A probabilistic approach for validating protein NMR chemical shift assignments

International Nuclear Information System (INIS)

Wang Bowei; Wang, Yunjun; Wishart, David S.

2010-01-01

It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program (SHIFTCOR) that is capable of handling both chemical shift mis-referencing and mis-assignments, requires the 3D structure coordinates of the target protein. Given that chemical shift mis-assignments and chemical shift re-referencing issues should ideally be addressed prior to 3D structure determination, there is a clear need to develop a structure-independent approach. Here, we present a new structure-independent protocol, which is based on using residue-specific and secondary structure-specific chemical shift distributions calculated over small (3-6 residue) fragments to identify mis-assigned resonances. The method is also able to identify and re-reference mis-referenced chemical shift assignments. Comparisons against existing re-referencing or mis-assignment detection programs show that the method is as good or superior to existing approaches. The protocol described here has been implemented into a freely available Java program called 'Probabilistic Approach for protein Nmr Assignment Validation (PANAV)' and as a web server (http://redpoll.pharmacy.ualberta.ca/PANAVhttp://redpoll.pharmacy.ualberta.ca/PANAV) which can be used to validate and/or correct as well as re-reference assigned protein chemical shifts.

Rapid and reliable protein structure determination via chemical shift threading.

Science.gov (United States)

Hafsa, Noor E; Berjanskii, Mark V; Arndt, David; Wishart, David S

2018-01-01

Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .

Bifurcation and stability analysis of rotating chemical spirals in circular domains: Boundary-induced meandering and stabilization

Science.gov (United States)

Bär, Markus; Bangia, Anil K.; Kevrekidis, Ioannis G.

2003-05-01

Recent experimental and model studies have revealed that the domain size may strongly influence the dynamics of rotating spirals in two-dimensional pattern forming chemical reactions. Hartmann et al. [Phys. Rev. Lett. 76, 1384 (1996)], report a frequency increase of spirals in circular domains with diameters substantially smaller than the spiral wavelength in a large domain for the catalytic NO+CO reaction on a microstructured platinum surface. Accompanying simulations with a simple reaction-diffusion system reproduced the behavior. Here, we supplement these studies by a numerical bifurcation and stability analysis of rotating spirals in a simple activator-inhibitor model. The problem is solved in a corotating frame of reference. No-flux conditions are imposed at the boundary of the circular domain. At large domain sizes, eigenvalues and eigenvectors very close to those corresponding to infinite medium translational invariance are observed. Upon decrease of domain size, we observe a simultaneous change in the rotation frequency and a deviation of these eigenvalues from being neutrally stable (zero real part). The latter phenomenon indicates that the translation symmetry of the spiral solution is appreciably broken due to the interaction with the (now nearby) wall. Various dynamical regimes are found: first, the spiral simply tries to avoid the boundary and its tip moves towards the center of the circular domain corresponding to a negative real part of the “translational” eigenvalues. This effect is noticeable at a domain radius of Rspiral subsequently exhibits an oscillatory instability: the tip trajectory displays a meandering motion, which may be characterized as boundary-induced spiral meandering. A systematic study of the spiral rotation as a function of a control parameter and the domain size reveals that the meandering instability in large domains becomes suppressed, and the spiral rotation becomes rigid, at a critical radius Rcr,0. Boundary

Tracking Target and Spiral Waves

DEFF Research Database (Denmark)

Jensen, Flemming G.; Sporring, Jon; Nielsen, Mads

2002-01-01

A new algorithm for analyzing the evolution of patterns of spiral and target waves in large aspect ratio chemical systems is introduced. The algorithm does not depend on finding the spiral tip but locates the center of the pattern by a new concept, called the spiral focus, which is defined...... by the evolutes of the actual spiral or target wave. With the use of Gaussian smoothing, a robust method is developed that permits the identification of targets and spirals foci independently of the wave profile. Examples of an analysis of long image sequences from experiments with the Belousov......–Zhabotinsky reaction catalyzed by ruthenium-tris-bipyridyl are presented. Moving target and spiral foci are found, and the speed and direction of movement of single as well as double spiral foci are investigated. For the experiments analyzed in this paper it is found that the movement of a focus correlates with foci...

Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

International Nuclear Information System (INIS)

Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei

2013-01-01

We introduce a Python-based program that utilizes the large database of 13 C and 15 N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D 13 C– 13 C, 15 N– 13 C, or 3D 15 N– 13 C– 13 C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D 13 C– 13 C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40–60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO–Cα–Cβ or N–Cα–Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

Solvable model of spiral wave chimeras.

Science.gov (United States)

Martens, Erik A; Laing, Carlo R; Strogatz, Steven H

2010-01-29

Spiral waves are ubiquitous in two-dimensional systems of chemical or biological oscillators coupled locally by diffusion. At the center of such spirals is a phase singularity, a topological defect where the oscillator amplitude drops to zero. But if the coupling is nonlocal, a new kind of spiral can occur, with a circular core consisting of desynchronized oscillators running at full amplitude. Here, we provide the first analytical description of such a spiral wave chimera and use perturbation theory to calculate its rotation speed and the size of its incoherent core.

Solvable Model of Spiral Wave Chimeras

DEFF Research Database (Denmark)

Martens, Erik Andreas; Laing, Carlo R.; Strogatz, Steven H.

2010-01-01

Spiral waves are ubiquitous in two-dimensional systems of chemical or biological oscillators coupled locally by diffusion. At the center of such spirals is a phase singularity, a topological defect where the oscillator amplitude drops to zero. But if the coupling is nonlocal, a new kind of spiral...... can occur, with a circular core consisting of desynchronized oscillators running at full amplitude. Here, we provide the first analytical description of such a spiral wave chimera and use perturbation theory to calculate its rotation speed and the size of its incoherent core....

Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

Energy Technology Data Exchange (ETDEWEB)

Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei, E-mail: mhong@iastate.edu [Iowa State University, Department of Chemistry (United States)

2013-06-15

We introduce a Python-based program that utilizes the large database of {sup 13}C and {sup 15}N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D {sup 13}C-{sup 13}C, {sup 15}N-{sup 13}C, or 3D {sup 15}N-{sup 13}C-{sup 13}C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D {sup 13}C-{sup 13}C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the C{alpha} and C{beta} chemical shifts, the highest-ranked PLUQ assignments were 40-60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO-C{alpha}-C{beta} or N-C{alpha}-C{beta}), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

Empirical correlation between protein backbone {sup 15}N and {sup 13}C secondary chemical shifts and its application to nitrogen chemical shift re-referencing

Energy Technology Data Exchange (ETDEWEB)

Wang Liya [Cold Spring Harbor Laboratory (United States); Markley, John L. [University of Wisconsin, Biochemistry Department (United States)], E-mail: markley@nmrfam.wisc.edu

2009-06-15

The linear analysis of chemical shifts (LACS) has provided a robust method for identifying and correcting {sup 13}C chemical shift referencing problems in data from protein NMR spectroscopy. Unlike other approaches, LACS does not require prior knowledge of the three-dimensional structure or inference of the secondary structure of the protein. It also does not require extensive assignment of the NMR data. We report here a way of extending the LACS approach to {sup 15}N NMR data from proteins, so as to enable the detection and correction of inconsistencies in chemical shift referencing for this nucleus. The approach is based on our finding that the secondary {sup 15}N chemical shift of the backbone nitrogen atom of residue i is strongly correlated with the secondary chemical shift difference (experimental minus random coil) between the alpha and beta carbons of residue i - 1. Thus once alpha and beta {sup 13}C chemical shifts are available (their difference is referencing error-free), the {sup 15}N referencing can be validated, and an appropriate offset correction can be derived. This approach can be implemented prior to a structure determination and can be used to analyze potential referencing problems in database data not associated with three-dimensional structure. Application of the LACS algorithm to the current BMRB protein chemical shift database, revealed that nearly 35% of the BMRB entries have {delta}{sup 15}N values mis-referenced by over 0.7 ppm and over 25% of them have {delta}{sup 1}H{sup N} values mis-referenced by over 0.12 ppm. One implication of the findings reported here is that a backbone {sup 15}N chemical shift provides a better indicator of the conformation of the preceding residue than of the residue itself.

Unraveling the meaning of chemical shifts in protein NMR.

Science.gov (United States)

Berjanskii, Mark V; Wishart, David S

2017-11-01

Chemical shifts are among the most informative parameters in protein NMR. They provide wealth of information about protein secondary and tertiary structure, protein flexibility, and protein-ligand binding. In this report, we review the progress in interpreting and utilizing protein chemical shifts that has occurred over the past 25years, with a particular focus on the large body of work arising from our group and other Canadian NMR laboratories. More specifically, this review focuses on describing, assessing, and providing some historical context for various chemical shift-based methods to: (1) determine protein secondary and super-secondary structure; (2) derive protein torsion angles; (3) assess protein flexibility; (4) predict residue accessible surface area; (5) refine 3D protein structures; (6) determine 3D protein structures and (7) characterize intrinsically disordered proteins. This review also briefly covers some of the methods that we previously developed to predict chemical shifts from 3D protein structures and/or protein sequence data. It is hoped that this review will help to increase awareness of the considerable utility of NMR chemical shifts in structural biology and facilitate more widespread adoption of chemical-shift based methods by the NMR spectroscopists, structural biologists, protein biophysicists, and biochemists worldwide. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

Evaluating amber force fields using computed NMR chemical shifts.

Science.gov (United States)

Koes, David R; Vries, John K

2017-10-01

NMR chemical shifts can be computed from molecular dynamics (MD) simulations using a template matching approach and a library of conformers containing chemical shifts generated from ab initio quantum calculations. This approach has potential utility for evaluating the force fields that underlie these simulations. Imperfections in force fields generate flawed atomic coordinates. Chemical shifts obtained from flawed coordinates have errors that can be traced back to these imperfections. We use this approach to evaluate a series of AMBER force fields that have been refined over the course of two decades (ff94, ff96, ff99SB, ff14SB, ff14ipq, and ff15ipq). For each force field a series of MD simulations are carried out for eight model proteins. The calculated chemical shifts for the 1 H, 15 N, and 13 C a atoms are compared with experimental values. Initial evaluations are based on root mean squared (RMS) errors at the protein level. These results are further refined based on secondary structure and the types of atoms involved in nonbonded interactions. The best chemical shift for identifying force field differences is the shift associated with peptide protons. Examination of the model proteins on a residue by residue basis reveals that force field performance is highly dependent on residue position. Examination of the time course of nonbonded interactions at these sites provides explanations for chemical shift differences at the atomic coordinate level. Results show that the newer ff14ipq and ff15ipq force fields developed with the implicitly polarized charge method perform better than the older force fields. © 2017 Wiley Periodicals, Inc.

Relative Configuration of Natural Products Using NMR Chemical Shifts

Science.gov (United States)

By comparing calculated with experimental NMR chemical shifts, we were able to determine the relative configurations of three monoterpene diastereomers produced by the walkingstick Anisomorpha buprestoides. The combined RMSDs of both 1H and 13C quantum chemically calculated shifts were able to predi...

SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database

Energy Technology Data Exchange (ETDEWEB)

Ginzinger, Simon W. [Center of Applied Molecular Engineering, University of Salzburg, Department of Molecular Biology, Division of Bioinformatics (Austria)], E-mail: simon@came.sbg.ac.at; Coles, Murray [Max-Planck-Institute for Developmental Biology, Department of Protein Evolution (Germany)], E-mail: Murray.Coles@tuebingen.mpg.de

2009-03-15

We present SimShiftDB, a new program to extract conformational data from protein chemical shifts using structural alignments. The alignments are obtained in searches of a large database containing 13,000 structures and corresponding back-calculated chemical shifts. SimShiftDB makes use of chemical shift data to provide accurate results even in the case of low sequence similarity, and with even coverage of the conformational search space. We compare SimShiftDB to HHSearch, a state-of-the-art sequence-based search tool, and to TALOS, the current standard tool for the task. We show that for a significant fraction of the predicted similarities, SimShiftDB outperforms the other two methods. Particularly, the high coverage afforded by the larger database often allows predictions to be made for residues not involved in canonical secondary structure, where TALOS predictions are both less frequent and more error prone. Thus SimShiftDB can be seen as a complement to currently available methods.

SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database

International Nuclear Information System (INIS)

Ginzinger, Simon W.; Coles, Murray

2009-01-01

We present SimShiftDB, a new program to extract conformational data from protein chemical shifts using structural alignments. The alignments are obtained in searches of a large database containing 13,000 structures and corresponding back-calculated chemical shifts. SimShiftDB makes use of chemical shift data to provide accurate results even in the case of low sequence similarity, and with even coverage of the conformational search space. We compare SimShiftDB to HHSearch, a state-of-the-art sequence-based search tool, and to TALOS, the current standard tool for the task. We show that for a significant fraction of the predicted similarities, SimShiftDB outperforms the other two methods. Particularly, the high coverage afforded by the larger database often allows predictions to be made for residues not involved in canonical secondary structure, where TALOS predictions are both less frequent and more error prone. Thus SimShiftDB can be seen as a complement to currently available methods

Role of quantitative chemical shift magnetic resonance imaging and chemical shift subtraction technique in discriminating adenomatous from non adenomatous adrenal solid lesions

Directory of Open Access Journals (Sweden)

Ahmed H. Afifi

2017-03-01

Conclusion: The signal intensity index and adrenal to spleen ratio are the most reliable quantitative chemical shift MRI methods in differentiation of adrenal adenomas from other non-adenomatous adrenal solid lesions. Chemical shift subtraction MRI is a recent technique that gives highly confident discrimination between two categories of pathology without using of any reference organ.

PPM-One: a static protein structure based chemical shift predictor

International Nuclear Information System (INIS)

Li, Dawei; Brüschweiler, Rafael

2015-01-01

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

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.

Holographic Chiral Magnetic Spiral

International Nuclear Information System (INIS)

Kim, Keun-Young; Sahoo, Bindusar; Yee, Ho-Ung

2010-06-01

We study the ground state of baryonic/axial matter at zero temperature chiral-symmetry broken phase under a large magnetic field, in the framework of holographic QCD by Sakai-Sugimoto. Our study is motivated by a recent proposal of chiral magnetic spiral phase that has been argued to be favored against previously studied phase of homogeneous distribution of axial/baryonic currents in terms of meson super-currents dictated by triangle anomalies in QCD. Our results provide an existence proof of chiral magnetic spiral in strong coupling regime via holography, at least for large axial chemical potentials, whereas we don't find the phenomenon in the case of purely baryonic chemical potential. (author)

The PROSECCO server for chemical shift predictions in ordered and disordered proteins.

Science.gov (United States)

Sanz-Hernández, Máximo; De Simone, Alfonso

2017-11-01

The chemical shifts measured in solution-state and solid-state nuclear magnetic resonance (NMR) are powerful probes of the structure and dynamics of protein molecules. The exploitation of chemical shifts requires methods to correlate these data with the protein structures and sequences. We present here an approach to calculate accurate chemical shifts in both ordered and disordered proteins using exclusively the information contained in their sequences. Our sequence-based approach, protein sequences and chemical shift correlations (PROSECCO), achieves the accuracy of the most advanced structure-based methods in the characterization of chemical shifts of folded proteins and improves the state of the art in the study of disordered proteins. Our analyses revealed fundamental insights on the structural information carried by NMR chemical shifts of structured and unstructured protein states.

Nonlinear dynamics of breathers in the spiral structures of magnets

Energy Technology Data Exchange (ETDEWEB)

Kiselev, V. V., E-mail: kiselev@imp.uran.ru; Raskovalov, A. A. [Russian Academy of Sciences, Mikheev Institute of Metal Physics, Ural Branch (Russian Federation)

2016-06-15

The structure and properties of pulsating solitons (breathers) in the spiral structures of magnets are analyzed within the sine-Gordon model. The breather core pulsations are shown to be accompanied by local shifts and oscillations of the spiral structure with the formation of “precursors” and “tails” in the moving soliton. The possibilities for the observation and excitation of breathers in the spiral structures of magnets and multiferroics are discussed.

Drug discovery for hearing loss: Phenotypic screening of chemical compounds on primary cultures of the spiral ganglion.

Science.gov (United States)

Whitlon, Donna S

2017-06-01

In the United States there are, at present, no drugs that are specifically FDA approved to treat hearing loss. Although several clinical trials are ongoing, including one testing D-methionine that is supported by the US Army, none of these trials directly address the effect of noise exposure on cochlear spiral ganglion neurons. We recently published the first report of a systematic chemical compound screen using primary, mammalian spiral ganglion cultures in which we were able to detect a compound and others in its class that increased neurite elongation, a critical step in restoring cochlear synapses after noise induced hearing loss. Here we discuss the issues, both pro and con, that influenced the development of our approach. These considerations may be useful for future compound screens that target the same or other attributes of cochlear spiral ganglion neurons. Copyright © 2016 Elsevier B.V. All rights reserved.

Chemical Shift Imaging (CSI) by precise object displacement

OpenAIRE

Leclerc, Sebastien; Trausch, Gregory; Cordier, Benoit; Grandclaude, Denis; Retournard, Alain; Fraissard, Jacques; Canet, Daniel

2006-01-01

International audience; A mechanical device (NMR lift) has been built for displacing vertically an object (typically a NMR sample tube) inside the NMR probe with an accuracy of 1 Μm. A series of single pulse experiments are performed for incremented vertical positions of the sample. With a sufficiently spatially selective rf field, one obtains chemical shift information along the displacement direction (one dimensional Chemical Shift Imaging – CSI). Knowing the vertical radio-frequency (rf) f...

Chemical shifts of oxygen-17 NMR in polyoxotungstates

International Nuclear Information System (INIS)

Kazanskij, L.P.; Fedotov, M.A.; Spitsyn, V.I.

1977-01-01

17 O NMR spectra of aqueous solutions containing paratungstate BH 2 W 12 O 42 10- and metatungstate H 2 W 12 O 40 6- anions have been measured. On the basis of the obtained data a scale of chemical shifts for oxygen atoms connected by various bonds with tungsten atoms is suggested. The obtained data are compared with the Raman spectra of crystalline salts and their aqueous solutions. Chemical shifts of 17 O NMR spectra have been also measured in other heteropolyanions

Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins

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.

Nucleic acid helix structure determination from NMR proton chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Werf, Ramon M. van der; Tessari, Marco; Wijmenga, Sybren S., E-mail: S.Wijmenga@science.ru.nl [Radboud University Nijmegen, Department of Biophysical Chemistry, Institute of Molecules and Materials (Netherlands)

2013-06-15

We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.

Accessible surface area from NMR chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Hafsa, Noor E.; Arndt, David; Wishart, David S., E-mail: david.wishart@ualberta.ca [University of Alberta, Department of Computing Science (Canada)

2015-07-15

Accessible surface area (ASA) is the surface area of an atom, amino acid or biomolecule that is exposed to solvent. The calculation of a molecule’s ASA requires three-dimensional coordinate data and the use of a “rolling ball” algorithm to both define and calculate the ASA. For polymers such as proteins, the ASA for individual amino acids is closely related to the hydrophobicity of the amino acid as well as its local secondary and tertiary structure. For proteins, ASA is a structural descriptor that can often be as informative as secondary structure. Consequently there has been considerable effort over the past two decades to try to predict ASA from protein sequence data and to use ASA information (derived from chemical modification studies) as a structure constraint. Recently it has become evident that protein chemical shifts are also sensitive to ASA. Given the potential utility of ASA estimates as structural constraints for NMR we decided to explore this relationship further. Using machine learning techniques (specifically a boosted tree regression model) we developed an algorithm called “ShiftASA” that combines chemical-shift and sequence derived features to accurately estimate per-residue fractional ASA values of water-soluble proteins. This method showed a correlation coefficient between predicted and experimental values of 0.79 when evaluated on a set of 65 independent test proteins, which was an 8.2 % improvement over the next best performing (sequence-only) method. On a separate test set of 92 proteins, ShiftASA reported a mean correlation coefficient of 0.82, which was 12.3 % better than the next best performing method. ShiftASA is available as a web server ( http://shiftasa.wishartlab.com http://shiftasa.wishartlab.com ) for submitting input queries for fractional ASA calculation.

Spiral loaded cavities for heavy ion acceleration

International Nuclear Information System (INIS)

Schempp, A.; Klein, H.

1976-01-01

A transmission line theory of the spiral resonator has been performed and the calculated and measured properties will be compared. Shunt impedances up to 50 MΩ/m have been measured. In a number of high power tests the structure has been tested and its electrical and mechanical stability has been investigated. The static frequency shift due to ponderomotoric forces was between 0.2 and 50 kHz/kW dependent on the geometrical parameters of the spirals. The maximum field strength obtained on the axis was 16 MV/m in pulsed operation and 9.2 MV/m in cw, corresponding to a voltage gain per cavity of up to 0.96 MV. The results show that spiral resonators are well suited as heavy ion accelerator cavities. (author)

Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps

Science.gov (United States)

Kumari, Amrita; Dorai, Kavita

2013-06-01

NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as α-helices, β-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.

Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Shen Yang; Bax, Ad, E-mail: bax@nih.go [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Laboratory of Chemical Physics (United States)

2010-03-15

We present a program, named Promega, to predict the Xaa-Pro peptide bond conformation on the basis of backbone chemical shifts and the amino acid sequence. Using a chemical shift database of proteins of known structure together with the PDB-extracted amino acid preference of cis Xaa-Pro peptide bonds, a cis/trans probability score is calculated from the backbone and {sup 13}C{sup {beta}} chemical shifts of the proline and its neighboring residues. For an arbitrary number of input chemical shifts, which may include Pro-{sup 13}C{sup {gamma}}, Promega calculates the statistical probability that a Xaa-Pro peptide bond is cis. Besides its potential as a validation tool, Promega is particularly useful for studies of larger proteins where Pro-{sup 13}C{sup {gamma}} assignments can be challenging, and for on-going efforts to determine protein structures exclusively on the basis of backbone and {sup 13}C{sup {beta}} chemical shifts.

Protein Structure Determination Using Chemical Shifts

DEFF Research Database (Denmark)

Christensen, Anders Steen

is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

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)

Further conventions for NMR shielding and chemical shifts (IUPAC Recommendations 2008)

International Nuclear Information System (INIS)

Harris, R.K.; Menezes, S.M. Cabral de; Granger, P.; Hoffman, R.E.; Zilm, K.W.

2008-01-01

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 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 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)

The direct measurement of the heteronuclear chemical shifts relative to tetramethylsilane

International Nuclear Information System (INIS)

Moritz, A.G.

1988-12-01

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

NMR chemical shifts in amino acids: Effects of environments, electric field, and amine group rotation

International Nuclear Information System (INIS)

Yoon, Young-Gui; Pfrommer, Bernd G.; Louie, Steven G.; Canning, Andrew

2002-01-01

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

Temperature dependence of 1H NMR chemical shifts and its influence on estimated metabolite concentrations.

Science.gov (United States)

Wermter, Felizitas C; Mitschke, Nico; Bock, Christian; Dreher, Wolfgang

2017-12-01

Temperature dependent chemical shifts of important brain metabolites measured by localised 1 H MRS were investigated to test how the use of incorrect prior knowledge on chemical shifts impairs the quantification of metabolite concentrations. Phantom measurements on solutions containing 11 metabolites were performed on a 7 T scanner between 1 and 43 °C. The temperature dependence of the chemical shift differences was fitted by a linear model. Spectra were simulated for different temperatures and analysed by the AQSES program (jMRUI 5.2) using model functions with chemical shift values for 37 °C. Large differences in the temperature dependence of the chemical shift differences were determined with a maximum slope of about ±7.5 × 10 -4  ppm/K. For 32-40 °C, only minor quantification errors resulted from using incorrect chemical shifts, with the exception of Cr and PCr. For 1-10 °C considerable quantification errors occurred if the temperature dependence of the chemical shifts was neglected. If 1 H MRS measurements are not performed at 37 °C, for which the published chemical shift values have been determined, the temperature dependence of chemical shifts should be considered to avoid systematic quantification errors, particularly for measurements on animal models at lower temperatures.

Theoretical Study of the NMR Chemical Shift of Xe in Supercritical Condition

DEFF Research Database (Denmark)

Lacerda Junior, Evanildo Gomes; Sauer, Stephan P. A.; Mikkelsen, Kurt Valentin

2018-01-01

In this work we investigate the level of theory necessary for reproducing the non-linear variation of the 129Xe nuclear magnetic resonance (NMR) chemical shift with the density of Xe in supercritical conditions. In detail we study how the 129Xe chemical shift depends under these conditions...... on electron correlation, relativistic and many-body effects. The latter are included using a sequential-QM/MM methodology, in which a classical MD simulation is performed first and the chemical shift is then obtained as an average of quantum calculations of 250 MD snapshots conformations carried out for Xen...... this approach we obtain very good agreement with the experimental data, showing that the chemical shift of 129Xe in supercritical conditions is very well described by cluster calculations at the HF level, with small contributions from relativistic and electron correlation effects....

29Si NMR Chemical Shift Calculation for Silicate Species by Gaussian Software

Science.gov (United States)

Azizi, S. N.; Rostami, A. A.; Godarzian, A.

2005-05-01

Hartree-Fock self-consistent-field (HF-SCF) theory and the Gauge-including atomic orbital (GIAO) methods are used in the calculation of 29Si NMR chemical shifts for ABOUT 90 units of 19 compounds of various silicate species of precursors for zeolites. Calculations have been performed at geometries optimized at the AM1 semi-empirical method. The GIAO-HF-SCF calculations were carried out with using three different basis sets: 6-31G*, 6-31+G** and 6-311+G(2d,p). To demonstrate the quality of the calculations the calculated chemical shifts, δ, were compared with the corresponding experimental values for the compounds in study. The results, especially with 6-31+g** are in excellent agreement with experimental values. The calculated chemical shifts, in practical point of view, appear to be accurate enough to aid in experimental peak assignments. The difference between the experimental and calculated 29Si chemical shift values not only depends on the Qn units but also it seems that basis set effects and the level of theory is more important. For the series of molecules studied here, the standard deviations and mean absolute errors for 29Si chemical shifts relative to TMS determined using Hartree--Fock 6-31+G** basis is nearly in all cases smaller than the errors for shifts determined using HF/6-311+G(2d,p).

Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy

International Nuclear Information System (INIS)

Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy

2015-01-01

Proton NMR spectroscopy in the solid state has recently attracted much attention owing to the significant enhancement in spectral resolution afforded by the remarkable advances in ultrafast magic angle spinning (MAS) capabilities. In particular, proton chemical shift anisotropy (CSA) has become an important tool for obtaining specific insights into inter/intra-molecular hydrogen bonding. However, even at the highest currently feasible spinning frequencies (110–120 kHz), 1 H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong 1 H– 1 H homonuclear dipolar couplings and narrow 1 H chemical shift (CS) ranges, which render it difficult to determine the CSA of specific proton sites in the standard CSA/single-quantum (SQ) chemical shift correlation experiment. Herein, we propose a three-dimensional (3D) 1 H double-quantum (DQ) chemical shift/CSA/SQ chemical shift correlation experiment to extract the CS tensors of proton sites whose signals are not well resolved along the single-quantum chemical shift dimension. As extracted from the 3D spectrum, the F1/F3 (DQ/SQ) projection provides valuable information about 1 H– 1 H proximities, which might also reveal the hydrogen-bonding connectivities. In addition, the F2/F3 (CSA/SQ) correlation spectrum, which is similar to the regular 2D CSA/SQ correlation experiment, yields chemical shift anisotropic line shapes at different isotropic chemical shifts. More importantly, since the F2/F1 (CSA/DQ) spectrum correlates the CSA with the DQ signal induced by two neighboring proton sites, the CSA spectrum sliced at a specific DQ chemical shift position contains the CSA information of two neighboring spins indicated by the DQ chemical shift. If these two spins have different CS tensors, both tensors can be extracted by numerical fitting. We believe that this robust and elegant single-channel proton-based 3D experiment provides useful atomistic-level structural and dynamical

Hypoxia Induces a Metabolic Shift and Enhances the Stemness and Expansion of Cochlear Spiral Ganglion Stem/Progenitor Cells

Directory of Open Access Journals (Sweden)

Hsin-Chien Chen

2015-01-01

Full Text Available Previously, we demonstrated that hypoxia (1% O2 enhances stemness markers and expands the cell numbers of cochlear stem/progenitor cells (SPCs. In this study, we further investigated the long-term effect of hypoxia on stemness and the bioenergetic status of cochlear spiral ganglion SPCs cultured at low oxygen tensions. Spiral ganglion SPCs were obtained from postnatal day 1 CBA/CaJ mouse pups. The measurement of oxygen consumption rate, extracellular acidification rate (ECAR, and intracellular adenosine triphosphate levels corresponding to 20% and 5% oxygen concentrations was determined using a Seahorse XF extracellular flux analyzer. After low oxygen tension cultivation for 21 days, the mean size of the hypoxia-expanded neurospheres was significantly increased at 5% O2; this correlated with high-level expression of hypoxia-inducible factor-1 alpha (Hif-1α, proliferating cell nuclear antigen (PCNA, cyclin D1, Abcg2, nestin, and Nanog proteins but downregulated expression of p27 compared to that in a normoxic condition. Low oxygen tension cultivation tended to increase the side population fraction, with a significant difference found at 5% O2 compared to that at 20% O2. In addition, hypoxia induced a metabolic energy shift of SPCs toward higher basal ECARs and higher maximum mitochondrial respiratory capacity but lower proton leak than under normoxia, where the SPC metabolism was switched toward glycolysis in long-term hypoxic cultivation.

Resolution of NMR chemical shift images into real and imaginary components

International Nuclear Information System (INIS)

Yamamoto, E.; Kohno, H.

1986-01-01

Fast chemical shift imaging of two-line materials is described using a modified spin-echo sequence. The method resolves the two chemical shift images into real and imaginary components representing the reconstructed image. The measuring time is reduced to half of that for the conventional method proposed by Dixon et al, and quantitative evaluation of the images becomes possible. Reference material with a single resonant line is used to eliminate the phase error caused by static field inhomogeneity and the inherent apparatus offset phase. Experiments are conducted using acetone and benzene with a medium-bore superconductive magnet operating at 0.5T. From these experiments, two chemical shift images are obtained. These images are then superimposed to produce a conventional density image. (author)

Suppression of Spiral Wave in Modified Orengonator Model

International Nuclear Information System (INIS)

Ma Jun; Wang Chunni; Jin Wuyin; Yi Ming

2008-01-01

In this paper, a spatial perturbation scheme is proposed to suppress the spiral wave in the modified Orengonator model, which is used to describe the chemical reaction in the light-sensitive media. The controllable external illumination Φ is perturbed with a spatial linear function. In our numerical simulation, the scheme is investigated by imposing the external controllable illumination on the space continuously and/or intermittently. The numerical simulation results confirm that the stable rotating spiral wave still can be removed with the scheme proposed in this paper even if the controllable Φ changed vs. time and space synchronously. Then the scheme is also used to control the spiral wave and turbulence in the modified Fitzhugh-Nagumo model. It is found that the scheme is effective to remove the sable rotating and meandering spiral wave but it costs long transient period and intensity of the gradient parameter to eliminate the spiral turbulence

Random coil chemical shifts in acidic 8 M urea: Implementation of random coil shift data in NMRView

International Nuclear Information System (INIS)

Schwarzinger, Stephan; Kroon, Gerard J.A.; Foss, Ted R.; Wright, Peter E.; Dyson, H. Jane

2000-01-01

Studies of proteins unfolded in acid or chemical denaturant can help in unraveling events during the earliest phases of protein folding. In order for meaningful comparisons to be made of residual structure in unfolded states, it is necessary to use random coil chemical shifts that are valid for the experimental system under study. We present a set of random coil chemical shifts obtained for model peptides under experimental conditions used in studies of denatured proteins. This new set, together with previously published data sets, has been incorporated into a software interface for NMRView, allowing selection of the random coil data set that fits the experimental conditions best

Prediction of proton chemical shifts in RNA - Their use in structure refinement and validation

International Nuclear Information System (INIS)

Cromsigt, Jenny A.M.T.C.; Hilbers, Cees W.; Wijmenga, Sybren S.

2001-01-01

An analysis is presented of experimental versus calculated chemical shifts of the non-exchangeable protons for 28 RNA structures deposited in the Protein Data Bank, covering a wide range of structural building blocks. We have used existing models for ring-current and magnetic-anisotropy contributions to calculate the proton chemical shifts from the structures. Two different parameter sets were tried: (i) parameters derived by Ribas-Prado and Giessner-Prettre (GP set) [(1981) J. Mol. Struct.,76, 81-92.]; (ii) parameters derived by Case [(1995) J. Biomol. NMR, 6, 341-346]. Both sets lead to similar results. The detailed analysis was carried using the GP set. The root-mean-square-deviation between the predicted and observed chemical shifts of the complete database is 0.16 ppm with a Pearson correlation coefficient of 0.79. For protons in the usually well-defined A-helix environment these numbers are, 0.08 ppm and 0.96, respectively. As a result of this good correspondence, a reliable analysis could be made of the structural dependencies of the 1 H chemical shifts revealing their physical origin. For example, a down-field shift of either H2' or H3' or both indicates a high-syn/syn χ-angle. In an A-helix it is essentially the 5'-neighbor that affects the chemical shifts of H5, H6 and H8 protons. The H5, H6 and H8 resonances can therefore be assigned in an A-helix on the basis of their observed chemical shifts. In general, the chemical shifts were found to be quite sensitive to structural changes. We therefore propose that a comparison between calculated and observed 1 H chemical shifts is a good tool for validation and refinement of structures derived from NOEs and J-couplings

A procedure to validate and correct the {sup 13}C chemical shift calibration of RNA datasets

Energy Technology Data Exchange (ETDEWEB)

Aeschbacher, Thomas; Schubert, Mario, E-mail: schubert@mol.biol.ethz.ch; Allain, Frederic H.-T., E-mail: allain@mol.biol.ethz.ch [ETH Zuerich, Institute for Molecular Biology and Biophysics (Switzerland)

2012-02-15

Chemical shifts reflect the structural environment of a certain nucleus and can be used to extract structural and dynamic information. Proper calibration is indispensable to extract such information from chemical shifts. Whereas a variety of procedures exist to verify the chemical shift calibration for proteins, no such procedure is available for RNAs to date. We present here a procedure to analyze and correct the calibration of {sup 13}C NMR data of RNAs. Our procedure uses five {sup 13}C chemical shifts as a reference, each of them found in a narrow shift range in most datasets deposited in the Biological Magnetic Resonance Bank. In 49 datasets we could evaluate the {sup 13}C calibration and detect errors or inconsistencies in RNA {sup 13}C chemical shifts based on these chemical shift reference values. More than half of the datasets (27 out of those 49) were found to be improperly referenced or contained inconsistencies. This large inconsistency rate possibly explains that no clear structure-{sup 13}C chemical shift relationship has emerged for RNA so far. We were able to recalibrate or correct 17 datasets resulting in 39 usable {sup 13}C datasets. 6 new datasets from our lab were used to verify our method increasing the database to 45 usable datasets. We can now search for structure-chemical shift relationships with this improved list of {sup 13}C chemical shift data. This is demonstrated by a clear relationship between ribose {sup 13}C shifts and the sugar pucker, which can be used to predict a C2 Prime - or C3 Prime -endo conformation of the ribose with high accuracy. The improved quality of the chemical shift data allows statistical analysis with the potential to facilitate assignment procedures, and the extraction of restraints for structure calculations of RNA.

Protein backbone angle restraints from searching a database for chemical shift and sequence homology

Energy Technology Data Exchange (ETDEWEB)

Cornilescu, Gabriel; Delaglio, Frank; Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

1999-03-15

Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local conformation, and homologous proteins show quite similar patterns of secondary chemical shifts. The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. The database contains 13C{alpha}, 13C{beta}, 13C', 1H{alpha} and 15N chemical shifts for 20 proteins for which a high resolution X-ray structure is available. The computer program TALOS was developed to search this database for strings of residues with chemical shift and residue type homology. The relative importance of the weighting factors attached to the secondary chemical shifts of the five types of resonances relative to that of sequence similarity was optimized empirically. TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of the query sequence. If the central residues in these 10 triplets exhibit similar {phi} and {psi} backbone angles, their averages can reliably be used as angular restraints for the protein whose structure is being studied. Tests carried out for proteins of known structure indicate that the root-mean-square difference (rmsd) between the output of TALOS and the X-ray derived backbone angles is about 15 deg. Approximately 3% of the predictions made by TALOS are found to be in error.

Benchmarking quantum mechanical calculations with experimental NMR chemical shifts of 2-HADNT

Science.gov (United States)

Liu, Yuemin; Junk, Thomas; Liu, Yucheng; Tzeng, Nianfeng; Perkins, Richard

2015-04-01

In this study, both GIAO-DFT and GIAO-MP2 calculations of nuclear magnetic resonance (NMR) spectra were benchmarked with experimental chemical shifts. The experimental chemical shifts were determined experimentally for carbon-13 (C-13) of seven carbon atoms for the TNT degradation product 2-hydroxylamino-4,6-dinitrotoluene (2-HADNT). Quantum mechanics GIAO calculations were implemented using Becke-3-Lee-Yang-Parr (B3LYP) and other six hybrid DFT methods (Becke-1-Lee-Yang-Parr (B1LYP), Becke-half-and-half-Lee-Yang-Parr (BH and HLYP), Cohen-Handy-3-Lee-Yang-Parr (O3LYP), Coulomb-attenuating-B3LYP (CAM-B3LYP), modified-Perdew-Wang-91-Lee-Yang-Parr (mPW1LYP), and Xu-3-Lee-Yang-Parr (X3LYP)) which use the same correlation functional LYP. Calculation results showed that the GIAO-MP2 method gives the most accurate chemical shift values, and O3LYP method provides the best prediction of chemical shifts among the B3LYP and other five DFT methods. Three types of atomic partial charges, Mulliken (MK), electrostatic potential (ESP), and natural bond orbital (NBO), were also calculated using MP2/aug-cc-pVDZ method. A reasonable correlation was discovered between NBO partial charges and experimental chemical shifts of carbon-13 (C-13).

Relation between chemical shift artifact and infiltration on MR imaging of renal cell carcinoma

International Nuclear Information System (INIS)

Yoshigoe, Fukuo; Makino, Hideki; Yanada, Syuichi; Ohishi, Yukihiko; Mashima, Yasuoki; Yamada, Hideo.

1994-01-01

Retrospective study on the relation between existence of the interruption and disturbance of chemical shift artifact and tumor infiltration at the periphery of the kidney on MR imaging was evaluated in 28 cases with renal cell carcinoma. Judgement was possible in 9 out of the 11 cases with pathological stage below pT2 and 14 cases out of 17 pT3 cases. Judgement was impracticable in 5 cases because the peripheral fat tissue of the kidney was too less to observe chemical shift artifact and the tumor was spreading at the side opposite to the chemical shift artifact. Chemical shift artifact on MRI in this study correlated well with renal tumor infiltration. (author)

Database proton NMR chemical shifts for RNA signal assignment and validation

Energy Technology Data Exchange (ETDEWEB)

Barton, Shawn; Heng Xiao [University of Maryland, Baltimore County, Howard Hughes Medical Institute (United States); Johnson, Bruce A., E-mail: bruce@onemoonscientific.com [University of Maryland, Baltimore County, Department of Chemistry and Biochemistry (United States); Summers, Michael F., E-mail: summers@hhmi.umbc.edu [University of Maryland, Baltimore County, Howard Hughes Medical Institute (United States)

2013-01-15

The Biological Magnetic Resonance Data Bank contains NMR chemical shift depositions for 132 RNAs and RNA-containing complexes. We have analyzed the {sup 1}H 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 4{sup 3} 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 {sup 1}H 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.

/sup 1/H-NMR chemical shift imaging suitable for low field systems

Energy Technology Data Exchange (ETDEWEB)

Yamamoto, Etsuji; Onodera, Takashi; Shiono, Hidemi; Kohno, Hideki

1986-12-01

An echo-time encoding proton NMR chemical shift imaging proposed by Dixon is extended to be applicable to low filed systems. The method utilizes the small phase angle between magnetic vectors of water and lipid protons to decrease the signal decays with spin-spin relaxation. The inevitable phase error caused by the static field inhomogeneity is corrected by using phase images of phantom measured under the same conditions as the actual measurements. The experiments were carried out using CuSO/sub 4/ doped water and vegetable oil at 0.5 T. Two chemical shift images could be clearly resolved with only one scan when the field inhomogeneity was larger than the chemical shift difference.

Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts.

Science.gov (United States)

Boomsma, Wouter; Tian, Pengfei; Frellsen, Jes; Ferkinghoff-Borg, Jesper; Hamelryck, Thomas; Lindorff-Larsen, Kresten; Vendruscolo, Michele

2014-09-23

Methods of protein structure determination based on NMR chemical shifts are becoming increasingly common. The most widely used approaches adopt the molecular fragment replacement strategy, in which structural fragments are repeatedly reassembled into different complete conformations in molecular simulations. Although these approaches are effective in generating individual structures consistent with the chemical shift data, they do not enable the sampling of the conformational space of proteins with correct statistical weights. Here, we present a method of molecular fragment replacement that makes it possible to perform equilibrium simulations of proteins, and hence to determine their free energy landscapes. This strategy is based on the encoding of the chemical shift information in a probabilistic model in Markov chain Monte Carlo simulations. First, we demonstrate that with this approach it is possible to fold proteins to their native states starting from extended structures. Second, we show that the method satisfies the detailed balance condition and hence it can be used to carry out an equilibrium sampling from the Boltzmann distribution corresponding to the force field used in the simulations. Third, by comparing the results of simulations carried out with and without chemical shift restraints we describe quantitatively the effects that these restraints have on the free energy landscapes of proteins. Taken together, these results demonstrate that the molecular fragment replacement strategy can be used in combination with chemical shift information to characterize not only the native structures of proteins but also their conformational fluctuations.

Protein Structure Validation and Refinement Using Chemical Shifts Derived from Quantum Mechanics

DEFF Research Database (Denmark)

Bratholm, Lars Andersen

to within 3 A. Furthermore, a fast quantum mechanics based chemical shift predictor was developed together with methodology for using chemical shifts in structure simulations. The developed predictor was used for renement of several protein structures and for reducing the computational cost of quantum...... mechanics / molecular mechanics (QM/MM) computations of chemical shieldings. Several improvements to the predictor is ongoing, where among other things, kernel based machine learning techniques have successfully been used to improve the quantum mechanical level of theory used in the predictions....

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)

Chemical Mass Shifts in a Digital Linear Ion Trap as Analytical Identity of o-, m-, and p-Xylene

Science.gov (United States)

Sun, Lulu; Xue, Bing; Huang, Zhengxu; Cheng, Ping; Ma, Li; Ding, Li; Zhou, Zhen

2018-04-01

Chemical mass shifts between isomeric ions of o-, m-, and p-xylene were measured using a digital linear ion trap, and the directions and values of the shifts were found to be correlated to the collision cross sections of the isomers. Both forward and reverse scans were used and the chemical shifts for each pair of isomers in scans of opposite directions were in opposite signs. Using different voltage settings (namely the voltage dividing ratio-VDR) of the ion trap allows adding high order field components in the quadrupole field and results in larger chemical mass shifts. The differential chemical mass shift which combined the shifts from forward and reverse scans doubled the amount of chemical shift, e.g., 0.077 Th between o- and p-xylene, enough for identification of the type of isomer without using an additional ion mobility spectrometer. The feature of equal and opposite chemical mass shifts also allowed to null out the chemical mass shift by calculating the mean m/z value between the two opposite scans and remove or reduce the mass error caused by chemical mass shift. [Figure not available: see fulltext.

Chemical Mass Shifts in a Digital Linear Ion Trap as Analytical Identity of o-, m-, and p-Xylene.

Science.gov (United States)

Sun, Lulu; Xue, Bing; Huang, Zhengxu; Cheng, Ping; Ma, Li; Ding, Li; Zhou, Zhen

2018-07-01

Chemical mass shifts between isomeric ions of o-, m-, and p-xylene were measured using a digital linear ion trap, and the directions and values of the shifts were found to be correlated to the collision cross sections of the isomers. Both forward and reverse scans were used and the chemical shifts for each pair of isomers in scans of opposite directions were in opposite signs. Using different voltage settings (namely the voltage dividing ratio-VDR) of the ion trap allows adding high order field components in the quadrupole field and results in larger chemical mass shifts. The differential chemical mass shift which combined the shifts from forward and reverse scans doubled the amount of chemical shift, e.g., 0.077 Th between o- and p-xylene, enough for identification of the type of isomer without using an additional ion mobility spectrometer. The feature of equal and opposite chemical mass shifts also allowed to null out the chemical mass shift by calculating the mean m/z value between the two opposite scans and remove or reduce the mass error caused by chemical mass shift. Graphical Abstract ᅟ.

Effects of Protein-pheromone Complexation on Correlated Chemical Shift Modulations

International Nuclear Information System (INIS)

Perazzolo, Chiara; Wist, Julien; Loth, Karine; Poggi, Luisa; Homans, Steve; Bodenhausen, Geoffrey

2005-01-01

Major urinary protein (MUP) is a pheromone-carrying protein of the lipocalin family. Previous studies by isothermal titration calorimetry (ITC) show that the affinity of MUP for the pheromone 2-methoxy-3-isobutylpyrazine (IBMP) is mainly driven by enthalpy, with a small unfavourable entropic contribution. Entropic terms can be attributed in part to changes in internal motions of the protein upon binding. Slow internal motions can lead to correlated or anti-correlated modulations of the isotropic chemical shifts of carbonyl C' and amide N nuclei. Correlated chemical shift modulations (CSM/CSM) in MUP have been determined by measuring differences of the transverse relaxation rates of zero- and double-quantum coherences ZQC{C'N} and DQC{C'N}, and by accounting for the effects of correlated fluctuations of dipole-dipole couplings (DD/DD) and chemical shift anisotropies (CSA/CSA). The latter can be predicted from tensor parameters of C' and N nuclei that have been determined in earlier work. The effects of complexation on slow time-scale protein dynamics can be determined by comparing the temperature dependence of the relaxation rates of APO-MUP (i.e., without ligand) and HOLO-MUP (i.e., with IBMP as a ligand)

Stereospecific assignment of the asparagine and glutamine sidechain amide protons in proteins from chemical shift analysis

Energy Technology Data Exchange (ETDEWEB)

Harsch, Tobias; Schneider, Philipp; Kieninger, Bärbel; Donaubauer, Harald; Kalbitzer, Hans Robert, E-mail: hans-robert.kalbitzer@biologie.uni-regensburg.de [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany)

2017-02-15

Side chain amide protons of asparagine and glutamine residues in random-coil peptides are characterized by large chemical shift differences and can be stereospecifically assigned on the basis of their chemical shift values only. The bimodal chemical shift distributions stored in the biological magnetic resonance data bank (BMRB) do not allow such an assignment. However, an analysis of the BMRB shows, that a substantial part of all stored stereospecific assignments is not correct. We show here that in most cases stereospecific assignment can also be done for folded proteins using an unbiased artificial chemical shift data base (UACSB). For a separation of the chemical shifts of the two amide resonance lines with differences ≥0.40 ppm for asparagine and differences ≥0.42 ppm for glutamine, the downfield shifted resonance lines can be assigned to H{sup δ21} and H{sup ε21}, respectively, at a confidence level >95%. A classifier derived from UASCB can also be used to correct the BMRB data. The program tool AssignmentChecker implemented in AUREMOL calculates the Bayesian probability for a given stereospecific assignment and automatically corrects the assignments for a given list of chemical shifts.

