Suppression of quantum phase interference in the molecular magnet Fe8 with dipolar-dipolar interaction

NASA Astrophysics Data System (ADS)

Chen, Zhi-De; Liang, J.-Q.; Shen, Shun-Qing

2002-09-01

Renormalized tunnel splitting with a finite distribution in the biaxial spin model for molecular magnets is obtained by taking into account the dipolar interaction of enviromental spins. Oscillation of the resonant tunnel splitting with a transverse magnetic field along the hard axis is smeared by the finite distribution, which subsequently affects the quantum steps of the hysteresis curve evaluated in terms of the modified Landau-Zener model of spin flipping induced by the sweeping field. We conclude that the dipolar-dipolar interaction drives decoherence of quantum tunneling in the molecular magnet Fe8, which explains why the quenching points of tunnel splitting between odd and even resonant tunneling predicted theoretically were not observed experimentally.

Stacking of purines in water: the role of dipolar interactions in caffeine.

PubMed

Tavagnacco, L; Di Fonzo, S; D'Amico, F; Masciovecchio, C; Brady, J W; Cesàro, A

2016-05-11

During the last few decades it has been ascertained that base stacking is one of the major contributions stabilizing nucleic acid conformations. However, the understanding of the nature of the interactions involved in the stacking process remains under debate and it is a subject of theoretical and experimental studies. Structural similarity between purine bases (guanine and adenine) in DNA and the caffeine molecule makes caffeine an excellent model for the purine bases. The present study clearly shows that dipolar interactions play a fundamental role in determining stacking of purine molecules in solution. In order to reach this achievement, polarized ultraviolet Raman resonant scattering experiments have been carried out on caffeine aqueous solutions as a function of concentration and temperature. The investigation pointed out at the aggregation and solvation properties, particularly at elevated temperatures. Kubo-Anderson theory was used as a framework to investigate the non-coincidence effect (NCE) occurring in the totally symmetric breathing modes of the purine rings, and in the bending modes of the methyl groups of caffeine. The NCE concentration dependence shows that caffeine aggregation at 80 °C occurs by planar stacking of the hydrophobic faces. The data clearly indicate that dipolar interactions determine the reorientational motion of the molecules in solution and are the driving force for the stacking of caffeine. In parallel, the observed dephasing times imply a change in caffeine interactions as a function of temperature and concentration. A decrease, at low water content, of the dephasing time for the ring breathing vibration mode indicates that self-association alters the solvation structure that is detectable at low concentration. These results are in agreement with simulation predictions and serve as an important validation of the models used in those calculations.

Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.

PubMed

Salmon, Loïc; Giambaşu, George M; Nikolova, Evgenia N; Petzold, Katja; Bhattacharya, Akash; Case, David A; Al-Hashimi, Hashim M

2015-10-14

Approaches that combine experimental data and computational molecular dynamics (MD) to determine atomic resolution ensembles of biomolecules require the measurement of abundant experimental data. NMR residual dipolar couplings (RDCs) carry rich dynamics information, however, difficulties in modulating overall alignment of nucleic acids have limited the ability to fully extract this information. We present a strategy for modulating RNA alignment that is based on introducing variable dynamic kinks in terminal helices. With this strategy, we measured seven sets of RDCs in a cUUCGg apical loop and used this rich data set to test the accuracy of an 0.8 μs MD simulation computed using the Amber ff10 force field as well as to determine an atomic resolution ensemble. The MD-generated ensemble quantitatively reproduces the measured RDCs, but selection of a sub-ensemble was required to satisfy the RDCs within error. The largest discrepancies between the RDC-selected and MD-generated ensembles are observed for the most flexible loop residues and backbone angles connecting the loop to the helix, with the RDC-selected ensemble resulting in more uniform dynamics. Comparison of the RDC-selected ensemble with NMR spin relaxation data suggests that the dynamics occurs on the ps-ns time scales as verified by measurements of R(1ρ) relaxation-dispersion data. The RDC-satisfying ensemble samples many conformations adopted by the hairpin in crystal structures indicating that intrinsic plasticity may play important roles in conformational adaptation. The approach presented here can be applied to test nucleic acid force fields and to characterize dynamics in diverse RNA motifs at atomic resolution.

The structure of ions and zwitterionic lipids regulates the charge of dipolar membranes.

PubMed

Szekely, Or; Steiner, Ariel; Szekely, Pablo; Amit, Einav; Asor, Roi; Tamburu, Carmen; Raviv, Uri

2011-06-21

In pure water, zwitterionic lipids form lamellar phases with an equilibrium water gap on the order of 2 to 3 nm as a result of the dominating van der Waals attraction between dipolar bilayers. Monovalent ions can swell those neutral lamellae by a small amount. Divalent ions can adsorb onto dipolar membranes and charge them. Using solution X-ray scattering, we studied how the structure of ions and zwitterionic lipids regulates the charge of dipolar membranes. We found that unlike monovalent ions that weakly interact with all of the examined dipolar membranes, divalent and trivalent ions adsorb onto membranes containing lipids with saturated tails, with an association constant on the order of ∼10 M(-1). One double bond in the lipid tail is sufficient to prevent divalent ion adsorption. We suggest that this behavior is due to the relatively loose packing of lipids with unsaturated tails that increases the area per lipid headgroup, enabling their free rotation. Divalent ion adsorption links two lipids and limits their free rotation. The ion-dipole interaction gained by the adsorption of the ions onto unsaturated membranes is insufficient to compensate for the loss of headgroup free-rotational entropy. The ion-dipole interaction is stronger for cations with a higher valence. Nevertheless, polyamines behave as monovalent ions near dipolar interfaces in the sense that they interact weakly with the membrane surface, whereas in the bulk their behavior is similar to that of multivalent cations. Advanced data analysis and comparison with theory provide insight into the structure and interactions between ion-induced regulated charged interfaces. This study models biologically relevant interactions between cell membranes and various ions and the manner in which the lipid structure governs those interactions. The ability to monitor these interactions creates a tool for probing systems that are more complex and forms the basis for controlling the interactions between dipolar

Dipolar excitation in the third stability region.

PubMed

Konenkov, Nikolai V; Chernyak, Eugenii Ya; Stepanov, Vladimir A

Dipole resonant excitation of ions creates instability bands which follow iso-β lines where β is the characteristic exponent (stability parameter). Instability bands are exited most effectively on the fundamental frequency π= βΩ/2. Here π is the angle resonance frequency of the dipolar voltage applied to x or y pair rods of the analyzer, and Ω is the angle frequency of the main drive voltage. Our goal is to study the mass peak shape in the third stability region with dipolar resonance excitation of the instability band with respect to the resonance frequency π and the dipolar potential amplitude. Numerical integration of the ion motion equations with a given ion source emittance is used to investigate peak shapes and ion transmission. We show that it is possible to vary the resolution power at any part of the third stability region. A change of the dipolar potential phase leads to a periodical variation of the resolution with period π.The most effective dipolar excitation in the y direction is along βy near the stability boundary. The mass peak shape is calculated also for a quadrupole with round rods. The best peak shape (small tails and high resolution) takes place for the rod set with r/r0=1.130. Dipolar excitation increases the transmission by approximately 5-10% at a given resolution.

Enhanced water vapor separation by temperature-controlled aligned-multiwalled carbon nanotube membranes.

PubMed

Jeon, Wonjae; Yun, Jongju; Khan, Fakhre Alam; Baik, Seunghyun

2015-09-14

Here we present a new strategy of selectively rejecting water vapor while allowing fast transport of dry gases using temperature-controlled aligned-multiwalled carbon nanotubes (aligned-MWNTs). The mechanism is based on the water vapor condensation at the entry region of nanotubes followed by removing aggregated water droplets at the tip of the superhydrophobic aligned-MWNTs. The first condensation step could be dramatically enhanced by decreasing the nanotube temperature. The permeate-side relative humidity was as low as ∼17% and the helium-water vapor separation factor was as high as 4.62 when a helium-water vapor mixture with a relative humidity of 100% was supplied to the aligned-MWNTs. The flow through the interstitial space of the aligned-MWNTs allowed the permeability of single dry gases an order of magnitude higher than the Knudsen prediction regardless of membrane temperature. The water vapor separation performance of hydrophobic polytetrafluoroethylene membranes could also be significantly enhanced at low temperatures. This work combines the membrane-based separation technology with temperature control to enhance water vapor separation performance.

Cluster Observations of Multiple Dipolarization Fronts

NASA Technical Reports Server (NTRS)

Hwang, Kyoung-Joo; Goldstein, Melvyn L.; Lee, Ensang; Pickett, Jolene S.

2011-01-01

We present Cluster observations of a series of dipolarization fronts (DF 1 to 6) at the central current sheet in Earth's magnetotail. The velocities of fast earthward flow following behind each DF 1-3, are comparable to the Alfven velocity, indicating that the flow bursts might have been generated by bursty reconnection that occurred tailward of the spacecraft. Based on multi-spacecraft timing analysis, DF normals are found to propagate mainly earthward at $160-335$ km/s with a thickness of 900-1500 km, which corresponds to the ion inertial length or gyroradius scale. Each DF is followed by significant fluctuations in the $x$ and $y$ components of the magnetic field whose peaks are found 1-2 minutes after the DF passage. These $(B_{x},B_{y} )$-fluctuations propagate dawnward (mainly) and earthward. Strongly enhanced field-aligned beams are observed coincidently with $(B_{x},B_{y})$ fluctuations, while an enhancement of cross-tail currents is associated with the DFs. From the observed pressure imbalance and flux-tube entropy changes between the two regions separated by the DF, we speculate that interchange instability destabilizes the DFs and causes the deformation of the mid-tail magnetic topology. This process generates significant field-aligned currents, and might power the auroral brightening in the ionosphere. However, this event is neither associated with the main substorm auroral breakup nor the poleward expansion, which might indicate that the observed multiple DFs have been dissipated before they reach the inner plasma sheet boundary.

Heat Transfer Through Dipolar Coupling: Sympathetic cooling without contact

NASA Astrophysics Data System (ADS)

Oktel, Mehmet; Renklioglu, Basak; Tanatar, Bilal

We consider two parallel layers of dipolar ultracold gases at different temperatures and calculate the heat transfer through dipolar coupling. As the simplest model we consider a system in which both of the layers contain two-dimensional spin-polarized Fermi gases. The effective interactions describing the correlation effects and screening between the dipoles are obtained by the Euler-Lagrange Fermi-hypernetted-chain approximation in a single layer. We use the random-phase approximation (RPA) for the interactions across the layers. We find that heat transfer through dipolar coupling becomes efficient when the layer separation is comparable to dipolar interaction length scale. We characterize the heat transfer by calculating the time constant for temperature equilibration between the layers and find that for the typical experimental parameter regime of dipolar molecules this is on the order of milliseconds. We generalize the initial model to Boson-Boson and Fermion-Boson layers and suggest that contactless sympathetic cooling may be used for ultracold dipolar molecules. Supported by TUBITAK 1002-116F030.

Cluster Observations of Multiple Dipolarization Fronts

NASA Technical Reports Server (NTRS)

Hwang, K.-J.; Goldstein, M. L.; Lee, E.; Pickett, J. S.

2011-01-01

We present Cluster observations of a series of dipolarization fronts (DF 1 to 6) at the central current sheet in Earth's magnetotail. The velocities of fast earthward flow following behind each DF 1.3 are comparable to the Alfven velocity, indicating that the flow bursts might have been generated by bursty reconnection that occurred tailward of the spacecraft. Based on multispacecraft timing analysis, DF normals are found to propagate mainly earthward at 160.335 km/s with a thickness of 900-1500 km, which corresponds to the ion inertial length or gyroradius scale. Each DF is followed by significant fluctuations in the x and y components of the magnetic field whose peaks are found 1.2 min after the DF passage. These (B(sub x), B(sub y)) fluctuations propagate dawnward (mainly) and earthward. Strongly enhanced field-aligned beams are observed coincidently with (B(sub x), B(sub y)) fluctuations, while an enhancement of cross-tail currents is associated with the DFs. From the observed pressure imbalance and flux tube entropy changes between the two regions separated by the DF, we speculate that interchange instability destabilizes the DFs and causes the deformation of the midtail magnetic topology. This process generates significant field-aligned currents and might power the auroral brightening in the ionosphere. However, this event is associated with neither the main substorm auroral breakup nor the poleward expansion, which might indicate that the observed multiple DFs have been dissipated before they reach the inner plasma sheet boundary.

Quantum Fluctuations in Quasi-One-Dimensional Dipolar Bose-Einstein Condensates

NASA Astrophysics Data System (ADS)

Edler, D.; Mishra, C.; Wächtler, F.; Nath, R.; Sinha, S.; Santos, L.

2017-08-01

Recent experiments have revealed that beyond-mean-field corrections are much more relevant in weakly interacting dipolar condensates than in their nondipolar counterparts. We show that in quasi-one-dimensional geometries quantum corrections in dipolar and nondipolar condensates are strikingly different due to the peculiar momentum dependence of the dipolar interactions. The energy correction of the condensate presents not only a modified density dependence, but it may even change from attractive to repulsive at a critical density due to the surprising role played by the transversal directions. The anomalous quantum correction translates into a strongly modified physics for quantum-stabilized droplets and dipolar solitons. Moreover, and for similar reasons, quantum corrections of three-body correlations, and hence of three-body losses, are strongly modified by the dipolar interactions. This intriguing physics can be readily probed in current experiments with magnetic atoms.

Quantum Fluctuations in Quasi-One-Dimensional Dipolar Bose-Einstein Condensates.

PubMed

Edler, D; Mishra, C; Wächtler, F; Nath, R; Sinha, S; Santos, L

2017-08-04

Recent experiments have revealed that beyond-mean-field corrections are much more relevant in weakly interacting dipolar condensates than in their nondipolar counterparts. We show that in quasi-one-dimensional geometries quantum corrections in dipolar and nondipolar condensates are strikingly different due to the peculiar momentum dependence of the dipolar interactions. The energy correction of the condensate presents not only a modified density dependence, but it may even change from attractive to repulsive at a critical density due to the surprising role played by the transversal directions. The anomalous quantum correction translates into a strongly modified physics for quantum-stabilized droplets and dipolar solitons. Moreover, and for similar reasons, quantum corrections of three-body correlations, and hence of three-body losses, are strongly modified by the dipolar interactions. This intriguing physics can be readily probed in current experiments with magnetic atoms.

Energetic Electron Acceleration and Injection During Dipolarization Events in Mercury's Magnetotail

NASA Astrophysics Data System (ADS)

Dewey, Ryan M.; Slavin, James A.; Raines, Jim M.; Baker, Daniel N.; Lawrence, David J.

2017-12-01

Energetic particle bursts associated with dipolarization events within Mercury's magnetosphere were first observed by Mariner 10. The events appear analogous to particle injections accompanying dipolarization events at Earth. The Energetic Particle Spectrometer (3 s resolution) aboard MESSENGER determined the particle bursts are composed entirely of electrons with energies ≳ 300 keV. Here we use the Gamma-Ray Spectrometer high-time-resolution (10 ms) energetic electron measurements to examine the relationship between energetic electron injections and magnetic field dipolarization in Mercury's magnetotail. Between March 2013 and April 2015, we identify 2,976 electron burst events within Mercury's magnetotail, 538 of which are closely associated with dipolarization events. These dipolarizations are detected on the basis of their rapid ( 2 s) increase in the northward component of the tail magnetic field (ΔBz 30 nT), which typically persists for 10 s. Similar to those at Earth, we find that these dipolarizations appear to be low-entropy, depleted flux tubes convecting planetward following the collapse of the inner magnetotail. We find that electrons experience brief, yet intense, betatron and Fermi acceleration during these dipolarizations, reaching energies 130 keV and contributing to nightside precipitation. Thermal protons experience only modest betatron acceleration. While only 25% of energetic electron events in Mercury's magnetotail are directly associated with dipolarization, the remaining events are consistent with the Near-Mercury Neutral Line model of magnetotail injection and eastward drift about Mercury, finding that electrons may participate in Shabansky-like closed drifts about the planet. Magnetotail dipolarization may be the dominant source of energetic electron acceleration in Mercury's magnetosphere.

Conformational analysis of the anti-obesity drug lorcaserin in water: how to take advantage of long-range residual dipolar couplings.

PubMed

Trigo-Mouriño, Pablo; de la Fuente, M Carmen; Gil, Roberto R; Sánchez-Pedregal, Víctor M; Navarro-Vázquez, Armando

2013-10-25

The conformational state of 8-chloro-1-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine hydrochloride (lorcaserin) in water has been determined on the basis of one-bond and long-range C-H residual dipolar coupling (RDC) data along with DFT computations and (3)J(HH) coupling-constant analysis. According to this analysis, lorcaserin exists as a conformational equilibrium of two crown-chair forms, of which the preferred conformation has the methyl group in an equatorial orientation. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nature of the water/aromatic parallel alignment interactions.

PubMed

Mitoraj, Mariusz P; Janjić, Goran V; Medaković, Vesna B; Veljković, Dušan Ž; Michalak, Artur; Zarić, Snežana D; Milčić, Miloš K

2015-01-30

The water/aromatic parallel alignment interactions are interactions where the water molecule or one of its O-H bonds is parallel to the aromatic ring plane. The calculated energies of the interactions are significant, up to ΔE(CCSD)(T)(limit) = -2.45 kcal mol(-1) at large horizontal displacement, out of benzene ring and CH bond region. These interactions are stronger than CH···O water/benzene interactions, but weaker than OH···π interactions. To investigate the nature of water/aromatic parallel alignment interactions, energy decomposition methods, symmetry-adapted perturbation theory, and extended transition state-natural orbitals for chemical valence (NOCV), were used. The calculations have shown that, for the complexes at large horizontal displacements, major contribution to interaction energy comes from electrostatic interactions between monomers, and for the complexes at small horizontal displacements, dispersion interactions are dominant binding force. The NOCV-based analysis has shown that in structures with strong interaction energies charge transfer of the type π → σ*(O-H) between the monomers also exists. © 2014 Wiley Periodicals, Inc.

Quantum Hall signatures of dipolar Mahan excitons

NASA Astrophysics Data System (ADS)

Schinner, G. J.; Repp, J.; Kowalik-Seidl, K.; Schubert, E.; Stallhofer, M. P.; Rai, A. K.; Reuter, D.; Wieck, A. D.; Govorov, A. O.; Holleitner, A. W.; Kotthaus, J. P.

2013-01-01

We explore the photoluminescence of spatially indirect, dipolar Mahan excitons in a gated double quantum well diode containing a mesoscopic electrostatic trap for neutral dipolar excitons at low temperatures down to 250 mK and in quantizing magnetic fields. Mahan excitons in the surrounding of the trap, consisting of individual holes interacting with a degenerate two-dimensional electron system confined in one of the quantum wells, exhibit strong quantum Hall signatures at integer filling factors and related anomalies around filling factor ν=(2)/(3),(3)/(5), and (1)/(2), reflecting the formation of composite fermions. Interactions across the trap perimeter are found to influence the energy of the confined neutral dipolar excitons by the presence of the quantum Hall effects in the two-dimensional electron system surrounding the trap.

Energetic electron injections and dipolarization events in Mercury's magnetotail: Substorm dynamics

NASA Astrophysics Data System (ADS)

Dewey, R. M.; Slavin, J. A.; Raines, J. M.; Imber, S.; Baker, D. N.; Lawrence, D. J.

2017-12-01

Despite its small size, Mercury's terrestrial-like magnetosphere experiences brief, yet intense, substorm intervals characterized by features similar to at Earth: loading/unloading of the tail lobes with open magnetic flux, dipolarization of the magnetic field at the inner edge of the plasma sheet, and, the focus of this presentation, energetic electron injection. We use the Gamma-Ray Spectrometer's high-time resolution (10 ms) energetic electron measurements to determine the relationship between substorm activity and energetic electron injections coincident with dipolarization fronts in the magnetotail. These dipolarizations were detected on the basis of their rapid ( 2 s) increase in the northward component of the tail magnetic field (ΔBz 30 nT), which typically persists for 10 s. We estimate the typical flow channel to be 0.15 RM, planetary convection speed of 750 km/s, cross-tail potential drop of 7 kV, and flux transport of 0.08 MWb for each dipolarization event, suggesting multiple simultaneous and sequential dipolarizations are required to unload the >1 MWb of magnetic flux typically returned to the dayside magnetosphere during a substorm interval. Indeed, while we observe most dipolarization-injections to be isolated or in small chains of events (i.e., 1-3 events), intervals of sawtooth-like injections with >20 sequential events are also present. The typical separation between dipolarization-injection events is 10 s. Magnetotail dipolarization, in addition to being a powerful source of electron acceleration, also plays a significant role in the substorm process at Mercury.

The extreme dipolarization during the Galaxy 15 spacecraft anomaly

NASA Astrophysics Data System (ADS)

Loto'aniu, P. T. M.; Redmon, R. J.; Welling, D. T.; Rodriguez, J. V.; Haiducek, J. D.

2016-12-01

The substorm just prior to the Galaxy 15 spacecraft anomaly on 5 April 2010 was intriguing for a number of reasons, including that multiple spacecraft were well located near-midnight to observe the event. Another reason is that the associated dipolarization was one of the most severe ever observed by GOES satellites, even though the solar wind conditions were moderate. In this study, we compare the Galaxy 15 event to other substorms in order to understand why the dipolarization was so extreme. Presented will be simulations from the Space Weather Modeling Framework (SWMF) of different storms and comparisons made to model results for the Galaxy 15 anomaly event. The SWMF does well in predicting some storms, particularly when heavier O+ ions outflowing from the ionosphere are included. However, the SWMF significantly under-predicts the magnitude of the Galaxy 15 event, regardless of the inclusion of a heavy ion outflow model. The model dipolarization occurs around 30 minutes later than the observed event, while the strength of the dipolarization in terms of the magnetic field was not predicted by the model, although, the model does well overall predicting Dst and Kp. We will also present statistical results representing a survey of dipolarizations observed by the GOES spacecraft over a solar cycle when the satellites were located in the near-midnight local time region. The statistical results are used to determine the occurrence rate and characteristics of similar events to the Galaxy 15 dipolarization event.

Extended Bose-Hubbard model with dipolar and contact interactions

NASA Astrophysics Data System (ADS)

Biedroń, Krzysztof; Łącki, Mateusz; Zakrzewski, Jakub

2018-06-01

We study the phase diagram of the one-dimensional boson gas trapped inside an optical lattice with contact and dipolar interaction, taking into account next-nearest terms for both tunneling and interaction. Using the density-matrix renormalization group, we calculate how the locations of phase transitions change with increasing dipolar interaction strength for average density ρ =1 . Furthermore, we show the emergence of pair-correlated phases for a large dipolar interaction strength and ρ ≥2 , including a supersolid phase with an incommensurate density wave ordering manifesting the corresponding spontaneous breaking of the translational symmetry.

When Ethyl Isocyanoacetate Meets Isatins: A 1,3-Dipolar/Inverse 1,3-Dipolar/Olefination Reaction for Access to 3-Ylideneoxindoles.

PubMed

Yuan, Wen-Kui; Cui, Tao; Liu, Wei; Wen, Li-Rong; Li, Ming

2018-03-16

A new CuI/1,10-phen-catalyzed reaction for the synthesis of 3-ylideneoxindoles from readily available isatins and ethyl isocyanoacetate, in which ethyl isocyanoacetate acts as a latent two-carbon donor like the Wittig reagent, is reported. A tandem procedure including 1,3-dipolar cycloaddition/inverse 1,3-dipolar ring opening/olefination allows the preparation of 3-ylideneoxindoles with broad functional group tolerance.

Dipolar and spinor bosonic systems

NASA Astrophysics Data System (ADS)

Yukalov, V. I.

2018-05-01

The main properties and methods of describing dipolar and spinor atomic systems, composed of bosonic atoms or molecules, are reviewed. The general approach for the correct treatment of Bose-condensed atomic systems with nonlocal interaction potentials is explained. The approach is applied to Bose-condensed systems with dipolar interaction potentials. The properties of systems with spinor interaction potentials are described. Trapped atoms and atoms in optical lattices are considered. Effective spin Hamiltonians for atoms in optical lattices are derived. The possibility of spintronics with cold atom is emphasized. The present review differs from the previous review articles by concentrating on a thorough presentation of basic theoretical points, helping the reader to better follow mathematical details and to make clearer physical conclusions.

Complex Dipolar Matter

DTIC Science & Technology

2014-11-10

opportunities for advanced material development and quantum simulators. These molecules include (1) the already quantum degenerate bi- alkali singlet sigma...case potassium-rubidium (KRb) and related molecules; (2) opto-electrically trapped symmetric top molecules soon to reach quantum degeneracy and...rubidium; (C) a correction of phase diagrams for dipolar gases necessary to understand experimental measurements and build accurate quantum simulators

Nuclear magnetic relaxation by the dipolar EMOR mechanism: Three-spin systems

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

Chang, Zhiwei; Halle, Bertil, E-mail: bertil.halle@bpc.lu.se

2016-07-21

In aqueous systems with immobilized macromolecules, including biological tissue, the longitudinal spin relaxation of water protons is primarily induced by exchange-mediated orientational randomization (EMOR) of intra- and intermolecular magnetic dipole-dipole couplings. Starting from the stochastic Liouville equation, we have developed a non-perturbative theory that can describe relaxation by the dipolar EMOR mechanism over the full range of exchange rates, dipole couplings, and Larmor frequencies. Here, we implement the general dipolar EMOR theory for a macromolecule-bound three-spin system, where one, two, or all three spins exchange with the bulk solution phase. In contrast to the previously studied two-spin system with amore » single dipole coupling, there are now three dipole couplings, so relaxation is affected by distinct correlations as well as by self-correlations. Moreover, relaxation can now couple the magnetizations with three-spin modes and, in the presence of a static dipole coupling, with two-spin modes. As a result of this complexity, three secondary dispersion steps with different physical origins can appear in the longitudinal relaxation dispersion profile, in addition to the primary dispersion step at the Larmor frequency matching the exchange rate. Furthermore, and in contrast to the two-spin system, longitudinal relaxation can be significantly affected by chemical shifts and by the odd-valued (“imaginary”) part of the spectral density function. We anticipate that the detailed studies of two-spin and three-spin systems that have now been completed will provide the foundation for developing an approximate multi-spin dipolar EMOR theory sufficiently accurate and computationally efficient to allow quantitative molecular-level interpretation of frequency-dependent water-proton longitudinal relaxation data from biophysical model systems and soft biological tissue.« less

Fluid transport by dipolar vortices

NASA Astrophysics Data System (ADS)

I, Eames; J.-B, Flór

1998-08-01

The transport properties of dipolar vortices propagating on an f-plane are studied experimentally by examining the distortion of a series of material surfaces. The observations are compared with a model based on characterising the flow around the dipole as irrotational flow past a rigid cylinder of volume V. Measurements made of the volume of fluid permanently displaced forward by the vortices, agree to within 20% of that predicted by the proposition of Darwin [Darwin, C., 1953. A note on hydrodynamics. Proc. Cambridge Philos. Soc., 49, 342-354], namely that the vortex will displace a volume CMV forward, where CM=1 for a Lamb's dipole. The results are applied to examine fluid transport by dipolar vortices propagating on the β-plane, where the ambient potential vorticity field causes easterly propagating dipolar vortices to meander sinusoidally between the North and South. We demonstrate that as the vortex moves between the North and South, it exchanges a volume CMV sin α by the drift effect (where α is the angle between the velocity of the dipole and the material surface), which is generally larger than that attributed to other mechanisms such as lobe shedding. The results are applied to give new insight to the effect of vortices in enhancing diffusion, and the secondary flow generated by the transport of ambient potential vorticity.

Monovalent Ions and Water Dipoles in Contact with Dipolar Zwitterionic Lipid Headgroups-Theory and MD Simulations

PubMed Central

Velikonja, Aljaž; Perutkova, Šarka; Gongadze, Ekaterina; Kramar, Peter; Polak, Andraž; Maček-Lebar, Alenka; Iglič, Aleš

2013-01-01

The lipid bilayer is a basic building block of biological membranes and can be pictured as a barrier separating two compartments filled with electrolyte solution. Artificial planar lipid bilayers are therefore commonly used as model systems to study the physical and electrical properties of the cell membranes in contact with electrolyte solution. Among them the glycerol-based polar phospholipids which have dipolar, but electrically neutral head groups, are most frequently used in formation of artificial lipid bilayers. In this work the electrical properties of the lipid layer composed of zwitterionic lipids with non-zero dipole moments are studied theoretically. In the model, the zwitterionic lipid bilayer is assumed to be in contact with aqueous solution of monovalent salt ions. The orientational ordering of water, resulting in spatial variation of permittivity, is explicitly taken into account. It is shown that due to saturation effect in orientational ordering of water dipoles the relative permittivity in the zwitterionic headgroup region is decreased, while the corresponding electric potential becomes strongly negative. Some of the predictions of the presented mean-field theoretical consideration are critically evaluated using the results of molecular dynamics (MD) simulation. PMID:23434651

Magnetospheric Multiscale Observations of Field-Aligned Currents in the Magnetotail

NASA Astrophysics Data System (ADS)

Strangeway, R. J.; Russell, C. T.; Zhao, C.; Plaschke, F.; Fischer, D.; Anderson, B. J.; Weygand, J. M.; Le, G.; Kepko, L.; Nakamura, R.; Baumjohann, W.; Slavin, J. A.; Paterson, W. R.; Giles, B. L.; Shuster, J. R.; Torbert, R. B.; Burch, J. L.

2017-12-01

Field-aligned currents (FACs) are frequently observed by Magnetospheric Multiscale (MMS) within the Earth's magnetotail. However, unlike the FACs observed by MMS at the dayside magnetopause, which are of the order 100s of nA/m2, the magnetotail FACs are relatively weak, of the order 10s of nA/m2. There appear to be a variety of sources for the FACs. FACs are observed in association with dipolarization fronts that are propagating both earthward and tailward, at the boundary of the current sheet, and in flux-ropes. FACs are also observed to be embedded in regions of high speed flow, both earthward and tailward, and not just at the dipolarization front frequently associated with high speed flows. As is the case for FACs observed at the dayside magnetopause, these observations raise questions as to how or where the FACs close.

Van Allen Probes Observations of Magnetic Field Dipolarization and Its Associated O+ Flux Variations in the Inner Magnetosphere at L 6.6

NASA Technical Reports Server (NTRS)

Nose, M.; Keika, K.; Kletzing, C. A.; Spence, H. E.; Smith, C. W.; MacDowall, R. J.; Reeves, G. D.; Larsen, B. A.; Mitchell, D. G.

2016-01-01

We investigate the magnetic field dipolarization in the inner magnetosphere and its associated ion flux variations, using the magnetic field and energetic ion flux data acquired by the Van Allen Probes. From a study of 74 events that appeared at L= 4.5-6.6 between 1 October 2012 and 31 October 2013, we reveal the following characteristics of the dipolarization in the inner magnetosphere: (1) its time scale is approximately 5 min; (2) it is accompanied by strong magnetic fluctuations that have a dominant frequency close to the O+ gyrofrequency; (3) ion fluxes at 20-50 keV are simultaneously enhanced with larger magnitudes for O+ than for H+; (4) after a few minutes of the dipolarization, the flux enhancement at 0.1-5 keV appears with a clear energy-dispersion signature only for O+; and (5) the energy-dispersed O+ flux enhancement appears in directions parallel or antiparallel to the magnetic field. From these characteristics, we discuss possible mechanisms that can provide selective acceleration to O+ ions at > 20 keV. We conclude that O+ ions at L= 5.4-6.6 undergo nonadiabatic local acceleration caused by oscillating electric field associated with the magnetic fluctuations and/or adiabatic convective transport from the plasma sheet to the inner magnetosphere by the impulsive electric field. At L= 4.5-5.4, however, only the former acceleration is plausible. We also conclude that the field-aligned energy-dispersed O+ ions at 0.1-5 keV originate from the ionosphere and are extracted nearly simultaneously to the onset of the dipolarization.

Dipolar eddies in a decaying stratified turbulent flow

NASA Astrophysics Data System (ADS)

Voropayev, S. I.; Fernando, H. J. S.; Morrison, R.

2008-02-01

Laboratory experiments on the evolution of dipolar (momentum) eddies in a stratified fluid in the presence of random background motions are described. A turbulent jet puff was used to generate the momentum eddies, and a decaying field of ambient random vortical motions was generated by a towed grid. Data on vorticity/velocity fields of momentum eddies, those of background motions, and their interactions were collected in the presence and absence of the other, and the main characteristics thereof were parametrized. Similarity arguments predict that dipolar eddies in stratified fluids may preserve their identity in decaying grid-generated stratified turbulence, which was verified experimentally. Possible applications of the results include mushroomlike currents and other naturally/artificially generated large dipolar eddies in strongly stratified layers of the ocean, the longevity of which is expected to be determined by the characteristics of the eddies and random background motions.

Field dipolarization in Saturn's magnetotail with planetward ion flows and energetic particle flow bursts: Evidence of quasi-steady reconnection.

PubMed

Jackman, C M; Thomsen, M F; Mitchell, D G; Sergis, N; Arridge, C S; Felici, M; Badman, S V; Paranicas, C; Jia, X; Hospodarksy, G B; Andriopoulou, M; Khurana, K K; Smith, A W; Dougherty, M K

2015-05-01

We present a case study of an event from 20 August (day 232) of 2006, when the Cassini spacecraft was sampling the region near 32 R S and 22 h LT in Saturn's magnetotail. Cassini observed a strong northward-to-southward turning of the magnetic field, which is interpreted as the signature of dipolarization of the field as seen by the spacecraft planetward of the reconnection X line. This event was accompanied by very rapid (up to ~1500 km s -1 ) thermal plasma flow toward the planet. At energies above 28 keV, energetic hydrogen and oxygen ion flow bursts were observed to stream planetward from a reconnection site downtail of the spacecraft. Meanwhile, a strong field-aligned beam of energetic hydrogen was also observed to stream tailward, likely from an ionospheric source. Saturn kilometric radiation emissions were stimulated shortly after the observation of the dipolarization. We discuss the field, plasma, energetic particle, and radio observations in the context of the impact this reconnection event had on global magnetospheric dynamics.

Dielectric relaxation in ionic liquid/dipolar solvent binary mixtures: A semi-molecular theory.

PubMed

Daschakraborty, Snehasis; Biswas, Ranjit

2016-03-14

A semi-molecular theory is developed here for studying dielectric relaxation (DR) in binary mixtures of ionic liquids (ILs) with common dipolar solvents. Effects of ion translation on DR time scale, and those of ion rotation on conductivity relaxation time scale are explored. Two different models for the theoretical calculations have been considered: (i) separate medium approach, where molecularities of both the IL and dipolar solvent molecules are retained, and (ii) effective medium approach, where the added dipolar solvent molecules are assumed to combine with the dipolar ions of the IL, producing a fictitious effective medium characterized via effective dipole moment, density, and diameter. Semi-molecular expressions for the diffusive DR times have been derived which incorporates the effects of wavenumber dependent orientational static correlations, ion dynamic structure factors, and ion translation. Subsequently, the theory has been applied to the binary mixtures of 1-butyl-3-methylimidazolium tetrafluoroborate ([Bmim][BF4]) with water (H2O), and acetonitrile (CH3CN) for which experimental DR data are available. On comparison, predicted DR time scales show close agreement with the measured DR times at low IL mole fractions (x(IL)). At higher IL concentrations (x(IL) > 0.05), the theory over-estimates the relaxation times and increasingly deviates from the measurements with x(IL), deviation being the maximum for the neat IL by almost two orders of magnitude. The theory predicts negligible contributions to this deviation from the x(IL) dependent collective orientational static correlations. The drastic difference between DR time scales for IL/solvent mixtures from theory and experiments arises primarily due to the use of the actual molecular volume (V(mol)(dip)) for the rotating dipolar moiety in the present theory and suggests that only a fraction of V(mol)(dip) is involved at high x(IL). Expectedly, nice agreement between theory and experiments appears when

Aligned Single Wall Carbon Nanotube Polymer Composites Using an Electric Field

NASA Technical Reports Server (NTRS)

Park, Cheol; Wiklinson, John; Banda, Sumanth; Ounaies, Zoubeida; Wise, Kristopher E.; Sauti, Godfrey; Lillehei, Peter T.; Harrison, Joycelyn S.

2005-01-01

While high shear alignment has been shown to improve the mechanical properties of single wall carbon nanotubes (SWNT)-polymer composites, it is difficult to control and often results in degradation of the electrical and dielectric properties of the composite. Here, we report a novel method to actively align SWNTs in a polymer matrix, which allows for control over the degree of alignment of SWNTs without the side effects of shear alignment. In this process, SWNTs are aligned via field-induced dipolar interactions among the nanotubes under an AC electric field in a liquid matrix followed by immobilization by photopolymerization while maintaining the electric field. Alignment of SWNTs was controlled as a function of magnitude, frequency, and application time of the applied electric field. The degree of SWNT alignment was assessed using optical microscopy and polarized Raman spectroscopy and the morphology of the aligned nanocomposites was investigated by high resolution scanning electron microscopy. The structure of the field induced aligned SWNTs is intrinsically different from that of shear aligned SWNTs. In the present work, SWNTs are not only aligned along the field, but also migrate laterally to form thick, aligned SWNT percolative columns between the electrodes. The actively aligned SWNTs amplify the electrical and dielectric properties in addition to improving the mechanical properties of the composite. All of these properties of the aligned nanocomposites exhibited anisotropic characteristics, which were controllable by tuning the applied field conditions.

Bose-Einstein condensation and superfluidity of dipolar excitons in a phosphorene double layer

NASA Astrophysics Data System (ADS)

Berman, Oleg L.; Gumbs, Godfrey; Kezerashvili, Roman Ya.

2017-07-01

We study the formation of dipolar excitons and their superfluidity in a phosphorene double layer. The analytical expressions for the single dipolar exciton energy spectrum and wave function are obtained. It is predicted that a weakly interacting gas of dipolar excitons in a double layer of black phosphorus exhibits superfluidity due to the dipole-dipole repulsion between the dipolar excitons. In calculations are employed the Keldysh and Coulomb potentials for the interaction between the charge carriers to analyze the influence of the screening effects on the studied phenomena. It is shown that the critical velocity of superfluidity, the spectrum of collective excitations, concentrations of the superfluid and normal component, and mean-field critical temperature for superfluidity are anisotropic and demonstrate the dependence on the direction of motion of dipolar excitons. The critical temperature for superfluidity increases if the exciton concentration and the interlayer separation increase. It is shown that the dipolar exciton binding energy and mean-field critical temperature for superfluidity are sensitive to the electron and hole effective masses. The proposed experiment to observe a directional superfluidity of excitons is addressed.

Vertical Phase Segregation Induced by Dipolar Interactions in Planar Polymer Brushes

DOE PAGES

Mahalik, Jyoti P.; Sumpter, Bobby G.; Kumar, Rajeev

2016-09-13

In this paper, we present a generalized theory for studying structural properties of a planar dipolar polymer brush immersed in a polar solvent. We show that an explicit treatment of the dipolar interactions yields a macroscopic concentration dependent effective “chi” (the Flory–Huggins-like interaction) parameter. Furthermore, it is shown that the concentration dependent chi parameter promotes phase segregation in polymer solutions and brushes so that the polymer-poor phase consists of a finite/nonzero polymer concentration. Such a destabilization of the homogeneous phase by the dipolar interactions appears as vertical phase segregation in a planar polymer brush. In a vertically phase segregated polymermore » brush, the polymer-rich phase near the grafting surface coexists with the polymer-poor phase at the other end. Predictions of the theory are directly compared with prior reported experimental results for dipolar polymers in polar solvents. Excellent agreements with the experimental results are found, hinting that the dipolar interactions play a significant role in vertical phase segregation of planar polymer brushes. We also compare our field theoretical approach with the two-state and other models invoking ad hoc concentration dependence of the chi parameter. Interplay between the short-ranged excluded volume interactions and long-ranged dipolar interactions is shown to play an important role in affecting the vertical phase separation. Finally, effects of mismatch between the dipole moments of the polymer segments and the solvent molecules are investigated in detail.« less

Structures and dynamics in a two-dimensional dipolar dust particle system

NASA Astrophysics Data System (ADS)

Hou, X. N.; Liu, Y. H.; Kravchenko, O. V.; Lapushkina, T. A.; Azarova, O. A.; Chen, Z. Y.; Huang, F.

2018-05-01

The effects of electric dipole moment, the number of dipolar particles, and system temperature on the structures and dynamics of a dipolar dust particle system are studied by molecular dynamics simulations. The results show that the larger electric dipole moment is favorable for the formation of a long-chain structure, the larger number of dipolar dust particles promotes the formation of the multi-chain structure, and the higher system temperature can cause higher rotation frequency. The trajectories, mean square displacement (MSD), and the corresponding spectrum functions of the MSDs are also calculated to illustrate the dynamics of the dipolar dust particle system, which is also closely related to the growth of dust particles. Some simulations are qualitatively in agreement with our experiments and can provide a guide for the study on dust growth, especially on the large-sized particles.

Probing the Dipolar Coupling in a Heterospin Endohedral Fullerene-Phthalocyanine Dyad.

PubMed

Zhou, Shen; Yamamoto, Masanori; Briggs, G Andrew D; Imahori, Hiroshi; Porfyrakis, Kyriakos

2016-02-03

Paramagnetic endohedral fullerenes and phthalocyanine (Pc) complexes are promising building blocks for molecular quantum information processing, for which tunable dipolar coupling is required. We have linked these two spin qubit candidates together and characterized the resulting electron paramagnetic resonance properties, including the spin dipolar coupling between the fullerene spin and the copper spin. Having interpreted the distance-dependent coupling strength quantitatively and further discussed the antiferromagnetic aggregation effect of the CuPc moieties, we demonstrate two ways of tuning the dipolar coupling in such dyad systems: changing the spacer group and adjusting the solution concentration.

Scissors Mode of Dipolar Quantum Droplets of Dysprosium Atoms

NASA Astrophysics Data System (ADS)

Ferrier-Barbut, Igor; Wenzel, Matthias; Böttcher, Fabian; Langen, Tim; Isoard, Mathieu; Stringari, Sandro; Pfau, Tilman

2018-04-01

We report on the observation of the scissors mode of a single dipolar quantum droplet. The existence of this mode is due to the breaking of the rotational symmetry by the dipole-dipole interaction, which is fixed along an external homogeneous magnetic field. By modulating the orientation of this magnetic field, we introduce a new spectroscopic technique for studying dipolar quantum droplets. This provides a precise probe for interactions in the system, allowing us to extract a background scattering length for 164Dy of 69 (4 )a0 . Our results establish an analogy between quantum droplets and atomic nuclei, where the existence of the scissors mode is also only due to internal interactions. They further open the possibility to explore physics beyond the available theoretical models for strongly dipolar quantum gases.

Propagation of Dipolarization Signatures Observed by the Van Allen Probes in the Inner Magnetosphere

NASA Astrophysics Data System (ADS)

Ohtani, S.; Motoba, T.; Gkioulidou, M.; Takahashi, K.; Kletzing, C.

2017-12-01

Dipolarization, the change of the local magnetic field from a stretched to a more dipolar configuration, is one of the most fundamental processes of magnetospheric physics. It is especially critical for the dynamics of the inner magnetosphere. The associated electric field accelerates ions and electrons and transports them closer to Earth. Such injected ions intensify the ring current, and electrons constitute the seed population of the radiation belt. Those ions and electrons may also excite various waves that play important roles in the enhancement and loss of the radiation belt electrons. Despite such critical consequences, the general characteristics of dipolarization in the inner magnetosphere still remain to be understood. The Van Allen Probes mission, which consists of two probes that orbit through the equatorial region of the inner magnetosphere, provides an ideal opportunity to examine dipolarization signatures in the core of the ring current. In the present study we investigate the spatial expansion of the dipolarization region by examining the correlation and time delay of dipolarization signatures observed by the two probes. Whereas in general it requires three-point measurements to deduce the propagation of a signal on a certain plane, we statically examined the observed time delays and found that dipolarization signatures tend to propagate radially inward as well as away from midnight. In this paper we address the propagation of dipolarization signatures quantitatively and compare with the propagation velocities reported previously based on observations made farther away from Earth. We also discuss how often and under what conditions the dipolarization region expands.

Equilibrium phases of dipolar lattice bosons in the presence of random diagonal disorder

NASA Astrophysics Data System (ADS)

Zhang, C.; Safavi-Naini, A.; Capogrosso-Sansone, B.

2018-01-01

Ultracold gases offer an unprecedented opportunity to engineer disorder and interactions in a controlled manner. In an effort to understand the interplay between disorder, dipolar interactions, and quantum degeneracy, we study two-dimensional hard-core dipolar lattice bosons in the presence of on-site bound disorder. Our results are based on large-scale path-integral quantum Monte Carlo simulations by the worm algorithm. We study the ground-state phase diagram at a fixed half-integer filling factor for which the clean system is either a superfluid at a lower dipolar interaction strength or a checkerboard solid at a larger dipolar interaction strength. We find that, even for weak dipolar interactions, superfluidity is destroyed in favor of a Bose glass at a relatively low disorder strength. Interestingly, in the presence of disorder, superfluidity persists for values of the dipolar interaction strength for which the clean system is a checkerboard solid. At a fixed disorder strength, as the dipolar interaction is increased, superfluidity is destroyed in favor of a Bose glass. As the interaction is further increased, the system eventually develops extended checkerboard patterns in the density distribution. Due to the presence of disorder, though, grain boundaries and defects, responsible for a finite residual compressibility, are present in the density distribution. Finally, we study the robustness of the superfluid phase against thermal fluctuations.

Effect of dipolar moments in domain sizes of lipid bilayers and monolayers

NASA Astrophysics Data System (ADS)

Travesset, A.

2006-08-01

Lipid domains are found in systems such as multicomponent bilayer membranes and single component monolayers at the air-water interface. It was shown by Keller et al. [J. Phys. Chem. 91, 6417 (1987)] that in monolayers, the size of the domains results from balancing the line tension, which favors the formation of a large single circular domain, against the electrostatic cost of assembling the dipolar moments of the lipids. In this paper, we present an exact analytical expression for the electric potential, ion distribution, and electrostatic free energy for different problems consisting of three different slabs with different dielectric constants and Debye lengths, with a circular homogeneous dipolar density in the middle slab. From these solutions, we extend the calculation of domain sizes for monolayers to include the effects of finite ionic strength, dielectric discontinuities (or image charges), and the polarizability of the dipoles and further generalize the calculations to account for domains in lipid bilayers. In monolayers, the size of the domains is dependent on the different dielectric constants but independent of ionic strength. In asymmetric bilayers, where the inner and outer leaflets have different dipolar densities, domains show a strong size dependence with ionic strength, with molecular-sized domains that grow to macroscopic phase separation with increasing ionic strength. We discuss the implications of the results for experiments and briefly consider their relation to other two dimensional systems such as Wigner crystals or heteroepitaxial growth.

