Wave equations in conformal gravity

NASA Astrophysics Data System (ADS)

Du, Juan-Juan; Wang, Xue-Jing; He, You-Biao; Yang, Si-Jiang; Li, Zhong-Heng

2018-05-01

We study the wave equation governing massless fields of all spins (s = 0, 1 2, 1, 3 2 and 2) in the most general spherical symmetric metric of conformal gravity. The equation is separable, the solution of the angular part is a spin-weighted spherical harmonic, and the radial wave function may be expressed in terms of solutions of the Heun equation which has four regular singular points. We also consider various special cases of the metric and find that the angular wave functions are the same for all cases, the actual shape of the metric functions affects only the radial wave function. It is interesting to note that each radial equation can be transformed into a known ordinary differential equation (i.e. Heun equation, or confluent Heun equation, or hypergeometric equation). The results show that there are analytic solutions for all the wave equations of massless spin fields in the spacetimes of conformal gravity. This is amazing because exact solutions are few and far between for other spacetimes.

Experimental Studies on Wave Interactions of Partially Perforated Wall under Obliquely Incident Waves

PubMed Central

Lee, Jong-In; Kim, Young-Taek; Shin, Sungwon

2014-01-01

This study presents wave height distribution in terms of stem wave evolution phenomena on partially perforated wall structures through three-dimensional laboratory experiments. The plain and partially perforated walls were tested to understand their effects on the stem wave evolution under the monochromatic and random wave cases with the various wave conditions, incident angle (from 10 to 40 degrees), and configurations of front and side walls. The partially perforated wall reduced the relative wave heights more effectively compared to the plain wall structure. Partially perforated walls with side walls showed a better performance in terms of wave height reduction compared to the structure without the side wall. Moreover, the relative wave heights along the wall were relatively small when the relative chamber width is large, within the range of the chamber width in this study. The wave spectra showed a frequency dependency of the wave energy dissipation. In most cases, the existence of side wall is a more important factor than the porosity of the front wall in terms of the wave height reduction even if the partially perforated wall was still effective compared to the plain wall. PMID:25254260

Experimental studies on wave interactions of partially perforated wall under obliquely incident waves.

PubMed

Lee, Jong-In; Kim, Young-Taek; Shin, Sungwon

2014-01-01

This study presents wave height distribution in terms of stem wave evolution phenomena on partially perforated wall structures through three-dimensional laboratory experiments. The plain and partially perforated walls were tested to understand their effects on the stem wave evolution under the monochromatic and random wave cases with the various wave conditions, incident angle (from 10 to 40 degrees), and configurations of front and side walls. The partially perforated wall reduced the relative wave heights more effectively compared to the plain wall structure. Partially perforated walls with side walls showed a better performance in terms of wave height reduction compared to the structure without the side wall. Moreover, the relative wave heights along the wall were relatively small when the relative chamber width is large, within the range of the chamber width in this study. The wave spectra showed a frequency dependency of the wave energy dissipation. In most cases, the existence of side wall is a more important factor than the porosity of the front wall in terms of the wave height reduction even if the partially perforated wall was still effective compared to the plain wall.

Nonrelativistic Conformed Symmetry in 2 + 1 Dimensional Field Theory.

NASA Astrophysics Data System (ADS)

Bergman, Oren

This thesis is devoted to the study of conformal invariance and its breaking in non-relativistic field theories. It is a well known feature of relativistic field theory that theories which are conformally invariant at the classical level can acquire a conformal anomaly upon quantization and renormalization. The anomaly appears through the introduction of an arbitrary, but dimensionful, renormalization scale. One does not usually associate the concepts of renormalization and anomaly with nonrelativistic quantum mechanics, but there are a few examples where these concepts are useful. The most well known case is the two-dimensional delta -function potential. In two dimensions the delta-function scales like the kinetic term of the Hamiltonian, and therefore the problem is classically conformally invariant. Another example of classical conformal invariance is the famous Aharonov-Bohm (AB) problem. In that case each partial wave sees a 1/r^2 potential. We use the second quantized formulation of these problems, namely the nonrelativistic field theories, to compute Green's functions and derive the conformal anomaly. In the case of the AB problem we also solve an old puzzle, namely how to reproduce the result of Aharonov and Bohm in perturbation theory. The thesis is organized in the following manner. Chapter 1 is an introduction to nonrelativistic field theory, nonrelativistic conformal invariance, contact interactions and the AB problem. In Chapter 2 we discuss nonrelativistic scalar field theory, and how its quantization produces the anomaly. Chapter 3 is devoted to the AB problem, and the resolution of the perturbation puzzle. In Chapter 4 we generalize the discussion of Chapter 3 to particles carrying nonabelian charges. The structure of the nonabelian theory is much richer, and deserves a separate discussion. We also comment on the issues of forward scattering and single -valuedness of wavefunctions, which are important for Chapter 3 as well. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.).

REVIEW: High pressure NMR study of proteins - seeking roots for function, evolution, disease and food applications

NASA Astrophysics Data System (ADS)

Akasaka, Kazuyuki

2010-12-01

NMR experiments at variable pressure reveal a wide range of conformation of a globular protein spanning from within the folded ensemble to the fully unfolded ensemble, herewith collectively called "high-energy conformers". The observation of "high-energy conformers" in a wide variety of globular proteins has led to the "volume theorem": the partial molar volume of a protein decreases with the decrease in its conformational order. Since "high-energy conformers" are intrinsically more reactive than the basic folded conformer, they could play decisive roles in all phenomena of proteins, namely function, environmental adaptation and misfolding. Based on the information on high-energy conformers and the rules on their partial volume in its monomeric state and amyloidosis, one may have a general view on what is happening on proteins under pressure. Moreover, one may even choose a high-energy conformer of a protein with pressure as variable for a particular purpose. Bridging "high-energy conformers" to macroscopic pressure effects could be a key to success in pressure application to biology, medicine, food technology and industry in the near future.

Excising das All: Evolving Maxwell waves beyond Scri

NASA Technical Reports Server (NTRS)

vanMeter, James R.; Fiske, David R.; Misner, Charles W.

2006-01-01

We study the numerical propagation of waves through future null infinity in a conformally compactified spacetime. We introduce an artificial cosmological constant, which allows us some control over the causal structure near null infinity. We exploit this freedom to ensure that all light cones are tilted outward in a region near null infinity, which allows us to impose excision-style boundary conditions in our finite difference code. In this preliminary study we consider electromagnetic waves propagating in a static, conformally compactified spacetime.

Wave impact on a deck or baffle

NASA Astrophysics Data System (ADS)

Md Noar, Nor Aida Zuraimi; Greenhow, Martin

2015-02-01

Some coastal or ocean structures have deck-like baffles or horizontal platforms that can be exposed to wave action in heavy seas. A similar situation may occur in partially-filled tanks with horizontal baffles that become engulfed by sloshing waves. This can result in dangerous wave impact loads (slamming) causing a rapid rise of pressures which may lead to local damaging by crack initiation and/or propagation. We consider the wave impact against the whole of underside of horizontal deck (or baffle) projecting from a seawall (or vertical tank wall), previously studied by Wood and Peregrine (1996) using a different method based on conformal mappings. The approach used is to simplify the highly time-dependent and very nonlinear problem by considering the time integral of the pressure over the duration of the impact pressure-impulse, P (x, y). Our method expresses this in terms of eigenfunctions that satisfy the boundary conditions apart from that on the impact region and the matching of the two regions (under the platform and under the free surface); this results in a matrix equation to be solved numerically. As in Wood and Peregrine, we found that the pressure impulse on the deck increases when the length of deck increases, there is a strong pressure gradient beneath the deck near the seaward edge and the maximum pressure impulse occurs at the landward end of the impact zone.

Treatment of Ion-Atom Collisions Using a Partial-Wave Expansion of the Projectile Wavefunction

ERIC Educational Resources Information Center

Wong, T. G.; Foster, M.; Colgan, J.; Madison, D. H.

2009-01-01

We present calculations of ion-atom collisions using a partial-wave expansion of the projectile wavefunction. Most calculations of ion-atom collisions have typically used classical or plane-wave approximations for the projectile wavefunction, since partial-wave expansions are expected to require prohibitively large numbers of terms to converge…

Millimeter and submillimeter wave spectroscopy of propanal

NASA Astrophysics Data System (ADS)

Zingsheim, Oliver; Müller, Holger S. P.; Lewen, Frank; Jørgensen, Jes K.; Schlemmer, Stephan

2017-12-01

The rotational spectra of the two stable conformers syn- and gauche-propanal (CH3CH2CHO) were studied in the millimeter and submillimeter wave regions from 75 to 500 GHz with the Cologne (Sub-)Millimeter wave Spectrometer. Furthermore, the first excited states associated with the aldehyde torsion and with the methyl torsion, respectively, of the syn-conformer were analyzed. The newly obtained spectroscopic parameters yield better predictions, thus fulfill sensitivity and resolution requirements in new astronomical observations in order to unambiguously assign pure rotational transitions of propanal. This is demonstrated on a radio astronomical spectrum from the Atacama Large Millimeter/submillimeter Array Protostellar Interferometric Line Survey (ALMA-PILS). In particular, an accurate description of observed splittings, caused by internal rotation of the methyl group in the syn-conformer and by tunneling rotation interaction from two stable degenerate gauche-conformers, is reported. The rotational spectrum of propanal is of additional interest because of its two large amplitude motions pertaining to the methyl and the aldehyde group, respectively.

Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations

PubMed Central

Okazaki, Kei-ichi; Koga, Nobuyasu; Takada, Shoji; Onuchic, Jose N.; Wolynes, Peter G.

2006-01-01

Biomolecules often undergo large-amplitude motions when they bind or release other molecules. Unlike macroscopic machines, these biomolecular machines can partially disassemble (unfold) and then reassemble (fold) during such transitions. Here we put forward a minimal structure-based model, the “multiple-basin model,” that can directly be used for molecular dynamics simulation of even very large biomolecular systems so long as the endpoints of the conformational change are known. We investigate the model by simulating large-scale motions of four proteins: glutamine-binding protein, S100A6, dihydrofolate reductase, and HIV-1 protease. The mechanisms of conformational transition depend on the protein basin topologies and change with temperature near the folding transition. The conformational transition rate varies linearly with driving force over a fairly large range. This linearity appears to be a consequence of partial unfolding during the conformational transition. PMID:16877541

Conformational transition of κ-casein in micellar environment: Insight from the tryptophan fluorescence

NASA Astrophysics Data System (ADS)

Mishra, Smruti; Meher, Geetanjali; Chakraborty, Hirak

2017-11-01

Intrinsically disordered proteins (IDPs) are under intense analysis due to their structural flexibility and importance in biological functions. Minuscule modulation in the microenvironment induces significant conformational changes in IDPs, and these non-native conformations of the IDPs often induce aggregation and cause cell death. Changes in the membrane composition often change the microenvironment, which promote conformational change and aggregation of IDPs. κ-Casein, an important milk protein, belongs to the class of IDPs containing net negative charges. In this present work, we have studied the interaction of κ-casein with cetyltrimethyl ammonium bromide (CTAB), a positively charged surfactant, utilizing various steady state fluorescence, time-resolved fluorescence and circular dichroism spectroscopy. Our results clearly indicate that κ-casein undergoes at least two conformational transitions in presence of various concentrations of CTAB. The intrinsically disordered κ-casein assumes a partially folded conformation at lower concentration of CTAB, which adopts an unstructured conformation at higher concentration of CTAB. The partially folded conformation of κ-casein at a lower CTAB concentration might be induced by the favorable electrostatic interaction between the positively charged surfactant headgroup and net negative charges of the protein, whereas surfactant nature of CTAB is being pronounced at higher concentration of CTAB.

Nucleon-nucleon interactions from dispersion relations: Elastic partial waves

NASA Astrophysics Data System (ADS)

Albaladejo, M.; Oller, J. A.

2011-11-01

We consider nucleon-nucleon (NN) interactions from chiral effective field theory. In this work we restrict ourselves to the elastic NN scattering. We apply the N/D method to calculate the NN partial waves taking as input the one-pion exchange discontinuity along the left-hand cut. This discontinuity is amenable to a chiral power counting as discussed by Lacour, Oller, and Meißner [Ann. Phys. (NY)APNYA60003-491610.1016/j.aop.2010.06.012 326, 241 (2011)], with one-pion exchange as its leading order contribution. The resulting linear integral equation for a partial wave with orbital angular momentum ℓ≥2 is solved in the presence of ℓ-1 constraints, so as to guarantee the right behavior of the D- and higher partial waves near threshold. The calculated NN partial waves are based on dispersion relations and are independent of regulator. This method can also be applied to higher orders in the calculation of the discontinuity along the left-hand cut and extended to triplet coupled partial waves.

Analysis of dispersion and attenuation of surface waves in poroelastic media in the exploration-seismic frequency band

USGS Publications Warehouse

Zhang, Y.; Xu, Y.; Xia, J.

2011-01-01

We analyse dispersion and attenuation of surface waves at free surfaces of possible vacuum/poroelastic media: permeable-'open pore', impermeable-'closed pore' and partially permeable boundaries, which have not been previously reported in detail by researchers, under different surface-permeable, viscous-damping, elastic and fluid-flowing conditions. Our discussion is focused on their characteristics in the exploration-seismic frequency band (a few through 200 Hz) for near-surface applications. We find two surface-wave modes exist, R1 waves for all conditions, and R2 waves for closed-pore and partially permeable conditions. For R1 waves, velocities disperse most under partially permeable conditions and least under the open-pore condition. High-coupling damping coefficients move the main dispersion frequency range to high frequencies. There is an f1 frequency dependence as a constant-Q model for attenuation at high frequencies. R1 waves for the open pore are most sensitive to elastic modulus variation, but least sensitive to tortuosities variation. R1 waves for partially permeable surface radiate as non-physical waves (Im(k) < 0) at low frequencies. For R2 waves, velocities are slightly lower than the bulk slow P2 waves. At low frequencies, both velocity and attenuation are diffusive of f1/2 frequency dependence, as P2 waves. It is found that for partially permeable surfaces, the attenuation displays -f1 frequency dependence as frequency increasing. High surface permeability, low-coupling damping coefficients, low Poisson's ratios, and low tortuosities increase the slope of the -f1 dependence. When the attenuation coefficients reach 0, R2 waves for partially permeable surface begin to radiate as non-physical waves. ?? 2011 The Authors Geophysical Journal International ?? 2011 RAS.

Conformal gravity holography in four dimensions.

PubMed

Grumiller, Daniel; Irakleidou, Maria; Lovrekovic, Iva; McNees, Robert

2014-03-21

We formulate four-dimensional conformal gravity with (anti-)de Sitter boundary conditions that are weaker than Starobinsky boundary conditions, allowing for an asymptotically subleading Rindler term concurrent with a recent model for gravity at large distances. We prove the consistency of the variational principle and derive the holographic response functions. One of them is the conformal gravity version of the Brown-York stress tensor, the other is a "partially massless response". The on shell action and response functions are finite and do not require holographic renormalization. Finally, we discuss phenomenologically interesting examples, including the most general spherically symmetric solutions and rotating black hole solutions with partially massless hair.

A New Energy Ordering and the Dipole Moment of Gas Phase Glycine via Plane-Wave Density Functional Theory Calculations

NASA Astrophysics Data System (ADS)

Min, Byeong June

2018-03-01

The abundance of glycine (Gly), the simplest amino acid, in meteorites leads us to the next question about its extraterrestrial origin. However, astronomers have not yet found glycine signature in interstellar medium. Laboratory microwave spectroscopy experiments report the most stable Gly conformer has a dipole moment of 4.5 - 5.45 Debye. Theoretical calculations, so far performed only with Gaussian basis functions, has predicted a dipole moment of about 1 Debye. This discrepancy has baffled astronomers. We study the energetics of glycine and its isomers and conformers via plane-wave density functional theory calculations. The geometric structures of the isomers and their conformers are identified, along with their relative stability and their dipole moment. In the case of glycine, we obtain the most stable conformer with a dipole moment of 5.76 Debye, close to the microwave spectroscopy experiments. If the plane wave energy cutoff is reduced to a lower value ( 400 eV) on purpose, the energy ordering reverses to the case with Gaussian basis calculations.

Resolving intramolecular-distortion changes induced by the partial fluorination of pentacene adsorbed on Cu(111)

NASA Astrophysics Data System (ADS)

Franco-Cañellas, Antoni; Wang, Qi; Broch, Katharina; Shen, Bin; Gerlach, Alexander; Bettinger, Holger F.; Duhm, Steffen; Schreiber, Frank

2018-04-01

We experimentally quantify the molecular bending of a partially fluorinated pentacene (PEN) compound, namely 2,3,9,10-tetrafluoropentacene (F4PEN), adsorbed on Cu(111). By means of the x-ray standing wave (XSW) technique, we directly measure the adsorption distance of three inequivalent carbon sites, the fluorine atoms as well as the total and backbone carbon average adsorption distances. The precise positioning of different sites within the carbon core allows us to resolve two adsorption behaviors, namely a PEN-like strong coupling between the backbone and the substrate, and a repulsive interaction involving the fluorinated short molecular edges, which are 0.91 ±0.09 Å above the central benzene ring. This finding is further supported by additional electronic and in-plane-structure measurements, thus showing that the selective fluorination of a PEN molecule has only a local conformational effect and it is not sufficient to modify its interface properties. Yet, in the multilayer regime, the electronic and growth properties of the film differ completely from those of PEN and its perfluorinated derivative.

Effects of partial sleep deprivation on slow waves during non-rapid eye movement sleep: A high density EEG investigation.

PubMed

Plante, David T; Goldstein, Michael R; Cook, Jesse D; Smith, Richard; Riedner, Brady A; Rumble, Meredith E; Jelenchick, Lauren; Roth, Andrea; Tononi, Giulio; Benca, Ruth M; Peterson, Michael J

2016-02-01

Changes in slow waves during non-rapid eye movement (NREM) sleep in response to acute total sleep deprivation are well-established measures of sleep homeostasis. This investigation utilized high-density electroencephalography (hdEEG) to examine topographic changes in slow waves during repeated partial sleep deprivation. Twenty-four participants underwent a 6-day sleep restriction protocol. Spectral and period-amplitude analyses of sleep hdEEG data were used to examine changes in slow wave energy, count, amplitude, and slope relative to baseline. Changes in slow wave energy were dependent on the quantity of NREM sleep utilized for analysis, with widespread increases during sleep restriction and recovery when comparing data from the first portion of the sleep period, but restricted to recovery sleep if the entire sleep episode was considered. Period-amplitude analysis was less dependent on the quantity of NREM sleep utilized, and demonstrated topographic changes in the count, amplitude, and distribution of slow waves, with frontal increases in slow wave amplitude, numbers of high-amplitude waves, and amplitude/slopes of low amplitude waves resulting from partial sleep deprivation. Topographic changes in slow waves occur across the course of partial sleep restriction and recovery. These results demonstrate a homeostatic response to partial sleep loss in humans. Copyright © 2015 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Supersymmetric Yang-Mills theory on conformal supergravity backgrounds in ten dimensions

NASA Astrophysics Data System (ADS)

de Medeiros, Paul; Figueroa-O'Farrill, José

2016-03-01

We consider bosonic supersymmetric backgrounds of ten-dimensional conformal supergravity. Up to local conformal isometry, we classify the maximally supersymmetric backgrounds, determine their conformal symmetry superalgebras and show how they arise as near-horizon geometries of certain half-BPS backgrounds or as a plane-wave limit thereof. We then show how to define Yang-Mills theory with rigid supersymmetry on any supersymmetric conformal supergravity background and, in particular, on the maximally supersymmetric backgrounds. We conclude by commenting on a striking resemblance between the supersymmetric backgrounds of ten-dimensional conformal supergravity and those of eleven-dimensional Poincaré supergravity.

Wave functions of symmetry-protected topological phases from conformal field theories

NASA Astrophysics Data System (ADS)

Scaffidi, Thomas; Ringel, Zohar

2016-03-01

We propose a method for analyzing two-dimensional symmetry-protected topological (SPT) wave functions using a correspondence with conformal field theories (CFTs) and integrable lattice models. This method generalizes the CFT approach for the fractional quantum Hall effect wherein the wave-function amplitude is written as a many-operator correlator in the CFT. Adopting a bottom-up approach, we start from various known microscopic wave functions of SPTs with discrete symmetries and show how the CFT description emerges at large scale, thereby revealing a deep connection between group cocycles and critical, sometimes integrable, models. We show that the CFT describing the bulk wave function is often also the one describing the entanglement spectrum, but not always. Using a plasma analogy, we also prove the existence of hidden quasi-long-range order for a large class of SPTs. Finally, we show how response to symmetry fluxes is easily described in terms of the CFT.

Probing Conformational Rescue Induced by a Chemical Corrector of F508del-Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Mutant*

PubMed Central

Yu, Wilson; Chiaw, Patrick Kim; Bear, Christine E.

2011-01-01

Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene that cause loss of function of the CFTR channel on the apical surface of epithelial cells. The major CF-causing mutation, F508del-CFTR, is misfolded, retained in the endoplasmic reticulum, and degraded. Small molecule corrector compounds have been identified using high throughput screens, which partially rescue the trafficking defect of F508del-CFTR, allowing a fraction of the mutant protein to escape endoplasmic reticulum retention and traffic to the plasma membrane, where it exhibits partial function as a cAMP-regulated chloride channel. A subset of such corrector compounds binds directly to the mutant protein, prompting the hypothesis that they rescue the biosynthetic defect by inducing improved protein conformation. We tested this hypothesis directly by evaluating the consequences of a corrector compound on the conformation of each nucleotide binding domain (NBD) in the context of the full-length mutant protein in limited proteolytic digest studies. Interestingly, we found that VRT-325 was capable of partially restoring compactness in NBD1. However, VRT-325 had no detectable effect on the conformation of the second half of the molecule. In comparison, ablation of the di-arginine sequence, R553XR555 (F508del-KXK-CFTR), modified protease susceptibility of NBD1, NBD2, and the full-length protein. Singly, each intervention led to a partial correction of the processing defect. Together, these interventions restored processing of F508del-CFTR to near wild type. Importantly, however, a defect in NBD1 conformation persisted, as did a defect in channel activation after the combined interventions. Importantly, this defect in channel activation can be fully corrected by the addition of the potentiator, VX-770. PMID:21602569

Amplitude reconstruction from complete photoproduction experiments and truncated partial-wave expansions

NASA Astrophysics Data System (ADS)

Workman, R. L.; Tiator, L.; Wunderlich, Y.; Döring, M.; Haberzettl, H.

2017-01-01

We compare the methods of amplitude reconstruction, for a complete experiment and a truncated partial-wave analysis, applied to the photoproduction of pseudoscalar mesons. The approach is pedagogical, showing in detail how the amplitude reconstruction (observables measured at a single energy and angle) is related to a truncated partial-wave analysis (observables measured at a single energy and a number of angles).

Amplitude reconstruction from complete photoproduction experiments and truncated partial-wave expansions

DOE PAGES

Workman, R. L.; Tiator, L.; Wunderlich, Y.; ...

2017-01-19

Here, we compare the methods of amplitude reconstruction, for a complete experiment and a truncated partial-wave analysis, applied to the photoproduction of pseudoscalar mesons. The approach is pedagogical, showing in detail how the amplitude reconstruction (observables measured at a single energy and angle) is related to a truncated partial-wave analysis (observables measured at a single energy and a number of angles).

75 FR 4793 - Availability for Non-Exclusive, Exclusive, or Partially Exclusive Licensing of U.S. Provisional...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-29

... Partially Exclusive Licensing of U.S. Provisional Patent Application Concerning Blast Wave Sensor AGENCY... ``Blast Wave Sensor,'' filed January 4, 2010. The United States Government, as represented by the... wave sensors and their use to detect blast induced pressure changes, and, in particular, a blast wave...

Infinitely dilute partial molar properties of proteins from computer simulation.

PubMed

Ploetz, Elizabeth A; Smith, Paul E

2014-11-13

A detailed understanding of temperature and pressure effects on an infinitely dilute protein's conformational equilibrium requires knowledge of the corresponding infinitely dilute partial molar properties. Established molecular dynamics methodologies generally have not provided a way to calculate these properties without either a loss of thermodynamic rigor, the introduction of nonunique parameters, or a loss of information about which solute conformations specifically contributed to the output values. Here we implement a simple method that is thermodynamically rigorous and possesses none of the above disadvantages, and we report on the method's feasibility and computational demands. We calculate infinitely dilute partial molar properties for two proteins and attempt to distinguish the thermodynamic differences between a native and a denatured conformation of a designed miniprotein. We conclude that simple ensemble average properties can be calculated with very reasonable amounts of computational power. In contrast, properties corresponding to fluctuating quantities are computationally demanding to calculate precisely, although they can be obtained more easily by following the temperature and/or pressure dependence of the corresponding ensemble averages.

[Development and application of CK-MB specific monoclonal antibodies].

PubMed

Chen, Zimin; Zhou, Guoliang; Xu, Weiling; Zheng, Xiaohong; Tong, Xunzhang; Ke, Qishen; Song, Liuwei; Ge, Shengxiang

2017-01-25

The aim of this study is to develop creatine kinase isoenzyme MB (CK-MB) specific monoclonal antibodies (mAb), and characterize the monoclonal antibody and further development of quantitative detection assay for CK-MB. The BALB/c mice were immunized with purchased CK-MB antigen, then monoclonal antibodies were prepared according to conventional hybridoma technique and screened by indirect and capture ELISA method. To identify the epitopes and evaluate the classification, purchased creatine kinase isoenzyme MB (CK-MM/BB/MB) antigen was used to identify the epitopes, with immunoblotting and synthetic CK-MM and CK-BB in different linear epitope. A double antibody sandwich ELISA was applied to screen the mAb pairs for CK-MB detection, and the quantitative detection assay for CK-MB was developed. We used 74 cases of clinical specimens for comparison of our assay with Roche's CK-MB assay. We successfully developed 22 strains of hybridoms against CK-MB, these mAbs can be divided into linear, partial conformational CK-MB, CK-MM or CK-BB cross monoclonal antibody and CK-MB specific reaction with partial conformational monoclonal antibody, and CK-MB quantitative detection assay was developed by using partial conformational monoclonal antibody. The correlation coefficient factor r of our reagent and Roche's was 0.930 9. This study established a screening method for CK-MB partial conformational specific monoclonal antibody, and these monoclonal antibodies were analyzed and an established quantitative detection assay was developed. The new assay had a high concordance with Roche's.

Partial Wave Dispersion Relations: Application to Electron-Atom Scattering

NASA Technical Reports Server (NTRS)

Temkin, A.; Drachman, Richard J.

1999-01-01

In this Letter we propose the use of partial wave dispersion relations (DR's) as the way of solving the long-standing problem of correctly incorporating exchange in a valid DR for electron-atom scattering. In particular a method is given for effectively calculating the contribution of the discontinuity and/or poles of the partial wave amplitude which occur in the negative E plane. The method is successfully tested in three cases: (i) the analytically solvable exponential potential, (ii) the Hartree potential, and (iii) the S-wave exchange approximation for electron-hydrogen scattering.

Statistical properties of nonlinear one-dimensional wave fields

NASA Astrophysics Data System (ADS)

Chalikov, D.

2005-06-01

A numerical model for long-term simulation of gravity surface waves is described. The model is designed as a component of a coupled Wave Boundary Layer/Sea Waves model, for investigation of small-scale dynamic and thermodynamic interactions between the ocean and atmosphere. Statistical properties of nonlinear wave fields are investigated on a basis of direct hydrodynamical modeling of 1-D potential periodic surface waves. The method is based on a nonstationary conformal surface-following coordinate transformation; this approach reduces the principal equations of potential waves to two simple evolutionary equations for the elevation and the velocity potential on the surface. The numerical scheme is based on a Fourier transform method. High accuracy was confirmed by validation of the nonstationary model against known solutions, and by comparison between the results obtained with different resolutions in the horizontal. The scheme allows reproduction of the propagation of steep Stokes waves for thousands of periods with very high accuracy. The method here developed is applied to simulation of the evolution of wave fields with large number of modes for many periods of dominant waves. The statistical characteristics of nonlinear wave fields for waves of different steepness were investigated: spectra, curtosis and skewness, dispersion relation, life time. The prime result is that wave field may be presented as a superposition of linear waves is valid only for small amplitudes. It is shown as well, that nonlinear wave fields are rather a superposition of Stokes waves not linear waves. Potential flow, free surface, conformal mapping, numerical modeling of waves, gravity waves, Stokes waves, breaking waves, freak waves, wind-wave interaction.

Hawking radiation by Kerr black holes and conformal symmetry.

PubMed

Agullo, Ivan; Navarro-Salas, José; Olmo, Gonzalo J; Parker, Leonard

2010-11-19

The exponential blueshift associated with the event horizon of a black hole makes conformal symmetry play a fundamental role in accounting for its thermal properties. Using a derivation based on two-point functions, we show that the full spectrum of thermal radiation of scalar particles by Kerr black holes can be explicitly derived on the basis of a conformal symmetry arising in the wave equation near the horizon. The simplicity of our approach emphasizes the depth of the connection between conformal symmetry and black hole radiance.

Correlations of π N partial waves for multireaction analyses

DOE PAGES

Doring, M.; Revier, J.; Ronchen, D.; ...

2016-06-15

In the search for missing baryonic resonances, many analyses include data from a variety of pion- and photon-induced reactions. For elastic πN scattering, however, usually the partial waves of the SAID (Scattering Analysis Interactive Database) or other groups are fitted, instead of data. We provide the partial-wave covariance matrices needed to perform correlated χ 2 fits, in which the obtained χ 2 equals the actual χ 2 up to nonlinear and normalization corrections. For any analysis relying on partial waves extracted from elastic pion scattering, this is a prerequisite to assess the significance of resonance signals and to assign anymore » uncertainty on results. Lastly, the influence of systematic errors is also considered.« less

Pseudopotential Method for Higher Partial Wave Scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Idziaszek, Zbigniew; Centrum Fizyki Teoretycznej, Polska Akademia Nauk, 02-668 Warsaw; Calarco, Tommaso

2006-01-13

We present a zero-range pseudopotential applicable for all partial wave interactions between neutral atoms. For p and d waves, we derive effective pseudopotentials, which are useful for problems involving anisotropic external potentials. Finally, we consider two nontrivial applications of the p-wave pseudopotential: we solve analytically the problem of two interacting spin-polarized fermions confined in a harmonic trap, and we analyze the scattering of p-wave interacting particles in a quasi-two-dimensional system.

Mechanism of partial agonism in AMPA-type glutamate receptors

PubMed Central

Salazar, Hector; Eibl, Clarissa; Chebli, Miriam; Plested, Andrew

2017-01-01

Neurotransmitters trigger synaptic currents by activating ligand-gated ion channel receptors. Whereas most neurotransmitters are efficacious agonists, molecules that activate receptors more weakly—partial agonists—also exist. Whether these partial agonists have weak activity because they stabilize less active forms, sustain active states for a lesser fraction of the time or both, remains an open question. Here we describe the crystal structure of an α-amino-3-hydroxy-5-methyl-4-isoxazolepropionate receptor (AMPAR) ligand binding domain (LBD) tetramer in complex with the partial agonist 5-fluorowillardiine (FW). We validate this structure, and others of different geometry, using engineered intersubunit bridges. We establish an inverse relation between the efficacy of an agonist and its promiscuity to drive the LBD layer into different conformations. These results suggest that partial agonists of the AMPAR are weak activators of the receptor because they stabilize multiple non-conducting conformations, indicating that agonism is a function of both the space and time domains. PMID:28211453

SU-F-T-446: Improving Craniospinal Irradiation Technique Using Volumetric Modulated Arc Therapy (VMAT) Planning and Its Dosimetric Verification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, X; Tejani, M; Jiang, X

2016-06-15

Purpose: The purpose of this study is to investigate a volumetric modulated arc therapy (VMAT) treatment planning technique for supine craniospinal irradiation (CSI). Evaluate the suitability of VMAT for CSI with dosimetric measurements and compare it to 3D conformal planning using specific plan metrics such as dose conformity, homogeneity, and dose of organs at risk (OAR). Methods: Ten CSI patients treated with conventional 3D technique were re-planned with VMAT. The PTV was contoured to include the whole contents of the brain and spinal canal with a uniform margin of 5 mm. VMAT plans were generated with two partial arcs coveringmore » the brain, two partial arcs for the superior portion of the spinal cord and two partial arcs covering the remaining inferior portion of the spinal cord. Conformity index (CI), heterogeneity indexes (HI) and max and mean doses of OAR were compared to 3D plans. VMAT plans were delivered onto an anthropomorphic phantom loaded with Gafchromic films and OSLDs placed at specific positions to evaluate the plan dose at the junctions and as well as the plan dose distributions. Results: This VMAT technique was validated with a clinical study of 10 patients. The average CI was 1.03±0.02 for VMAT plans and 1.96±0.32 for conformal plans. And the average HI was 1.15±0.01 for VMAT plans and 1.51±0.21 for conformal plans. The mean and max doses to the all OARs for VMAT plans were significantly lower than conformal plans. The measured dose in phantom for VAMT plans was comparable to the calculated dose in Eclipse and the doses at junctions were verified. Conclusion: VMAT CSI was able to achieve better dose conformity and heterogeneity as well as significantly reducing the dose to Heart, esophagus and larynx. VMAT CSI appears to be a dosimterically advantageous, faster delivery, has better reproducibility CSI treatment.« less

Millimeter and Submillimeter Wave Spectroscopy of Higher Energy Conformers of 1,2-PROPANEDIOL

NASA Astrophysics Data System (ADS)

Zakharenko, Olena; Bossa, Jean-Baptiste; Lewen, Frank; Schlemmer, Stephan; Müller, Holger S. P.

2017-06-01

We have performed a study of the millimeter/submillimeter wave spectrum of four higher energy conformers of 1,2-propanediol (continuation of the previous study on the three lowest energy conformers. The present analysis of rotational transitions carried out in the frequency range 38 - 400 GHz represents a significant extension of previous microwave work. The new data were combined with previously-measured microwave transitions and fitted using a Watson's S-reduced Hamiltonian. The final fits were within experimental accuracy, and included spectroscopic parameters up to sixth order of angular momentum, for the ground states of the four higher energy conformers following previously studied ones: g'Ga, gG'g', aGg' and g'Gg. The present analysis provides reliable frequency predictions for astrophysical detection of 1,2-propanediol by radio telescope arrays at millimeter wavelengths. J.-B. Bossa, M.H. Ordu, H.S.P. Müller, F. Lewen, S. Schlemmer, A&A 570 (2014) A12)

On the Conformable Fractional Quantum Mechanics

NASA Astrophysics Data System (ADS)

Mozaffari, F. S.; Hassanabadi, H.; Sobhani, H.; Chung, W. S.

2018-05-01

In this paper, a conformable fractional quantum mechanic has been introduced using three postulates. Then in such a formalism, Schr¨odinger equation, probability density, probability flux and continuity equation have been derived. As an application of considered formalism, a fractional-radial harmonic oscillator has been considered. After obtaining its wave function and energy spectrum, effects of the conformable fractional parameter on some quantities have been investigated and plotted for different excited states.

Breakthroughs in Low-Profile Leaky-Wave HPM Antennas

DTIC Science & Technology

2015-03-18

presentation of our work at the 17th annual DEPS conference. 15. SUBJECT TERMS Leaky-wave Antennas. High Power Microwaves (HPM) Antennas. Low-profile...the performance, behavior, and design of innovative High Power Microwave (HPM, GW-class) antennas of the forward-traveling, fast-wave, leaky-wave...Conformal Antennas. 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER OF PAGES 19a. NAME OF RESPONSIBLE PERSON (Monitor

Infinitely Dilute Partial Molar Properties of Proteins from Computer Simulation

PubMed Central

2015-01-01

A detailed understanding of temperature and pressure effects on an infinitely dilute protein’s conformational equilibrium requires knowledge of the corresponding infinitely dilute partial molar properties. Established molecular dynamics methodologies generally have not provided a way to calculate these properties without either a loss of thermodynamic rigor, the introduction of nonunique parameters, or a loss of information about which solute conformations specifically contributed to the output values. Here we implement a simple method that is thermodynamically rigorous and possesses none of the above disadvantages, and we report on the method’s feasibility and computational demands. We calculate infinitely dilute partial molar properties for two proteins and attempt to distinguish the thermodynamic differences between a native and a denatured conformation of a designed miniprotein. We conclude that simple ensemble average properties can be calculated with very reasonable amounts of computational power. In contrast, properties corresponding to fluctuating quantities are computationally demanding to calculate precisely, although they can be obtained more easily by following the temperature and/or pressure dependence of the corresponding ensemble averages. PMID:25325571

Helical unwinding and side-chain unlocking unravel the outward open conformation of the melibiose transporter

NASA Astrophysics Data System (ADS)

Wang, Li-Ying; Ravi, Vidhya M.; Leblanc, Gérard; Padrós, Esteve; Cladera, Josep; Perálvarez-Marín, Alex

2016-09-01

Molecular dynamics simulations have been used to study the alternate access mechanism of the melibiose transporter from Escherichia coli. Starting from the outward-facing partially occluded form, 2 out of 12 simulations produced an outward full open form and one partially open, whereas the rest yielded fully or partially occluded forms. The shape of the outward-open form resembles other outward-open conformations of secondary transporters. During the transporter opening, conformational changes in some loops are followed by changes in the periplasm region of transmembrane helix 7. Helical curvature relaxation and unlocking of hydrophobic and ionic locks promote the outward opening of the transporter making accessible the substrate binding site. In particular, FRET studies on mutants of conserved aromatic residues of extracellular loop 4 showed lack of substrate binding, emphasizing the importance of this loop for making crucial interactions that control the opening of the periplasmic side. This study indicates that the alternate access mechanism for the melibiose transporter fits better into a flexible gating mechanism rather than the archetypical helical rigid-body rocker-switch mechanism.

Direct Calculation of the Scattering Amplitude Without Partial Wave Decomposition. III; Inclusion of Correlation Effects

NASA Technical Reports Server (NTRS)

Shertzer, Janine; Temkin, Aaron

2007-01-01

In the first two papers in this series, we developed a method for studying electron-hydrogen scattering that does not use partial wave analysis. We constructed an ansatz for the wave function in both the static and static exchange approximations and calculated the full scattering amplitude. Here we go beyond the static exchange approximation, and include correlation in the wave function via a modified polarized orbital. This correlation function provides a significant improvement over the static exchange approximation: the resultant elastic scattering amplitudes are in very good agreement with fully converged partial wave calculations for electron-hydrogen scattering. A fully variational modification of this approach is discussed in the conclusion of the article Popular summary of Direct calculation of the scattering amplitude without partial wave expansion. III ....." by J. Shertzer and A. Temkin. In this paper we continue the development of In this paper we continue the development of a new approach to the way in which researchers have traditionally used to calculate the scattering cross section of (low-energy) electrons from atoms. The basic mathematical problem is to solve the Schroedinger Equation (SE) corresponding the above physical process. Traditionally it was always the case that the SE was reduced to a sequence of one-dimensional (ordinary) differential equations - called partial waves which were solved and from the solutions "phase shifts" were extracted, from which the scattering cross section was calculated.

Calculation of the Full Scattering Amplitude without Partial Wave Decomposition. 2; Inclusion of Exchange

NASA Technical Reports Server (NTRS)

Shertzer, Janine; Temkin, Aaron

2004-01-01

The development of a practical method of accurately calculating the full scattering amplitude, without making a partial wave decomposition is continued. The method is developed in the context of electron-hydrogen scattering, and here exchange is dealt with by considering e-H scattering in the static exchange approximation. The Schroedinger equation in this approximation can be simplified to a set of coupled integro-differential equations. The equations are solved numerically for the full scattering wave function. The scattering amplitude can most accurately be calculated from an integral expression for the amplitude; that integral can be formally simplified, and then evaluated using the numerically determined wave function. The results are essentially identical to converged partial wave results.

Effect of Gravity Waves from Small Islands in the Southern Ocean on the Southern Hemisphere Atmospheric Circulation

NASA Technical Reports Server (NTRS)

Garfinkel, C. I.; Oman, L. D.

2018-01-01

The effect of small islands in the Southern Ocean on the atmospheric circulation in the Southern Hemisphere is considered with a series of simulations using the NASA Goddard Earth Observing System Chemistry-Climate Model in which the gravity wave stress generated by these islands is increased to resemble observed values. The enhanced gravity wave drag leads to a 2 K warming of the springtime polar stratosphere, partially ameliorating biases in this region. Resolved wave drag declines in the stratospheric region in which the added orographic gravity waves deposit their momentum, such that changes in gravity waves are partially compensated by changes in resolved waves, though resolved wave drag increases further poleward. The orographic drag from these islands has impacts for surface climate, as biases in tropospheric jet position are also partially ameliorated. These results suggest that these small islands are likely contributing to the missing drag near 60 degrees S in the upper stratosphere evident in many data assimilation products.

Factors Influencing Army Accessions.

DTIC Science & Technology

1982-12-01

partial autocorrelations were examined for significant lags or a recognizable pattern such as a damped exponential or a sine wave. The TSP prugrams...decreasing function indicating nonstation- *arity or a very long sine wave where only a small portion of the wave is plotted. The partial...plot of the raw data appeared (Appendix E-1) to be either the middle of a long sine wave or a linearly decreasing function. This pattern is recognized

Identification of seismic anomalies caused by gas saturation on the basis of theoretical P and PS wavefield in the Carpathian Foredeep, SE Poland

NASA Astrophysics Data System (ADS)

Pietsch, Kaja; Marzec, Paweł; Kobylarski, Marcin; Danek, Tomasz; Leśniak, Andrzej; Tatarata, Artur; Gruszczyk, Edward

2007-06-01

The thin-layer build of the Carpathian Foredeep Miocene formations and large petrophysical parameter variation cause seismic images of gas-saturated zones to be ambiguous, and the location of prospection wells on the basis of anomalous seismic record is risky. A method that assists reservoir interpretation of standard recorded seismic profiles (P waves) can be a converted wave recording (PS waves). This paper presents the results of application of a multicomponent seismic survey for the reservoir interpretation over the Chałupki Dębniańskie gas deposit, carried out for the first time in Poland by Geofizyka Kraków Ltd. for the Polish Oil and Gas Company. Seismic modeling was applied as the basic research tool, using the SeisMod program based on the finite-difference solution of the acoustic wave equation and equations of motion. Seismogeological models for P waves were developed using Acoustic Logs; S-wave model (records only from part of the well) was developed on the basis of theoretical curves calculated by means of the Estymacja program calibrated with average S-velocities, calculated by correlation of recorded P and PS wavefields with 1D modeling. The conformity between theoretical and recorded wavefields makes it possible to apply the criteria established on the basis of modeling for reservoir interpretation. Direct hydrocarbon indicators (bright spots, phase change, time sag) unambiguously identify gas-prone layers within the ChD-2 prospect. A partial range of the indicators observed in the SW part of the studied profile (bright spot that covers a single, anticlinally bent seismic horizon) points to saturation of the horizon. The proposed location is confirmed by criteria determined for converted waves (continuous seismic horizons with constant, high amplitude) despite poorer agreement between theoretical and recorded wavefields.

The formation mechanism of defects, spiral wave in the network of neurons.

PubMed

Wu, Xinyi; Ma, Jun

2013-01-01

A regular network of neurons is constructed by using the Morris-Lecar (ML) neuron with the ion channels being considered, and the potential mechnism of the formation of a spiral wave is investigated in detail. Several spiral waves are initiated by blocking the target wave with artificial defects and/or partial blocking (poisoning) in ion channels. Furthermore, possible conditions for spiral wave formation and the effect of partial channel blocking are discussed completely. Our results are summarized as follows. 1) The emergence of a target wave depends on the transmembrane currents with diversity, which mapped from the external forcing current and this kind of diversity is associated with spatial heterogeneity in the media. 2) Distinct spiral wave could be induced to occupy the network when the target wave is broken by partially blocking the ion channels of a fraction of neurons (local poisoned area), and these generated spiral waves are similar with the spiral waves induced by artificial defects. It is confirmed that partial channel blocking of some neurons in the network could play a similar role in breaking a target wave as do artificial defects; 3) Channel noise and additive Gaussian white noise are also considered, and it is confirmed that spiral waves are also induced in the network in the presence of noise. According to the results mentioned above, we conclude that appropriate poisoning in ion channels of neurons in the network acts as 'defects' on the evolution of the spatiotemporal pattern, and accounts for the emergence of a spiral wave in the network of neurons. These results could be helpful to understand the potential cause of the formation and development of spiral waves in the cortex of a neuronal system.

The Formation Mechanism of Defects, Spiral Wave in the Network of Neurons

PubMed Central

Wu, Xinyi; Ma, Jun

2013-01-01

A regular network of neurons is constructed by using the Morris-Lecar (ML) neuron with the ion channels being considered, and the potential mechnism of the formation of a spiral wave is investigated in detail. Several spiral waves are initiated by blocking the target wave with artificial defects and/or partial blocking (poisoning) in ion channels. Furthermore, possible conditions for spiral wave formation and the effect of partial channel blocking are discussed completely. Our results are summarized as follows. 1) The emergence of a target wave depends on the transmembrane currents with diversity, which mapped from the external forcing current and this kind of diversity is associated with spatial heterogeneity in the media. 2) Distinct spiral wave could be induced to occupy the network when the target wave is broken by partially blocking the ion channels of a fraction of neurons (local poisoned area), and these generated spiral waves are similar with the spiral waves induced by artificial defects. It is confirmed that partial channel blocking of some neurons in the network could play a similar role in breaking a target wave as do artificial defects; 3) Channel noise and additive Gaussian white noise are also considered, and it is confirmed that spiral waves are also induced in the network in the presence of noise. According to the results mentioned above, we conclude that appropriate poisoning in ion channels of neurons in the network acts as ‘defects’ on the evolution of the spatiotemporal pattern, and accounts for the emergence of a spiral wave in the network of neurons. These results could be helpful to understand the potential cause of the formation and development of spiral waves in the cortex of a neuronal system. PMID:23383179

Evaluation of Density Functionals and Basis Sets for Carbohydrates

USDA-ARS?s Scientific Manuscript database

Correlated ab initio wave function calculations using MP2/aug-cc-pVTZ model chemistry have been performed for three test sets of gas phase saccharide conformations to provide reference values for their relative energies. The test sets consist of 15 conformers of alpha and beta-D-allopyranose, 15 of ...

The Microwave Spectroscopy Study of 1,2-DIMETHOXYETHANE

NASA Astrophysics Data System (ADS)

Li, Weixing; Vigorito, Annalisa; Calabrese, Camilla; Evangelisti, Luca; Favero, Laura B.; Maris, Assimo; Melandri, Sonia

2017-06-01

With Pulsed-Jet Fourier Transform MicroWave (PJ-FTMW) spectroscopy and Stark modulated Free Jet Millimeter-Wave absorption (FJ-AMMW) spectroscopy, the rotational spectra of two conformers of 1,2-Dimethoxyethane were identified and characterized. Besides the normal species, the spectra of all the mono-substituted ^{13}C isotopologues in natural abundance were also measured. By fitting the rotational transitions split by the methyl internal rotations using both XIAM and ERHAM programs, the spectroscopic parameters were obtained and compared. The rotational constants indicated the conformers to be TGT and TGG', respectively. With the rotational constants of the normal and ^{13}C species, the coordinates of the substituted carbon atoms could be calculated with Kraitchmann's equations. The carbon-frameworks further confirmed the assignment of the two conformations. The V_{3} barriers of the two methyl groups' internal rotations were also experimentally determined.

Connection between angle-dependent phase ambiguities and the uniqueness of the partial-wave decomposition

NASA Astrophysics Data System (ADS)

Švarc, A.; Wunderlich, Y.; Osmanović, H.; Hadžimehmedović, M.; Omerović, R.; Stahov, J.; Kashevarov, V.; Nikonov, K.; Ostrick, M.; Tiator, L.; Workman, R.

2018-05-01

Unconstrained partial -wave amplitudes, obtained at discrete energies from fits to complete sets of eight independent observables, may be used to reconstruct reaction amplitudes. These partial-wave amplitudes do not vary smoothly with energy and are in principle nonunique. We demonstrate how this behavior can be ascribed to the continuum ambiguity. Starting from the spinless scattering case, we show how an unknown overall phase, depending on energy and angle, mixes the structures seen in the associated partial-wave amplitudes. This process is illustrated using a simple toy model. We then apply these principles to pseudoscalar meson photoproduction, showing how the above effect can be removed through a phase rotation, allowing a consistent comparison with model amplitudes. The effect of this phase ambiguity is also considered for Legendre expansions of experimental observables.

Sequential allosteric mechanism of ATP hydrolysis by the CCT/TRiC chaperone is revealed through Arrhenius analysis

PubMed Central

Gruber, Ranit; Levitt, Michael; Horovitz, Amnon

2017-01-01

Knowing the mechanism of allosteric switching is important for understanding how molecular machines work. The CCT/TRiC chaperonin nanomachine undergoes ATP-driven conformational changes that are crucial for its folding function. Here, we demonstrate that insight into its allosteric mechanism of ATP hydrolysis can be achieved by Arrhenius analysis. Our results show that ATP hydrolysis triggers sequential ‟conformational waves.” They also suggest that these waves start from subunits CCT6 and CCT8 (or CCT3 and CCT6) and proceed clockwise and counterclockwise, respectively. PMID:28461478

Sequential allosteric mechanism of ATP hydrolysis by the CCT/TRiC chaperone is revealed through Arrhenius analysis.

PubMed

Gruber, Ranit; Levitt, Michael; Horovitz, Amnon

2017-05-16

Knowing the mechanism of allosteric switching is important for understanding how molecular machines work. The CCT/TRiC chaperonin nanomachine undergoes ATP-driven conformational changes that are crucial for its folding function. Here, we demonstrate that insight into its allosteric mechanism of ATP hydrolysis can be achieved by Arrhenius analysis. Our results show that ATP hydrolysis triggers sequential ‟conformational waves." They also suggest that these waves start from subunits CCT6 and CCT8 (or CCT3 and CCT6) and proceed clockwise and counterclockwise, respectively.

Experimental observation of water saturation effects on shear wave splitting in synthetic rock with fractures aligned at oblique angles

NASA Astrophysics Data System (ADS)

Amalokwu, Kelvin; Chapman, Mark; Best, Angus I.; Sothcott, Jeremy; Minshull, Timothy A.; Li, Xiang-Yang

2015-01-01

Fractured rocks are known to exhibit seismic anisotropy and shear wave splitting (SWS). SWS is commonly used for fractured rock characterization and has been shown to be sensitive to fluid type. The presence of partial liquid/gas saturation is also known to affect the elastic properties of rocks. The combined effect of both fractures and partial liquid/gas saturation is still unknown. Using synthetic, silica-cemented sandstones with aligned penny-shaped voids, we conducted laboratory ultrasonic experiments to investigate the effect fractures aligned at an oblique angle to wave propagation would have on SWS under partial liquid/gas saturation conditions. The result for the fractured rock shows a saturation dependence which can be explained by combining a fractured rock model and a partial saturation model. At high to full water saturation values, SWS decreases as a result of the fluid bulk modulus effect on the quasi-shear wave. This bulk modulus effect is frequency dependent as a result of wave-induced fluid flow mechanisms, which would in turn lead to frequency dependent SWS. This result suggests the possible use of SWS for discriminating between full liquid saturation and partial liquid/gas saturation.

Faddeev calculation for ^9_ΛBe hypernucleus

NASA Astrophysics Data System (ADS)

Suslov, Vladimir; Filikhin, Igor; Vlahovic, Branislav

2003-04-01

Faddeev calculations are performed for the ^9_ΛBe hypernucleus in terms of α's and Λ clusters using various Λα potential models. The main goal of our calculations is to estimate higher partial waves contribution in binding energy of ^9_ΛBe ground state (1/2^+) and particularly contribution from the high partial waves of the Λα pair. Phenomenological Ali-Bodmer potential is employed for description of the αα interaction. This potential has s, d and g - waves components. For a Λα potential both form and parameters are uncertain, because Λα interaction data are limited by the experimental value of binding energy of the ^5_ΛHe hypernucleus, which is considered as the bound s-wave state of the Λα system. The binding energy of the ^9_ΛBe is calculated for two different cases. First the s-wave Λα potential acting in all partial waves in the Λα subsystem is used. Second, a recent more realistic Λα potential model including the s and p-partial components from work [1] is employed. We compared these models and discussed validity of the s-wave approximation for calculation of ^9_ΛBe hypernucleus. This work was partially supported by Department of Defenses through the grant No.DAAD 19-01-1-0795. The work of V.M.S and I.N.F was supported by the RFFI under Grant No. 02-02-16562. References: [1] K.S. Myint, S. Shinmura and Y. Akaishi, nucl-th/0209090.

Partial-wave analysis of nucleon-nucleon elastic scattering data

DOE PAGES

Workman, Ron L.; Briscoe, William J.; Strakovsky, Igor I.

2016-12-19

Energy-dependent and single-energy fits to the existing nucleon-nucleon database have been updated to incorporate recent measurements. The fits cover a region from threshold to 3 GeV, in the laboratory kinetic energy, for proton-proton scattering, with an upper limit of 1.3 GeV for neutron-proton scattering. Experiments carried out at the COSY-WASA and COSY-ANKE facilities have had a significant impact on the partial-wave solutions. Lastly, results are discussed in terms of both partial-wave and direct reconstruction amplitudes.

Non-local Effects of Conformal Anomaly

NASA Astrophysics Data System (ADS)

Meissner, Krzysztof A.; Nicolai, Hermann

2018-03-01

It is shown that the nonlocal anomalous effective actions corresponding to the quantum breaking of the conformal symmetry can lead to observable modifications of Einstein's equations. The fact that Einstein's general relativity is in perfect agreement with all observations including cosmological or recently observed gravitational waves imposes strong restrictions on the field content of possible extensions of Einstein's theory: all viable theories should have vanishing conformal anomalies. It is shown that a complete cancellation of conformal anomalies in D=4 for both the C^2 invariant and the Euler (Gauss-Bonnet) invariant can only be achieved for N-extended supergravity multiplets with N ≥ 5.

On discrete field theory properties of the dimer and Ising models and their conformal field theory limits

NASA Astrophysics Data System (ADS)

Kriz, Igor; Loebl, Martin; Somberg, Petr

2013-05-01

We study various mathematical aspects of discrete models on graphs, specifically the Dimer and the Ising models. We focus on proving gluing formulas for individual summands of the partition function. We also obtain partial results regarding conjectured limits realized by fermions in rational conformal field theories.

Scattering of plane evanescent waves by buried cylinders: Modeling the coupling to guided waves and resonances

NASA Astrophysics Data System (ADS)

Marston, Philip L.

2003-04-01

The coupling of sound to buried targets can be associated with acoustic evanescent waves when the sea bottom is smooth. To understand the excitation of guided waves on buried fluid cylinders and shells by acoustic evanescent waves and the associated target resonances, the two-dimensional partial wave series for the scattering is found for normal incidence in an unbounded medium. The shell formulation uses the simplifications of thin-shell dynamics. The expansion of the incident wave becomes a double summation with products of modified and ordinary Bessel functions [P. L. Marston, J. Acoust. Soc. Am. 111, 2378 (2002)]. Unlike the case of an ordinary incident wave, the counterpropagating partial waves of the same angular order have unequal magnitudes when the incident wave is evanescent. This is a consequence of the exponential dependence of the incident wave amplitude on depth. Some consequences of this imbalance of partial-wave amplitudes are given by modifying previous ray theory for the scattering [P. L. Marston and N. H. Sun, J. Acoust. Soc. Am. 97, 777-783 (1995)]. The exponential dependence of the scattering on the location of a scatterer was previously demonstrated in air [T. J. Matula and P. L. Marston, J. Acoust. Soc. Am. 93, 1192-1195 (1993)].

Unification of the general non-linear sigma model and the Virasoro master equation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boer, J. de; Halpern, M.B.

1997-06-01

The Virasoro master equation describes a large set of conformal field theories known as the affine-Virasoro constructions, in the operator algebra (affinie Lie algebra) of the WZW model, while the einstein equations of the general non-linear sigma model describe another large set of conformal field theories. This talk summarizes recent work which unifies these two sets of conformal field theories, together with a presumable large class of new conformal field theories. The basic idea is to consider spin-two operators of the form L{sub ij}{partial_derivative}x{sup i}{partial_derivative}x{sup j} in the background of a general sigma model. The requirement that these operators satisfymore » the Virasoro algebra leads to a set of equations called the unified Einstein-Virasoro master equation, in which the spin-two spacetime field L{sub ij} cuples to the usual spacetime fields of the sigma model. The one-loop form of this unified system is presented, and some of its algebraic and geometric properties are discussed.« less

Relativistic optical model on the basis of the Moscow potential and lower phase shifts for nucleon-nucleon scattering at laboratory energies of up to 3 GeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knyr, V. A.; Neudatchin, V. G.; Khokhlov, N. A.

Data of a partial-wave analysis of nucleon-nucleon scattering at energies of up to E{sub lab} = 3 GeV (lower partial waves) and the properties of the deuteron are described within the relativistic optical model based on deep attractive quasipotentials involving forbidden states (as exemplified by the Moscow potential). Partial-wave potentials are derived by the inverse-scattering-problem method based on the Marchenko equation by using present-day data from the partial-wave analysis of nucleon-nucleon scattering at energies of up to 3 GeV. Channel coupling is taken into account. The imaginary parts of the potentials are deduced from the phase equation of the variable-phasemore » approach. The general situation around the manifestation of quark effects in nucleon-nucleon interaction is discussed.« less

Matrix product state description of Halperin states

NASA Astrophysics Data System (ADS)

Crépel, V.; Estienne, B.; Bernevig, B. A.; Lecheminant, P.; Regnault, N.

2018-04-01

Many fractional quantum Hall states can be expressed as a correlator of a given conformal field theory used to describe their edge physics. As a consequence, these states admit an economical representation as an exact matrix product state (MPS) that was extensively studied for the systems without any spin or any other internal degrees of freedom. In that case, the correlators are built from a single electronic operator, which is primary with respect to the underlying conformal field theory. We generalize this construction to the archetype of Abelian multicomponent fractional quantum Hall wave functions, the Halperin states. These can be written as conformal blocks involving multiple electronic operators and we explicitly derive their exact MPS representation. In particular, we deal with the caveat of the full wave-function symmetry and show that any additional SU(2) symmetry is preserved by the natural MPS truncation scheme provided by the conformal dimension. We use our method to characterize the topological order of the Halperin states by extracting the topological entanglement entropy. We also evaluate their bulk correlation lengths, which are compared to plasma analogy arguments.

Conformational state interactions provide clues to the pharmacochaperone potential of serotonin transporter partial substrates

PubMed Central

Bhat, Shreyas; Hasenhuetl, Peter S.; Kasture, Ameya; El-Kasaby, Ali; Baumann, Michael H.; Blough, Bruce E.; Sucic, Sonja; Sandtner, Walter; Freissmuth, Michael

2017-01-01

Point mutations in SLC6 transporters cause misfolding, which can be remedied by pharmacochaperones. The serotonin transporter (SERT/SLC6A4) has a rich pharmacology including inhibitors, releasers (amphetamines, which promote the exchange mode), and more recently, discovered partial substrates. We hypothesized that partial substrates trapped the transporter in one or several states of the transport cycle. This conformational trapping may also be conducive to folding. We selected naphthylpropane-2-amines of the phenethylamine library (PAL) including the partial substrate PAL1045 and its congeners PAL287 and PAL1046. We analyzed their impact on the transport cycle of SERT by biochemical approaches and by electrophysiological recordings; substrate-induced peak currents and steady-state currents monitored the translocation of substrate and co-substrate Na+ across the lipid bilayer and the transport cycle, respectively. These experiments showed that PAL1045 and its congeners bound with different affinities (ranging from nm to μm) to various conformational intermediates of SERT during the transport cycle. Consistent with the working hypothesis, PAL1045 was the most efficacious compound in restoring surface expression and transport activity to the folding-deficient mutant SERT-601PG602-AA. These experiments provide a proof-of-principle for a rational search for pharmacochaperones, which may be useful to restore function to clinically relevant folding-deficient transporter mutants. PMID:28842491

Conformal surface plasmons propagating on ultrathin and flexible films

PubMed Central

Shen, Xiaopeng; Cui, Tie Jun; Martin-Cano, Diego; Garcia-Vidal, Francisco J.

2013-01-01

Surface plasmon polaritons (SPPs) are localized surface electromagnetic waves that propagate along the interface between a metal and a dielectric. Owing to their inherent subwavelength confinement, SPPs have a strong potential to become building blocks of a type of photonic circuitry built up on 2D metal surfaces; however, SPPs are difficult to control on curved surfaces conformably and flexibly to produce advanced functional devices. Here we propose the concept of conformal surface plasmons (CSPs), surface plasmon waves that can propagate on ultrathin and flexible films to long distances in a wide broadband range from microwave to mid-infrared frequencies. We present the experimental realization of these CSPs in the microwave regime on paper-like dielectric films with a thickness 600-fold smaller than the operating wavelength. The flexible paper-like films can be bent, folded, and even twisted to mold the flow of CSPs. PMID:23248311

Conductance of P2X4 purinergic receptor is determined by conformational equilibrium in the transmembrane region.

PubMed

Minato, Yuichi; Suzuki, Shiho; Hara, Tomoaki; Kofuku, Yutaka; Kasuya, Go; Fujiwara, Yuichiro; Igarashi, Shunsuke; Suzuki, Ei-Ichiro; Nureki, Osamu; Hattori, Motoyuki; Ueda, Takumi; Shimada, Ichio

2016-04-26

Ligand-gated ion channels are partially activated by their ligands, resulting in currents lower than the currents evoked by the physiological full agonists. In the case of P2X purinergic receptors, a cation-selective pore in the transmembrane region expands upon ATP binding to the extracellular ATP-binding site, and the currents evoked by α,β-methylene ATP are lower than the currents evoked by ATP. However, the mechanism underlying the partial activation of the P2X receptors is unknown although the crystal structures of zebrafish P2X4 receptor in the apo and ATP-bound states are available. Here, we observed the NMR signals from M339 and M351, which were introduced in the transmembrane region, and the endogenous alanine and methionine residues of the zebrafish P2X4 purinergic receptor in the apo, ATP-bound, and α,β-methylene ATP-bound states. Our NMR analyses revealed that, in the α,β-methylene ATP-bound state, M339, M351, and the residues that connect the ATP-binding site and the transmembrane region, M325 and A330, exist in conformational equilibrium between closed and open conformations, with slower exchange rates than the chemical shift difference (<100 s(-1)), suggesting that the small population of the open conformation causes the partial activation in this state. Our NMR analyses also revealed that the transmembrane region adopts the open conformation in the state bound to the inhibitor trinitrophenyl-ATP, and thus the antagonism is due to the closure of ion pathways, except for the pore in the transmembrane region: i.e., the lateral cation access in the extracellular region.

Conductance of P2X4 purinergic receptor is determined by conformational equilibrium in the transmembrane region

PubMed Central

Minato, Yuichi; Suzuki, Shiho; Hara, Tomoaki; Kofuku, Yutaka; Kasuya, Go; Fujiwara, Yuichiro; Igarashi, Shunsuke; Suzuki, Ei-ichiro; Nureki, Osamu; Hattori, Motoyuki; Ueda, Takumi; Shimada, Ichio

2016-01-01

Ligand-gated ion channels are partially activated by their ligands, resulting in currents lower than the currents evoked by the physiological full agonists. In the case of P2X purinergic receptors, a cation-selective pore in the transmembrane region expands upon ATP binding to the extracellular ATP-binding site, and the currents evoked by α,β-methylene ATP are lower than the currents evoked by ATP. However, the mechanism underlying the partial activation of the P2X receptors is unknown although the crystal structures of zebrafish P2X4 receptor in the apo and ATP-bound states are available. Here, we observed the NMR signals from M339 and M351, which were introduced in the transmembrane region, and the endogenous alanine and methionine residues of the zebrafish P2X4 purinergic receptor in the apo, ATP-bound, and α,β-methylene ATP-bound states. Our NMR analyses revealed that, in the α,β-methylene ATP-bound state, M339, M351, and the residues that connect the ATP-binding site and the transmembrane region, M325 and A330, exist in conformational equilibrium between closed and open conformations, with slower exchange rates than the chemical shift difference (<100 s−1), suggesting that the small population of the open conformation causes the partial activation in this state. Our NMR analyses also revealed that the transmembrane region adopts the open conformation in the state bound to the inhibitor trinitrophenyl-ATP, and thus the antagonism is due to the closure of ion pathways, except for the pore in the transmembrane region: i.e., the lateral cation access in the extracellular region. PMID:27071117

Scalar gravitational waves in the effective theory of gravity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mottola, Emil

As a low energy effective field theory, classical General Relativity receives an infrared relevant modification from the conformal trace anomaly of the energy-momentum tensor of massless, or nearly massless, quantum fields. The local form of the effective action associated with the trace anomaly is expressed in terms of a dynamical scalar field that couples to the conformal factor of the spacetime metric, allowing it to propagate over macroscopic distances. Linearized around flat spacetime, this semi-classical EFT admits scalar gravitational wave solutions in addition to the transversely polarized tensor waves of the classical Einstein theory. The amplitude of the scalar wavemore » modes, as well as their energy and energy flux which are positive and contain a monopole moment, are computed. As a result, astrophysical sources for scalar gravitational waves are considered, with the excited gluonic condensates in the interiors of neutron stars in merger events with other compact objects likely to provide the strongest burst signals.« less

Scalar gravitational waves in the effective theory of gravity

DOE PAGES

Mottola, Emil

2017-07-10

As a low energy effective field theory, classical General Relativity receives an infrared relevant modification from the conformal trace anomaly of the energy-momentum tensor of massless, or nearly massless, quantum fields. The local form of the effective action associated with the trace anomaly is expressed in terms of a dynamical scalar field that couples to the conformal factor of the spacetime metric, allowing it to propagate over macroscopic distances. Linearized around flat spacetime, this semi-classical EFT admits scalar gravitational wave solutions in addition to the transversely polarized tensor waves of the classical Einstein theory. The amplitude of the scalar wavemore » modes, as well as their energy and energy flux which are positive and contain a monopole moment, are computed. As a result, astrophysical sources for scalar gravitational waves are considered, with the excited gluonic condensates in the interiors of neutron stars in merger events with other compact objects likely to provide the strongest burst signals.« less

Flat connections and nonlocal conserved quantities in irrational conformal field theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Halpern, M.B.; Obers, N.A.

1995-03-01

Irrational conformal field theory (ICFT) includes rational conformal field theory as a small subspace, and the affine-Virasoro Ward identities describe the biconformal correlators of ICFT. The Ward identities are reformulated as an equivalent linear partial differential system with flat connections and new nonlocal conserved quantities. As examples of the formulation, the system of flat connections is solved for the coset correlators, the correlators of the affine-Sugawara nests, and the high-level [ital n]-point correlators of ICFT.

Direct conformational analysis of a 10 nm long oligothiophene wire.

PubMed

Nishiyama, Fumitaka; Ogawa, Kengo; Tanaka, Shoji; Yokoyama, Takashi

2008-05-01

Conformational variations of a 10 nm long oligothiophene wire comprising 24 thiophene rings on Au(111), which are related to the various straight and bent shapes of the long wires, have been directly visualized by scanning tunneling microscopy (STM). The local bending angles within the wire are well characterized as s-cis/s-trans configurations of individual thiophene rings. We find that the partial stabilization of the metastable s-cis conformation results in the wire bending, which should be influenced by solvent and substituents.