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 nega...

Solvent Effects on Oxygen-17 Chemical Shifts in Amides. Quantitative Linear Solvation Shift Relationships

Science.gov (United States)

Díez, Ernesto; Fabián, Jesús San; Gerothanassis, Ioannis P.; Esteban, Angel L.; Abboud, José-Luis M.; Contreras, Ruben H.; de Kowalewski, Dora G.

1997-01-01

A multiple-linear-regression analysis (MLRA) has been carried out using the Kamlet-Abboud-Taft (KAT) solvatochromic parameters in order to elucidate and quantify the solvent effects on the17O chemical shifts ofN-methylformamide (NMF),N,N-dimethylformamide (DMF),N-methylacetamide (NMA), andN,N-dimethylacetamide (DMA). The chemical shifts of the four molecules show the same dependence (in ppm) on the solvent polarity-polarizability, i.e., -22π*. The influence of the solvent hydrogen-bond-donor (HBD) acidities is slightly larger for the acetamides NMA and DMA, i.e., -48α, than for the formamides NMF and DMF, i.e., -42α. The influence of the solvent hydrogen-bond-acceptor (HBA) basicities is negligible for the nonprotic molecules DMF and DMA but significant for the protic molecules NMF and NMA, i.e., -9β. The effect of substituting the N-H hydrogen by a methyl group amounts to -5.9 ppm in NMF and 5.4 ppm in NMA. The effect of substituting the O=C-H hydrogen amounts to 5.5 ppm in NMF and 16.8 ppm in DMF. The model of specific hydration sites of amides by I. P. Gerothanassis and C. Vakka [J. Org. Chem.59,2341 (1994)] is settled in a more quantitative basis and the model by M. I. Burgar, T. E. St. Amour, and D. Fiat [J. Phys. Chem.85,502 (1981)] is critically evaluated.17O hydration shifts have been calculated for formamide (FOR) by the ab initio LORG method at the 6-31G* level. For a formamide surrounded by the four in-plane molecules of water in the first hydration shell, the calculated17O shift change due to the four hydrogen bonds, -83.2 ppm, is smaller than the empirical hydration shift, -100 ppm. The17O shift change from each out-of-plane water molecule hydrogen-bonded to the amide oxygen is -18.0 ppm. These LORG results support the conclusion that no more than four water molecules are hydrogen-bonded to the amide oxygen in formamide.

Spiral density waves in M81. I. Stellar spiral density waves

International Nuclear Information System (INIS)

Feng, Chien-Chang; Lin, Lien-Hsuan; Wang, Hsiang-Hsu; Taam, Ronald E.

2014-01-01

Aside from the grand-design stellar spirals appearing in the disk of M81, a pair of stellar spiral arms situated well inside the bright bulge of M81 has been recently discovered by Kendall et al. The seemingly unrelated pairs of spirals pose a challenge to the theory of spiral density waves. To address this problem, we have constructed a three-component model for M81, including the contributions from a stellar disk, a bulge, and a dark matter halo subject to observational constraints. Given this basic state for M81, a modal approach is applied to search for the discrete unstable spiral modes that may provide an understanding for the existence of both spiral arms. It is found that the apparently separated inner and outer spirals can be interpreted as a single trailing spiral mode. In particular, these spirals share the same pattern speed 25.5 km s –1 kpc –1 with a corotation radius of 9.03 kpc. In addition to the good agreement between the calculated and the observed spiral pattern, the variation of the spiral amplitude can also be naturally reproduced.

Logarithmic Spiral

Indian Academy of Sciences (India)

Switzerland) even today can see the. Archimedian spiral and the inscription under it on the tombstone of Jacob Bernoulli 1. Logarithmic Spiral in Nature. Apart from logarithmic spiral no other curve seems to have attracted the attention of scientists, ...

Identify Beta-Hairpin Motifs with Quadratic Discriminant Algorithm Based on the Chemical Shifts.

Directory of Open Access Journals (Sweden)

Feng YongE

Full Text Available Successful prediction of the beta-hairpin motif will be helpful for understanding the of the fold recognition. Some algorithms have been proposed for the prediction of beta-hairpin motifs. However, the parameters used by these methods were primarily based on the amino acid sequences. Here, we proposed a novel model for predicting beta-hairpin structure based on the chemical shift. Firstly, we analyzed the statistical distribution of chemical shifts of six nuclei in not beta-hairpin and beta-hairpin motifs. Secondly, we used these chemical shifts as features combined with three algorithms to predict beta-hairpin structure. Finally, we achieved the best prediction, namely sensitivity of 92%, the specificity of 94% with 0.85 of Mathew's correlation coefficient using quadratic discriminant analysis algorithm, which is clearly superior to the same method for the prediction of beta-hairpin structure from 20 amino acid compositions in the three-fold cross-validation. Our finding showed that the chemical shift is an effective parameter for beta-hairpin prediction, suggesting the quadratic discriminant analysis is a powerful algorithm for the prediction of beta-hairpin.

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.

Identification of helix capping and β-turn motifs from NMR chemical shifts

International Nuclear Information System (INIS)

Shen Yang; Bax, Ad

2012-01-01

We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and 13 C β chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of β-turns: I, II, I′, II′ 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 β-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.

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.)

Frequency spirals

International Nuclear Information System (INIS)

Ottino-Löffler, Bertrand; Strogatz, Steven H.

2016-01-01

We study the dynamics of coupled phase oscillators on a two-dimensional Kuramoto lattice with periodic boundary conditions. For coupling strengths just below the transition to global phase-locking, we find localized spatiotemporal patterns that we call “frequency spirals.” These patterns cannot be seen under time averaging; they become visible only when we examine the spatial variation of the oscillators' instantaneous frequencies, where they manifest themselves as two-armed rotating spirals. In the more familiar phase representation, they appear as wobbly periodic patterns surrounding a phase vortex. Unlike the stationary phase vortices seen in magnetic spin systems, or the rotating spiral waves seen in reaction-diffusion systems, frequency spirals librate: the phases of the oscillators surrounding the central vortex move forward and then backward, executing a periodic motion with zero winding number. We construct the simplest frequency spiral and characterize its properties using analytical and numerical methods. Simulations show that frequency spirals in large lattices behave much like this simple prototype.

Frequency spirals

Energy Technology Data Exchange (ETDEWEB)

Ottino-Löffler, Bertrand; Strogatz, Steven H., E-mail: strogatz@cornell.edu [Center for Applied Mathematics, Cornell University, Ithaca, New York 14853 (United States)

2016-09-15

We study the dynamics of coupled phase oscillators on a two-dimensional Kuramoto lattice with periodic boundary conditions. For coupling strengths just below the transition to global phase-locking, we find localized spatiotemporal patterns that we call “frequency spirals.” These patterns cannot be seen under time averaging; they become visible only when we examine the spatial variation of the oscillators' instantaneous frequencies, where they manifest themselves as two-armed rotating spirals. In the more familiar phase representation, they appear as wobbly periodic patterns surrounding a phase vortex. Unlike the stationary phase vortices seen in magnetic spin systems, or the rotating spiral waves seen in reaction-diffusion systems, frequency spirals librate: the phases of the oscillators surrounding the central vortex move forward and then backward, executing a periodic motion with zero winding number. We construct the simplest frequency spiral and characterize its properties using analytical and numerical methods. Simulations show that frequency spirals in large lattices behave much like this simple prototype.

Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution

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....... The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each residue's effect on glycine chemical shifts. Due to its unusual conformational freedom, glycine may be particularly unrepresentative for the remaining residue types. In this study, we...... 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...

Effects of Protein-pheromone Complexation on Correlated Chemical Shift Modulations

Energy Technology Data Exchange (ETDEWEB)

Perazzolo, Chiara; Wist, Julien [Ecole Polytechnique Federale de Lausanne, Institut des Sciences et Ingenierie Chimiques (Switzerland); Loth, Karine; Poggi, Luisa [Ecole Normale Superieure, Departement de chimie, associe au CNRS (France); Homans, Steve [University of Leeds, School of Biochemistry and Microbiology (United Kingdom); Bodenhausen, Geoffrey [Ecole Polytechnique Federale de Lausanne, Institut des Sciences et Ingenierie Chimiques (Switzerland)], E-mail: Geoffrey.Bodenhausen@ens.fr

2005-12-15

Major urinary protein (MUP) is a pheromone-carrying protein of the lipocalin family. Previous studies by isothermal titration calorimetry (ITC) show that the affinity of MUP for the pheromone 2-methoxy-3-isobutylpyrazine (IBMP) is mainly driven by enthalpy, with a small unfavourable entropic contribution. Entropic terms can be attributed in part to changes in internal motions of the protein upon binding. Slow internal motions can lead to correlated or anti-correlated modulations of the isotropic chemical shifts of carbonyl C' and amide N nuclei. Correlated chemical shift modulations (CSM/CSM) in MUP have been determined by measuring differences of the transverse relaxation rates of zero- and double-quantum coherences ZQC{l_brace}C'N{r_brace} and DQC{l_brace}C'N{r_brace}, and by accounting for the effects of correlated fluctuations of dipole-dipole couplings (DD/DD) and chemical shift anisotropies (CSA/CSA). The latter can be predicted from tensor parameters of C' and N nuclei that have been determined in earlier work. The effects of complexation on slow time-scale protein dynamics can be determined by comparing the temperature dependence of the relaxation rates of APO-MUP (i.e., without ligand) and HOLO-MUP (i.e., with IBMP as a ligand)

Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

International Nuclear Information System (INIS)

Fritzsching, Keith J.; Hong, Mei; Schmidt-Rohr, Klaus

2016-01-01

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

Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

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

Spiral symmetry

CERN Document Server

Hargittai, Istvan

1992-01-01

From the tiny twisted biological molecules to the gargantuan curling arms of many galaxies, the physical world contains a startling repetition of spiral patterns. Today, researchers have a keen interest in identifying, measuring, and defining these patterns in scientific terms. Spirals play an important role in the growth processes of many biological forms and organisms. Also, through time, humans have imitated spiral motifs in their art forms, and invented new and unusual spirals which have no counterparts in the natural world. Therefore, one goal of this multiauthored book is to stress the c

DFT/GIAO calculations of the relative contributions of hyperconjugation to the chemical shifts of ethanol

International Nuclear Information System (INIS)

Carneiro, J. Walkimar de M.; Dias, Jacques F.; Seidl, Peter R.; Tostes, J. Glauco R.

2002-01-01

Our previous DFT/GIAO calculations on different types of alcohols reveal that the rotation of the hydroxyl group can affect the chemical shift of carbons and hydrogens close to the substituent in different ways. Besides the steric and electrostatic effects that have been widely studied, hyperconjugation with the lone pairs on oxygen of the hydroxyl group leads to changes in bond lengths and angles as well as to different charge distributions. As all three of these factors also affect chemical shifts, we undertook a systematic investigation of their relative contributions to the chemical shifts of ethanol, a molecule in which there is minimum interference among these factors. Calculations by the B3LYP method at the 6-31G(d) level for ethanol conformers corresponding to a rotation around the carbon-oxygen bond at 30 dec increments are used to show how relative contributions vary with the dihedral angle formed between the carbon-carbon and oxygen-hydrogen bonds (C-C-O-H). Largest contributions to carbon chemical shifts can be attributed to changes in bond lengths while for hydrogen chemical shifts also contribute significantly differences in charge distribution. (author)

Triangular spiral tilings

International Nuclear Information System (INIS)

Sushida, Takamichi; Hizume, Akio; Yamagishi, Yoshikazu

2012-01-01

The topology of spiral tilings is intimately related to phyllotaxis theory and continued fractions. A quadrilateral spiral tiling is determined by a suitable chosen triple (ζ, m, n), where ζ element of D/R, and m and n are relatively prime integers. We give a simple characterization when (ζ, m, n) produce a triangular spiral tiling. When m and n are fixed, the admissible generators ζ form a curve in the unit disk. The family of triangular spiral tilings with opposed parastichy pairs (m, n) is parameterized by the divergence angle arg (ζ), while triangular spiral tilings with non-opposed parastichy pairs are parameterized by the plastochrone ratio 1/|ζ|. The generators for triangular spiral tilings with opposed parastichy pairs are not dense in the complex parameter space, while those with non-opposed parastichy pairs are dense. The proofs will be given in a general setting of spiral multiple tilings. We present paper-folding (origami) sheets that build spiral towers whose top-down views are triangular tilings. (paper)

Anisotropy of the fluorine chemical shift tensor in UF6

International Nuclear Information System (INIS)

Rigny, P.

1965-04-01

An 19 F magnetic resonance study of polycrystalline UF 6 is presented. The low temperature complex line can be analyzed as the superposition of two distinct lines, which is attributed to a distortion of the UF 6 octahedron in the solid. The shape of the two components is studied. Their width is much larger than the theoretical dipolar width, and must be explained by large anisotropies of the fluorine chemical shift tensors. The resulting shape functions of the powder spectra are determined. The values of the parameters of the chemical shift tensors yield estimates of the characters of the U-F bonds, and this gives some information on the ground state electronic wave function of the UF 6 molecule in the solid. (author) [fr

Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression

Energy Technology Data Exchange (ETDEWEB)

Brown, Joshua D.; Summers, Michael F. [University of Maryland Baltimore County, Howard Hughes Medical Institute (United States); Johnson, Bruce A., E-mail: bruce.johnson@asrc.cuny.edu [University of Maryland Baltimore County, Department of Chemistry and Biochemistry (United States)

2015-09-15

The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the {sup 1}H NMR and {sup 13}C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and {sup 1}H and {sup 13}C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA {sup 1}H and {sup 13}C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides.

Skeletal and chlorine effects on 13C-NMR chemical shifts of chlorinated polycyclic systems

Directory of Open Access Journals (Sweden)

Costa V.E.U.

1999-01-01

Full Text Available In order to establish a comparative analysis of chemical shifts caused by ring compression effects or by the presence of a chlorine atom on strained chlorinated carbons, a series of the chlorinated and dechlorinated polycyclic structures derived from "aldrin" (5 and "isodrin" (14 was studied. Compounds were classified in four different groups, according to their conformation and number of ring such as: endo-exo and endo-endo tetracyclics, pentacyclics and hexacyclics. The 13C chemical shift comparison between the chlorinated and dechlorinated compounds showed that when C-9 and C-10 are olefinic carbons, it occurs a shielding of 0.5-2.4 ppm for endo-endo tetracyclics and of 4.7-7.6 ppm for endo-exo tetracyclic. The chemical shift variation for C-11 reaches 49-53 ppm for endo-exo and endo-endo tetracyclics, 54 ppm for pentacyclic and 56-59 ppm for hexacyclic compounds. From these data, it was possible to observe the influence of ring compression on the chemical shifts.

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

International Nuclear Information System (INIS)

Shen Yang; Bax, Ad

2010-01-01

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 13 C β 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 13 C β atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for δ 15 N, δ 13 C', δ 13 C α , δ 13 C β , δ 1 H α and δ 1 H 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.

Cyclohexanecarbonitriles: Assigning Configurations at Quaternary Centers From 13C NMR CN Chemical Shifts.1

Science.gov (United States)

Wei, Guoqing

2009-01-01

13C NMR chemical shifts of the nitrile carbon in cyclohexanecarbonitriles directly correlate with the configuration of the quaternary, nitrile-bearing stereocenter. Comparing 13C NMR chemical shifts for over 200 cyclohexanecarbonitriles reveals that equatorially oriented nitriles resonate 3.3 ppm downfield, on average, from their axial counterparts. Pairs of axial/equatorial diastereomers varying only at the nitrile-bearing carbon consistently exhibit downfield shifts of δ 0.4–7.2 for the equatorial nitrile carbon, even in angularly substituted decalins and hydrindanes. PMID:19348434

Continuing research on the classical spiraling photon model

Science.gov (United States)

Li, Hongrui

2014-11-01

Based no the classical spiraling photon model proposed by Hongrui Li, the laws of reflection, refraction of a single photon can be derived. Moreover, the polarization, total reflection, evanescent wave and Goos-Hanchen shift of a single photon can be elucidated. However, this photon model is still unfinished. Especially, the spiraling diameter of a photon is not definite. In this paper, the continuous research works on this new theory are reported. According to the facts that the diffraction limit of light and the smallest diameter of the focal spot of lenses are all equal to the wavelength λ of the light, we can get that the spiraling diameter of a photon equals to the wavelength λ, so we gain that the angle between the linear velocity of the spiraling photon υ and the component of the linear velocity in the forward direction υb is 45°, and the energy of a classical spiraling photon E = (1/2)mυ2 = (1/2)m2c2 = mc2. This coincides with Einstein's mass-energy relation. While it is obtained that the velocity of the evanescent wave in the vacuum is slower than the velocity of light in glass in straight line. In such a way, the optical fiber can slow the light down. In addition, the force analysis of a single photon in optical tweezers system is discussed. And the reason that the laser beam can capture the particle slightly downstream from the focal point can be explained.

Linking phylogenetic and functional diversity to nutrient spiraling in microbial mats from Lower Kane Cave (USA).

Science.gov (United States)

Engel, Annette Summers; Meisinger, Daniela B; Porter, Megan L; Payn, Robert A; Schmid, Michael; Stern, Libby A; Schleifer, K H; Lee, Natuschka M

2010-01-01

Microbial mats in sulfidic cave streams offer unique opportunities to study redox-based biogeochemical nutrient cycles. Previous work from Lower Kane Cave, Wyoming, USA, focused on the aerobic portion of microbial mats, dominated by putative chemolithoautotrophic, sulfur-oxidizing groups within the Epsilonproteobacteria and Gammaproteobacteria. To evaluate nutrient cycling and turnover within the whole mat system, a multidisciplinary strategy was used to characterize the anaerobic portion of the mats, including application of the full-cycle rRNA approach, the most probable number method, and geochemical and isotopic analyses. Seventeen major taxonomic bacterial groups and one archaeal group were retrieved from the anaerobic portions of the mats, dominated by Deltaproteobacteria and uncultured members of the Chloroflexi phylum. A nutrient spiraling model was applied to evaluate upstream to downstream changes in microbial diversity based on carbon and sulfur nutrient concentrations. Variability in dissolved sulfide concentrations was attributed to changes in the abundance of sulfide-oxidizing microbial groups and shifts in the occurrence and abundance of sulfate-reducing microbes. Gradients in carbon and sulfur isotopic composition indicated that released and recycled byproduct compounds from upstream microbial activities were incorporated by downstream communities. On the basis of the type of available chemical energy, the variability of nutrient species in a spiraling model may explain observed differences in microbial taxonomic affiliations and metabolic functions, thereby spatially linking microbial diversity to nutrient spiraling in the cave stream ecosystem.

1H NMR spectra part 31: 1H chemical shifts of amides in DMSO solvent.

Science.gov (United States)

Abraham, Raymond J; Griffiths, Lee; Perez, Manuel

2014-07-01

The (1)H chemical shifts of 48 amides in DMSO solvent are assigned and presented. The solvent shifts Δδ (DMSO-CDCl3 ) are large (1-2 ppm) for the NH protons but smaller and negative (-0.1 to -0.2 ppm) for close range protons. A selection of the observed solvent shifts is compared with calculated shifts from the present model and from GIAO calculations. Those for the NH protons agree with both calculations, but other solvent shifts such as Δδ(CHO) are not well reproduced by the GIAO calculations. The (1)H chemical shifts of the amides in DMSO were analysed using a functional approach for near ( ≤ 3 bonds removed) protons and the electric field, magnetic anisotropy and steric effect of the amide group for more distant protons. The chemical shifts of the NH protons of acetanilide and benzamide vary linearly with the π density on the αN and βC atoms, respectively. The C=O anisotropy and steric effect are in general little changed from the values in CDCl3. The effects of substituents F, Cl, Me on the NH proton shifts are reproduced. The electric field coefficient for the protons in DMSO is 90% of that in CDCl3. There is no steric effect of the C=O oxygen on the NH proton in an NH…O=C hydrogen bond. The observed deshielding is due to the electric field effect. The calculated chemical shifts agree well with the observed shifts (RMS error of 0.106 ppm for the data set of 257 entries). Copyright © 2014 John Wiley & Sons, Ltd.

Characterization of the conformational equilibrium between the two major substates of RNase A using NMR chemical shifts.

Science.gov (United States)

Camilloni, Carlo; Robustelli, Paul; De Simone, Alfonso; Cavalli, Andrea; Vendruscolo, Michele

2012-03-07

Following the recognition that NMR chemical shifts can be used for protein structure determination, rapid advances have recently been made in methods for extending this strategy for proteins and protein complexes of increasing size and complexity. A remaining major challenge is to develop approaches to exploit the information contained in the chemical shifts about conformational fluctuations in native states of proteins. In this work we show that it is possible to determine an ensemble of conformations representing the free energy surface of RNase A using chemical shifts as replica-averaged restraints in molecular dynamics simulations. Analysis of this surface indicates that chemical shifts can be used to characterize the conformational equilibrium between the two major substates of this protein. © 2012 American Chemical Society

Sharp corners as sources of spiral pairs

International Nuclear Information System (INIS)

Biton, Y.; Rabinovitch, A.; Braunstein, D.; Friedman, M.; Aviram, I.

2010-01-01

It is demonstrated that using the FitzHugh-Nagumo model, stimulation of excitable media inside a region possessing sharp corners, can lead to the appearance of sources of spiral-pairs of sustained activity. The two conditions for such source creation are: The corners should be less than 120 deg. and the range of stimulating amplitudes should be small, occurring just above the threshold value and decreasing with the corner angle. The basic mechanisms driving the phenomenon are discussed. These include: A. If the corner angle is below 120 deg., the wave generated inside cannot emerge at the corner tip, resulting in the creation of two free edges which start spiraling towards each other. B. Spiraling must be strong enough; otherwise annihilation of the rotating arms would occur too soon to create a viable source. C. The intricacies of the different radii involved are elucidated. Possible applications in heart stimulation and in chemical reactions are considered.

Sequential nearest-neighbor effects on computed {sup 13}C{sup {alpha}} chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Vila, Jorge A. [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States); Serrano, Pedro; Wuethrich, Kurt [The Scripps Research Institute, Department of Molecular Biology (United States); Scheraga, Harold A., E-mail: has5@cornell.ed [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States)

2010-09-15

To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of {sup 13}C{sup {alpha}} chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue {alpha}/{beta} protein, which contains 9 prolines and has 50% of its residues located in loops and turns. Overall, the results presented here show that sizeable nearest-neighbor effects are seen only for residues preceding proline, where Pro introduces an overestimation, on average, of 1.73 ppm in the computed {sup 13}C{sup {alpha}} chemical shifts. A new ensemble of 20 conformers representing the NMR structure of the NAB, which was calculated with an input containing backbone torsion angle constraints derived from the theoretical {sup 13}C{sup {alpha}} chemical shifts as supplementary data to the NOE distance constraints, exhibits very similar topology and comparable agreement with the NOE constraints as the published NMR structure. However, the two structures differ in the patterns of differences between observed and computed {sup 13}C{sup {alpha}} chemical shifts, {Delta}{sub ca,i}, for the individual residues along the sequence. This indicates that the {Delta}{sub ca,i} -values for the NAB protein are primarily a consequence of the limited sampling by the bundles of 20 conformers used, as in common practice, to represent the two NMR structures, rather than of local flaws in the structures.

Isotope effects on chemical shifts in tautomeric systems with double proton transfer. Citronin

International Nuclear Information System (INIS)

Hansen, P.E.; Langgard, M.; Bolvig, S.

1998-01-01

Primary and secondary deuterium isotope effects on 1 H and 13 C chemical shifts are measured in citrinin, a tautomeric compound with an unusual doubly intramolecularly hydrogen bonded structure. The isotope effects are to a large extent dominated by equilibrium contributions and deuteration leads to more of the deuterated enol forms rather than the deuterated acid form. 1 H 13 C and 17 O nuclear shieldings are calculated using density functional ab initio methods. A very good correlation between calculated nuclear shieldings and experimental 1 H and 13 C chemical shifts is obtained. The tautomeric equilibrium can be analyzed based on the isotope effects on B-6 and C-8 carbons and shows an increase in the o-quinone form on lowering the temperature. Furthermore, upon deuteration the largest equilibrium shift is found for deuteration at OH-8 and the shift in the tautomeric equilibrium upon deuteration at OH-8 and the shift in the tautomeric equilibrium upon deuteration is increasing at lower temperature. (author)

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

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.

The interplay between transient a-helix formation and side chain rotamer distributions in disordered proteins probed by methyl chemical shifts

DEFF Research Database (Denmark)

Kjærgaard, Magnus; Iesmantavicius, Vytautas; Poulsen, Flemming M

2011-01-01

and retinoid receptors (ACTR). We find that small differences in the methyl carbon chemical shifts due to the ¿-gauche effect may provide information about the side chain rotamer distributions. However, the effects of neighboring residues on the methyl group chemical shifts obscure the direct observation...... 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...

What can we learn by computing 13Cα chemical shifts for X-ray protein models?

International Nuclear Information System (INIS)

Arnautova, Yelena A.; Vila, Jorge A.; Martin, Osvaldo A.; Scheraga, Harold A.

2009-01-01

The room-temperature X-ray structures of two proteins, solved at 1.8 and 1.9 Å resolution, are used to investigate whether a set of conformations, rather than a single X-ray structure, provides better agreement with both the X-ray data and the observed 13 C α chemical shifts in solution. The room-temperature X-ray structures of ubiquitin and of the RNA-binding domain of nonstructural protein 1 of influenza A virus solved at 1.8 and 1.9 Å resolution, respectively, were used to investigate whether a set of conformations rather than a single X-ray structure provides better agreement with both the X-ray data and the observed 13 C α chemical shifts in solution. For this purpose, a set of new conformations for each of these proteins was generated by fitting them to the experimental X-ray data deposited in the PDB. For each of the generated structures, which show R and R free factors similar to those of the deposited X-ray structure, the 13 C α chemical shifts of all residues in the sequence were computed at the DFT level of theory. The sets of conformations were then evaluated by their ability to reproduce the observed 13 C α chemical shifts by using the conformational average root-mean-square-deviation (ca-r.m.s.d.). For ubiquitin, the computed set of conformations is a better representation of the observed 13 C α chemical shifts in terms of the ca-r.m.s.d. than a single X-ray-derived structure. However, for the RNA-binding domain of nonstructural protein 1 of influenza A virus, consideration of an ensemble of conformations does not improve the agreement with the observed 13 C α chemical shifts. Whether an ensemble of conformations rather than any single structure is a more accurate representation of a protein structure in the crystal as well as of the observed 13 C α chemical shifts is determined by the dispersion of coordinates, in terms of the all-atom r.m.s.d. among the generated models; these generated models satisfy the experimental X-ray data with

Conformational analysis of the chemical shifts for molecules containing diastereotopic methylene protons

Science.gov (United States)

Borowski, Piotr

2012-01-01

Quantum chemistry SCF/GIAO calculations were carried out on a set of compounds containing diastereotopic protons. Five molecules, including recently synthesized 1,3-di(2,3-epoxypropoxy)benzene, containing the chiral or pro-chiral center and the neighboring methylene group, were chosen. The rotational averages (i.e. normalized averages with respect to the rotation about the torsional angle τ with the exponential energy weight at temperature T) calculated individually for each of the methylene protons in 1,3-di(2,3-epoxypropoxy)benzene differ by ca. 0.6 ppm, which is significantly less than the value calculated for the lowest energy conformer. This value turned out to be low enough to guarantee the proper ordering of theoretical chemical shifts, supporting the interpretation of the 1H NMR spectrum of this important compound. The rotational averages of chemical shifts for methylene protons for a given type of conformer are shown to be essentially equal to the Boltzmann averages (here, the population-weighted averages for the individual conformers representing minima on the E( τ) cross-section). The calculated Boltzmann averages in the representative conformational space may exhibit completely different ordering as compared to the chemical shifts calculated for the lowest-energy conformer. This is especially true in the case of molecules, for which no significant steric effects are present. In this case, only Boltzmann averages account for the experimental pattern of proton signals. In addition, better overall agreement with experiment (lower value of the root-mean-square deviation between calculated and measured chemical shifts) is typically obtained when Boltzmann averages are used.

Spiral Countercurrent Chromatography

Science.gov (United States)

Ito, Yoichiro; Knight, Martha; Finn, Thomas M.

2013-01-01

For many years, high-speed countercurrent chromatography conducted in open tubing coils has been widely used for the separation of natural and synthetic compounds. In this method, the retention of the stationary phase is solely provided by the Archimedean screw effect by rotating the coiled column in the centrifugal force field. However, the system fails to retain enough of the stationary phase for polar solvent systems such as the aqueous–aqueous polymer phase systems. To address this problem, the geometry of the coiled channel was modified to a spiral configuration so that the system could utilize the radially acting centrifugal force. This successfully improved the retention of the stationary phase. Two different types of spiral columns were fabricated: the spiral disk assembly, made by stacking multiple plastic disks with single or four interwoven spiral channels connected in series, and the spiral tube assembly, made by inserting the tetrafluoroethylene tubing into a spiral frame (spiral tube support). The capabilities of these column assemblies were successfully demonstrated by separations of peptides and proteins with polar two-phase solvent systems whose stationary phases had not been well retained in the earlier multilayer coil separation column for high-speed countercurrent chromatography. PMID:23833207

Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

International Nuclear Information System (INIS)

Shen Yang; Bax, Ad

2007-01-01

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/χ 1 torsion angles and sequence similarity to the query triplet of interest. The database contains 15 N, 1 H N , 1 H α , 13 C α , 13 C β and 13 C' 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/χ 1 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 15 N, 1 H N , 1 H α , 13 C α , 13 C β and 13 C', respectively, including outliers

Wavelength conversion of QAM signals in a low loss CMOS compatible spiral waveguide

DEFF Research Database (Denmark)

Da Ros, Francesco; Porto da Silva, Edson; Zibar, Darko

2017-01-01

We demonstrate wavelength conversion of quadrature amplitude modulation (QAM) signals, including 32-GBd quadrature phase-shift keying and 10-GBd 16-QAM, in a 50-cm long high index doped glass spiral waveguide. The quality of the generated idlers for up to 20 nm of wavelength shift is sufficient...... to achieve a BER performance below the hard decision forward error correction threshold BER performance (...

Chemical Evolution and Star Formation History of the Disks of Spirals in Local Group

Science.gov (United States)

Yin, J.

2011-05-01

Milky Way (MW), M31 and M33 are the only three spiral galaxies in our Local group. MW and M31 have similar mass, luminosity and morphology, while M33 is only about one tenth of MW in terms of its baryonic mass. Detailed theoretical researches on these three spirals will help us to understand the formation and evolution history of both spiral galaxies and Local group. Referring to the phenomenological chemical evolution model adopted in MW disk, a similar model is established to investigate the star formation and chemical enrichment history of these three local spirals. Firstly, the properties of M31 disk are studied by building a similar chemical evolution model which is able to successfully describe the MW disk. It is expected that a simple unified phenomenological chemical evolution model could successfully describe the radial and global properties of both disks. Comparing with the former work, we adopt an extensive data set as model constraints, including the star formation profile of M31 disk derived from the recent UV data of GALEX. The comparison among the observed properties of these two disks displays very interesting similarities in their radial profiles when the distance from the galactic center is expressed in terms of the corresponding scale length. This implies some common processes in their formation and evolution history. Based on the observed data of the gas mass surface density and SFR surface density, the SFR radial profile of MW can be well described by Kennicutt-Schmidt star formation law (K-S law) or modified K-S law (SFR is inversely proportional to the distance from the galactic center), but this is not applicable to the M31 disk. Detailed calculations show that our unified model describes fairly well all the main properties of the MW disk and most properties of M31 disk, provided that the star formation efficiency of M31 disk is adjusted to be twice as large as that of MW disk (as anticipated from the lower gas fraction of M31). However, the

Transition from Spirals to Defect-Mediated Turbulence Driven by a Doppler Instability

International Nuclear Information System (INIS)

Ouyang, Qi; Swinney, Harry L.; Li, Ge

2000-01-01

A transition from rotating chemical spirals to turbulence is observed in experiments on the Belousov-Zhabotinsky reaction. The transition occurs when the waves near the spiral tip spontaneously break, generating defects. Measurements reveal that this defect-mediated turbulence is caused by the Doppler effect on the traveling waves. The observations are in good accord with numerical simulations and theory. (c) 2000 The American Physical Society

Implementation of the NMR CHEmical Shift Covariance Analysis (CHESCA): A Chemical Biologist's Approach to Allostery.

Science.gov (United States)

Boulton, Stephen; Selvaratnam, Rajeevan; Ahmed, Rashik; Melacini, Giuseppe

2018-01-01

Mapping allosteric sites is emerging as one of the central challenges in physiology, pathology, and pharmacology. Nuclear Magnetic Resonance (NMR) spectroscopy is ideally suited to map allosteric sites, given its ability to sense at atomic resolution the dynamics underlying allostery. Here, we focus specifically on the NMR CHEmical Shift Covariance Analysis (CHESCA), in which allosteric systems are interrogated through a targeted library of perturbations (e.g., mutations and/or analogs of the allosteric effector ligand). The atomic resolution readout for the response to such perturbation library is provided by NMR chemical shifts. These are then subject to statistical correlation and covariance analyses resulting in clusters of allosterically coupled residues that exhibit concerted responses to the common set of perturbations. This chapter provides a description of how each step in the CHESCA is implemented, starting from the selection of the perturbation library and ending with an overview of different clustering options.

Proton chemical shift imaging after myocardial infarction

International Nuclear Information System (INIS)

Bouchard, A.; Doyle, M.; Pohost, G.M.

1989-01-01

The present study was undertaken to test whether chemical shift imaging could detect spatially the lipids known to accumulate in myocardium after an ischemic insult. Seven dogs underwent a 24-hour coronary artery occlusion. Hearts were removed and imaged ex vivo by the Dixon method (1.5 T), and myocardial samples were obtained for high-resolution H-1 spectroscopy. Lipid images revealed regions of increased signal intensity in the periphery f the myocardial infarction. The zones of high lipid signal corresponded to zones with elevated mobile lipids as detected by H-1 spectroscopy

Accuracy and precision of protein–ligand interaction kinetics determined from chemical shift titrations

International Nuclear Information System (INIS)

Markin, Craig J.; Spyracopoulos, Leo

2012-01-01

NMR-monitored chemical shift titrations for the study of weak protein–ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K D ) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K D value of a 1:1 protein–ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125–138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of 1 H– 15 N 2D HSQC NMR spectra acquired using precise protein–ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k off ). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k off ∼ 3,000 s −1 in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k off from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k off values over a wide range, from 100 to 15,000 s −1 . The validity of line shape analysis for k off values approaching intermediate exchange (∼100 s −1 ), may be facilitated by more accurate K D measurements from NMR

Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations.

Science.gov (United States)

Markin, Craig J; Spyracopoulos, Leo

2012-12-01

NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K ( D )) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K ( D ) value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of (1)H-(15)N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k ( off )). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k ( off ) ~ 3,000 s(-1) in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k ( off ) from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k ( off ) values over a wide range, from 100 to 15,000 s(-1). The validity of line shape analysis for k ( off ) values approaching intermediate exchange (~100 s(-1)), may be facilitated by more accurate K ( D ) measurements

13C NMR Chemical Shifts of the Triclinic and Monoclinic Crystal forms of Valinomycin

International Nuclear Information System (INIS)

Kameda, Tsunenori; McGeorge, Gary; Orendt, Anita M.; Grant, David M.

2004-01-01

Two different crystalline polymorphs of valinomycin, the triclinic and monoclinic forms, have been studied by high resolution, solid state 13 C CP-MAS NMR spectroscopy. Although the two polymorphs of the crystal are remarkably similar, there are distinct differences in the isotropic chemical shifts between the two spectra. For the triclinic form, the carbon chemical shift tensor components for the alpha carbons adjacent to oxygen in the lactic acid and hydroxyisovaleric acid residues and the ester carbonyls of the valine residue were obtained using the FIREMAT experiment. From the measured components, it was found that the behavior of the isotropic chemical shift, δ iso , for valine residue ester carbonyl carbons is predominately influenced by the intermediate component, δ 22 . Additionally it was found that the smallest shift component, δ 33 , for the L-lactic acid (L-Lac) and D-α-hydroxyisovaleric acid (D-Hyi) C α -O carbon was significantly displaced depending upon the nature of individual amino acid residues, and it is the δ 33 component that governs the behavior of δ iso in these alpha carbons

Generation of spirally polarized propagation-invariant beam using fiber microaxicon.

Science.gov (United States)

Philip, Geo M; Viswanathan, Nirmal K

2011-10-01

We present here a fiber microaxicon (MA)based method to generate spirally polarized propagation-invariant optical beam. MA chemically etched in the tip of a two-mode fiber efficiently converts the generic cylindrically polarized vortex fiber mode into a spirally polarized propagation-invariant (Bessel-type) beam via radial dependence of polarization rotation angle. The combined roles of helico-conical phase and nonparaxial propagation in the generation and characteristics of the output beam from the fiber MA are discussed. © 2011 Optical Society of America

Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics.

Science.gov (United States)

Klukowski, Piotr; Schubert, Mario

2018-06-15

A better understanding of oligosaccharides and their wide-ranging functions in almost every aspect of biology and medicine promises to uncover hidden layers of biology and will support the development of better therapies. Elucidating the chemical structure of an unknown oligosaccharide is still a challenge. Efficient tools are required for non-targeted glycomics. Chemical shifts are a rich source of information about the topology and configuration of biomolecules, whose potential is however not fully explored for oligosaccharides. We hypothesize that the chemical shifts of each monosaccharide are unique for each saccharide type with a certain linkage pattern, so that correlated data measured by NMR spectroscopy can be used to identify the chemical nature of a carbohydrate. We present here an efficient search algorithm, GlycoNMRSearch, that matches either a subset or the entire set of chemical shifts of an unidentified monosaccharide spin system to all spin systems in an NMR database. The search output is much more precise than earlier search functions and highly similar matches suggest the chemical structure of the spin system within the oligosaccharide. Thus searching for connected chemical shift correlations within all electronically available NMR data of oligosaccharides is a very efficient way of identifying the chemical structure of unknown oligosaccharides. With an improved database in the future, GlycoNMRSearch will be even more efficient deducing chemical structures of oligosaccharides and there is a high chance that it becomes an indispensable technique for glycomics. The search algorithm presented here, together with a graphical user interface, is available at http://glyconmrsearch.santos.pwr.edu.pl. Supplementary data are available at Bioinformatics online.

Robustness, Death of Spiral Wave in the Network of Neurons under Partial Ion Channel Block

International Nuclear Information System (INIS)

Jun, Ma; Long, Huang; Chun-Ni, Wang; Zhong-Sheng, Pu

2013-01-01

The development of spiral wave in a two-dimensional square array due to partial ion channel block (Potassium, Sodium) is investigated, the dynamics of the node is described by Hodgkin—Huxley neuron and these neurons are coupled with nearest neighbor connection. The parameter ratio x Na (and x K ), which defines the ratio of working ion channel number of sodium (potassium) to the total ion channel number of sodium (and potassium), is used to measure the shift conductance induced by channel block. The distribution of statistical variable R in the two-parameter phase space (parameter ratio vs. poisoning area) is extensively calculated to mark the parameter region for transition of spiral wave induced by partial ion channel block, the area with smaller factors of synchronization R is associated the parameter region that spiral wave keeps alive and robust to the channel poisoning. Spiral wave keeps alive when the poisoned area (potassium or sodium) and degree of intoxication are small, distinct transition (death, several spiral waves coexist or multi-arm spiral wave emergence) occurs under moderate ratio x Na (and x K ) when the size of blocked area exceeds certain thresholds. Breakup of spiral wave occurs and multi-arm of spiral waves are observed when the channel noise is considered. (interdisciplinary physics and related areas of science and technology)

Elucidation of the substitution pattern of 9,10-anthraquinones through the chemical shifts of peri-hydroxyl protons

DEFF Research Database (Denmark)

Schripsema, Jan; Danigno, Denise

1996-01-01

In 9,10-anthraquinones the chemical shift of a peri-hydroxyl proton is affected by the substituents in the other benzenoid ring. These effects are additive. They are useful for the determination of substitution patterns and have been used to revise the structures of six previously reported...... anthraquinones containing methoxyl, hydroxyl, methylenedioxy and beta-methyl substituents. Because the chemical shifts of the other protons are hardly affected by substitutions in the other ring, the characteristic chemical shifts for a wide variety of substitution patterns could be derived....

Vanadium NMR Chemical Shifts of (Imido)vanadium(V) Dichloride Complexes with Imidazolin-2-iminato and Imidazolidin-2-iminato Ligands: Cooperation with Quantum-Chemical Calculations and Multiple Linear Regression Analyses.

Science.gov (United States)

Yi, Jun; Yang, Wenhong; Sun, Wen-Hua; Nomura, Kotohiro; Hada, Masahiko

2017-11-30

The NMR chemical shifts of vanadium ( 51 V) in (imido)vanadium(V) dichloride complexes with imidazolin-2-iminato and imidazolidin-2-iminato ligands were calculated by the density functional theory (DFT) method with GIAO. The calculated 51 V NMR chemical shifts were analyzed by the multiple linear regression (MLR) analysis (MLRA) method with a series of calculated molecular properties. Some of calculated NMR chemical shifts were incorrect using the optimized molecular geometries of the X-ray structures. After the global minimum geometries of all of the molecules were determined, the trend of the observed chemical shifts was well reproduced by the present DFT method. The MLRA method was performed to investigate the correlation between the 51 V NMR chemical shift and the natural charge, band energy gap, and Wiberg bond index of the V═N bond. The 51 V NMR chemical shifts obtained with the present MLR model were well reproduced with a correlation coefficient of 0.97.

Electromechanics of graphene spirals

Energy Technology Data Exchange (ETDEWEB)

Korhonen, Topi; Koskinen, Pekka, E-mail: pekka.koskinen@iki.fi [NanoScience Center, Department of Physics, University of Jyväskylä, 40014 Jyväskylä (Finland)

2014-12-15

Among the most fascinating nanostructure morphologies are spirals, hybrids of somewhat obscure topology and dimensionality with technologically attractive properties. Here, we investigate mechanical and electromechanical properties of graphene spirals upon elongation by using density-functional tight-binding, continuum elasticity theory, and classical force field molecular dynamics. It turns out that electronic properties are governed by interlayer interactions as opposed to strain effects. The structural behavior is governed by van der Waals interaction: in its absence spirals unfold with equidistant layer spacings, ripple formation at spiral perimeter, and steadily increasing axial force; in its presence, on the contrary, spirals unfold via smooth local peeling, complex geometries, and nearly constant axial force. These electromechanical trends ought to provide useful guidelines not only for additional theoretical investigations but also for forthcoming experiments on graphene spirals.

Evaluation of the application of chemical shift for the detection of lipid in brain lesion

Energy Technology Data Exchange (ETDEWEB)

Lim, C.J. [Department of Biomedical Imaging, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur (Malaysia); Ng, K.H., E-mail: ngkh@um.edu.m [Department of Biomedical Imaging, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur (Malaysia); Ramli, N.; Azman, R.R. [Department of Biomedical Imaging, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur (Malaysia)

2011-02-15

Non-invasive detection of the presence of lipids is particularly important in staging of intracranial tumours. Presence of lipid peak in aggressive intracranial tumours has been reported widely using MR spectroscopy. However this method has limitation due to long imaging time and artefacts formed by adjacent bones. Chemical shift MR imaging (with has shorter imaging time) is an alternative method that had been used to detect presence of lipid in vivo by means of signal intensity loss. The purpose of this study was to evaluate gradient echo in- and opposed-phase chemical shift pulse sequences for detection of lipid elements in brain lesion. Ten cylindered phantoms measuring 3 x 3 cm were filled with various mixtures of lipid and water: 0-90% lipid, in 10% step by weight. The gradient echo in- and opposed-phase chemical shift sequences were performed using a 1.5 T MRI (Magnetom Vision, Siemens) with a head coil. In addition, we performed MRI and chemical shift studies on 32 patients with brain lesion. We then analysed the association between out of phase intensity value and classification of the lesions. For phantom containing 50% lipid, maximum signal loss on opposed-phase images was observed. There were significant differences between in- and opposed-phase lipid-water phantom images (P = 0.0054). Most of the benign lesions fall into the positive out of phase intensity value, and malignant lesions fall into negative out of phase intensity value. We conclude that chemical shift artefact can be applied in detecting and characterising lipid elements in brain lesion.

Evaluation of the application of chemical shift for the detection of lipid in brain lesion

International Nuclear Information System (INIS)

Lim, C.J.; Ng, K.H.; Ramli, N.; Azman, R.R.

2011-01-01

Non-invasive detection of the presence of lipids is particularly important in staging of intracranial tumours. Presence of lipid peak in aggressive intracranial tumours has been reported widely using MR spectroscopy. However this method has limitation due to long imaging time and artefacts formed by adjacent bones. Chemical shift MR imaging (with has shorter imaging time) is an alternative method that had been used to detect presence of lipid in vivo by means of signal intensity loss. The purpose of this study was to evaluate gradient echo in- and opposed-phase chemical shift pulse sequences for detection of lipid elements in brain lesion. Ten cylindered phantoms measuring 3 x 3 cm were filled with various mixtures of lipid and water: 0-90% lipid, in 10% step by weight. The gradient echo in- and opposed-phase chemical shift sequences were performed using a 1.5 T MRI (Magnetom Vision, Siemens) with a head coil. In addition, we performed MRI and chemical shift studies on 32 patients with brain lesion. We then analysed the association between out of phase intensity value and classification of the lesions. For phantom containing 50% lipid, maximum signal loss on opposed-phase images was observed. There were significant differences between in- and opposed-phase lipid-water phantom images (P = 0.0054). Most of the benign lesions fall into the positive out of phase intensity value, and malignant lesions fall into negative out of phase intensity value. We conclude that chemical shift artefact can be applied in detecting and characterising lipid elements in brain lesion.

Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations

Energy Technology Data Exchange (ETDEWEB)

Markin, Craig J.; Spyracopoulos, Leo, E-mail: leo.spyracopoulos@ualberta.ca [University of Alberta, Department of Biochemistry (Canada)

2012-12-15

NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K{sub D}) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K{sub D} value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of {sup 1}H-{sup 15}N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k{sub off}). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k{sub off} {approx} 3,000 s{sup -1} in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k{sub off} from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k{sub off} values over a wide range, from 100 to 15,000 s{sup -1}. The validity of line shape analysis for k{sub off} values approaching intermediate exchange ({approx}100 s{sup -1}), may be facilitated by

An extrapolation scheme for solid-state NMR chemical shift calculations

Science.gov (United States)

Nakajima, Takahito

2017-06-01

Conventional quantum chemical and solid-state physical approaches include several problems to accurately calculate solid-state nuclear magnetic resonance (NMR) properties. We propose a reliable computational scheme for solid-state NMR chemical shifts using an extrapolation scheme that retains the advantages of these approaches but reduces their disadvantages. Our scheme can satisfactorily yield solid-state NMR magnetic shielding constants. The estimated values have only a small dependence on the low-level density functional theory calculation with the extrapolation scheme. Thus, our approach is efficient because the rough calculation can be performed in the extrapolation scheme.

Observations of barred spirals

International Nuclear Information System (INIS)

Elmegreen, D.M.