Development of New Supramolecular Lyotropic Liquid Crystals and Their Application as Alignment Media for Organic Compounds.

PubMed

Leyendecker, Martin; Meyer, Nils-Christopher; Thiele, Christina M

2017-09-11

Most alignment media for the residual dipolar coupling (RDC) based molecular structure determination of small organic compounds consist of rod-like polymers dissolved in organic solvents or of swollen cross-linked polymer gels. Thus far, the synthesis of polymer-based alignment media has been a challenging process, which is often followed by a time-consuming sample preparation. We herein propose the use of non-polymeric alignment media based on benzenetricarboxamides (BTAs), which self-assemble into rod-like supramolecules. Our newly found supramolecular lyotropic liquid crystals (LLCs) are studied in terms of their LLC properties and their suitability as alignment media in NMR spectroscopy. Scalable enantiodifferentiating properties are introduced through a sergeant-and-soldier principle by blending achiral with chiral substituted BTAs. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Energetic electron acceleration and injection during dipolarization events in Mercury's magnetotail

NASA Astrophysics Data System (ADS)

Dewey, R. M.; Slavin, J. A.; Raines, J. M.; Baker, D. N.; Lawrence, D. J.

2017-12-01

MESSENGER frequently observed bursts of energetic electrons (>10 keV to 300 keV) within Mercury's miniature terrestrial-like magnetosphere. These bursts are observed most often in the post-midnight sector near the magnetic equator, suggestive of the acceleration and injection of electrons from the magnetotail and their eastward drift about the planet. We use the Gamma-Ray Spectrometer's high-time resolution (10 ms) energetic electron measurements to examine the relationship between energetic electron injections and magnetospheric dynamics in Mercury's magnetotail. We find that these electron injections were observed most frequently in association with magnetic field dipolarization. Between March 2013 and April 2015, we identified 2976 magnetotail electron events of which 538 were coincident with the leading edge of a dipolarization event. These dipolarization fronts were detected on the basis of their rapid ( 2 s) increase in the northward component of the tail magnetic field (ΔBz 30 nT), which typically persists for 10 s. We find electrons experience brief, yet intense, betatron and Fermi acceleration during these dipolarization events, reaching energies 160 keV and contributing to nightside precipitation. Dipolarization events, and subsequently, the electron acceleration associated with them, display a strong dawn-dusk asymmetry, suggestive of a post-midnight maximum in magnetotail reconnection.

Isospin equilibration processes and dipolar signals: Coherent cluster production

NASA Astrophysics Data System (ADS)

Papa, M.; Berceanu, I.; Acosta, L.; Agodi, C.; Auditore, L.; Cardella, G.; Chatterjee, M. B.; Dell'Aquila, D.; De Filippo, E.; Francalanza, L.; Lanzalone, G.; Lombardo, I.; Maiolino, C.; Martorana, N.; Pagano, A.; Pagano, E. V.; Pirrone, S.; Politi, G.; Quattrocchi, L.; Rizzo, F.; Russotto, P.; Trifiró, A.; Trimarchi, M.; Verde, G.; Vigilante, M.

2017-11-01

The total dipolar signal related to multi-break-up processes induced on the system ^{48}Ca +{^{27}Al} at 40MeV/nucleon has been investigated with the CHIMERA multi-detector. Experimental data related to semi-peripheral collisions are shown and compared with CoMD-III calculations. The strong connection between the dipolar signal as obtained from the detected fragments and the dynamics of the isospin equilibration processes is also shortly discussed.

Internal structure of vortices in a dipolar spinor Bose-Einstein condensate

NASA Astrophysics Data System (ADS)

Borgh, Magnus O.; Lovegrove, Justin; Ruostekoski, Janne

2017-04-01

We demonstrate how dipolar interactions (DI) can have pronounced effects on the structure of vortices in atomic spinor Bose-Einstein condensates and illustrate generic physical principles that apply across dipolar spinor systems. We then find and analyze the cores of singular non-Abelian vortices in a spin-3 52Cr condensate. Using a simpler spin-1 model system, we analyze the underlying dipolar physics and show how a dipolar healing length interacts with the hierarchy of healing lengths of the contact interaction and leads to simple criteria for the core structure: vortex core size is restricted to the shorter spin-dependent healing length when the interactions both favor the ground-state spin condition, but can conversely be enlarged by DI when interactions compete. We further demonstrate manifestations of spin-ordering induced by the DI anisotropy, including DI-dependent angular momentum of nonsingular vortices, as a result of competition with adaptation to rotation, and potentially observable internal vortex-core spin textures. We acknowledge financial support from the EPSRC.

Random acoustic metamaterial with a subwavelength dipolar resonance.

PubMed

Duranteau, Mickaël; Valier-Brasier, Tony; Conoir, Jean-Marc; Wunenburger, Régis

2016-06-01

The effective velocity and attenuation of longitudinal waves through random dispersions of rigid, tungsten-carbide beads in an elastic matrix made of epoxy resin in the range of beads volume fraction 2%-10% are determined experimentally. The multiple scattering model proposed by Luppé, Conoir, and Norris [J. Acoust. Soc. Am. 131(2), 1113-1120 (2012)], which fully takes into account the elastic nature of the matrix and the associated mode conversions, accurately describes the measurements. Theoretical calculations show that the rigid particles display a local, dipolar resonance which shares several features with Minnaert resonance of bubbly liquids and with the dipolar resonance of core-shell particles. Moreover, for the samples under study, the main cause of smoothing of the dipolar resonance of the scatterers and the associated variations of the effective mass density of the dispersions is elastic relaxation, i.e., the finite time required for the shear stresses associated to the translational motion of the scatterers to propagate through the matrix. It is shown that its influence is governed solely by the value of the particle to matrix mass density contrast.

Laboratory Study of Wave Generation Near Dipolarization Fronts

NASA Astrophysics Data System (ADS)

Tejero, E. M.; Enloe, C. L.; Amatucci, B.; Crabtree, C. E.; Ganguli, G.; Malaspina, D.

2017-12-01

Experiments conducted in the Space Physics Simulation Chamber at the Naval Research Laboratory (NRL) create plasma equilibria that replicate those found in dipolarization fronts. These experiments were designed to study the dynamics of boundary layers, such as dipolarization fronts, and it was found that there are instabilities generated by highly inhomogeneous plasma flows. It has previously been shown that these highly inhomogeneous flows can generate waves in the lower hybrid frequency range. Analysis of satellite observations indicate that the sheared flows are a plausible explanation for the observed lower hybrid waves at dipolarization fronts since they can generate longer wavelengths compared to the electron gyroradius, which is consistent with observations. Recent experiments at NRL have demonstrated that these flows can also generate electromagnetic waves in the whistler band. These waves are large amplitude, bursty waves that exhibit frequency chirps similar to whistler mode chorus. Recent results from these experiments and comparisons to in situ observations will be presented. * Work supported by the Naval Research Laboratory Base Program and NASA Grant No. NNH17AE70I.

Improved heteronuclear dipolar decoupling sequences for liquid-crystal NMR

NASA Astrophysics Data System (ADS)

Thakur, Rajendra Singh; Kurur, Narayanan D.; Madhu, P. K.

2007-04-01

Recently we introduced a radiofrequency pulse scheme for heteronuclear dipolar decoupling in solid-state nuclear magnetic resonance under magic-angle spinning [R.S. Thakur, N.D. Kurur, P.K. Madhu, Swept-frequency two-pulse phase modulation for heteronuclear dipolar decoupling in solid-state NMR, Chem. Phys. Lett. 426 (2006) 459-463]. Variants of this sequence, swept-frequency TPPM, employing frequency modulation of different types have been further tested to improve the efficiency of heteronuclear dipolar decoupling. Among these, certain sequences that were found to perform well at lower spinning speeds are demonstrated here on a liquid-crystal sample of MBBA for application in static samples. The new sequences are compared with the standard TPPM and SPINAL schemes and are shown to perform better than them. These modulated schemes perform well at low decoupler radiofrequency power levels and are easy to implement on standard spectrometers.

Response of energetic particles to local magnetic dipolarization inside geosynchronous orbit

NASA Astrophysics Data System (ADS)

Motoba, T.; Ohtani, S.; Gkioulidou, M.; Takahashi, K.

2017-12-01

Magnetic field dipolarization and energetic particle injections are the most distinct phenomena observed in the inner magnetosphere during the substorm expansion phase. Compared to a wealth of knowledge about the phenomenology of magnetic dipolarizations and particle injections at/outside geosynchronous orbit (GEO), our understanding of them inside GEO remains incomplete because of a very limited number of previous studies. In the present study, we statistically examine the response of 1-1000 keV energetic particles to local magnetic dipolarization by performing a superposed epoch analysis of energetic particle fluxes with the zero epoch defined as the dipolarization onset times. Based on data from the Van Allen Probes tail seasons in 2012-2016, we identified a total of 97 magnetic dipolarization events which occurred closer to the magnetic equator (i.e., BH, which is antiparallel to the Earth's dipole axis, is the dominant component of the local magnetic field at least for 5 min before the onset). For major ion species (hydrogen, helium, and oxygen ions), the relative flux intensity to the pre-onset level increases at > 50 keV and decreases at < 30 keV. The hydrogen and helium ion fluxes in the hundreds of keV range sharply increase within a minute after the onset and then decay. Compared to the short-lived nature of hydrogen and helium ion flux enhancements, oxygen ion fluxes are enhanced more gradually (on the order of several minutes). The relative ion flux intensity and peak energy generally tend to increase for stronger dipolarization-related impulsive westward electric field. This suggests that the impulsive electric field is responsible for the energization and/or transport of energetic ions inside GEO. On the other hand, the electron flux enhancement first appears from several tens of keV to a few hundreds of keV, and then exhibits an inverse energy dispersion. For dipolarizations with strong impulsive westward electric fields, the relative electron flux

Influence of solvent and salt concentration on the alignment properties of acrylamide copolymer gels for the measurement of RDC.

PubMed

Trigo-Mouriño, Pablo; Navarro-Vázquez, Armando; Sánchez-Pedregal, Víctor M

2012-12-01

The dependence of molecular alignment with solvent nature and salt concentration has been investigated for mechanically stretched polyacrylamide copolymer gels. Residual dipolar couplings (RDCs) were recorded for D(2)O, DMSO-d(6), and DMSO-d(6)/D(2)O solutions containing different proportions of the solvents and different sodium chloride concentrations. Alignment tensors were determined by fitting the experimental RDCs to the DFT-computed structure of N-methylcodeinium ion. Analysis of the tensors shows that the degree of alignment decreases with the proportion of DMSO-d(6) as well as with the concentration of sodium chloride, most likely due to enhanced ion-pair aggregation. Furthermore, rotation of the alignment tensor is observed when increasing the salt concentration. Copyright © 2012 John Wiley & Sons, Ltd.

Phase behavior of a simple dipolar fluid under shear flow in an electric field.

PubMed

McWhirter, J Liam

2008-01-21

Nonequilibrium molecular dynamics simulations are performed on a dense simple dipolar fluid under a planar Couette shear flow. Shear generates heat, which is removed by thermostatting terms added to the equations of motion of the fluid particles. The spatial structure of simple fluids at high shear rates is known to depend strongly on the thermostatting mechanism chosen. Kinetic thermostats are either biased or unbiased: biased thermostats neglect the existence of secondary flows that appear at high shear rates superimposed upon the linear velocity profile of the fluid. Simulations that employ a biased thermostat produce a string phase where particles align in strings with hexagonal symmetry along the direction of the flow. This phase is known to be a simulation artifact of biased thermostatting, and has not been observed by experiments on colloidal suspensions under shear flow. In this paper, we investigate the possibility of using a suitably directed electric field, which is coupled to the dipole moments of the fluid particles, to stabilize the string phase. We explore several thermostatting mechanisms where either the kinetic or configurational fluid degrees of freedom are thermostated. Some of these mechanisms do not yield a string phase, but rather a shear-thickening phase; in this case, we find the influence of the dipolar interactions and external field on the packing structure, and in turn their influence on the shear viscosity at the onset of this shear-thickening regime.

Designing Hysteresis with Dipolar Chains.

PubMed

Concha, Andrés; Aguayo, David; Mellado, Paula

2018-04-13

Materials that have hysteretic response to an external field are essential in modern information storage and processing technologies. A myriad of magnetization curves of several natural and artificial materials have previously been measured and each has found a particular mechanism that accounts for it. However, a phenomenological model that captures all the hysteresis loops and at the same time provides a simple way to design the magnetic response of a material while remaining minimal is missing. Here, we propose and experimentally demonstrate an elementary method to engineer hysteresis loops in metamaterials built out of dipolar chains. We show that by tuning the interactions of the system and its geometry we can shape the hysteresis loop which allows for the design of the softness of a magnetic material at will. Additionally, this mechanism allows for the control of the number of loops aimed to realize multiple-valued logic technologies. Our findings pave the way for the rational design of hysteretical responses in a variety of physical systems such as dipolar cold atoms, ferroelectrics, or artificial magnetic lattices, among others.

Designing Hysteresis with Dipolar Chains

NASA Astrophysics Data System (ADS)

Concha, Andrés; Aguayo, David; Mellado, Paula

2018-04-01

Materials that have hysteretic response to an external field are essential in modern information storage and processing technologies. A myriad of magnetization curves of several natural and artificial materials have previously been measured and each has found a particular mechanism that accounts for it. However, a phenomenological model that captures all the hysteresis loops and at the same time provides a simple way to design the magnetic response of a material while remaining minimal is missing. Here, we propose and experimentally demonstrate an elementary method to engineer hysteresis loops in metamaterials built out of dipolar chains. We show that by tuning the interactions of the system and its geometry we can shape the hysteresis loop which allows for the design of the softness of a magnetic material at will. Additionally, this mechanism allows for the control of the number of loops aimed to realize multiple-valued logic technologies. Our findings pave the way for the rational design of hysteretical responses in a variety of physical systems such as dipolar cold atoms, ferroelectrics, or artificial magnetic lattices, among others.

Electrostatic contribution to the persistence length of a semiflexible dipolar chain.

PubMed

Podgornik, Rudi

2004-09-01

We investigate the electrostatic contribution to the persistence length of a semiflexible polymer chain whose segments interact via a screened Debye-Hückel dipolar interaction potential. We derive the expressions for the renormalized persistence length on the level of a 1/D-expansion method already successfully used in other contexts of polyelectrolye physics. We investigate different limiting forms of the renormalized persistence length of the dipolar chain and show that, in, general, it depends less strongly on the screening length than in the context of a monopolar chain. We show that for a dipolar chain the electrostatic persistence length in the same regime of the parameter phase space as the original Odijk-Skolnick-Fixman (OSF) form for a monopolar chain depends logarithmically on the screening length rather than quadratically. This can be understood solely on the basis of a swifter decay of the dipolar interactions with separation compared to the monopolar electrostatic interactions. We comment also on the general contribution of higher multipoles to the electrostatic renormalization of the bending rigidity.

Quantum Landau damping in dipolar Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Mendonça, J. T.; Terças, H.; Gammal, A.

2018-06-01

We consider Landau damping of elementary excitations in Bose-Einstein condensates (BECs) with dipolar interactions. We discuss quantum and quasiclassical regimes of Landau damping. We use a generalized wave-kinetic description of BECs which, apart from the long-range dipolar interactions, also takes into account the quantum fluctuations and the finite-energy corrections to short-range interactions. Such a description is therefore more general than the usual mean-field approximation. The present wave-kinetic approach is well suited for the study of kinetic effects in BECs, such as those associated with Landau damping, atom trapping, and turbulent diffusion. The inclusion of quantum fluctuations and energy corrections changes the dispersion relation and the damping rates, leading to possible experimental signatures of these effects. Quantum Landau damping is described with generality, and particular examples of dipolar condensates in two and three dimensions are studied. The occurrence of roton-maxon excitations, and their relevance to Landau damping, are also considered in detail. The present approach is mainly based on a linear perturbative procedure, but the nonlinear regime of Landau damping, which includes atom trapping and atom diffusion, is also briefly discussed.

Demixing in simple dipolar mixtures: Integral equation versus density functional results

NASA Astrophysics Data System (ADS)

Range, Gabriel M.; Klapp, Sabine H. L.

2004-09-01

Using reference hypernetted chain (RHNC) integral equations and density functional theory in the modified mean-field (MMF) approximation we investigate the phase behavior of binary mixtures of dipolar hard spheres. The two species ( A and B ) differ only in their dipole moments mA and mB , and the central question investigated is under which conditions these asymmetric mixtures can exhibit demixing phase transitions in the fluid phase regime. Results from our two theoretical approaches turn out to strongly differ. Within the RHNC (which we apply to the isotropic high-temperature phase) demixing does indeed occur for dense systems with small interaction parameters Γ=mB2/mA2 . This result generalizes previously reported observations on demixing in mixtures of dipolar and neutral hard spheres (Γ=0) to the case of true dipolar hard sphere mixtures. The RHNC approach also indicates that these demixed fluid phases are isotropic at temperatures accessible by the theory, whereas isotropic-to-ferroelectric transitions occur only at larger Γ . The MMF theory, on the other hand, yields a different picture in which demixing occurs in combination with spontaneous ferroelectricity at all Γ considered. This discrepancy underlines the relevance of correlational effects for the existence of demixing transitions in dipolar systems without dispersive interactions. Indeed, supplementing the dipolar interactions by small, asymmetric amounts of van der Waals-like interactions (and thereby supporting the systems tendency to demix) one finally reaches good agreement between MMF and RHNC results.

Nonlocal and nonlinear electrostatics of a dipolar Coulomb fluid.

PubMed

Sahin, Buyukdagli; Ralf, Blossey

2014-07-16

We study a model Coulomb fluid consisting of dipolar solvent molecules of finite extent which generalizes the point-like dipolar Poisson-Boltzmann model (DPB) previously introduced by Coalson and Duncan (1996 J. Phys. Chem. 100 2612) and Abrashkin et al (2007 Phys. Rev. Lett. 99 077801). We formulate a nonlocal Poisson-Boltzmann equation (NLPB) and study both linear and nonlinear dielectric response in this model for the case of a single plane geometry. Our results shed light on the relevance of nonlocal versus nonlinear effects in continuum models of material electrostatics.

Acceleration and Precipitation of Electrons during Substorm Dipolarization Events

NASA Astrophysics Data System (ADS)

Ashour-Abdalla, Maha; Richard, Robert; Donovan, Eric; Zhou, Meng; Goldstein, Mevlyn; El-Alaoui, Mostafa; Schriver, David; Walker, Raymond

Observations and modeling have established that during geomagnetically disturbed times the Earth’s magnetotail goes through large scale changes that result in enhanced electron precipitation into the ionosphere and earthward propagating dipolarization fronts that contain highly energized plasma. Such events originate near reconnection regions in the magnetotail at about 20-30 R_E down tail. As the dipolarization fronts propagate earthward, strong acceleration of both ions and electrons occurs due to a combination of non-adiabatic and adiabatic (betatron and Fermi) acceleration, with particle energies reaching up to 100 keV within the dipolarization front. One consequence of the plasma transport that occurs during these events is direct electron precipitation into the ionosphere, which form auroral precipitation. Using global kinetic simulations along with spacecraft and ground-based data, causes of electron precipitation are determined during well-documented, disturbed events. It is found that precipitation of keV electrons in the pre-midnight sector at latitudes around 70(°) occur due to two distinct physical processes: (1) higher latitude (≥72(°) ) precipitation due to electrons that undergo relatively rapid non-adiabatic pitch angle scattering into the loss cone just earthward of the reconnection region at around 20 R_E downtail, and (2) lower latitude (≤72(°) ) precipitation due to electrons that are more gradually accelerated primarily parallel to the geomagnetic field during its bounce motion by Fermi acceleration and enter the loss cone much closer to the Earth at 10-15 R_E, somewhat tailward of the dipolarization front. As the dipolarization fronts propagate earthward, the electron precipitation shifts to lower latitudes and occurs over a wider region in the auroral ionosphere. Our results show a direct connection between electron acceleration in the magnetotail and electron precipitation in the ionosphere during disturbed times. The electron

Critical Time Crystals in Dipolar Systems

NASA Astrophysics Data System (ADS)

Ho, Wen Wei; Choi, Soonwon; Lukin, Mikhail D.; Abanin, Dmitry A.

2017-07-01

We analyze the quantum dynamics of periodically driven, disordered systems in the presence of long-range interactions. Focusing on the stability of discrete time crystalline (DTC) order in such systems, we use a perturbative procedure to evaluate its lifetime. For 3D systems with dipolar interactions, we show that the corresponding decay is parametrically slow, implying that robust, long-lived DTC order can be obtained. We further predict a sharp crossover from the stable DTC regime into a regime where DTC order is lost, reminiscent of a phase transition. These results are in good agreement with the recent experiments utilizing a dense, dipolar spin ensemble in diamond [Nature (London) 543, 221 (2017), 10.1038/nature21426]. They demonstrate the existence of a novel, critical DTC regime that is stabilized not by many-body localization but rather by slow, critical dynamics. Our analysis shows that the DTC response can be used as a sensitive probe of nonequilibrium quantum matter.

Hole localization, water dissociation mechanisms, and band alignment at aqueous-titania interfaces

NASA Astrophysics Data System (ADS)

Lyons, John L.

Photocatalytic water splitting is a promising method for generating clean energy, but materials that can efficiently act as photocatalysts are scarce. This is in part due to the fact that exposure to water can strongly alter semiconductor surfaces and therefore photocatalyst performance. Many materials are not stable in aqueous environments; in other cases, local changes in structure may occur, affecting energy-level alignment. Even in the simplest case, dynamic fluctuations modify the organization of interface water. Accounting for such effects requires knowledge of the dominant local structural motifs and also accurate semiconductor band-edge positions, making quantitative prediction of energy-level alignments computationally challenging. Here we employ a combined theoretical approach to study the structure, energy alignment, and hole localization at aqueous-titania interfaces. We calculate the explicit aqueous-semiconductor interface using ab initio molecular dynamics, which provides the fluctuating atomic structure, the extent of water dissociation, and the resulting electrostatic potential. For both anatase and rutile TiO2 we observe spontaneous water dissociation and re-association events that occur via distinct mechanisms. We also find a higher-density water layer occurring on anatase. In both cases, we find that the second monolayer of water plays a crucial role in controlling the extent of water dissociation. Using hybrid functional calculations, we then investigate the propensity for dissociated waters to stabilize photo-excited carriers, and compare the results of rutile and anatase aqueous interfaces. Finally, we use the GW approach from many-body perturbation theory to obtain the position of semiconductor band edges relative to the occupied 1b1 level and thus the redox levels of water, and examine how local structural modifications affect these offsets. This work was performed in collaboration with N. Kharche, M. Z. Ertem, J. T. Muckerman, and M. S

Dipolar collisions of ultracold 23Na87Rb molecules.

NASA Astrophysics Data System (ADS)

Guo, Mingyang; Ye, Xin; He, Junyu; Quéméner, Goulven; González-Martínez, Maykel; Dulieu, Olivier; Wang, Dajun

2017-04-01

Although ultracold polar molecules have long been proposed as a primary candidate for investigating dipolar many body physics, many of their basic properties, like their collisions in external electric fields, are still largely unknown. In fact, despite the successful production of several new ultracold molecular species in the last two years, so far the only available dipolar collision data is still from JILA's fermionic 40K87Rb experiment in 2010. In this talk, we will describe our investigation on dipolar collisions of ultracold bosonic and chemically stable 23Na87Rb molecules which possess a large permanent electric dipole moment. With a moderate electric field, an effective dipole moment large enough to strongly couple higher partial waves into the collisions can be achieved. We will report the influence of this effect on the molecular collisions observed in our experiment. Our theoretical model for understanding these observations will also be presented. This work is supported by the Hong Kong RGC CUHK404712 and the ANR/RGC Joint Research Scheme ACUHK403/13.

Reconstruction of interatomic vectors by principle component analysis of nuclear magnetic resonance data in multiple alignments

NASA Astrophysics Data System (ADS)

Hus, Jean-Christophe; Bruschweiler, Rafael

2002-07-01

A general method is presented for the reconstruction of interatomic vector orientations from nuclear magnetic resonance (NMR) spectroscopic data of tensor interactions of rank 2, such as dipolar coupling and chemical shielding anisotropy interactions, in solids and partially aligned liquid-state systems. The method, called PRIMA, is based on a principal component analysis of the covariance matrix of the NMR parameters collected for multiple alignments. The five nonzero eigenvalues and their eigenvectors efficiently allow the approximate reconstruction of the vector orientations of the underlying interactions. The method is demonstrated for an isotropic distribution of sample orientations as well as for finite sets of orientations and internuclear vectors encountered in protein systems.

Electron heating and Tp/Te variations during magnetic dipolarizations

NASA Astrophysics Data System (ADS)

Grigorenko, Elena; Kronberg, Elena; Daly, Patrick; Ganushkina, Natalia; Lavraud, Benoit; Sauvaud, Jean-Andre; Zelenyi, Lev

2017-04-01

The proton-to-electron temperature ratio (Tp/Te) in the plasma sheet (PS) of the Earth's magnetotail is studied by using 5 years of Cluster observations (2001-2005). The PS intervals are searched within a region defined with -19dipolarizations. A superposed epoch analysis applied to these events shows that the minimum value of Tp/Te is observed after the dipolarization onset during the "turbulent phase" of dipolarization, when a number of transient Bz pulses are reduced, but the value of Bz field is still large and an intensification of wave activity is observed. The Tp/Te drops and associated increases of Te often coincide either with bursts of broadband electrostatic emissions, which may include electron cyclotron harmonics, or with broadband electromagnetic emission in a frequency range from proton plasma frequency (fpp) up to the electron gyrofrequency (fce). These findings show that the wave activity developing in the current sheet after dipolarization onset may play a role in the additional electron heating and the associated Tp/Te decrease. This work was supported by the Volskwagen Foundation (grant Az 90 312).

Lorentz microscopy sheds light on the role of dipolar interactions in magnetic hyperthermia

NASA Astrophysics Data System (ADS)

Campanini, M.; Ciprian, R.; Bedogni, E.; Mega, A.; Chiesi, V.; Casoli, F.; de Julián Fernández, C.; Rotunno, E.; Rossi, F.; Secchi, A.; Bigi, F.; Salviati, G.; Magén, C.; Grillo, V.; Albertini, F.

2015-04-01

Monodispersed Fe3O4 nanoparticles with comparable size distributions have been synthesized by two different synthesis routes, co-precipitation and thermal decomposition. Thanks to the different steric stabilizations, the described samples can be considered as a model system to investigate the effects of magnetic dipolar interactions on the aggregation states of the nanoparticles. Moreover, the presence of magnetic dipolar interactions can strongly affect the nanoparticle efficiency as a hyperthermic mediator. In this paper, we present a novel way to visualize and map the magnetic dipolar interactions in different kinds of nanoparticle aggregates by the use of Lorentz microscopy, an easy and reliable in-line electron holographic technique. By exploiting Lorentz microscopy, which is complementary to the magnetic measurements, it is possible to correlate the interaction degrees of magnetic nanoparticles with their magnetic behaviors. In particular, we demonstrate that Lorentz microscopy is successful in visualizing the magnetic configurations stabilized by dipolar interactions, thus paving the way to the comprehension of the power loss mechanisms for different nanoparticle aggregates.Monodispersed Fe3O4 nanoparticles with comparable size distributions have been synthesized by two different synthesis routes, co-precipitation and thermal decomposition. Thanks to the different steric stabilizations, the described samples can be considered as a model system to investigate the effects of magnetic dipolar interactions on the aggregation states of the nanoparticles. Moreover, the presence of magnetic dipolar interactions can strongly affect the nanoparticle efficiency as a hyperthermic mediator. In this paper, we present a novel way to visualize and map the magnetic dipolar interactions in different kinds of nanoparticle aggregates by the use of Lorentz microscopy, an easy and reliable in-line electron holographic technique. By exploiting Lorentz microscopy, which is

Collective excitation frequencies and stationary states of trapped dipolar Bose-Einstein condensates in the Thomas-Fermi regime

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

Bijnen, R. M. W. van; Department of Physics and Astronomy, McMaster University, Hamilton, Ontario L8S 4M1; Parker, N. G.

We present a general method for obtaining the exact static solutions and collective excitation frequencies of a trapped Bose-Einstein condensate (BEC) with dipolar atomic interactions in the Thomas-Fermi regime. The method incorporates analytic expressions for the dipolar potential of an arbitrary polynomial density profile, thereby reducing the problem of handling nonlocal dipolar interactions to the solution of algebraic equations. We comprehensively map out the static solutions and excitation modes, including non-cylindrically-symmetric traps, and also the case of negative scattering length where dipolar interactions stabilize an otherwise unstable condensate. The dynamical stability of the excitation modes gives insight into the onsetmore » of collapse of a dipolar BEC. We find that global collapse is consistently mediated by an anisotropic quadrupolar collective mode, although there are two trapping regimes in which the BEC is stable against quadrupole fluctuations even as the ratio of the dipolar to s-wave interactions becomes infinite. Motivated by the possibility of a fragmented condensate in a dipolar Bose gas due to the partially attractive interactions, we pay special attention to the scissors modes, which can provide a signature of superfluidity, and identify a long-range restoring force which is peculiar to dipolar systems. As part of the supporting material for this paper we provide the computer program used to make the calculations, including a graphical user interface.« less

Plasma Entry from Tail into the Dipolar Magnetosphere During Substorms

NASA Astrophysics Data System (ADS)

Haerendel, Gerhard

Plasma entering the dipolar magnetosphere from the tail has to overcome the obstacle presented by the conductivity enhancements caused by the poleward arc(s). While the arcs move poleward, the plasma proceeds equatorward as testified by the existence of a westward electric field. The arcs break into smaller-scale structures and loops with a tendency of eastward growth and expansion, although the basic driving force is directed earthward/equatorward. The likely reason is that the arc-related conductivity enhancements act as flow barriers and convert normal into shear stresses. The energy derived from the release of the shear stresses and dissipated in the arcs lowers the entropy content of the flux tubes and enables their earthward progression. In addition, poleward jumps of the breakup arcs are quite common. They result from refreshments of the generator plasma by the sequential arrival of flow bursts from the near-Earth neutral line. Once inside the oval, the plasma continues to move equatorward as manifested through north-south aligned auroral forms. Owing to the existence of an inner border of the oval, marked by the Region 2 currents, all flows are eventually diverted sunward.

Tight coupling of metabolic oscillations and intracellular water dynamics in Saccharomyces cerevisiae.

PubMed

Thoke, Henrik Seir; Tobiesen, Asger; Brewer, Jonathan; Hansen, Per Lyngs; Stock, Roberto P; Olsen, Lars F; Bagatolli, Luis A

2015-01-01

We detected very strong coupling between the oscillating concentration of ATP and the dynamics of intracellular water during glycolysis in Saccharomyces cerevisiae. Our results indicate that: i) dipolar relaxation of intracellular water is heterogeneous within the cell and different from dilute conditions, ii) water dipolar relaxation oscillates with glycolysis and in phase with ATP concentration, iii) this phenomenon is scale-invariant from the subcellular to the ensemble of synchronized cells and, iv) the periodicity of both glycolytic oscillations and dipolar relaxation are equally affected by D2O in a dose-dependent manner. These results offer a new insight into the coupling of an emergent intensive physicochemical property of the cell, i.e. cell-wide water dipolar relaxation, and a central metabolite (ATP) produced by a robustly oscillating metabolic process.

Tight Coupling of Metabolic Oscillations and Intracellular Water Dynamics in Saccharomyces cerevisiae

PubMed Central

Thoke, Henrik Seir; Tobiesen, Asger; Brewer, Jonathan; Hansen, Per Lyngs; Stock, Roberto P.; Olsen, Lars F.; Bagatolli, Luis A.

2015-01-01

We detected very strong coupling between the oscillating concentration of ATP and the dynamics of intracellular water during glycolysis in Saccharomyces cerevisiae. Our results indicate that: i) dipolar relaxation of intracellular water is heterogeneous within the cell and different from dilute conditions, ii) water dipolar relaxation oscillates with glycolysis and in phase with ATP concentration, iii) this phenomenon is scale-invariant from the subcellular to the ensemble of synchronized cells and, iv) the periodicity of both glycolytic oscillations and dipolar relaxation are equally affected by D2O in a dose-dependent manner. These results offer a new insight into the coupling of an emergent intensive physicochemical property of the cell, i.e. cell-wide water dipolar relaxation, and a central metabolite (ATP) produced by a robustly oscillating metabolic process. PMID:25705902

Ion Transport and Acceleration at Dipolarization Fronts: High-Resolution MHD/Test-Particle Simulations

NASA Astrophysics Data System (ADS)

Ukhorskiy, A. Y.; Sorathia, K.; Merkin, V. G.; Sitnov, M. I.; Mitchell, D. G.; Wiltberger, M. J.; Lyon, J.

2017-12-01

Much of plasma heating and transport from the magnetotail into the inner magnetosphere occurs in the form of mesoscale discrete injections associated with sharp dipolarizations of magnetic field (dipolarization fronts). In this study we investigate the mechanisms of ion acceleration at dipolarization fronts in a high-resolution global magnetospheric MHD model (LFM). We use large-scale three-dimensional test-particle simulations (CHIMP) to address the following science questions: 1) what are the characteristic scales of dipolarization regions that can stably trap ions? 2) what role does the trapping play in ion transport and acceleration? 3) how does it depend on particle energy and distance from Earth? 4) to what extent ion acceleration is adiabatic? High-resolution LFM was run using idealized solar wind conditions with fixed nominal values of density and velocity and a southward IMF component of -5 nT. To simulate ion interaction with dipolarization fronts, a large ensemble of test particles distributed in energy, pitch-angle, and gyrophase was initialized inside one of the LFM dipolarization channels in the magnetotail. Full Lorentz ion trajectories were then computed over the course of the front inward propagation from the distance of 17 to 6 Earth radii. A large fraction of ions with different initial energies stayed in phase with the front over the entire distance. The effect of magnetic trapping at different energies was elucidated with a correlation of the ion guiding center and the ExB drift velocities. The role of trapping in ion energization was quantified by comparing the partial pressure of ions that exhibit trapping to the pressure of all trapped ions.

Pitch angle distributions of electrons at dipolarization sites during geomagnetic activity: THEMIS observations

NASA Astrophysics Data System (ADS)

Wang, Kaiti; Lin, Ching-Huei; Wang, Lu-Yin; Hada, Tohru; Nishimura, Yukitoshi; Turner, Drew L.; Angelopoulos, Vassilis

2014-12-01

Changes in pitch angle distributions of electrons with energies from a few eV to 1 MeV at dipolarization sites in Earth's magnetotail are investigated statistically to determine the extent to which adiabatic acceleration may contribute to these changes. Forty-two dipolarization events from 2008 and 2009 observed by Time History of Events and Macroscale Interactions during Substorms probes covering the inner plasma sheet from 8 RE to 12 RE during geomagnetic activity identified by the AL index are analyzed. The number of observed events with cigar-type distributions (peaks at 0° and 180°) decreases sharply below 1 keV after dipolarization because in many of these events, electron distributions became more isotropized. From above 1 keV to a few tens of keV, however, the observed number of cigar-type events increases after dipolarization and the number of isotropic events decreases. These changes can be related to the ineffectiveness of Fermi acceleration below 1 keV (at those energies, dipolarization time becomes comparable to electron bounce time). Model-calculated pitch angle distributions after dipolarization with the effect of betatron and Fermi acceleration tested indicate that these adiabatic acceleration mechanisms can explain the observed patterns of event number changes over a large range of energies for cigar events and isotropic events. Other factors still need to be considered to assess the observed increase in cigar events around 2 keV. Indeed, preferential directional increase/loss of electron fluxes, which may contribute to the formation of cigar events, was observed. Nonadiabatic processes to accelerate electrons in a parallel direction may also be important for future study.

Observation of Dipolar Spin-Exchange Interactions with Polar Molecules in a Lattice

DTIC Science & Technology

2013-01-01

extend beyond nearest neighbours. This allows coherent spin dynamics to persist even for gases with relatively high entropy and low lattice filling...dynamics to persist even for gases with relatively high entropy and low lat- tice filling. While measured effects of dipolar interactions in ultracold...limits superexchange to nearest-neighbor interactions and requires extremely low temperature and entropy . In contrast, long-range dipolar

Empirical parameters for solvent acidity, basicity, dipolarity, and polarizability of the ionic liquids [BMIM][BF4] and [BMIM][PF6].

PubMed

del Valle, J C; García Blanco, F; Catalán, J

2015-04-02

The empirical solvent scales for polarizability (SP), dipolarity (SdP), acidity (SA), and basicity (SB) have been successfully used to interpret the solvatochromism of compounds dissolved in organic solvents and their solvent mixtures. Providing that the published solvatochromic parameters for the ionic liquids 1-(1-butyl)-3-methylimidazolium tetrafluoroborate, [BMIM][BF4] and 1-(1-butyl)-3-methylimidazolium hexafluorophosphate, [BMIM][PF6], are excessively widespread, their SP, SdP, SA, and SB values are measured herein at temperatures from 293 to 353 K. Four key points are emphasized herein: (i) the origin of the solvatochromic solvent scales--the gas phase, that is the absence of any medium perturbation--; (ii) the separation of the polarizability and dipolarity effects; (iii) the simplification of the probing process in order to obtain the solvatochromic parameters; and (iv) the SP, SdP, SA, and SB solvent scales can probe the polarizability, dipolarity, acidity, and basicity of ionic liquids as well as of organic solvents and water-organic solvent mixtures. From the multiparameter approach using the four pure solvent scales one can draw the conclusion that (a) the solvent influence of [BMIM][BF4] parallels that of formamide at 293 K, both of them miscible with water; (b) [BMIM][PF6] shows a set of solvatochromic parameters similar to that of chloroacetonitrile, both of them water insoluble; and (c) that the corresponding solvent acidity and basicity of the ionic liquids can be explained to a great extent from the cation species by comparing the empirical parameters of [BMIM](+) with those of the solvent 1-methylimidazole. The insolubility of [BMIM][PF6] in water as compared to [BMIM][BF4] is tentatively connected to some extent to the larger molar volume of the anion [PF6](-), and to the difference in basicity of [PF6](-) and [BF4](-).

Manipulation and control of the interfacial polarization in organic light-emitting diodes by dipolar doping

NASA Astrophysics Data System (ADS)

Jäger, Lars; Schmidt, Tobias D.; Brütting, Wolfgang

2016-09-01

Most of the commonly used electron transporting materials in organic light-emitting diodes exhibit interfacial polarization resulting from partially aligned permanent dipole moments of the molecules. This property modifies the internal electric field distribution of the device and therefore enables an earlier flat band condition for the hole transporting side, leading to improved charge carrier injection. Recently, this phenomenon was studied with regard to different materials and degradation effects, however, so far the influence of dilution has not been investigated. In this paper we focus on dipolar doping of the hole transporting material 4,4-bis[N-(1-naphthyl)-N-phenylamino]-biphenyl (NPB) with the polar electron transporting material tris-(8-hydroxyquinolate) aluminum (Alq3). Impedance spectroscopy reveals that changes of the hole injection voltage do not scale in a simple linear fashion with the effective thickness of the doped layer. In fact, the measured interfacial polarization reaches a maximum value for a 1:1 blend. Taking the permanent dipole moment of Alq3 into account, an increasing degree of dipole alignment is found for decreasing Alq3 concentration. This observation can be explained by the competition between dipole-dipole interactions leading to dimerization and the driving force for vertical orientation of Alq3 dipoles at the surface of the NPB layer.

The inhibition of methane hydrate formation by water alignment underneath surface adsorption of surfactants

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

Nguyen, Ngoc N.; Nguyen, Anh V.; Dang, Liem X.

Sodium dodecyl sulfate (SDS) has been widely shown to strongly promote the formation of methane hydrate. Here we show that SDS displays an extraordinary inhibition effect on methane hydrate formation when the surfactant is used in sub-millimolar concentration (around 0.3 mM). We have also employed Sum Frequency Generation vibrational spectroscopy (SFG) and molecular dynamics simulation (MDS) to elucidate the molecular mechanism of this inhibition. The SFG and MDS results revealed a strong alignment of water molecules underneath surface adsorption of SDS in its sub-millimolar solution. Interestingly, both the alignment of water and the inhibition effect (in 0.3 mM SDS solution)more » went vanishing when an oppositely-charged surfactant (tetra-n-butylammonium bromide, TBAB) was suitably added to produce a mixed solution of 0.3 mM SDS and 3.6 mM TBAB. Combining structural and kinetic results, we pointed out that the alignment of water underneath surface adsorption of dodecyl sulfate (DS-) anions gave rise to the unexpected inhibition of methane hydration formation in sub-millimolar solution of SDS. The adoption of TBAB mitigated the SDS-induced electrostatic field at the solution’s surface and, therefore, weakened the alignment of interfacial water which, in turn, erased the inhibition effect. We discussed this finding using the concept of activation energy of the interfacial formation of gas hydrate. The main finding of this work is to reveal the interplay of interfacial water in governing gas hydrate formation which sheds light on a universal molecular-scale understanding of the influence of surfactants on gas hydrate formation. This work was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.« less

Nuclear magnetic relaxation by the dipolar EMOR mechanism: General theory with applications to two-spin systems.

PubMed

Chang, Zhiwei; Halle, Bertil

2016-02-28

In aqueous systems with immobilized macromolecules, including biological tissue, the longitudinal spin relaxation of water protons is primarily induced by exchange-mediated orientational randomization (EMOR) of intra- and intermolecular magnetic dipole-dipole couplings. We have embarked on a systematic program to develop, from the stochastic Liouville equation, a general and rigorous theory that can describe relaxation by the dipolar EMOR mechanism over the full range of exchange rates, dipole coupling strengths, and Larmor frequencies. Here, we present a general theoretical framework applicable to spin systems of arbitrary size with symmetric or asymmetric exchange. So far, the dipolar EMOR theory is only available for a two-spin system with symmetric exchange. Asymmetric exchange, when the spin system is fragmented by the exchange, introduces new and unexpected phenomena. Notably, the anisotropic dipole couplings of non-exchanging spins break the axial symmetry in spin Liouville space, thereby opening up new relaxation channels in the locally anisotropic sites, including longitudinal-transverse cross relaxation. Such cross-mode relaxation operates only at low fields; at higher fields it becomes nonsecular, leading to an unusual inverted relaxation dispersion that splits the extreme-narrowing regime into two sub-regimes. The general dipolar EMOR theory is illustrated here by a detailed analysis of the asymmetric two-spin case, for which we present relaxation dispersion profiles over a wide range of conditions as well as analytical results for integral relaxation rates and time-dependent spin modes in the zero-field and motional-narrowing regimes. The general theoretical framework presented here will enable a quantitative analysis of frequency-dependent water-proton longitudinal relaxation in model systems with immobilized macromolecules and, ultimately, will provide a rigorous link between relaxation-based magnetic resonance image contrast and molecular parameters.

Nuclear magnetic relaxation by the dipolar EMOR mechanism: General theory with applications to two-spin systems

NASA Astrophysics Data System (ADS)

Chang, Zhiwei; Halle, Bertil

2016-02-01

In aqueous systems with immobilized macromolecules, including biological tissue, the longitudinal spin relaxation of water protons is primarily induced by exchange-mediated orientational randomization (EMOR) of intra- and intermolecular magnetic dipole-dipole couplings. We have embarked on a systematic program to develop, from the stochastic Liouville equation, a general and rigorous theory that can describe relaxation by the dipolar EMOR mechanism over the full range of exchange rates, dipole coupling strengths, and Larmor frequencies. Here, we present a general theoretical framework applicable to spin systems of arbitrary size with symmetric or asymmetric exchange. So far, the dipolar EMOR theory is only available for a two-spin system with symmetric exchange. Asymmetric exchange, when the spin system is fragmented by the exchange, introduces new and unexpected phenomena. Notably, the anisotropic dipole couplings of non-exchanging spins break the axial symmetry in spin Liouville space, thereby opening up new relaxation channels in the locally anisotropic sites, including longitudinal-transverse cross relaxation. Such cross-mode relaxation operates only at low fields; at higher fields it becomes nonsecular, leading to an unusual inverted relaxation dispersion that splits the extreme-narrowing regime into two sub-regimes. The general dipolar EMOR theory is illustrated here by a detailed analysis of the asymmetric two-spin case, for which we present relaxation dispersion profiles over a wide range of conditions as well as analytical results for integral relaxation rates and time-dependent spin modes in the zero-field and motional-narrowing regimes. The general theoretical framework presented here will enable a quantitative analysis of frequency-dependent water-proton longitudinal relaxation in model systems with immobilized macromolecules and, ultimately, will provide a rigorous link between relaxation-based magnetic resonance image contrast and molecular parameters.

Topological defect formation in rotating binary dipolar Bose–Einstein condensate

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

Zhang, Xiao-Fei, E-mail: xfzhang@ntsc.ac.cn; University of Chinese Academy of Sciences, Beijing 100049; Department of Engineering Science, University of Electro-Communications, Tokyo 182-8585

We investigate the topological defects and spin structures of a rotating binary Bose–Einstein condensate, which consists of both dipolar and scalar bosonic atoms confined in spin-dependent optical lattices, for an arbitrary orientation of the dipoles with respect to their plane of motion. Our results show that the tunable dipolar interaction, especially the orientation of the dipoles, can be used to control the direction of stripe phase and its related half-vortex sheets. In addition, it can also be used to obtain a regular arrangement of various topological spin textures, such as meron, circular and cross disgyration spin structures. We point outmore » that such topological defects and regular arrangement of spin structures arise primarily from the long-range and anisotropic nature of dipolar interaction and its competition with the spin-dependent optical lattices and rotation. - Highlights: • Effects of both strength and orientation of the dipoles are discussed. • Various topological defects can be formed in different parameter regions. • Present one possible way to obtain regular arrangements of spin textures.« less

Dipolar particles in a double-trap confinement: Response to tilting the dipolar orientation

NASA Astrophysics Data System (ADS)

Bjerlin, J.; Bengtsson, J.; Deuretzbacher, F.; Kristinsdóttir, L. H.; Reimann, S. M.

2018-02-01

We analyze the microscopic few-body properties of dipolar particles confined in two parallel quasi-one-dimensional harmonic traps. In particular, we show that an adiabatic rotation of the dipole orientation about the trap axes can drive an initially nonlocalized few-fermion state into a localized state with strong intertrap pairing. With an instant, nonadiabatic rotation, however, localization is inhibited and a highly excited state is reached. This state may be interpreted as the few-body analog of a super-Tonks-Girardeau state, known from one-dimensional systems with contact interactions.

Quantum phases of dipolar rotors on two-dimensional lattices

NASA Astrophysics Data System (ADS)

Abolins, B. P.; Zillich, R. E.; Whaley, K. B.