Penetration and screening of perpendicularly launched electromagnetic waves through bounded supercritical plasma confined in multicusp magnetic field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dey, Indranuj; Bhattacharjee, Sudeep

2011-02-15

The question of electromagnetic wave penetration and screening by a bounded supercritical ({omega}{sub p}>{omega} with {omega}{sub p} and {omega} being the electron-plasma and wave frequencies, respectively) plasma confined in a minimum B multicusp field, for waves launched in the k perpendicular B{sub o} mode, is addressed through experiments and numerical simulations. The scale length of radial plasma nonuniformity (|n{sub e}/({partial_derivative}n{sub e}/{partial_derivative}r)|) and magnetostatic field (B{sub o}) inhomogeneity (|B{sub o}/({partial_derivative}B{sub o}/{partial_derivative}r)|) are much smaller than the free space ({lambda}{sub o}) and guided wavelengths ({lambda}{sub g}). Contrary to predictions of plane wave dispersion theory and the Clemow-Mullaly-Allis (CMA) diagram, for a boundedmore » plasma a finite propagation occurs through the central plasma regions where {alpha}{sub p}{sup 2}={omega}{sub p}{sup 2}/{omega}{sup 2}{>=}1 and {beta}{sub c}{sup 2}={omega}{sub ce}{sup 2}/{omega}{sup 2}<<1({approx}10{sup -4}), with {omega}{sub ce} being the electron cyclotron frequency. Wave screening, as predicted by the plane wave model, does not remain valid due to phase mixing and superposition of reflected waves from the conducting boundary, leading to the formation of electromagnetic standing wave modes. The waves are found to satisfy a modified upper hybrid resonance (UHR) relation in the minimum B field and are damped at the local electron cyclotron resonance (ECR) location.« less

Stressful Events and Other Predictors of Remission from Drug Dependence in the United States: Longitudinal Results from a National Survey

PubMed Central

McCabe, Sean Esteban; Cranford, James A.; Boyd, Carol J.

2016-01-01

This study examined stressful life events and other predictors associated with remission from DSM-IV drug dependence involving cannabis, cocaine, hallucinogens, heroin, inhalants, non-heroin opioids, sedatives, stimulants, tranquilizers, or other drugs. Waves 1 and 2 of the National Epidemiologic Survey on Alcohol and Related Conditions were used to examine the prevalence and predictors of past-year remission status. Among U.S. adults with previous (i.e., prior-to-past-year) drug dependence (n = 921) at baseline (Wave 1), the prevalence of past-year remission status at Wave 1 was: abstinence (60.5%), asymptomatic drug use (18.8%), partial remission (7.1%), and still drug dependent (13.5%). Similarly, the prevalence of past-year remission status three years after baseline at Wave 2 was: abstinence (69.1%), asymptomatic drug use (15.5%), partial remission (8.4%), and still drug dependent (7.0%). Remission three years after baseline at Wave 2 was much more likely among formerly drug dependent U.S. adults who abstained from drug use at baseline (Wave 1) relative to those who reported asymptomatic drug use, partial remission, or remained drug dependent. Design-based weighted multinomial logistic regression analysis showed that relative to abstinence, past-year stressful events at baseline (Wave 1) predicted higher odds of partial remission and drug dependence at both Waves 1 and 2. This is the first national study to examine the potential role of stressful life events associated with remission from drug dependence. Although the majority of those who reported previous drug dependence transitioned to full remission, a sizeable percentage were either still drug dependent or in partial remission. Higher levels of stressful life events appear to create barriers for remission and should remain a focus for relapse prevention programs. PMID:27776676

Influences of periodic mechanical deformation on pinned spiral waves

NASA Astrophysics Data System (ADS)

Chen, Jiang-Xing; Peng, Liang; Zheng, Qiang; Zhao, Ye-Hua; Ying, He-Ping

2014-09-01

In a generic model of excitable media, we study the behavior of spiral waves interacting with obstacles and their dynamics under the influences of simple periodic mechanical deformation (PMD). Depending on the characteristics of the obstacles, i.e., size and excitability, the rotation of a pinned spiral wave shows different scenarios, e.g., embedding into or anchoring on an obstacle. Three different drift phenomena induced by PMD are observed: scattering on small partial-excitable obstacles, meander-induced unpinning on big partial-excitable obstacles, and drifting around small unexcitable obstacles. Their underlying mechanisms are discussed. The dependence of the threshold amplitude of PMD on the characteristics of the obstacles to successfully remove pinned spiral waves on big partial-excitable obstacles is studied.

Food as a way to convey masculinities: How conformity to hegemonic masculinity norms influences men's and women's food consumption.

PubMed

Campos, Lúcia; Bernardes, Sónia; Godinho, Cristina

2018-05-01

This study investigated how conformity to hegemonic masculinity norms affects men's and women's food consumption and whether such influence was contextually modulated. A total of 519 individuals (65% women; M = 44 years old) participated in a 2 (gender salience: low vs high) × 2 (participants' sex: male vs female) quasi-experimental between-subjects design, completing the Conformity to Masculinity Norms Inventory (Portuguese version) and reporting their past week's food consumption. Gender salience moderated the relation between men's conformity to masculinity norms and food consumption; sex-related differences in food consumption were partially mediated by conformity to masculinity norms. Implications for food consumption interventions are discussed.

Full Wave Analysis of Passive Microwave Monolithic Integrated Circuit Devices Using a Generalized Finite Difference Time Domain (GFDTD) Algorithm

NASA Technical Reports Server (NTRS)

Lansing, Faiza S.; Rascoe, Daniel L.

1993-01-01

This paper presents a modified Finite-Difference Time-Domain (FDTD) technique using a generalized conformed orthogonal grid. The use of the Conformed Orthogonal Grid, Finite Difference Time Domain (GFDTD) enables the designer to match all the circuit dimensions, hence eliminating a major source o error in the analysis.

Picosecond to nanosecond dynamics provide a source of conformational entropy for protein folding.

PubMed

Stadler, Andreas M; Demmel, Franz; Ollivier, Jacques; Seydel, Tilo

2016-08-03

Myoglobin can be trapped in fully folded structures, partially folded molten globules, and unfolded states under stable equilibrium conditions. Here, we report an experimental study on the conformational dynamics of different folded conformational states of apo- and holomyoglobin in solution. Global protein diffusion and internal molecular motions were probed by neutron time-of-flight and neutron backscattering spectroscopy on the picosecond and nanosecond time scales. Global protein diffusion was found to depend on the α-helical content of the protein suggesting that charges on the macromolecule increase the short-time diffusion of protein. With regard to the molten globules, a gel-like phase due to protein entanglement and interactions with neighbouring macromolecules was visible due to a reduction of the global diffusion coefficients on the nanosecond time scale. Diffusion coefficients, residence and relaxation times of internal protein dynamics and root mean square displacements of localised internal motions were determined for the investigated structural states. The difference in conformational entropy ΔSconf of the protein between the unfolded and the partially or fully folded conformations was extracted from the measured root mean square displacements. Using thermodynamic parameters from the literature and the experimentally determined ΔSconf values we could identify the entropic contribution of the hydration shell ΔShydr of the different folded states. Our results point out the relevance of conformational entropy of the protein and the hydration shell for stability and folding of myoglobin.

Conformational switching upon phosphorylation: a predictive framework based on energy landscape principles.

PubMed

Lätzer, Joachim; Shen, Tongye; Wolynes, Peter G

2008-02-19

We investigate how post-translational phosphorylation modifies the global conformation of a protein by changing its free energy landscape using two test proteins, cystatin and NtrC. We first examine the changes in a free energy landscape caused by phosphorylation using a model containing information about both structural forms. For cystatin the free energy cost is fairly large indicating a low probability of sampling the phosphorylated conformation in a perfectly funneled landscape. The predicted barrier for NtrC conformational transition is several times larger than the barrier for cystatin, indicating that the switch protein NtrC most probably follows a partial unfolding mechanism to move from one basin to the other. Principal component analysis and linear response theory show how the naturally occurring conformational changes in unmodified proteins are captured and stabilized by the change of interaction potential. We also develop a partially guided structure prediction Hamiltonian which is capable of predicting the global structure of a phosphorylated protein using only knowledge of the structure of the unphosphorylated protein or vice versa. This algorithm makes use of a generic transferable long-range residue contact potential along with details of structure short range in sequence. By comparing the results obtained with this guided transferable potential to those from the native-only, perfectly funneled Hamiltonians, we show that the transferable Hamiltonian correctly captures the nature of the global conformational changes induced by phosphorylation and can sample substantially correct structures for the modified protein with high probability.

An Accurate Method for Measuring Airplane-Borne Conformal Antenna's Radar Cross Section

NASA Astrophysics Data System (ADS)

Guo, Shuxia; Zhang, Lei; Wang, Yafeng; Hu, Chufeng

2016-09-01

The airplane-borne conformal antenna attaches itself tightly with the airplane skin, so the conventional measurement method cannot determine the contribution of the airplane-borne conformal antenna to its radar cross section (RCS). This paper uses the 2D microwave imaging to isolate and extract the distribution of the reflectivity of the airplane-borne conformal antenna. It obtains the 2D spatial spectra of the conformal antenna through the wave spectral transform between the 2D spatial image and the 2D spatial spectrum. After the interpolation from the rectangular coordinate domain to the polar coordinate domain, the spectral domain data for the variation of the scatter of the conformal antenna with frequency and angle is obtained. The experimental results show that the measurement method proposed in this paper greatly enhances the airplane-borne conformal antenna's RCS measurement accuracy, essentially eliminates the influences caused by the airplane skin and more accurately reveals the airplane-borne conformal antenna's RCS scatter properties.

Dispersion relation for hadronic light-by-light scattering: two-pion contributions

DOE PAGES

Colangelo, Gilberto; Hoferichter, Martin; Procura, Massimiliano; ...

2017-04-27

In our third paper of a series dedicated to a dispersive treatment of the hadronic light-by-light (HLbL) tensor, we derive a partial-wave formulation for two-pion intermediate states in the HLbL contribution to the anomalous magnetic moment of the muon (g - 2) μ, including a detailed discussion of the unitarity relation for arbitrary partial waves. We show that obtaining a final expression free from unphysical helicity partial waves is a subtle issue, which we thoroughly clarify. As a by-product, we obtain a set of sum rules that could be used to constrain future calculations of γ*γ* → ππ. We validate the formalism extensively using the pion-box contribution, defined by two-pion intermediate states with a pion-pole left-hand cut, and demonstrate how the full known result is reproduced when resumming the partial waves. Using dispersive fits to high-statistics data for the pion vector form factor, we provide an evaluation of the full pion box, amore » $$π-box\\atop{μ}$$ =-15.9(2) × 10 -11. As an application of the partial-wave formalism, we present a first calculation of ππ-rescattering effects in HLbL scattering, with γ*γ* → ππ helicity partial waves constructed dispersively using ππ phase shifts derived from the inverse-amplitude method. In this way, the isospin-0 part of our calculation can be interpreted as the contribution of the f0(500) to HLbL scattering in (g - 2) μ. We also argue that the contribution due to charged-pion rescattering implements corrections related to the corresponding pion polarizability and show that these are moderate. Our final result for the sum of pion-box contribution and its S-wave rescattering corrections reads a$$π-box\\atop{μ}$$ + a$$ππ, π-pole LHC\\atop{μ, J=0}$$ = -24(1) × 10 -11.« less

Dispersion relation for hadronic light-by-light scattering: two-pion contributions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Colangelo, Gilberto; Hoferichter, Martin; Procura, Massimiliano

In our third paper of a series dedicated to a dispersive treatment of the hadronic light-by-light (HLbL) tensor, we derive a partial-wave formulation for two-pion intermediate states in the HLbL contribution to the anomalous magnetic moment of the muon (g - 2) μ, including a detailed discussion of the unitarity relation for arbitrary partial waves. We show that obtaining a final expression free from unphysical helicity partial waves is a subtle issue, which we thoroughly clarify. As a by-product, we obtain a set of sum rules that could be used to constrain future calculations of γ*γ* → ππ. We validate the formalism extensively using the pion-box contribution, defined by two-pion intermediate states with a pion-pole left-hand cut, and demonstrate how the full known result is reproduced when resumming the partial waves. Using dispersive fits to high-statistics data for the pion vector form factor, we provide an evaluation of the full pion box, amore » $$π-box\\atop{μ}$$ =-15.9(2) × 10 -11. As an application of the partial-wave formalism, we present a first calculation of ππ-rescattering effects in HLbL scattering, with γ*γ* → ππ helicity partial waves constructed dispersively using ππ phase shifts derived from the inverse-amplitude method. In this way, the isospin-0 part of our calculation can be interpreted as the contribution of the f0(500) to HLbL scattering in (g - 2) μ. We also argue that the contribution due to charged-pion rescattering implements corrections related to the corresponding pion polarizability and show that these are moderate. Our final result for the sum of pion-box contribution and its S-wave rescattering corrections reads a$$π-box\\atop{μ}$$ + a$$ππ, π-pole LHC\\atop{μ, J=0}$$ = -24(1) × 10 -11.« less

High Order Numerical Simulation of Waves Using Regular Grids and Non-conforming Interfaces

DTIC Science & Technology

2013-10-06

SECURITY CLASSIFICATION OF: We study the propagation of waves over large regions of space with smooth, but not necessarily constant, material...of space with smooth, but not necessarily constant, material characteristics, separated into sub-domains by interfaces of arbitrary shape. We...Abstract We study the propagation of waves over large regions of space with smooth, but not necessarily constant, material characteristics, separated into

Hall viscosity of hierarchical quantum Hall states

NASA Astrophysics Data System (ADS)

Fremling, M.; Hansson, T. H.; Suorsa, J.

2014-03-01

Using methods based on conformal field theory, we construct model wave functions on a torus with arbitrary flat metric for all chiral states in the abelian quantum Hall hierarchy. These functions have no variational parameters, and they transform under the modular group in the same way as the multicomponent generalizations of the Laughlin wave functions. Assuming the absence of Berry phases upon adiabatic variations of the modular parameter τ, we calculate the quantum Hall viscosity and find it to be in agreement with the formula, given by Read, which relates the viscosity to the average orbital spin of the electrons. For the filling factor ν =2/5 Jain state, which is at the second level in the hierarchy, we compare our model wave function with the numerically obtained ground state of the Coulomb interaction Hamiltonian in the lowest Landau level, and find very good agreement in a large region of the complex τ plane. For the same example, we also numerically compute the Hall viscosity and find good agreement with the analytical result for both the model wave function and the numerically obtained Coulomb wave function. We argue that this supports the notion of a generalized plasma analogy that would ensure that wave functions obtained using the conformal field theory methods do not acquire Berry phases upon adiabatic evolution.

The discovery of 9/8-ribbons, β/γ-peptides with curved shapes governed by a combined configuration-conformation code.

PubMed

Grison, Claire M; Robin, Sylvie; Aitken, David J

2015-11-21

The de novo design of a β/γ-peptidic foldamer motif has led to the discovery of an unprecedented 9/8-ribbon featuring an uninterrupted alternating C9/C8 hydrogen-bonding network. The ribbons adopt partially curved topologies determined synchronistically by the β-residue configuration and the γ-residue conformation sets.

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

NASA Astrophysics Data System (ADS)

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

2013-02-01

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 xNa (and xK), 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 xNa (and xK) 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.

Generalized wave operators, weighted Killing fields, and perturbations of higher dimensional spacetimes

NASA Astrophysics Data System (ADS)

Araneda, Bernardo

2018-04-01

We present weighted covariant derivatives and wave operators for perturbations of certain algebraically special Einstein spacetimes in arbitrary dimensions, under which the Teukolsky and related equations become weighted wave equations. We show that the higher dimensional generalization of the principal null directions are weighted conformal Killing vectors with respect to the modified covariant derivative. We also introduce a modified Laplace–de Rham-like operator acting on tensor-valued differential forms, and show that the wave-like equations are, at the linear level, appropriate projections off shell of this operator acting on the curvature tensor; the projection tensors being made out of weighted conformal Killing–Yano tensors. We give off shell operator identities that map the Einstein and Maxwell equations into weighted scalar equations, and using adjoint operators we construct solutions of the original field equations in a compact form from solutions of the wave-like equations. We study the extreme and zero boost weight cases; extreme boost corresponding to perturbations of Kundt spacetimes (which includes near horizon geometries of extreme black holes), and zero boost to static black holes in arbitrary dimensions. In 4D our results apply to Einstein spacetimes of Petrov type D and make use of weighted Killing spinors.

Rigidity in vacuum under conformal symmetry

NASA Astrophysics Data System (ADS)

Galloway, Gregory J.; Vega, Carlos

2018-04-01

Motivated in part by Eardley et al. (Commun Math Phys 106(1):137-158, 1986), in this note we obtain a rigidity result for globally hyperbolic vacuum spacetimes in arbitrary dimension that admit a timelike conformal Killing vector field. Specifically, we show that if M is a Ricci flat, timelike geodesically complete spacetime with compact Cauchy surfaces that admits a timelike conformal Killing field X, then M must split as a metric product, and X must be Killing. This gives a partial proof of the Bartnik splitting conjecture in the vacuum setting.

Rotational Spectroscopy and Conformational Studies of 4-PENTYNENITRILE, 4-PENTENENITRILE, and Glutaronitrile

NASA Astrophysics Data System (ADS)

Hays, Brian M.; Mehta-Hurt, Deepali; Jawad, Khadija M.; Hernandez-Castillo, Alicia O.; Abeysekera, Chamara; Zhang, Di; Zwier, Timothy S.

2017-06-01

The pure rotational spectra of 4-pentynenitrile, 4-pentenenitrile, and glutaronitrile were acquired using chirped pulse Fouirer transform microwave spectroscopy. 4-pentynenitrile and 4-pentenenitrile are the recombination products of two resonance stabilized radicals, propargyl + cyanomethyl or allyl + cyanomethyl, respectively, and are thus anticipated to be significant among the more complex nitriles in Titan's atmosphere. Indeed, these partially unsaturated alkyl cyanides have been found in laboratory analogs of tholins and are also expected to have interesting photochemistry. The optimized structures of all conformers below predicted energies of 500 \\wn were calculated for each molecule. Both of the conformers, trans and gauche, for 4-pentynenitrile have been identified and assigned. Five conformers were assigned in 4-pentenenitrile. The eclipsed conformers, with respect to the vinyl group, dominate the spectrum but some population was found in the syn conformers including the syn-gauche conformer, calculated to be 324 \\wn above the global minimum. The glutaronitrile spectrum contained only the two conformers below 500 \\wn, with reduced amount of the gauche trans conformer. The assigned spectra and structural assignments will be presented.

Next Generation of Magneto-Dielectric Antennas and Optimum Flux Channels

NASA Astrophysics Data System (ADS)

Yousefi, Tara

There is an ever-growing need for broadband conformal antennas to not only reduce the number of antennas utilized to cover a broad range of frequencies (VHF-UHF) but also to reduce visual and RF signatures associated with communication systems. In many applications antennas needs to be very close to low-impedance mediums or embedded inside low-impedance mediums. However, for conventional metal and dielectric antennas to operate efficiently in such environments either a very narrow bandwidth must be tolerated, or enough loss added to expand the bandwidth, or they must be placed one quarter of a wavelength above the conducting surface. The latter is not always possible since in the HF through low UHF bands, critical to Military and Security functions, this quarter-wavelength requirement would result in impractically large antennas. Despite an error based on a false assumption in the 1950’s, which had severely underestimated the efficiency of magneto-dielectric antennas, recently demonstrated magnetic-antennas have been shown to exhibit extraordinary efficiency in conformal applications. Whereas conventional metal-and-dielectric antennas carrying radiating electric currents suffer a significant disadvantage when placed conformal to the conducting surface of a platform, because they induce opposing image currents in the surface, magnetic-antennas carrying magnetic radiating currents have no such limitation. Their magnetic currents produce co-linear image currents in electrically conducting surfaces. However, the permeable antennas built to date have not yet attained the wide bandwidth expected because the magnetic-flux-channels carrying the wave have not been designed to guide the wave near the speed of light at all frequencies. Instead, they tend to lose the wave by a leaky fast-wave mechanism at low frequencies or they over-bind a slow-wave at high frequencies. In this dissertation, we have studied magnetic antennas in detail and presented the design approach and apparatus required to implement a flux-channel carrying the magnetic current wave near the speed of light over a very broad frequency range which also makes the design of a frequency independent antenna (spiral) possible. We will learn how to construct extremely thin conformal antennas, frequency-independent permeable antennas, and even micron-sized antennas that can be embedded inside the brain without damaging the tissue.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Jun; Byrne, Noel; Wang, John

Clinical studies indicate that partial agonists of the G-protein-coupled, free fatty acid receptor 1 GPR40 enhance glucose-dependent insulin secretion and represent a potential mechanism for the treatment of type 2 diabetes mellitus. Full allosteric agonists (AgoPAMs) of GPR40 bind to a site distinct from partial agonists and can provide additional efficacy. We report the 3.2-Å crystal structure of human GPR40 (hGPR40) in complex with both the partial agonist MK-8666 and an AgoPAM, which exposes a novel lipid-facing AgoPAM-binding pocket outside the transmembrane helical bundle. Comparison with an additional 2.2-Å structure of the hGPR40–MK-8666 binary complex reveals an induced-fit conformational couplingmore » between the partial agonist and AgoPAM binding sites, involving rearrangements of the transmembrane helices 4 and 5 (TM4 and TM5) and transition of the intracellular loop 2 (ICL2) into a short helix. These conformational changes likely prime GPR40 to a more active-like state and explain the binding cooperativity between these ligands.« less

Sound Source Localization Using Non-Conformal Surface Sound Field Transformation Based on Spherical Harmonic Wave Decomposition

PubMed Central

Zhang, Lanyue; Ding, Dandan; Yang, Desen; Wang, Jia; Shi, Jie

2017-01-01

Spherical microphone arrays have been paid increasing attention for their ability to locate a sound source with arbitrary incident angle in three-dimensional space. Low-frequency sound sources are usually located by using spherical near-field acoustic holography. The reconstruction surface and holography surface are conformal surfaces in the conventional sound field transformation based on generalized Fourier transform. When the sound source is on the cylindrical surface, it is difficult to locate by using spherical surface conformal transform. The non-conformal sound field transformation by making a transfer matrix based on spherical harmonic wave decomposition is proposed in this paper, which can achieve the transformation of a spherical surface into a cylindrical surface by using spherical array data. The theoretical expressions of the proposed method are deduced, and the performance of the method is simulated. Moreover, the experiment of sound source localization by using a spherical array with randomly and uniformly distributed elements is carried out. Results show that the non-conformal surface sound field transformation from a spherical surface to a cylindrical surface is realized by using the proposed method. The localization deviation is around 0.01 m, and the resolution is around 0.3 m. The application of the spherical array is extended, and the localization ability of the spherical array is improved. PMID:28489065

Conformal Infinity.

PubMed

Frauendiener, Jörg

2000-01-01

The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, "conformal infinity" is related with almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved out of physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation and how it lends itself very naturally to solve radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

Conformal Infinity.

PubMed

Frauendiener, Jörg

2004-01-01

The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, "conformal infinity" is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation, and how it lends itself very naturally to the solution of radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

Series expansion solutions for the multi-term time and space fractional partial differential equations in two- and three-dimensions

NASA Astrophysics Data System (ADS)

Ye, H.; Liu, F.; Turner, I.; Anh, V.; Burrage, K.

2013-09-01

Fractional partial differential equations with more than one fractional derivative in time describe some important physical phenomena, such as the telegraph equation, the power law wave equation, or the Szabo wave equation. In this paper, we consider two- and three-dimensional multi-term time and space fractional partial differential equations. The multi-term time-fractional derivative is defined in the Caputo sense, whose order belongs to the interval (1,2],(2,3],(3,4] or (0, m], and the space-fractional derivative is referred to as the fractional Laplacian form. We derive series expansion solutions based on a spectral representation of the Laplacian operator on a bounded region. Some applications are given for the two- and three-dimensional telegraph equation, power law wave equation and Szabo wave equation.

Experimental study of the evanescent-wave photonic sensors response in presence of molecular beacon conformational changes.

PubMed

Ruiz-Tórtola, Ángela; Prats-Quílez, Francisco; Gónzalez-Lucas, Daniel; Bañuls, María-José; Maquieira, Ángel; Wheeler, Guy; Dalmay, Tamas; Griol, Amadeu; Hurtado, Juan; Bohlmann, Helge; Götzen, Reiner; García-Rupérez, Jaime

2018-04-17

An experimental study of the influence of the conformational change suffered by molecular beacon (MB) probes -upon the biorecognition of nucleic acid target oligonucleotides over evanescent wave photonic sensors- is reported. To this end, high sensitivity photonic sensors based on silicon photonic bandgap (PBG) structures were used, where the MB probes were immobilized via their 5' termination. Those MBs incorporate a biotin moiety close to their 3' termination in order to selectively bind a streptavidin molecule to them. The different photonic sensing responses obtained towards the target oligonucleotide detection, when the streptavidin molecule was bound to the MB probes or not, demonstrate the conformational change suffered by the MB upon hybridization, which promotes the displacement of the streptavidin molecule away from the surface of the photonic sensing structure. Schematic diagram of the PBG sensing structure on which the streptavidin-labeled MB probes were immobilized. This article is protected by copyright. All rights reserved.

Direct manipulation of wave amplitude and phase through inverse design of isotropic media

NASA Astrophysics Data System (ADS)

Liu, Y.; Vial, B.; Horsley, S. A. R.; Philbin, T. G.; Hao, Y.

2017-07-01

In this article we propose a new design methodology allowing us to control both amplitude and phase of electromagnetic waves from a cylindrical incident wave. This results in isotropic materials and does not resort to transformation optics or its quasi-conformal approximations. Our method leads to two-dimensional isotropic, inhomogeneous material profiles of permittivity and permeability, to which a general class of scattering-free wave solutions arise. Our design is based on the separation of the complex wave solution into amplitude and phase. We give two types of examples to validate our methodology.

Spatial and temporal compact equations for water waves

NASA Astrophysics Data System (ADS)

Dyachenko, Alexander; Kachulin, Dmitriy; Zakharov, Vladimir

2016-04-01

A one-dimensional potential flow of an ideal incompressible fluid with a free surface in a gravity field is the Hamiltonian system with the Hamiltonian: H = 1/2intdxint-∞^η |nablaφ|^2dz + g/2ont η^2dxŗφ(x,z,t) - is the potential of the fluid, g - gravity acceleration, η(x,t) - surface profile Hamiltonian can be expanded as infinite series of steepness: {Ham4} H &=& H2 + H3 + H4 + dotsŗH2 &=& 1/2int (gη2 + ψ hat kψ) dx, ŗH3 &=& -1/2int \\{(hat kψ)2 -(ψ_x)^2}η dx,ŗH4 &=&1/2int {ψxx η2 hat kψ + ψ hat k(η hat k(η hat kψ))} dx. where hat k corresponds to the multiplication by |k| in Fourier space, ψ(x,t)= φ(x,η(x,t),t). This truncated Hamiltonian is enough for gravity waves of moderate amplitudes and can not be reduced. We have derived self-consistent compact equations, both spatial and temporal, for unidirectional water waves. Equations are written for normal complex variable c(x,t), not for ψ(x,t) and η(x,t). Hamiltonian for temporal compact equation can be written in x-space as following: {SPACE_C} H = intc^*hat V c dx + 1/2int [ i/4(c2 partial/partial x {c^*}2 - {c^*}2 partial/partial x c2)- |c|2 hat K(|c|^2) ]dx Here operator hat V in K-space is so that Vk = ω_k/k. If along with this to introduce Gardner-Zakharov-Faddeev bracket (for the analytic in the upper half-plane function) {GZF} partial^+x Leftrightarrow ikθk Hamiltonian for spatial compact equation is the following: {H24} &&H=1/gint1/ω|cω|2 dω +ŗ&+&1/2g^3int|c|^2(ddot c^*c + ddot c c^*)dt + i/g^2int |c|^2hatω(dot c c* - cdot c^*)dt. equation of motion is: {t-space} &&partial /partial xc +i/g partial^2/partial t^2c =ŗ&=& 1/2g^3partial^3/partial t3 [ partial^2/partial t^2(|c|^2c) +2 |c|^2ddot c +ddot c^*c2 ]+ŗ&+&i/g3 partial^3/partial t3 [ partial /partial t( chatω |c|^2) + dot c hatω |c|2 + c hatω(dot c c* - cdot c^*) ]. It solves the spatial Cauchy problem for surface gravity wave on the deep water. Main features of the equations are: Equations are written for complex normal variable c(x,t) which is analytic function in the upper half-planeHamiltonians both for temporal and spatial equations are very simple It can be easily implemented for numerical simulation The equations can be generalized for "almost" 2-D waves like KdV is generalized to KP. This work was supported by was Grant "Wave turbulence: theory, numerical simulation, experiment" #14-22-00174 of Russian Science Foundation.

Accurate Drift Time Determination by Traveling Wave Ion Mobility Spectrometry: The Concept of the Diffusion Calibration.

PubMed

Kune, Christopher; Far, Johann; De Pauw, Edwin

2016-12-06

Ion mobility spectrometry (IMS) is a gas phase separation technique, which relies on differences in collision cross section (CCS) of ions. Ionic clouds of unresolved conformers overlap if the CCS difference is below the instrumental resolution expressed as CCS/ΔCCS. The experimental arrival time distribution (ATD) peak is then a superimposition of the various contributions weighted by their relative intensities. This paper introduces a strategy for accurate drift time determination using traveling wave ion mobility spectrometry (TWIMS) of poorly resolved or unresolved conformers. This method implements through a calibration procedure the link between the peak full width at half-maximum (fwhm) and the drift time of model compounds for wide range of settings for wave heights and velocities. We modified a Gaussian equation, which achieves the deconvolution of ATD peaks where the fwhm is fixed according to our calibration procedure. The new fitting Gaussian equation only depends on two parameters: The apex of the peak (A) and the mean drift time value (μ). The standard deviation parameter (correlated to fwhm) becomes a function of the drift time. This correlation function between μ and fwhm is obtained using the TWIMS calibration procedure which determines the maximum instrumental ion beam diffusion under limited and controlled space charge effect using ionic compounds which are detected as single conformers in the gas phase. This deconvolution process has been used to highlight the presence of poorly resolved conformers of crown ether complexes and peptides leading to more accurate CCS determinations in better agreement with quantum chemistry predictions.

Confinement-induced p-wave resonances from s-wave interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nishida, Yusuke; Tan, Shina; School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332

2010-12-15

We show that a purely s-wave interaction in three dimensions (3D) can induce higher partial-wave resonances in mixed dimensions. We develop two-body scattering theories in all three cases of 0D-3D, 1D-3D, and 2D-3D mixtures and determine the positions of higher partial-wave resonances in terms of the 3D s-wave scattering length assuming a harmonic confinement potential. We also compute the low-energy scattering parameters in the p-wave channel (scattering volume and effective momentum) that are necessary for the low-energy effective theory of the p-wave resonance. We point out that some of the resonances observed in the Florence group experiment [Phys. Rev. Lett.more » 104, 153202 (2010)] can be interpreted as the p-wave resonances in the 2D-3D mixed dimensions. Our study paves the way for a variety of physics, such as Anderson localization of matter waves under p-wave resonant scatterers.« less

Numerical simulation of solitary waves on deep water with constant vorticity

NASA Astrophysics Data System (ADS)

Dosaev, A. S.; Shishina, M. I.; Troitskaya, Yu I.

2018-01-01

Characteristics of solitary deep water waves on a flow with constant vorticity are investigated by numerical simulation within the framework of fully nonlinear equations of motion (Euler equations) using the method of surface-tracking conformal coordinates. To ensure that solutions observed are stable, soliton formation as a result of disintegration of an initial pulse-like disturbance is modeled. Evidence is obtained that solitary waves with height above a certain threshold are unstable.

Classification of the Lie and Noether point symmetries for the Wave and the Klein-Gordon equations in pp-wave spacetimes

NASA Astrophysics Data System (ADS)

Paliathanasis, A.; Tsamparlis, M.; Mustafa, M. T.

2018-02-01

A complete classification of the Lie and Noether point symmetries for the Klein-Gordon and the wave equation in pp-wave spacetimes is obtained. The classification analysis is carried out by reducing the problem of the determination of the point symmetries to the problem of existence of conformal killing vectors on the pp-wave spacetimes. Employing the existing results for the isometry classes of the pp-wave spacetimes, the functional form of the potential is determined for which the Klein-Gordon equation admits point symmetries and Noetherian conservation law. Finally the Lie and Noether point symmetries of the wave equation are derived.

Acoustic radiation force expansions in terms of partial wave phase shifts for scattering: Applications

NASA Astrophysics Data System (ADS)

Marston, Philip L.; Zhang, Likun

2016-11-01

When evaluating radiation forces on spheres in soundfields (with or without orbital-angular momentum) the interpretation of analytical results is greatly simplified by retaining the use of s-function notation for partial-wave coefficients imported into acoustics from quantum scattering theory in the 1970s. This facilitates easy interpretation of various efficiency factors. For situations in which dissipation is negligible, each partial-wave s-function becomes characterized by a single parameter: a phase shift allowing for all possible situations. These phase shifts are associated with scattering by plane traveling waves and the incident wavefield of interest is separately parameterized. (When considering outcomes, the method of fabricating symmetric objects having a desirable set of phase shifts becomes a separate issue.) The existence of negative radiation force "islands" for beams reported in 2006 by Marston is manifested. This approach and consideration of conservation theorems illustrate the unphysical nature of various claims made by other researchers. This approach is also directly relevant to objects in standing waves. Supported by ONR.

Ambiguities in model-independent partial-wave analysis

NASA Astrophysics Data System (ADS)

Krinner, F.; Greenwald, D.; Ryabchikov, D.; Grube, B.; Paul, S.

2018-06-01

Partial-wave analysis is an important tool for analyzing large data sets in hadronic decays of light and heavy mesons. It commonly relies on the isobar model, which assumes multihadron final states originate from successive two-body decays of well-known undisturbed intermediate states. Recently, analyses of heavy-meson decays and diffractively produced states have attempted to overcome the strong model dependences of the isobar model. These analyses have overlooked that model-independent, or freed-isobar, partial-wave analysis can introduce mathematical ambiguities in results. We show how these ambiguities arise and present general techniques for identifying their presence and for correcting for them. We demonstrate these techniques with specific examples in both heavy-meson decay and pion-proton scattering.

Updated analysis of NN elastic scattering to 3 GeV

NASA Astrophysics Data System (ADS)

Arndt, R. A.; Briscoe, W. J.; Strakovsky, I. I.; Workman, R. L.

2007-08-01

A partial-wave analysis of NN elastic scattering data has been updated to include a number of recent measurements. Experiments carried out at the Cooler Synchrotron (COSY) by the EDDA Collaboration have had a significant impact above 1 GeV. Results are discussed in terms of the partial-wave and direct-reconstruction amplitudes.

Laser backscattered from partially convex targets of large sizes in random media for E-wave polarization.

PubMed

El-Ocla, Hosam

2006-08-01

The characteristics of a radar cross section (RCS) of partially convex targets with large sizes up to five wavelengths in free space and random media are studied. The nature of the incident wave is an important factor in remote sensing and radar detection applications. I investigate the effects of beam wave incidence on the performance of RCS, drawing on the method I used in a previous study on plane-wave incidence. A beam wave can be considered a plane wave if the target size is smaller than the beam width. Therefore, to have a beam wave with a limited spot on the target, the target size should be larger than the beam width (assuming E-wave incidence wave polarization. The effects of the target configuration, random medium parameters, and the beam width on the laser RCS and the enhancement in the radar cross section are numerically analyzed, resulting in the possibility of having some sort of control over radar detection using beam wave incidence.

Leap-dynamics: efficient sampling of conformational space of proteins and peptides in solution.

PubMed

Kleinjung, J; Bayley, P; Fraternali, F

2000-03-31

A molecular simulation scheme, called Leap-dynamics, that provides efficient sampling of protein conformational space in solution is presented. The scheme is a combined approach using a fast sampling method, imposing conformational 'leaps' to force the system over energy barriers, and molecular dynamics (MD) for refinement. The presence of solvent is approximated by a potential of mean force depending on the solvent accessible surface area. The method has been successfully applied to N-acetyl-L-alanine-N-methylamide (alanine dipeptide), sampling experimentally observed conformations inaccessible to MD alone under the chosen conditions. The method predicts correctly the increased partial flexibility of the mutant Y35G compared to native bovine pancreatic trypsin inhibitor. In particular, the improvement over MD consists of the detection of conformational flexibility that corresponds closely to slow motions identified by nuclear magnetic resonance techniques.

Light cone thermodynamics

NASA Astrophysics Data System (ADS)

De Lorenzo, Tommaso; Perez, Alejandro

2018-02-01

We show that null surfaces defined by the outgoing and infalling wave fronts emanating from and arriving at a sphere in Minkowski spacetime have thermodynamical properties that are in strict formal correspondence with those of black hole horizons in curved spacetimes. Such null surfaces, made of pieces of light cones, are bifurcate conformal Killing horizons for suitable conformally stationary observers. They can be extremal and nonextremal depending on the radius of the shining sphere. Such conformal Killing horizons have a constant light cone (conformal) temperature, given by the standard expression in terms of the generalization of surface gravity for conformal Killing horizons. Exchanges of conformally invariant energy across the horizon are described by a first law where entropy changes are given by 1 /(4 ℓp2) of the changes of a geometric quantity with the meaning of horizon area in a suitable conformal frame. These conformal horizons satisfy the zeroth to the third laws of thermodynamics in an appropriate way. In the extremal case they become light cones associated with a single event; these have vanishing temperature as well as vanishing entropy.

Improved optical filter

NASA Technical Reports Server (NTRS)

Title, A. M.

1978-01-01

Filter includes partial polarizer between birefrigent elements. Plastic film on partial polarizer compensates for any polarization rotation by partial polarizer. Two quarter-wave plates change incident, linearly polarized light into elliptically polarized light.

On mass transport in porosity waves

NASA Astrophysics Data System (ADS)

Jordan, Jacob S.; Hesse, Marc A.; Rudge, John F.

2018-03-01

Porosity waves arise naturally from the equations describing fluid migration in ductile rocks. Here, we show that higher-dimensional porosity waves can transport mass and therefore preserve geochemical signatures, at least partially. Fluid focusing into these high porosity waves leads to recirculation in their center. This recirculating fluid is separated from the background flow field by a circular dividing streamline and transported with the phase velocity of the porosity wave. Unlike models for one-dimensional chromatography in geological porous media, tracer transport in higher-dimensional porosity waves does not produce chromatographic separations between relatively incompatible elements due to the circular flow pattern. This may allow melt that originated from the partial melting of fertile heterogeneities or fluid produced during metamorphism to retain distinct geochemical signatures as they rise buoyantly towards the surface.

Exact Solutions for the Integrable Sixth-Order Drinfeld-Sokolov-Satsuma-Hirota System by the Analytical Methods.

PubMed

Manafian Heris, Jalil; Lakestani, Mehrdad

2014-01-01

We establish exact solutions including periodic wave and solitary wave solutions for the integrable sixth-order Drinfeld-Sokolov-Satsuma-Hirota system. We employ this system by using a generalized (G'/G)-expansion and the generalized tanh-coth methods. These methods are developed for searching exact travelling wave solutions of nonlinear partial differential equations. It is shown that these methods, with the help of symbolic computation, provide a straightforward and powerful mathematical tool for solving nonlinear partial differential equations.

Ionic cleaning after wave solder and before conformal coat

NASA Astrophysics Data System (ADS)

Nguygen, Tochau N.; Sutherland, Thomas H.

An account is given of efforts made by a military electronics manufacturer to upgrade product reliability in response to the printed writing board (PWB) ionic cleanliness requirements recently set out in MIL-P-28809 Rev. A. These requirements had to be met both after wave soldering, involving the immediate removal of ionically active RA flux, and immediately before conformal coating, in order to remove the less active RMA flux and bonding contaminants. Attention is given to the results of a test program which compared the effectiveness with which five different solvents and two (batch and conveyorized vapor degreasing) cleaning methods cleaned representative PWBs containing many components. Alcohol-containing fluorocarbon blends were adequate, but the most densely packed PWBs required a supplemental water rinse.

SU-E-T-548: How To Decrease Spine Dose In Patients Who Underwent Sterotactic Spine Radiosurgery?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Acar, H; Altinok, A; Kucukmorkoc, E

2014-06-01

Purpose: Stereotactic radiosurgery for spine metastases involves irradiation using a single high dose fraction. The purpose of this study was to dosimetrically compare stereotactic spine radiosurgery(SRS) plans using a recently new volumetric modulated arc therapy(VMAT) technique against fix-field intensity-modulated radiotherapy(IMRT). Plans were evaluated for target conformity and spinal cord sparing. Methods: Fifteen previously treated patients were replanned using the Eclipse 10.1 TPS AAA calculation algorithm. IMRT plans with 7 fields were generated. The arc plans used 2 full arc configurations. Arc and IMRT plans were normalized and prescribed to deliver 16.0 Gy in a single fraction to 90% of themore » planning target volume(PTV). PTVs consisted of the vertebral body expanded by 3mm, excluding the PRV-cord, where the cord was expanded by 2mm.RTOG 0631 recommendations were applied for treatment planning. Partial spinal cord volume was defined as 5mm above and below the radiosurgery target volume. Plans were compared for conformity and gradient index as well as spinal cord sparing. Results: The conformity index values of fifteen patients for two different treatment planning techniques were shown in table 1. Conformity index values for 2 full arc planning (average CI=0.84) were higher than that of IMRT planning (average CI=0.79). The gradient index values of fifteen patients for two different treatment planning techniques were shown in table 2. Gradient index values for 2 full arc planning (average GI=3.58) were higher than that of IMRT planning (average GI=2.82).The spinal cord doses of fifteen patients for two different treatment planning techniques were shown in table 3. D0.35cc, D0.03cc and partial spinal cord D10% values in 2 full arc plannings (average D0.35cc=819.3cGy, D0.03cc=965.4cGy, 10%partial spinal=718.1cGy) were lower than IMRT plannings (average D0.35cc=877.4cGy, D0.03c=1071.4cGy, 10%partial spinal=805.1cGy). Conclusions: The two arc VMAT technique is superior to 7 field IMRT technique in terms of both spinal cord sparing and better conformity and gradient indexes.« less

Side-chain conformational space analysis (SCSA): A multi conformation-based QSAR approach for modeling and prediction of protein-peptide binding affinities

NASA Astrophysics Data System (ADS)

Zhou, Peng; Chen, Xiang; Shang, Zhicai

2009-03-01

In this article, the concept of multi conformation-based quantitative structure-activity relationship (MCB-QSAR) is proposed, and based upon that, we describe a new approach called the side-chain conformational space analysis (SCSA) to model and predict protein-peptide binding affinities. In SCSA, multi-conformations (rather than traditional single-conformation) have received much attention, and the statistical average information on multi-conformations of side chains is determined using self-consistent mean field theory based upon side chain rotamer library. Thereby, enthalpy contributions (including electrostatic, steric, hydrophobic interaction and hydrogen bond) and conformational entropy effects to the binding are investigated in terms of occurrence probability of residue rotamers. Then, SCSA was applied into the dataset of 419 HLA-A*0201 binding peptides, and nonbonding contributions of each position in peptide ligands are well determined. For the peptides, the hydrogen bond and electrostatic interactions of the two ends are essential to the binding specificity, van der Waals and hydrophobic interactions of all the positions ensure strong binding affinity, and the loss of conformational entropy at anchor positions partially counteracts other favorable nonbonding effects.

Quantum mechanics of conformally and minimally coupled Friedmann-Robertson-Walker cosmology

NASA Astrophysics Data System (ADS)

Kim, Sang Pyo

1992-10-01

The expansion method by a time-dependent basis of the eigenfunctions for the space-coordinate-dependent sub-Hamiltonian is one of the most natural frameworks for quantum systems, relativistic as well as nonrelativistic. The complete set of wave functions is found in the product integral formulation, whose constants of integration are fixed by Cauchy initial data. The wave functions for the Friedmann-Robertson-Walker (FRW) cosmology conformally and minimally coupled to a scalar field with a power-law potential or a polynomial potential are expanded in terms of the eigenfunctions of the scalar field sub-Hamiltonian part. The resultant gravitational field part which is an ``intrinsic'' timelike variable-dependent matrix-valued differential equation is solved again in the product integral formulation. There are classically allowed regions for the ``intrinsic'' timelike variable depending on the scalar field quantum numbers and these regions increase accordingly as the quantum numbers increase. For a fixed large three-geometry the wave functions corresponding to the low excited (small quantum number) states of the scalar field are exponentially damped or diverging and the wave functions corresponding to the high excited (large quantum number) states are still oscillatory but become eventually exponential as the three-geometry becomes larger. Furthermore, a proposal is advanced that the wave functions exponentially damped for a large three-geometry may be interpreted as ``tunneling out'' wave functions into, and the wave functions exponentially diverging as ``tunneling in'' from, different universes with the same or different topologies, the former being interpreted as the recently proposed Hawking-Page wormhole wave functions. It is observed that there are complex as well as Euclidean actions depending on the quantum numbers of the scalar field part outside the classically allowed region both of the gravitational and scalar fields, suggesting the usefulness of complex geometry and complex trajectories. From the most general wave functions for the FRW cosmology conformally coupled to scalar field, the boundary conditions for the wormhole wave functions are modified so that the modulus of wave functions, instead of the wave functions themselves, should be exponentially damped for a large three-geometry and be regular up to some negative power of the three-geometry as the three-geometry collapses. The wave functions for the FRW cosmology minimally coupled to an inhomogeneous scalar field are similarly found in the product integral formulation. The role of a large number of the inhomogeneous modes of the scalar field is not only to increase the classically allowed regions for the gravitational part but also to provide a mechanism of the decoherence of quantum interferences between the different sizes of the universe.

Scattering of plane evanescent waves by cylindrical shells and wave vector coupling conditions for exciting flexural waves

NASA Astrophysics Data System (ADS)

Marston, Philip L.

2002-05-01

The coupling of sound to buried targets can be associated with acoustic evanescent waves when the sea bottom is smooth. To understand the excitation of flexural waves on buried shells by acoustic evanescent waves, the partial wave series for the scattering is found for cylindrical shells at normal incidence in an unbounded medium. The formulation uses the simplifications of thin-shell dynamics. In the case of ordinary waves incident on a shell, a ray formulation is available to describe the coupling to subsonic flexural waves [P. L. Marston and N. H. Sun, J. Acoust. Soc. Am. 97, 777-783 (1995)]. When the incident wave is evanescent, the distance between propagating plane wavefronts is smaller than the ordinary acoustical wavelength at the same frequency and the coupling condition for the excitation of flexural waves on shells or plates is modified. Instead of matching the flexural wave number with the propagating part of the acoustic wave number only at the coincidence frequency, a second low-frequency wave number matching condition is found for highly evanescent waves. Numerical evaluation of the modified partial-wave-series appropriate for an evanescent wave is used to investigate the low-frequency coupling of evanescent waves with flexural wave resonances of shells.

Calculation of the Full Scattering Amplitude without Partial Wave Decomposition II: Inclusion of Exchange

NASA Technical Reports Server (NTRS)

Shertzer, Janine; Temkin, A.

2003-01-01

As is well known, the full scattering amplitude can be expressed as an integral involving the complete scattering wave function. We have shown that the integral can be simplified and used in a practical way. Initial application to electron-hydrogen scattering without exchange was highly successful. The Schrodinger equation (SE), which can be reduced to a 2d partial differential equation (pde), was solved using the finite element method. We have now included exchange by solving the resultant SE, in the static exchange approximation, which is reducible to a pair of coupled pde's. The resultant scattering amplitudes, both singlet and triplet, calculated as a function of energy are in excellent agreement with converged partial wave results.

Bound states and propagating modes in quantum wires with sharp bends and/or constrictions

NASA Astrophysics Data System (ADS)

Razavy, M.

1997-06-01

A number of interesting problems of quantum wires with different geometries can be studied with the help of conformal mapping. These include crossed wires, twisting wires, conductors with constrictions, and wires with a bend. Here the Helmholz equation with Dirichlet boundary condition on the surface of the wire is transformed to a Schröautdinger-like equation with an energy-dependent nonseparable potential but with boundary conditions given on two straight lines. By expanding the wave function in terms of the Fourier series of one of the variables one obtains an infinite set of coupled ordinary differential equations. Only the propagating modes plus a few of the localized modes contribute significantly to the total wave function. Once the problem is solved, one can express the results in terms of the original variables using the inverse conformal mapping. As an example, the total wave function, the components of the current density, and the bound-state energy for a Γ-shaped quantum wire is calculated in detail.

Monomerization alters the dynamics of the lid region in Campylobacter jejuni CstII: an MD simulation study.

PubMed

Prabhakar, Pradeep Kumar; Srivastava, Alka; Rao, K Krishnamurthy; Balaji, Petety V

2016-01-01

CstII, a bifunctional (α2,3/8) sialyltransferase from Campylobacter jejuni, is a homotetramer. It has been reported that mutation of the interface residues Phe121 (F121D) or Tyr125 (Y125Q) leads to monomerization and partial loss of enzyme activity, without any change in the secondary or tertiary structures. MD simulations of both tetramer and monomer, with and without bound donor substrate, were performed for the two mutants and WT to understand the reasons for partial loss of activity due to monomerization since the active site is located within each monomer. RMSF values were found to correlate with the crystallographic B-factor values indicating that the simulations are able to capture the flexibility of the molecule effectively. There were no gross changes in either the secondary or tertiary structure of the proteins during MD simulations. However, interface is destabilized by the mutations, and more importantly the flexibility of the lid region (Gly152-Lys190) is affected. The lid region accesses three major conformations named as open, intermediate, and closed conformations. In both Y121Q and F121D mutants, the closed conformation is accessed predominantly. In this conformation, the catalytic base His188 is also displaced. Normal mode analysis also revealed differences in the lid movement in tetramer and monomer. This provides a possible explanation for the partial loss of enzyme activity in both interface mutants. The lid region controls the traffic of substrates and products in and out of the active site, and the dynamics of this region is regulated by tetramerization. Thus, this study provides valuable insights into the role of loop dynamics in enzyme activity of CstII.

Systematic Improvement of Potential-Derived Atomic Multipoles and Redundancy of the Electrostatic Parameter Space.

PubMed

Jakobsen, Sofie; Jensen, Frank

2014-12-09

We assess the accuracy of force field (FF) electrostatics at several levels of approximation from the standard model using fixed partial charges to conformational specific multipole fits including up to quadrupole moments. Potential-derived point charges and multipoles are calculated using least-squares methods for a total of ∼1000 different conformations of the 20 natural amino acids. Opposed to standard charge fitting schemes the procedure presented in the current work employs fitting points placed on a single isodensity surface, since the electrostatic potential (ESP) on such a surface determines the ESP at all points outside this surface. We find that the effect of multipoles beyond partial atomic charges is of the same magnitude as the effect due to neglecting conformational dependency (i.e., polarizability), suggesting that the two effects should be included at the same level in FF development. The redundancy at both the partial charge and multipole levels of approximation is quantified. We present an algorithm which stepwise reduces or increases the dimensionality of the charge or multipole parameter space and provides an upper limit of the ESP error that can be obtained at a given truncation level. Thereby, we can identify a reduced set of multipole moments corresponding to ∼40% of the total number of multipoles. This subset of parameters provides a significant improvement in the representation of the ESP compared to the simple point charge model and close to the accuracy obtained using the complete multipole parameter space. The selection of the ∼40% most important multipole sites is highly transferable among different conformations, and we find that quadrupoles are of high importance for atoms involved in π-bonding, since the anisotropic electric field generated in such regions requires a large degree of flexibility.

An ansatz for solving nonlinear partial differential equations in mathematical physics.

PubMed

Akbar, M Ali; Ali, Norhashidah Hj Mohd

2016-01-01

In this article, we introduce an ansatz involving exact traveling wave solutions to nonlinear partial differential equations. To obtain wave solutions using direct method, the choice of an appropriate ansatz is of great importance. We apply this ansatz to examine new and further general traveling wave solutions to the (1+1)-dimensional modified Benjamin-Bona-Mahony equation. Abundant traveling wave solutions are derived including solitons, singular solitons, periodic solutions and general solitary wave solutions. The solutions emphasize the nobility of this ansatz in providing distinct solutions to various tangible phenomena in nonlinear science and engineering. The ansatz could be more efficient tool to deal with higher dimensional nonlinear evolution equations which frequently arise in many real world physical problems.

Interactions of ligands with active and inactive conformations of the dopamine D2 receptor.

PubMed

Malmberg, A; Mohell, N; Backlund Höök, B; Johansson, A M; Hacksell, U; Nordvall, G

1998-04-10

The affinities of 19 pharmacologically diverse dopamine D2 receptor ligands were determined for the active and inactive conformations of cloned human dopamine D2 receptors expressed in Ltk cells. The agonist [3H]quinpirole was used to selectively label the guanine nucleotide-binding protein-coupled, active receptor conformation. The antagonist [3H]raclopride, in the presence of the non-hydrolysable GTP-analogue Gpp(NH)p and sodium ions and in the absence of magnesium ions, was used to label the free inactive receptor conformation. The intrinsic activities of the ligands were determined in a forskolin-stimulated cyclic AMP assay using the same cells. An excellent correlation was shown between the affinity ratios (KR/KRG) of the ligands for the two receptor conformations and their intrinsic activity (r=0.96). The ligands included eight structurally related and enantiopure 2-aminotetralin derivatives; the enantiomers of 5-hydroxy-2-(dipropylamino)tetralin, 5-methoxy-2-(dipropylamino)tetralin, 5-fluoro-2-(dipropylamino)tetralin and 2-(dipropylamino)tetralin. The (S)-enantiomers behaved as full agonists in the cyclic AMP assay and displayed a large KR/KRG ratio. The (R)-enantiomers were classified as partial agonists and had lower ratios. The structure-affinity relationships of these compounds at the active and the inactive receptor conformations were analysed separately, and used in conjunction with a homology based receptor model of the dopamine D2 receptor. This led to proposed binding modes for agonists, antagonists and partial agonists in the 2-aminotetralin series. The concepts used in this study should be of value in the design of ligands with predetermined affinity and intrinsic activity.

Conformational distribution of baclofen analogues by 1H and 13C NMR analysis and ab initio HF MO STO-3G or STO-3G* calculations

NASA Astrophysics Data System (ADS)

Vaccher, Claude; Berthelot, Pascal; Debaert, Michel; Vermeersch, Gaston; Guyon, René; Pirard, Bernard; Vercauteren, Daniel P.; Dory, Magdalena; Evrard, Guy; Durant, François

1993-12-01

The conformations of 3-(substituted furan-2-yl) and 3-(substituted thien-2-yl)-γ-aminobutyric acid 1-9 in solution (D 2O) are estimated from high-resolution (300 MHz) 1H NMR coupling data. Conformations and populations of conformers are calculated by means of a modified Karplus-like relationship for the vicinal coupling constants. The results are compared with X-ray crystallographic investigations (torsion angles) and ab initio HF MO ST-3G or STO-3G* calculations. 1H NMR spectral analysis shows how 1-9 in solution retain the preferred g- conformation around the C3C4 bond, as found in the solid state, while a partial rotation is set up around the C2C3 bond: the conformations about C2C3 are all highly populated in solution. The 13C spin-lattice relaxation times are also discussed.

Conformational switching in the coiled-coil domains of a proteasomal ATPase regulates substrate processing.

PubMed

Snoberger, Aaron; Brettrager, Evan J; Smith, David M

2018-06-18

Protein degradation in all domains of life requires ATPases that unfold and inject proteins into compartmentalized proteolytic chambers. Proteasomal ATPases in eukaryotes and archaea contain poorly understood N-terminally conserved coiled-coil domains. In this study, we engineer disulfide crosslinks in the coiled-coils of the archaeal proteasomal ATPase (PAN) and report that its three identical coiled-coil domains can adopt three different conformations: (1) in-register and zipped, (2) in-register and partially unzipped, and (3) out-of-register. This conformational heterogeneity conflicts with PAN's symmetrical OB-coiled-coil crystal structure but resembles the conformational heterogeneity of the 26S proteasomal ATPases' coiled-coils. Furthermore, we find that one coiled-coil can be conformationally constrained even while unfolding substrates, and conformational changes in two of the coiled-coils regulate PAN switching between resting and active states. This switching functionally mimics similar states proposed for the 26S proteasome from cryo-EM. These findings thus build a mechanistic framework to understand regulation of proteasome activity.

Guiding Conformation Space Search with an All-Atom Energy Potential

PubMed Central

Brunette, TJ; Brock, Oliver

2009-01-01

The most significant impediment for protein structure prediction is the inadequacy of conformation space search. Conformation space is too large and the energy landscape too rugged for existing search methods to consistently find near-optimal minima. To alleviate this problem, we present model-based search, a novel conformation space search method. Model-based search uses highly accurate information obtained during search to build an approximate, partial model of the energy landscape. Model-based search aggregates information in the model as it progresses, and in turn uses this information to guide exploration towards regions most likely to contain a near-optimal minimum. We validate our method by predicting the structure of 32 proteins, ranging in length from 49 to 213 amino acids. Our results demonstrate that model-based search is more effective at finding low-energy conformations in high-dimensional conformation spaces than existing search methods. The reduction in energy translates into structure predictions of increased accuracy. PMID:18536015

Theory of electron-impact ionization of atoms

NASA Astrophysics Data System (ADS)

Kadyrov, A. S.; Mukhamedzhanov, A. M.; Stelbovics, A. T.; Bray, I.

2004-12-01

The existing formulations of electron-impact ionization of a hydrogenic target suffer from a number of formal problems including an ambiguous and phase-divergent definition of the ionization amplitude. An alternative formulation of the theory is given. An integral representation for the ionization amplitude which is free of ambiguity and divergence problems is derived and is shown to have four alternative, but equivalent, forms well suited for practical calculations. The extension to amplitudes of all possible scattering processes taking place in an arbitrary three-body system follows. A well-defined conventional post form of the breakup amplitude valid for arbitrary potentials including the long-range Coulomb interaction is given. Practical approaches are based on partial-wave expansions, so the formulation is also recast in terms of partial waves and partial-wave expansions of the asymptotic wave functions are presented. In particular, expansions of the asymptotic forms of the total scattering wave function, developed from both the initial and the final state, for electron-impact ionization of hydrogen are given. Finally, the utility of the present formulation is demonstrated on some well-known model problems.

Polymorphism of DNA conformation inside the bacteriophage capsid.

PubMed

Leforestier, Amélie

2013-03-01

Double-stranded DNA bacteriophage genomes are packaged into their icosahedral capsids at the highest densities known so far (about 50 % w:v). How the molecule is folded at such density and how its conformation changes upon ejection or packaging are fascinating questions still largely open. We review cryo-TEM analyses of DNA conformation inside partially filled capsids as a function of the physico-chemical environment (ions, osmotic pressure, temperature). We show that there exists a wide variety of DNA conformations. Strikingly, the different observed structures can be described by some of the different models proposed over the years for DNA organisation inside bacteriophage capsids: either spool-like structures with axial or concentric symmetries, or liquid crystalline structures characterised by a DNA homogeneous density. The relevance of these conformations for the understanding of DNA folding and unfolding upon ejection and packaging in vivo is discussed.

Conformational plasticity of the Ebola virus matrix protein.

PubMed

Radzimanowski, Jens; Effantin, Gregory; Weissenhorn, Winfried

2014-11-01

Filoviruses are the causative agents of a severe and often fatal hemorrhagic fever with repeated outbreaks in Africa. They are negative sense single stranded enveloped viruses that can cross species barriers from its natural host bats to primates including humans. The small size of the genome poses limits to viral adaption, which may be partially overcome by conformational plasticity. Here we review the different conformational states of the Ebola virus (EBOV) matrix protein VP40 that range from monomers, to dimers, hexamers, and RNA-bound octamers. This conformational plasticity that is required for the viral life cycle poses a unique opportunity for development of VP40 specific drugs. Furthermore, we compare the structure to homologous matrix protein structures from Paramyxoviruses and Bornaviruses and we predict that they do not only share the fold but also the conformational flexibility of EBOV VP40. © 2014 The Protein Society.

Loop-driven conformational transition between the alternative and collapsed form of prethrombin-2: targeted molecular dynamics study.

PubMed

Wu, Sangwook

2017-01-01

Two distinct crystal structures of prethrombin-2, the alternative and collapsed forms, are elucidated by X-ray crystallogrphy. We analyzed the conformational transition from the alternative to the collapsed form employing targeted molecular dynamics (TMD) simulation. Despite small RMSD difference in the two X-ray crystal structures, some hydrophobic residues (W60d, W148, W215, and F227) show a significant difference between the two conformations. TMD simulation shows that the four hydrophobic residues undergo concerted movement from dimer to trimer transition via tetramer state in the conformational change from the alternative to the collapsed form. We reveal that the concerted movement of the four hydrophobic residues is controlled by movement of specific loop regions behind. In this paper, we propose a sequential scenario for the conformational transition from the alternative form to the collapsed form, which is partially supported by the mutant W148A simulation.

High-order modes of spoof surface plasmonic wave transmission on thin metal film structure.

PubMed

Liu, Xiaoyong; Feng, Yijun; Zhu, Bo; Zhao, Junming; Jiang, Tian

2013-12-16

Recently, conformal surface plasmon (CSP) structure has been successfully proposed that could support spoof surface plasmon polaritons (SPPs) on corrugated metallic strip with ultrathin thickness [Proc. Natl. Acad. Sci. U.S.A. 110, 40-45 (2013)]. Such concept provides a flexible, conformal, and ultrathin wave-guiding element, very promising for application of plasmonic devices, and circuits in the frequency ranging from microwave to mid-infrared. In this work, we investigated the dispersions and field patterns of high-order modes of spoof SPPs along CSP structure of thin metal film with corrugated edge of periodic array of grooves, and carried out direct measurement on the transmission spectrum of multi-band of surface wave propagation at microwave frequency. It is found that the mode number and mode bands are mainly determined by the depth of the grooves, providing a way to control the multi-band transmission spectrum. We have also experimentally verified the high-order mode spoof SPPs propagation on curved CSP structure with acceptable bending loss. The multi-band propagation of spoof surface wave is believed to be applicable for further design of novel planar devices such as filters, resonators, and couplers, and the concept can be extended to terahertz frequency range.

Ethanol Dimer: Observation of Three New Conformers by Broadband Rotational Spectroscopy

NASA Astrophysics Data System (ADS)

Loru, Donatella; Peña, Isabel; Sanz, M. Eugenia

2017-06-01

The conformational behaviour of the hydrogen-bonded cluster ethanol dimer has been reinvestigated by chirped pulse Fourier transform microwave spectroscopy in the 2-8 GHz frequency region. Three new conformers ({tt}, {tg}+, and {g}-{g}+) have been identified together with the three ({g}+{g}+, {g}-{t}, and {g}+{t}) previously observed by Hearn et al. (J. Chem. Phys. 123, 134324, 2005) and their rotational and centrifugal distortion constants have been determined. By using different carrier gases in the supersonic expansion, the relative abundances of the observed conformers have been estimated. The monosubstituted ^{13}C species and some of the ^{18}O species of the most abundant conformers {g}+{g}+, {g}-{t}, and {tt} have been observed in their natural abundance, which led to the partial determination of their r_{s} structures, and the r_{0} structure for the {tt} conformer. The six observed conformers are stabilized by the delicate interplay of primary O-H...O and secondary C-H...O hydrogen bonds, and dispersion interactions between the methyl groups. Density functional and ab initio methods with different basis sets are benchmarked against the experimental data.

QSPR models for various physical properties of carbohydrates based on molecular mechanics and quantum chemical calculations.

PubMed

Dyekjaer, Jane Dannow; Jónsdóttir, Svava Osk

2004-01-22

Quantitative Structure-Property Relationships (QSPR) have been developed for a series of monosaccharides, including the physical properties of partial molar heat capacity, heat of solution, melting point, heat of fusion, glass-transition temperature, and solid state density. The models were based on molecular descriptors obtained from molecular mechanics and quantum chemical calculations, combined with other types of descriptors. Saccharides exhibit a large degree of conformational flexibility, therefore a methodology for selecting the energetically most favorable conformers has been developed, and was used for the development of the QSPR models. In most cases good correlations were obtained for monosaccharides. For five of the properties predictions were made for disaccharides, and the predicted values for the partial molar heat capacities were in excellent agreement with experimental values.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Medvedev, Ivan R.; De Lucia, Frank C.; Herbst, Eric

Since methyl formate (HCOOCH{sub 3}) is found to have a high abundance in hot molecular cores and other types of clouds in the galactic center, it is reasonable to search among such sources for detectable abundances of the more complex analog ethyl formate (HCOOC{sub 2}H{sub 5}). Following a previous study of the millimeter-wave spectrum of ethyl formate, we have extended the analysis of the vibrational ground state of the trans and gauche conformers of ethyl formate into the submillimeter-wave range. Over 2200 new spectral lines have been measured and analyzed at frequencies up to 380 GHz. Fitting the data formore » each conformer to a Watson A-reduced asymmetric-top Hamiltonian has allowed us to predict the frequencies and intensities of many more transitions through 380 GHz.« less

Peer pressure and alcohol use in young men: a mediation analysis of drinking motives.

PubMed

Studer, Joseph; Baggio, Stéphanie; Deline, Stéphane; N'Goran, Alexandra A; Henchoz, Yves; Mohler-Kuo, Meichun; Daeppen, Jean-Bernard; Gmel, Gerhard

2014-07-01

Peer pressure (PP) has been shown to play a major role in the development and continuation of alcohol use and misuse. To date, almost all the studies investigating the association of PP with alcohol use only considered the PP for misconduct but largely ignored other aspects of PP, such as pressure for peer involvement and peer conformity. Moreover, it is not clear whether the association of PP with alcohol use is direct or mediated by other factors. The aim of the present study was to investigate the association of different aspects of peer pressure (PP) with drinking volume (DV) and risky single-occasion drinking (RSOD), and to explore whether these associations were mediated by drinking motives (DM). A representative sample of 5521 young Swiss men, aged around 20 years old, completed a questionnaire assessing their usual weekly DV, the frequency of RSOD, DM (i.e. enhancement, social, coping, and conformity motives), and 3 aspects of PP (i.e. misconduct, peer involvement, and peer conformity). Associations between PP and alcohol outcomes (DV and RSOD) as well as the mediation of DM were tested using structural equation models. Peer pressure to misconduct was associated with more alcohol use, whereas peer involvement and peer conformity were associated with less alcohol use. Associations of drinking outcomes with PP to misconduct and peer involvement were partially mediated by enhancement and coping motives, while the association with peer conformity was partially mediated by enhancement and conformity motives. Results suggest that PP to misconduct constitutes a risk factor, while peer conformity and peer involvement reflect protective factors with regard to alcohol use. Moreover, results from the mediation analyses suggest that part of the association of PP with alcohol use came indirectly through DM: PP was associated with DM, which in turn were associated with alcohol use. Copyright © 2014 Elsevier B.V. All rights reserved.

Holographic multiverse and conformal invariance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garriga, Jaume; Vilenkin, Alexander, E-mail: jaume.garriga@ub.edu, E-mail: vilenkin@cosmos.phy.tufts.edu

2009-11-01

We consider a holographic description of the inflationary multiverse, according to which the wave function of the universe is interpreted as the generating functional for a lower dimensional Euclidean theory. We analyze a simple model where transitions between inflationary vacua occur through bubble nucleation, and the inflating part of spacetime consists of de Sitter regions separated by thin bubble walls. In this model, we present some evidence that the dual theory is conformally invariant in the UV.

On mass transport in magmatic porosity waves

NASA Astrophysics Data System (ADS)

Jordan, J.; Hesse, M. A.; Rudge, J. F.