1990-01-01

Observations of barred spiral galaxies are discussed which show that the presence of a bar increases the likelihood for grand design spiral structure only in early Hubble types. This result is contrary to the more common notion that grand design spiral structure generally accompanies bars in galaxies. Enhanced deprojected color images are shown which reveal that a secondary set of spiral arms commonly occurs in barred galaxies and also occasionally in ovally distorted galaxies. 6 refs

Analisa Kekuatan Spiral Bevel Gear Dengan Variasi Sudut Spiral Menggunakan Metode Elemen Hingga

OpenAIRE

Deta Rachmat Andika; Agus Sigit Pramono

2017-01-01

Seiring perkembangan zaman,  teknologi roda gigi dituntut untuk mampu mentransmisikan daya yang besar dengan efisiensi yang besar pula. Pada jenis intersecting shaft gear, tipe roda gigi payung spiral (spiral bevel gear)  merupakan perkembangan dari roda gigi payung bergigi lurus (straight bevel gear). Kelebihan dari spiral bevel gear antara  lain adalah kemampuan transmisi daya dan efisiensi yang lebih besar pada geometri yang sama serta tidak terlalu berisik. Akan tetapi spiral bevel gear j...

Barred spiral structure of galaxies

International Nuclear Information System (INIS)

Chen, Z.; Weng, s.; Xu, M.

1982-01-01

Observational data indicate the grand design of spiral or barred spiral structure in disk galaxies. The problem of spiral structure has been thoroughly investigated by C. C. Lin and his collaborators, but yet the problem of barred spiral structure has not been investigated systematically, although much work has been done, such as in Ref. 3--7. Using the gasdynamic model for galaxies and a method of integral transform presented in Ref. 1, we investigated the barred spiral structure and obtained an analytical solution. It gives the large-scale pattern of barred-spirals, which is in fairly good agreement with observational data

Spiral branches and star formation

International Nuclear Information System (INIS)

Zasov, A.V.

1974-01-01

Origin of spiral branches of galaxies and formation of stars in them are considered from the point of view of the theory of the gravitational gas condensation, one of comparatively young theories. Arguments are presented in favour of the stellar condensation theory. The concept of the star formation of gas is no longer a speculative hypothesis. This is a theory which assumes quantitative verification and explains qualitatively many facts observed. And still our knowledge on the nature of spiral branches is very poor. It still remains vague what processes give origin to spiral branches, why some galaxies have spirals and others have none. And shapes of spiral branches are diverse. Some cases are known when spiral branches spread outside boundaries of galaxies themselves. Such spirals arise exclusively in the region where there are two or some interacting galaxies. Only first steps have been made in the explanation of the galaxy spiral branches, and it is necessary to carry out new observations and new theoretical calculations

Plasma Generator Using Spiral Conductors

Science.gov (United States)

Szatkowski, George N. (Inventor); Dudley, Kenneth L. (Inventor); Ticatch, Larry A. (Inventor); Smith, Laura J. (Inventor); Koppen, Sandra V. (Inventor); Nguyen, Truong X. (Inventor); Ely, Jay J. (Inventor)

2016-01-01

A plasma generator includes a pair of identical spiraled electrical conductors separated by dielectric material. Both spiraled conductors have inductance and capacitance wherein, in the presence of a time-varying electromagnetic field, the spiraled conductors resonate to generate a harmonic electromagnetic field response. The spiraled conductors lie in parallel planes and partially overlap one another in a direction perpendicular to the parallel planes. The geometric centers of the spiraled conductors define endpoints of a line that is non-perpendicular with respect to the parallel planes. A voltage source coupled across the spiraled conductors applies a voltage sufficient to generate a plasma in at least a portion of the dielectric material.

Experimental and DFT evaluation of the 1H and 13C NMR chemical shifts for calix[4]arenes

Science.gov (United States)

Guzzo, Rodrigo N.; Rezende, Michelle Jakeline Cunha; Kartnaller, Vinicius; Carneiro, José Walkimar de M.; Stoyanov, Stanislav R.; Costa, Leonardo Moreira da

2018-04-01

The density functional theory is employed to determine the efficiency of 11 exchange-correlation (XC) functionals to compute the 1H and 13C NMR chemical shifts of p-tert-butylcalix[4]arene (ptcx4, R1 = C(CH3)3) and congeners using the 6-31G(d,p) basis set. The statistical analysis shows that B3LYP, B3PW91 and PBE1PBE are the best XC functionals for the calculation of 1H chemical shifts. Moreover, the best results for the 13C chemical shifts are obtained using the LC-WPBE, M06-2X and wB97X-D functionals. The performance of these XC functionals is tested for three other calix[4]arenes: p-sulfonic acid calix[4]arene (sfxcx4 - R1 = SO3H), p-nitro-calix[4]arene (ncx4, R1 = NO2) and calix[4]arene (cx4 - R1 = H). For 1H chemical shifts B3LYP, B3PW91 and PBE1PBE yield similar results, although B3PW91 shows more consistency in the calculated error for the different structures. For 13C NMR chemical shifts, the XC functional that stood out as best is LC-WPBE. Indeed, the three functionals selected for each of 1H and 13C show good accuracy and can be used in future studies involving the prediction of 1H and 13C chemical shifts for this type of compounds.

Investigation of DOTA-Metal Chelation Effects on the Chemical Shift of ¹²⁹ Xe

Energy Technology Data Exchange (ETDEWEB)

Jeong, K; Slack, CC; Vassiliou, CC; Dao, P; Gomes, MD; Kennedy, DJ; Truxal, AE; Sperling, LJ; Francis, MB; Wemmer, DE; Pines, A

2015-09-17

Recent work has shown that xenon chemical shifts in cryptophane-cage sensors are affected when tethered chelators bind to metals. Here in this paper, we explore the xenon shifts in response to a wide range of metal ions binding to diastereomeric forms of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) linked to cryptophane-A. The shifts induced by the binding of Ca²⁺, Cu²⁺, Ce³⁺, Zn²⁺, Cd²⁺, Ni²⁺, Co²⁺, Cr²⁺, Fe³⁺, and Hg²⁺ are distinct. In addition, the different responses of the diastereomers for the same metal ion indicate that shifts are affected by partial folding with a correlation between the expected coordination number of the metal in the DOTA complex and the chemical shift of ¹²⁹Xe. Lastly, these sensors may be used to detect and quantify many important metal ions, and a better understanding of the basis for the induced shifts could enhance future designs.

The different star formation histories of blue and red spiral and elliptical galaxies

Science.gov (United States)

Tojeiro, Rita; Masters, Karen L.; Richards, Joshua; Percival, Will J.; Bamford, Steven P.; Maraston, Claudia; Nichol, Robert C.; Skibba, Ramin; Thomas, Daniel

2013-06-01

We study the spectral properties of intermediate mass galaxies (M* ˜ 1010.7 M⊙) as a function of colour and morphology. We use Galaxy Zoo to define three morphological classes of galaxies, namely early types (ellipticals), late-type (disc-dominated) face-on spirals and early-type (bulge-dominated) face-on spirals. We classify these galaxies as blue or red according to their Sloan Digital Sky Survey (SDSS) g - r colour and use the spectral fitting code Versatile Spectral Analyses to calculate time-resolved star formation histories, metallicity and total starlight dust extinction from their SDSS fibre spectra. We find that red late-type spirals show less star formation in the last 500 Myr than blue late-type spirals by up to a factor of 3, but share similar star formation histories at earlier times. This decline in recent star formation explains their redder colour: their chemical and dust content are the same. We postulate that red late-type spirals are recent descendants of blue late-type spirals, with their star formation curtailed in the last 500 Myr. The red late-type spirals are however still forming stars ≃17 times faster than red ellipticals over the same period. Red early-type spirals lie between red late-type spirals and red ellipticals in terms of recent-to-intermediate star formation and dust content. Therefore, it is plausible that these galaxies represent an evolutionary link between these two populations. They are more likely to evolve directly into red ellipticals than red late-type spirals, which show star formation histories and dust content closer to blue late-type spirals. Blue ellipticals show similar star formation histories as blue spirals (regardless of type), except that they have formed less stars in the last 100 Myr. However, blue ellipticals have different dust content, which peaks at lower extinction values than all spiral galaxies. Therefore, many blue ellipticals are unlikely to be descendants of blue spirals, suggesting there may

Pressure-dependent {sup 13}C chemical shifts in proteins: origins and applications

Energy Technology Data Exchange (ETDEWEB)

Wilton, David J. [University of Sheffield, Department of Molecular Biology and Biotechnology (United Kingdom); Kitahara, Ryo [Ritsumeikan University, College of Pharmaceutical Sciences (Japan); Akasaka, Kazuyuki [Kinki University, Department of Biotechnological Science, School of Biology-Oriented Science and Technology (Japan); Williamson, Mike P. [University of Sheffield, Department of Molecular Biology and Biotechnology (United Kingdom)], E-mail: m.williamson@sheffield.ac.uk

2009-05-15

Pressure-dependent {sup 13}C chemical shifts have been measured for aliphatic carbons in barnase and Protein G. Up to 200 MPa (2 kbar), most shift changes are linear, demonstrating pressure-independent compressibilities. CH{sub 3}, CH{sub 2} and CH carbon shifts change on average by +0.23, -0.09 and -0.18 ppm, respectively, due to a combination of bond shortening and changes in bond angles, the latter matching one explanation for the {gamma}-gauche effect. In addition, there is a residue-specific component, arising from both local compression and conformational change. To assess the relative magnitudes of these effects, residue-specific shift changes for protein G were converted into structural restraints and used to calculate the change in structure with pressure, using a genetic algorithm to convert shift changes into dihedral angle restraints. The results demonstrate that residual {sup 13}C{alpha} shifts are dominated by dihedral angle changes and can be used to calculate structural change, whereas {sup 13}C{beta} shifts retain significant dependence on local compression, making them less useful as structural restraints.

Utilization of the ion traps by SPIRAL

International Nuclear Information System (INIS)

Le Brun, C.; Lienard, E.; Mauger, F.; Tamain, B.

1997-01-01

An ion trap is a device capable of confine particles, ions or atoms in a well-controlled environment isolated from any exterior perturbations. There are different traps. They are utilized to collect or stock ions, to cool them after in order to subject them to high precision measurement of masses, magnetic moments, hyperfine properties, beta decay properties, etc. Some dozen of traps are currently used all over the world to study stable or radioactive ions.. SPIRAL has been designed and built to produce radioactive ions starting from various heavy ion beams. SPIRAL has the advantage that the projectile parameters, the target and the energy can be chosen to optimize the production in various regions of the nuclear chart. Also, in SPIRAL it is possible to extract more rapidly the radioactive ions formed in the targets. In addition, in SPIRAL the multicharged ion production in a ECR source is possible. The utilization of multicharged ions is indeed very useful for fast mass measurements or for the study of the interaction between the nucleus and the electronic cloud. Finally, utilization of a ion trap on SPIRAL can be designed first at the level of production target by installing a low energy output line. Than, the trap system could be up-graded and brought to its full utilization behind of the recoil spectrometer. It must be capable of selecting and slowing down the ions produced in the reactions (fusion transfer, very inelastic collisions, etc.) induced by the radioactive ions accelerated in CIME. At present, the collaboration is debating on the most favored subject to study and the most suited experimental setups. The following subjects were selected: ion capture, purification and manipulation; isomers (separation and utilization); mass measurements; hyperfine interactions; lifetimes, nuclear electric cloud; β decays; study of the N = Z nuclei close to the proton drip line; physical and chemical properties of transuranium systems

Spiral CT for evaluation of chest trauma; Spiral-CT beim Thoraxtrauma

Energy Technology Data Exchange (ETDEWEB)

Roehnert, W. [Universitaetsklinikum Dresden (Germany). Inst. und Poliklinik fuer Radiologische Diagnostik; Weise, R. [Universitaetsklinikum Dresden (Germany). Inst. und Poliklinik fuer Radiologische Diagnostik

1997-07-01

After implementation of spiral CT in our department, we carried out an analysis for determining anew the value of CT as a modality of chest trauma diagnosis in the emergency department. The retrospective study covers a period of 10 months and all emergency patients with chest trauma exmined by spiral CT. The major lesions of varying seriousness covered by this study are: pneumothorax, hematothorax, pulmonary contusion or laceration, mediastinal hematoma, rupture of a vessel, injury of the heart and pericardium. The various fractures are not included in this study. In many cases, spiral CT within relatively short time yields significant diagnostic findings, frequently saving additional angiography. A rigid diagnostic procedure cannot be formulated. Plain-film chest radiography still remains a diagnostic modality of high value. (Orig.) [Deutsch] Nach Einfuehrung der Spiral-CT in unserer Einrichtung versuchten wir, den Stellenwert der Computertomographie in der Notfalldiagnostik des Thoraxtraumas neu zu bestimmen. Dazu wurden retrospektiv ueber einen Zeitraum von 10 Monaten alle mittels Spiral-CT untersuchten Notfallpatienten mit Thoraxverletzungen ausgewertet. Im Vordergrund standen folgende Befunde unterschiedlichen Schweregrades: Pneumothorax, Haematothorax, Lungenkontusion/-lazeration, Mediastinalhaematom, Gefaessruptur, Herz- und Herzbeutelverletzung. Auf die unterschiedlichen Frakturen wird bewusst nicht naeher eingegangen. In vielen Faellen liefert die Spiral-CT mit relativ geringem Zeitaufwand wesentliche diagnostische Aussagen. Haeufig kann auf eine Angiographie verzichtet werden. Ein starres diagnostisches Stufenschema laesst sich nicht definieren. Die Thoraxuebersichtsaufnahme besitzt einen unveraendert hohen Stellenwert. (orig.)

Spin-echo based diagonal peak suppression in solid-state MAS NMR homonuclear chemical shift correlation spectra

Science.gov (United States)

Wang, Kaiyu; Zhang, Zhiyong; Ding, Xiaoyan; Tian, Fang; Huang, Yuqing; Chen, Zhong; Fu, Riqiang

2018-02-01

The feasibility of using the spin-echo based diagonal peak suppression method in solid-state MAS NMR homonuclear chemical shift correlation experiments is demonstrated. A complete phase cycling is designed in such a way that in the indirect dimension only the spin diffused signals are evolved, while all signals not involved in polarization transfer are refocused for cancellation. A data processing procedure is further introduced to reconstruct this acquired spectrum into a conventional two-dimensional homonuclear chemical shift correlation spectrum. A uniformly 13C, 15N labeled Fmoc-valine sample and the transmembrane domain of a human protein, LR11 (sorLA), in native Escherichia coli membranes have been used to illustrate the capability of the proposed method in comparison with standard 13C-13C chemical shift correlation experiments.

Physical basis of the effect of hemoglobin on the 31P NMR chemical shifts of various phosphoryl compounds

International Nuclear Information System (INIS)

Kirk, K.; Kuchel, P.W.

1988-01-01

The marked difference between the intra- and extracellular 31 P NMR chemical shifts of various phosphoryl compounds when added to a red cell suspension may be largely understood in terms of the effects of hemoglobin on the 31 P NMR chemical shifts. The presence of [oxy- or (carbonmonoxy)-] hemoglobin inside the red cell causes the bulk magnetic susceptibility of the cell cytoplasm to be significantly less than that of the external solution. This difference is sufficient to account for the difference in the intra- and extracellular chemical shifts of the two phosphate esters trimethyl phosphate and triethyl phosphate. However, in the case of the compounds dimethyl methylphosphonate, diethyl methylphosphonate, and trimethylphosphine oxide as well as the hypophosphite, phenylphosphinate, and diphenylphosphinate ions, hemoglobin exerts an additional, much larger, effect, causing the 31 P NMR resonances to shift to lower frequency in a manner that cannot be accounted for in terms of magnetic susceptibility. Lysozyme is a protein structurally unrelated to hemoglobin and was shown to cause similar shifts to lower frequency of the resonances of these six compounds; this suggests that the mechanism may involve a property of proteins in general and not a specific property of hemoglobin. The effect of different solvents on the chemical shifts of the eight phosphoryl compounds provided an insight into the possible physical basis of the effect. It is proposed that, in addition to magnetic susceptibility effects, hemoglobin exerts its influence on phosphoryl chemical shifts by disrupting the hydrogen bonding of the phosphoryl group to solvent water

High assurance SPIRAL

Science.gov (United States)

Franchetti, Franz; Sandryhaila, Aliaksei; Johnson, Jeremy R.

2014-06-01

In this paper we introduce High Assurance SPIRAL to solve the last mile problem for the synthesis of high assurance implementations of controllers for vehicular systems that are executed in today's and future embedded and high performance embedded system processors. High Assurance SPIRAL is a scalable methodology to translate a high level specification of a high assurance controller into a highly resource-efficient, platform-adapted, verified control software implementation for a given platform in a language like C or C++. High Assurance SPIRAL proves that the implementation is equivalent to the specification written in the control engineer's domain language. Our approach scales to problems involving floating-point calculations and provides highly optimized synthesized code. It is possible to estimate the available headroom to enable assurance/performance trade-offs under real-time constraints, and enables the synthesis of multiple implementation variants to make attacks harder. At the core of High Assurance SPIRAL is the Hybrid Control Operator Language (HCOL) that leverages advanced mathematical constructs expressing the controller specification to provide high quality translation capabilities. Combined with a verified/certified compiler, High Assurance SPIRAL provides a comprehensive complete solution to the efficient synthesis of verifiable high assurance controllers. We demonstrate High Assurance SPIRALs capability by co-synthesizing proofs and implementations for attack detection and sensor spoofing algorithms and deploy the code as ROS nodes on the Landshark unmanned ground vehicle and on a Synthetic Car in a real-time simulator.

Simulations of the flocculent spiral M33: what drives the spiral structure?

Science.gov (United States)

Dobbs, C. L.; Pettitt, A. R.; Corbelli, E.; Pringle, J. E.

2018-05-01

We perform simulations of isolated galaxies in order to investigate the likely origin of the spiral structure in M33. In our models, we find that gravitational instabilities in the stars and gas are able to reproduce the observed spiral pattern and velocity field of M33, as seen in HI, and no interaction is required. We also find that the optimum models have high levels of stellar feedback which create large holes similar to those observed in M33, whilst lower levels of feedback tend to produce a large amount of small scale structure, and undisturbed long filaments of high surface density gas, hardly detected in the M33 disc. The gas component appears to have a significant role in producing the structure, so if there is little feedback, both the gas and stars organise into clear spiral arms, likely due to a lower combined Q (using gas and stars), and the ready ability of cold gas to undergo spiral shocks. By contrast models with higher feedback have weaker spiral structure, especially in the stellar component, compared to grand design galaxies. We did not see a large difference in the behaviour of Qstars with most of these models, however, because Qstars stayed relatively constant unless the disc was more strongly unstable. Our models suggest that although the stars produce some underlying spiral structure, this is relatively weak, and the gas physics has a considerable role in producing the large scale structure of the ISM in flocculent spirals.

Binding energies and chemical shifts of least bound core electron excitations in cubic Asub(N)Bsub(8-N) semiconductors

International Nuclear Information System (INIS)

Bechstedt, F.; Enderlein, R.; Wischnewski, R.

1981-01-01

Core electron binding energies Esup(B) with respect to the vacuum level and their chemical shifts are calculated for the least bound core levels of cations and anions of cubic Asub(N)Bsub(8-N) semiconductors. Starting from the HF-binding energy of the free atom absolute values of Esup(B) are obtained by adding core level shifts and relaxation energies. Core level shifts are calculated by means of an electrostatic model with ionic and bond charges according to Phillips' bond charge model. For the calculation of relaxation energies the linear dielectric theory of electronic polarization is applied. Valence and core electrons, and diagonal and non-diagonal screening are taken into account. The theoretical results for chemical shifts of binding energies are compared with experimental values from XPS-measurements corrected by work function data. Good agreement is obtained in all cases within the error limit of about one eV. Chemical and atomic trends of core level shifts, relaxation energies, and binding energies are discussed in terms of changes of atomic and solid state parameters. Chemical shifts and relaxation energies are predicted for various ternary Asub(N)Bsub(8-N) compounds. (author)

Multiple mechanisms quench passive spiral galaxies

Science.gov (United States)

Fraser-McKelvie, Amelia; Brown, Michael J. I.; Pimbblet, Kevin; Dolley, Tim; Bonne, Nicolas J.

2018-02-01

We examine the properties of a sample of 35 nearby passive spiral galaxies in order to determine their dominant quenching mechanism(s). All five low-mass (M⋆ environments. We postulate that cluster-scale gas stripping and heating mechanisms operating only in rich clusters are required to quench low-mass passive spirals, and ram-pressure stripping and strangulation are obvious candidates. For higher mass passive spirals, while trends are present, the story is less clear. The passive spiral bar fraction is high: 74 ± 15 per cent, compared with 36 ± 5 per cent for a mass, redshift and T-type matched comparison sample of star-forming spiral galaxies. The high mass passive spirals occur mostly, but not exclusively, in groups, and can be central or satellite galaxies. The passive spiral group fraction of 74 ± 15 per cent is similar to that of the comparison sample of star-forming galaxies at 61 ± 7 per cent. We find evidence for both quenching via internal structure and environment in our passive spiral sample, though some galaxies have evidence of neither. From this, we conclude no one mechanism is responsible for quenching star formation in passive spiral galaxies - rather, a mixture of mechanisms is required to produce the passive spiral distribution we see today.

Are spiral galaxies heavy smokers?

International Nuclear Information System (INIS)

Davies, J.; Disney, M.; Phillipps, S

1990-01-01

The dustiness of spiral galaxies is discussed. Starburst galaxies and the shortage of truly bright spiral galaxies is cited as evidence that spiral galaxies are far dustier than has been thought. The possibility is considered that the dust may be hiding missing mass

Spiral silicon drift detectors

International Nuclear Information System (INIS)

Rehak, P.; Gatti, E.; Longoni, A.; Sampietro, M.; Holl, P.; Lutz, G.; Kemmer, J.; Prechtel, U.; Ziemann, T.

1988-01-01

An advanced large area silicon photodiode (and x-ray detector), called Spiral Drift Detector, was designed, produced and tested. The Spiral Detector belongs to the family of silicon drift detectors and is an improvement of the well known Cylindrical Drift Detector. In both detectors, signal electrons created in silicon by fast charged particles or photons are drifting toward a practically point-like collection anode. The capacitance of the anode is therefore kept at the minimum (0.1pF). The concentric rings of the cylindrical detector are replaced by a continuous spiral in the new detector. The spiral geometry detector design leads to a decrease of the detector leakage current. In the spiral detector all electrons generated at the silicon-silicon oxide interface are collected on a guard sink rather than contributing to the detector leakage current. The decrease of the leakage current reduces the parallel noise of the detector. This decrease of the leakage current and the very small capacities of the detector anode with a capacitively matched preamplifier may improve the energy resolution of Spiral Drift Detectors operating at room temperature down to about 50 electrons rms. This resolution is in the range attainable at present only by cooled semiconductor detectors. 5 refs., 10 figs

Fragment-based {sup 13}C nuclear magnetic resonance chemical shift predictions in molecular crystals: An alternative to planewave methods

Energy Technology Data Exchange (ETDEWEB)

Hartman, Joshua D.; Beran, Gregory J. O., E-mail: gregory.beran@ucr.edu [Department of Chemistry, University of California, Riverside, California 92521 (United States); Monaco, Stephen; Schatschneider, Bohdan [The Pennsylvania State University, The Eberly Campus, 2201 University Dr, Lemont Furnace, Pennsylvania 15456 (United States)

2015-09-14

We assess the quality of fragment-based ab initio isotropic {sup 13}C chemical shift predictions for a collection of 25 molecular crystals with eight different density functionals. We explore the relative performance of cluster, two-body fragment, combined cluster/fragment, and the planewave gauge-including projector augmented wave (GIPAW) models relative to experiment. When electrostatic embedding is employed to capture many-body polarization effects, the simple and computationally inexpensive two-body fragment model predicts both isotropic {sup 13}C chemical shifts and the chemical shielding tensors as well as both cluster models and the GIPAW approach. Unlike the GIPAW approach, hybrid density functionals can be used readily in a fragment model, and all four hybrid functionals tested here (PBE0, B3LYP, B3PW91, and B97-2) predict chemical shifts in noticeably better agreement with experiment than the four generalized gradient approximation (GGA) functionals considered (PBE, OPBE, BLYP, and BP86). A set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided based on these benchmark calculations. Statistical cross-validation procedures are used to demonstrate the robustness of these fits.

Carbon 13 nuclear magnetic resonance chemical shifts empiric calculations of polymers by multi linear regression and molecular modeling

International Nuclear Information System (INIS)

Da Silva Pinto, P.S.; Eustache, R.P.; Audenaert, M.; Bernassau, J.M.

1996-01-01

This work deals with carbon 13 nuclear magnetic resonance chemical shifts empiric calculations by multi linear regression and molecular modeling. The multi linear regression is indeed one way to obtain an equation able to describe the behaviour of the chemical shift for some molecules which are in the data base (rigid molecules with carbons). The methodology consists of structures describer parameters definition which can be bound to carbon 13 chemical shift known for these molecules. Then, the linear regression is used to determine the equation significant parameters. This one can be extrapolated to molecules which presents some resemblances with those of the data base. (O.L.). 20 refs., 4 figs., 1 tab

Cα and Cβ Carbon-13 Chemical Shifts in Proteins From an Empirical Database

International Nuclear Information System (INIS)

Iwadate, Mitsuo; Asakura, Tetsuo; Williamson, Michael P.

1999-01-01

We have constructed an extensive database of 13C Cα and Cβ chemical shifts in proteins of solution, for proteins of which a high-resolution crystal structure exists, and for which the crystal structure has been shown to be essentially identical to the solution structure. There is no systematic effect of temperature, reference compound, or pH on reported shifts, but there appear to be differences in reported shifts arising from referencing differences of up to 4.2 ppm. The major factor affecting chemical shifts is the backbone geometry, which causes differences of ca. 4 ppm between typical α- helix and β-sheet geometries for Cα, and of ca. 2 ppm for Cβ. The side-chain dihedral angle χ1 has an effect of up to 0.5 ppm on the Cα shift, particularly for amino acids with branched side-chains at Cβ. Hydrogen bonding to main-chain atoms has an effect of up to 0.9 ppm, which depends on the main- chain conformation. The sequence of the protein and ring-current shifts from aromatic rings have an insignificant effect (except for residues following proline). There are significant differences between different amino acid types in the backbone geometry dependence; the amino acids can be grouped together into five different groups with different φ,ψ shielding surfaces. The overall fit of individual residues to a single non-residue-specific surface, incorporating the effects of hydrogen bonding and χ1 angle, is 0.96 ppm for both Cα and Cβ. The results from this study are broadly similar to those from ab initio studies, but there are some differences which could merit further attention

Nature of galaxy spiral arms

International Nuclear Information System (INIS)

Efremov, Yu.N.

1984-01-01

The nature of galaxy spiral arms is discussed in a popular form. Two approaches in the theory of spiral arms are considered; they are related to the problem of differential galaxy rotation and the spiral structure wave theory. The example of Galaxy M31 is considered to compare the structural peculiarity of its spiral arms with the wave theory predictions. The situation in the central and south-eastern part of arm S4 in Galaxy M31 noted to be completely explained by the wave theory and modern concepts on the origin of massive stars

Three phase spiral liver Scanning

International Nuclear Information System (INIS)

Kanyanja, T.A.

2006-01-01

The ability to perform rapid back-to-back spiral acquisitions is an important recent technical advantage of spiral CT. this allows imaging of the upper abdomen (liver) during peak arterial enhancement (arterial phase) and during peak hepatic parenchymal enhancement (portal venous phase). Breatheld spiral CT has completely replaced dynamic incremental CT for evaluation of the liver. in selected patients with hyper vascular metastasis (hepatoma, neuroendocrine tumors, renal cell carcinoma, etc.) a biphasic examination is performed with one spiral acquisition obtained during the hepatic arterial phase and a second acquisition during the portal venous phase

Propulsion using the electron spiral toroid

International Nuclear Information System (INIS)

Seward, Clint

1998-01-01

A new propulsion method is proposed which could potentially reduce propellant needed for space travel by three orders of magnitude. It uses the newly patented electron spiral toroid (EST), which stores energy as magnetic field energy. The EST is a hollow toroid of electrons, all spiraling in parallel paths in a thin outer shell. The electrons satisfy the coupling condition, forming an electron matrix. Stability is assured as long as the coupling condition is satisfied. The EST is held in place with a small external electric field; without an external magnetic field. The EST system is contained in a vacuum chamber. The EST can be thought of as an energetic entity, with electrons at 10,000 electron volts. Propulsion would not use combustion, but would heat propellant through elastic collisions with the EST surface and eject them for thrust. Chemical rocket combustion heats propellant to 4000 deg. C; an EST will potentially heat the propellant 29,000 times as much, reducing propellant needs accordingly. The thrust can be turned ON and OFF. The EST can be recharged as needed

The perfect shape spiral stories

CERN Document Server

Hammer, Øyvind

2016-01-01

This book uses the spiral shape as a key to a multitude of strange and seemingly disparate stories about art, nature, science, mathematics, and the human endeavour. In a way, the book is itself organized as a spiral, with almost disconnected chapters circling around and closing in on the common theme. A particular strength of the book is its extremely cross-disciplinary nature - everything is fun, and everything is connected! At the same time, the author puts great emphasis on mathematical and scientific correctness, in contrast, perhaps, with some earlier books on spirals. Subjects include the mathematical properties of spirals, sea shells, sun flowers, Greek architecture, air ships, the history of mathematics, spiral galaxies, the anatomy of the human hand, the art of prehistoric Europe, Alfred Hitchcock, and spider webs, to name a few.

Band-notched spiral antenna

Science.gov (United States)

Jeon, Jae; Chang, John

2018-03-13

A band-notched spiral antenna having one or more spiral arms extending from a radially inner end to a radially outer end for transmitting or receiving electromagnetic radiation over a frequency range, and one or more resonance structures positioned adjacent one or more segments of the spiral arm associated with a notch frequency band or bands of the frequency range so as to resonate and suppress the transmission or reception of electromagnetic radiation over said notch frequency band or bands.

The 40th anniversary of the discovery of NMR-chemical shift and nuclear spin-spin coupling

International Nuclear Information System (INIS)

Zhu Zhenghe; Gou Qingquan

1989-01-01

After the discovery of NMR Phenomenon in the physics laboratories of E.M.Purcell at Harvard and F.Bloch at Stanford in 1946, W.G.Proctor and F.C.Yu made the successful discovery of NMR-chemical shift and nuclear spin-spin coupling at Stanford in 1950, Which brought NMR spectroscopy from the physics laboratory to the laboratories of many different fields. This is worth memorizing. Retrospecting the past 40 years, it is sure that chemical shift theory will be much more prosperous prospects

High-Assurance Spiral

Science.gov (United States)

2017-11-01

HIGH-ASSURANCE SPIRAL CARNEGIE MELLON UNIVERSITY NOVEMBER 2017 FINAL TECHNICAL REPORT APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED STINFO...MU 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Carnegie Mellon University 5000 Forbes Ave Pittsburgh, PA 15217 8. PERFORMING ORGANIZATION...Approved for Public Release; Distribution Unlimited. Carnegie Mellon Carnegie Mellon HA SPIRAL Code Synthesis KeYmaera X Hybrid Theorem Prover

Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations.

Science.gov (United States)

Kraus, Jodi; Gupta, Rupal; Yehl, Jenna; Lu, Manman; Case, David A; Gronenborn, Angela M; Akke, Mikael; Polenova, Tatyana

2018-03-22

Magic angle spinning NMR spectroscopy is uniquely suited to probe the structure and dynamics of insoluble proteins and protein assemblies at atomic resolution, with NMR chemical shifts containing rich information about biomolecular structure. Access to this information, however, is problematic, since accurate quantum mechanical calculation of chemical shifts in proteins remains challenging, particularly for 15 N H . Here we report on isotropic chemical shift predictions for the carbohydrate recognition domain of microcrystalline galectin-3, obtained from using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, implemented using an automated fragmentation approach, and using very high resolution (0.86 Å lactose-bound and 1.25 Å apo form) X-ray crystal structures. The resolution of the X-ray crystal structure used as an input into the AF-NMR program did not affect the accuracy of the chemical shift calculations to any significant extent. Excellent agreement between experimental and computed shifts is obtained for 13 C α , while larger scatter is observed for 15 N H chemical shifts, which are influenced to a greater extent by electrostatic interactions, hydrogen bonding, and solvation.

H-1 chemical shift imaging characterization of human brain tumor and edema

NARCIS (Netherlands)

Sijens, PE; Oudkerk, M

Longitudinal (T1) and transverse (T2) relaxation times of metabolites in human brain tumor, peritumoral edema, and unaffected brain tissue were assessed from point resolved spectroscopy (PRESS) H-1 chemical shift imaging results at different repetition times (TR = 1500 and 5000 ms; T1: n = 19) and

Measuring nutrient spiralling in streams

Energy Technology Data Exchange (ETDEWEB)

Newbold, J D; Elwood, J W; O' Neill, R V; Van Winkle, W

1981-01-01

Nutrient cycling in streams involves some downstream transport before the cycle is completed. Thus, the path traveled by a nutrient atom in passing through the cycle can be visualized as a spiral. As an index of the spiralling process, we introduce spiralling length, defined as the average distance associated with one complete cycle of a nutrient atom. This index provides a measure of the utilization of nutrients relative to the available supply from upstream. Using /sup 32/p as a tracer, we estimated a spiralling length of 193 m for phosphorus in a small woodland stream.

TESTING THEORIES IN BARRED-SPIRAL GALAXIES

International Nuclear Information System (INIS)

Martínez-García, Eric E.

2012-01-01

According to one version of the recently proposed 'manifold' theory that explains the origin of spirals and rings in relation to chaotic orbits, galaxies with stronger bars should have a higher spiral arms pitch angle when compared to galaxies with weaker bars. A subsample of barred-spiral galaxies in the Ohio State University Bright Galaxy Survey was used to analyze the spiral arms pitch angle. These were compared with bar strengths taken from the literature. It was found that the galaxies in which the spiral arms maintain a logarithmic shape for more than 70° seem to corroborate the predicted trend.

PACSY, a relational database management system for protein structure and chemical shift analysis.

Science.gov (United States)

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

2012-10-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

PACSY, a relational database management system for protein structure and chemical shift analysis

Energy Technology Data Exchange (ETDEWEB)

Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison, and Biochemistry Department (United States); Yu, Wookyung [Center for Proteome Biophysics, Pusan National University, Department of Physics (Korea, Republic of); Kim, Suhkmann [Pusan National University, Department of Chemistry and Chemistry Institute for Functional Materials (Korea, Republic of); Chang, Iksoo [Center for Proteome Biophysics, Pusan National University, Department of Physics (Korea, Republic of); Lee, Weontae, E-mail: wlee@spin.yonsei.ac.kr [Yonsei University, Structural Biochemistry and Molecular Biophysics Laboratory, Department of Biochemistry (Korea, Republic of); Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison, and Biochemistry Department (United States)

2012-10-15

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.eduhttp://pacsy.nmrfam.wisc.edu.

PACSY, a relational database management system for protein structure and chemical shift analysis

Science.gov (United States)

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo

2012-01-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu. PMID:22903636

PACSY, a relational database management system for protein structure and chemical shift analysis

International Nuclear Information System (INIS)

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L.

2012-01-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.eduhttp://pacsy.nmrfam.wisc.edu.

Collective excitations in itinerant spiral magnets

International Nuclear Information System (INIS)

Kampf, A.P.

1996-01-01

We investigate the coupled charge and spin collective excitations in the spiral phases of the two-dimensional Hubbard model using a generalized random-phase approximation. Already for small doping the spin-wave excitations are strongly renormalized due to low-energy particle-hole excitations. Besides the three Goldstone modes of the spiral state the dynamical susceptibility reveals an extra zero mode for low doping and strong coupling values signaling an intrinsic instability of the homogeneous spiral state. In addition, near-zero modes are found in the vicinity of the spiral pitch wave number for out-of-plane spin fluctuations. Their origin is found to be the near degeneracy with staggered noncoplanar spiral states which, however, are not the lowest energy Hartree-Fock solutions among the homogeneous spiral states. copyright 1996 The American Physical Society

Results and technical problems of therapeutic vascular embolization with special reference to the use of spirals

International Nuclear Information System (INIS)

Grosse-Vorholt, R.; Zeitler, E.

1980-01-01

31 therapeutic vascular embolizations were performed: 4 for osteolytic lesions; 24 for renal tumors and 3 for malignant hypertension in 3 patients with chronic pyelonephritis and corresponding bilateral kidney shrinkage with the kidneys left in the patients (-one patient being put on chronic dialysis and 2 having undergone renal transplantation). Opacifying chemical substances (Ethibloc) and nonopacifying chemical substances (Fibrospum, Butyl-2-Cyanoacrylat) were sometimes used for embolization; but most of the time, metal spiral (licenced by Cianturco) were taken, because of the following advantages: Their insertion is simple and easily controlled by fluoroscopy; they cause less pain, and they induce progressive thrombosis in the embolised artery. In cases, however, where catheterisation is difficult or impossible (narrow lumen/collaterals), embolization with chemical substances has to be done in addition to that by spiral. (orig.) [de

Chiral Magnetic Spirals

International Nuclear Information System (INIS)

Basar, Goekce; Dunne, Gerald V.; Kharzeev, Dmitri E.

2010-01-01

We argue that the presence of a very strong magnetic field in the chirally broken phase induces inhomogeneous expectation values, of a spiral nature along the magnetic field axis, for the currents of charge and chirality, when there is finite baryon density or an imbalance between left and right chiralities. This 'chiral magnetic spiral' is a gapless excitation transporting the currents of (i) charge (at finite chirality), and (ii) chirality (at finite baryon density) along the direction of the magnetic field. In both cases it also induces in the transverse directions oscillating currents of charge and chirality. In heavy ion collisions, the chiral magnetic spiral possibly provides contributions both to the out-of-plane and the in-plane dynamical charge fluctuations recently observed at BNL RHIC.

Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides.

Science.gov (United States)

Sumowski, Chris Vanessa; Hanni, Matti; Schweizer, Sabine; Ochsenfeld, Christian

2014-01-14

The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.

Modelling the acid/base 1H NMR chemical shift limits of metabolites in human urine.

Science.gov (United States)

Tredwell, Gregory D; Bundy, Jacob G; De Iorio, Maria; Ebbels, Timothy M D

2016-01-01

Despite the use of buffering agents the 1 H NMR spectra of biofluid samples in metabolic profiling investigations typically suffer from extensive peak frequency shifting between spectra. These chemical shift changes are mainly due to differences in pH and divalent metal ion concentrations between the samples. This frequency shifting results in a correspondence problem: it can be hard to register the same peak as belonging to the same molecule across multiple samples. The problem is especially acute for urine, which can have a wide range of ionic concentrations between different samples. To investigate the acid, base and metal ion dependent 1 H NMR chemical shift variations and limits of the main metabolites in a complex biological mixture. Urine samples from five different individuals were collected and pooled, and pre-treated with Chelex-100 ion exchange resin. Urine samples were either treated with either HCl or NaOH, or were supplemented with various concentrations of CaCl 2 , MgCl 2 , NaCl or KCl, and their 1 H NMR spectra were acquired. Nonlinear fitting was used to derive acid dissociation constants and acid and base chemical shift limits for peaks from 33 identified metabolites. Peak pH titration curves for a further 65 unidentified peaks were also obtained for future reference. Furthermore, the peak variations induced by the main metal ions present in urine, Na + , K + , Ca 2+ and Mg 2+ , were also measured. These data will be a valuable resource for 1 H NMR metabolite profiling experiments and for the development of automated metabolite alignment and identification algorithms for 1 H NMR spectra.

Quantum-Chemical Approach to NMR Chemical Shifts in Paramagnetic Solids Applied to LiFePO4 and LiCoPO4.

Science.gov (United States)

Mondal, Arobendo; Kaupp, Martin

2018-04-05

A novel protocol to compute and analyze NMR chemical shifts for extended paramagnetic solids, accounting comprehensively for Fermi-contact (FC), pseudocontact (PC), and orbital shifts, is reported and applied to the important lithium ion battery cathode materials LiFePO 4 and LiCoPO 4 . Using an EPR-parameter-based ansatz, the approach combines periodic (hybrid) DFT computation of hyperfine and orbital-shielding tensors with an incremental cluster model for g- and zero-field-splitting (ZFS) D-tensors. The cluster model allows the use of advanced multireference wave function methods (such as CASSCF or NEVPT2). Application of this protocol shows that the 7 Li shifts in the high-voltage cathode material LiCoPO 4 are dominated by spin-orbit-induced PC contributions, in contrast with previous assumptions, fundamentally changing interpretations of the shifts in terms of covalency. PC contributions are smaller for the 7 Li shifts of the related LiFePO 4 , where FC and orbital shifts dominate. The 31 P shifts of both materials finally are almost pure FC shifts. Nevertheless, large ZFS contributions can give rise to non-Curie temperature dependences for both 7 Li and 31 P shifts.

Relativistic Spin-Orbit Heavy Atom on the Light Atom NMR Chemical Shifts: General Trends Across the Periodic Table Explained.

Science.gov (United States)

Vícha, Jan; Komorovsky, Stanislav; Repisky, Michal; Marek, Radek; Straka, Michal

2018-05-10

The importance of relativistic effects on the NMR parameters in heavy-atom (HA) compounds, particularly the SO-HALA (Spin-Orbit Heavy Atom on the Light Atom) effect on NMR chemical shifts, has been known for about 40 years. Yet, a general correlation between the electronic structure and SO-HALA effect has been missing. By analyzing 1 H NMR chemical shifts of the sixth-period hydrides (Cs-At), we discovered general electronic-structure principles and mechanisms that dictate the size and sign of the SO-HALA NMR chemical shifts. In brief, partially occupied HA valence shells induce relativistic shielding at the light atom (LA) nuclei, while empty HA valence shells induce relativistic deshielding. In particular, the LA nucleus is relativistically shielded in 5d 2 -5d 8 and 6p 4 HA hydrides and deshielded in 4f 0 , 5d 0 , 6s 0 , and 6p 0 HA hydrides. This general and intuitive concept explains periodic trends in the 1 H NMR chemical shifts along the sixth-period hydrides (Cs-At) studied in this work. We present substantial evidence that the introduced principles have a general validity across the periodic table and can be extended to nonhydride LAs. The decades-old question of why compounds with occupied frontier π molecular orbitals (MOs) cause SO-HALA shielding at the LA nuclei, while the frontier σ MOs cause deshielding is answered. We further derive connection between the SO-HALA NMR chemical shifts and Spin-Orbit-induced Electron Deformation Density (SO-EDD), a property that can be obtained easily from differential electron densities and can be represented graphically. SO-EDD provides an intuitive understanding of the SO-HALA effect in terms of the depletion/concentration of the electron density at LA nuclei caused by spin-orbit coupling due to HA in the presence of a magnetic field. Using an analogy between the SO-EDD concept and arguments from classic NMR theory, the complex question of the SO-HALA NMR chemical shifts becomes easily understandable for a wide

Rebuilding Spiral Galaxies

Science.gov (United States)

2005-01-01

occurring in less than 1,000 million years, the existence of such a large fraction of these LIRGs in the past Universe has important consequences on the total stellar formation rate. As François Hammer (Paris Observatory, France), leader of the team, states: "We are thus led to the conclusion that during the time span from roughly 8,000 million to 4,000 million years ago, intermediate mass galaxies converted about half of their total mass into stars. Moreover, this star formation must have taken place in very intense bursts when galaxies were emitting huge amount of infrared radiation and appeared as LIRGs." Another result could be secured using the spectra obtained with the Very Large Telescope: the astronomers measured the chemical abundances in several of the observed galaxies (PR Photo 02a/05). They find that galaxies with large redshifts show oxygen abundances two times lower than present-day spirals. As it is stars which produce oxygen in a galaxy, this again gives support to the fact that these galaxies have been actively forming stars in the period between 8,000 and 4,000 million years ago. And because it is believed that galaxy collisions and mergers play an important role in triggering such phases of enhanced star-forming activity, these observations indicate that galaxy merging still occurred frequently less than 8,000 million years ago. Spiral Rebuilding ESO PR Photo 02b/05 ESO PR Photo 02b/05 The Spiral Rebuilding Scenario [Preview - JPEG: 471 x 400 pix - 80k] [Normal - JPEG: 941 x 800 pix - 207k] Caption: ESO PR Photo 02b/05: Schematic representation of the newly proposed scenario of "spiral galaxy rebuilding": galaxies collide (1), then merge (2), inducing a burst of stellar formation activity. After the merging, the gas and the stars fall towards the centre in a very compact structure (3). Part of the gas which did not fall back initially, gradually rebuilds a disc around the compact structure, making a new spiral galaxy (4 and 5). The images are pictures

Forming Spirals From Shadows

Science.gov (United States)

Kohler, Susanna

2016-07-01

What causes the large-scale spiral structures found in some protoplanetary disks? Most models assume theyre created by newly-forming planets, but a new study suggests that planets might have nothing to do with it.Perturbations from Planets?In some transition disks protoplanetary disks with gaps in their inner regions weve directly imaged large-scale spiral arms. Many theories currently attribute the formation of these structures to young planets: either the direct perturbations of a planet embedded in the disk cause the spirals, or theyre indirectly caused by the orbit of a planetary body outside of the arms.Another example of spiral arms detected in a protoplanetary disk, MWC 758. [NASA/ESA/ESO/M. Benisty et al.]But what if you could get spirals without any planets? A team of scientists led by Matas Montesinos (University of Chile) have recently published a study in which they examine what happens to a shadowed protoplanetary disk.Casting Shadows with WarpsIn the teams setup, they envision a protoplanetary disk that is warped: the inner region is slightly tilted relative to the outer region. As the central star casts light out over its protoplanetary disk, this disk warping would cause some regions of the disk to be shaded in a way that isnt axially symmetric with potentially interesting implications.Montesinos and collaborators ran 2D hydrodynamics simulations to determine what happens to the motion of particles within the disk when they pass in and out of the shadowed regions. Since the shadowed regions are significantly colder than the illuminated disk, the pressure in these regions is much lower. Particles are therefore accelerated and decelerated as they pass through these regions, and the lack of axial symmetry causes spiral density waves to form in the disk as a result.Initial profile for the stellar heating rate per unit area for one of the authors simulations. The regions shadowed as a result of the disk warp subtend 0.5 radians each (shown on the left

TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Shen Yang; Delaglio, Frank [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Cornilescu, Gabriel [National Magnetic Resonance Facility (United States); Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: bax@nih.gov

2009-08-15

NMR chemical shifts in proteins depend strongly on local structure. The program TALOS establishes an empirical relation between {sup 13}C, {sup 15}N and {sup 1}H chemical shifts and backbone torsion angles {phi} and {psi} (Cornilescu et al. J Biomol NMR 13 289-302, 1999). Extension of the original 20-protein database to 200 proteins increased the fraction of residues for which backbone angles could be predicted from 65 to 74%, while reducing the error rate from 3 to 2.5%. Addition of a two-layer neural network filter to the database fragment selection process forms the basis for a new program, TALOS+, which further enhances the prediction rate to 88.5%, without increasing the error rate. Excluding the 2.5% of residues for which TALOS+ makes predictions that strongly differ from those observed in the crystalline state, the accuracy of predicted {phi} and {psi} angles, equals {+-}13{sup o}. Large discrepancies between predictions and crystal structures are primarily limited to loop regions, and for the few cases where multiple X-ray structures are available such residues are often found in different states in the different structures. The TALOS+ output includes predictions for individual residues with missing chemical shifts, and the neural network component of the program also predicts secondary structure with good accuracy.