2018-03-01

The quantum phase transitions of dipoles confined to the vertices of two-dimensional lattices of square and triangular geometry is studied using path integral ground state quantum Monte Carlo. We analyze the phase diagram as a function of the strength of both the dipolar interaction and a transverse electric field. The study reveals the existence of a class of orientational phases of quantum dipolar rotors whose properties are determined by the ratios between the strength of the anisotropic dipole-dipole interaction, the strength of the applied transverse field, and the rotational constant. For the triangular lattice, the generic orientationally disordered phase found at zero and weak values of both dipolar interaction strength and applied field is found to show a transition to a phase characterized by net polarization in the lattice plane as the strength of the dipole-dipole interaction is increased, independent of the strength of the applied transverse field, in addition to the expected transition to a transverse polarized phase as the electric field strength increases. The square lattice is also found to exhibit a transition from a disordered phase to an ordered phase as the dipole-dipole interaction strength is increased, as well as the expected transition to a transverse polarized phase as the electric field strength increases. In contrast to the situation with a triangular lattice, on square lattices, the ordered phase at high dipole-dipole interaction strength possesses a striped ordering. The properties of these quantum dipolar rotor phases are dominated by the anisotropy of the interaction and provide useful models for developing quantum phases beyond the well-known paradigms of spin Hamiltonian models, implementing in particular a novel physical realization of a quantum rotor-like Hamiltonian that possesses an anisotropic long range interaction.

Adaptation of a 3-D Quadrupole Ion Trap for Dipolar DC Collisional Activation

PubMed Central

Prentice, Boone M.; Santini, Robert E.; McLuckey, Scott A.

2011-01-01

Means to allow for the application of a dipolar DC pulse to the end-cap electrodes of a three-dimensional (3-D) quadrupole ion trap for as short as a millisecond to as long as hundreds of milliseconds are described. The implementation of dipolar DC does not compromise the ability to apply AC waveforms to the end-cap electrodes at other times in the experiment. Dipolar DC provides a nonresonant means for ion acceleration by displacing ions from the center of the ion trap where they experience stronger rf electric fields, which increases the extent of micro-motion. The evolution of the product ion spectrum to higher generation products with time, as shown using protonated leucine enkephalin as a model protonated peptide, illustrates the broad-band nature of the activation. Dipolar DC activation is also shown to be effective as an ion heating approach in mimicking high amplitude short time excitation (HASTE)/pulsed Q dissociation (PQD) resonance excitation experiments that are intended to enhance the likelihood for observing low m/z products in ion trap tandem mass spectrometry. PMID:21953251

Gas-liquid coexistence in a system of dipolar soft spheres.

PubMed

Jia, Ran; Braun, Heiko; Hentschke, Reinhard

2010-12-01

The existence of gas-liquid coexistence in dipolar fluids with no other contribution to attractive interaction than dipole-dipole interaction is a basic and open question in the theory of fluids. Here we compute the gas-liquid critical point in a system of dipolar soft spheres subject to an external electric field using molecular dynamics computer simulation. Tracking the critical point as the field strength is approaching zero we find the following limiting values: T(c)=0.063 and ρ(c)=0.0033 (dipole moment μ=1). These values are confirmed by independent simulation at zero field strength.

Ground-state candidate for the classical dipolar kagome Ising antiferromagnet

NASA Astrophysics Data System (ADS)

Chioar, I. A.; Rougemaille, N.; Canals, B.

2016-06-01

We have investigated the low-temperature thermodynamic properties of the classical dipolar kagome Ising antiferromagnet using Monte Carlo simulations, in the quest for the ground-state manifold. In spite of the limitations of a single-spin-flip approach, we managed to identify certain ordering patterns in the low-temperature regime and we propose a candidate for this unknown state. This configuration presents some intriguing features and is fully compatible with the extrapolations of the at-equilibrium thermodynamic behavior sampled so far, making it a very likely choice for the dipolar long-range ordered state of the classical kagome Ising antiferromagnet.

Cooling without contact in bilayer dipolar Fermi gases

NASA Astrophysics Data System (ADS)

Tanatar, Bilal; Renklioglu, Basak; Oktel, M. Ozgur

2016-05-01

We consider two parallel layers of dipolar ultracold Fermi gases at different temperatures and calculate the heat transfer between them. The effective interactions describing screening and correlation effects between the dipoles in a single layer are modelled within the Euler-Lagrange Fermi-hypernetted chain approximation. The random-phase approximation is employed for the interactions across the layers. We investigate the amount of transferred power between the layers as a function of the temperature difference. Energy transfer proceeds via the long-range dipole-dipole interactions. A simple thermal model is developed to investigate the feasibility of using the contactless sympathetic cooling of the ultracold polar atoms/molecules. Our calculations indicate that dipolar heat transfer is effective for typical polar molecule experiments and may be utilized as a cooling process. Supported by TUBA and TUBITAK (112T974).

Dipolarization Fronts from Reconnection Onset

NASA Astrophysics Data System (ADS)

Sitnov, M. I.; Swisdak, M. M.; Merkin, V. G.; Buzulukova, N.; Moore, T. E.

2012-12-01

Dipolarization fronts observed in the magnetotail are often viewed as signatures of bursty magnetic reconnection. However, until recently spontaneous reconnection was considered to be fully prohibited in the magnetotail geometry because of the linear stability of the ion tearing mode. Recent theoretical studies showed that spontaneous reconnection could be possible in the magnetotail geometries with the accumulation of magnetic flux at the tailward end of the thin current sheet, a distinctive feature of the magnetotail prior to substorm onset. That result was confirmed by open-boundary full-particle simulations of 2D current sheet equilibria, where two magnetotails were separated by an equilibrium X-line and weak external electric field was imposed to nudge the system toward the instability threshold. To investigate the roles of the equilibrium X-line, driving electric field and other parameters in the reconnection onset process we performed a set of 2D PIC runs with different initial settings. The investigated parameter space includes the critical current sheet thickness, flux tube volume per unit magnetic flux and the north-south component of the magnetic field. Such an investigation is critically important for the implementation of kinetic reconnection onset criteria into global MHD codes. The results are compared with Geotail visualization of the magnetotail during substorms, as well as Cluster and THEMIS observations of dipolarization fronts.

Nuclear magnetic relaxation by the dipolar EMOR mechanism: Multi-spin systems

NASA Astrophysics Data System (ADS)

Chang, Zhiwei; Halle, Bertil

2017-08-01

In aqueous systems with immobilized macromolecules, including biological tissues, the longitudinal spin relaxation of water protons is primarily induced by exchange-mediated orientational randomization (EMOR) of intra- and intermolecular magnetic dipole-dipole couplings. Starting from the stochastic Liouville equation, we have previously developed a rigorous EMOR relaxation theory for dipole-coupled two-spin and three-spin systems. Here, we extend the stochastic Liouville theory to four-spin systems and use these exact results as a guide for constructing an approximate multi-spin theory, valid for spin systems of arbitrary size. This so-called generalized stochastic Redfield equation (GSRE) theory includes the effects of longitudinal-transverse cross-mode relaxation, which gives rise to an inverted step in the relaxation dispersion profile, and coherent spin mode transfer among solid-like spins, which may be regarded as generalized spin diffusion. The GSRE theory is compared to an existing theory, based on the extended Solomon equations, which does not incorporate these phenomena. Relaxation dispersion profiles are computed from the GSRE theory for systems of up to 16 protons, taken from protein crystal structures. These profiles span the range from the motional narrowing limit, where the coherent mode transfer plays a major role, to the ultra-slow motion limit, where the zero-field rate is closely related to the strong-collision limit of the dipolar relaxation rate. Although a quantitative analysis of experimental data is beyond the scope of this work, it is clear from the magnitude of the predicted relaxation rate and the shape of the relaxation dispersion profile that the dipolar EMOR mechanism is the principal cause of water-1H low-field longitudinal relaxation in aqueous systems of immobilized macromolecules, including soft biological tissues. The relaxation theory developed here therefore provides a basis for molecular-level interpretation of endogenous soft

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.

Attraction between Opposing Planar Dipolar Polymer Brushes

DOE PAGES

Mahalik, J. P.; Sumpter, Bobby G.; Kumar, Rajeev

2017-08-01

In this paper, we use a field theory approach to study the effects of permanent dipoles on interpenetration and free energy changes as a function of distance between two identical planar polymer brushes. Melts (i.e., solvent-free) and solvated brushes made up of polymers grafted on nonadsorbing substrates are studied. In particular, the weak coupling limit of the dipolar interactions is considered, which leads to concentration-dependent pairwise interactions, and the effects of orientational order are neglected. It is predicted that a gradual increase in the dipole moment of the polymer segments can lead to attractive interactions between the brushes at intermediatemore » separation distances. Finally, because classical theory of polymer brushes based on the strong stretching limit (SSL) and the standard self-consistent field theory (SCFT) simulations using the Flory’s χ parameter always predicts repulsive interactions at all separations, our work highlights the importance of dipolar interactions in tailoring and accurately predicting forces between polar polymeric interfaces in contact with each other.« less

Solid-state NMR detection of 14N-13C dipolar couplings between amino acid side groups provides constraints on amyloid fibril architecture.

PubMed

Middleton, David A

2011-02-01

Solid-state nuclear magnetic resonance (SSNMR) is a powerful technique for the structural analysis of amyloid fibrils. With suitable isotope labelling patterns, SSNMR can provide constraints on the secondary structure, alignment and registration of β-strands within amyloid fibrils and identify the tertiary and quaternary contacts defining the packing of the β-sheet layers. Detection of (14)N-(13)C dipolar couplings may provide potentially useful additional structural constraints on β-sheet packing within amyloid fibrils but has not until now been exploited for this purpose. Here a frequency-selective, transfer of population in double resonance SSNMR experiment is used to detect a weak (14)N-(13)C dipolar coupling in amyloid-like fibrils of the peptide H(2)N-SNNFGAILSS-COOH, which was uniformly (13)C and (15)N labelled across the four C-terminal amino acids. The (14)N-(13)C interatomic distance between leucine and asparagine side groups is constrained between 2.4 and 3.8 Å, which allows current structural models of the β-spine arrangement within the fibrils to be refined. This procedure could be useful for the general structural analysis of other proteins in condensed phases and environments, such as biological membranes. Copyright © 2011 John Wiley & Sons, Ltd.

Electric Dipolar Kondo Effect Emerging from a Vibrating Magnetic Ion

NASA Astrophysics Data System (ADS)

Hotta, Takashi; Ueda, Kazuo

2012-06-01

When a magnetic ion vibrates in a metal, it inevitably introduces a new channel of hybridization with conduction electrons, and in general, the vibrating ion induces an electric dipole moment. In such a situation, we find that magnetic and nonmagnetic Kondo effects alternatively occur due to the screening of the spin moment and electric dipole moment of the vibrating ion. In particular, the electric dipolar two-channel Kondo effect is found to occur for a weak Coulomb interaction. We also show that a magnetically robust heavy-electron state appears near the fixed point of the electric dipolar two-channel Kondo effect. We believe that the vibrating magnetic ion opens a new door in Kondo physics.

Water saturation effects on elastic wave attenuation in porous rocks with aligned fractures

NASA Astrophysics Data System (ADS)

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

2014-05-01

Elastic wave attenuation anisotropy in porous rocks with aligned fractures is of interest to seismic remote sensing of the Earth's structure and to hydrocarbon reservoir characterization in particular. We investigated the effect of partial water saturation on attenuation in fractured rocks in the laboratory by conducting ultrasonic pulse-echo measurements on synthetic, silica-cemented, sandstones with aligned penny-shaped voids (fracture density of 0.0298 ± 0.0077), chosen to simulate the effect of natural fractures in the Earth according to theoretical models. Our results show, for the first time, contrasting variations in the attenuation (Q-1) of P and S waves with water saturation in samples with and without fractures. The observed Qs/Qp ratios are indicative of saturation state and the presence or absence of fractures, offering an important new possibility for remote fluid detection and characterization.

1,3-Dipolar Cycloadditions of Diazo Compounds in the Presence of Azides.

PubMed

Aronoff, Matthew R; Gold, Brian; Raines, Ronald T

2016-04-01

The diazo group has untapped utility in chemical biology. The tolerance of stabilized diazo groups to cellular metabolism is comparable to that of azido groups. However, chemoselectivity has been elusive, as both groups undergo 1,3-dipolar cycloadditions with strained alkynes. Removing strain and tuning dipolarophile electronics yields diazo group selective 1,3-dipolar cycloadditions that can be performed in the presence of an azido group. For example, diazoacetamide but not its azido congener react with dehydroalanine residues, as in the natural product nisin.

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

NASA Astrophysics Data System (ADS)

Hou, Guangjin; Lu, Xingyu; Vega, Alexander J.; Polenova, Tatyana

2014-09-01

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

Weyl Superfluidity in a Three-dimensional Dipolar Fermi Gas

NASA Astrophysics Data System (ADS)

Liu, Bo; Li, Xiaopeng; Yin, Lan; Liu, W. Vincent

2015-03-01

Weyl superconductivity or superfluidity, a fascinating topological state of matter, features novel phenomena such as emergent Weyl fermionic excitations and anomalies. Here we report that an anisotropic Weyl superfluid state can arise as a low temperature stable phase in a 3D dipolar Fermi gas. A crucial ingredient of our model is a direction-dependent two-body effective attraction generated by a rotating external field. Experimental signatures are predicted for cold gases in radio-frequency spectroscopy. The finite temperature phase diagram of this system is studied and the transition temperature of the Weyl superfluidity is found to be within the experimental scope for atomic dipolar Fermi gases. Work supported in part by U.S. ARO, AFOSR, DARPA-OLE-ARO, Charles E. Kaufman Foundation and The Pittsburgh Foundation, JQI-NSF-PFC, ARO-Atomtronics-MURI, and NSF of China.

The Plasma Sheet as Natural Symmetry Plane for Dipolarization Fronts in the Earth's Magnetotail

NASA Astrophysics Data System (ADS)

Frühauff, D.; Glassmeier, K.-H.

2017-11-01

In this work, observations of multispacecraft mission Time History of Events and Macroscale Interactions during Substorms are used for statistical investigation of dipolarization fronts in the near-Earth plasma sheet of the magnetotail. Using very stringent criteria, 460 events are detected in almost 10 years of mission data. Minimum variance analysis is used to determine the normal directions of the phase fronts, providing evidence for the existence of a natural symmetry of these phenomena, given by the neutral sheet of the magnetotail. This finding enables the definition of a local coordinate system based on the Tsyganenko model, reflecting the intrinsic orientation of the neutral sheet and, therefore, the dipolarization fronts. In this way, the comparison of events with very different background conditions is improved. Through this study, the statistical results of Liu, Angelopoulos, Runov, et al. (2013) are both confirmed and extended. In a case study, the knowledge of this plane of symmetry helps to explain the concave curvature of dipolarization fronts in the XZ plane through phase propagation speeds of magnetoacoustic waves. A second case study is presented to determine the central current system of a passing dipolarization front through a constellation of three spacecraft. With this information, a statistical analysis of spacecraft observations above and below the neutral sheet is used to provide further evidence for the neutral sheet as the symmetry plane and the central current system. Furthermore, it is shown that the signatures of dipolarization fronts are under certain conditions closely related to that of flux ropes, indicating a possible relationship between these two transient phenomena.

Overflow of a dipolar exciton trap at high magnetic fields

NASA Astrophysics Data System (ADS)

Dietl, Sebastian; Kowalik-Seidl, Katarzyna; Hammer, Lukas; Schuh, Dieter; Wegscheider, Werner; Holleitner, Alexander; Wurstbauer, Ursula

We study the photoluminescence of trapped dipolar excitons (IX) in coupled double GaAs quantum wells at low temperatures and high magnetic fields. A voltage-tunable electrode geometry controls the strength of the quantum confined Stark effect and defines the lateral trapping potential. Furthermore, it enhances the IX lifetime, enabling them to cool down to lattice temperature. We show that a magnetic field in Faraday configuration effectively prevents the escape of unbound photogenerated charge carriers from the trap area, thus increasing the density of dipolar excitons. For large magnetic fields, we observe an overflow of the IX trap and an effectively suppressed quantum confined Stark effect. We acknowledge financial support by the German Excellence Initiative via the Nanosystems Initiative Munich (NIM).

Stepwise π-extension of meso-alkylidenyl porphyrins through sequential 1,3-dipolar cycloaddition and redox reactions.

PubMed

Park, Dowoo; Jeong, Seung Doo; Ishida, Masatoshi; Lee, Chang-Hee

2014-08-25

Several regioselectively π-extended, pyrrole fused porphyrinoids have been synthesized by the 1,3-dipolar cycloaddition of meso-alkylidene-(benzi)porphyrins. Pd(II) complexes gave oxidation resistant, bis-pyrrole fused adducts. The repeated 1,3-dipolar cycloaddition followed by oxidation-reduction of pentaphyrin analogs afforded π-extended porphyrin analogs.

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

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

Hou, Guangjin, E-mail: hou@udel.edu, E-mail: tpolenov@udel.edu; Lu, Xingyu, E-mail: luxingyu@udel.edu, E-mail: lexvega@comcast.net; Vega, Alexander J., E-mail: luxingyu@udel.edu, E-mail: lexvega@comcast.net

2014-09-14

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

Conformational response of the phosphatidylcholine headgroup to bilayer surface charge: torsion angle constraints from dipolar and quadrupolar couplings in bicelles.

PubMed

Semchyschyn, Darlene J; Macdonald, Peter M

2004-02-01

The effects of bilayer surface charge on the conformation of the phosphocholine group of phosphatidylcholine were investigated using a torsion angle analysis of quadrupolar and dipolar splittings in, respectively, (2)H and (13)C NMR spectra of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) labelled in the phosphocholine group with either deuterons (POPC-alpha-d(2), POPC-beta-d(2) and POPC-gamma-d(9)) or carbon-13 (POPC-alpha-(13)C and POPC-alphabeta-(13)C(2)) and incorporated into magnetically aligned bicelles containing various amounts of either the cationic amphiphile 1,2-dimyristoyl-3-trimethylammoniumpropane (DMTAP) or the anionic amphiphile 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol (DMPG). Three sets of quadrupolar splittings, one from each of the three deuteron labelling positions, and three sets of dipolar splittings ((13)C(alpha)-(31)P, (13)C(alpha)-(13)C(beta), (13)C(beta)-(14)N), were measured at each surface charge, along with the (31)P residual chemical shift anisotropy. The torsion angle analysis assumed fast anisotropic rotation of POPC about its long molecular axis, thus projecting all NMR interactions onto that director axis of motion. Dipolar, quadrupolar and chemical shift anisotropies were calculated as a function of the phosphocholine internal torsion angles by first transforming into a common reference frame affixed to the phosphocholine group prior to motional averaging about the director axis. A comparison of experiment and calculation provided the two order parameters specifying the director orientation relative to the molecule, plus the torsion angles alpha(3), alpha(4) and alpha(5). Surface charge was found to have little effect on the torsion angle alpha(5) (rotations about C(alpha)-C(beta)), but to have large and inverse effects on torsion angles alpha(3) [rotations about P-O(11)] and alpha(4) [rotations about O(11)-C(alpha)], yielding a net upwards tilt of the P-N vector in the presence of cationic surface charge, and a

Assessing fit, interplay, and scale: Aligning governance and information for improved water management in a changing climate

NASA Astrophysics Data System (ADS)

Kirchhoff, C.; Dilling, L.

2011-12-01

Water managers have long experienced the challenges of managing water resources in a variable climate. However, climate change has the potential to reshape the experiential landscape by, for example, increasing the intensity and duration of droughts, shifting precipitation timing and amounts, and changing sea levels. Given the uncertainty in evaluating potential climate risks as well as future water availability and water demands, scholars suggest water managers employ more flexible and adaptive science-based management to manage uncertainty (NRC 2009). While such an approach is appropriate, for adaptive science-based management to be effective both governance and information must be concordant across three measures: fit, interplay and scale (Young 2002)(Note 1). Our research relies on interviews of state water managers and related experts (n=50) and documentary analysis in five U.S. states to understand the drivers and constraints to improving water resource planning and decision-making in a changing climate using an assessment of fit, interplay and scale as an evaluative framework. We apply this framework to assess and compare how water managers plan and respond to current or anticipated water resource challenges within each state. We hypothesize that better alignment between the data and management framework and the water resource problem improves water managers' facility to understand (via available, relevant, timely information) and respond appropriately (through institutional response mechanisms). In addition, better alignment between governance mechanisms (between the scope of the problem and identified appropriate responses) improves water management. Moreover, because many of the management challenges analyzed in this study concern present day issues with scarcity brought on by a combination of growth and drought, better alignment of fit, interplay, and scale today will enable and prepare water managers to be more successful in adapting to climate change

FORMATION AND ALIGNMENT OF ELONGATED, FRACTAL-LIKE WATER-ICE GRAINS IN EXTREMELY COLD, WEAKLY IONIZED PLASMA

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

Chai, Kil-Byoung; Bellan, Paul M., E-mail: kbchai@caltech.edu, E-mail: pbellan@caltech.edu

2015-04-01

Elongated, fractal-like water-ice grains are observed to form spontaneously when water vapor is injected into a weakly ionized laboratory plasma formed in a background gas cooled to an astrophysically relevant temperature. The water-ice grains form in 1–2 minutes, levitate with regular spacing, and are aligned parallel to the sheath electric field. Water-ice grains formed in plasma where the neutrals and ions have low mass, such as hydrogen and helium, are larger, more elongated, and more fractal-like than water-ice grains formed in plasmas where the neutrals and ions have high mass such as argon and krypton. Typical aspect ratios (length tomore » width ratio) are as great as 5 while typical fractal dimensions are ∼1.7. Water-ice grain lengths in plasmas with low neutral and ion masses can be several hundred microns long. Infrared absorption spectroscopy reveals that the water-ice grains are crystalline and so are similar in constitution to the water-ice grains in protoplanetary disks, Saturn’s rings, and mesospheric clouds. The properties and behavior of these laboratory water-ice grains may provide insights into morphology and alignment behavior of water-ice grains in astrophysical dusty plasmas.« less

Contrasting dynamics of electrons and protons in the near-Earth plasma sheet during dipolarization

NASA Astrophysics Data System (ADS)

Malykhin, Andrey Y.; Grigorenko, Elena E.; Kronberg, Elena A.; Koleva, Rositza; Ganushkina, Natalia Y.; Kozak, Ludmila; Daly, Patrick W.

2018-05-01

The fortunate location of Cluster and the THEMIS P3 probe in the near-Earth plasma sheet (PS) (at X ˜ -7-9 RE) allowed for the multipoint analysis of properties and spectra of electron and proton injections. The injections were observed during dipolarization and substorm current wedge formation associated with braking of multiple bursty bulk flows (BBFs). In the course of dipolarization, a gradual growth of the BZ magnetic field lasted ˜ 13 min and it was comprised of several BZ pulses or dipolarization fronts (DFs) with duration ≤ 1 min. Multipoint observations have shown that the beginning of the increase in suprathermal ( > 50 keV) electron fluxes - the injection boundary - was observed in the PS simultaneously with the dipolarization onset and it propagated dawnward along with the onset-related DF. The subsequent dynamics of the energetic electron flux was similar to the dynamics of the magnetic field during the dipolarization. Namely, a gradual linear growth of the electron flux occurred simultaneously with the gradual growth of the BZ field, and it was comprised of multiple short ( ˜ few minutes) electron injections associated with the BZ pulses. This behavior can be explained by the combined action of local betatron acceleration at the BZ pulses and subsequent gradient drifts of electrons in the flux pile up region through the numerous braking and diverting DFs. The nonadiabatic features occasionally observed in the electron spectra during the injections can be due to the electron interactions with high-frequency electromagnetic or electrostatic fluctuations transiently observed in the course of dipolarization. On the contrary, proton injections were detected only in the vicinity of the strongest BZ pulses. The front thickness of these pulses was less than a gyroradius of thermal protons that ensured the nonadiabatic acceleration of protons. Indeed, during the injections in the energy spectra of protons the pronounced bulge was clearly observed in a

Quantum Theory of Atoms in Molecules Charge-Charge Transfer-Dipolar Polarization Classification of Infrared Intensities.

PubMed

Duarte, Leonardo J; Richter, Wagner E; Silva, Arnaldo F; Bruns, Roy E

2017-10-26

Fundamental infrared vibrational transition intensities of gas-phase molecules are sensitive probes of changes in electronic structure accompanying small molecular distortions. Models containing charge, charge transfer, and dipolar polarization effects are necessary for a successful classification of the C-H, C-F, and C-Cl stretching and bending intensities. C-H stretching and in-plane bending vibrations involving sp 3 carbon atoms have small equilibrium charge contributions and are accurately modeled by the charge transfer-counterpolarization contribution and its interaction with equilibrium charge movement. Large C-F and C═O stretching intensities have dominant equilibrium charge movement contributions compared to their charge transfer-dipolar polarization ones and are accurately estimated by equilibrium charge and the interaction contribution. The C-F and C-Cl bending modes have charge and charge transfer-dipolar polarization contribution sums that are of similar size but opposite sign to their interaction values resulting in small intensities. Experimental in-plane C-H bends have small average intensities of 12.6 ± 10.4 km mol -1 owing to negligible charge contributions and charge transfer-counterpolarization cancellations, whereas their average out-of-plane experimental intensities are much larger, 65.7 ± 20.0 km mol -1 , as charge transfer is zero and only dipolar polarization takes place. The C-F bending intensities have large charge contributions but very small intensities. Their average experimental out-of-plane intensity of 9.9 ± 12.6 km mol -1 arises from the cancellation of large charge contributions by dipolar polarization contributions. The experimental average in-plane C-F bending intensity, 5.8 ± 7.3 km mol -1 , is also small owing to charge and charge transfer-counterpolarization sums being canceled by their interaction contributions. Models containing only atomic charges and their fluxes are incapable of describing electronic structure

Effect of magnetic dipolar interactions on temperature dependent magnetic hyperthermia in ferrofluids

NASA Astrophysics Data System (ADS)

Palihawadana-Arachchige, Maheshika; Nemala, Humeshkar; Naik, Vaman M.; Naik, Ratna

2017-01-01

Magnetic hyperthermia (MHT), where localized heating is generated when magnetic nanoparticles (MNPs) are subjected to a radiofrequency magnetic field, has a great potential as a non-invasive cancer therapy treatment. The efficiency of heat generation depends on the magnetic properties of MNPs, such as saturation magnetization (Ms) and magnetic anisotropy (K), as well as the particle size distribution and magnetic dipolar interactions. We have investigated MHT in two Fe3O4 ferrofluids prepared by co-precipitation (CP) and hydrothermal (HT) synthesis methods showing similar physical particle size distribution (14 ± 4 nm) and saturation magnetization (70 ± 2 emu/g of Fe3O4) but very different specific absorption rates (SAR) of ˜110 W/g and ˜40 W/g at room temperature (measured with an ac magnetic field amplitude of 240 Oe and a frequency of 375 kHz). This observed reduction in SAR has been explained by taking into account the dipolar interactions and the distribution of the magnetic core size of MNPs in ferrofluids. The HT ferrofluid shows a higher effective dipolar interaction and a wider distribution of the magnetic core size of MNPs compared to those of the CP ferrofluid. We have fitted the temperature dependent SAR data using the linear response theory, incorporating an effective dipolar interaction, to determine the magnetic anisotropy constant of MNPs prepared by CP (22 ± 2 kJ/m3) and HT (26 ± 2 kJ/m3) synthesis methods. These values are in good agreement with the magnetic anisotropy constant determined using frequency and temperature dependent magnetic susceptibility data obtained on powder samples.

Adimensional theory of shielding in ultracold collisions of dipolar rotors

NASA Astrophysics Data System (ADS)

González-Martínez, Maykel L.; Bohn, John L.; Quéméner, Goulven

2017-09-01

We investigate the electric field shielding of ultracold collisions of dipolar rotors, initially in their first rotational excited state, using an adimensional approach. We establish a map of good and bad candidates for efficient evaporative cooling based on this shielding mechanism, by presenting the ratio of elastic over quenching processes as a function of a rescaled rotational constant B ˜=B /sE3 and a rescaled electric field F ˜=d F /B . B ,d ,F ,andsE 3 are respectively the rotational constant, the full electric dipole moment of the molecules, the applied electric field, and a characteristic dipole-dipole energy. We identify two groups of bi-alkali-metal dipolar molecules. The first group, including RbCs, NaK, KCs, LiK, NaRb, LiRb, NaCs, and LiCs, is favorable with a ratio over 1000 at collision energies equal to (or even higher than) their characteristic dipolar energy. The second group, including LiNa and KRb, is not favorable. More generally, for molecules well described by Hund's case b, our adimensional study provides the conditions of efficient evaporative cooling. The range of appropriate rescaled rotational constant and rescaled field is approximately B ˜≥108 and 3.25 ≤F ˜≤3.8 , with a maximum ratio reached for F ˜≃3.4 for a given B ˜. We also discuss the importance of the electronic van der Waals interaction on the adimensional character of our study.

NMR dipolar constants of motion in liquid crystals: Jeener-Broekaert, double quantum coherence experiments and numerical calculation on a 10-spin cluster.

PubMed

Segnorile, H H; Bonin, C J; González, C E; Acosta, R H; Zamar, R C

2009-10-01

Two proton quasi-equilibrium states were previously observed in nematic liquid crystals, namely the S and W quasi-invariants. Even though the experimental evidence suggested that they originate in a partition of the spin dipolar energy into a strong and a weak part, respectively, from a theoretical viewpoint, the existence of an appropriate energy scale which allows such energy separation remains to be confirmed and a representation of the quasi-invariants is still to be given. We compare the dipolar NMR signals yielded both by the Jeener-Broekaert (JB) experiment as a function of the preparation time and the free evolution of the double quantum coherence (DQC) spectra excited from the S state, with numerical calculations carried out from first principles under different models for the dipolar quasi-invariants, in a 10-spin cluster which represents the 5CB (4(')-pentyl-4-biphenyl-carbonitrile) molecule. The calculated signals qualitatively agree with the experiments and the DQC spectra as a function of the single-quantum detection time are sensible enough to the different models to allow both to probe the physical nature of the initial dipolar-ordered state and to assign a subset of dipolar interactions to each constant of motion, which are compatible with the experiments. As a criterion for selecting a suitable quasi-equilibrium model of the 5CB molecule, we impose on the time evolution operator consistency with the occurrence of two dipolar quasi-invariants, that is, the calculated spectra must be unaffected by truncation of non-secular terms of the weaker dipolar energy. We find that defining the S quasi-invariant as the subset of the dipolar interactions of each proton with its two nearest neighbours yields a realistic characterization of the dipolar constants of motion in 5CB. We conclude that the proton-spin system of the 5CB molecule admits a partition of the dipolar energy into a bilinear strong and a multiple-spin weak contributions therefore providing two

Second Harmonic Generation Mediated by Aligned Water in Starch Granules.

PubMed

Cisek, Richard; Tokarz, Danielle; Krouglov, Serguei; Steup, Martin; Emes, Michael J; Tetlow, Ian J; Barzda, Virginijus

2014-12-26

The origin of second harmonic generation (SHG) in starch granules was investigated using ab initio quantum mechanical modeling and experimentally examined using polarization-in, polarization-out (PIPO) second harmonic generation microscopy. Ab initio calculations revealed that the largest contribution to the SHG signal from A- and B-type allomorphs of starch originates from the anisotropic organization of hydroxide and hydrogen bonds mediated by aligned water found in the polymers. The hypothesis was experimentally tested by imaging maize starch granules under various hydration and heat treatment conditions that alter the hydrogen bond network. The highest SHG intensity was found in fully hydrated starch granules, and heat treatment diminished the SHG intensity. The PIPO SHG imaging showed that dried starch granules have a much higher nonlinear optical susceptibility component ratio than fully hydrated granules. In contrast, deuterated starch granules showed a smaller susceptibility component ratio demonstrating that SHG is highly sensitive to the organization of the hydroxyl and hydrogen bond network. The polarization SHG imaging results of potato starch granules, representing starch allomorph B, were compared to those of maize starch granules representing allomorph A. The results showed that the amount of aligned water was higher in the maize granules. Nonlinear microscopy of starch granules provides evidence that varying hydration conditions leads to significant changes in the nonlinear susceptibility ratio as well as the SHG intensity, supporting the hypothesis from ab initio calculations that the dominant contribution to SHG is due to the ordered hydroxide and hydrogen bond network.

Arrays of dipolar molecular rotors in Tris(o-phenylenedioxy) cyclotriphosphazene.

PubMed

Zhao, Ke; Dron, Paul I; Kaleta, Jiří; Rogers, Charles T; Michl, Josef

2014-01-01

Regular two-dimensional or three-dimensional arrays of mutually interacting dipolar molecular rotors represent a worthy synthetic objective. Their dielectric properties, including possible collective behavior, will be a sensitive function of the location of the rotors, the orientation of their axes, and the size of their dipoles. Host-guest chemistry is one possible approach to gaining fine control over these factors. We describe the progress that has been achieved in recent years using tris (o-phenylenedioxy)cyclotriphosphazene as a host and a series of rod-shaped dipolar molecular rotors as guests. Structures of both surface and bulk inclusion compounds have been established primarily by solid-state nuclear magnetic resonance (NMR) and powder X-ray diffraction (XRD) techniques. Low-temperature dielectric spectroscopy revealed rotational barriers as low as 1.5 kcal/mol, but no definitive evidence for collective behavior has been obtained so far.

Coherent manipulation of dipolar coupled spins in an anisotropic environment

NASA Astrophysics Data System (ADS)

Baibekov, E. I.; Gafurov, M. R.; Zverev, D. G.; Kurkin, I. N.; Malkin, B. Z.; Barbara, B.

2014-11-01

We study coherent dynamics in a system of dipolar coupled spin qubits diluted in a solid and subjected to a driving microwave field. In the case of rare earth ions, an anisotropic crystal background results in anisotropic g tensor and thus modifies the dipolar coupling. We develop a microscopic theory of spin relaxation in a transient regime for the frequently encountered case of axially symmetric crystal field. The calculated decoherence rate is nonlinear in the Rabi frequency. We show that the direction of a static magnetic field that corresponds to the highest spin g factor is preferable in order to obtain a higher number of coherent qubit operations. The results of calculations are in excellent agreement with our experimental data on Rabi oscillations recorded for a series of CaW O4 crystals with different concentrations of N d3 + ions.

Cascade oxime formation, cyclization to a nitrone, and intermolecular dipolar cycloaddition.

PubMed

Furnival, Rachel C; Saruengkhanphasit, Rungroj; Holberry, Heather E; Shewring, Jonathan R; Guerrand, Hélène D S; Adams, Harry; Coldham, Iain

2016-11-22

Simple haloaldehydes, including enolisable aldehydes, were found to be suitable for the formation of cyclic products by cascade (domino) condensation, cyclisation, dipolar cycloaddition chemistry. This multi-component reaction approach to heterocyclic compounds was explored by using hydroxylamine, a selection of aldehydes, and a selection of activated dipolarophiles. Initial condensation gives intermediate oximes that undergo cyclisation with displacement of halide to give intermediate nitrones; these nitrones undergo in situ intermolecular dipolar cycloaddition reactions to give isoxazolidines. The cycloadducts from using dimethyl fumarate were treated with zinc/acetic acid to give lactam products and this provides an easy way to prepare pyrrolizinones, indolizinones, and pyrrolo[2,1-a]isoquinolinones. The chemistry is illustrated with a very short synthesis of the pyrrolizidine alkaloid macronecine and a formal synthesis of petasinecine.

The effect of bottom friction on tidal dipolar vortices and the associated transport

NASA Astrophysics Data System (ADS)

Duran-Matute, Matias; Kamp, Leon; van Heijst, Gertjan

2016-11-01

Tidal dipolar vortices can be formed in a semi-enclosed basin as the tides flow in and out through an inlet. If they are strong enough to overcome the opposing tidal currents, these vortices can travel away from the inlet due to their self-propelling mechanism, and hence, act as an efficient transport agent for suspended material. We present results of two-dimensional numerical simulations of the flow through an idealized tidal inlet, with either a linear or a nonlinear parameterization of the bottom friction. We then quantify the effect of the bottom friction on the propagation of the dipolar vortex and on its ability as a transport agent by computing the flushing and residence times of passive particles. Bottom friction is detrimental to the ability of tidal dipolar vortices to propagate and hinders transport away from the inlet. The magnitude of this effect is related to the relative duration of the tidal period as compared to the typical decay time scale of the vortex dipole. This research is funded by NWO (the Netherlands) through the VENI Grant 863.13.022.

Monte Carlo simulations of kagome lattices with magnetic dipolar interactions

NASA Astrophysics Data System (ADS)

Plumer, Martin; Holden, Mark; Way, Andrew; Saika-Voivod, Ivan; Southern, Byron

Monte Carlo simulations of classical spins on the two-dimensional kagome lattice with only dipolar interactions are presented. In addition to revealing the sixfold-degenerate ground state, the nature of the finite-temperature phase transition to long-range magnetic order is discussed. Low-temperature states consisting of mixtures of degenerate ground-state configurations separated by domain walls can be explained as a result of competing exchange-like and shape-anisotropy-like terms in the dipolar coupling. Fluctuations between pairs of degenerate spin configurations are found to persist well into the ordered state as the temperature is lowered until locking in to a low-energy state. Results suggest that the system undergoes a continuous phase transition at T ~ 0 . 43 in agreement with previous MC simulations but the nature of the ordering process differs. Preliminary results which extend this analysis to the 3D fcc ABC-stacked kagome systems will be presented.

Geometric stability spectra of dipolar Bose gases in tunable optical lattices

NASA Astrophysics Data System (ADS)

Corson, John P.; Wilson, Ryan M.; Bohn, John L.

2013-07-01

We examine the stability of quasi-two-dimensional dipolar Bose-Einstein condensates in the presence of weak optical lattices of various geometries. We find that when the condensate possesses a roton-maxon quasiparticle dispersion, the conditions for stability exhibit a strong dependence both on the lattice geometry and the polarization tilt. This results in rich structures in the system's stability diagram akin to spectroscopic signatures. We show how these structures originate from the mode matching of rotons to the perturbing lattice. In the case of a one-dimensional lattice, some of the features emerge only when the polarization axis is tilted into the plane of the condensate. Our results suggest that the stability diagram may be used as a novel means to spectroscopically measure rotons in dipolar condensates.

Off-equatorial current-driven instabilities ahead of approaching dipolarization fronts

NASA Astrophysics Data System (ADS)

Zhang, Xu; Angelopoulos, V.; Pritchett, P. L.; Liu, Jiang

2017-05-01

Recent kinetic simulations have revealed that electromagnetic instabilities near the ion gyrofrequency and slightly away from the equatorial plane can be driven by a current parallel to the magnetic field prior to the arrival of dipolarization fronts. Such instabilities are important because of their potential contribution to global electromagnetic energy conversion near dipolarization fronts. Of the several instabilities that may be consistent with such waves, the most notable are the current-driven electromagnetic ion cyclotron instability and the current-driven kink-like instability. To confirm the existence and characteristics of these instabilities, we used observations by two Time History of Events and Macroscale Interactions during Substorms satellites, one near the neutral sheet observing dipolarization fronts and the other at the boundary layer observing precursor waves and currents. We found that such instabilities with monochromatic signatures are rare, but one of the few cases was selected for further study. Two different instabilities, one at about 0.3 Hz and the other at a much lower frequency, 0.02 Hz, were seen in the data from the off-equatorial spacecraft. A parallel current attributed to an electron beam coexisted with the waves. Our instability analysis attributes the higher-frequency instability to a current-driven ion cyclotron instability and the lower frequency instability to a kink-like instability. The current-driven kink-like instability we observed is consistent with the instabilities observed in the simulation. We suggest that the currents needed to excite these low-frequency instabilities are so intense that the associated electron beams are easily thermalized and hence difficult to observe.

Synthesis of Trifluoromethylated Isoxazolidines: 1,3-Dipolar Cycloaddition of Nitrosoarenes, (Trifluoromethyl)diazomethane, and Alkenes

PubMed Central

Molander, Gary A.; Cavalcanti, Livia N.

2013-01-01

Isoxazolidines have proven to be important substrates in synthetic organic chemistry. Limited examples in the literature that provide trifluoromethylated versions of these compounds have prompted us to investigate a 1,3-dipolar cycloaddition route providing access to N-functionalized isoxazolidines containing a trifluoromethyl group. Thus, a 1,3-dipolar cycloaddition of nitrosoarenes, (trifluoromethyl)diazomethane, and alkenes was developed. The starting materials can be synthesized from easy to handle and accessible reagents. The reaction proved to be tolerant of a variety of electron-deficient alkenes and nitrosoarenes. PMID:24490778

Magnetic Field Dipolarization and Its Associated Ion Flux Variations in the Inner Magnetosphere: Simultaneous Observations by Arase and Michibiki Satellites

NASA Astrophysics Data System (ADS)

Nose, M.; Matsuoka, A.; Kasahara, S.; Yokota, S.; Higashio, N.; Koshiishi, H.; Imajo, S.; Teramoto, M.; Nomura, R.; Fujimoto, A.; Keika, K.; Tanaka, Y.; Shinohara, M.; Shinohara, I.; Yoshizumi, M.

2017-12-01

Recent satellite observations by MDS-1 and Van Allen Probes statistically revealed that magnetic field dipolarization can be detected over a wide range of L in the deep inner magnetosphere (i.e., L = 3.5-6.5, which is far inside the geosynchronous altitude). It is accompanied by magnetic field fluctuations having a characteristic timescale of a few to 10 s, which is comparable to the local gyroperiod of O+ ions. These magnetic field fluctuations are considered to cause nonadiabatic local acceleration of ions. In this study, we intend to confirm the above-mentioned characteristics of magnetic field dipolarization in the inner magnetosphere, using the magnetic field data and the energetic ion flux data measured by the Exploration of energization and Radiation in Geospace (ERG) "Arase" satellite. The Arase satellite was launched on December 20, 2016 into an elliptical orbit having an apogee of 6.0 Re, a perigee of 440 km altitude, an orbital period of 9.5 h, and an orbital inclination of 32 degrees. During the first magnetic storm of March 27, 2017 after Arase started scientific operation, Arase observes clear dipolarization signatures around 1500 UT at L 4.6 and MLT 5.7 hr. Strong magnetic field fluctuations are embedded in the magnetic field dipolarization and their characteristic frequency is close to the local gyrofrequency of O+ ions. Both H+ and O+ flux enhancements are observed in accordance with the dipolarization. These results are consistent with the previous results. In this event, the Quasi-Zenith Satellite (QZS)-1 "Michibiki" satellite was located at L 7.0 and MLT 23.8 hr, and observes similar dipolarization signatures with a few minute time difference. Simultaneous observations by both Arase and Michibiki provides us a unique opportunity to investigate how fast and wide the dipolarization propagates in the inner magnetosphere. In the presentation, we will show detailed analysis results of the dipolarization event on March 27, 2017 as well as similar

Tuning dipolar magnetic interactions by controlling individual silica coating of iron oxide nanoparticles

NASA Astrophysics Data System (ADS)

Rivas Rojas, P. C.; Tancredi, P.; Moscoso Londoño, O.; Knobel, M.; Socolovsky, L. M.

2018-04-01

Single and fixed size core, core-shell nanoparticles of iron oxides coated with a silica layer of tunable thickness were prepared by chemical routes, aiming to generate a frame of study of magnetic nanoparticles with controlled dipolar interactions. The batch of iron oxides nanoparticles of 4.5 nm radii, were employed as cores for all the coated samples. The latter was obtained via thermal decomposition of organic precursors, resulting on nanoparticles covered with an organic layer that was subsequently used to promote the ligand exchange in the inverse microemulsion process, employed to coat each nanoparticle with silica. The amount of precursor and times of reaction was varied to obtain different silica shell thicknesses, ranging from 0.5 nm to 19 nm. The formation of the desired structures was corroborated by TEM and SAXS measurements, the core single-phase spinel structure was confirmed by XRD, and superparamagnetic features with gradual change related to dipolar interaction effects were obtained by the study of the applied field and temperature dependence of the magnetization. To illustrate that dipolar interactions are consistently controlled, the main magnetic properties are presented and analyzed as a function of center to center minimum distance between the magnetic cores.

NMR Detection Using Laser-Polarized Xenon as a DipolarSensor

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

Granwehr, Josef; Urban, Jeffry T.; Trabesinger, Andreas H.

2005-02-28

Hyperpolarized Xe-129 can be used as a sensor to indirectly detect NMR spectra of heteronuclei that are neither covalently bound nor necessarily in direct contact with the Xe atoms, but coupled through long-range intermolecular dipolar couplings. In order to reintroduce long-range dipolar couplings the sample symmetry has to be broken. This can be done either by an asymmetric sample arrangement, or by breaking the symmetry of the spin magnetization with field gradient pulses. Experiments are performed where only a small fraction of the available Xe-129 magnetization is used for each point, so that a single batch of xenon suffices formore » the point-by-point acquisition of a heteronuclear NMR spectrum. Examples with H-1 as analyte nucleus show that these methods have the potential to obtain spectra with a resolution that is high enough to determine homonuclear J couplings. The applicability of this technique with remote detection is discussed.« less

A novel dipolar dephasing method for the slow magic angle turning experiment.

PubMed

Hu, J Z; Taylor, C M; Pugmire, R J; Grant, D M

2001-09-01

Complete suppression of the resonances from protonated carbons in a slow magic angle spinning experiment can be achieved using five dipolar dephasing (Five-DD) periods distributed in one rotor period. This produces a spectrum containing only the spinning sidebands (SSB) from the nonprotonated carbons. It is shown that the SSB patterns corresponding to the nonprotonated carbons are not distorted over a wide range of dipolar dephasing times. Hence, this method can be used to obtain reliable principal values of the chemical shift tensors for each nonprotonated carbon. The Five-DD method can be readily incorporated into isotropic-anisotropic 2D experiments such as FIREMAT and 2D-PASS to facilitate the measurement of the (13)C chemical shift tensors in complex systems. Copyright 2001 Academic Press.

Aligning nanodiscs at the air-water interface, a neutron reflectivity study.

PubMed

Wadsäter, Maria; Simonsen, Jens B; Lauridsen, Torsten; Tveten, Erlend Grytli; Naur, Peter; Bjørnholm, Thomas; Wacklin, Hanna; Mortensen, Kell; Arleth, Lise; Feidenhans'l, Robert; Cárdenas, Marité

2011-12-20

Nanodiscs are self-assembled nanostructures composed of a belt protein and a small patch of lipid bilayer, which can solubilize membrane proteins in a lipid bilayer environment. We present a method for the alignment of a well-defined two-dimensional layer of nanodiscs at the air-water interface by careful design of an insoluble surfactant monolayer at the surface. We used neutron reflectivity to demonstrate the feasibility of this approach and to elucidate the structure of the nanodisc layer. The proof of concept is hereby presented with the use of nanodiscs composed of a mixture of two different lipid (DMPC and DMPG) types to obtain a net overall negative charge of the nanodiscs. We find that the nanodisc layer has a thickness or 40.9 ± 2.6 Å with a surface coverage of 66 ± 4%. This layer is located about 15 Å below a cationic surfactant layer at the air-water interface. The high level of organization within the nanodiscs layer is reflected by a low interfacial roughness (~4.5 Å) found. The use of the nanodisc as a biomimetic model of the cell membrane allows for studies of single membrane proteins isolated in a confined lipid environment. The 2D alignment of nanodiscs could therefore enable studies of high-density layers containing membrane proteins that, in contrast to membrane proteins reconstituted in a continuous lipid bilayer, remain isolated from influences of neighboring membrane proteins within the layer. © 2011 American Chemical Society

Diazo Compounds as Highly Tunable Reactants in 1,3-Dipolar Cycloaddition Reactions with Cycloalkynes†

PubMed Central

McGrath, Nicholas A.