2017-12-01

Geochemical analyses of oceanic basalts indicate the mantle is lithologically heterogenous and subject to partial melting. Here we show that porosity waves-which arise naturally in models of buoyancy driven melt migration-transport mass and preserve geochemical signatures, at least partially. Prior studies of tracer transport in one dimensional porosity waves conclude that porosity waves do not transfer mass. However, it is well known that one-dimensional porosity waves are unstable in two and three dimensions and break up into sets of cylindrical or spherical porosity waves. We show that tracer transport in higher dimensional porosity waves is dramatically different than in one dimension. Lateral melt focusing into these high porosity regions leads to melt recirculating in the center of the wave. Melt focusing and recirculation are not resolvable in one dimension where no sustained transport is observed in numerical experiments of solitary porosity waves. In two and three dimensions, the recirculating melt is separated from the background melt-flow field by a circular or spherical dividing streamline and transported with the phase velocity of the porosity wave. The amount of melt focusing that occurs within any given porosity wave, and thus, the extent of the dividing streamline, and resultant volume of transported melt is extremely sensitive to the selection of porosity-permeability and porosity-rheology relationships. Therefore, we present a regime diagram spanning common parameterizations that illustrates the minimum amplitude and phase velocity required for a solitary porosity wave to transport mass as a function of material properties and common parameters used in magma dynamics and mid-ocean ridge models. The realization that solitary waves are capable of sustaining melt transport may require the reinterpretation of previous studies. For example, transport in porosity waves may allow melts that originated from the partial melting of fertile heterogeneities to retain their incompatible trace element signatures as they rise through the mantle. Porosity waves may also provide a mechanism for mixing melts derived from heterogeneities with ambient melts derived from different depths in the mantle.

SU-F-T-650: The Comparison of Robotic Partial Breast Stereotactic Irradiation Using MLC Vs. Iris Cone

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ding, C; Timmerman, R; Jiang, S

Purpose: To evaluate the dosimetric impact on treatment planning for partial breast stereotactic irradiation using Cyberknife with MLC versus Iris Cone. Methods: Ten patients whom underwent lumpectomy for DCIS or stage I invasive non-lobular epithelial breast cancer were included in this study. All patients were previously treated on the Cyberknife using Iris cone with the prescription dose of 37.5Gy in 5 fractions covering at least 95% of PTV on our phase I SBRT 5 fraction partial breast irradiation trial. Retrospectively, treatment planning was performed and compared using the new Cyberknife M6 MLC system for each patient. Using the same contoursmore » and critical organ constraints for both MLC and Iris cone plans, the dose on target and critical organs were analyzed accordingly. Results: Dose to critical organs such as ipsilateral lung, contralateral lung, heart, skin, ipsilateral breast, and rib were analyzed, as well as conformity index and high dose spillage of the target area. In 9 of 10 patients, the MLC plans had less total ipsilateral breast volume encompassing the 50% prescription isodose (mean:22.3±8.2% MLC vs. 31.6±8.0 Iris, p=0.00014) .The MLC plans mean estimated treatment delivery time was significantly less than the Iris plans (51±3.9min vs. 56.2±9min, p=0.03) Both MLC and Iris cone plans were able to meet all dose constraints and there was no statistical difference between those dose constraints. Conclusion: Both MLC and Iris Cone can deliver conformal dose to a partial breast target and satisfy the dose constraints of critical organs. The new Cyberknife with MLC can deliver a more conformal dose in the lower dose region and spare more ipsilateral breast tissue to the 50% prescription isodose. The treatment time for partial breast SBRT plans was also reduced using MLC. Project receives research support from Accuray Inc.« less

Investigation of the Dirac Equation by Using the Conformable Fractional Derivative

NASA Astrophysics Data System (ADS)

Mozaffari, F. S.; Hassanabadi, H.; Sobhani, H.; Chung, W. S.

2018-05-01

In this paper,the Dirac equation is constructed using the conformable fractional derivative so that in its limit for the fractional parameter, the normal version is recovered. Then, the Cornell potential is considered as the interaction of the system. In this case, the wave function and the energy eigenvalue equation are derived with the aim of the bi-confluent Heun functions. use of the conformable fractional derivative is proven to lead to a branching treatment for the energy of the system. Such a treatment is obvious for small values of the fractional parameter, and a united value as the fractional parameter approaches unity.

INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Multi-mode Spiral Wave in a Coupled Oscillatory Medium

NASA Astrophysics Data System (ADS)

Wang, Qun; Gao, Qing-Yu; Lü, Hua-Ping; Zheng, Zhi-Gang

2010-05-01

Multi-mode spiral wave and its breakup in 1-d and 2-d coupled oscillatory media is studied here by theoretic analysis and numerical simulations. The analysis in 1-d system shows that the dispersion relation curve could be non-monotonic depending on the coupling strength. It may also lead to the coexistence of different wave numbers within one system. Direct numerical observations in 1-d and 2-d systems conform to the prediction of dispersion relation analysis. Our findings indicate that the wave grouping can also be observed in oscillatory media without tip meandering and waves with negative group velocity can occur without inhomogeneity.

Relationship of scattering phase shifts to special radiation force conditions for spheres in axisymmetric wave-fields.

PubMed

Marston, Philip L; Zhang, Likun

2017-05-01

When investigating the radiation forces on spheres in complicated wave-fields, the interpretation of analytical results can be simplified by retaining the s-function notation and associated phase shifts imported into acoustics from quantum scattering theory. For situations in which dissipation is negligible, as taken to be the case in the present investigation, there is an additional simplification in that partial-wave phase shifts become real numbers that vanish when the partial-wave index becomes large and when the wave-number-sphere-radius product vanishes. By restricting attention to monopole and dipole phase shifts, transitions in the axial radiation force for axisymmetric wave-fields are found to be related to wave-field parameters for traveling and standing Bessel wave-fields by considering the ratio of the phase shifts. For traveling waves, the special force conditions concern negative forces while for standing waves, the special force conditions concern vanishing radiation forces. An intermediate step involves considering the functional dependence on phase shifts. An appendix gives an approximation for zero-force plane standing wave conditions. Connections with early investigations of acoustic levitation are mentioned and some complications associated with viscosity are briefly noted.

Scattering of acoustic evanescent waves by circular cylinders: Partial wave series solution

NASA Astrophysics Data System (ADS)

Marston, Philip L.

2002-05-01

Evanescent acoustical waves occur in a variety of situations such as when sound is incident on a fluid interface beyond the critical angle and when flexural waves on a plate are subsonic with respect to the surrounding fluid. The scattering by circular cylinders at normal incidence was calculated to give insight into the consequences on the scattering of the evanescence of the incident wave. To analyze the scattering, it is necessary to express the incident wave using a modified expansion involving cylindrical functions. For plane evanescent waves, the expansion becomes a double summation with products of modified and ordinary Bessel functions. The resulting modified series is found for the scattering by a fluid cylinder in an unbounded medium. The perfectly soft and rigid cases are also examined. Unlike the case of an ordinary incident wave, the counterpropagating partial waves of the same angular order have unequal magnitudes when the incident wave is evanescent. This is a consequence of the exponential dependence of the incident wave amplitude on the transverse coordinate. The associated exponential dependence of the scattering on the location of a scatterer was previously demonstrated [T. J. Matula and P. L. Marston, J. Acoust. Soc. Am. 93, 1192-1195 (1993)].

Explaining the Relationship Between Sexually Explicit Internet Material and Casual Sex: A Two-Step Mediation Model.

PubMed

Vandenbosch, Laura; van Oosten, Johanna M F

2018-07-01

Despite increasing interest in the implications of adolescents' use of sexually explicit Internet material (SEIM), we still know little about the relationship between SEIM use and adolescents' casual sexual activities. Based on a three-wave online panel survey study among Dutch adolescents (N = 1079; 53.1% boys; 93.5% with an exclusively heterosexual orientation; M age  = 15.11; SD = 1.39), we found that watching SEIM predicted engagement in casual sex over time. In turn, casual sexual activities partially predicted adolescents' use of SEIM. A two-step mediation model was tested to explain the relationship between watching SEIM and casual sex. It was partially confirmed. First, watching SEIM predicted adolescents' perceptions of SEIM as a relevant information source from Wave 2 to Wave 3, but not from Wave 1 to Wave 2. Next, such perceived utility of SEIM was positively related to stronger instrumental attitudes toward sex and thus their views about sex as a core instrument for sexual gratification. Lastly, adolescents' instrumental attitudes toward sex predicted adolescents' engagement in casual sex activities consistently across waves. Partial support emerged for a reciprocal relationship between watching SEIM and perceived utility. We did not find a reverse relationship between casual sex activities and instrumental attitudes toward sex. No significant gender differences emerged.

Smoking policy change at a homeless shelter: attitudes and effects.

PubMed

Businelle, Michael S; Poonawalla, Insiya B; Kendzor, Darla E; Rios, Debra M; Cuate, Erica L; Savoy, Elaine J; Ma, Ping; Baggett, Travis P; Reingle, Jennifer; Reitzel, Lorraine R

2015-01-01

Homeless adults are exposed to more smokers and smoke in response to environmental tobacco cues more than other socioeconomically disadvantaged groups. Addressing the culture of smoking in homeless shelters through policy initiatives may support cessation and improve health in this vulnerable and understudied population. This study examined support for and expected/actual effects of a smoking ban at a homeless shelter. A 2-wave cross-sectional study with an embedded cohort was conducted in the summer of 2013 two weeks before (wave 1) and two months after (wave 2) a partial outdoor smoking ban was implemented. A total of 394 homeless adults were surveyed (i.e., wave 1 [n=155]; wave 2 [n=150]; and 89 additional participants completed both waves). On average, participants were 43 years old, primarily African American (63%), male (72%), and had been homeless for the previous 12 months (median). Most participants were smokers (76%) smoking 12 cigarettes per day on average. Most participants supported the creation of a large smoke-free zone on the shelter campus, but there was less support for a shelter-wide smoking ban. Average cigarettes smoked per day did not differ between study waves. However, participants who completed both study waves experienced a reduction in expired carbon monoxide at wave 2 (W1=18.2 vs. W2=15.8 parts per million, p=.02). Expected effects of the partial ban were similar to actual effects. Partial outdoor smoking bans may be well supported by homeless shelter residents and may have a positive impact on shelter resident health. Copyright © 2014 Elsevier Ltd. All rights reserved.

Surface wave energy absorption by a partially submerged bio-inspired canopy.

PubMed

Nové-Josserand, C; Castro Hebrero, F; Petit, L-M; Megill, W M; Godoy-Diana, R; Thiria, B

2018-03-27

Aquatic plants are known to protect coastlines and riverbeds from erosion by damping waves and fluid flow. These flexible structures absorb the fluid-borne energy of an incoming fluid by deforming mechanically. In this paper we focus on the mechanisms involved in these fluid-elasticity interactions, as an efficient energy harvesting system, using an experimental canopy model in a wave tank. We study an array of partially-submerged flexible structures that are subjected to the action of a surface wave field, investigating in particular the role of spacing between the elements of the array on the ability of our system to absorb energy from the flow. The energy absorption potential of the canopy model is examined using global wave height measurements for the wave field and local measurements of the elastic energy based on the kinematics of each element of the canopy. We study different canopy arrays and show in particular that flexibility improves wave damping by around 40%, for which half is potentially harvestable.

Multi-fluid Approach to High-frequency Waves in Plasmas. III. Nonlinear Regime and Plasma Heating

NASA Astrophysics Data System (ADS)

Martínez-Gómez, David; Soler, Roberto; Terradas, Jaume

2018-03-01

The multi-fluid modeling of high-frequency waves in partially ionized plasmas has shown that the behavior of magnetohydrodynamic waves in the linear regime is heavily influenced by the collisional interaction between the different species that form the plasma. Here, we go beyond linear theory and study large-amplitude waves in partially ionized plasmas using a nonlinear multi-fluid code. It is known that in fully ionized plasmas, nonlinear Alfvén waves generate density and pressure perturbations. Those nonlinear effects are more pronounced for standing oscillations than for propagating waves. By means of numerical simulations and analytical approximations, we examine how the collisional interaction between ions and neutrals affects the nonlinear evolution. The friction due to collisions dissipates a fraction of the wave energy, which is transformed into heat and consequently raises the temperature of the plasma. As an application, we investigate frictional heating in a plasma with physical conditions akin to those in a quiescent solar prominence.

Collision cross sections of high-mannose N-glycans in commonly observed adduct states--identification of gas-phase conformers unique to [M-H](-) ions.

PubMed

Struwe, W B; Benesch, J L; Harvey, D J; Pagel, K

2015-10-21

We report collision cross sections (CCS) of high-mannose N-glycans as [M + Na](+), [M + K](+), [M + H](+), [M + Cl](-), [M + H2PO4](-) and [M - H](-) ions, measured by drift tube (DT) ion mobility-mass spectrometry (IM-MS) in helium and nitrogen gases. Further analysis using traveling wave (TW) IM-MS reveal the existence of distinct conformers exclusive to [M - H](-) ions.

Calculation of the Full Scattering Amplitude without Partial Wave Decomposition II

NASA Technical Reports Server (NTRS)

Shertzer, J.; Temkin, A.

2003-01-01

As is well known, the full scattering amplitude can be expressed as an integral involving the complete scattering wave function. We have shown that the integral can be simplified and used in a practical way. Initial application to electron-hydrogen scattering without exchange was highly successful. The Schrodinger equation (SE) can be reduced to a 2d partial differential equation (pde), and was solved using the finite element method. We have now included exchange by solving the resultant SE, in the static exchange approximation. The resultant equation can be reduced to a pair of coupled pde's, to which the finite element method can still be applied. The resultant scattering amplitudes, both singlet and triplet, as a function of angle can be calculated for various energies. The results are in excellent agreement with converged partial wave results.

Water saturation effects on P-wave anisotropy in synthetic sandstone with aligned fractures

NASA Astrophysics Data System (ADS)

Amalokwu, Kelvin; Chapman, Mark; Best, Angus I.; Minshull, Timothy A.; Li, Xiang-Yang

2015-08-01

The seismic properties of rocks are known to be sensitive to partial liquid or gas saturation, and to aligned fractures. P-wave anisotropy is widely used for fracture characterization and is known to be sensitive to the saturating fluid. However, studies combining the effect of multiphase saturation and aligned fractures are limited even though such conditions are common in the subsurface. An understanding of the effects of partial liquid or gas saturation on P-wave anisotropy could help improve seismic characterization of fractured, gas bearing reservoirs. Using octagonal-shaped synthetic sandstone samples, one containing aligned penny-shaped fractures and the other without fractures, we examined the influence of water saturation on P-wave anisotropy in fractured rocks. In the fractured rock, the saturation related stiffening effect at higher water saturation values is larger in the direction across the fractures than along the fractures. Consequently, the anisotropy parameter `ε' decreases as a result of this fluid stiffening effect. These effects are frequency dependent as a result of wave-induced fluid flow mechanisms. Our observations can be explained by combining a frequency-dependent fractured rock model and a frequency-dependent partial saturation model.

Rotational superradiant scattering in a vortex flow

NASA Astrophysics Data System (ADS)

Torres, Theo; Patrick, Sam; Coutant, Antonin; Richartz, Maurício; Tedford, Edmund W.; Weinfurtner, Silke

2017-09-01

When an incident wave scatters off of an obstacle, it is partially reflected and partially transmitted. In theory, if the obstacle is rotating, waves can be amplified in the process, extracting energy from the scatterer. Here we describe in detail the first laboratory detection of this phenomenon, known as superradiance. We observed that waves propagating on the surface of water can be amplified after being scattered by a draining vortex. The maximum amplification measured was 14% +/- 8%, obtained for 3.70 Hz waves, in a 6.25-cm-deep fluid, consistent with the superradiant scattering caused by rapid rotation. We expect our experimental findings to be relevant to black-hole physics, since shallow water waves scattering on a draining fluid constitute an analogue of a black hole, as well as to hydrodynamics, due to the close relation to over-reflection instabilities.

Mathematical Methods in Wave Propagation: Part 2--Non-Linear Wave Front Analysis

ERIC Educational Resources Information Center

Jeffrey, Alan

1971-01-01

The paper presents applications and methods of analysis for non-linear hyperbolic partial differential equations. The paper is concluded by an account of wave front analysis as applied to the piston problem of gas dynamics. (JG)

Gravitational waves from plunges into Gargantua

NASA Astrophysics Data System (ADS)

Compère, Geoffrey; Fransen, Kwinten; Hertog, Thomas; Long, Jiang

2018-05-01

We analytically compute time domain gravitational waveforms produced in the final stages of extreme mass ratio inspirals of non-spinning compact objects into supermassive nearly extremal Kerr black holes. Conformal symmetry relates all corotating equatorial orbits in the geodesic approximation to circular orbits through complex conformal transformations. We use this to obtain the time domain Teukolsky perturbations for generic equatorial corotating plunges in closed form. The resulting gravitational waveforms consist of an intermediate polynomial ringdown phase in which the decay rate depends on the impact parameters, followed by an exponential quasi-normal mode decay. The waveform amplitude exhibits critical behavior when the orbital angular momentum tends to a minimal value determined by the innermost stable circular orbit. We show that either near-critical or large angular momentum leads to a significant extension of the LISA observable volume of gravitational wave sources of this kind.

Conformal field theory construction for non-Abelian hierarchy wave functions

NASA Astrophysics Data System (ADS)

Tournois, Yoran; Hermanns, Maria

2017-12-01

The fractional quantum Hall effect is the paradigmatic example of topologically ordered phases. One of its most fascinating aspects is the large variety of different topological orders that may be realized, in particular non-Abelian ones. Here we analyze a class of non-Abelian fractional quantum Hall model states which are generalizations of the Abelian Haldane-Halperin hierarchy. We derive their topological properties and show that the quasiparticles obey non-Abelian fusion rules of type su (q)k . For a subset of these states we are able to derive the conformal field theory description that makes the topological properties—in particular braiding—of the state manifest. The model states we study provide explicit wave functions for a large variety of interesting topological orders, which may be relevant for certain fractional quantum Hall states observed in the first excited Landau level.

Reciprocal links among differential parenting, perceived partiality, and self-worth: a three-wave longitudinal study.

PubMed

Shebloski, Barbara; Conger, Katherine J; Widaman, Keith F

2005-12-01

This study examined reciprocal links between parental differential treatment, siblings' perception of partiality, and self-worth with 3 waves of data from 384 adolescent sibling dyads. Results suggest that birth-order status was significantly associated with self-worth and perception of maternal and paternal differential treatment. There was a consistent across-time effect of self-worth on perception of parental partiality for later born siblings, but not earlier born siblings, and a consistent effect of differential treatment on perception of partiality for earlier born but not later born siblings. The results contribute new insight into the associations between perception of differential parenting and adolescents' adjustment and the role of birth order. Copyright 2006 APA, all rights reserved).

A Rosetta Stone Relating Conventions In Photo-Meson Partial Wave Analyses

DOE Office of Scientific and Technical Information (OSTI.GOV)

A.M. Sandorfi, B. Dey, A. Sarantsev, L. Tiator, R. Workman

2012-04-01

A new generation of complete experiments in pseudoscalar meson photo-production is being pursued at several laboratories. While new data are emerging, there is some confusion regarding definitions of asymmetries and the conventions used in partial wave analyses (PWA). We present expressions for constructing asymmetries as coordinate-system independent ratios of cross sections, along with the names used for these ratios by different PWA groups.

Effect of H-wave polarization on laser radar detection of partially convex targets in random media.

PubMed

El-Ocla, Hosam

2010-07-01

A study on the performance of laser radar cross section (LRCS) of conducting targets with large sizes is investigated numerically in free space and random media. The LRCS is calculated using a boundary value method with beam wave incidence and H-wave polarization. Considered are those elements that contribute to the LRCS problem including random medium strength, target configuration, and beam width. The effect of the creeping waves, stimulated by H-polarization, on the LRCS behavior is manifested. Targets taking large sizes of up to five wavelengths are sufficiently larger than the beam width and are sufficient for considering fairly complex targets. Scatterers are assumed to have analytical partially convex contours with inflection points.

Collision effects on propagation characteristics of electromagnetic waves in a sub-wavelength plasma slab of partially ionized dense plasmas

NASA Astrophysics Data System (ADS)

Bowen, LI; Zhibin, WANG; Qiuyue, NIE; Xiaogang, WANG; Fanrong, KONG; Zhenyu, WANG

2018-01-01

Intensive collisions between electrons and neutral particles in partially ionized plasmas generated in atmospheric/sub-atmospheric pressure environments can sufficiently affect the propagation characteristics of electromagnetic waves, particularly in the sub-wavelength regime. To investigate the collisional effect in such plasmas, we introduce a simplified plasma slab model with a thickness on the order of the wavelength of the incident electromagnetic wave. The scattering matrix method (SMM) is applied to solve the wave equation in the plasma slab with significant nonuniformity. Results show that the collisions between the electrons and the neutral particles, as well as the incident angle and the plasma thickness, can disturb the transmission and reduce reflection significantly.

Functional Coordination of WAVE and WASP in C. elegans Neuroblast Migration.

PubMed

Zhu, Zhiwen; Chai, Yongping; Jiang, Yuxiang; Li, Wenjing; Hu, Huifang; Li, Wei; Wu, Jia-Wei; Wang, Zhi-Xin; Huang, Shanjin; Ou, Guangshuo

2016-10-24

Directional cell migration is critical for metazoan development. We define two molecular pathways that activate the Arp2/3 complex during neuroblast migration in Caenorhabditis elegans. The transmembrane protein MIG-13/Lrp12 is linked to the Arp2/3 nucleation-promoting factors WAVE or WASP through direct interactions with ABL-1 or SEM-5/Grb2, respectively. WAVE mutations partially impaired F-actin organization and decelerated cell migration, and WASP mutations did not inhibit cell migration but enhanced migration defects in WAVE-deficient cells. Purified SEM-5 and MIG-2 synergistically stimulated the F-actin branching activity of WASP-Arp2/3 in vitro. In GFP knockin animals, WAVE and WASP were largely organized into separate clusters at the leading edge, and the amount of WASP was less than WAVE but could be elevated by WAVE mutations. Our results indicate that the MIG-13-WAVE pathway provides the major force for directional cell motility, whereas MIG-13-WASP partially compensates for its loss, underscoring their coordinated activities in facilitating robust cell migration. Copyright © 2016 Elsevier Inc. All rights reserved.

Endocytosis of ABCG2 drug transporter caused by binding of 5D3 antibody: trafficking mechanisms and intracellular fate.

PubMed

Studzian, Maciej; Bartosz, Grzegorz; Pulaski, Lukasz

2015-08-01

ABCG2, a metabolite and xenobiotic transporter located at the plasma membrane (predominantly in barrier tissues and progenitor cells), undergoes a direct progressive endocytosis process from plasma membrane to intracellular compartments upon binding of 5D3 monoclonal antibody. This antibody is specific to an external epitope on the protein molecule and locks it in a discrete conformation within its activity cycle, presumably providing a structural trigger for the observed internalization phenomenon. Using routine and novel assays, we show that ABCG2 is endocytosed by a mixed mechanism: partially via a rapid, clathrin-dependent pathway and partially in a cholesterol-dependent, caveolin-independent manner. While the internalization process is entirely dynamin-dependent and converges initially at the early endosome, subsequent intracellular fate of ABCG2 is again twofold: endocytosis leads to only partial lysosomal degradation, while a significant fraction of the protein is retained in a post-endosomal compartment with the possibility of at least partial recycling back to the cell surface. This externally triggered, conformation-related trafficking pathway may serve as a general regulatory paradigm for membrane transporters, and its discovery was made possible thanks to consistent application of quantitative methods. Copyright © 2015 Elsevier B.V. All rights reserved.

Spontaneous emergence of rogue waves in partially coherent waves: A quantitative experimental comparison between hydrodynamics and optics

NASA Astrophysics Data System (ADS)

El Koussaifi, R.; Tikan, A.; Toffoli, A.; Randoux, S.; Suret, P.; Onorato, M.

2018-01-01

Rogue waves are extreme and rare fluctuations of the wave field that have been discussed in many physical systems. Their presence substantially influences the statistical properties of a partially coherent wave field, i.e., a wave field characterized by a finite band spectrum with random Fourier phases. Their understanding is fundamental for the design of ships and offshore platforms. In many meteorological conditions waves in the ocean are characterized by the so-called Joint North Sea Wave Project (JONSWAP) spectrum. Here we compare two unique experimental results: the first one has been performed in a 270 m wave tank and the other in optical fibers. In both cases, waves characterized by a JONSWAP spectrum and random Fourier phases have been launched at the input of the experimental device. The quantitative comparison, based on an appropriate scaling of the two experiments, shows a very good agreement between the statistics in hydrodynamics and optics. Spontaneous emergence of heavy tails in the probability density function of the wave amplitude is observed in both systems. The results demonstrate the universal features of rogue waves and provide a fundamental and explicit bridge between two important fields of research. Numerical simulations are also compared with experimental results.

Spontaneous emergence of rogue waves in partially coherent waves: A quantitative experimental comparison between hydrodynamics and optics.

PubMed

El Koussaifi, R; Tikan, A; Toffoli, A; Randoux, S; Suret, P; Onorato, M

2018-01-01

Rogue waves are extreme and rare fluctuations of the wave field that have been discussed in many physical systems. Their presence substantially influences the statistical properties of a partially coherent wave field, i.e., a wave field characterized by a finite band spectrum with random Fourier phases. Their understanding is fundamental for the design of ships and offshore platforms. In many meteorological conditions waves in the ocean are characterized by the so-called Joint North Sea Wave Project (JONSWAP) spectrum. Here we compare two unique experimental results: the first one has been performed in a 270 m wave tank and the other in optical fibers. In both cases, waves characterized by a JONSWAP spectrum and random Fourier phases have been launched at the input of the experimental device. The quantitative comparison, based on an appropriate scaling of the two experiments, shows a very good agreement between the statistics in hydrodynamics and optics. Spontaneous emergence of heavy tails in the probability density function of the wave amplitude is observed in both systems. The results demonstrate the universal features of rogue waves and provide a fundamental and explicit bridge between two important fields of research. Numerical simulations are also compared with experimental results.

Conformational Entropy of Intrinsically Disordered Proteins from Amino Acid Triads

PubMed Central

Baruah, Anupaul; Rani, Pooja; Biswas, Parbati

2015-01-01

This work quantitatively characterizes intrinsic disorder in proteins in terms of sequence composition and backbone conformational entropy. Analysis of the normalized relative composition of the amino acid triads highlights a distinct boundary between globular and disordered proteins. The conformational entropy is calculated from the dihedral angles of the middle amino acid in the amino acid triad for the conformational ensemble of the globular, partially and completely disordered proteins relative to the non-redundant database. Both Monte Carlo (MC) and Molecular Dynamics (MD) simulations are used to characterize the conformational ensemble of the representative proteins of each group. The results show that the globular proteins span approximately half of the allowed conformational states in the Ramachandran space, while the amino acid triads in disordered proteins sample the entire range of the allowed dihedral angle space following Flory’s isolated-pair hypothesis. Therefore, only the sequence information in terms of the relative amino acid triad composition may be sufficient to predict protein disorder and the backbone conformational entropy, even in the absence of well-defined structure. The predicted entropies are found to agree with those calculated using mutual information expansion and the histogram method. PMID:26138206

Structural alphabets derived from attractors in conformational space

PubMed Central

2010-01-01

Background The hierarchical and partially redundant nature of protein structures justifies the definition of frequently occurring conformations of short fragments as 'states'. Collections of selected representatives for these states define Structural Alphabets, describing the most typical local conformations within protein structures. These alphabets form a bridge between the string-oriented methods of sequence analysis and the coordinate-oriented methods of protein structure analysis. Results A Structural Alphabet has been derived by clustering all four-residue fragments of a high-resolution subset of the protein data bank and extracting the high-density states as representative conformational states. Each fragment is uniquely defined by a set of three independent angles corresponding to its degrees of freedom, capturing in simple and intuitive terms the properties of the conformational space. The fragments of the Structural Alphabet are equivalent to the conformational attractors and therefore yield a most informative encoding of proteins. Proteins can be reconstructed within the experimental uncertainty in structure determination and ensembles of structures can be encoded with accuracy and robustness. Conclusions The density-based Structural Alphabet provides a novel tool to describe local conformations and it is specifically suitable for application in studies of protein dynamics. PMID:20170534

5-D interpolation with wave-front attributes

NASA Astrophysics Data System (ADS)

Xie, Yujiang; Gajewski, Dirk

2017-11-01

Most 5-D interpolation and regularization techniques reconstruct the missing data in the frequency domain by using mathematical transforms. An alternative type of interpolation methods uses wave-front attributes, that is, quantities with a specific physical meaning like the angle of emergence and wave-front curvatures. In these attributes structural information of subsurface features like dip and strike of a reflector are included. These wave-front attributes work on 5-D data space (e.g. common-midpoint coordinates in x and y, offset, azimuth and time), leading to a 5-D interpolation technique. Since the process is based on stacking next to the interpolation a pre-stack data enhancement is achieved, improving the signal-to-noise ratio (S/N) of interpolated and recorded traces. The wave-front attributes are determined in a data-driven fashion, for example, with the Common Reflection Surface (CRS method). As one of the wave-front-attribute-based interpolation techniques, the 3-D partial CRS method was proposed to enhance the quality of 3-D pre-stack data with low S/N. In the past work on 3-D partial stacks, two potential problems were still unsolved. For high-quality wave-front attributes, we suggest a global optimization strategy instead of the so far used pragmatic search approach. In previous works, the interpolation of 3-D data was performed along a specific azimuth which is acceptable for narrow azimuth acquisition but does not exploit the potential of wide-, rich- or full-azimuth acquisitions. The conventional 3-D partial CRS method is improved in this work and we call it as a wave-front-attribute-based 5-D interpolation (5-D WABI) as the two problems mentioned above are addressed. Data examples demonstrate the improved performance by the 5-D WABI method when compared with the conventional 3-D partial CRS approach. A comparison of the rank-reduction-based 5-D seismic interpolation technique with the proposed 5-D WABI method is given. The comparison reveals that there are significant advantages for steep dipping events using the 5-D WABI method when compared to the rank-reduction-based 5-D interpolation technique. Diffraction tails substantially benefit from this improved performance of the partial CRS stacking approach while the CPU time is comparable to the CPU time consumed by the rank-reduction-based method.

Pseudo-phase-matched four-wave mixing in soliton wavelength-division multiplexing transmission.

PubMed

Mamyshev, P V; Mollenauer, L F

1996-03-15

In a soliton transmission system using lumped amplifiers, pseudo phase matching allows four-wave mixing fields from soliton-soliton collisions to grow uncontrollably and inf lict severe penalties. Through numerical simulation, we show that this growth can be eliminated, or at least greatly reduced, through the use of fiber whose dispersion is tapered, either continuously or in steps, in conformity with the fiber loss curve.

Pathway towards Programmable Wave Anisotropy in Cellular Metamaterials

NASA Astrophysics Data System (ADS)

Celli, Paolo; Zhang, Weiting; Gonella, Stefano

2018-01-01

In this work, we provide a proof-of-concept experimental demonstration of the wave-control capabilities of cellular metamaterials endowed with populations of tunable electromechanical resonators. Each independently tunable resonator comprises a piezoelectric patch and a resistor-inductor shunt, and its resonant frequency can be seamlessly reprogrammed without interfering with the cellular structure's default properties. We show that, by strategically placing the resonators in the lattice domain and by deliberately activating only selected subsets of them, chosen to conform to the directional features of the beamed wave response, it is possible to override the inherent wave anisotropy of the cellular medium. The outcome is the establishment of tunable spatial patterns of energy distillation resulting in a nonsymmetric correction of the wave fields.

The Bach equations in spin-coefficient form

NASA Astrophysics Data System (ADS)

Forbes, Hamish

2018-06-01

Conformal gravity theories are defined by field equations that determine only the conformal structure of the spacetime manifold. The Bach equations represent an early example of such a theory, we present them here in component form in terms of spin- and boost-weighted spin-coefficients using the compacted spin-coefficient formalism. These equations can be used as an efficient alternative to the standard tensor form. As a simple application we solve the Bach equations for pp-wave and static spherically symmetric spacetimes.

Enhanced biosensor performance using an avidin-biotin bridge for antibody immobilization

NASA Astrophysics Data System (ADS)

Narang, Upvan; Anderson, George P.; King, Keeley D.; Liss, Heidi S.; Ligler, Frances S.

1997-05-01

Maintaining antibody function after immobilization is critical to the performance of a biosensor. The conventional methods to immobilize antibodies onto surfaces are via covalent attachment using a crosslinker or by adsorption. Often, these methods of immobilization result in partial denaturation of the antibody and conformational changes leading to a reduced activity of the antibody. In this paper, we report on the immobilization of antibodies onto the surface of an optical fiber through an avidin-biotin bridge for the detection of ricin, ovalbumin, and Bacillus globigii (Bg). The assays are performed in a sandwich format. First, a capture antibody is immobilized, followed by the addition of the analyte. Finally, a fluorophore- labeled antibody is added for the specific detection of the analyte. The evanescent wave-induced fluorescence is coupled back through the same fiber to be detected using a photodiode. In all cases, we observe an improved performance of the biosensor, i.e., lower limit of detection and wide linear dynamic range, for the assays in which the antibody is immobilized via avidin-biotin bridges compared to covalent attachment method.

Gender, health, and initiation of breastfeeding.

PubMed

Colodro-Conde, Lucía; Limiñana-Gras, Rosa M; Sánchez-López, M Pilar; Ordoñana, Juan R

2015-01-01

The aim of this study was to explore the associations of health, gender, and motherhood with the decisions about breastfeeding. The sample consisted of 265 pregnant women (mean age: 32.34, SD: 4.01 years) who were recruited in healthcare centers and hospitals in southeast Spain between 2010 and 2011. Mental health was measured by the 12-Item General Health Questionnaire and gender by the Conformity to Feminine Norms Inventory. Women in our sample showed a higher conformity to gender norms than women surveyed in the adaptation of the inventory to the Spanish population (t = 11.25, p < 0.001, effect estimate (Cohen's d) = 0.59). After adjustment for covariates, women who exclusively breastfed did not differ significantly in their conformity to gender norms from those who used partial breastfeeding or bottle feeding. Although good, our expectant mothers had worse mental health than the women aged 15-44 years in the Spanish National Health Survey (t = 2.96, p < 0.001, d = 0.26). Those who partially breastfed had significantly better mental health values. Gender norms were modulators in a model of factors related to initiation of breastfeeding. This study provides information about health and social construction of gender norms.

Interactions of solitary waves and compression/expansion waves in core-annular flows

NASA Astrophysics Data System (ADS)

Maiden, Michelle; Anderson, Dalton; El, Gennady; Franco, Nevil; Hoefer, Mark

2017-11-01

The nonlinear hydrodynamics of an initial step leads to the formation of rarefaction waves and dispersive shock waves in dispersive media. Another hallmark of these media is the soliton, a localized traveling wave whose speed is amplitude dependent. Although compression/expansion waves and solitons have been well-studied individually, there has been no mathematical description of their interaction. In this talk, the interaction of solitons and shock/rarefaction waves for interfacial waves in viscous, miscible core-annular flows are modeled mathematically and explored experimentally. If the interior fluid is continuously injected, a deformable conduit forms whose interfacial dynamics are well-described by a scalar, dispersive nonlinear partial differential equation. The main focus is on interactions of solitons with dispersive shock waves and rarefaction waves. Theory predicts that a soliton can either be transmitted through or trapped by the extended hydrodynamic state. The notion of reciprocity is introduced whereby a soliton interacts with a shock wave in a reciprocal or dual fashion as with the rarefaction. Soliton reciprocity, trapping, and transmission are observed experimentally and are found to agree with the modulation theory and numerical simulations. This work was partially supported by NSF CAREER DMS-1255422 (M.A.H.) and NSF GRFP (M.D.M.).

Line-source excitation of realistic conformal metasurface cloaks

NASA Astrophysics Data System (ADS)

Padooru, Yashwanth R.; Yakovlev, Alexander B.; Chen, Pai-Yen; Alù, Andrea

2012-11-01

Following our recently introduced analytical tools to model and design conformal mantle cloaks based on metasurfaces [Padooru et al., J. Appl. Phys. 112, 034907 (2012)], we investigate their performance and physical properties when excited by an electric line source placed in their close proximity. We consider metasurfaces formed by 2-D arrays of slotted (meshes and Jerusalem cross slots) and printed (patches and Jerusalem crosses) sub-wavelength elements. The electromagnetic scattering analysis is carried out using a rigorous analytical model, which utilizes the two-sided impedance boundary conditions at the interface of the sub-wavelength elements. It is shown that the homogenized grid-impedance expressions, originally derived for planar arrays of sub-wavelength elements and plane-wave excitation, may be successfully used to model and tailor the surface reactance of cylindrical conformal mantle cloaks illuminated by near-field sources. Our closed-form analytical results are in good agreement with full-wave numerical simulations, up to sub-wavelength distances from the metasurface, confirming that mantle cloaks may be very effective to suppress the scattering of moderately sized objects, independent of the type of excitation and point of observation. We also discuss the dual functionality of these metasurfaces to boost radiation efficiency and directivity from confined near-field sources.

Tailoring of the partial magnonic gap in three-dimensional magnetoferritin-based magnonic crystals

NASA Astrophysics Data System (ADS)

Mamica, S.

2013-07-01

We investigate theoretically the use of magnetoferritin nanoparticles, self-assembled in the protein crystallization process, as the basis for the realization of 3D magnonic crystals in which the interparticle space is filled with a ferromagnetic material. Using the plane wave method we study the dependence of the width of the partial band gap and its central frequency on the total magnetic moment of the magnetoferritin core and the lattice constant of the magnetoferritin crystal. We show that by adjusting the combination of these two parameters the partial gap can be tailored in a wide frequency range and shifted to sub-terahertz frequencies. Moreover, the difference in the width of the partial gap for spin waves propagating in planes parallel and perpendicular to the external field allows for switching on and off the partial magnonic gap by changing the direction of the applied field.

Determining the dominant partial wave contributions from angular distributions of single- and double-polarization observables in pseudoscalar meson photoproduction

NASA Astrophysics Data System (ADS)

Wunderlich, Y.; Afzal, F.; Thiel, A.; Beck, R.

2017-05-01

This work presents a simple method to determine the significant partial wave contributions to experimentally determined observables in pseudoscalar meson photoproduction. First, fits to angular distributions are presented and the maximum orbital angular momentum Lmax needed to achieve a good fit is determined. Then, recent polarization measurements for γ p → π0 p from ELSA, GRAAL, JLab and MAMI are investigated according to the proposed method. This method allows us to project high-spin partial wave contributions to any observable as long as the measurement has the necessary statistical accuracy. We show, that high precision and large angular coverage in the polarization data are needed in order to be sensitive to high-spin resonance states and thereby also for the finding of small resonance contributions. This task can be achieved via interference of these resonances with the well-known states. For the channel γ p → π0 p, those are the N(1680)5/2+ and Δ(1950)7/2+, contributing to the F-waves.

Turbulence in the Ott-Antonsen equation for arrays of coupled phase oscillators

NASA Astrophysics Data System (ADS)

Wolfrum, M.; Gurevich, S. V.; Omel'chenko, O. E.

2016-02-01

In this paper we study the transition to synchrony in an one-dimensional array of oscillators with non-local coupling. For its description in the continuum limit of a large number of phase oscillators, we use a corresponding Ott-Antonsen equation, which is an integro-differential equation for the evolution of the macroscopic profiles of the local mean field. Recently, it was reported that in the spatially extended case at the synchronisation threshold there appear partially coherent plane waves with different wave numbers, which are organised in the well-known Eckhaus scenario. In this paper, we show that for Kuramoto-Sakaguchi phase oscillators the phase lag parameter in the interaction function can induce a Benjamin-Feir-type instability of the partially coherent plane waves. The emerging collective macroscopic chaos appears as an intermediate stage between complete incoherence and stable partially coherent plane waves. We give an analytic treatment of the Benjamin-Feir instability and its onset in a codimension-two bifurcation in the Ott-Antonsen equation as well as a numerical study of the transition from phase turbulence to amplitude turbulence inside the Benjamin-Feir unstable region.

Analytic computation of energy derivatives - Relationships among partial derivatives of a variationally determined function

NASA Technical Reports Server (NTRS)

King, H. F.; Komornicki, A.

1986-01-01

Formulas are presented relating Taylor series expansion coefficients of three functions of several variables, the energy of the trial wave function (W), the energy computed using the optimized variational wave function (E), and the response function (lambda), under certain conditions. Partial derivatives of lambda are obtained through solution of a recursive system of linear equations, and solution through order n yields derivatives of E through order 2n + 1, extending Puley's application of Wigner's 2n + 1 rule to partial derivatives in couple perturbation theory. An examination of numerical accuracy shows that the usual two-term second derivative formula is less stable than an alternative four-term formula, and that previous claims that energy derivatives are stationary properties of the wave function are fallacious. The results have application to quantum theoretical methods for the computation of derivative properties such as infrared frequencies and intensities.

Power counting in peripheral partial waves: The singlet channels

NASA Astrophysics Data System (ADS)

Valderrama, M. Pavón; Sánchez, M. Sánchez; Yang, C.-J.; Long, Bingwei; Carbonell, J.; van Kolck, U.

2017-05-01

We analyze the power counting of the peripheral singlet partial waves in nucleon-nucleon scattering. In agreement with conventional wisdom, we find that pion exchanges are perturbative in the peripheral singlets. We quantify from the effective field theory perspective the well-known suppression induced by the centrifugal barrier in the pion-exchange interactions. By exploring perturbation theory up to fourth order, we find that the one-pion-exchange potential in these channels is demoted from leading to subleading order by a given power of the expansion parameter that grows with the orbital angular momentum. We discuss the implications of these demotions for few-body calculations: though higher partial waves have been known for a long time to be irrelevant in these calculations (and are hence ignored), here we explain how to systematize the procedure in a way that is compatible with the effective field theory expansion.

Teaching Modeling with Partial Differential Equations: Several Successful Approaches

ERIC Educational Resources Information Center

Myers, Joseph; Trubatch, David; Winkel, Brian

2008-01-01

We discuss the introduction and teaching of partial differential equations (heat and wave equations) via modeling physical phenomena, using a new approach that encompasses constructing difference equations and implementing these in a spreadsheet, numerically solving the partial differential equations using the numerical differential equation…

Trajectory modulated prone breast irradiation: a LINAC-based technique combining intensity modulated delivery and motion of the couch.

PubMed

Fahimian, Benjamin; Yu, Victoria; Horst, Kathleen; Xing, Lei; Hristov, Dimitre

2013-12-01

External beam radiation therapy (EBRT) provides a non-invasive treatment alternative for accelerated partial breast irradiation (APBI), however, limitations in achievable dose conformity of current EBRT techniques have been correlated to reported toxicity. To enhance the conformity of EBRT APBI, a technique for conventional LINACs is developed, which through combined motion of the couch, intensity modulated delivery, and a prone breast setup, enables wide-angular coronal arc irradiation of the ipsilateral breast without irradiating through the thorax and contralateral breast. A couch trajectory optimization technique was developed to determine the trajectories that concurrently avoid collision with the LINAC and maintain the target within the MLC apertures. Inverse treatment planning was performed along the derived trajectory. The technique was experimentally implemented by programming the Varian TrueBeam™ STx in Developer Mode. The dosimetric accuracy of the delivery was evaluated by ion chamber and film measurements in phantom. The resulting optimized trajectory was shown to be necessarily non-isocentric, and contain both translation and rotations of the couch. Film measurements resulted in 93% of the points in the measured two-dimensional dose maps passing the 3%/3mm Gamma criterion. Preliminary treatment plan comparison to 5-field 3D-conformal, IMRT, and VMAT demonstrated enhancement in conformity, and reduction of the normal tissue V50% and V100% parameters that have been correlated with EBRT toxicity. The feasibility of wide-angular intensity modulated partial breast irradiation using motion of the couch has been demonstrated experimentally on a standard LINAC for the first time. For patients eligible for a prone setup, the technique may enable improvement of dose conformity and associated dose-volume parameters correlated with toxicity. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Endoscopic stenting as bridge-to-surgery (BTS) in left-sided obstructing colorectal cancer: Experience with conformable stents.

PubMed

Parodi, Andrea; De Ceglie, Antonella; De Luca, Luca; Conigliaro, Rita; Naspetti, Riccardo; Arpe, Paola; Coccia, Gianni; Conio, Massimo

2016-11-01

Compared to emergency surgery, self-expandable metallic stents are effective and safe when used as bridge-to-surgery (BTS) in operable patients with acute colorectal cancer obstruction. In this study, we report data on the new conformable colonic stents. To evaluate clinical effectiveness of conformable stents as BTS in patients with acute colorectal cancer obstruction. This was a retrospective study. The study was conducted at six Italian Endoscopic Units. Data about patients with acute malignant colorectal obstruction were collected between 2007 and 2012. All patients were treated with conformable stents as BTS. Technical success, clinical success, rate of primary anastomosis and colostomy, early and late complications were evaluated. Data about 88 patients (62 males) were reviewed in this study. Conformable SEMS were correctly deployed in 86 out of 88 patients, with resolution of obstruction in all treated patients. Tumor resection with primary anastomosis was possible in all patients. A temporary colostomy was performed in 40. Early complications did not occur. Late complications occurred in 11 patients. Stent migration was significantly higher in patients treated with partially-covered stents compared to the uncovered group (35% vs. 0%, P<0.001). Endoscopical re-intervention was required in 12% of patients. One patient with rectal cancer had an anastomotic dehiscence after surgery and he was successfully treated with endoscopic clipping. One year after surgery, all patients were alive and local recurrence have not been documented. This was a retrospective and uncontrolled study. Preliminary data from this large case series are encouraging, with a high rate of technical and clinical success and low rate of clinically relevant complications. Partially-covered SEMS should be avoided in order to reduce the risk of endoscopic re-intervention. Copyright © 2016. Published by Elsevier Masson SAS.

The butyrophilin 3A1 intracellular domain undergoes a conformational change involving the juxtamembrane region.

PubMed

Nguyen, Khiem; Li, Jin; Puthenveetil, Robbins; Lin, Xiaochen; Poe, Michael M; Hsiao, Chia-Hung Christine; Vinogradova, Olga; Wiemer, Andrew J

2017-11-01

Small isoprenoid diphosphates, such as ( E )-4-hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP), are ligands of the internal domain of BTN3A1. Ligand binding in target cells promotes activation of Vγ9Vδ2 T cells. We demonstrate by small-angle X-ray scattering (SAXS) that HMBPP binding to the internal domain of BTN3A1 induces a conformational change in the position of the B30.2 domain relative to the juxtamembrane (JM) region. To better understand the molecular details of this conformational rearrangement, NMR spectroscopy was used to discover that the JM region interacts with HMBPP, specifically at the diphosphate. The spectral location of the affected amide peaks, partial NMR assignments, and JM mutants (ST 296 AA or T 304 A) investigated, confirm that the backbone amide of at least one Thr (Thr 304 ), adjacent to conserved Ser, comes close to the HMBPP diphosphate, whereas double mutation of nonconserved residues (Ser/Thr 296/297 ) may perturb the local fold. Cellular mutation of either of the identified Thr residues reduces the activation of Vγ9Vδ2 T cells by HMBPP, zoledronate, and POM 2 -C-HMBP, but not by a partial agonist BTN3 antibody. Taken together, our results show that ligand binding to BTN3A1 induces a conformational change within the intracellular domain that involves the JM region and is required for full activation.-Nguyen, K., Li, J., Puthenveetil, R., Lin, X., Poe, M. M., Hsiao, C.-H. C., Vinogradova, O., Wiemer, A. J. The butyrophilin 3A1 intracellular domain undergoes a conformational change involving the juxtamembrane region. © FASEB.

Pure quasi-P-wave calculation in transversely isotropic media using a hybrid method

NASA Astrophysics Data System (ADS)

Wu, Zedong; Liu, Hongwei; Alkhalifah, Tariq

2018-07-01

The acoustic approximation for anisotropic media is widely used in current industry imaging and inversion algorithms mainly because Pwaves constitute the majority of the energy recorded in seismic exploration. The resulting acoustic formulae tend to be simpler, resulting in more efficient implementations, and depend on fewer medium parameters. However, conventional solutions of the acoustic wave equation with higher-order derivatives suffer from shear wave artefacts. Thus, we derive a new acoustic wave equation for wave propagation in transversely isotropic (TI) media, which is based on a partially separable approximation of the dispersion relation for TI media and free of shear wave artefacts. Even though our resulting equation is not a partial differential equation, it is still a linear equation. Thus, we propose to implement this equation efficiently by combining the finite difference approximation with spectral evaluation of the space-independent parts. The resulting algorithm provides solutions without the constraint ɛ ≥ δ. Numerical tests demonstrate the effectiveness of the approach.

Contributions of aortic pulse wave velocity and backward wave pressure to variations in left ventricular mass are independent of each other.

PubMed

Bello, Hamza; Norton, Gavin R; Ballim, Imraan; Libhaber, Carlos D; Sareli, Pinhas; Woodiwiss, Angela J

2017-05-01

Aortic pulse wave velocity (PWV) and backward waves, as determined from wave separation analysis, predict cardiovascular events beyond brachial blood pressure. However, the extent to which these aortic hemodynamic variables contribute independent of each other is uncertain. In 749 randomly selected participants of African ancestry, we therefore assessed the extent to which relationships between aortic PWV or backward wave pressures (Pb) (and hence central aortic pulse pressure [PPc]) and left ventricular mass index (LVMI) occur independent of each other. Aortic PWV, PPc, forward wave pressure (Pf), and Pb were determined using radial applanation tonometry and SphygmoCor software and LVMI using echocardiography; 44.5% of participants had an increased left ventricular mass indexed to height 1.7 . With adjustments for age, brachial systolic blood pressure or PP, and additional confounders, PPc and Pb, but not Pf, were independently related to LVMI and left ventricular hypertrophy (LVH) in both men and women. However, PWV was independently associated with LVMI in women (partial r = 0.16, P < .001), but not in men (partial r = 0.03), and PWV was independently associated with LVH in women (P < .05), but not in men (P = .07). With PWV and Pb included in the same multivariate regression models, PWV (partial r = 0.14, P < .005) and Pb (partial r = 0.10, P < .05) contributed to a similar extent to variations in LVMI in women. In addition, with PWV and Pb included in the same multivariate regression models, PWV (P < .05) and Pb (P < .02) contributed to LVH in women. In conclusion, aortic PWV and Pb (and hence pulse pressure) although both associated with LVMI and LVH produce effects which are independent of each other. Copyright © 2017 American Society of Hypertension. Published by Elsevier Inc. All rights reserved.

{omega} meson production in pp collisions with a polarized beam

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balasubramanyam, J.; Venkataraya,; Ramachandran, G.

2008-07-15

Model independent formulas are derived for the beam analyzing power A{sub y} and beam to meson spin transfers in pp{yields}pp{omega}, taking into consideration all six threshold partial wave amplitudes f{sub 1},...,f{sub 6} covering the Ss, Sp, and Ps channels. It is shown that the lowest three partial wave amplitudes f{sub 1},f{sub 2},f{sub 3} can be determined empirically without any discrete ambiguities. Partial information with regard to the amplitudes f{sub 4},f{sub 5},f{sub 6} covering the Ps channel may be extracted, if the measurements are carried through at the double differential level.

White-light parametric instabilities in plasmas.

PubMed

Santos, J E; Silva, L O; Bingham, R

2007-06-08

Parametric instabilities driven by partially coherent radiation in plasmas are described by a generalized statistical Wigner-Moyal set of equations, formally equivalent to the full wave equation, coupled to the plasma fluid equations. A generalized dispersion relation for stimulated Raman scattering driven by a partially coherent pump field is derived, revealing a growth rate dependence, with the coherence width sigma of the radiation field, scaling with 1/sigma for backscattering (three-wave process), and with 1/sigma1/2 for direct forward scattering (four-wave process). Our results demonstrate the possibility to control the growth rates of these instabilities by properly using broadband pump radiation fields.

Evidence for a magma reservoir beneath the Taipei metropolis of Taiwan from both S-wave shadows and P-wave delays.

PubMed

Lin, Cheng-Horng

2016-12-23

There are more than 7 million people living near the Tatun volcano group in northern Taiwan. For the safety of the Taipei metropolis, in particular, it has been debated for decades whether or not these volcanoes are active. Here I show evidence of a deep magma reservoir beneath the Taipei metropolis from both S-wave shadows and P-wave delays. The reservoir is probably composed of either a thin magma layer overlay or many molten sills within thick partially molten rocks. Assuming that 40% of the reservoir is partially molten, its total volume could be approximately 350 km 3 . The exact location and geometry of the magma reservoir will be obtained after dense seismic arrays are deployed in 2017-2020.

Coulomb wave functions in momentum space

DOE PAGES

Eremenko, V.; Upadhyay, N. J.; Thompson, I. J.; ...

2015-10-15

We present an algorithm to calculate non-relativistic partial-wave Coulomb functions in momentum space. The arguments are the Sommerfeld parameter η, the angular momentum l, the asymptotic momentum q and the 'running' momentum p, where both momenta are real. Since the partial-wave Coulomb functions exhibit singular behavior when p → q, different representations of the Legendre functions of the 2nd kind need to be implemented in computing the functions for the values of p close to the singularity and far away from it. The code for the momentum-space Coulomb wave functions is applicable for values of vertical bar eta vertical barmore » in the range of 10 -1 to 10, and thus is particularly suited for momentum space calculations of nuclear reactions.« less

Strongly interacting high-partial-wave Bose gas

NASA Astrophysics Data System (ADS)

Yao, Juan; Qi, Ran; Zhang, Pengfei

2018-04-01

Motivated by recent experimental progress, we make an investigation of p - and d -wave resonant Bose gas. An explanation of the Nozières and Schmitt-Rink (NSR) scheme in terms of two-channel model is provided. Different from the s -wave case, high-partial-wave interaction supports a quasibound state in the weak-coupling regime. Within the NSR approximation, we study the equation of state, critical temperature, and particle population distributions. We clarify the effect of the quasibound state on the phase diagram and the dimer production. A multicritical point where normal phase, atomic superfluid phase, and molecular superfluid phase meet is predicted within the phase diagram. We also show the occurrence of a resonant conversion between solitary atoms and dimers when temperature kBT approximates the quasibound energy.

Matrix product state representation of quasielectron wave functions

NASA Astrophysics Data System (ADS)

Kjäll, J.; Ardonne, E.; Dwivedi, V.; Hermanns, M.; Hansson, T. H.

2018-05-01

Matrix product state techniques provide a very efficient way to numerically evaluate certain classes of quantum Hall wave functions that can be written as correlators in two-dimensional conformal field theories. Important examples are the Laughlin and Moore-Read ground states and their quasihole excitations. In this paper, we extend the matrix product state techniques to evaluate quasielectron wave functions, a more complex task because the corresponding conformal field theory operator is not local. We use our method to obtain density profiles for states with multiple quasielectrons and quasiholes, and to calculate the (mutual) statistical phases of the excitations with high precision. The wave functions we study are subject to a known difficulty: the position of a quasielectron depends on the presence of other quasiparticles, even when their separation is large compared to the magnetic length. Quasielectron wave functions constructed using the composite fermion picture, which are topologically equivalent to the quasielectrons we study, have the same problem. This flaw is serious in that it gives wrong results for the statistical phases obtained by braiding distant quasiparticles. We analyze this problem in detail and show that it originates from an incomplete screening of the topological charges, which invalidates the plasma analogy. We demonstrate that this can be remedied in the case when the separation between the quasiparticles is large, which allows us to obtain the correct statistical phases. Finally, we propose that a modification of the Laughlin state, that allows for local quasielectron operators, should have good topological properties for arbitrary configurations of excitations.

Plan-graph Based Heuristics for Conformant Probabilistic Planning

NASA Technical Reports Server (NTRS)

Ramakrishnan, Salesh; Pollack, Martha E.; Smith, David E.

2004-01-01

In this paper, we introduce plan-graph based heuristics to solve a variation of the conformant probabilistic planning (CPP) problem. In many real-world problems, it is the case that the sensors are unreliable or take too many resources to provide knowledge about the environment. These domains are better modeled as conformant planning problems. POMDP based techniques are currently the most successful approach for solving CPP but have the limitation of state- space explosion. Recent advances in deterministic and conformant planning have shown that plan-graphs can be used to enhance the performance significantly. We show that this enhancement can also be translated to CPP. We describe our process for developing the plan-graph heuristics and estimating the probability of a partial plan. We compare the performance of our planner PVHPOP when used with different heuristics. We also perform a comparison with a POMDP solver to show over a order of magnitude improvement in performance.

Perpetual Motion with Maxwell's Demon

NASA Astrophysics Data System (ADS)

Gordon, Lyndsay G. M.

2002-11-01

A method for producing a temperature gradient by Brownian motion in an equilibrated isolated system composed of two fluid compartments and a separating adiabatic membrane is discussed. This method requires globular protein molecules, partially embedded in the membrane, to alternate between two conformations which lie on opposite sides of the membrane. The greater part of each conformer is bathed by one of the fluids and rotates in Brownian motion around its axis, perpendicular to the membrane. Rotational energy is transferred through the membrane during conformational changes. Angular momentum is conserved during the transitions. The energy flow becomes asymmetrical when the conformational changes of the protein are sterically hindered by two of its side-chains, the positions of which are affected by the angular velocity of the rotor. The heat flow increases the temperature gradient in contravention of the Second Law. A second hypothetical model which illustrates solute transfer at variance with the Second Law is also discussed.

Plateau Waves of Intracranial Pressure and Partial Pressure of Cerebral Oxygen.

PubMed

Lang, Erhard W; Kasprowicz, Magdalena; Smielewski, Peter; Pickard, John; Czosnyka, Marek

2016-01-01

This study investigates 55 intracranial pressure (ICP) plateau waves recorded in 20 patients after severe traumatic brain injury (TBI) with a focus on a moving correlation coefficient between mean arterial pressure (ABP) and ICP, called PRx, which serves as a marker of cerebrovascular reactivity, and a moving correlation coefficient between ABP and cerebral partial pressure of oxygen (pbtO2), called ORx, which serves as a marker for cerebral oxygen reactivity. ICP and ICPamplitude increased significantly during the plateau waves, whereas CPP and pbtO2 decreased significantly. ABP, ABP amplitude, and heart rate remained unchanged. In 73 % of plateau waves PRx increased during the wave. ORx showed an increase during and a decrease after the plateau waves, which was not statistically significant. Our data show profound cerebral vasoparalysis on top of the wave and, to a lesser extent, impairment of cerebral oxygen reactivity. The different behavior of the indices may be due to the different latencies of the cerebral blood flow and oxygen level control mechanisms. While cerebrovascular reactivity is a rapidly reacting mechanism, cerebral oxygen reactivity is slower.

Simulations of flow induced structural transition of the β-switch region of glycoprotein Ibα.

PubMed

Han, Mengzhi; Xu, Ji; Ren, Ying; Li, Jinghai

2016-02-01

Binding of glycoprotein Ibα to von Willebrand factor induces platelet adhesion to injured vessel walls and initiates a multistep hemostatic process. It has been hypothesized that the flow condition could induce a loop to β-sheet conformational change in the β-switch region of glycoprotein Ibα, which regulates it binding to the von Willebrand factor and facilitates the blood clot formation and wound healing. In this work, direct molecular dynamics (MD), flow MD and metadynamics, were employed to investigate the mechanisms of this flow induced conformational transition process. Specifically, the free energy landscape of the whole transition process was drawn by metadynamics with the path collective variable approach. The results reveal that without flow, the free energy landscape has two main basins, including a random loop basin stabilized by large conformational entropy and a partially folded β-sheet basin. The free energy barrier separating these two basins is relatively high and the β-switch could not fold from loop to β-sheet state spontaneously. The fully β-sheet conformations located in high free energy regions, which are also unstable and gradually unfold into partially folded β-sheet state with flow. Relatively weak flow could trigger some folding of the β-switch but could not fold it into fully β-sheet state. Under strong flow conditions, the β-switch could readily overcome the high free energy barrier and fold into fully β-sheet state. Copyright © 2015 Elsevier B.V. All rights reserved.

The uncertain trajectory of a pilot-wave

NASA Astrophysics Data System (ADS)

Nachbin, Andre

2015-11-01

Yves Couder (Paris 7) and coworkers reported on walking droplets on the surface of a vibrating bath. John Bush (MIT) and coworkers also produced laboratory experiments which were compared to theoretical predictions. Both groups discussed the pilot-wave properties previously thought to be peculiar to the microscopic, quantum realm. Of particular interest is the wavelike statistics for pilot-wave dynamics in a confined domain. We present a one dimensional water wave model for a droplet bouncing in a confined domain. The mathematical model makes use of conformal mapping which allows for the presence of submerged barriers. The computational simulations produce tunneling events. Work supported by CNPq grant 454027/2008-7 and by FAPERJ Cientistas do Nosso Estado grant 102917/2011.

Entanglement entropy of 2D conformal quantum critical points: hearing the shape of a quantum drum.

PubMed

Fradkin, Eduardo; Moore, Joel E

2006-08-04

The entanglement entropy of a pure quantum state of a bipartite system A union or logical sumB is defined as the von Neumann entropy of the reduced density matrix obtained by tracing over one of the two parts. In one dimension, the entanglement of critical ground states diverges logarithmically in the subsystem size, with a universal coefficient that for conformally invariant critical points is related to the central charge of the conformal field theory. We find that the entanglement entropy of a standard class of z=2 conformal quantum critical points in two spatial dimensions, in addition to a nonuniversal "area law" contribution linear in the size of the AB boundary, generically has a universal logarithmically divergent correction, which is completely determined by the geometry of the partition and by the central charge of the field theory that describes the critical wave function.

Conformational dependence of a protein kinase phosphate transfer reaction

NASA Astrophysics Data System (ADS)

Labute, Montiago; Henkelman, Graeme; Tung, Chang-Shung; Fenimore, Paul; McMahon, Ben

2007-03-01

Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase have been calculated using plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In TC, we calculate that the reactants and products are nearly isoenergetic with a 20-kJ/mol barrier, whereas phosphate transfer is unfavorable by 120 kJ/mol in the RC, with an even higher barrier. Our results demonstrate that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an angstrom in the catalytic site [1]. [1] G.H. Henkelman, M.X. LaBute, C.-S. Tung, P.W. Fenimore, B.H. McMahon, Proc. Natl. Acad. Sci. USA vol. 102, no. 43:15347-15351 (2005).

Self-Focusing and the Talbot Effect in Conformal Transformation Optics.

PubMed

Wang, Xiangyang; Chen, Huanyang; Liu, Hui; Xu, Lin; Sheng, Chong; Zhu, Shining

2017-07-21

Transformation optics has been used to propose various novel optical devices. With the help of metamaterials, several intriguing designs, such as invisibility cloaks, have been implemented. However, as the basic units should be much smaller than the working wavelengths to achieve the effective material parameters, and the sizes of devices should be much larger than the wavelengths of illumination to work within the light-ray approximation, it is a big challenge to implement an experimental system that works simultaneously for both geometric optics and wave optics. In this Letter, by using a gradient-index microstructured optical waveguide, we realize a device of conformal transformation optics (CTO) and demonstrate its self-focusing property for geometry optics and the Talbot effect for wave optics. In addition, the Talbot effect in such a system has a potential application to transfer digital information without diffraction. Our findings demonstrate the photon controlling ability of CTO in a feasible experiment system.

Self-Focusing and the Talbot Effect in Conformal Transformation Optics

NASA Astrophysics Data System (ADS)

Wang, Xiangyang; Chen, Huanyang; Liu, Hui; Xu, Lin; Sheng, Chong; Zhu, Shining

2017-07-01

Transformation optics has been used to propose various novel optical devices. With the help of metamaterials, several intriguing designs, such as invisibility cloaks, have been implemented. However, as the basic units should be much smaller than the working wavelengths to achieve the effective material parameters, and the sizes of devices should be much larger than the wavelengths of illumination to work within the light-ray approximation, it is a big challenge to implement an experimental system that works simultaneously for both geometric optics and wave optics. In this Letter, by using a gradient-index microstructured optical waveguide, we realize a device of conformal transformation optics (CTO) and demonstrate its self-focusing property for geometry optics and the Talbot effect for wave optics. In addition, the Talbot effect in such a system has a potential application to transfer digital information without diffraction. Our findings demonstrate the photon controlling ability of CTO in a feasible experiment system.

Electromagnetic retroreflection augmented by spherical and conical metasurfaces

NASA Astrophysics Data System (ADS)

Shang, Yuping; Shen, Zhongxiang

2017-11-01

The focus of this paper is on phase gradient metasurfaces conformal to spherical and conical bodies of revolution, with an aim of engineering retroreflections and therefore augmenting backscattering cross-sections of those three-dimensional geometries under the illumination of a plane electromagnetic wave. Based on the conducting sphere and cone, the effect of the geometric revolution property on the selection of the unit inclusion of metasurfaces is considered. The procedure for using the selected unit inclusion to implement the proper reflection phase gradient onto the illuminated surfaces of those objects is formulated in detail. Retroreflections resembling conducting plates under normal incidence are observed for both the conducting sphere and cone coated with conformal metasurfaces. As a result, the redirection-induced retroreflection effectively contributes to the backscattering cross-section enhancement. A good agreement between full-wave simulations and measurements demonstrates the validity and effectiveness of backscattering cross-section enhancement using spherical and conical metasurfaces.

Travelling-wave ion mobility and negative ion fragmentation of high mannose N-glycans

PubMed Central

Harvey, David J.; Scarff, Charlotte A.; Edgeworth, Matthew; Struwe, Weston B.; Pagel, Kevin; Thalassinos, Konstantinos; Crispin, Max; Scrivens, Jim

2016-01-01

The isomeric structure of high-mannose N-glycans can significantly impact biological recognition events. Here, the utility of travelling-wave ion mobility-mass spectrometry (TW IM-MS)for isomer separation of high-mannose N-glycans is investigated. Negative ion fragmentation using collision-induced dissociation (CID) gave more informative spectra than positive ion spectra with mass-different fragment ions characterizing many of the isomers. Isomer separation by ion mobility in both ionization modes was generally limited, with the arrival time distributions (ATD) often showing little sign of isomers. However, isomers could be partially resolved by plotting extracted fragment ATDs of the diagnostic fragment ions from the negative ion spectra and the fragmentation spectra of the isomers could be extracted by using ions from limited areas of the ATD peak. In some cases, asymmetric ATDs were observed but no isomers could be detected by fragmentation. In these cases, it was assumed that conformers were being separated. Collision cross sections (CCSs) of the isomers in positive and negative fragmentation mode were estimated from TW IM-MS data using dextran glycans as calibrant. More complete CCS data were achieved in negative ion mode by utilizing the diagnostic fragment ions. Examples of isomer separations are shown for N-glycans released from the well-characterized glycoproteins chicken ovalbumin, porcine thyroglobulin and gp120 from the human immunodeficiency virus. In addition to the cross sectional data, details of the negative ion collision-induced dissociation (CID) spectra of all resolved isomers are discussed. PMID:26956389

Teaching graphical simulations of Fourier series expansion of some periodic waves using spreadsheets

NASA Astrophysics Data System (ADS)

Singh, Iqbal; Kaur, Bikramjeet

2018-05-01

The present article demonstrates a way of programming using an Excel spreadsheet to teach Fourier series expansion in school/colleges without the knowledge of any typical programming language. By using this, a student learns to approximate partial sum of the n terms of Fourier series for some periodic signals such as square wave, saw tooth wave, half wave rectifier and full wave rectifier signals.