Spirals on the sea

Directory of Open Access Journals (Sweden)

Walter Munk

2001-12-01

Full Text Available Spiral eddies were first seen in the sun glitter on the Apollo Mission 30 years ago; they have since been recorded on SAR missions and in the infrared. The spirals are globally distributed, 10-25 km in size and overwhelmingly cyclonic. They have not been explained. Under light winds favorable to visualization, linear surface features with high surfactant density and low surface roughness are of common occurrence. We have proposed that frontal formations concentrate the ambient shear and prevailing surfactants. Horizontal shear instabilities ensue when the shear becomes comparable to the coriolis frequency. The resulting vortices wind the liner features into spirals. The hypothesis needs to be tested by prolonged measurements and surface truth. Spiral eddies are a manifestation of a sub-mesoscale oceanography associated with upper ocean stirring; dimensional considerations suggest a horizontal diffusivity of order 103 m2 s-1.

A comparison of chemical shift sensitivity of trifluoromethyl tags: optimizing resolution in {sup 19}F NMR studies of proteins

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.

Quasicrystallography on the spiral of Archimedes

International Nuclear Information System (INIS)

Bursill, L.A.

1990-01-01

The concept of a spiral lattice is discussed. Some examples of known mineral structures, namely clino asbestos, halloysite and cylindrite, are then interpreted in terms of this structural principle. An example of a synthetic sulphide catalyst spiral structure having atomic dimensions is also described. All of these inorganic spiral structures are based on the sprial of Archimedes. The principles for a new type of crystallography, based on the Archimedian spiral, are then presented. 45 refs., 8 figs

Embracing the Spiral

Directory of Open Access Journals (Sweden)

Li Mao

2016-12-01

Full Text Available Critical research demands that we interrogate our own positionality and social location. Critical reflexivity is a form of researcher critical consciousness that is constant and dynamic in a complex spiral-like process starting within our own experiences as racialized, gendered, and classed beings embedded in particular sociopolitical contexts. Across diverse critical methodologies, a group of graduate students and their supervisor explored their own conceptualization of the reflexivity spiral by reflecting on how their research motivations and methodologies emerged from their racializing, colonizing, language-learning, parenting, and identity negotiating experiences. In this article, they present a spiral model of the critical reflexivity process, review the literature on reflexivity, and conclude with a description of critical reflexivity as a social practice within a supportive and collaborative graduate school experience.

Quantitative chemical shift-encoded MRI is an accurate method to quantify hepatic steatosis.

Science.gov (United States)

Kühn, Jens-Peter; Hernando, Diego; Mensel, Birger; Krüger, Paul C; Ittermann, Till; Mayerle, Julia; Hosten, Norbert; Reeder, Scott B

2014-06-01

To compare the accuracy of liver fat quantification using a three-echo chemical shift-encoded magnetic resonance imaging (MRI) technique without and with correction for confounders with spectroscopy (MRS) as the reference standard. Fifty patients (23 women, mean age 56.6 ± 13.2 years) with fatty liver disease were enrolled. Patients underwent T2-corrected single-voxel MRS and a three-echo chemical shift-encoded gradient echo (GRE) sequence at 3.0T. MRI fat fraction (FF) was calculated without and with T2* and T1 correction and multispectral modeling of fat and compared with MRS-FF using linear regression. The spectroscopic range of liver fat was 0.11%-38.7%. Excellent correlation between MRS-FF and MRI-FF was observed when using T2* correction (R(2)  = 0.96). With use of T2* correction alone, the slope was significantly different from 1 (1.16 ± 0.03, P fat were addressed, the results showed equivalence between fat quantification using MRI and MRS (slope: 1.02 ± 0.03, P = 0.528; intercept: 0.26% ± 0.46%, P = 0.572). Complex three-echo chemical shift-encoded MRI is equivalent to MRS for quantifying liver fat, but only with correction for T2* decay and T1 recovery and use of spectral modeling of fat. This is necessary because T2* decay, T1 recovery, and multispectral complexity of fat are processes which may otherwise bias the measurements. Copyright © 2013 Wiley Periodicals, Inc.

Chemical shift of Mn and Cr K-edges in X-ray absorption

Indian Academy of Sciences (India)

... Lecture Workshops · Refresher Courses · Symposia · Live Streaming. Home; Journals; Bulletin of Materials Science; Volume 36; Issue 6. Chemical shift of Mn and Cr K-edges in X-ray absorption spectroscopy with synchrotron radiation. D Joseph A K Yadav S N Jha D Bhattacharyya. Volume 36 Issue 6 November 2013 pp ...

Assignment of protein backbone resonances using connectivity, torsion angles and 13Cα chemical shifts

International Nuclear Information System (INIS)

Morris, Laura C.; Valafar, Homayoun; Prestegard, James H.

2004-01-01

A program is presented which will return the most probable sequence location for a short connected set of residues in a protein given just 13 C α chemical shifts (δ( 13 C α )) and data restricting the φ and ψ backbone angles. Data taken from both the BioMagResBank and the Protein Data Bank were used to create a probability density function (PDF) using a multivariate normal distribution in δ( 13 C α ), φ, and ψ space for each amino acid residue. Extracting and combining probabilities for particular amino acid residues in a short proposed sequence yields a score indicative of the correctness of the proposed assignment. The program is illustrated using several proteins for which structure and 13 C α chemical shift data are available

Spiral 2 Week

Energy Technology Data Exchange (ETDEWEB)

NONE

2007-07-01

The main goal of this meeting is to present and discuss the current status of the Spiral-2 project at GANIL in front of a large community of scientists and engineers. Different issues have been tackled particularly the equipment around Spiral-2 like injectors, cryo-modules or beam diagnostics, a workshop was devoted to other facilities dedicated to radioactive ion beam production. This document gathers only the slides of the presentations.

Spiral 2 Week

International Nuclear Information System (INIS)

2007-01-01

The main goal of this meeting is to present and discuss the current status of the Spiral-2 project at GANIL in front of a large community of scientists and engineers. Different issues have been tackled particularly the equipment around Spiral-2 like injectors, cryo-modules or beam diagnostics, a workshop was devoted to other facilities dedicated to radioactive ion beam production. This document gathers only the slides of the presentations

Wave-particle dualism of spiral waves dynamics.

Science.gov (United States)

Biktasheva, I V; Biktashev, V N

2003-02-01

We demonstrate and explain a wave-particle dualism of such classical macroscopic phenomena as spiral waves in active media. That means although spiral waves appear as nonlocal processes involving the whole medium, they respond to small perturbations as effectively localized entities. The dualism appears as an emergent property of a nonlinear field and is mathematically expressed in terms of the spiral waves response functions, which are essentially nonzero only in the vicinity of the spiral wave core. Knowledge of the response functions allows quantitatively accurate prediction of the spiral wave drift due to small perturbations of any nature, which makes them as fundamental characteristics for spiral waves as mass is for the condensed matter.

Spiral-arm instability: giant clump formation via fragmentation of a galactic spiral arm

Science.gov (United States)

Inoue, Shigeki; Yoshida, Naoki

2018-03-01

Fragmentation of a spiral arm is thought to drive the formation of giant clumps in galaxies. Using linear perturbation analysis for self-gravitating spiral arms, we derive an instability parameter and define the conditions for clump formation. We extend our analysis to multicomponent systems that consist of gas and stars in an external potential. We then perform numerical simulations of isolated disc galaxies with isothermal gas, and compare the results with the prediction of our analytic model. Our model describes accurately the evolution of the spiral arms in our simulations, even when spiral arms dynamically interact with one another. We show that most of the giant clumps formed in the simulated disc galaxies satisfy the instability condition. The clump masses predicted by our model are in agreement with the simulation results, but the growth time-scale of unstable perturbations is overestimated by a factor of a few. We also apply our instability analysis to derive scaling relations of clump properties. The expected scaling relation between the clump size, velocity dispersion, and circular velocity is slightly different from that given by the Toomre instability analyses, but neither is inconsistent with currently available observations. We argue that the spiral-arm instability is a viable formation mechanism of giant clumps in gas-rich disc galaxies.

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

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...

Chemical shift-selective snapshot FLASH MR imaging in combination with inversion-recovery T1 contrast at different field strengths

International Nuclear Information System (INIS)

Matthaei, D.; Haase, A.; Henrich, D.; Duhmke, E.

1991-01-01

With fast MR imaging, chemical shift contract becomes available to the clinician in seconds. The purpose of this paper is to evaluate the combination of chemical shift selective (CHESS) MR imaging using the snapshot FLASH MR method with the inversion-recovery technique and to obtain information concerning the signal-to-noise and chemical shift with the presaturation method at different field strengths. Investigations with volunteers and experimental animals were done at 2 and 3 T (whole body) and in a 4.7-T animal image. For the inversion-recovery experiments, saturation was done before every snapshot FLASH image. With increasing field strength due to signal-to-noise and chemical shift advantages, the method performs better. Increasing T1 values are also important at high field strengths. The combined technique is useful only for T1 water images with fat saturation. It also allows fast quantification of T1 in water-containing organs and pathologic processes. At high field strengths, fast CHESS and T1 imaging promise fast quantitative information. This is a possible argument for clinical high-field-strength MR imagining along with MR spectroscopy

Calculation of NMR chemical shifts. 7. Gauge-invariant INDO method

Science.gov (United States)

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.

Determination of the bonding of alkyl monolayers to the Si(111) surface using chemical-shift, scanned-energy photoelectron diffraction

Energy Technology Data Exchange (ETDEWEB)

Terry, J.; Linford, M.R.; Wigren, C.; Cao, R.; Pianetta, P.; Chidsey, C.E. [Stanford University, Stanford, California 94309 (United States)

1997-08-01

The bonding of alkyl monolayers to Si(111) surfaces has been studied by conventional x-ray photoelectron spectroscopy (XPS) and chemical-shift, scanned-energy photoelectron diffraction (PED) using synchrotron radiation. Two very different wet-chemical methods have been used to prepare the alkyl monolayers: (i) olefin insertion into the H{endash}Si bond on the H{endash}Si(111) surface, and (ii) replacement of Cl on the Cl{endash}Si(111) surface by an alkyl group from an alkyllithium reagent. In both cases, XPS has revealed a C 1s signal chemically shifted to lower binding energy, which we have assigned to carbon bonded to silicon. PED has shown that both preparative methods result in carbon bonded in an atop site with the expected C{endash}Si bond length of 1.85{plus_minus}0.05{Angstrom}. Chemical-shift, scanned-energy photoelectron diffraction is a particularly valuable probe of local structure at surfaces that contain the same element in multiple, chemically distinct environments. {copyright} {ital 1997 American Institute of Physics.}

Determination of the bonding of alkyl monolayers to the Si(111) surface using chemical-shift, scanned-energy photoelectron diffraction

International Nuclear Information System (INIS)

Terry, J.; Linford, M.R.; Wigren, C.; Cao, R.; Pianetta, P.; Chidsey, C.E.

1997-01-01

The bonding of alkyl monolayers to Si(111) surfaces has been studied by conventional x-ray photoelectron spectroscopy (XPS) and chemical-shift, scanned-energy photoelectron diffraction (PED) using synchrotron radiation. Two very different wet-chemical methods have been used to prepare the alkyl monolayers: (i) olefin insertion into the H endash Si bond on the H endash Si(111) surface, and (ii) replacement of Cl on the Cl endash Si(111) surface by an alkyl group from an alkyllithium reagent. In both cases, XPS has revealed a C 1s signal chemically shifted to lower binding energy, which we have assigned to carbon bonded to silicon. PED has shown that both preparative methods result in carbon bonded in an atop site with the expected C endash Si bond length of 1.85±0.05 Angstrom. Chemical-shift, scanned-energy photoelectron diffraction is a particularly valuable probe of local structure at surfaces that contain the same element in multiple, chemically distinct environments. copyright 1997 American Institute of Physics

Solvation effects on chemical shifts by embedded cluster integral equation theory.

Science.gov (United States)

Frach, Roland; Kast, Stefan M

2014-12-11

The accurate computational prediction of nuclear magnetic resonance (NMR) parameters like chemical shifts represents a challenge if the species studied is immersed in strongly polarizing environments such as water. Common approaches to treating a solvent in the form of, e.g., the polarizable continuum model (PCM) ignore strong directional interactions such as H-bonds to the solvent which can have substantial impact on magnetic shieldings. We here present a computational methodology that accounts for atomic-level solvent effects on NMR parameters by extending the embedded cluster reference interaction site model (EC-RISM) integral equation theory to the prediction of chemical shifts of N-methylacetamide (NMA) in aqueous solution. We examine the influence of various so-called closure approximations of the underlying three-dimensional RISM theory as well as the impact of basis set size and different treatment of electrostatic solute-solvent interactions. We find considerable and systematic improvement over reference PCM and gas phase calculations. A smaller basis set in combination with a simple point charge model already yields good performance which can be further improved by employing exact electrostatic quantum-mechanical solute-solvent interaction energies. A larger basis set benefits more significantly from exact over point charge electrostatics, which can be related to differences of the solvent's charge distribution.

Interaction of multiarmed spirals in bistable media.

Science.gov (United States)

He, Ya-feng; Ai, Bao-quan; Liu, Fu-cheng

2013-05-01

We study the interaction of both dense and sparse multiarmed spirals in bistable media modeled by equations of the FitzHugh-Nagumo type. A dense one-armed spiral is characterized by its fixed tip. For dense multiarmed spirals, when the initial distance between tips is less than a critical value, the arms collide, connect, and disconnect continuously as the spirals rotate. The continuous reconstruction between the front and the back drives the tips to corotate along a rough circle and to meander zigzaggedly. The rotation frequency of tip, the frequency of zigzagged displacement, the frequency of spiral, the oscillation frequency of media, and the number of arms satisfy certain relations as long as the control parameters of the model are fixed. When the initial distance between tips is larger than the critical value, the behaviors of individual arms within either dense or sparse multiarmed spirals are identical to that of corresponding one-armed spirals.

Benchmark fragment-based 1H, 13C, 15N and 17O chemical shift predictions in molecular crystals†

Science.gov (United States)

Hartman, Joshua D.; Kudla, Ryan A.; Day, Graeme M.; Mueller, Leonard J.; Beran, Gregory J. O.

2016-01-01

The performance of fragment-based ab initio 1H, 13C, 15N and 17O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. 1H, 13C, 15N, and 17O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same 1H, 13C, 15N, and 17O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tertbutyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2. PMID:27431490

Benchmark fragment-based (1)H, (13)C, (15)N and (17)O chemical shift predictions in molecular crystals.

Science.gov (United States)

Hartman, Joshua D; Kudla, Ryan A; Day, Graeme M; Mueller, Leonard J; Beran, Gregory J O

2016-08-21

The performance of fragment-based ab initio(1)H, (13)C, (15)N and (17)O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. (1)H, (13)C, (15)N, and (17)O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same (1)H, (13)C, (15)N, and (17)O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tert-butyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2.

Transitions between Taylor vortices and spirals via wavy Taylor vortices and wavy spirals

International Nuclear Information System (INIS)

Hoffmann, Ch; Altmeyer, S; Pinter, A; Luecke, M

2009-01-01

We present numerical simulations of closed wavy Taylor vortices and of helicoidal wavy spirals in the Taylor-Couette system. These wavy structures appearing via a secondary bifurcation out of Taylor vortex flow and out of spiral vortex flow, respectively, mediate transitions between Taylor and spiral vortices and vice versa. Structure, dynamics, stability and bifurcation behaviour are investigated in quantitative detail as a function of Reynolds numbers and wave numbers for counter-rotating as well as corotating cylinders. These results are obtained by solving the Navier-Stokes equations subject to axial periodicity for a radius ratio η=0.5 with a combination of a finite differences method and a Galerkin method.

SIGNATURES OF LONG-LIVED SPIRAL PATTERNS

International Nuclear Information System (INIS)

Martínez-García, Eric E.; González-Lópezlira, Rosa A.

2013-01-01

Azimuthal age/color gradients across spiral arms are a signature of long-lived spirals. From a sample of 19 normal (or weakly barred) spirals where we have previously found azimuthal age/color gradient candidates, 13 objects were further selected if a two-armed grand-design pattern survived in a surface density stellar mass map. Mass maps were obtained from optical and near-infrared imaging, by comparison with a Monte Carlo library of stellar population synthesis models that allowed us to obtain the mass-to-light ratio in the J band, (M/L) J , as a function of (g – i) versus (i – J) color. The selected spirals were analyzed with Fourier methods in search of other signatures of long-lived modes related to the gradients, such as the gradient divergence toward corotation, and the behavior of the phase angle of the two-armed spiral in different wavebands, as expected from theory. The results show additional signatures of long-lived spirals in at least 50% of the objects.

Scaling effects in spiral capsule robots.

Science.gov (United States)

Liang, Liang; Hu, Rong; Chen, Bai; Tang, Yong; Xu, Yan

2017-04-01

Spiral capsule robots can be applied to human gastrointestinal tracts and blood vessels. Because of significant variations in the sizes of the inner diameters of the intestines as well as blood vessels, this research has been unable to meet the requirements for medical applications. By applying the fluid dynamic equations, using the computational fluid dynamics method, to a robot axial length ranging from 10 -5 to 10 -2  m, the operational performance indicators (axial driving force, load torque, and maximum fluid pressure on the pipe wall) of the spiral capsule robot and the fluid turbulent intensity around the robot spiral surfaces was numerically calculated in a straight rigid pipe filled with fluid. The reasonableness and validity of the calculation method adopted in this study were verified by the consistency of the calculated values by the computational fluid dynamics method and the experimental values from a relevant literature. The results show that the greater the fluid turbulent intensity, the greater the impact of the fluid turbulence on the driving performance of the spiral capsule robot and the higher the energy consumption of the robot. For the same level of size of the robot, the axial driving force, the load torque, and the maximum fluid pressure on the pipe wall of the outer spiral robot were larger than those of the inner spiral robot. For different requirements of the operating environment, we can choose a certain kind of spiral capsule robot. This study provides a theoretical foundation for spiral capsule robots.

Echo-Interleaved-Spiral MR Imaging

International Nuclear Information System (INIS)

Rosenthal, Shirrie; Azhari, Haim; Montag, Avram

1998-01-01

Interleaved-Spiral imaging is an efficient method for MRI fast scans. However, images suffer from blurring and artifacts due to field inhomogeneities and the long readout times. In this paper, we combine interleaved-spirals with spin-echo for 3D scans. The refocusing RF-pulses (echoes) refocus off-resonance spins, thus allowing longer acquisition times per excitation, by limiting inhomogeneity effects. The total number of excitations for a 3D scan is reduced by half. The 3D Fourier transform of an object is divided into pairs of slices, one slice is scanned in an outgoing interleaved-spiral, initiated after a 90 degree pulse has been applied. The second slice is scanned in an ingoing interleaved-spiral, after a 180 degree pulse has been applied, thus reaching the slice origin at the echo time. (authors)

The Spiral of Euroscepticism

DEFF Research Database (Denmark)

Galpin, Charlotte; Trenz, Hans-Jörg

2017-01-01

of Euroscepticism’, taking media autonomy seriously to understand how media logics and selective devices contribute to the shaping of public discourse about the EU. We review the literature on the media and EU legitimacy to show how media frames and their amplification on social media can account for the salience......Media scholars have increasingly examined the effects of a negativity bias that applies to political news. In the ‘spiral of cynicism’, journalist preferences for negative news correspond to public demands for sensational news. We argue that this spiral of cynicism in EU news results in a ‘spiral...... of Eurosceptic opinions in the public sphere that then push parties to contest the EU in predominantly negative terms....

SPIRAL DENSITY WAVES IN M81. II. HYDRODYNAMIC SIMULATIONS OF THE GAS RESPONSE TO STELLAR SPIRAL DENSITY WAVES

International Nuclear Information System (INIS)

Wang, Hsiang-Hsu; Lee, Wing-Kit; Taam, Ronald E.; Feng, Chien-Chang; Lin, Lien-Hsuan

2015-01-01

The gas response to the underlying stellar spirals is explored for M81 using unmagnetized hydrodynamic simulations. Constrained within the uncertainty of observations, 18 simulations are carried out to study the effects of self-gravity and to cover the parameter space comprising three different sound speeds and three different arm strengths. The results are confronted with the data observed at wavelengths of 8 μm and 21 cm. In the outer disk, the ring-like structure observed in the 8 μm image is consistent with the response of cold neutral medium with an effective sound speed 7 km s –1 . For the inner disk, the presence of spiral shocks can be understood as a result of 4:1 resonances associated with the warm neutral medium with an effective sound speed 19 km s –1 . Simulations with a single effective sound speed alone cannot simultaneously explain the structures in the outer and inner disks. Instead this justifies the coexistence of cold and warm neutral media in M81. The anomalously high streaming motions observed in the northeast arm and the outward shifted turning points in the iso-velocity contours seen along the southwest arm are interpreted as signatures of interactions with companion galaxies. The level of simulated streaming motions narrows down the uncertainty of the observed arm strength toward larger amplitudes

SPIRAL DENSITY WAVES IN M81. II. HYDRODYNAMIC SIMULATIONS OF THE GAS RESPONSE TO STELLAR SPIRAL DENSITY WAVES

Energy Technology Data Exchange (ETDEWEB)

Wang, Hsiang-Hsu; Lee, Wing-Kit; Taam, Ronald E.; Feng, Chien-Chang; Lin, Lien-Hsuan, E-mail: hhwang@asiaa.sinica.edu.tw [Institute of Astronomy and Astrophysics, Academia Sinica, P.O. Box 23-141, Taipei 10617, Taiwan, ROC (China)

2015-02-20

The gas response to the underlying stellar spirals is explored for M81 using unmagnetized hydrodynamic simulations. Constrained within the uncertainty of observations, 18 simulations are carried out to study the effects of self-gravity and to cover the parameter space comprising three different sound speeds and three different arm strengths. The results are confronted with the data observed at wavelengths of 8 μm and 21 cm. In the outer disk, the ring-like structure observed in the 8 μm image is consistent with the response of cold neutral medium with an effective sound speed 7 km s{sup –1}. For the inner disk, the presence of spiral shocks can be understood as a result of 4:1 resonances associated with the warm neutral medium with an effective sound speed 19 km s{sup –1}. Simulations with a single effective sound speed alone cannot simultaneously explain the structures in the outer and inner disks. Instead this justifies the coexistence of cold and warm neutral media in M81. The anomalously high streaming motions observed in the northeast arm and the outward shifted turning points in the iso-velocity contours seen along the southwest arm are interpreted as signatures of interactions with companion galaxies. The level of simulated streaming motions narrows down the uncertainty of the observed arm strength toward larger amplitudes.

Echo-Interleaved-Spiral MR Imaging

Energy Technology Data Exchange (ETDEWEB)

Rosenthal, Shirrie; Azhari, Haim [Department of Biomedical Engineering, Technion, Israel Institute of Technology, Haifa 32000 (Israel); Montag, Avram [Elscint Ltd., MRI division, Haifa (Israel)

1999-12-31

Interleaved-Spiral imaging is an efficient method for MRI fast scans. However, images suffer from blurring and artifacts due to field inhomogeneities and the long readout times. In this paper, we combine interleaved-spirals with spin-echo for 3D scans. The refocusing RF-pulses (echoes) refocus off-resonance spins, thus allowing longer acquisition times per excitation, by limiting inhomogeneity effects. The total number of excitations for a 3D scan is reduced by half. The 3D Fourier transform of an object is divided into pairs of slices, one slice is scanned in an outgoing interleaved-spiral, initiated after a 90 degree pulse has been applied. The second slice is scanned in an ingoing interleaved-spiral, after a 180 degree pulse has been applied, thus reaching the slice origin at the echo time. (authors) 4 refs., 3 figs.

Orientation-dependent surface core-level shifts and chemical shifts on clean and H 2S-covered GaAs

Science.gov (United States)

Ranke, W.; Finster, J.; Kuhr, H. J.

1987-08-01

Photoelectron spectra of the As 3d and Ga 3d core levels were studied in situ on a cylindrically shaped GaAs single crystal for the six inequivalent orientations (001), (113), (111), (110), (11¯1) and (11¯3). On the clean surface, prepared by molecular beam epitaxy (MBE), surface core levels are shifted by 0.25 to 0.55 eV towards smaller binding energy (BE) for As 3d and -0.25 to -0.35 eV towards higher BE for Ga, depending on orientation. Additional As causes As 3d contributions shifted between -0.45 and -0.7 eV towards higher BE. The position and intensity of them is influenced by H 2S adsorption. At 150 K, H 2S adsorbs preferentially on As sites. As chemical shifts appear at -0.6 to -0.9 eV towards higher BE. Simultaneously, As accumulation occurs on all orientations with the exception of (110). High temperature adsorption (550 K, 720 K) influences mainly the Ga 3d peaks. Two peaks shifted by about -0.45 and -0.8 eV towards higher Be were found which are attributed to Ga atoms with one or two sulfur ligands, respectively. At 720 K, also As depletion is observed. The compatibility of surface core-level positions and intensities with recent structural models for the (111) and (11¯1) surfaces is discussed.

Criteria to average out the chemical shift anisotropy in solid-state NMR when irradiated with BABA I, BABA II, and C7 radiofrequency pulse sequences.

Science.gov (United States)

Stephane Mananga, Eugene

2013-01-01

Floquet-Magnus expansion is used to study the effect of chemical shift anisotropy in solid-state NMR of rotating solids. The chemical shift interaction is irradiated with two types of radiofrequency pulse sequences: BABA and C7. The criteria for the chemical shift anisotropy to be averaged out in each rotor period are obtained. Copyright © 2013 Elsevier Inc. All rights reserved.

Investigation of logarithmic spiral nanoantennas at optical frequencies

Science.gov (United States)

Verma, Anamika; Pandey, Awanish; Mishra, Vigyanshu; Singh, Ten; Alam, Aftab; Dinesh Kumar, V.

2013-12-01

The first study is reported of a logarithmic spiral antenna in the optical frequency range. Using the finite integration technique, we investigated the spectral and radiation properties of a logarithmic spiral nanoantenna and a complementary structure made of thin gold film. A comparison is made with results for an Archimedean spiral nanoantenna. Such nanoantennas can exhibit broadband behavior that is independent of polarization. Two prominent features of logarithmic spiral nanoantennas are highly directional far field emission and perfectly circularly polarized radiation when excited by a linearly polarized source. The logarithmic spiral nanoantenna promises potential advantages over Archimedean spirals and could be harnessed for several applications in nanophotonics and allied areas.

Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

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...

Differentiation of osteoporotic and neoplastic vertebral fractures by chemical shift {in-phase and out-of phase} MR imaging

International Nuclear Information System (INIS)

Ragab, Yasser; Emad, Yasser; Gheita, Tamer; Mansour, Maged; Abou-Zeid, A.; Ferrari, Serge; Rasker, Johannes J.

2009-01-01

Objective: The objective of this study was to establish the cut-off value of the signal intensity drop on chemical shift magnetic resonance imaging (MRI) with appropriate sensitivity and specificity to differentiate osteoporotic from neoplastic wedging of the spine. Patients and methods: All patients with wedging of vertebral bodies were included consecutively between February 2006 and January 2007. A chemical shift MRI was performed and signal intensity after (in-phase and out-phase) images were obtained. A DXA was performed in all. Results: A total of 40 patients were included, 20 with osteoporotic wedging (group 1) and 20 neoplastic (group 2). They were 21 males and 19 females. Acute vertebral collapse was observed in 15 patients in group 1 and subacute collapse in another 5 patients, while in group 2, 11 patients showed acute collapse and 9 patients (45%) showed subacute vertebral collapse. On the chemical shift MRI a substantial reduction in signal intensity was found in all lesions in both groups. The proportional changes observed in signal intensity of bone marrow lesions on in-phase compared with out-of-phase images showed significant differences in both groups (P < 0.05). At a cut-off value of 35%, the observed sensitivity of out-of-phase images was 95%, specificity was 100%, positive predictive value was 100% and negative predictive value was 95.2%. Conclusion: A chemical shift MRI is useful in order to differentiate patients with vertebral collapse due to underlying osteoporosis or neoplastic process.

Measuring 13Cβ chemical shifts of invisible excited states in proteins by relaxation dispersion NMR spectroscopy

International Nuclear Information System (INIS)

Lundstroem, Patrik; Lin Hong; Kay, Lewis E.

2009-01-01

A labeling scheme is introduced that facilitates the measurement of accurate 13 C β chemical shifts of invisible, excited states of proteins by relaxation dispersion NMR spectroscopy. The approach makes use of protein over-expression in a strain of E. coli in which the TCA cycle enzyme succinate dehydrogenase is knocked out, leading to the production of samples with high levels of 13 C enrichment (30-40%) at C β side-chain carbon positions for 15 of the amino acids with little 13 C label at positions one bond removed (∼5%). A pair of samples are produced using [1- 13 C]-glucose/NaH 12 CO 3 or [2- 13 C]-glucose as carbon sources with isolated and enriched (>30%) 13 C β positions for 11 and 4 residues, respectively. The efficacy of the labeling procedure is established by NMR spectroscopy. The utility of such samples for measurement of 13 C β chemical shifts of invisible, excited states in exchange with visible, ground conformations is confirmed by relaxation dispersion studies of a protein-ligand binding exchange reaction in which the extracted chemical shift differences from dispersion profiles compare favorably with those obtained directly from measurements on ligand free and fully bound protein samples

How does a planet excite multiple spiral arms?

Science.gov (United States)

Bae, Jaehan; Zhu, Zhaohuan

2018-01-01

Protoplanetary disk simulations show that a single planet excites multiple spiral arms in the background disk, potentially supported by the multi-armed spirals revealed with recent high-resolution observations in some disks. The existence of multiple spiral arms is of importance in many aspects. It is empirically found that the arm-to-arm separation increases as a function of the planetary mass, so one can use the morphology of observed spiral arms to infer the mass of unseen planets. In addition, a spiral arm opens a radial gap as it steepens into a shock, so when a planet excites multiple spiral arms it can open multiple gaps in the disk. Despite the important implications, however, the formation mechanism of multiple spiral arms has not been fully understood by far.In this talk, we explain how a planet excites multiple spiral arms. The gravitational potential of a planet can be decomposed into a Fourier series, a sum of individual azimuthal modes having different azimuthal wavenumbers. Using a linear wave theory, we first demonstrate that appropriate sets of Fourier decomposed waves can be in phase, raising a possibility that constructive interference among the waves can produce coherent structures - spiral arms. More than one spiral arm can form since such constructive interference can occur at different positions in the disk for different sets of waves. We then verify this hypothesis using a suite of two-dimensional hydrodynamic simulations. Finally, we present non-linear behavior in the formation of multiple spiral arms.

Empirical isotropic chemical shift surfaces

International Nuclear Information System (INIS)

Czinki, Eszter; Csaszar, Attila G.

2007-01-01

A list of proteins is given for which spatial structures, with a resolution better than 2.5 A, are known from entries in the Protein Data Bank (PDB) and isotropic chemical shift (ICS) values are known from the RefDB database related to the Biological Magnetic Resonance Bank (BMRB) database. The structures chosen provide, with unknown uncertainties, dihedral angles φ and ψ characterizing the backbone structure of the residues. The joint use of experimental ICSs of the same residues within the proteins, again with mostly unknown uncertainties, and ab initio ICS(φ,ψ) surfaces obtained for the model peptides For-(l-Ala) n -NH 2 , with n = 1, 3, and 5, resulted in so-called empirical ICS(φ,ψ) surfaces for all major nuclei of the 20 naturally occurring α-amino acids. Out of the many empirical surfaces determined, it is the 13C α ICS(φ,ψ) surface which seems to be most promising for identifying major secondary structure types, α-helix, β-strand, left-handed helix (α D ), and polyproline-II. Detailed tests suggest that Ala is a good model for many naturally occurring α-amino acids. Two-dimensional empirical 13C α - 1 H α ICS(φ,ψ) correlation plots, obtained so far only from computations on small peptide models, suggest the utility of the experimental information contained therein and thus they should provide useful constraints for structure determinations of proteins

Lanthanide shift reagents, binding, shift mechanisms and exchange

International Nuclear Information System (INIS)

Boer, J.W.M. de

1977-01-01

Paramagnetic lanthanide shift reagents, when added to a solution of a substrate, induce shifts in the nuclear magnetic resonance (NMR) spectrum of the substrate molecules. The induced shifts contain information about the structure of the shift reagent substrate complex. The structural information, however, may be difficult to extract because of the following effects: (1) different complexes between shift reagent and substrate may be present in solution, e.g. 1:1 and 1:2 complexes, and the shift observed is a weighed average of the shifts of the substrate nuclei in the different complexes; (2) the Fermi contact interaction, arising from the spin density at the nucleus, contributes to the induced shift; (3) chemical exchange effects may complicate the NMR spectrum. In this thesis, the results of an investigation into the influence of these effects on the NMR spectra of solutions containing a substrate and LSR are presented. The equations describing the pseudo contact and the Fermi contact shift are derived. In addition, it is shown how the modified Bloch equations describing the effect of the chemical exchange processes occurring in the systems studied can be reduced to the familiar equations for a two-site exchange case. The binding of mono- and bifunctional ethers to the shift reagent are reported. An analysis of the induced shifts is given. Finally, the results of the experiments performed to study the exchange behavior of dimethoxyethane and heptafluorodimethyloctanedionato ligands are presented

Origins of galactic spiral structures

International Nuclear Information System (INIS)

Piddington, J.H.

1978-01-01

Theories of galactic structure are reviewed briefly before comparing them with recent observations. Also reviewed is the evidence for an intergalactic magnetic field and its possible effects on gas concentrations and patterns of star creation, including spiral arms. It is then shown that normal spiral galaxies may be divided into the M51-type and others. The rare M51-type have H I gas arms coincident with unusually filamentary and luminous optical arms; they also have a companion galaxy. The remaining great majority of spirals have no well-defined gas arms and their optical arms are irregular, broader and less luminous; they have no companion galaxy. It appears that without exception the half-dozen or so galaxies whose structures appear to support the density-wave theory show one or more of the characteristics of the rare type of spiral, and that 'the three principal confirmations of the spiral-wave idea' (M51, M81, M101) have companions which may account for their arms. Toomre has rejected this idea on the grounds that his models do not agree with the observed structures. It is shown that these models are inadequate in two major respects, and when replaced by magneto-tidal models using non-uniform gas disks one might expect agreement. The original hydromagnetic model of spiral arms is now reserved for non-interacting galaxies, of which M33 might be taken as a prototype. The model predicts broad or 'massive' optical arms and no corresponding arms of neutral hydrogen, as observed. (Auth.)

Pressure dependence of side chain 13C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

Science.gov (United States)

Beck Erlach, Markus; Koehler, Joerg; Crusca, Edson; Munte, Claudia E; Kainosho, Masatsune; Kremer, Werner; Kalbitzer, Hans Robert

2017-10-01

For evaluating the pressure responses of folded as well as intrinsically unfolded proteins detectable by NMR spectroscopy the availability of data from well-defined model systems is indispensable. In this work we report the pressure dependence of 13 C chemical shifts of the side chain atoms in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH 2 (Xxx, one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of a number of nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The size of the polynomial pressure coefficients B 1 and B 2 is dependent on the type of atom and amino acid studied. For H N , N and C α the first order pressure coefficient B 1 is also correlated to the chemical shift at atmospheric pressure. The first and second order pressure coefficients of a given type of carbon atom 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 also are weakly correlated. The downfield shifts of the methyl resonances suggest that gauche conformers of the side chains are not preferred with pressure. The valine and leucine methyl groups in the model peptides were assigned using stereospecifically 13 C enriched amino acids with the pro-R carbons downfield shifted relative to the pro-S carbons.

Reassigning the Structures of Natural Products Using NMR Chemical Shifts Computed with Quantum Mechanics: A Laboratory Exercise

Science.gov (United States)

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…

Flocculent and grand design spiral galaxies in groups: time scales for the persistence of grand design spiral structures

International Nuclear Information System (INIS)

Elmegreen, B.G.; Elmegreen, D.M.

1983-01-01

Spiral arm classifications were made for 261 low-inclination galaxies in groups listed by Huchra and Geller. The fractional occurrence of grand design spiral structure in nonbarred galaxies was found to increase from approx.0.1 to approx.0.6 and then level off as the group crossing rate or galaxy collision rate in a group increases. A simple model is discussed where the random encounters between galaxies of any type and flocculent galaxies induce transient grand design spirals in the flocculent galaxies. If this grand-design stimulation occurs for binary collisions with impact parameters less than αR 25 , were R 25 is the galactic radius at 25 mag arcsec - 2 , and if the induced grand design spirals persist for an average time equal to #betta# galactic rotations, then the quantity α 2 #betta# equals approximately 3 x 10 4 . If binary collisions are responsible for grand design spirals, then this result implies either that the induced spirals last for many galactic rotations (#betta#>15), or that they can be stimulated by very remote encounters (α>45.) Alternatively, grand design spirals may be stimulated by multiple galaxy encounters, which would be the case for such large α, or by interactions with the potential well of the associated group, rather than by simple binary encounters. Weak correlations between the grand design fraction and the galaxy size, or between this fraction and the total number of galaxies in a group, were also found. Spiral structures of barred galaxies show no correlations with group environment

Identifying Stereoisomers by ab-initio Calculation of Secondary Isotope Shifts on NMR Chemical Shieldings

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.

Identifying stereoisomers by ab-initio calculation of secondary isotope shifts on NMR chemical shieldings.

Science.gov (United States)

Böhm, Karl-Heinz; Banert, Klaus; Auer, Alexander A

2014-04-23

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(2-2H)ethane 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.

Global extinction in spiral galaxies

NARCIS (Netherlands)

Tully, RB; Pierce, MJ; Saunders, W; Verheijen, MAW; Witchalls, PL

Magnitude-limited samples of spiral galaxies drawn from the Ursa Major and Pisces Clusters are used to determine their extinction properties as a function of inclination. Imaging photometry is available for 87 spirals in the B, R, I, and K' bands. Extinction causes systematic scatter in

Dynamics of the off axis intense beam propagation in a spiral inflector

Energy Technology Data Exchange (ETDEWEB)

Goswami, A., E-mail: animesh@vecc.gov.in; Sing Babu, P., E-mail: psb@vecc.gov.in; Pandit, V.S., E-mail: pandit@vecc.gov.in

2017-01-01

In this paper the dynamics of space charge dominated beam in a spiral inflector is discussed by developing equations of motion for centroid and beam envelope for the off axis beam propagation. Evolution of the beam centroid and beam envelope is studied as a function of the beam current for various input beam parameters. The transmission of beam through the inflector is also estimated as a function of the beam current for an on axis and off axis beam by tracking a large number of particles. Simulation studies show that shift of the centroid from the axis at the inflector entrance affects the centroid location at the exit of the inflector and causes reduction in the beam transmission. The centroid shift at the entrance in the horizontal plane (h plane) is more critical as it affects the centroid shift in the vertical plane (u plane) by a large amount near the inflector exit where the available aperture is small. The beam transmission is found to reduce with increase in the centroid shift as well as with the beam current.

A study of spiral galaxies

International Nuclear Information System (INIS)

Wevers, B.M.H.R.

1984-01-01

Attempts have been made to look for possible correlations between integral properties of spiral galaxies as a function of morphological type. To investigate this problem, one needs the detailed distribution of both the gaseous and the stellar components for a well-defined sample of spiral galaxies. A sample of about 20 spiral galaxies was therefore defined; these galaxies were observed in the 21 cm neutral hydrogen line with the Westerbork Synthesis Radio Telescope and in three broad-band optical colours with the 48-inch Palomar Smidt Telescope. First, an atlas of the combined radio and optical observations of 16 nearby northern-hemisphere spiral galaxies is presented. Luminosity profiles are discussed and the scale lengths of the exponential disks and extrapolated central surface brightnesses are derived, as well as radial color distributions; azimuthal surface brightness distributions and rotation curves. Possible correlations with optical features are investigated. It is found that 20 to 50 per cent of the total mass is in the disk. (Auth.)

Calculation of the NMR chemical shift for a 4d1 system in a strong crystal field environment of trigonal symmetry with a threefold axis of quantization

International Nuclear Information System (INIS)

Ahn, Sang Woon; Oh, Se Woung; Ro, Seung Woo

1986-01-01

The NMR chemical shift arising from 4d electron angular momentum and 4d electron angular momentum and 4d electron spin dipolar-nuclear spin angular momentum interactions for a 4d 1 system in a strong crystal field environment of trigonal symmetry, where the threefold axis is chosen to be the axis of quantization axis, has been examined. A general expression using the nonmultipole expansion method (exact method) is derived for the NMR chemical shift. From this expression all the multipolar terms are determined. we observe that along the (100), (010), (110), and (111) axes the NMR chemical shifts are positive while along the (001) axis, it is negative. We observe that the dipolar term (1/R 3 ) is the dominant contribution to the NMR chemical shift except for along the (111) axis. A comparison of the multipolar terms with the exact values shows also that the multipolar results are exactly in agreement with the exact values around R≥0.2 nm. The temperature dependence analysis on the NMR chemical shifts may imply that along the (111) axis the contribution to the NMR chemical shift is dominantly pseudo contact interaction. Separation of the contributions of the Fermi and the pseudo contact interactions would correctly imply that the dipolar interaction is the dominant contribution to the NMR chemical shifts along the (100), (010), (001), and (110) axes, but along the (111) axis the Fermi contact interaction is incorrectly the dominant contribution to the NMR chemical shift. (Author)

Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

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.

Imaging of head and neck tumors -- methods: CT, spiral-CT, multislice-spiral-CT

International Nuclear Information System (INIS)

Baum, Ulrich; Greess, Holger; Lell, Michael; Noemayr, Anton; Lenz, Martin

2000-01-01

Spiral-CT is standard for imaging neck tumors. In correspondence with other groups we routinely use spiral-CT with thin slices (3 mm), a pitch of 1.3-1.5 and an overlapping reconstruction increment (2-3 mm). In patients with dental fillings a short additional spiral parallel to the corpus of the mandible reduces artifacts behind the dental arches and improves the diagnostic value of CT. For the assessment of the base of the skull, the orbital floor, the palate and paranasal sinuses an additional examination in the coronal plane is helpful. Secondary coronal reconstructions of axial scans are helpful in the evaluation of the crossing of the midline by small tumors of the tongue base or palate. For an optimal vascular or tissue contrast a sufficient volume of contrast medium and a start delay greater than 70-80 s are necessary. In our opinion the best results can be achieved with a volume of 150 ml, a flow of 2.5 ml/s and a start delay of 80 s. Dynamic enhanced CT is only necessary in some special cases. There is clear indication for dynamic enhanced CT where a glomus tumor is suspected. Additional functional CT imaging during i-phonation and/or Valsalva's maneuver are of great importance to prove vocal cords mobility. Therefore, imaging during i-phonation is an elemental part of every thorough examination of the hypopharynx and larynx region. Multislice-spiral-CT allows almost isotropic imaging of the head and neck region and improves the assessment of tumor spread and lymph node metastases in arbitrary oblique planes. Thin structures (the base of the skull, the orbital floor, the hard palate) as well as the floor of the mouth can be evaluated sufficiently with multiplanar reformations. Usually, additional coronal scanning is not necessary with multislice-spiral-CT. Multislice-spiral-CT is especially advantageous in defining the critical relationships of tumor and lymph node metastases and for functional imaging of the hypopharynx and larynx not only in the

Galaxy Zoo: dust in spiral galaxies

Science.gov (United States)

Masters, Karen L.; Nichol, Robert; Bamford, Steven; Mosleh, Moein; Lintott, Chris J.; Andreescu, Dan; Edmondson, Edward M.; Keel, William C.; Murray, Phil; Raddick, M. Jordan; Schawinski, Kevin; Slosar, Anže; Szalay, Alexander S.; Thomas, Daniel; Vandenberg, Jan

2010-05-01

We investigate the effect of dust on spiral galaxies by measuring the inclination dependence of optical colours for 24276 well-resolved Sloan Digital Sky Survey (SDSS) galaxies visually classified via the Galaxy Zoo project. We find clear trends of reddening with inclination which imply a total extinction from face-on to edge-on of 0.7, 0.6, 0.5 and 0.4mag for the ugri passbands (estimating 0.3mag of extinction in z band). We split the sample into `bulgy' (early-type) and `discy' (late-type) spirals using the SDSS fracdeV (or fDeV) parameter and show that the average face-on colour of `bulgy' spirals is redder than the average edge-on colour of `discy' spirals. This shows that the observed optical colour of a spiral galaxy is determined almost equally by the spiral type (via the bulge-disc ratio and stellar populations), and reddening due to dust. We find that both luminosity and spiral type affect the total amount of extinction, with discy spirals at Mr ~ -21.5mag having the most reddening - more than twice as much as both the lowest luminosity and most massive, bulge-dominated spirals. An increase in dust content is well known for more luminous galaxies, but the decrease of the trend for the most luminous has not been observed before and may be related to their lower levels of recent star formation. We compare our results with the latest dust attenuation models of Tuffs et al. We find that the model reproduces the observed trends reasonably well but overpredicts the amount of u-band attenuation in edge-on galaxies. This could be an inadequacy in the Milky Way extinction law (when applied to external galaxies), but more likely indicates the need for a wider range of dust-star geometries. We end by discussing the effects of dust on large galaxy surveys and emphasize that these effects will become important as we push to higher precision measurements of galaxy properties and their clustering. This publication has been made possible by the participation of more than

Polarization study of spiral galaxies

Energy Technology Data Exchange (ETDEWEB)

Ward-Thompson, D

1987-01-01

Optical polarimetry results are presented for four spiral galaxies: NGC 5194 (M51), NGC 1068, NGC 4565 and NGC 4594 (M104). M51 and NGC 1068 show spiral polarization patterns interpreted as indicating a spiral magnetic field in each case. NGC 4565 and M104 show polarizations in their dust lanes which are parallel to their galactic planes, and which are interpreted in terms of a magnetic field in the plane of each. It is hypothesized that the observed magnetic fields may be linked to galactic shocks. A discussion of the origin of galactic magnetic fields concludes that there is not evidence that necessitates a primordial magnetic field.

Spiral phases of doped antiferromagnets

International Nuclear Information System (INIS)

Shraiman, B.I.; Siggia, E.D.

1990-01-01

The dipole density field describing the holls in a doped antiferromagnet is considered for law hole density in the semiclassical limit. This yields a phase in which the order parameter is planar and spirals round a fixed direction. The single spiral state breaks the continuous spin rotational symmetry and exhibits long-range order at zero temperature. In it there is a global spin direction as rotation axis. The double spiral state, in which there are two perpendicular directions, is isotropic in both spin and real space. Several results of microscopic calculations, carried out to understand the electronic states, quantum fluctuations, lattice effects and normal mode dynamics, are recapitulated. 8 refs

Properties of spiral resonators

International Nuclear Information System (INIS)

Haeuser, J.

