)
Severyukhin A. P.
2012-12-01
Full Text Available A finite rank separable approximation for the quasiparticle random phase approximation (QRPA with Skyrme interactions is applied to study properties of the Gamow-Teller (GT resonances in the neutron-rich Cd isotopes. This approximation enables one to reduce considerably the dimension of matrix that must be diagonalized to perform QRPA calculations in a very large configuration space. Our results from the SGII Skyrme interaction with the tensor interactions and the density-dependent zero-range pairing interaction show that the GT distribution is noticeably modified when the tensor correlations are taken into account. In particular, for 130Cd the dominant peak is moved 3.6 MeV downward and 10% of the GT distribution is shifted to the high excitation energy region near E=50MeV.
Energy-momentum tensor on the lattice: non-perturbative renormalization in Yang--Mills theory
Giusti, Leonardo
2015-01-01
We construct an energy-momentum tensor on the lattice which satisfies the appropriate Ward Identities (WIs) and has the right trace anomaly in the continuum limit. It is defined by imposing suitable WIs associated to the Poincare` invariance of the continuum theory. These relations come forth when the length of the box in the temporal direction is finite, and they take a particularly simple form if the coordinate and the periodicity axes are not aligned. We implement the method for the SU(3) Yang--Mills theory discretized with the standard Wilson action in presence of shifted boundary conditions in the (short) temporal direction. By carrying out extensive numerical simulations, the renormalization constants of the traceless components of the tensor are determined with a precision of roughly half a percent for values of the bare coupling constant in the range 0<= g^2_0<=1.
Tensor modes on the string theory landscape
Energy Technology Data Exchange (ETDEWEB)
Westphal, Alexander
2012-06-15
We attempt an estimate for the distribution of the tensor mode fraction r 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 then follows the number frequency distributions of inflationary mechanisms of string theory over the landscape. We show that an estimate of the relative number frequencies for small-field vs large-field inflation, while unattainable on the whole landscape, may be within reach as a regional answer for warped Calabi-Yau flux compactifications of type IIB string theory.
Damage Tensor Analysis on Regional Seismic Status
Institute of Scientific and Technical Information of China (English)
Zhong Jimao; Cheng Wanzheng
2006-01-01
In this paper, we researched the regional seismic status by using theories of the Damage Mechanics. The macroscopic damage status of the earth crust block, which is caused by earthquake fracture, is described with several concepts-the damage degree, the damage rate and the strain rate. In the earthquake process, the average strain rate of the studied block is equal to the sum of all seismic moment tensors of the earthquakes taking place in unit time and physical volume. To describe the anisotropy of microdamage of the crust block, we use the damage tensor that is expressed in the fissure density. By means of the transformation from the focal coordinate system to the observation system, we obtained the external normal vector of the focal fault plane expressed in its observation system and obtained the macrodamage degree of the researched block, which is calculated in dyadic. This provides a new analysis method for recognizing the underground damage status and the stress status.
Extended Scalar-Tensor Theories of Gravity
Crisostomi, Marco; Tasinato, Gianmassimo
2016-01-01
We determine new consistent scalar-tensor theories of gravity, with potentially interesting cosmological applications. We develop a general method to find the conditions for the existence of a primary constraint, which is necessary to prevent the propagation of an additional dangerous mode associated with higher order equations of motion. We then classify the most general, consistent scalar-tensor theories that are at most quadratic in the second derivatives of the scalar field. In addition, we investigate the possible connection between these theories and (beyond) Horndeski through conformal and disformal transformations. Finally, we point out that these theories can be associated with new operators in the effective field theory of dark energy, which might open up new possibilities to test dark energy models in future surveys.
Tensor modes on the string theory landscape
International Nuclear Information System (INIS)
We attempt an estimate for the distribution of the tensor mode fraction r 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 then follows the number frequency distributions of inflationary mechanisms of string theory over the landscape. We show that an estimate of the relative number frequencies for small-field vs large-field inflation, while unattainable on the whole landscape, may be within reach as a regional answer for warped Calabi-Yau flux compactifications of type IIB string theory.
Tensor modes on the string theory landscape
Westphal, Alexander
2012-01-01
We attempt an estimate for the distribution of the tensor mode fraction $r$ 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 then follows the number frequency distributions of inflationary mechanisms of string theory over the landscape. We show that an estimate of the relative number frequencies for small-field vs large-field inflation, while unattainable on the whole landscape, may be within reach as a regional answer for warped Calabi-Yau flux compactifications of type IIB string theory.