2012-01-01

Diazo compounds, which can be accessed directly from azides by deimidogenation, are shown to be extremely versatile dipoles in 1,3-dipolar cycloaddition reactions with a cyclooctyne. The reactivity of a diazo compound can be much greater or much less than its azide analog, and is enhanced markedly in polar-protic solvents. These reactivities are predictable from frontier molecular orbital energies. The most reactive diazo compound exhibited the highest known second-order rate constant to date for a dipolar cycloaddition with a cycloalkyne. These data provide a new modality for effecting chemoselective reactions in a biological context. PMID:23227302

Temperature Dependence of the Thermal Conductivity of a Trapped Dipolar Bose-Condensed Gas

NASA Astrophysics Data System (ADS)

Yavari, H.

2018-02-01

The thermal conductivity of a trapped dipolar Bose condensed gas is calculated as a function of temperature in the framework of linear response theory. The contributions of the interactions between condensed and noncondensed atoms and between noncondensed atoms in the presence of both contact and dipole-dipole interactions are taken into account to the thermal relaxation time, by evaluating the self-energies of the system in the Beliaev approximation. We will show that above the Bose-Einstein condensation temperature ( T > T BEC ) in the absence of dipole-dipole interaction, the temperature dependence of the thermal conductivity reduces to that of an ideal Bose gas. In a trapped Bose-condensed gas for temperature interval k B T << n 0 g B , E p << k B T ( n 0 is the condensed density and g B is the strength of the contact interaction), the relaxation rates due to dipolar and contact interactions between condensed and noncondensed atoms change as {τ}_{dd12}^{-1}∝ {e}^{-E/{k}_BT} and τ c12 ∝ T -5, respectively, and the contact interaction plays the dominant role in the temperature dependence of the thermal conductivity, which leads to the T -3 behavior of the thermal conductivity. In the low-temperature limit, k B T << n 0 g B , E p >> k B T, since the relaxation rate {τ}_{c12}^{-1} is independent of temperature and the relaxation rate due to dipolar interaction goes to zero exponentially, the T 2 temperature behavior for the thermal conductivity comes from the thermal mean velocity of the particles. We will also show that in the high-temperature limit ( k B T > n 0 g B ) and low momenta, the relaxation rates {τ}_{c12}^{-1} and {τ}_{dd12}^{-1} change linearly with temperature for both dipolar and contact interactions and the thermal conductivity scales linearly with temperature.

Quantitative ionization chamber alignment to a water surface: Theory and simulation.

PubMed

Siebers, Jeffrey V; Ververs, James D; Tessier, Frédéric

2017-07-01

To examine the response properties of cylindrical cavity ionization chambers (ICs) in the depth-ionization buildup region so as to obtain a robust chamber-signal - based method for definitive water surface identification, hence absolute ionization chamber depth localization. An analytical model with simplistic physics and geometry is developed to explore the theoretical aspects of ionization chamber response near a phantom water surface. Monte Carlo simulations with full physics and ionization chamber geometry are utilized to extend the model's findings to realistic ion chambers in realistic beams and to study the effects of IC design parameters on the entrance dose response. Design parameters studied include full and simplified IC designs with varying central electrode thickness, wall thickness, and outer chamber radius. Piecewise continuous fits to the depth-ionization signal gradient are used to quantify potential deviation of the gradient discontinuity from the chamber outer radius. Exponential, power, and hyperbolic sine functional forms are used to model the gradient for chamber depths of zero to the depth of the gradient discontinuity. The depth-ionization gradient as a function of depth is maximized and discontinuous when a submerged IC's outer radius coincides with the water surface. We term this depth the gradient chamber alignment point (gCAP). The maximum deviation between the gCAP location and the chamber outer radius is 0.13 mm for a hypothetical 4 mm thick wall, 6.45 mm outer radius chamber using the power function fit, however, the chamber outer radius is within the 95% confidence interval of the gCAP determined by this fit. gCAP dependence on the chamber wall thickness is possible, but not at a clinically relevant level. The depth-ionization gradient has a discontinuity and is maximized when the outer-radius of a submerged IC coincides with the water surface. This feature can be used to auto-align ICs to the water surface at the time of scanning

Transfer of dipolar gas through the discrete localized mode.

PubMed

Bai, Xiao-Dong; Zhang, Ai-Xia; Xue, Ju-Kui

2013-12-01

By considering the discrete nonlinear Schrödinger model with dipole-dipole interactions for dipolar condensate, the existence, the types, the stability, and the dynamics of the localized modes in a nonlinear lattice are discussed. It is found that the contact interaction and the dipole-dipole interactions play important roles in determining the existence, the type, and the stability of the localized modes. Because of the coupled effects of the contact interaction and the dipole-dipole interactions, rich localized modes and their stability nature can exist: when the contact interaction is larger and the dipole-dipole interactions is smaller, a discrete bright breather occurs. In this case, while the on-site interaction can stabilize the discrete breather, the dipole-dipole interactions will destabilize the discrete breather; when both the contact interaction and the dipole-dipole interactions are larger, a discrete kink appears. In this case, both the on-site interaction and the dipole-dipole interactions can stabilize the discrete kink, but the discrete kink is more unstable than the ordinary discrete breather. The predicted results provide a deep insight into the dynamics of blocking, filtering, and transfer of the norm in nonlinear lattices for dipolar condensates.

Columnar domains and anisotropic growth laws in dipolar systems.

PubMed

Bupathy, Arunkumar; Banerjee, Varsha; Puri, Sanjay

2017-06-01

Magnetic and dielectric solids are well-represented by the Ising model with dipolar interactions (IM+DI). The latter are long-ranged, fluctuating in sign, and anisotropic. Equilibrium studies have revealed novel consequences of these complicated interactions, but their effect on nonequilibrium behavior is not explored. We perform a deep temperature quench to study the kinetics of domain growth in the d=3 IM+DI. Our main observations are (i) the emergence of columnar domains along the z axis (Ising axis) with a transient periodicity in the xy plane; (ii) anisotropic growth laws: ℓ_{ρ}(t)∼t^{ϕ}; ℓ_{z}(t)∼t^{ψ}, where ρ[over ⃗]=(x,y) and ℓ is the characteristic length scale; (iii) generalized dynamical scaling for the correlation function: C(ρ,z;t)=g(ρ/ℓ_{ρ},z/ℓ_{z}); and (iv) an asymptotic Porod tail in the corresponding structure factor: S(k_{ρ},0;t)∼k_{ρ}^{-3}; S(0,k_{z};t)∼k_{z}^{-2}. Our results explain the experimentally observed columnar morphologies in a wide range of dipolar systems, and they have important technological implications.

Nuclear reactor alignment plate configuration

DOEpatents

Altman, David A; Forsyth, David R; Smith, Richard E; Singleton, Norman R

2014-01-28

An alignment plate that is attached to a core barrel of a pressurized water reactor and fits within slots within a top plate of a lower core shroud and upper core plate to maintain lateral alignment of the reactor internals. The alignment plate is connected to the core barrel through two vertically-spaced dowel pins that extend from the outside surface of the core barrel through a reinforcement pad and into corresponding holes in the alignment plate. Additionally, threaded fasteners are inserted around the perimeter of the reinforcement pad and into the alignment plate to further secure the alignment plate to the core barrel. A fillet weld also is deposited around the perimeter of the reinforcement pad. To accomodate thermal growth between the alignment plate and the core barrel, a gap is left above, below and at both sides of one of the dowel pins in the alignment plate holes through with the dowel pins pass.

Refocused continuous-wave decoupling: a new approach to heteronuclear dipolar decoupling in solid-state NMR spectroscopy.

PubMed

Vinther, Joachim M; Nielsen, Anders B; Bjerring, Morten; van Eck, Ernst R H; Kentgens, Arno P M; Khaneja, Navin; Nielsen, Niels Chr

2012-12-07

A novel strategy for heteronuclear dipolar decoupling in magic-angle spinning solid-state nuclear magnetic resonance (NMR) spectroscopy is presented, which eliminates residual static high-order terms in the effective Hamiltonian originating from interactions between oscillating dipolar and anisotropic shielding tensors. The method, called refocused continuous-wave (rCW) decoupling, is systematically established by interleaving continuous wave decoupling with appropriately inserted rotor-synchronized high-power π refocusing pulses of alternating phases. The effect of the refocusing pulses in eliminating residual effects from dipolar coupling in heteronuclear spin systems is rationalized by effective Hamiltonian calculations to third order. In some variants the π pulse refocusing is supplemented by insertion of rotor-synchronized π/2 purging pulses to further reduce the residual dipolar coupling effects. Five different rCW decoupling sequences are presented and their performance is compared to state-of-the-art decoupling methods. The rCW decoupling sequences benefit from extreme broadbandedness, tolerance towards rf inhomogeneity, and improved potential for decoupling at relatively low average rf field strengths. In numerical simulations, the rCW schemes clearly reveal superior characteristics relative to the best decoupling schemes presented so far, which we to some extent also are capable of demonstrating experimentally. A major advantage of the rCW decoupling methods is that they are easy to set up and optimize experimentally.

Quantum spin ices and magnetic states from dipolar-octupolar doublets on the pyrochlore lattice

NASA Astrophysics Data System (ADS)

Chen, Gang

We consider a class of electron systems in which dipolar-octupolar Kramers doublets arise on the pyrochlore lattice. In the localized limit, the Kramers doublets are described by the effective spin 1/2 pseudospins. The most general nearest-neighbor exchange model between these pseudospins is the XYZ model. In additional to dipolar ordered and octupolar ordered magnetic states, we show that this XYZ model exhibits two distinct quantum spin ice (QSI) phases, that we dub dipolar QSI and octupolar QSI. These two QSIs are distinct symmetry enriched U(1) quantum spin liquids, enriched by the lattice symmetry. Moreover, the XYZ model is absent from the notorious sign problem for a quantum Monte Carlo simulation in a large parameter space. We discuss the potential relevance to real material systems such as Dy2Ti2O7, Nd2Zr2O7, Nd2Hf2O7, Nd2Ir2O7, Nd2Sn2O7 and Ce2Sn2O7. chggst@gmail.com, Refs: Y-P Huang, G Chen, M Hermele, Phys. Rev. Lett. 112, 167203 (2014).

Branching points in the low-temperature dipolar hard sphere fluid

NASA Astrophysics Data System (ADS)

Rovigatti, Lorenzo; Kantorovich, Sofia; Ivanov, Alexey O.; Tavares, José Maria; Sciortino, Francesco

2013-10-01

In this contribution, we investigate the low-temperature, low-density behaviour of dipolar hard-sphere (DHS) particles, i.e., hard spheres with dipoles embedded in their centre. We aim at describing the DHS fluid in terms of a network of chains and rings (the fundamental clusters) held together by branching points (defects) of different nature. We first introduce a systematic way of classifying inter-cluster connections according to their topology, and then employ this classification to analyse the geometric and thermodynamic properties of each class of defects, as extracted from state-of-the-art equilibrium Monte Carlo simulations. By computing the average density and energetic cost of each defect class, we find that the relevant contribution to inter-cluster interactions is indeed provided by (rare) three-way junctions and by four-way junctions arising from parallel or anti-parallel locally linear aggregates. All other (numerous) defects are either intra-cluster or associated to low cluster-cluster interaction energies, suggesting that these defects do not play a significant part in the thermodynamic description of the self-assembly processes of dipolar hard spheres.

Nuclear magnetic resonance signal dynamics of liquids in the presence of distant dipolar fields, revisited

PubMed Central

Barros, Wilson; Gochberg, Daniel F.; Gore, John C.

2009-01-01

The description of the nuclear magnetic resonance magnetization dynamics in the presence of long-range dipolar interactions, which is based upon approximate solutions of Bloch–Torrey equations including the effect of a distant dipolar field, has been revisited. New experiments show that approximate analytic solutions have a broader regime of validity as well as dependencies on pulse-sequence parameters that seem to have been overlooked. In order to explain these experimental results, we developed a new method consisting of calculating the magnetization via an iterative formalism where both diffusion and distant dipolar field contributions are treated as integral operators incorporated into the Bloch–Torrey equations. The solution can be organized as a perturbative series, whereby access to higher order terms allows one to set better boundaries on validity regimes for analytic first-order approximations. Finally, the method legitimizes the use of simple analytic first-order approximations under less demanding experimental conditions, it predicts new pulse-sequence parameter dependencies for the range of validity, and clarifies weak points in previous calculations. PMID:19425789

Decreasing Distortion Energies without Strain: Diazo-Selective 1,3-Dipolar Cycloadditions.

PubMed

Gold, Brian; Aronoff, Matthew R; Raines, Ronald T

2016-07-15

The diazo group has attributes that complement those of the azido group for applications in chemical biology. Here, we use computational analyses to provide insights into the chemoselectivity of the diazo group in 1,3-dipolar cycloadditions. Dipole distortion energies are responsible for ∼80% of the overall energetic barrier for these reactions. Here, we show that diazo compounds, unlike azides, provide an opportunity to decrease that barrier substantially without introducing strain into the dipolarophile. The ensuing rate enhancement is due to the greater nucleophilic character of a diazo group compared to that of an azido group, which can accommodate decreased distortion energies without predistortion. The tuning of distortion energies with substituents in a diazo compound or dipolarophile can enhance reactivity and selectivity in a predictable manner. Notably, these advantages of diazo groups are amplified in water. Our findings provide a theoretical framework that can guide the design and application of both diazo compounds and azides in "orthogonal" contexts, especially for biological investigations.

Finite-size corrections in simulation of dipolar fluids

NASA Astrophysics Data System (ADS)

Belloni, Luc; Puibasset, Joël

2017-12-01

Monte Carlo simulations of dipolar fluids are performed at different numbers of particles N = 100-4000. For each size of the cubic cell, the non-spherically symmetric pair distribution function g(r,Ω) is accumulated in terms of projections gmnl(r) onto rotational invariants. The observed N dependence is in very good agreement with the theoretical predictions for the finite-size corrections of different origins: the explicit corrections due to the absence of fluctuations in the number of particles within the canonical simulation and the implicit corrections due to the coupling between the environment around a given particle and that around its images in the neighboring cells. The latter dominates in fluids of strong dipolar coupling characterized by low compressibility and high dielectric constant. The ability to clean with great precision the simulation data from these corrections combined with the use of very powerful anisotropic integral equation techniques means that exact correlation functions both in real and Fourier spaces, Kirkwood-Buff integrals, and bridge functions can be derived from box sizes as small as N ≈ 100, even with existing long-range tails. In the presence of dielectric discontinuity with the external medium surrounding the central box and its replica within the Ewald treatment of the Coulombic interactions, the 1/N dependence of the gmnl(r) is shown to disagree with the, yet well-accepted, prediction of the literature.

Quasi-parallel whistler mode waves observed by THEMIS during near-earth dipolarizations

NASA Astrophysics Data System (ADS)

Le Contel, O.; Roux, A.; Jacquey, C.; Robert, P.; Berthomier, M.; Chust, T.; Grison, B.; Angelopoulos, V.; Sibeck, D.; Chaston, C. C.; Cully, C. M.; Ergun, B.; Glassmeier, K.-H.; Auster, U.; McFadden, J.; Carlson, C.; Larson, D.; Bonnell, J. W.; Mende, S.; Russell, C. T.; Donovan, E.; Mann, I.; Singer, H.

2009-06-01

We report on quasi-parallel whistler emissions detected by the near-earth satellites of the THEMIS mission before, during, and after local dipolarization. These emissions are associated with an electron temperature anisotropy α=T⊥e/T||e>1 consistent with the linear theory of whistler mode anisotropy instability. When the whistler mode emissions are observed the measured electron anisotropy varies inversely with β||e (the ratio of the electron parallel pressure to the magnetic pressure) as predicted by Gary and Wang (1996). Narrow band whistler emissions correspond to the small α existing before dipolarization whereas the broad band emissions correspond to large α observed during and after dipolarization. The energy in the whistler mode is leaving the current sheet and is propagating along the background magnetic field, towards the Earth. A simple time-independent description based on the Liouville's theorem indicates that the electron temperature anisotropy decreases with the distance along the magnetic field from the equator. Once this variation of α is taken into account, the linear theory predicts an equatorial origin for the whistler mode. The linear theory is also consistent with the observed bandwidth of wave emissions. Yet, the anisotropy required to be fully consistent with the observations is somewhat larger than the measured one. Although the discrepancy remains within the instrumental error bars, this could be due to time-dependent effects which have been neglected. The possible role of the whistler waves in the substorm process is discussed.

Influence of dipolar interactions on the angular-dependent coercivity of nickel nanocylinders

NASA Astrophysics Data System (ADS)

Bender, P.; Krämer, F.; Tschöpe, A.; Birringer, R.

2015-04-01

In this study the influence of dipolar interactions on the orientation-dependent magnetization behavior of an ensemble of single-domain nickel nanorods was investigated. The rods were synthesized by electrodeposition of nickel into porous alumina templates. Some of the rods were released from the oxide and embedded in gelatine hydrogels (ferrogel) at a sufficiently large average interparticle distance to suppress dipolar interactions. By comparing the orientation-dependent hystereses of the two ensembles in the template and the gel-matrix it could be shown that the dipolar interactions in the template considerably alter the functional form of the angular-dependent coercivity. Analysis of the magnetization curves for an angle of 60° between the rod-axes and the field revealed a significantly reduced coercivity of the template compared to the ferrogel, which could be directly attributed to a stray field induced magnetization reversal of a steadily increasing number of rods with increasing field strength. The magnetization curve of the template could be approximated by a weighted linear superposition of the hysteresis branches of the ferrogel. The magnetization reversal process of the rods was investigated by analyzing the angular-dependent coercivity of the non-interacting nanorods. Comparison of the functional form with analytical models and micromagnetic simulations emphasized the assumption of a localized magnetization reversal. Additionally, it could be shown that the nucleation field of rods with diameters in the range 18-29 nm tends to increase with increasing diameter.

Absence of Long-Range Order in a Triangular Spin System with Dipolar Interactions

NASA Astrophysics Data System (ADS)

Keleş, Ahmet; Zhao, Erhai

2018-05-01

The antiferromagnetic Heisenberg model on the triangular lattice is perhaps the best known example of frustrated magnets, but it orders at low temperatures. Recent density matrix renormalization group (DMRG) calculations find that the next nearest neighbor interaction J2 enhances the frustration, and it leads to a spin liquid for J2/J1∈(0.08 ,0.15 ). In addition, a DMRG study of a dipolar Heisenberg model with longer range interactions gives evidence for a spin liquid at a small dipole tilting angle θ ∈[0 ,1 0 ° ). In both cases, the putative spin liquid region appears to be small. Here, we show that for the triangular lattice dipolar Heisenberg model, a robust quantum paramagnetic phase exists in a surprisingly wide region, θ ∈[0 ,5 4 ° ) , for dipoles tilted along the lattice diagonal direction. We obtain the phase diagram of the model by functional renormalization group (RG), which treats all magnetic instabilities on equal footing. The quantum paramagnetic phase is characterized by a smooth continuous flow of vertex functions and spin susceptibility down to the lowest RG scale, in contrast to the apparent breakdown of RG flow in phases with stripe or spiral order. Our finding points to a promising direction to search for quantum spin liquids in ultracold dipolar molecules.

Angular resolution and range of dipole-dipole correlations in water

NASA Astrophysics Data System (ADS)

Mathias, Gerald; Tavan, Paul

2004-03-01

We investigate the dipolar correlations in liquid water at angular resolution by molecular-dynamics simulations of a large periodic simulation system containing about 40 000 molecules. Because we are particularly interested in the long-range ordering, we use a simple three-point model for these molecules. The electrostatics is treated both by Ewald summation and by minimum image truncation combined with a reaction field approach. To gain insight into the angular dependence of the simulated dipolar ordering we introduce a suitable expansion of the molecular pair distribution function into a set of two-dimensional correlation functions. We show that these functions enable detailed insights into the shell structure of the dipolar ordering around a given water molecule. For these functions we derive analytical expressions in the particular case in which liquid water is conceived as a dielectric continuum. Comparisons of these continuum models with the correlation functions derived from the simulations yield the key result that liquid water behaves like a continuum dielectric beyond distances of about 15 Å from a given water molecule. We argue that this should be a generic property of water independent of our modeling. By comparison of the results of the two different electrostatics treatments with the continuum description we show that the boundary artifacts occurring in both methods are isotropically distributed and are locally small in the respective boundary regions.

Vertically Aligned Graphene Sheets Membrane for Highly Efficient Solar Thermal Generation of Clean Water.

PubMed

Zhang, Panpan; Li, Jing; Lv, Lingxiao; Zhao, Yang; Qu, Liangti

2017-05-23

Efficient utilization of solar energy for clean water is an attractive, renewable, and environment friendly way to solve the long-standing water crisis. For this task, we prepared the long-range vertically aligned graphene sheets membrane (VA-GSM) as the highly efficient solar thermal converter for generation of clean water. The VA-GSM was prepared by the antifreeze-assisted freezing technique we developed, which possessed the run-through channels facilitating the water transport, high light absorption capacity for excellent photothermal transduction, and the extraordinary stability in rigorous conditions. As a result, VA-GSM has achieved average water evaporation rates of 1.62 and 6.25 kg m -2 h -1 under 1 and 4 sun illumination with a superb solar thermal conversion efficiency of up to 86.5% and 94.2%, respectively, better than that of most carbon materials reported previously, which can efficiently produce the clean water from seawater, common wastewater, and even concentrated acid and/or alkali solutions.

Nanoscale control of competing interactions and geometrical frustration in a dipolar trident lattice

DOE PAGES

Farhan, Alan; Petersen, Charlotte F.; Dhuey, Scott; ...

2017-10-17

Geometrical frustration occurs when entities in a system, subject to given lattice constraints, are hindered to simultaneously minimize their local interactions. In magnetism, systems incorporating geometrical frustration are fascinating, as their behavior is not only hard to predict, but also leads to the emergence of exotic states of matter. Here, we provide a first look into an artificial frustrated system, the dipolar trident lattice, where the balance of competing interactions between nearest-neighbor magnetic moments can be directly controlled, thus allowing versatile tuning of geometrical frustration and manipulation of ground state configurations. Our findings not only provide the basis for futuremore » studies on the low-temperature physics of the dipolar trident lattice, but also demonstrate how this frustration-by-design concept can deliver magnetically frustrated metamaterials.« less

Fingering instabilities and pattern formation in a two-component dipolar Bose-Einstein condensate

NASA Astrophysics Data System (ADS)

Xi, Kui-Tian; Byrnes, Tim; Saito, Hiroki

2018-02-01

We study fingering instabilities and pattern formation at the interface of an oppositely polarized two-component Bose-Einstein condensate with strong dipole-dipole interactions in three dimensions. It is shown that the rotational symmetry is spontaneously broken by fingering instability when the dipole-dipole interactions are strengthened. Frog-shaped and mushroom-shaped patterns emerge during the dynamics due to the dipolar interactions. We also demonstrate the spontaneous density modulation and domain growth of a two-component dipolar BEC in the dynamics. Bogoliubov analyses in the two-dimensional approximation are performed, and the characteristic lengths of the domains are estimated analytically. Patterns resembling those in magnetic classical fluids are modulated when the number ratio of atoms, the trap ratio of the external potential, or tilted polarization with respect to the z direction is varied.

Intense Current Structures Observed at Electron Kinetic Scales in the Near-Earth Magnetotail During Dipolarization and Substorm Current Wedge Formation

NASA Astrophysics Data System (ADS)

Grigorenko, E. E.; Dubyagin, S.; Malykhin, A. Yu.; Khotyaintsev, Yu V.; Kronberg, E. A.; Lavraud, B.; Ganushkina, N. Yu

2018-01-01

We use data from the 2013-2014 Cluster Inner Magnetosphere Campaign, with its uniquely small spacecraft separations (less than or equal to electron inertia length, λe), to study multiscale magnetic structures in 14 substorm-related prolonged dipolarizations in the near-Earth magnetotail. Three time scales of dipolarization are identified: (i) a prolonged growth of the BZ component with duration ≤20 min; (ii) BZ pulses with durations ≤1 min during the BZ growth; and (iii) strong magnetic field gradients with durations ≤2 s during the dipolarization growth. The values of these gradients observed at electron scales are several dozen times larger than the corresponding values of magnetic gradients simultaneously detected at ion scales. These nonlinear features in magnetic field gradients denote the formation of intense and localized (approximately a few λe) current structures during the dipolarization and substorm current wedge formation. These observations highlight the importance of electron scale processes in the formation of a 3-D substorm current system.

Experimental Evidence of Dipolar Interaction in Bilayer Nanocomposite Magnets

DTIC Science & Technology

2010-11-25

corporated to improve experimental systems. However, re- ported bulk nanocomposite magnets exhibit (BH)max val- ues that are far below the...Appl Phys A DOI 10.1007/s00339-010-6073-6 Experimental evidence of dipolar interaction in bilayer nanocomposite magnets A.J. Zambano · H. Oguchi · I...Abstract We use magnetic thin film hard/non/soft-mag- netic trilayer systems to probe the nature of the hard–soft phase interaction and the role

Thermal entanglement and teleportation in a dipolar interacting system

NASA Astrophysics Data System (ADS)

Castro, C. S.; Duarte, O. S.; Pires, D. P.; Soares-Pinto, D. O.; Reis, M. S.

2016-04-01

Quantum teleportation, which depends on entangled states, is a fascinating subject and an important branch of quantum information processing. The present work reports the use of a dipolar spin thermal system as a noisy quantum channel to perform quantum teleportation. Non-locality, tested by violation of Bell's inequality and thermal entanglement, measured by negativity, shows that for the present model all entangled states, even those that do not violate Bell's inequality, are useful for teleportation.

Characteristics of high-latitude precursor flows ahead of dipolarization fronts

NASA Astrophysics Data System (ADS)

Li, Jia-Zheng; Zhou, Xu-Zhi; Runov, Andrei; Angelopoulos, Vassilis; Liu, Jiang; Pan, Dong-Xiao; Zong, Qiu-Gang

2017-05-01

Dipolarization fronts (DFs), earthward propagating structures in the magnetotail current sheet characterized by sharp enhancements of northward magnetic field, are capable of converting electromagnetic energy into particle kinetic energy. The ions previously accelerated and reflected at the DFs can contribute to plasma flows ahead of the fronts, which have been identified as DF precursor flows in both the near-equatorial plasma sheet and far from it, near the plasma sheet boundary. Using observations from the THEMIS (Time History of Events and Macroscale Interactions during Substorms) spacecraft, we show that the earthward particle and energy flux enhancements ahead of DFs are statistically larger farther away from the neutral sheet (at high latitudes) than in the near-equatorial region. High-latitude particle and energy fluxes on the DF dawnside are found to be significantly greater than those on the duskside, which is opposite to the dawn-dusk asymmetries previously found near the equatorial region. Using forward and backward tracing test-particle simulations, we then explain and reproduce the observed latitude-dependent characteristics of DF precursor flows, providing a better understanding of ion dynamics associated with dipolarization fronts.

Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex.

PubMed

Ortega-Roldan, Jose Luis; Jensen, Malene Ringkjøbing; Brutscher, Bernhard; Azuaga, Ana I; Blackledge, Martin; van Nuland, Nico A J

2009-05-01

The description of the interactome represents one of key challenges remaining for structural biology. Physiologically important weak interactions, with dissociation constants above 100 muM, are remarkably common, but remain beyond the reach of most of structural biology. NMR spectroscopy, and in particular, residual dipolar couplings (RDCs) provide crucial conformational constraints on intermolecular orientation in molecular complexes, but the combination of free and bound contributions to the measured RDC seriously complicates their exploitation for weakly interacting partners. We develop a robust approach for the determination of weak complexes based on: (i) differential isotopic labeling of the partner proteins facilitating RDC measurement in both partners; (ii) measurement of RDC changes upon titration into different equilibrium mixtures of partially aligned free and complex forms of the proteins; (iii) novel analytical approaches to determine the effective alignment in all equilibrium mixtures; and (iv) extraction of precise RDCs for bound forms of both partner proteins. The approach is demonstrated for the determination of the three-dimensional structure of the weakly interacting CD2AP SH3-C:Ubiquitin complex (K(d) = 132 +/- 13 muM) and is shown, using cross-validation, to be highly precise. We expect this methodology to extend the remarkable and unique ability of NMR to study weak protein-protein complexes.

Progressive Stereo Locking (PSL): A Residual Dipolar Coupling Based Force Field Method for Determining the Relative Configuration of Natural Products and Other Small Molecules.

PubMed

Cornilescu, Gabriel; Ramos Alvarenga, René F; Wyche, Thomas P; Bugni, Tim S; Gil, Roberto R; Cornilescu, Claudia C; Westler, William M; Markley, John L; Schwieters, Charles D

2017-08-18

Establishing the relative configuration of a bioactive natural product represents the most challenging part in determining its structure. Residual dipolar couplings (RDCs) are sensitive probes of the relative spatial orientation of internuclear vectors. We adapted a force field structure calculation methodology to allow free sampling of both R and S configurations of the stereocenters of interest. The algorithm uses a floating alignment tensor in a simulated annealing protocol to identify the conformations and configurations that best fit experimental RDC and distance restraints (from NOE and J-coupling data). A unique configuration (for rigid molecules) or a very small number of configurations (for less rigid molecules) of the structural models having the lowest chiral angle energies and reasonable magnitudes of the alignment tensor are provided as the best predictions of the unknown configuration. For highly flexible molecules, the progressive locking of their stereocenters into their statistically dominant R or S state dramatically reduces the number of possible relative configurations. The result is verified by checking that the same configuration is obtained by initiating the locking from different regions of the molecule. For all molecules tested having known configurations (with conformations ranging from mostly rigid to highly flexible), the method accurately determined the correct configuration.

Dielectric metamaterials with toroidal dipolar response

DOE PAGES

Basharin, Alexey A.; Kafesaki, Maria; Economou, Eleftherios N.; ...

2015-03-27

Toroidal multipoles are the terms missing in the standard multipole expansion; they are usually overlooked due to their relatively weak coupling to the electromagnetic fields. Here, we propose and theoretically study all-dielectric metamaterials of a special class that represent a simple electromagnetic system supporting toroidal dipolar excitations in the THz part of the spectrum. In addition, we show that resonant transmission and reflection of such metamaterials is dominated by toroidal dipole scattering, the neglect of which would result in a misunderstanding interpretation of the metamaterials’ macroscopic response. Due to the unique field configuration of the toroidal mode, the proposed metamaterialsmore » could serve as a platform for sensing or enhancement of light absorption and optical nonlinearities.« less

Dipolar induced para-hydrogen-induced polarization.

PubMed

Buntkowsky, Gerd; Gutmann, Torsten; Petrova, Marina V; Ivanov, Konstantin L; Bommerich, Ute; Plaumann, Markus; Bernarding, Johannes

2014-01-01

Analytical expressions for the signal enhancement in solid-state PHIP NMR spectroscopy mediated by homonuclear dipolar interactions and single pulse or spin-echo excitation are developed and simulated numerically. It is shown that an efficient enhancement of the proton NMR signal in solid-state NMR studies of chemisorbed hydrogen on surfaces is possible. Employing typical reaction efficacy, enhancement-factors of ca. 30-40 can be expected both under ALTADENA and under PASADENA conditions. This result has important consequences for the practical application of the method, since it potentially allows the design of an in-situ flow setup, where the para-hydrogen is adsorbed and desorbed from catalyst surfaces inside the NMR magnet. Copyright © 2014 Elsevier Inc. All rights reserved.

Low density mesostructures of confined dipolar particles in an external field

NASA Astrophysics Data System (ADS)

Richardi, J.; Weis, J.-J.

2011-09-01

Mesostructures formed by dipolar particles confined between two parallel walls and subjected to an external field are studied by Monte Carlo simulations. The main focus of the work is the structural behavior of the Stockmayer fluid in the low density regime. The dependence of cluster thickness and ordering is estimated as a function of density and wall separation, the two most influential parameters, for large dipole moments and high field strengths. The great sensitivity of the structure to details of the short-range part of the interactions is pointed out. In particular, the attractive part of the Lennard-Jones potential is shown to play a major role in driving chain aggregation. The effect of confinement, evaluated by comparison with results for a bulk system, is most pronounced for a short range hard sphere potential. No evidence is found for a novel "gel-like" phase recently uncovered in low density dipolar colloidal suspensions [A. K. Agarwal and A. Yethiraj, Phys. Rev. Lett. 102, 198301 (2009), 10.1103/PhysRevLett.102.198301].

The 3D Kasteleyn transition in dipolar spin ice: a numerical study with the conserved monopoles algorithm

NASA Astrophysics Data System (ADS)

Baez, M. L.; Borzi, R. A.

2017-02-01

We study the three-dimensional Kasteleyn transition in both nearest neighbours and dipolar spin ice models using an algorithm that conserves the number of excitations. We first limit the interactions range to nearest neighbours to test the method in the presence of a field applied along ≤ft[1 0 0\\right] , and then focus on the dipolar spin ice model. The effect of dipolar interactions, which is known to be greatly self screened at zero field, is particularly strong near full polarization. It shifts the Kasteleyn transition to lower temperatures, which decreases  ≈0.4 K for the parameters corresponding to the best known spin ice materials, \\text{D}{{\\text{y}}2}\\text{T}{{\\text{i}}2}{{\\text{O}}7} and \\text{H}{{\\text{o}}2}\\text{T}{{\\text{i}}2}{{\\text{O}}7} . This shift implies effective dipolar fields as big as 0.05 T opposing the applied field, and thus favouring the creation of ‘strings’ of reversed spins. We compare the reduction in the transition temperature with results in previous experiments, and study the phenomenon quantitatively using a simple molecular field approach. Finally, we relate the presence of the effective residual field to the appearance of string-ordered phases at low fields and temperatures, and we check numerically that for fields applied along ≤ft[1 0 0\\right] there are only three different stable phases at zero temperature.

The Earth's magnetic field is primarily dipolar

NASA Astrophysics Data System (ADS)

Besse, J.; Cogne, J. P.; Courtillot, V.; Gilder, S.

2003-04-01

The question of the geometry of the Earth's magnetic field has been, and should remain, a central concern for all paleomagnetists. The founding assumption that the field has always been dominantly dipolar has been under recent challenge; stable, long standing octupolar contributions of up to 10% of the main dipole have been proposed for several periods in the Phanerozoic (e.g. ref. 1). Uncertainties that limit interpretation of paleomagnetic data arise from physical, field and laboratory problems. We note mainly uncertainties in rock or magnetization age, inclination shallowing in sediments, possible remagnetization, lack of proper averaging of secular variation in lavas, improperly modeled tectonics or unnoticed deformations of large blocks or plates, failure of reference APWPs to be valid, or uncertainties in past plate motions based on oceanic kinematic parameters... There are so many instances in which these problems have been demonstrated to occur or are likely (at no major cost to geophysical hypotheses and theories) that they must have been all excluded with satisfactory likelihood before the major and 'expensive' hypothesis that the field could be very significantly non-dipolar over long geological periods must be entertained. We will discuss a number of data that pertain to this problem. (a) In a recent review of the global paleomagnetic data base (ref. 2), when all data were averaged in 20 Ma windows, we were unable to find conclusive evidence for significant long term departures from a dipolar geometry, except for a contribution from a quadrupolar component of some 3% pm 2% (grand average) of the axial dipole. This confirms a result which had been suggested since the early 70's and vindicated by all recent analyses of the best data sets from the last 5 Ma (with a value up to possibly ca. 7%; see for instance Elmaleh et al, this meeting). Detailed analyses of key time periods when enough data with widespread enough coverage are available are clearly

Constraining the dipolar magnetic field of M82 X-2 by the accretion model

NASA Astrophysics Data System (ADS)

Chen, Wen-Cong

2017-02-01

Recently, ultraluminous X-ray source (ULX) M82 X-2 has been identified to be an accreting neutron star, which has a P = 1.37 s spin period, and is spinning up at a rate dot{P}=-2.0× 10^{-10} s s^{-1}. Interestingly, its isotropic X-ray luminosity Liso = 1.8 × 1040 erg s- 1 during outbursts is 100 times the Eddington limit for a 1.4 M⊙ neutron star. In this Letter, based on the standard accretion model we attempt to constrain the dipolar magnetic field of the pulsar in ULX M82 X-2. Our calculations indicate that the accretion rate at the magnetospheric radius must be super-Eddington during outbursts. To support such a super-Eddington accretion, a relatively high multipole field ( ≳ 1013 G) near the surface of the accretor is invoked to produce an accreting gas column. However, our constraint shows that the surface dipolar magnetic field of the pulsar should be in the range of 1.0-3.5 × 1012 G. Therefore, our model supports that the neutron star in ULX M82 X-2 could be a low-magnetic-field magnetar (proposed by Tong) with a normal dipolar field (˜1012 G) and relatively strong multipole field. For the large luminosity variations of this source, our scenario can also present a self-consistency interpretation.

The Relationship Between Dipolarization Fronts and Pi2 Pulsations in the Near-Earth Magnetotail - A MHD Case Study

NASA Astrophysics Data System (ADS)

Ream, J. B.; Walker, R. J.; Ashour-Abdalla, M.; El-Alaoui, M.

2011-12-01

We performed a global MHD simulation of a substorm event on 14 September 2004 in order to investigate the link between Pi2 generation and dipolarization fronts. Pi2 pulsations (T = 40-150 s) measured by ground-based instruments are typically used as an indicator of substorm onset, therefore, understanding how and where they are generated is vital to understanding the series of events leading up to onset. Kepko et al. [1999] suggested that the compression regions and velocity variations associated with earthward propagating dipolarization fronts directly drive Pi2 pulsations. Similarly, Panov et al. [2011] suggested that Pi2 pulsations are generated by the overshoot and rebound of bursty bulk flows. Dipolarization fronts are step-wise enhancements in Bz which are associated with fast (>100km/s) earthward flows and are followed by tailward expansion due to pile-up at the high pressure region where the magnetic field lines transition from a stretched to a dipolar configuration. Cao et al. [2009] have presented observations from Double Star (TC1), Cluster 4 and Polar of a substorm with onset at 18:22 UT. During this event a dipolarization front was observed by Double Star at ~18:25, and dipolarization associated expansion was observed by Cluster 4 at ~18:50 and Polar at ~18:55 UT. The spacecraft were positioned at (-10.2, -1.6, 1.2), (-16.4, 1.6, 2.2) and (-7.5, -1.8, -4.9) RE in GSM coordinates respectively. The simulation was carried out with the UCLA global MHD code [El-Alaoui (2001), Raeder (1998)], using Geotail, located near the bow shock at ~24 RE, as the solar wind monitor. The solar wind magnetic field data were rotated into a minimum variance frame to be used as input for the simulation. The results from the simulation have been compared to observations and do a good job reproducing the structures observed by all three satellites. Around the time of onset, we have identified a dipolarization front near midnight which originates at ~12 RE. We show that as the

Recoupling of Heteronuclear Dipolar Interactions with Rotational-Echo Double-Resonance at High Magic-Angle Spinning Frequencies

NASA Astrophysics Data System (ADS)

Jaroniec, Christopher P.; Tounge, Brett A.; Rienstra, Chad M.; Herzfeld, Judith; Griffin, Robert G.

2000-09-01

Heteronuclear dipolar recoupling with rotational-echo double-resonance (REDOR) is investigated in the rapid magic-angle spinning regime, where radiofrequency irradiation occupies a significant fraction of the rotor period (10-60%). We demonstrate, in two model 13C-15N spin systems, [1-13C, 15N] and [2-13C, 15N]glycine, that REDOR ΔS/S0 curves acquired at high MAS rates and relatively low recoupling fields are nearly identical to the ΔS/S0 curve expected for REDOR with ideal δ-function pulses. The only noticeable effect of the finite π pulse length on the recoupling is a minor scaling of the dipolar oscillation frequency. Experimental results are explained using both numerical calculations and average Hamiltonian theory, which is used to derive analytical expressions for evolution under REDOR recoupling sequences with different π pulse phasing schemes. For xy-4 and extensions thereof, finite pulses scale only the dipolar oscillation frequency by a well-defined factor. For other phasing schemes (e.g., xx-4 and xx¯-4) both the frequency and amplitude of the oscillation are expected to change.

Linear polarimetry of AP stars. IV. The influence of deviations from a pure dipolar model.

NASA Astrophysics Data System (ADS)

Leroy, J. L.; Landolfi, M.; Landi Degl'Innocenti, M.; Landi Degl'Innocenti, E.; Bagnulo, S.; Laporte, P.

1995-09-01

In the previous papers of this series we have described a new observational program of broadband linear polarimetry aimed at Ap stars. At the same time, we have established a canonical model, based on the oblique rotator geometry, which describes successfully the main features of the observed polarization: in some cases the linear polarization data, combined with the classical circular polarization measurements, allow one to determine the characteristic parameters which define the oblique dipolar rotator. However, we have also observed polarization diagrams that depart clearly from those predicted by the canonical model, which means that it is not always possible to rely on a pure dipolar model (nor on a combination of a dipole plus a linear quadrupole parallel to the dipole). Although an interpretation of the polarization peculiarities in terms of magnetic `anomalies' (i.e. deviations from the dipolar configuration) is quite natural, one must also take into account the possible influence of local abundance inhomogeneities. Therefore, we have first studied the sensitivity of the polarized signal (which is known to be due to the differential saturation of Zeeman components in spectral lines) to a variation of the metallic absorption spectrum. Then we have examined how a local enhancement (or reduction) of the polarization produced by a dipolar magnetic field affects the Fourier spectrum of the observed polarization signal. Finally, we have designed an inversion program making possible the recovery - under certain restrictions - of the spatial modulations of the polarization generated by a dipole, which are necessary to explain `odd' polarimetric data. This program has been applied to the data gathered from three stars (49 Cam, β CrB, HD 71866). As far as the last star is concerned, none of the spatial modulations considered was able to reproduce the observations. On the contrary, good solutions are found for the other two. However, if one interprets the variations

Observation of roton mode population in a dipolar quantum gas

NASA Astrophysics Data System (ADS)

Chomaz, L.; van Bijnen, R. M. W.; Petter, D.; Faraoni, G.; Baier, S.; Becher, J. H.; Mark, M. J.; Wächtler, F.; Santos, L.; Ferlaino, F.

2018-05-01

The concept of a roton, a special kind of elementary excitation forming a minimum of energy at finite momentum, has been essential for the understanding of the properties of superfluid 4He (ref. 1). In quantum liquids, rotons arise from the strong interparticle interactions, whose microscopic description remains debated2. In the realm of highly controllable quantum gases, a roton mode has been predicted to emerge due to magnetic dipole-dipole interactions despite their weakly interacting character3. This prospect has raised considerable interest4-12; yet roton modes in dipolar quantum gases have remained elusive to observations. Here we report experimental and theoretical studies of the momentum distribution in Bose-Einstein condensates of highly magnetic erbium atoms, revealing the existence of the long-sought roton mode. Following an interaction quench, the roton mode manifests itself with the appearance of symmetric peaks at well-defined finite momentum. The roton momentum follows the predicted geometrical scaling with the inverse of the confinement length along the magnetization axis. From the growth of the roton population, we probe the roton softening of the excitation spectrum in time and extract the corresponding imaginary roton gap. Our results provide a further step in the quest towards supersolidity in dipolar quantum gases13.

Renormalization group analysis of dipolar Heisenberg model on square lattice

NASA Astrophysics Data System (ADS)

Keleş, Ahmet; Zhao, Erhai

2018-06-01

We present a detailed functional renormalization group analysis of spin-1/2 dipolar Heisenberg model on square lattice. This model is similar to the well-known J1-J2 model and describes the pseudospin degrees of freedom of polar molecules confined in deep optical lattice with long-range anisotropic dipole-dipole interactions. Previous study of this model based on tensor network ansatz indicates a paramagnetic ground state for certain dipole tilting angles which can be tuned in experiments to control the exchange couplings. The tensor ansatz formulated on a small cluster unit cell is inadequate to describe the spiral order, and therefore the phase diagram at high azimuthal tilting angles remains undetermined. Here, we obtain the full phase diagram of the model from numerical pseudofermion functional renormalization group calculations. We show that an extended quantum paramagnetic phase is realized between the Néel and stripe/spiral phases. In this region, the spin susceptibility flows smoothly down to the lowest numerical renormalization group scales with no sign of divergence or breakdown of the flow, in sharp contrast to the flow towards the long-range-ordered phases. Our results provide further evidence that the dipolar Heisenberg model is a fertile ground for quantum spin liquids.

Spreading dynamics of 2D dipolar Langmuir monolayer phases.

PubMed

Heinig, P; Wurlitzer, S; Fischer, Th M

2004-07-01

We study the spreading of a liquid 2D dipolar droplet in a Langmuir monolayer. Interfacial tensions (line tensions) and microscopic contact angles depend on the scale on which they are probed and obey a scaling law. Assuming rapid equilibration of the microscopic contact angle and ideal slippage of the 2D solid/liquid and solid/gas boundary, the driving force of spreading is merely expressed by the shape-dependent long-range interaction integrals. We obtain good agreement between experiment and numerical simulations using this theory.

Dipolar ferromagnetic phase transition in Fe3O4 nanoparticle arrays observed by Lorentz microscopy and electron holography

NASA Astrophysics Data System (ADS)

Yamamoto, Kazuo; Hogg, Charles R.; Yamamuro, Saeki; Hirayama, Tsukasa; Majetich, Sara A.

2011-02-01

Dipolar ferromagnetism formed in Fe3O4 nanoparticle arrays is revealed by Fresnel Lorentz microscopy and electron holography. Dipolar domain walls do not lie preferentially along macrograin boundaries but depend on the overall shape of the assembly, meaning magnetostatic energy dominates. The domain structures are imaged at different temperatures for both monolayer and bilayer arrays. The domain wall contrast in the monolayer region is visible until 575 °C, and the magnetic order parameter steeply drops toward the temperature. In the bilayer region, finer and more complicated domains are formed.

Quantum Electric Dipole Lattice - Water Molecules Confined to Nanocavities in Beryl

NASA Astrophysics Data System (ADS)

Dressel, Martin; Zhukova, Elena S.; Thomas, Victor G.; Gorshunov, Boris P.