1989-10-01

The present thesis deals with the calculation and the study of the application possibilities of single and double spiral resonators. The main aim was the development and the construction of reliable and effective high-power spiral resonators for the UNILAC of the GSI in Darmstadt and the H - -injector for the storage ring HERA of DESY in Hamburg. After the presentation of the construction and the properties of spiral resonators and their description by oscillating-circuit models the theoretical foundations of the bunching are presented and some examples of a rebuncher and debuncher and their influence on the longitudinal particle dynamics are shown. After the description of the characteristic accelerator quantities by means of an oscillating-circuit model and the theory of an inhomogeneous λ/4 line it is shown, how the resonance frequency and the efficiency of single and double spiral resonators can be calculated from the geometrical quantities of the structure. In the following the dependence of the maximal reachable resonator voltage in dependence on the gap width and the surface of the drift tubes is studied. Furthermore the high-power resonators are presented, which were built for the different applications for the GSI in Darmstadt, DESY in Hamburg, and for the FOM Institute in Amsterdam. (orig./HSI) [de

Orientation decoding: Sense in spirals?

Science.gov (United States)

Clifford, Colin W G; Mannion, Damien J

2015-04-15

The orientation of a visual stimulus can be successfully decoded from the multivariate pattern of fMRI activity in human visual cortex. Whether this capacity requires coarse-scale orientation biases is controversial. We and others have advocated the use of spiral stimuli to eliminate a potential coarse-scale bias-the radial bias toward local orientations that are collinear with the centre of gaze-and hence narrow down the potential coarse-scale biases that could contribute to orientation decoding. The usefulness of this strategy is challenged by the computational simulations of Carlson (2014), who reported the ability to successfully decode spirals of opposite sense (opening clockwise or counter-clockwise) from the pooled output of purportedly unbiased orientation filters. Here, we elaborate the mathematical relationship between spirals of opposite sense to confirm that they cannot be discriminated on the basis of the pooled output of unbiased or radially biased orientation filters. We then demonstrate that Carlson's (2014) reported decoding ability is consistent with the presence of inadvertent biases in the set of orientation filters; biases introduced by their digital implementation and unrelated to the brain's processing of orientation. These analyses demonstrate that spirals must be processed with an orientation bias other than the radial bias for successful decoding of spiral sense. Copyright © 2014 Elsevier Inc. All rights reserved.

Accuracy of chemical shift MR imaging in diagnosing indeterminate bone marrow lesions in the pelvis: review of a single institution's experience

International Nuclear Information System (INIS)

Kohl, Chad A.; Chivers, F.S.; Lorans, Roxanne; Roberts, Catherine C.; Kransdorf, Mark J.

2014-01-01

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.)

Diagnosis of pancreatic tumors by spiral angio CT

International Nuclear Information System (INIS)

Miura, Kohi; Nakao, Norio; Takayasu, Yukio; Okawa, Tomohisa

1995-01-01

Spiral angio were performed with injection of 30 ml of contrast material at a rate of 1 ml/sec with a scan delay of 6 sec through catheter into the celiac artery while the blood flow of the superior mesenteric artery (SMA) was occluded by the inflated balloon catheter. Spiral CT scans were obtained using Somatom Plus (Siemens). Parameter for spiral CT were 24-sec acquisition time, 5 mm collimation, 5 mm/sec table incrementation. Reconstructions were performed every 5 mm. Pancreatic cancers were characteristically depicted with spiral angio CT as hypodensity relative to normal enhanced pancreatic parenchyma. On dynamic angio CT studies performed in pancreatic cancers, the area of cancer and normal parenchyma had maximum level of enhancement at 10-15 sec after injection of contrast material via catheter into the celiac, and there was no difference in enhancement between tumor and normal parenchyma. On the other hand, the lesions of cancer were revealed as hypodensity with spiral angio CT. In case of chronic pancreatitis, the enhancement of the entire pancreas obtained with spiral angio CT was homogeneous. Insulinoma in the tail of pancreas was detected by spiral angio CT but was not detected by both selective angiography and conventional CT. Three-dimensional (3-D) rendering spiral angio CT data shows the extent of vascular involvement by pancreatic cancer and provides useful information for surgical planning. Spiral angio CT is the most useful procedure for diagnosis of pancreatic tumor. (author)

Comparison of experimental and DFT-calculated NMR chemical shifts of 2-amino and 2-hydroxyl substituted phenyl benzimidazoles, benzoxazoles and benzothiazoles in four solvents using the IEF-PCM solvation model.

Science.gov (United States)

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. Copyright © 2015 John Wiley & Sons, Ltd.

IMRT delivery verification using a spiral phantom

International Nuclear Information System (INIS)

Richardson, Susan L.; Tome, Wolfgang A.; Orton, Nigel P.; McNutt, Todd R.; Paliwal, Bhudatt R.

2003-01-01

In this paper we report on the testing and verification of a system for IMRT delivery quality assurance that uses a cylindrical solid water phantom with a spiral trajectory for radiographic film placement. This spiral film technique provides more complete dosimetric verification of the entire IMRT treatment than perpendicular film methods, since it samples a three-dimensional dose subspace rather than using measurements at only one or two depths. As an example, the complete analysis of the predicted and measured spiral films is described for an intracranial IMRT treatment case. The results of this analysis are compared to those of a single field perpendicular film technique that is typically used for IMRT QA. The comparison demonstrates that both methods result in a dosimetric error within a clinical tolerance of 5%, however the spiral phantom QA technique provides a more complete dosimetric verification while being less time consuming. To independently verify the dosimetry obtained with the spiral film, the same IMRT treatment was delivered to a similar phantom in which LiF thermoluminescent dosimeters were arranged along the spiral trajectory. The maximum difference between the predicted and measured TLD data for the 1.8 Gy fraction was 0.06 Gy for a TLD located in a high dose gradient region. This further validates the ability of the spiral phantom QA process to accurately verify delivery of an IMRT plan

Cochlea and other spiral forms in nature and art.

Science.gov (United States)

Marinković, Slobodan; Stanković, Predrag; Štrbac, Mile; Tomić, Irina; Ćetković, Mila

2012-01-01

The original appearance of the cochlea and the specific shape of a spiral are interesting for both the scientists and artists. Yet, a correlation between the cochlea and the spiral forms in nature and art has been very rarely mentioned. The aim of this study was to investigate the possible correlation between the cochlea and the other spiral objects in nature, as well as the artistic presentation of the spiral forms. We explored data related to many natural objects and examined 13,625 artworks created by 2049 artists. We also dissected 2 human cochleas and prepared histologic slices of a rat cochlea. The cochlea is a spiral, cone-shaped osseous structure that resembles certain other spiral forms in nature. It was noticed that parts of some plants are arranged in a spiral manner, often according to Fibonacci numbers. Certain animals, their parts, or their products also represent various types of spirals. Many of them, including the cochlea, belong to the logarithmic type. Nature created spiral forms in the living world to pack a larger number of structures in a limited space and also to improve their function. Because the cochlea and other spiral forms have a certain aesthetic value, many artists presented them in their works of art. There is a mathematical and geometric correlation between the cochlea and natural spiral objects, and the same functional reason for their formation. The artists' imagery added a new aspect to those domains. Obviously, the creativity of nature and Homo sapiens has no limits--like the infinite distal part of the spiral. Copyright © 2012 Elsevier Inc. All rights reserved.

Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

Energy Technology Data Exchange (ETDEWEB)

Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States); Assadi, Amir [University of Wisconsin-Madison, Mathematics Department (United States); Markley, John L. [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States)], E-mail: eghbalni@nmrfam.wisc.edu

2005-05-15

We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states.

Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

International Nuclear Information System (INIS)

Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash; Assadi, Amir; Markley, John L.

2005-01-01

We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states

Stacking the Equiangular Spiral

OpenAIRE

Agrawal, A.; Azabi, Y. O.; Rahman, B. M.

2013-01-01

We present an algorithm that adapts the mature Stack and Draw (SaD) methodology for fabricating the exotic Equiangular Spiral Photonic Crystal Fiber. (ES-PCF) The principle of Steiner chains and circle packing is exploited to obtain a non-hexagonal design using a stacking procedure based on Hexagonal Close Packing. The optical properties of the proposed structure are promising for SuperContinuum Generation. This approach could make accessible not only the equiangular spiral but also other qua...

Spiral-shaped disinfection reactors

KAUST Repository

Ghaffour, Noreddine

2015-08-20

This disclosure includes disinfection reactors and processes for the disinfection of water. Some disinfection reactors include a body that defines an inlet, an outlet, and a spiral flow path between the inlet and the outlet, in which the body is configured to receive water and a disinfectant at the inlet such that the water is exposed to the disinfectant as the water flows through the spiral flow path. Also disclosed are processes for disinfecting water in such disinfection reactors.

Spiral Wave in Small-World Networks of Hodgkin-Huxley Neurons

International Nuclear Information System (INIS)

Ma Jun; Zhang Cairong; Yang Lijian; Wu Ying

2010-01-01

The effect of small-world connection and noise on the formation and transition of spiral wave in the networks of Hodgkin-Huxley neurons are investigated in detail. Some interesting results are found in our numerical studies. i) The quiescent neurons are activated to propagate electric signal to others by generating and developing spiral wave from spiral seed in small area. ii) A statistical factor is defined to describe the collective properties and phase transition induced by the topology of networks and noise. iii) Stable rotating spiral wave can be generated and keeps robust when the rewiring probability is below certain threshold, otherwise, spiral wave can not be developed from the spiral seed and spiral wave breakup occurs for a stable rotating spiral wave. iv) Gaussian white noise is introduced on the membrane of neurons to study the noise-induced phase transition on spiral wave in small-world networks of neurons. It is confirmed that Gaussian white noise plays active role in supporting and developing spiral wave in the networks of neurons, and appearance of smaller factor of synchronization indicates high possibility to induce spiral wave. (interdisciplinary physics and related areas of science and technology)

Six Decades of Spiral Density Wave Theory

Science.gov (United States)

Shu, Frank H.

2016-09-01

The theory of spiral density waves had its origin approximately six decades ago in an attempt to reconcile the winding dilemma of material spiral arms in flattened disk galaxies. We begin with the earliest calculations of linear and nonlinear spiral density waves in disk galaxies, in which the hypothesis of quasi-stationary spiral structure (QSSS) plays a central role. The earliest success was the prediction of the nonlinear compression of the interstellar medium and its embedded magnetic field; the earliest failure, seemingly, was not detecting color gradients associated with the migration of OB stars whose formation is triggered downstream from the spiral shock front. We give the reasons for this apparent failure with an update on the current status of the problem of OB star formation, including its relationship to the feathering substructure of galactic spiral arms. Infrared images can show two-armed, grand design spirals, even when the optical and UV images show flocculent structures. We suggest how the nonlinear response of the interstellar gas, coupled with overlapping subharmonic resonances, might introduce chaotic behavior in the dynamics of the interstellar medium and Population I objects, even though the underlying forces to which they are subject are regular. We then move to a discussion of resonantly forced spiral density waves in a planetary ring and their relationship to the ideas of disk truncation, and the shepherding of narrow rings by satellites orbiting nearby. The back reaction of the rings on the satellites led to the prediction of planet migration in protoplanetary disks, which has had widespread application in the exploding data sets concerning hot Jupiters and extrasolar planetary systems. We then return to the issue of global normal modes in the stellar disk of spiral galaxies and its relationship to the QSSS hypothesis, where the central theoretical concepts involve waves with negative and positive surface densities of energy and angular

Chiralities of spiral waves and their transitions.

Science.gov (United States)

Pan, Jun-ting; Cai, Mei-chun; Li, Bing-wei; Zhang, Hong

2013-06-01

The chiralities of spiral waves usually refer to their rotation directions (the turning orientations of the spiral temporal movements as time elapses) and their curl directions (the winding orientations of the spiral spatial geometrical structures themselves). Traditionally, they are the same as each other. Namely, they are both clockwise or both counterclockwise. Moreover, the chiralities are determined by the topological charges of spiral waves, and thus they are conserved quantities. After the inwardly propagating spirals were experimentally observed, the relationship between the chiralities and the one between the chiralities and the topological charges are no longer preserved. The chiralities thus become more complex than ever before. As a result, there is now a desire to further study them. In this paper, the chiralities and their transition properties for all kinds of spiral waves are systemically studied in the framework of the complex Ginzburg-Landau equation, and the general relationships both between the chiralities and between the chiralities and the topological charges are obtained. The investigation of some other models, such as the FitzHugh-Nagumo model, the nonuniform Oregonator model, the modified standard model, etc., is also discussed for comparison.

Mechanism of spiral formation in heterogeneous discretized excitable media.

Science.gov (United States)

Kinoshita, Shu-ichi; Iwamoto, Mayuko; Tateishi, Keita; Suematsu, Nobuhiko J; Ueyama, Daishin

2013-06-01

Spiral waves on excitable media strongly influence the functions of living systems in both a positive and negative way. The spiral formation mechanism has thus been one of the major themes in the field of reaction-diffusion systems. Although the widely believed origin of spiral waves is the interaction of traveling waves, the heterogeneity of an excitable medium has recently been suggested as a probable cause. We suggest one possible origin of spiral waves using a Belousov-Zhabotinsky reaction and a discretized FitzHugh-Nagumo model. The heterogeneity of the reaction field is shown to stochastically generate unidirectional sites, which can induce spiral waves. Furthermore, we found that the spiral wave vanished with only a small reduction in the excitability of the reaction field. These results reveal a gentle approach for controlling the appearance of a spiral wave on an excitable medium.

SELF-DESTRUCTING SPIRAL WAVES: GLOBAL SIMULATIONS OF A SPIRAL-WAVE INSTABILITY IN ACCRETION DISKS

International Nuclear Information System (INIS)

Bae, Jaehan; Hartmann, Lee; Nelson, Richard P.; Richard, Samuel

2016-01-01

We present results from a suite of three-dimensional global hydrodynamic simulations that shows that spiral density waves propagating in circumstellar disks are unstable to the growth of a parametric instability that leads to break down of the flow into turbulence. This spiral wave instability (SWI) arises from a resonant interaction between pairs of inertial waves, or inertial-gravity waves, and the background spiral wave. The development of the instability in the linear regime involves the growth of a broad spectrum of inertial modes, with growth rates on the order of the orbital time, and results in a nonlinear saturated state in which turbulent velocity perturbations are of a similar magnitude to those induced by the spiral wave. The turbulence induces angular momentum transport and vertical mixing at a rate that depends locally on the amplitude of the spiral wave (we obtain a stress parameter α ∼ 5 × 10 −4 in our reference model). The instability is found to operate in a wide range of disk models, including those with isothermal or adiabatic equations of state, and in viscous disks where the dimensionless kinematic viscosity ν ≤ 10 −5 . This robustness suggests that the instability will have applications to a broad range of astrophysical disk-related phenomena, including those in close binary systems, planets embedded in protoplanetary disks (including Jupiter in our own solar system) and FU Orionis outburst models. Further work is required to determine the nature of the instability and to evaluate its observational consequences in physically more complete disk models than we have considered in this paper.

pH-Dependent spin state population and 19F NMR chemical shift via remote ligand protonation in an iron(ii) complex.

Science.gov (United States)

Gaudette, Alexandra I; Thorarinsdottir, Agnes E; Harris, T David

2017-11-30

An Fe II complex that features a pH-dependent spin state population, by virtue of a variable ligand protonation state, is described. This behavior leads to a highly pH-dependent 19 F NMR chemical shift with a sensitivity of 13.9(5) ppm per pH unit at 37 °C, thereby demonstrating the potential utility of the complex as a 19 F chemical shift-based pH sensor.

Spiral blood flow in aorta-renal bifurcation models.

Science.gov (United States)

Javadzadegan, Ashkan; Simmons, Anne; Barber, Tracie

2016-01-01

The presence of a spiral arterial blood flow pattern in humans has been widely accepted. It is believed that this spiral component of the blood flow alters arterial haemodynamics in both positive and negative ways. The purpose of this study was to determine the effect of spiral flow on haemodynamic changes in aorta-renal bifurcations. In this regard, a computational fluid dynamics analysis of pulsatile blood flow was performed in two idealised models of aorta-renal bifurcations with and without flow diverter. The results show that the spirality effect causes a substantial variation in blood velocity distribution, while causing only slight changes in fluid shear stress patterns. The dominant observed effect of spiral flow is on turbulent kinetic energy and flow recirculation zones. As spiral flow intensity increases, the rate of turbulent kinetic energy production decreases, reducing the region of potential damage to red blood cells and endothelial cells. Furthermore, the recirculation zones which form on the cranial sides of the aorta and renal artery shrink in size in the presence of spirality effect; this may lower the rate of atherosclerosis development and progression in the aorta-renal bifurcation. These results indicate that the spiral nature of blood flow has atheroprotective effects in renal arteries and should be taken into consideration in analyses of the aorta and renal arteries.

Model for the local spiral structure of the galaxy

International Nuclear Information System (INIS)

Humphreys, R.M.

1976-01-01

The spatial distribution of the most luminous stars, associations, clusters, and H II regions in the region l = 270 0 to 30 0 reveal a major spiral arm, Sagittarius-Carina, which can be observed to 9 or 10 kpc from the sun in the direction l = 290 0 to 305 0 . Evidence is also presented for a spur at l = 305 0 to 310 0 on the inner side of the Saggitarius-Carina arm. The noncircular motions observed in the Carina and Sagittarius spiral features agree in both magnitude and direction and support the suggestion that Sagittarius-Carina is a major spiral arm. A model is presented for the local spiral structure with wide, massive, spiral arms which show fragmentation in our region of the Galaxy. On the basis of the optical spiral structure, the Milky Way is an Sc type spiral galaxy, perhaps of the M 101 type

Ablation acceleration of macroparticle in spiral magnetic fields

International Nuclear Information System (INIS)

Ikuta, Kazunari.

1981-05-01

The rocket motion of macroparticles heated by energetic pulses in a spiral magnetic field was studied. The purpose of the present work is to study the ablation acceleration of a macroparticle in a spiral magnetic field with the help of the law of conservation of angular momentum. The basic equation of motion of ablatively accelerated projectile in a spiral magnetic field was derived. Any rocket which is ejecting fully ionized plasma in an intense magnetic field with rotational transform is able to have spin by the law of conservation of momentum. The effect of spiral magnetic field on macroparticle acceleration is discussed. The necessary mass ratio increase exponentially with respect to the field parameter. The spiral field should be employed with care to have only to stabilize the position of macroparticles. As conclusion, it can be said that the ablation acceleration of the projectile in a spiral field can give the accelerated body spin quite easily. (Kato, T.)

Are Elias 2-27's Spiral Arms Driven by Self-gravity, or by a Companion? A Comparative Spiral Morphology Study

Science.gov (United States)

Forgan, Duncan H.; Ilee, John D.; Meru, Farzana

2018-06-01

The spiral waves detected in the protostellar disk surrounding Elias 2-27 have been suggested as evidence of the disk being gravitationally unstable. However, previous work has shown that a massive, stable disk undergoing an encounter with a massive companion are also consistent with the observations. We compare the spiral morphology of smoothed particle hydrodynamic simulations modeling both cases. The gravitationally unstable disk produces symmetric, tightly wound spiral arms with constant pitch angle, as predicted by the literature. The companion disk’s arms are asymmetric, with pitch angles that increase with radius. However, these arms are not well-fitted by standard analytic expressions, due to the high disk mass and relatively low companion mass. We note that differences (or indeed similarities) in morphology between pairs of spirals is a crucial discriminant between scenarios for Elias 2-27, and hence future studies must fit spiral arms individually. If Elias 2-27 continues to show symmetric tightly wound spiral arms in future observations, then we posit that it is the first observed example of a gravitationally unstable protostellar disk.

Planet-driven Spiral Arms in Protoplanetary Disks. II. Implications

Science.gov (United States)

Bae, Jaehan; Zhu, Zhaohuan

2018-06-01

We examine whether various characteristics of planet-driven spiral arms can be used to constrain the masses of unseen planets and their positions within their disks. By carrying out two-dimensional hydrodynamic simulations varying planet mass and disk gas temperature, we find that a larger number of spiral arms form with a smaller planet mass and a lower disk temperature. A planet excites two or more spiral arms interior to its orbit for a range of disk temperatures characterized by the disk aspect ratio 0.04≤slant {(h/r)}p≤slant 0.15, whereas exterior to a planet’s orbit multiple spiral arms can form only in cold disks with {(h/r)}p≲ 0.06. Constraining the planet mass with the pitch angle of spiral arms requires accurate disk temperature measurements that might be challenging even with ALMA. However, the property that the pitch angle of planet-driven spiral arms decreases away from the planet can be a powerful diagnostic to determine whether the planet is located interior or exterior to the observed spirals. The arm-to-arm separations increase as a function of planet mass, consistent with previous studies; however, the exact slope depends on disk temperature as well as the radial location where the arm-to-arm separations are measured. We apply these diagnostics to the spiral arms seen in MWC 758 and Elias 2–27. As shown in Bae et al., planet-driven spiral arms can create concentric rings and gaps, which can produce a more dominant observable signature than spiral arms under certain circumstances. We discuss the observability of planet-driven spiral arms versus rings and gaps.

Improved reconstruction for IDEAL spiral CSI

DEFF Research Database (Denmark)

Hansen, Rie Beck; Mariager, Christian; Laustsen, Christoffer

2017-01-01

In this study we demonstrate how reconstruction for IDEAL spiral CSI (spectroscopic imaging scheme developed for hyperpolarized dynamic metabolic MR imaging) can be improved by using regularization with a sparsity constraint. By exploiting sparsity of the spectral domain, IDEAL spiral CSI can...

Magnetic spiral arms in galaxy haloes

Science.gov (United States)

Henriksen, R. N.

2017-08-01

We seek the conditions for a steady mean field galactic dynamo. The parameter set is reduced to those appearing in the α2 and α/ω dynamo, namely velocity amplitudes, and the ratio of sub-scale helicity to diffusivity. The parameters can be allowed to vary on conical spirals. We analyse the mean field dynamo equations in terms of scale invariant logarithmic spiral modes and special exact solutions. Compatible scale invariant gravitational spiral arms are introduced and illustrated in an appendix, but the detailed dynamical interaction with the magnetic field is left for another work. As a result of planar magnetic spirals `lifting' into the halo, multiple sign changes in average rotation measures forming a regular pattern on each side of the galactic minor axis, are predicted. Such changes have recently been detected in the Continuum Halos in Nearby Galaxies-an EVLA Survey (CHANG-ES) survey.

Kidney spiral CT, indications, realization, results

International Nuclear Information System (INIS)

Braunschweig, R.; Beilicke, M.; Hundt, W.; Breiteneder, T.; Reiser, M.

1999-01-01

The introduction of spiral computed tomography (spiral CT) has vastly enriched the methodologically diversity of computer-tomographic scans. It allows for the recording of different perfusion or excretion stages of the kidney parenchyma of the urine draining paths by carrying out long-distance, phase-identical multiple examinations of the retroperitoneum. The description of the findings which are characterized by their local and contrasts behavior is possible. The following report describes the indications and technological process of kidney spiral CT using kidney-typical intravenous contrast media. Special emphasis is put on the advantages and limits of multiple phase spiral CT. Decisive preconditions are: 1. Specific clinical query, 2. selection of the corresponding phase contrasts of the kidneys and uretra or bladder, 3. exact technical and temporal adjustment of the acquisition parameters. Scanning times are in the range of seconds. The overall examination can be carried out quick and without any major strain on the part of the patient. A sound proof and a general differentiation of focal kideny lesions can be derived from the acquired data. This is also true for kidneys and ureters findings. Bladder findings can be localized and differentiated according to stage. More than two 'spiral acquisitions' should be carried out with restraint taking exposure to radiation into account. Due to the sound registration of focal lesions, its capability of reproduction and its short-time examination, the spiral CT of the kidneys can be said to be the most effective current scanning method of the retroperitoneum following clinical examinations and sonography. (orig.) [de

High-displacement spiral piezoelectric actuators

Science.gov (United States)

Mohammadi, F.; Kholkin, A. L.; Jadidian, B.; Safari, A.

1999-10-01

A high-displacement piezoelectric actuator, employing spiral geometry of a curved piezoelectric strip is described. The monolithic actuators are fabricated using a layered manufacturing technique, fused deposition of ceramics, which is capable of prototyping electroceramic components with complex shapes. The spiral actuators (2-3 cm in diameter) consisted of 4-5 turns of a lead zirconate titanate ceramic strip with an effective length up to 28 cm. The width was varied from 0.9 to 1.75 mm with a height of 3 mm. When driven by the electric field applied across the width of the spiral wall, the tip of the actuator was found to displace in both radial and tangential directions. The tangential displacement of the tip was about 210 μm under the field of 5 kV/cm. Both the displacement and resonant frequency of the spirals could be tailored by changing the effective length and wall width. The blocking force of the actuator in tangential direction was about 1 N under the field of 5 kV/cm. These properties are advantageous for high-displacement low-force applications where bimorph or monomorph actuators are currently employed.

SELF-DESTRUCTING SPIRAL WAVES: GLOBAL SIMULATIONS OF A SPIRAL-WAVE INSTABILITY IN ACCRETION DISKS

Energy Technology Data Exchange (ETDEWEB)

Bae, Jaehan; Hartmann, Lee [Department of Astronomy, University of Michigan, 1085 S. University Ave., Ann Arbor, MI 48109 (United States); Nelson, Richard P.; Richard, Samuel, E-mail: jaehbae@umich.edu, E-mail: lhartm@umich.edu, E-mail: r.p.nelson@qmul.ac.uk, E-mail: samuel.richard@qmul.ac.uk [Astronomy Unit, Queen Mary University of London, Mile End Road, London E1 4NS (United Kingdom)

2016-09-20

We present results from a suite of three-dimensional global hydrodynamic simulations that shows that spiral density waves propagating in circumstellar disks are unstable to the growth of a parametric instability that leads to break down of the flow into turbulence. This spiral wave instability (SWI) arises from a resonant interaction between pairs of inertial waves, or inertial-gravity waves, and the background spiral wave. The development of the instability in the linear regime involves the growth of a broad spectrum of inertial modes, with growth rates on the order of the orbital time, and results in a nonlinear saturated state in which turbulent velocity perturbations are of a similar magnitude to those induced by the spiral wave. The turbulence induces angular momentum transport and vertical mixing at a rate that depends locally on the amplitude of the spiral wave (we obtain a stress parameter α ∼ 5 × 10{sup −4} in our reference model). The instability is found to operate in a wide range of disk models, including those with isothermal or adiabatic equations of state, and in viscous disks where the dimensionless kinematic viscosity ν ≤ 10{sup −5}. This robustness suggests that the instability will have applications to a broad range of astrophysical disk-related phenomena, including those in close binary systems, planets embedded in protoplanetary disks (including Jupiter in our own solar system) and FU Orionis outburst models. Further work is required to determine the nature of the instability and to evaluate its observational consequences in physically more complete disk models than we have considered in this paper.

NMR chemical shift and J coupling parameterization and quantum mechanical reference spectrum simulation for selected nerve agent degradation products in aqueous conditions.

Science.gov (United States)

Koskela, Harri; Anđelković, Boban

2017-10-01

The spectral parameters of selected nerve agent degradation products relevant to the Chemical Weapons Convention, namely, ethyl methylphosphonate, isopropyl methylphosphonate, pinacolyl methylphosphonate and methylphosphonic acid, were studied in wide range of pH conditions and selected temperatures. The pH and temperature dependence of chemical shifts and J couplings was parameterized using Henderson-Hasselbalch-based functions. The obtained parameters allowed calculation of precise chemical shifts and J coupling constants in arbitrary pH conditions and typical measurement temperatures, thus facilitating quantum mechanical simulation of reference spectra in the chosen magnetic field strength for chemical verification. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Mapping the gas-to-dust ratio in the edge-on spiral galaxy IC2531

Science.gov (United States)

Baes, Maarten; Gentile, Gianfranco; Allaert, Flor; Kuno, Nario; Verstappen, Joris

2012-04-01

The gas-to-dust ratio is an important diagnostic of the chemical evolution of galaxies, but unfortunately, there are only a few unbiased studies of the gas-to-dust ratio within galaxies and among different galaxies. We want to take advantage of the revolutionary capabilities of the Herschel Space Observatory and the special geometry of edge-on spiral galaxies to derive accurate gas and dust mass profiles in the edge-on spiral galaxy IC2531, the only southern galaxy from a sample of large edge-on spirals observed with Herschel. We already have a wealth of ancillary data and detailed radiative transfer modelling at our disposal for this galaxy, and now request CO observations to map the molecular gas distribution. With our combined dataset, we will investigate the radial behaviour of the gas-to-dust ratio, compare it with the properties of the stellar population and the dark matter distribution, and test the possibility to use the far-infrared emission from dust to determine the total ISM mass in galaxies.

The dynamics of the spiral galaxy M81

International Nuclear Information System (INIS)

Visser, H.C.D.

1978-01-01

A detailed comparison of the observations of the spiral galaxy M81 with the density-wave theory for tightly-wound spirals is presented. In particular, hydrogen-line observations are compared with the nonlinear density-wave theory for the gas with the aim of constructing a density-wave model for the spiral galaxy M81

SPIRAL2 Week 2012 - Slides of the presentations

International Nuclear Information System (INIS)

Staley, F.; Jacquemet, M.; Lewitowicz, M.; Bertrand, P.; Tuske, O.; Caruso, A.; Leyge, J.F.; Perrot, L.; Di Giacomo, M.; Ausset, P.; Moscatello, M.H.; Savalle, A.; Rannou, B.; Lambert, M.; Petit, E.; Hulin, X.; Barre-Boscher, N.; Tusseau-Nenez, S.; Tecchio, L.B.

2013-01-01

The main goal of the 5. edition of the SPIRAL2 Week is to present and discuss the current status of the SPIRAL2 project in front of a large community of scientists and engineers. The program of the meeting will include presentations on scientific and technical developments related to the baseline project, experiments and theory. The main topics to be discussed at the conference are: -) physics and detectors at SPIRAL2, -) driver accelerators, -) production of radioactive ion beams (RIB), -) safety, -) buildings and infrastructure, -) RIB facilities worldwide, and -) SPIRAL2 preparatory phase. This document is made up of the slides of the presentations

Safe Control for Spiral Recovery of Unmanned Aerial Vehicle

Directory of Open Access Journals (Sweden)

Chang-Jian Ru

2014-01-01

Full Text Available With unmanned aerial vehicles (UAVs widely used in both military and civilian fields, many events affecting their safe flying have emerged. That UAV’s entering into the spiral is such a typical safety issue. To solve this safety problem, a novel recovery control approach is proposed. First, the factors of spiral are analyzed. Then, based on control scheduling of state variables and nonlinear dynamic inversion control laws, the spiral recovery controller is designed to accomplish guidance and control of spiral recovery. Finally, the simulation results have illustrated that the proposed control method can ensure the UAV autonomous recovery from spiral effectively.

ANGULAR-MOMENTUM IN BINARY SPIRAL GALAXIES

NARCIS (Netherlands)

OOSTERLOO, T

In order to investigate the relative orientations of spiral galaxies in pairs, the distribution of the angle between the spin-vectors for a new sample of 40 binary spiral galaxies is determined. From this distribution it is found, contrary to an earlier result obtained by Helou (1984), that there is

Galaxy Zoo: constraining the origin of spiral arms

Science.gov (United States)

Hart, Ross E.; Bamford, Steven P.; Keel, William C.; Kruk, Sandor J.; Masters, Karen L.; Simmons, Brooke D.; Smethurst, Rebecca J.

2018-05-01

Since the discovery that the majority of low-redshift galaxies exhibit some level of spiral structure, a number of theories have been proposed as to why these patterns exist. A popular explanation is a process known as swing amplification, yet there is no observational evidence to prove that such a mechanism is at play. By using a number of measured properties of galaxies, and scaling relations where there are no direct measurements, we model samples of SDSS and S4G spiral galaxies in terms of their relative halo, bulge and disc mass and size. Using these models, we test predictions of swing amplification theory with respect to directly measured spiral arm numbers from Galaxy Zoo 2. We find that neither a universal cored or cuspy inner dark matter profile can correctly predict observed numbers of arms in galaxies. However, by invoking a halo contraction/expansion model, a clear bimodality in the spiral galaxy population emerges. Approximately 40 per cent of unbarred spiral galaxies at z ≲ 0.1 and M* ≳ 1010M⊙ have spiral arms that can be modelled by swing amplification. This population display a significant correlation between predicted and observed spiral arm numbers, evidence that they are swing amplified modes. The remainder are dominated by two-arm systems for which the model predicts significantly higher arm numbers. These are likely driven by tidal interactions or other mechanisms.

Pulsatile spiral blood flow through arterial stenosis.

Science.gov (United States)

Linge, Fabian; Hye, Md Abdul; Paul, Manosh C

2014-11-01

Pulsatile spiral blood flow in a modelled three-dimensional arterial stenosis, with a 75% cross-sectional area reduction, is investigated by using numerical fluid dynamics. Two-equation k-ω model is used for the simulation of the transitional flow with Reynolds numbers 500 and 1000. It is found that the spiral component increases the static pressure in the vessel during the deceleration phase of the flow pulse. In addition, the spiral component reduces the turbulence intensity and wall shear stress found in the post-stenosis region of the vessel in the early stages of the flow pulse. Hence, the findings agree with the results of Stonebridge et al. (2004). In addition, the results of the effects of a spiral component on time-varying flow are presented and discussed along with the relevant pathological issues.

Planet-driven Spiral Arms in Protoplanetary Disks. I. Formation Mechanism

Science.gov (United States)

Bae, Jaehan; Zhu, Zhaohuan

2018-06-01

Protoplanetary disk simulations show that a single planet can excite more than one spiral arm, possibly explaining the recent observations of multiple spiral arms in some systems. In this paper, we explain the mechanism by which a planet excites multiple spiral arms in a protoplanetary disk. Contrary to previous speculations, the formation of both primary and additional arms can be understood as a linear process when the planet mass is sufficiently small. A planet resonantly interacts with epicyclic oscillations in the disk, launching spiral wave modes around the Lindblad resonances. When a set of wave modes is in phase, they can constructively interfere with each other and create a spiral arm. More than one spiral arm can form because such constructive interference can occur for different sets of wave modes, with the exact number and launching position of the spiral arms being dependent on the planet mass as well as the disk temperature profile. Nonlinear effects become increasingly important as the planet mass increases, resulting in spiral arms with stronger shocks and thus larger pitch angles. This is found to be common for both primary and additional arms. When a planet has a sufficiently large mass (≳3 thermal masses for (h/r) p = 0.1), only two spiral arms form interior to its orbit. The wave modes that would form a tertiary arm for smaller mass planets merge with the primary arm. Improvements in our understanding of the formation of spiral arms can provide crucial insights into the origin of observed spiral arms in protoplanetary disks.

Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

Science.gov (United States)

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.

Pathomorphism of spiral tibial fractures in computed tomography imaging.

Science.gov (United States)

Guzik, Grzegorz

2011-01-01

Spiral fractures of the tibia are virtually homogeneous with regard to their pathomorphism. The differences that are seen concern the level of fracture of the fibula, and, to a lesser extent, the level of fracture of the tibia, the length of fracture cleft, and limb shortening following the trauma. While conventional radiographs provide sufficient information about the pathomorphism of fractures, computed tomography can be useful in demonstrating the spatial arrangement of bone fragments and topography of soft tissues surrounding the fracture site. Multiple cross-sectional computed tomography views of spiral fractures of the tibia show the details of the alignment of bone chips at the fracture site, axis of the tibial fracture cleft, and topography of soft tissues that are not visible on standard radiographs. A model of a spiral tibial fracture reveals periosteal stretching with increasing spiral and longitudinal displacement. The cleft in tibial fractures has a spiral shape and its line is invariable. Every spiral fracture of both crural bones results in extensive damage to the periosteum and may damage bellies of the long flexor muscle of toes, flexor hallucis longus as well as the posterior tibial muscle. Computed tomography images of spiral fractures of the tibia show details of damage that are otherwise invisible on standard radiographs. Moreover, CT images provide useful information about the spatial location of the bone chips as well as possible threats to soft tissues that surround the fracture site. Every spiral fracture of the tibia is associated with disruption of the periosteum. 1. Computed tomography images of spiral fractures of the tibia show details of damage otherwise invisible on standard radiographs, 2. The sharp end of the distal tibial chip can damage the tibialis posterior muscle, long flexor muscles of the toes and the flexor hallucis longus, 3. Every spiral fracture of the tibia is associated with disruption of the periosteum.

Profiles of the stochastic star formation process in spiral galaxies

International Nuclear Information System (INIS)

Comins, N.

1981-01-01

The formation of spiral arms in disc galaxies is generally attributed to the effects of spiral density waves. These relatively small (i.e. 5 per cent) non-axisymmetric perturbations of the interstellar medium cause spiral arms highlighted by O and B type stars to be created. In this paper another mechanism for spiral arm formation, the stochastic self-propagating star formation (SSPSF) process is examined. The SSPSF process combines the theory that shock waves from supernovae will compress the interstellar medium to create new stars, some of which will be massive enough to also supernova, with a disc galaxy's differential rotation to create spiral arms. The present work extends this process to the case where the probability of star formation from supernova shocks decreases with galactic radius. Where this work and previous investigations overlap (namely the uniform probability case), the agreement is very good, pretty spirals with various numbers of arms are generated. The decreasing probability cases, taken to vary as rsup(-j), still form spiral arms for 0 1.5 the spiral structure is essentially non-existent. (author)

Benchmarking Hydrogen and Carbon NMR Chemical Shifts at HF, DFT, and MP2 Levels.

Science.gov (United States)

Flaig, Denis; Maurer, Marina; Hanni, Matti; Braunger, Katharina; Kick, Leonhard; Thubauville, Matthias; Ochsenfeld, Christian

2014-02-11

An extensive study of error distributions for calculating hydrogen and carbon NMR chemical shifts at Hartree-Fock (HF), density functional theory (DFT), and Møller-Plesset second-order perturbation theory (MP2) levels is presented. Our investigation employs accurate CCSD(T)/cc-pVQZ calculations for providing reference data for 48 hydrogen and 40 carbon nuclei within an extended set of chemical compounds covering a broad range of the NMR scale with high relevance to chemical applications, especially in organic chemistry. Besides the approximations of HF, a variety of DFT functionals, and conventional MP2, we also present results with respect to a spin component-scaled MP2 (GIAO-SCS-MP2) approach. For each method, the accuracy is analyzed in detail for various basis sets, allowing identification of efficient combinations of method and basis set approximations.

The spinning ball spiral

International Nuclear Information System (INIS)

Dupeux, Guillaume; Le Goff, Anne; Quere, David; Clanet, Christophe

2010-01-01

We discuss the trajectory of a fast revolving solid ball moving in a fluid of comparable density. As the ball slows down owing to drag, its trajectory follows an exponential spiral as long as the rotation speed remains constant: at the characteristic distance L where the ball speed is significantly affected by the drag, the bending of the trajectory increases, surprisingly. Later, the rotation speed decreases, which makes the ball follow a second kind of spiral, also described in the paper. Finally, the use of these highly curved trajectories is shown to be relevant to sports.

The handedness of historiated spiral columns.

Science.gov (United States)

Couzin, Robert

2017-09-01

Trajan's Column in Rome (AD 113) was the model for a modest number of other spiral columns decorated with figural, narrative imagery from antiquity to the present day. Most of these wind upwards to the right, often with a congruent spiral staircase within. A brief introductory consideration of antique screw direction in mechanical devices and fluted columns suggests that the former may have been affected by the handedness of designers and the latter by a preference for symmetry. However, for the historiated columns that are the main focus of this article, the determining factor was likely script direction. The manner in which this operated is considered, as well as competing mechanisms that might explain exceptions. A related phenomenon is the reversal of the spiral in a non-trivial number of reproductions of the antique columns, from Roman coinage to Renaissance and baroque drawings and engravings. Finally, the consistent inattention in academic literature to the spiral direction of historiated columns and the repeated publication of erroneous earlier reproductions warrants further consideration.

Spiral CT: An innovative method of volumetric recording. Pt. 1

International Nuclear Information System (INIS)

Kalender, W.A.; Vock, P.; Polacin, A.; Soucek, M.

1990-01-01

A major advance in the field of CT diagnosis has been made with the development of spiral computed tomography. It permits a complete photographic recording of volumes in such a way that even 'minor' pathological changes can be detected and reconstructed providing the absence of respiration-induced organ displacement. During one session, in which up to 24 360deg scans may be obtained within 24 seconds, the patient is continuously shifted at a speed of 10 mm/s, which permits the volumes recorded to be increased up to a height of 24 cm. The underlying methodology is described, as is the procedure to be used in the reconstruction of planar pictures from the volumes recorded. (orig./GDG) [de

Analysis of spiral components in 16 galaxies

International Nuclear Information System (INIS)

Considere, S.; Athanassoula, E.

1988-01-01

A Fourier analysis of the intensity distributions in the plane of 16 spiral galaxies of morphological types from 1 to 7 is performed. The galaxies processed are NGC 300,598,628,2403,2841,3031,3198,3344,5033,5055,5194,5247,6946,7096,7217, and 7331. The method, mathematically based upon a decomposition of a distribution into a superposition of individual logarithmic spiral components, is first used to determine for each galaxy the position angle PA and the inclination ω of the galaxy plane onto the sky plane. Our results, in good agreement with those issued from different usual methods in the literature, are discussed. The decomposition of the deprojected galaxies into individual spiral components reveals that the two-armed component is everywhere dominant. Our pitch angles are then compared to the previously published ones and their quality is checked by drawing each individual logarithmic spiral on the actual deprojected galaxy images. Finally, the surface intensities for angular periodicities of interest are calculated. A choice of a few of the most important ones is used to elaborate a composite image well representing the main spiral features observed in the deprojected galaxies

Single-shot spiral imaging at 7 T.

Science.gov (United States)

Engel, Maria; Kasper, Lars; Barmet, Christoph; Schmid, Thomas; Vionnet, Laetitia; Wilm, Bertram; Pruessmann, Klaas P

2018-03-25

The purpose of this work is to explore the feasibility and performance of single-shot spiral MRI at 7 T, using an expanded signal model for reconstruction. Gradient-echo brain imaging is performed on a 7 T system using high-resolution single-shot spiral readouts and half-shot spirals that perform dual-image acquisition after a single excitation. Image reconstruction is based on an expanded signal model including the encoding effects of coil sensitivity, static off-resonance, and magnetic field dynamics. The latter are recorded concurrently with image acquisition, using NMR field probes. The resulting image resolution is assessed by point spread function analysis. Single-shot spiral imaging is achieved at a nominal resolution of 0.8 mm, using spiral-out readouts of 53-ms duration. High depiction fidelity is achieved without conspicuous blurring or distortion. Effective resolutions are assessed as 0.8, 0.94, and 0.98 mm in CSF, gray matter and white matter, respectively. High image quality is also achieved with half-shot acquisition yielding image pairs at 1.5-mm resolution. Use of an expanded signal model enables single-shot spiral imaging at 7 T with unprecedented image quality. Single-shot and half-shot spiral readouts deploy the sensitivity benefit of high field for rapid high-resolution imaging, particularly for functional MRI and arterial spin labeling. © 2018 International Society for Magnetic Resonance in Medicine.

Hermite-Gaussian beams with self-forming spiral phase distribution

Science.gov (United States)

Zinchik, Alexander A.; Muzychenko, Yana B.

2014-05-01

Spiral laser beams is a family of laser beams that preserve the structural stability up to scale and rotate with the propagation. Properties of spiral beams are of practical interest for laser technology, medicine and biotechnology. Researchers use a spiral beams for movement and manipulation of microparticles. Spiral beams have a complicated phase distribution in cross section. This paper describes the results of analytical and computer simulation of Hermite-Gaussian beams with self-forming spiral phase distribution. In the simulation used a laser beam consisting of the sum of the two modes HG TEMnm and TEMn1m1. The coefficients n1, n, m1, m were varied. Additional phase depending from the coefficients n, m, m1, n1 imposed on the resulting beam. As a result, formed the Hermite Gaussian beam phase distribution which takes the form of a spiral in the process of distribution. For modeling was used VirtualLab 5.0 (manufacturer LightTrans GmbH).

Spiral modes in cold cylindrical systems

International Nuclear Information System (INIS)

Robe, H.

1975-01-01

The linearized hydrodynamical equations governing the non-axisymmetric free modes of oscillation of cold cylindrical stellar systems are separated in cylindrical coordinates and solved numerically for two models. Short-wavelength unstable modes corresponding to tight spirals do not exist; but there exists an unstable growing mode which has the form of trailing spirals which are quite open. (orig.) [de

Colours and morphology of spiral galaxies

International Nuclear Information System (INIS)

Wyse, R.F.G.

1981-01-01

Tinsley has proposed that late-type spirals have relatively more non-luminous material than early-type spirals. A re-examination of the data indicates that this proposal is equally consistent with dark matter being more dominant in barred galaxies than in unbarred galaxies. Neither conclusion can be firm, since the dataset is far from ideal. (author)

Optical and theoretical studies of giant clouds in spiral galaxies

International Nuclear Information System (INIS)

Elmegreen, B.G.; Elmegreen, D.M.

1980-01-01

An optical study of four spiral galaxies, combined with radiative transfer models for transmitted and scattered light, has led to a determination of the opacities and masses of numerous dark patches and dust lanes that outline spiral structure. The observed compression factors for the spiral-like dust lanes are in accord with expectations from the theory of gas flow in spiral density waves. Several low density (10 2 cm -3 ) clouds containing 10 6 to 10 7 solar masses were also studied. These results are discussed in terms of recent theoretical models of cloud and star formation in spiral galaxies. The long-term evolution of giant molecular clouds is shown to have important consequences for the positions and ages of star formation sites in spiral arms. (Auth.)

Neutral hydrogen and spiral structure in M33

International Nuclear Information System (INIS)

Newton, K.

1980-01-01

Observations of neutral hydrogen (H I) in the galaxy M33 are presented which have sufficient angular resolution (47 x 93 arcsec) to distinguish detailed H I spiral structure for the first time. H I spiral features extend over the entire disc; the pattern is broken and multi-armed with the best-defined arms lying at radii outside the brightest optical features. Several very narrow spiral 'filaments' are unresolved by the beam, implying true widths -1 , is perturbed near the inner spiral arms. These perturbations agree with the predictions of density-wave theory but may simply arise from the self-gravity of massive arms whether or not they are a quasi-stationary wave phenomenon. If the outer spiral features form a rigidly rotating density-wave pattern, the absence of large radial streaming motions along the features implies a small pattern speed ( -1 kpc -1 ), with corotation in the outer parts of the disc. (author)

The effect of pitch in multislice spiral/helical CT

International Nuclear Information System (INIS)

Wang, G.; Vannier, M.W.

2000-01-01

The purpose of this study is to understand the effect of pitch on raw data interpolation in multislice spiral/helical computed tomography (CT) and provide guidelines for scanner design and protocol optimization. Multislice spiral CT is mainly characterized by the three parameters: the number of detector arrays, the detector collimation, and the table increment per x-ray source rotation. The pitch in multislice spiral CT is defined as the ratio of the table increment over the detector collimation in this study. In parallel to the current framework for studying longitudinal image resolution, the central fan-beam rays of direct and opposite directions are considered, assuming a narrow cone-beam angle. Generally speaking, sampling in the Radon domain by the direct and opposite central rays is nonuniform along the longitudinal axis. Using a recently developed methodology for quantifying the sensibility of signal reconstruction from non-uniformly sampled finite points, the effect of pitch on raw data interpolation is analyzed in multislice spiral CT. Unlike single-slice spiral CT, in which image quality decreases monotonically as the pitch increases, the sensibility of raw data interpolation in multislice spiral CT increases, suggesting that image quality does not decrease monotonically in this case. The most favorable pitch can be found from the sensitivity-slice spiral CT is provided. The study on the effect of pitch using the sensitivity analysis approach reveals the fundamental characteristics of raw data interpolation in multislice spiral CT, and gives insights into interaction between pitch and image quality. These results may be valuable for design of multislice spiral CT scanners and imaging protocol optimization in clinical applications. (authors)

Optimal voxel size for measuring global gray and white matter proton metabolite concentrations using chemical shift imaging

DEFF Research Database (Denmark)

Hanson, Lars Peter Grüner; Adalsteinsson, E; Pfefferbaum, A

2000-01-01

Quantification of gray and white matter levels of spectroscopically visible metabolites can provide important insights into brain development and pathological conditions. Chemical shift imaging offers a gain in efficiency for estimation of global gray and white matter metabolite concentrations co...