A Traveling Wave Ion Mobility Spectrometry (TWIMS) Study of the Robo1-Heparan Sulfate Interaction

NASA Astrophysics Data System (ADS)

Zhao, Yuejie; Yang, Jeong Yeh; Thieker, David F.; Xu, Yongmei; Zong, Chengli; Boons, Geert-Jan; Liu, Jian; Woods, Robert J.; Moremen, Kelley W.; Amster, I. Jonathan

2018-03-01

Roundabout 1 (Robo1) interacts with its receptor Slit to regulate axon guidance, axon branching, and dendritic development in the nervous system and to regulate morphogenesis and many cell functions in the nonneuronal tissues. This interaction is known to be critically regulated by heparan sulfate (HS). Previous studies suggest that HS is required to promote the binding of Robo1 to Slit to form the minimal signaling complex, but the molecular details and the structural requirements of HS for this interaction are still unclear. Here, we describe the application of traveling wave ion mobility spectrometry (TWIMS) to study the conformational details of the Robo1-HS interaction. The results suggest that Robo1 exists in two conformations that differ by their compactness and capability to interact with HS. The results also suggest that the highly flexible interdomain hinge region connecting the Ig1 and Ig2 domains of Robo1 plays an important functional role in promoting the Robo1-Slit interaction. Moreover, variations in the sulfation pattern and size of HS were found to affect its binding affinity and selectivity to interact with different conformations of Robo1. Both MS measurements and CIU experiments show that the Robo1-HS interaction requires the presence of a specific size and pattern of modification of HS. Furthermore, the effect of N-glycosylation on the conformation of Robo1 and its binding modes with HS is reported. [Figure not available: see fulltext.

Tapping of Love waves in an isotropic surface waveguide by surface-to-bulk wave transduction.

NASA Technical Reports Server (NTRS)

Tuan, H.-S.; Chang, C.-P.

1972-01-01

A theoretical study of tapping a Love wave in an isotropic microacoustic surface waveguide is given. The surface Love wave is tapped by partial transduction into a bulk wave at a discontinuity. It is shown that, by careful design of the discontinuity, the converted bulk wave power and the radiation pattern may be controlled. General formulas are derived for the calculation of these important characteristics from a relatively general surface contour deformation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Workman, Ron L.; Briscoe, William J.; Strakovsky, Igor I.

Energy-dependent and single-energy fits to the existing nucleon-nucleon database have been updated to incorporate recent measurements. The fits cover a region from threshold to 3 GeV, in the laboratory kinetic energy, for proton-proton scattering, with an upper limit of 1.3 GeV for neutron-proton scattering. Experiments carried out at the COSY-WASA and COSY-ANKE facilities have had a significant impact on the partial-wave solutions. Lastly, results are discussed in terms of both partial-wave and direct reconstruction amplitudes.

a Partial Wave Analysis of the Reaction Negative Pion Proton ---> Positive Pion Negative Pion Neutral Pion Neutron at 8.45 Gev/c.

NASA Astrophysics Data System (ADS)

Dankowych, John Alexander

1980-06-01

We have performed an isobar model partial wave analysis (PWA) of a high statistics sample of the reaction (pi)('-)p (,(--->)) (pi)('+)(pi)('-)(pi)('0)n at 8.45 GeV/c. We present strong evidence for the existence of the unnatural parity, isoscalar (H) and isovector (A(,1)) axial-vector mesons. The intensity distributions show significant structure while the forward phase motion relative to the isospin-2 axial-vector partial wave is consistent with that expected for Breit-Wigner resonances. The A(,1) production is mainly via M = 1, natural parity exchange while the H is produced mainly in M = 0, natural parity exchange. From a Deck model fit we obtain for the A(,1) a mass of 1241 (+OR-) 80 MeV and a width of 380 (+OR-) 100 MeV; for the H we obtain a mass of 1194 (+OR-) 55 MeV and a width of 320 (+OR-) 50 MeV. In nucleon spin flip we have evidence for an isovector, pseudoscalar resonance ((pi)') under the A(,2). The natural parity states : the (omega)(IJP = 01-), the A(,2) (IJP = 12+) and the (omega)(,g )(IJP = 03-) are strong features of the data. In the IJP = 01- partial wave thre is more cross-section than that expected for just the (omega)(783) tail.

Conformational plasticity of DM43, a metalloproteinase inhibitor from Didelphis marsupialis: chemical and pressure-induced equilibrium (un)folding studies.

PubMed

Chapeaurouge, Alex; Martins, Samantha M; Holub, Oliver; Rocha, Surza L G; Valente, Richard H; Neves-Ferreira, Ana G C; Ferreira, Sérgio T; Domont, Gilberto B; Perales, Jonas

2009-10-01

We have investigated the folding of DM43, a homodimeric metalloproteinase inhibitor isolated from the serum of the South American opossum Didelphis marsupialis. Denaturation of the protein induced by GdnHCl (guanidine hydrochloride) was monitored by extrinsic and intrinsic fluorescence spectroscopy. While the equilibrium (un)folding of DM43 followed by tryptophan fluorescence was well described by a cooperative two-state transition, bis-ANS (4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid) fluorescence measurements revealed an intensity maximum at the midpoint of the unfolding transition (2 M GdnHCl), indicating a partially folded intermediate state. We further investigated the DM43 intermediate stabilized at 2 M GdnHCl using size exclusion chromatography. This analysis revealed that the folding intermediate can be best described as partially folded DM43 monomers. Thermodynamic analysis of the GdnHCl-induced denaturation of DM43 revealed Gibbs free-energy changes of 13.57 kcal/mol for dimer dissociation and 1.86 kcal/mol for monomer unfolding, pointing to a critical role of dimerization as a determinant of the structure and stability of this protein. In addition, by using hydrostatic pressure (up to 3.5 kbar) we were able to stabilize partially folded states different from those stabilized in the presence of GdnHCl. Taken together, these results indicate that the conformational plasticity of DM43 could provide this protein with the ability to adapt its conformation to a variety of different environments and biological partners during its biological lifetime.

Hexafluoroisopropanol-induced helix-sheet transition of stem bromelain: correlation to function.

PubMed

Dave, Sandeep; Dkhar, H Kitdorlang; Singh, Manvendra Pratap; Gupta, Garima; Chandra, Vemika; Mahajan, Sahil; Gupta, Pawan

2010-06-01

Stem bromelain is a proteolytic phytoprotein with a variety of therapeutic effects. Understanding its structural properties could provide insight into the mechanisms underlying its clinical utility. Stem bromelain was evaluated for its conformational and folding properties at the pH conditions it encounters when administered orally. It exists as a partially folded intermediate at pH 2.0. The conformational changes to this intermediate state were evaluated using fluorinated alcohols known to induce changes similar to those seen in vivo. Studies using circular dichroism, fluorescence emission spectroscopy, binding of the hydrophobic dye 1-anilino-8-naphthalene sulfonic acid and mass spectrometry indicate that treatment with 10-30% hexafluoroisopropanol induces the partially folded intermediate to adopt much of the native protein's secondary structure, but only a rudimentary tertiary structure, characteristic of the molten globule state. Addition of slightly higher concentrations of hexafluoroisopropanol caused transformation from an alpha-helix to a beta-sheet and induced formation of a compact nonnative structure. This nonnative form was more inhibitory of cell survival than either the native or the partially folded intermediate forms, as measured by enhanced suppression of proliferative cues (e.g., extracellular-signal-regulated kinase) and initiation of apoptotic events. The nonnative form also showed better antitumorigenic properties, as evaluated using an induced two-stage mouse skin papilloma model. In contrast, the nonnative state showed only a fraction of the proteolytic activity of the native form. This study demonstrates that hexafluoroisopropanol can induce a conformational change in stem bromelain to a form with potentially useful therapeutic properties different from those of the native protein. Copyright 2010 Elsevier Ltd. All rights reserved.

Dissipative instability in a partially ionised prominence plasma slab

NASA Astrophysics Data System (ADS)

Ballai, I.; Pintér, B.; Oliver, R.; Alexandrou, M.

2017-07-01

Aims: We aim to investigate the nature of dissipative instability appearing in a prominence planar thread filled with partially ionised plasma in the incompressible limit. The importance of partial ionisation is investigated in terms of the ionisation factor and the wavelength of sausage and kink waves propagating in the slab. Methods: In order to highlight the role of partial ionisation, we have constructed models describing various situations we can meet in solar prominence fine structure. Matching the solutions for the transversal component of the velocity and total pressure at the interfaces between the prominence slab and surrounding plasmas, we derived a dispersion relation whose imaginary part describes the evolution of the instability. Results were obtained in the limit of weak dissipation. We have investigated the appearance of instabilities in prominence dark plumes using single and two-fluid approximations. Results: Using simple analytical methods, we show that dissipative instabilities appear for flow speeds that are less than the Kelvin-Helmholtz instability threshold. The onset of instability is determined by the equilibrium flow strength, the ionisation factor of the plasma, the wavelength of waves and the ion-neutral collisional rate. For a given wavelength and for ionisation degrees closer to a neutral gas, the propagating waves become unstable for a narrow band of flow speeds, meaning that neutrals have a stabilising effect. Our results show that the partially ionised plasma describing prominence dark plumes becomes unstable only in a two-fluid (charged particles-neutrals) model, that is for periods that are smaller than the ion-neutral collision time. Conclusions: The present study improves our understanding of the complexity of dynamical processes and stability of solar prominences and the role partial ionisation in destabilising the plasma. We showed the necessity of two-fluid approximation when discussing the nature of instabilities: waves in a single fluid approximation show a great deal of stability. Our results clearly show that the problem of partial ionisation introduces new aspects of plasma stability with consequences on the evolution of partially ionised plasmas and solar prominences, in particular.

Partial Reflection and Trapping of a Fast-mode Wave in Solar Coronal Arcade Loops

NASA Astrophysics Data System (ADS)

Kumar, Pankaj; Innes, D. E.

2015-04-01

We report on the first direct observation of a fast-mode wave propagating along and perpendicular to cool (171 Å) arcade loops observed by the Solar Dynamics Observatory/Atmospheric Imaging Assembly (AIA). The wave was associated with an impulsive/compact flare near the edge of a sunspot. The EUV wavefront expanded radially outward from the flare center and decelerated in the corona from 1060 to 760 km s-1 within ˜3-4 minutes. Part of the EUV wave propagated along a large-scale arcade of cool loops and was partially reflected back to the flare site. The phase speed of the wave was about 1450 km s-1, which is interpreted as a fast-mode wave. A second overlying loop arcade, orientated perpendicular to the cool arcade, is heated and becomes visible in the AIA hot channels. These hot loops sway in time with the EUV wave, as it propagated to and fro along the lower loop arcade. We suggest that an impulsive energy release at one of the footpoints of the arcade loops causes the onset of an EUV shock wave that propagates along and perpendicular to the magnetic field.

THE CM-, MM-, AND SUB-MM-WAVE SPECTRUM OF ALLYL ISOCYANIDE AND RADIOASTRONOMICAL OBSERVATIONS IN ORION KL AND THE SgrB2 LINE SURVEYS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haykal, I.; Margulès, L.; Huet, T. R.

2013-11-10

Organic isocyanides have an interesting astrochemistry and some of these molecules have been detected in the interstellar medium (ISM). However, rotational spectral data for this class of compounds are still scarce. We provide laboratory spectra of the four-carbon allyl isocyanide covering the full microwave region, thus allowing a potential astrophysical identification in the ISM. We assigned the rotational spectrum of the two cis (synperiplanar) and gauche (anticlinal) conformations of allyl isocyanide in the centimeter-wave region (4-18 GHz), resolved its {sup 14}N nuclear quadrupole coupling (NQC) hyperfine structure, and extended the measurements into the millimeter and submillimeter-wave (150-900 GHz) ranges formore » the title compound. Rotational constants for all the monosubstituted {sup 13}C and {sup 15}N isotopologues are additionally provided. Laboratory observations are supplemented with initial radioastronomical observations. Following analysis of an extensive dataset (>11000 rotational transitions), accurate ground-state molecular parameters are reported for the cis and gauche conformations of the molecule, including rotational constants, NQC parameters, and centrifugal distortion terms up to octic contributions. Molecular parameters have also been obtained for the two first excited states of the cis conformation, with a dataset of more than 3300 lines. The isotopic data allowed determining substitution and effective structures for the title compound. We did not detect allyl isocyanide either in the IRAM 30 m line survey of Orion KL or in the PRIMOS survey toward SgrB2. Nevertheless, we provided an upper limit to its column density in Orion KL.« less

Analysis of the Conformally Flat Approximation for Binary Neutron Star Initial Conditions

DOE PAGES

Suh, In-Saeng; Mathews, Grant J.; Haywood, J. Reese; ...

2017-01-09

The spatially conformally flat approximation (CFA) is a viable method to deduce initial conditions for the subsequent evolution of binary neutron stars employing the full Einstein equations. Here in this paper, we analyze the viability of the CFA for the general relativistic hydrodynamic initial conditions of binary neutron stars. We illustrate the stability of the conformally flat condition on the hydrodynamics by numerically evolving ~100 quasicircular orbits. We illustrate the use of this approximation for orbiting neutron stars in the quasicircular orbit approximation to demonstrate the equation of state dependence of these initial conditions and how they might affect themore » emergent gravitational wave frequency as the stars approach the innermost stable circular orbit.« less

The Structure of a High Fidelity DNA Polymerase Bound to a Mismatched Nucleotide Reveals an “Ajar” Intermediate Conformation in the Nucleotide Selection Mechanism*

PubMed Central

Wu, Eugene Y.; Beese, Lorena S.

2011-01-01

To achieve accurate DNA synthesis, DNA polymerases must rapidly sample and discriminate against incorrect nucleotides. Here we report the crystal structure of a high fidelity DNA polymerase I bound to DNA primer-template caught in the act of binding a mismatched (dG:dTTP) nucleoside triphosphate. The polymerase adopts a conformation in between the previously established “open” and “closed” states. In this “ajar” conformation, the template base has moved into the insertion site but misaligns an incorrect nucleotide relative to the primer terminus. The displacement of a conserved active site tyrosine in the insertion site by the template base is accommodated by a distinctive kink in the polymerase O helix, resulting in a partially open ternary complex. We suggest that the ajar conformation allows the template to probe incoming nucleotides for complementarity before closure of the enzyme around the substrate. Based on solution fluorescence, kinetics, and crystallographic analyses of wild-type and mutant polymerases reported here, we present a three-state reaction pathway in which nucleotides either pass through this intermediate conformation to the closed conformation and catalysis or are misaligned within the intermediate, leading to destabilization of the closed conformation. PMID:21454515

Conformational analysis of HAMLET, the folding variant of human alpha-lactalbumin associated with apoptosis.

PubMed

Casbarra, Annarita; Birolo, Leila; Infusini, Giuseppe; Dal Piaz, Fabrizio; Svensson, Malin; Pucci, Piero; Svanborg, Catharina; Marino, Gennaro

2004-05-01

A combination of hydrogen/deuterium (H/D) exchange and limited proteolysis experiments coupled to mass spectrometry analysis was used to depict the conformation in solution of HAMLET, the folding variant of human alpha-lactalbumin, complexed to oleic acid, that induces apoptosis in tumor and immature cells. Although near- and far-UV CD and fluorescence spectroscopy were not able to discriminate between HAMLET and apo-alpha-lactalbumin, H/D exchange experiments clearly showed that they correspond to two distinct conformational states, with HAMLET incorporating a greater number of deuterium atoms than the apo and holo forms. Complementary proteolysis experiments revealed that HAMLET and apo are both accessible to proteases in the beta-domain but showed substantial differences in accessibility to proteases at specific sites. The overall results indicated that the conformational changes associated with the release of Ca2+ are not sufficient to induce the HAMLET conformation. Metal depletion might represent the first event to produce a partial unfolding in the beta-domain of alpha-lactalbumin, but some more unfolding is needed to generate the active conformation HAMLET, very likely allowing the protein to bind the C18:1 fatty acid moiety. On the basis of these data, a putative binding site of the oleic acid, which stabilizes the HAMLET conformation, is proposed.

Gas-phase spectroscopy of synephrine by laser desorption supersonic jet technique.

PubMed

Ishiuchi, Shun-ichi; Asakawa, Toshiro; Mitsuda, Haruhiko; Miyazaki, Mitsuhiko; Chakraborty, Shamik; Fujii, Masaaki

2011-09-22

In our previous work, we found that synephrine has six conformers in the gas phase, while adrenaline, which is a catecholamine and has the same side chain as synephrine, has been reported to have only two conformers. To determine the conformational geometries of synephrine, we measured resonance enhanced multiphoton ionization, ultraviolet-ultraviolet hole burning, and infrared dip spectra by utilizing the laser desorption supersonic jet technique. By comparing the observed infrared spectra with theoretical ones, we assigned geometries except for the orientations of the phenolic OH group. Comparison between the determined structures of synephrine and those of 2-methylaminno-1-phenylethanol, which has the same side chain as synephrine but no phenol OH group, leads to the conclusion that the phenolic OH group in synephrine does not affect the conformational flexibility of the side chain. In the case of adrenaline, which is expected to have 12 conformers if there are no interactions between the catecholic OH groups and the side chain, some interactions possibly exist between them because only two conformations are observed. By estimation of the dipole-dipole interaction energy between partial dipole moments of the catecholic OH groups and the side chain, it was concluded that the dipole-dipole interaction stabilizes specific conformers which are actually observed. © 2011 American Chemical Society

Quantifying polymer deformation in viscoelastic turbulence: the geometric decomposition and a Riemannian approach to scalar measures

NASA Astrophysics Data System (ADS)

Hameduddin, Ismail; Meneveau, Charles; Zaki, Tamer; Gayme, Dennice

2017-11-01

We develop a new framework to quantify the fluctuating behaviour of the conformation tensor in viscoelastic turbulent flows. This framework addresses two shortcomings of the classical approach based on Reynolds decomposition: the fluctuating part of the conformation tensor is not guaranteed to be positive definite and it does not consistently represent polymer expansions and contractions about the mean. Our approach employs a geometric decomposition that yields a positive-definite fluctuating conformation tensor with a clear physical interpretation as a deformation to the mean conformation. We propose three scalar measures of this fluctuating conformation tensor, which respect the non-Euclidean Riemannian geometry of the manifold of positive-definite tensors: fluctuating polymer volume, geodesic distance from the mean, and an anisotropy measure. We use these scalar quantities to investigate drag-reduced viscoelastic turbulent channel flow. Our approach establishes a systematic method to study viscoelastic turbulence. It also uncovers interesting phenomena that are not apparent using traditional analysis tools, including a logarithmic decrease in anisotropy of the mean conformation tensor away from the wall and polymer fluctuations peaking beyond the buffer layer. This work has been partially funded by the following NSF Grants: CBET-1652244, OCE-1633124, CBET-1511937.

The K-π+ S-wave from the D+→K-π+π+ decay

NASA Astrophysics Data System (ADS)

FOCUS Collaboration; Link, J. M.; Yager, P. M.; Anjos, J. C.; Bediaga, I.; Castromonte, C.; Machado, A. A.; Magnin, J.; Massafferri, A.; de Miranda, J. M.; Pepe, I. M.; Polycarpo, E.; Dos Reis, A. C.; Carrillo, S.; Cuautle, E.; Sánchez-Hernández, A.; Uribe, C.; Vázquez, F.; Agostino, L.; Cinquini, L.; Cumalat, J. P.; Frisullo, V.; O'Reilly, B.; Segoni, I.; Stenson, K.; Butler, J. N.; Cheung, H. W. K.; Chiodini, G.; Gaines, I.; Garbincius, P. H.; Garren, L. A.; Gottschalk, E.; Kasper, P. H.; Kreymer, A. E.; Kutschke, R.; Wang, M.; Benussi, L.; Bianco, S.; Fabbri, F. L.; Zallo, A.; Casimiro, E.; Reyes, M.; Cawlfield, C.; Kim, D. Y.; Rahimi, A.; Wiss, J.; Gardner, R.; Kryemadhi, A.; Chung, Y. S.; Kang, J. S.; Ko, B. R.; Kwak, J. W.; Lee, K. B.; Cho, K.; Park, H.; Alimonti, G.; Barberis, S.; Boschini, M.; Cerutti, A.; D'Angelo, P.; Dicorato, M.; Dini, P.; Edera, L.; Erba, S.; Inzani, P.; Leveraro, F.; Malvezzi, S.; Menasce, D.; Mezzadri, M.; Moroni, L.; Pedrini, D.; Pontoglio, C.; Prelz, F.; Rovere, M.; Sala, S.; Davenport, T. F.; Arena, V.; Boca, G.; Bonomi, G.; Gianini, G.; Liguori, G.; Pegna, D. Lopes; Merlo, M. M.; Pantea, D.; Ratti, S. P.; Riccardi, C.; Vitulo, P.; Göbel, C.; Otalora, J.; Hernandez, H.; Lopez, A. M.; Mendez, H.; Paris, A.; Quinones, J.; Ramirez, J. E.; Zhang, Y.; Wilson, J. R.; Handler, T.; Mitchell, R.; Engh, D.; Hosack, M.; Johns, W. E.; Luiggi, E.; Moore, J. E.; Nehring, M.; Sheldon, P. D.; Vaandering, E. W.; Webster, M.; Sheaff, M.

2009-10-01

Using data from FOCUS (E831) experiment at Fermilab, we present a model independent partial-wave analysis of the K-π+ S-wave amplitude from the decay D+→K-π+π+. The S-wave is a generic complex function to be determined directly from the data fit. The P- and D-waves are parameterized by a sum of Breit-Wigner amplitudes. The measurement of the S-wave amplitude covers the whole elastic range of the K-π+ system.

Crustal Structure of the Iceland Region from Spectrally Correlated Free-air and Terrain Gravity Data

NASA Technical Reports Server (NTRS)

Leftwich, T. E.; vonFrese, R. R. R. B.; Potts, L. V.; Roman, D. R.; Taylor, Patrick T.

2003-01-01

Seismic refraction studies have provided critical, but spatially restricted constraints on the structure of the Icelandic crust. To obtain a more comprehensive regional view of this tectonically complicated area, we spectrally correlated free-air gravity anomalies against computed gravity effects of the terrain for a crustal thickness model that also conforms to regional seismic and thermal constraints. Our regional crustal thickness estimates suggest thickened crust extends up to 500 km on either side of the Greenland-Scotland Ridge with the Iceland-Faeroe Ridge crust being less extended and on average 3-5 km thinner than the crust of the Greenland-Iceland Ridge. Crustal thickness estimates for Iceland range from 25-35 km in conformity with seismic predictions of a cooler, thicker crust. However, the deepening of our gravity-inferred Moho relative to seismic estimates at the thermal plume and rift zones of Iceland suggests partial melting. The amount of partial melting may range from about 8% beneath the rift zones to perhaps 20% above the plume core where mantle temperatures may be 200-400 C above normal. Beneath Iceland, areally limited regions of partial melting may also be compositionally and mechanically layered

The role of family communication in individual health attitudes and behaviors concerning diet and physical activity.

PubMed

Baiocchi-Wagner, Elizabeth A; Talley, Amelia E

2013-01-01

This study explored associations among family communication patterns (conversation and conformity orientations), health-specific communication variables, health attitudes, and health behaviors in a sample of 433 family dyads (N = 866). As expected, results of multilevel models revealed that individuals' health attitudes were strongly associated with their self-reported health behaviors. Findings also suggested that perceived confirmation from a family member during health-specific conversations (a) directly influenced health attitudes, (b) partially accounted for the positive relationship between family conversation orientation and health attitudes, and (c) partially accounted for the inverse relationship between family conformity orientation and health attitudes. Similarly, frequency of health-specific communication (a) directly influenced health attitudes, (b) partially accounted for the positive relationship between family conversation orientation and health attitudes, and (c) directly associated with health behaviors. Results from an actor-partner interdependence model (APIM) supported the aforementioned within-person association between a person's own health attitudes and health behaviors, as well as a positive relationship between young adults' health attitudes and their influential family member's health behaviors. Implications of these findings are discussed as they relate to theory and obesity prevention.

Can misfolded proteins be beneficial? The HAMLET case.

PubMed

Pettersson-Kastberg, Jenny; Aits, Sonja; Gustafsson, Lotta; Mossberg, Anki; Storm, Petter; Trulsson, Maria; Persson, Filip; Mok, K Hun; Svanborg, Catharina

2009-01-01

By changing the three-dimensional structure, a protein can attain new functions, distinct from those of the native protein. Amyloid-forming proteins are one example, in which conformational change may lead to fibril formation and, in many cases, neurodegenerative disease. We have proposed that partial unfolding provides a mechanism to generate new and useful functional variants from a given polypeptide chain. Here we present HAMLET (Human Alpha-lactalbumin Made LEthal to Tumor cells) as an example where partial unfolding and the incorporation of cofactor create a complex with new, beneficial properties. Native alpha-lactalbumin functions as a substrate specifier in lactose synthesis, but when partially unfolded the protein binds oleic acid and forms the tumoricidal HAMLET complex. When the properties of HAMLET were first described they were surprising, as protein folding intermediates and especially amyloid-forming protein intermediates had been regarded as toxic conformations, but since then structural studies have supported functional diversity arising from a change in fold. The properties of HAMLET suggest a mechanism of structure-function variation, which might help the limited number of human protein genes to generate sufficient structural diversity to meet the diverse functional demands of complex organisms.

Synthesis and conformational studies of carrabiose and its 4'-sulphate and 2,4'-disulphate.

PubMed

Parra, E; Caro, H N; Jiménez-Barbero, J; Martín-Lomas, M; Bernabé, M

1990-12-15

Methyl alpha-carrabioside (13), and its 4-sulphate (19) and 2,4-disulphate (20) have been synthesised via glycosylation of methyl 3,6-anhydro-2-O-benzyl-alpha-D-galactopyranoside with 2,3,6-tri-O-acetyl-4-O-benzyl-beta-D-galactopyranosyl bromide and subsequent partial or complete debenzylation, sulphation, and deprotection of the resulting disaccharide derivatives. Conformational studies have been carried out on 13, 19, and 20 on the basis of 1D and 2D 1H-n.m.r. spectroscopy and molecular mechanics calculations.

Standing spin-wave mode structure and linewidth in partially disordered hexagonal arrays of perpendicularly magnetized sub-micron Permalloy discs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ross, N., E-mail: rossn2282@gmail.com; Kostylev, M., E-mail: mikhail.kostylev@uwa.edu.au; Stamps, R. L.

2014-09-21

Standing spin wave mode frequencies and linewidths in partially disordered perpendicular magnetized arrays of sub-micron Permalloy discs are measured using broadband ferromagnetic resonance and compared to analytical results from a single, isolated disc. The measured mode structure qualitatively reproduces the structure expected from the theory. Fitted demagnetizing parameters decrease with increasing array disorder. The frequency difference between the first and second radial modes is found to be higher in the measured array systems than predicted by theory for an isolated disc. The relative frequencies between successive spin wave modes are unaffected by reduction of the long-range ordering of discs inmore » the array. An increase in standing spin wave resonance linewidth at low applied magnetic fields is observed and grows more severe with increased array disorder.« less

Evidence for a magma reservoir beneath the Taipei metropolis of Taiwan from both S-wave shadows and P-wave delays

PubMed Central

Lin, Cheng-Horng

2016-01-01

There are more than 7 million people living near the Tatun volcano group in northern Taiwan. For the safety of the Taipei metropolis, in particular, it has been debated for decades whether or not these volcanoes are active. Here I show evidence of a deep magma reservoir beneath the Taipei metropolis from both S-wave shadows and P-wave delays. The reservoir is probably composed of either a thin magma layer overlay or many molten sills within thick partially molten rocks. Assuming that 40% of the reservoir is partially molten, its total volume could be approximately 350 km3. The exact location and geometry of the magma reservoir will be obtained after dense seismic arrays are deployed in 2017–2020. PMID:28008931

TU-CD-304-03: Dosimetric Verification and Preliminary Comparison of Dynamic Wave Arc for SBRT Treatments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burghelea, M; BRAINLAB AG, Munich; Babes Bolyai University, Cluj-Napoca

2015-06-15

Purpose: To evaluate the potential dosimetric benefits and verify the delivery accuracy of Dynamic Wave Arc, a novel treatment delivery approach for the Vero SBRT system. Methods: Dynamic Wave Arc (DWA) combines simultaneous movement of gantry/ring with inverse planning optimization, resulting in an uninterrupted non-coplanar arc delivery technique. Thirteen SBRT complex cases previously treated with 8–10 conformal static beams (CRT) were evaluated in this study. Eight primary centrally-located NSCLC (prescription dose 4×12Gy or 8×7.5Gy) and five oligometastatic cases (2×2 lesions, 10×5Gy) were selected. DWA and coplanar VMAT plans, partially with dual arcs, were generated for each patient using identical objectivemore » functions for target volumes and OARs on the same TPS (RayStation, RaySearch Laboratories). Dosimetric differences and delivery time among these three planning schemes were evaluated. The DWA delivery accuracy was assessed using the Delta4 diode array phantom (ScandiDos AB). The gamma analysis was performed with the 3%/3mm dose and distance-to-agreement criteria. Results: The target conformity for CRT, VMAT and DWA were 0.95±0.07, 0.96±0.04 and 0.97±0.04, while the low dose spillage gradient were 5.52±1.36, 5.44±1.11, and 5.09±0.98 respectively. Overall, the bronchus, esophagus and spinal cord maximum doses were similar between VMAT and DWA, but highly reduced compared with CRT. For the lung cases, the mean dose and V20Gy were lower for the arc techniques compares with CRT, while for the liver cases, the mean dose and the V30Gy presented slightly higher values. The average delivery time of VMAT and DWA were 2.46±1.10 min and 4.25±1.67 min, VMAT presenting shorter treatment time in all cases. The DWA dosimetric verification presented an average gamma index passing rate of 95.73±1.54% (range 94.2%–99.8%). Conclusion: Our preliminary data indicated that the DWA is deliverable with clinically acceptable accuracy and has the potential to further improve the plan quality. This collaborative work was supported by the Flemish government through the Hercules foundation and corporate funding from BrainLab AG. The first and the sixth author are financially supported by Brainlab AG. The other authors have no conflict of interest.« less

Calculation of total electron excitation cross-sections and partial electron ionization cross-sections for the elements. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Green, T. J.

1973-01-01

Computer programs were used to calculate the total electron excitation cross-section for atoms and the partial ionization cross-section. The approximations to the scattering amplitude used are as follows: (1) Born, Bethe, and Modified Bethe for non-exchange excitation; (2) Ochkur for exchange excitation; and (3) Coulomb-Born of non-exchange ionization. The amplitudes are related to the differential cross-sections which are integrated to give the total excitation (or partial ionization) cross-section for the collision. The atomic wave functions used are Hartree-Fock-Slater functions for bound states and the coulomb wave function for the continuum. The programs are presented and the results are examined.

The Lockheed alternate partial polarizer universal filter

NASA Technical Reports Server (NTRS)

Title, A. M.

1976-01-01

A tunable birefringent filter using an alternate partial polarizer design has been built. The filter has a transmission of 38% in polarized light. Its full width at half maximum is .09A at 5500A. It is tunable from 4500 to 8500A by means of stepping motor actuated rotating half wave plates and polarizers. Wave length commands and thermal compensation commands are generated by a PPD 11/10 minicomputer. The alternate partial polarizer universal filter is compared with the universal birefringent filter and the design techniques, construction methods, and filter performance are discussed in some detail. Based on the experience of this filter some conclusions regarding the future of birefringent filters are elaborated.

Validation of an Accurate Three-Dimensional Helical Slow-Wave Circuit Model

NASA Technical Reports Server (NTRS)

Kory, Carol L.

1997-01-01

The helical slow-wave circuit embodies a helical coil of rectangular tape supported in a metal barrel by dielectric support rods. Although the helix slow-wave circuit remains the mainstay of the traveling-wave tube (TWT) industry because of its exceptionally wide bandwidth, a full helical circuit, without significant dimensional approximations, has not been successfully modeled until now. Numerous attempts have been made to analyze the helical slow-wave circuit so that the performance could be accurately predicted without actually building it, but because of its complex geometry, many geometrical approximations became necessary rendering the previous models inaccurate. In the course of this research it has been demonstrated that using the simulation code, MAFIA, the helical structure can be modeled with actual tape width and thickness, dielectric support rod geometry and materials. To demonstrate the accuracy of the MAFIA model, the cold-test parameters including dispersion, on-axis interaction impedance and attenuation have been calculated for several helical TWT slow-wave circuits with a variety of support rod geometries including rectangular and T-shaped rods, as well as various support rod materials including isotropic, anisotropic and partially metal coated dielectrics. Compared with experimentally measured results, the agreement is excellent. With the accuracy of the MAFIA helical model validated, the code was used to investigate several conventional geometric approximations in an attempt to obtain the most computationally efficient model. Several simplifications were made to a standard model including replacing the helical tape with filaments, and replacing rectangular support rods with shapes conforming to the cylindrical coordinate system with effective permittivity. The approximate models are compared with the standard model in terms of cold-test characteristics and computational time. The model was also used to determine the sensitivity of various circuit parameters including typical manufacturing dimensional tolerances and support rod permittivity. By varying the circuit parameters of an accurate model using MAFIA, these sensitivities can be computed for manufacturing concerns, and design optimization previous to fabrication, thus eliminating the need for costly experimental iterations. Several variations were made to a standard helical circuit using MAFIA to investigate the effect that variations on helical tape and support rod width, metallized loading height and support rod permittivity, have on TWT cold-test characteristics.

Equivalent equations of motion for gravity and entropy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Czech, Bartlomiej; Lamprou, Lampros; McCandlish, Samuel

We demonstrate an equivalence between the wave equation obeyed by the entanglement entropy of CFT subregions and the linearized bulk Einstein equation in Anti-de Sitter space. In doing so, we make use of the formalism of kinematic space and fields on this space. We show that the gravitational dynamics are equivalent to a gauge invariant wave-equation on kinematic space and that this equation arises in natural correspondence to the conformal Casimir equation in the CFT.

Equivalent equations of motion for gravity and entropy

DOE PAGES

Czech, Bartlomiej; Lamprou, Lampros; McCandlish, Samuel; ...

2017-02-01

We demonstrate an equivalence between the wave equation obeyed by the entanglement entropy of CFT subregions and the linearized bulk Einstein equation in Anti-de Sitter space. In doing so, we make use of the formalism of kinematic space and fields on this space. We show that the gravitational dynamics are equivalent to a gauge invariant wave-equation on kinematic space and that this equation arises in natural correspondence to the conformal Casimir equation in the CFT.

Disentangling the dynamical origin of P11 nucleon resonances.

PubMed

Suzuki, N; Juliá-Díaz, B; Kamano, H; Lee, T-S H; Matsuyama, A; Sato, T

2010-01-29

We show that two almost degenerate poles near the piDelta threshold and the next higher mass pole in the P11 partial wave of piN scattering evolve from a single bare state through its coupling with piN, etaN, and pipiN reaction channels. This finding provides new information on understanding the dynamical origins of the Roper N{*}(1440) and N{*}(1710) resonances listed by Particle Data Group. Our results for the resonance poles in other piN partial waves are also presented.

S-matrix method for the numerical determination of bound states.

NASA Technical Reports Server (NTRS)

Bhatia, A. K.; Madan, R. N.

1973-01-01

A rapid numerical technique for the determination of bound states of a partial-wave-projected Schroedinger equation is presented. First, one needs to integrate the equation only outwards as in the scattering case, and second, the number of trials necessary to determine the eigenenergy and the corresponding eigenfunction is considerably less than in the usual method. As a nontrivial example of the technique, bound states are calculated in the exchange approximation for the e-/He+ system and l equals 1 partial wave.

Hidden conformal symmetry of rotating black holes in minimal five-dimensional gauged supergravity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Setare, M. R.; Kamali, V.

2010-10-15

In the present paper we show that for a low frequency limit the wave equation of a massless scalar field in the background of nonextremal charged rotating black holes in five-dimensional minimal gauged and ungauged supergravity can be written as the Casimir of an SL(2,R) symmetry. Our result shows that the entropy of the black hole is reproduced by the Cardy formula. Also the absorption cross section is consistent with the finite temperature absorption cross section for a two-dimensional conformal field theory.

Solving the Helmholtz equation in conformal mapped ARROW structures using homotopy perturbation method.

PubMed

Reck, Kasper; Thomsen, Erik V; Hansen, Ole

2011-01-31

The scalar wave equation, or Helmholtz equation, describes within a certain approximation the electromagnetic field distribution in a given system. In this paper we show how to solve the Helmholtz equation in complex geometries using conformal mapping and the homotopy perturbation method. The solution of the mapped Helmholtz equation is found by solving an infinite series of Poisson equations using two dimensional Fourier series. The solution is entirely based on analytical expressions and is not mesh dependent. The analytical results are compared to a numerical (finite element method) solution.

On irregular singularity wave functions and superconformal indices

NASA Astrophysics Data System (ADS)

Buican, Matthew; Nishinaka, Takahiro

2017-09-01

We generalize, in a manifestly Weyl-invariant way, our previous expressions for irregular singularity wave functions in two-dimensional SU(2) q-deformed Yang-Mills theory to SU( N). As an application, we give closed-form expressions for the Schur indices of all ( A N - 1 , A N ( n - 1)-1) Argyres-Douglas (AD) superconformal field theories (SCFTs), thus completing the computation of these quantities for the ( A N , A M ) SCFTs. With minimal effort, our wave functions also give new Schur indices of various infinite sets of "Type IV" AD theories. We explore the discrete symmetries of these indices and also show how highly intricate renormalization group (RG) flows from isolated theories and conformal manifolds in the ultraviolet to isolated theories and (products of) conformal manifolds in the infrared are encoded in these indices. We compare our flows with dimensionally reduced flows via a simple "monopole vev RG" formalism. Finally, since our expressions are given in terms of concise Lie algebra data, we speculate on extensions of our results that might be useful for probing the existence of hypothetical SCFTs based on other Lie algebras. We conclude with a discussion of some open problems.

Simultaneous quarter-wave plate and half-mirror operation through a highly flexible single layer anisotropic metasurface.

PubMed

Khan, M Ismail; Tahir, Farooq A

2017-11-22

A highly flexible single-layer metasurface manifesting quarter-wave plate as well as half-mirror (1:1 beam-splitter) operation in the microwave frequency regime is being presented in this research. The designed metasurface reflects half power of the impinging linearly polarized electromagnetic wave as circularly polarized wave while the remaining half power is transmitted as circularly polarized wave at resonance frequency. Similarly, a circularly polarized incident wave is reflected and transmitted as linearly polarized wave with equal half powers. Moreover, the response of the metasurface is quite stable against the variations in the incidence angle up to 45°. The measurements performed on the fabricated prototype exhibit a good agreement with the simulation results. The compact size, flexible structure, angular stability and two in one operation (operating as a quarter-wave plate and beam-splitter at the same time) are the main characteristics of the subject metasurface that makes it a potential candidate for numerous applications in communication and miniaturized and conformal polarization control devices.

The Third Wave: A Position Paper.

ERIC Educational Resources Information Center

Dyrud, Marilyn A.

2000-01-01

Describes the Third Wave as an "information bomb... exploding in our midst, showering us with a shrapnel of images and drastically changing the way each of us perceives and acts upon our private world." Begins with a description of A. Toffler's Third Wave as an attempt to partially explain what is happening in higher education,…

All-dielectric ultrathin conformal metasurfaces: lensing and cloaking applications at 532 nm wavelength

NASA Astrophysics Data System (ADS)

Cheng, Jierong; Jafar-Zanjani, Samad; Mosallaei, Hossein

2016-12-01

Metasurfaces are ideal candidates for conformal wave manipulation on curved objects due to their low profiles and rich functionalities. Here we design and analyze conformal metasurfaces for practical optical applications at 532 nm visible band for the first time. The inclusions are silicon disk nanoantennas embedded in a flexible supporting layer of polydimethylsiloxane (PDMS). They behave as local phase controllers in subwavelength dimensions for successful modification of electromagnetic responses point by point, with merits of high efficiency, at visible regime, ultrathin films, good tolerance to the incidence angle and the grid stretching due to the curvy substrate. An efficient modeling technique based on field equivalence principle is systematically proposed for characterizing metasurfaces with huge arrays of nanoantennas oriented in a conformal manner. Utilizing the robust nanoantenna inclusions and benefiting from the powerful analyzing tool, we successfully demonstrate the superior performances of the conformal metasurfaces in two specific areas, with one for lensing and compensation of spherical aberration, and the other carpet cloak, both at 532 nm visible spectrum.

Influence of two-stream relativistic electron beam parameters on the space-charge wave with broad frequency spectrum formation

NASA Astrophysics Data System (ADS)

Alexander, LYSENKO; Iurii, VOLK

2018-03-01

We developed a cubic non-linear theory describing the dynamics of the multiharmonic space-charge wave (SCW), with harmonics frequencies smaller than the two-stream instability critical frequency, with different relativistic electron beam (REB) parameters. The self-consistent differential equation system for multiharmonic SCW harmonic amplitudes was elaborated in a cubic non-linear approximation. This system considers plural three-wave parametric resonant interactions between wave harmonics and the two-stream instability effect. Different REB parameters such as the input angle with respect to focusing magnetic field, the average relativistic factor value, difference of partial relativistic factors, and plasma frequency of partial beams were investigated regarding their influence on the frequency spectrum width and multiharmonic SCW saturation levels. We suggested ways in which the multiharmonic SCW frequency spectrum widths could be increased in order to use them in multiharmonic two-stream superheterodyne free-electron lasers, with the main purpose of forming a powerful multiharmonic electromagnetic wave.

Application of hyperspherical harmonics expansion method to the low-lying bound S-states of exotic two-muon three-body systems

NASA Astrophysics Data System (ADS)

Khan, Md. Abdul

2014-09-01

In this paper, energies of the low-lying bound S-states (L = 0) of exotic three-body systems, consisting a nuclear core of charge +Ze (Z being atomic number of the core) and two negatively charged valence muons, have been calculated by hyperspherical harmonics expansion method (HHEM). The three-body Schrödinger equation is solved assuming purely Coulomb interaction among the binary pairs of the three-body systems XZ+μ-μ- for Z = 1 to 54. Convergence pattern of the energies have been checked with respect to the increasing number of partial waves Λmax. For available computer facilities, calculations are feasible up to Λmax = 28 partial waves, however, calculation for still higher partial waves have been achieved through an appropriate extrapolation scheme. The dependence of bound state energies has been checked against increasing nuclear charge Z and finally, the calculated energies have been compared with the ones of the literature.

Solution of two-body relativistic bound state equations with confining plus Coulomb interactions

NASA Technical Reports Server (NTRS)

Maung, Khin Maung; Kahana, David E.; Norbury, John W.

1992-01-01

Studies of meson spectroscopy have often employed a nonrelativistic Coulomb plus Linear Confining potential in position space. However, because the quarks in mesons move at an appreciable fraction of the speed of light, it is necessary to use a relativistic treatment of the bound state problem. Such a treatment is most easily carried out in momentum space. However, the position space Linear and Coulomb potentials lead to singular kernels in momentum space. Using a subtraction procedure we show how to remove these singularities exactly and thereby solve the Schroedinger equation in momentum space for all partial waves. Furthermore, we generalize the Linear and Coulomb potentials to relativistic kernels in four dimensional momentum space. Again we use a subtraction procedure to remove the relativistic singularities exactly for all partial waves. This enables us to solve three dimensional reductions of the Bethe-Salpeter equation. We solve six such equations for Coulomb plus Confining interactions for all partial waves.

Prestack reverse time migration for tilted transversely isotropic media

NASA Astrophysics Data System (ADS)

Jang, Seonghyung; Hien, Doan Huy

2013-04-01

According to having interest in unconventional resource plays, anisotropy problem is naturally considered as an important step for improving the seismic image quality. Although it is well known prestack depth migration for the seismic reflection data is currently one of the powerful tools for imaging complex geological structures, it may lead to migration error without considering anisotropy. Asymptotic analysis of wave propagation in transversely isotropic (TI) media yields a dispersion relation of couple P- and SV wave modes that can be converted to a fourth order scalar partial differential equation (PDE). By setting the shear wave velocity equal zero, the fourth order PDE, called an acoustic wave equation for TI media, can be reduced to couple of second order PDE systems and we try to solve the second order PDE by the finite difference method (FDM). The result of this P wavefield simulation is kinematically similar to elastic and anisotropic wavefield simulation. We develop prestack depth migration algorithm for tilted transversely isotropic media using reverse time migration method (RTM). RTM is a method for imaging the subsurface using inner product of source wavefield extrapolation in forward and receiver wavefield extrapolation in backward. We show the subsurface image in TTI media using the inner product of partial derivative wavefield with respect to physical parameters and observation data. Since the partial derivative wavefields with respect to the physical parameters require extremely huge computing time, so we implemented the imaging condition by zero lag crosscorrelation of virtual source and back propagating wavefield instead of partial derivative wavefields. The virtual source is calculated directly by solving anisotropic acoustic wave equation, the back propagating wavefield on the other hand is calculated by the shot gather used as the source function in the anisotropic acoustic wave equation. According to the numerical model test for a simple geological model including syncline and anticline, the prestack depth migration using TTI-RTM in weak anisotropic media shows the subsurface image is similar to the true geological model used to generate the shot gathers.

Multi-fluid Approach to High-frequency Waves in Plasmas. II. Small-amplitude Regime in Partially Ionized Media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martínez-Gómez, David; Soler, Roberto; Terradas, Jaume, E-mail: david.martinez@uib.es

2017-03-01

The presence of neutral species in a plasma has been shown to greatly affect the properties of magnetohydrodynamic waves. For instance, the interaction between ions and neutrals through momentum transfer collisions causes the damping of Alfvén waves and alters their oscillation frequency and phase speed. When the collision frequencies are larger than the frequency of the waves, single-fluid magnetohydrodynamic approximations can accurately describe the effects of partial ionization, since there is a strong coupling between the various species. However, at higher frequencies, the single-fluid models are not applicable and more complex approaches are required. Here, we use a five-fluid modelmore » with three ionized and two neutral components, which takes into consideration Hall’s current and Ohm’s diffusion in addition to the friction due to collisions between different species. We apply our model to plasmas composed of hydrogen and helium, and allow the ionization degree to be arbitrary. By analyzing the corresponding dispersion relation and numerical simulations, we study the properties of small-amplitude perturbations. We discuss the effect of momentum transfer collisions on the ion-cyclotron resonances and compare the importance of magnetic resistivity, and ion–neutral and ion–ion collisions on the wave damping at various frequency ranges. Applications to partially ionized plasmas of the solar atmosphere are performed.« less

Partially Unfolded Forms of the Prion Protein Populated under Misfolding-promoting Conditions

PubMed Central

Moulick, Roumita; Das, Ranabir; Udgaonkar, Jayant B.

2015-01-01

The susceptibility of the cellular prion protein (PrPC) to convert to an alternative misfolded conformation (PrPSc), which is the key event in the pathogenesis of prion diseases, is indicative of a conformationally flexible native (N) state. In the present study, hydrogen-deuterium exchange (HDX) in conjunction with mass spectrometry and nuclear magnetic resonance spectroscopy were used for the structural and energetic characterization of the N state of the full-length mouse prion protein, moPrP(23–231), under conditions that favor misfolding. The kinetics of HDX of 34 backbone amide hydrogens in the N state were determined at pH 4. In contrast to the results of previous HDX studies on the human and Syrian hamster prion proteins at a higher pH, various segments of moPrP were found to undergo different extents of subglobal unfolding events at pH 4, a pH at which the protein is known to be primed to misfold to a β-rich conformation. No residual structure around the disulfide bond was observed for the unfolded state at pH 4. The N state of the prion protein was observed to be at equilibrium with at least two partially unfolded forms (PUFs). These PUFs, which are accessed by stochastic fluctuations of the N state, have altered surface area exposure relative to the N state. One of these PUFs resembles a conformation previously implicated to be an initial intermediate in the conversion of monomeric protein into misfolded oligomer at pH 4. PMID:26306043

On some 3-point functions in the W 4 CFT and related braiding matrix

NASA Astrophysics Data System (ADS)

Furlan, P.; Petkova, V. B.

2015-12-01

We construct a class of 3-point constants in the sl(4) Toda conformal theory W 4, extending the examples in Fateev and Litvinov [1]. Their knowledge allows to determine the braiding/fusing matrix transforming 4-point conformal blocks of one fundamental, labelled by the 6-dimensional sl(4) representation, and three partially degenerate vertex operators. It is a 3 × 3 submatrix of the generic 6 × 6 fusing matrix consistent with the fusion rules for the particular class of representations. We check a braiding relation which has wider applications to conformal models with sl(4) symmetry. The 3-point constants in dual regions of central charge are compared in preparation for a BPS like relation in the widehat{sl}(4) WZW model.

Understanding the power reflection and transmission coefficients of a plane wave at a planar interface

NASA Astrophysics Data System (ADS)

Ye, Qian; Jiang, Yikun; Lin, Haoze

2017-03-01

In most textbooks, after discussing the partial transmission and reflection of a plane wave at a planar interface, the power (energy) reflection and transmission coefficients are introduced by calculating the normal-to-interface components of the Poynting vectors for the incident, reflected and transmitted waves, separately. Ambiguity arises among students since, for the Poynting vector to be interpreted as the energy flux density, on the incident (reflected) side, the electric and magnetic fields involved must be the total fields, namely, the sum of incident and reflected fields, instead of the partial fields which are just the incident (reflected) fields. The interpretation of the cross product of partial fields as energy flux has not been obviously justified in most textbooks. Besides, the plane wave is actually an idealisation that is only ever found in textbooks, then what do the reflection and transmission coefficients evaluated for a plane wave really mean for a real beam of limited extent? To provide a clearer physical picture, we exemplify a light beam of finite transverse extent by a fundamental Gaussian beam and simulate its reflection and transmission at a planar interface. Due to its finite transverse extent, we can then insert the incident fields or reflected fields as total fields into the expression of the Poynting vector to evaluate the energy flux and then power reflection and transmission coefficients. We demonstrate that the power reflection and transmission coefficients of a beam of finite extent turn out to be the weighted sum of the corresponding coefficients for all constituent plane wave components that form the beam. The power reflection and transmission coefficients of a single plane wave serve, in turn, as the asymptotes for the corresponding coefficients of a light beam as its width expands infinitely.

Group Velocity for Leaky Waves

NASA Astrophysics Data System (ADS)

Rzeznik, Andrew; Chumakova, Lyubov; Rosales, Rodolfo

2017-11-01

In many linear dispersive/conservative wave problems one considers solutions in an infinite medium which is uniform everywhere except for a bounded region. In general, localized inhomogeneities of the medium cause partial internal reflection, and some waves leak out of the domain. Often one only desires the solution in the inhomogeneous region, with the exterior accounted for by radiation boundary conditions. Formulating such conditions requires definition of the direction of energy propagation for leaky waves in multiple dimensions. In uniform media such waves have the form exp (d . x + st) where d and s are complex and related by a dispersion relation. A complex s is required since these waves decay via radiation to infinity, even though the medium is conservative. We present a modified form of Whitham's Averaged Lagrangian Theory along with modulation theory to extend the classical idea of group velocity to leaky waves. This allows for solving on the bounded region by representing the waves as a linear combination of leaky modes, each exponentially decaying in time. This presentation is part of a joint project, and applications of these results to example GFD problems will be presented by L. Chumakova in the talk ``Leaky GFD Problems''. This work is partially supported by NSF Grants DMS-1614043, DMS-1719637, and 1122374, and by the Hertz Foundation.

Application of ANNs approach for wave-like and heat-like equations

NASA Astrophysics Data System (ADS)

Jafarian, Ahmad; Baleanu, Dumitru

2017-12-01

Artificial neural networks are data processing systems which originate from human brain tissue studies. The remarkable abilities of these networks help us to derive desired results from complicated raw data. In this study, we intend to duplicate an efficient iterative method to the numerical solution of two famous partial differential equations, namely the wave-like and heat-like problems. It should be noted that many physical phenomena such as coupling currents in a flat multi-strand two-layer super conducting cable, non-homogeneous elastic waves in soils and earthquake stresses, are described by initial-boundary value wave and heat partial differential equations with variable coefficients. To the numerical solution of these equations, a combination of the power series method and artificial neural networks approach, is used to seek an appropriate bivariate polynomial solution of the mentioned initial-boundary value problem. Finally, several computer simulations confirmed the theoretical results and demonstrating applicability of the method.

Investigation of Solitary wave solutions for Vakhnenko-Parkes equation via exp-function and Exp(-ϕ(ξ))-expansion method.

PubMed

Roshid, Harun-Or; Kabir, Md Rashed; Bhowmik, Rajandra Chadra; Datta, Bimal Kumar

2014-01-01

In this paper, we have described two dreadfully important methods to solve nonlinear partial differential equations which are known as exp-function and the exp(-ϕ(ξ)) -expansion method. Recently, there are several methods to use for finding analytical solutions of the nonlinear partial differential equations. The methods are diverse and useful for solving the nonlinear evolution equations. With the help of these methods, we are investigated the exact travelling wave solutions of the Vakhnenko- Parkes equation. The obtaining soliton solutions of this equation are described many physical phenomena for weakly nonlinear surface and internal waves in a rotating ocean. Further, three-dimensional plots of the solutions such as solitons, singular solitons, bell type solitary wave i.e. non-topological solitons solutions and periodic solutions are also given to visualize the dynamics of the equation.

Initial-value problem for the Gardner equation applied to nonlinear internal waves

NASA Astrophysics Data System (ADS)

Rouvinskaya, Ekaterina; Kurkina, Oxana; Kurkin, Andrey; Talipova, Tatiana; Pelinovsky, Efim

2017-04-01

The Gardner equation is a fundamental mathematical model for the description of weakly nonlinear weakly dispersive internal waves, when cubic nonlinearity cannot be neglected. Within this model coefficients of quadratic and cubic nonlinearity can both be positive as well as negative, depending on background conditions of the medium, where waves propagate (sea water density stratification, shear flow profile) [Rouvinskaya et al., 2014, Kurkina et al., 2011, 2015]. For the investigation of weakly dispersive behavior in the framework of nondimensional Gardner equation with fixed (positive) sign of quadratic nonlinearity and positive or negative cubic nonlinearity {eq1} partial η/partial t+6η( {1± η} )partial η/partial x+partial ^3η/partial x^3=0, } the series of numerical experiments of initial-value problem was carried out for evolution of a bell-shaped impulse of negative polarity (opposite to the sign of quadratic nonlinear coefficient): {eq2} η(x,t=0)=-asech2 ( {x/x0 } ), for which amplitude a and width x0 was varied. Similar initial-value problem was considered in the paper [Trillo et al., 2016] for the Korteweg - de Vries equation. For the Gardner equation with different signs of cubic nonlinearity the initial-value problem for piece-wise constant initial condition was considered in detail in [Grimshaw et al., 2002, 2010]. It is widely known, for example, [Pelinovsky et al., 2007], that the Gardner equation (1) with negative cubic nonlinearity has a family of classic solitary wave solutions with only positive polarity,and with limiting amplitude equal to 1. Therefore evolution of impulses (2) of negative polarity (whose amplitudes a were varied from 0.1 to 3, and widths at the level of a/2 were equal to triple width of solitons with the same amplitude for a 1) was going on a universal scenario with the generation of nonlinear Airy wave. For the Gardner equation (1) with the positive cubic nonlinearity coefficient there exist two one-parametric families of solitons (family with positive polarity, and family with negative polarity bounded below by the amplitude of 2) and two-parametric family of breathers (oscillatory wave packets). In this case varying amplitude and width of bell-shaped initial impulse leads to plenty of different evolutionary scenarios with the generation of solitary waves, breathers, solibores and nonlinear Airy wave in their various combinations. Statistical analysis of the wave field in time shows almost permanent substantial exceedance of the level of the significant wave height in some position in spatial coordinate. Evolution of Fourier spectrum of the wave field is also analyzed, and its behavior after a long time of initial wave evolution demonstrates the power asymptotic for small wave numbers and exponential asymptotic for large wave numbers. The presented results of research are obtained with the support of the grant of the President of the Russian Federation for state support of the young Russian scientists - Candidates of Sciences (MK-5208.2016.5) and Russian Foundation for Basic Research grant 16-05-00049. References: Grimshaw R., Pelinovsky D., Pelinovsky E and Slunyaev A. Generation of large-amplitude solitons in the extended Korteweg-de Vries equation // Chaos, 2002. - V.12. - No 4. - 1070-1076. Grimshaw, R., Slunyaev, A., and Pelinovsky, E. Generation of solitons and breathers in the extended Korteweg-de Vries equation with positive cubic nonlinearity //Chaos, 2010. - vol. 20.-013102. Kurkina O.E., Kurkin A.A., Soomere T., Pelinovsky E.N., Rouvinskaya E.A. Higher-order (2+4) Korteweg-de Vries - like equation for interfacial waves in a symmetric three-layer fluid // Physics of Fluids, 2011. - Volume 23. - Issue 11. - p.116602--1--13. Kurkina O., Rouvinskaya E., Talipova T., Kurkin A., Pelinovsky E. Nonlinear disintegration of sine wave in the framework of the Gardner equation // Physica D: Nonlinear Phenomena, 2015. - doi:10.1016/j.physd.2015.12.007. Pelinovsky E., Polukhina O., Slunyaev A., Talipova T. Internal solitary waves // Chapter 4 in the book ``Solitary Waves in Fluids''. WIT Press. Southampton, Boston. 2007. P. 85 - 110. Rouvinskaya E., Kurkina O., Kurkin A. Dynamics of nonlinear internal gravity waves in layered fluids // NNSTU n.a. R.E. Alekseev Press - Nizhny Novgorod, 2014 - 160 p. [In Russian] Trillo S., Klein M., Clauss G., Onorato M. Observation of dispersive shock waves developing from initial depressions in shallow water // Physica D, 2016. - http://dx.doi.org/10.1016/j.physd.2016.01.007.

Solitary Waves, Periodic Peakons and Pseudo-Peakons of the Nonlinear Acoustic Wave Model in Rotating Magnetized Plasma

NASA Astrophysics Data System (ADS)

Li, Jibin

The dynamical model of the nonlinear acoustic wave in rotating magnetized plasma is governed by a partial differential equation system. Its traveling system is a singular traveling wave system of first class depending on two parameters. By using the bifurcation theory and method of dynamical systems and the theory of singular traveling wave systems, in this paper, we show that there exist parameter groups such that this singular system has pseudo-peakons, periodic peakons and compactons as well as different solitary wave solutions.

Basis for ligand discrimination between ON and OFF state riboswitch conformations: The case of the SAM-I riboswitch

PubMed Central

Boyapati, Vamsi Krishna; Huang, Wei; Spedale, Jessica; Aboul-ela, Fareed

2012-01-01

Riboswitches are RNA elements that bind to effector ligands and control gene expression. Most consist of two domains. S-Adenosyl Methionine (SAM) binds the aptamer domain of the SAM-I riboswitch and induces conformational changes in the expression domain to form an intrinsic terminator (transcription OFF state). Without SAM the riboswitch forms the transcription ON state, allowing read-through transcription. The mechanistic link between the SAM/aptamer recognition event and subsequent secondary structure rearrangement by the riboswitch is unclear. We probed for those structural features of the Bacillus subtilis yitJ SAM-I riboswitch responsible for discrimination between the ON and OFF states by SAM. We designed SAM-I riboswitch RNA segments forming “hybrid” structures of the ON and OFF states. The choice of segment constrains the formation of a partial P1 helix, characteristic of the OFF state, together with a partial antiterminator (AT) helix, characteristic of the ON state. For most choices of P1 vs. AT helix lengths, SAM binds with micromolar affinity according to equilibrium dialysis. Mutational analysis and in-line probing confirm that the mode of SAM binding by hybrid structures is similar to that of the aptamer. Altogether, binding measurements and in-line probing are consistent with the hypothesis that when SAM is present, stacking interactions with the AT helix stabilize a partially formed P1 helix in the hybrids. Molecular modeling indicates that continuous stacking between the P1 and the AT helices is plausible with SAM bound. Our findings raise the possibility that conformational intermediates may play a role in ligand-induced aptamer folding. PMID:22543867

Basis for ligand discrimination between ON and OFF state riboswitch conformations: the case of the SAM-I riboswitch.

PubMed

Boyapati, Vamsi Krishna; Huang, Wei; Spedale, Jessica; Aboul-Ela, Fareed

2012-06-01

Riboswitches are RNA elements that bind to effector ligands and control gene expression. Most consist of two domains. S-Adenosyl Methionine (SAM) binds the aptamer domain of the SAM-I riboswitch and induces conformational changes in the expression domain to form an intrinsic terminator (transcription OFF state). Without SAM the riboswitch forms the transcription ON state, allowing read-through transcription. The mechanistic link between the SAM/aptamer recognition event and subsequent secondary structure rearrangement by the riboswitch is unclear. We probed for those structural features of the Bacillus subtilis yitJ SAM-I riboswitch responsible for discrimination between the ON and OFF states by SAM. We designed SAM-I riboswitch RNA segments forming "hybrid" structures of the ON and OFF states. The choice of segment constrains the formation of a partial P1 helix, characteristic of the OFF state, together with a partial antiterminator (AT) helix, characteristic of the ON state. For most choices of P1 vs. AT helix lengths, SAM binds with micromolar affinity according to equilibrium dialysis. Mutational analysis and in-line probing confirm that the mode of SAM binding by hybrid structures is similar to that of the aptamer. Altogether, binding measurements and in-line probing are consistent with the hypothesis that when SAM is present, stacking interactions with the AT helix stabilize a partially formed P1 helix in the hybrids. Molecular modeling indicates that continuous stacking between the P1 and the AT helices is plausible with SAM bound. Our findings raise the possibility that conformational intermediates may play a role in ligand-induced aptamer folding.

The stability of freak waves with regard to external impact and perturbation of initial data

NASA Astrophysics Data System (ADS)

Smirnova, Anna; Shamin, Roman

2014-05-01

We investigate solutions of the equations, describing freak waves, in perspective of stability with regard to external impact and perturbation of initial data. The modeling of freak waves is based on numerical solution of equations describing a non-stationary potential flow of the ideal fluid with a free surface. We consider the two-dimensional infinitely deep flow. For waves modeling we use the equations in conformal variables. The variant of these equations is offered in [1]. Mathematical correctness of these equations was discussed in [2]. These works establish the uniqueness of solutions, offer the effective numerical solution calculation methods, prove the numerical convergence of these methods. The important aspect of numerical modeling of freak waves is the stability of solutions, describing these waves. In this work we study the questions of stability with regards to external impact and perturbation of initial data. We showed the stability of freak waves numerical model, corresponding to the external impact. We performed series of computational experiments with various freak wave initial data and random external impact. This impact means the power density on free surface. In each experiment examine two waves: the wave that was formed by external impact and without one. In all the experiments we see the stability of equation`s solutions. The random external impact practically does not change the time of freak wave formation and its form. Later our work progresses to the investigation of solution's stability under perturbations of initial data. We take the initial data that provide a freak wave and get the numerical solution. In common we take the numerical solution of equation with perturbation of initial data. The computing experiments showed that the freak waves equations solutions are stable under perturbations of initial data.So we can make a conclusion that freak waves are stable relatively external perturbation and perturbation of initial data both. 1. Zakharov V.E., Dyachenko A.I., Vasilyev O.A. New method for numerical simulation of a nonstationary potential flow of incompressible fluid with a free surface// Eur. J.~Mech. B Fluids. 2002. V. 21. P. 283-291. 2. R.V. Shamin. Dynamics of an Ideal Liquid with a Free Surface in Conformal Variables // Journal of Mathematical Sciences, Vol. 160, No. 5, 2009. P. 537-678. 3. R.V. Shamin, V.E. Zakharov, A.I. Dyachenko. How probability for freak wave formation can be found // THE EUROPEAN PHYSICAL JOURNAL - SPECIAL TOPICS Volume 185, Number 1, 113-124, DOI: 10.1140/epjst/e2010-01242-y

Anderson localization of partially incoherent light

DOE Office of Scientific and Technical Information (OSTI.GOV)

Capeta, D.; Radic, J.; Buljan, H.

We study Anderson localization and propagation of partially spatially incoherent wavepackets in linear disordered potentials, motivated by the insight that interference phenomena resulting from multiple scattering are affected by the coherence of the waves. We find that localization is delayed by incoherence: the more incoherent the waves are, the longer they diffusively spread while propagating in the medium. However, if all the eigenmodes of the system are exponentially localized (as in one- and two-dimensional disordered systems), any partially incoherent wavepacket eventually exhibits localization with exponentially decaying tails, after sufficiently long propagation distances. Interestingly, we find that the asymptotic behavior ofmore » the incoherent beam is similar to that of a single instantaneous coherent realization of the beam.« less

Monitoring conformational heterogeneity of the lid of DnaK substrate-binding domain during its chaperone cycle.

PubMed

Banerjee, Rupa; Jayaraj, Gopal Gunanathan; Peter, Joshua Jebakumar; Kumar, Vignesh; Mapa, Koyeli

2016-08-01

DnaK or Hsp70 of Escherichia coli is a master regulator of the bacterial proteostasis network. Allosteric communication between the two functional domains of DnaK, the N-terminal nucleotide-binding domain (NBD) and the C-terminal substrate- or peptide-binding domain (SBD) regulate its activity. X-ray crystallography and NMR studies have provided snapshots of distinct conformations of Hsp70 proteins in various physiological states; however, the conformational heterogeneity and dynamics of allostery-driven Hsp70 activity remains underexplored. In this work, we employed single-molecule Förster resonance energy transfer (sm-FRET) measurements to capture distinct intradomain conformational states of a region within the DnaK-SBD known as the lid. Our data conclusively demonstrate prominent conformational heterogeneity of the DnaK lid in ADP-bound states; in contrast, the ATP-bound open conformations are homogeneous. Interestingly, a nonhydrolysable ATP analogue, AMP-PNP, imparts heterogeneity to the lid conformations mimicking the ADP-bound state. The cochaperone DnaJ confers ADP-like heterogeneous lid conformations to DnaK, although the presence of the cochaperone accelerates the substrate-binding rate by a hitherto unknown mechanism. Irrespective of the presence of DnaJ, binding of a peptide substrate to the DnaK-SBD leads to prominent lid closure. Lid closure is only partial upon binding to molten globule-like authentic cellular substrates, probably to accommodate non-native substrate proteins of varied structures. © 2016 Federation of European Biochemical Societies.

Conformational Heterogeneity of the HIV Envelope Glycan Shield.

PubMed

Yang, Mingjun; Huang, Jing; Simon, Raphael; Wang, Lai-Xi; MacKerell, Alexander D

2017-06-30

To better understand the conformational properties of the glycan shield covering the surface of the HIV gp120/gp41 envelope (Env) trimer, and how the glycan shield impacts the accessibility of the underlying protein surface, we performed enhanced sampling molecular dynamics (MD) simulations of a model glycosylated HIV Env protein and related systems. Our simulation studies revealed a conformationally heterogeneous glycan shield with a network of glycan-glycan interactions more extensive than those observed to date. We found that partial preorganization of the glycans potentially favors binding by established broadly neutralizing antibodies; omission of several specific glycans could increase the accessibility of other glycans or regions of the protein surface to antibody or CD4 receptor binding; the number of glycans that can potentially interact with known antibodies is larger than that observed in experimental studies; and specific glycan conformations can maximize or minimize interactions with individual antibodies. More broadly, the enhanced sampling MD simulations described here provide a valuable tool to guide the engineering of specific Env glycoforms for HIV vaccine design.