Tensors: A guide for undergraduate students
Battaglia, Franco; George, Thomas F.
2013-07-01
A guide on tensors is proposed for undergraduate students in physics or engineering that ties directly to vector calculus in orthonormal coordinate systems. We show that once orthonormality is relaxed, a dual basis, together with the contravariant and covariant components, naturally emerges. Manipulating these components requires some skill that can be acquired more easily and quickly once a new notation is adopted. This notation distinguishes multi-component quantities in different coordinate systems by a differentiating sign on the index labelling the component rather than on the label of the quantity itself. This tiny stratagem, together with simple rules openly stated at the beginning of this guide, allows an almost automatic, easy-to-pursue procedure for what is otherwise a cumbersome algebra. By the end of the paper, the reader will be skillful enough to tackle many applications involving tensors of any rank in any coordinate system, without index-manipulation obstacles standing in the way.
Oscillating Chiral Tensor Spectrum from Axionic Inflation
Obata, Ippei
2016-01-01
We study the axionic inflation with a modulated potential and examine if the primordial tensor power spectrum exhibits oscillatory feature, which is testable with future space-based gravitational wave experiments such as DECIGO and BBO. In the case of the single-field axion monodromy inflation, it turns out that it is difficult to detect the oscillation in the spectrum due to suppression of the sub-Planckian decay constant of axion. On the other hand, in the case of aligned chromo-natural inflation where the axion is coupled to a SU(2) gauge field, it turns out that the sizable oscillation in the tensor spectrum can occur due to the enhancement of chiral gravitational waves sourced by the gauge field. We expect that this feature will be a new probe to axion phenomenologies in early universe through the chiral gravitational waves.
A Near Horizon Stress Tensor for Blackfold
Sadeghi, J
2016-01-01
In literature, it is nicely proved that Einstein's field equations could be written near a horizon as a thermodynamical equation for the 4 dimensional spherically symmetric static and stationary spacetimes and also axisymmetric cases. In addition, for few types of higher dimensional black branes this thermodynamical equation has been derived. We determine the stress energy tensor for another interesting higher dimensional black branes which are known as blackfolds. Computations are done for two cases of charged and neutral blackfols. The method used is the near horizon expansion of the metrics of neutral and charged blackfolds. Using some rules and conditions, thermodynamic quantities of blackfolds have been calculated. Results surprisingly show that temperature, entropy, pressure and energy density are proportional to $n$ and $\\Omega_{n+1}$. Although temperatures (and entropies) differ from each other, the obtained stress energy tensor is the same for neutral and charged blackfolds. It proves that local dist...
Tensor Tilt from Primordial B-modes
Powell, Brian A
2011-01-01
A primordial cosmic microwave background B-mode is widely considered a "smoking gun" signature of an early period of inflationary expansion. However, competing theories of the origin of structure, including string gases and bouncing cosmologies, also produce primordial tensor perturbations that give rise to a B-mode. These models can be differentiated by the scale dependence of their tensor spectra: inflation predicts a red tilt ($n_T0$), while a nonsingular matter bounce gives zero tilt ($n_T=0$). We perform a Bayesian analysis to determine how far $|n_T|$ must deviate from zero before a tilt can be detected with current and future B-mode experiments. We find that Planck in conjunction with QUIET (II) will decisively detect $n_T \
Fermionic orbital optimisation in tensor network states
Krumnow, C; Eisert, J
2015-01-01
Tensor network states and specifically matrix-product states have proven to be a powerful tool for simulating ground states of strongly correlated spin models. Recently, they have also been applied to interacting fermionic problems, specifically in the context of quantum chemistry. A new freedom arising in such non-local fermionic systems is the choice of orbitals, it being far from clear what choice of fermionic orbitals to make. In this work, we propose a way to overcome this challenge. We suggest a method intertwining the optimisation over matrix product states with suitable fermionic Gaussian mode transformations, hence bringing the advantages of both approaches together. The described algorithm generalises basis changes in the spirit of the Hartree-Fock methods to matrix-product states, and provides a black box tool for basis optimisations in tensor network methods.