Influence of excitability on unpinning and termination of spiral waves.

Science.gov (United States)

Luengviriya, Jiraporn; Sutthiopad, Malee; Phantu, Metinee; Porjai, Porramain; Kanchanawarin, Jarin; Müller, Stefan C; Luengviriya, Chaiya

2014-11-01

Application of electrical forcing to release pinned spiral waves from unexcitable obstacles and to terminate the rotation of free spiral waves at the boundary of excitable media has been investigated in thin layers of the Belousov-Zhabotinsky (BZ) reaction, prepared with different initial concentrations of H_{2}SO_{4}. Increasing [H_{2}SO_{4}] raises the excitability of the reaction and reduces the core diameter of free spiral waves as well as the wave period. An electric current with density stronger than a critical value Junpin causes a pinned spiral wave to drift away from the obstacle. For a given obstacle size, Junpin increases with [H_{2}SO_{4}]. Under an applied electrical current, the rotation center of a free spiral wave drifts along a straight path to the boundary. When the current density is stronger than a critical value Jterm, the spiral tip is forced to hit the boundary, where the spiral wave is terminated. Similar to Junpin for releasing a pinned spiral wave, Jterm also increases with [H_{2}SO_{4}]. These experimental findings were confirmed by numerical simulations using the Oregonator model, in which the excitability was adjusted via the ratio of the excitation rate to the recovery rate of the BZ reaction. Therefore, our investigation shows that decreasing the excitability can facilitate elimination of spiral waves by electrical forcing, either in the presence of obstacles or not.

THE STRUCTURE OF SPIRAL SHOCKS EXCITED BY PLANETARY-MASS COMPANIONS

International Nuclear Information System (INIS)

Zhu, Zhaohuan; Stone, James M.; Rafikov, Roman R.; Dong, Ruobing

2015-01-01

Direct imaging observations have revealed spiral structures in protoplanetary disks. Previous studies have suggested that planet-induced spiral arms cannot explain some of these spiral patterns, due to the large pitch angle and high contrast of the spiral arms in observations. We have carried out three-dimensional (3D) hydrodynamical simulations to study spiral wakes/shocks excited by young planets. We find that, in contrast with linear theory, the pitch angle of spiral arms does depend on the planet mass, which can be explained by the nonlinear density wave theory. A secondary (or even a tertiary) spiral arm, especially for inner arms, is also excited by a massive planet. With a more massive planet in the disk, the excited spiral arms have larger pitch angle and the separation between the primary and secondary arms in the azimuthal direction is also larger. We also find that although the arms in the outer disk do not exhibit much vertical motion, the inner arms have significant vertical motion, which boosts the density perturbation at the disk atmosphere. Combining hydrodynamical models with Monte-Carlo radiative transfer calculations, we find that the inner spiral arms are considerably more prominent in synthetic near-IR images using full 3D hydrodynamical models than images based on two-dimensional models assuming vertical hydrostatic equilibrium, indicating the need to model observations with full 3D hydrodynamics. Overall, companion-induced spiral arms not only pinpoint the companion’s position but also provide three independent ways (pitch angle, separation between two arms, and contrast of arms) to constrain the companion’s mass

THE STRUCTURE OF SPIRAL SHOCKS EXCITED BY PLANETARY-MASS COMPANIONS

Energy Technology Data Exchange (ETDEWEB)

Zhu, Zhaohuan; Stone, James M.; Rafikov, Roman R. [Department of Astrophysical Sciences, 4 Ivy Lane, Peyton Hall, Princeton University, Princeton, NJ 08544 (United States); Dong, Ruobing, E-mail: zhzhu@astro.princeton.edu, E-mail: rdong2013@berkeley.edu [Lawrence Berkeley National Lab, Berkeley, CA 94720 (United States)

2015-11-10

Direct imaging observations have revealed spiral structures in protoplanetary disks. Previous studies have suggested that planet-induced spiral arms cannot explain some of these spiral patterns, due to the large pitch angle and high contrast of the spiral arms in observations. We have carried out three-dimensional (3D) hydrodynamical simulations to study spiral wakes/shocks excited by young planets. We find that, in contrast with linear theory, the pitch angle of spiral arms does depend on the planet mass, which can be explained by the nonlinear density wave theory. A secondary (or even a tertiary) spiral arm, especially for inner arms, is also excited by a massive planet. With a more massive planet in the disk, the excited spiral arms have larger pitch angle and the separation between the primary and secondary arms in the azimuthal direction is also larger. We also find that although the arms in the outer disk do not exhibit much vertical motion, the inner arms have significant vertical motion, which boosts the density perturbation at the disk atmosphere. Combining hydrodynamical models with Monte-Carlo radiative transfer calculations, we find that the inner spiral arms are considerably more prominent in synthetic near-IR images using full 3D hydrodynamical models than images based on two-dimensional models assuming vertical hydrostatic equilibrium, indicating the need to model observations with full 3D hydrodynamics. Overall, companion-induced spiral arms not only pinpoint the companion’s position but also provide three independent ways (pitch angle, separation between two arms, and contrast of arms) to constrain the companion’s mass.

Study of chemical shifts of the chloroform complexes with cyclic donors of electrons

International Nuclear Information System (INIS)

Blaszkiewicz, B.; Pajak, Z.

1973-01-01

Chemical shifts of chloroform complexes with the heterocyclic electron donors: pyridine, piperidine, alpha-picoline and gamma-picoline have been studied using the high resolution (5.10 -9 ) spectrometer operating at 80 MHz. An attempt has also been made to study the three - component solutions of : chloroform, a heterocyclic donor of electrons and carbon tetrachloride. The results, which have been obtained, indicate that the complex-forming power of pyridine and other electron donors is greater in carbon tetrachloride than in other solvents. (S.B.)

Coronary artery atherosclerosis associated with shift work in chemical plant workers by using coronary CT angiography.

Science.gov (United States)

Kang, WonYang; Park, Won-Ju; Jang, Keun-Ho; Kim, Soo-Hyeon; Gwon, Do-Hyeong; Lim, Hyeong-Min; Ahn, Ji-Sung; Moon, Jai-Dong

2016-08-01

The aim of this study was to investigate whether shift work is related to elevated risk of coronary artery disease (CAD) by determining the coronary artery calcium (CAC) score and the presence of coronary artery stenosis by using coronary artery CT angiography (CCTA). In this study, 110 male workers participated and underwent a CCTA examination for CAC scoring, which represents coronary artery plaque, and were evaluated for luminal stenosis. All of the participants were working in the same chemical plant, of whom 70 worked day shifts and 40 worked rotating shifts. In a multivariate logistic regression analysis, including age, smoking status, alcohol consumption, regular exercise and waist circumference, shift work was associated with a 2.89-fold increase in the odds of developing coronary plaque compared with day work (OR, 2.89; 95% CI 1.07 to 7.82). The association between shift work and coronary plaque was strong after adjustment for age, low-density lipoprotein cholesterol, hypertension and diabetes mellitus (OR, 2.92; 95% CI 1.02 to 8.33). In addition, the number of years of shift work employment was associated with coronary plaque. However, no association was found between shift work and coronary artery stenosis. Shift work could induce CAD onset via the atherosclerotic process, and shift work employment duration was associated with an increased risk of atherosclerosis in male workers. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

CHARACTERISTICS OF SPIRAL ARMS IN LATE-TYPE GALAXIES

International Nuclear Information System (INIS)

Honig, Z. N.; Reid, M. J.

2015-01-01

We have measured the positions of large numbers of H II regions in four nearly face-on, late-type, spiral galaxies: NGC 628 (M74), NGC 1232, NGC 3184, and NGC 5194 (M51). Fitting log-periodic spiral models to segments of each arm yields local estimates of spiral pitch angle and arm width. While pitch angles vary considerably along individual arms, among arms within a galaxy, and among galaxies, we find no systematic trend with galactocentric distance. We estimate the widths of the arm segments from the scatter in the distances of the H II regions from the spiral model. All major arms in these galaxies show spiral arm width increasing with distance from the galactic center, similar to the trend seen in the Milky Way. However, in the outermost parts of the galaxies, where massive star formation declines, some arms reverse this trend and narrow. We find that spiral arms often appear to be composed of segments of ∼5 kpc length, which join to form kinks and abrupt changes in pitch angle and arm width; these characteristics are consistent with properties seen in the large N-body simulations of D'Onghia et al. and others

Using 1H and 13C NMR chemical shifts to determine cyclic peptide conformations: a combined molecular dynamics and quantum mechanics approach.

Science.gov (United States)

Nguyen, Q Nhu N; Schwochert, Joshua; Tantillo, Dean J; Lokey, R Scott

2018-05-10

Solving conformations of cyclic peptides can provide insight into structure-activity and structure-property relationships, which can help in the design of compounds with improved bioactivity and/or ADME characteristics. The most common approaches for determining the structures of cyclic peptides are based on NMR-derived distance restraints obtained from NOESY or ROESY cross-peak intensities, and 3J-based dihedral restraints using the Karplus relationship. Unfortunately, these observables are often too weak, sparse, or degenerate to provide unequivocal, high-confidence solution structures, prompting us to investigate an alternative approach that relies only on 1H and 13C chemical shifts as experimental observables. This method, which we call conformational analysis from NMR and density-functional prediction of low-energy ensembles (CANDLE), uses molecular dynamics (MD) simulations to generate conformer families and density functional theory (DFT) calculations to predict their 1H and 13C chemical shifts. Iterative conformer searches and DFT energy calculations on a cyclic peptide-peptoid hybrid yielded Boltzmann ensembles whose predicted chemical shifts matched the experimental values better than any single conformer. For these compounds, CANDLE outperformed the classic NOE- and 3J-coupling-based approach by disambiguating similar β-turn types and also enabled the structural elucidation of the minor conformer. Through the use of chemical shifts, in conjunction with DFT and MD calculations, CANDLE can help illuminate conformational ensembles of cyclic peptides in solution.

Is the Lamb shift chemically significant?

Science.gov (United States)

Dyall, Kenneth G.; Bauschlicher, Charles W., Jr.; Schwenke, David W.; Pyykko, Pekka; Arnold, James (Technical Monitor)

2001-01-01

The contribution of the Lamb shift to the atomization energies of some prototype molecules, BF3, AlF3, and GaF3, is estimated by a perturbation procedure. It is found to be in the range of 3-5% of the one-electron scalar relativistic contribution to the atomization energy. The maximum absolute value is 0.2 kcal/mol for GaF3. These sample calculations indicate that the Lamb shift is probably small enough to be neglected for energetics of molecules containing light atoms if the target accuracy is 1 kcal/mol, but for higher accuracy calculations and for molecules containing heavy elements it must be considered.

Investigation of spiral blood flow in a model of arterial stenosis.

Science.gov (United States)

Paul, Manosh C; Larman, Arkaitz

2009-11-01

The spiral component of blood flow has both beneficial and detrimental effects in human circulatory system [Stonebridge PA, Brophy CM. Spiral laminar flow in arteries? Lancet 1991; 338: 1360-1]. We investigate the effects of the spiral blood flow in a model of three-dimensional arterial stenosis with a 75% cross-sectional area reduction at the centre by means of computational fluid dynamics (CFD) techniques. The standard k-omega model is employed for simulation of the blood flow for the Reynolds number of 500 and 1000. We find that for Re=500 the spiral component of the blood flow increases both the total pressure and velocity of the blood, and some significant differences are found between the wall shear stresses of the spiral and non-spiral induced flow downstream of the stenosis. The turbulent kinetic energy is reduced by the spiral flow as it induces the rotational stabilities in the forward flow. For Re=1000 the tangential component of the blood velocity is most influenced by the spiral speed, but the effect of the spiral flow on the centreline turbulent kinetic energy and shear stress is mild. The results of the effects of the spiral flow are discussed in the paper along with the relevant pathological issues.

Non-local coexistence of multiple spiral waves with independent frequencies

International Nuclear Information System (INIS)

Zhan Meng; Luo Jinming

2009-01-01

The interactions of several spiral waves with different independent rotation frequencies are studied in a model of two-dimensional complex Ginzburg-Laudau equation. We find a general coexistence phenomenon, non-local non-phase-locking-invasion coexistence, that is, the non-slowest spiral wave can survive and not be killed by the fastest spiral wave as it is insulated from the fastest one with the sacrifice of the slowest one, which stays in the spatial position between the fastest spiral and the non-slowest one. Both the parameter non-monotonicity and the non-phase-locking invasion between the fastest and the slowest spiral waves play key roles in this phenomenon. Importantly, the results could give a general idea for extensively observed coexistence of spiral waves in various inhomogeneous circumstances.

Magnetization reversal in ferromagnetic spirals via domain wall motion

Science.gov (United States)

Schumm, Ryan D.; Kunz, Andrew

2016-11-01

Domain wall dynamics have been investigated in a variety of ferromagnetic nanostructures for potential applications in logic, sensing, and recording. We present a combination of analytic and simulated results describing the reliable field driven motion of a domain wall through the arms of a ferromagnetic spiral nanowire. The spiral geometry is capable of taking advantage of the benefits of both straight and circular wires. Measurements of the in-plane components of the spirals' magnetization can be used to determine the angular location of the domain wall, impacting the magnetoresistive applications dependent on the domain wall location. The spirals' magnetization components are found to depend on the spiral parameters: the initial radius and spacing between spiral arms, along with the domain wall location. The magnetization is independent of the parameters of the rotating field used to move the domain wall, and therefore the model is valid for current induced domain wall motion as well. The speed of the domain wall is found to depend on the frequency of the rotating driving field, and the domain wall speeds can be reliably varied over several orders of magnitude. We further demonstrate a technique capable of injecting multiple domain walls and show the reliable and unidirectional motion of domain walls through the arms of the spiral.

Molecular clouds and galactic spiral structure

International Nuclear Information System (INIS)

Dame, T.M.

1984-02-01

Galactic CO line emission at 115 GHz was surveyed in order to study the distribution of molecular clouds in the inner galaxy. Comparison of this survey with similar H1 data reveals a detailed correlation with the most intense 21 cm features. To each of the classical 21 cm H1 spiral arms of the inner galaxy there corresponds a CO molecular arm which is generally more clearly defined and of higher contrast. A simple model is devised for the galactic distribution of molecular clouds. The modeling results suggest that molecular clouds are essentially transient objects, existing for 15 to 40 million years after their formation in a spiral arm, and are largely confined to spiral features about 300 pc wide

Spiral CT manifestations of spherical pneumonia

International Nuclear Information System (INIS)

Li Xiaohong; Yang Hongwei; Xu Chunmin; Qin Xiu

2008-01-01

Objective: To explore the Spiral CT manifestations and differential diagnosis of spherical pneumonia. Methods: 18 cases of spherical pneumonia and 20 cases of peripheral pulmonary carcinoma were selected, both of them were confirmed by clinic and/or pathology. The SCT findings of both groups were compared retrospectively. Results: Main spiral CT findings of spherical pneumonia were showed as followings: square or triangular lesions adjacent to pleura; with irregular shape, blurry, slightly lobulated margin, sometimes with halo sign. Small inflammatory patches and intensified vascular markings around the lesions were seen. Lesions became smaller or vanished after short-term anti-inflammatory treatment. Conclusion: Spherical pneumonia showed some characteristics on Spiral CT scan, which are helpful in diagnosis and differential diagnosis of this disease. (authors)

Diffusion-weighted imaging of the liver at 3 T using section-selection gradient reversal: emphasis on chemical shift artefacts and lesion conspicuity

International Nuclear Information System (INIS)

Lee, J.S.; Kim, Y.K.; Jeong, W.K.; Choi, D.; Lee, W.J.

2015-01-01

Aim: To assess the value of section-selection gradient reversal (SSGR) in liver diffusion-weighted imaging (DWI) by comparing it to conventional DWI with an emphasis on chemical shift artefacts and lesion conspicuity. Materials and methods: Forty-eight patients (29 men and 19 women; age range 33–80 years) with 48 liver lesions underwent two DWI examinations using spectral presaturation with inversion recovery fat suppression with and without SSGR at 3 T. Two reviewers evaluated each DWI (b = 100 and b = 800 image) with respect to chemical shift artefacts and liver lesion conspicuity using five-point scales and performed pairwise comparisons between the two DWIs. The signal-to-noise ratio (SNR) of the liver and the lesion and the lesion–liver contrast-to-noise ratio (CNR) were also calculated. Results: SSGR-DWI was significantly better than conventional DWI with respect to chemical shift artefacts and lesion conspicuity in both separate reviews and pairwise comparisons (p < 0.05). There were significant differences in the SNR of the liver (b = 100 and b = 800 images) and lesion (b = 800) between SSGR-DWI and conventional DWI (p < 0.05). Conclusion: Applying the SSGR method to DWI using SPIR fat suppression at 3 T could significantly reduce chemical shift artefacts without incurring additional acquisition time or SNR penalties, which leads to increased conspicuity of focal liver lesions. - Highlights: • Chemical shift artefact in liver DWI is markedly decreased by applying SSGR. • Liver lesion conspicuity is improved by applying SSGR to DWI. • In SNR of the liver, SSGR-DWI is better than conventional DWI

Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction

International Nuclear Information System (INIS)

Lehtivarjo, Juuso; Tuppurainen, Kari; Hassinen, Tommi; Laatikainen, Reino; Peräkylä, Mikael

2012-01-01

While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1 H chemical shifts in which molecular motions, the 4th dimension, were modeled using molecular dynamics (MD) simulations. Although the approach clearly improved the prediction, the X-ray structures and single NMR conformers used in the model cannot be considered fully realistic models of protein in solution. In this work, NMR ensembles (NMRE) were used to expand the conformational space of proteins (e.g. side chains, flexible loops, termini), followed by MD simulations for each conformer to map the local fluctuations. Compared with the non-dynamic model, the NMRE+MD model gave 6–17% lower root-mean-square (RMS) errors for different backbone nuclei. The improved prediction indicates that NMR ensembles with MD simulations can be used to obtain a more realistic picture of protein structures in solutions and moreover underlines the importance of short and long time-scale dynamics for the prediction. The RMS errors of the NMRE+MD model were 0.24, 0.43, 0.98, 1.03, 1.16 and 2.39 ppm for 1 Hα, 1 HN, 13 Cα, 13 Cβ, 13 CO and backbone 15 N chemical shifts, respectively. The model is implemented in the prediction program 4DSPOT, available at http://www.uef.fi/4dspothttp://www.uef.fi/4dspot.

Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction

Energy Technology Data Exchange (ETDEWEB)

Lehtivarjo, Juuso, E-mail: juuso.lehtivarjo@uef.fi; Tuppurainen, Kari; Hassinen, Tommi; Laatikainen, Reino [University of Eastern Finland, School of Pharmacy (Finland); Peraekylae, Mikael [University of Eastern Finland, Institute of Biomedicine (Finland)

2012-03-15

While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein {sup 1}H chemical shifts in which molecular motions, the 4th dimension, were modeled using molecular dynamics (MD) simulations. Although the approach clearly improved the prediction, the X-ray structures and single NMR conformers used in the model cannot be considered fully realistic models of protein in solution. In this work, NMR ensembles (NMRE) were used to expand the conformational space of proteins (e.g. side chains, flexible loops, termini), followed by MD simulations for each conformer to map the local fluctuations. Compared with the non-dynamic model, the NMRE+MD model gave 6-17% lower root-mean-square (RMS) errors for different backbone nuclei. The improved prediction indicates that NMR ensembles with MD simulations can be used to obtain a more realistic picture of protein structures in solutions and moreover underlines the importance of short and long time-scale dynamics for the prediction. The RMS errors of the NMRE+MD model were 0.24, 0.43, 0.98, 1.03, 1.16 and 2.39 ppm for {sup 1}H{alpha}, {sup 1}HN, {sup 13}C{alpha}, {sup 13}C{beta}, {sup 13}CO and backbone {sup 15}N chemical shifts, respectively. The model is implemented in the prediction program 4DSPOT, available at http://www.uef.fi/4dspothttp://www.uef.fi/4dspot.

Classifying and modelling spiral structures in hydrodynamic simulations of astrophysical discs

Science.gov (United States)

Forgan, D. H.; Ramón-Fox, F. G.; Bonnell, I. A.

2018-05-01

We demonstrate numerical techniques for automatic identification of individual spiral arms in hydrodynamic simulations of astrophysical discs. Building on our earlier work, which used tensor classification to identify regions that were `spiral-like', we can now obtain fits to spirals for individual arm elements. We show this process can even detect spirals in relatively flocculent spiral patterns, but the resulting fits to logarithmic `grand-design' spirals are less robust. Our methods not only permit the estimation of pitch angles, but also direct measurements of the spiral arm width and pattern speed. In principle, our techniques will allow the tracking of material as it passes through an arm. Our demonstration uses smoothed particle hydrodynamics simulations, but we stress that the method is suitable for any finite-element hydrodynamics system. We anticipate our techniques will be essential to studies of star formation in disc galaxies, and attempts to find the origin of recently observed spiral structure in protostellar discs.

A FUNDAMENTAL PLANE OF SPIRAL STRUCTURE IN DISK GALAXIES

Energy Technology Data Exchange (ETDEWEB)

Davis, Benjamin L.; Kennefick, Daniel; Kennefick, Julia; Shields, Douglas W. [Arkansas Center for Space and Planetary Sciences, University of Arkansas, 346 1/2 North Arkansas Avenue, Fayetteville, AR 72701 (United States); Westfall, Kyle B. [Kapteyn Astronomical Institute, University of Groningen, P.O. Box 800, NL-9700 AV Groningen (Netherlands); Flatman, Russell [School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332 (United States); Hartley, Matthew T. [Department of Physics, University of Arkansas, 226 Physics Building, 835 West Dickson Street, Fayetteville, AR 72701 (United States); Berrier, Joel C. [Department of Physics and Astronomy, Rutgers, The State University of New Jersey, 136 Frelinghuysen Road, Piscataway, NJ 08854-8019 (United States); Martinsson, Thomas P. K. [Leiden Observatory, P.O. Box 9513, NL-2300 RA Leiden (Netherlands); Swaters, Rob A., E-mail: bld002@email.uark.edu [National Optical Astronomy Observatory, 950 North Cherry Avenue, Tucson, AZ 85719 (United States)

2015-03-20

Spiral structure is the most distinctive feature of disk galaxies and yet debate persists about which theory of spiral structure is correct. Many versions of the density wave theory demand that the pitch angle be uniquely determined by the distribution of mass in the bulge and disk of the galaxy. We present evidence that the tangent of the pitch angle of logarithmic spiral arms in disk galaxies correlates strongly with the density of neutral atomic hydrogen in the disk and with the central stellar bulge mass of the galaxy. These three quantities, when plotted against each other, form a planar relationship that we argue should be fundamental to our understanding of spiral structure in disk galaxies. We further argue that any successful theory of spiral structure must be able to explain this relationship.

Impact of Bounded Noise and Rewiring on the Formation and Instability of Spiral Waves in a Small-World Network of Hodgkin-Huxley Neurons.

Science.gov (United States)

Yao, Yuangen; Deng, Haiyou; Ma, Chengzhang; Yi, Ming; Ma, Jun

2017-01-01

Spiral waves are observed in the chemical, physical and biological systems, and the emergence of spiral waves in cardiac tissue is linked to some diseases such as heart ventricular fibrillation and epilepsy; thus it has importance in theoretical studies and potential medical applications. Noise is inevitable in neuronal systems and can change the electrical activities of neuron in different ways. Many previous theoretical studies about the impacts of noise on spiral waves focus an unbounded Gaussian noise and even colored noise. In this paper, the impacts of bounded noise and rewiring of network on the formation and instability of spiral waves are discussed in small-world (SW) network of Hodgkin-Huxley (HH) neurons through numerical simulations, and possible statistical analysis will be carried out. Firstly, we present SW network of HH neurons subjected to bounded noise. Then, it is numerically demonstrated that bounded noise with proper intensity σ, amplitude A, or frequency f can facilitate the formation of spiral waves when rewiring probability p is below certain thresholds. In other words, bounded noise-induced resonant behavior can occur in the SW network of neurons. In addition, rewiring probability p always impairs spiral waves, while spiral waves are confirmed to be robust for small p, thus shortcut-induced phase transition of spiral wave with the increase of p is induced. Furthermore, statistical factors of synchronization are calculated to discern the phase transition of spatial pattern, and it is confirmed that larger factor of synchronization is approached with increasing of rewiring probability p, and the stability of spiral wave is destroyed.

Wireless Displacement Sensing of Micromachined Spiral-Coil Actuator Using Resonant Frequency Tracking

Directory of Open Access Journals (Sweden)

Mohamed Sultan Mohamed Ali

2014-07-01

Full Text Available This paper reports a method that enables real-time displacement monitoring and control of micromachined resonant-type actuators using wireless radiofrequency (RF. The method is applied to an out-of-plane, spiral-coil microactuator based on shape-memory-alloy (SMA. The SMA spiral coil forms an inductor-capacitor resonant circuit that is excited using external RF magnetic fields to thermally actuate the coil. The actuation causes a shift in the circuit’s resonance as the coil is displaced vertically, which is wirelessly monitored through an external antenna to track the displacements. Controlled actuation and displacement monitoring using the developed method is demonstrated with the microfabricated device. The device exhibits a frequency sensitivity to displacement of 10 kHz/µm or more for a full out-of-plane travel range of 466 µm and an average actuation velocity of up to 155 µm/s. The method described permits the actuator to have a self-sensing function that is passively operated, thereby eliminating the need for separate sensors and batteries on the device, thus realizing precise control while attaining a high level of miniaturization in the device.

A model of the formation of spiral galaxies

International Nuclear Information System (INIS)

Brown, W.K.; Gritzo, L.A.

1980-01-01

It has been verified that the analytical results in a previous article for elliptical galaxies may also be used to describe spiral galaxies. Exploration of the model for small values of the principal parameter THETA yields surface mass density distributions as functions of radius which, while always displaying the exponential disk, describe both of the subcategories of spiral galaxies. Within the constraints of the model, the two main questions concerning spirals posed some years ago by Freeman appear to be successfully addressed. An intrinsic model mechanism has been identified that could account for the extended state of elliptical galaxies, as opposed to the flat disks of spirals. In general, the model correctly describes the relative sizes of the various types of galaxies. (orig.)

Spiral: a new equipment for exotic nuclei; Spiral: un nouvel equipement pour les noyaux exotiques

Energy Technology Data Exchange (ETDEWEB)

NONE

2002-02-01

This document presents the GANIL activities and more specially the SPIRAL project. The missions of the GANIL are to allow scientists fundamental researches in Nuclear Physics and to develop applications for heavy ions in other domains. Spiral is an european project, decided by NuPECC (NUclear Physics European Collaboration Committee). It is a first generation equipment allowing the production and the acceleration of light and moderately heavy nuclei at energy range of 2 to 25 MeV/nucleus. (A.L.B.)

Superconducting spiral phase in the two-dimensional t-J model

International Nuclear Information System (INIS)

Sushkov, Oleg P.; Kotov, Valeri N.

2004-01-01

We analyze the t-t ' -t '' -J model, relevant to the superconducting cuprates. By using chiral perturbation theory we have determined the ground state to be a spiral for small doping δ1 near half filling. In this limit the solution does not contain any uncontrolled approximations. We evaluate the spin-wave Green's functions and address the issue of stability of the spiral state, leading to the phase diagram of the model. At t ' =t '' =0 the spiral state is unstable towards a local enhancement of the spiral pitch, and the nature of the true ground state remains unclear. However, for values of t ' and t '' corresponding to real cuprates the (1,0) spiral state is stabilized by quantum fluctuations ('order from disorder' effect). We show that at δ≅0.119 the spiral is commensurate with the lattice with a period of eight lattice spacings. It is also demonstrated that spin-wave mediated superconductivity develops in the spiral state and a lower limit for the superconducting gap is derived. Even though one cannot classify the gap symmetry according to the lattice representations (s,p,d, ellipsis (horizontal)) since the symmetry of the lattice is spontaneously broken by the spiral, the gap always has lines of nodes along the (1,±1) directions

Propagation of spiral waves pinned to circular and rectangular obstacles.

Science.gov (United States)

Sutthiopad, Malee; Luengviriya, Jiraporn; Porjai, Porramain; Phantu, Metinee; Kanchanawarin, Jarin; Müller, Stefan C; Luengviriya, Chaiya

2015-05-01

We present an investigation of spiral waves pinned to circular and rectangular obstacles with different circumferences in both thin layers of the Belousov-Zhabotinsky reaction and numerical simulations with the Oregonator model. For circular objects, the area always increases with the circumference. In contrast, we varied the circumference of rectangles with equal areas by adjusting their width w and height h. For both obstacle forms, the propagating parameters (i.e., wavelength, wave period, and velocity of pinned spiral waves) increase with the circumference, regardless of the obstacle area. Despite these common features of the parameters, the forms of pinned spiral waves depend on the obstacle shapes. The structures of spiral waves pinned to circles as well as rectangles with the ratio w/h∼1 are similar to Archimedean spirals. When w/h increases, deformations of the spiral shapes are observed. For extremely thin rectangles with w/h≫1, these shapes can be constructed by employing semicircles with different radii which relate to the obstacle width and the core diameter of free spirals.

Mechanical response of spiral interconnect arrays for highly stretchable electronics

KAUST Repository

Qaiser, Nadeem

2017-11-21

A spiral interconnect array is a commonly used architecture for stretchable electronics, which accommodates large deformations during stretching. Here, we show the effect of different geometrical morphologies on the deformation behavior of the spiral island network. We use numerical modeling to calculate the stresses and strains in the spiral interconnects under the prescribed displacement of 1000 μm. Our result shows that spiral arm elongation depends on the angular position of that particular spiral in the array. We also introduce the concept of a unit-cell, which fairly replicates the deformation mechanism for full complex hexagon, diamond, and square shaped arrays. The spiral interconnects which are axially connected between displaced and fixed islands attain higher stretchability and thus experience the maximum deformations. We perform tensile testing of 3D printed replica and find that experimental observations corroborate with theoretical study.

Mechanical response of spiral interconnect arrays for highly stretchable electronics

KAUST Repository

Qaiser, Nadeem; Khan, S. M.; Nour, Maha A.; Rehman, M. U.; Rojas, J. P.; Hussain, Muhammad Mustafa

2017-01-01

A spiral interconnect array is a commonly used architecture for stretchable electronics, which accommodates large deformations during stretching. Here, we show the effect of different geometrical morphologies on the deformation behavior of the spiral island network. We use numerical modeling to calculate the stresses and strains in the spiral interconnects under the prescribed displacement of 1000 μm. Our result shows that spiral arm elongation depends on the angular position of that particular spiral in the array. We also introduce the concept of a unit-cell, which fairly replicates the deformation mechanism for full complex hexagon, diamond, and square shaped arrays. The spiral interconnects which are axially connected between displaced and fixed islands attain higher stretchability and thus experience the maximum deformations. We perform tensile testing of 3D printed replica and find that experimental observations corroborate with theoretical study.

QS Spiral: Visualizing Periodic Quantified Self Data

DEFF Research Database (Denmark)

Larsen, Jakob Eg; Cuttone, Andrea; Jørgensen, Sune Lehmann

2013-01-01

In this paper we propose an interactive visualization technique QS Spiral that aims to capture the periodic properties of quantified self data and let the user explore those recurring patterns. The approach is based on time-series data visualized as a spiral structure. The interactivity includes ...

Research on performance of upstream pumping mechanical seal with different deep spiral groove

International Nuclear Information System (INIS)

Wang, Q; Chen, H L; Liu, T; Liu, Y H; Liu, Z B; Liu, D H

2012-01-01

As one new type of mechanical seal, Upstream Pumping Mechanical Seal has been widely used in fluid machinery. In this paper, structure of spiral groove is innovatively optimized to improve performance of Upstream Pumping Mechanical Seal with Spiral Groove: keeping the dam zone and the weir zone not changed, changing the bottom shape of spiral groove only, substituting different deep spiral groove for equal deep spiral groove. The simulation on Upstream Pumping Mechanical Seal with different deep spiral grooves is done using FVM method. According to calculation, the performances of opening force and pressure distribution on seals face are obtained. Five types of spiral grooves are analyzed, namely equal deep spiral groove, circumferential convergent ladder-like different deep spiral groove, circumferential divergent ladder-like different deep spiral groove, radial convergent ladder-like different deep spiral groove and radial divergent ladder-like different deep spiral groove. This paper works on twenty-five working conditions. The results indicate the performances of circumferential divergent 2-ladder different deep spiral groove are better than the others, with more opening force and better stabilization, while with the same leakage. The outcome provides theoretical support for application of Upstream Pumping Mechanical Seal with circumferential convergent ladder-like different deep spiral groove.

Research on performance of upstream pumping mechanical seal with different deep spiral groove

Science.gov (United States)

Wang, Q.; Chen, H. L.; Liu, T.; Liu, Y. H.; Liu, Z. B.; Liu, D. H.

2012-11-01

As one new type of mechanical seal, Upstream Pumping Mechanical Seal has been widely used in fluid machinery. In this paper, structure of spiral groove is innovatively optimized to improve performance of Upstream Pumping Mechanical Seal with Spiral Groove: keeping the dam zone and the weir zone not changed, changing the bottom shape of spiral groove only, substituting different deep spiral groove for equal deep spiral groove. The simulation on Upstream Pumping Mechanical Seal with different deep spiral grooves is done using FVM method. According to calculation, the performances of opening force and pressure distribution on seals face are obtained. Five types of spiral grooves are analyzed, namely equal deep spiral groove, circumferential convergent ladder-like different deep spiral groove, circumferential divergent ladder-like different deep spiral groove, radial convergent ladder-like different deep spiral groove and radial divergent ladder-like different deep spiral groove. This paper works on twenty-five working conditions. The results indicate the performances of circumferential divergent 2-ladder different deep spiral groove are better than the others, with more opening force and better stabilization, while with the same leakage. The outcome provides theoretical support for application of Upstream Pumping Mechanical Seal with circumferential convergent ladder-like different deep spiral groove.

Attraction and repulsion of spiral waves by inhomogeneity of conduction anisotropy--a model of spiral wave interaction with electrical remodeling of heart tissue.

Science.gov (United States)

Kuklik, Pawel; Sanders, Prashanthan; Szumowski, Lukasz; Żebrowski, Jan J

2013-01-01

Various forms of heart disease are associated with remodeling of the heart muscle, which results in a perturbation of cell-to-cell electrical coupling. These perturbations may alter the trajectory of spiral wave drift in the heart muscle. We investigate the effect of spatially extended inhomogeneity of transverse cell coupling on the spiral wave trajectory using a simple active media model. The spiral wave was either attracted or repelled from the center of inhomogeneity as a function of cell excitability and gradient of the cell coupling. High levels of excitability resulted in an attraction of the wave to the center of inhomogeneity, whereas low levels resulted in an escape and termination of the spiral wave. The spiral wave drift velocity was related to the gradient of the coupling and the initial position of the wave. In a diseased heart, a region of altered transverse coupling corresponds with local gap junction remodeling that may be responsible for stabilization-destabilization of spiral waves and hence reflect potentially important targets in the treatment of heart arrhythmias.

The potentials of spiral CT for detection of focal liver lesions; Moeglichkeiten der Spiral-CT zur Diagnostik fokaler Leberlaesionen

Energy Technology Data Exchange (ETDEWEB)

Helmberger, H. [Technische Univ. Muenchen, Klinikum rechts der Iser, Inst. fuer Roentgendiagnostik (Germany); Kersting-Sommerhoff, B. [Technische Univ. Muenchen, Klinikum rechts der Iser, Inst. fuer Roentgendiagnostik (Germany); Lenz, M. [Technische Univ. Muenchen, Klinikum rechts der Iser, Inst. fuer Roentgendiagnostik (Germany); Kirsten, R. [Technische Univ. Muenchen, Klinikum rechts der Iser, Inst. fuer Roentgendiagnostik (Germany); Bautz, W. [Technische Univ. Muenchen, Klinikum rechts der Iser, Inst. fuer Roentgendiagnostik (Germany)

1996-03-01

Spiral CT currently is the modality of choice for all aspects of diagnostic evaluation of the liver. Optimal selection of treatment should be based inter alia on the findings obtained by spiral CT with arterial application of contrast medium, as for example S-CTA (primary liver tumors), or S-CTAP (secondary liver tumors). Ultrasonography is the major supplementing modality. In the near future, MR imaging applying liver-specific contrast-enhancing agents is expected to become an important competing technique, and further developments of interest in diagnostic imaging of the liver are in the offing: it is not yet known which technique will be the modality of choice at the onset of the 21st century. (orig.) [Deutsch] Die Spiral-CT ist zur Zeit das empfehlenswerte Verfahren fuer alle Fragen der Leberdiagnostik. Zur optimalen praetherapeutischen Beurteilung der Leber sollte die Spiral-CT mit arterieller Kontrastmittelapplikation als S-CTA (primaere Lebertumoren) bzw. S-CTAP (sekundaere Lebertumoren) durchgefuehrt werden. Der US kommt ein Stellenwert als ergaenzende Methode zu. In Zukunft wird die MRT mit leberspezifischen Kontrastmitteln ein konkurrierendes Verfahren zur Spiral-CT darstellen, wobei eine weitere interessante Entwicklung auf dem Gebiet der hepatischen Bildgebung zu erwarten ist: Das diagnostische Verfahren der Wahl fuer die Leber zu Beginn des 21. Jahrhunderts ist noch nicht definiert. (orig.)

Spiral groove seal. [for rotating shaft

Science.gov (United States)

Ludwig, L. P.; Strom, T. N. (Inventor)

1974-01-01

Mating flat surfaces inhibit leakage of a fluid around a stationary shaft. A spiral groove produces a pumping action toward the fluid when the shaft rotates. This prevents leakage while a generated hydraulic lifting force separates the mating surfaces to minimize wear. Provision is made for placing these spiral grooves in communication with the fluid to accelerate the generation of the hydraulic lifting force.

Smooth-arm spiral galaxies: their properties and significance to cluster-galaxy evolution

International Nuclear Information System (INIS)

Wilkerson, M.S.

1979-01-01

In this dissertation a number of galaxies with optical appearances between those of normal, actively-star-forming spirals and SO galaxies have been examined. These so-called smooth-arm spiral galaxies exhibit spiral arms without any of the spiral tracers - H II regions, O-B star associations, dust - indicative of current star formation. Tests were made to find if, perhaps, these smooth-arm spirals could have, at one time, been normal, actively-star-forming spirals whose gas had been somehow removed; and that are currently transforming into SO galaxies. This scenario proceeds as (1) removal of gas, (2) gradual dying of disk density wave, (3) emergence of SO galaxy. If the dominant method of gas removal is ram-pressure stripping by a hot, intracluster medium, then smooth-arm spirals should occur primarily in x-ray clusters. Some major findings of this dissertation are as follows: (1) Smooth-arm spirals are redder than normal spirals of the same morphological type. Most smooth-arm spirals cannot be distinguished by color from SO galaxies. (2) A weak trend exists for smooth-arm spirals with stronger arms to be bluer than those with weaker arms; thus implying that the interval since gas removal has been shorter for the galaxies with stronger arms. (3) Smooth-arm spirals are deficient in neutral hydrogen - sometimes by an order of magnitude or, possibly, more

Chemical shift of U L3 edges in different uranium compounds obtained by X-ray absorption spectroscopy with synchrotron radiation

International Nuclear Information System (INIS)

Joseph, D.; Jha, S.N.; Nayak, C.; Bhattacharyya, D.; Babu, P. Venu

2014-01-01

Uranium L 3 X-ray absorption edge was measured in various compounds containing uranium in U 4+ , U 5+ and U 5+ 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 L 3 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. (author)

Radial distributions of arm-gas offsets as an observational test of spiral theories

OpenAIRE

Baba, Junichi; Morokuma-Matsui, Kana; Egusa, Fumi

2015-01-01

Theories of stellar spiral arms in disk galaxies can be grouped into two classes based on the longevity of a spiral arm. Although the quasi-stationary density wave theory supposes that spirals are rigidly-rotating, long-lived patterns, the dynamic spiral theory predicts that spirals are differentially-rotating, transient, recurrent patterns. In order to distinguish between the two spiral models from observations, we performed hydrodynamic simulations with steady and dynamic spiral models. Hyd...

Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH{sub 2}

Energy Technology Data Exchange (ETDEWEB)

Erlach, Markus Beck; Koehler, Joerg [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany); Crusca, Edson [University of São Paulo, Physics Institute of São Carlos (Brazil); Kremer, Werner [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany); Munte, Claudia E. [University of São Paulo, Physics Institute of São Carlos (Brazil); Kalbitzer, Hans Robert, E-mail: hans-robert.kalbitzer@biologie.uni-regensburg.de [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany)

2016-06-15

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 {sup 1}H{sup α}, {sup 13}C{sup α} and {sup 13}C′ in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH{sub 2} (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{sub 1} and B{sub 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.Graphical Abstract.

Application of the Fenske-Hall molecular orbital method to the calculation of 11B NMR chemical shifts. Antipodal substituent effects in deltahedral clusters

International Nuclear Information System (INIS)

Fehlner, T.P.; Czech, P.T.; Fenske, R.F.

1990-01-01

Utilizing Fenske-Hall wave functions and eigenvalues combined with the Ramsey sum over states (SOS) approximation, it is demonstrated that the sign and magnitude of the paramagnetic contribution to the shielding correlates well with the observed 11 B chemical shifts of a substantial variety of boron- and metal-containing compounds. Analysis of the molecular orbital (MO) contributions in the SOS approximation leads to an explanation of the large downfield shifts associated with metal-rich metallaboranes. A similar analysis demonstrates the importance of selected cluster occupied and unoccupied MO's in explaining both exo-cage substituent effects in which the antipodal boron resonance is shifted upfield and endo-cage substituent effects (interchange of isolobal fragments within the cage framework) in which the antipodal boron resonance is shifted downfield. Exo- and endo-cage substitution perturbs these MO's in an understandable fashion, leading to an internally consistent explanation of the observed chemical shift changes. 36 refs., 8 figs., 4 tabs

Nonuniqueness of self-propagating spiral galaxy models

International Nuclear Information System (INIS)

Freedman, W.L.; Madore, B.F.

1984-01-01

We demonstrate the nonuniqueness of the basic assumptions leading to spiral structure in self-propagating star formation models. Even in the case where star formation occurs purely spontaneously and does not propagate, we have generated spiral structure by adopting the radically different assumption where star formation is systematically inhibited

Unusually large chemical potential shift in a degenerate semiconductor: Angle-resolved photoemission study of SnSe and Na-doped SnSe

Science.gov (United States)

Maeda, M.; Yamamoto, K.; Mizokawa, T.; Saini, N. L.; Arita, M.; Namatame, H.; Taniguchi, M.; Tan, G.; Zhao, L. D.; Kanatzidis, M. G.

2018-03-01

We have studied the electronic structure of SnSe and Na-doped SnSe by means of angle-resolved photoemission spectroscopy. The valence-band top reaches the Fermi level by the Na doping, indicating that Na-doped SnSe can be viewed as a degenerate semiconductor. However, in the Na-doped system, the chemical potential shift with temperature is unexpectedly large and is apparently inconsistent with the degenerate semiconductor picture. The large chemical potential shift and anomalous spectral shape are key ingredients for an understanding of the novel metallic state with the large thermoelectric performance in Na-doped SnSe.

Differentiation of osteoporotic and neoplastic vertebral fractures by chemical shift {l_brace}in-phase and out-of phase{r_brace} MR imaging

Energy Technology Data Exchange (ETDEWEB)

Ragab, Yasser [Radiology Department, Faculty of Medicine, Cairo University (Egypt); Radiology Department, Dr Erfan and Bagedo General Hospital (Saudi Arabia)], E-mail: yragab61@hotmail.com; Emad, Yasser [Rheumatology and Rehabilitation Department, Faculty of Medicine, Cairo University (Egypt); Rheumatology and Rehabilitation Department, Dr Erfan and Bagedo General Hospital (Saudi Arabia)], E-mail: yasseremad68@yahoo.com; Gheita, Tamer [Rheumatology and Rehabilitation Department, Faculty of Medicine, Cairo University (Egypt)], E-mail: gheitamer@yahoo.com; Mansour, Maged [Oncology Department, Faculty of Medicine, Cairo University (Egypt); Oncology Department, Dr Erfan and Bagedo General Hospital (Saudi Arabia)], E-mail: magedmansour@yahoo.com; Abou-Zeid, A. [Public Health Department, Faculty of Medicine, Cairo University, Cairo (Egypt)], E-mail: alaabouzeid@yahoo.com; Ferrari, Serge [Division of Bone Diseases, Department of Rehabilitation and Geriatrics, and WHO, Collaborating Center for Osteoporosis Prevention, Geneva University Hospital (Switzerland)], E-mail: serge.ferrari@medecine.unige.ch; Rasker, Johannes J. [Rheumatologist University of Twente, Enschede (Netherlands)], E-mail: j.j.rasker@utwente.nl

2009-10-15

Objective: The objective of this study was to establish the cut-off value of the signal intensity drop on chemical shift magnetic resonance imaging (MRI) with appropriate sensitivity and specificity to differentiate osteoporotic from neoplastic wedging of the spine. Patients and methods: All patients with wedging of vertebral bodies were included consecutively between February 2006 and January 2007. A chemical shift MRI was performed and signal intensity after (in-phase and out-phase) images were obtained. A DXA was performed in all. Results: A total of 40 patients were included, 20 with osteoporotic wedging (group 1) and 20 neoplastic (group 2). They were 21 males and 19 females. Acute vertebral collapse was observed in 15 patients in group 1 and subacute collapse in another 5 patients, while in group 2, 11 patients showed acute collapse and 9 patients (45%) showed subacute vertebral collapse. On the chemical shift MRI a substantial reduction in signal intensity was found in all lesions in both groups. The proportional changes observed in signal intensity of bone marrow lesions on in-phase compared with out-of-phase images showed significant differences in both groups (P < 0.05). At a cut-off value of 35%, the observed sensitivity of out-of-phase images was 95%, specificity was 100%, positive predictive value was 100% and negative predictive value was 95.2%. Conclusion: A chemical shift MRI is useful in order to differentiate patients with vertebral collapse due to underlying osteoporosis or neoplastic process.