Molecular conformation of linear alkane molecules: From gas phase to bulk water through the interface

NASA Astrophysics Data System (ADS)

Murina, Ezequiel L.; Fernández-Prini, Roberto; Pastorino, Claudio

2017-08-01

We studied the behavior of long chain alkanes (LCAs) as they were transferred from gas to bulk water, through the liquid-vapor interface. These systems were studied using umbrella sampling molecular dynamics simulation and we have calculated properties like free energy profiles, molecular orientation, and radius of gyration of the LCA molecules. The results show changes in conformation of the solutes along the path. LCAs adopt pronounced molecular orientations and the larger ones extend appreciably when partially immersed in the interface. In bulk water, their conformations up to dodecane are mainly extended. However, larger alkanes like eicosane present a more stable collapsed conformation as they approach bulk water. We have characterized the more probable configurations in all interface and bulk regions. The results obtained are of interest for the study of biomatter processes requiring the transfer of hydrophobic matter, especially chain-like molecules like LCAs, from gas to bulk aqueous systems through the interface.

Molecular Dynamics Simulations of the Human Glucose Transporter GLUT1

PubMed Central

Park, Min-Sun

2015-01-01

Glucose transporters (GLUTs) provide a pathway for glucose transport across membranes. Human GLUTs are implicated in devastating diseases such as heart disease, hyper- and hypo-glycemia, type 2 diabetes and caner. The human GLUT1 has been recently crystalized in the inward-facing open conformation. However, there is no other structural information for other conformations. The X-ray structures of E. coli Xylose permease (XylE), a glucose transporter homolog, are available in multiple conformations with and without the substrates D-xylose and D-glucose. XylE has high sequence homology to human GLUT1 and key residues in the sugar-binding pocket are conserved. Here we construct a homology model for human GLUT1 based on the available XylE crystal structure in the partially occluded outward-facing conformation. A long unbiased all atom molecular dynamics simulation starting from the model can capture a new fully opened outward-facing conformation. Our investigation of molecular interactions at the interface between the transmembrane (TM) domains and the intracellular helices (ICH) domain in the outward- and inward-facing conformation supports that the ICH domain likely stabilizes the outward-facing conformation in GLUT1. Furthermore, inducing a conformational transition, our simulations manifest a global asymmetric rocker switch motion and detailed molecular interactions between the substrate and residues through the water-filled selective pore along a pathway from the extracellular to the intracellular side. The results presented here are consistent with previously published biochemical, mutagenesis and functional studies. Together, this study shed light on the structure and functional relationships of GLUT1 in multiple conformational states. PMID:25919356

Conformational diversity analysis reveals three functional mechanisms in proteins

PubMed Central

Fornasari, María Silvina

2017-01-01

Protein motions are a key feature to understand biological function. Recently, a large-scale analysis of protein conformational diversity showed a positively skewed distribution with a peak at 0.5 Å C-alpha root-mean-square-deviation (RMSD). To understand this distribution in terms of structure-function relationships, we studied a well curated and large dataset of ~5,000 proteins with experimentally determined conformational diversity. We searched for global behaviour patterns studying how structure-based features change among the available conformer population for each protein. This procedure allowed us to describe the RMSD distribution in terms of three main protein classes sharing given properties. The largest of these protein subsets (~60%), which we call “rigid” (average RMSD = 0.83 Å), has no disordered regions, shows low conformational diversity, the largest tunnels and smaller and buried cavities. The two additional subsets contain disordered regions, but with differential sequence composition and behaviour. Partially disordered proteins have on average 67% of their conformers with disordered regions, average RMSD = 1.1 Å, the highest number of hinges and the longest disordered regions. In contrast, malleable proteins have on average only 25% of disordered conformers and average RMSD = 1.3 Å, flexible cavities affected in size by the presence of disordered regions and show the highest diversity of cognate ligands. Proteins in each set are mostly non-homologous to each other, share no given fold class, nor functional similarity but do share features derived from their conformer population. These shared features could represent conformational mechanisms related with biological functions. PMID:28192432

Galactic conformity measured in semi-analytic models

NASA Astrophysics Data System (ADS)

Lacerna, I.; Contreras, S.; González, R. E.; Padilla, N.; Gonzalez-Perez, V.

2018-03-01

We study the correlation between the specific star formation rate of central galaxies and neighbour galaxies, also known as `galactic conformity', out to 20 h^{-1} {Mpc} using three semi-analytic models (SAMs, one from L-GALAXIES and other two from GALFORM). The aim is to establish whether SAMs are able to show galactic conformity using different models and selection criteria. In all the models, when the selection of primary galaxies is based on an isolation criterion in real space, the mean fraction of quenched (Q) galaxies around Q primary galaxies is higher than that around star-forming primary galaxies of the same stellar mass. The overall signal of conformity decreases when we remove satellites selected as primary galaxies, but the effect is much stronger in GALFORM models compared with the L-GALAXIES model. We find this difference is partially explained by the fact that in GALFORM once a galaxy becomes a satellite remains as such, whereas satellites can become centrals at a later time in L-GALAXIES. The signal of conformity decreases down to 60 per cent in the L-GALAXIES model after removing central galaxies that were ejected from their host halo in the past. Galactic conformity is also influenced by primary galaxies at fixed stellar mass that reside in dark matter haloes of different masses. Finally, we explore a proxy of conformity between distinct haloes. In this case, the conformity is weak beyond ˜3 h^{-1} {Mpc} (<3 per cent in L-GALAXIES, <1-2 per cent in GALFORM models). Therefore, it seems difficult that conformity is directly related with a long-range effect.

Characterizing Solution Surface Loop Conformational Flexibility of the GM2 Activator Protein

PubMed Central

2015-01-01

GM2AP has a β-cup topology with numerous X-ray structures showing multiple conformations for some of the surface loops, revealing conformational flexibility that may be related to function, where function is defined as either membrane binding associated with ligand binding and extraction or interaction with other proteins. Here, site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy and molecular dynamic (MD) simulations are used to characterize the mobility and conformational flexibility of various structural regions of GM2AP. A series of 10 single cysteine amino acid substitutions were generated, and the constructs were chemically modified with the methanethiosulfonate spin label. Continuous wave (CW) EPR line shapes were obtained and subsequently simulated using the microscopic order macroscopic disorder (MOMD) program. Line shapes for sites that have multiple conformations in the X-ray structures required two spectral components, whereas spectra of the remaining sites were adequately fit with single-component parameters. For spin labeled sites L126C and I66C, spectra were acquired as a function of temperature, and simulations provided for the determination of thermodynamic parameters associated with conformational change. Binding to GM2 ligand did not alter the conformational flexibility of the loops, as evaluated by EPR and NMR spectroscopies. These results confirm that the conformational flexibility observed in the surface loops of GM2AP crystals is present in solution and that the exchange is slow on the EPR time scale (>ns). Furthermore, MD simulation results are presented and agree well with the conformational heterogeneity revealed by SDSL. PMID:25127419

Numerical grid generation techniques. [conference

NASA Technical Reports Server (NTRS)

1980-01-01

The state of the art in topology and flow geometry is presented. Solution techniques for partial differential equations are reviewed and included developments in coordinate transformations, conformal mapping, and invariant imbeddings. Applications of these techniques in fluid mechanics, flow geometry, boundary value problems, and fluidics are presented.

Calculation of incompressible fluid flow through cambered blades

NASA Technical Reports Server (NTRS)

Hsu, C. C.

1970-01-01

Conformal mapping technique yields linear, approximate solutions for calculating flow of an incompressible fluid through staggered array of cambered blades for the cases of flow with partial cavitation and supercavitation. Lift and drag coefficients, cavitation number, cavity shape, and exit flow conditions can be determined.

Symptomatic Radiation Pneumonitis After Accelerated Partial Breast Irradiation Using Three-dimensional Conformal Radiotherapy.

PubMed

Shikama, Naoto; Kumazaki, Y U; Miyazawa, Kazunari; Miyaura, Kazunori; Kato, Shingo; Nakamura, Naoki; Kawamori, Jiro; Shimizuguchi, Takuya; Saito, Naoko; Saeki, Toshiaki

2016-05-01

To examine the relationship between symptomatic radiation pneumonitis and lung dose-volume parameters for patients receiving accelerated partial breast irradiation (APBI) using three dimensional-conformal radiotherapy (3D-CRT). The prescribed radiation dose was 30 Gy in 5 fractions over 10 days. Toxicity was graded according to the Common Terminology Criteria for Adverse Events (version 4.0). Fifty-five patients were enrolled from August 2010 to October 2013 and the median follow-up time was 30 months (range=18-46 months). Three patients (5%) developed grade 2 symptomatic radiation pneumonitis after 3D-CRT APBI. Among 16 patients with ILV10Gy (% ipsilateral lung receiving ≥10 Gy) of 10% or higher, three patients (19%) developed symptomatic radiation pneumonitis. This trend was not observed in any of the patients with ILV10Gy less than 10% (p=0.005). High ILV10Gy might be associated with symptomatic radiation pneumonitis after 3D-CRT APBI. Copyright© 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

High Energy Scattering in the AdS/CFT Correspondence

NASA Astrophysics Data System (ADS)

Penedones, Joao

2007-12-01

This work explores the celebrated AdS/CFT correspondence in the regime of high energy scattering in Anti--de Sitter (AdS) spacetime. In particular, we develop the eikonal approximation to high energy scattering in AdS and explore its consequences for the dual Conformal Field Theory (CFT). Using position space Feynman rules, we rederive the eikonal approximation for high energy scattering in flat space. Following this intuitive position space perspective, we then generalize the eikonal approximation for high energy scattering in AdS and other spacetimes. Remarkably, we are able to resum, in terms of a generalized phase shift, ladder and cross ladder Witten diagrams associated to the exchange of an AdS spin j field, to all orders in the coupling constant. By the AdS/CFT correspondence, the eikonal amplitude in AdS is related to the four point function of CFT primary operators in the regime of large 't Hooft coupling, including all terms of the 1/N expansion. We then show that the eikonal amplitude determines the behavior of the CFT four point function for small values of the cross ratios in a Lorentzian regime and that this controls its high spin and dimension conformal partial wave decomposition. These results allow us to determine the anomalous dimension of high spin and dimension double trace primary operators, by relating it to the AdS eikonal phase shift. Finally we find that, at large energies and large impact parameters in AdS, the gravitational interaction dominates all other interactions, as in flat space. Therefore, the anomalous dimension of double trace operators, associated to graviton exchange in AdS, yields a universal prediction for CFT's with AdS gravitational duals.

The second Cu(II)-binding site in a proton-rich environment interferes with the aggregation of amyloid-beta(1-40) into amyloid fibrils.

PubMed

Jun, Sangmi; Gillespie, Joel R; Shin, Byong-kyu; Saxena, Sunil

2009-11-17

The overall morphology and Cu(II) ion coordination for the aggregated amyloid-beta(1-40) [Abeta(1-40)] in N-ethylmorpholine (NEM) buffer are affected by Cu(II) ion concentration. This effect is investigated by transmission electron microscopy (TEM), atomic force microscopy (AFM), and electron spin echo envelope modulation (ESEEM) spectroscopy. At lower than equimolar concentrations of Cu(II) ions, fibrillar aggregates of Abeta(1-40) are observed. At these concentrations of Cu(II), the monomeric and fibrillar Abeta(1-40) ESEEM data indicate that the Cu(II) ion is coordinated by histidine residues. For aggregated Abeta(1-40) at a Cu(II):Abeta molar ratio of 2:1, TEM and AFM images show both linear fibrils and granular amorphous aggregates. The ESEEM spectra show that the multi-histidine coordination for Cu(II) ion partially breaks up and becomes exposed to water or exchangeable protons of the peptide at a higher Cu(II) concentration. Since the continuous-wave electron spin resonance results also suggest two copper-binding sites in Abeta(1-40), the proton ESEEM peak may arise from the second copper-binding site, which may be significantly involved in the formation of granular amorphous aggregates. Thioflavin T fluorescence and circular dichroism experiments also show that Cu(II) inhibits the formation of fibrils and induces a nonfibrillar beta-sheet conformation. Therefore, we propose that Abeta(1-40) has a second copper-binding site in a proton-rich environment and the second binding Cu(II) ion interferes with a conformational transition into amyloid fibrils, inducing the formation of granular amorphous aggregates.

Propagation of large-amplitude waves on dielectric liquid sheets in a tangential electric field: exact solutions in three-dimensional geometry.

PubMed

Zubarev, Nikolay M; Zubareva, Olga V

2010-10-01

Nonlinear waves on sheets of dielectric liquid in the presence of an external tangential electric field are studied theoretically. It is shown that waves of arbitrary shape in three-dimensional geometry can propagate along (or against) the electric field direction without distortion, i.e., the equations of motion admit a wide class of exact traveling wave solutions. This unusual situation occurs for nonconducting ideal liquids with high dielectric constants in the case of a sufficiently strong field strength. Governing equations for evolution of plane symmetric waves on fluid sheets are derived using conformal variables. A dispersion relation for the evolution of small perturbations of the traveling wave solutions is obtained. It follows from this relation that, regardless of the wave shape, the amplitudes of small-scale perturbations do not increase with time and, hence, the traveling waves are stable. We also study the interaction of counterpropagating symmetric waves with small but finite amplitudes. The corresponding solution of the equations of motion describes the nonlinear superposition of the oppositely directed waves. The results obtained are applicable for the description of long waves on fluid sheets in a horizontal magnetic field.

Direct measurement of conformational strain energy in protofilaments curling outward from disassembling microtubule tips.

PubMed

Driver, Jonathan W; Geyer, Elisabeth A; Bailey, Megan E; Rice, Luke M; Asbury, Charles L

2017-06-19

Disassembling microtubules can generate movement independently of motor enzymes, especially at kinetochores where they drive chromosome motility. A popular explanation is the 'conformational wave' model, in which protofilaments pull on the kinetochore as they curl outward from a disassembling tip. But whether protofilaments can work efficiently via this spring-like mechanism has been unclear. By modifying a previous assay to use recombinant tubulin and feedback-controlled laser trapping, we directly demonstrate the spring-like elasticity of curling protofilaments. Measuring their mechanical work output suggests they carry ~25% of the energy of GTP hydrolysis as bending strain, enabling them to drive movement with efficiency similar to conventional motors. Surprisingly, a β-tubulin mutant that dramatically slows disassembly has no effect on work output, indicating an uncoupling of disassembly speed from protofilament strain. These results show the wave mechanism can make a major contribution to kinetochore motility and establish a direct approach for measuring tubulin mechano-chemistry.

Closed form solutions of two time fractional nonlinear wave equations

NASA Astrophysics Data System (ADS)

Akbar, M. Ali; Ali, Norhashidah Hj. Mohd.; Roy, Ripan

2018-06-01

In this article, we investigate the exact traveling wave solutions of two nonlinear time fractional wave equations. The fractional derivatives are described in the sense of conformable fractional derivatives. In addition, the traveling wave solutions are accomplished in the form of hyperbolic, trigonometric, and rational functions involving free parameters. To investigate such types of solutions, we implement the new generalized (G‧ / G) -expansion method. The extracted solutions are reliable, useful and suitable to comprehend the optimal control problems, chaotic vibrations, global and local bifurcations and resonances, furthermore, fission and fusion phenomena occur in solitons, the relativistic energy-momentum relation, scalar electrodynamics, quantum relativistic one-particle theory, electromagnetic interactions etc. The results reveal that the method is very fruitful and convenient for exploring nonlinear differential equations of fractional order treated in theoretical physics.

Does aquatic foraging impact head shape evolution in snakes?

PubMed Central

Cornette, Raphaël; Fabre, Anne-Claire; Godoy-Diana, Ramiro; Herrel, Anthony

2016-01-01

Evolutionary trajectories are often biased by developmental and historical factors. However, environmental factors can also impose constraints on the evolutionary trajectories of organisms leading to convergence of morphology in similar ecological contexts. The physical properties of water impose strong constraints on aquatic feeding animals by generating pressure waves that can alert prey and potentially push them away from the mouth. These hydrodynamic constraints have resulted in the independent evolution of suction feeding in most groups of secondarily aquatic tetrapods. Despite the fact that snakes cannot use suction, they have invaded the aquatic milieu many times independently. Here, we test whether the aquatic environment has constrained head shape evolution in snakes and whether shape converges on that predicted by biomechanical models. To do so, we used three-dimensional geometric morphometrics and comparative, phylogenetically informed analyses on a large sample of aquatic snake species. Our results show that aquatic snakes partially conform to our predictions and have a narrower anterior part of the head and dorsally positioned eyes and nostrils. This morphology is observed, irrespective of the phylogenetic relationships among species, suggesting that the aquatic environment does indeed drive the evolution of head shape in snakes, thus biasing the evolutionary trajectory of this group of animals. PMID:27581887

Fully pseudospectral solution of the conformally invariant wave equation near the cylinder at spacelike infinity. III: nonspherical Schwarzschild waves and singularities at null infinity

NASA Astrophysics Data System (ADS)

Frauendiener, Jörg; Hennig, Jörg

2018-03-01

We extend earlier numerical and analytical considerations of the conformally invariant wave equation on a Schwarzschild background from the case of spherically symmetric solutions, discussed in Frauendiener and Hennig (2017 Class. Quantum Grav. 34 045005), to the case of general, nonsymmetric solutions. A key element of our approach is the modern standard representation of spacelike infinity as a cylinder. With a decomposition into spherical harmonics, we reduce the four-dimensional wave equation to a family of two-dimensional equations. These equations can be used to study the behaviour at the cylinder, where the solutions turn out to have, in general, logarithmic singularities at infinitely many orders. We derive regularity conditions that may be imposed on the initial data, in order to avoid the first singular terms. We then demonstrate that the fully pseudospectral time evolution scheme can be applied to this problem leading to a highly accurate numerical reconstruction of the nonsymmetric solutions. We are particularly interested in the behaviour of the solutions at future null infinity, and we numerically show that the singularities spread to null infinity from the critical set, where the cylinder approaches null infinity. The observed numerical behaviour is consistent with similar logarithmic singularities found analytically on the critical set. Finally, we demonstrate that even solutions with singularities at low orders can be obtained with high accuracy by virtue of a coordinate transformation that converts solutions with logarithmic singularities into smooth solutions.

Rescattering Effects in the Hadronic-Light-by-Light Contribution to the Anomalous Magnetic Moment of the Muon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Colangelo, Gilberto; Hoferichter, Martin; Procura, Massimiliano

We present a first model-independent calculation of ππ intermediate states in the hadronic-light-by-light (HLBL) contribution to the anomalous magnetic moment of the muon (g - 2) μ that goes beyond the scalar QED pion loop. To this end, we combine a recently developed dispersive description of the HLBL tensor with a partial-wave expansion and demonstrate that the known scalar-QED result is recovered after partial-wave resummation. Using dispersive fits to high-statistics data for the pion vector form factor, we provide an evaluation of the full pion box a π μ box = –15.9(2) x 10 -11. We then construct a suitablemore » input for the γ*γ* → ππ helicity partial waves, based on a pion-pole left-hand cut and show that for the dominant charged-pion contribution, this representation is consistent with the two-loop chiral prediction and the COMPASS measurement for the pion polarizability. This allows us to reliably estimate S-wave rescattering effects to the full pion box and leads to our final estimate for the sum of these two contributions a π μ box + a ππ,π-pole μ,J=0 LHC = –24(1) x 10 -11.« less

Rescattering Effects in the Hadronic-Light-by-Light Contribution to the Anomalous Magnetic Moment of the Muon

DOE PAGES

Colangelo, Gilberto; Hoferichter, Martin; Procura, Massimiliano; ...

2017-06-09

We present a first model-independent calculation of ππ intermediate states in the hadronic-light-by-light (HLBL) contribution to the anomalous magnetic moment of the muon (g - 2) μ that goes beyond the scalar QED pion loop. To this end, we combine a recently developed dispersive description of the HLBL tensor with a partial-wave expansion and demonstrate that the known scalar-QED result is recovered after partial-wave resummation. Using dispersive fits to high-statistics data for the pion vector form factor, we provide an evaluation of the full pion box a π μ box = –15.9(2) x 10 -11. We then construct a suitablemore » input for the γ*γ* → ππ helicity partial waves, based on a pion-pole left-hand cut and show that for the dominant charged-pion contribution, this representation is consistent with the two-loop chiral prediction and the COMPASS measurement for the pion polarizability. This allows us to reliably estimate S-wave rescattering effects to the full pion box and leads to our final estimate for the sum of these two contributions a π μ box + a ππ,π-pole μ,J=0 LHC = –24(1) x 10 -11.« less

Polymer Morphological Change Induced by Terahertz Irradiation

NASA Astrophysics Data System (ADS)

Hoshina, Hiromichi; Suzuki, Hal; Otani, Chiko; Nagai, Masaya; Kawase, Keigo; Irizawa, Akinori; Isoyama, Goro

2016-06-01

As terahertz (THz) frequencies correspond to those of the intermolecular vibrational modes in a polymer, intense THz wave irradiation affects the macromolecular polymorph, which determines the polymer properties and functions. THz photon energy is quite low compared to the covalent bond energy; therefore, conformational changes can be induced “softly,” without damaging the chemical structures. Here, we irradiate a poly(3-hydroxybutylate) (PHB) / chloroform solution during solvent casting crystallization using a THz wave generated by a free electron laser (FEL). Morphological observation shows the formation of micrometer-sized crystals in response to the THz wave irradiation. Further, a 10-20% increase in crystallinity is observed through analysis of the infrared (IR) absorption spectra. The peak power density of the irradiating THz wave is 40 MW/cm2, which is significantly lower than the typical laser intensities used for material manipulation. We demonstrate for the first time that the THz wave effectively induces the intermolecular rearrangement of polymer macromolecules.

Jet formation at the interaction of localized waves on the free surface of dielectric liquid in a tangential electric field

NASA Astrophysics Data System (ADS)

Kochurin, E. A.; Zubarev, N. M.

2018-01-01

Nonlinear dynamics of the free surface of finite depth non-conducting fluid with high dielectric constant subjected to a strong horizontal electric field is considered. Using the conformal transformation of the region occupied by the fluid into a strip, the process of interaction of counter-propagating waves is numerically simulated. The nonlinear solitary waves on the surface can separately propagate along or against the direction of electric field without distortion. At the same time, the shape of the oppositely traveling waves can be distorted as the result of their interaction. In the problem under study, the nonlinearity leads to increasing the wave amplitudes and the duration of their interaction. This effect is inversely proportional to the fluid depth. In the shallow water limit, the tendency to the formation of a vertical liquid jet is observed.

Prevalence and Axis I Comorbidity of Full and Partial Posttraumatic Stress Disorder in the United States: Results from Wave 2 of the National Epidemiologic Survey on Alcohol and Related Conditions

PubMed Central

Pietrzak, Robert H.; Goldstein, Risë B.; Southwick, Steven M.; Grant, Bridget F.

2010-01-01

The present study used data from the Wave 2 National Epidemiologic Survey on Alcohol and Related Conditions (n=34,653) to examine lifetime Axis I psychiatric comorbidity of posttraumatic stress disorder (PTSD) in a nationally representative sample of U.S. adults. Lifetime prevalences±standard errors of PTSD and partial PTSD were 6.4%±0.18 and 6.6%±0.18, respectively. Rates of PTSD and partial PTSD were higher among women (8.6%±0.26 and 8.6%±0.26) than men (4.1%±0.19 and 4.5%±0.21). Respondents with both PTSD and partial PTSD most commonly reported unexpected death of someone close, serious illness or injury to someone close, and sexual assault as their worst stressful experiences. PTSD and partial PTSD were associated with elevated lifetime rates of mood, anxiety, and substance use disorders, and suicide attempts. Respondents with partial PTSD generally had intermediate odds of comorbid Axis I disorders and psychosocial impairment relative to trauma controls and full PTSD. PMID:21168991

Teaching Graphical Simulations of Fourier Series Expansion of Some Periodic Waves Using Spreadsheets

ERIC Educational Resources Information Center

Singh, Iqbal; Kaur, Bikramjeet

2018-01-01

The present article demonstrates a way of programming using an Excel spreadsheet to teach Fourier series expansion in school/colleges without the knowledge of any typical programming language. By using this, a student learns to approximate partial sum of the n terms of Fourier series for some periodic signals such as square wave, saw tooth wave,…

Intracavity frequency doubling of a continuous wave Ti:sapphire ring laser and application in resonance Raman spectroscopy of heme protein dynamics

NASA Astrophysics Data System (ADS)

Buchter, Scott C.; Williams, Curtis; Schulte, Alfons; Alekel, Theodore, III; Mizell, Gregory J.; Fay, William R.

1995-04-01

Noncritical temperature-tuned phase-matching and large nonlinear coefficients make potassium niobate an attractive material for frequency doubling tuneable near-infrared radiation. We have mounted a KNbO3 crystal intracavity in an argon ion pumped, continuous wave Ti:Sapphire ring laser to increase the power level of the second harmonic. Wavelength selection at the fundamental frequency is accomplished with a birefringent filter. By using the crystal orientation that defines the d32 coefficient of KNbO3 we have obtained a blue second harmonic output tuneable from 425-445 nm. The laser is also characterized by the narrow linewidth of the Ti:Sapphire ring oscillator and good temporal stability. A continuous wave, frequency doubled Ti:sapphire laser is well suited to excite the resonance Raman spectrum in heme proteins with strong absorption bands in the range of 400 to 450 nm. We demonstrate the feasibility of such a setup for Raman studies of ligand binding to myoglobin. The Raman bands yield information on the reaction dynamics and on conformational changes near the linkage between the heme and the protein. In particular, a shift of the stretch frequency of the iron- histidine bond with high pressure may be attributed to a protein conformational change.

Langmuir instability in partially spin polarized bounded degenerate plasma

NASA Astrophysics Data System (ADS)

Iqbal, Z.; Jamil, M.; Murtaza, G.

2018-04-01

Some new features of waves inside the cylindrical waveguide on employing the separated spin evolution quantum hydrodynamic model are evoked. Primarily, the instability of Langmuir wave due to the electron beam in a partially spin polarized degenerate plasma considering a nano-cylindrical geometry is discussed. Besides, the evolution of a new spin-dependent wave (spin electron acoustic wave) due to electron spin polarization effects in the real wave spectrum is elaborated. Analyzing the growth rate, it is found that in the absence of Bohm potential, the electron spin effects or exchange interaction reduce the growth rate as well as k-domain but the inclusion of Bohm potential increases both the growth rate and k-domain. Further, we investigate the geometry effects expressed by R and pon and find that they have opposite effects on the growth rate and k-domain of the instability. Additionally, how the other parameters like electron beam density or streaming speed of beam electrons influence the growth rate is also investigated. This study may find its applications for the signal analysis in solid state devices at nanoscales.

Probing coherence in microcavity frequency combs via optical pulse shaping

NASA Astrophysics Data System (ADS)

Ferdous, Fahmida; Miao, Houxun; Wang, Pei-Hsun; Leaird, Daniel E.; Srinivasan, Kartik; Chen, Lei; Aksyuk, Vladimir; Weiner, Andrew M.

2012-09-01

Recent investigations of microcavity frequency combs based on cascaded four-wave mixing have revealed a link between the evolution of the optical spectrum and the observed temporal coherence. Here we study a silicon nitride microresonator for which the initial four-wave mixing sidebands are spaced by multiple free spectral ranges (FSRs) from the pump, then fill in to yield a comb with single FSR spacing, resulting in partial coherence. By using a pulse shaper to select and manipulate the phase of various subsets of spectral lines, we are able to probe the structure of the coherence within the partially coherent comb. Our data demonstrate strong variation in the degree of mutual coherence between different groups of lines and provide support for a simple model of partially coherent comb formation.

Geometrical and wave optics of paraxial beams.

PubMed

Meron, M; Viccaro, P J; Lin, B

1999-06-01

Most calculational techniques used to evaluate beam propagation are geared towards either fully coherent or fully incoherent beams. The intermediate partial-coherence regime, while in principle known for a long time, has received comparably little attention so far. The resulting shortage of adequate calculational techniques is currently being felt in the realm of x-ray optics where, with the advent of third generation synchrotron light sources, partially coherent beams become increasingly common. The purpose of this paper is to present a calculational approach which, utilizing a "variance matrix" representation of paraxial beams, allows for a straightforward evaluation of wave propagation through an optical system. Being capable of dealing with an arbitrary degree of coherence, this approach covers the whole range from wave to ray optics, in a seamless fashion.

Copper plasmonics and catalysis: role of electron-phonon interactions in dephasing localized surface plasmons

NASA Astrophysics Data System (ADS)

Sun, Qi-C.; Ding, Yuchen; Goodman, Samuel M.; H. Funke, Hans; Nagpal, Prashant

2014-10-01

Copper metal can provide an important alternative for the development of efficient, low-cost and low-loss plasmonic nanoparticles, and selective nanocatalysts. However, poor chemical stability and lack of insight into photophysics and plasmon decay mechanisms has impeded study. Here, we use smooth conformal ALD coating on copper nanoparticles to prevent surface oxidation, and study dephasing time for localized surface plasmons on different sized copper nanoparticles. Using dephasing time as a figure of merit, we elucidate the role of electron-electron, electron-phonon, impurity, surface and grain boundary scattering on the decay of localized surface plasmon waves. Using our quantitative analysis and different temperature dependent measurements, we show that electron-phonon interactions dominate over other scattering mechanisms in dephasing plasmon waves. While interband transitions in copper metal contributes substantially to plasmon losses, tuning surface plasmon modes to infrared frequencies leads to a five-fold enhancement in the quality factor. These findings demonstrate that conformal ALD coatings can improve the chemical stability for copper nanoparticles, even at high temperatures (>300 °C) in ambient atmosphere, and nanoscaled copper is a good alternative material for many potential applications in nanophotonics, plasmonics, catalysis and nanoscale electronics.Copper metal can provide an important alternative for the development of efficient, low-cost and low-loss plasmonic nanoparticles, and selective nanocatalysts. However, poor chemical stability and lack of insight into photophysics and plasmon decay mechanisms has impeded study. Here, we use smooth conformal ALD coating on copper nanoparticles to prevent surface oxidation, and study dephasing time for localized surface plasmons on different sized copper nanoparticles. Using dephasing time as a figure of merit, we elucidate the role of electron-electron, electron-phonon, impurity, surface and grain boundary scattering on the decay of localized surface plasmon waves. Using our quantitative analysis and different temperature dependent measurements, we show that electron-phonon interactions dominate over other scattering mechanisms in dephasing plasmon waves. While interband transitions in copper metal contributes substantially to plasmon losses, tuning surface plasmon modes to infrared frequencies leads to a five-fold enhancement in the quality factor. These findings demonstrate that conformal ALD coatings can improve the chemical stability for copper nanoparticles, even at high temperatures (>300 °C) in ambient atmosphere, and nanoscaled copper is a good alternative material for many potential applications in nanophotonics, plasmonics, catalysis and nanoscale electronics. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr04719b

Inverse Problems for Semilinear Wave Equations on Lorentzian Manifolds

NASA Astrophysics Data System (ADS)

Lassas, Matti; Uhlmann, Gunther; Wang, Yiran

2018-06-01

We consider inverse problems in space-time ( M, g), a 4-dimensional Lorentzian manifold. For semilinear wave equations {\\square_g u + H(x, u) = f}, where {\\square_g} denotes the usual Laplace-Beltrami operator, we prove that the source-to-solution map {L: f → u|_V}, where V is a neighborhood of a time-like geodesic {μ}, determines the topological, differentiable structure and the conformal class of the metric of the space-time in the maximal set, where waves can propagate from {μ} and return back. Moreover, on a given space-time ( M, g), the source-to-solution map determines some coefficients of the Taylor expansion of H in u.

Breaking Wave Impact on a Partially Submerged Rigid Cube in Deep Water

NASA Astrophysics Data System (ADS)

Ikeda, C. M.; Choquette, M.; Duncan, J. H.

2011-11-01

The impact of a plunging breaking wave on a partially submerged cube is studied experimentally. The experiments are performed in a wave tank that is 14.8 m long, 1.15 m wide and 2.2 m high with a water depth of 0.91 m. A single repeatable plunging breaker is generated from a dispersively focused wave packet (average frequency of 1.4 Hz) that is created with a programmable wave maker. The rigid (L = 30 . 5 cm) cube is centered in the width of the tank and mounted from above with one face oriented normal to the oncoming wave. The position of the center of the front face of the cube is varied from the breaker location (xb ~ 6 . 35 m) to xb + 0 . 05 m in the streamwise direction and from - 0 . 25 L to 0 . 25 L vertically relative to the mean water level. A high-speed digital camera is used to record both white-light and laser-induced fluorescence (LIF) movies of the free surface shape in front of the cube before and after the wave impact. When the wave hits the cube just as the plunging jet is formed, a high-velocity vertical jet is created and the trajectory and maximum height of the jet are strongly influenced by the vertical position of the cube. Supported by the Office of Naval Research, Contract Monitor R. D. Joslin.

Novel two-way artificial boundary condition for 2D vertical water wave propagation modelled with Radial-Basis-Function Collocation Method

NASA Astrophysics Data System (ADS)

Mueller, A.

2018-04-01

A new transparent artificial boundary condition for the two-dimensional (vertical) (2DV) free surface water wave propagation modelled using the meshless Radial-Basis-Function Collocation Method (RBFCM) as boundary-only solution is derived. The two-way artificial boundary condition (2wABC) works as pure incidence, pure radiation and as combined incidence/radiation BC. In this work the 2wABC is applied to harmonic linear water waves; its performance is tested against the analytical solution for wave propagation over horizontal sea bottom, standing and partially standing wave as well as wave interference of waves with different periods.

Comparison study of the partial-breast irradiation techniques: Dosimetric analysis of three-dimensional conformal radiation therapy, electron beam therapy, and helical tomotherapy depending on various tumor locations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Min-Joo; Park, So-Hyun; Research Institute of Biomedical Engineering, The Catholic University of Korea, Seoul

2013-10-01

The partial-breast irradiation (PBI) technique, an alternative to whole-breast irradiation, is a beam delivery method that uses a limited range of treatment volume. The present study was designed to determine the optimal PBI treatment modalities for 8 different tumor locations. Treatment planning was performed on computed tomography (CT) data sets of 6 patients who had received lumpectomy treatments. Tumor locations were classified into 8 subsections according to breast quadrant and depth. Three-dimensional conformal radiation therapy (3D-CRT), electron beam therapy (ET), and helical tomotherapy (H-TOMO) were utilized to evaluate the dosimetric effect for each tumor location. Conformation number (CN), radical dosemore » homogeneity index (rDHI), and dose delivered to healthy tissue were estimated. The Kruskal-Wallis, Mann-Whitney U, and Bonferroni tests were used for statistical analysis. The ET approach showed good sparing effects and acceptable target coverage for the lower inner quadrant—superficial (LIQ-S) and lower inner quadrant—deep (LIQ-D) locations. The H-TOMO method was the least effective technique as no evaluation index achieved superiority for all tumor locations except CN. The ET method is advisable for treating LIQ-S and LIQ-D tumors, as opposed to 3D-CRT or H-TOMO, because of acceptable target coverage and much lower dose applied to surrounding tissue.« less

Crystal structure of Halobacterium salinarum halorhodopsin with a partially depopulated primary chloride-binding site.

PubMed

Schreiner, Madeleine; Schlesinger, Ramona; Heberle, Joachim; Niemann, Hartmut H

2016-09-01

The transmembrane pump halorhodopsin in halophilic archaea translocates chloride ions from the extracellular to the cytoplasmic side upon illumination. In the ground state a tightly bound chloride ion occupies the primary chloride-binding site (CBS I) close to the protonated Schiff base that links the retinal chromophore to the protein. The light-triggered trans-cis isomerization of retinal causes structural changes in the protein associated with movement of the chloride ion. In reverse, chemical depletion of CBS I in Natronomonas pharaonis halorhodopsin (NpHR) through deprotonation of the Schiff base results in conformational changes of the protein: a state thought to mimic late stages of the photocycle. Here, crystals of Halobacterium salinarum halorhodopsin (HsHR) were soaked at high pH to provoke deprotonation of the Schiff base and loss of chloride. The crystals changed colour from purple to yellow and the occupancy of CBS I was reduced from 1 to about 0.5. In contrast to NpHR, this chloride depletion did not cause substantial conformational changes in the protein. Nevertheless, two observations indicate that chloride depletion could eventually result in structural changes similar to those found in NpHR. Firstly, the partially chloride-depleted form of HsHR has increased normalized B factors in the region of helix C that is close to CBS I and changes its conformation in NpHR. Secondly, prolonged soaking of HsHR crystals at high pH resulted in loss of diffraction. In conclusion, the conformation of the chloride-free protein may not be compatible with this crystal form of HsHR despite a packing arrangement that hardly restrains helices E and F that presumably move during ion transport.

A projection-based model reduction strategy for the wave and vibration analysis of rotating periodic structures

NASA Astrophysics Data System (ADS)

Beli, D.; Mencik, J.-M.; Silva, P. B.; Arruda, J. R. F.

2018-05-01

The wave finite element method has proved to be an efficient and accurate numerical tool to perform the free and forced vibration analysis of linear reciprocal periodic structures, i.e. those conforming to symmetrical wave fields. In this paper, its use is extended to the analysis of rotating periodic structures, which, due to the gyroscopic effect, exhibit asymmetric wave propagation. A projection-based strategy which uses reduced symplectic wave basis is employed, which provides a well-conditioned eigenproblem for computing waves in rotating periodic structures. The proposed formulation is applied to the free and forced response analysis of homogeneous, multi-layered and phononic ring structures. In all test cases, the following features are highlighted: well-conditioned dispersion diagrams, good accuracy, and low computational time. The proposed strategy is particularly convenient in the simulation of rotating structures when parametric analysis for several rotational speeds is usually required, e.g. for calculating Campbell diagrams. This provides an efficient and flexible framework for the analysis of rotordynamic problems.

Asymptotically simple spacetimes and mass loss due to gravitational waves

NASA Astrophysics Data System (ADS)

Saw, Vee-Liem

The cosmological constant Λ used to be a freedom in Einstein’s theory of general relativity (GR), where one had a proclivity to set it to zero purely for convenience. The signs of Λ or Λ being zero would describe universes with different properties. For instance, the conformal structure of spacetime directly depends on Λ: null infinity ℐ is a spacelike, null, or timelike hypersurface, if Λ > 0, Λ = 0, or Λ < 0, respectively. Recent observations of distant supernovae have taught us that our universe expands at an accelerated rate, and this can be accounted for by choosing Λ > 0 in Einstein’s theory of GR. A quantity that depends on the conformal structure of spacetime, especially on the nature of ℐ, is the Bondi mass which in turn dictates the mass loss of an isolated gravitating system due to energy carried away by gravitational waves. This problem of extending the Bondi mass to a universe with Λ > 0 has spawned intense research activity over the past several years. Some aspects include a closer inspection on the conformal properties, working with linearization, attempts using a Hamiltonian formulation based on “linearized” asymptotic symmetries, as well as obtaining the general asymptotic solutions of de Sitter-like spacetimes. We consolidate on the progress thus far from the various approaches that have been undertaken, as well as discuss the current open problems and possible directions in this area.

A Measure of the Conformity of a Parameter Set to a Trend: The Partially Ordered Case.

DTIC Science & Technology

1983-05-01

A-A3214 A MEASURE OF THE CONFORMIYO QAPARAMEfERSETO QA / TREND: THE PARTIAL .U) IOWA UNIV IOWA CIT DEPT OF ......STATISTICS AND ACTURIAL SCIENCE.T...and j with i o j. Such a vector 0 = (Oi,0j,.... 0k is said to be isotone (with respect to _). In studying such inference procedures it is helpful to...noticed that none of the measures studied here are applicable in alIl the situations considered. In studying locat ion pa rameter- wlhich are not

Acoustic scattering of a Bessel vortex beam by a rigid fixed spheroid

NASA Astrophysics Data System (ADS)

Mitri, F. G.

2015-12-01

Partial-wave series representation of the acoustic scattering field of high-order Bessel vortex beams by rigid oblate and prolate spheroids using the modal matching method is developed. The method, which is applicable to slightly elongated objects at low-to-moderate frequencies, requires solving a system of linear equations which depends on the partial-wave index n and the order of the Bessel vortex beam m using truncated partial-wave series expansions (PWSEs), and satisfying the Neumann boundary condition for a rigid immovable surface in the least-squares sense. This original semi-analytical approach developed for Bessel vortex beams is demonstrated for finite oblate and prolate spheroids, where the mathematical functions describing the spheroidal geometry are written in a form involving single angular (polar) integrals that are numerically computed. The transverse (θ = π / 2) and 3D scattering directivity patterns are evaluated in the far-field for both prolate and oblate spheroids, with particular emphasis on the aspect ratio (i.e., the ratio of the major axis over the minor axis of the spheroid) not exceeding 3:1, the half-cone angle β and order m of the Bessel vortex beam, as well as the dimensionless size parameter kr0. Periodic oscillations in the magnitude plots of the far-field scattering form function are observed, which result from the interference of the reflected waves with the circumferential (Franz') waves circumnavigating the surface of the spheroid in the surrounding fluid. Moreover, the 3D directivity patterns illustrate the far-field scattering from the spheroid, that vanishes in the forward (θ = 0) and backward (θ = π) directions. Particular applications in underwater acoustics and scattering, acoustic levitation and the detection of submerged elongated objects using Bessel vortex waves to name a few, would benefit from the results of the present investigation.

Dosimetric comparison of 3D conformal, IMRT, and V-MAT techniques for accelerated partial-breast irradiation (APBI)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qiu, Jian-Jian; Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai

2014-07-01

The purpose is to dosimetrically compare the following 3 delivery techniques: 3-dimensional conformal radiation therapy (3D-CRT), intensity-modulated arc therapy (IMRT), and volumetric-modulated arc therapy (V-MAT) in the treatment of accelerated partial-breast irradiation (APBI). Overall, 16 patients with T1/2N0 breast cancer were treated with 3D-CRT (multiple, noncoplanar photon fields) on the RTOG 0413 partial-breast trial. These cases were subsequently replanned using static gantry IMRT and V-MAT technology to understand dosimetric differences among these 3 techniques. Several dosimetric parameters were used in plan quality evaluation, including dose conformity index (CI) and dose-volume histogram analysis of normal tissue coverage. Quality assurance studies includingmore » gamma analysis were performed to compare the measured and calculated dose distributions. The IMRT and V-MAT plans gave more conformal target dose distributions than the 3D-CRT plans (p < 0.05 in CI). The volume of ipsilateral breast receiving 5 and 10 Gy was significantly less using the V-MAT technique than with either 3D-CRT or IMRT (p < 0.05). The maximum lung dose and the ipsilateral lung volume receiving 10 (V{sub 10}) or 20 Gy (V{sub 20}) were significantly less with both V-MAT and IMRT (p < 0.05). The IMRT technique was superior to 3D-CRT and V-MAT of low dose distributions in ipsilateral lung (p < 0.05 in V{sub 5} and D{sub 5}). The total mean monitor units (MUs) for V-MAT (621.0 ± 111.9) were 12.2% less than those for 3D-CRT (707.3 ± 130.9) and 46.5% less than those for IMRT (1161.4 ± 315.6) (p < 0.05). The average machine delivery time was 1.5 ± 0.2 minutes for the V-MAT plans, 7.0 ± 1.6 minutes for the 3D-CRT plans, and 11.5 ± 1.9 minutes for the IMRT plans, demonstrating much less delivery time for V-MAT. Based on this preliminary study, V-MAT and IMRT techniques offer improved dose conformity as compared with 3D-CRT techniques without increasing dose to the ipsilateral lung. In terms of MU and delivery time, V-MAT is significantly more efficient for APBI than for conventional 3D-CRT and static-beam IMRT.« less

Pyruvate Dehydrogenase Kinase-4 Structures Reveal a Metastable Open Conformation Fostering Robust Core-free Basal Activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wynn, R. Max; Kato, Masato; Chuang, Jacinta L.

2008-10-21

Human pyruvate dehydrogenase complex (PDC) is down-regulated by pyruvate dehydrogenase kinase (PDK) isoforms 1-4. PDK4 is overexpressed in skeletal muscle in type 2 diabetes, resulting in impaired glucose utilization. Here we show that human PDK4 has robust core-free basal activity, which is considerably higher than activity levels of other PDK isoforms stimulated by the PDC core. PDK4 binds the L3 lipoyl domain, but its activity is not significantly stimulated by any individual lipoyl domains or the core of PDC. The 2.0-{angstrom} crystal structures of the PDK4 dimer with bound ADP reveal an open conformation with a wider active-site cleft, comparedmore » with that in the closed conformation epitomized by the PDK2-ADP structure. The open conformation in PDK4 shows partially ordered C-terminal cross-tails, in which the conserved DW (Asp{sup 394}-Trp{sup 395}) motif from one subunit anchors to the N-terminal domain of the other subunit. The open conformation fosters a reduced binding affinity for ADP, facilitating the efficient removal of product inhibition by this nucleotide. Alteration or deletion of the DW-motif disrupts the C-terminal cross-tail anchor, resulting in the closed conformation and the nearly complete inactivation of PDK4. Fluorescence quenching and enzyme activity data suggest that compounds AZD7545 and dichloroacetate lock PDK4 in the open and the closed conformational states, respectively. We propose that PDK4 with bound ADP exists in equilibrium between the open and the closed conformations. The favored metastable open conformation is responsible for the robust basal activity of PDK4 in the absence of the PDC core.« less

Pyruvate dehydrogenase kinase-4 structures reveal a metastable open conformation fostering robust core-free basal activity.

PubMed

Wynn, R Max; Kato, Masato; Chuang, Jacinta L; Tso, Shih-Chia; Li, Jun; Chuang, David T

2008-09-12

Human pyruvate dehydrogenase complex (PDC) is down-regulated by pyruvate dehydrogenase kinase (PDK) isoforms 1-4. PDK4 is overexpressed in skeletal muscle in type 2 diabetes, resulting in impaired glucose utilization. Here we show that human PDK4 has robust core-free basal activity, which is considerably higher than activity levels of other PDK isoforms stimulated by the PDC core. PDK4 binds the L3 lipoyl domain, but its activity is not significantly stimulated by any individual lipoyl domains or the core of PDC. The 2.0-A crystal structures of the PDK4 dimer with bound ADP reveal an open conformation with a wider active-site cleft, compared with that in the closed conformation epitomized by the PDK2-ADP structure. The open conformation in PDK4 shows partially ordered C-terminal cross-tails, in which the conserved DW (Asp(394)-Trp(395)) motif from one subunit anchors to the N-terminal domain of the other subunit. The open conformation fosters a reduced binding affinity for ADP, facilitating the efficient removal of product inhibition by this nucleotide. Alteration or deletion of the DW-motif disrupts the C-terminal cross-tail anchor, resulting in the closed conformation and the nearly complete inactivation of PDK4. Fluorescence quenching and enzyme activity data suggest that compounds AZD7545 and dichloroacetate lock PDK4 in the open and the closed conformational states, respectively. We propose that PDK4 with bound ADP exists in equilibrium between the open and the closed conformations. The favored metastable open conformation is responsible for the robust basal activity of PDK4 in the absence of the PDC core.

Analysis of an Hp-Non-conforming Discontinuous Galerkin Spectral Element Method for Wave

DTIC Science & Technology

2011-04-01

Scientific Computing, 36 (2008), pp. 351–390. [25] Eleuterio F . Toro , Riemann Solvers and Numerical Methods for Fluid Dynamics, Springer, 1999. [26...denoted by ñ, and the contravariant flux [15] is defined as F̃i = Jeai · F , i = 1, 2, 3, with ai as the contravariant basis vectors. We now describe...wave propagation case by the following definitions, q = ( E v ) ∈ V, Q = ( I 0 0 ρI ) , g = ( 0 f ) ∈ V, with I denoting the fourth-order identity tensor

Stability of the sum of two solitary waves for (gDNLS) in the energy space

NASA Astrophysics Data System (ADS)

Tang, Xingdong; Xu, Guixiang

2018-03-01

In this paper, we continue the study in [18]. We use the perturbation argument, modulational analysis and the energy argument in [15,16] to show the stability of the sum of two solitary waves with weak interactions for the generalized derivative Schrödinger equation (gDNLS) in the energy space. Here (gDNLS) hasn't the Galilean transformation invariance, the pseudo-conformal invariance and the gauge transformation invariance, and the case σ > 1 we considered corresponds to the L2-supercritical case.

S-Matrix to potential inversion of low-energy α-12C phase shifts

NASA Astrophysics Data System (ADS)

Cooper, S. G.; Mackintosh, R. S.

1990-10-01

The IP S-matrix to potential inversion procedure is applied to phase shifts for selected partial waves over a range of energies below the inelastic threshold for α-12C scattering. The phase shifts were determined by Plaga et al. Potentials found by Buck and Rubio to fit the low-energy alpha cluster resonances need only an increased attraction in the surface to accurately reproduce the phase-shift behaviour. Substantial differences between the potentials for odd and even partial waves are necessary. The surface tail of the potential is postulated to be a threshold effect.

Huygens-Fresnel picture for electron-molecule elastic scattering★

NASA Astrophysics Data System (ADS)

Baltenkov, Arkadiy S.; Msezane, Alfred Z.

2017-11-01

The elastic scattering cross sections for a slow electron by C2 and H2 molecules have been calculated within the framework of the non-overlapping atomic potential model. For the amplitudes of the multiple electron scattering by a target the wave function of the molecular continuum is represented as a combination of a plane wave and two spherical waves generated by the centers of atomic spheres. This wave function obeys the Huygens-Fresnel principle according to which the electron wave scattering by a system of two centers is accompanied by generation of two spherical waves; their interaction creates a diffraction pattern far from the target. Each of the Huygens waves, in turn, is a superposition of the partial spherical waves with different orbital angular momenta l and their projections m. The amplitudes of these partial waves are defined by the corresponding phases of electron elastic scattering by an isolated atomic potential. In numerical calculations the s- and p-phase shifts are taken into account. So the number of interfering electron waves is equal to eight: two of which are the s-type waves and the remaining six waves are of the p-type with different m values. The calculation of the scattering amplitudes in closed form (rather than in the form of S-matrix expansion) is reduced to solving a system of eight inhomogeneous algebraic equations. The differential and total cross sections of electron scattering by fixed-in-space molecules and randomly oriented ones have been calculated as well. We conclude by discussing the special features of the S-matrix method for the case of arbitrary non-spherical potentials. Contribution to the Topical Issue "Low energy positron and electron interactions", edited by James Sullivan, Ron White, Michael Bromley, Ilya Fabrikant, and David Cassidy.

Tradition and Innovation in Russian Church Slavonic Hymnography

ERIC Educational Resources Information Center

Nelson, Elena Margaret

2010-01-01

The focus of this dissertation is the highly specialized and stylized liturgical language of Russian Church Slavonic (RCS). Historically, RCS has been strictly controlled by authorities and has conformed to established norms, but innovations have nevertheless arisen in response to various conditions. One major wave of innovations was a long,…

Supersonic flow with feeding of energy

NASA Technical Reports Server (NTRS)

Zaremba, W.

1985-01-01

The present work discusses the results of some experimental studies on the possibility of attenuating shock waves in a supersonic flow. The shock waves were formed by an external source of electrical energy. An electromechanical method is described that permits partial recovery of the expended energy.

A study of 3π production in γp → n -π +π +π - and γ-p → Δ + +π +π -π - with CLAS at Jefferson Lab ->n

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsaris, Aristedis

2016-02-22

Apart from the mesons that the constituent quark model predicts, QCD allows for additional states beyond the qq system. Previous experiments have performed partial wave analysis on pion-production data and claim observation of an exotic J PC = 1 -+ state decaying via p-π. The g12 experiment took place at Jefferson Lab using the CLAS spectrometer, a liquid hydrogen target was used and a tagged photon beam. By studying the reactions γp → n -π +π +π - and γp → Δ + +π +π -π -, the photoproduction of mesons decaying to 3-pi was studied using two different butmore » complimentary channels. Events are selected with low four-momentum transfer to the baryon, in order to enhance one pion exchange production. For both 3-pi systems the data exhibit two intermediate decays, p-pi and f 2π. For the γp → n -π +π +π - reaction over 600k events were acquired resulting in the largest 3 photoproduction dataset to date. The exotic J PC = 1 -+ partial wave does not show resonant behavior and more so it is strongly consistent with a non-resonant non-interfering wave relative to a resonant π 2(1670). Furthermore, the partial wave analysis shows production of the a 2(1320) and π 2(1670) mesons. For the first time we report observation of a photoproduced a 1(1260) meson. For the γp → Δ + +π +π -π - reaction nearly 350k events were analyzed. A partial wave analysis was performed for the first time on this channel. The a1(1260), a2(1320), and the 2(1670) mesons were observed. Observation of the a1(1260) confirms the result first reported in γp → n -π +π +π - reaction.« less

Nucleic Acid-Dependent Conformational Changes in CRISPR-Cas9 Revealed by Site-Directed Spin Labeling.

PubMed

Vazquez Reyes, Carolina; Tangprasertchai, Narin S; Yogesha, S D; Nguyen, Richard H; Zhang, Xiaojun; Rajan, Rakhi; Qin, Peter Z

2017-06-01

In a type II clustered regularly interspaced short palindromic repeats (CRISPR) system, RNAs that are encoded at the CRISPR locus complex with the CRISPR-associated (Cas) protein Cas9 to form an RNA-guided nuclease that cleaves double-stranded DNAs at specific sites. In recent years, the CRISPR-Cas9 system has been successfully adapted for genome engineering in a wide range of organisms. Studies have indicated that a series of conformational changes in Cas9, coordinated by the RNA and the target DNA, direct the protein into its active conformation, yet details on these conformational changes, as well as their roles in the mechanism of function of Cas9, remain to be elucidated. Here, nucleic acid-dependent conformational changes in Streptococcus pyogenes Cas9 (SpyCas9) were investigated using the method of site-directed spin labeling (SDSL). Single nitroxide spin labels were attached, one at a time, at one of the two native cysteine residues (Cys80 and Cys574) of SpyCas9, and the spin-labeled proteins were shown to maintain their function. X-band continuous-wave electron paramagnetic resonance spectra of the nitroxide attached at Cys80 revealed conformational changes of SpyCas9 that are consistent with a large-scale domain re-arrangement upon binding to its RNA partner. The results demonstrate the use of SDSL to monitor conformational changes in CRISPR-Cas9, which will provide key information for understanding the mechanism of CRISPR function.

Personality Disorders Associated with Full and Partial Posttraumatic Stress Disorder in the U.S. Population: Results from Wave 2 of the National Epidemiologic Survey on Alcohol and Related Conditions

PubMed Central

Pietrzak, Robert H.; Goldstein, Risë B.; Southwick, Steven M.; Grant, Bridget F.

2010-01-01

Background While it is well known that personality disorders are associated with trauma exposure and PTSD, limited nationally representative data are available on DSM-IV personality disorders that co-occur with posttraumatic stress disorder (PTSD) and partial PTSD. Methods Face-to-face interviews were conducted with 34,653 adults participating in the Wave 2 National Epidemiologic Survey on Alcohol and Related Conditions. Logistic regression analyses controlling for sociodemographics and additional psychiatric comorbidity evaluated associations of PTSD and partial PTSD with personality disorders. Results Prevalence rates of lifetime PTSD and partial PTSD were 6.4% and 6.6%, respectively. After adjustment for sociodemographic characteristics and additional psychiatric comorbidity, respondents with full PTSD were more likely than trauma controls to meet criteria for schizotypal, narcissistic, and borderline personality disorders (ORs=2.1–2.5); and respondents with partial PTSD were more likely than trauma controls to meet diagnostic criteria for borderline (OR=2.0), schizotypal (OR=1.8), and narcissistic (OR=1.6) PDs. Women with PTSD were more likely than controls to have obsessive-compulsive PD. Women with partial PTSD were more likely than controls to have antisocial PD; and men with partial PTSD were less likely than women with partial PTSD to have avoidant PD. Conclusions PTSD and partial PTSD are associated with borderline, schizotypal, and narcissistic personality disorders. Modestly higher rates of obsessive-compulsive PD were observed among women with full PTSD, and of antisocial PD among women with partial PTSD. PMID:20950823

Electron acceleration by inertial Alfven waves

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, B.J.; Lysak, R.L.

1996-03-01

Alfven waves reflected by the ionosphere and by inhomogeneities in the Alfven speed can develop an oscillating parallel electric field when electron inertial effects are included. These waves, which have wavelengths of the order of an Earth radius, can develop a coherent structure spanning distances of several Earth radii along geomagnetic field lines. This system has characteristic frequencies in the range of 1 Hz and can exhibit electric fields capable of accelerating electrons in several senses: via Landua resonance, bounce or transit time resonance as discussed by Andre and Eliasson or through the effective potential drop which appears when themore » transit time of the electrons is much smaller than the wave period, so that the electric fields appear effectively static. A time-dependent model of wave propagation is developed which represents inertial Alfven wave propagation along auroral field lines. The disturbance is modeled as it travels earthward, experiences partial reflections in regions of rapid variation, and finally reflects off a conducting ionosphere to continue propagating antiearthward. The wave experiences partial trapping by the ionospheric and the Alfven speed peaks discussed earlier by Polyakov and Rapoport and Trakhtengerts and Feldstein and later by Lysak. Results of the wave simulation and an accompanying test particle simulation are presented, which indicate that inertial Alfven waves are a possible mechanism for generating electron conic distributions and field-aligned particle precipitation. The model incorporates conservation of energy by allowing electrons to affect the wave via Landau damping, which appears to enhance the effect of the interactions which heat electron populations. 22 refs., 14 figs.« less

On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brokaw, Jason B.; Chu, Jhih-wei

2010-11-17

We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier worksmore » of coarse-grained modeling. The trajectories of the all-atom molecular-dynamics simulations revealed the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK did not show prominent variation during the transition between closed and open forms. Finally, we characterized the effects of local unfolding of an important hinge near Pro177 on the closed-to-open transition of AK and identified a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro177 hinge induces alternative tertiary contacts that stabilize the closed structure and prevent the opening transition.« less

On conforming mixed finite element methods for incompressible viscous flow problems

NASA Technical Reports Server (NTRS)

Gunzburger, M. D; Nicolaides, R. A.; Peterson, J. S.

1982-01-01

The application of conforming mixed finite element methods to obtain approximate solutions of linearized Navier-Stokes equations is examined. Attention is given to the convergence rates of various finite element approximations of the pressure and the velocity field. The optimality of the convergence rates are addressed in terms of comparisons of the approximation convergence to a smooth solution in relation to the best approximation available for the finite element space used. Consideration is also devoted to techniques for efficient use of a Gaussian elimination algorithm to obtain a solution to a system of linear algebraic equations derived by finite element discretizations of linear partial differential equations.

On the Weyl anomaly of 4D conformal higher spins: a holographic approach

NASA Astrophysics Data System (ADS)

Acevedo, S.; Aros, R.; Bugini, F.; Diaz, D. E.

2017-11-01

We present a first attempt to derive the full (type-A and type-B) Weyl anomaly of four dimensional conformal higher spin (CHS) fields in a holographic way. We obtain the type-A and type-B Weyl anomaly coefficients for the whole family of 4D CHS fields from the one-loop effective action for massless higher spin (MHS) Fronsdal fields evaluated on a 5D bulk Poincaré-Einstein metric with an Einstein metric on its conformal boundary. To gain access to the type-B anomaly coefficient we assume, for practical reasons, a Lichnerowicz-type coupling of the bulk Fronsdal fields with the bulk background Weyl tensor. Remarkably enough, our holographic findings under this simplifying assumption are certainly not unknown: they match the results previously found on the boundary counterpart under the assumption of factorization of the CHS higher-derivative kinetic operator into Laplacians of "partially massless" higher spins on Einstein backgrounds.

Maximum entropy analysis of NMR data of flexible multirotor molecules partially oriented in nematic solution: 2,2':5',2″-terthiophene, 2,2'- and 3,3'-dithiophene

NASA Astrophysics Data System (ADS)

Caldarelli, Stefano; Catalano, Donata; Di Bari, Lorenzo; Lumetti, Marco; Ciofalo, Maurizio; Alberto Veracini, Carlo

1994-07-01

The dipolar couplings observed by NMR spectroscopy of solutes in nematic solvents (LX-NMR) are used to build up the maximum entropy (ME) probability distribution function of the variables describing the orientational and internal motion of the molecule. The ME conformational distributions of 2,2'- and 3,3'-dithiophene and 2,2':5',2″-terthiophene (α-terthienyl)thus obtained are compared with the results of previous studies. The 2,2'- and 3,3'-dithiophene molecules exhibit equilibria among cisoid and transoid forms; the probability maxima correspond to planar and twisted conformers for 2,2'- or 3,3'-dithiophene, respectively, 2,2':5',2″-Terthiophene has two internal degrees of freedom; the ME approach indicates that the trans, trans and cis, trans planar conformations are the most probable. The correlation between the two intramolecular rotations is also discussed.

Hidden symmetry in the presence of fluxes

NASA Astrophysics Data System (ADS)

Kubizňák, David; Warnick, Claude M.; Krtouš, Pavel

2011-03-01

We derive the most general first-order symmetry operator for the Dirac equation coupled to arbitrary fluxes. Such an operator is given in terms of an inhomogeneous form ω which is a solution to a coupled system of first-order partial differential equations which we call the generalized conformal Killing-Yano system. Except trivial fluxes, solutions of this system are subject to additional constraints. We discuss various special cases of physical interest. In particular, we demonstrate that in the case of a Dirac operator coupled to the skew symmetric torsion and U(1) field, the system of generalized conformal Killing-Yano equations decouples into the homogeneous conformal Killing-Yano equations with torsion introduced in D. Kubiznak et al. (2009) [8] and the symmetry operator is essentially the one derived in T. Houri et al. (2010) [9]. We also discuss the Dirac field coupled to a scalar potential and in the presence of 5-form and 7-form fluxes.

Quantitative determination of the conformational properties of partially folded and intrinsically disordered proteins using NMR dipolar couplings.

PubMed

Jensen, Malene Ringkjøbing; Markwick, Phineus R L; Meier, Sebastian; Griesinger, Christian; Zweckstetter, Markus; Grzesiek, Stephan; Bernadó, Pau; Blackledge, Martin

2009-09-09

Intrinsically disordered proteins (IDPs) inhabit a conformational landscape that is too complex to be described by classical structural biology, posing an entirely new set of questions concerning the molecular understanding of functional biology. The characterization of the conformational properties of IDPs, and the elucidation of the role they play in molecular function, is therefore one of the major challenges remaining for modern structural biology. NMR is the technique of choice for studying this class of proteins, providing information about structure, flexibility, and interactions at atomic resolution even in completely disordered states. In particular, residual dipolar couplings (RDCs) have been shown to be uniquely sensitive and powerful tools for characterizing local and long-range structural behavior in disordered proteins. In this review we describe recent applications of RDCs to quantitatively describe the level of local structure and transient long-range order in IDPs involved in viral replication, neurodegenerative disease, and cancer.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suh, In-Saeng; Mathews, Grant J.; Haywood, J. Reese

The spatially conformally flat approximation (CFA) is a viable method to deduce initial conditions for the subsequent evolution of binary neutron stars employing the full Einstein equations. Here in this paper, we analyze the viability of the CFA for the general relativistic hydrodynamic initial conditions of binary neutron stars. We illustrate the stability of the conformally flat condition on the hydrodynamics by numerically evolving ~100 quasicircular orbits. We illustrate the use of this approximation for orbiting neutron stars in the quasicircular orbit approximation to demonstrate the equation of state dependence of these initial conditions and how they might affect themore » emergent gravitational wave frequency as the stars approach the innermost stable circular orbit.« less

The analytic structure of conformal blocks and the generalized Wilson-Fisher fixed points

DOE PAGES

Gliozzi, Ferdinando; Guerrieri, Andrea L.; Petkou, Anastasios C.; ...

2017-04-11

Here, we describe in detail the method used in our previous work arXiv:1611.10344 to study the Wilson-Fisher critical points nearby generalized free CFTs, exploiting the analytic structure of conformal blocks as functions of the conformal dimension of the exchanged operator. Our method is equivalent to the mechanism of conformal multiplet recombination set up by null states. We also compute, to the first non-trivial order in the ε-expansion, the anomalous dimensions and the OPE coefficients of infinite classes of scalar local operators using just CFT data. We study single-scalar and O(N)-invariant theories, as well as theories with multiple deformations. When availablemore » we agree with older results, but we also produce a wealth of new ones. Furthermore, unitarity and crossing symmetry are not used in our approach and we are able to apply our method to non-unitary theories as well. Some implications of our results for the study of the non-unitary theories containing partially conserved higher-spin currents are briefly mentioned.« less

Separability of black holes in string theory

NASA Astrophysics Data System (ADS)

Keeler, Cynthia; Larsen, Finn

2012-10-01

We analyze the origin of separability for rotating black holes in string theory, considering both massless and massive geodesic equations as well as the corresponding wave equations. We construct a conformal Killing-Stackel tensor for a general class of black holes with four independent charges, then identify two-charge configurations where enhancement to an exact Killing-Stackel tensor is possible. We show that further enhancement to a conserved Killing-Yano tensor is possible only for the special case of Kerr-Newman black holes. We construct natural null congruences for all these black holes and use the results to show that only the Kerr-Newman black holes are algebraically special in the sense of Petrov. Modifying the asymptotic behavior by the subtraction procedure that induces an exact SL(2)2 also preserves only the conformal Killing-Stackel tensor. Similarly, we find that a rotating Kaluza-Klein black hole possesses a conformal Killing-Stackel tensor but has no further enhancements.

Impact of plunging breaking waves on a partially submerged cube

NASA Astrophysics Data System (ADS)

Wang, A.; Ikeda, C.; Duncan, J. H.

2013-11-01

The impact of a deep-water plunging breaking wave on a partially submerged cube is studied experimentally in a tank that is 14.8 m long and 1.2 m wide with a water depth of 0.91 m. The breakers are created from dispersively focused wave packets generated by a programmable wave maker. The water surface profile in the vertical center plane of the cube is measured using a cinematic laser-induced fluorescence technique with movie frame rates ranging from 300 to 4,500 Hz. The pressure distribution on the front face of the cube is measured with 24 fast-response sensors simultaneously with the wave profile measurements. The cube is positioned vertically at three heights relative to the mean water level and horizontally at a distance from the wave maker where a strong vertical water jet is formed. The portion of the water surface between the contact point on the front face of the cube and the wave crest is fitted with a circular arc and the radius and vertical position of the fitted circle is tracked during the impact. The vertical acceleration of the contact point reaches more than 50 times the acceleration of gravity and the pressure distribution just below the free surface shows a localized high-pressure region with a very high vertical pressure gradient. This work is supported by the Office of Naval Research under grant N000141110095.

Paths to equilibrium in non-conformal collisions

NASA Astrophysics Data System (ADS)

Attems, Maximilian; Bea, Yago; Casalderrey-Solana, Jorge; Mateos, David; Santos-Oliván, Daniel; Sopuerta, Carlos F.; Triana, Miquel; Zilhão, Miguel

2018-03-01

Ever since fast hydrodynamization has been observed in heavy ion collisions the understanding of the hot early out-of-equilibrium stage of such collisions has been a topic of intense research. We use the gauge/gravity duality to model the creation of a strongly coupled Quark-Gluon plasma in a non-conformal gauge theory. This numerical relativity study is the first non-conformal holographic simulation of a heavy ion collision and reveals the existence of new relaxation channels due to the presence of non-vanishing bulk viscosity. We study shock wave collisions at different energies in gauge theories with different degrees of non-conformality and compare three relaxation times which can occur in different orderings: the hydrodynamization time (when hydrodynamics becomes applicable), the EoSization time (when the average pressure approaches its equilibrium value) and the condensate relaxation time (when the expectation value of a scalar operator approaches its equilibrium value). We find that these processes can occur in several different orderings. In particular, the condensate can remain far from equilibrium even long after the plasma has hydrodynamized and EoSized.

Conformational dependence of a protein kinase phosphate transfer reaction.