Entanglement, Tensor Networks and Black Hole Horizons
Molina-Vilaplana, Javier
2014-01-01
We elaborate on a previous proposal by Hartman and Maldacena on a tensor network which accounts for the scaling of the entanglement entropy in a system at a finite temperature. In this construction, the ordinary entanglement renormalization flow given by the class of tensor networks known as the Multi Scale Entanglement Renormalization Ansatz (MERA), is supplemented by an additional entanglement structure at the length scale fixed by the temperature. The network comprises two copies of a MERA circuit with a fixed number of layers and a pure matrix product state which joins both copies by entangling the infrared degrees of freedom of both MERA networks. The entanglement distribution within this bridge state defines reduced density operators on both sides which cause analogous effects to the presence of a black hole horizon when computing the entanglement entropy at finite temperature in the AdS/CFT correspondence. The entanglement and correlations during the thermalization process of a system after a quantum q...
General Metasurface Synthesis Based on Susceptibility Tensors
Achouri, Karim; Salem, Mohamed Ahmed; Caloz, Christophe
2014-01-01
A general method, based on susceptibility tensors, is proposed for the synthesis of metasurfaces transforming arbitrary incident waves into arbitrary reflected and transmitted waves. The proposed method exhibits two advantages: 1)it is inherently vectorial, and therefore better suited for full vectorial (beyond paraxial) electromagnetic problems, 2) it provides closed-form solutions, and is therefore extremely fast. Incidentally, the method reveals that a metasurface is fundamentally capable ...
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...... is demonstrated by detailed finite element time and frequency analysis of a concentrated force in infinite three-dimensional space, and by a time analysis of a pulse load in a two-dimensional underground gallery....
Ab initio mass tensor molecular dynamics
Tsuchida, Eiji
2010-01-01
Mass tensor molecular dynamics was first introduced by Bennett [J. Comput. Phys. 19, 267 (1975)] for efficient sampling of phase space through the use of generalized atomic masses. Here, we show how to apply this method to ab initio molecular dynamics simulations with minimal computational overhead. Test calculations on liquid water show a threefold reduction in computational effort without making the fixed geometry approximation. We also present a simple recipe for estimating the optimal ato...
Vector-tensor interaction of gravitation
Energy Technology Data Exchange (ETDEWEB)
Zhang Yuan-zhong; Guo han-ying
1982-11-01
In the paper, by using the equation of motion a particle, we show that the antigravity exist in the vector-tensor model of gravitation. Thus the motion of a particle deviates from the geodesic equation. In Newtonian approximation and weak gravitational field, acceleration of a particle in a spherically symmetric and astatic gravitation field is zero. The result is obviously not in agreement with gravitational phenomena.
Proofs of Vector Identities Using Tensors
Uddin, Zaheer; Ulfat, Intikhab
2014-01-01
The vector algebra and calculus are frequently used in many branches of Physics, for example, classical mechanics, electromagnetic theory, Astrophysics, Spectroscopy, etc. Important vector identities with the help of Levi-Civita symbols and Kronecker delta tensor are proved and presented in this paper. Some of the identities have been proved using Levi-Civita Symbols by other mathematicians and Physicists. The rests are presented for the first time. The derivations are of interest for both gr...
Monte Carlo Volcano Seismic Moment Tensors
Waite, G. P.; Brill, K. A.; Lanza, F.
2015-12-01
Inverse modeling of volcano seismic sources can provide insight into the geometry and dynamics of volcanic conduits. But given the logistical challenges of working on an active volcano, seismic networks are typically deficient in spatial and temporal coverage; this potentially leads to large errors in source models. In addition, uncertainties in the centroid location and moment-tensor components, including volumetric components, are difficult to constrain from the linear inversion results, which leads to a poor understanding of the model space. In this study, we employ a nonlinear inversion using a Monte Carlo scheme with the objective of defining robustly resolved elements of model space. The model space is randomized by centroid location and moment tensor eigenvectors. Point sources densely sample the summit area and moment tensors are constrained to a randomly chosen geometry within the inversion; Green's functions for the random moment tensors are all calculated from modeled single forces, making the nonlinear inversion computationally reasonable. We apply this method to very-long-period (VLP) seismic events that accompany minor eruptions at Fuego volcano, Guatemala. The library of single force Green's functions is computed with a 3D finite-difference modeling algorithm through a homogeneous velocity-density model that includes topography, for a 3D grid of nodes, spaced 40 m apart, within the summit region. The homogenous velocity and density model is justified by long wavelength of VLP data. The nonlinear inversion reveals well resolved model features and informs the interpretation through a better understanding of the possible models. This approach can also be used to evaluate possible station geometries in order to optimize networks prior to deployment.