Spatial and mass distributions of molecular clouds and spiral structure

International Nuclear Information System (INIS)

Kwan, J.; Valdes, F.; National Optical Astronomy Observatories, Tucson, AZ)

1987-01-01

The growth of molecular clouds resulting from cloud-cloud collisions and coalescence in the Galactic ring between 4 and 8 kpc are modeled, taking into account the presence of a spiral potential and the mutual cloud-cloud gravitational attraction. The mean lifetime of molecular clouds is determined to be about 200 million years. The clouds are present in both spiral arm and interarm regions, but a spiral pattern in their spatial distribution is clearly discernible, with the more massive clouds showing a stronger correlation with the spiral arms. As viewed from within the Galactic disk, however, it is very difficult to ascertain that the molecular cloud distribution in longitude-velocity space has a spiral pattern. 19 references

Dark matter in spiral galaxies

International Nuclear Information System (INIS)

Persic, M.; Salucci, P.

1990-01-01

The Tully-Fisher relation is used to probe dark matter (DM) in the optical regions of spiral galaxies. By establishing it at several different isophotal radii in an appropriate sample of 58 galaxies with good B-band photometry and rotation curves, it is shown that some of its attributes (such as scatter, residuals, nonlinearity, and bias) dramatically decrease moving from the disk edge inward. This behavior challenges any mass model which assumes no DM or a luminosity-independent DM mass fraction interior to the optical radius of spiral galaxies. 58 refs

SPIRAL COUNTER-CURRENT CHROMATOGRAPHY OF SMALL MOLECULES, PEPTIDES AND PROTEINS USING THE SPIRAL TUBING SUPPORT ROTOR

OpenAIRE

Knight, Martha; Finn, Thomas M.; Zehmer, John; Clayton, Adam; Pilon, Aprile

2011-01-01

An important advance in countercurrent chromatography (CCC) carried out in open flow-tubing coils, rotated in planetary centrifuges, is the new design to spread out the tubing in spirals. More spacing between the tubing was found to significantly increase the stationary phase retention, such that now all types of two-phase solvent systems can be used for liquid-liquid partition chromatography in the J-type planetary centrifuges. A spiral tubing support (STS) frame with circular channels was c...

Correlations of the chemical shift on fasly rotating biological solids by means of NMR spectroscopy

International Nuclear Information System (INIS)

Herbst, Christian

2010-01-01

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 13 C- 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 n ν and RN n ν mixing sequences as well as heteronuclear RN n ν s ,ν 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) 97 -RNA. This thesis deals furthermore with the possibility to acquire simultaneously different signals with several receivers. By means of numerically optimized RN n ν s ,ν k pulse sequences both 15 N- 13 C and 13 C- 15 N correlation spectra were simultaneously generated. Furthermore it could be shown that the simultaneous acquisition of 3D- 15 N- 13 C- 13 C and 13 C- 15 N-( 1 H)- 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 χ in RNA. This was demonstrated by means of the (CUG) 97 -RNA. The simultaneous acquisition of all relevant crossing signals of the correlation spectra leads not only to an essential time saving, but

Floating venous thrombi: diagnosis with spiral-CT-venography; Diagnose flottierender venoeser Thromben mittels Phlebo-Spiral-CT

Energy Technology Data Exchange (ETDEWEB)

Gartenschlaeger, M. [Mainz Univ. (Germany). Klinik fuer Radiologie; Klose, K.J. [Univ. Marburg, Medizinisches Zentrum fuer Innere Medizin, Abt. Poliklinik (Germany); Schmidt, J.A. [Univ. Marburg, Medizinisches Zentrum fuer Radiologie, Abt. fuer Strahlendiagnostik (Germany)

1996-05-01

Local application of contrast agent into an ipsilateral dorsal foot vein and spiral CT were used to examine 16 consecutive cases with deep venous thrombosis proven at conventional venography; in addition, colour Doppler flow imaging was performed. At conventional venography, 8/16 thrombi appeared to be floating and the remaining 8/16 were adherent to the vessel wall. Spiral-CT showed 15/16 thrombi to be adherent to the vessel wall; the floating thrombus correlated with findings in conventional venography. At colour Doppler flow imaging 3/16 thrombi were considered floating, one of them was discordant to conventional venography. The comparison of conventional venography to spiral-CT demonstrates complete agreement for adherence to vessel wall seen in conventional venography (p=1,0) and significant discordance in cases with free-floating appearance in conventional venography. Adherence of thrombi to the wall of the vessel at conventional venography is in agreement with computed tomography. Conventional venography probably overestimates the prevalence of free floating thrombi. (orig./MG) [Deutsch] Mittels lokaler Kontrastmittelapplikation in eine ipsilaterale Fussrueckenvene und Spiral-CT wurden 16 konsekutive Faelle konventionell phlebographisch gesicherter Phlebothrombose untersucht, zusaetzlich wurde die farbkodierte Doppler-Ultraschalluntersuchung durchgefuehrt. In der konventionellen Phlebographie waren 8/16 Thromben flottierend, die uebrigen 8/16 wandadhaerent. In der Spiral-CT zeigten sich Wandadhaerenzen in 15/16 Faellen; der nachgewiesene flottierende Thrombus stimmte mit der konventionellen Phlebographie ueberein. Im farbkodierten Doppler-Ultraschall erschienen die Thromben in 3/16 Faellen flottierend, darunter ein von der konventionellen Phlebographie abweichender Befund. Der Vergleich von konventioneller und CT-Phlebographie ergab eine komplette Uebereinstimmung fuer konventionell phlebographisch nachgewiesene Wandadhaerenz und eine signifikante Abweichung

Determination of hydration numbers of electrolytes from temperature dependence of PMR chemical shifts

International Nuclear Information System (INIS)

Subramanian, N.

1979-01-01

The method proposed by Malinowski et al. for the determination of effective hydration numbers (h) of electrolytes leads to a consistent incrrease in the observed values of 'h' with increase in solution concentration. An attempt is made to rationalize the experimental results by cosidering the simultaneous effects of temperature and concentration on the proton chemical shift. It is suggested that Malinowski's technique might yeld 'h' values very close to the true value for those ions for which there is a fortuitous cancellation of structure-making and structure-breaking properties. (Author) [pt

Spiral 2 workshop

International Nuclear Information System (INIS)

2004-01-01

The accelerator and experimental facilities at GANIL will be transformed over the next 5-10 years. The centerpiece of the additions to the accelerator complex will be Spiral-2. This is the first phase of a new radioactive beam facility based on the ISOL principle. The main aim of Spiral-2 will be to produce intense, high quality beams of neutron-rich nuclei created in neutron-induced fission of heavy elements and accelerated by the existing CIME cyclotron. The principal aims of this workshop will be a) to publicize the new facilities, b) to discuss and define the science which might be carried out with them, c) to discuss the instrumentation and infrastructure required to exploit the new facilities and d) to help form collaborations of scientists wishing to design and construct the equipment needed to undertake the science programme. This document gathers most of the slides presented in the workshop

Spiral 2 workshop

Energy Technology Data Exchange (ETDEWEB)

NONE

2004-07-01

The accelerator and experimental facilities at GANIL will be transformed over the next 5-10 years. The centerpiece of the additions to the accelerator complex will be Spiral-2. This is the first phase of a new radioactive beam facility based on the ISOL principle. The main aim of Spiral-2 will be to produce intense, high quality beams of neutron-rich nuclei created in neutron-induced fission of heavy elements and accelerated by the existing CIME cyclotron. The principal aims of this workshop will be a) to publicize the new facilities, b) to discuss and define the science which might be carried out with them, c) to discuss the instrumentation and infrastructure required to exploit the new facilities and d) to help form collaborations of scientists wishing to design and construct the equipment needed to undertake the science programme. This document gathers most of the slides presented in the workshop.

Organic carbon spiralling in stream ecosystems

Energy Technology Data Exchange (ETDEWEB)

Newbold, J D; Mulholland, P J; Elwood, J W; O' Neill, R V

1982-01-01

The term spiralling has been used to describe the combined processes of cycling and longitudinal transport in streams. As a measure or organic carbon spiralling, we introduced organic carbon turnover length, S, defined as the average or expected downstream distance travelled by a carbon atom between its entry or fixation in the stream and its oxidation. Using a simple model for organic carbon dynamics in a stream, we show that S is closely related to fisher and Likens' ecosystem efficiency. Unlike efficiency, however, S is independent of the length of the study reach, and values of S determined in streams of differing lengths can be compared. Using data from three different streams, we found the relationship between S and efficiency to agree closely with the model prediction. Hypotheses of stream functioning are discussed in the context of organic carbeon spiralling theory.

SPIRAL CHAMBERS OF COMBINED PUMP-TURBINE UNITS AND CENTRIFUGAL PUMPS

Directory of Open Access Journals (Sweden)

Mihajlov Ivan Evgrafovich

2012-10-01

The loss of energy (pressure in spiral chambers and trail races of the above machines can be reduced, if the output section of the spiral has the shape of a torus with a central angle φ= 45….55o, taken in-between the output section of the spiral and its tooth, while the cross sectional area is equal to the section area calculated as Vu ∙ r = const or Vср ∙ r = const (this section of the spiral is the initial section of the torus.

Neutrons for science (NFS) at spiral-2

International Nuclear Information System (INIS)

Ridikas, D.

2005-01-01

Both cross section measurements and various applications could be realised successfully using the high energy neutrons that will be produced at SPIRAL-2. Two particular cases were examined in more detail, namely: (a) neutron time-of-flight (nToF) measurements with pulsed neutron beams, and (b) material activation-irradiation with high-energy high-intensity neutron fluxes. Thanks to the high energy and high intensity neutron flux available, SPIRAL-2 offers a unique opportunity for material irradiations both for fission and fusion related research, tests of various detection systems and of resistance of electronics components to irradiations, etc. SPIRAL-2 also could be considered as an intermediate step towards new generation dedicated irradiation facilities as IFMIF previewed only beyond 2015. Equally, the interval from 0.1 MeV to 40 MeV for neutron cross section measurements is an energy range that is of particular importance for energy applications, notably accelerator driven systems (ADS) and Gen-IV fast reactors, as well as for fusion related devices. It is also the region where pre-equilibrium approaches are often used to link the low (evaporation) and high energy (intra-nuclear cascade) reaction models. With very intense neutron beams of SPIRAL-2 measurements of very low mass (often radioactive) targets and small cross sections become feasible in short experimental campaigns. Production of radioactive targets for dedicated physics experiments is also an attractive feature of SPIRAL-2. In brief, it was shown that SPIRAL-2 has got a remarkable potential for neutron based research both for fundamental physics and various applications. In addition, in the neutron energy range from a few MeV to, say, 35 MeV this research would have a leading position for the next 10-15 years if compared to other neutron facilities in operation or under construction worldwide. (author)

Logarithmic spiral trajectories generated by Solar sails

Science.gov (United States)

Bassetto, Marco; Niccolai, Lorenzo; Quarta, Alessandro A.; Mengali, Giovanni

2018-02-01

Analytic solutions to continuous thrust-propelled trajectories are available in a few cases only. An interesting case is offered by the logarithmic spiral, that is, a trajectory characterized by a constant flight path angle and a fixed thrust vector direction in an orbital reference frame. The logarithmic spiral is important from a practical point of view, because it may be passively maintained by a Solar sail-based spacecraft. The aim of this paper is to provide a systematic study concerning the possibility of inserting a Solar sail-based spacecraft into a heliocentric logarithmic spiral trajectory without using any impulsive maneuver. The required conditions to be met by the sail in terms of attitude angle, propulsive performance, parking orbit characteristics, and initial position are thoroughly investigated. The closed-form variations of the osculating orbital parameters are analyzed, and the obtained analytical results are used for investigating the phasing maneuver of a Solar sail along an elliptic heliocentric orbit. In this mission scenario, the phasing orbit is composed of two symmetric logarithmic spiral trajectories connected with a coasting arc.

Fabrication techniques of X-ray spiral zone plates

International Nuclear Information System (INIS)

Gao Nan; Zhu Xiaoli; Li Hailiang; Xie Changqing

2010-01-01

The techniques to make X-ray spiral zone plates using electron beam and X-ray lithography were studied. A master mask was fabricated on polyimide membrane by E-beam lithography and micro-electroplating. Spiral zone plates were efficiently replicated by X-ray lithography and micro-electroplating. By combining the techniques, spiral zone plates at 1 keV were successfully fabricate. With an outermost zone width of the 200 nm, and the gold absorbers thickness of 700 nm, the high quality zone plates can be used for X-ray phase contrast microscopy.(authors)

Spiral scan long object reconstruction through PI line reconstruction

International Nuclear Information System (INIS)

Tam, K C; Hu, J; Sourbelle, K

2004-01-01

The response of a point object in a cone beam (CB) spiral scan is analysed. Based on the result, a reconstruction algorithm for long object imaging in spiral scan cone beam CT is developed. A region-of-interest (ROI) of the long object is scanned with a detector smaller than the ROI, and a portion of it can be reconstructed without contamination from overlaying materials. The top and bottom surfaces of the ROI are defined by two sets of PI lines near the two ends of the spiral path. With this novel definition of the top and bottom ROI surfaces and through the use of projective geometry, it is straightforward to partition the cone beam image into regions corresponding to projections of the ROI, the overlaying objects or both. This also simplifies computation at source positions near the spiral ends, and makes it possible to reduce radiation exposure near the spiral ends substantially through simple hardware collimation. Simulation results to validate the algorithm are presented

Low surface brightness spiral galaxies

International Nuclear Information System (INIS)

Romanishin, W.

1980-01-01

This dissertation presents an observational overview of a sample of low surface brightness (LSB) spiral galaxies. The sample galaxies were chosen to have low surface brightness disks and indications of spiral structure visible on the Palomar Sky Survey. They are of sufficient angular size (diameter > 2.5 arcmin), to allow detailed surface photometry using Mayall 4-m prime focus plates. The major findings of this dissertation are: (1) The average disk central surface brightness of the LSB galaxies is 22.88 magnitude/arcsec 2 in the B passband. (2) From broadband color measurements of the old stellar population, we infer a low average stellar metallicity, on the order of 1/5 solar. (3) The spectra and optical colors of the HII regions in the LSB galaxies indicate a lack of hot ionizing stars compared to HII regions in other late-type galaxies. (4) The average surface mass density, measured within the radius containing half the total mass, is less than half that of a sample of normal late-type spirals. (5) The average LSB galaxy neutral hydrogen mass to blue luminosity ratio is about 0.6, significantly higher than in a sample of normal late-type galaxies. (6) We find no conclusive evidence of an abnormal mass-to-light ratio in the LSB galaxies. (7) Some of the LSB galaxies exhibit well-developed density wave patterns. (8) A very crude calculation shows the lower metallicity of the LSB galaxies compared with normal late-type spirals might be explained simply by the deficiency of massive stars in the LSB galaxies

The dynamics of spiral tip adjacent to inhomogeneity in cardiac tissue

Science.gov (United States)

Zhang, Juan; Tang, Jun; Ma, Jun; Luo, Jin Ming; Yang, Xian Qing

2018-02-01

Rotating spiral waves in cardiac tissue are implicated in life threatening cardiac arrhythmias. Experimental and theoretical evidences suggest the inhomogeneities in cardiac tissue play a significant role in the dynamics of spiral waves. Based on a modified 2D cardiac tissue model, the interaction of inhomogeneity on the nearby rigidly rotating spiral wave is numerically studied. The adjacent area of the inhomogeneity is divided to two areas, when the initial rotating center of the spiral tip is located in the two areas, the spiral tip will be attracted and anchor on the inhomogeneity finally, or be repulsed away. The width of the area is significantly dependent on the intensity and size of the inhomogeneity. Our numerical study sheds some light on the mechanism of the interaction of inhomogeneity on the spiral wave in cardiac tissue.

Simple theory of how spiral galaxies acquire their principal global properties

International Nuclear Information System (INIS)

Burstein, D.; Sarazin, C.L.

1983-01-01

The strongest correlations among the global properties of spiral galaxies are the power law correlations between luminosity and rotation velocity (the Tully-Fisher relation) and between luminosity and luminous radius. Both of these relations are derived from a single density-radius power-law relation for spiral galaxies, assuming that the total mass-to-luminosity ratio is fixed by the Hubble type of the spiral, and that spirals gain their angular momentum through tidal interactions. The predictions of this simple theory are consistent with the observed luminosity and mass properties of the Hubble type-restricted samples of spiral galaxies studied by Rubin et al. This model suggests that many of the physical properties of spiral galaxies, and of the Hubble sequence, originate before or during the formation of galaxies

The scientific objectives of the SPIRAL 2 Project

Energy Technology Data Exchange (ETDEWEB)

Ackermann, D.; Adoui, L.; Angelis, G. de [GANIL, Grand Accelerateur National d' Ions Lourds, BP 55027, 14076 Caen cedex 5 (France)] (and others)

2006-06-15

The construction of SPIRAL 2 at GANIL will open completely new possibilities for parallel beam operation of the whole facility. The whole GANIL/SPIRAL/SPIRAL2 accelerator complex will allow for the simultaneous use of up to 5 different radioactive and stable beams. Several combinations of different beams delivered in parallel for experiments at low (keV/u), medium (few MeV/u) and high (up to 100 MeV/u) energies will be possible. Presently the GANIL/SPIRAL facility delivers about 60 weeks per year of stable and radioactive beams (up to 3 simultaneous beams). Thanks to SPIRAL 2 and the construction of a new beam line connecting the CIME cyclotron and the G1 and G2 experimental rooms the available beam time for experiments may be extended up to about 120 (up to 5 simultaneous beams) weeks per year. The chapters which follow a general introduction deal with the detailed questions to be addressed by experiments with the beams from SPIRAL2. In chapter 2 the many unanswered questions related to the structure of exotic nuclei are posed and the role of SPIRAL2 in answering them outlined. Chapter 3 deals with the dynamics and thermodynamics of asymmetric nuclear systems. Chapter 4 is concerned with questions of nuclear astrophysics which are intimately related to the properties of exotic nuclei. Chapter 5 indicates how the atomic nucleus can act as a laboratory for tests of the Standard model of Particle Physics and Chapter 6 shows how the production of intense fluxes of neutrons at SPIRAL2 make it an excellent tool to address both questions related to damage in materials of importance in nuclear installations and to the s- and r-processes of nucleosynthesis. In chapter 7 we turn to the application, of the radioactive beams from SPIRAL2 and the radionuclides produced by it, to study condensed matter and radiobiology. Finally in the eight and last chapter the reader can find an account of the historical development of the SPIRAL2 facility and this is followed by an outline of

The scientific objectives of the SPIRAL 2 Project

International Nuclear Information System (INIS)

Ackermann, D.; Adoui, L.; Angelis, G. de

2006-06-01

The construction of SPIRAL 2 at GANIL will open completely new possibilities for parallel beam operation of the whole facility. The whole GANIL/SPIRAL/SPIRAL2 accelerator complex will allow for the simultaneous use of up to 5 different radioactive and stable beams. Several combinations of different beams delivered in parallel for experiments at low (keV/u), medium (few MeV/u) and high (up to 100 MeV/u) energies will be possible. Presently the GANIL/SPIRAL facility delivers about 60 weeks per year of stable and radioactive beams (up to 3 simultaneous beams). Thanks to SPIRAL 2 and the construction of a new beam line connecting the CIME cyclotron and the G1 and G2 experimental rooms the available beam time for experiments may be extended up to about 120 (up to 5 simultaneous beams) weeks per year. The chapters which follow a general introduction deal with the detailed questions to be addressed by experiments with the beams from SPIRAL2. In chapter 2 the many unanswered questions related to the structure of exotic nuclei are posed and the role of SPIRAL2 in answering them outlined. Chapter 3 deals with the dynamics and thermodynamics of asymmetric nuclear systems. Chapter 4 is concerned with questions of nuclear astrophysics which are intimately related to the properties of exotic nuclei. Chapter 5 indicates how the atomic nucleus can act as a laboratory for tests of the Standard model of Particle Physics and Chapter 6 shows how the production of intense fluxes of neutrons at SPIRAL2 make it an excellent tool to address both questions related to damage in materials of importance in nuclear installations and to the s- and r-processes of nucleosynthesis. In chapter 7 we turn to the application, of the radioactive beams from SPIRAL2 and the radionuclides produced by it, to study condensed matter and radiobiology. Finally in the eight and last chapter the reader can find an account of the historical development of the SPIRAL2 facility and this is followed by an outline of

Grand-design Spiral Arms in a Young Forming Circumstellar Disk

Energy Technology Data Exchange (ETDEWEB)

Tomida, Kengo; Lin, Chia Hui [Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 560-0043 (Japan); Machida, Masahiro N. [Department of Earth and Planetary Sciences, Faculty of Sciences, Kyushu University, Nishi-ku, Fukuoka 819-0395 (Japan); Hosokawa, Takashi [Department of Physics, Kyoto University, Sakyo-ku, Kyoto 606-8502 (Japan); Sakurai, Yuya, E-mail: tomida@vega.ess.sci.osaka-u.ac.jp [Department of Physics, The University of Tokyo, Tokyo 113-0033 (Japan)

2017-01-20

We study formation and long-term evolution of a circumstellar disk in a collapsing molecular cloud core using a resistive magnetohydrodynamic simulation. While the formed circumstellar disk is initially small, it grows as accretion continues, and its radius becomes as large as 200 au toward the end of the Class-I phase. A pair of grand-design spiral arms form due to gravitational instability in the disk, and they transfer angular momentum in the highly resistive disk. Although the spiral arms disappear in a few rotations as expected in a classical theory, new spiral arms form recurrently as the disk, soon becoming unstable again by gas accretion. Such recurrent spiral arms persist throughout the Class-0 and I phases. We then perform synthetic observations and compare our model with a recent high-resolution observation of a young stellar object Elias 2–27, whose circumstellar disk has grand-design spiral arms. We find good agreement between our theoretical model and the observation. Our model suggests that the grand-design spiral arms around Elias 2–27 are consistent with material arms formed by gravitational instability. If such spiral arms commonly exist in young circumstellar disks, it implies that young circumstellar disks are considerably massive and gravitational instability is the key process of angular momentum transport.

Grand-design Spiral Arms in a Young Forming Circumstellar Disk

International Nuclear Information System (INIS)

Tomida, Kengo; Lin, Chia Hui; Machida, Masahiro N.; Hosokawa, Takashi; Sakurai, Yuya

2017-01-01

We study formation and long-term evolution of a circumstellar disk in a collapsing molecular cloud core using a resistive magnetohydrodynamic simulation. While the formed circumstellar disk is initially small, it grows as accretion continues, and its radius becomes as large as 200 au toward the end of the Class-I phase. A pair of grand-design spiral arms form due to gravitational instability in the disk, and they transfer angular momentum in the highly resistive disk. Although the spiral arms disappear in a few rotations as expected in a classical theory, new spiral arms form recurrently as the disk, soon becoming unstable again by gas accretion. Such recurrent spiral arms persist throughout the Class-0 and I phases. We then perform synthetic observations and compare our model with a recent high-resolution observation of a young stellar object Elias 2–27, whose circumstellar disk has grand-design spiral arms. We find good agreement between our theoretical model and the observation. Our model suggests that the grand-design spiral arms around Elias 2–27 are consistent with material arms formed by gravitational instability. If such spiral arms commonly exist in young circumstellar disks, it implies that young circumstellar disks are considerably massive and gravitational instability is the key process of angular momentum transport.

Tissue-engineered spiral nerve guidance conduit for peripheral nerve regeneration.

Science.gov (United States)

Chang, Wei; Shah, Munish B; Lee, Paul; Yu, Xiaojun

2018-06-01

Recently in peripheral nerve regeneration, preclinical studies have shown that the use of nerve guidance conduits (NGCs) with multiple longitudinally channels and intra-luminal topography enhance the functional outcomes when bridging a nerve gap caused by traumatic injury. These features not only provide guidance cues for regenerating nerve, but also become the essential approaches for developing a novel NGC. In this study, a novel spiral NGC with aligned nanofibers and wrapped with an outer nanofibrous tube was first developed and investigated. Using the common rat sciatic 10-mm nerve defect model, the in vivo study showed that a novel spiral NGC (with and without inner nanofibers) increased the successful rate of nerve regeneration after 6 weeks recovery. Substantial improvements in nerve regeneration were achieved by combining the spiral NGC with inner nanofibers and outer nanofibrous tube, based on the results of walking track analysis, electrophysiology, nerve histological assessment, and gastrocnemius muscle measurement. This demonstrated that the novel spiral NGC with inner aligned nanofibers and wrapped with an outer nanofibrous tube provided a better environment for peripheral nerve regeneration than standard tubular NGCs. Results from this study will benefit for future NGC design to optimize tissue-engineering strategies for peripheral nerve regeneration. We developed a novel spiral nerve guidance conduit (NGC) with coated aligned nanofibers. The spiral structure increases surface area by 4.5 fold relative to a tubular NGC. Furthermore, the aligned nanofibers was coated on the spiral walls, providing cues for guiding neurite extension. Finally, the outside of spiral NGC was wrapped with randomly nanofibers to enhance mechanical strength that can stabilize the spiral NGC. Our nerve histological data have shown that the spiral NGC had 50% more myelinated axons than a tubular structure for nerve regeneration across a 10 mm gap in a rat sciatic nerve

Galactic models with variable spiral structure

International Nuclear Information System (INIS)

James, R.A.; Sellwood, J.A.

1978-01-01

A series of three-dimensional computer simulations of disc galaxies has been run in which the self-consistent potential of the disc stars is supplemented by that arising from a small uniform Population II sphere. The models show variable spiral structure, which is more pronounced for thin discs. In addition, the thin discs form weak bars. In one case variable spiral structure associated with this bar has been seen. The relaxed discs are cool outside resonance regions. (author)

Spiral arms, comets and terrestrial catastrophism

International Nuclear Information System (INIS)

Clube, S.V.M.; Napier, W.M.

1982-01-01

A review is presented of an hypothesis of terrestrial catastrophism in which comets grow in molecular clouds and are captured by the Sun as it passes through the spiral arms of the Galaxy. Assuming that comets are a major supplier of the Earth-crossing (Appollo) asteroid population, the latter fluctuates correspondingly and leads to episodes of terrestrial bombardment. Changes in the rotational momentum of core and mantle, generated by impacts, lead to episodes of magnetic field reversal and tectonic activity, while surface phenomena lead to ice-ages and mass extinctions. An episodic geophysical history with an interstellar connection is thus implied. If comets in spiral arms are necessary intermediaries in the process of star formation, the theory also has implications relating to early solar system history and galactic chemistry. These aspects are briefly discussed with special reference to the nature of spiral arms. (author)

Molecular clouds and galactic spiral structure

International Nuclear Information System (INIS)

Dame, T.M.

1983-01-01

Galactic CO line emission at 115 GHz has been surveyed in the region 12 0 less than or equal to l less than or equal to 60 0 and -1 0 less than or equal to b less than or equal to 1 0 in order to study the distribution of molecular clouds in the inner galaxy; an inner strip 0 0 .5 wide has been sampled every beamwidth (0 0 .125), the rest every two beamwidths. Comparison of the survey with similar HI data reveals a detailed correlation with the most intense 21-cm features, implying that the CO and HI trace the same galactic features and have the same large-scale kinematics. To each of the classical 21-cm (HI) spiral arms of the inner galaxy there corresponds a CO molecular arm which is generally more clearly defined and of higher contrast. A simple model is developed in which all of the CO emission from the inner galaxy arises from spiral arms. The modeling results suggest that molecular clouds are essentially transient objects, existing for 15 to 40 million years after their formation in a spiral arm, and are largely confined to spiral features about 300 pc wide. A variety of methods are employed to estimate distances and masses for the largest clouds detected by the inner-galaxy survey and a catalogue is compiled. The catalogued clouds, the largest of which have masses of several 10 6 M/sub sunmass/ and linear dimensions in excess of 100 pc, are found to be excellent spiral-arm tracers. One of the nearest of the clouds, that associated with the supernova remnant W44, is fully mapped in both CO and 13 CO and is discussed in detail

Chemical constituents of Ottonia corcovadensis Miq. from Amazon forest: 1H and 13C chemical shift assignments

International Nuclear Information System (INIS)

Facundo, Valdir A.; Morais, Selene M.; Braz Filho, Raimundo

2004-01-01

In an ethanolic extract of leaves of Ottonia corcovadensis (Piperaceae) were identified sixteen terpenoids of essential oil and the three flavonoids 3',4',5,5',7-penta methoxyflavone (1), 3',4',5,7-tetra methoxyflavone (2) and 5-hydroxy-3',4',5',7-tetra methoxyflavone (3) and cafeic acid (4). Two amides (5 and 6) were isolated from an ethanolic extract of the roots. The structures were established by spectral analysis, meanly NMR (1D and 2D) and mass spectra. Extensive NMR analysis was also used to complete 1 H and 13 C chemical shift assignments of the flavonoids and amides. The components of the essential oil were identified by computer library search, retention indices and visual interpretation of mass spectra. (author)

The effect of cellular aging on the dynamics of spiral waves

International Nuclear Information System (INIS)

Deng Min-Yi; Chen Xi-Qiong; Tang Guo-Ning

2014-01-01

Cellular aging can result in deterioration of electrical coupling, the extension of the action potential duration, and lower excitability of the cell. Those factors are introduced into the Greenberg—Hastings cellular automaton model and the effects of the cellular aging on the dynamics of spiral waves are studied. The numerical results show that a 50% reduction of the coupling strength of aging cells has a little influence on spiral waves. If the coupling strength of aging cells equals zero, the ability for the medium to maintain spiral waves will be reduced by approximately 50% when the aging cell ratio increases from 0 to 0.5, where the reduction of cell excitability plays a major role in inducing disappearance of spiral waves. When the relevant parameters are properly chosen, the cellular aging can lead to the meandering of spiral waves, the emergence of the binary spiral waves, and even the disappearance of spiral waves via the stopping rotation or shrinkage of wave. Physical mechanisms of the above phenomena are analyzed briefly. (general)

Molecular gas and star formation in the centers of Virgo spirals

International Nuclear Information System (INIS)

Canzian, B.

1990-01-01

The CO and H alpha flux distributions for a sample of Virgo spirals were mapped out in an attempt to understand the coupling between gas dynamics and star formation in spiral galaxies. A broad range of morphological types were observed (types Sab through Scd) under the hypothesis that the gas dynamics is most influential in determining the overall appearance of a spiral galaxy. Only non-barred spirals were considered so that the well-studied but complicated properties of bars and their role in inducing star formation would not be a factor. All galaxies were chosen from the Virgo cluster to eliminate uncertainties due to distance errors. Since the dynamical seat of a spiral is at its center, it was expected that the dynamics of the central region would influence global properties of the rest of the disk. This could happen through the existence or absence of an inner Lindblad resonance (according to the degree of central concentration of mass) to modulate swing amplification of spiral waves, or the persistence of an oval distortion to initiate an instability which leads to spiral structure

Thalassiosira spp. community composition shifts in response to chemical and physical forcing in the northeast Pacific Ocean.

Directory of Open Access Journals (Sweden)

Phoebe Dreux Chappell

2013-09-01

Full Text Available Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here we examine shifts in Thalassiosira spp. composition along a coastal to open ocean transect that encountered a three-month-old Haida eddy in the northeast Pacific Ocean. To quantify shifts in Thalassiosira species composition, we developed a targeted automated ribosomal intergenic spacer analysis (ARISA method to identify Thalassiosira spp. in environmental samples. As many specific fragment lengths are indicative of individual Thalassiosira spp., the ARISA method is a useful screening tool to identify changes in the relative abundance and distribution of specific species. The method also enabled us to assess changes in Thalassiosira community composition in response to chemical and physical forcing. Thalassiosira spp. community composition in the core of a three-month-old Haida eddy remained largely (>80% similar over a two-week period, despite moving 24 km southwestward. Shifts in Thalassiosira species correlated with changes in dissolved iron (Fe and temperature throughout the sampling period. Simultaneously tracking community composition and relative abundance of Thalassiosira species within the physical and chemical context they occurred allowed us to identify quantitative linkages between environmental conditions and community response.

Digitized Spiral Drawing: A Possible Biomarker for Early Parkinson's Disease.

Science.gov (United States)

San Luciano, Marta; Wang, Cuiling; Ortega, Roberto A; Yu, Qiping; Boschung, Sarah; Soto-Valencia, Jeannie; Bressman, Susan B; Lipton, Richard B; Pullman, Seth; Saunders-Pullman, Rachel

2016-01-01

Pre-clinical markers of Parkinson's Disease (PD) are needed, and to be relevant in pre-clinical disease, they should be quantifiably abnormal in early disease as well. Handwriting is impaired early in PD and can be evaluated using computerized analysis of drawn spirals, capturing kinematic, dynamic, and spatial abnormalities and calculating indices that quantify motor performance and disability. Digitized spiral drawing correlates with motor scores and may be more sensitive in detecting early changes than subjective ratings. However, whether changes in spiral drawing are abnormal compared with controls and whether changes are detected in early PD are unknown. 138 PD subjects (50 with early PD) and 150 controls drew spirals on a digitizing tablet, generating x, y, z (pressure) data-coordinates and time. Derived indices corresponded to overall spiral execution (severity), shape and kinematic irregularity (second order smoothness, first order zero-crossing), tightness, mean speed and variability of spiral width. Linear mixed effect adjusted models comparing these indices and cross-validation were performed. Receiver operating characteristic analysis was applied to examine discriminative validity of combined indices. All indices were significantly different between PD cases and controls, except for zero-crossing. A model using all indices had high discriminative validity (sensitivity = 0.86, specificity = 0.81). Discriminative validity was maintained in patients with early PD. Spiral analysis accurately discriminates subjects with PD and early PD from controls supporting a role as a promising quantitative biomarker. Further assessment is needed to determine whether spiral changes are PD specific compared with other disorders and if present in pre-clinical PD.

Spiral-structured, nanofibrous, 3D scaffolds for bone tissue engineering.

Science.gov (United States)

Wang, Junping; Valmikinathan, Chandra M; Liu, Wei; Laurencin, Cato T; Yu, Xiaojun

2010-05-01

Polymeric nanofiber matrices have already been widely used in tissue engineering. However, the fabrication of nanofibers into complex three-dimensional (3D) structures is restricted due to current manufacturing techniques. To overcome this limitation, we have incorporated nanofibers onto spiral-structured 3D scaffolds made of poly (epsilon-caprolactone) (PCL). The spiral structure with open geometries, large surface areas, and porosity will be helpful for improving nutrient transport and cell penetration into the scaffolds, which are otherwise limited in conventional tissue-engineered scaffolds for large bone defects repair. To investigate the effect of structure and fiber coating on the performance of the scaffolds, three groups of scaffolds including cylindrical PCL scaffolds, spiral PCL scaffolds (without fiber coating), and spiral-structured fibrous PCL scaffolds (with fiber coating) have been prepared. The morphology, porosity, and mechanical properties of the scaffolds have been characterized. Furthermore, human osteoblast cells are seeded on these scaffolds, and the cell attachment, proliferation, differentiation, and mineralized matrix deposition on the scaffolds are evaluated. The results indicated that the spiral scaffolds possess porosities within the range of human trabecular bone and an appropriate pore structure for cell growth, and significantly lower compressive modulus and strength than cylindrical scaffolds. When compared with the cylindrical scaffolds, the spiral-structured scaffolds demonstrated enhanced cell proliferation, differentiation, and mineralization and allowed better cellular growth and penetration. The incorporation of nanofibers onto spiral scaffolds further enhanced cell attachment, proliferation, and differentiation. These studies suggest that spiral-structured nanofibrous scaffolds may serve as promising alternatives for bone tissue engineering applications. Copyright 2009 Wiley Periodicals, Inc.

Investigation of Spiral and Sweeping Holes

Science.gov (United States)

Thurman, Douglas; Poinsatte, Philip; Ameri, Ali; Culley, Dennis; Raghu, Surya; Shyam, Vikram

2015-01-01

Surface infrared thermography, hotwire anemometry, and thermocouple surveys were performed on two new film cooling hole geometries: spiral/rifled holes and fluidic sweeping holes. The spiral holes attempt to induce large-scale vorticity to the film cooling jet as it exits the hole to prevent the formation of the kidney shaped vortices commonly associated with film cooling jets. The fluidic sweeping hole uses a passive in-hole geometry to induce jet sweeping at frequencies that scale with blowing ratios. The spiral hole performance is compared to that of round holes with and without compound angles. The fluidic hole is of the diffusion class of holes and is therefore compared to a 777 hole and Square holes. A patent-pending spiral hole design showed the highest potential of the non-diffusion type hole configurations. Velocity contours and flow temperature were acquired at discreet cross-sections of the downstream flow field. The passive fluidic sweeping hole shows the most uniform cooling distribution but suffers from low span-averaged effectiveness levels due to enhanced mixing. The data was taken at a Reynolds number of 11,000 based on hole diameter and freestream velocity. Infrared thermography was taken for blowing rations of 1.0, 1.5, 2.0, and 2.5 at a density ration of 1.05. The flow inside the fluidic sweeping hole was studied using 3D unsteady RANS.

Spiral CT for evaluation of chest trauma

International Nuclear Information System (INIS)

Roehnert, W.; Weise, R.

1997-01-01

After implementation of spiral CT in our department, we carried out an analysis for determining anew the value of CT as a modality of chest trauma diagnosis in the emergency department. The retrospective study covers a period of 10 months and all emergency patients with chest trauma exmined by spiral CT. The major lesions of varying seriousness covered by this study are: pneumothorax, hematothorax, pulmonary contusion or laceration, mediastinal hematoma, rupture of a vessel, injury of the heart and pericardium. The various fractures are not included in this study. In many cases, spiral CT within relatively short time yields significant diagnostic findings, frequently saving additional angiography. A rigid diagnostic procedure cannot be formulated. Plain-film chest radiography still remains a diagnostic modality of high value. (Orig.) [de

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.

Generation of spiral waves pinned to obstacles in a simulated excitable system

Science.gov (United States)

Phantu, Metinee; Kumchaiseemak, Nakorn; Porjai, Porramain; Sutthiopad, Malee; Müller, Stefan C.; Luengviriya, Chaiya; Luengviriya, Jiraporn

2017-09-01

Pinning phenomena emerge in many dynamical systems. They are found to stabilize extreme conditions such as superconductivity and super fluidity. The dynamics of pinned spiral waves, whose tips trace the boundary of obstacles, also play an important role in the human health. In heart, such pinned waves cause longer tachycardia. In this article, we present two methods for generating pinned spiral waves in a simulated excitable system. In method A, an obstacle is set in the system prior to an ignition of a spiral wave. This method may be suitable only for the case of large obstacles since it often fails when used for small obstacles. In method B, a spiral wave is generated before an obstacle is placed at the spiral tip. With this method, a pinned spiral wave is always obtained, regardless the obstacle size. We demonstrate that after a transient interval the dynamics of the pinned spiral waves generated by the methods A and B are identical. The initiation of pinned spiral waves in both two- and three-dimensional systems is illustrated.

A spiral, bi-planar gradient coil design for open magnetic resonance imaging.

Science.gov (United States)

Zhang, Peng; Shi, Yikai; Wang, Wendong; Wang, Yaohui

2018-01-01

To design planar gradient coil for MRI applications without discretization of continuous current density and loop-loop connection errors. In the new design method, the coil current is represented using a spiral curve function described by just a few control parameters. Using a proper parametric equation set, an ensemble of spiral contours is reshaped to satisfy the coil design requirements, such as gradient linearity, inductance and shielding. In the given case study, by using the spiral coil design, the magnetic field errors in the imaging area were reduced from 5.19% (non-spiral design) to 4.47% (spiral design) for the transverse gradient coils, and for the longitudinal gradient coil design, the magnetic field errors were reduced to 5.02% (spiral design). The numerical evaluation shows that when compared with conventional wire loop, the inductance and resistance of spiral coil was reduced by 11.55% and 8.12% for x gradient coil, respectively. A novel spiral gradient coil design for biplanar MRI systems, the new design offers better magnetic field gradients, smooth contours than the conventional connected counterpart, which improves manufacturability.

Improvement of chemical shift selective saturation (CHESS) pulse for MR angiography

International Nuclear Information System (INIS)

Ishimori, Yoshiyuki; Sashie, Hiroyuki; Hiraga, Akira; Matsuda, Tsuyoshi

2000-01-01

We improved the fat suppression technique based on chemical shift selective saturation (CHESS). To do this, we shortened the duration of the CHESS pulse to achieve a short repetition time (TR) for MR angiography (MRA). A short-duration CHESS pulse causes broad frequency band saturation, creating extensive offset from the resonance frequency of water. In our phantom experiment, the best parameters of the short-duration CHESS pulse were 3.84 ms in duration, -650 Hz in offset frequency from water resonance, and had a 130-degree flip angle. With this technique, MRA will be able to be carried out without a significant increase in TR. Thus, better vessel contrast will be maintained in time-of-flight (TOF) MRA or contrast-enhanced MRA when using the maximum intensity projection (MIP) method. (author)

Isomer shifts and chemical bonding in crystalline Sn(II) and Sn(IV) compounds

International Nuclear Information System (INIS)

Terra, J.; Guenzburger, D.

1991-01-01

First-principles self-consistent Local Density calculations of the electronic structure of clusters representing Sn(II) (SnO, SnF 2 , SnS, SnSe) and Sn(IV) (SnO 2 , SnF 4 ) crystalline compounds were performed. Values of the electron density at the Sn nucleus were obtained and related to measured values of the Moessbauer Isomer Shifts reported in the literature. The nuclear parameter of 119 Sn derived was ΔR/R=(1.58±0.14)x10 -4 . The chemical bonding in the solids was analysed and related to the electron densities obtained. (author)

Propagating star formation and irregular structure in spiral galaxies

International Nuclear Information System (INIS)

Mueller, M.W.; Arnett, W.D.

1976-01-01

A simple model is proposed which describes the irregular optical appearance often seen in late-type spiral galaxies. If high-mass stars produce spherical shock waves which induce star formation, new high-mass stars will be born which, in turn, produce new shock waves. When this process operates in a differentially rotating disk, our numerical model shows that large-scale spiral-shaped regions of star formation are built up. The structure is seen to be most sensitive to a parameter which governs how often a region of the interstellar medium can undergo star formation. For a proper choice of this parameter, large-scale features disappear before differential rotation winds them up. New spiral features continuously form, so some spiral structure is seen indefinitely. The structure is not the classical two-armed symmetric spiral pattern which the density-wave theory attempts to explain, but it is asymmetric and disorderly.The mechanism of propagating star formation used in our model is consistent with observations which connect young OB associations with expanding shells of gas. We discuss the possible interaction of this mechanism with density waves

A comment on spiral motions in projective relativity

International Nuclear Information System (INIS)

Muzzio, J.C.; Lousto, C.O.; Instituto de Astronomia y Fisica del Espacio de la Republica Argentina)

1985-01-01

Astronomical evidence has been inadequately invoked to support projective relativity. The spiral structure cannot be explained just by the existence of spiral orbits, and the use of Oort's constant to support the theory is also a misunderstanding. Besides, some mathematical inaccuracies make the application invalid. (author)

Predicting Heats of Explosion of Nitroaromatic Compounds through NBO Charges and 15N NMR Chemical Shifts of Nitro Groups

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.

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

Science.gov (United States)

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. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Properties of the outer regions of spiral disks: abundances, colors and ages

Science.gov (United States)

Mollá, Mercedes; Díaz, Angeles I.; Gibson, Brad K.; Cavichia, Oscar; López-Sánchez, Ángel-R.

2017-03-01

We summarize the results obtained from our suite of chemical evolution models for spiral disks, computed for different total masses and star formation efficiencies. Once the gas, stars and star formation radial distributions are reproduced, we analyze the Oxygen abundances radial profiles for gas and stars, in addition to stellar averaged ages and global metallicity. We examine scenarios for the potential origin of the apparent flattening of abundance gradients in the outskirts of disk galaxies, in particular the role of molecular gas formation prescriptions.

Design and evaluation of a high sensitivity spiral TDR scour sensor

Science.gov (United States)

Gao, Quan; (Bill Yu, Xiong

2015-08-01

Bridge scour accounts for more than half of the reported bridge failures in the United States. Scour monitoring technology based on time domain reflectometry (TDR) features the advantages of being automatic and inexpensive. The senior author’s team has developed a few generations of a TDR bridge scour monitoring system, which have succeeded in both laboratory and field evaluations. In this study, an innovative spiral TDR sensor is proposed to further improve the sensitivity of the TDR sensor in scour detection. The spiral TDR sensor is made of a parallel copper wire waveguide wrapped around a mounting rod. By using a spiral path for the waveguide, the TDR sensor achieves higher sensitivity than the traditional straight TDR probes due to longer travel distance of the electromagnetic (EM) wave per unit length in the spiral probe versus traditional probe. The performance of the new TDR spiral scour sensor is validated by calibration with liquids with known dielectric constant and wet soils. Laboratory simulated scour-refilling experiments are performed to evaluate the performance of the new spiral probe in detecting the sediment-water interface and therefore the scour-refill process. The tests results indicate that scour depth variation of less than 2 cm can be easily detected by this new spiral sensor. A theory is developed based on the dielectric mixing model to simplify the TDR signal analyses for scour depth detection. The sediment layer thickness (directly related to scour depth) varies linearly with the square root of the bulk dielectric constant of the water-sediment mixture measured by the spiral TDR probe, which matches the results of theoretical prediction. The estimated sediment layer thickness and therefore scour depth from the spiral TDR sensor agrees very well with that by direct physical measurement. The spiral TDR sensor is four times more sensitive than a traditional straight TDR probe.

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...

Adaptation of the control system in view of SPIRAL integration

International Nuclear Information System (INIS)

Lecorche, E.

1998-01-01

As soon as the collaboration between the SPIRAL project and the Control Group has been defined, the first implementation of the SPIRAL control system started following various directions. Both the global hardware and software architectures has been specified and some practical works have been undertaken such as the Ethernet network installation or the first SPIRAL oriented software design and coding. (authors)

Model for Simulating a Spiral Software-Development Process

Science.gov (United States)

Mizell, Carolyn; Curley, Charles; Nayak, Umanath

2010-01-01

A discrete-event simulation model, and a computer program that implements the model, have been developed as means of analyzing a spiral software-development process. This model can be tailored to specific development environments for use by software project managers in making quantitative cases for deciding among different software-development processes, courses of action, and cost estimates. A spiral process can be contrasted with a waterfall process, which is a traditional process that consists of a sequence of activities that include analysis of requirements, design, coding, testing, and support. A spiral process is an iterative process that can be regarded as a repeating modified waterfall process. Each iteration includes assessment of risk, analysis of requirements, design, coding, testing, delivery, and evaluation. A key difference between a spiral and a waterfall process is that a spiral process can accommodate changes in requirements at each iteration, whereas in a waterfall process, requirements are considered to be fixed from the beginning and, therefore, a waterfall process is not flexible enough for some projects, especially those in which requirements are not known at the beginning or may change during development. For a given project, a spiral process may cost more and take more time than does a waterfall process, but may better satisfy a customer's expectations and needs. Models for simulating various waterfall processes have been developed previously, but until now, there have been no models for simulating spiral processes. The present spiral-process-simulating model and the software that implements it were developed by extending a discrete-event simulation process model of the IEEE 12207 Software Development Process, which was built using commercially available software known as the Process Analysis Tradeoff Tool (PATT). Typical inputs to PATT models include industry-average values of product size (expressed as number of lines of code

Nonplanar spiral states of the t-J model with classical spins

International Nuclear Information System (INIS)

Hamada, M.; Shimahara, H.; Mori, H.