PubMed

Henkelman, Graeme; LaBute, Montiago X; Tung, Chang-Shung; Fenimore, P W; McMahon, Benjamin H

2005-10-25

Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In TC, we calculate that the reactants and products are nearly isoenergetic with a 20-kJ/mol barrier, whereas phosphate transfer is unfavorable by 120 kJ/mol in the RC, with an even higher barrier. With the protein in TC, the motions involved in reaction are small, with only P(gamma) and the catalytic proton moving >0.5 A. Examination of the structures reveals that in the RC the active site cleft is not completely closed and there is insufficient space for the phosphorylated serine residue in the product state. Together, these observations imply that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an angstrom in the catalytic site.

The Shock and Vibration Digest. Volume 16, Number 11

DTIC Science & Technology

1984-11-01

wave [19], a secular equation for Rayleigh waves on ing, seismic risk, and related problems are discussed. the surface of an anisotropic half-space...waves in an !so- tive equation of an elastic-plastic rack medium was....... tropic linear elastic half-space with plane material used; the coefficient...pair of semi-linear hyperbolic partial differential -- " Conditions under which the equations of motion equations governing slow variations in amplitude

Biliary lithotripsy can be enhanced with proper ultrasound probe position.

PubMed

Affronti, J; Flournoy, T; Akers, S; Baillie, J

1992-04-01

We have demonstrated in our in vitro system that an extracorporeal lithotripter utilizing a movable ultrasound probe can fragment gallstones more effectively when the ultrasound probe is not partially blocking shock waves. Using a pressure transducer we measured the pressures in the focal volume of a Wolf Piezolith 2300 lithotripter with the ultrasound probe fully extended and fully retracted. We also chose 12 pairs of twin gallstones, each taken from the same gallbladder. One stone from each pair was subjected to shock waves while the ultrasound probe was fully extended and the other treated while the probe was fully retracted. Shock wave pressures (which are converted to a measurable voltage output by our transducer) were clearly lower when the ultrasound probe was extended (5.45 volts; SEM = 0.10 volts) as compared to when the ultrasound scanner was retracted (6.7 volts: SEM = 0.08 volts). Significantly more shock waves were required to completely fragment stones when the ultrasound scanner was extended than when it was retracted (p = 0.01 using the nonparametric Wilcoxon's signed rank test). These results show that, in the lithotripter tested, an extended in-line ultrasound scanner can partially block shock waves. Retraction of an extendible ultrasound probe may enhance stone fragmentation when operating at the highest shock wave intensity.

SU-E-T-217: Comprehensive Dosimetric Evaluation On 3D-CRT, IMRT and Non-Coplanar Arc Treatment for Prone Accelerated Partial Breast Irradiation (APBI)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chiu, T; Yan, Y; Ramirez, E

2015-06-15

Purpose: Accelerated partial breast irradiation (APBI) is an effective treatment for early stage breast-cancer. Irradiation in a prone position can mitigate breast motion and spare heart and lung. In this study, a comprehensive study is performed to evaluate various treatment techniques for prone APBI treatment including: 3D-CRT, IMRT, co-planar and non-coplanar partial arcs treatment. Methods: In this treatment planning study, a left breast patient treated in prone position in our clinic was imported into Varian Eclipse TPS. Six beams tangential to chest wall were used in both 3D-CRT and IMRT plans. These six beams were coplanar in a transactional planemore » achieved by both gantry and couch rotation. A 60-beam IMRT plan was also created to explore the maximum benefit of co-planar IMRT. Within deliverable couch rotation range (±30°), partial arc treatment plans with one and up to ten couch positions were generated for comparison. For each plan, 30Gy in 6 fractions was prescribed to 95% PTV volume. Critical dosimetric parameters, such as conformity index, mean, maximum, and volume dose of organ at risk, are evaluated. Results: The conformity indexes (CI) are 3.53, 3.17, 2.21 and 1.08 respectively to 3D-CRT, 6-beam IMRT, 60-beam IMRT, and two-partial-arcs coplanar plans. However, arc plans increase heart dose. CI for non-coplanar arc plans decreases from 1.19 to 1.10 when increases couch positions. Maximum dose in ipsilateral lung (1.98 to 1.13 Gy), and heart (0.62 to 0.43 Gy) are steadily decreased with the increased number of non-coplanar arcs. Conclusions: The dosimetric evaluation results show that partial arc plans have improved CIs compared to conventional 3D-CRT and IMRT plans. Increasing number of partial arcs decreases lung and heart dose. The dosimetric benefit obtained from non-coplanar arcs should be considered with treatment delivery time.« less

The C-terminal region of translesion synthesis DNA polymerase η is partially unstructured and has high conformational flexibility

PubMed Central

Powers, Kyle T; Washington, M Todd

2018-01-01

Abstract Eukaryotic DNA polymerase η catalyzes translesion synthesis of thymine dimers and 8-oxoguanines. It is comprised of a polymerase domain and a C-terminal region, both of which are required for its biological function. The C-terminal region mediates interactions with proliferating cell nuclear antigen (PCNA) and other translesion synthesis proteins such as Rev1. This region contains a ubiquitin-binding/zinc-binding (UBZ) motif and a PCNA-interacting protein (PIP) motif. Currently little structural information is available for this region of polymerase η. Using a combination of approaches—including genetic complementation assays, X-ray crystallography, Langevin dynamics simulations, and small-angle X-ray scattering—we show that the C-terminal region is partially unstructured and has high conformational flexibility. This implies that the C-terminal region acts as a flexible tether linking the polymerase domain to PCNA thereby increasing its local concentration. Such tethering would facilitate the sampling of translesion synthesis polymerases to ensure that the most appropriate one is selected to bypass the lesion. PMID:29385534

Atomic Charge Parameters for the Finite Difference Poisson-Boltzmann Method Using Electronegativity Neutralization.

PubMed

Yang, Qingyi; Sharp, Kim A

2006-07-01

An optimization of Rappe and Goddard's charge equilibration (QEq) method of assigning atomic partial charges is described. This optimization is designed for fast and accurate calculation of solvation free energies using the finite difference Poisson-Boltzmann (FDPB) method. The optimization is performed against experimental small molecule solvation free energies using the FDPB method and adjusting Rappe and Goddard's atomic electronegativity values. Using a test set of compounds for which experimental solvation energies are available and a rather small number of parameters, very good agreement was obtained with experiment, with a mean unsigned error of about 0.5 kcal/mol. The QEq atomic partial charge assignment method can reflect the effects of the conformational changes and solvent induction on charge distribution in molecules. In the second section of the paper we examined this feature with a study of the alanine dipeptide conformations in water solvent. The different contributions to the energy surface of the dipeptide were examined and compared with the results from fixed CHARMm charge potential, which is widely used for molecular dynamics studies.

Studies on interaction of norbixin with DNA: Multispectroscopic and in silico analysis

NASA Astrophysics Data System (ADS)

Anantharaman, Amrita; Priya, Rajendra Rao; Hemachandran, Hridya; Sivaramakrishna, Akella; Babu, Subramanian; Siva, Ramamoorthy

2015-06-01

The interaction of food colorant norbixin with calf thymus DNA (CTDNA) was investigated through UV-Visible spectroscopy, Fourier Transform Infrared (FTIR), Circular Dichroism (CD), Nuclear Magnetic Resonance (NMR), DNA melting studies, electrophoretic analysis, histological staining technique and molecular docking studies. The results indicated that norbixin interacted with CTDNA by partial intercalation mode. The binding constant (K) of norbixin with CTDNA was calculated to be 5.08 × 105 Mol-1 L. FTIR and CD studies were coupled with 1H NMR spectra revealed that norbixin intercalates partially and binds to the groove's, phosphate group, deoxyribose sugar of DNA and also induces conformational transition of B-form to A-form DNA. Agarose gel electrophoretic and histological staining technique results further prove that, norbixin specifically binds to the DNA in the cell. Moreover, molecular docking studies on the specific binding of norbixin with CTDNA have exhibited lowest conformation energy score of -3.2. Therefore, this food colorant has the ability to interact with DNA and it could emerge as a promising class of natural DNA targeted therapeutic.

A magnesium-induced triplex pre-organizes the SAM-II riboswitch

PubMed Central

Roy, Susmita; Lammert, Heiko; Dayie, T. Kwaku; Sanbonmatsu, Karissa Y.

2017-01-01

Our 13C- and 1H-chemical exchange saturation transfer (CEST) experiments previously revealed a dynamic exchange between partially closed and open conformations of the SAM-II riboswitch in the absence of ligand. Here, all-atom structure-based molecular simulations, with the electrostatic effects of Manning counter-ion condensation and explicit magnesium ions are employed to calculate the folding free energy landscape of the SAM-II riboswitch. We use this analysis to predict that magnesium ions remodel the landscape, shifting the equilibrium away from the extended, partially unfolded state towards a compact, pre-organized conformation that resembles the ligand-bound state. Our CEST and SAXS experiments, at different magnesium ion concentrations, quantitatively confirm our simulation results, demonstrating that magnesium ions induce collapse and pre-organization. Agreement between theory and experiment bolsters microscopic interpretation of our simulations, which shows that triplex formation between helix P2b and loop L1 is highly sensitive to magnesium and plays a key role in pre-organization. Pre-organization of the SAM-II riboswitch allows rapid detection of ligand with high selectivity, which is important for biological function. PMID:28248966

Infrared-induced conformational isomerization and vibrational relaxation dynamics in melatonin and 5-methoxy-N-acetyl tryptophan methyl amide

NASA Astrophysics Data System (ADS)

Dian, Brian C.; Florio, Gina M.; Clarkson, Jasper R.; Longarte, Asier; Zwier, Timothy S.

2004-05-01

The conformational isomerization dynamics of melatonin and 5-methoxy N-acetyltryptophan methyl amide (5-methoxy NATMA) have been studied using the methods of IR-UV hole-filling spectroscopy and IR-induced population transfer spectroscopy. Using these techniques, single conformers of melatonin were excited via a well-defined NH stretch fundamental with an IR pump laser. This excess energy was used to drive conformational isomerization. By carrying out the infrared excitation early in a supersonic expansion, the excited molecules were re-cooled into their zero-point levels, partially re-filling the hole created in the ground state population of the excited conformer, and creating gains in population of the other conformers. These changes in population were detected using laser-induced fluorescence downstream in the expansion via an UV probe laser. The isomerization quantum yields for melatonin show some conformation specificity but no hint of vibrational mode specificity. In 5-methoxy NATMA, no isomerization was observed out of the single conformational well populated in the expansion in the absence of the infrared excitation. In order to study the dependence of the isomerization on the cooling rate, the experimental arrangement was modified so that faster cooling conditions could be studied. In this arrangement, the pump and probe lasers were overlapped in space in the high density region of the expansion, and the time dependence of the zero-point level populations of the conformers was probed following selective excitation of a single conformation. The analysis needed to extract isomerization quantum yields from the timing scans was developed and applied to the melatonin timing scans. Comparison between the frequency and time domain isomerization quantum yields under identical experimental conditions produced similar results. Under fast cooling conditions, the product quantum yields were shifted from their values under standard conditions. The results for melatonin are compared with those for N-acetyl tryptophan methyl amide.

Crustal Structure of the Iceland Region from Spectrally Correlated Free-air and Terrain Gravity Data

NASA Technical Reports Server (NTRS)

Leftwich, T. E.; vonFrese, R. R. B.; Potts, L. V.; Roman, D. R.; Taylor, P. T.

2003-01-01

Seismic refraction studies have provided critical, but spatially restricted constraints on the structure of the Icelandic crust. To obtain a more comprehensive regional view of this tectonically complicated area, we spectrally correlated free-air gravity anomalies against computed gravity effects of the terrain for a crustal thickness model that also conforms to regional seismic and thermal constraints. Our regional crustal thickness estimates suggest thickened crust extends up to 500 km on either side of the Greenland-Scotland Ridge with the Iceland-Faeroe Ridge crust being less extended and on average 3-5 km thinner than the crust of the Greenland-Iceland Ridge. Crustal thickness estimates for Iceland range from 25-35 km in conformity with seismic predictions of a cooler, thicker crust. However, the deepening of our gravity-inferred Moho relative to seismic estimates at the thermal plume and rift zones of Iceland suggests partial melting. The amount of partial melting may range from about 8% beneath the rift zones to perhaps 20% above the plume core where mantle temperatures may be 200-400 C above normal. Beneath Iceland, areally limited regions of partial melting may also be compositionally and mechanically layered and intruded. The mantle plume appears to be centered at (64.6 deg N, 17.4 deg W) near the Vatnajokull Glacier and the central Icelandic neovolcanic zones.

Electrostatic Unfolding and Interactions of Albumin Driven by pH Changes: A Molecular Dynamics Study

PubMed Central

2015-01-01

A better understanding of protein aggregation is bound to translate into critical advances in several areas, including the treatment of misfolded protein disorders and the development of self-assembling biomaterials for novel commercial applications. Because of its ubiquity and clinical potential, albumin is one of the best-characterized models in protein aggregation research; but its properties in different conditions are not completely understood. Here, we carried out all-atom molecular dynamics simulations of albumin to understand how electrostatics can affect the conformation of a single albumin molecule just prior to self-assembly. We then analyzed the tertiary structure and solvent accessible surface area of albumin after electrostatically triggered partial denaturation. The data obtained from these single protein simulations allowed us to investigate the effect of electrostatic interactions between two proteins. The results of these simulations suggested that hydrophobic attractions and counterion binding may be strong enough to effectively overcome the electrostatic repulsions between the highly charged monomers. This work contributes to our general understanding of protein aggregation mechanisms, the importance of explicit consideration of free ions in protein solutions, provides critical new insights about the equilibrium conformation of albumin in its partially denatured state at low pH, and may spur significant progress in our efforts to develop biocompatible protein hydrogels driven by electrostatic partial denaturation. PMID:24393011

Line narrowing spectroscopic studies of DNA-carcinogen adducts and DNA-dye complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suh, Myungkoo

1995-12-06

Laser-induced fluorescence line narrowing and non-line narrowing spectroscopic methods were applied to conformational studies of stable DNA adducts of the 7β, 8α-dihydoxy-9α, l0α-epoxy-7,8,9, 10-tetrahydrobenzo[α]pyrene (anti-BPDE). Stereochemically distinct (+)-trans-, (-)-trans-, (+)-cis- and (-)-cis adducts of anti-BPDE bound to exocyclic amino group of the central guanine in an 11-mer oligonucleotide, exist in a mixture of conformations in frozen aqueous buffer matrices. The (+)-trans adduct adopts primarily an external conformation with a smaller fraction ( ~25 %) exists in a partially base-stacked conformation. Both cis adducts were found to be intercalated with significant π-π stacking interactions between the pyrenyl residues and the bases.more » Conformations of the trans-adduct of (+)-anti -BPDE in 11-mer oligonucleotides were studied as a function of flanking bases. In single stranded form the adduct at G 2 or G 3 (5 ft-flanking, base guanine) adopts a conformation with strong, interaction with the bases. In contrast, the adduct with a 5ft-flanking, thymine exists in a primarily helixexternal conformation. Similar differences were observed in the double stranded oligonucleotides. The nature of the 3ft-flanking base has little influence on the conformational equilibrium of the (+)-trans-anti BPDE-dG adduct. The formation and repair of BPDE-N 2-dG in DNA isolated from the skin of mice treated topically with benzo[α]pyrene (BP) was studied. Low-temperature fluorescence spectroscopy of the intact DNA identified the major adduct as (+)-trans-anti-BPDE-N-dG, and the minor adduct fraction consisted mainly of (+)-cis-anti-BPDE-N 2-dG.« less

Cosolvent-Based Molecular Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein Conformations.

PubMed

Uehara, Shota; Tanaka, Shigenori

2017-04-24

Protein flexibility is a major hurdle in current structure-based virtual screening (VS). In spite of the recent advances in high-performance computing, protein-ligand docking methods still demand tremendous computational cost to take into account the full degree of protein flexibility. In this context, ensemble docking has proven its utility and efficiency for VS studies, but it still needs a rational and efficient method to select and/or generate multiple protein conformations. Molecular dynamics (MD) simulations are useful to produce distinct protein conformations without abundant experimental structures. In this study, we present a novel strategy that makes use of cosolvent-based molecular dynamics (CMD) simulations for ensemble docking. By mixing small organic molecules into a solvent, CMD can stimulate dynamic protein motions and induce partial conformational changes of binding pocket residues appropriate for the binding of diverse ligands. The present method has been applied to six diverse target proteins and assessed by VS experiments using many actives and decoys of DEKOIS 2.0. The simulation results have revealed that the CMD is beneficial for ensemble docking. Utilizing cosolvent simulation allows the generation of druggable protein conformations, improving the VS performance compared with the use of a single experimental structure or ensemble docking by standard MD with pure water as the solvent.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gupta, Preeti; Deep, Shashank, E-mail: sdeep@chemistry.iitd.ac.in

Highlights: • HCAII forms amyloid-like aggregates at moderate concentration of trifluoroethanol. • Protein adopts a state between β-sheet and α-helix at moderate % of TFE. • Hydrophobic surface(s) of partially structured conformation forms amyloid. • High % of TFE induces stable α-helical state preventing aggregation. - Abstract: In the present work, we examined the correlation between 2,2,2-trifluoroethanol (TFE)-induced conformational transitions of human carbonic anhydrase II (HCAII) and its aggregation propensity. Circular dichroism data indicates that protein undergoes a transition from β-sheet to α-helix on addition of TFE. The protein was found to aggregate maximally at moderate concentration of TFE atmore » which it exists somewhere between β-sheet and α-helix, probably in extended non-native β-sheet conformation. Thioflavin-T (ThT) and Congo-Red (CR) assays along with fluorescence microscopy and transmission electron microscopy (TEM) data suggest that the protein aggregates induced by TFE possess amyloid-like features. Anilino-8-naphthalene sulfonate (ANS) binding studies reveal that the exposure of hydrophobic surface(s) was maximum in intermediate conformation. Our study suggests that the exposed hydrophobic surface and/or the disruption of the structural features protecting a β-sheet protein might be the major reason(s) for the high aggregation propensity of non-native intermediate conformation of HCAII.« less

Ab initio conformational analysis of N-formyl ?-alanine amide including electron correlation

NASA Astrophysics Data System (ADS)

Yu, Ching-Hsing; Norman, Mya A.; Schäfer, Lothar; Ramek, Michael; Peeters, Anik; van Alsenoy, Christian

2001-06-01

The conformational properties of N-formyl L-alanine amide (ALA) were investigated using RMP2/6-311G∗∗ ab initio gradient geometry optimization. One hundred forty four structures of ALA were optimized at 30° grid points in its φ(N-C(α)), ψ(C(α)-C‧) conformational space. Using cubic spline functions, the grid structures were then used to construct analytical representations of complete surfaces, in φ,ψ-space, of bond lengths, bond angles, torsional sensitivity and electrostatic atomic charges. Analyses show that, in agreement with previous studies, the right-handed helical conformation, αR, is not a local energy minimum of the potential energy surface of ALA. Comparisons with protein crystallographic data show that the characteristic differences between geometrical trends in dipeptides and proteins, previously found for ab initio dipeptide structures obtained without electron correlation, are also found in the electron-correlated geometries. In contrast to generally accepted features of force fields used in empirical molecular modeling, partial atomic charges obtained by the CHELPG method are found to be not constant, but to vary significantly throughout the φ,ψ-space. By comparing RHF and MP2 structures, the effects of dispersion forces on ALA were studied, revealing molecular contractions for those conformations, in which small adjustments of torsional angles entail large changes in non-bonded distances.

Sodium ion effect on silk fibroin conformation characterized by solid-state NMR and generalized 2D NMR NMR correlation

NASA Astrophysics Data System (ADS)

Ruan, Qing-Xia; Zhou, Ping

2008-07-01

In the present work, we investigated Na + ion effect on the silk fibroin (SF) conformation. Samples are Na +-involved regenerated silk fibroin films. 13C CP-MAS NMR demonstrates that as added [Na +] increases, partial silk fibroin conformation transit from helix-form to β-form at certain Na + ion concentration which is much higher than that in Bombyx mori silkworm gland. The generalized two-dimensional NMR-NMR correlation analysis reveals that silk fibroin undergoes several intermediate states during its conformation transition process as [Na +] increase. The appearance order of the intermediates is followed as: helix and/or random coil → helix-like → β-sheet-like → β-sheet, which is the same as that produced by pH decrease from 6.8 to 4.8 in the resultant regenerated silk fibroin films. The binding sites of Na + to silk fibroin might involve the carbonyl oxygen atom of certain amino acids sequence which could promote the formation of β-sheet conformation. Since the Na +sbnd O bond is weak, the ability of Na + inducing the secondary structure transition is weaker than those of Ca 2+, Cu 2+ and even K +. It is maybe a reason why the sodium content is much lower than potassium in the silkworm gland.

Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes

PubMed Central

Duchi, Diego; Gryte, Kristofer; Robb, Nicole C; Morichaud, Zakia; Sheppard, Carol; Wigneshweraraj, Sivaramesh

2018-01-01

Abstract Transcription initiation is a major step in gene regulation for all organisms. In bacteria, the promoter DNA is first recognized by RNA polymerase (RNAP) to yield an initial closed complex. This complex subsequently undergoes conformational changes resulting in DNA strand separation to form a transcription bubble and an RNAP-promoter open complex; however, the series and sequence of conformational changes, and the factors that influence them are unclear. To address the conformational landscape and transitions in transcription initiation, we applied single-molecule Förster resonance energy transfer (smFRET) on immobilized Escherichia coli transcription open complexes. Our results revealed the existence of two stable states within RNAP–DNA complexes in which the promoter DNA appears to adopt closed and partially open conformations, and we observed large-scale transitions in which the transcription bubble fluctuated between open and closed states; these transitions, which occur roughly on the 0.1 s timescale, are distinct from the millisecond-timescale dynamics previously observed within diffusing open complexes. Mutational studies indicated that the σ70 region 3.2 of the RNAP significantly affected the bubble dynamics. Our results have implications for many steps of transcription initiation, and support a bend-load-open model for the sequence of transitions leading to bubble opening during open complex formation. PMID:29177430

A broadband transformation-optics metasurface lens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wan, Xiang; Xiang Jiang, Wei; Feng Ma, Hui

2014-04-14

We present a transformational metasurface Luneburg lens based on the quasi-conformal mapping method, which has weakly anisotropic constitutive parameters. We design the metasurface lens using inhomogeneous artificial structures to realize the required surface refractive indexes. The transformational metasurface Luneburg lens is fabricated and the measurement results demonstrate very good performance in controlling the radiated surface waves.

Application of the Schwinger multichannel formulation to electron-impact excitation of the B 1Sigma(+)u state of H2

NASA Technical Reports Server (NTRS)

Gibson, Thomas L.; Lima, Marco A. P.; Mckoy, Vincent; Huo, Winifred M.

1987-01-01

The paper reports cross sections for electron-impact excitation of the X 1Sigma(+)g - BISigma(+)u transition in H2 for collision energies of 15, 20, and 30 eV. For this dipole-allowed transition with its associated long-range potential, the contributions of the more strongly scattered low-angular-momentum partial waves to the cross section were obtained from a two-state Schwinger multichannel calculation, and a modified Born-closure scheme was used to include the contributions from the remaining weakly scattered partial waves. Agreement between the calculated differential cross sections and available experimental data is encouraging.

N(1520) 3/2- Helicity Amplitudes from an Energy-Independent Multipole Analysis Based on New Polarization Data on Photoproduction of Neutral Pions

NASA Astrophysics Data System (ADS)

Hartmann, J.; Dutz, H.; Anisovich, A. V.; Bayadilov, D.; Beck, R.; Becker, M.; Beloglazov, Y.; Berlin, A.; Bichow, M.; Böse, S.; Brinkmann, K.-Th.; Crede, V.; Dieterle, M.; Eberhardt, H.; Elsner, D.; Fornet-Ponse, K.; Friedrich, St.; Frommberger, F.; Funke, Ch.; Gottschall, M.; Gridnev, A.; Grüner, M.; Gutz, E.; Hammann, Ch.; Hannappel, J.; Hannen, V.; Herick, J.; Hillert, W.; Hoffmeister, Ph.; Honisch, Ch.; Jahn, O.; Jude, T.; Käser, A.; Kaiser, D.; Kalinowsky, H.; Kalischewski, F.; Klassen, P.; Keshelashvili, I.; Klein, F.; Klempt, E.; Koop, K.; Krusche, B.; Kube, M.; Lang, M.; Lopatin, I.; Makonyi, K.; Messi, F.; Metag, V.; Meyer, W.; Müller, J.; Nanova, M.; Nikonov, V.; Novinski, D.; Novotny, R.; Piontek, D.; Rosenbaum, C.; Roth, B.; Reicherz, G.; Rostomyan, T.; Sarantsev, A.; Schmidt, Ch.; Schmieden, H.; Schmitz, R.; Seifen, T.; Sokhoyan, V.; Thämer, Ph.; Thiel, A.; Thoma, U.; Urban, M.; van Pee, H.; Walther, D.; Wendel, Ch.; Wiedner, U.; Wilson, A.; Winnebeck, A.; Witthauer, L.; Wunderlich, Y.; Cbelsa/Taps Collaboration

2014-08-01

New data on the polarization observables T, P, and H for the reaction γp→pπ0 are reported. The results are extracted from azimuthal asymmetries when a transversely polarized butanol target and a linearly polarized photon beam are used. The data were taken at the Bonn electron stretcher accelerator ELSA using the CBELSA/TAPS detector. These and earlier data are used to perform a truncated energy-independent partial wave analysis in sliced-energy bins. This energy-independent analysis is compared to the results from energy-dependent partial wave analyses.

A Phase Correction Technique Based on Spatial Movements of Antennas in Real-Time (S.M.A.R.T.) for Designing Self-Adapting Conformal Array Antennas

NASA Astrophysics Data System (ADS)

Roy, Sayan

This research presents a real-time adaptive phase correction technique for flexible phased array antennas on conformal surfaces of variable shapes. Previously reported pattern correctional methods for flexible phased array antennas require prior knowledge on the possible non-planar shapes in which the array may adapt for conformal applications. For the first time, this initial requirement of shape curvature knowledge is no longer needed and the instantaneous information on the relative location of array elements is used here for developing a geometrical model based on a set of Bezier curves. Specifically, by using an array of inclinometer sensors and an adaptive phase-correctional algorithm, it has been shown that the proposed geometrical model can successfully predict different conformal orientations of a 1-by-4 antenna array in real-time without the requirement of knowing the shape-changing characteristics of the surface the array is attached upon. Moreover, the phase correction technique is validated by determining the field patterns and broadside gain of the 1-by-4 antenna array on four different conformal surfaces with multiple points of curvatures. Throughout this work, measurements are shown to agree with the analytical solutions and full-wave simulations.

Experimental demonstration of conformal phased array antenna via transformation optics.

PubMed

Lei, Juan; Yang, Juxing; Chen, Xi; Zhang, Zhiya; Fu, Guang; Hao, Yang

2018-02-28

Transformation Optics has been proven a versatile technique for designing novel electromagnetic devices and it has much wider applicability in many subject areas related to general wave equations. Among them, quasi-conformal transformation optics (QCTO) can be applied to minimize anisotropy of transformed media and has opened up the possibility to the design of broadband antennas with arbitrary geometries. In this work, a wide-angle scanning conformal phased array based on all-dielectric QCTO lens is designed and experimentally demonstrated. Excited by the same current distribution as such in a conventional planar array, the conformal system in presence of QCTO lens can preserve the same radiation characteristics of a planar array with wide-angle beam-scanning and low side lobe level (SLL). Laplace's equation subject to Dirichlet-Neumann boundary conditions is adopted to construct the mapping between the virtual and physical spaces. The isotropic lens with graded refractive index is realized by all-dielectric holey structure after an effective parameter approximation. The measurements of the fabricated system agree well with the simulated results, which demonstrate its excellent wide-angle beam scanning performance. Such demonstration paves the way to a robust but efficient array synthesis, as well as multi-beam and beam forming realization of conformal arrays via transformation optics.

Photon beam asymmetry Σ in the reaction γ → p → pω for Eγ = 1.152 to 1.876 GeV

NASA Astrophysics Data System (ADS)

Collins, P.; Ritchie, B. G.; Dugger, M.; Klein, F. J.; Anisovich, A. V.; Klempt, E.; Nikonov, V. A.; Sarantsev, A.; Adhikari, K. P.; Adhikari, S.; Adikaram, D.; Akbar, Z.; Anefalos Pereira, S.; Avakian, H.; Ball, J.; Baltzell, N. A.; Bashkanov, M.; Battaglieri, M.; Batourine, V.; Bedlinskiy, I.; Biselli, A. S.; Boiarinov, S.; Briscoe, W. J.; Brooks, W. K.; Burkert, V. D.; Cao, Frank Thanh; Cao, T.; Carman, D. S.; Celentano, A.; Charles, G.; Chetry, T.; Ciullo, G.; Clark, L.; Cole, P. L.; Contalbrigo, M.; Cortes, O.; Crede, V.; Dashyan, N.; De Vita, R.; De Sanctis, E.; Defurne, M.; Deur, A.; Djalali, C.; Dupre, R.; Egiyan, H.; El Alaoui, A.; El Fassi, L.; Eugenio, P.; Fedotov, G.; Filippi, A.; Fleming, J. A.; Ghandilyan, Y.; Gilfoyle, G. P.; Giovanetti, K. L.; Girod, F. X.; Glazier, D. I.; Gleason, C.; Golovatch, E.; Gothe, R. W.; Griffioen, K. A.; Guidal, M.; Hafidi, K.; Hakobyan, H.; Hanretty, C.; Harrison, N.; Hattawy, M.; Heddle, D.; Hicks, K.; Hollis, G.; Holtrop, M.; Hughes, S. M.; Ilieva, Y.; Ireland, D. G.; Ishkhanov, B. S.; Isupov, E. L.; Jenkins, D.; Jiang, H.; Jo, H. S.; Joosten, S.; Keller, D.; Khachatryan, G.; Khachatryan, M.; Khandaker, M.; Kim, A.; Kim, W.; Klein, A.; Kubarovsky, V.; Kuleshov, S. V.; Lanza, L.; Lenisa, P.; Livingston, K.; MacGregor, I. J. D.; Markov, N.; McKinnon, B.; Meyer, C. A.; Meziani, Z. E.; Mineeva, T.; Mokeev, V.; Montgomery, R. A.; Movsisyan, A.; Munevar, E.; Munoz Camacho, C.; Nadel-Turonski, P.; Net, L. A.; Niccolai, S.; Niculescu, G.; Niculescu, I.; Osipenko, M.; Ostrovidov, A. I.; Paolone, M.; Paremuzyan, R.; Park, K.; Pasyuk, E.; Phelps, W.; Pisano, S.; Pogorelko, O.; Price, J. W.; Procureur, S.; Prok, Y.; Protopopescu, D.; Raue, B. A.; Ripani, M.; Rizzo, A.; Rosner, G.; Sabatié, F.; Salgado, C.; Schumacher, R. A.; Sharabian, Y. G.; Simonyan, A.; Skorodumina, Iu.; Smith, G. D.; Sober, D. I.; Sokhan, D.; Sparveris, N.; Stankovic, I.; Stepanyan, S.; Strakovsky, I. I.; Strauch, S.; Taiuti, M.; Ungaro, M.; Voskanyan, H.; Voutier, E.; Walford, N. K.; Watts, D. P.; Wei, X.; Wood, M. H.; Zachariou, N.; Zhang, J.; Zhao, Z. W.

2017-10-01

Photon beam asymmetry Σ measurements for ω photoproduction in the reaction γ → p → ωp are reported for photon energies from 1.152 to 1.876 GeV. Data were taken using a linearly-polarized tagged photon beam, a cryogenic hydrogen target, and the CLAS spectrometer in Hall B at Jefferson Lab. The measurements obtained markedly increase the size of the database for this observable, extend coverage to higher energies, and resolve discrepancies in previously published data. Comparisons of these new results with predictions from a chiral-quark-based model and from a dynamical coupled-channels model indicate the importance of interferences between t-channel meson exchange and s- and u-channel contributions, underscoring sensitivity to the nucleon resonances included in those descriptions. Comparisons with the Bonn-Gatchina partial-wave analysis indicate the Σ data reported here help to fix the magnitudes of the interference terms between the leading amplitudes in that calculation (Pomeron exchange and the resonant portion of the JP = 3 /2+ partial wave), as well as the resonant portions of the smaller partial waves with JP = 1 /2-, 3 /2-, and 5 /2+.

Full-scale testing of leakage of blast waves inside a partially vented room exposed to external air blast loading

NASA Astrophysics Data System (ADS)

Codina, R.; Ambrosini, D.

2018-03-01

For the last few decades, the effects of blast loading on structures have been studied by many researchers around the world. Explosions can be caused by events such as industrial accidents, military conflicts or terrorist attacks. Urban centers have been prone to various threats including car bombs, suicide attacks, and improvised explosive devices. Partially vented constructions subjected to external blast loading represent an important topic in protective engineering. The assessment of blast survivability inside structures and the development of design provisions with respect to internal elements require the study of the propagation and leakage of blast waves inside buildings. In this paper, full-scale tests are performed to study the effects of the leakage of blast waves inside a partially vented room that is subjected to different external blast loadings. The results obtained may be useful for proving the validity of different methods of calculation, both empirical and numerical. Moreover, the experimental results are compared with those computed using the empirical curves of the US Defense report/manual UFC 3-340. Finally, results of the dynamic response of the front masonry wall are presented in terms of accelerations and an iso-damage diagram.

The Search for Exotic Mesons in gamma p -> pi+pi+pi-n with CLAS at Jefferson Lab

DOE Office of Scientific and Technical Information (OSTI.GOV)

Craig Bookwalter

2011-12-01

The {pi}{sub 1}(1600), a J{sup PC} = 1{sup {-+}} exotic meson has been observed by experiments using pion beams. Theorists predict that photon beams could produce gluonic hybrid mesons, of which the {pi}{sub 1}(1600) is a candidate, at enhanced levels relative to pion beams. The g12 rungroup at Jefferson Lab's CEBAF Large Acceptance Spectrometer (CLAS) has recently acquired a large photoproduction dataset, using a liquid hydrogen target and tagged photons from a 5.71 GeV electron beam. A partial-wave analysis of 502K {gamma}p {yields} {pi}{sup +}{pi}{sup +}{pi}{sup -}n events selected from the g12 dataset has been performed, and preliminary fit resultsmore » show strong evidence for well-known states such as the a{sub 1}(1260), a{sub 2}(1320), and {pi}{sub 2}(1670). However, we observe no evidence for the production of the {pi}{sub 1}(1600) in either the partial-wave intensities or the relative complex phase between the 1{sup {-+}} and the 2{sup {-+}} (corresponding to the {pi}{sub 2}) partial waves.« less

Polymer Morphological Change Induced by Terahertz Irradiation

PubMed Central

Hoshina, Hiromichi; Suzuki, Hal; Otani, Chiko; Nagai, Masaya; Kawase, Keigo; Irizawa, Akinori; Isoyama, Goro

2016-01-01

As terahertz (THz) frequencies correspond to those of the intermolecular vibrational modes in a polymer, intense THz wave irradiation affects the macromolecular polymorph, which determines the polymer properties and functions. THz photon energy is quite low compared to the covalent bond energy; therefore, conformational changes can be induced “softly,” without damaging the chemical structures. Here, we irradiate a poly(3-hydroxybutylate) (PHB) / chloroform solution during solvent casting crystallization using a THz wave generated by a free electron laser (FEL). Morphological observation shows the formation of micrometer-sized crystals in response to the THz wave irradiation. Further, a 10−20% increase in crystallinity is observed through analysis of the infrared (IR) absorption spectra. The peak power density of the irradiating THz wave is 40 MW/cm2, which is significantly lower than the typical laser intensities used for material manipulation. We demonstrate for the first time that the THz wave effectively induces the intermolecular rearrangement of polymer macromolecules. PMID:27272984

Conformational statistics of stiff macromolecules as solutions to partial differential equations on the rotation and motion groups

PubMed

Chirikjian; Wang

2000-07-01

Partial differential equations (PDE's) for the probability density function (PDF) of the position and orientation of the distal end of a stiff macromolecule relative to its proximal end are derived and solved. The Kratky-Porod wormlike chain, the Yamakawa helical wormlike chain, and the original and revised Marko-Siggia models are examples of stiffness models to which the present formulation is applied. The solution technique uses harmonic analysis on the rotation and motion groups to convert PDE's governing the PDF's of interest into linear algebraic equations which have mathematically elegant solutions.

Theory of wave propagation in partially saturated double-porosity rocks: a triple-layer patchy model

NASA Astrophysics Data System (ADS)

Sun, Weitao; Ba, Jing; Carcione, José M.

2016-04-01

Wave-induced local fluid flow is known as a key mechanism to explain the intrinsic wave dissipation in fluid-saturated rocks. Understanding the relationship between the acoustic properties of rocks and fluid patch distributions is important to interpret the observed seismic wave phenomena. A triple-layer patchy (TLP) model is proposed to describe the P-wave dissipation process in a double-porosity media saturated with two immiscible fluids. The double-porosity rock consists of a solid matrix with unique host porosity and inclusions which contain the second type of pores. Two immiscible fluids are considered in concentric spherical patches, where the inner pocket and the outer sphere are saturated with different fluids. The kinetic and dissipation energy functions of local fluid flow (LFF) in the inner pocket are formulated through oscillations in spherical coordinates. The wave propagation equations of the TLP model are based on Biot's theory and the corresponding Lagrangian equations. The P-wave dispersion and attenuation caused by the Biot friction mechanism and the local fluid flow (related to the pore structure and the fluid distribution) are obtained by a plane-wave analysis from the Christoffel equations. Numerical examples and laboratory measurements indicate that P-wave dispersion and attenuation are significantly influenced by the spatial distributions of both, the solid heterogeneity and the fluid saturation distribution. The TLP model is in reasonably good agreement with White's and Johnson's models. However, differences in phase velocity suggest that the heterogeneities associated with double-porosity and dual-fluid distribution should be taken into account when describing the P-wave dispersion and attenuation in partially saturated rocks.

Periodic Peakons, Pseudo-Peakons and Compactons of Ion-Acoustic Wave Model in Electronegative Plasmas with Electrons Featuring Tsallis Distribution

NASA Astrophysics Data System (ADS)

Li, Jibin

The dynamical model of the nonlinear ion-acoustic oscillations is governed by a partial differential equation system. Its traveling system is just a singular traveling wave system of first class depending on four parameters. By using the method of dynamical systems and the theory of singular traveling wave systems, in this paper, we show that there exist parameter groups such that this singular system has pseudo-peakons, periodic peakons and compactons as well as kink and anti-kink wave solutions.

Scaling Observations of Surface Waves in the Beaufort Sea

DTIC Science & Technology

2016-04-14

the treatment of wind input can be improved in partial ice cover using the ice concentration, where wave energy is a function of open water distance...drifting buoys during the 2014 open water season, are interpreted using open water distances determined from satellite ice products and wind forcing time...series measured in situ with the buoys. A significant portion of the wave observations were found to be limited by open water distance (fetch) when

An algorithm for solving the perturbed gas dynamic equations

NASA Technical Reports Server (NTRS)

Davis, Sanford

1993-01-01

The present application of a compact, higher-order central-difference approximation to the linearized Euler equations illustrates the multimodal character of these equations by means of computations for acoustic, vortical, and entropy waves. Such dissipationless central-difference methods are shown to propagate waves exhibiting excellent phase and amplitude resolution on the basis of relatively large time-steps; they can be applied to wave problems governed by systems of first-order partial differential equations.

Analysis of partial-reflection data from the solar eclipse of 10 Jul. 1972. [ground-based experiment using vertical incident radio waves partially reflected from D region

NASA Technical Reports Server (NTRS)

Bean, T. A.; Bowhill, S. A.

1973-01-01

Partial-reflection data collected for the eclipse of July 10, 1972 as well as for July 9 and 11, 1972, are analyzed to determine eclipse effects on D-region electron densities. The partial-reflection experiment was set up to collect data using an on-line PDP-15 computer and DECtape storage. The electron-density profiles show good agreement with results from other eclipses. The partial-reflection programs were changed after the eclipse data collection to improve the operation of the partial-reflection system. These changes were mainly due to expanded computer hardware and have simplified the operations of the system considerably.

More on asymptotically anti-de Sitter spaces in topologically massive gravity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henneaux, Marc; Physique theorique et mathematique, Universite Libre de Bruxelles and International Solvay Institutes, ULB Campus Plaine C.P. 231, B-1050 Bruxelles; Martinez, Cristian

2010-09-15

Recently, the asymptotic behavior of three-dimensional anti-de Sitter (AdS) gravity with a topological mass term was investigated. Boundary conditions were given that were asymptotically invariant under the two dimensional conformal group and that included a falloff of the metric sufficiently slow to consistently allow pp-wave type of solutions. Now, pp waves can have two different chiralities. Above the chiral point and at the chiral point, however, only one chirality can be considered, namely, the chirality that has the milder behavior at infinity. The other chirality blows up faster than AdS and does not define an asymptotically AdS spacetime. By contrast,more » both chiralities are subdominant with respect to the asymptotic behavior of AdS spacetime below the chiral point. Nevertheless, the boundary conditions given in the earlier treatment only included one of the two chiralities (which could be either one) at a time. We investigate in this paper whether one can generalize these boundary conditions in order to consider simultaneously both chiralities below the chiral point. We show that this is not possible if one wants to keep the two-dimensional conformal group as asymptotic symmetry group. Hence, the boundary conditions given in the earlier treatment appear to be the best possible ones compatible with conformal symmetry. In the course of our investigations, we provide general formulas controlling the asymptotic charges for all values of the topological mass (not just below the chiral point).« less

Effects of subsurface ocean dynamics on instability waves in the tropical Pacific

NASA Astrophysics Data System (ADS)

Lawrence, Sean P.; Allen, Myles R.; Anderson, David L. T.; Llewellyn-Jones, David T.

1998-08-01

Tropical instability waves in a primitive equation model of the tropical Pacific Ocean, forced with analyzed wind stresses updated daily, show unexpectedly close phase correspondence with observation through the latter half of 1992. This suggests that these waves are not pure instabilities developing from infinitesimal disturbances, but that their phases and phase speeds are at least partially determined by the wind stress forcing. To quantify and explain this observation, we perfomed several numerical experiments, which indicate that remotely forced Rossby waves can influence both the phase and phase speed of tropical instability waves. We suggest that a remote wind forcing determines the high model/observation phase correspondence of tropical instability waves through a relatively realistic simulation of equatorial Kelvin and Rossby wave activity.

Characteristics of dilatational infrasonic pulses accompanying low-frequency earthquakes at Miyakejima Volcano, Japan

NASA Astrophysics Data System (ADS)

Fujiwara, Yoshiaki; Yamasato, Hitoshi; Shimbori, Toshiki; Sakai, Takayuki

2014-12-01

Since the caldera-forming eruption of Miyakejima Volcano in 2000, low-frequency (LF) earthquakes have occurred frequently beneath the caldera. Some of these LF earthquakes are accompanied by emergent infrasonic pulses that start with dilatational phases and may be accompanied by the eruption of small amounts of ash. The estimated source locations of both the LF earthquakes and the infrasonic signals are within the vent at shallow depth. Moreover, the maximum seismic amplitude roughly correlates with the maximum amplitude of the infrasonic pulses. From these observations, we hypothesized that the infrasonic waves were excited by partial subsidence within the vent associated with the LF earthquakes. To verify our hypothesis, we used the infrasonic data to estimate the volumetric change due to the partial subsidence associated with each LF earthquake. The results showed that partial subsidence in the vent can well explain the generation of infrasonic waves.

Compact representations of partially coherent undulator radiation suitable for wave propagation

DOE PAGES

Lindberg, Ryan R.; Kim, Kwang -Je

2015-09-28

Undulator radiation is partially coherent in the transverse plane, with the degree of coherence depending on the ratio of the electron beam phase space area (emittance) to the characteristic radiation wavelength λ. Numerical codes used to predict x-ray beam line performance can typically only propagate coherent fields from the source to the image plane. We investigate methods for representing partially coherent undulator radiation using a suitably chosen set of coherent fields that can be used in standard wave propagation codes, and discuss such “coherent mode expansions” for arbitrary degrees of coherence. In the limit when the electron beam emittance alongmore » at least one direction is much larger than λ the coherent modes are orthogonal and therefore compact; when the emittance approaches λ in both planes we discuss an economical method of defining the relevant coherent fields that samples the electron beam phase space using low-discrepancy sequences.« less

Angular Momentum Content of the ρ Meson in Lattice QCD

NASA Astrophysics Data System (ADS)

Glozman, Leonid Ya.; Lang, C. B.; Limmer, Markus

2009-09-01

The variational method allows one to study the mixing of interpolators with different chiral transformation properties in the nonperturbatively determined physical state. It is then possible to define and calculate in a gauge-invariant manner the chiral as well as the partial wave content of the quark-antiquark component of a meson in the infrared, where mass is generated. Using a unitary transformation from the chiral basis to the LJ2S+1 basis one may extract a partial wave content of a meson. We present results for the ground state of the ρ meson using quenched simulations as well as simulations with nf=2 dynamical quarks, all for lattice spacings close to 0.15 fm. We point out that these results indicate a simple S13-wave composition of the ρ meson in the infrared, like in the SU(6) flavor-spin quark model.

Angular momentum content of the rho meson in lattice QCD.

PubMed

Glozman, Leonid Ya; Lang, C B; Limmer, Markus

2009-09-18

The variational method allows one to study the mixing of interpolators with different chiral transformation properties in the nonperturbatively determined physical state. It is then possible to define and calculate in a gauge-invariant manner the chiral as well as the partial wave content of the quark-antiquark component of a meson in the infrared, where mass is generated. Using a unitary transformation from the chiral basis to the ;{2S+1}L_{J} basis one may extract a partial wave content of a meson. We present results for the ground state of the rho meson using quenched simulations as well as simulations with n_{f} = 2 dynamical quarks, all for lattice spacings close to 0.15 fm. We point out that these results indicate a simple ;{3}S_{1}-wave composition of the rho meson in the infrared, like in the SU(6) flavor-spin quark model.

Spin Dependence of η Meson Production in Proton-Proton Collisions Close to Threshold.

PubMed

Adlarson, P; Augustyniak, W; Bardan, W; Bashkanov, M; Bass, S D; Bergmann, F S; Berłowski, M; Bondar, A; Büscher, M; Calén, H; Ciepał, I; Clement, H; Czerwiński, E; Demmich, K; Engels, R; Erven, A; Erven, W; Eyrich, W; Fedorets, P; Föhl, K; Fransson, K; Goldenbaum, F; Goswami, A; Grigoryev, K; Gullström, C-O; Heijkenskjöld, L; Hejny, V; Hüsken, N; Jarczyk, L; Johansson, T; Kamys, B; Kemmerling, G; Khatri, G; Khoukaz, A; Khreptak, O; Kirillov, D A; Kistryn, S; Kleines, H; Kłos, B; Krzemień, W; Kulessa, P; Kupść, A; Kuzmin, A; Lalwani, K; Lersch, D; Lorentz, B; Magiera, A; Maier, R; Marciniewski, P; Mariański, B; Morsch, H-P; Moskal, P; Ohm, H; Parol, W; Perez Del Rio, E; Piskunov, N M; Prasuhn, D; Pszczel, D; Pysz, K; Pyszniak, A; Ritman, J; Roy, A; Rudy, Z; Rundel, O; Sawant, S; Schadmand, S; Schätti-Ozerianska, I; Sefzick, T; Serdyuk, V; Shwartz, B; Sitterberg, K; Skorodko, T; Skurzok, M; Smyrski, J; Sopov, V; Stassen, R; Stepaniak, J; Stephan, E; Sterzenbach, G; Stockhorst, H; Ströher, H; Szczurek, A; Trzciński, A; Wolke, M; Wrońska, A; Wüstner, P; Yamamoto, A; Zabierowski, J; Zieliński, M J; Złomańczuk, J; Żuprański, P; Żurek, M

2018-01-12

Taking advantage of the high acceptance and axial symmetry of the WASA-at-COSY detector, and the high polarization degree of the proton beam of COSY, the reaction p[over →]p→ppη has been measured close to threshold to explore the analyzing power A_{y}. The angular distribution of A_{y} is determined with the precision improved by more than 1 order of magnitude with respect to previous results, allowing a first accurate comparison with theoretical predictions. The determined analyzing power is consistent with zero for an excess energy of Q=15  MeV, signaling s-wave production with no evidence for higher partial waves. At Q=72  MeV the data reveal strong interference of Ps and Pp partial waves and cancellation of (Pp)^{2} and Ss^{*}Sd contributions. These results rule out the presently available theoretical predictions for the production mechanism of the η meson.

Resolution of quantum singularities

NASA Astrophysics Data System (ADS)

Konkowski, Deborah; Helliwell, Thomas

2017-01-01

A review of quantum singularities in static and conformally static spacetimes is given. A spacetime is said to be quantum mechanically non-singular if a quantum wave packet does not feel, in some sense, the presence of a singularity; mathematically, this means that the wave operator is essentially self-adjoint on the space of square integrable functions. Spacetimes with classical mild singularities (quasiregular ones) to spacetimes with classical strong curvature singularities have been tested. Here we discuss the similarities and differences between classical singularities that are healed quantum mechanically and those that are not. Possible extensions of the mathematical technique to more physically realistic spacetimes are discussed.

Optical conformal mapping.

PubMed

Leonhardt, Ulf

2006-06-23

An invisibility device should guide light around an object as if nothing were there, regardless of where the light comes from. Ideal invisibility devices are impossible, owing to the wave nature of light. This study develops a general recipe for the design of media that create perfect invisibility within the accuracy of geometrical optics. The imperfections of invisibility can be made arbitrarily small to hide objects that are much larger than the wavelength. With the use of modern metamaterials, practical demonstrations of such devices may be possible. The method developed here can also be applied to escape detection by other electromagnetic waves or sound.

Travelling-wave ion mobility mass spectrometry and negative ion fragmentation of hybrid and complex N-glycans

PubMed Central

Harvey, David J.; Scarff, Charlotte A.; Edgeworth, Matthew; Pagel, Kevin; Thalassinos, Konstantinos; Struwe, Weston B.; Crispin, Max; Scrivens, Jim

2016-01-01

Nitrogen cross sections of hybrid and complex glycans released from the glycoproteins IgG, gp120 (from human immunodeficiency virus), ovalbumin, α1-acid glycoprotein, thyroglobulin and fucosylated glycoproteins from the human parotid gland were measured with a travelling-wave ion mobility mass spectrometer using dextran as the calibrant. The utility of this instrument for isomer separation was also investigated. Some isomers, such as Man3GlcNAc3 from chicken ovalbumin and Man3GlcNAc3Fuc1 from thyroglobulin could be partially resolved and identified by their negative ion fragmentation spectra. Several other larger glycans, however, although existing as isomers, produced only asymmetric rather than separated arrival time distributions (ATDs). Nevertheless, in these cases, isomers could often be detected by plotting extracted fragment ATDs of diagnostic fragment ions from the negative ion spectra obtained in the transfer cell of the Waters Synapt mass spectrometer. Coincidence in the drift times of all fragment ions with an overall asymmetric ATD profile usually suggested that separations were due to conformers or anomers, whereas symmetrical ATDs of fragments showing differences in drift times indicated isomer separation. Although some significant differences in cross sections were found for the smaller isomeric glycans, the differences found for the larger compounds were usually too small to be analytically useful. Possible correlations between cross sections and structural types were also investigated and it was found that complex glycans tended to have slightly smaller cross sections than high-mannose glycans of comparable molecular weight. In addition, biantennary glycans containing a core fucose and/or a bisecting GlcNAc residue fell on different mobility-m/z trend lines to those glycans not so substituted with both of these substituents contributing to larger cross sections. PMID:27477117

Relationship between ionospheric plasma bubble occurrence and lightning strikes over the Amazon region

NASA Astrophysics Data System (ADS)

Sousasantos, Jonas; Sobral, José Humberto Andrade; Alam Kherani, Esfhan; Magalhães Fares Saba, Marcelo; Rodolfo de Campos, Diovane

2018-03-01

The vertical coupling between the troposphere and the ionosphere presents some remarkable features. Under intense tropospheric convection, gravity waves may be generated, and once they reach the ionosphere, these waves may seed instabilities and spread F and equatorial plasma bubble events may take place. Additionally, there is a close association between severe tropospheric convection and lightning strikes. In this work an investigation covering an equinox period (September-October) during the deep solar minimum (2009) presents the relation between lightning strike activity and spread F (equatorial plasma bubble) detected over a low-latitude Brazilian region. The results show a considerable correlation between these two phenomena. The common element in the center of this conformity seems to be the gravity waves. Once gravity waves and lightning strikes share the same source (intense tropospheric convection) and the effects of such gravity waves in the ionosphere include the seeding of instabilities according to the gravity waves magnitude, the monitoring of the lightning strike activity seems to offer some information about the subsequent development of spread F over the equatorial region.

Exact traveling wave solutions of modified KdV-Zakharov-Kuznetsov equation and viscous Burgers equation.

PubMed

Islam, Md Hamidul; Khan, Kamruzzaman; Akbar, M Ali; Salam, Md Abdus

2014-01-01

Mathematical modeling of many physical systems leads to nonlinear evolution equations because most physical systems are inherently nonlinear in nature. The investigation of traveling wave solutions of nonlinear partial differential equations (NPDEs) plays a significant role in the study of nonlinear physical phenomena. In this article, we construct the traveling wave solutions of modified KDV-ZK equation and viscous Burgers equation by using an enhanced (G '/G) -expansion method. A number of traveling wave solutions in terms of unknown parameters are obtained. Derived traveling wave solutions exhibit solitary waves when special values are given to its unknown parameters. 35C07; 35C08; 35P99.

Helioseismic Implications of Mode Conversion

NASA Astrophysics Data System (ADS)

Moradi, H.; Cally, P. S.

2013-12-01

The Sun leaks waves through its active regions. The leakage of acoustic waves into the atmosphere through these ‘magnetoacoustic portals’ is well known, but magnetic (fast) waves also enter the atmosphere there. Fast waves ultimately reflect because of the increase in Alfvén speed with height, but when they do so they can partially convert to Alfvén waves. The weakened fast waves then re-enter the interior, to rejoin the seismic p-mode field. But how has the Alfvénic loss they suffered affected the seismology? We present results from simulations that compare Alfvénic losses with travel-time shifts, and draw general conclusions about the role of active region atmospheres in local helioseismology.

System engineering study of electrodynamic tether as a spaceborne generator and radiator of electromagnetic waves in the ULF/ELF frequency band

NASA Technical Reports Server (NTRS)

Estes, Robert D.

1987-01-01

An electrodynamic tether deployed from a satellite in low-Earth orbit can perform, if properly instrumented, as a partially self-powered generator of electromagnetic waves in the ULF/ELF band, potentially at power levels high enough to be of practical use. Two basic problems are examined. The first is that of the level of wave power that the system can be expected to generate in the ULF/ELF radiation band. The second major question is whether an electrodynamic tethered satellite system for transmitting waves can be made partially self-powering so that power requirements for drag compensation can be met within economical constraints of mass, cost, and complexity. The theoretical developments and the system applications study are presented. The basic design criteria, the drag-compensation method, the effects on the propagation paths from orbit to Earth surface of high-altitude nuclear debris patches, and the estimate of masses and sizes are covered. An outline of recommended analytical work, to be performed as a follow-on to the present study, is contained.

Conformation study of HA(306-318) antigenic peptide of the haemagglutinin influenza virus protein

NASA Astrophysics Data System (ADS)

Bertrand, A.; Brito, R. M.; Alix, A. J. P.; Lancelin, J. M.; Carvalho, R. A.; Geraldes, C. F. G. C.; Lakhdar-Ghazal, F.

2006-11-01

Several HLA-DR alleles present the immunodominant HA(306-318) peptide of haemagglutinin of the influenza virus to T cells. NMR data of the peptide in various water solutions exclude any α-helix or turn conformations. Circular dichroism and Fourier transform infrared spectroscopies indicate an estimated β-extended structure in water of 31% and 28%, respectively, with spectra shape similar to the ones observed for β-sheet containing proteins. The H/D amide exchange suggests a stable length-dependent interchain hydrogen-bonding. The partially β-extended conformation of HA(306-318) in solution might be close to the one found in HA(306-318)-HLA-DR1 complex. These results suggest different interconverting extended conformations of HA(306-318), depending on the microenvironment of the solution medium. This flexibility emphasizes the ability of some peptides to fit more easily the binding site of several HLA-DR molecules. Similar results were obtained on the HIV P25(263-277) peptide which has been previously shown to be a good DR1 binder. From a vibrational point of view, infrared Amide I frequencies of secondary structures in peptides were ascertained. As previously demonstrated for proteins in solution, Fourier transform infrared and circular dichroism spectroscopies appear to be valuable tools for conformational properties of peptides. Their use may contribute to the detection of peptide conformation-binding relationship which has to be further tested by biochemical and biological studies.

Brain Surface Conformal Parameterization Using Riemann Surface Structure

PubMed Central

Wang, Yalin; Lui, Lok Ming; Gu, Xianfeng; Hayashi, Kiralee M.; Chan, Tony F.; Toga, Arthur W.; Thompson, Paul M.; Yau, Shing-Tung

2011-01-01

In medical imaging, parameterized 3-D surface models are useful for anatomical modeling and visualization, statistical comparisons of anatomy, and surface-based registration and signal processing. Here we introduce a parameterization method based on Riemann surface structure, which uses a special curvilinear net structure (conformal net) to partition the surface into a set of patches that can each be conformally mapped to a parallelogram. The resulting surface subdivision and the parameterizations of the components are intrinsic and stable (their solutions tend to be smooth functions and the boundary conditions of the Dirichlet problem can be enforced). Conformal parameterization also helps transform partial differential equations (PDEs) that may be defined on 3-D brain surface manifolds to modified PDEs on a two-dimensional parameter domain. Since the Jacobian matrix of a conformal parameterization is diagonal, the modified PDE on the parameter domain is readily solved. To illustrate our techniques, we computed parameterizations for several types of anatomical surfaces in 3-D magnetic resonance imaging scans of the brain, including the cerebral cortex, hippocampi, and lateral ventricles. For surfaces that are topologically homeomorphic to each other and have similar geometrical structures, we show that the parameterization results are consistent and the subdivided surfaces can be matched to each other. Finally, we present an automatic sulcal landmark location algorithm by solving PDEs on cortical surfaces. The landmark detection results are used as constraints for building conformal maps between surfaces that also match explicitly defined landmarks. PMID:17679336

Monitoring Conformational Landscape of Ovine Prion Protein Monomer Using Ion Mobility Coupled to Mass Spectrometry

NASA Astrophysics Data System (ADS)

Van der Rest, Guillaume; Rezaei, Human; Halgand, Frédéric

2017-02-01

Prion protein is involved in deadly neurodegenerative diseases. Its pathogenicity is linked to its structural conversion (α-helix to β-strand transition). However, recent studies suggest that prion protein can follow a plurality of conversion pathways, which hints towards different conformers that might coexist in solution. To gain insights on the plasticity of the ovine prion protein (PrP) monomer, wild type (A136, R154, Q171), mutants and deletions of ARQ were studied by traveling wave ion mobility experiments coupled to mass spectrometry. In order to perform the analysis of a large body of data sets, we designed and evaluated the performance of a processing pipeline based on Driftscope peak detection and a homemade script for automated peak assignment, annotation, and quantification on specific multiply charged protein data. Using this approach, we showed that in the gas phase, PrPs are represented by at least three conformer families differing in both charge state distribution and collisional cross-section, in agreement with the work of Hilton et al. (2010). We also showed that this plasticity is borne both by the N- and C-terminal domains. Effect of protein concentration, pH and temperature were also assessed, showing that (1) pH does not affect conformer distributions, (2) protein concentration modifies the conformational landscape of one mutant (I208M) only, and (3) heating leads to other unfolded species and to a modification of the conformer intensity ratios.

State-resolved differential and integral cross sections for the Ne + H{sub 2}{sup +} (v = 0–2, j = 0) → NeH{sup +} + H reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Hui; Yao, Cui-Xia; He, Xiao-Hu

State-to-state quantum dynamic calculations for the proton transfer reaction Ne + H{sub 2}{sup +} (v = 0–2, j = 0) are performed on the most accurate LZHH potential energy surface, with the product Jacobi coordinate based time-dependent wave packet method including the Coriolis coupling. The J = 0 reaction probabilities for the title reaction agree well with previous results in a wide range of collision energy of 0.2-1.2 eV. Total integral cross sections are in reasonable agreement with the available experiment data. Vibrational excitation of the reactant is much more efficient in enhancing the reaction cross sections than translational andmore » rotational excitation. Total differential cross sections are found to be forward-backward peaked with strong oscillations, which is the indication of the complex-forming mechanism. As the collision energy increases, state-resolved differential cross section changes from forward-backward symmetric peaked to forward scattering biased. This forward bias can be attributed to the larger J partial waves, which makes the reaction like an abstraction process. Differential cross sections summed over two different sets of J partial waves for the v = 0 reaction at the collision energy of 1.2 eV are plotted to illustrate the importance of large J partial waves in the forward bias of the differential cross sections.« less

Mesospheric gravity-wave climatology at Adelaide

NASA Technical Reports Server (NTRS)

Vincent, R. A.

1986-01-01

The MF Adelaide partial-reflection radar has been operating continuously since November 1983. This has enabled a climatology of gravity-wave activity to be constructed for the mesosphere. The data have been analyzed for a medium-period range of 1 to 8 hr. and a longer period range between 8 and 24 hr. covering the inertio-period waves. The tidal motions have been filtered out prior to analysis. For the data analyses so far (Nov. 1983 to Dec. 1984), a number of interesting features emerged. Firstly, the wave activity at heights above 80 km shows a small seimannual variation with season with the activity being strongest in summer and winter. At heights below 80 km however, there is a similar but more marked variation with the weakest amplitudes occurring at the time of the changeovers in the prevailing circulation. If breaking gravity waves are responsible for much of the turbulence in the mesosphere, then the periods March to April and September to October might also be expected to be periods of weak turbulence. The wave field appears to be partially polarized. The meridional amplitudes are larger than the zonal amplitudes, especially in water. It is found that the degree of polarization is about 15% in summer and 30% in winter. The polarized component is found to propagate in the opposite direction to the background flow in the stratosphere, which suggests that the polarization arises through directional filtering of the waves as they propagate up from below.

Abundant closed form solutions of the conformable time fractional Sawada-Kotera-Ito equation using (G‧ / G) -expansion method

NASA Astrophysics Data System (ADS)

Al-Shawba, Altaf Abdulkarem; Gepreel, K. A.; Abdullah, F. A.; Azmi, A.

2018-06-01

In current study, we use the (G‧ / G) -expansion method to construct the closed form solutions of the seventh order time fractional Sawada-Kotera-Ito (TFSKI) equation based on conformable fractional derivative. As a result, trigonometric, hyperbolic and rational functions solutions with arbitrary constants are obtained. When the arbitrary constants are taken some special values, the periodic and soliton solutions are obtained from the travelling wave solutions. The obtained solutions are new and not found elsewhere. The effect of the fractional order on some of these solutions are represented graphically to illustrate the behavior of the exact solutions when the parameter take some special choose.

Topics in two-body hadronic decays of D mesons

NASA Astrophysics Data System (ADS)

El Aaoud, El Hassan

We have carried out an analysis of helicity and partial- wave amplitudes for the decay of D mesons to two vector mesons V 1V2, D --> V1V2. In particular we have studied the Cabibbo-favored decays D+s --> ρφ and D --> K*ρ in the factorization approximation using several models for the form factors. All the models, with the exception of one, generate partial-wave amplitudes with the hierarchy |S| > |P| > | D|. Even though in most models the D-wave amplitude is an order of magnitude smaller than the S-wave amplitude, its effect on the longitudinal polarization could be as large as 30%. Due to a misidentification of the partial-wave amplitudes in terms of the Lorentz structures in the relevant literature, we cast doubt on the veracity of the listed data for the decay D --> K*ρ, particularly the partial-wave branching ratios. We have also investigated the effect of the isospin ½, JP = 0+ resonant state K*0 (1950) on the decays D0 --> K¯0η and D0 --> K¯0η' as a function of the branching ratio sum r = Br( K*0 (1950) --> K¯0η) + Br( K*0 (1950) --> K¯0η ') and the coupling constants gK*0 K0h , and gK*0 K0h' . We have used a factorized input for the D 0 --> K*0 (1950) weak transition through a πK loop. We estimated both on- and off-shell contributions from the loop. Our calculation shows that the off-shell effects are significant. For r >= 30% a fit to the decay amplitude |A(D 0 --> K¯0η' )| was possible, but the amplitude A(D 0 --> K¯0η) remained at its factorized value and hence a branching ratio too low compared to data. For small values of r, r <= 18%, we were able to fit |A(D0 --> K¯0η)|, and despite the fact that | A(D0 --> K¯ 0η') | could be raised by almost 100% over its factorized value, it still falls short of its experimental value. A simultaneous fit to both amplitudes |(A(D0 --> K¯0η')| and | A(D0 --> K¯ 0η| was not possible. We have also determined the strong phase of the resonant amplitudes for both decays.

Aspects of String Dualities

NASA Astrophysics Data System (ADS)

Orgera, Jacopo

In this thesis we investigate some aspects of String Dualities. In particular, in the context of Twistor-String/Field Theories duality, we present some partial results toward the understanding of Conformal Supergravity amplitudes. Also, in the context of AdS/CFT duality, we investigate: the role of Euclidean Wormholes in quantum de-coherence and the semiclassical decay of certain non-supersimmetric vacua.

The temporal behaviour of MHD waves in a partially ionized prominence-like plasma: Effect of heating and cooling

NASA Astrophysics Data System (ADS)

Ballester, J. L.; Carbonell, M.; Soler, R.; Terradas, J.

2018-01-01

Context. During heating or cooling processes in prominences, the plasma microscopic parameters are modified due to the change of temperature and ionization degree. Furthermore, if waves are excited on this non-stationary plasma, the changing physical conditions of the plasma also affect wave dynamics. Aims: Our aim is to study how temporal variation of temperature and microscopic plasma parameters modify the behaviour of magnetohydrodynamic (MHD) waves excited in a prominence-like hydrogen plasma. Methods: Assuming optically thin radiation, a constant external heating, the full expression of specific internal energy, and a suitable energy equation, we have derived the profiles for the temporal variation of the background temperature. We have computed the variation of the ionization degree using a Saha equation, and have linearized the single-fluid MHD equations to study the temporal behaviour of MHD waves. Results: For all the MHD waves considered, the period and damping time become time dependent. In the case of Alfvén waves, the cut-off wavenumbers also become time dependent and the attenuation rate is completely different in a cooling or heating process. In the case of slow waves, while it is difficult to distinguish the slow wave properties in a cooling partially ionized plasma from those in an almost fully ionized plasma, the period and damping time of these waves in both plasmas are completely different when the plasma is heated. The temporal behaviour of the Alfvén and fast wave is very similar in the cooling case, but in the heating case, an important difference appears that is related with the time damping. Conclusions: Our results point out important differences in the behaviour of MHD waves when the plasma is heated or cooled, and show that a correct interpretation of the observed prominence oscillations is very important in order to put accurate constraints on the physical situation of the prominence plasma under study, that is, to perform prominence seismology.

Relationship between P-wave attenuation and water saturation in an homogeneous unconsolidated and partially saturated porous media : An experimental study

NASA Astrophysics Data System (ADS)

Barrière, J.; Sénéchal, P.; Bordes, C.; Perroud, H.