Cho, ChangSoo
2015-04-01
Moment tensor inversion method using waveform is not widely used in identification of fault direction for earthquake but also in identification of explosion experiment such as north korea nuclear test. TDMT inversion code as open source was used for 1-D focal mechanism to moderate earthquake. But TDMT code caused some problems to fit waveform data of earthquake. This software was modified and improved with using the extraction bandwidth for event data and using waveform fitting of maximum cross-correlation with limit of shifting time. Improved algorithm was applied to moderate earthquakes occurred in and around the korean peninsula and showed the result of good data fitting in deriving focal mechanism. CMT centeroid locations were calculated with this algorithm. Earthquakes occurred rarely in the korean peninsula and instrumental recording started from 1990's late. But quality of measurement ground motion is very good after the beginning of instrumental recording. 61 moderate earthquakes occurred analyzed between 2000 to present were analyzed. most of all focal mechanism of earthquake showed strike slip or reverse fault as intraplate earthquake. The horizontal direction of tectonic stress of the korean peninsula is ENE-WSW derived with focal mechanisms that were calculated with 1D moment tensor inversion for moderate earthquake by Zoback(1992)'s method of tectonic stress. 3D-moment tensor inversion method was also developed with simulation code of 3-D viscoelastic finite difference method with ADE(auxiliary differential equation)-PML(perfectly matched layer) and applied to main moderate earthquakes. Forward modeling of 3D seismic wave propagation for moment tensor inversion require much time and expensive cost. Forward simulation with domain decomposition of having only thin model between source and receiver in moment tensor inversion could reduce much time, memory and computational cost in 3D moment tensor inversion even though this method was not more effective
Energy Technology Data Exchange (ETDEWEB)
Hansen, Tobias
2015-07-15
This thesis covers two main topics: the tensorial structure of quantum field theory correlators in general spacetime dimensions and a method for computing string theory scattering amplitudes directly in target space. In the first part tensor structures in generic bosonic CFT correlators and scattering amplitudes are studied. To this end arbitrary irreducible tensor representations of SO(d) (traceless mixed-symmetry tensors) are encoded in group invariant polynomials, by contracting with sets of commuting and anticommuting polarization vectors which implement the index symmetries of the tensors. The tensor structures appearing in CFT{sub d} correlators can then be inferred by studying these polynomials in a d + 2 dimensional embedding space. It is shown with an example how these correlators can be used to compute general conformal blocks describing the exchange of mixed-symmetry tensors in four-point functions, which are crucial for advancing the conformal bootstrap program to correlators of operators with spin. Bosonic string theory lends itself as an ideal example for applying the same methods to scattering amplitudes, due to its particle spectrum of arbitrary mixed-symmetry tensors. This allows in principle the definition of on-shell recursion relations for string theory amplitudes. A further chapter introduces a different target space definition of string scattering amplitudes. As in the case of on-shell recursion relations, the amplitudes are expressed in terms of their residues via BCFW shifts. The new idea here is that the residues are determined by use of the monodromy relations for open string theory, avoiding the infinite sums over the spectrum arising in on-shell recursion relations. Several checks of the method are presented, including a derivation of the Koba-Nielsen amplitude in the bosonic string. It is argued that this method provides a target space definition of the complete S-matrix of string theory at tree-level in a at background in terms of a
International Nuclear Information System (INIS)
This thesis covers two main topics: the tensorial structure of quantum field theory correlators in general spacetime dimensions and a method for computing string theory scattering amplitudes directly in target space. In the first part tensor structures in generic bosonic CFT correlators and scattering amplitudes are studied. To this end arbitrary irreducible tensor representations of SO(d) (traceless mixed-symmetry tensors) are encoded in group invariant polynomials, by contracting with sets of commuting and anticommuting polarization vectors which implement the index symmetries of the tensors. The tensor structures appearing in CFTd correlators can then be inferred by studying these polynomials in a d + 2 dimensional embedding space. It is shown with an example how these correlators can be used to compute general conformal blocks describing the exchange of mixed-symmetry tensors in four-point functions, which are crucial for advancing the conformal bootstrap program to correlators of operators with spin. Bosonic string theory lends itself as an ideal example for applying the same methods to scattering amplitudes, due to its particle spectrum of arbitrary mixed-symmetry