2018-02-01

Water is subject to intense investigations due to its importance in biological matter but keeps many of its secrets. Here, we unveil an even other aspect by confining H2O molecules to nanosize cages. Our THz and infrared spectra of water in the gemstone beryl evidence quantum tunneling of H2O molecules in the crystal lattice. The water molecules are spread out when confined in a nanocage. In combination with low-frequency dielectric measurements, we were also able to show that dipolar coupling among the H2O molecules leads towards a ferroelectric state at low temperatures. Upon cooling, a ferroelectric soft mode shifts through the THz range. Only quantum fluctuations prevent perfect macroscopic order to be fully achieved. Beside the significance to life science and possible application, nanoconfined water may become the prime example of a quantum electric dipolar lattice.

Carrier-envelope phase effects for a dipolar molecule interacting with two-color pump-probe laser pulses

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

Cheng Taiwang; Brown, Alex

2004-12-01

The interaction of a two-level dipolar molecule with two laser pulses, where one laser's frequency is tuned to the energy level separation (pump laser) while the second laser's frequency is extremely small (probe laser), is investigated. A dipolar molecule is one with a nonzero difference between the permanent dipole moments of the molecular states. As shown previously [A. Brown, Phys. Rev. A 66, 053404 (2002)], the final population transfer between the two levels exhibits a dependence on the carrier-envelope phase of the probe laser. Based on the rotating-wave approximation (RWA), an effective Hamiltonian is derived to account for the basicmore » characteristics of the carrier-envelope phase dependence effect. By analysis of the effective Hamiltonian, scaling properties of the system are found with regard to field strengths, pulse durations, and frequencies. According to these scaling properties, the final-state population transfer can be controlled by varying the carrier-envelope phase of the probe laser field using lasers with weak field strengths (low intensities) and relatively long pulse durations. In order to examine the possible roles of background states, the investigation is extended to a three-level model. It is demonstrated that the carrier-envelope phase effect still persists in a well-defined manner even when neighboring energy levels are present. These results illustrate the potential of utilizing excitation in dipolar molecules as a means of measuring the carrier-envelope phase of a laser pulse or if one can manipulate the carrier envelope phase, as a method of controlling population transfer in dipolar molecules. The results also suggest that the carrier-envelope phases must be taken into account properly when performing calculations involving pump-probe excitation schemes with laser frequencies which differ widely in magnitude.« less

Evidence for several dipolar quasi-invariants in liquid crystals

NASA Astrophysics Data System (ADS)

Bonin, C. J.; González, C. E.; Segnorile, H. H.; Zamar, R. C.

2013-10-01

The quasi-equilibrium states of an observed quantum system involve as many constants of motion as the dimension of the operator basis which spans the blocks of all the degenerate eigenvalues of the Hamiltonian that drives the system dynamics, however, the possibility of observing such quasi-invariants in solid-like spin systems in Nuclear Magnetic Resonance (NMR) is not a strictly exact prediction. The aim of this work is to provide experimental evidence of several quasi-invariants, in the proton NMR of small spin clusters, like nematic liquid crystal molecules, in which the use of thermodynamic arguments is not justified. We explore the spin states prepared with the Jeener-Broekaert pulse sequence by analyzing the time-domain signals yielded by this sequence as a function of the preparation times, in a variety of dipolar networks, solids, and liquid crystals. We observe that the signals can be explained with two dipolar quasi-invariants only within a range of short preparation times, however at longer times liquid crystal signals show an echo-like behaviour whose description requires assuming more quasi-invariants. We study the multiple quantum coherence content of such signals on a basis orthogonal to the z-basis and see that such states involve a significant number of correlated spins. Therefore, we show that the NMR signals within the whole preparation time-scale can only be reconstructed by assuming the occurrence of multiple quasi-invariants which we experimentally isolate.

Ion trajectory simulations of axial ac dipolar excitation in the Orbitrap

NASA Astrophysics Data System (ADS)

Wu, Guangxiang; Noll, Robert J.; Plass, Wolfgang R.; Hu, Qizhi; Perry, Richard H.; Cooks, R. Graham

2006-07-01

The newly developed version of the multi-particle ion trajectory simulation program, ITSIM 6.0, was applied to simulate ac dipolar excitation of ion axial motion in the Orbitrap. The Orbitrap inner and outer electrodes were generated in AutoCAD, a 3D drawing program. The electrode geometry was imported into the 3D field solver COMSOL; the field array was then imported into ITSIM 6.0. Ion trajectories were calculated by solving Newton's equations using Runge-Kutta integration methods. Compared to the analytical solution, calculated radial components of the field at the device's "equator" (z = 0) were within 0.5% and calculated axial components midway between the inner and outer electrodes were within 0.2%. The experiments simulated here involved the control of axial motion of ions in the Orbitrap by the application of dipolar ac signals to the split outer electrodes, as described in a recently published paper from this laboratory [Hu et al., J. Phys. Chem. A 110 (2006) 2682]. In these experiments, ac signal was applied at the axial resonant frequency of a selected ion. Axial excitation and eventual ion ejection resulted when the ac was in phase with, i.e., had 0° phase relative to ion axial motion. De-excitation of ion axial motion until the ions were at z = 0 and at rest with respect to the z-axis resulted if the applied ac was out of phase with ion motion, with re-excitation of ion axial motion occurring if the dipolar ac was continued beyond this point. Both de-excitation and re-excitation could be achieved mass-selectively and depended on the amplitude and duration (number of cycles) of the applied ac. The effects of ac amplitude, frequency, phase relative to ion motion, and bandwidth of applied waveform were simulated. All simulation results were compared directly with the experimental data and good agreement was observed. Such ion motion control experiments and their simulation provide the possibility to improve Orbitrap performance and to develop tandem mass

Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex

PubMed Central

Ortega-Roldan, Jose Luis; Jensen, Malene Ringkjøbing; Brutscher, Bernhard; Azuaga, Ana I.; Blackledge, Martin; van Nuland, Nico A. J.

2009-01-01

The description of the interactome represents one of key challenges remaining for structural biology. Physiologically important weak interactions, with dissociation constants above 100 μM, are remarkably common, but remain beyond the reach of most of structural biology. NMR spectroscopy, and in particular, residual dipolar couplings (RDCs) provide crucial conformational constraints on intermolecular orientation in molecular complexes, but the combination of free and bound contributions to the measured RDC seriously complicates their exploitation for weakly interacting partners. We develop a robust approach for the determination of weak complexes based on: (i) differential isotopic labeling of the partner proteins facilitating RDC measurement in both partners; (ii) measurement of RDC changes upon titration into different equilibrium mixtures of partially aligned free and complex forms of the proteins; (iii) novel analytical approaches to determine the effective alignment in all equilibrium mixtures; and (iv) extraction of precise RDCs for bound forms of both partner proteins. The approach is demonstrated for the determination of the three-dimensional structure of the weakly interacting CD2AP SH3-C:Ubiquitin complex (Kd = 132 ± 13 μM) and is shown, using cross-validation, to be highly precise. We expect this methodology to extend the remarkable and unique ability of NMR to study weak protein–protein complexes. PMID:19359362

Freezing point and solid-liquid interfacial free energy of Stockmayer dipolar fluids: a molecular dynamics simulation study.

PubMed

Wang, Jun; Apte, Pankaj A; Morris, James R; Zeng, Xiao Cheng

2013-09-21

Stockmayer fluids are a prototype model system for dipolar fluids. We have computed the freezing temperatures of Stockmayer fluids at zero pressure using three different molecular-dynamics simulation methods, namely, the superheating-undercooling method, the constant-pressure and constant-temperature two-phase coexistence method, and the constant-pressure and constant-enthalpy two-phase coexistence method. The best estimate of the freezing temperature (in reduced unit) for the Stockmayer (SM) fluid with the dimensionless dipole moment μ*=1, √2, √3 is 0.656 ± 0.001, 0.726 ± 0.002, and 0.835 ± 0.005, respectively. The freezing temperature increases with the dipolar strength. Moreover, for the first time, the solid-liquid interfacial free energies γ of the fcc (111), (110), and (100) interfaces are computed using two independent methods, namely, the cleaving-wall method and the interfacial fluctuation method. Both methods predict that the interfacial free energy increases with the dipole moment. Although the interfacial fluctuation method suggests a weaker interfacial anisotropy, particularly for strongly dipolar SM fluids, both methods predicted the same trend of interfacial anisotropy, i.e., γ100 > γ110 > γ111.

Observation of plasmonic dipolar anti-bonding mode in silver nanoring structures.

PubMed

Ye, Jian; Van Dorpe, Pol; Lagae, Liesbet; Maes, Guido; Borghs, Gustaaf

2009-11-18

We report on a clear experimental observation of the plasmonic dipolar anti-bonding resonance in silver nanorings. The data can be explained effectively by the plasmon hybridization model, which is confirmed by the numerical calculations of the electromagnetic field and surface charge distribution profiles. The experimental demonstration of the plasmon hybridization model indicates its usefulness as a valuable tool to understand, design and predict optical properties of metallic nanostructures.

Observation of plasmonic dipolar anti-bonding mode in silver nanoring structures

NASA Astrophysics Data System (ADS)

Ye, Jian; Van Dorpe, Pol; Lagae, Liesbet; Maes, Guido; Borghs, Gustaaf

2009-11-01

We report on a clear experimental observation of the plasmonic dipolar anti-bonding resonance in silver nanorings. The data can be explained effectively by the plasmon hybridization model, which is confirmed by the numerical calculations of the electromagnetic field and surface charge distribution profiles. The experimental demonstration of the plasmon hybridization model indicates its usefulness as a valuable tool to understand, design and predict optical properties of metallic nanostructures.

Supra Arcade Downflows with XRT Informed by Dipolarization Fronts with THEMIS

NASA Technical Reports Server (NTRS)

Kobelski, Adam; Savage, Sabrina Leah; Malaspina, David

2016-01-01

Magnetic reconnection can rapidly reconfigure the magnetic field of the corona, accelerating plasma through the site of reconnection. Ambiguities due to the nature of remote sensing have complicated the interpretation of observations of the inflowing and outflowing plasma in reconnecting regions. In particular, the interpretation of sunward moving density depletions above flare arcades (known as Supra Arcade Downflows - SADs) is still debated. Hinode/XRT has provided a wealth of observations for SADs and helped inform our current understanding of these structures. SADs have been interpreted as wakes behind newly reconnected and outflowing loops (Supra Arcade Downflowing Loops - SADLs). Models have shown the plausibility of this interpretation, though this interpretation has not yet been fully accepted. We present here observations of newly reconnected outflowing loops observed via in situ instruments in the magnetosphere. These observations, provided by five THEMIS spacecraft, show that around retracting loops (dipolarization fronts in this context) similar dynamic temperature and density structures are found as seen in SADs. We compare data from multiple SADs and dipolarization fronts to show that the observational signatures implied in the corona can be directly observed in similar plasma regimes in the magnetosphere, strongly favoring the interpretation of SADs as wakes behind retracting loops.

Characterizing Ion Flows Across a Dipolarization Front

NASA Astrophysics Data System (ADS)

Arnold, H.; Drake, J. F.; Swisdak, M.

2017-12-01

In light of the Magnetospheric Multiscale Mission (MMS) moving to study predominately symmetric magnetic reconnection in the Earth's magnetotail, it is of interest to investigate various methods for determining the relative location of the satellites with respect to the x line or a dipolarization front. We use a 2.5 dimensional PIC simulation to explore the dependence of various characteristics of a front, or flux bundle, on the width of the front in the dawn-dusk direction. In particular, we characterize the ion flow in the x-GSM direction across the front. We find a linear relationship between the width of a front, w, and the maximum velocity of the ion flow in the x-GSM direction, Vxi, for small widths: Vxi/VA=w/di*1/2*(mVA2)/Ti*Bz/Bxwhere m, VA, di, Ti, Bz, and Bx are the ion mass, upstream Alfven speed, ion inertial length, ion temperature, and magnetic fields in the z-GSM and x-GSM directions respectively. However, once the width reaches around 5 di, the relationship gradually approaches the well-known theoretical limit for ion flows, the upstream Alfven speed. Furthermore, we note that there is a reversal in the Hall magnetic field near the current sheet on the positive y-GSM side of the front. This reversal is most likely due to conservation of momentum in the y-GSM direction as the ions accelerate towards the x-GSM direction. This indicates that while the ions are primarily energized in the x-GSM direction by the front, they transfer energy to the electromagnetic fields in the y-GSM direction. The former energy transfer is greater than the latter, but the reversal of the Hall magnetic field drags the frozen-in electrons along with it outside of the front. These simulations should better able researchers to determine the relative location of a satellite crossing a dipolarization front.

High-Temperature and High-Energy-Density Dipolar Glass Polymers Based on Sulfonylated Poly(2,6-dimethyl-1,4-phenylene oxide).

PubMed

Zhang, Zhongbo; Wang, David H; Litt, Morton H; Tan, Loon-Seng; Zhu, Lei

2018-02-05

A new class of high-temperature dipolar polymers based on sulfonylated poly(2,6-dimethyl-1,4-phenylene oxide) (SO 2 -PPO) was synthesized by post-polymer functionalization. Owing to the efficient rotation of highly polar methylsulfonyl side groups below the glass transition temperature (T g ≈220 °C), the dipolar polarization of these SO 2 -PPOs was enhanced, and thus the dielectric constant was high. Consequently, the discharge energy density reached up to 22 J cm -3 . Owing to its high T g  , the SO 2 -PPO 25 sample also exhibited a low dielectric loss. For example, the dissipation factor (tan δ) was 0.003, and the discharge efficiency at 800 MV m -1 was 92 %. Therefore, these dipolar glass polymers are promising for high-temperature, high-energy-density, and low-loss electrical energy storage applications. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Overcoming low-alignment signal contrast induced alignment failure by alignment signal enhancement

NASA Astrophysics Data System (ADS)

Lee, Byeong Soo; Kim, Young Ha; Hwang, Hyunwoo; Lee, Jeongjin; Kong, Jeong Heung; Kang, Young Seog; Paarhuis, Bart; Kok, Haico; de Graaf, Roelof; Weichselbaum, Stefan; Droste, Richard; Mason, Christopher; Aarts, Igor; de Boeij, Wim P.

2016-03-01

Overlay is one of the key factors which enables optical lithography extension to 1X node DRAM manufacturing. It is natural that accurate wafer alignment is a prerequisite for good device overlay. However, alignment failures or misalignments are commonly observed in a fab. There are many factors which could induce alignment problems. Low alignment signal contrast is one of the main issues. Alignment signal contrast can be degraded by opaque stack materials or by alignment mark degradation due to processes like CMP. This issue can be compounded by mark sub-segmentation from design rules in combination with double or quadruple spacer process. Alignment signal contrast can be improved by applying new material or process optimization, which sometimes lead to the addition of another process-step with higher costs. If we can amplify the signal components containing the position information and reduce other unwanted signal and background contributions then we can improve alignment performance without process change. In this paper we use ASML's new alignment sensor (as was introduced and released on the NXT:1980Di) and sample wafers with special stacks which can induce poor alignment signal to demonstrate alignment and overlay improvement.

Did the Moon have a dipolar field?

NASA Astrophysics Data System (ADS)

Boutin, D.; Arkani-Hamed, J.

2012-12-01

Did the Moon have a dipolar core field? Daniel Boutin1 (dboutin003@sympatico.ca) Jafar Arkani-Hamed2 (jafar@physics.utoronto.ca) 1Earth and Planetary Sciences, McGill University, Montreal, QC, H3A-2A7, Canada 2Physics, University of Toronto, Toronto, ON M5S 1A7, Canada The lack of a global scale magnetic field at present and the observed strong magnetic anomalies of the Moon suggest that the magnetic source bodies have been magnetized in the past. The origin of the magnetizing field is poorly understood. Several scenarios have been proposed including a strong core dynamo [1] and the external origin due to giant impacts such as the enhancement of an existing weak field by impact-generated plasmas or a transient field possibly generated during the impacts [2,3]. It is also possible that the existing field was not very strong but the source bodies are highly magnetic [4]. Here we test the hypothesis that the magnetizing field was of internal origin using two sets of data: the 150 degree spherical harmonic representation of the lunar crustal field by Purucker [5] and the raw magnetic data acquired by the Lunar Prospector magnetometer. Although 17 isolated magnetic anomalies are easily identified on the basis of the spherical harmonic representation, we model only 10 anomalies because of the lack of sufficient raw data over others. The isolated magnetic anomalies allow us to model each anomaly by a simple uniformly magnetized elliptical source body. We model the radial component of the magnetic field following the procedure adopted by Boutin and Arkani-Hamed [6] for the martian magnetic anomalies, and determine the three components of the magnetization vector. Seven out of 10 anomalies result in consistent source bodies obtained using the two sets of data. Assuming that each of the source bodies is magnetized by a dipole core field, the paleomagnetic pole of the Moon is determined on the basis of the corresponding magnetization vector. The resulting paleomagnetic pole

Confocal shift interferometry of coherent emission from trapped dipolar excitons

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

Repp, J.; Nanosystems Initiative Munich; Center for NanoScience and Fakultät für Physik, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München

2014-12-15

We introduce a confocal shift-interferometer based on optical fibers. The presented spectroscopy allows measuring coherence maps of luminescent samples with a high spatial resolution even at cryogenic temperatures. We apply the spectroscopy onto electrostatically trapped, dipolar excitons in a semiconductor double quantum well. We find that the measured spatial coherence length of the excitonic emission coincides with the point spread function of the confocal setup. The results are consistent with a temporal coherence of the excitonic emission down to temperatures of 250 mK.

Numerical simulations of motion-insensitive diffusion imaging based on the distant dipolar field effects.

PubMed

Lin, Tao; Sun, Huijun; Chen, Zhong; You, Rongyi; Zhong, Jianhui

2007-12-01

Diffusion weighting in MRI is commonly achieved with the pulsed-gradient spin-echo (PGSE) method. When combined with spin-warping image formation, this method often results in ghosts due to the sample's macroscopic motion. It has been shown experimentally (Kennedy and Zhong, MRM 2004;52:1-6) that these motion artifacts can be effectively eliminated by the distant dipolar field (DDF) method, which relies on the refocusing of spatially modulated transverse magnetization by the DDF within the sample itself. In this report, diffusion-weighted images (DWIs) using both DDF and PGSE methods in the presence of macroscopic sample motion were simulated. Numerical simulation results quantify the dependence of signals in DWI on several key motion parameters and demonstrate that the DDF DWIs are much less sensitive to macroscopic sample motion than the traditional PGSE DWIs. The results also show that the dipolar correlation distance (d(c)) can alter contrast in DDF DWIs. The simulated results are in good agreement with the experimental results reported previously.

Nanoscale control of competing interactions and geometrical frustration in a dipolar trident lattice.

PubMed

Farhan, Alan; Petersen, Charlotte F; Dhuey, Scott; Anghinolfi, Luca; Qin, Qi Hang; Saccone, Michael; Velten, Sven; Wuth, Clemens; Gliga, Sebastian; Mellado, Paula; Alava, Mikko J; Scholl, Andreas; van Dijken, Sebastiaan

2017-10-17

Geometrical frustration occurs when entities in a system, subject to given lattice constraints, are hindered to simultaneously minimize their local interactions. In magnetism, systems incorporating geometrical frustration are fascinating, as their behavior is not only hard to predict, but also leads to the emergence of exotic states of matter. Here, we provide a first look into an artificial frustrated system, the dipolar trident lattice, where the balance of competing interactions between nearest-neighbor magnetic moments can be directly controlled, thus allowing versatile tuning of geometrical frustration and manipulation of ground state configurations. Our findings not only provide the basis for future studies on the low-temperature physics of the dipolar trident lattice, but also demonstrate how this frustration-by-design concept can deliver magnetically frustrated metamaterials.Artificial magnetic nanostructures enable the study of competing frustrated interactions with more control over the system parameters than is possible in magnetic materials. Farhan et al. present a two-dimensional lattice geometry where the frustration can be controlled by tuning the unit cell parameters.

Influence of anisotropic dipolar interaction on the spin dynamics of Ni80Fe20 nanodot arrays arranged in honeycomb and octagonal lattices

NASA Astrophysics Data System (ADS)

Mondal, Sucheta; Barman, Saswati; Choudhury, Samiran; Otani, Yoshichika; Barman, Anjan

2018-07-01

Ultrafast spin dynamics in ferromagnetic nanodot arrays with dot diameter 100 nm and thickness 20 nm arranged in honeycomb and octagonal lattice symmetries are studied to explore the tunability of the collective magnetization dynamics. By varying the inter-dot separation between 30 nm and 300 nm drastic variation in the precessional dynamics from strongly collective to completely isolated regime has been observed by using all-optical time-resolved magneto-optical Kerr microscope. Micromagnetic simulation is exploited to gain insights about the resonant mode profiles and magnetic coupling between the nanodots. A significant spectral and spatial variation in the resonant mode with increasing dipolar interaction is demonstrated with increasing inter-dot separation. The spins driven by effective field inside single nanodots are prone to precess independently, generating two self-standing centre and edge modes in the array that are influenced by the relative orientation between the inter-dot coupling direction and bias magnetic field. The anisotropic behavior of dipolar field is rigorously investigated here. Splitting of the centre mode in case of octagonal lattice is experimentally observed here as a consequence of the anisotropic dipolar field between the nanodot pairs coupled horizontally and vertically, which is not found in the honeycomb lattice. In addition, proper understanding of the modification of dynamic mode profile by neighboring dipolar interaction built up here, is imperative for further control of the dynamic dipolar interaction and the corresponding collective excitation in magnonic crystals. The usage of nanodot lattices with complex basis structures can be advantageous for the designing of high density magnetic recording media, spin-wave filter and logic devices.

Oxygen-promoted catalyst sintering influences number density, alignment, and wall number of vertically aligned carbon nanotubes.

PubMed

Shi, Wenbo; Li, Jinjing; Polsen, Erik S; Oliver, C Ryan; Zhao, Yikun; Meshot, Eric R; Barclay, Michael; Fairbrother, D Howard; Hart, A John; Plata, Desiree L

2017-04-20

A lack of synthetic control and reproducibility during vertically aligned carbon nanotube (CNT) synthesis has stifled many promising applications of organic nanomaterials. Oxygen-containing species are particularly precarious in that they have both beneficial and deleterious effects and are notoriously difficult to control. Here, we demonstrated diatomic oxygen's ability, independent of water, to tune oxide-supported catalyst thin film dewetting and influence nanoscale (diameter and wall number) and macro-scale (alignment and density) properties for as-grown vertically aligned CNTs. In particular, single- or few-walled CNT forests were achieved at very low oxygen loading, with single-to-multi-walled CNT diameters ranging from 4.8 ± 1.3 nm to 6.4 ± 1.1 nm over 0-800 ppm O 2 , and an expected variation in alignment, where both were related to the annealed catalyst morphology. Morphological differences were not the result of subsurface diffusion, but instead occurred via Ostwald ripening under several hundred ppm O 2 , and this effect was mitigated by high H 2 concentrations and not due to water vapor (as confirmed in O 2 -free water addition experiments), supporting the importance of O 2 specifically. Further characterization of the interface between the Fe catalyst and Al 2 O 3 support revealed that either oxygen-deficit metal oxide or oxygen-adsorption on metals could be functional mechanisms for the observed catalyst nanoparticle evolution. Taken as a whole, our results suggest that the impacts of O 2 and H 2 on the catalyst evolution have been underappreciated and underleveraged in CNT synthesis, and these could present a route toward facile manipulation of CNT forest morphology through control of the reactive gaseous atmosphere alone.

Rapid water disinfection using vertically aligned MoS 2 nanofilms and visible light

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

Liu, Chong; Kong, Desheng; Hsu, Po -Chun

Here, solar energy is readily available in most climates and can be used for water purification. However, solar disinfection of drinking water (SODIS) mostly relies on ultraviolet light, which represents only 4% of total solar energy, and this leads to slow treatment speed. The development of new materials that can harvest visible light for water disinfection, and speed up solar water purification, is therefore highly desirable. Here, we show that few-layered vertically aligned MoS 2 (FLV-MoS 2) films can be used to harvest the whole spectrum of visible light (~ 50% of solar energy) and achieve highly efficient water disinfection.more » The bandgap of MoS 2 was increased from 1.3 eV to 1.55 eV by decreasing the domain size, which allowed the FLV-MoS 2 to generate reactive oxygen species (ROS) for bacterial inactivation in water. The FLV-MoS 2 showed ~15 times better log inactivation efficiency of indicator bacteria compared to bulk MoS 2, and much faster inactivation of bacteria under both visible light and sunlight illumination compared to widely used TiO 2. Moreover, by using a 5 nm copper film on top of the FLV-MoS 2 as a catalyst to facilitate electron-hole pair separation and promote the generation of ROS, the disinfection rate was further increased 6 fold. With our approach, we achieved water disinfection of >99.999% inactivation of bacteria in 20 minutes with a small amount of material (1.6 mg/L) under simulated visible light.« less

Rapid water disinfection using vertically aligned MoS 2 nanofilms and visible light

DOE PAGES

Liu, Chong; Kong, Desheng; Hsu, Po -Chun; ...

2016-08-15

Here, solar energy is readily available in most climates and can be used for water purification. However, solar disinfection of drinking water (SODIS) mostly relies on ultraviolet light, which represents only 4% of total solar energy, and this leads to slow treatment speed. The development of new materials that can harvest visible light for water disinfection, and speed up solar water purification, is therefore highly desirable. Here, we show that few-layered vertically aligned MoS 2 (FLV-MoS 2) films can be used to harvest the whole spectrum of visible light (~ 50% of solar energy) and achieve highly efficient water disinfection.more » The bandgap of MoS 2 was increased from 1.3 eV to 1.55 eV by decreasing the domain size, which allowed the FLV-MoS 2 to generate reactive oxygen species (ROS) for bacterial inactivation in water. The FLV-MoS 2 showed ~15 times better log inactivation efficiency of indicator bacteria compared to bulk MoS 2, and much faster inactivation of bacteria under both visible light and sunlight illumination compared to widely used TiO 2. Moreover, by using a 5 nm copper film on top of the FLV-MoS 2 as a catalyst to facilitate electron-hole pair separation and promote the generation of ROS, the disinfection rate was further increased 6 fold. With our approach, we achieved water disinfection of >99.999% inactivation of bacteria in 20 minutes with a small amount of material (1.6 mg/L) under simulated visible light.« less

Magnetic holes in the dipolarized magnetotail: ion and electron anisotropies

NASA Astrophysics Data System (ADS)

Shustov, P.; Artemyev, A.; Zhang, X. J.; Yushkov, E.; Petrukovich, A. A.

2017-12-01

We conduct statistics on magnetic holes observed by THEMIS spacecraft in the near-Earth magnetotail. Groups of holes are detected after dipolarizations in the quiet, equatorial plasma sheet. Magnetic holes are characterized by significant magnetic field depressions (up to 50%) and strong electron currents ( 10-50 nA/m2), with spatial scales much smaller than the ion gyroradius. These magnetic holes are populated by hot (>10 keV), transversely anisotropic electrons supporting the pressure balance. We present statistical properties of these sub-ion scale magnetic holes and discuss possible mechanisms on the hole formation.

New metal phthalocyanines/metal simple hydroxide multilayers: experimental evidence of dipolar field-driven magnetic behavior.

PubMed

Bourzami, Riadh; Eyele-Mezui, Séraphin; Delahaye, Emilie; Drillon, Marc; Rabu, Pierre; Parizel, Nathalie; Choua, Sylvie; Turek, Philippe; Rogez, Guillaume

2014-01-21

A series of new hybrid multilayers has been synthesized by insertion-grafting of transition metal (Cu(II), Co(II), Ni(II), and Zn(II)) tetrasulfonato phthalocyanines between layers of Cu(II) and Co(II) simple hydroxides. The structural and spectroscopic investigations confirm the formation of new layered hybrid materials in which the phthalocyanines act as pillars between the inorganic layers. The magnetic investigations show that all copper hydroxide-based compounds behave similarly, presenting an overall antiferromagnetic behavior with no ordering down to 1.8 K. On the contrary, the cobalt hydroxide-based compounds present a ferrimagnetic ordering around 6 K, regardless of the nature of the metal phthalocyanine between the inorganic layers. The latter observation points to strictly dipolar interactions between the inorganic layers. The amplitude of the dipolar field has been evaluated from X-band and Q-band EPR spectroscopy investigation (Bdipolar ≈ 30 mT).

Gold (I)-Catalyzed Diastereo- and Enantioselective 1,3-Dipolar Cycloaddition and Mannich Reactions of Azlactones

PubMed Central

Melhado, Asa D.; Amarante, Giovanni W.; Wang, Z. Jane; Luparia, Marco; Toste, F. Dean

2011-01-01

Azlactones participate in stereoselective reactions with electron-deficient alkenes and N-sulfonyl aldimines to give products of 1,3-dipolar cycloaddition and Mannich addition reactions respectively. Both of these reactions proceed with good to excellent diastereo- and enantioselectivity using a single class of gold-catalysts, namely C2-symmetric bis(phosphinegold(I) carboxylate)complexes. The development of the azlactone Mannich reaction to provide fully protected anti-α,β-diamino acid derivatives is described. 1,3-Dipolar cycloaddition reactions of several acyclic 1,2-disubstituted alkenes, and the chemistry of the resultant cycloadducts, are examined to probe the stereochemical course of this reaction. Reaction kinetics and tandem MS studies of both the cycloaddition and Mannich reactions are reported. These studies support a mechanism in which the gold complexes catalyze addition reactions through nucleophile activation rather than the more typical activation of the electrophilic reaction component. PMID:21341677

Development and application of high-resolution solid- state NMR dipolar recovery techniques for spin-1/2 nuclei

NASA Astrophysics Data System (ADS)

Joers, James M.

The use of magic angle spinning to obtain high resolution solid state spectra has been well documented. This resolution occurs by coherently averaging the chemical shift anisotropy and dipolar interactions to zero over the period of a full rotation. While this allows for higher resolution, the structural information is seemingly lost to the spectrometer eye. Thus, high resolution spectra and structural information appear to be mutually exlusive. Recently, the push in solid state NMR is the development of recoupling techniques which afford both high resolution and structural information. The following dissertation demonstrates the feasibility of implementing such experiments in solving real world problems, and is centered on devising a method to recover homonuclear dipolar interactions in the high resolution regime.

Self-assembly in Dipolar Fluids

NASA Astrophysics Data System (ADS)

Ronti, Michela; Kantorovich, Sofia

We are studying low temperature structural transitions in dipolar hard spheres (DHS), combining grand-canonical Monte Carlo simulations and direct analytical theoretical calculations. DHS is characterized by long-range anisotropic interactions: it consists of a point dipole at the center of a hard sphere. We are interested in low temperature and low density phase behaviour of DHS systems. From a theoretical point of view the process of self-assembly is not responsible for a phase transition; this belief was completely reverted by theoretical studies showing that the process of self-assembly is alone capable to induce phase transition. On the other hand in the last years it was proved that no sign of critical behaviour is observed, implementing efficient and tailored Monte Carlo algorithms. Moreover a theoretical approach based on Density Functional Theory was developed: a series of structural transitions were discovered providing evidence of a hierarchy in the structures on cooling. We are performing free-energy calculations in order to draw the phase diagram of DHS model. Comparing the numerical results with the theoretical ones shed light on the scenario of temperature induced structural transitions in magnetic nanocolloids. Etn-COLLDENSE (H2020-MCSA-ITN-2014, Grant No. 642774).

Dipolar sources of the early scalp somatosensory evoked potentials to upper limb stimulation. Effect of increasing stimulus rates.

PubMed

Valeriani, M; Restuccia, D; Di Lazzaro, V; Le Pera, D; Barba, C; Tonali, P; Mauguiere, F

1998-06-01

Brain electrical source analysis (BESA) of the scalp electroencephalographic activity is well adapted to distinguish neighbouring cerebral generators precisely. Therefore, we performed dipolar source modelling in scalp medium nerve somatosensory evoked potentials (SEPs) recorded at 1.5-Hz stimulation rate, where all the early components should be identifiable. We built a four-dipole model, which was issued from the grand average, and applied it also to recordings from single individuals. Our model included a dipole at the base of the skull and three other perirolandic dipoles. The first of the latter dipoles was tangentially oriented and was active at the same latencies as the N20/P20 potential and, with opposite polarity, the P24/N24 response. The second perirolandic dipole showed an initial peak of activity slightly earlier than that of the N20/P20 dipolar source and, later, it was active at the same latency as the central P22 potential. Lastly, the third perirolandic dipole explaining the fronto-central N30 potential scalp distribution was constantly more posterior than the first one. In order to evaluate the effect of an increasing repetition frequency on the activity of SEP dipolar sources, we applied the model built from 1.5-Hz SEPs to traces recorded at 3-Hz and 10-Hz repetition rates. We found that the 10-Hz stimulus frequency reduced selectively the later of the two activity phases of the first perirolandic dipole. The decrement in strength of this dipolar source can be explained if we assume that: (a) the later activity of the first perirolandic dipole can represent the inhibitory phase of a "primary response"; (b) two different clusters of cells generate the opposite activities of the tangential perirolandic dipole. An additional finding in our model was that two different perirolandic dipoles contribute to the centro-parietal N20 potential generation.

Communication: Strong laser alignment of solvent-solute aggregates in the gas-phase

NASA Astrophysics Data System (ADS)

Trippel, Sebastian; Wiese, Joss; Mullins, Terry; Küpper, Jochen

2018-03-01

Strong quasi-adiabatic laser alignment of the indole-water-dimer clusters, an amino-acid chromophore bound to a single water molecule through a hydrogen bond, was experimentally realized. The alignment was visualized through ion and electron imaging following strong-field ionization. Molecular-frame photoelectron angular distributions showed a clear suppression of the electron yield in the plane of the ionizing laser's polarization, which was analyzed as strong alignment of the molecular cluster with ⟨cos2 θ2D⟩ ≥ 0.9.

15N CSA tensors and 15N-1H dipolar couplings of protein hydrophobic core residues investigated by static solid-state NMR

NASA Astrophysics Data System (ADS)

Vugmeyster, Liliya; Ostrovsky, Dmitry; Fu, Riqiang

2015-10-01

In this work, we assess the usefulness of static 15N NMR techniques for the determination of the 15N chemical shift anisotropy (CSA) tensor parameters and 15N-1H dipolar splittings in powder protein samples. By using five single labeled samples of the villin headpiece subdomain protein in a hydrated lyophilized powder state, we determine the backbone 15N CSA tensors at two temperatures, 22 and -35 °C, in order to get a snapshot of the variability across the residues and as a function of temperature. All sites probed belonged to the hydrophobic core and most of them were part of α-helical regions. The values of the anisotropy (which include the effect of the dynamics) varied between 130 and 156 ppm at 22 °C, while the values of the asymmetry were in the 0.32-0.082 range. The Leu-75 and Leu-61 backbone sites exhibited high mobility based on the values of their temperature-dependent anisotropy parameters. Under the assumption that most differences stem from dynamics, we obtained the values of the motional order parameters for the 15N backbone sites. While a simple one-dimensional line shape experiment was used for the determination of the 15N CSA parameters, a more advanced approach based on the ;magic sandwich; SAMMY pulse sequence (Nevzorov and Opella, 2003) was employed for the determination of the 15N-1H dipolar patterns, which yielded estimates of the dipolar couplings. Accordingly, the motional order parameters for the dipolar interaction were obtained. It was found that the order parameters from the CSA and dipolar measurements are highly correlated, validating that the variability between the residues is governed by the differences in dynamics. The values of the parameters obtained in this work can serve as reference values for developing more advanced magic-angle spinning recoupling techniques for multiple labeled samples.

Reply to "Comment on 'Origin of tilted-phase generation in systems of ellipsoidal molecules with dipolar interactions' "

NASA Astrophysics Data System (ADS)

Bose, Tushar Kanti; Saha, Jayashree

2014-04-01

In a recent article [T. K. Bose and J. Saha, Phys. Rev. E 86, 050701 (2012), 10.1103/PhysRevE.86.050701], we have presented the results of a Monte Carlo simulation study of the systems of dipolar Gay-Berne ellipsoids where two terminal antiparallel dipoles are placed symmetrically on the long axis of each ellipsoid, and the results revealed the combined contribution of dipolar separation and transverse orientations in controlling the tilt angle in the tilted hexatic smectic phase. The tilt angle changed from zero to a significant value, in the case of transverse dipoles, with a change in the dipolar separation. In the related comment, Madhusudana [preceding Comment, Phys. Rev. E 89, 046501 (2014), 10.1103/PhysRevE.89.046501] has claimed that the physical origin of the molecular tilt in the significantly tilted phases found in the simulations is similar to that proposed by McMillan [Phys. Rev. A 8, 1921 (1973), 10.1103/PhysRevA.8.1921]. Here, we explain that the claim is not correct and make it clear that the two compared pictures are quite different. In the preceding Comment, Madhusudana has also suggested an alternative explanation for tilt generation in the simulations by criticizing the original one proposed by us. We argue here in support of the original explanation and clarify that his explanation does not follow the simulation results.

Variations of High-Energy Ions during Fast Plasma Flows and Dipolarization in the Plasma Sheet: Comparison Among Different Ion Species

NASA Astrophysics Data System (ADS)

Ohtani, S.; Nose, M.; Miyashita, Y.; Lui, A.

2014-12-01

We investigate the responses of different ion species (H+, He+, He++, and O+) to fast plasma flows and local dipolarization in the plasma sheet in terms of energy density. We use energetic (9-210 keV) ion composition measurements made by the Geotail satellite at r = 10~31 RE. The results are summarized as follows: (1) whereas the O+-to-H+ ratio decreases with earthward flow velocity, it increases with tailward flow velocity with Vx dependence steeper for perpendicular flows than for parallel flows; (2) for fast earthward flows, the energy density of each ion species increases without any clear preference for heavy ions; (3) for fast tailward flows the ion energy density increases initially, then it decreases to below pre-flow levels except for O+; (4) the O+-to-H+ ratio does not increase through local dipolarization irrespective of dipolarization amplitude, background BZ, X distance, and VX; (5) in general, the H+ and He++ ions behave similarly. Result (1) can be attributed to radial transport along with the earthward increase of the background O+-to-H+ ratio. Results (2) and (4) indicate that ion energization associated with local dipolarization is not mass-dependent possibly because in the energy range of our interest the ions are not magnetized irrespective of species. In the tailward outflow region of reconnection, where the plasma sheet becomes thinner, the H+ ions escape along the field line more easily than the O+ ions, which possibly explains result (3). Result (5) suggests that the solar wind is the primary source of the high-energy H+ ions.

Characteristics of Ion Distribution Functions in Dipolarizing FluxBundles: THEMIS Event Studies

NASA Astrophysics Data System (ADS)

Runov, A.; Artemyev, A.; Birn, J.; Pritchett, P. L.; Zhou, X.

2016-12-01

Taking advantage of multi-point observations from repeating configuration of the Time History of Events and Macroscale Interactions during Substorms (THEMIS) fleet with probe separation of 1 to 2 Earth radii (RE) along X, Y, and Z in the geocentric solar magnetospheric system (GSM), we study ion distribution functions observed by the probes during three transient dipolarization events. Comparing observations by the multiple probes, we characterize changes in the ion distribution functions with respect to geocentric distance (X), cross-tail probe separation (Y), and levels of |Bx|, which characterize the distance from the neutral sheet. We examined 2-D and 1-D cuts of the 3-D velocity distribution functions by the {Vb,Vbxv} plane. The results indicate that the velocity distribution functions observed inside the dipolarizing flux bundles (DFB) close to the magnetic equator are often perpendicularly anisotropic for velocities Vth≤v≤2Vth, where Vth is the ion thermal velocity. Ions of higher energies (v>2Vth) are isotropic. Hence, interaction of DFBs and ambient ions may result in the perpendicular anisotropy of the injecting energetic ions, which is an important factor for plasma waves and instabilities excitation and further particle acceleration in the inner magnetosphere. We also compare the observations with the results of test-particles and PIC simulations.

Oxygen-promoted catalyst sintering influences number density, alignment, and wall number of vertically aligned carbon nanotubes

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

Shi, Wenbo; Li, Jinjing; Polsen, Erik S.

A lack of synthetic control and reproducibility during vertically aligned carbon nanotube (CNT) synthesis has stifled many promising applications of organic nanomaterials. Oxygen-containing species are particularly precarious in that they have both beneficial and deleterious effects and are notoriously difficult to control. In this paper, we demonstrated diatomic oxygen's ability, independent of water, to tune oxide-supported catalyst thin film dewetting and influence nanoscale (diameter and wall number) and macro-scale (alignment and density) properties for as-grown vertically aligned CNTs. In particular, single- or few-walled CNT forests were achieved at very low oxygen loading, with single-to-multi-walled CNT diameters ranging from 4.8 ±more » 1.3 nm to 6.4 ± 1.1 nm over 0–800 ppm O 2, and an expected variation in alignment, where both were related to the annealed catalyst morphology. Morphological differences were not the result of subsurface diffusion, but instead occurred via Ostwald ripening under several hundred ppm O 2, and this effect was mitigated by high H 2 concentrations and not due to water vapor (as confirmed in O 2-free water addition experiments), supporting the importance of O 2 specifically. Further characterization of the interface between the Fe catalyst and Al 2O 3 support revealed that either oxygen-deficit metal oxide or oxygen-adsorption on metals could be functional mechanisms for the observed catalyst nanoparticle evolution. Finally, taken as a whole, our results suggest that the impacts of O 2 and H 2 on the catalyst evolution have been underappreciated and underleveraged in CNT synthesis, and these could present a route toward facile manipulation of CNT forest morphology through control of the reactive gaseous atmosphere alone.« less

Oxygen-promoted catalyst sintering influences number density, alignment, and wall number of vertically aligned carbon nanotubes

DOE PAGES

Shi, Wenbo; Li, Jinjing; Polsen, Erik S.; ...

2017-04-11

A lack of synthetic control and reproducibility during vertically aligned carbon nanotube (CNT) synthesis has stifled many promising applications of organic nanomaterials. Oxygen-containing species are particularly precarious in that they have both beneficial and deleterious effects and are notoriously difficult to control. In this paper, we demonstrated diatomic oxygen's ability, independent of water, to tune oxide-supported catalyst thin film dewetting and influence nanoscale (diameter and wall number) and macro-scale (alignment and density) properties for as-grown vertically aligned CNTs. In particular, single- or few-walled CNT forests were achieved at very low oxygen loading, with single-to-multi-walled CNT diameters ranging from 4.8 ±more » 1.3 nm to 6.4 ± 1.1 nm over 0–800 ppm O 2, and an expected variation in alignment, where both were related to the annealed catalyst morphology. Morphological differences were not the result of subsurface diffusion, but instead occurred via Ostwald ripening under several hundred ppm O 2, and this effect was mitigated by high H 2 concentrations and not due to water vapor (as confirmed in O 2-free water addition experiments), supporting the importance of O 2 specifically. Further characterization of the interface between the Fe catalyst and Al 2O 3 support revealed that either oxygen-deficit metal oxide or oxygen-adsorption on metals could be functional mechanisms for the observed catalyst nanoparticle evolution. Finally, taken as a whole, our results suggest that the impacts of O 2 and H 2 on the catalyst evolution have been underappreciated and underleveraged in CNT synthesis, and these could present a route toward facile manipulation of CNT forest morphology through control of the reactive gaseous atmosphere alone.« less

Aligning the unalignable: bacteriophage whole genome alignments.

PubMed

Bérard, Sèverine; Chateau, Annie; Pompidor, Nicolas; Guertin, Paul; Bergeron, Anne; Swenson, Krister M

2016-01-13

In recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for comparing whole genomes exist: dot plots diagrams give a mostly qualitative assessment of the similarity/dissimilarity between two or more genomes, and clustering techniques are used to classify genomes. Multiple alignments are conspicuously absent from this scene. Indeed, whole genome aligners interpret lack of similarity between sequences as an indication of rearrangements, insertions, or losses. This behavior makes them ill-prepared to align bacteriophage genomes, where even closely related strains can accomplish the same biological function with highly dissimilar sequences. In this paper, we propose a multiple alignment strategy that exploits functional collinearity shared by related strains of bacteriophages, and uses partial orders to capture mosaicism of sets of genomes. As classical alignments do, the computed alignments can be used to predict that genes have the same biological function, even in the absence of detectable similarity. The Alpha aligner implements these ideas in visual interactive displays, and is used to compute several examples of alignments of Staphylococcus aureus and Mycobacterium bacteriophages, involving up to 29 genomes. Using these datasets, we prove that Alpha alignments are at least as good as those computed by standard aligners. Comparison with the progressive Mauve aligner - which implements a partial order strategy, but whose alignments are linearized - shows a greatly improved interactive graphic display, while avoiding misalignments. Multiple alignments of whole bacteriophage genomes work, and will become an important conceptual and visual tool in comparative genomics of sets of related strains. A python implementation of Alpha, along with installation instructions for Ubuntu and OSX, is available on bitbucket (https://bitbucket.org/thekswenson/alpha).

Rapid water disinfection using vertically aligned MoS2 nanofilms and visible light

NASA Astrophysics Data System (ADS)

Liu, Chong; Kong, Desheng; Hsu, Po-Chun; Yuan, Hongtao; Lee, Hyun-Wook; Liu, Yayuan; Wang, Haotian; Wang, Shuang; Yan, Kai; Lin, Dingchang; Maraccini, Peter A.; Parker, Kimberly M.; Boehm, Alexandria B.; Cui, Yi

2016-12-01

Solar energy is readily available in most climates and can be used for water purification. However, solar disinfection of drinking water mostly relies on ultraviolet light, which represents only 4% of the total solar energy, and this leads to a slow treatment speed. Therefore, the development of new materials that can harvest visible light for water disinfection, and so speed up solar water purification, is highly desirable. Here we show that few-layered vertically aligned MoS2 (FLV-MoS2) films can be used to harvest the whole spectrum of visible light (∼50% of solar energy) and achieve highly efficient water disinfection. The bandgap of MoS2 was increased from 1.3 to 1.55 eV by decreasing the domain size, which allowed the FLV-MoS2 to generate reactive oxygen species (ROS) for bacterial inactivation in the water. The FLV-MoS2 showed a ∼15 times better log inactivation efficiency of the indicator bacteria compared with that of bulk MoS2, and a much faster inactivation of bacteria under both visible light and sunlight illumination compared with the widely used TiO2. Moreover, by using a 5 nm copper film on top of the FLV-MoS2 as a catalyst to facilitate electron-hole pair separation and promote the generation of ROS, the disinfection rate was increased a further sixfold. With our approach, we achieved water disinfection of >99.999% inactivation of bacteria in 20 min with a small amount of material (1.6 mg l-1) under simulated visible light.