2010-12-01

Nowadays, it is well known that hydrogeological properties of the porous media (porosity, fluid saturation and permeability) can influence seismic properties. The major theory which links hydrogeological and seismic parameters is poroelasticity proposed by Biot (1956) for saturated porous media in a wetting phase fluid. However the Biot relaxation process can't explain the level of attenuation of seismic waves generally measured on field from seismic to sonic frequency range in the case of partially saturated media. Laboratory experiments are necessary to better understand the effects of fluids on the attenuation of waves but few ones are done in the low frequency range (1Hz to 10 kHz) where the wavelength is greater than heterogeneities size. We propose an experimental study to determine the attenuation of propagative P-wave in the sonic frequency range on unconsolidated and partially saturated porous media, typical of near surface hydrogeological media. 10 accelerometers (0.0001-17kHz) and 6 capacitance probes (soil moisture sensors) are placed in a container (107 cm x 34 cm x 35cm) full of homogeneous sand (99% silica). An acoustic source (0 - 20 kHz) generate seismic waves which are recorded by the accelerometers during three cycles of imbibition-drainage (corresponding to a water saturation range from 0% to 95%). Values of attenuation (quality factor Q) versus water saturation and frequency are calculated with the well-known spectral ratio method. The spectrum of each recorded P-wave is obtained by a continuous wavelet transform, more adapted than Fourier transform for a non-stationary signal, such as seismic signal, whose frequency content varies with time. The first analyses show a strong dependence of the quality factor with frequency and water saturation, notably at high water saturation (above 60 %) where the attenuation is maximum. Knowing some important parameters of the studied media such as porosity and permeability, we interpret physically our results in accordance with some recent poroelastic models.

A Relation Between the Eikonal Equation Associated to a Potential Energy Surface and a Hyperbolic Wave Equation.

PubMed

Bofill, Josep Maria; Quapp, Wolfgang; Caballero, Marc

2012-12-11

The potential energy surface (PES) of a molecule can be decomposed into equipotential hypersurfaces. We show in this article that the hypersurfaces are the wave fronts of a certain hyperbolic partial differential equation, a wave equation. It is connected with the gradient lines, or the steepest descent, or the steepest ascent lines of the PES. The energy seen as a reaction coordinate plays the central role in this treatment.

Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins

PubMed Central

Kurkcuoglu, Zeynep; Doruker, Pemra

2016-01-01

Incorporating receptor flexibility in small ligand-protein docking still poses a challenge for proteins undergoing large conformational changes. In the absence of bound structures, sampling conformers that are accessible by apo state may facilitate docking and drug design studies. For this aim, we developed an unbiased conformational search algorithm, by integrating global modes from elastic network model, clustering and energy minimization with implicit solvation. Our dataset consists of five diverse proteins with apo to complex RMSDs 4.7–15 Å. Applying this iterative algorithm on apo structures, conformers close to the bound-state (RMSD 1.4–3.8 Å), as well as the intermediate states were generated. Dockings to a sequence of conformers consisting of a closed structure and its “parents” up to the apo were performed to compare binding poses on different states of the receptor. For two periplasmic binding proteins and biotin carboxylase that exhibit hinge-type closure of two dynamics domains, the best pose was obtained for the conformer closest to the bound structure (ligand RMSDs 1.5–2 Å). In contrast, the best pose for adenylate kinase corresponded to an intermediate state with partially closed LID domain and open NMP domain, in line with recent studies (ligand RMSD 2.9 Å). The docking of a helical peptide to calmodulin was the most challenging case due to the complexity of its 15 Å transition, for which a two-stage procedure was necessary. The technique was first applied on the extended calmodulin to generate intermediate conformers; then peptide docking and a second generation stage on the complex were performed, which in turn yielded a final peptide RMSD of 2.9 Å. Our algorithm is effective in producing conformational states based on the apo state. This study underlines the importance of such intermediate states for ligand docking to proteins undergoing large transitions. PMID:27348230

Three-year outcomes of a once daily fractionation scheme for accelerated partial breast irradiation (APBI) using 3-D conformal radiotherapy (3D-CRT)

PubMed Central

Goyal, Sharad; Daroui, Parima; Khan, Atif J; Kearney, Thomas; Kirstein, Laurie; Haffty, Bruce G

2013-01-01

The aim of this study was to report 3-year outcomes of toxicity, cosmesis, and local control using a once daily fractionation scheme (49.95 Gy in 3.33 Gy once daily fractions) for accelerated partial breast irradiation (APBI) using three-dimensional conformal radiotherapy (3D-CRT). Between July 2008 and August 2010, women aged ≥40 years with ductal carcinoma in situ or node-negative invasive breast cancer ≤3 cm in diameter, treated with breast-conserving surgery achieving negative margins, were accrued to a prospective study. Women were treated with APBI using 3–5 photon beams, delivering 49.95 Gy over 15 once daily fractions over 3 weeks. Patients were assessed for toxicities, cosmesis, and local control rates before APBI and at specified time points. Thirty-four patients (mean age 60 years) with Tis 0 (n = 9) and T1N0 (n = 25) breast cancer were treated and followed up for an average of 39 months. Only 3% (1/34) patients experienced a grade 3 subcutaneous fibrosis and breast edema and 97% of the patients had good/excellent cosmetic outcome at 3 years. The 3-year rate of ipsilateral breast tumor recurrence (IBTR) was 0% while the rate of contralateral breast events was 6%. The 3-year disease-free survival (DFS), overall survival (OS), and breast cancer-specific survival (BCSS) was 94%, 100%, and 100%, respectively. Our novel accelerated partial breast fractionation scheme of 15 once daily fractions of 3.33 Gy (49.95 Gy total) is a remarkably well-tolerated regimen of 3D-CRT-based APBI. A larger cohort of patients is needed to further ascertain the toxicity of this accelerated partial breast regimen. PMID:24403270

A phase II prospective, non-comparative assessment of a new silver sodium carboxymethylcellulose (AQUACEL(®) Ag BURN) glove in the management of partial thickness hand burns.

PubMed

Duteille, Franck; Jeffery, Steven L A

2012-11-01

Nylon-reinforced silver sodium carboxymethylcellulose (AQUACEL(®) Ag BURN) dressings were developed to be pliable and conforming for the management of partial-thickness burns. This study evaluated the AQUACEL(®) Ag BURN glove for the management of hand burns. This 21-day, phase II, prospective, non-comparative study included 23 patients with partial-thickness hand burn of at least two fingers. The AQUACEL(®) Ag BURN glove was applied to one hand and could remain in place up to 21 days until clinically indicated to change the glove. Dressings were evaluated 1, 2, 4, 6, 8, 14, and 21 days after initial application. Safety was the primary study endpoint. Sixteen (70%) hand burns re-epithelialized fully over a mean of 15.6 days. Initial application was easy/very easy for 20 (87%) patients. Mean time for initial dressing application was 5.4 min. At final evaluation, most patients gave ratings of excellent/good for conformability (91%), overall glove performance (74%), and appropriateness of sizes (83%). Mean pain score from 0 (none) to 10 (worst imaginable) was 3.43 at baseline; during the study, mean scores were 1.15 at rest and 2.29 during movement. Of 61 glove removals, most (72%) were easy/very easy, and 12% had fallen off. Adverse events (wound site or elsewhere) occurred in 15 (65%) patients. Treatment-related adverse events were wound pain (17%), maceration (9%), and stiff fingers (4%). The AQUACEL(®) Ag BURN glove was well tolerated in the management of partial-thickness hand burn. Many patients used only one glove. When glove changes were required, they were usually quick and easy. Copyright © 2012 Elsevier Ltd and ISBI. All rights reserved.

Does aquatic foraging impact head shape evolution in snakes?

PubMed

Segall, Marion; Cornette, Raphaël; Fabre, Anne-Claire; Godoy-Diana, Ramiro; Herrel, Anthony

2016-08-31

Evolutionary trajectories are often biased by developmental and historical factors. However, environmental factors can also impose constraints on the evolutionary trajectories of organisms leading to convergence of morphology in similar ecological contexts. The physical properties of water impose strong constraints on aquatic feeding animals by generating pressure waves that can alert prey and potentially push them away from the mouth. These hydrodynamic constraints have resulted in the independent evolution of suction feeding in most groups of secondarily aquatic tetrapods. Despite the fact that snakes cannot use suction, they have invaded the aquatic milieu many times independently. Here, we test whether the aquatic environment has constrained head shape evolution in snakes and whether shape converges on that predicted by biomechanical models. To do so, we used three-dimensional geometric morphometrics and comparative, phylogenetically informed analyses on a large sample of aquatic snake species. Our results show that aquatic snakes partially conform to our predictions and have a narrower anterior part of the head and dorsally positioned eyes and nostrils. This morphology is observed, irrespective of the phylogenetic relationships among species, suggesting that the aquatic environment does indeed drive the evolution of head shape in snakes, thus biasing the evolutionary trajectory of this group of animals. © 2016 The Author(s).

Hyperthermophile Protein Behavior: Partially-Structured Conformations of Pyrococcus furiosus Rubredoxin Monomers Generated through Forced Cold-Denaturation and Refolding

PubMed Central

Ahmed, Shubbir; Guptasarma, Purnananda

2014-01-01

Some years ago, we showed that thermo-chemically denatured, partially-unfolded forms of Pyrococcus furiosus triosephosphateisomerase (PfuTIM) display cold-denaturation upon cooling, and heat-renaturation upon reheating, in proportion with the extent of initial partial unfolding achieved. This was the first time that cold-denaturation was demonstrated for a hyperthermophile protein, following unlocking of surface salt bridges. Here, we describe the behavior of another hyperthermophile protein, the small, monomeric, 53 residues-long rubredoxin from Pyrococcus furiosus (PfRd), which is one of the most thermostable proteins known to man. Like PfuTIM, PfRd too displays cold-denaturation after initial thermo-chemical perturbation, however, with two differences: (i) PfRd requires considerably higher temperatures as well as higher concentrations of guanidium hydrochloride (Gdm.HCl) than PfuTIM; (ii) PfRd's cold-denaturation behavior during cooling after thermo-chemical perturbation is incompletely reversible, unlike PfuTIM's, which was clearly reversible (from each different conformation generated). Differential cold-denaturation treatments allow PfRd to access multiple partially-unfolded states, each of which is clearly highly kinetically-stable. We refer to these as ‘Trishanku’ unfolding intermediates (or TUIs). Fascinatingly, refolding of TUIs through removal of Gdm.HCl generates multiple partially-refolded, monomeric, kinetically-trapped, non-native ‘Trishanku’ refolding intermediates (or TRIs), which differ from each other and from native PfRd and TUIs, in structural content and susceptibility to proteolysis. We find that the occurrence of cold denaturation and observations of TUI and TRI states is contingent on the oxidation status of iron, with redox agents managing to modulate the molecule's behavior upon gaining access to PfRd's iron atom. Mass spectrometric examination provides no evidence of the formation of disulfide bonds, but other experiments suggest that the oxidation status of iron (and its extent of burial) together determine whether or not PfRd shows cold denaturation, and also whether redox agents are able to modulate its behavior. PMID:24603413

The calculation of the contributions to low energy e+H2 scattering from sigma u+ and Pion u symmetries using the Kohn variational method

NASA Technical Reports Server (NTRS)

Armour, E. A. G.; Baker, D. J.; Plummer, M.

1990-01-01

Above incident energies of about 2 eV, the contribution to the total cross section in positron+H2 scattering from the sigma g+ symmetry is insufficient to account for the experimental value. Calculations carried out of the lowest partial waves of sigma u+ symmetry and Pion u symmetry using the Kohn variational method are described. The contributions to the total cross section from the two equivalent partial waves of Pion u symmetry significantly reduce the discrepancy with experiment up to incident energies of 4 to 5 eV. Comparisons are made with recent R-matrix calculations performed by Danby and Tennyson.

SU-F-T-625: Optimal Treatment Planning Strategy Among Arc Arrangements for Prostate SBRT with VMAT Technique

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chung, J; Kim, J; Eom, K

Purpose: The purpose of this study is to determine the optimal treatment planning strategy among the different arc arrangements for prostate stereotactic body radiotherapy (SBRT) plans with volumetric modulated arc therapy (VMAT). Methods: Ten patients with prostate cancer were selected. The SBRT-VMAT plans for each patient were generated with single-full (181° to 179°; 1FA), single-partial (240° to 120°; 1PA), double-full (181° to 179° and 179° to 181°; 2FA), and double-partial (240° to 120° and 120° to 240°; 2PA) arc arrangements. The prescription dose was 42.7 Gy in 7 fractions. Dose distribution was calculated using a 10-MV flattening-filter-free beam and themore » Acuros XB algorithm. Dosimetric parameters of target volume and organs at risk (OARs) were evaluated from cumulative dose-volume histograms on prostate SBRT-VMAT plans between single-arc (1FA and 1PA) and double-arc (2FA and 2PA) arrangements. Results: All plans using four arc arrangements were highly conformal with conformity index (CI)<1.05 and conformation number (CN)=0.91, and the doses to target volume were homogeneous (homogeneity index (HI)= 0.09 0.12). Pertaining to the dose to the OARs, there were significant differences in the rectum, left and right femoral head doses while having no difference in the bladder dose. The partial-arc (1PA and 2PA) had relatively high reductions for the mean rectum dose compared to full-arc (1FA and 2FA). The near-to-maximum dose (D2%) and mean dose of the left and right femoral head were always lower on prostate SBRT-VMAT plan using the full-arc, when compared to the partial-arc arrangement. Conclusion: This study confirmed that prostate SBRT-VMAT using 1PA was feasible fast delivery time and produced equivalent target coverage and better rectum sparing, although the D2% and mean dose of the left and right femoral head increased slightly. Therefore, the results of this study suggest that the use of 1PA is an attractive choice for delivering prostate SBRT-VMAT.« less

Stability of nonlinear waves and patterns and related topics

NASA Astrophysics Data System (ADS)

Ghazaryan, Anna; Lafortune, Stephane; Manukian, Vahagn

2018-04-01

Periodic and localized travelling waves such as wave trains, pulses, fronts and patterns of more complex structure often occur in natural and experimentally built systems. In mathematics, these objects are realized as solutions of nonlinear partial differential equations. The existence, dynamic properties and bifurcations of those solutions are of interest. In particular, their stability is important for applications, as the waves that are observable are usually stable. When the waves are unstable, further investigation is warranted of the way the instability is exhibited, i.e. the nature of the instability, and also coherent structures that appear as a result of an instability of travelling waves. A variety of analytical, numerical and hybrid techniques are used to study travelling waves and their properties. This article is part of the theme issue `Stability of nonlinear waves and patterns and related topics'.

Dissecting Antibodies with Regards to Linear and Conformational Epitopes

PubMed Central

Forsström, Björn; Bisławska Axnäs, Barbara; Rockberg, Johan; Danielsson, Hanna; Bohlin, Anna; Uhlen, Mathias

2015-01-01

An important issue for the performance and specificity of an antibody is the nature of the binding to its protein target, including if the recognition involves linear or conformational epitopes. Here, we dissect polyclonal sera by creating epitope-specific antibody fractions using a combination of epitope mapping and an affinity capture approach involving both synthesized peptides and recombinant protein fragments. This allowed us to study the relative amounts of antibodies to linear and conformational epitopes in the polyclonal sera as well as the ability of each antibody-fraction to detect its target protein in Western blot assays. The majority of the analyzed polyclonal sera were found to have most of the target-specific antibodies directed towards linear epitopes and these were in many cases giving Western blot bands of correct molecular weight. In contrast, many of the antibodies towards conformational epitopes did not bind their target proteins in the Western blot assays. The results from this work have given us insights regarding the nature of the antibody response generated by immunization with recombinant protein fragments and has demonstrated the advantage of using antibodies recognizing linear epitopes for immunoassay involving wholly or partially denatured protein targets. PMID:25816293

Conformational distribution of n-hexane in a nematic liquid crystal obtained from nuclear spin dipolar couplings by Monte Carlo sampling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luzar, M.; Rosen, M.E.; Caldarelli, S.

Motionally averaged proton-proton dipolar couplings measured by nuclear magnetic resonance (NMR) spectroscopy can provide information about the conformations and orientations sampled by partially oriented molecules. In this study, the measured dipolar couplings between pairs of protons on n-hexane dissolved in a nematic liquid crystal solvent are used as constraints in a Monte Carlo sampling of the conformations and orientations of n-hexane. Rotation about each carbon-carbon bond in the molecule is modeled by the complete sinusoidal torsional potential of Ryckaert and Bellemans rather than by the three-state rotational isomeric states (RIS) model that has been used in previous studies. Comparison ofmore » the results of the simulations using the Ryckaert-Bellemans potential and the RIS model indicates little difference in the values of the adjustable parameters and the quality of the fits to the experimental data. The primary difference between the models appears in the calculated conformer probability distributions for n-hexane, highlighting the importance of the exact shape of the torsional potential used to model carbon-carbon bond rotation in organic molecules. 23 refs., 3 figs., 4 tabs.« less

Toward the definition of stereochemical requirements for MT2-selective antagonists and partial agonists by studying 4-phenyl-2-propionamidotetralin derivatives.

PubMed

Bedini, Annalida; Lucarini, Simone; Spadoni, Gilberto; Tarzia, Giorgio; Scaglione, Francesco; Dugnani, Silvana; Pannacci, Marilou; Lucini, Valeria; Carmi, Caterina; Pala, Daniele; Rivara, Silvia; Mor, Marco

2011-12-22

New derivatives of 4-phenyl-2-propionamidotetralin (4-P-PDOT) were prepared and tested on cloned MT1 and MT2 receptors, with the purpose of merging previously reported pharmacophores for nonselective agonists and for MT2-selective antagonists. A 8-methoxy group increases binding affinity of both (±)-cis- and (±)-trans-4-P-PDOT, and it can be bioisosterically replaced by a bromine. Conformational analysis of 8-methoxy-4-P-PDOT by molecular dynamics, supported by NMR data, revealed an energetically favored conformation for the (2S,4S)-cis isomer and a less favorable conformation for the (2R,4S)-trans one, fulfilling the requirements of a pharmacophore model for nonselective melatonin receptor agonists. A new superposition model, including features characteristic of MT2-selective antagonists, suggests that MT1/MT2 agonists and MT2 antagonists can share the same arrangement for their pharmacophoric elements. The model correctly predicted the eutomers of (±)-cis- and (±)-trans-4-P-PDOT. The model was validated by preparing three dihydronaphthalene derivatives, either able or not able to reproduce the putative active conformation of 4-P-PDOT.

Solar eclipses at high latitudes: ionospheric effects in the lower ionosphere

NASA Astrophysics Data System (ADS)

Cherniakov, S.

2017-12-01

The partial reflection facility of the Polar Geophysical Institute (the Tumanny observatory, 69.0N, 35.7E) has observed behavior of the high-latitude lower ionosphere during the 20 March 2015 total solar eclipse. There were several effects during the eclipse. At the heights of 60-80 km the ionosphere has shown the effect of a "short night", but at the higher altitudes local enhanced electron concentration had a wave-like form. Data received by the riometer of the Tumanny observatory have also shown wave-like behavior. The behavior can be explained by influence of acoustic-gravity waves which originated after cooling of the atmosphere during the lunar shadow supersonic movement, and transport processes during the eclipse. During the 21 August 2017 solar eclipse there was a substorm at the high latitudes. But after the end of the substorm in the region of the Tumanny observatory the observed amplitudes of the reflected waves had wave effects which could be connected with the coming waves from the region of the eclipse. The wave features were also shown in the behavior of the total electron content (TEC) of the lower ionosphere. During several solar eclipses it was implemented observations of lower ionosphere behavior by the partial reflection facility of the Tumanny observatory. The consideration of the lower ionosphere TEC had revealed common features in the TEC behavior during the eclipses. The photochemical theory of processes in the lower ionosphere is very complicated and up to now it is not completely developed. Therefore introduction of the effective coefficients determining the total speed of several important reactions has been widely adopted when modeling the D-region of the ionosphere. However, experimental opportunities for obtaining effective recombination coefficients are rather limited. One of the methods to estimate effective recombination coefficients uses the phenomenon of a solar eclipse. During solar eclipses at the partial reflection facility of the Tumanny observatory observations were carried out. It gave possibility to obtain the behavior of the electron concentration in time at the selected heights. Using the obtained experimental profiles, the effective recombination coefficients at the D-region heights of the ionosphere have been evaluated.

SPATIAL DAMPING OF PROPAGATING KINK WAVES IN PROMINENCE THREADS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soler, R.; Oliver, R.; Ballester, J. L., E-mail: roberto.soler@wis.kuleuven.be

Transverse oscillations and propagating waves are frequently observed in threads of solar prominences/filaments and have been interpreted as kink magnetohydrodynamic (MHD) modes. We investigate the spatial damping of propagating kink MHD waves in transversely nonuniform and partially ionized prominence threads. Resonant absorption and ion-neutral collisions (Cowling's diffusion) are the damping mechanisms taken into account. The dispersion relation of resonant kink waves in a partially ionized magnetic flux tube is numerically solved by considering prominence conditions. Analytical expressions of the wavelength and damping length as functions of the kink mode frequency are obtained in the thin tube and thin boundary approximations.more » For typically reported periods of thread oscillations, resonant absorption is an efficient mechanism for the kink mode spatial damping, while ion-neutral collisions have a minor role. Cowling's diffusion dominates both the propagation and damping for periods much shorter than those observed. Resonant absorption may explain the observed spatial damping of kink waves in prominence threads. The transverse inhomogeneity length scale of the threads can be estimated by comparing the observed wavelengths and damping lengths with the theoretically predicted values. However, the ignorance of the form of the density profile in the transversely nonuniform layer introduces inaccuracies in the determination of the inhomogeneity length scale.« less

Steepened magnetosonic waves in the high beta plasma surrounding Comet Giacobini-Zinner

NASA Technical Reports Server (NTRS)

Tsurutani, B. T.; Smith, E. J.; Thorne, R. M.; Gosling, J. T.; Matsumoto, H.

1986-01-01

Studies of intense hydromagnetic waves at Giacobini-Zinner are extended to investigate the mode and direction of wave propagation. Simultaneous high-resolution measurements of electron density fluctuations demonstrate that long period waves propagate in the magnetosonic mode. Principal axis analyses of the long period waves and accompanying partial rotations show that the sum of the wave phase rotations is 360 deg, indicating that both are parts of the same wave oscillation. The time sequence of the steepened waveforms observed by ICE shows that the waves must propagate towards the Sun with Cph less than Vsw. Observations are consistent with wave generation by resonant ion ring or ion beam instability which predicts right-hand polarized waves propagating in the ion beam (solar) direction. The large amplitudes and small scale sizes of the cometary waves suggest that rapid pitch-angle scattering and energy transfer with energetic ions should occur. Since the waves are highly compressive, first-order Fermi acceleration is forecast.

Demonstration of a robust magnonic spin wave interferometer.

PubMed

Kanazawa, Naoki; Goto, Taichi; Sekiguchi, Koji; Granovsky, Alexander B; Ross, Caroline A; Takagi, Hiroyuki; Nakamura, Yuichi; Inoue, Mitsuteru

2016-07-22

Magnonics is an emerging field dealing with ultralow power consumption logic circuits, in which the flow of spin waves, rather than electric charges, transmits and processes information. Waves, including spin waves, excel at encoding information via their phase using interference. This enables a number of inputs to be processed in one device, which offers the promise of multi-input multi-output logic gates. To realize such an integrated device, it is essential to demonstrate spin wave interferometers using spatially isotropic spin waves with high operational stability. However, spin wave reflection at the waveguide edge has previously limited the stability of interfering waves, precluding the use of isotropic spin waves, i.e., forward volume waves. Here, a spin wave absorber is demonstrated comprising a yttrium iron garnet waveguide partially covered by gold. This device is shown experimentally to be a robust spin wave interferometer using the forward volume mode, with a large ON/OFF isolation value of 13.7 dB even in magnetic fields over 30 Oe.

Demonstration of a robust magnonic spin wave interferometer

PubMed Central

Kanazawa, Naoki; Goto, Taichi; Sekiguchi, Koji; Granovsky, Alexander B.; Ross, Caroline A.; Takagi, Hiroyuki; Nakamura, Yuichi; Inoue, Mitsuteru

2016-01-01

Magnonics is an emerging field dealing with ultralow power consumption logic circuits, in which the flow of spin waves, rather than electric charges, transmits and processes information. Waves, including spin waves, excel at encoding information via their phase using interference. This enables a number of inputs to be processed in one device, which offers the promise of multi-input multi-output logic gates. To realize such an integrated device, it is essential to demonstrate spin wave interferometers using spatially isotropic spin waves with high operational stability. However, spin wave reflection at the waveguide edge has previously limited the stability of interfering waves, precluding the use of isotropic spin waves, i.e., forward volume waves. Here, a spin wave absorber is demonstrated comprising a yttrium iron garnet waveguide partially covered by gold. This device is shown experimentally to be a robust spin wave interferometer using the forward volume mode, with a large ON/OFF isolation value of 13.7 dB even in magnetic fields over 30 Oe. PMID:27443989

Simulating Seismic Wave Propagation in Viscoelastic Media with an Irregular Free Surface

NASA Astrophysics Data System (ADS)

Liu, Xiaobo; Chen, Jingyi; Zhao, Zhencong; Lan, Haiqiang; Liu, Fuping

2018-05-01

In seismic numerical simulations of wave propagation, it is very important for us to consider surface topography and attenuation, which both have large effects (e.g., wave diffractions, conversion, amplitude/phase change) on seismic imaging and inversion. An irregular free surface provides significant information for interpreting the characteristics of seismic wave propagation in areas with rugged or rapidly varying topography, and viscoelastic media are a better representation of the earth's properties than acoustic/elastic media. In this study, we develop an approach for seismic wavefield simulation in 2D viscoelastic isotropic media with an irregular free surface. Based on the boundary-conforming grid method, the 2D time-domain second-order viscoelastic isotropic equations and irregular free surface boundary conditions are transferred from a Cartesian coordinate system to a curvilinear coordinate system. Finite difference operators with second-order accuracy are applied to discretize the viscoelastic wave equations and the irregular free surface in the curvilinear coordinate system. In addition, we select the convolutional perfectly matched layer boundary condition in order to effectively suppress artificial reflections from the edges of the model. The snapshot and seismogram results from numerical tests show that our algorithm successfully simulates seismic wavefields (e.g., P-wave, Rayleigh wave and converted waves) in viscoelastic isotropic media with an irregular free surface.

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Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-14

..., or Partially-Exclusive Licensing of an Invention Concerning a Device and Method for Inducing Brain... Application Serial No. 61/521,446, entitled ``A Device and Method for Inducing Brain Injury in Animal Test... and method for inducing brain injury in animal test subjects through inflicting pressure-wave or...

Three-wave electron vortex lattices for measuring nanofields.

PubMed

Dwyer, C; Boothroyd, C B; Chang, S L Y; Dunin-Borkowski, R E

2015-01-01

It is demonstrated how an electron-optical arrangement consisting of two electron biprisms can be used to generate three-wave vortex lattices with effective lattice spacings between 0.1 and 1 nm. The presence of vortices in these lattices was verified by using a third biprism to perform direct phase measurements via off-axis electron holography. The use of three-wave lattices for nanoscale electromagnetic field measurements via vortex interferometry is discussed, including the accuracy of vortex position measurements and the interpretation of three-wave vortex lattices in the presence of partial spatial coherence. Copyright © 2014 Elsevier B.V. All rights reserved.

Structural insights into selective agonist actions of tamoxifen on human estrogen receptor alpha.

PubMed

Chakraborty, Sandipan; Biswas, Pradip Kumar

2014-08-01

Tamoxifen-an anti-estrogenic ligand in breast tissues used as a first-line treatment in estrogen receptor (ER)-positive breast cancers-is associated with the development of resistance followed by resumption of tumor growth in about 30 % of cases. Whether tamoxifen assists in proliferation in such cases or whether any ligand-independent pathway to transcription exists is not fully understood; also, no ERα mutants have been detected so far that could lead to tamoxifen resistance. Using in silico conformational analysis of the ERα ligand binding domain (LBD), in the absence and presence of selective agonist (diethylstilbestrol; DES), antagonist (Faslodex; ICI), and selective estrogen receptor modulator (SERM; 4-hydroxy tamoxifen; 4-OHT) ligands, we have elucidated ligand-responsive structural modulations of the ERα-LBD dimer in its agonist and antagonist complexes to address the issue of "tamoxifen resistance". DES and ICI were found to stabilize the dimer in their agonist and antagonist conformations, respectively. The ERα-LBD dimer without the presence of any bound ligand also led to a stable structure in agonist conformation. However, binding of 4-OHT to the antagonist structure led to a flexible conformation allowing the protein to visit conformations populated by agonists as was evident from principal component analysis and radius of gyration plots. Further, the relaxed conformations of the 4-OHT bound protein exhibited a diminished size of the co-repressor binding pocket in the LBD, thus signaling a partial blockage of the co-repressor binding motif. Thus, the ability of 4-OHT-bound ERα-LBD to assume flexible conformations visited by agonists and reduced co-repressor binding surface at the LBD provide crucial structural insights into tamoxifen-resistance that complement our existing understanding.

Ligand Size and Conformation Affect the Behavior of Nanoparticles Coated with in Vitro and in Vivo Protein Corona.

PubMed

Zhang, Huajin; Wu, Tianmu; Yu, Wenqi; Ruan, Shaobo; He, Qin; Gao, Huile

2018-03-14

Protein corona is immediately established on the surface of nanoparticles upon their introduction into biological milieu. Several studies have shown that the targeting efficiency of ligand-modified nanoparticles is attenuated or abolished owing to the protein adsorption. Here, transferrin receptor-targeting ligands, including LT7 (CHAIYPRH), DT7 (hrpyiahc, all d-form amino acids), and transferrin, were used to identify the influence of the ligand size and conformation on protein corona formation. The results showed that the targeting capacity of ligand-modified nanoparticles was lost after incubation with plasma in vitro, whereas it was partially retained after in vivo corona formation. Results from sodium dodecyl sulfate polyacrylamide gel electrophoresis and liquid chromatography-mass spectrometry revealed the difference in the composition of in vitro and in vivo corona, wherein the ligand size and conformation played a critical role. Differences were observed in cellular internalization and exocytosis profiles on the basis of the ligand and corona source.

Initial steps of inactivation at the K+ channel selectivity filter

PubMed Central

Thomson, Andrew S.; Heer, Florian T.; Smith, Frank J.; Hendron, Eunan; Bernèche, Simon; Rothberg, Brad S.

2014-01-01

K+ efflux through K+ channels can be controlled by C-type inactivation, which is thought to arise from a conformational change near the channel’s selectivity filter. Inactivation is modulated by ion binding near the selectivity filter; however, the molecular forces that initiate inactivation remain unclear. We probe these driving forces by electrophysiology and molecular simulation of MthK, a prototypical K+ channel. Either Mg2+ or Ca2+ can reduce K+ efflux through MthK channels. However, Ca2+, but not Mg2+, can enhance entry to the inactivated state. Molecular simulations illustrate that, in the MthK pore, Ca2+ ions can partially dehydrate, enabling selective accessibility of Ca2+ to a site at the entry to the selectivity filter. Ca2+ binding at the site interacts with K+ ions in the selectivity filter, facilitating a conformational change within the filter and subsequent inactivation. These results support an ionic mechanism that precedes changes in channel conformation to initiate inactivation. PMID:24733889

The spatial configuration of ordered polynucleotide chains. II. The poly(rA) helix.

PubMed Central

Olson, W K

1975-01-01

Approximate details of the spatial configuration of the ordered single-stranded poly(rA) molecule in dilute solution have been obtained in a combined theoretical analysis of base stacking and chain flexibility. Only those regularly repeating structures which fulfill the criterion of conformational flexibility (based upon all available experimental and theoretical evidence of preferred bond rotations) and which also exhibit the right-handed base stacking pattern observed in nmr investigations of poly(rA) are deemed suitable single-stranded helices. In addition, the helical geometry of the stacked structures is required to be consistent with the experimentally observed dimensions of both completely ordered and partially ordered poly(rA) chains. Only a single category of poly(rA) helices (very similar in all conformational details to the individual chains of the poly(rA) double-stranded X-ray structure) is thus obtained. Other conformationally feasible polynucleotide helices characterized simply by a parallel and overlapping base stacking arrangement are also discussed. PMID:1052529

Modeled and Measured Partially Coherent Illumination Speckle Effects from Sloped Surfaces for Tactical Tracking

DTIC Science & Technology

2015-03-26

long-wave infrared ( LWIR ) passive imaging, or eliminating dependence upon target emission and solar reflection. Figure 1.1 shows one example of a...levels of illumination nonuniformity were still present in each IFOV. Thus, further expansion of the beam such that the minimum diffraction- limited... LWIR – long-wave infrared, sometimes defined as the 8 to 12 µm spectral window MWIR – mid-wave infrared, sometimes defined as the 3 to 5 µm spectral

Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale

PubMed Central

Candotti, Michela; Pérez, Alberto; Ferrer-Costa, Carles; Rueda, Manuel; Meyer, Tim; Gelpí, Josep Lluís; Orozco, Modesto

2013-01-01

After decades of using urea as denaturant, the kinetic role of this molecule in the unfolding process is still undefined: does urea actively induce protein unfolding or passively stabilize the unfolded state? By analyzing a set of 30 proteins (representative of all native folds) through extensive molecular dynamics simulations in denaturant (using a range of force-fields), we derived robust rules for urea unfolding that are valid at the proteome level. Irrespective of the protein fold, presence or absence of disulphide bridges, and secondary structure composition, urea concentrates in the first solvation shell of quasi-native proteins, but with a density lower than that of the fully unfolded state. The presence of urea does not alter the spontaneous vibration pattern of proteins. In fact, it reduces the magnitude of such vibrations, leading to a counterintuitive slow down of the atomic-motions that opposes unfolding. Urea stickiness and slow diffusion is, however, crucial for unfolding. Long residence urea molecules placed around the hydrophobic core are crucial to stabilize partially open structures generated by thermal fluctuations. Our simulations indicate that although urea does not favor the formation of partially open microstates, it is not a mere spectator of unfolding that simply displaces to the right of the folded←→unfolded equilibrium. On the contrary, urea actively favors unfolding: it selects and stabilizes partially unfolded microstates, slowly driving the protein conformational ensemble far from the native one and also from the conformations sampled during thermal unfolding. PMID:24348236

Account of an optical beam spreading caused by turbulence for the problem of partially coherent wavefield propagation through inhomogeneous absorbing media

NASA Astrophysics Data System (ADS)

Dudorov, Vadim V.; Kolosov, Valerii V.

2003-04-01

The propagation problem for partially coherent wave fields in inhomogeneous media is considered in this work. The influence of refraction, inhomogeneity of gain medium properties and refraction parameter fluctuations on target characteristics of radiation are taken into consideration. Such problems arise in the study of laser propagation on atmosphere paths, under investigation of directional radiation pattern forming for lasers which gain media is characterized by strong fluctuation of dielectric constant and for lasers which resonator have an atmosphere area. The ray-tracing technique allows us to make effective algorithms for modeling of a partially coherent wave field propagation through inhomogeneous random media is presented for case when the influecne of an optical wave refraction, the influence of the inhomogeiety of radiaitn amplification or absorption, and also the influence of fluctuations of a refraction parameter on target radiation parameters are basic. Novelty of the technique consists in the account of the additional refraction caused by inhomogeneity of gain, and also in the method of an account of turbulent distortions of a beam with any initial coherence allowing to execute construction of effective numerical algorithms. The technique based on the solution of the equation for coherence function of the second order.

Photon beam asymmetry Σ in the reaction γ → p → p ω for E γ = 1.152 to 1.876 GeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Collins, P.; Ritchie, B. G.; Dugger, M.

Photon beam asymmetrymore » $$\\Sigma$$ measurements for $$\\omega$$ photoproduction in the reaction $$\\vec{\\gamma} p \\to \\omega p$$ are reported for photon energies from 1.152 to 1.876 GeV. Data were taken using a linearly-polarized tagged photon beam, a cryogenic hydrogen target, and the CLAS spectrometer in Hall B at Jefferson Lab. The measurements we obtained markedly increase the size of the database for this observable, extend coverage to higher energies, and resolve discrepancies in previously published data. Comparisons of these new results with predictions from a chiral-quark-based model and from a dynamical coupled-channels model indicate the importance of interferences between $t$-channel meson exchange and $s$- and $u$-channel contributions, underscoring sensitivity to the nucleon resonances included in those descriptions. Comparisons with the Bonn-Gatchina partial-wave analysis indicate the $$\\Sigma$$ data reported here help to fix the magnitudes of the interference terms between the leading amplitudes in that calculation (Pomeron exchange and the resonant portion of the $J^P=3/2^+$ partial wave), as well as the resonant portions of the smaller partial waves with $J^P$= $1/2^-$, $3/2^-$, and $5/2^+$.« less

Statistics of partially-polarized fields: beyond the Stokes vector and coherence matrix

NASA Astrophysics Data System (ADS)

Charnotskii, Mikhail

2017-08-01

Traditionally, the partially-polarized light is characterized by the four Stokes parameters. Equivalent description is also provided by correlation tensor of the optical field. These statistics specify only the second moments of the complex amplitudes of the narrow-band two-dimensional electric field of the optical wave. Electric field vector of the random quasi monochromatic wave is a nonstationary oscillating two-dimensional real random variable. We introduce a novel statistical description of these partially polarized waves: the Period-Averaged Probability Density Function (PA-PDF) of the field. PA-PDF contains more information on the polarization state of the field than the Stokes vector. In particular, in addition to the conventional distinction between the polarized and depolarized components of the field PA-PDF allows to separate the coherent and fluctuating components of the field. We present several model examples of the fields with identical Stokes vectors and very distinct shapes of PA-PDF. In the simplest case of the nonstationary, oscillating normal 2-D probability distribution of the real electrical field and stationary 4-D probability distribution of the complex amplitudes, the newly-introduced PA-PDF is determined by 13 parameters that include the first moments and covariance matrix of the quadrature components of the oscillating vector field.

Photon beam asymmetry Σ in the reaction γ → p → p ω for E γ = 1.152 to 1.876 GeV

DOE PAGES

Collins, P.; Ritchie, B. G.; Dugger, M.; ...

2017-08-18

Photon beam asymmetrymore » $$\\Sigma$$ measurements for $$\\omega$$ photoproduction in the reaction $$\\vec{\\gamma} p \\to \\omega p$$ are reported for photon energies from 1.152 to 1.876 GeV. Data were taken using a linearly-polarized tagged photon beam, a cryogenic hydrogen target, and the CLAS spectrometer in Hall B at Jefferson Lab. The measurements we obtained markedly increase the size of the database for this observable, extend coverage to higher energies, and resolve discrepancies in previously published data. Comparisons of these new results with predictions from a chiral-quark-based model and from a dynamical coupled-channels model indicate the importance of interferences between $t$-channel meson exchange and $s$- and $u$-channel contributions, underscoring sensitivity to the nucleon resonances included in those descriptions. Comparisons with the Bonn-Gatchina partial-wave analysis indicate the $$\\Sigma$$ data reported here help to fix the magnitudes of the interference terms between the leading amplitudes in that calculation (Pomeron exchange and the resonant portion of the $J^P=3/2^+$ partial wave), as well as the resonant portions of the smaller partial waves with $J^P$= $1/2^-$, $3/2^-$, and $5/2^+$.« less

Quantum theory of the structure and bonding in proteins. Part 11. A simplified method and its application to the α-amino-isobutyric acid residue

NASA Astrophysics Data System (ADS)

Peters, David; Peters, Jane

Information about the preferred conformation of the α-amino-isobutyric acid residue (α-AIB) is obtained without explicit computation of its wave function. The conformation of lowest energy of this residue is close to the usual helical conformation and so the residue may occur at the 2 position of a type I or I' bend or in either position of a type III or III' bend. The available experimental information refers to a β bend formed from α-AIB-PRO and then the theory and experiment agree that the only possibility is a type III bend. It is predicted that a β sheet structure may be formed at rather higher energy and in the planar and not the pleated form. There is no apparent reason why this residue should not form an α helix. The simplified method used here is closely related to the partitioned potential energy methods which are widely used in this subject.

Explicit and exact nontraveling wave solutions of the (3+1)-dimensional potential Yu-Toda-Sasa-Fukuyama equation

NASA Astrophysics Data System (ADS)

Yuan, Na

2018-04-01

With the aid of the symbolic computation, we present an improved ( G ‧ / G ) -expansion method, which can be applied to seek more types of exact solutions for certain nonlinear evolution equations. In illustration, we choose the (3 + 1)-dimensional potential Yu-Toda-Sasa-Fukuyama equation to demonstrate the validity and advantages of the method. As a result, abundant explicit and exact nontraveling wave solutions are obtained including two solitary waves solutions, nontraveling wave solutions and dromion soliton solutions. Some particular localized excitations and the interactions between two solitary waves are researched. The method can be also applied to other nonlinear partial differential equations.

Conformal flight path symbology for head-up displays: Defining the distribution of visual attention in three-dimensional space

NASA Astrophysics Data System (ADS)

Ververs, Patricia May

An extensive investigation of the format for head-up display (HUD) instrumentation was conducted in a two-part experiment. First, a pilot's information requirements for the tasks of approach, landing, and taxi were determined through a survey administered to professional commercial pilots via the world wide web. The results of the survey were applied in the development of two symbology sets, one set for flight navigation and the second for ground navigation. Second, twenty pilots from the University of Illinois at Urbana-Champaign were recruited to participate in a 3-day experiment. The study was designed to investigate the format for symbology on HUDs and the performance effects of using conformal and partially conformal symbology to support the pilots' tasks. In addition, two different methods were investigated for supporting the pilots' transition between the task of flying and the task of landing. A seamless transition used visual momentum techniques to smoothly guide the pilots' cognitive transition between the serial displays and the associated tasks. A seamed approach employed an abrupt change between the displays to alert the pilots of the task switch. The results indicate that incorporating a virtually conformal, tunnel-in-the-sky symbology into a complete HUD instrumentation set offers promising pilot performance effects. Pilots easily navigated the complex curved approaches with little to no deviation from the flight path (approximately 10 feet), while performing the secondary tasks of the scanning their instruments and the environment. The seamless transition between the flight and ground symbology offered the pilots a preview of the upcoming landing task, thereby preparing them for the task switch. On the ground, the perspective (scene-linked) symbology set supported landing and taxi navigation tasks with the equal efficiency to the plan view display but with much greater precision. Theories of allocation of attention were used to interpret the experimental findings. Attention was found to be more widely distributed in X-Y space when the pilots were flying with the conformal, tunnel-in-the-sky as compared to the partially conformal ILS (instrument landing system) symbology set. There was little evidence that the air-based navigation displays were supporting divided attention in three-dimensional space. The ground-based scene-linked (truly conformal) display indicated promising effects of dividing attention in depth without negative consequences to processing the near domain symbology. Event expectancy was found to modulate pilot performance in the detection of events both on the symbology and in the environment. The phenomenon known as cognitive tunneling is discussed as a possible cause of the inadequate response times in resolving the anomalous events.

A Proof of Friedman's Ergosphere Instability for Scalar Waves

NASA Astrophysics Data System (ADS)

Moschidis, Georgios

2018-03-01

Let {(M^{3+1},g)} be a real analytic, stationary and asymptotically flat spacetime with a non-empty ergoregion E and no future event horizon H}^{+. In Friedman (Commun Math Phys 63(3):243-255, 1978), Friedman observed that, on such spacetimes, there exist solutions φ to the wave equation \\squaregφ=0 such that their local energy does not decay to 0 as time increases. In addition, Friedman provided a heuristic argument that the energy of such solutions actually grows to +∞. In this paper, we provide a rigorous proof of Friedman's instability. Our setting is, in fact, more general. We consider smooth spacetimes {(M^{d+1},g)}, for any {d≥2}, not necessarily globally real analytic. We impose only a unique continuation condition for the wave equation across the boundary partial{E} of E on a small neighborhood of a point p\\inpartialE. This condition always holds if {(M,g)} is analytic in that neighborhood of p, but it can also be inferred in the case when {(M,g)} possesses a second Killing field {Φ} such that the span of {Φ} and the stationary Killing field T is timelike on partial{E}. We also allow the spacetimes {(M,g)} under consideration to possess a (possibly empty) future event horizon H}^{+, such that, however, {H+\\cap E=\\emptyset} (excluding, thus, the Kerr exterior family). As an application of our theorem, we infer an instability result for the acoustical wave equation on the hydrodynamic vortex, a phenomenon first investigated numerically by Oliveira et al. in (Phys Rev D 89(12):124008, 2014). Furthermore, as a side benefit of our proof, we provide a derivation, based entirely on the vector field method, of a Carleman-type estimate on the exterior of the ergoregion for a general class of stationary and asymptotically flat spacetimes. Applications of this estimate include a Morawetz-type bound for solutions φ of \\squaregφ=0 with frequency support bounded away from {{ω}=0} and {{ω}=±∞}.

Water-hammer pressure waves interaction at cross-section changes in series in viscoelastic pipes

NASA Astrophysics Data System (ADS)

Meniconi, S.; Brunone, B.; Ferrante, M.

2012-08-01

In view of scarcity of both experimental data and numerical models concerning transient behavior of cross-section area changes in pressurized liquid flow, the paper presents laboratory data and numerical simulation of the interaction of a surge wave with a partial blockage by a valve, a single pipe contraction or expansion and a series of pipe contraction/expansion in close proximity.With regard to a single change of cross-section area, laboratory data point out the completely different behavior with respect to one of the partially closed in-line valves with the same area ratio. In fact, for the former the pressure wave interaction is not regulated by the steady-state local head loss. With regard to partial blockages, transient tests have shown that the smaller the length, the more intense the overlapping of pressure waves due to the expansion and contraction in series.Numerically, the need for taking into account both the viscoelasticity and unsteady friction is demonstrated, since the classical water-hammer theory does not simulate the relevant damping of pressure peaks and gives rise to a time shifting between numerical and laboratory data. The transient behavior of a single local head loss has been checked by considering tests carried out in a system with a partially closed in-line valve. As a result, the reliability of the quasi steady-state approach for local head loss simulation has been demonstrated in viscoelastic pipes. The model parameters obtained on the basis of transients carried out in single pipe systems have then been used to simulate transients in the more complex pipe systems. These numerical experiments show the great importance of the length of the small-bore pipe with respect to one of the large-bore pipes. Precisely, until a gradually flow establishes in the small-bore pipe, the smaller such a length, the better the quality of the numerical simulation.

Is Congo red an amyloid-specific dye?

PubMed

Khurana, R; Uversky, V N; Nielsen, L; Fink, A L

2001-06-22

Congo red (CR) binding, monitored by characteristic yellow-green birefringence under crossed polarization has been used as a diagnostic test for the presence of amyloid in tissue sections for several decades. This assay is also widely used for the characterization of in vitro amyloid fibrils. In order to probe the structural specificity of Congo red binding to amyloid fibrils we have used an induced circular dichroism (CD) assay. Amyloid fibrils from insulin and the variable domain of Ig light chain demonstrate induced CD spectra upon binding to Congo red. Surprisingly, the native conformations of insulin and Ig light chain also induced Congo red circular dichroism, but with different spectral shapes than those from fibrils. In fact, a wide variety of native proteins exhibited induced CR circular dichroism indicating that CR bound to representative proteins from different classes of secondary structure such as alpha (citrate synthase), alpha + beta (lysozyme), beta (concavalin A), and parallel beta-helical proteins (pectate lyase). Partially folded intermediates of apomyoglobin induced different Congo red CD bands than the corresponding native conformation, however, no induced CD bands were observed with unfolded protein. Congo red was also found to induce oligomerization of native proteins, as demonstrated by covalent cross-linking and small angle x-ray scattering. Our data suggest that Congo red is sandwiched between two protein molecules causing protein oligomerization. The fact that Congo red binds to native, partially folded conformations and amyloid fibrils of several proteins shows that it must be used with caution as a diagnostic test for the presence of amyloid fibrils in vitro.

Effect of temperature on the conformation of natively unfolded protein 4E-BP1 in aqueous and mixed solutions containing trifluoroethanol and hexafluoroisopropanol.

PubMed

Hackl, Ellen V

2015-02-01

Natively unfolded (intrinsically disordered) proteins have attracted growing attention due to their high abundance in nature, involvement in various signalling and regulatory pathways and direct association with many diseases. In the present work the combined effect of temperature and alcohols, trifluoroethanol (TFE) and hexafluoroisopropanol (HFIP), on the natively unfolded 4E-BP1 protein was studied to elucidate the balance between temperature-induced folding and unfolding in intrinsically disordered proteins. It was shown that elevated temperatures induce reversible partial folding of 4E-BP1 both in buffer and in the mixed solutions containing denaturants. In the mixed solutions containing TFE (HFIP) 4E-BP1 adopts a partially folded helical conformation. As the temperature increases, the initial temperature-induced protein folding is replaced by irreversible unfolding/melting only after a certain level of the protein helicity has been reached. Onset unfolding temperature decreases with TFE (HFIP) concentration in solution. It was shown that an increase in the temperature induces two divergent processes in a natively unfolded protein--hydrophobicity-driven folding and unfolding. Balance between these two processes determines thermal behaviour of a protein. The correlation between heat-induced protein unfolding and the amount of helical content in a protein is revealed. Heat-induced secondary structure formation can be a valuable test to characterise minor changes in the conformations of natively unfolded proteins as a result of site-directed mutagenesis. Mutants with an increased propensity to fold into a structured form reveal different temperature behaviour.

Mechanism of cAMP Partial Agonism in Protein Kinase G (PKG)*♦

PubMed Central

VanSchouwen, Bryan; Selvaratnam, Rajeevan; Giri, Rajanish; Lorenz, Robin; Herberg, Friedrich W.; Kim, Choel; Melacini, Giuseppe

2015-01-01

Protein kinase G (PKG) is a major receptor of cGMP and controls signaling pathways often distinct from those regulated by cAMP. Hence, the selective activation of PKG by cGMP versus cAMP is critical. However, the mechanism of cGMP-versus-cAMP selectivity is only limitedly understood. Although the C-terminal cyclic nucleotide-binding domain B of PKG binds cGMP with higher affinity than cAMP, the intracellular concentrations of cAMP are typically higher than those of cGMP, suggesting that the cGMP-versus-cAMP selectivity of PKG is not controlled uniquely through affinities. Here, we show that cAMP is a partial agonist for PKG, and we elucidate the mechanism for cAMP partial agonism through the comparative NMR analysis of the apo, cGMP-, and cAMP-bound forms of the PKG cyclic nucleotide-binding domain B. We show that although cGMP activation is adequately explained by a two-state conformational selection model, the partial agonism of cAMP arises from the sampling of a third, partially autoinhibited state. PMID:26370085

Pink truck ads: second-wave feminism and gendered marketing.

PubMed

Howard, Ella

2010-01-01

Second-wave feminist media had a contentious relationship with corporate advertisers. This article uses automotive advertisements to explore the role of gender, class, and race in the construction of consumer markets from the 1970s through the 1980s. It analyzes the struggle of Gloria Steinem and other liberal feminists to navigate the terrain between the women's movement and corporate advertisers. The increased economic power of women, stemming from the Equal Credit Opportunity Act as well as broader social and political shifts, facilitated their efforts. In the 1980s, automobiles continued to be marketed to women, albeit through "feminine" imagery conforming to the era's dominant trends.

A relativistic toy model for Unruh black holes

NASA Astrophysics Data System (ADS)

Carbonaro, P.

2014-08-01

We consider the wave propagation in terms of acoustic geometry in a quantum relativistic system. This reduces, in the hydrodynamic limit, to the equations which govern the motion of a relativistic Fermi-degenerate gas in one space dimension. The derivation of an acoustic metric for one-dimensional (1D) systems is in general plagued with the impossibility of defining a conformal factor. Here we show that, although the system is intrinsically one-dimensional, the Unruh procedure continues to work because of the particular structure symmetry of the model. By analyzing the dispersion relation, attention is also paid to the quantum effects on the wave propagation.

40 CFR 1068.262 - What are the provisions for temporarily exempting engines for shipment to secondary engine...

Code of Federal Regulations, 2011 CFR

2011-07-01

... manufacturers may finish assembly of partially complete engines in the following cases: (1) You obtain an engine... with the intent to modify it before it reaches the ultimate purchaser. (3) You obtain an engine with... of conformity but before the certificate's effective date. In this case, all the provisions of § 1068...

49 CFR 176.907 - Polymeric Beads and Plastic Molding Compounds.

Code of Federal Regulations, 2013 CFR

2013-10-01

...: (1) Packed in hermetically sealed packagings or IBC's which conform to packing group II performance level for liquid dangerous goods with a total pressure in the packaging (i.e., the vapor pressure of the material plus the partial pressure of air or other inert gases, less 100kPa (15 psia)) at 55 °C (131 °F...

49 CFR 176.907 - Polymeric Beads and Plastic Molding Compounds.

Code of Federal Regulations, 2014 CFR

2014-10-01

...: (1) Packed in hermetically sealed packagings or IBC's which conform to packing group II performance level for liquid dangerous goods with a total pressure in the packaging (i.e., the vapor pressure of the material plus the partial pressure of air or other inert gases, less 100kPa (15 psia)) at 55 °C (131 °F...

Theoretical study of hydrated copper(II) interactions with guanine: a computational density functional theory study.

PubMed

Pavelka, Matej; Shukla, Manoj K; Leszczynski, Jerzy; Burda, Jaroslav V

2008-01-17

Optimization of the hydrated Cu(II)(N7-guanine) structures revealed a number of minima on the potential energy surface. For selected structures, energy decompositions together with the determination of electronic properties (partial charges and electron spin densities) were performed. In the complexes of guanine with the bare copper cation and that with the monoaqua ligated cation, an electron transfer from guanine to Cu(II) was observed, resulting in a Cu(I)-guanine(+) type of complex. Conformers with two aqua ligands are borderline systems characterized by a Cu partial charge of +0.7e and a similar value of the spin density (0.6e) localized on guanine. When tetracoordination of copper was achieved, only then the prevailing electron spin density is unambiguously localized on copper. The energetic preference of diaqua-Cu-(N7,O6-guanine) over triaqua-Cu-(N7-guanine) was found for the four-coordinate structures. However, the energy difference between these two conformations decreases with the number of water molecules present in the systems, and in complexes with five water molecules this preference is preserved only at DeltaG level where thermal and entropy terms are included.

Medical Comorbidity of Full and Partial Posttraumatic Stress Disorder in United States Adults: Results from Wave 2 of the National Epidemiologic Survey on Alcohol and Related Conditions

PubMed Central

Pietrzak, Robert H.; Goldstein, Risë B.; Southwick, Steven M.; Grant, Bridget F.

2011-01-01

Objective This study examined associations between lifetime trauma exposures, PTSD and partial PTSD, and past-year medical conditions in a nationally representative sample of U.S. adults. Methods Face-to-face interviews were conducted with 34,653 participants in the Wave 2 National Epidemiologic Survey on Alcohol and Related Conditions. Logistic regression analyses evaluated associations of trauma exposure, PTSD and partial PTSD with respondent-reported medical diagnoses. Results After adjustment for sociodemographic characteristics and comorbid Axis I and II disorders, respondents with full PTSD were more likely than traumatized respondents without full or partial PTSD (comparison group) to report diagnoses of diabetes mellitus, noncirrhotic liver disease, angina pectoris, tachycardia, hypercholesterolemia, other heart disease, stomach ulcer, HIV seropositivity, gastritis, and arthritis (odds ratios [ORs]=1.2-2.5). Respondents with partial PTSD were more likely than the comparison group to report past-year diagnoses of stomach ulcer, angina pectoris, tachycardia, and arthritis (ORs=1.3-1.6). Men with full and partial PTSD were more likely than controls to report diagnoses of hypertension (both ORs=1.6), and both men and women with PTSD (ORs=1.8 and 1.6, respectively), and men with partial PTSD (OR=2.0) were more likely to report gastritis. Total number of lifetime traumatic event types was associated with many assessed medical conditions (ORs=1.04-1.16), reducing the magnitudes and rendering non-significant some of the associations between PTSD status and medical conditions. Conclusions Greater lifetime trauma exposure and PTSD are associated with numerous medical conditions, many of which are stress-related and chronic, in U.S. adults. Partial PTSD is associated with intermediate odds of some of these conditions. PMID:21949429

Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Laowanapiban, Poramaet; Kapustina, Maryna; Vonrhein, Clemens

2009-03-05

Two new crystal structures of Bacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS) afford evidence that a closed interdomain hinge angle requires a covalent bond between AMP and an occupant of either pyrophosphate or tryptophan subsite. They also are within experimental error of a cluster of structures observed in a nonequilibrium molecular dynamics simulation showing partial active-site assembly. Further, the highest energy structure in a minimum action pathway computed by using elastic network models for Open and Pretransition state (PreTS) conformations for the fully liganded TrpRS monomer is intermediate between that simulated structure and a partially disassembled structure from a nonequilibrium molecular dynamicsmore » trajectory for the unliganded PreTS. These mutual consistencies provide unexpected validation of inferences drawn from molecular simulations.« less

Boundary-fitted coordinate systems for numerical solution of partial differential equations - A review

NASA Technical Reports Server (NTRS)

Thompson, J. F.; Warsi, Z. U. A.; Mastin, C. W.

1982-01-01

A comprehensive review of methods of numerically generating curvilinear coordinate systems with coordinate lines coincident with all boundary segments is given. Some general mathematical framework and error analysis common to such coordinate systems is also included. The general categories of generating systems are those based on conformal mapping, orthogonal systems, nearly orthogonal systems, systems produced as the solution of elliptic and hyperbolic partial differential equations, and systems generated algebraically by interpolation among the boundaries. Also covered are the control of coordinate line spacing by functions embedded in the partial differential operators of the generating system and by subsequent stretching transformation. Dynamically adaptive coordinate systems, coupled with the physical solution, and time-dependent systems that follow moving boundaries are treated. References reporting experience using such coordinate systems are reviewed as well as those covering the system development.

Exploring the binding energy profiles of full agonists, partial agonists, and antagonists of the α7 nicotinic acetylcholine receptor.

PubMed

Tabassum, Nargis; Ma, Qianyun; Wu, Guanzhao; Jiang, Tao; Yu, Rilei

2017-09-01

Nicotinic acetylcholine receptors (nAChRs) belong to the Cys-loop receptor family and are important drug targets for the treatment of neurological diseases. However, the precise determinants of the binding efficacies of ligands for these receptors are unclear. Therefore, in this study, the binding energy profiles of various ligands (full agonists, partial agonists, and antagonists) were quantified by docking those ligands with structural ensembles of the α7 nAChR exhibiting different degrees of C-loop closure. This approximate treatment of interactions suggested that full agonists, partial agonists, and antagonists of the α7 nAChR possess distinctive binding energy profiles. Results from docking revealed that ligand binding efficacy may be related to the capacity of the ligand to stabilize conformational states with a closed C loop.

Study of diffusion of wave packets in a square lattice under external fields along the discrete nonlinear Schrödinger equation

NASA Astrophysics Data System (ADS)

de Brito, P. E.; Nazareno, H. N.

2012-09-01

The object of the present work is to analyze the effect of nonlinearity on wave packet propagation in a square lattice subject to a magnetic and an electric field in the Hall configuration, by using the Discrete Nonlinear Schrödinger Equation (DNLSE). In previous works we have shown that without the nonlinear term, the presence of the magnetic field induces the formation of vortices that remain stationary, while a wave packet is introduced in the system. As for the effect of an applied electric field, it was shown that the vortices propagate in a direction perpendicular to the electric field, similar behavior as presented in the classical treatment, we provide a quantum mechanics explanation for that. We have performed the calculations considering first the action of the magnetic field as well as the nonlinearity. The results indicate that for low values of the nonlinear parameter U the vortices remain stationary while preserving the form. For greater values of the parameter the picture gets distorted, the more so, the greater the nonlinearity. As for the inclusion of the electric field, we note that for small U, the wave packet propagates perpendicular to the applied field, until for greater values of U the wave gets partially localized in a definite region of the lattice. That is, for strong nonlinearity the wave packet gets partially trapped, while the tail of it can propagate through the lattice. Note that this tail propagation is responsible for the over-diffusion for long times of the wave packet under the action of an electric field. We have produced short films that show clearly the time evolution of the wave packet, which can add to the understanding of the dynamics.

Propagation of Torsional Alfvén Waves from the Photosphere to the Corona: Reflection, Transmission, and Heating in Expanding Flux Tubes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soler, Roberto; Terradas, Jaume; Oliver, Ramón

It has been proposed that Alfvén waves play an important role in the energy propagation through the solar atmospheric plasma and its heating. Here we theoretically investigate the propagation of torsional Alfvén waves in magnetic flux tubes expanding from the photosphere up to the low corona and explore the reflection, transmission, and dissipation of wave energy. We use a realistic variation of the plasma properties and the magnetic field strength with height. Dissipation by ion–neutral collisions in the chromosphere is included using a multifluid partially ionized plasma model. Considering the stationary state, we assume that the waves are driven belowmore » the photosphere and propagate to the corona, while they are partially reflected and damped in the chromosphere and transition region. The results reveal the existence of three different propagation regimes depending on the wave frequency: low frequencies are reflected back to the photosphere, intermediate frequencies are transmitted to the corona, and high frequencies are completely damped in the chromosphere. The frequency of maximum transmissivity depends on the magnetic field expansion rate and the atmospheric model, but is typically in the range of 0.04–0.3 Hz. Magnetic field expansion favors the transmission of waves to the corona and lowers the reflectivity of the chromosphere and transition region compared to the case with a straight field. As a consequence, the chromospheric heating due to ion–neutral dissipation systematically decreases when the expansion rate of the magnetic flux tube increases.« less

Spectral modification of seismic waves propagating through solids exhibiting a resonance frequency: a 1-D coupled wave propagation-oscillation model

NASA Astrophysics Data System (ADS)

Frehner, Marcel; Schmalholz, Stefan M.; Podladchikov, Yuri

2009-02-01

A 1-D model is presented that couples the microscale oscillations of non-wetting fluid blobs in a partially saturated poroelastic medium with the macroscale wave propagation through the elastic skeleton. The fluid oscillations are caused by surface tension forces that act as the restoring forces driving the oscillations. The oscillations are described mathematically with the equation for a linear oscillator and the wave propagation is described with the 1-D elastic wave equation. Coupling is done using Hamilton's variational principle for continuous systems. The resulting linear system of two partial differential equations is solved numerically with explicit finite differences. Numerical simulations are used to analyse the effect of solids exhibiting internal oscillations, and consequently a resonance frequency, on seismic waves propagating through such media. The phase velocity dispersion relation shows a higher phase velocity in the high-frequency limit and a lower phase velocity in the low-frequency limit. At the resonance frequency a singularity in the dispersion relation occurs. Seismic waves can initiate oscillations of the fluid by transferring energy from solid to fluid at the resonance frequency. Due to this transfer, the spectral amplitude of the solid particle velocity decreases at the resonance frequency. After initiation, the oscillatory movement of the fluid continuously transfers energy at the resonance frequency back to the solid. Therefore, the spectral amplitude of the solid particle velocity is increased at the resonance frequency. Once initiated, fluid oscillations decrease in amplitude with increasing time. Consequently, the spectral peak of the solid particle velocity at the resonance frequency decreases with time.

Hydrogen bonding in the neutron structure of the mononucleotide 5'-UMP disodium salt

NASA Astrophysics Data System (ADS)

Chitra, R.; Ranjan-Choudhury, R.; Ramanadham, M.

Disodium uridine 5'-monophosphate heptahydrate (5'-UMPNa2), Na2[C9H11N2O9P].7H2O, crystallises in space group C2221 with a=22.985, b=8.911 and c=19.494Å. A neutron beam of λ=1.216Å was used; Z=8 and V=3992.75Å3. Data consisted of 1785 unique reflections. Na ions were connected to the main molecule through water molecules and sugar oxygens. One of the Na ions occupied a special position, and the other at a general position was partially disordered. The uracil base was planar, and had anti conformation about the glycosidic bond. The sugar had C(2') endo conformation and was gauche-gauche.

The nucleotide-free state of heterotrimeric G proteins α-subunit adopts a highly stable conformation.

PubMed

Andhirka, Sai Krishna; Vignesh, Ravichandran; Aradhyam, Gopala Krishna

2017-08-01

Deciphering the mechanism of activation of heterotrimeric G proteins by their cognate receptors continues to be an intriguing area of research. The recently solved crystal structure of the ternary complex captured the receptor-bound α-subunit in an open conformation, without bound nucleotide has improved our understanding of the activation process. Despite these advancements, the mechanism by which the receptor causes GDP release from the α-subunit remains elusive. To elucidate the mechanism of activation, we studied guanine nucleotide-induced structural stability of the α-subunit (in response to thermal/chaotrope-mediated stress). Inherent stabilities of the inactive (GDP-bound) and active (GTP-bound) forms contribute antagonistically to the difference in conformational stability whereas the GDP-bound protein is able to switch to a stable intermediate state, GTP-bound protein loses this ability. Partial perturbation of the protein fold reveals the underlying influence of the bound nucleotide providing an insight into the mechanism of activation. An extra stable, pretransition intermediate, 'empty pocket' state (conformationally active-state like) in the unfolding pathway of GDP-bound protein mimics a gating system - the activation process having to overcome this stable intermediate state. We demonstrate that a relatively more complex conformational fold of the GDP-bound protein is at the core of the gating system. We report capturing this threshold, 'metastable empty pocket' conformation (the gate) of α-subunit of G protein and hypothesize that the receptor activates the G protein by enabling it to achieve this structure through mild structural perturbation. © 2017 Federation of European Biochemical Societies.

Discordant U waves in the setting of hyperkalaemia.

PubMed

Chhabra, Lovely; Spodick, David H

2013-07-04

Physiological U wave genesis occurs likely secondary to either late repolarisation of Purkinje fibres, or late repolarisation of some myocardial cells and/or delayed after depolarisation of the ventricular wall occurring during ventricular filling. Hypokalaemia has a well-known association with pathological 'U wave' which actually combines with the T wave (TU complex) and results from slowing of phase 3 of the action potential with resultant electrical interaction between the three myocardial layers. U waves usually tend to disappear in the setting of hyperkalaemia. We report an unusual case where hyperkalaemia and discordant U waves coexisted. We believe that this may have occurred as a result of partial clinical adaptation of cardiac myocytes to the long-standing effects of hyperkalaemia as the patient had underlying history of chronic kidney disease. We also discuss the possible mechanisms of the U wave genesis and the importance of different U wave morphologies encountered in the real clinical practice.

Grating formation by a high power radio wave in near-equator ionosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Rohtash; Sharma, A. K.; Tripathi, V. K.

2011-11-15

The formation of a volume grating in the near-equator regions of ionosphere due to a high power radio wave is investigated. The radio wave, launched from a ground based transmitter, forms a standing wave pattern below the critical layer, heating the electrons in a space periodic manner. The thermal conduction along the magnetic lines of force inhibits the rise in electron temperature, limiting the efficacy of heating to within a latitude of few degrees around the equator. The space periodic electron partial pressure leads to ambipolar diffusion creating a space periodic density ripple with wave vector along the vertical. Suchmore » a volume grating is effective to cause strong reflection of radio waves at a frequency one order of magnitude higher than the maximum plasma frequency in the ionosphere. Linearly mode converted plasma wave could scatter even higher frequency radio waves.« less

Stability of nonlinear waves and patterns and related topics.

PubMed

Ghazaryan, Anna; Lafortune, Stephane; Manukian, Vahagn

2018-04-13

Periodic and localized travelling waves such as wave trains, pulses, fronts and patterns of more complex structure often occur in natural and experimentally built systems. In mathematics, these objects are realized as solutions of nonlinear partial differential equations. The existence, dynamic properties and bifurcations of those solutions are of interest. In particular, their stability is important for applications, as the waves that are observable are usually stable. When the waves are unstable, further investigation is warranted of the way the instability is exhibited, i.e. the nature of the instability, and also coherent structures that appear as a result of an instability of travelling waves. A variety of analytical, numerical and hybrid techniques are used to study travelling waves and their properties.This article is part of the theme issue 'Stability of nonlinear waves and patterns and related topics'. © 2018 The Author(s).