tensors. This allows in principle the definition of on-shell recursion relations for string theory amplitudes. A further chapter introduces a different target space definition of string scattering amplitudes. As in the case of on-shell recursion relations, the amplitudes are expressed in terms of their residues via BCFW shifts. The new idea here is that the residues are determined by use of the monodromy relations for open string theory, avoiding the infinite sums over the spectrum arising in on-shell recursion relations. Several checks of the method are presented, including a derivation of the Koba-Nielsen amplitude in the bosonic string. It is argued that this method provides a target space definition of the complete S-matrix of string theory at tree-level in a at background in terms of a small
On Tensors, Sparsity, and Nonnegative Factorizations
Chi, Eric C
2011-01-01
Tensors have found application in a variety of fields, ranging from chemometrics to signal processing and beyond. In this paper, we consider the problem of multilinear modeling of sparse count data. Our goal is to develop a descriptive tensor factorization model of such data, along with appropriate algorithms and theory. To do so, we propose that the random variation is best described via a Poisson distribution, which better describes the zeros observed in the data as compared to the typical assumption of a Gaussian distribution. Under a Poisson assumption, we fit a model to observed data using the negative log-likelihood score. We present a new algorithm for Poisson tensor factorization called CANDECOMP--PARAFAC Alternating Poisson Regression (CP-APR) that is based on a majorization-minimization approach. It can be shown that CP-APR is a generalization of the Lee-Seung multiplicative updates. We show how to prevent the algorithm from converging to non-KKT points and prove convergence of CP-APR under mild con...
Diffusion tensor image registration using polynomial expansion
International Nuclear Information System (INIS)
In this paper, we present a deformable registration framework for the diffusion tensor image (DTI) using polynomial expansion. The use of polynomial expansion in image registration has previously been shown to be beneficial due to fast convergence and high accuracy. However, earlier work was developed only for 3D scalar medical image registration. In this work, it is shown how polynomial expansion can be applied to DTI registration. A new measurement is proposed for DTI registration evaluation, which seems to be robust and sensitive in evaluating the result of DTI registration. We present the algorithms for DTI registration using polynomial expansion by the fractional anisotropy image, and an explicit tensor reorientation strategy is inherent to the registration process. Analytic transforms with high accuracy are derived from polynomial expansion and used for transforming the tensor's orientation. Three measurements for DTI registration evaluation are presented and compared in experimental results. The experiments for algorithm validation are designed from simple affine deformation to nonlinear deformation cases, and the algorithms using polynomial expansion give a good performance in both cases. Inter-subject DTI registration results are presented showing the utility of the proposed method. (paper)
Scalable Tensor Factorizations for Incomplete Data
Acar, Evrim; Dunlavy, Daniel M; Morup, Morten
2010-01-01
The problem of incomplete data - i.e., data with missing or unknown values - in multi-way arrays is ubiquitous in biomedical signal processing, network traffic analysis, bibliometrics, social network analysis, chemometrics, computer vision, communication networks, etc. We consider the problem of how to 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 the presence of missing data, CP can be formulated as a weighted least squares problem that models only the known entries. We develop an algorithm called CP-WOPT (CP Weighted OPTimization) that uses a first-order optimization approach to solve the weighted least squares problem. Based on extensive numerical experiments, our algorithm is shown to successfully factorize tensors with noise and up to 99% missing d...
Tensors, BICEP2, prior dependence, and dust
Cortês, Marina; Parkinson, David
2014-01-01
We investigate the prior dependence on the inferred spectrum of primordial tensor perturbations, in light of recent results from BICEP2 and taking into account a possible dust contribution to polarized anisotropies. We highlight an optimized parameterization of the tensor power spectrum, and adoption of a logarithmic prior on its amplitude $A_T$, leading to results that transform more evenly under change of pivot scale. In the absence of foregrounds the tension between the results of BICEP2 and Planck drives the tensor spectral index $n_T$ to be blue-tilted in a joint analysis, which would be in contradiction to the standard inflation prediction ($n_T<0$). When foregrounds are accounted for, the BICEP2 results no longer require non-standard inflationary parameter regions. We present limits on primordial $A_T$ and $n_T$, adopting foreground scenarios put forward by Mortonson & Seljak and motivated by Planck 353 GHz observations, and assess what dust contribution leaves a detectable cosmological signal. ...