Pure dipolar-interacted CoFe{sub 2}O{sub 4} nanoparticles and their magnetic properties

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

Xu, Shi-tao; School of Physics and Electronic Information, Huaibei Normal University, Huaibei 235000; Ma, Yong-qing, E-mail: yqma@ahu.edu.cn

2015-02-15

Graphical abstract: The mono-dispersed CoFe{sub 2}O{sub 4} nanoparticles with the uniform size of 10.5 ± 2 nm were first synthesized and then they were embedded in amorphous SiO{sub 2} matrix with different CoFe{sub 2}O{sub 4} nanoparticles’ concentrations. The large coercivity (3056 Oe) and the remanence ratio (0.63) were obtained by suitably diluting CoFe{sub 2}O{sub 4} nanoparticles into the SiO{sub 2} matrix. The reciprocal of the absolute maximum of δm and the M{sub r}/M{sub s} ratio behave in the same trend (as shown in (e)), indicating that the M{sub r}/M{sub s} ratio was dominated by the interparticle dipolar interaction. The presentmore » work is meaningful for revealing the underlying mechanism in nano-scaled magnetic system and improving the magnetic performance. - Highlights: • The mono-dispersed CoFe{sub 2}O{sub 4} nanoparticles with the uniform size of 10.5 ± 2 nm were synthesized by the thermal decomposition of metals acetylacetonates in solvents with high boiling point. • The large coercivity (3056 Oe) and the remanence ratio (0.63) were obtained by diluting CoFe{sub 2}O{sub 4} nanoparticles into the SiO{sub 2} matrix with a suitable concentration. • The surface anisotropy and interparticle dipolar interaction affect the magnetic performance and magnetic ordering state. • It was observed that the M{sub r}/M{sub s} ratio was dominated by the interparticle dipolar interaction. - Abstract: The mono-dispersed and uniform CoFe{sub 2}O{sub 4} nanoparticles were synthesized by the thermal decomposition of Fe(acac){sub 3} and Co(acac){sub 2}. Then the CoFe{sub 2}O{sub 4} nanoparticles were diluted in amorphous SiO{sub 2} matrix with different CoFe{sub 2}O{sub 4} nanoparticles’ concentrations. All samples show the positive or negative exchange bias behavior, indicating the presence of canted spin layer at the CoFe{sub 2}O{sub 4} nanoparticles’ surface. The large effective anisotropy constant (3.38 × 10{sup 6} erg/cm{sup 3}) was observed

MaxAlign: maximizing usable data in an alignment.

PubMed

Gouveia-Oliveira, Rodrigo; Sackett, Peter W; Pedersen, Anders G

2007-08-28

The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. MaxAlign is a program that optimizes the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid) symbols that are present in gap-free columns - the alignment area - by selecting the optimal subset of sequences to exclude from the alignment. MaxAlign can be used prior to phylogenetic and bioinformatical analyses as well as in other situations where this form of alignment improvement is useful. In this work we test MaxAlign's performance in these tasks and compare the accuracy of phylogenetic estimates including and excluding gapped columns from the analysis, with and without processing with MaxAlign. In this paper we also introduce a new simple measure of tree similarity, Normalized Symmetric Similarity (NSS) that we consider useful for comparing tree topologies. We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also show that it is not advisable to exclude gapped columns from phylogenetic analyses unless MaxAlign is used first. Finally, we find that the sequences removed by MaxAlign from an alignment tend to be those that would otherwise be associated with low phylogenetic accuracy, and that the presence of gaps in any given sequence does not seem to disturb the phylogenetic estimates of other sequences. The MaxAlign web-server is freely available online at http://www.cbs.dtu.dk/services/MaxAlign where supplementary information can also be found. The program is also freely available as a Perl stand-alone package.

Heat transport in electrically aligned multiwalled carbon nanotubes dispersed in water

NASA Astrophysics Data System (ADS)

Cervantes-Alvarez, F.; Macias, J. D.; Alvarado-Gil, J. J.

2018-02-01

A modified Ångström method was used to determine the thermal diffusivity and thermal conductivity of aqueous dispersions of multiwalled carbon nanotubes as a function of their weight fraction concentration and in the presence of an externally applied electric field. Measurements were performed in planar samples, with a fixed thickness of 3.18 mm applying an AC voltage in the range from 0 to 70~V_RMS and for concentrations of carbon nanotubes from 0 to 2 wf%. It is shown that this field induces the formation of clusters followed by their alignment along the electric field, which can favor heat transfer in that direction. Heat transfer measurements show two regimes, in the first one under 0.5 wf%, voltages lower than 30~V_RMS are not strong enough to induce the adequate order of the carbon nanostructures, and as a consequence, thermal diffusivity of the dispersion remains close to the thermal diffusivity of water. In contrast for higher concentrations (above 1.5 wf%), 10~V_RMS are enough to get a good alignment. Above such thresholds of concentrations and voltages, thermal diffusivity and conductivity increase, when the electric field is increased, in such a way that for an applied voltage of 20~V_RMS and for a concentration of 1.5 wf%, an increase of 49% of the thermal conductivity was obtained. It is also shown that this approach exhibits limits, due to the fact that the electric-field induced structure, can act as a heating element at high electric field intensities and carbon nanotubes concentrations, which can induce convection and evaporation of the liquid matrix.

Application of Alignment Methodologies to Spatial Ontologies in the Hydro Domain

NASA Astrophysics Data System (ADS)

Lieberman, J. E.; Cheatham, M.; Varanka, D.

2015-12-01

Ontologies are playing an increasing role in facilitating mediation and translation between datasets representing diverse schemas, vocabularies, or knowledge communities. This role is relatively straightforward when there is one ontology comprising all relevant common concepts that can be mapped to entities in each dataset. Frequently, one common ontology has not been agreed to. Either each dataset is represented by a distinct ontology, or there are multiple candidates for commonality. Either the one most appropriate (expressive, relevant, correct) ontology must be chosen, or else concepts and relationships matched across multiple ontologies through an alignment process so that they may be used in concert to carry out mediation or other semantic operations. A resulting alignment can be effective to the extent that entities in in the ontologies represent differing terminology for comparable conceptual knowledge. In cases such as spatial ontologies, though, ontological entities may also represent disparate conceptualizations of space according to the discernment methods and application domains on which they are based. One ontology's wetland concept may overlap in space with another ontology's recharge zone or wildlife range or water feature. In order to evaluate alignment with respect to spatial ontologies, alignment has been applied to a series of ontologies pertaining to surface water that are used variously in hydrography (characterization of water features), hydrology (study of water cycling), and water quality (nutrient and contaminant transport) application domains. There is frequently a need to mediate between datasets in each domain in order to develop broader understanding of surface water systems, so there is a practical as well theoretical value in the alignment. From a domain expertise standpoint, the ontologies under consideration clearly contain some concepts that are spatially as well as conceptually identical and then others with less clear

Self-replication with magnetic dipolar colloids

NASA Astrophysics Data System (ADS)

Dempster, Joshua M.; Zhang, Rui; Olvera de la Cruz, Monica

2015-10-01

Colloidal self-replication represents an exciting research frontier in soft matter physics. Currently, all reported self-replication schemes involve coating colloidal particles with stimuli-responsive molecules to allow switchable interactions. In this paper, we introduce a scheme using ferromagnetic dipolar colloids and preprogrammed external magnetic fields to create an autonomous self-replication system. Interparticle dipole-dipole forces and periodically varying weak-strong magnetic fields cooperate to drive colloid monomers from the solute onto templates, bind them into replicas, and dissolve template complexes. We present three general design principles for autonomous linear replicators, derived from a focused study of a minimalist sphere-dimer magnetic system in which single binding sites allow formation of dimeric templates. We show via statistical models and computer simulations that our system exhibits nonlinear growth of templates and produces nearly exponential growth (low error rate) upon adding an optimized competing electrostatic potential. We devise experimental strategies for constructing the required magnetic colloids based on documented laboratory techniques. We also present qualitative ideas about building more complex self-replicating structures utilizing magnetic colloids.

Particle-in-cell Simulation of Dipolarization Front Associated Whistlers

NASA Astrophysics Data System (ADS)

Lin, D.; Scales, W.; Ganguli, G.; Crabtree, C. E.

2017-12-01

Dipolarization fronts (DFs) are dipolarized magnetic field embedded in the Earthward propagating bursty bulk flows (BBFs), which separates the hot, tenuous high-speed flow from the cold, dense, and slowly convecting surrounding plasma [Runov et al. 2011]. Broadband fluctuations have been observed at DFs including the electromagnetic whistler waves and electrostatic lower hybrid waves in the Very Low Frequency (VLF) range [e.g., Zhou et al. 2009, Deng et al. 2010]. There waves are suggested to be able heat electrons and play a critical role in the plasma sheet dynamics [Chaston et al., 2012, Angelopoulos et al., 2013]. However, their generation mechanism and role in the energy conversion are still under debate. The gradient scale of magnetic field, plasma density at DFs in the near-Earth magnetotail is comparable to or lower than the ion gyro radius [Runov et al., 2011, Fu et al., 2012, Breuillard et al., 2016]. Such strongly inhomogeneous configuration could be unstable to the electron-ion hybrid (EIH) instability, which arises from strongly sheared transverse flow and is in the VLF range [Ganguli et al. 1988, Ganguli et al. 2014]. The equilibrium of the EIH theory implies an anisotropy of electron temperature, which are likely to drive the whistler waves observed in DFs [Deng et al., 2010, Gary et al., 2011]. In order to better understand how the whistler waves are generated in DFs and whether the EIH theory is applicable, a fully electromagnetic particle-in-cell (EMPIC) model is used to simulate the EIH instability with similar equilibrium configurations in DF observations. The EMPIC model deals with three dimensions in the velocity space and two dimensions in the configuration space, which is quite ready to include the third configuration dimension. Simulation results will be shown in this presentation.

Dipolar filtered magic-sandwich-echoes as a tool for probing molecular motions using time domain NMR

NASA Astrophysics Data System (ADS)

Filgueiras, Jefferson G.; da Silva, Uilson B.; Paro, Giovanni; d'Eurydice, Marcel N.; Cobo, Márcio F.; deAzevedo, Eduardo R.

2017-12-01

We present a simple 1 H NMR approach for characterizing intermediate to fast regime molecular motions using 1 H time-domain NMR at low magnetic field. The method is based on a Goldmann Shen dipolar filter (DF) followed by a Mixed Magic Sandwich Echo (MSE). The dipolar filter suppresses the signals arising from molecular segments presenting sub kHz mobility, so only signals from mobile segments are detected. Thus, the temperature dependence of the signal intensities directly evidences the onset of molecular motions with rates higher than kHz. The DF-MSE signal intensity is described by an analytical function based on the Anderson Weiss theory, from where parameters related to the molecular motion (e.g. correlation times and activation energy) can be estimated when performing experiments as function of the temperature. Furthermore, we propose the use of the Tikhonov regularization for estimating the width of the distribution of correlation times.

Independent EEG Sources Are Dipolar

PubMed Central

Delorme, Arnaud; Palmer, Jason; Onton, Julie; Oostenveld, Robert; Makeig, Scott

2012-01-01

Independent component analysis (ICA) and blind source separation (BSS) methods are increasingly used to separate individual brain and non-brain source signals mixed by volume conduction in electroencephalographic (EEG) and other electrophysiological recordings. We compared results of decomposing thirteen 71-channel human scalp EEG datasets by 22 ICA and BSS algorithms, assessing the pairwise mutual information (PMI) in scalp channel pairs, the remaining PMI in component pairs, the overall mutual information reduction (MIR) effected by each decomposition, and decomposition ‘dipolarity’ defined as the number of component scalp maps matching the projection of a single equivalent dipole with less than a given residual variance. The least well-performing algorithm was principal component analysis (PCA); best performing were AMICA and other likelihood/mutual information based ICA methods. Though these and other commonly-used decomposition methods returned many similar components, across 18 ICA/BSS algorithms mean dipolarity varied linearly with both MIR and with PMI remaining between the resulting component time courses, a result compatible with an interpretation of many maximally independent EEG components as being volume-conducted projections of partially-synchronous local cortical field activity within single compact cortical domains. To encourage further method comparisons, the data and software used to prepare the results have been made available (http://sccn.ucsd.edu/wiki/BSSComparison). PMID:22355308

Flow-driven alignment of carbon nanotubes during floating evaporative self assembly

NASA Astrophysics Data System (ADS)

Berson, Arganthael; Jinkins, Katherine; Chan, Jason; Brady, Gerald; Gronski, Kjerstin; Gopalan, Padma; Evensen, Harold; Arnold, Michael

2017-11-01

Individual semi-conducting single-wall carbon nanotubes (s-SWCNTs) exhibit exceptional electronic properties, which makes them promising candidates for the next generation of semi-conductor electronics. In practice, field-effect transistors (FETs) are fabricated from arrays of s-SWCNTs deposited onto a substrate. In order to achieve high electronic performance, the s-SWCNTs in these arrays must be densely packed and well aligned. Floating Evaporative Self Assembly (FESA) is a new deposition technique developed at the UW-Madison that can achieve such high-quality s-SWCNT alignment. For example, it was used to fabricate the first s-SWCNT-based FETs to outperform gallium arsenide and silicon FETs. In FESA, a droplet of ink containing the s-SWCNTs is deposited onto a pool of water. The ink spreads on the water surface towards a substrate that is vertically pulled out of the water. A band of aligned s-SWCNTs is deposited with each drop of ink. High-speed imaging is combined with cross-polarized microscopy to elucidate the mechanisms behind the exceptional alignment of s-SWCNTs. Two key mechanisms are 1) the collection of s-SWCNTs at the ink-water interface and 2) the depinning of the air-ink-substrate contact line. Avenues for scaling up FESA will be presented.

Dipolarizing flux bundles in the cis-geosynchronous magnetosphere: relationship between electric fields and energetic particle injections

NASA Astrophysics Data System (ADS)

Liu, J.; Angelopoulos, V.; Zhang, X. J.; Turner, D. L.; Gabrielse, C.; Runov, A.; Funsten, H. O.; Spence, H. E.

2015-12-01

Dipolarizing flux bundles (DFBs) are small flux tubes (typically < 3 RE in XGSM and YGSM) in the nightside magnetosphere that have magnetic field more dipolar than the background field. Although DFBs are known to accelerate particles to create energetic particle injections, their acceleration mechanism and importance in generating injections inside geosynchronous orbit remain open questions. To answer these questions, we investigate DFBs in the inner magnetosphere by conducting a statistical study with data from the Van Allen Probes. The results show that just like DFBs outside geosynchronous orbit, those inside that orbit occur most often in the pre-midnight sector. Half the DFBs are accompanied by energetic particle injection. Statistically, DFBs with injection have an electric field three times that of those without. All the injections accompanying DFBs appear dispersionless within the temporal and energy resolution considered. These findings suggest that the injections are ushered or locally produced by the DFB, and the DFB's strong electric field is an important aspect of the injection generation mechanism.

Dramatic improvement in water retention and proton conductivity in electrically aligned functionalized CNT/SPEEK nanohybrid PEM.

PubMed

Gahlot, Swati; Kulshrestha, Vaibhav

2015-01-14

Nanohybrid membranes of electrically aligned functionalized carbon nanotube f CNT with sulfonated poly ether ether ketone (SPEEK) have been successfully prepared by solution casting. Functionalization of CNTs was done through a carboxylation and sulfonation route. Further, a constant electric field (500 V·cm(-2)) has been applied to align CNTs in the same direction during the membrane drying process. All the membranes are characterized chemically, thermally, and mechanically by the means of FTIR, DSC, DMA, UTM, SEM, TEM, and AFM techniques. Intermolecular interactions between the components in hybrid membranes are established by FTIR. Physicochemical measurements were done to analyze membrane stability. Membranes are evaluated for proton conductivity (30-90 °C) and methanol crossover resistance to reveal their potential for direct methanol fuel cell application. Incorporation of f CNT reasonably increases the ion-exchange capacity, water retention, and proton conductivity while it reduces the methanol permeability. The maximum proton conductivity has been found in the S-sCNT-5 nanohybrid PEM with higher methanol crossover resistance. The prepared membranes can be also used for electrode material for fuel cells and batteries.

Quantum-Fluctuation-Driven Crossover from a Dilute Bose-Einstein Condensate to a Macrodroplet in a Dipolar Quantum Fluid

NASA Astrophysics Data System (ADS)

Chomaz, L.; Baier, S.; Petter, D.; Mark, M. J.; Wächtler, F.; Santos, L.; Ferlaino, F.

2016-10-01

In a joint experimental and theoretical effort, we report on the formation of a macrodroplet state in an ultracold bosonic gas of erbium atoms with strong dipolar interactions. By precise tuning of the s -wave scattering length below the so-called dipolar length, we observe a smooth crossover of the ground state from a dilute Bose-Einstein condensate to a dense macrodroplet state of more than 2 ×104 atoms . Based on the study of collective excitations and loss features, we prove that quantum fluctuations stabilize the ultracold gas far beyond the instability threshold imposed by mean-field interactions. Finally, we perform expansion measurements, showing that although self-bound solutions are prevented by losses, the interplay between quantum stabilization and losses results in a minimal time-of-flight expansion velocity at a finite scattering length.

AlignMe—a membrane protein sequence alignment web server

PubMed Central

Stamm, Marcus; Staritzbichler, René; Khafizov, Kamil; Forrest, Lucy R.

2014-01-01

We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences. Access is available at http://www.bioinfo.mpg.de/AlignMe PMID:24753425

Isoxazolodihydropyridinones: 1,3-dipolar cycloaddition of nitrile oxides onto 2,4-dioxopiperidines

PubMed Central

Coffman, Keith C.; Hartley, Timothy P.; Dallas, Jerry L.; Kurth, Mark J.

2012-01-01

Practical and efficient methods have been developed for the diversity-oriented synthesis of isoxazolodihydropyridinones via the 1,3-dipolar cycloaddition of nitrile oxides onto 2,4-dioxopiperidines. A select few of these isoxazolodihydropyridinones were further elaborated with triazoles by copper catalyzed azide-alkyne cycloaddition reactions. A total of 70 compounds and intermediates were synthesized and analyzed for drug likeness. Sixty-four of these novel compounds were submitted to the NIH Molecular Libraries Small Molecule Repository for high-throughput biological screening. PMID:22352295

Reversible switching of liquid crystalline order permits synthesis of homogeneous populations of dipolar patchy microparticles

DOE PAGES

Wang, Xiaoguang; Miller, Daniel S.; de Pablo, Juan J.; ...

2014-08-15

The spontaneous positioning of colloids on the surfaces of micrometer-sized liquid crystal (LC) droplets and their subsequent polymerization offers the basis of a general and facile method for the synthesis of patchy microparticles. The existence of multiple local energetic minima, however, can generate kinetic traps for colloids on the surfaces of the LC droplets and result in heterogeneous populations of patchy microparticles. To address this issue, in this paper it is demonstrated that adsorbate-driven switching of the internal configurations of LC droplets can be used to sweep colloids to a single location on the LC droplet surfaces, thus resulting inmore » the synthesis of homogeneous populations of patchy microparticles. The surface-driven switching of the LC can be triggered by addition of surfactant or salts, and permits the synthesis of dipolar microparticles as well as “Janus-like” microparticles. Finally, by using magnetic colloids, the utility of the approach is illustrated by synthesizing magnetically responsive patchy microdroplets of LC with either dipolar or quadrupolar symmetry that exhibit distinct optical responses upon application of an external magnetic field.« less

Weaker axially dipolar time-averaged paleomagnetic field based on multidomain-corrected paleointensities from Galapagos lavas.

PubMed

Wang, Huapei; Kent, Dennis V; Rochette, Pierre

2015-12-08

The geomagnetic field is predominantly dipolar today, and high-fidelity paleomagnetic mean directions from all over the globe strongly support the geocentric axial dipole (GAD) hypothesis for the past few million years. However, the bulk of paleointensity data fails to coincide with the axial dipole prediction of a factor-of-2 equator-to-pole increase in mean field strength, leaving the core dynamo process an enigma. Here, we obtain a multidomain-corrected Pliocene-Pleistocene average paleointensity of 21.6 ± 11.0 µT recorded by 27 lava flows from the Galapagos Archipelago near the Equator. Our new result in conjunction with a published comprehensive study of single-domain-behaved paleointensities from Antarctica (33.4 ± 13.9 µT) that also correspond to GAD directions suggests that the overall average paleomagnetic field over the past few million years has indeed been dominantly dipolar in intensity yet only ∼ 60% of the present-day field strength, with a long-term average virtual axial dipole magnetic moment of the Earth of only 4.9 ± 2.4 × 10(22) A ⋅ m(2).

Creation of a strongly dipolar gas of ultracold ground-state 23 Na87 Rb molecules

NASA Astrophysics Data System (ADS)

Guo, Mingyang; Zhu, Bing; Lu, Bo; Ye, Xin; Wang, Fudong; Wang, Dajun; Vexiau, Romain; Bouloufa-Maafa, Nadia; Quéméner, Goulven; Dulieu, Olivier

2016-05-01

We report on successful creation of an ultracold sample of ground-state 23 Na87 Rb molecules with a large effective electric dipole moment. Through a carefully designed two-photon Raman process, we have successfully transferred the magneto-associated Feshbach molecules to the singlet ground state with high efficiency, obtaining up to 8000 23 Na87 Rb molecules with peak number density over 1011 cm-3 in their absolute ground-state level. With an external electric field, we have induced an effective dipole moment over 1 Debye, making 23 Na87 Rb the most dipolar ultracold particle ever achieved. Contrary to the expectation, we observed a rather fast population loss even for 23 Na87 Rb in the absolute ground state with the bi-molecular exchange reaction energetically forbidden. The origin for the short lifetime and possible ways of mitigating it are currently under investigation. Our achievements pave the way toward investigation of ultracold bosonic molecules with strong dipolar interactions. This work is supported by the Hong Kong RGC CUHK404712 and the ANR/RGC Joint Research Scheme ACUHK403/13.

Weaker axially dipolar time-averaged paleomagnetic field based on multidomain-corrected paleointensities from Galapagos lavas

PubMed Central

Wang, Huapei; Kent, Dennis V.; Rochette, Pierre

2015-01-01

The geomagnetic field is predominantly dipolar today, and high-fidelity paleomagnetic mean directions from all over the globe strongly support the geocentric axial dipole (GAD) hypothesis for the past few million years. However, the bulk of paleointensity data fails to coincide with the axial dipole prediction of a factor-of-2 equator-to-pole increase in mean field strength, leaving the core dynamo process an enigma. Here, we obtain a multidomain-corrected Pliocene–Pleistocene average paleointensity of 21.6 ± 11.0 µT recorded by 27 lava flows from the Galapagos Archipelago near the Equator. Our new result in conjunction with a published comprehensive study of single-domain–behaved paleointensities from Antarctica (33.4 ± 13.9 µT) that also correspond to GAD directions suggests that the overall average paleomagnetic field over the past few million years has indeed been dominantly dipolar in intensity yet only ∼60% of the present-day field strength, with a long-term average virtual axial dipole magnetic moment of the Earth of only 4.9 ± 2.4 × 1022 A⋅m2. PMID:26598664

Ground state of dipolar hard spheres confined in channels

NASA Astrophysics Data System (ADS)

Deißenbeck, Florian; Löwen, Hartmut; Oǧuz, Erdal C.

2018-05-01

We investigate the ground state of a classical two-dimensional system of hard-sphere dipoles confined between two hard walls. Using lattice sum minimization techniques we reveal that at fixed wall separations, a first-order transition from a vacuum to a straight one-dimensional chain of dipoles occurs upon increasing the density. Further increase in the density yields the stability of an undulated chain as well as nontrivial buckling structures. We explore the close-packed configurations of dipoles in detail, and we find that, in general, the densest packings of dipoles possess complex magnetizations along the principal axis of the slit. Our predictions serve as a guideline for experiments with granular dipolar and magnetic colloidal suspensions confined in slitlike channel geometry.

Hidden magnetism in periodically modulated one dimensional dipolar fermions

NASA Astrophysics Data System (ADS)

Fazzini, S.; Montorsi, A.; Roncaglia, M.; Barbiero, L.

2017-12-01

The experimental realization of time-dependent ultracold lattice systems has paved the way towards the implementation of new Hubbard-like Hamiltonians. We show that in a one-dimensional two-components lattice dipolar Fermi gas the competition between long range repulsion and correlated hopping induced by periodically modulated on-site interaction allows for the formation of hidden magnetic phases, with degenerate protected edge modes. The magnetism, characterized solely by string-like nonlocal order parameters, manifests in the charge and/or in the spin degrees of freedom. Such behavior is enlighten by employing Luttinger liquid theory and numerical methods. The range of parameters for which hidden magnetism is present can be reached by means of the currently available experimental setups and probes.

CHARGED TORI IN SPHERICAL GRAVITATIONAL AND DIPOLAR MAGNETIC FIELDS

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

Slany, P.; Kovar, J.; Stuchlik, Z.

2013-03-01

A Newtonian model of non-conductive, charged, perfect fluid tori orbiting in combined spherical gravitational and dipolar magnetic fields is presented and stationary, axisymmetric toroidal structures are analyzed. Matter in such tori exhibits a purely circulatory motion and the resulting convection carries charges into permanent rotation around the symmetry axis. As a main result, we demonstrate the possible existence of off-equatorial charged tori and equatorial tori with cusps that also enable outflows of matter from the torus in the Newtonian regime. These phenomena qualitatively represent a new consequence of the interplay between gravity and electromagnetism. From an astrophysical point of view,more » our investigation can provide insight into processes that determine the vertical structure of dusty tori surrounding accretion disks.« less

Interpretation of magnetization transfer from inhomogeneously broadened lines (ihMT) in tissues as a dipolar order effect within motion restricted molecules

NASA Astrophysics Data System (ADS)

Varma, G.; Girard, O. M.; Prevost, V. H.; Grant, A. K.; Duhamel, G.; Alsop, D. C.

2015-11-01

Comparison of off-resonance saturation with single and dual frequency irradiation indicates a contribution of inhomogeneously broadened lines to magnetization transfer in tissues. This inhomogeneous magnetization transfer (ihMT) phenomenon can be exploited to produce images that highlight tissues containing myelin, in vivo. Here, a model for ihMT is described that includes dipolar order effects from magnetization associated with motion-restricted macromolecules. In this model, equal irradiation at positive and negative frequency offsets eliminates dipolar order and achieves greater saturation than irradiation at a single offset frequency using the same power. Fitting of mouse and human volunteer brain data at different irradiation powers and offset frequencies was performed to assess the relevance of the model and approximate tissue parameters. A key parameter in determining ihMT signal was found to be the relaxation time T1D associated with the dipolar order reservoir and the fraction f of the semi-solid, bound magnetization that possessed a nonzero T1D. Indeed, better fits of myelinated tissue were achieved when assuming f ≠ 1. From such fits, estimated T1Ds of mice in the white matter, (34 ± 14)ms, were much longer than in muscle, T1D = (1 ± 1)ms and the average f from white matter volunteer data was 2.2 times greater than that in grey matter. The combination of f and longer T1Ds was primarily responsible for the much higher ihMT in myelinated tissues, and provided explanation for the species variation. This dipolar order ihMT model should help guide future research, pulse sequence optimization, and clinical applications.

Collective alignment of nanorods in thin Newtonian films

NASA Astrophysics Data System (ADS)

Gu, Yu; Burtovyy, Ruslan; Townsend, James; Owens, Jeffery; Luzinov, Igor; Kornev, Konstantin

2013-11-01

We provide a complete analytical description of the alignment kinetics of magnetic nanorods in magnetic field. Nickel nanorods were formed by template electrochemical deposition in alumina membranes from a dispersion in a water-glycerol mixture. To ensure uniformity of the dispersion, the surface of the nickel nanorods was covered with polyvinylpyrrolidone (PVP). A 40-70 nm coating prevented aggregation of nanoroda. These modifications allowed us to control alignment of the nanorods in a magnetic field and test the proposed theory. An orientational distribution function of nanorods was introduced. We demonstrated that the 0.04% volume fraction of nanorods in the glycerol-water mixture behaves as a system of non-interacting particles. However, the kinetics of alignment of a nanorod assembly does not follow the predictions of the single-nanorod theory. The distribution function theory explains the kinetics of alignment of a nanorod assembly and shows the significance of the initial distribution of nanorods in the film. It can be used to develop an experimental protocol for controlled ordering of magnetic nanorods in thin films. This work was supported by the Air Force Office of Scientific Research, Grant numbers FA9550-12-1-0459 and FA8650-09-D-507 5900.

Frustrated Magnetism of Dipolar Molecules on a Square Optical Lattice: Prediction of a Quantum Paramagnetic Ground State

NASA Astrophysics Data System (ADS)

Zou, Haiyuan; Zhao, Erhai; Liu, W. Vincent

2017-08-01

Motivated by the experimental realization of quantum spin models of polar molecule KRb in optical lattices, we analyze the spin 1 /2 dipolar Heisenberg model with competing anisotropic, long-range exchange interactions. We show that, by tilting the orientation of dipoles using an external electric field, the dipolar spin system on square lattice comes close to a maximally frustrated region similar, but not identical, to that of the J1-J2 model. This provides a simple yet powerful route to potentially realize a quantum spin liquid without the need for a triangular or kagome lattice. The ground state phase diagrams obtained from Schwinger-boson and spin-wave theories consistently show a spin disordered region between the Néel, stripe, and spiral phase. The existence of a finite quantum paramagnetic region is further confirmed by an unbiased variational ansatz based on tensor network states and a tensor renormalization group.

Dipolar DC Collisional Activation in a "Stretched" 3-D Ion Trap: The Effect of Higher Order Fields on rf-Heating

NASA Astrophysics Data System (ADS)

Prentice, Boone M.; McLuckey, Scott A.

2012-04-01

Applying dipolar DC (DDC) to the end-cap electrodes of a 3-D ion trap operated with a bath gas at roughly 1 mTorr gives rise to `rf-heating' and can result in collision-induced dissociation (CID). This approach to ion trap CID differs from the conventional single-frequency resonance excitation approach in that it does not rely on tuning a supplementary frequency to coincide with the fundamental secular frequeny of the precursor ion of interest. Simulations using the program ITSIM 5.0 indicate that application of DDC physically displaces ions solely in the axial (inter end-cap) dimension whereupon ion acceleration occurs via power absorption from the drive rf. Experimental data shows that the degree of rf-heating in a stretched 3-D ion trap is not dependent solely on the ratio of the dipolar DC voltage/radio frequency (rf) amplitude, as a model based on a pure quadrupole field suggests. Rather, ion temperatures are shown to increase as the absolute values of the dipolar DC and rf amplitude both decrease. Simulations indicate that the presence of higher order multi-pole fields underlies this unexpected behavior. These findings have important implications for the use of DDC as a broad-band activation approach in multi-pole traps.

Pushing the limit of NMR-based distance measurements - retrieving dipolar couplings to spins with extensively large quadrupolar frequencies.

PubMed

Makrinich, M; Nimerovsky, E; Goldbourt, A

2018-04-14

Dipolar recoupling under magic-angle spinning allows to measure accurate inter-nuclear distances provided that the two interacting spins can be efficiently and uniformly excited. Alexander (Lex) Vega has shown that adiabatic transfers of populations in quadrupolar spins during the application of constant-wave (cw) radio-frequency pulses lead to efficient and quantifiable dipolar recoupling curves. Accurate distance determination within and beyond the adiabatic regime using cw pulses is limited by the size of the quadrupolar coupling constant. Here we show that using the approach of long-pulse phase modulation, dipolar recoupling and accurate distances can be obtained for nuclei having extensively large quadrupolar frequencies of 5-10 MHz. We demonstrate such results by obtaining a 31 P- 79/81 Br distance in a compound for which bromine-79 (spin-3/2) has a quadrupolar coupling constant of 11.3 MHz, and a 13 C- 209 Bi distance where the bismuth (spin-9/2) has a quadrupolar coupling constant of 256 MHz, equaling a quadrupolar frequency of 10.7 MHz. For Bromine, we demonstrate that an analytical curve based on the assumption of complete spin saturation fits the data. In the case of bismuth acetate, a C-Bi 3 spin system must be used in order to match the correct saturation recoupling curve, and results are in agreement with the crystallographic structure. Copyright © 2018 Elsevier Inc. All rights reserved.

Quantum rotor model for a Bose-Einstein condensate of dipolar molecules.

PubMed

Armaitis, J; Duine, R A; Stoof, H T C

2013-11-22

We show that a Bose-Einstein condensate of heteronuclear molecules in the regime of small and static electric fields is described by a quantum rotor model for the macroscopic electric dipole moment of the molecular gas cloud. We solve this model exactly and find the symmetric, i.e., rotationally invariant, and dipolar phases expected from the single-molecule problem, but also an axial and planar nematic phase due to many-body effects. Investigation of the wave function of the macroscopic dipole moment also reveals squeezing of the probability distribution for the angular momentum of the molecules.

Photoinduced Bioorthogonal 1,3-Dipolar Poly-cycloaddition Promoted by Oxyanionic Substrates for Spatiotemporal Operation of Molecular Glues.

PubMed

Hatano, Junichi; Okuro, Kou; Aida, Takuzo

2016-01-04

PGlue(PZ), a pyrazoline (PZ)-based fluorescent adhesive which can be generated spatiotemporally in living systems, was developed. Since PGlue(PZ) carries many guanidinium ion (Gu(+)) pendants, it strongly adheres to various oxyanionic substrates through a multivalent salt-bridge interaction. PGlue(PZ) is given by bioorthogonal photopolymerization of a Gu(+)-appended monomer (Glue(TZ)), bearing tetrazole (TZ) and olefinic termini. Upon exposure to UV light, Glue(TZ) transforms into a nitrileimine (NI) intermediate (Glue(NI)), which is eligible for 1,3-dipolar polycycloaddition. However, Glue(NI) in aqueous media can concomitantly be deactivated into Glue(WA) by the addition of water, and the polymerization hardly occurs unless Glue(NI) is concentrated. We found that, even under high dilution, Glue(NI) is concentrated on oxyanionic substrates to a sufficient level for the polymerization, so that their surfaces can be point-specifically functionalized with PGlue(PZ) by the use of a focused beam of UV light. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Energy conversion and dissipation at dipolarization fronts: Theory, modeling and MMS observations

NASA Astrophysics Data System (ADS)

Sitnov, M. I.; Motoba, T.; Merkin, V. G.; Ohtani, S.; Cohen, I. J.; Mauk, B.; Vines, S. K.; Anderson, B. J.; Moore, T. E.; Torbert, R. B.; Giles, B. L.; Burch, J. L.

2017-12-01

Magnetic reconnection is one of the most important energy conversion mechanisms in space plasmas. In the classical picture it converts the energy of antiparallel magnetic fields into the kinetic and thermal energy of accelerated plasma particles in reconnection exhausts. It also involves energy dissipation near the X-line. This classical picture may be substantially modified in real space plasma configurations, such as the dayside magnetopause and the magnetotail. In particular, in the magnetotail the flows of accelerated particles may be strongly asymmetric along the tail with the domination of earthward flows. At the same time, strong energy conversion and even dissipation may occur away from the X-line, in particular, at dipolarization fronts. Here we present a theoretical picture of spontaneous magnetotail reconnection based on 3-D PIC simulations with the focus on plasma bulk flows, energy conversion and dissipation. This picture is compared with some observations from the MMS tail season. An important finding from these observations is that dipolarizations fronts may not only be regions of the total energy conversion with jE>0, but they may also be the sites of energy dissipation, both positive (jE'>0, E' is the electric field E in the system moving with one of the plasma species) and negative (jE'<0). Observations are further compared with theory and modeling that predict the specific location and sign of the energy dissipation at fronts depending on their evolution phase (e.g., formation, propagation, braking).

Condensation to a strongly correlated dark fluid of two dimensional dipolar excitons

NASA Astrophysics Data System (ADS)

Mazuz-Harpaz, Yotam; Cohen, Kobi; Rapaport, Ronen

2017-08-01

Recently we reported on the condensation of cold, electrostatically trapped dipolar excitons in GaAs bilayer heterostructure into a new, dense and dark collective phase. Here we analyze and discuss in detail the experimental findings and the emerging evident properties of this collective liquid-like phase. We show that the phase transition is characterized by a sharp increase of the number of non-emitting dipoles, by a clear contraction of the fluid spatial extent into the bottom of the parabolic-like trap, and by spectral narrowing. We extract the total density of the condensed phase which we find to be consistent with the expected density regime of a quantum liquid. We show that there are clear critical temperature and excitation power onsets for the phase transition and that as the power further increases above the critical power, the strong darkening is reduced down until no clear darkening is observed. At this point another transition appears which we interpret as a transition to a strongly repulsive yet correlated e-h plasma. Based on the experimental findings, we suggest that the physical mechanism that may be responsible for the transition is a dynamical final-state stimulation of the dipolar excitons to their dark spin states, which have a long lifetime and thus support the observed sharp increase in density. Further experiments and modeling will hopefully be able to unambiguously identify the physical mechanism behind these recent observations.

Monte Carlo simulation of Hamaker nanospheres coated with dipolar particles

NASA Astrophysics Data System (ADS)

Meyra, Ariel G.; Zarragoicoechea, Guillermo J.; Kuz, Victor A.

2012-01-01

Parallel tempering Monte Carlo simulation is carried out in systems of N attractive Hamaker spheres dressed with n dipolar particles, able to move on the surface of the spheres. Different cluster configurations emerge for given values of the control parameters. Energy per sphere, pair distribution functions of spheres and dipoles as function of temperature, density, external electric field, and/or the angular orientation of dipoles are used to analyse the state of aggregation of the system. As a consequence of the non-central interaction, the model predicts complex structures like self-assembly of spheres by a double crown of dipoles. This interesting result could be of help in understanding some recent experiments in colloidal science and biology.

Anisotropic properties of phase separation in two-component dipolar Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Wang, Wei; Li, Jinbin

2018-03-01

Using Crank-Nicolson method, we calculate ground state wave functions of two-component dipolar Bose-Einstein condensates (BECs) and show that, due to dipole-dipole interaction (DDI), the condensate mixture displays anisotropic phase separation. The effects of DDI, inter-component s-wave scattering, strength of trap potential and particle numbers on the density profiles are investigated. Three types of two-component profiles are present, first cigar, along z-axis and concentric torus, second pancake (or blood cell), in xy-plane, and two non-uniform ellipsoid, separated by the pancake and third two dumbbell shapes.

Relaxation spectra and dipolar correlations for flexible polymers with bulky side groups

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

Diaz-Calleja, R.; Riande, E.; Roman, J.S.

1992-08-06

This paper discusses how relaxation spectra and dipolar correlations for flexible polymers with bulky side groups (PBPA chains) suggest that intermolecular correlations are not very important in this polymer and that {alpha}, {beta}, and {gamma} absorptions exist. TSDC techniques reveal that the {gamma} peak has a smaller activation energy than the {beta}, and the coupling scheme is used to interpret the complex dielectric and mechanical {alpha} relaxations. The anomalous temperature dependence of the glass-rubber relaxation is discussed in terms of the bulkiness of the side group. 23 refs., 8 figs., 3 tabs.

Corresponding-states behavior of a dipolar model fluid with variable dispersion interactions and its relevance to the anomalies of hydrogen fluoride

NASA Astrophysics Data System (ADS)

Weiss, Volker C.; Leroy, Frédéric

2016-06-01

More than two decades ago, the elusiveness of a liquid-vapor equilibrium and a corresponding critical point in simulations of the supposedly simple model of dipolar hard spheres came as a surprise to many liquid matter theorists. van Leeuwen and Smit [Phys. Rev. Lett. 71, 3991 (1993)] showed that a minimum of attractive dispersion interactions among the dipolar particles may be needed to observe regular fluid behavior. Here, we adopt their approach and use an only slightly modified model, in which the original point dipole is replaced by a dipole moment produced by charges that are separated in space, to study the influence of dispersion interactions of variable strength on the coexistence and interfacial properties of a polar fluid. The thermophysical properties are discussed in terms of Guggenheim's corresponding-states approach. In this way, the coexistence curve, the critical compressibility factor, the surface tension, Guggenheim's ratio, and modifications of Guldberg's and Trouton's rules (related to the vapor pressure and the enthalpy of vaporization) are analyzed. As the importance of dispersion is decreased, a crossover from simple-fluid behavior to that characteristic of strongly dipolar systems takes place; for some properties, this transition is monotonic, but for others it occurs non-monotonically. For strongly dipolar systems, the reduced surface tension is very low, whereas Guggenheim's ratio and Guldberg's ratio are found to be high. The critical compressibility factor is smaller, and the coexistence curve is wider and more skewed than for simple fluids. For very weak dispersion, liquid-vapor equilibrium is still observable, but the interfacial tension is extremely low and may, eventually, vanish marking the end of the existence of a liquid phase. We discuss the implications of our findings for real fluids, in particular, for hydrogen fluoride.

Electron acceleration behind a wavy dipolarization front

NASA Astrophysics Data System (ADS)

Wu, Mingyu; Lu, Quanming; Volwerk, Martin; Nakamura, Rumi; Zhang, Tielong

2018-02-01

In this paper, with the in-situ observations from the Time History of Events and Macroscale Interactions during Substorms (THEMIS) probes we report a wavy dipolarization front (DF) event, where the DF has different magnetic structures and electron distributions at different y positions in the Geocentric Solar Magnetospheric (GSM) coordinates. At y ˜2.1RE (RE is the radius of Earth), the DF has a relatively simple structure, which is similar to that of a conventional DF. At y ˜3.0RE, the DF is revealed to have a multiple DF structure, where the plasma exhibits a vortex flow. Such a wavy DF could be the results of the interchange instability. The different structure of such a wavy DF at different sites has a great effect on electron acceleration. Fermi acceleration can occur at the site of the DF with a simple or multiple DF structure, while betatron acceleration as a local process has the contribution to energetic electrons only at the site of the DF with a simple structure.

IUS prerelease alignment

NASA Technical Reports Server (NTRS)

Evans, F. A.

1978-01-01

Space shuttle orbiter/IUS alignment transfer was evaluated. Although the orbiter alignment accuracy was originally believed to be the major contributor to the overall alignment transfer error, it was shown that orbiter alignment accuracy is not a factor affecting IUS alignment accuracy, if certain procedures are followed. Results are reported of alignment transfer accuracy analysis.

Dipolarizing flux bundles in the cis-geosynchronous magnetosphere: Relationship between electric fields and energetic particle injections

NASA Astrophysics Data System (ADS)

Liu, Jiang; Angelopoulos, V.; Zhang, Xiao-Jia; Turner, D. L.; Gabrielse, C.; Runov, A.; Li, Jinxing; Funsten, H. O.; Spence, H. E.

2016-02-01

Dipolarizing flux bundles (DFBs) are small flux tubes (typically <3 RE in XGSM and YGSM) in the nightside magnetosphere that have magnetic field more dipolar than the background. Although DFBs are known to accelerate particles, creating energetic particle injections outside geosynchronous orbit (trans-GEO), the nature of the acceleration mechanism and the importance of DFBs in generating injections inside geosynchronous orbit (cis-GEO) are unclear. Our statistical study of cis-GEO DFBs using data from the Van Allen Probes reveals that just like trans-GEO DFBs, cis-GEO DFBs occur most often in the premidnight sector, but their occurrence rate is ~1/3 that of trans-GEO DFBs. Half the cis-GEO DFBs are accompanied by an energetic particle injection and have an electric field 3 times stronger than that of the injectionless half. All DFB injections are dispersionless within the temporal resolution considered (11 s). Our findings suggest that these injections are ushered or produced locally by the DFB, and the DFB's strong electric field is an important aspect of the injection generation mechanism.

Electron Injections: A Study of Electron Acceleration by Multiple Dipolarizing Flux Bundles Using an Analytical Model

NASA Astrophysics Data System (ADS)

Gabrielse, C.; Angelopoulos, V.; Artemyev, A.; Runov, A.; Harris, C.

2016-12-01

We study energetic electron injections using an analytical model that self-consistently describes electric and magnetic field perturbations of transient, localized dipolarizing flux bundles (DFBs). Previous studies using THEMIS, Van Allen Probes, and the Magnetospheric Multiscale Mission have shown that injections can occur on short (minutes) or long (10s of minutes) timescales. These studies suggest that the short timescale injections correspond to a single DFB, whereas long timescale injections are likely caused by an aggregate of multiple DFBs, each incrementally heating the particle population. We therefore model the effects of multiple DFBs on the electron population using multi-spacecraft observations of the fields and particle fluxes to constrain the model parameters. The analytical model is the first of its kind to model multiple dipolarization fronts in order to better understand the transport and acceleration process throughout the plasma sheet. It can reproduce most injection signatures at multiple locations simultaneously, reaffirming earlier findings that multiple earthward-traveling DFBs can both transport and accelerate electrons to suprathermal energies, and can thus be considered the injections' primary driver.

Monte Carlo simulations of dipolar and quadrupolar linear Kihara fluids. A test of thermodynamic perturbation theory

NASA Astrophysics Data System (ADS)

Garzon, B.

Several simulations of dipolar and quadrupolar linear Kihara fluids using the Monte Carlo method in the canonical ensemble have been performed. Pressure and internal energy have been directly determined from simulations and Helmholtz free energy using thermodynamic integration. Simulations were carried out for fluids of fixed elongation at two different densities and several values of temperature and dipolar or quadrupolar moment for each density. Results are compared with the perturbation theory developed by Boublik for this same type of fluid and good agreement between simulated and theoretical values was obtained especially for quadrupole fluids. Simulations are also used to obtain the liquid structure giving the first few coefficients of the expansion of pair correlation functions in terms of spherical harmonics. Estimations of the triple point temperature to critical temperature ratio are given for some dipole and quadrupole linear fluids. The stability range of the liquid phase of these substances is shortly discussed and an analysis about the opposite roles of the dipole moment and the molecular elongation on this stability is also given.

Experimental quantification of decoherence via the Loschmidt echo in a many spin system with scaled dipolar Hamiltonians

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

Buljubasich, Lisandro; Dente, Axel D.; Levstein, Patricia R.