1995-01-01

The spiral state in the two-dimensional t-J model is studied by numerical diagonalization of an effective Hamiltonian. We examine all possibilities of the spiral spin states including the nonplanar states. It is found that nonplanar spiral states occur, but the deviations from the planar spiral state in the nonplanar spiral states are small for small hole concentrations where our effective Hamiltonian is valid. The modulation of the spin configuration increases continuously from the antiferromagnetic order as the hole concentration increases, and discontinuously changes at a critical hole concentration. Then the state undergoes the first-order phase transition either to the (π,0) phase or to the ferromagnetic phase, depending on the value of J/t

Packing of equal discs on a parabolic spiral lattice

International Nuclear Information System (INIS)

Xudong, F.; Bursill, L.A.; Julin, P.

1989-01-01

A contact disc model is investigated to determine the most closely-packed parabolic spiral lattice. The most space-efficient packings have divergence angles in agreement with the priority ranking of natural spiral structures

Computerized spiral analysis using the iPad.

Science.gov (United States)

Sisti, Jonathan A; Christophe, Brandon; Seville, Audrey Rakovich; Garton, Andrew L A; Gupta, Vivek P; Bandin, Alexander J; Yu, Qiping; Pullman, Seth L

2017-01-01

Digital analysis of writing and drawing has become a valuable research and clinical tool for the study of upper limb motor dysfunction in patients with essential tremor, Parkinson's disease, dystonia, and related disorders. We developed a validated method of computerized spiral analysis of hand-drawn Archimedean spirals that provides insight into movement dynamics beyond subjective visual assessment using a Wacom graphics tablet. While the Wacom tablet method provides robust data, more widely available mobile technology platforms exist. We introduce a novel adaptation of the Wacom-based method for the collection of hand-drawn kinematic data using an Apple iPad. This iPad-based system is stand-alone, easy-to-use, can capture drawing data with either a finger or capacitive stylus, is precise, and potentially ubiquitous. The iPad-based system acquires position and time data that is fully compatible with our original spiral analysis program. All of the important indices including degree of severity, speed, presence of tremor, tremor amplitude, tremor frequency, variability of pressure, and tightness are calculated from the digital spiral data, which the application is able to transmit. While the iPad method is limited by current touch screen technology, it does collect data with acceptable congruence compared to the current Wacom-based method while providing the advantages of accessibility and ease of use. The iPad is capable of capturing precise digital spiral data for analysis of motor dysfunction while also providing a convenient, easy-to-use modality in clinics and potentially at home. Copyright © 2016 Elsevier B.V. All rights reserved.

Compression of interstellar clouds in spiral density-wave shocks

International Nuclear Information System (INIS)

Woodward, P.R.

1979-01-01

A mechanism of triggering star formation by galactic shocks is discussed. The possibilty that shocks may form along spiral arms in the gaseous component of a galactic disk is by now a familiar feature of spiral wave theory. It was suggested by Roberts (1969) that these shocks could trigger star formation in narrow bands forming a coherent spiral pattern over most of the disk of a galaxy. Some results of computer simulations of such a triggering process for star formation are reported. (Auth.)

Boundary layer circulation in disk-halo galaxies. III. The dispersion relation for local disturbances and large-scale spiral waves

International Nuclear Information System (INIS)

Waxman, A.M.

1980-01-01

This paper concerns the geometry and physical properties of waves which arise from a shear-flow (i.e. inflection point) instability of the galactic boundary layer circulation. This circulation was shown to exist in the meridional plane of a model galaxy containing a gaseous disk embedded in a rotating gaseous halo. Previously derived equations describe the local effects of Boussinesq perturbations, in the form of spiral waves with aribitrary pitch angle, on the model disk-halo system. The equations are solved asymptotically for large values of the local Reynolds number. In passing to the limit of inviscid waves, it is possible to derive a locally valid dispersion relation. A perturbation technique is developed whereby the inviscid wave eigenvalues can be corrected for the effects of small but finite viscosity. In this way the roles of the buoyancy force, Coriolis acceleration, viscous stresses, and their interactions can be studied. It is found that, locally, the most unstable inviscid waves are leading and open with large azimuthal wavenumbers. However, these waves display little or no coherence over the face of the disk and so would not emerge as modes in a global analysis.The geometry of the dominant inviscid waves is found to be leading, tightly wound spirals. Viscous corrections shift the dominant wave form to trailing, tightly wound spirals with small azimuthal wavenumbers. These waves grow on a time scale of about 10 7 years. It is suggested that these waves can initiate spiral structure in galaxies during disk formation and that a subsequent transition to a self-gravitating acoustical mode with the same spiral geometry may occur. This transition becomes possible once the contrast in gas densities between the disk and surrounding halo becomes sufficiently large

A Bayesian-probability-based method for assigning protein backbone dihedral angles based on chemical shifts and local sequences

Energy Technology Data Exchange (ETDEWEB)

Wang Jun; Liu Haiyan [University of Science and Technology of China, Hefei National Laboratory for Physical Sciences at the Microscale, and Key Laboratory of Structural Biology, School of Life Sciences (China)], E-mail: hyliu@ustc.edu.cn

2007-01-15

Chemical shifts contain substantial information about protein local conformations. We present a method to assign individual protein backbone dihedral angles into specific regions on the Ramachandran map based on the amino acid sequences and the chemical shifts of backbone atoms of tripeptide segments. The method uses a scoring function derived from the Bayesian probability for the central residue of a query tripeptide segment to have a particular conformation. The Ramachandran map is partitioned into representative regions at two levels of resolution. The lower resolution partitioning is equivalent to the conventional definitions of different secondary structure regions on the map. At the higher resolution level, the {alpha} and {beta} regions are further divided into subregions. Predictions are attempted at both levels of resolution. We compared our method with TALOS using the original TALOS database, and obtained comparable results. Although TALOS may produce the best results with currently available databases which are much enlarged, the Bayesian-probability-based approach can provide a quantitative measure for the reliability of predictions.

HI-deficient spiral galaxies in the Coma cluster and Abell 1367

International Nuclear Information System (INIS)

Sullivan, W.T. III; Johnson, P.E.

1978-01-01

A sample of 11 spiral galaxies in each of the clusters Abell 1367 and Coma (Abell 1656) was observed in the 21-cm H I line with the Arecibo 305-m radio telescope. Nine galaxies are detected in Al367 and three in Coma. Comparison of the quantity log M/sub H/L/sub pg/ for each galaxy with the mean value for its Hubble type from the standard samples of nearby spirals compiled by Balkowski and by Roberts indicates that the A1367 and Coma spirals have lower values of log M/sub H/L/sub pg/ than field spirals by a factor of at least 4, with the Coma values probably more extreme. It is argued that little of this effect (perhaps a factor approx. 1.5) can be attributed to the bias toward high luminosities in the sample, and thus that these spirals are deficient in H I by factors of at least 3 to 5 in comparison with the standard samples. For the present limited sample, several mechanisms seem adequate to account qualitatively for stripping of H I from the Coma cluster spirals, but the case of the A1367 spirals is puzzling. 2 figures

Elimination of spiral chaos by periodic force for the Aliev-Panfilov model

OpenAIRE

Sakaguchi, Hidetsugu; Fujimoto, Takefumi

2003-01-01

Spiral chaos appears in the two dimensional Aliev-Panfilov model. The generation mechanism of the spiral chaos is related to the breathing instability of pulse trains. The spiral chaos can be eliminated by applying periodic force uniformly. The elimination of spiral chaos is most effective, when the frequency of the periodic force is close to that of the breathing motion.

On the nature of the ramified spiral structure of galaxies

International Nuclear Information System (INIS)

Mishurov, Yu.N.; Suchkov, A.A.

1976-01-01

The nature of large-scale branching of spiral arms observed in a number of galaxies has been explained in the framework of the density wave theory. The solutions of the dispersion equation of spiral waves of density relative to the wave number k(r) in the models of galaxies in the form of two discs rotating with different angular velocities have been shown to be branching functions of the parameter r (r is the galacto-centric distance) under definite conditions; it corresponds to the branching of spiral arms. Hydrodynamic and kinetic considerations are also presented. The last one makes possible the understanding several other structural properties of spiral galaxies

Principles of spiral CT: III. Quality assurance

International Nuclear Information System (INIS)

Suess, C.; Kalender, W.A.

1998-01-01

Since its introduction in 1989 spiral CT has gained wide clinical acceptance and meanwhile it covers a large range of CT applications. This new technology, however, has not yet been recognized and acknowledged in the national or international regulations on scanner quality assurance (QA) programs. The conventional QA procedures should be extended to check the distribution of resolution and noise within the image plane. Imaging performance in the axial direction constitutes one of the major advantages of spiral scanning. Therefore, the slice sensitivity profiles and the spatial and low-contrast resolution along the z-axis have to be assessed. The high demands on table feed accuracy require additional tests. We suggest phantoms and procedures to check and quantify these parameters. Thereby, we hope to support the ongoing discussion about spiral CT quality assurance. (orig.) [de

Nuclear Spiral Shocks and Induced Gas Inflows in Weak Oval Potentials

Energy Technology Data Exchange (ETDEWEB)

Kim, Woong-Tae [Department of Physics and Astronomy, Seoul National University, Seoul 151-742 (Korea, Republic of); Elmegreen, Bruce G., E-mail: wkim@astro.snu.ac.kr, E-mail: bge@us.ibm.com [IBM T. J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY 10598 (United States)

2017-05-20

Nuclear spirals are ubiquitous in galaxy centers. They exist not only in strong barred galaxies but also in galaxies without noticeable bars. We use high-resolution hydrodynamic simulations to study the properties of nuclear gas spirals driven by weak bar-like and oval potentials. The amplitude of the spirals increases toward the center by a geometric effect, readily developing into shocks at small radii even for very weak potentials. The shape of the spirals and shocks depends rather sensitively on the background shear. When shear is low, the nuclear spirals are loosely wound and the shocks are almost straight, resulting in large mass inflows toward the center. When shear is high, on the other hand, the spirals are tightly wound and the shocks are oblique, forming a circumnuclear disk through which gas flows inward at a relatively lower rate. The induced mass inflow rates are enough to power black hole accretion in various types of Seyfert galaxies as well as to drive supersonic turbulence at small radii.

Chemical evolution of galaxies

International Nuclear Information System (INIS)

Pagel, B.E.J.

1979-01-01

The chemical evolution of disk galaxies is discussed with special reference to results obtained from studies of the oxygen abundance in H II regions. Normal spirals (including our own) display the by now well known radial abundance gradient, which is discussed on the basis of the simple enrichment model and other models. The Magellanic Clouds, on the other hand, and the barred spiral NGC 1365, have been found to have little or no abundance gradient, implying a very different sort of evolution that may involve large-scale mixing. Finally, the simple model is tested against a number of results in H II regions where the ratio of total mass to mass of residual gas can be estimated. It turns out to fit adequately the Magellanic Clouds and a number of H II regions in the outer parts of spiral galaxies, but in more inner parts it fails, as do more sophisticated models involving infall during the formation of galactic disks that have proved very successful in other respects. (Auth.)

Topographic Beta Spiral and Onshore Intrusion of the Kuroshio Current

Science.gov (United States)

Yang, De-Zhou; Huang, Rui Xin; Yin, Bao-shu; Feng, Xing-Ru; Chen, Hai-ying; Qi, Ji-Feng; Xu, Ling-jing; Shi, Yun-long; Cui, Xuan; Gao, Guan-Dong; Benthuysen, Jessica A.

2018-01-01

The Kuroshio intrusion plays a vitally important role in carrying nutrients to marginal seas. However, the key mechanism leading to the Kuroshio intrusion remains unclear. In this study we postulate a mechanism: when the Kuroshio runs onto steep topography northeast of Taiwan, the strong inertia gives rise to upwelling over topography, leading to a left-hand spiral in the stratified ocean. This is called the topographic beta spiral, which is a major player regulating the Kuroshio intrusion; this spiral can be inferred from hydrographic surveys. In the world oceans, the topographic beta spirals can be induced by upwelling generated by strong currents running onto steep topography. This is a vital mechanism regulating onshore intruding flow and the cross-shelf transport of energy and nutrients from the Kuroshio Current to the East China Sea. This topographic beta spiral reveals a long-term missing link between the oceanic general circulation theory and shelf dynamic theory.

Multi-armed spirals and multi-pairs antispirals in spatial rock–paper–scissors games

Energy Technology Data Exchange (ETDEWEB)

Jiang, Luo-Luo, E-mail: jiangluoluo@gmail.com [College of Physics and Electronic Information Engineering, Wenzhou University, Wenzhou 325035 (China); College of Physics and Technology, Guangxi Normal University, Guilin, Guangxi 541004 (China); Wang, Wen-Xu [School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ 85287 (United States); Department of Physics, Beijing Normal University, Beijing 100875 (China); Lai, Ying-Cheng [School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ 85287 (United States); Department of Physics, Arizona State University, Tempe, AZ 85287 (United States); Ni, Xuan [School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ 85287 (United States)

2012-07-09

We study the formation of multi-armed spirals and multi-pairs antispirals in spatial rock–paper–scissors games with mobile individuals. We discover a set of seed distributions of species, which is able to produce multi-armed spirals and multi-pairs antispirals with a finite number of arms and pairs based on stochastic processes. The joint spiral waves are also predicted by a theoretical model based on partial differential equations associated with specific initial conditions. The spatial entropy of patterns is introduced to differentiate the multi-armed spirals and multi-pairs antispirals. For the given mobility, the spatial entropy of multi-armed spirals is higher than that of single armed spirals. The stability of the waves is explored with respect to individual mobility. Particularly, we find that both two armed spirals and one pair antispirals transform to the single armed spirals. Furthermore, multi-armed spirals and multi-pairs antispirals are relatively stable for intermediate mobility. The joint spirals with lower numbers of arms and pairs are relatively more stable than those with higher numbers of arms and pairs. In addition, comparing to large amount of previous work, we employ the no flux boundary conditions which enables quantitative studies of pattern formation and stability in the system of stochastic interactions in the absence of excitable media. -- Highlights: ► Multi-armed spirals and multi-pairs antispirals are observed. ► Patterns are predicted by computer simulations and partial differential equations. ► The spatial entropy of patterns is introduced. ► Patterns are relatively stable for intermediate mobility. ► The joint spirals with lower numbers of arms and pairs are relatively more stable.

Multi-armed spirals and multi-pairs antispirals in spatial rock–paper–scissors games

International Nuclear Information System (INIS)

Jiang, Luo-Luo; Wang, Wen-Xu; Lai, Ying-Cheng; Ni, Xuan

2012-01-01

We study the formation of multi-armed spirals and multi-pairs antispirals in spatial rock–paper–scissors games with mobile individuals. We discover a set of seed distributions of species, which is able to produce multi-armed spirals and multi-pairs antispirals with a finite number of arms and pairs based on stochastic processes. The joint spiral waves are also predicted by a theoretical model based on partial differential equations associated with specific initial conditions. The spatial entropy of patterns is introduced to differentiate the multi-armed spirals and multi-pairs antispirals. For the given mobility, the spatial entropy of multi-armed spirals is higher than that of single armed spirals. The stability of the waves is explored with respect to individual mobility. Particularly, we find that both two armed spirals and one pair antispirals transform to the single armed spirals. Furthermore, multi-armed spirals and multi-pairs antispirals are relatively stable for intermediate mobility. The joint spirals with lower numbers of arms and pairs are relatively more stable than those with higher numbers of arms and pairs. In addition, comparing to large amount of previous work, we employ the no flux boundary conditions which enables quantitative studies of pattern formation and stability in the system of stochastic interactions in the absence of excitable media. -- Highlights: ► Multi-armed spirals and multi-pairs antispirals are observed. ► Patterns are predicted by computer simulations and partial differential equations. ► The spatial entropy of patterns is introduced. ► Patterns are relatively stable for intermediate mobility. ► The joint spirals with lower numbers of arms and pairs are relatively more stable.

Spiral wave drift and complex-oscillatory spiral waves caused by heterogeneities in two-dimensional in vitro cardiac tissues

International Nuclear Information System (INIS)

Woo, Sung-Jae; Hong, Jin Hee; Kim, Tae Yun; Bae, Byung Wook; Lee, Kyoung J

2008-01-01

Understanding spiral reentry wave dynamics in cardiac systems is important since it underlies various cardiac arrhythmia including cardiac fibrillation. Primary cultures of dissociated cardiac cells have been a convenient and useful system for studying cardiac wave dynamics, since one can carry out systematic and quantitative studies with them under well-controlled environments. One key drawback of the dissociated cell culture is that, inevitably, some spatial inhomogeneities in terms of cell types and density, and/or the degree of gap junction connectivity, are introduced to the system during the preparation. These unintentional spatial inhomogeneities can cause some non-trivial wave dynamics, for example, the entrainment dynamics among different spiral waves and the generation of complex-oscillatory spiral waves. The aim of this paper is to quantify these general phenomena in an in vitro cardiac system and provide explanations for them with a simple physiological model having some realistic spatial inhomogeneities incorporated

The instability of the spiral wave induced by the deformation of elastic excitable media

International Nuclear Information System (INIS)

Ma Jun; Jia Ya; Wang Chunni; Li Shirong

2008-01-01

There are some similarities between the spiral wave in excitable media and in cardiac tissue. Much evidence shows that the appearance and instability of the spiral wave in cardiac tissue can be linked to one kind of heart disease. There are many models that can be used to investigate the formation and instability of the spiral wave. Cardiac tissue is excitable and elastic, and it is interesting to simulate the transition and instability of the spiral wave induced by media deformation. For simplicity, a class of the modified Fitzhugh-Nagumo (MFHN) model, which can generate a stable rotating spiral wave, meandering spiral wave and turbulence within appropriate parameter regions, will be used to simulate the instability of the spiral wave induced by the periodical deformation of media. In the two-dimensional case, the total acreage of elastic media is supposed to be invariable in the presence of deformation, and the problem is described with L x x L y = N x ΔxN x Δy = L' x L' y = N x Δx'N x Δy'. In our studies, elastic media are decentralized into N x N sites and the space of the adjacent sites is changed to simulate the deformation of elastic media. Based on the nonlinear dynamics theory, the deformation effect on media is simplified and simulated by perturbing the diffusion coefficients D x and D y with different periodical signals, but the perturbed diffusion coefficients are compensatory. The snapshots of our numerical results find that the spiral wave can coexist with the spiral turbulence, instability of the spiral wave and weak deformation of the spiral wave in different conditions. The ratio parameter ε and the frequency of deformation forcing play a deterministic role in inducing instability of the spiral wave. Extensive studies confirm that the instability of the spiral wave can be induced and developed only if an appropriate frequency for deformation is used. We analyze the power spectrum for the time series of the mean activator of four sampled sites

The instability of the spiral wave induced by the deformation of elastic excitable media

Science.gov (United States)

Ma, Jun; Jia, Ya; Wang, Chun-Ni; Li, Shi-Rong

2008-09-01

There are some similarities between the spiral wave in excitable media and in cardiac tissue. Much evidence shows that the appearance and instability of the spiral wave in cardiac tissue can be linked to one kind of heart disease. There are many models that can be used to investigate the formation and instability of the spiral wave. Cardiac tissue is excitable and elastic, and it is interesting to simulate the transition and instability of the spiral wave induced by media deformation. For simplicity, a class of the modified Fitzhugh-Nagumo (MFHN) model, which can generate a stable rotating spiral wave, meandering spiral wave and turbulence within appropriate parameter regions, will be used to simulate the instability of the spiral wave induced by the periodical deformation of media. In the two-dimensional case, the total acreage of elastic media is supposed to be invariable in the presence of deformation, and the problem is described with Lx × Ly = N × ΔxN × Δy = L'xL'y = N × Δx'N × Δy'. In our studies, elastic media are decentralized into N × N sites and the space of the adjacent sites is changed to simulate the deformation of elastic media. Based on the nonlinear dynamics theory, the deformation effect on media is simplified and simulated by perturbing the diffusion coefficients Dx and Dy with different periodical signals, but the perturbed diffusion coefficients are compensatory. The snapshots of our numerical results find that the spiral wave can coexist with the spiral turbulence, instability of the spiral wave and weak deformation of the spiral wave in different conditions. The ratio parameter ɛ and the frequency of deformation forcing play a deterministic role in inducing instability of the spiral wave. Extensive studies confirm that the instability of the spiral wave can be induced and developed only if an appropriate frequency for deformation is used. We analyze the power spectrum for the time series of the mean activator of four sampled sites

Nonsuppressing normal thymus on chemical-shift MR imaging and anterior mediastinal lymphoma. Differentiation with diffusion-weighted MR imaging by using the apparent diffusion coefficient

International Nuclear Information System (INIS)

Priola, Adriano Massimiliano; Priola, Sandro Massimo; Gned, Dario; Veltri, Andrea; Giraudo, Maria Teresa

2018-01-01

To prospectively evaluate usefulness of the apparent diffusion coefficient (ADC) in differentiating anterior mediastinal lymphoma from nonsuppressing normal thymus on chemical-shift MR, and to look at the relationship between patient age and ADC. Seventy-three young subjects (25 men, 48 women; age range, 9-29 years), who underwent chemical-shift MR and diffusion-weighted MR were divided into a normal thymus group (group A, 40 subjects), and a lymphoma group (group B, 33 patients). For group A, all subjects had normal thymus with no suppression on opposed-phase chemical-shift MR. Two readers measured the signal intensity index (SII) and ADC. Differences in SII and ADC between groups were tested using t-test. ADC was correlated with age using Pearson correlation coefficient. Mean SII±standard deviation was 2.7±1.8% for group A and 2.2±2.4% for group B, with no significant difference between groups (P=.270). Mean ADC was 2.48±0.38 x 10 -3 mm 2 /s for group A and 1.24±0.23 x 10 -3 mm 2 /s for group B. A significant difference between groups was found (P<.001), with no overlap in range. Lastly, significant correlation was found between age and ADC (r=0.935, P<.001) in group A. ADC of diffusion-weighted MR is a noninvasive and accurate parameter for differentiating lymphoma from nonsuppressing thymus on chemical-shift MR in young subjects. (orig.)

Spiral-shaped disinfection reactors

KAUST Repository

Ghaffour, NorEddine; Ait-Djoudi, Fariza; Naceur, Wahib Mohamed; Soukane, Sofiane

2015-01-01

This disclosure includes disinfection reactors and processes for the disinfection of water. Some disinfection reactors include a body that defines an inlet, an outlet, and a spiral flow path between the inlet and the outlet, in which the body

Spiral structure and star formation. II. Stellar lifetimes and cloud kinematics

International Nuclear Information System (INIS)

Hausman, M.A.; Roberts, W.W. Jr.

1984-01-01

We present further results of our model, introduced in Paper I, of star formation and star-gas interactions in the cloud-dominated ISMs of spiral density wave galaxies. The global density distribution and velocity field of the gas clouds are virtually independent of stellar parameters and even of mean free path for the wide range of values studied, but local density variations are found which superficially resemble cloud complexes. Increasing the average life span of ''spiral tracer'' stellar associations beyond about 20 Myr washes out the spiral pattern which younger associations show. Allowing clouds to form several successive associations (sequential star formation) slightly increases the frequency of interarm, young-star spurs and substantially increases the average star formation rate. The mean velocity field of clouds shows tipped oval streamlines, similar to both continuum gas dynamical models and stellar-kinematic models of spiral density waves. These streamlines are almost ballistic orbits except close to the spiral arms. Newly formed stellar associations leave the spiral density peak with initial tangential velocitie shigher than ''postshock'' values and do not fall back into the ''preshock'' region. By varying our stellar parametes within physically reasonable limits, we may reproduce spiral galaxies with a wide range of morphological appearaces

A Spiral Task as a Model for In-Service Teacher Education

Science.gov (United States)

Fried, Michael N.; Amit, Miriam

2005-01-01

The spiral approach has long been used by curriculum designers to deepen students' knowledge of scientific and mathematical concepts and to bring students to higher levels of abstraction. The benefits of a spiral approach, however, can also be extended to teacher education. This paper describes a spiral activity employed by the "Kidumatica"…

STRUCTURED MOLECULAR GAS REVEALS GALACTIC SPIRAL ARMS

Energy Technology Data Exchange (ETDEWEB)

Sawada, Tsuyoshi [Joint ALMA Office, Alonso de Cordova 3107, Vitacura, Santiago 763-0355 (Chile); Hasegawa, Tetsuo [NAOJ Chile Observatory, Joaquin Montero 3000 Oficina 702, Vitacura, Santiago 763-0409 (Chile); Koda, Jin, E-mail: sawada.tsuyoshi@nao.ac.jp [Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800 (United States)

2012-11-01

We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory {sup 13}CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.

MR chemical shift imaging and spectroscopy of atherosclerotic plaque

International Nuclear Information System (INIS)

Vinitski, S.; Consigny, P.M.; Shapiro, M.J.; Janes, N.; Smullens, S.N.; Rifkin, M.D.

1989-01-01

The purpose of this study was to develop a technique for in vivo imaging and characterization of atherosclerotic plaque. The authors used a spin-echo technique with a short echo time (TE) of 11 msec. Lipid/water suppression was achieved by means of hybrid chemical shift imaging. Lesions were induced in three rabbits by a combination of balloon denudation of the abdominal aorta and a high-cholesterol diet. Following in vivo imaging of these rabbit aortas and human carotid arteries (1.5 T), the animals were killed or carotid endarterectomy was performed so that the plaques could be excised. The plaques were then analyzed in vitro both histologically and with high-resolution spectroscopy (8.5 T). Use of the short TE improved lesion visualization. The fat/water suppression showed only a small amount of mobile lipids in plaque. Both MR spectroscopic and histologic analysis corroborated these images. The composition of atherosclerotic plaques in both humans and rabbits was demonstrated to be heterogeneous, with predominantly nonmobile lipids. These results suggest that the combination of short TE MR imaging and fat/water suppression can identify plaque and delineate areas containing mobile lipids

Measurement of lung volumes : usefulness of spiral CT

International Nuclear Information System (INIS)

Kang, Ho Yeong; Kwak, Byung Kook; Lee, Sang Yoon; Kim, Soo Ran; Lee, Shin Hyung; Lee, Chang Joon; Park, In Won

1996-01-01

To evaluate the usefulness of spiral CT in the measurement of lung volumes. Fifteen healthy volunteers were studied by both spirometer and spiral CT at full inspiration and expiration in order to correlated their results, including total lung capacity (TLC), vital capacity (VC) and residual volume (RV). 3-D images were reconstructed from spiral CT, and we measured lung volumes at a corresponding CT window range ; their volumes were compared with the pulmonary function test (paired t-test). The window range corresponding to TLC was from -1000HU to -150HU (p=0.279, r=0.986), and for VC from -910HU to -800HU (p=0.366, r=0.954) in full-inspiratory CT. The optimal window range for RV in full-expiratory CT was from -1000HU to -450HU (p=0.757, r=0.777), and TLC-VC in full-inspiratory CT was also calculated (p=0.843, r=0.847). Spiral CT at full inspiration can used to lung volumes such as TLC, VC and RV

Advanced Manufacture of Spiral Bevel and Hypoid Gears

Directory of Open Access Journals (Sweden)

Vilmos Simon

2016-11-01

Full Text Available In this study, an advanced method for the manufacture of spiral bevel and hypoid gears on CNC hypoid generators is proposed. The optmal head-cutter geometry and machine tool settings are determined to introduce the optimal tooth surface modifications into the teeth of spiral bevel and hypoid gears. The aim of these tooth surface modifications is to simultaneously reduce the tooth contact pressure and the transmission errors, to maximize the EHD load carrying capacity of the oil film, and to minimize power losses in the oil film. The proposed advanced method for the manufacture of spiral bevel and hypoid gears is based on machine tool setting variation on the cradle-type generator conducted by optimal polynomial functions and on the use of a CNC hypoid generator. An algorithm is developed for the execution of motions on the CNC hypoid generator using the optimal relations on the cradle-type machine. Effectiveness of the method was demonstrated by using spiral bevel and hypoid gear examples. Significant improvements in the operating characteristics of the gear pairs are achieved.

Drift of Spiral Waves in Complex Ginzburg-Landau Equation

International Nuclear Information System (INIS)

Yang Junzhong; Zhang Mei

2006-01-01

The spontaneous drift of the spiral wave in a finite domain in the complex Ginzburg-Landau equation is investigated numerically. By using the interactions between the spiral wave and its images, we propose a phenomenological theory to explain the observations.

Pulmonary embolism: spiral CT evaluation; Embolie pulmonaire: apport de la tomodensitometrie helicoidale

Energy Technology Data Exchange (ETDEWEB)

Senac, J.P.; Vernhet, H.; Bousquet, C.; Giron, J.; Pieuchot, P.; Durand, G.; Benezet, O.; Aubas, P. [Centre Hospitalier Universitaire, 34 - Montpellier (France)

1995-06-01

Purpose: Spiral computed tomography was compared retrospectively with digital substraction pulmonary angiography (PA) in 45 patients suspected of having acute or chronic pulmonary embolism. Materials and method : 45 patients in whom the presence of acute or chronic pulmonary embolism was suspected underwent examination by spiral CT and PA. Diagnosis of pulmonary embolism was based on the direct visualization of intraluminal clots. The study of the agreement between the two methods was based on the Kappa test. In 35 cases, pulmonary emboli were proved. Acute pulmonary emboli were present in 28 cases and chronic in 7 cases. Results: Spiral computed tomography represents an excellent way to detect acute pulmonary embolism. In the chronic form, spiral CT is better than PA to detect intraluminal clots. However, Spiral CT can fail to detect small emboli in the peripheral arterial bed. In the 10 patients without pulmonary embolism, the spiral CT proved diagnosis pulmonary oedema (n=3), lymphangi-carcinoma (n=4), pleural effusion (n=3). Conclusion: This study suggest that the spiral CT examination is accurate for diagnosis of pulmonary embolism specifically in case of suspected important embolism. The advantages of spiral CT are multiple (non invasive, wide diagnosis spectrum). However, may be a limitation to is use is insufficient distal thrombi detection. This eventuality (5 to 10% in the Pioped study) justify the practice of pulmonary angiography. Spiral CT improvements should reduce this insufficiency in the next future. (Authors). 16 refs., 4 figs., 3 tabs.

Shunt impedance of spiral loaded resonant rf cavities

International Nuclear Information System (INIS)

Peebles, P.Z. Jr.; Parvarandeh, M.

1975-01-01

Based upon a treatment of the spiral loaded resonant radio frequency cavity as a shorted quarter-wave transmission line, a model for shunt impedance is developed. The model is applicable to loosely wound spirals in large diameter containers. Theoretical shunt impedance is given for spirals wound from tubing of circular or rectangular cross section. The former produces higher shunt impedance. Measurements made at Oak Ridge National Laboratory on 17 copper cavities are described which support the theoretical results. Theoretical results are also compared to data from twenty-three additional cavities measured at Los Alamos Scientific Laboratory. It is shown that the theoretical function forms a useful means of interpreting the quality of constructed cavities. (author)

Statistical analysis of metallicity in spiral galaxies

Energy Technology Data Exchange (ETDEWEB)

Galeotti, P [Consiglio Nazionale delle Ricerche, Turin (Italy). Lab. di Cosmo-Geofisica; Turin Univ. (Italy). Ist. di Fisica Generale)

1981-04-01

A principal component analysis of metallicity and other integral properties of 33 spiral galaxies is presented; the involved parameters are: morphological type, diameter, luminosity and metallicity. From the statistical analysis it is concluded that the sample has only two significant dimensions and additonal tests, involving different parameters, show similar results. Thus it seems that only type and luminosity are independent variables, being the other integral properties of spiral galaxies correlated with them.

: Nuclear Spirals and Mass Accretion to Supermassive Black Holes in Weakly-Barred Galaxies

Science.gov (United States)

Kim, Woong-Tae; Elmegreen, Bruce

2018-01-01

Disk galaxies, especially barred-spiral galaxies, abound with rings and spirals in their nuclear regions. Nuclear spirals existing even in weakly barred galaxies are thought to channel gas inflows to supermassive black holes residing at the centers. We use high-resolution hydrodynamic simulations to study the properties of nuclear gas spirals driven by weak bar-like or oval potentials. The amplitude of the spirals increases toward the center by a geometric effect, readily developing into shocks at small radii even for very weak potentials. The shape of the spirals and shocks depends rather sensitively on the background shear. When shear is low, the nuclear spirals are loosely wound and the shocks are almost straight, resulting in large mass inflows toward the center. When shear is high, on the other hand, the spirals are tightly wound and the shocks are oblique, forming a circumnuclear disk through which gas flows inward at a relatively lower rate. The induced mass inflow rates are enough to power black hole accretion in various types of Seyfert galaxies.

Density wave theory and the classification of spiral galaxies

International Nuclear Information System (INIS)

Roberts, W.W. Jr.; Roberts, M.S.; Shu, F.H.

1975-01-01

Axisymmetric models of disk galaxies taken together with the density wave theory allow us to distinguish and categorize spiral galaxies by means of two fundamental galactic parameters: the total mass of the galaxy, divided by a characteristic dimension; and the degree of concentration of mass toward the galactic center. These two parameters govern the strength of the galactic shocks in the interstellar gas and the geometry of the spiral wave pattern. In turn, the shock strength and the theoretical pitch angle of the spiral arms play a major role in determining the degree of development of spiral structure in a galaxy and its Hubble type. The application of these results to 24 external galaxies demonstrates that the categorization of galaxies according to this theoretical framework correlates well with the accepted classification of these galaxies within the observed sequences of luminosity class and Hubble type

On the possibility of simultaneous spiral and superfluid ordering in a Fermi-liquid

International Nuclear Information System (INIS)

Peletminskij, S.V.; Yatsenko, A.A.; Shulga, S.N.

2004-01-01

The paper concerns a particular possibility of ordering for Fermi systems - a superfluid spiral ordering, at which in addition to the phase invariance breakdown there occurs a violence of the translational and the spin rotation invariance. A general approach of studying of the superfluid spiral ordering is formulated on the basis of the Fermi liquid method. For a monocomponent Fermi system self-consistency equations for four order parameters and the temperature of simultaneous transition to spiral and superfluid states are obtained. The system of equations is studied under the assumption of two order parameters being distinct from zero. The spiral parameter dependences of the transition temperature and the energy gap in the spectrum of elementary fermion excitations are calculated. An interval of the spiral parameter values within which the superfluid spiral ordering can exist is determined. The spin correlation function at the spiral ordering is studied

Gastric spiral bacteria in small felids.

Science.gov (United States)

Kinsel, M J; Kovarik, P; Murnane, R D

1998-06-01

Nine small cats, including one bobcat (Felis rufus), one Pallas cat (F. manul), one Canada lynx (F. lynx canadensis), two fishing cats (F. viverrina), two margays (F. wiedii), and two sand cats (F. margarita), necropsied between June 1995 and March 1997 had large numbers of gastric spiral bacteria, whereas five large cats, including one African lion (Panthera leo), two snow leopards (P. uncia), one Siberian tiger (P. tigris altaica), and one jaguar (P. onca), necropsied during the same period had none. All of the spiral organisms from the nine small cats were histologically and ultrastructurally similar. Histologically, the spiral bacteria were 5-14 microm long with five to nine coils per organism and were located both extracellularly within gastric glands and surface mucus, and intracellularly in parietal cells. Spiral bacteria in gastric mucosal scrapings from the Canada lynx, one fishing cat, and the two sand cats were gram negative and had corkscrewlike to tumbling motility when viewed with phase contrast microscopy. The bacteria were 0.5-0.7 microm wide, with a periodicity of 0.65-1.1 microm in all cats. Bipolar sheathed flagella were occasionally observed, and no periplasmic fibrils were seen. The bacteria were extracellular in parietal cell canaliculi and intracellular within parietal cells. Culture of mucosal scrapings from the Canada lynx and sand cats was unsuccessful. Based on morphology, motility, and cellular tropism, the bacteria were probably Helicobacter-like organisms. Although the two margays had moderate lymphoplasmacytic gastritis, the other cats lacked or had only mild gastric lymphoid infiltrates, suggesting that these organisms are either commensals or opportunistic pathogens.

Spiral counter-current chromatography of small molecules, peptides and proteins using the spiral tubing support rotor.

Science.gov (United States)

Knight, Martha; Finn, Thomas M; Zehmer, John; Clayton, Adam; Pilon, Aprile

2011-09-09

An important advance in countercurrent chromatography (CCC) carried out in open flow-tubing coils, rotated in planetary centrifuges, is the new design to spread out the tubing in spirals. More spacing between the tubing was found to significantly increase the stationary phase retention, such that now all types of two-phase solvent systems can be used for liquid-liquid partition chromatography in the J-type planetary centrifuges. A spiral tubing support (STS) frame with circular channels was constructed by laser sintering technology into which FEP tubing was placed in 4 spiral loops per layer from the bottom to the top and a cover affixed allowing the tubing to connect to flow-tubing of the planetary centrifuge. The rotor was mounted and run in a P.C. Inc. type instrument. Examples of compounds of molecular weights ranging from <300 to approximately 15,000 were chromatographed in appropriate two-phase solvent systems to assess the capability for separation and purification. A mixture of small molecules including aspirin was completely separated in hexane-ethyl acetate-methanol-water. Synthetic peptides including a very hydrophobic peptide were each purified to a very high purity level in a sec-butanol solvent system. In the STS rotor high stationary phase retention was possible with the aqueous sec-butanol solvent system at a normal flow rate. Finally, the two-phase aqueous polyethylene glycol-potassium phosphate solvent system was applied to separate a protein from a lysate of an Escherichia coli expression system. These experiments demonstrate the versatility of spiral CCC using the STS rotor. Copyright © 2011 Elsevier B.V. All rights reserved.

Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra

International Nuclear Information System (INIS)

Bellstedt, Peter; Herbst, Christian; Häfner, Sabine; Leppert, Jörg; Görlach, Matthias; Ramachandran, Ramadurai

2012-01-01

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′C and 3D C′NCA with sequential 13 C acquisitions, 3D NHH and 3D NC′H with sequential 1 H acquisitions and 3D CANH and 3D C’NH with broadband 13 C– 15 N mixing are demonstrated using microcrystalline samples of the β1 immunoglobulin binding domain of protein G (GB1) and the chicken α-spectrin SH3 domain.

Calculation of 125Te NMR Chemical Shifts at the Full Four-Component Relativistic Level with Taking into Account Solvent and Vibrational Corrections: A Gateway to Better Agreement with Experiment.

Science.gov (United States)

Rusakova, Irina L; Rusakov, Yuriy Yu; Krivdin, Leonid B

2017-06-29

Four-component relativistic calculations of 125 Te NMR chemical shifts were performed in the series of 13 organotellurium compounds, potential precursors of the biologically active species, at the density functional theory level under the nonrelativistic and four-component fully relativistic conditions using locally dense basis set scheme derived from relativistic Dyall's basis sets. The relativistic effects in tellurium chemical shifts were found to be of as much as 20-25% of the total calculated values. The vibrational and solvent corrections to 125 Te NMR chemical shifts are about, accordingly, 6 and 8% of their total values. The PBE0 exchange-correlation functional turned out to give the best agreement of calculated tellurium shifts with their experimental values giving the mean absolute percentage error of 4% in the range of ∼1000 ppm, provided all corrections are taken into account.

Can cluster environment modify the dynamical evolution of spiral galaxies?

Science.gov (United States)

Amram, P.; Balkowski, C.; Cayatte, V.; Marcelin, M.; Sullivan, W. T., III

1993-01-01

Over the past decade many effects of the cluster environment on member galaxies have been established. These effects are manifest in the amount and distribution of gas in cluster spirals, the luminosity and light distributions within galaxies, and the segregation of morphological types. All these effects could indicate a specific dynamical evolution for galaxies in clusters. Nevertheless, a more direct evidence, such as a different mass distribution for spiral galaxies in clusters and in the field, is not yet clearly established. Indeed, Rubin, Whitmore, and Ford (1988) and Whitmore, Forbes, and Rubin (1988) (referred to as RWF) presented evidence that inner cluster spirals have falling rotation curves, unlike those of outer cluster spirals or the great majority of field spirals. If falling rotation curves exist in centers of clusters, as argued by RWF, it would suggest that dark matter halos were absent from cluster spirals, either because the halos had become stripped by interactions with other galaxies or with an intracluster medium, or because the halos had never formed in the first place. Even if they didn't disagree with RWF, other researchers pointed out that the behaviour of the slope of the rotation curves of spiral galaxies (in Virgo) is not so clear. Amram, using a different sample of spiral galaxies in clusters, found only 10% of declining rotation curves (2 declining vs 17 flat or rising) in opposition to RWF who find about 40% of declining rotation curves in their sample (6 declining vs 10 flat or rising), we will hereafter briefly discuss the Amram data paper and compare it to the results of RWF. We have measured the rotation curves for a sample of 21 spiral galaxies in 5 nearby clusters. These rotation curves have been constructed from detailed two-dimensional maps of each galaxy's velocity field as traced by emission from the Ha line. This complete mapping, combined with the sensitivity of our CFHT 3.60 m. + Perot-Fabry + CCD observations, allows

Angular momentum redistribution by spiral waves in computer models of disc galaxies

International Nuclear Information System (INIS)

Sellwood, J.A.; James, R.A.

1979-01-01

It is shown that the spiral patterns which develop spontaneously in computer models of galaxies are generated through angular momentum transfer. By adjusting the distribution of mass in the rigid halo components of the models it is possible to alter radically the rotation curve of the disc component. Either trailing or leading spiral arms develop in the models, dependent only on the sense of the differential shear; no spirals are seen in models where the disc rotates uniformly. It is found that the distribution of angular momentum in the disc is altered by the spiral evolution. Although some spiral structure can be seen for a long period, the life of each pattern is very short. It is shown that resonances are of major importance even for these transient patterns. All spiral wave patterns which have been seen possess both an inner Lindblad resonance and a co-rotation resonance. (author)

Spiral nonimaging optical designs

Science.gov (United States)

Zamora, Pablo; Benítez, Pablo; Miñano, Juan C.; Vilaplana, Juan

2011-10-01

Manufacturing technologies as injection molding or embossing specify their production limits for minimum radii of the vertices or draft angle for demolding, for instance. In some demanding nonimaging applications, these restrictions may limit the system optical efficiency or affect the generation of undesired artifacts on the illumination pattern. A novel manufacturing concept is presented here, in which the optical surfaces are not obtained from the usual revolution symmetry with respect to a central axis (z axis), but they are calculated as free-form surfaces describing a spiral trajectory around z axis. The main advantage of this new concept lies in the manufacturing process: a molded piece can be easily separated from its mold just by applying a combination of rotational movement around axis z and linear movement along axis z, even for negative draft angles. Some of these spiral symmetry examples will be shown here, as well as their simulated results.

Theory of spiral structure

International Nuclear Information System (INIS)

Lin, C.C.

1977-01-01

The density wave theory of galactic spirals has now developed into a form suitable for consideration by experts in Applied Mechanics. On the one hand, comparison of theoretical deductions with observational data has convinced astrophysicists of the validity of the basic physical picture and the calculated results. On the other hand, the dynamical problems of a stellar system, such as those concerning the origin of spiral structure in galaxies, have not been completely solved. This paper reviews the current status of such developments, including a brief summary of comparison with observations. A particularly important mechanism, currently called the mechanism of energy exchange, is described in some detail. The mathematical problems and the physical processes involved are similar to those occurring in certain instability mechanisms in the 'magnetic bottle' designed for plasma containment. Speculations are given on the future developments of the theory and on observational programs. (Auth.)

A Software Development Simulation Model of a Spiral Process

Science.gov (United States)

Mizell, Carolyn; Malone, Linda

2007-01-01

There is a need for simulation models of software development processes other than the waterfall because processes such as spiral development are becoming more and more popular. The use of a spiral process can make the inherently difficult job of cost and schedule estimation even more challenging due to its evolutionary nature, but this allows for a more flexible process that can better meet customers' needs. This paper will present a discrete event simulation model of spiral development that can be used to analyze cost and schedule effects of using such a process in comparison to a waterfall process.

A New Paradigm for Chemical Engineering?

DEFF Research Database (Denmark)

Gani, Rafiqul

evidence of this change comes from the jobs taken by graduating chemical engineering professionals in North America, Europe, and some of the Asian countries. In terms of where the graduating chemical engineers are going to work, a clear shift from the commodity chemical industry to the product oriented...... businesses has been observed. There is an increasing trend within the chemical industry to focus on products and the sustainable processes that can make them. Do these changes point to a paradigm shift in chemical engineering as a discipline? Historically, two previous paradigm shifts in chemical engineering...... corresponded to major shifts in chemical engineering as a discipline, which affected not only the education of chemical engineers, but also the development of chemical engineering as a discipline. Has the time come for a new paradigm shift that will prepare the current and future chemical engineering graduates...

On wave dark matter in spiral and barred galaxies

International Nuclear Information System (INIS)

Martinez-Medina, Luis A.; Matos, Tonatiuh; Bray, Hubert L.

2015-01-01

We recover spiral and barred spiral patterns in disk galaxy simulations with a Wave Dark Matter (WDM) background (also known as Scalar Field Dark Matter (SFDM), Ultra-Light Axion (ULA) dark matter, and Bose-Einstein Condensate (BEC) dark matter). Here we show how the interaction between a baryonic disk and its Dark Matter Halo triggers the formation of spiral structures when the halo is allowed to have a triaxial shape and angular momentum. This is a more realistic picture within the WDM model since a non-spherical rotating halo seems to be more natural. By performing hydrodynamic simulations, along with earlier test particles simulations, we demonstrate another important way in which wave dark matter is consistent with observations. The common existence of bars in these simulations is particularly noteworthy. This may have consequences when trying to obtain information about the dark matter distribution in a galaxy, the mere presence of spiral arms or a bar usually indicates that baryonic matter dominates the central region and therefore observations, like rotation curves, may not tell us what the DM distribution is at the halo center. But here we show that spiral arms and bars can develop in DM dominated galaxies with a central density core without supposing its origin on mechanisms intrinsic to the baryonic matter

Considerations of an oscillating spiral universe cosmology

International Nuclear Information System (INIS)

Sachs, M.

1989-01-01

It is proposed that if the spiral configuration of galaxies is explicable in terms of the equations of motion of its constituent stars, as an expression of global laws of nature, then the universe as a whole may be similarly described in terms of the motions of its constituent galaxies with a similar spiral dynamics. With the functional form of the spiral paths in terms of Fresnel integrals, taken from solutions of equations in general relativity (from previous analyses of galactic configurations) the density of the universe at the big bang stage is determined. It is found to depend, numerically, on the neutron lifetime and the period of oscillation of the universe as a whole. There is some concluding discussion of the implications of this analysis of the matter of the universe at the big bang stage vis a vis the black hole state of matter

The Fundamental Structure and the Reproduction of Spiral Wave in a Two-Dimensional Excitable Lattice.

Science.gov (United States)

Qian, Yu; Zhang, Zhaoyang

2016-01-01

In this paper we have systematically investigated the fundamental structure and the reproduction of spiral wave in a two-dimensional excitable lattice. A periodically rotating spiral wave is introduced as the model to reproduce spiral wave artificially. Interestingly, by using the dominant phase-advanced driving analysis method, the fundamental structure containing the loop structure and the wave propagation paths has been revealed, which can expose the periodically rotating orbit of spiral tip and the charity of spiral wave clearly. Furthermore, the fundamental structure is utilized as the core for artificial spiral wave. Additionally, the appropriate parameter region, in which the artificial spiral wave can be reproduced, is studied. Finally, we discuss the robustness of artificial spiral wave to defects.

Nutrient spiraling in streams and river networks