Testing gravity theories using tensor perturbations
Lin, Weikang
2016-01-01
Primordial gravitational waves constitute a promising probe of the very-early universe and the laws of gravity. We study changes to tensor mode perturbations that can arise in various proposed modified gravity (MG) theories. These include additional friction effects, non-standard dispersion relations involving a massive graviton, a modified speed, and a small-scale modification. We introduce a physically-motivated parameterization of these effects and use current available data to obtain exclusion regions in the parameter spaces. Taking into account the foreground subtraction, we then perform a forecast analysis focusing on the tensor mode MG parameters as constrained by the future experiments COrE, Stage-IV and PIXIE. For a fiducial value of the tensor-to-scalar ratio r=0.01, we find that an additional friction of 3.5-4.5% compared to GR will be detected at $3\\sigma$ by these experiments while a decrease in friction will be more difficult to detect. The speed of gravitational waves needs to be 5-15% differen...
Scalable tensor factorizations with incomplete data.
Energy Technology Data Exchange (ETDEWEB)
Morup, Morten (Technical University of Denmark); Dunlavy, Daniel M. (Sandia National Laboratories, Albuquerque, NM); Acar, Evrim (Information Technologies Institute, Turkey); Kolda, Tamara Gibson
2010-07-01
The problem of incomplete data - i.e., data with missing or unknown values - in multi-way arrays is ubiquitous in biomedical signal processing, network traffic analysis, bibliometrics, social network analysis, chemometrics, computer vision, communication networks, etc. We consider the problem of how to 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 the presence of missing data, CP can be formulated as a weighted least squares problem that models only the known entries. We develop an algorithm called CP-WOPT (CP Weighted OPTimization) that uses a first-order optimization approach to solve the weighted least squares problem. Based on extensive 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 x 1000 x 1000 with five million known entries (0.5% dense). We further demonstrate the usefulness of CP-WOPT on two real-world applications: a novel EEG (electroencephalogram) application where missing data is frequently encountered due to disconnections of electrodes and the problem of modeling computer network traffic where data may be absent due to the expense of the data collection process.
Tensor integrand reduction via Laurent expansion
Hirschi, Valentin
2016-01-01
We introduce a new method for the application of one-loop integrand reduction via the Laurent expansion algorithm, as implemented in the public C++ library Ninja. We show how the coefficients of the Laurent expansion can be computed by suitable contractions of the loop numerator tensor with cut-dependent projectors, making it possible to interface Ninja to any one-loop matrix element generator that can provide the components of this tensor. We implemented this technique in the Ninja library and interfaced it to MadLoop, which is part of the public MadGraph5_aMC@NLO framework. We performed a detailed performance study, comparing against other public reduction tools, namely CutTools, Samurai, IREGI, PJFry++ and Golem. We find that Ninja outperforms traditional integrand reduction in both speed and numerical stability, the latter being on par with that of the tensor integral reduction tool Golem which is however more limited and slower than Ninja. We considered many benchmark multi-scale processes of increasing ...
An $OSp$ extension of Canonical Tensor Model
Narain, Gaurav
2015-01-01
Tensor models are generalizations of matrix models, and are studied as discrete models of quantum gravity for arbitrary dimensions. Among them, the canonical tensor model (CTM for short) is a rank-three tensor model formulated as a totally constrained system with a number of first-class constraints, which have a similar algebraic structure as the constraints of the ADM formalism of general relativity. In this paper, we formulate a super-extension of CTM as an attempt to incorporate fermionic degrees of freedom. The kinematical symmetry group is extended from $O(N)$ to $OSp(N,\\tilde N)$, and the constraints are constructed so that they form a first-class constraint super-Poisson algebra. This is a straightforward super-extension, and the constraints and their algebraic structure are formally unchanged from the purely bosonic case, except for the additional signs associated to the order of the fermionic indices and dynamical variables. However, this extension of CTM leads to the existence of negative norm state...