2015-10-28

We performed Loschmidt echo nuclear magnetic resonance experiments to study decoherence under a scaled dipolar Hamiltonian by means of a symmetrical time-reversal pulse sequence denominated Proportionally Refocused Loschmidt (PRL) echo. The many-spin system represented by the protons in polycrystalline adamantane evolves through two steps of evolution characterized by the secular part of the dipolar Hamiltonian, scaled down with a factor |k| and opposite signs. The scaling factor can be varied continuously from 0 to 1/2, giving access to a range of complexity in the dynamics. The experimental results for the Loschmidt echoes showed a spreading of the decay rates thatmore » correlate directly to the scaling factors |k|, giving evidence that the decoherence is partially governed by the coherent dynamics. The average Hamiltonian theory was applied to give an insight into the spin dynamics during the pulse sequence. The calculations were performed for every single radio frequency block in contrast to the most widely used form. The first order of the average Hamiltonian numerically computed for an 8-spin system showed decay rates that progressively decrease as the secular dipolar Hamiltonian becomes weaker. Notably, the first order Hamiltonian term neglected by conventional calculations yielded an explanation for the ordering of the experimental decoherence rates. However, there is a strong overall decoherence observed in the experiments which is not reflected by the theoretical results. The fact that the non-inverted terms do not account for this effect is a challenging topic. A number of experiments to further explore the relation of the complete Hamiltonian with this dominant decoherence rate are proposed.« less

Direct Investigation of Slow Correlated Dynamics in Proteins via Dipolar Interactions

PubMed Central

Fenwick, R. Bryn; Schwieters, Charles D.; Vögeli, Beat

2016-01-01

The synchronization of native state motions as they transition between microstates influences catalysis kinetics, mediates allosteric interactions and reduces the conformational entropy of proteins. However, it has proven difficult to describe native microstates because they are usually minimally frustrated and may interconvert on the μs-ms time scale. Direct observation of concerted equilibrium fluctuations would therefore be an important tool for describing protein native states. Here we propose a strategy that relates NMR cross-correlated relaxation (CCR) rates between dipolar interactions to residual dipolar couplings (RDCs) of individual consecutive HN–N and Hα–Cα bonds, which act as a proxy for the peptide planes and the side chains respectively. Using Xplor-NIH ensemble structure calculations restrained with the RDC and CCR data we observe collective motions on time scales slower than nanoseconds in the backbone for GB3. To directly access the correlations from CCR we develop a structure-free data analysis. The resulting dynamic correlation map is consistent with the ensemble-restrained simulations and reveals a complex network. In general we find that the bond motions are on average slightly correlated, and that the local environment dominates many observations. Despite this, some patterns are typical over entire secondary structure elements. In the β-sheet, nearly all bonds are weakly correlated and there is an approximately binary alternation in correlation intensity corresponding to the solvent exposure/shielding alternation of the side chains. For α-helices there is also a weak correlation in the HN-N bonds and the degree of correlation involving Hα-Cα bonds is directly affected by side-chain fluctuations, while loops show complex and non-uniform behavior. PMID:27331619

Optical Switching Using Transition from Dipolar to Charge Transfer Plasmon Modes in Ge2Sb2Te5 Bridged Metallodielectric Dimers

PubMed Central

Ahmadivand, Arash; Gerislioglu, Burak; Sinha, Raju; Karabiyik, Mustafa; Pala, Nezih

2017-01-01

Capacitive coupling and direct shuttling of charges in nanoscale plasmonic components across a dielectric spacer and through a conductive junction lead to excitation of significantly different dipolar and charge transfer plasmon (CTP) resonances, respectively. Here, we demonstrate the excitation of dipolar and CTP resonant modes in metallic nanodimers bridged by phase-change material (PCM) sections, material and electrical characteristics of which can be controlled by external stimuli. Ultrafast switching (in the range of a few nanoseconds) between amorphous and crystalline phases of the PCM section (here Ge2Sb2Te5 (GST)) allows for designing a tunable plasmonic switch for optical communication applications with significant modulation depth (up to 88%). Judiciously selecting the geometrical parameters and taking advantage of the electrical properties of the amorphous phase of the GST section we adjusted the extinction peak of the dipolar mode at the telecommunication band (λ~1.55 μm), which is considered as the OFF state. Changing the GST phase to crystalline via optical heating allows for direct transfer of charges through the junction between nanodisks and formation of a distinct CTP peak at longer wavelengths (λ~1.85 μm) far from the telecommunication wavelength, which constitutes the ON state. PMID:28205643

Optical Switching Using Transition from Dipolar to Charge Transfer Plasmon Modes in Ge2Sb2Te5 Bridged Metallodielectric Dimers.

PubMed

Ahmadivand, Arash; Gerislioglu, Burak; Sinha, Raju; Karabiyik, Mustafa; Pala, Nezih

2017-02-16

Capacitive coupling and direct shuttling of charges in nanoscale plasmonic components across a dielectric spacer and through a conductive junction lead to excitation of significantly different dipolar and charge transfer plasmon (CTP) resonances, respectively. Here, we demonstrate the excitation of dipolar and CTP resonant modes in metallic nanodimers bridged by phase-change material (PCM) sections, material and electrical characteristics of which can be controlled by external stimuli. Ultrafast switching (in the range of a few nanoseconds) between amorphous and crystalline phases of the PCM section (here Ge 2 Sb 2 Te 5 (GST)) allows for designing a tunable plasmonic switch for optical communication applications with significant modulation depth (up to 88%). Judiciously selecting the geometrical parameters and taking advantage of the electrical properties of the amorphous phase of the GST section we adjusted the extinction peak of the dipolar mode at the telecommunication band (λ~1.55 μm), which is considered as the OFF state. Changing the GST phase to crystalline via optical heating allows for direct transfer of charges through the junction between nanodisks and formation of a distinct CTP peak at longer wavelengths (λ~1.85 μm) far from the telecommunication wavelength, which constitutes the ON state.

Optical Switching Using Transition from Dipolar to Charge Transfer Plasmon Modes in Ge2Sb2Te5 Bridged Metallodielectric Dimers

NASA Astrophysics Data System (ADS)

Ahmadivand, Arash; Gerislioglu, Burak; Sinha, Raju; Karabiyik, Mustafa; Pala, Nezih

2017-02-01

Capacitive coupling and direct shuttling of charges in nanoscale plasmonic components across a dielectric spacer and through a conductive junction lead to excitation of significantly different dipolar and charge transfer plasmon (CTP) resonances, respectively. Here, we demonstrate the excitation of dipolar and CTP resonant modes in metallic nanodimers bridged by phase-change material (PCM) sections, material and electrical characteristics of which can be controlled by external stimuli. Ultrafast switching (in the range of a few nanoseconds) between amorphous and crystalline phases of the PCM section (here Ge2Sb2Te5 (GST)) allows for designing a tunable plasmonic switch for optical communication applications with significant modulation depth (up to 88%). Judiciously selecting the geometrical parameters and taking advantage of the electrical properties of the amorphous phase of the GST section we adjusted the extinction peak of the dipolar mode at the telecommunication band (λ~1.55 μm), which is considered as the OFF state. Changing the GST phase to crystalline via optical heating allows for direct transfer of charges through the junction between nanodisks and formation of a distinct CTP peak at longer wavelengths (λ~1.85 μm) far from the telecommunication wavelength, which constitutes the ON state.

Theoretical studies to elucidate the influence of magnetic dipolar interactions occurring in the magnetic nanoparticle systems, for biomedical applications

NASA Astrophysics Data System (ADS)

Osaci, M.; Cacciola, M.

2016-02-01

In recent years, the study of magnetic nanoparticles has been intensively developed not only for their fundamental theoretical interest, but also for their many technological applications, especially biomedical applications, ranging from contrast agents for magnetic resonance imaging to the deterioration of cancer cells via hyperthermia treatment. The theoretical and experimental research has shown until now that the magnetic dipolar interactions between nanoparticles can have a significant influence on the magnetic behaviour of the system. But, this influence is not well understood. It is clear that the magnetic dipolar interaction intensity is correlated with the nanoparticle concentration, volume fraction and magnetic moment orientations. In this paper, we try to understand the influence of magnetic dipolar interactions on the behaviour of magnetic nanoparticle systems, for biomedical applications. For the model, we considered spherical nanoparticles with uniaxial anisotropy and lognormal distribution of the sizes. The model involves a simulation stage of the spatial distribution and orientation of the nanoparticles and their easy axes of magnetic anisotropy, and an evaluation stage of the Néel relaxation time. To assess the Néel relaxation time, we are going to discretise and adapt, to the local magnetic field, the Coffey analytical solution for the equation Fokker-Planck describing the dynamics of magnetic moments of nanoparticles in oblique external magnetic field. There are three fundamental aspects of interest in our studies on the magnetic nanoparticles: their spatial & orientational distributions, concentrations and sizes.

Kinematically aligned TKA can align knee joint line to horizontal.

PubMed

Ji, Hyung-Min; Han, Jun; Jin, Dong San; Seo, Hyunseok; Won, Ye-Yeon

2016-08-01

The joint line of the native knee is horizontal to the floor and perpendicular to the vertical weight-bearing axis of the patient in a bipedal stance. The purposes of this study were as follows: (1) to find out the distribution of the native joint line in a population of normal patients with normal knees; (2) to compare the native joint line orientation between patients receiving conventional mechanically aligned total knee arthroplasty (TKA), navigated mechanically aligned TKA, and kinematically aligned TKA; and (3) to determine which of the three TKA methods aligns the postoperative knee joint perpendicular to the weight-bearing axis of the limb in bipedal stance. To determine the joint line orientation of a native knee, 50 full-length standing hip-to-ankle digital radiographs were obtained in 50 young, healthy individuals. The angle between knee joint line and the line parallel to the floor was measured and defined as joint line orientation angle (JLOA). JLOA was also measured prior to and after conventional mechanically aligned TKA (65 knees), mechanically aligned TKA using imageless navigation (65 knees), and kinematically aligned TKA (65 knees). The proportion of the knees similar to the native joint line was calculated for each group. The mean JLOA in healthy individuals was parallel to the floor (0.2° ± 1.1°). The pre-operative JLOA of all treatment groups slanted down to the lateral side. Postoperative JLOA slanted down to the lateral side in conventional mechanically aligned TKA (-3.3° ± 2.2°) and in navigation mechanically aligned TKA (-2.6° ± 1.8°), while it was horizontal to the floor in kinematically aligned TKA (0.6° ± 1.7°). Only 6.9 % of the conventional mechanically aligned TKA and 16.9 % of the navigation mechanically aligned TKA were within one SD of the mean JLOA of the native knee, while the proportion was significantly higher (50.8 %) in kinematically aligned TKA. The portion was statistically greater in mechanically

Electron Jet Detected by MMS at Dipolarization Front

NASA Astrophysics Data System (ADS)

Liu, C. M.; Fu, H. S.; Vaivads, A.; Khotyaintsev, Y. V.; Gershman, D. J.; Hwang, K.-J.; Chen, Z. Z.; Cao, D.; Xu, Y.; Yang, J.; Peng, F. Z.; Huang, S. Y.; Burch, J. L.; Giles, B. L.; Ergun, R. E.; Russell, C. T.; Lindqvist, P.-A.; Le Contel, O.

2018-01-01

Using MMS high-resolution measurements, we present the first observation of fast electron jet (Ve 2,000 km/s) at a dipolarization front (DF) in the magnetotail plasma sheet. This jet, with scale comparable to the DF thickness ( 0.9 di), is primarily in the tangential plane to the DF current sheet and mainly undergoes the E × B drift motion; it contributes significantly to the current system at the DF, including a localized ring-current that can modify the DF topology. Associated with this fast jet, we observed a persistent normal electric field, strong lower hybrid drift waves, and strong energy conversion at the DF. Such strong energy conversion is primarily attributed to the electron-jet-driven current (E ṡ je ≈ 2 E ṡ ji), rather than the ion current suggested in previous studies.

Effect of dipolar fields, surface termination, and surface orientation on photochemical reactions on transition metal oxides

NASA Astrophysics Data System (ADS)

Giocondi, Jennifer Lynn

Experiments have been conducted to determine the effects of dipolar fields, surface termination, and surface orientation on the photochemical reactivity of several transition metal oxides. These compounds include BaTiO3, SrTiO3, BaTi4O9, Sr2Nb2O 7, and Sr2Ta2O7 which were studied as polycrystalline ceramics, single crystals, micron-sized faceted particles, or some combination of these forms. The reduction of Ag+ from an aqueous AgNO3 solution (Ag0 product) and the oxidation of Pb2+ from an aqueous lead acetate solution (PbO 2 product) were selected as probe reactions because they leave insoluble products on the oxide surfaces. The reactivity of ferroelectric BaTiO3 was dominated by the effect of dipolar fields on the transport of photogenerated charge carriers. Silver was reduced on domains with a positive surface charge while lead was oxidized on domains with a negative surface charge. This reactivity implies that the dipolar field in individual domains drives photogenerated charge carriers to oppositely charged surfaces. This reaction mechanism results in a physical separation of the photogenerated charge carriers and the locations of the oxidation and reduction half reactions on the catalyst surface. Experiments performed on polycrystalline ceramics, single crystals, and micron-sized particles all showed this domain specific reactivity. SrTiO3 has the ideal cubic perovskite structure from which the tetragonally distorted ferroelectric BaTiO3 phase is derived. Polished and annealed surfaces of randomly oriented grain surfaces were bound by some combination of the following three planes: {110}, {111}, and a complex facet inclined approximately 24° from {100}. Surfaces with the complex {100} facet were found to be the most active for Ag reduction. Single crystal studies also showed that the nonpolar (100) surface is the most reactive and that the composition of the termination layer does not influence this reaction. However, the polar (111) and (110) surfaces had

Axial dipolar dynamo action in the Taylor-Green vortex.

PubMed

Krstulovic, Giorgio; Thorner, Gentien; Vest, Julien-Piera; Fauve, Stephan; Brachet, Marc

2011-12-01

We present a numerical study of the magnetic field generated by the Taylor-Green vortex. We show that periodic boundary conditions can be used to mimic realistic boundary conditions by prescribing the symmetries of the velocity and magnetic fields. This gives insight into some problems of central interest for dynamos: the possible effect of velocity fluctuations on the dynamo threshold, and the role of boundary conditions on the threshold and on the geometry of the magnetic field generated by dynamo action. In particular, we show that an axial dipolar dynamo similar to the one observed in a recent experiment can be obtained with an appropriate choice of the symmetries of the magnetic field. The nonlinear saturation is studied and a simple model explaining the magnetic Prandtl number dependence of the super- and subcritical nature of the dynamo transition is given.

Vortex dipolar structures in a rigid model of the larynx at flow onset

NASA Astrophysics Data System (ADS)

Chisari, N. E.; Artana, G.; Sciamarella, D.

2011-02-01

Starting jet airflow is investigated in a channel with a pair of consecutive slitted constrictions approximating the true and false vocal folds in the human larynx. The flow is visualized using the Schlieren optical technique and simulated by solving the Navier-Stokes equations for an incompressible two-dimensional viscous flow. Laboratory and numerical experiments show the spontaneous formation of three different classes of vortex dipolar structures in several regions of the laryngeal profile under conditions that may be assimilated to those of voice onset.

Synthesis of Functionalized Pyrazoles via 1,3-Dipolar Cycloaddition of α-Diazo-β-ketophosphonates, Sufones and Esters with Electron-Deficient Alkenes.

PubMed

Baiju, T V; Namboothiri, Irishi N N

2017-10-01

1,3-Dipolar cycloaddition of diazo compounds with olefinic substrates is a promising atom-economic strategy for the construction of functionalized pyrazoles. Over the last few years, our group has been engaged in the synthesis of phosphonyl/sulfonylpyrazoles and pyrazole esters by employing Bestmann-Ohira Reagent (BOR) and its sulfur and ester analogs as 1,3-dipole precursors with various dipolarophiles. This account describes the novel synthetic methods developed in our laboratory, in the perspective of closely related work by others, for the synthesis of phosphonyl/sulfonylpyrazoles, pyrazole esters and the total synthesis of Withasomnine, a natural product, by using 1,3-dipolar cycloaddition as the key step. © 2017 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantifying entanglement of rotor chains using basis truncation: Application to dipolar endofullerene peapods.

PubMed

Halverson, Tom; Iouchtchenko, Dmitri; Roy, Pierre-Nicholas

2018-02-21

We propose a variational approach for the calculation of the quantum entanglement entropy of assemblies of rotating dipolar molecules. A basis truncation scheme based on the total angular momentum quantum number is proposed. The method is tested on hydrogen fluoride (HF) molecules confined in C 60 fullerene cages themselves trapped in a nanotube to form a carbon peapod. The rotational degrees of freedom of the HF molecules and dipolar interactions between neighboring molecules are considered in our model Hamiltonian. Both screened and unscreened dipoles are simulated and results are obtained for the ground state and one excited state that is expected to be accessible via a far-infrared collective excitation. The effect of basis truncation on energetic and entanglement properties is examined and discussed in terms of size extensivity. It is empirically found that for unscreened dipoles, a total angular momentum cutoff that increases linearly with the number of rotors is required in order to obtain proper system size scaling of the chemical potential and entanglement entropy. Recent experiments [A. Krachmalnicoff et al., Nat. Chem. 8, 953 (2016)] suggest substantial screening of the HF dipole moment, so much smaller basis sets are required to obtain converged results in this realistic case. Static correlation functions are also computed and are shown to decay much quicker in the case of screened dipoles. Our variational results are also used to test the accuracy of perturbative and pairwise ansatz treatments.

CW dipolar broadening EPR spectroscopy and mechanically aligned bilayers used to measure distance and relative orientation between two TOAC spin labels on an antimicrobial peptide

NASA Astrophysics Data System (ADS)

Sahu, Indra D.; Hustedt, Eric J.; Ghimire, Harishchandra; Inbaraj, Johnson J.; McCarrick, Robert M.; Lorigan, Gary A.

2014-12-01

An EPR membrane alignment technique was applied to measure distance and relative orientations between two spin labels on a protein oriented along the surface of the membrane. Previously we demonstrated an EPR membrane alignment technique for measuring distances and relative orientations between two spin labels using a dual TOAC-labeled integral transmembrane peptide (M2δ segment of Acetylcholine receptor) as a test system. In this study we further utilized this technique and successfully measured the distance and relative orientations between two spin labels on a membrane peripheral peptide (antimicrobial peptide magainin-2). The TOAC-labeled magainin-2 peptides were mechanically aligned using DMPC lipids on a planar quartz support, and CW-EPR spectra were recorded at specific orientations. Global analysis in combination with rigorous spectral simulation was used to simultaneously analyze data from two different sample orientations for both single- and double-labeled peptides. We measured an internitroxide distance of 15.3 Å from a dual TOAC-labeled magainin-2 peptide at positions 8 and 14 that closely matches with the 13.3 Å distance obtained from a model of the labeled magainin peptide. In addition, the angles determining the relative orientations of the two nitroxides have been determined, and the results compare favorably with molecular modeling. This study demonstrates the utility of the technique for proteins oriented along the surface of the membrane in addition to the previous results for proteins situated within the membrane bilayer.

Computing distance distributions from dipolar evolution data with overtones: RIDME spectroscopy with Gd(iii)-based spin labels.

PubMed

Keller, Katharina; Mertens, Valerie; Qi, Mian; Nalepa, Anna I; Godt, Adelheid; Savitsky, Anton; Jeschke, Gunnar; Yulikov, Maxim

2017-07-21

Extraction of distance distributions between high-spin paramagnetic centers from relaxation induced dipolar modulation enhancement (RIDME) data is affected by the presence of overtones of dipolar frequencies. As previously proposed, we account for these overtones by using a modified kernel function in Tikhonov regularization analysis. This paper analyzes the performance of such an approach on a series of model compounds with the Gd(iii)-PyMTA complex serving as paramagnetic high-spin label. We describe the calibration of the overtone coefficients for the RIDME kernel, demonstrate the accuracy of distance distributions obtained with this approach, and show that for our series of Gd-rulers RIDME technique provides more accurate distance distributions than Gd(iii)-Gd(iii) double electron-electron resonance (DEER). The analysis of RIDME data including harmonic overtones can be performed using the MATLAB-based program OvertoneAnalysis, which is available as open-source software from the web page of ETH Zurich. This approach opens a perspective for the routine use of the RIDME technique with high-spin labels in structural biology and structural studies of other soft matter.

Wetting behavior of nonpolar nanotubes in simple dipolar liquids for varying nanotube diameter and solute-solvent interactions

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

Rana, Malay Kumar; Chandra, Amalendu, E-mail: amalen@iitk.ac.in

2015-01-21

Atomistic simulations of model nonpolar nanotubes in a Stockmayer liquid are carried out for varying nanotube diameter and nanotube-solvent interactions to investigate solvophobic interactions in generic dipolar solvents. We have considered model armchair type single-walled nonpolar nanotubes with increasing radii from (5,5) to (12,12). The interactions between solute and solvent molecules are modeled by the well-known Lennard-Jones and repulsive Weeks-Chandler-Andersen potentials. We have investigated the density profiles and microscopic arrangement of Stockmayer molecules, orientational profiles of their dipole vectors, time dependence of their occupation, and also the translational and rotational motion of solvent molecules in confined environments of the cylindricalmore » nanopores and also in their external peripheral regions. The present results of structural and dynamical properties of Stockmayer molecules inside and near atomistically rough nonpolar surfaces including their wetting and dewetting behavior for varying interactions provide a more generic picture of solvophobic effects experienced by simple dipolar liquids without any specific interactions such as hydrogen bonds.« less

Near-earth injection of MeV electrons associated with intense dipolarization electric fields: Van Allen Probes observations

DOE PAGES

Dai, Lei; Wang, Chi; Duan, Suping; ...

2015-08-10

Substorms generally inject tens to hundreds of keV electrons, but intense substorm electric fields have been shown to inject MeV electrons as well. An intriguing question is whether such MeVelectron injections can populate the outer radiation belt. Here we present observations of a substorm injection of MeV electrons into the inner magnetosphere. In the premidnight sector at L ~ 5.5, Van Allen Probes (Radiation Belt Storm Probes)-A observed a large dipolarization electric field (50 mV/m) over ~40 s and a dispersionless injection of electrons up to ~3 MeV. Pitch angle observations indicated betatron acceleration of MeV electrons at the dipolarizationmore » front. Corresponding signals of MeV electron injection were observed at LANL-GEO, THEMIS-D, and GOES at geosynchronous altitude. Through a series of dipolarizations, the injections increased the MeV electron phase space density by 1 order of magnitude in less than 3 h in the outer radiation belt (L > 4.8). Our observations provide evidence that deep injections can supply significant MeV electrons.« less

Multidimensional oriented solid-state NMR experiments enable the sequential assignment of uniformly 15N labeled integral membrane proteins in magnetically aligned lipid bilayers.

PubMed

Mote, Kaustubh R; Gopinath, T; Traaseth, Nathaniel J; Kitchen, Jason; Gor'kov, Peter L; Brey, William W; Veglia, Gianluigi

2011-11-01

Oriented solid-state NMR is the most direct methodology to obtain the orientation of membrane proteins with respect to the lipid bilayer. The method consists of measuring (1)H-(15)N dipolar couplings (DC) and (15)N anisotropic chemical shifts (CSA) for membrane proteins that are uniformly aligned with respect to the membrane bilayer. A significant advantage of this approach is that tilt and azimuthal (rotational) angles of the protein domains can be directly derived from analytical expression of DC and CSA values, or, alternatively, obtained by refining protein structures using these values as harmonic restraints in simulated annealing calculations. The Achilles' heel of this approach is the lack of suitable experiments for sequential assignment of the amide resonances. In this Article, we present a new pulse sequence that integrates proton driven spin diffusion (PDSD) with sensitivity-enhanced PISEMA in a 3D experiment ([(1)H,(15)N]-SE-PISEMA-PDSD). The incorporation of 2D (15)N/(15)N spin diffusion experiments into this new 3D experiment leads to the complete and unambiguous assignment of the (15)N resonances. The feasibility of this approach is demonstrated for the membrane protein sarcolipin reconstituted in magnetically aligned lipid bicelles. Taken with low electric field probe technology, this approach will propel the determination of sequential assignment as well as structure and topology of larger integral membrane proteins in aligned lipid bilayers. © Springer Science+Business Media B.V. 2011

Ion Velocity Distributions in Dipolarization Events: Beams in the Vicinity of the Plasma Sheet Boundary

NASA Technical Reports Server (NTRS)

Birn, J.; Chandler, M.; Moore, T.; Runov, A.

2017-01-01

Using combined MHD/test particle simulations, we further explore characteristic ion velocity distributions in relation to magnetotail reconnection and dipolarization events, focusing on distributions at and near the plasma sheet boundary layer (PSBL). Simulated distributions right at the boundary are characterized by a single earthward beam, as discussed earlier. However, farther inside, the distributions consist of multiple beams parallel and antiparallel to the magnetic field, remarkably similar to recent Magnetospheric Multiscale observations. The simulations provide insight into the mechanisms: the lowest earthward beam results from direct acceleration at an earthward propagating dipolarization front (DF), with a return beam at somewhat higher energy. A higher-energy earthward beam results from dual acceleration, first near the reconnection site and then at the DF, again with a corresponding return beam resulting from mirroring closer to Earth. Multiple acceleration at the X line or the propagating DF with intermediate bounces may produce even higher-energy beams. Particles contributing to the lower energy beams are found to originate from the PSBL with thermal source energies, increasing with increasing beam energy. In contrast, the highest-energy beams consist mostly of particles that have entered the acceleration region via cross-tail drift with source energies in the suprathermal range.

Ion velocity distributions in dipolarization events: Beams in the vicinity of the plasma sheet boundary

NASA Astrophysics Data System (ADS)

Birn, J.; Chandler, M.; Moore, T.; Runov, A.

2017-08-01

Using combined MHD/test particle simulations, we further explore characteristic ion velocity distributions in relation to magnetotail reconnection and dipolarization events, focusing on distributions at and near the plasma sheet boundary layer (PSBL). Simulated distributions right at the boundary are characterized by a single earthward beam, as discussed earlier. However, farther inside, the distributions consist of multiple beams parallel and antiparallel to the magnetic field, remarkably similar to recent Magnetospheric Multiscale observations. The simulations provide insight into the mechanisms: the lowest earthward beam results from direct acceleration at an earthward propagating dipolarization front (DF), with a return beam at somewhat higher energy. A higher-energy earthward beam results from dual acceleration, first near the reconnection site and then at the DF, again with a corresponding return beam resulting from mirroring closer to Earth. Multiple acceleration at the X line or the propagating DF with intermediate bounces may produce even higher-energy beams. Particles contributing to the lower energy beams are found to originate from the PSBL with thermal source energies, increasing with increasing beam energy. In contrast, the highest-energy beams consist mostly of particles that have entered the acceleration region via cross-tail drift with source energies in the suprathermal range.

First order reversal curve study of the dipolar interaction in Ni three-dimensional antidot arrays

NASA Astrophysics Data System (ADS)

Li, Bingqing; Chai, Xuzhao; Moeendarbari, Sina; Hao, Yaowu; Gilbert, Dustin A.; Liu, Kai; Zhang, Di; Feng, Gang; Han, Ping; Cheng, X. M.

2014-03-01

Three-dimensional antidot arrays (3DAAs) have attracted considerable attention due to potential applications in sensors, energy storage and transducers. Magnetic 3DAAs also provide an ideal system for studying the effect of dimensionality and morphology on magnetic properties. We report study of dipolar interactions in Ni 3DAAs using the first-order reversal curve (FORC) method. Ordered Ni 3DAAs were fabricated by electrochemical deposition into colloidal crystal templates of self-assembled polystyrene spheres. The samples have the same pore size of about 500 nm but different thicknesses, ranging from 0.3 μm to 1.2 μm, confirmed by scanning electron microscopy (SEM) and atomic force microscopy (AFM). FORCs of the samples with thicknesses of 0.3 μm, 0.8 μm, and 1.2 μm were measured by a vibrating sample magnetometer. The FORC diagram analysis reveals a demagnetizing magnetic dipolar interaction, and a decrease in the interaction strength with the increasing sample thickness, evidenced by a decrease in the spread of the irreversible peak in the bias distribution, as well as a decrease in the tilting of the FORC distribution from the local coercivity axis. Work at BMC and UCD is supported by NSF DMR-1207085 and DMR-1008791, respectively.

Triangular Alignment (TAME). A Tensor-based Approach for Higher-order Network Alignment

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

Mohammadi, Shahin; Gleich, David F.; Kolda, Tamara G.

2015-11-01

Network alignment is an important tool with extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the network alignment problem that extends topological similarity to higher-order structures and provide a new objective function that maximizes the number of aligned substructures. This objective function corresponds to an integer programming problem, which is NP-hard. Consequently, we approximate this objective function as a surrogate function whose maximization results in a tensor eigenvalue problem. Based on this formulation, we present an algorithm called Triangularmore » AlignMEnt (TAME), which attempts to maximize the number of aligned triangles across networks. We focus on alignment of triangles because of their enrichment in complex networks; however, our formulation and resulting algorithms can be applied to general motifs. Using a case study on the NAPABench dataset, we show that TAME is capable of producing alignments with up to 99% accuracy in terms of aligned nodes. We further evaluate our method by aligning yeast and human interactomes. Our results indicate that TAME outperforms the state-of-art alignment methods both in terms of biological and topological quality of the alignments.« less

Strongly scale-dependent CMB dipolar asymmetry from super-curvature fluctuations

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

Byrnes, Christian; Domènech, Guillem; Sasaki, Misao

2016-12-01

We reconsider the observed CMB dipolar asymmetry in the context of open inflation, where a supercurvature mode might survive the bubble nucleation. If such a supercurvature mode modulates the amplitude of the curvature power spectrum, it would easily produce an asymmetry in the power spectrum. We show that current observational data can be accommodated in a three-field model, with simple quadratic potentials and a non-trivial field-space metric. Despite the presence of three fields, we believe this model is so far the simplest that can match current observations. We are able to match the observed strong scale dependence of the dipolarmore » asymmetry, without a fine tuning of initial conditions, breaking slow roll or adding a feature to the evolution of any field.« less

Dipolar dark matter with massive bigravity

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

Blanchet, Luc; Heisenberg, Lavinia; Department of Physics & The Oskar Klein Centre, AlbaNova University Centre,Roslagstullsbacken 21, 10691 Stockholm

2015-12-14

Massive gravity theories have been developed as viable IR modifications of gravity motivated by dark energy and the problem of the cosmological constant. On the other hand, modified gravity and modified dark matter theories were developed with the aim of solving the problems of standard cold dark matter at galactic scales. Here we propose to adapt the framework of ghost-free massive bigravity theories to reformulate the problem of dark matter at galactic scales. We investigate a promising alternative to dark matter called dipolar dark matter (DDM) in which two different species of dark matter are separately coupled to the twomore » metrics of bigravity and are linked together by an internal vector field. We show that this model successfully reproduces the phenomenology of dark matter at galactic scales (i.e. MOND) as a result of a mechanism of gravitational polarisation. The model is safe in the gravitational sector, but because of the particular couplings of the matter fields and vector field to the metrics, a ghost in the decoupling limit is present in the dark matter sector. However, it might be possible to push the mass of the ghost beyond the strong coupling scale by an appropriate choice of the parameters of the model. Crucial questions to address in future work are the exact mass of the ghost, and the cosmological implications of the model.« less

Dipolar dark matter with massive bigravity

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

Blanchet, Luc; Heisenberg, Lavinia, E-mail: blanchet@iap.fr, E-mail: laviniah@kth.se

2015-12-01

Massive gravity theories have been developed as viable IR modifications of gravity motivated by dark energy and the problem of the cosmological constant. On the other hand, modified gravity and modified dark matter theories were developed with the aim of solving the problems of standard cold dark matter at galactic scales. Here we propose to adapt the framework of ghost-free massive bigravity theories to reformulate the problem of dark matter at galactic scales. We investigate a promising alternative to dark matter called dipolar dark matter (DDM) in which two different species of dark matter are separately coupled to the twomore » metrics of bigravity and are linked together by an internal vector field. We show that this model successfully reproduces the phenomenology of dark matter at galactic scales (i.e. MOND) as a result of a mechanism of gravitational polarisation. The model is safe in the gravitational sector, but because of the particular couplings of the matter fields and vector field to the metrics, a ghost in the decoupling limit is present in the dark matter sector. However, it might be possible to push the mass of the ghost beyond the strong coupling scale by an appropriate choice of the parameters of the model. Crucial questions to address in future work are the exact mass of the ghost, and the cosmological implications of the model.« less

Alignment-Annotator web server: rendering and annotating sequence alignments

PubMed Central

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-01-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. Availability: http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. PMID:24813445

Does water belong to the homologous series of hydroxyl compounds H(CH2)nOH?

PubMed

Swiergiel, Jolanta; Jadżyn, Jan

2017-04-12

The main objective of this paper is to find a source of anomalously high value of the equilibrium permittivity of water. The source is identified to be the unusually high deformation polarizability. The conclusion follows from the analysis of the behavior of the orientational entropy increment induced by an external electric field applied to the liquids belonging to the homologous series of hydroxyl compounds H(CH 2 ) n OH at the end of which water is located. The finding reflects the "indecision" of water about its dielectric relationship with the alcohol family: the value of the permittivity of water absolutely does not fit into alcohols (is too high), while the dipolar orientation effects (which normally determine the permittivity level) fit into alcohols quite well. It results from the presented experimental data that among all the diversity of intermolecular hydrogen-bonded structures existing in liquid water, predominant are the polar entities, i.e. the structures which more or less resemble the chains. Otherwise, the dipolar orientational effects would behave in a quite different way than what is observed in the experiment. The result is convergent with the conclusion of Wernet et al., based on the high-performance X-ray studies of water (Science, 2004).

Experimental findings on the underwater measurements uncertainty of speed of sound and the alignment system

NASA Astrophysics Data System (ADS)

Santos, T. Q.; Alvarenga, A. V.; Oliveira, D. P.; Mayworm, R. C.; Souza, R. M.; Costa-Félix, R. P. B.

2016-07-01

Speed of sound is an important quantity to characterize reference materials for ultrasonic applications, for instance. The alignment between the transducer and the test body is an key activity in order to perform reliable and consistent measurement. The aim of this work is to evaluate the influence of the alignment system to the expanded uncertainty of such measurement. A stainless steel cylinder was previously calibrated on an out of water system typically used for calibration of non-destructive blocks. Afterwards, the cylinder was calibrated underwater with two distinct alignment system: fixed and mobile. The values were statistically compared to the out-of-water measurement, considered the golden standard for such application. For both alignment systems, the normalized error was less than 0.8, leading to conclude that the both measurement system (under and out-of-water) do not diverge significantly. The gold standard uncertainty was 2.7 m-s-1, whilst the fixed underwater system resulted in 13 m-s-1, and the mobile alignment system achieved 6.6 m-s-1. After the validation of the underwater system for speed of sound measurement, it will be applied to certify Encapsulated Tissue Mimicking Material as a reference material for biotechnology application.

The role of the substrate surface morphology and water in growth of vertically aligned single-walled carbon nanotubes.

PubMed

Pint, Cary; Pheasant, Sean; Nicholas, Nolan; Horton, Charles; Hauge, Robert

2008-11-01

Growth of high quality, vertically aligned single-walled carbon nanotubes (carpets) is achieved using a rapid insertion hot filament chemical vapor deposition (HF-CVD) technique. The effect of the substrate morphology on growth is explored by comparing carpets grown on epitaxially polished MgO substrates to those grown on "as-cut", macroscopically rough MgO substrates. Depending on the substrate morphology, we observe differences in both the overall carpet morphology as well as the diameter distribution of nanotubes grown in the carpet based on optical measurements. In addition, we explore the role of water in the growth of carpets on MgO and the conventional Al2O3 coated Si substrates. We find that the addition of a small amount of water is beneficial to the growth rates of the SWNT carpets, enhancing the growth rates by up to eight times.

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

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

Kharkov, B. B.; Chizhik, V. I.; Dvinskikh, S. V., E-mail: sergeid@kth.se

2016-01-21

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

Alignment-Annotator web server: rendering and annotating sequence alignments.

PubMed

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-07-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Evolution of multiple quantum coherences with scaled dipolar Hamiltonian

NASA Astrophysics Data System (ADS)

Sánchez, Claudia M.; Buljubasich, Lisandro; Pastawski, Horacio M.; Chattah, Ana K.

2017-08-01

In this article, we introduce a pulse sequence which allows the monitoring of multiple quantum coherences distribution of correlated spin states developed with scaled dipolar Hamiltonian. The pulse sequence is a modification of our previous Proportionally Refocused Loschmidt echo (PRL echo) with phase increment, in order to verify the accuracy of the weighted coherent quantum dynamics. The experiments were carried out with different scaling factors to analyze the evolution of the total magnetization, the time dependence of the multiple quantum coherence orders, and the development of correlated spins clusters. In all cases, a strong dependence between the evolution rate and the weighting factor is observed. Remarkably, all the curves appeared overlapped in a single trend when plotted against the self-time, a new time scale that includes the scaling factor into the evolution time. In other words, the spin system displayed always the same quantum evolution, slowed down as the scaling factor decreases, confirming the high performance of the new pulse sequence.

Stabilized nonlinear optical chromophore alignment in high-? guest - host polycarbonates

NASA Astrophysics Data System (ADS)

Healy, D.; Bloor, D.; Gray, D.; Cross, G. H.

1997-11-01

Electric-field-poling studies of two polycarbonates doped with 2-(N,N dimethylamino)-5-nitroacetanilide revealed a long-term room-temperature alignment stability. This stability at room temperature is compared with that of similarly doped poly(methyl methacrylate) (PMMA) which displays short-term relaxation. Despite several previous suggestions that hydrogen bonding between guest and host plays a major role in these effects, infra-red spectroscopic studies refuted the idea that stronger hydrogen bond formation in the polycarbonate rather than in PMMA is the dominant influence. Rather we show, using an examination of the poling currents during poling, that the re-orientation dynamics in the polycarbonate systems are markedly different. In the case of PMMA-doped films, the deposited surface charge is compensated by poling currents at a rate at least comparable to the rate of deposition of corona charge. The compensation rate for polycarbonate-doped systems was markedly lower, however, suggesting that polar re-orientation is slower. Studies of the second-order optical nonlinearities of poled thin films using second-harmonic generation revealed an apparent enhancement of the second-harmonic coefficient compared with the predictions of conventional theories. However, we note that the use of microscopic parameters (the dipole moment and the first hyperpolarizability) obtained from measurements in non-dipolar media may give rise to the apparent anomaly since high reaction fields in polycarbonate films may act to modify these parameters.

All-dielectric perforated metamaterials with toroidal dipolar response (Conference Presentation)

NASA Astrophysics Data System (ADS)

Stenishchev, Ivan; Basharin, Alexey A.

2017-05-01

We present metamaterials based on dielectric slab with perforated identical cylindrical clusters with perforated holes, which allow to support the toroidal dipolar response due to Mie-resonances in each hole. Note that proposed metamaterial is technologically simple for fabrication in optical frequency range. Metamaterial can be fabricated by several methods. For instance, we may apply the molecular beam epitaxy method for deposition of Si or GaAs layers, which have permittivity close to 16. Next step, nanometer/micrometer holes are perforated by focused ion beam method or laser cutting method. Fundamental difference of proposed metamaterial is technological fabrication process. Classically all- dielectric optical metamaterials consist of nano-spheres or nano-discs, which are complicated for fabrication, while our idea and suggested metamaterials are promising prototype of various optical/THz all-dielectic devices as sensor, nano-antennas elements for nanophotonics.

Arrangement at the nanoscale: Effect on magnetic particle hyperthermia

NASA Astrophysics Data System (ADS)

Myrovali, E.; Maniotis, N.; Makridis, A.; Terzopoulou, A.; Ntomprougkidis, V.; Simeonidis, K.; Sakellari, D.; Kalogirou, O.; Samaras, T.; Salikhov, R.; Spasova, M.; Farle, M.; Wiedwald, U.; Angelakeris, M.

2016-11-01

In this work, we present the arrangement of Fe3O4 magnetic nanoparticles into 3D linear chains and its effect on magnetic particle hyperthermia efficiency. The alignment has been performed under a 40 mT magnetic field in an agarose gel matrix. Two different sizes of magnetite nanoparticles, 10 and 40 nm, have been examined, exhibiting room temperature superparamagnetic and ferromagnetic behavior, in terms of DC magnetic field, respectively. The chain formation is experimentally visualized by scanning electron microscopy images. A molecular Dynamics anisotropic diffusion model that outlines the role of intrinsic particle properties and inter-particle distances on dipolar interactions has been used to simulate the chain formation process. The anisotropic character of the aligned samples is also reflected to ferromagnetic resonance and static magnetometry measurements. Compared to the non-aligned samples, magnetically aligned ones present enhanced heating efficiency increasing specific loss power value by a factor of two. Dipolar interactions are responsible for the chain formation of controllable density and thickness inducing shape anisotropy, which in turn enhances magnetic particle hyperthermia efficiency.

Evaporative cooling of the dipolar hydroxyl radical.

PubMed

Stuhl, Benjamin K; Hummon, Matthew T; Yeo, Mark; Quéméner, Goulven; Bohn, John L; Ye, Jun

2012-12-20

Atomic physics was revolutionized by the development of forced evaporative cooling, which led directly to the observation of Bose-Einstein condensation, quantum-degenerate Fermi gases and ultracold optical lattice simulations of condensed-matter phenomena. More recently, substantial progress has been made in the production of cold molecular gases. Their permanent electric dipole moment is expected to generate systems with varied and controllable phases, dynamics and chemistry. However, although advances have been made in both direct cooling and cold-association techniques, evaporative cooling has not been achieved so far. This is due to unfavourable ratios of elastic to inelastic scattering and impractically slow thermalization rates in the available trapped species. Here we report the observation of microwave-forced evaporative cooling of neutral hydroxyl (OH(•)) molecules loaded from a Stark-decelerated beam into an extremely high-gradient magnetic quadrupole trap. We demonstrate cooling by at least one order of magnitude in temperature, and a corresponding increase in phase-space density by three orders of magnitude, limited only by the low-temperature sensitivity of our spectroscopic thermometry technique. With evaporative cooling and a sufficiently large initial population, much colder temperatures are possible; even a quantum-degenerate gas of this dipolar radical (or anything else it can sympathetically cool) may be within reach.

Using Quasi-Horizontal Alignment in the absence of the actual alignment.

PubMed

Banihashemi, Mohamadreza

2016-10-01

Horizontal alignment is a major roadway characteristic used in safety and operational evaluations of many facility types. The Highway Safety Manual (HSM) uses this characteristic in crash prediction models for rural two-lane highways, freeway segments, and freeway ramps/C-D roads. Traffic simulation models use this characteristic in their processes on almost all types of facilities. However, a good portion of roadway databases do not include horizontal alignment data; instead, many contain point coordinate data along the roadways. SHRP 2 Roadway Information Database (RID) is a good example of this type of data. Only about 5% of this geodatabase contains alignment information and for the rest, point data can easily be produced. Even though the point data can be used to extract actual horizontal alignment data but, extracting horizontal alignment is a cumbersome and costly process, especially for a database of miles and miles of highways. This research introduces a so called "Quasi-Horizontal Alignment" that can be produced easily and automatically from point coordinate data and can be used in the safety and operational evaluations of highways. SHRP 2 RID for rural two-lane highways in Washington State is used in this study. This paper presents a process through which Quasi-Horizontal Alignments are produced from point coordinates along highways by using spreadsheet software such as MS EXCEL. It is shown that the safety and operational evaluations of the highways with Quasi-Horizontal Alignments are almost identical to the ones with the actual alignments. In the absence of actual alignment the Quasi-Horizontal Alignment can easily be produced from any type of databases that contain highway coordinates such geodatabases and digital maps. Copyright © 2016 Elsevier Ltd. All rights reserved.

CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.

PubMed

Zhou, Carol L Ecale

2015-01-01

In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure. This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA). The use and utility of CombAlign was demonstrated by generating gapped MSSAs using sets of pairwise structure-based sequence alignments between structure models of the matrix protein (VP40) and pre-small/secreted glycoprotein (sGP) of Reston Ebolavirus and the corresponding proteins of several other filoviruses. The gapped MSSAs revealed structure-based residue-residue correspondences, which enabled identification of structurally similar versus differing regions in the Reston proteins compared to each of the other corresponding proteins. CombAlign is a new Python code that generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related proteins. CombAlign was developed in Python 2.6, and the source code is available for download from the GitHub code repository.

Collective excitations and ultrafast dipolar solvation dynamics in water-ethanol binary mixture

NASA Astrophysics Data System (ADS)

Hazra, Milan K.; Bagchi, Biman

2018-03-01

In order to understand the intermolecular vibrational spectrum and the collective excitations of water-ethanol binary mixture, we investigate the density of states and the power spectrum using computer simulations aided by theory. We investigate in particular the spectra at intermediate to low frequencies (a few hundreds to few tens of cm-1) by calculating (i) the density of states from quenched normal modes, (ii) the power spectrum from velocity time correlation function, and (iii) the far infrared and dielectric spectra (that is, the Cole-Cole plot) from the total dipole moment time correlation function. The different spectra are in broad agreement with each other and at the same time reveal unique characteristics of the water-ethanol mixture. Inverse participation ratio reveals several interesting features. Libration of pure ethanol is more localized than that of pure water. With increasing ethanol content, we observe localization of the collective libration mode as well as of the hindered translational and rotational mode. An interesting mixing between the libration of water and ethanol is observed. Solvation dynamics of tryptophan measured by equilibrium energy fluctuation time correlation function show surprisingly strong non-linear dependence on composition that can be tested against experiments.

Collective excitations and ultrafast dipolar solvation dynamics in water-ethanol binary mixture.

PubMed

Hazra, Milan K; Bagchi, Biman

2018-03-21

In order to understand the intermolecular vibrational spectrum and the collective excitations of water-ethanol binary mixture, we investigate the density of states and the power spectrum using computer simulations aided by theory. We investigate in particular the spectra at intermediate to low frequencies (a few hundreds to few tens of cm -1 ) by calculating (i) the density of states from quenched normal modes, (ii) the power spectrum from velocity time correlation function, and (iii) the far infrared and dielectric spectra (that is, the Cole-Cole plot) from the total dipole moment time correlation function. The different spectra are in broad agreement with each other and at the same time reveal unique characteristics of the water-ethanol mixture. Inverse participation ratio reveals several interesting features. Libration of pure ethanol is more localized than that of pure water. With increasing ethanol content, we observe localization of the collective libration mode as well as of the hindered translational and rotational mode. An interesting mixing between the libration of water and ethanol is observed. Solvation dynamics of tryptophan measured by equilibrium energy fluctuation time correlation function show surprisingly strong non-linear dependence on composition that can be tested against experiments.

Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation.

PubMed

Sharma, Virag; Hiller, Michael

2017-08-21

Genome alignments provide a powerful basis to transfer gene annotations from a well-annotated reference genome to many other aligned genomes. The completeness of these annotations crucially depends on the sensitivity of the underlying genome alignment. Here, we investigated the impact of the genome alignment parameters and found that parameters with a higher sensitivity allow the detection of thousands of novel alignments between orthologous exons that have been missed before. In particular, comparisons between species separated by an evolutionary distance of >0.75 substitutions per neutral site, like human and other non-placental vertebrates, benefit from increased sensitivity. To systematically test if increased sensitivity improves comparative gene annotations, we built a multiple alignment of 144 vertebrate genomes and used this alignment to map human genes to the other 143 vertebrates with CESAR. We found that higher alignment sensitivity substantially improves the completeness of comparative gene annotations by adding on average 2382 and 7440 novel exons and 117 and 317 novel genes for mammalian and non-mammalian species, respectively. Our results suggest a more sensitive alignment strategy that should generally be used for genome alignments between distantly-related species. Our 144-vertebrate genome alignment and the comparative gene annotations (https://bds.mpi-cbg.de/hillerlab/144VertebrateAlignment_CESAR/) are a valuable resource for comparative genomics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Role of dipolar interactions on morphologies and tunnel magnetoresistance in assemblies of magnetic nanoparticles

NASA Astrophysics Data System (ADS)

Anand, Manish; Carrey, Julian; Banerjee, Varsha

2018-05-01

We undertake comprehensive simulations of 2d arrays (Lx ×Ly) of magnetic nanoparticles (MNPs) with dipole-dipole interactions by solving LLG equations. Our primary interest is to understand the correspondence between equilibrium spin (ES) morphologies and tunnel magnetoresistance (TMR) as a function of Θ - the ratio of the dipolar to the anisotropy strength, sample size Lx , aspect ratio Ar =Ly /Lx and the direction of the applied field H → = HêH . The parameter Θ is varied by choosing three distinct particles: (i) α -Fe2O3 (Θ ≃ 0) , (ii) Co (Θ ≃ 0.37) and (iii) Fe3O4 (Θ ≃ 1.28) . Our main observations are as follows: (a) For weakly interacting spins (Θ ≃ 0) , the morphology has randomly oriented magnetic moments for all sample sizes and aspect ratios. The TMR exhibits a peak value of 50% at the coercive field Hc . It is robust with respect to Lx and Ar , and isotropic with respect to êH . (b) For strong interactions (Θ > 1) , the moments order in the plane of the sample. The ES morphology comprises of magnetically aligned regions interspersed with flux closure loops. For fields along x or y, the maximum TMR amplitude decrease to ∼30%. For êH = z ̂ , it drops to ∼3%. The TMR is robust with respect to Lx and Ar and isotropic in the x and y directions only. (c) In strongly interacting samples (Θ > 1) with Lx comparable to the size of a flux closure loop, increasing Ar creates ferromagnetic chains in the sample oriented along y or - y . Consequently, for êH = y ̂ , the TMR magnitude for Ar = 1 is ∼33% while that for Ar = 32 drops to ∼16%. For êH = x ̂ on the other hand, it is ∼30% and independent of Ar . The TMR of long ribbons of MNPs has a strong dependence on Ar and is anisotropic in all three directions.