Low-frequency dispersion and attenuation in anisotropic partially saturated rocks

NASA Astrophysics Data System (ADS)

Cavallini, Fabio; Carcione, José M.; Vidal de Ventós, Daniel; Engell-Sørensen, Lisbeth

2017-06-01

The mesoscopic-loss mechanism is believed to be the most important attenuation mechanism in porous media at seismic frequencies. It is caused by P-wave conversion to slow diffusion (Biot) modes at material inhomogeneity on length scales of the order of centimetres. It is very effective in partially saturated media, particularly in the presence of gas. We explicitly extend the theory of wave propagation at normal incidence to three periodic thin layers and using this result we obtain the five complex and frequency-dependent stiffness components of the corresponding periodic finely layered medium, where the equivalent medium is anisotropic, specifically transversely isotropic. The relaxation behaviour can be described by a single complex and frequency-dependent stiffness component, since the medium consists of plane homogeneous layers. The media can be dissimilar in any property, but a relevant example in hydrocarbon exploration is the case of partial saturation and the same frame skeleton, where the fluid can be brine, oil and gas. The numerical examples illustrate the implementation of the theory to compute the wave velocities (phase and energy) and quality factors. We consider two main cases, namely, the same frame (or skeleton) and different fluids, and the same fluid and different frame properties. Unlike the two-phase case (two fluids), the results show two relaxation peaks. This scenario is more realistic since usually reservoirs rocks contain oil, brine and gas. The theory is quite general since it is not only restricted to partial saturation, but also applies to important properties such as porosity and permeability heterogeneities.

Multiconfiguration Pair-Density Functional Theory: A New Way To Treat Strongly Correlated Systems.

PubMed

Gagliardi, Laura; Truhlar, Donald G; Li Manni, Giovanni; Carlson, Rebecca K; Hoyer, Chad E; Bao, Junwei Lucas

2017-01-17

The electronic energy of a system provides the Born-Oppenheimer potential energy for internuclear motion and thus determines molecular structure and spectra, bond energies, conformational energies, reaction barrier heights, and vibrational frequencies. The development of more efficient and more accurate ways to calculate the electronic energy of systems with inherently multiconfigurational electronic structure is essential for many applications, including transition metal and actinide chemistry, systems with partially broken bonds, many transition states, and most electronically excited states. Inherently multiconfigurational systems are called strongly correlated systems or multireference systems, where the latter name refers to the need for using more than one ("multiple") configuration state function to provide a good zero-order reference wave function. This Account describes multiconfiguration pair-density functional theory (MC-PDFT), which was developed as a way to combine the advantages of wave function theory (WFT) and density functional theory (DFT) to provide a better treatment of strongly correlated systems. First we review background material: the widely used Kohn-Sham DFT (which uses only a single Slater determinant as reference wave function), multiconfiguration WFT methods that treat inherently multiconfigurational systems based on an active space, and previous attempts to combine multiconfiguration WFT with DFT. Then we review the formulation of MC-PDFT. It is a generalization of Kohn-Sham DFT in that the electron kinetic energy and classical electrostatic energy are calculated from a reference wave function, while the rest of the energy is obtained from a density functional. However, there are two main differences with respent to Kohn-Sham DFT: (i) The reference wave function is multiconfigurational rather than being a single Slater determinant. (ii) The density functional is a function of the total density and the on-top pair density rather than being a function of the spin-up and spin-down densities. In work carried out so far, the multiconfigurational wave function is a multiconfiguration self-consistent-field wave function. The new formulation has the advantage that the reference wave function has the correct spatial and spin symmetry and can describe bond dissociation (of both single and multiple bonds) and electronic excitations in a formally and physically correct way. We then review the formulation of density functionals in terms of the on-top pair density. Finally we review successful applications of the theory to bond energies and bond dissociation potential energy curves of main-group and transition metal bonds, to barrier heights (including pericyclic reactions), to proton affinities, to the hydrogen bond energy of water dimer, to ground- and excited-state charge transfer, to valence and Rydberg excitations of molecules, and to singlet-triplet splittings of radicals. We find that that MC-PDFT can give accurate results not only with complete-active-space multiconfiguration wave functions but also with generalized-active-space multiconfiguration wave functions, which are practical for larger numbers of active electrons and active orbitals than are complete-active-space wave functions. The separated-pair approximation, which is a special case of generalized active space self-consistent-field theory, is especially promising. MC-PDFT, because it requires much less computer time and storage than pure WFT methods, has the potential to open larger and more complex strongly correlated systems to accurate simulation.

Damage detection in composite materials using Lamb wave methods

NASA Astrophysics Data System (ADS)

Kessler, Seth S.; Spearing, S. Mark; Soutis, Constantinos

2002-04-01

Cost-effective and reliable damage detection is critical for the utilization of composite materials. This paper presents part of an experimental and analytical survey of candidate methods for in situ damage detection of composite materials. Experimental results are presented for the application of Lamb wave techniques to quasi-isotropic graphite/epoxy test specimens containing representative damage modes, including delamination, transverse ply cracks and through-holes. Linear wave scans were performed on narrow laminated specimens and sandwich beams with various cores by monitoring the transmitted waves with piezoceramic sensors. Optimal actuator and sensor configurations were devised through experimentation, and various types of driving signal were explored. These experiments provided a procedure capable of easily and accurately determining the time of flight of a Lamb wave pulse between an actuator and sensor. Lamb wave techniques provide more information about damage presence and severity than previously tested methods (frequency response techniques), and provide the possibility of determining damage location due to their local response nature. These methods may prove suitable for structural health monitoring applications since they travel long distances and can be applied with conformable piezoelectric actuators and sensors that require little power.

Shock and Rarefaction Waves in a Heterogeneous Mantle

NASA Astrophysics Data System (ADS)

Jordan, J.; Hesse, M. A.

2012-12-01

We explore the effect of heterogeneities on partial melting and melt migration during active upwelling in the Earth's mantle. We have constructed simple, explicit nonlinear models in one dimension to examine heterogeneity and its dynamic affects on porosity, temperature and the magnesium number in a partially molten, porous medium comprised of olivine. The composition of the melt and solid are defined by a closed, binary phase diagram for a simplified, two-component olivine system. The two-component solid solution is represented by a phase loop where concentrations 0 and 1 to correspond to fayalite and forsterite, respectively. For analysis, we examine an advective system with a Riemann initial condition. Chromatographic tools and theory have primarily been used to track large, rare earth elements as tracers. In our case, we employ these theoretical tools to highlight the importance of the magnesium number, enthalpy and overall heterogeneity in the dynamics of melt migration. We calculate the eigenvectors and eigenvalues in the concentration-enthalpy space in order to glean the characteristics of the waves emerging the Riemann step. Analysis on Riemann problems of this nature shows us that the composition-enthalpy waves can be represented by self-similar solutions. The eigenvalues of the composition-enthalpy system represent the characteristic wave propagation speeds of the compositions and enthalpy through the domain. Furthermore, the corresponding eigenvectors are the directions of variation, or ``pathways," in concentration-enthalpy space that the characteristic waves follow. In the two-component system, the Riemann problem yields two waves connected by an intermediate concentration-enthalpy state determined by the intersections of the integral curves of the eigenvectors emanating from both the initial and boundary states. The first wave, ``slow path," and second wave, ``fast path," follow the aformentioned pathways set by the eigenvectors. The slow path wave has a zero eigenvalue, corresponding to a wave speed of zero, which preserves a residual imprint of the initial condition. Freezing fronts textemdash those that result in a negative change in porositytextemdash feature fast path waves that travel as shocks, whereas the fast path waves of melting fronts travel as spreading, rarefaction waves.

Concatenons as the solutions for non-linear partial differential equations

NASA Astrophysics Data System (ADS)

Kudryashov, N. A.; Volkov, A. K.

2017-07-01

New class of solutions for nonlinear partial differential equations is introduced. We call them the concaten solutions. As an example we consider equations for the description of wave processes in the Fermi-Pasta-Ulam mass chain and construct the concatenon solutions for these equation. Stability of the concatenon-type solutions is investigated numerically. Interaction between the concatenon and solitons is discussed.

Ultrasonic Acoustic Velocities During Partial Melting of a Mantle Peridotite KLB-1

NASA Astrophysics Data System (ADS)

Weidner, Donald J.; Li, Li; Whitaker, Matthew L.; Triplett, Richard

2018-02-01

Knowledge of the elastic properties of partially molten rocks is crucial for understanding low-velocity regions in the interior of the Earth. Models of fluid and solid mixtures have demonstrated that significant decreases in seismic velocity are possible with small amounts of melt, but there is very little available data for testing these models, particularly with both P and S waves for mantle compositions. We report ultrasonic measurements of P and S velocities on a partially molten KLB-1 sample at mantle conditions using a multi-anvil device at a synchrotron facility. The P, S, and bulk sound velocities decrease as melting occurs. We find that the quantity, ∂lnVS/∂lnVB (where VB is the bulk sound velocity) is lower than mechanical models estimate. Instead, our data, as well as previous data in the literature, are consistent with a dynamic melting model in which melting and solidification interact with the stress field of the acoustic wave.

Electron-pair-production cross section in the tip region of the positron spectrum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sud, K.K.; Sharma, D.K.

1984-11-01

The radial integrals for electron-pair production in a point Coulomb potential have been expressed by Sud, Sharma, and Sud in terms of the matrix generalization of the GAMMA function. Two new partial differential equations in photon energy satisfied by the matrix GAMMA function are obtained. We have obtained, on integrating the partial differential equations, accurate radial integrals as a function of photon energy for the pair production by intermediate-energy photons. The cross section in the tip region of the spectrum are calculated for photons of energy 5.0 to 10.0 MeV for /sup 92/U. The new technique results in extensive savingmore » in computer time as the basic radial integrals in terms of the hypergeometric function F/sub 2/ are computed at one photon energy for each pair of partial waves. The results of our calculations are compared with plane-wave Born-approximation results and with the calculations of Dugne and of Deck, Moroi, and Alling.« less

Pulse-like partial ruptures and high-frequency radiation at creeping-locked transition during megathrust earthquakes

NASA Astrophysics Data System (ADS)

Michel, Sylvain; Avouac, Jean-Philippe; Lapusta, Nadia; Jiang, Junle

2017-08-01

Megathrust earthquakes tend to be confined to fault areas locked in the interseismic period and often rupture them only partially. For example, during the 2015 M7.8 Gorkha earthquake, Nepal, a slip pulse propagating along strike unzipped the bottom edge of the locked portion of the Main Himalayan Thrust (MHT). The lower edge of the rupture produced dominant high-frequency (>1 Hz) radiation of seismic waves. We show that similar partial ruptures occur spontaneously in a simple dynamic model of earthquake sequences. The fault is governed by standard laboratory-based rate-and-state friction with the aging law and contains one homogenous velocity-weakening (VW) region embedded in a velocity-strengthening (VS) area. Our simulations incorporate inertial wave-mediated effects during seismic ruptures (they are thus fully dynamic) and account for all phases of the seismic cycle in a self-consistent way. Earthquakes nucleate at the edge of the VW area and partial ruptures tend to stay confined within this zone of higher prestress, producing pulse-like ruptures that propagate along strike. The amplitude of the high-frequency sources is enhanced in the zone of higher, heterogeneous stress at the edge of the VW area.

Pulse-Like Partial Ruptures and High-Frequency Radiation at Creeping-Locked Transition during Megathrust Earthquakes

NASA Astrophysics Data System (ADS)

Michel, S. G. R. M.; Avouac, J. P.; Lapusta, N.; Jiang, J.

2017-12-01

Megathrust earthquakes tend to be confined to fault areas locked in the interseismic period and often rupture them only partially. For example, during the 2015 M7.8 Gorkha earthquake, Nepal, a slip pulse propagating along strike unzipped the bottom edge of the locked portion of the Main Himalayan Thrust (MHT). The lower edge of the rupture produced dominant high-frequency (>1 Hz) radiation of seismic waves. We show that similar partial ruptures occur spontaneously in a simple dynamic model of earthquake sequences. The fault is governed by standard laboratory-based rate-and-state friction with the ageing law and contains one homogenous velocity-weakening (VW) region embedded in a velocity-strengthening (VS) area. Our simulations incorporate inertial wave-mediated effects during seismic ruptures (they are thus fully dynamic) and account for all phases of the seismic cycle in a self-consistent way. Earthquakes nucleate at the edge of the VW area and partial ruptures tend to stay confined within this zone of higher prestress, producing pulse-like ruptures that propagate along strike. The amplitude of the high-frequency sources is enhanced in the zone of higher, heterogeneous stress at the edge of the VW area.

DAMPING OF MAGNETOHYDRODYNAMIC TURBULENCE IN PARTIALLY IONIZED PLASMA: IMPLICATIONS FOR COSMIC RAY PROPAGATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Siyao; Yan, Huirong; Lazarian, A., E-mail: syxu@pku.edu.cn, E-mail: huirong.yan@desy.de, E-mail: lazarian@astro.wisc.edu

2016-08-01

We study the damping processes of both incompressible and compressible magnetohydrodynamic (MHD) turbulence in a partially ionized medium. We start from the linear analysis of MHD waves, applying both single-fluid and two-fluid treatments. The damping rates derived from the linear analysis are then used in determining the damping scales of MHD turbulence. The physical connection between the damping scale of MHD turbulence and the cutoff boundary of linear MHD waves is investigated. We find two branches of slow modes propagating in ions and neutrals, respectively, below the damping scale of slow MHD turbulence, and offer a thorough discussion of theirmore » propagation and dissipation behavior. Our analytical results are shown to be applicable in a variety of partially ionized interstellar medium (ISM) phases and the solar chromosphere. The importance of neutral viscosity in damping the Alfvenic turbulence in the interstellar warm neutral medium and the solar chromosphere is demonstrated. As a significant astrophysical utility, we introduce damping effects to the propagation of cosmic rays in partially ionized ISM. The important role of turbulence damping in both transit-time damping and gyroresonance is identified.« less

X-ray standing wave analysis of nanostructures using partially coherent radiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tiwari, M. K., E-mail: mktiwari@rrcat.gov.in; Das, Gangadhar; Bedzyk, M. J.

2015-09-07

The effect of longitudinal (or temporal) coherence on total reflection assisted x-ray standing wave (TR-XSW) analysis of nanoscale materials is quantitatively demonstrated by showing how the XSW fringe visibility can be strongly damped by decreasing the spectral resolution of the incident x-ray beam. The correction for nonzero wavelength dispersion (δλ ≠ 0) of the incident x-ray wave field is accounted for in the model computations of TR-XSW assisted angle dependent fluorescence yields of the nanostructure coatings on x-ray mirror surfaces. Given examples include 90 nm diameter Au nanospheres deposited on a Si(100) surface and a 3 nm thick Zn layer trapped on top amore » 100 nm Langmuir-Blodgett film coating on a Au mirror surface. Present method opens up important applications, such as enabling XSW studies of large dimensioned nanostructures using conventional laboratory based partially coherent x-ray sources.« less

Use of the Lorentz-operator in relativistic quantum mechanics to guarentee a single-energy root

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ritchie, A B

1998-08-01

The Lorentz-operator form of relativistic quantum mechanics, with relativistic wave equation i{h_bar}{partial_derivative}{psi}/{partial_derivative}t=(mc{sup 2}{gamma}+e{Phi}){psi}, is implemented to guarantee a single-energy root. The Lorentz factor as modified by Pauli's ansatz is given by {gamma}={radical}1+[{rvec {sigma}}{center_dot}(i{h_bar}{rvec {del}}+(e/c){rvec A})]{sup 2}/m{sup 2}c{sup 2}, such that the theory is appropriate for electrons. Magnetic fine structure in the Lorentz relativistic wave equation emerges on the use of an appropriate operator form of the Lienard-Wiechert four- potential ({Phi},{rvec A}) from electromagnetic theory. Although computationally more intensive the advantage of the theory is the elimination of the negative-root of the energy and an interpretation of the wave function basedmore » on a one-particle, positive definite probability density like that of nonrelativistic quantum mechanics.« less

Transformation elastodynamics and cloaking for flexural waves

NASA Astrophysics Data System (ADS)

Colquitt, D. J.; Brun, M.; Gei, M.; Movchan, A. B.; Movchan, N. V.; Jones, I. S.

2014-12-01

The paper addresses an important issue of cloaking transformations for fourth-order partial differential equations representing flexural waves in thin elastic plates. It is shown that, in contrast with the Helmholtz equation, the general form of the partial differential equation is not invariant with respect to the cloaking transformation. The significant result of this paper is the analysis of the transformed equation and its interpretation in the framework of the linear theory of pre-stressed plates. The paper provides a formal framework for transformation elastodynamics as applied to elastic plates. Furthermore, an algorithm is proposed for designing a broadband square cloak for flexural waves, which employs a regularised push-out transformation. Illustrative numerical examples show high accuracy and efficiency of the proposed cloaking algorithm. In particular, a physical configuration involving a perturbation of an interference pattern generated by two coherent sources is presented. It is demonstrated that the perturbation produced by a cloaked defect is negligibly small even for such a delicate interference pattern.

Fast neural solution of a nonlinear wave equation

NASA Technical Reports Server (NTRS)

Toomarian, Nikzad; Barhen, Jacob

1992-01-01

A neural algorithm for rapidly simulating a certain class of nonlinear wave phenomena using analog VLSI neural hardware is presented and applied to the Korteweg-de Vries partial differential equation. The corresponding neural architecture is obtained from a pseudospectral representation of the spatial dependence, along with a leap-frog scheme for the temporal evolution. Numerical simulations demonstrated the robustness of the proposed approach.

Seismic seiches

USGS Publications Warehouse

McGarr, Arthur; Gupta, Harsh K.

2011-01-01

Seismic seiche is a term first used by Kvale (1955) to discuss oscillations of lake levels in Norway and England caused by the Assam earthquake of August 15, 1950. This definition has since been generalized to apply to standing waves set up in closed, or partially closed, bodies of water including rivers, shipping channels, lakes, swimming pools and tanks due to the passage of seismic waves from an earthquake.

Coherence for vectorial waves and majorization.

PubMed

Luis, Alfredo

2016-11-15

We show that comparison via majorization provides a powerful tool to examine the coherence of partially polarized electromagnetic waves, including the idea that two field states may or may not be comparable. Through two relevant scenarios, we show that when superimposing comparable unpolarized fields majorization agrees with interferometric visibility, while when combining fields of different degrees of polarization the situation turns out to be richer.

The dynamics of a forced coupled network of active elements

NASA Astrophysics Data System (ADS)

Parks, Helen F.; Ermentrout, Bard; Rubin, Jonathan E.

2011-03-01

This paper presents the derivation and analysis of mathematical models motivated by the experimental induction of contour phosphenes in the retina. First, a spatially discrete chain of periodically forced coupled oscillators is considered via reduction to a chain of scalar phase equations. Each isolated oscillator locks in a 1:2 manner with the forcing so that there is intrinsic bistability, with activity peaking on either the odd or even cycles of the forcing. If half the chain is started on the odd cycle and half on the even cycle (“split state”), then with sufficiently strong coupling, a wave can be produced that can travel in either direction due to symmetry. Numerical and analytic methods are employed to determine the size of coupling necessary for the split state solution to destabilize such that waves appear. Taking a continuum limit, we reduce the chain to a partial differential equation. We use a Melnikov function to compute, to leading order, the speed of the traveling wave solution to the partial differential equation as a function of the form of coupling and the forcing parameters and compare our result to the numerically computed discrete and continuum wave speeds.

Time-domain comparisons of power law attenuation in causal and noncausal time-fractional wave equations

PubMed Central

Zhao, Xiaofeng; McGough, Robert J.

2016-01-01

The attenuation of ultrasound propagating in human tissue follows a power law with respect to frequency that is modeled by several different causal and noncausal fractional partial differential equations. To demonstrate some of the similarities and differences that are observed in three related time-fractional partial differential equations, time-domain Green's functions are calculated numerically for the power law wave equation, the Szabo wave equation, and for the Caputo wave equation. These Green's functions are evaluated for water with a power law exponent of y = 2, breast with a power law exponent of y = 1.5, and liver with a power law exponent of y = 1.139. Simulation results show that the noncausal features of the numerically calculated time-domain response are only evident very close to the source and that these causal and noncausal time-domain Green's functions converge to the same result away from the source. When noncausal time-domain Green's functions are convolved with a short pulse, no evidence of noncausal behavior remains in the time-domain, which suggests that these causal and noncausal time-fractional models are equally effective for these numerical calculations. PMID:27250193

A novel principle for partial agonism of liver X receptor ligands. Competitive recruitment of activators and repressors.

PubMed

Albers, Michael; Blume, Beatrix; Schlueter, Thomas; Wright, Matthew B; Kober, Ingo; Kremoser, Claus; Deuschle, Ulrich; Koegl, Manfred

2006-02-24

Partial, selective activation of nuclear receptors is a central issue in molecular endocrinology but only partly understood. Using LXRs as an example, we show here that purely agonistic ligands can be clearly and quantitatively differentiated from partial agonists by the cofactor interactions they induce. Although a pure agonist induces a conformation that is incompatible with the binding of repressors, partial agonists such as GW3965 induce a state where the interaction not only with coactivators, but also corepressors is clearly enhanced over the unliganded state. The activities of the natural ligand 22(R)-hydroxycholesterol and of a novel quinazolinone ligand, LN6500 can be further differentiated from GW3965 and T0901317 by their weaker induction of coactivator binding. Using biochemical and cell-based assays, we show that the natural ligand of LXR is a comparably weak partial agonist. As predicted, we find that a change in the coactivator to corepressor ratio in the cell will affect NCoR recruiting compounds more dramatically than NCoR-dissociating compounds. Our data show how competitive binding of coactivators and corepressors can explain the tissue-specific behavior of partial agonists and open up new routes to a rational design of partial agonists for LXRs.

Structural Characterization of Two Metastable ATP-Bound States of P-Glycoprotein

PubMed Central

O’Mara, Megan L.; Mark, Alan E.

2014-01-01

ATP Binding Cassette (ABC) transporters couple the binding and hydrolysis of ATP to the transport of substrate molecules across the membrane. The mechanism by which ATP binding and/or hydrolysis drives the conformational changes associated with substrate transport has not yet been characterized fully. Here, changes in the conformation of the ABC export protein P-glycoprotein on ATP binding are examined in a series of molecular dynamics simulations. When one molecule of ATP is placed at the ATP binding site associated with each of the two nucleotide binding domains (NBDs), the membrane-embedded P-glycoprotein crystal structure adopts two distinct metastable conformations. In one, each ATP molecule interacts primarily with the Walker A motif of the corresponding NBD. In the other, the ATP molecules interacts with both Walker A motif of one NBD and the Signature motif of the opposite NBD inducing the partial dimerization of the NBDs. This interaction is more extensive in one of the two ATP binding site, leading to an asymmetric structure. The overall conformation of the transmembrane domains is not altered in either of these metastable states, indicating that the conformational changes associated with ATP binding observed in the simulations in the absence of substrate do not lead to the outward-facing conformation and thus would be insufficient in themselves to drive transport. Nevertheless, the metastable intermediate ATP-bound conformations observed are compatible with a wide range of experimental cross-linking data demonstrating the simulations do capture physiologically important conformations. Analysis of the interaction between ATP and its cofactor Mg2+ with each NBD indicates that the coordination of ATP and Mg2+ differs between the two NBDs. The role structural asymmetry may play in ATP binding and hydrolysis is discussed. Furthermore, we demonstrate that our results are not heavily influenced by the crystal structure chosen for initiation of the simulations. PMID:24632881

Analysis of the Association Between Electrocardiographic P-wave Characteristics and Atrial Fibrillation in the REGICOR Study.

PubMed

Massó-van Roessel, Albert; Escobar-Robledo, Luis Alberto; Dégano, Irene R; Grau, María; Sala, Joan; Ramos, Rafel; Marrugat, Jaume; Bayés de Luna, Antoni; Elosua, Roberto

2017-10-01

Atrial fibrillation (AF) is the most common clinically significant cardiac arrhythmia. P-wave duration and interatrial blocks (IAB) have been reported to be associated with AF. Our aim was to determine the individual and combined association of P-wave duration and advanced IAB morphology with AF. We designed an age-, sex-, and survey-matched case-control study nested in a population-based cohort (REGICOR: REgistre GIroní del COR). Two different surveys recruited a total of 9380 participants from 1999 to 2005; all participants were invited to a second examination between 2009 and 2013. For the present study, we selected participants aged 25 to 79 years with follow-up through the end of the study. All electrocardiograms were analyzed by 2 observers to determine P-wave duration and morphology (normal, partial, or advanced IAB). The median follow-up was 7.12 years. Eighty participants presented with AF, had a legible baseline electrocardiogram, and were included in the study, along with 160 controls. P-wave duration and the presence of partial or advanced IAB were associated with AF. When P-wave duration and morphology were considered together, only P-wave duration (≥ 110 milliseconds) showed an independent and strong association with AF. The odds ratio for AF of P-wave duration between 110-119, 120-129 and ≥ 130 milliseconds vs < 110 milliseconds were 5.33; 95%CI, 1.74-16.33, 5.08; 95%CI, 1.73-14.90 and 5.44; 95%CI, 1.95-15.15, respectively. A P-wave longer than 110 milliseconds increases the risk of AF. Advanced IAB morphology did not seem to provide an additional AF risk beyond that of P-wave duration. Copyright © 2017 Sociedad Española de Cardiología. Published by Elsevier España, S.L.U. All rights reserved.

Origin choice and petal loss in the flower garden of spiral wave tip trajectories

PubMed Central

Gray, Richard A.; Wikswo, John P.; Otani, Niels F.

2009-01-01

Rotating spiral waves have been observed in numerous biological and physical systems. These spiral waves can be stationary, meander, or even degenerate into multiple unstable rotating waves. The spatiotemporal behavior of spiral waves has been extensively quantified by tracking spiral wave tip trajectories. However, the precise methodology of identifying the spiral wave tip and its influence on the specific patterns of behavior remains a largely unexplored topic of research. Here we use a two-state variable FitzHugh–Nagumo model to simulate stationary and meandering spiral waves and examine the spatiotemporal representation of the system’s state variables in both the real (i.e., physical) and state spaces. We show that mapping between these two spaces provides a method to demarcate the spiral wave tip as the center of rotation of the solution to the underlying nonlinear partial differential equations. This approach leads to the simplest tip trajectories by eliminating portions resulting from the rotational component of the spiral wave. PMID:19791998

Origin choice and petal loss in the flower garden of spiral wave tip trajectories.

PubMed

Gray, Richard A; Wikswo, John P; Otani, Niels F

2009-09-01

Rotating spiral waves have been observed in numerous biological and physical systems. These spiral waves can be stationary, meander, or even degenerate into multiple unstable rotating waves. The spatiotemporal behavior of spiral waves has been extensively quantified by tracking spiral wave tip trajectories. However, the precise methodology of identifying the spiral wave tip and its influence on the specific patterns of behavior remains a largely unexplored topic of research. Here we use a two-state variable FitzHugh-Nagumo model to simulate stationary and meandering spiral waves and examine the spatiotemporal representation of the system's state variables in both the real (i.e., physical) and state spaces. We show that mapping between these two spaces provides a method to demarcate the spiral wave tip as the center of rotation of the solution to the underlying nonlinear partial differential equations. This approach leads to the simplest tip trajectories by eliminating portions resulting from the rotational component of the spiral wave.

Add-on unidirectional elastic metamaterial plate cloak

PubMed Central

Lee, Min Kyung; Kim, Yoon Young

2016-01-01

Metamaterial cloaks control the propagation of waves to make an object invisible or insensible. To manipulate elastic waves in space, a metamaterial cloak is typically embedded in a base system that includes or surrounds a target object. The embedding is undesirable because it structurally weakens or permanently alters the base system. In this study, we propose a new add-on metamaterial elastic cloak that can be placed over and mechanically coupled with a base structure without embedding. We designed an add-on type annular metamaterial plate cloak through conformal mapping, fabricated it and performed cloaking experiments in a thin-plate with a hole. Experiments were performed in a thin plate by using the lowest symmetric Lamb wave centered at 100 kHz. As a means to check the cloaking performance of the add-on elastic plate cloak, possibly as a temporary stress reliever or a so-called “stress bandage”, the degree of stress concentration mitigation and the recovery from the perturbed wave field due to a hole were investigated. PMID:26860896

Broadband diffuse terahertz wave scattering by flexible metasurface with randomized phase distribution

PubMed Central

Zhang, Yin; Liang, Lanju; Yang, Jing; Feng, Yijun; Zhu, Bo; Zhao, Junming; Jiang, Tian; Jin, Biaobing; Liu, Weiwei

2016-01-01

Suppressing specular electromagnetic wave reflection or backward radar cross section is important and of broad interests in practical electromagnetic engineering. Here, we present a scheme to achieve broadband backward scattering reduction through diffuse terahertz wave reflection by a flexible metasurface. The diffuse scattering of terahertz wave is caused by the randomized reflection phase distribution on the metasurface, which consists of meta-particles of differently sized metallic patches arranged on top of a grounded polyimide substrate simply through a certain computer generated pseudorandom sequence. Both numerical simulations and experimental results demonstrate the ultralow specular reflection over a broad frequency band and wide angle of incidence due to the re-distribution of the incident energy into various directions. The diffuse scattering property is also polarization insensitive and can be well preserved when the flexible metasurface is conformably wrapped on a curved reflective object. The proposed design opens up a new route for specular reflection suppression, and may be applicable in stealth and other technology in the terahertz spectrum. PMID:27225031

Broadband diffuse terahertz wave scattering by flexible metasurface with randomized phase distribution.

PubMed

Zhang, Yin; Liang, Lanju; Yang, Jing; Feng, Yijun; Zhu, Bo; Zhao, Junming; Jiang, Tian; Jin, Biaobing; Liu, Weiwei

2016-05-26

Suppressing specular electromagnetic wave reflection or backward radar cross section is important and of broad interests in practical electromagnetic engineering. Here, we present a scheme to achieve broadband backward scattering reduction through diffuse terahertz wave reflection by a flexible metasurface. The diffuse scattering of terahertz wave is caused by the randomized reflection phase distribution on the metasurface, which consists of meta-particles of differently sized metallic patches arranged on top of a grounded polyimide substrate simply through a certain computer generated pseudorandom sequence. Both numerical simulations and experimental results demonstrate the ultralow specular reflection over a broad frequency band and wide angle of incidence due to the re-distribution of the incident energy into various directions. The diffuse scattering property is also polarization insensitive and can be well preserved when the flexible metasurface is conformably wrapped on a curved reflective object. The proposed design opens up a new route for specular reflection suppression, and may be applicable in stealth and other technology in the terahertz spectrum.

Add-on unidirectional elastic metamaterial plate cloak

NASA Astrophysics Data System (ADS)

Lee, Min Kyung; Kim, Yoon Young

2016-02-01

Metamaterial cloaks control the propagation of waves to make an object invisible or insensible. To manipulate elastic waves in space, a metamaterial cloak is typically embedded in a base system that includes or surrounds a target object. The embedding is undesirable because it structurally weakens or permanently alters the base system. In this study, we propose a new add-on metamaterial elastic cloak that can be placed over and mechanically coupled with a base structure without embedding. We designed an add-on type annular metamaterial plate cloak through conformal mapping, fabricated it and performed cloaking experiments in a thin-plate with a hole. Experiments were performed in a thin plate by using the lowest symmetric Lamb wave centered at 100 kHz. As a means to check the cloaking performance of the add-on elastic plate cloak, possibly as a temporary stress reliever or a so-called “stress bandage”, the degree of stress concentration mitigation and the recovery from the perturbed wave field due to a hole were investigated.

Stability of the Zagreb realization of the Carnegie-Mellon-Berkeley coupled-channels unitary model

NASA Astrophysics Data System (ADS)

Osmanović, H.; Ceci, S.; Švarc, A.; Hadžimehmedović, M.; Stahov, J.

2011-09-01

In Hadžimehmedović [Phys. Rev. CPRVCAN0556-281310.1103/PhysRevC.84.035204 84, 035204 (2011)] we have used the Zagreb realization of Carnegie-Melon-Berkeley coupled-channel, unitary model as a tool for extracting pole positions from the world collection of partial-wave data, with the aim of eliminating model dependence in pole-search procedures. In order that the method is sensible, we in this paper discuss the stability of the method with respect to the strong variation of different model ingredients. We show that the Zagreb CMB procedure is very stable with strong variation of the model assumptions and that it can reliably predict the pole positions of the fitted partial-wave amplitudes.

Effect of partial wave parameter identification on IOS opacities and integral cross sections for rotationally inelastic collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pack, R.T

1977-02-15

The effect of identification of the partial wave parameter of the J/sub z/ CCS and IOS approximations as an orbital angular momentum rather than the total angular momentum is studied. Comparison with accurate close coupling calculations for Ar--N/sub 2/ and He--CO/sub 2/ collisions is made, and it is found that this identification results in a marked improvement, both quantitative and qualitative, in calculated IOS opacity functions and integral cross sections for both elastic and inelastic collisions. Use of the correct energy in the cross section formula also makes a marked improvement even though T matrices are computed with an averagemore » energy. (AIP)« less

The Chiral and Angular Momentum Content of the ρ-Meson

NASA Astrophysics Data System (ADS)

Glozman, L. Ya.; Lang, C. B.; Limmer, M.

2010-01-01

It is possible to define and calculate in a gauge-invariant manner the chiral as well as the partial wave content of the quark-antiquark Fock component of a meson in the infrared, where mass is generated. Using the variational method and a set of interpolators that span a complete chiral basis we extract in a lattice QCD Monte Carlo simulation with n f = 2 dynamical light quarks the orbital angular momentum and spin content of the ρ-meson. We obtain in the infrared a simple 3 S 1 component as a leading component of the ρ-meson with a small admixture of the 3 D 1 partial wave, in agreement with the SU(6) flavor-spin symmetry.

Interference and partial which-way information: A quantitative test of duality in two-atom resonance

NASA Astrophysics Data System (ADS)

Abranyos, Y.; Jakob, M.; Bergou, J.

2000-01-01

We propose for the experimental verification of an inequality concerning wave-particle duality by Englert [Phys. Rev. Lett. 77, 2154 (1996)] relating (or setting) an upper limit on distinguishability and visibility in a two-way interferometer. The inequality, quantifies the concept of wave-particle duality. The considered two-way interferometer is a Young's double-slit experiment involving two four-level atoms and is a slightly modified version of that of the recent experiment by Eichmann et al. [Phys. Rev. Lett. 70, 2359 (1993)]. The fringe visibility depends on the detected polarization direction of the scattered light and a read out of the internal state of one of the two atoms provides a partial which-way information.

Baryon Spectroscopy Through Partial-Wave Analysis and Meson Photoproduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manley, D. Mark

2016-09-08

The principal goal of this project is the experimental and phenomenological study of baryon spectroscopy. The PI's group consists of himself and three graduate students. This final report summarizes research activities by the PI's group during the period 03/01/2015 to 08/14/2016. During this period, the PI co-authored 11 published journal papers and one proceedings article and presented three invited talks. The PI's general interest is the investigation of the baryon resonance spectrum up to masses of ~ 2 GeV. More detail is given on two research projects: Neutral Kaon Photoproduction and Partial-Wave Analyses of γp → η p, γn →more » η n, and γp → K⁺ Λ.« less

Uncertainties of α-particle optical potential assessment around and below the Coulomb barrier

NASA Astrophysics Data System (ADS)

Avrigeanu, V.; Avrigeanu, M.; Mǎnǎilescu, C.

2017-06-01

A competition of the low-energy Coulomb excitation (CE) with the compound nucleus (CN) formation in α-induced reactions below the Coulomb barrier has recently been assumed in order to make possible the description of the latter as well as the α-particle emission by the same optical model (OM) potential. However, we show in the present work that the corresponding partial waves and integration radii provide evidence for the distinct account of the CE cross section and OM total-reaction cross section σR. Thus the largest contribution to CE cross section comes by far from partial waves larger than the ones contributing to the σR values. Finally, effects of statistical model parameters are comparatively discussed.

The production of phantom partials due to nonlinearities in the structural components of the piano.

PubMed

Rokni, Eric; Neldner, Lauren M; Adkison, Camille; Moore, Thomas R

2017-10-01

Phantom partials are anomalous overtones in the spectrum of the piano sound that occur at sum and difference frequencies of the natural overtones of the string. Although they are commonly assumed to be produced by forced longitudinal waves in the string, analysis of the sound of a piano produced by mechanically vibrating the soundboard while all the strings are damped indicates that phantom partials can occur in the absence of string motion. The magnitude of the effect leads to the conclusion that nonlinearity in the non-string components may be responsible for some of the power in the phantom partials.

Universal power law of the gravity wave manifestation in the AIM CIPS polar mesospheric cloud images

NASA Astrophysics Data System (ADS)

Rong, Pingping; Yue, Jia; Russell, James M., III; Siskind, David E.; Randall, Cora E.

2018-01-01

We aim to extract a universal law that governs the gravity wave manifestation in polar mesospheric clouds (PMCs). Gravity wave morphology and the clarity level of display vary throughout the wave population manifested by the PMC albedo data. Higher clarity refers to more distinct exhibition of the features, which often correspond to larger variances and a better-organized nature. A gravity wave tracking algorithm based on the continuous Morlet wavelet transform is applied to the PMC albedo data at 83 km altitude taken by the Aeronomy of Ice in the Mesosphere (AIM) Cloud Imaging and Particle Size (CIPS) instrument to obtain a large ensemble of the gravity wave detections. The horizontal wavelengths in the range of ˜ 20-60 km are the focus of the study. It shows that the albedo (wave) power statistically increases as the background gets brighter. We resample the wave detections to conform to a normal distribution to examine the wave morphology and display clarity beyond the cloud brightness impact. Sample cases are selected at the two tails and the peak of the normal distribution to represent the full set of wave detections. For these cases the albedo power spectra follow exponential decay toward smaller scales. The high-albedo-power category has the most rapid decay (i.e., exponent = -3.2) and corresponds to the most distinct wave display. The wave display becomes increasingly blurrier for the medium- and low-power categories, which hold the monotonically decreasing spectral exponents of -2.9 and -2.5, respectively. The majority of waves are straight waves whose clarity levels can collapse between the different brightness levels, but in the brighter background the wave signatures seem to exhibit mildly turbulent-like behavior.

Protective measurement of the wave function of a single squeezed harmonic-oscillator state

NASA Astrophysics Data System (ADS)

Alter, Orly; Yamamoto, Yoshihisa

1996-05-01

A scheme for the "protective measurement"

An exact solution for effects of topography on free Rayleigh waves

USGS Publications Warehouse

Savage, W.Z.

2004-01-01

An exact solution for the effects of topography on Rayleigh wave amplification is presented. The solution is obtained by incorporating conformal mapping into complex-variable stress functions developed for free Rayleigh wave propagation in an elastic half-space with a flat upper surface. Results are presented for free Rayleigh wave propagation across isolated symmetric ridges and valleys. It is found for wavelengths that are comparable to ridge widths that horizontal Rayleigh wave amplitudes are amplified at ridge crests and that vertical amplitudes are strongly reduced near ridge crests relative to horizontal and vertical amplitudes of free Rayleigh waves in the flat case. Horizontal amplitudes are strongly deamplified at valley bottoms relative to those for the flat case for Rayleigh wavelengths comparable to valley widths. Wave amplitudes in the symmetric ridges and valleys asymptotically approach those for the flat case with increased wavelengths, increased ridge and valley widths, and with horizontal distance from and depth below the isolated ridges and valleys. Also, prograde particle motion is predicted near crests of narrow ridges and near the bottoms of narrow valleys. Finally, application of the theory at two sites known for topographic wave amplification gives a predicted surface wave amplification ratio of 3.80 at the ridge center for a frequency of 1.0 Hz at Robinwood Ridge in northern California and a predicted surface wave amplification ratio of 1.67 at the ridge center for the same frequency at the Cedar Hill Nursery site at Tarzana in southern California.

Chiral dynamics of the p wave in K-p and coupled states

NASA Astrophysics Data System (ADS)

Jido, D.; Oset, E.; Ramos, A.

2002-11-01

We perform an evaluation of the p-wave amplitudes of meson-baryon scattering in the strangeness S=-1 sector starting from the lowest order chiral Lagrangians and introducing explicitly the Σ* field with couplings to the meson-baryon states obtained using SU(6) symmetry. The N/D method of unitarization is used, equivalent, in practice, to the use of the Bethe-Salpeter equation with a cutoff. The procedure leaves no freedom for the p-waves once the s-waves are fixed and thus one obtains genuine predictions for the p-wave scattering amplitudes, which are in good agreement with experimental results for differential cross sections, as well as for the width and partial decay widths of the Σ*(1385).

Axial acoustic radiation force on rigid oblate and prolate spheroids in Bessel vortex beams of progressive, standing and quasi-standing waves.

PubMed

Mitri, F G

2017-02-01

The analysis using the partial-wave series expansion (PWSE) method in spherical coordinates is extended to evaluate the acoustic radiation force experienced by rigid oblate and prolate spheroids centered on the axis of wave propagation of high-order Bessel vortex beams composed of progressive, standing and quasi-standing waves, respectively. A coupled system of linear equations is derived after applying the Neumann boundary condition for an immovable surface in a non-viscous fluid, and solved numerically by matrix inversion after performing a single numerical integration procedure. The system of linear equations depends on the partial-wave index n and the order of the Bessel vortex beam m using truncated but converging PWSEs in the least-squares sense. Numerical results for the radiation force function, which is the radiation force per unit energy density and unit cross-sectional surface, are computed with particular emphasis on the amplitude ratio describing the transition from the progressive to the pure standing waves cases, the aspect ratio (i.e., the ratio of the major axis over the minor axis of the spheroid), the half-cone angle and order of the Bessel vortex beam, as well as the dimensionless size parameter. A generalized expression for the radiation force function is derived for cases encompassing the progressive, standing and quasi-standing waves of Bessel vortex beams. This expression can be reduced to other types of beams/waves such as the zeroth-order Bessel non-vortex beam or the infinite plane wave case by appropriate selection of the beam parameters. The results for progressive waves reveal a tractor beam behavior, characterized by the emergence of an attractive pulling force acting in opposite direction of wave propagation. Moreover, the transition to the quasi-standing and pure standing wave cases shows the acoustical tweezers behavior in dual-beam Bessel vortex beams. Applications in acoustic levitation, particle manipulation and acousto-fluidics would benefit from the results of the present investigation. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular dynamics studies of protein folding and aggregation

NASA Astrophysics Data System (ADS)

Ding, Feng

This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation. Most small proteins fold into their native states via a first-order-like phase transition with a major free energy barrier between the folded and unfolded states. A set of protein conformations corresponding to the free energy barrier, Delta G >> kBT, are the folding transition state ensemble (TSE). Due to their evasive nature, TSE conformations are hard to capture (probability ∝ exp(-DeltaG/k BT)) and characterize. A coarse-grained discrete molecular dynamics model with realistic steric constraints is constructed to reproduce the experimentally observed two-state folding thermodynamics. A kinetic approach is proposed to identify the folding TSE. A specific set of contacts, common to the TSE conformations, is identified as the folding nuclei which are necessary to be formed in order for the protein to fold. Interestingly, the amino acids at the site of the identified folding nuclei are highly conserved for homologous proteins sharing the same structures. Such conservation suggests that amino acids that are important for folding kinetics are under selective pressure to be preserved during the course of molecular evolution. In addition, studies of the conformations close to the transition states uncover the importance of topology in the construction of order parameter for protein folding transition. Misfolded proteins often form insoluble aggregates, amyloid fibrils, that deposit in the extracellular space and lead to a type of disease known as amyloidosis. Due to its insoluble and non-crystalline nature, the aggregation structure and, thus the aggregation mechanism, has yet to be uncovered. Discrete molecular dynamics studies reveal an aggregate structure with the same structural signatures as in experimental observations and show a nucleation aggregation scenario. The simulations also suggest a generic aggregation mechanism that globular proteins under a denaturing environment partially unfold and aggregate by forming stabilizing hydrogen bonds between the backbones of the partial folded substructures. Proteins or peptides rich in alpha-helices also aggregate into beta-rich amyloid fibrils. Upon aggregation, the protein or peptide undergoes a conformational transition from alpha-helices to beta-sheets. The transition of alpha-helix to beta-hairpin (two-stranded beta-sheet) is studied in an all-heavy-atom discrete molecular dynamics model of a polyalanine chain. An entropical driving scenario for the alpha-helix to beta-hairpin transition is discovered.

Scattering and absorption of massless scalar waves by Born-Infeld black holes

NASA Astrophysics Data System (ADS)

Sanchez, Pablo Alejandro; Bretón, Nora; Bergliaffa, Santiago Esteban Perez

2018-06-01

We present the results of a study of the scattering of massless planar scalar waves by a Born-Infeld black hole. The scattering and absorption cross sections are calculated using partial-wave methods. The numerical results are checked by reproducing those of the Reissner-Nordstrom black hole, and also using several approximations, with which our results are in very good agreement. The dependence of these phenomena on the effective potential, the charge of the black hole, and the value of the Born-Infeld parameter is discussed.

Transition of torque pattern in undulatory locomotion due to wave number variation in resistive force dominated media

NASA Astrophysics Data System (ADS)

Ding, Yang; Ming, Tingyu

2016-11-01

In undulatory locomotion, torque (bending moment) is required along the body to overcome the external forces from environments and bend the body. Previous observations on animals using less than two wavelengths on the body showed such torque has a single traveling wave pattern. Using resistive force theory model and considering the torque generated by external force in a resistive force dominated media, we found that as the wave number (number of wavelengths on the locomotor's body) increases from 0.5 to 1.8, the speed of the traveling wave of torque decreases. When the wave number increases to 2 and greater, the torque pattern transits from a single traveling wave to a two traveling waves and then a complex pattern that consists two wave-like patterns. By analyzing the force distribution and its contribution to the torque, we explain the speed decrease of the torque wave and the pattern transition. This research is partially supported by the Recruitment Program of Global Young Experts (China).

New soliton solution to the longitudinal wave equation in a magneto-electro-elastic circular rod

NASA Astrophysics Data System (ADS)

Seadawy, Aly R.; Manafian, Jalil

2018-03-01

This paper examines the effectiveness of an integration scheme which called the extended trial equation method (ETEM) in exactly solving a well-known nonlinear equation of partial differential equations (PDEs). In this respect, the longitudinal wave equation (LWE) that arises in mathematical physics with dispersion caused by the transverse Poisson's effect in a magneto-electro-elastic (MEE) circular rod, which a series of exact traveling wave solutions for the aforementioned equation is formally extracted. Explicit new exact solutions are derived in different form such as dark solitons, bright solitons, solitary wave, periodic solitary wave, rational function, and elliptic function solutions of the longitudinal wave equation. The movements of obtained solutions are shown graphically, which helps to understand the physical phenomena of this longitudinal wave equation. Many other such types of nonlinear equations arising in non-destructive evaluation of structures made of the advanced MEE material can also be solved by this method.

Determination of s- and p-wave I = 1/2 Kπ scattering amplitudes in Nf = 2 + 1 lattice QCD

NASA Astrophysics Data System (ADS)

Brett, Ruairí; Bulava, John; Fallica, Jacob; Hanlon, Andrew; Hörz, Ben; Morningstar, Colin

2018-07-01

The elastic I = 1 / 2, s- and p-wave kaon-pion scattering amplitudes are calculated using a single ensemble of anisotropic lattice QCD gauge field configurations with Nf = 2 + 1 flavors of dynamical Wilson-clover fermions at mπ = 230 MeV. A large spatial extent of L = 3.7 fm enables a good energy resolution while partial wave mixing due to the reduced symmetries of the finite volume is treated explicitly. The p-wave amplitude is well described by a Breit-Wigner shape with parameters mK* /mπ = 3.808 (18) and gK*Kπ BW = 5.33 (20) which are insensitive to the inclusion of d-wave mixing and variation of the s-wave parametrization. An effective range description of the near-threshold s-wave amplitude yields mπa0 = - 0.353 (25).

Quantum chemical calculation (electronic and topologic) and experimental (FT-IR, FT-Raman and UV) analysis of isonicotinic acid N-oxide

NASA Astrophysics Data System (ADS)

Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

2015-04-01

In this work, the molecular conformation, vibrational and electronic analysis of isonicotinic acid N-oxide (iso-NANO) were presented in the ground state using experimental techniques (FT-IR, FT-Raman and UV) and density functional theory (DFT) employing B3LYP exchange correlation with the 6-311++G(d,p) basis set. The geometry optimization and energies associated possible two conformers (Rot-I and Rot-II) were computed. The vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The obtained structures were analyzed with the Atoms in Molecules (AIMs) methodology. The computational results diagnose the most stable conformer of iso-NANO as the Rot-I form. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (OPDOS) diagrams analysis for the most stable conformer (Rot-I) were calculated using the same method. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures were calculated. As a result, the optimized geometry and calculated spectroscopic data show a good agreement with the experimental results.

Conformational stability as a design target to control protein aggregation.

PubMed

Costanzo, Joseph A; O'Brien, Christopher J; Tiller, Kathryn; Tamargo, Erin; Robinson, Anne Skaja; Roberts, Christopher J; Fernandez, Erik J

2014-05-01

Non-native protein aggregation is a prevalent problem occurring in many biotechnological manufacturing processes and can compromise the biological activity of the target molecule or induce an undesired immune response. Additionally, some non-native aggregation mechanisms lead to amyloid fibril formation, which can be associated with debilitating diseases. For natively folded proteins, partial or complete unfolding is often required to populate aggregation-prone conformational states, and therefore one proposed strategy to mitigate aggregation is to increase the free energy for unfolding (ΔGunf) prior to aggregation. A computational design approach was tested using human γD crystallin (γD-crys) as a model multi-domain protein. Two mutational strategies were tested for their ability to reduce/increase aggregation rates by increasing/decreasing ΔGunf: stabilizing the less stable domain and stabilizing the domain-domain interface. The computational protein design algorithm, RosettaDesign, was implemented to identify point variants. The results showed that although the predicted free energies were only weakly correlated with the experimental ΔGunf values, increased/decreased aggregation rates for γD-crys correlated reasonably well with decreases/increases in experimental ΔGunf, illustrating improved conformational stability as a possible design target to mitigate aggregation. However, the results also illustrate that conformational stability is not the sole design factor controlling aggregation rates of natively folded proteins.

Pauling and Corey's alpha-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease.

PubMed

Armen, Roger S; DeMarco, Mari L; Alonso, Darwin O V; Daggett, Valerie

2004-08-10

Transthyretin, beta(2)-microglobulin, lysozyme, and the prion protein are four of the best-characterized proteins implicated in amyloid disease. Upon partial acid denaturation, these proteins undergo conformational change into an amyloidogenic intermediate that can self-assemble into amyloid fibrils. Many experiments have shown that pH-mediated changes in structure are required for the formation of the amyloidogeneic intermediate, but it has proved impossible to characterize these conformational changes at high resolution using experimental means. To probe these conformational changes at atomic resolution, we have performed molecular dynamics simulations of these proteins at neutral and low pH. In low-pH simulations of all four proteins, we observe the formation of alpha-pleated sheet secondary structure, which was first proposed by L. Pauling and R. B. Corey [(1951) Proc. Natl. Acad. Sci. USA 37, 251-256]. In all beta-sheet proteins, transthyretin and beta(2)-microglobulin, alpha-pleated sheet structure formed over the strands that are highly protected in hydrogen-exchange experiments probing amyloidogenic conditions. In lysozyme and the prion protein, alpha-sheets formed in the specific regions of the protein implicated in the amyloidogenic conversion. We propose that the formation of alpha-pleated sheet structure may be a common conformational transition in amyloidosis.

Pauling and Corey's α-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease

PubMed Central

Armen, Roger S.; DeMarco, Mari L.; Alonso, Darwin O. V.; Daggett, Valerie

2004-01-01

Transthyretin, β2-microglobulin, lysozyme, and the prion protein are four of the best-characterized proteins implicated in amyloid disease. Upon partial acid denaturation, these proteins undergo conformational change into an amyloidogenic intermediate that can self-assemble into amyloid fibrils. Many experiments have shown that pH-mediated changes in structure are required for the formation of the amyloidogeneic intermediate, but it has proved impossible to characterize these conformational changes at high resolution using experimental means. To probe these conformational changes at atomic resolution, we have performed molecular dynamics simulations of these proteins at neutral and low pH. In low-pH simulations of all four proteins, we observe the formation of α-pleated sheet secondary structure, which was first proposed by L. Pauling and R. B. Corey [(1951) Proc. Natl. Acad. Sci. USA 37, 251–256]. In all β-sheet proteins, transthyretin and β2-microglobulin, α-pleated sheet structure formed over the strands that are highly protected in hydrogen-exchange experiments probing amyloidogenic conditions. In lysozyme and the prion protein, α-sheets formed in the specific regions of the protein implicated in the amyloidogenic conversion. We propose that the formation of α-pleated sheet structure may be a common conformational transition in amyloidosis. PMID:15280548

Open and closed conformations of two SpoIIAA-like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding

PubMed Central

Kumar, Abhinav; Lomize, Andrei; Jin, Kevin K.; Carlton, Dennis; Miller, Mitchell D.; Jaroszewski, Lukasz; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Chiu, Hsiu-Ju; Clayton, Thomas; Das, Debanu; Deller, Marc C.; Duan, Lian; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Anna; Han, Gye Won; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Marciano, David; McMullan, Daniel; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; van den Bedem, Henry; Weekes, Dana; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

2010-01-01

The crystal structures of the proteins encoded by the YP_749275.1 and YP_001095227.1 genes from Shewanella frigidimarina and S. loihica, respectively, have been determined at 1.8 and 2.25 Å resolution, respectively. These proteins are members of a novel family of bacterial proteins that adopt the α/β SpoIIAA-like fold found in STAS and CRAL-TRIO domains. Despite sharing 54% sequence identity, these two proteins adopt distinct conformations arising from different dispositions of their α2 and α3 helices. In the ‘open’ conformation (YP_001095227.1), these helices are 15 Å apart, leading to the creation of a deep nonpolar cavity. In the ‘closed’ structure (YP_749275.1), the helices partially unfold and rearrange, occluding the cavity and decreasing the solvent-exposed hydrophobic surface. These two complementary structures are reminiscent of the conformational switch in CRAL-TRIO carriers of hydrophobic compounds. It is suggested that both proteins may associate with the lipid bilayer in their ‘open’ monomeric state by inserting their amphiphilic helices, α2 and α3, into the lipid bilayer. These bacterial proteins may function as carriers of nonpolar substances or as interfacially activated enzymes. PMID:20944218

High-Throughput Biophysical Analysis and Data Visualization of Conformational Stability of an IgG1 Monoclonal Antibody (mAb) After Deglycosylation

PubMed Central

Alsenaidy, Mohammad A.; Kim, Jae Hyun; Majumdar, Ranajoy; Weis, David D.; Joshi, Sangeeta B.; Tolbert, Thomas J.; Middaugh, C. Russell; Volkin, David B.

2013-01-01

The structural integrity and conformational stability of an IgG1 monoclonal antibody (mAb), after partial and complete enzymatic removal of the N-linked Fc glycan, was compared to the untreated mAb over a wide range of temperature (10° to 90°C) and solution pH (3 to 8) using circular dichroism, fluorescence spectroscopy, and static light scattering combined with data visualization employing empirical phase diagrams (EPDs). Subtle to larger stability differences between the different glycoforms were observed. Improved detection of physical stability differences was then demonstrated over narrower pH range (4.0-6.0) using smaller temperature increments, especially when combined with an alternative data visualization method (radar plots). Differential scanning calorimetry and differential scanning fluorimetry were then utilized and also showed an improved ability to detect differences in mAb glycoform physical stability. Based on these results, a two-step methodology was used in which mAb glycoform conformational stability is first screened with a wide variety of instruments and environmental stresses, followed by a second evaluation with optimally sensitive experimental conditions, analytical techniques and data visualization methods. With this approach, high-throughput biophysical analysis to assess relatively subtle conformational stability differences in protein glycoforms is demonstrated. PMID:24114789

Inherent flexibility determines the transition mechanisms of the EF-hands of calmodulin.

PubMed

Tripathi, Swarnendu; Portman, John J

2009-02-17

We explore how inherent flexibility of a protein molecule influences the mechanism controlling allosteric transitions by using a variational model inspired from work in protein folding. The striking differences in the predicted transition mechanism for the opening of the two domains of calmodulin (CaM) emphasize that inherent flexibility is key to understanding the complex conformational changes that occur in proteins. In particular, the C-terminal domain of CaM (cCaM), which is inherently less flexible than its N-terminal domain (nCaM), reveals "cracking" or local partial unfolding during the open/closed transition. This result is in harmony with the picture that cracking relieves local stresses caused by conformational deformations of a sufficiently rigid protein. We also compare the conformational transition in a recently studied even-odd paired fragment of CaM. Our results rationalize the different relative binding affinities of the EF-hands in the engineered fragment compared with the intact odd-even paired EF-hands (nCaM and cCaM) in terms of changes in flexibility along the transition route. Aside from elucidating general theoretical ideas about the cracking mechanism, these studies also emphasize how the remarkable intrinsic plasticity of CaM underlies conformational dynamics essential for its diverse functions.

Acid-enhanced conformation changes of yeast cytochrome c coated onto gold nanoparticles, a FT-IR spectroscopic analysis.

PubMed

Dong, Aichun; Brown, Corina; Bai, Shufeng; Dong, Jian

2018-06-01

Under conditions with or without linker molecules, the effects of acidic pH on the conformation of yeast iso-1-cytochrome c coated onto gold nanoparticles (AuNPs) in correlation with color changes of a Cyt c-coated AuNPs solution/suspension were examined by Fourier transform infrared (FT-IR) spectroscopy and correlated to color change. The results of detailed secondary structural analysis revealed that although the color changes coincide with acid-induced conformational changes in Cyt c coated onto AuNPs, the pH-related conformational unfolding of Cyt c coated onto AuNPs differed dramatically from that of its counterpart in solution. For Cyt c free in solution, the acid-induced unfolding did not occur until the pH was below 3.0, whereas for Cyt c coated onto AuNPs via C102 coordination near the C-terminal, a partial unfolding was observed even at near neutral pH which continuously intensified as pH decreased. Insertion of a short alkanethiol (3-mercaptoproprionic acid, 3-MPA) molecule between Cyt c and AuNP, which changes the interaction mode from a thiol coordination between Cyt c and AuNP to an electrostatic interaction between Cyt c and 3-MPA, which stabilized the conformation of Cyt c significantly, but did not prevent the acid-induced aggregation of Cyt c-3MPA-AuNPs. Copyright © 2018 Elsevier B.V. All rights reserved.

Improved Modeling of Open Waveguide Aperture Radiators for use in Conformal Antenna Arrays

NASA Astrophysics Data System (ADS)

Nelson, Gregory James

Open waveguide apertures have been used as radiating elements in conformal arrays. Individual radiating element model patterns are used in constructing overall array models. The existing models for these aperture radiating elements may not accurately predict the array pattern for TEM waves which are not on boresight for each radiating element. In particular, surrounding structures can affect the far field patterns of these apertures, which ultimately affects the overall array pattern. New models of open waveguide apertures are developed here with the goal of accounting for the surrounding structure effects on the aperture far field patterns such that the new models make accurate pattern predictions. These aperture patterns (both E plane and H plane) are measured in an anechoic chamber and the manner in which they deviate from existing model patterns are studied. Using these measurements as a basis, existing models for both E and H planes are updated with new factors and terms which allow the prediction of far field open waveguide aperture patterns with improved accuracy. These new and improved individual radiator models are then used to predict overall conformal array patterns. Arrays of open waveguide apertures are constructed and measured in a similar fashion to the individual aperture measurements. These measured array patterns are compared with the newly modeled array patterns to verify the improved accuracy of the new models as compared with the performance of existing models in making array far field pattern predictions. The array pattern lobe characteristics are then studied for predicting fully circularly conformal arrays of varying radii. The lobe metrics that are tracked are angular location and magnitude as the radii of the conformal arrays are varied. A constructed, measured array that is close to conforming to a circular surface is compared with a fully circularly conformal modeled array pattern prediction, with the predicted lobe angular locations and magnitudes tracked, plotted and tabulated. The close match between the patterns of the measured array and the modeled circularly conformal array verifies the validity of the modeled circularly conformal array pattern predictions.

Study of cross-shaped ultrasonic array sensor applied to partial discharge location in transformer oil.

PubMed

Li, Jisheng; Xin, Xiaohu; Luo, Yongfen; Ji, Haiying; Li, Yanming; Deng, Junbo

2013-11-01

A conformal combined sensor is designed and it is used in Partial Discharge (PD) location experiments in transformer oil. The sensor includes a cross-shaped ultrasonic phased array of 13 elements and an ultra-high-frequency (UHF) electromagnetic rectangle array of 2 × 2 elements. Virtual expansion with high order cumulants, the ultrasonic array can achieve the effect of array with 61 elements. This greatly improves the aperture and direction sharpness of original array and reduces the cost of follow-up hardware. With the cross-shaped ultrasonic array, the results of PD location experiments are precise and the maximum error of the direction of arrival (DOA) is less than 5°.

Quantum information and the problem of mechanisms of biological evolution.

PubMed

Melkikh, Alexey V

2014-01-01

One of the most important conditions for replication in early evolution is the de facto elimination of the conformational degrees of freedom of the replicators, the mechanisms of which remain unclear. In addition, realistic evolutionary timescales can be established based only on partially directed evolution, further complicating this issue. A division of the various evolutionary theories into two classes has been proposed based on the presence or absence of a priori information about the evolving system. A priori information plays a key role in solving problems in evolution. Here, a model of partially directed evolution, based on the learning automata theory, which includes a priori information about the fitness space, is proposed. A potential repository of such prior information is the states of biologically important molecules. Thus, the need for extended evolutionary synthesis is discussed. Experiments to test the hypothesis of partially directed evolution are proposed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Reversible Aggregation Plays a Crucial Role on the Folding Landscape of p53 Core Domain

PubMed Central

Ishimaru, Daniella; Lima, Luis M. T. R.; Maia, Lenize F.; Lopez, Priscila M.; Ano Bom, Ana P.; Valente, Ana P.; Silva, Jerson L.

2004-01-01

The role of tumor suppressor protein p53 in cell cycle control depends on its flexible and partially unstructured conformation, which makes it crucial to understand its folding landscape. Here we report an intermediate structure of the core domain of the tumor suppressor protein p53 (p53C) during equilibrium and kinetic folding/unfolding transitions induced by guanidinium chloride. This partially folded structure was undetectable when investigated by intrinsic fluorescence. Indeed, the fluorescence data showed a simple two-state transition. On the other hand, analysis of far ultraviolet circular dichroism in 1.0 M guanidinium chloride demonstrated a high content of secondary structure, and the use of an extrinsic fluorescent probe, 4,4′-dianilino-1,1′ binaphthyl-5,5′-disulfonic acid, indicated an increase in exposure of the hydrophobic core at 1 M guanidinium chloride. This partially folded conformation of p53C was plagued by aggregation, as suggested by one-dimensional NMR and demonstrated by light-scattering and gel-filtration chromatography. Dissociation by high pressure of these aggregates reveals the reversibility of the process and that the aggregates have water-excluded cavities. Kinetic measurements show that the intermediate formed in a parallel reaction between unfolded and folded structures and that it is under fine energetic control. They are not only crucial to the folding pathway of p53C but may explain as well the vulnerability of p53C to undergo departure of the native to an inactive state, which makes the cell susceptible to malignant transformation. PMID:15298872

Rogue Wave Modes for the Long Wave-Short Wave Resonance and the Derivative Nonlinear Schrödinger Models

NASA Astrophysics Data System (ADS)

Chan, Hiu Ning; Chow, Kwok Wing; Kedziora, David Jacob; Grimshaw, Roger Hamilton James; Ding, Edwin

2014-11-01

Rogue waves are unexpectedly large displacements of the water surface and will obviously pose threat to maritime activities. Recently, the formation of rogue waves is correlated with the onset of modulation instabilities of plane waves of the system. The long wave-short wave resonance and the derivative nonlinear Schrödinger models are considered. They are relevant in a two-layer fluid and a fourth order perturbation expansion of free surface waves respectively. Analytical solutions of rogue wave modes for the two models are derived by the Hirota bilinear method. Properties and amplitudes of these rogue wave modes are investigated. Conditions for modulation instability of the plane waves are shown to be precisely the requirements for the occurrence of rogue waves. In contrast with the nonlinear Schrödinger equation, rogue wave modes for the derivative nonlinear Schrödinger model exist even if the dispersion and cubic nonlinearity are of the opposite signs, provided that a sufficiently strong self-steepening nonlinearity is present. Extensions to the coupled case (multiple waveguides) will be discussed. This work is partially supported by the Research Grants Council General Research Fund Contract HKU 711713E.

Investigations on the Aerodynamic Characteristics and Blade Excitations of the Radial Turbine with Pulsating Inlet Flow

NASA Astrophysics Data System (ADS)

Liu, Yixiong; Yang, Ce; Yang, Dengfeng; Zhang, Rui

2016-04-01

The aerodynamic performance, detailed unsteady flow and time-based excitations acting on blade surfaces of a radial flow turbine have been investigated with pulsation flow condition. The results show that the turbine instantaneous performance under pulsation flow condition deviates from the quasi-steady value significantly and forms obvious hysteretic loops around the quasi-steady conditions. The detailed analysis of unsteady flow shows that the characteristic of pulsation flow field in radial turbine is highly influenced by the pulsation inlet condition. The blade torque, power and loading fluctuate with the inlet pulsation wave in a pulse period. For the blade excitations, the maximum and the minimum blade excitations conform to the wave crest and wave trough of the inlet pulsation, respectively, in time-based scale. And toward blade chord direction, the maximum loading distributes along the blade leading edge until 20% chord position and decreases from the leading to trailing edge.

Concircular vector fields on Lorentzian manifold of Bianchi type-I spacetimes

NASA Astrophysics Data System (ADS)

Mahmood, Amjad; Ali, Ahmad T.; Khan, Suhail

2018-04-01

Our aim in this paper is to obtain concircular vector fields (CVFs) on the Lorentzian manifold of Bianchi type-I spacetimes. For this purpose, two different sets of coupled partial differential equations comprising ten equations each are obtained. The first ten equations, known as conformal Killing equations are solved completely and components of conformal Killing vector fields (CKVFs) are obtained in different possible cases. These CKVFs are then substituted into second set of ten differential equations to obtain CVFs. It comes out that Bianchi type-I spacetimes admit four-, five-, six-, seven- or 15-dimensional CVFs for particular choices of the metric functions. In many cases, the CKVFs of a particular metric are same as CVFs while there exists few cases where proper CKVFs are not CVFs.

Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

PubMed Central

Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

2016-01-01

We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method. PMID:27025410

Group identity and positive deviance in work groups.

PubMed

Kim, Moon Joung; Choi, Jin Nam

2017-12-05

This study examines why and how identity cognitions, including group identification and individual differentiation, influence the positive deviance of employees. We identify the risk-taking intention of employees as a critical psychological mechanism to overcome stigma-induced identity threat of positive deviance. The analysis of data collected from 293 members comprising 66 work teams reveals that the relationship between individual differentiation and positive deviance is partially mediated by risk-taking intention. The indirect effect of group identification on positive deviance through risk-taking intention is also significant and positive in groups with low conformity pressure, whereas the same indirect effect is neutralized in groups with high conformity pressure. The current analysis offers new insights into the way the group context and the identity cognition of members explain the development of positive deviance and workplace creativity.

Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

NASA Astrophysics Data System (ADS)

Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

2016-03-01

We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method.