Murg, V; Verstraete, F; Schneider, R; Nagy, P R; Legeza, Ö
2015-03-10
We study the tree-tensor-network-state (TTNS) method with variable tensor orders for quantum chemistry. TTNS is a variational method to efficiently approximate complete active space (CAS) configuration interaction (CI) wave functions in a tensor product form. TTNS can be considered as a higher order generalization of the matrix product state (MPS) method. The MPS wave function is formulated as products of matrices in a multiparticle basis spanning a truncated Hilbert space of the original CAS-CI problem. These matrices belong to active orbitals organized in a one-dimensional array, while tensors in TTNS are defined upon a tree-like arrangement of the same orbitals. The tree-structure is advantageous since the distance between two arbitrary orbitals in the tree scales only logarithmically with the number of orbitals N, whereas the scaling is linear in the MPS array. It is found to be beneficial from the computational costs point of view to keep strongly correlated orbitals in close vicinity in both arrangements; therefore, the TTNS ansatz is better suited for multireference problems with numerous highly correlated orbitals. To exploit the advantages of TTNS a novel algorithm is designed to optimize the tree tensor network topology based on quantum information theory and entanglement. The superior performance of the TTNS method is illustrated on the ionic-neutral avoided crossing of LiF. It is also shown that the avoided crossing of LiF can be localized using only ground state properties, namely one-orbital entanglement.
Kim, Eng-Chan; Cho, Jae-Hwan; Kim, Min-Hye; Kim, Ki-Hong; Choi, Cheon-Woong; Seok, Jong-min; Na, Kil-Ju; Han, Man-Seok
2013-03-01
This study was conducted on 20 patients who had undergone pedicle screw fixation between March and December 2010 to quantitatively compare a conventional fat suppression technique, CHESS (chemical shift selection suppression), and a new technique, IDEAL (iterative decomposition of water and fat with echo asymmetry and least squares estimation). The general efficacy and usefulness of the IDEAL technique was also evaluated. Fat-suppressed transverse-relaxation-weighed images and longitudinal-relaxation-weighted images were obtained before and after contrast injection by using these two techniques with a 1.5T MR (magnetic resonance) scanner. The obtained images were analyzed for image distortion, susceptibility artifacts and homogenous fat removal in the target region. The results showed that the image distortion due to the susceptibility artifacts caused by implanted metal was lower in the images obtained using the IDEAL technique compared to those obtained using the CHESS technique. The results of a qualitative analysis also showed that compared to the CHESS technique, fewer susceptibility artifacts and more homogenous fat removal were found in the images obtained using the IDEAL technique in a comparative image evaluation of the axial plane images before and after contrast injection. In summary, compared to the CHESS technique, the IDEAL technique showed a lower occurrence of susceptibility artifacts caused by metal and lower image distortion. In addition, more homogenous fat removal was shown in the IDEAL technique.
Energy Technology Data Exchange (ETDEWEB)
Alizai, Hamza; Nardo, Lorenzo; Karampinos, Dimitrios C.; Joseph, Gabby B.; Yap, Samuel P.; Baum, Thomas; Krug, Roland; Majumdar, Sharmila; Link, Thomas M. [University of California, San Francisco, Musculoskeletal and Quantitative Imaging Research Group, Department of Radiology and Biomedical Imaging, San Francisco, CA (United States)
2012-07-15
The goal of this study was to compare the semi-quantitative Goutallier classification for fat infiltration with quantitative fat-fraction derived from a magnetic resonance imaging (MRI) chemical shift-based water/fat separation technique. Sixty-two women (age 61 {+-} 6 years), 27 of whom had diabetes, underwent MRI of the calf using a T1-weighted fast spin-echo sequence and a six-echo spoiled gradient-echo sequence at 3 T. Water/fat images and fat fraction maps were reconstructed using the IDEAL algorithm with T2* correction and a multi-peak model for the fat spectrum. Two radiologists scored fat infiltration on the T1-weighted images using the Goutallier classification in six muscle compartments. Spearman correlations between the Goutallier grades and the fat fraction were calculated; in addition, intra-observer and inter-observer agreement were calculated. A significant correlation between the clinical grading and the fat fraction values was found for all muscle compartments (P < 0.0001, R values ranging from 0.79 to 0.88). Goutallier grades 0-4 had a fat fraction ranging from 3.5 to 19%. Intra-observer and inter-observer agreement values of 0.83 and 0.81 were calculated for the semi-quantitative grading. Semi-quantitative grading of intramuscular fat and quantitative fat fraction were significantly correlated and both techniques had excellent reproducibility. However, the clinical grading was found to overestimate muscle fat. (orig.)
Ohlsson, Henrik; Eldar, Yonina C.; Yang, Allen Y.; Sastry, S. Shankar
2014-08-01
The classical shift retrieval problem considers two signals in vector form that are related by a shift. The problem is of great importance in many applications and is typically solved by maximizing the cross-correlation between the two signals. Inspired by compressive sensing, in this paper, we seek to estimate the shift directly from compressed signals. We show that under certain conditions, the shift can be recovered using fewer samples and less computation compared to the classical setup. Of particular interest is shift estimation from Fourier coefficients. We show that under rather mild conditions only one Fourier coefficient suffices to recover the true shift.
Physical states in the canonical tensor model from the perspective of random tensor networks
Narain, Gaurav; Sato, Yuki
2014-01-01
Tensor models, generalization of matrix models, are studied aiming for quantum gravity in dimensions larger than two. Among them, the canonical tensor model is formulated as a totally constrained system with first-class constraints, the algebra of which resembles the Dirac algebra of general relativity. When quantized, the physical states are defined to be vanished by the quantized constraints. In explicit representations, the constraint equations are a set of partial differential equations for physical wave-functions, which do not seem straightforward to solve due to their non-linear character. In this paper, after providing some explicit solutions for N = 2,3, we show that certain scale-free integration of partition functions of statistical systems on random networks, or random tensor networks more generally, provides a series of solutions for general N. Then, by generalizing this form, we also obtain various solutions for general N. Moreover, we show that the solutions for the cases with a cosmological con...
Component reduction in N=2 supergravity: the vector, tensor, and vector-tensor multiplets
Butter, Daniel
2012-01-01
Recent advances in curved N=2 superspace methods have rendered the component reduction of superspace actions more feasible than in the past. In this paper, we consider models involving both vector and tensor multiplets coupled to supergravity and demonstrate explicitly how component actions may be efficiently obtained. In addition, tensor multiplets coupled to conformal supergravity are considered directly within projective superspace, where their formulation is most natural. We then demonstrate how the inverse procedure -- the lifting of component results to superspace -- can simplify the analysis of complicated multiplets. We address the off-shell N=2 vector-tensor multiplet coupled to conformal supergravity with a central charge and demonstrate explicitly how its constraints and Lagrangian can be written in a simpler way using superfields.
Suppression of clock shifts at field-insensitive transitions
Arnold, Kyle J
2016-01-01
We show that it is possible to significantly reduce quadrupole and tensor polarizability shifts of a clock transition by operating at a judiciously chosen field-insensitive point. In some cases shifts are almost completely eliminated making the transition an effective J = 0 to J = 0 candidate. This significantly improves the feasibility of a recent proposal for clock operation with large ion crystals. For such multi-ion clocks, geometric constraints and selection rules naturally divide clock operation into two categories based on the orientation of the magnetic field. We discuss the limitations imposed on each type and how calibrations might be carried out for clock operation.
Tensor-polarized structure functions: Tensor structure of deuteron in 2020's
Kumano, S.
2014-10-01
We explain spin structure for a spin-one hadron, in which there are new structure functions, in addition to the ones (F1, F2, g1, g2) which exist for the spin-1/2 nucleon, associated with its tensor structure. The new structure functions are b1, b2, b3, and b4 in deep inelastic scattering of a charged-lepton from a spin-one hadron such as the deuteron. Among them, twist- two functions are related by the Callan-Gross type relation b2 = 2xb1 in the Bjorken scaling limit. First, these new structure functions are introduced, and useful formulae are derived for projection operators of b1-4 from a hadron tensor Wμν. Second, a sum rule is explained for b1, and possible tensor-polarized distributions are discussed by using HERMES data in order to propose future experimental measurements and to compare them with theoretical models. A proposal was approved to measure b1 at the Thomas Jefferson National Accelerator Facility (JLab), so that much progress is expected for b1 in the near future. Third, formalisms of polarized proton-deuteron Drell-Yan processes are explained for probing especially tensor- polarized antiquark distributions, which were suggested by the HERMES data. The studies of the tensor-polarized structure functions will open a new era in 2020's for tensor-structure studies in terms of quark and gluon degrees of freedom, which are very different from ordinary descriptions in terms of nucleons and mesons.