Controlling electric, magnetic, and chiral dipolar emission with PT-symmetric potentials

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

Alaeian, Hadiseh; Dionne, Jennifer A.

We investigate the effect of parity-time (PT) symmetric optical potentials on the radiation of achiral and chiral dipole sources. Two properties unique to PT-symmetric potentials are observed. First, the dipole can be tuned to behave as a strong optical emitter or absorber based on the non-Hermiticity parameter and the dipole location. Second, exceptional points give rise to new system resonances that lead to orders-of-magnitude enhancements in the dipolar emitted or absorbed power. Utilizing these properties, we show that enantiomers of chiral molecules near PT-symmetric metamaterials exhibit a 4.5-fold difference in their emitted power and decay rate. The results of thismore » work could enable new atom-cavity interactions for quantum optics, as well as all-optical enantioselective separation.« less

Aligning for Innovation - Alignment Strategy to Drive Innovation

NASA Technical Reports Server (NTRS)

Johnson, Hurel; Teltschik, David; Bussey, Horace, Jr.; Moy, James

2010-01-01

With the sudden need for innovation that will help the country achieve its long-term space exploration objectives, the question of whether NASA is aligned effectively to drive the innovation that it so desperately needs to take space exploration to the next level should be entertained. Authors such as Robert Kaplan and David North have noted that companies that use a formal system for implementing strategy consistently outperform their peers. They have outlined a six-stage management systems model for implementing strategy, which includes the aligning of the organization towards its objectives. This involves the alignment of the organization from the top down. This presentation will explore the impacts of existing U.S. industrial policy on technological innovation; assess the current NASA organizational alignment and its impacts on driving technological innovation; and finally suggest an alternative approach that may drive the innovation needed to take the world to the next level of space exploration, with NASA truly leading the way.

Fluctuation-dissipation theorem in an isolated system of quantum dipolar bosons after a quench.

PubMed

Khatami, Ehsan; Pupillo, Guido; Srednicki, Mark; Rigol, Marcos

2013-08-02

We examine the validity of fluctuation-dissipation relations in isolated quantum systems taken out of equilibrium by a sudden quench. We focus on the dynamics of trapped hard-core bosons in one-dimensional lattices with dipolar interactions whose strength is changed during the quench. We find indications that fluctuation-dissipation relations hold if the system is nonintegrable after the quench, as well as if it is integrable after the quench if the initial state is an equilibrium state of a nonintegrable Hamiltonian. On the other hand, we find indications that they fail if the system is integrable both before and after quenching.

Ultrafast responses of dipolar and V-shaped dipicolinate derivatives with potential applications in the labeling of biomolecules

NASA Astrophysics Data System (ADS)

Wang, Yaochuan; Liu, Siyuan; Liu, Dajun; Wang, Guiqiu; Xiao, Haibo

2016-02-01

A dipolar dipicolinate derivative, trans-dimethyl-4-[4'-(N,N-diphenylamino)-styry1]-pyridin-2,6-dicarboxylate (P-1), and a P-1based V-shaped compound, {4-[(E)-2-(2,6-dimethoxycarbonylpyridin-4-yl) vinyl]}-N-phenyl-N-{4-[(E)-2-(2,6-dimethoxycarbonylpyridin-4-yl)vinylphenyl]}aniline (P-2), with intense two-photon fluorescence emission properties were systematically investigated by using steady-state absorption and fluorescence spectroscopy, open-aperture Z-scans, and two-photon excited fluorescence (TPF). The two-photon absorption cross-section of the V-shaped compound P-2 in tetrahydrofuran (THF) was determined to be 208 GM, which represents a 6.5-fold enhancement compared with its dipolar counterpart P-1 (32 GM). Extension of the intramolecular charge transfer (ICT) in the V-shaped dipicolinate derivative has been suggested as the mechanism of enhancement. The excited state dynamics from transient absorption spectroscopy were analyzed and discussed. The formation and relaxation lifetimes of the ICT state for these dipicolinate derivatives in THF solutions were found to be several picoseconds and several hundred picoseconds, respectively. The results show an increased ICT character of the V-shaped compound and a potential application for this compound in two-photon fluorescence imaging fields.

Gd(III) complexes for electron-electron dipolar spectroscopy: Effects of deuteration, pH and zero field splitting.

PubMed

Garbuio, Luca; Zimmermann, Kaspar; Häussinger, Daniel; Yulikov, Maxim

2015-10-01

Spectral parameters of Gd(III) complexes are intimately linked to the performance of the Gd(III)-nitroxide or Gd(III)-Gd(III) double electron-electron resonance (DEER or PELDOR) techniques, as well as to that of relaxation induced dipolar modulation enhancement (RIDME) spectroscopy with Gd(III) ions. These techniques are of interest for applications in structural biology, since they can selectively detect site-to-site distances in biomolecules or biomolecular complexes in the nanometer range. Here we report relaxation properties, echo detected EPR spectra, as well as the magnitude of the echo reduction effect in Gd(III)-nitroxide DEER for a series of Gadolinium(III) complexes with chelating agents derived from tetraazacyclododecane. We observed that solvent deuteration does not only lengthen the relaxation times of Gd(III) centers but also weakens the DEER echo reduction effect. Both of these phenomena lead to an improved signal-to-noise ratios or, alternatively, longer accessible distance range in pulse EPR measurements. The presented data enrich the knowledge on paramagnetic Gd(III) chelate complexes in frozen solutions, and can help optimize the experimental conditions for most types of the pulse measurements of the electron-electron dipolar interactions. Copyright © 2015 Elsevier Inc. All rights reserved.

The α-helix alignment of proteins in water solution toward a high-frequency electromagnetic field: A FTIR spectroscopy study.

PubMed

Calabrò, Emanuele; Magazù, Salvatore

2017-01-01

The aim of this article was to study the effects of mobile phone electromagnetic waves at 1750 MHz on the Amide I and Amide II vibration bands of some proteins in bidistilled water solution by means of Fourier transform infrared (FTIR) spectroscopy and Fourier self-deconvolution (FSD) analysis. The proteins that were used for the experiment were hemoglobin, myoglobin, bovine serum albumin and lysozyme. The exposure system consisted of microwaves emitted by an operational mobile phone at the frequency at 1750 MHz at the average power density of 1 W/m 2 . Exposed and control samples were analyzed using FTIR spectroscopy and FSD analysis. The main result was that Amide I band of the proteins that were used increased significantly (p < 0.05) after 4 h of exposure to MWs, whereas Amide II band did not change significantly. This result can be explained assuming that the α-helix structure of the proteins aligned itself with the direction of the electromagnetic field due to the alignment of C = O stretching and N - H bending ligands that are oriented along with the α-helix axis that give rise to the Amide I mode.

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.

StructAlign, a Program for Alignment of Structures of DNA-Protein Complexes.

PubMed

Popov, Ya V; Galitsyna, A A; Alexeevski, A V; Karyagina, A S; Spirin, S A

2015-11-01

Comparative analysis of structures of complexes of homologous proteins with DNA is important in the analysis of DNA-protein recognition. Alignment is a necessary stage of the analysis. An alignment is a matching of amino acid residues and nucleotides of one complex to residues and nucleotides of the other. Currently, there are no programs available for aligning structures of DNA-protein complexes. We present the program StructAlign, which should fill this gap. The program inputs a pair of complexes of DNA double helix with proteins and outputs an alignment of DNA chains corresponding to the best spatial fit of the protein chains.

First-Principles Approach to Energy Level Alignment at Aqueous Semiconductor Interfaces

NASA Astrophysics Data System (ADS)

Hybertsen, Mark

2015-03-01

We have developed a first principles method to calculate the energy level alignment between semiconductor band edges and reference energy levels at aqueous interfaces. This alignment is fundamental to understand the electrochemical characteristics of any semiconductor electrode in general and the potential for photocatalytic activity in particular. For example, in the search for new photo-catalytic materials, viable candidates must demonstrate both efficient absorption of the solar spectrum and an appropriate alignment of the band edge levels in the semiconductor to the redox levels for the target reactions. In our approach, the interface-specific contribution to the electrostatic step across the interface is evaluated using density functional theory (DFT) based molecular dynamics to sample the physical interface structure and the corresponding change in the electrostatic potential at the interface. The reference electronic levels in the semiconductor and in the water are calculated using the GW approach, which naturally corrects for errors inherent in the use of Kohn-Sham energy eigenvalues to approximate the electronic excitation energies in each material. Taken together, our calculations provide the alignment of the semiconductor valence band edge to the centroid of the highest occupied 1b1 level in water. The known relationship of the 1b1 level to the normal hydrogen electrode completes the connection to electrochemical levels. We discuss specific results for GaN, ZnO, and TiO2. The effect of interface structural motifs, such as different degrees of water dissociation, and of dynamical characteristics, will be presented together with available experimental data. Work supported by the US Department of Energy, Office of Basic Energy Sciences under Contract No. DE-AC02-98CH10886.

CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

PubMed

Terashi, Genki; Takeda-Shitaka, Mayuko

2015-01-01

Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both

Structural anomaly and dynamic heterogeneity in cycloether/water binary mixtures: Signatures from composition dependent dynamic fluorescence measurements and computer simulations

NASA Astrophysics Data System (ADS)

Indra, Sandipa; Guchhait, Biswajit; Biswas, Ranjit

2016-03-01

We have performed steady state UV-visible absorption and time-resolved fluorescence measurements and computer simulations to explore the cosolvent mole fraction induced changes in structural and dynamical properties of water/dioxane (Diox) and water/tetrahydrofuran (THF) binary mixtures. Diox is a quadrupolar solvent whereas THF is a dipolar one although both are cyclic molecules and represent cycloethers. The focus here is on whether these cycloethers can induce stiffening and transition of water H-bond network structure and, if they do, whether such structural modification differentiates the chemical nature (dipolar or quadrupolar) of the cosolvent molecules. Composition dependent measured fluorescence lifetimes and rotation times of a dissolved dipolar solute (Coumarin 153, C153) suggest cycloether mole-fraction (XTHF/Diox) induced structural transition for both of these aqueous binary mixtures in the 0.1 ≤ XTHF/Diox ≤ 0.2 regime with no specific dependence on the chemical nature. Interestingly, absorption measurements reveal stiffening of water H-bond structure in the presence of both the cycloethers at a nearly equal mole-fraction, XTHF/Diox ˜ 0.05. Measurements near the critical solution temperature or concentration indicate no role for the solution criticality on the anomalous structural changes. Evidences for cycloether aggregation at very dilute concentrations have been found. Simulated radial distribution functions reflect abrupt changes in respective peak heights at those mixture compositions around which fluorescence measurements revealed structural transition. Simulated water coordination numbers (for a dissolved C153) and number of H-bonds also exhibit minima around these cosolvent concentrations. In addition, several dynamic heterogeneity parameters have been simulated for both the mixtures to explore the effects of structural transition and chemical nature of cosolvent on heterogeneous dynamics of these systems. Simulated four-point dynamic

Exp6-polar thermodynamics of dense supercritical water

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

Bastea, S; Fried, L E

2007-12-13

We introduce a simple polar fluid model for the thermodynamics of dense supercritical water based on a Buckingham (exp-6) core and point dipole representation of the water molecule. The proposed exp6-polar thermodynamics, based on ideas originally applied to dipolar hard spheres, performs very well when tested against molecular dynamics simulations. Comparisons of the model predictions with experimental data available for supercritical water yield excellent agreement for the shock Hugoniot, isotherms and sound speeds, and are also quite good for the self-diffusion constant and relative dielectric constant. We expect the present approach to be also useful for other small polar moleculesmore » and their mixtures.« less

Relaxation dynamics of a driven two-level system coupled to a Bose-Einstein condensate: application to quantum dot-dipolar exciton gas hybrid systems.

PubMed

Kovalev, Vadim M; Tse, Wang-Kong

2017-11-22

We develop a microscopic theory for the relaxation dynamics of an optically pumped two-level system (TLS) coupled to a bath of weakly interacting Bose gas. Using Keldysh formalism and diagrammatic perturbation theory, expressions for the relaxation times of the TLS Rabi oscillations are derived when the boson bath is in the normal state and the Bose-Einstein condensate (BEC) state. We apply our general theory to consider an irradiated quantum dot coupled with a boson bath consisting of a two-dimensional dipolar exciton gas. When the bath is in the BEC regime, relaxation of the Rabi oscillations is due to both condensate and non-condensate fractions of the bath bosons for weak TLS-light coupling and pre dominantly due to the non-condensate fraction for strong TLS-light coupling. Our theory also shows that a phase transition of the bath from the normal to the BEC state strongly influences the relaxation rate of the TLS Rabi oscillations. The TLS relaxation rate is approximately independent of the pump field frequency and monotonically dependent on the field strength when the bath is in the low-temperature regime of the normal phase. Phase transition of the dipolar exciton gas leads to a non-monotonic dependence of the TLS relaxation rate on both the pump field frequency and field strength, providing a characteristic signature for the detection of BEC phase transition of the coupled dipolar exciton gas.

Broadband high-frequency waves and intermittent energy conversion at dipolarization fronts

NASA Astrophysics Data System (ADS)

Yang, J.; Cao, J.; Fu, H.; Wang, T.; Liu, W.; Yao, Z., Sr.

2017-12-01

Dipolarization front (DF) is a sharp boundary most probably separating the reconnection jet from the background plasma sheet. So far at this boundary, the observed waves are mainly in low-frequency range (e.g., magnetosonic waves and lower hybrid waves). Few high-frequency waves are observed in this region. In this paper, we report the broadband high-frequency wave emissions at the DF. These waves, having frequencies extending from the electron cyclotron frequency fce, up to the electron plasma frequency fpe, could contribute 10% to the in situ measurement of intermittent energy conversion at the DF layer. Their generation may be attributed to electron beams, which are simultaneously observed at the DF as well. Furthermore, we find intermittent energy conversion is primarily to the broadband fluctuations in the lower hybrid frequency range although the net energy conversion is small.

Superfluidity of dipolar excitons in a transition metal dichalcogenide double layer

NASA Astrophysics Data System (ADS)

Berman, Oleg L.; Kezerashvili, Roman Ya.

2017-09-01

We study formation and superfluidity of dipolar excitons in double layer heterostructures formed by two transition metal dichalcogenide (TMDC) atomically thin layers. Considering screening effects for an electron-hole interaction via the harmonic oscillator approximation for the Keldysh potential, the analytical expressions for the exciton energy spectrum and the mean field critical temperature Tc for the superfluidity are obtained. It is shown that binding energies of A excitons are larger than for B excitons. The mean field critical temperature for a two-component dilute exciton system in a TMDC double layer is analyzed and shown that the latter is an increasing function of the factor Q , determined by the effective masses of A and B excitons and their reduced mass. Comparison of the calculations for Tc performed by employing the Coulomb and Keldysh interactions demonstrates the importance of screening effects in TMDC.

Stakeholder Alignment and Changing Geospatial Information Capabilities

NASA Astrophysics Data System (ADS)

Winter, S.; Cutcher-Gershenfeld, J.; King, J. L.

2015-12-01

Changing geospatial information capabilities can have major economic and social effects on activities such as drought monitoring, weather forecasts, agricultural productivity projections, water and air quality assessments, the effects of forestry practices and so on. Whose interests are served by such changes? Two common mistakes are assuming stability in the community of stakeholders and consistency in stakeholder behavior. Stakeholder communities can reconfigure dramatically as some leave the discussion, others enter, and circumstances shift — all resulting in dynamic points of alignment and misalignment . New stakeholders can bring new interests, and existing stakeholders can change their positions. Stakeholders and their interests need to be be considered as geospatial information capabilities change, but this is easier said than done. New ways of thinking about stakeholder alignment in light of changes in capability are presented.

Evidence for a dipolar-coupled AM system in carnosine in human calf muscle from in vivo 1H NMR spectroscopy

NASA Astrophysics Data System (ADS)

Schröder, Leif; Bachert, Peter

2003-10-01

Spin systems with residual dipolar couplings such as creatine, taurine, and lactate in skeletal muscle tissue exhibit first-order spectra in in vivo 1H NMR spectroscopy at 1.5 T because the coupled protons are represented by (nearly) symmetrized eigenfunctions. The imidazole ring protons (H2, H4) of carnosine are suspected to form also a coupled system. The ring's stiffness could enable a connectivity between these anisochronous protons with the consequence of second-order spectra at low field strength. Our purpose was to study whether this deviation from the Paschen-Back condition can be used to detect the H2-H4 coupling in localized 1D 1H NMR spectra obtained at 1.5 T (64 MHz) from the human calf in a conventional whole-body scanner. As for the hydrogen hyperfine interaction, a Breit-Rabi equation was derived to describe the transition from Zeeman to Paschen-Back regime for two dipolar-coupled protons. The ratio of the measurable coupling strength ( Sk) and the difference in resonance frequencies of the coupled spins (Δ ω) induces quantum-state mixing of various degree upon definition of an appropriate eigenbase of the coupled spin system. The corresponding Clebsch-Gordan coefficients manifest in characteristic energy corrections in the Breit-Rabi formula. These additional terms were used to define an asymmetry parameter of the line positions as a function of Sk and Δ ω. The observed frequency shifts of the resonances were found to be consistent with this parameter within the accuracy achievable in in vivo NMR spectroscopy. Thus it was possible to identify the origin of satellite peaks of H2, H4 and to describe this so far not investigated type of residual dipolar coupling in vivo.

Geometry-dependent distributed polarizability models for the water molecule

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

Loboda, Oleksandr; Ingrosso, Francesca; Ruiz-López, Manuel F.

2016-01-21

Geometry-dependent distributed polarizability models have been constructed by fits to ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set for the water molecule in the field of a point charge. The investigated models include (i) charge-flow polarizabilities between chemically bonded atoms, (ii) isotropic or anisotropic dipolar polarizabilities on oxygen atom or on all atoms, and (iii) combinations of models (i) and (ii). For each model, the polarizability parameters have been optimized to reproduce the induction energy of a water molecule polarized by a point charge successivelymore » occupying a grid of points surrounding the molecule. The quality of the models is ascertained by examining their ability to reproduce these induction energies as well as the molecular dipolar and quadrupolar polarizabilities. The geometry dependence of the distributed polarizability models has been explored by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For each considered model, the distributed polarizability components have been fitted as a function of the geometry by a Taylor expansion in monomer coordinate displacements up to the sum of powers equal to 4.« less

Simulation study of localization of electromagnetic waves in two-dimensional random dipolar systems.

PubMed

Wang, Ken Kang-Hsin; Ye, Zhen

2003-12-01

We study the propagation and scattering of electromagnetic waves by random arrays of dipolar cylinders in a uniform medium. A set of self-consistent equations, incorporating all orders of multiple scattering of the electromagnetic waves, is derived from first principles and then solved numerically for electromagnetic fields. For certain ranges of frequencies, spatially localized electromagnetic waves appear in such a simple but realistic disordered system. Dependence of localization on the frequency, radiation damping, and filling factor is shown. The spatial behavior of the total, coherent, and diffusive waves is explored in detail, and found to comply with a physical intuitive picture. A phase diagram characterizing localization is presented, in agreement with previous investigations on other systems.

Hydrophilic Channel Alignment of Perfluoronated Sulfonic-Acid Ionomers for Vanadium Redox Flow Batteries.

PubMed

So, Soonyong; Cha, Min Suc; Jo, Sang-Woo; Kim, Tae-Ho; Lee, Jang Yong; Hong, Young Taik

2018-06-13

It is known that uniaxially drawn perfluoronated sulfonic-acid ionomers (PFSAs) show diffusion anisotropy because of the aligned water channels along the deformation direction. We apply the uniaxially stretched membranes to vanadium redox flow batteries (VRFBs) to suppress the permeation of active species, vanadium ions through the transverse directions. The aligned water channels render much lower vanadium permeability, resulting in higher Coulombic efficiency (>98%) and longer self-discharge time (>250 h). Similar to vanadium ions, proton conduction through the membranes also decreases as the stretching ratio increases, but the thinned membranes show the enhanced voltage and energy efficiencies over the range of current density, 50-100 mA/cm 2 . Hydrophilic channel alignment of PFSAs is also beneficial for long-term cycling of VRFBs in terms of capacity retention and cell performances. This simple pretreatment of membranes offers an effective and facile way to overcome high vanadium permeability of PFSAs for VRFBs.

Dry contact transfer printing of aligned carbon nanotube patterns and characterization of their optical properties for diameter distribution and alignment.

PubMed

Pint, Cary L; Xu, Ya-Qiong; Moghazy, Sharief; Cherukuri, Tonya; Alvarez, Noe T; Haroz, Erik H; Mahzooni, Salma; Doorn, Stephen K; Kono, Junichiro; Pasquali, Matteo; Hauge, Robert H

2010-02-23

A scalable and facile approach is demonstrated where as-grown patterns of well-aligned structures composed of single-walled carbon nanotubes (SWNT) synthesized via water-assisted chemical vapor deposition (CVD) can be transferred, or printed, to any host surface in a single dry, room-temperature step using the growth substrate as a stamp. We demonstrate compatibility of this process with multiple transfers for large-scale device and specifically tailored pattern fabrication. Utilizing this transfer approach, anisotropic optical properties of the SWNT films are probed via polarized absorption, Raman, and photoluminescence spectroscopies. Using a simple model to describe optical transitions in the large SWNT species present in the aligned samples, polarized absorption data are demonstrated as an effective tool for accurate assignment of the diameter distribution from broad absorption features located in the infrared. This can be performed on either well-aligned samples or unaligned doped samples, allowing simple and rapid feedback of the SWNT diameter distribution that can be challenging and time-consuming to obtain in other optical methods. Furthermore, we discuss challenges in accurately characterizing alignment in structures of long versus short carbon nanotubes through optical techniques, where SWNT length makes a difference in the information obtained in such measurements. This work provides new insight to the efficient transfer and optical properties of an emerging class of long, large diameter SWNT species typically produced in the CVD process.

Characteristics of DC electric fields at dipolarization fronts

NASA Astrophysics Data System (ADS)

Laakso, Harri; Escoubet, Philippe; Masson, Arnaud

2016-04-01

We investigate the characteristics of DC electric field at dipolarization fronts and BBF's using multi-point Cluster observations. There are plenty of important issues that are considered, such as what kind of DC electric fields exist in such events and what are their spatial scales. One can also recognize if electrons and ions perform ExB drift motions in these events. To investigate this, we take an advantage of five different DC electric field measurements in the plasma sheet available from the EFW double probe experiment, EDI electron drift instrument, CODIF and HIA ion spectrometers, and PEACE electron spectrometer. The calibrated observations of the three spectrometers are used to determine the proton and electron drift velocity and furthermore the DC electric field, assuming that the electron and proton velocity perpendicular to the magnetic field is dominated by the ExB drift motion. Naturally when ions and electrons do not perform a proper drift motion, which can happen in the plasma sheet, the estimated DC electric field from ion and electron motion is not correct. However, surprisingly often the DC electric fields estimated from electron and ion motions are identical suggesting that this field is a real DC electric field around the measurement point. This investigation also helps understand how well different measurements are calibrated.

Colour stabilities of three types of orthodontic clear aligners exposed to staining agents

PubMed Central

Liu, Chen-Lu; Sun, Wen-Tian; Liao, Wen; Lu, Wen-Xin; Li, Qi-Wen; Jeong, Yunho; Liu, Jun; Zhao, Zhi-He

2016-01-01

The aim of this study was to evaluate and compare the colour stabilities of three types of orthodontic clear aligners exposed to staining agents in vitro. Sixty clear orthodontic aligners produced by three manufacturers (Invisalign, Angelalign, and Smartee) were immersed in three staining solutions (coffee, black tea, and red wine) and one control solution (distilled water). After 12-h and 7-day immersions, the aligners were washed in an ultrasonic cleaner and measured with a colourimeter. The colour changes (ΔE*) were calculated on the basis of the Commission Internationale de I'Eclairage L*a*b* colour system (CIE L*a*b*), and the results were then converted into National Bureau of Standards (NBS) units. Fourier transformation infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM) were conducted to observe the molecular and morphologic alterations to the aligner surfaces, respectively. The three types of aligners exhibited slight colour changes after 12 h of staining, with the exception of the Invisalign aligners stained with coffee. The Invisalign aligners exhibited significantly higher ΔE* values (ranging from 0.30 to 27.81) than those of the Angelalign and Smartee aligners (ΔE* values ranging from 0.33 to 1.89 and 0.32 to 1.61, respectively, P<0.05). FT-IR analysis confirmed that the polymer-based structure of aligners did not exhibit significant chemical differences before and after the immersions. The SEM results revealed different surface alterations to the three types of aligner materials after the 7-day staining. The three types of aesthetic orthodontic appliances exhibited colour stability after the 12-h immersion, with the exception of the Invisalign aligners stained by coffee. The Invisalign aligners were more prone than the Angelalign and Smartee aligners to pigmentation. Aligner materials may be improved by considering aesthetic colour stability properties. PMID:27660048

Colour stabilities of three types of orthodontic clear aligners exposed to staining agents.

PubMed

Liu, Chen-Lu; Sun, Wen-Tian; Liao, Wen; Lu, Wen-Xin; Li, Qi-Wen; Jeong, Yunho; Liu, Jun; Zhao, Zhi-He

2016-12-16

The aim of this study was to evaluate and compare the colour stabilities of three types of orthodontic clear aligners exposed to staining agents in vitro. Sixty clear orthodontic aligners produced by three manufacturers (Invisalign, Angelalign, and Smartee) were immersed in three staining solutions (coffee, black tea, and red wine) and one control solution (distilled water). After 12-h and 7-day immersions, the aligners were washed in an ultrasonic cleaner and measured with a colourimeter. The colour changes (ΔE*) were calculated on the basis of the Commission Internationale de I'Eclairage L*a*b* colour system (CIE L*a*b*), and the results were then converted into National Bureau of Standards (NBS) units. Fourier transformation infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM) were conducted to observe the molecular and morphologic alterations to the aligner surfaces, respectively. The three types of aligners exhibited slight colour changes after 12 h of staining, with the exception of the Invisalign aligners stained with coffee. The Invisalign aligners exhibited significantly higher ΔE* values (ranging from 0.30 to 27.81) than those of the Angelalign and Smartee aligners (ΔE* values ranging from 0.33 to 1.89 and 0.32 to 1.61, respectively, P<0.05). FT-IR analysis confirmed that the polymer-based structure of aligners did not exhibit significant chemical differences before and after the immersions. The SEM results revealed different surface alterations to the three types of aligner materials after the 7-day staining. The three types of aesthetic orthodontic appliances exhibited colour stability after the 12-h immersion, with the exception of the Invisalign aligners stained by coffee. The Invisalign aligners were more prone than the Angelalign and Smartee aligners to pigmentation. Aligner materials may be improved by considering aesthetic colour stability properties.

Van-der-Waals interaction of atoms in dipolar Rydberg states

NASA Astrophysics Data System (ADS)

Kamenski, Aleksandr A.; Mokhnenko, Sergey N.; Ovsiannikov, Vitaly D.

2018-02-01

An asymptotic expression for the van-der-Waals constant C 6( n) ≈ -0.03 n 12 K p ( x) is derived for the long-range interaction between two highly excited hydrogen atoms A and B in their extreme Stark states of equal principal quantum numbers n A = n B = n ≫ 1 and parabolic quantum numbers n 1(2) = n - 1, n 2(1) = m = 0 in the case of collinear orientation of the Stark-state dipolar electric moments and the interatomic axis. The cubic polynomial K 3( x) in powers of reciprocal values of the principal quantum number x = 1/ n and quadratic polynomial K 2( y) in powers of reciprocal values of the principal quantum number squared y = 1/ n 2 were determined on the basis of the standard curve fitting polynomial procedure from the calculated data for C 6( n). The transformation of attractive van-der-Waals force ( C 6 > 0) for low-energy states n < 23 into repulsive force ( C 6 < 0) for all higher-energy states of n ≥ 23, is observed from the results of numerical calculations based on the second-order perturbation theory for the operator of the long-range interaction between neutral atoms. This transformation is taken into account in the asymptotic formulas (in both cases of p = 2, 3) by polynomials K p tending to unity at n → ∞ ( K p (0) = 1). The transformation from low- n attractive van-der-Waals force into high- n repulsive force demonstrates the gradual increase of the negative contribution to C 6( n) from the lower-energy two-atomic states, of the A(B)-atom principal quantum numbers n'A(B) = n-Δ n (where Δ n = 1, 2, … is significantly smaller than n for the terms providing major contribution to the second-order series), which together with the states of n″B(A) = n+Δ n make the joint contribution proportional to n 12. So, the hydrogen-like manifold structure of the energy spectrum is responsible for the transformation of the power-11 asymptotic dependence C 6( n) ∝ n 11of the low-angular-momenta Rydberg states in many-electron atoms into the power

Nuclear magnetic resonance studies of quadrupolar nuclei and dipolar field effects

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

Urban, Jeffry Todd

Experimental and theoretical research conducted in two areas in the field of nuclear magnetic resonance (NMR) spectroscopy is presented: (1) studies of the coherent quantum-mechanical control of the angular momentum dynamics of quadrupolar (spin I > 1/2) nuclei and its application to the determination of molecular structure; and (2) applications of the long-range nuclear dipolar field to novel NMR detection methodologies.The dissertation is organized into six chapters. The first two chapters and associated appendices are intended to be pedagogical and include an introduction to the quantum mechanical theory of pulsed NMR spectroscopy and the time dependent theory of quantum mechanics.more » The third chapter describes investigations of the solid-state multiple-quantum magic angle spinning (MQMAS) NMR experiment applied to I = 5/2 quadrupolar nuclei. This work reports the use of rotary resonance-matched radiofrequency irradiation for sensitivity enhancement of the I = 5/2 MQMAS experiment. These experiments exhibited certain selective line narrowing effects which were investigated theoretically.The fourth chapter extends the discussion of multiple quantum spectroscopy of quadrupolar nuclei to a mostly theoretical study of the feasibility of enhancing the resolution of nitrogen-14 NMR of large biomolecules in solution via double-quantum spectroscopy. The fifth chapter continues to extend the principles of multiple quantum NMR spectroscopy of quadrupolar nuclei to make analogies between experiments in NMR/nuclear quadrupolar resonance (NQR) and experiments in atomic/molecular optics (AMO). These analogies are made through the Hamiltonian and density operator formalism of angular momentum dynamics in the presence of electric and magnetic fields.The sixth chapter investigates the use of the macroscopic nuclear dipolar field to encode the NMR spectrum of an analyte nucleus indirectly in the magnetization of a sensor nucleus. This technique could potentially serve as an

A Dipolar Anthracene Dye: Synthesis, Optical Properties and Two-photon Tissue Imaging.

PubMed

Moon, Hyunsoo; Jun, Yong Woong; Kim, Dokyoung; Ryu, Hye Gun; Wang, Taejun; Kim, Ki Hean; Huh, Youngbuhm; Jung, Junyang; Ahn, Kyo Han

2016-09-20

Two-photon microscopy is a powerful tool for studying biological systems. In search of novel two-photon absorbing dyes for bioimaging, we synthesized a new anthracene-based dipolar dye (anthradan) and evaluated its two-photon absorbing and imaging properties. The new anthradan, 9,10-bis(o-dimethoxy-phenyl)-anthradan, absorbs and emits at longer wavelengths than acedan, a well-known two-photon absorbing dye. It is also stable under two-photon excitation conditions and biocompatible, and thus used for two-photon imaging of mouse organ tissues to show bright, near-red fluorescence along with negligible autofluorescence. Such an anthradan thus holds promise as a new class of two-photon absorbing dyes for the development of fluorescent probes and tags for biological systems. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Reducing beam shaper alignment complexity: diagnostic techniques for alignment and tuning

NASA Astrophysics Data System (ADS)

Lizotte, Todd E.

2011-10-01

Safe and efficient optical alignment is a critical requirement for industrial laser systems used in a high volume manufacturing environment. Of specific interest is the development of techniques to align beam shaping optics within a beam line; having the ability to instantly verify by a qualitative means that each element is in its proper position as the beam shaper module is being aligned. There is a need to reduce these types of alignment techniques down to a level where even a newbie to optical alignment will be able to complete the task. Couple this alignment need with the fact that most laser system manufacturers ship their products worldwide and the introduction of a new set of variables including cultural and language barriers, makes this a top priority for manufacturers. Tools and methodologies for alignment of complex optical systems need to be able to cross these barriers to ensure the highest degree of up time and reduce the cost of maintenance on the production floor. Customers worldwide, who purchase production laser equipment, understand that the majority of costs to a manufacturing facility is spent on system maintenance and is typically the largest single controllable expenditure in a production plant. This desire to reduce costs is driving the trend these days towards predictive and proactive, not reactive maintenance of laser based optical beam delivery systems [10]. With proper diagnostic tools, laser system developers can develop proactive approaches to reduce system down time, safe guard operational performance and reduce premature or catastrophic optics failures. Obviously analytical data will provide quantifiable performance standards which are more precise than qualitative standards, but each have a role in determining overall optical system performance [10]. This paper will discuss the use of film and fluorescent mirror devices as diagnostic tools for beam shaper module alignment off line or in-situ. The paper will also provide an overview

Making Macroscopic Assemblies of Aligned Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Smalley, Richard E.; Colbert, Daniel T.; Smith, Ken A.; Walters, Deron A.; Casavant, Michael J.; Qin, Xiaochuan; Yakobson, Boris; Hauge, Robert H.; Saini, Rajesh Kumar; Chiung, Wan-Ting;

Creating Polymer Hydrogel Microfibres with Internal Alignment via Electrical and Mechanical Stretching

PubMed Central

Zhang, Shuming; Liu, Xi; Barreto-Ortiz, Sebastian F.; Yu, Yixuan; Ginn, Brian; DeSantis, Nicholas; Hutton, Daphne L; Grayson, Warren; Cui, Fu-Zhai; Korgel, Brian A.; Gerecht, Sharon; Mao, Hai-Quan

2014-01-01

Hydrogels have been widely used for 3-dimensional (3D) cell culture and tissue regeneration due to their tunable biochemical and physicochemical properties as well as their high water content, which resembles the aqueous microenvironment of the natural extracellular matrix. While many properties of natural hydrogel matrices are modifiable, their intrinsic isotropic structure limits the control over cellular organization, which is critical to restore tissue function. Here we report a generic approach to incorporate alignment topography inside the hydrogel matrix using a combination of electrical and mechanical stretching. Hydrogel fibres with uniaxial alignment were prepared from aqueous solutions of natural polymers such as alginate, fibrin, gelatin, and hyaluronic acid under ambient conditions. The unique internal alignment feature drastically enhances the mechanical properties of the hydrogel microfibres. Furthermore, the facile, organic solvent-free processing conditions are amenable to the incorporation of live cells within the hydrogel fibre or on the fibre surface; both approaches effectively induce cellular alignment. This work demonstrates a versatile and scalable strategy to create aligned hydrogel microfibres from various natural polymers. PMID:24439410

Van Allen Probe measurements of intense Poynting Flux, magnetic dipolarization, and particle energization and auroral arcs.

NASA Astrophysics Data System (ADS)

Wygant, J. R.; Tian, S.; Thaller, S. A.; Breneman, A. W.; Cattell, C. A.; Engel, A.; Mozer, F.; Bonnell, J. W.; Chaston, C. C.; Donovan, E.; Spanswick, E.; Reeves, G.; Kistler, L. M.; Mouikis, C.; Hudson, M.; Smith, C. W.; Fennell, J. F.; Blake, J. B.; Turner, D. L.; Baker, D. N.; Kletzing, C.

2017-12-01

In recent years, there has been a focus on measurements in the near Earth plasmasheet of intervals of intense parallel Poynting flux, magnetic dipolarizations, and energetic particle injection/ and acceleration, as well as, ion ouflow from low altitudes (Ergun et al., 2015; Wygant et al., 2015 and Tian et. al. this meeting). We describe observations from an event on 5/1/2013 and related events on 6/01/2013 and 4/14/2013. Measurements from Van Allen Probes demonstrate that intrinsic to the structure of these dipolarization events are intense pulses (>100 mW/m2) of Poynting flux lasting 1 minute at the leading edge of the dipolarization front. The electric field associated with the Poynting flux burst is primarily in the poloidal direction (70 mV/m) but does also have a significant azimuthal (dawn-dusk) component of 20 mV/m capable of injecting electrons earthward and energizing them via conservation of the first adiabatic invariant. The THEMIS auroral array is used to show that these intervals of Poynting flux are nearly exactly coincident with thin (30 km wide) intense auroral arcs, which also have durations comparable to the Poynting flux. The correspondence between the arc and the Poynting flux allows us to infer the spatial dimensions of the electric fields, which might accelerate particles. Based on the dimensions of the arc, we estimate that at the spacecraft, the region of strong electric field is 1- 1.5 Re in azimuthal extent and 600- 900 km in poloidal direction. The associated EMF along the longitudinal direction is 150-200 kilovolts while the EMF in the poloidal direction is 30-60 kilovolts.Van Allen Probe measurements show that there are abrupt peaks in energetic electrons between 30 keV to 2 MeV coincident with these fields.The enhancements are dispersion-less locally but show energy-time dispersion as seen by LANL spacecraft displaced in MLT. Subsequent to the initial pulse of Poynting flux, there is a longer term (5-30 minutes) second phase of the

HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks.

PubMed

Hashemifar, Somaye; Xu, Jinbo

2014-09-01

High-throughput experimental techniques have produced a large amount of protein-protein interaction (PPI) data. The study of PPI networks, such as comparative analysis, shall benefit the understanding of life process and diseases at the molecular level. One way of comparative analysis is to align PPI networks to identify conserved or species-specific subnetwork motifs. A few methods have been developed for global PPI network alignment, but it still remains challenging in terms of both accuracy and efficiency. This paper presents a novel global network alignment algorithm, denoted as HubAlign, that makes use of both network topology and sequence homology information, based upon the observation that topologically important proteins in a PPI network usually are much more conserved and thus, more likely to be aligned. HubAlign uses a minimum-degree heuristic algorithm to estimate the topological and functional importance of a protein from the global network topology information. Then HubAlign aligns topologically important proteins first and gradually extends the alignment to the whole network. Extensive tests indicate that HubAlign greatly outperforms several popular methods in terms of both accuracy and efficiency, especially in detecting functionally similar proteins. HubAlign is available freely for non-commercial purposes at http://ttic.uchicago.edu/∼hashemifar/software/HubAlign.zip. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Comparative SEM analysis of nine F22 aligner cleaning strategies.

PubMed

Lombardo, Luca; Martini, Marco; Cervinara, Francesca; Spedicato, Giorgio Alfredo; Oliverio, Teresa; Siciliani, Giuseppe

2017-12-01

The orthodontics industry has paid great attention to the aesthetics of orthodontic appliances, seeking to make them as invisible as possible. There are several advantages to clear aligner systems, including aesthetics, comfort, chairside time reduction, and the fact that they can be removed for meals and oral hygiene procedures. Five patients were each given a series of F22 aligners, each to be worn for 14 days and nights, with the exception of meal and brushing times. Patients were instructed to clean each aligner using a prescribed strategy, and sections of the used aligners were observed under SEM. One grey-scale SEM image was saved per aligner in JPEG format with an 8-bit colour depth, and a total of 45 measurements on the grey scale ("Value" variable) were made. This dataset was analysed statistically via repeated measures ANOVA to determine the effect of each of the nine cleaning strategies in each of the five patients. A statistically significant difference in the efficacy of the cleaning strategies was detected. Specifically, rinsing with water alone was significantly less efficacious, and a combination of cationic detergent solution and ultrasonication was significantly more efficacious than the other methods (p < 0.05). Of the nine cleaning strategies examined, only that involving 5 min of ultrasonication at 42 k Hz combined with a 0.3% germicidal cationic detergent was observed to be statistically effective at removing the bacterial biofilm from the surface of F22 aligners.

Preparation of aligned nanotube membranes for water and gas separation applications

DOEpatents

Lulevich, Valentin; Bakajin, Olgica; Klare, Jennifer E.; Noy, Aleksandr

2016-01-05

Fabrication methods for selective membranes that include aligned nanotubes can advantageously include a mechanical polishing step. The nanotubes have their ends closed off during the step of infiltrating a polymer precursor around the nanotubes. This prevents polymer precursor from flowing into the nanotubes. The polishing step is performed after the polymer matrix is formed, and can open up the ends of the nanotubes.

Effect of Dipolar Cross Correlation on Model-Free Motional Parameters Obtained from 13C Relaxation in AX 2 Systems

NASA Astrophysics Data System (ADS)

Zhu, L. Y.; Kemple, M. D.; Landy, S. B.; Buckley, P.

The importance of dipolar cross correlation in 13C relaxation studies of molecular motion in AX 2 spin systems (A = 13C, X = 1H) was examined. Several different models for the internal motion, including two restricted-diffusion, and two-site jump models, the Kinosita model [K. Kinosita, Jr., S. Kawato, and A. Ikegami, Biophys. J.20, 289 (1977)], and an axially symmetric model, were applied through the Lipari and Szabo [ J. Am. Chem. Soc.104, 4546 (1982)] formalism to calculate errors in 13C T1, obtained from inversion-recovery measurements under proton saturation, and NOE when dipolar cross correlation is neglected. Motional parameters in the Lipari and Szabo formalism, τ m, S2, and τ e, were then determined from T1 and NOE (including the errors) and compared with parameters initially used to simulate the relaxation data. The resulting differences in the motional parameters, while model dependent, were generally small for plausible motions. At larger S2 values (≥ 0.6), the errors in both τ m and S2 were <5%. Errors in τ e increased with S2 but were usually less than 10%. Larger errors in the parameters were found for an axially symmetric model, but with τ m fixed even those were >5% only for the τ m = 1 ns, τ e = 10 ps case. Furthermore, it was observed that deviations in a given motional parameter were mostly of the same sign, which allows bounds to be set on experimentally derived parameters. Relaxation data for the peptide melittin synthesized with gly enriched with 13C at the backbone cu position and with lys enriched with 13C in the side chain were examined in light of the results of the simulations. All in all, it appears that neglect of dipolar cross correlation in 13C T1 (With proton saturation) and NOE measurements in AX 2 systems does not lead to major problems in interpretation of the results in terms of molecular motion.

ATP Bioluminometers Analysis on the Surfaces of Removable Orthodontic Aligners after the Use of Different Cleaning Methods

PubMed Central

Levrini, Luca; Mangano, Alessandro; Margherini, Silvia; Tenconi, Camilla; Vigetti, Davide; Muollo, Raffaele; Marco Abbate, Gian

2016-01-01

Purpose. The aim was to quantify the bacteria concentration on the surface of orthodontic clear aligners using three different cleaning methods. Furthermore the objective was to validate the efficacy of the bioluminometer in assessing the bacteria concentration. Materials and Methods. Twenty subjects (six males and fourteen females) undergoing orthodontic therapy with clear aligners (Invisalign® Align Technology, Santa Clara, California) were enrolled in this study. The observation time was of six weeks. The patients were instructed to use different cleaning methods (water, brushing with toothpaste, and brushing with toothpaste and use of sodium carbonate and sulphate tablet). At the end of each phase a microbiological analysis was performed using the bioluminometer. Results. The highest bacteria concentration was found on aligners cleaned using only water (583 relative light units); a value of 189 relative light units was found on aligners cleaned with brushing and toothpaste. The lowest bacteria concentration was recorded on aligners cleaned with brushing and toothpaste and the use of sodium carbonate and sulfate tablet. Conclusions. The mechanical removal of the bacterial biofilm proved to be effective with brushing and toothpaste. The best results in terms of bacteria concentration were achieved adding the use of sodium carbonate and sulfate tablet. PMID:27242901

Influence of the black hole spin on the chaotic particle dynamics within a dipolar halo

NASA Astrophysics Data System (ADS)

Nag, Sankhasubhra; Sinha, Siddhartha; Ananda, Deepika B.; Das, Tapas K.

2017-04-01

We investigate the role of the spin angular momentum of astrophysical black holes in controlling the special relativistic chaotic dynamics of test particles moving under the influence of a post-Newtonian pseudo-Kerr black hole potential, along with a perturbative potential created by an asymmetrically placed (dipolar) halo. Proposing a Lyapunov-like exponent to be the effective measure of the degree of chaos observed in the system under consideration, it has been found that black hole spin anti-correlates with the degree of chaos for the aforementioned dynamics. Our findings have been explained applying the general principles of dynamical systems analysis.

Tidal alignment of galaxies

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

Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš

We develop an analytic model for galaxy intrinsic alignments (IA) based on the theory of tidal alignment. We calculate all relevant nonlinear corrections at one-loop order, including effects from nonlinear density evolution, galaxy biasing, and source density weighting. Contributions from density weighting are found to be particularly important and lead to bias dependence of the IA amplitude, even on large scales. This effect may be responsible for much of the luminosity dependence in IA observations. The increase in IA amplitude for more highly biased galaxies reflects their locations in regions with large tidal fields. We also consider the impact ofmore » smoothing the tidal field on halo scales. We compare the performance of this consistent nonlinear model in describing the observed alignment of luminous red galaxies with the linear model as well as the frequently used "nonlinear alignment model," finding a significant improvement on small and intermediate scales. We also show that the cross-correlation between density and IA (the "GI" term) can be effectively separated into source alignment and source clustering, and we accurately model the observed alignment down to the one-halo regime using the tidal field from the fully nonlinear halo-matter cross correlation. Inside the one-halo regime, the average alignment of galaxies with density tracers no longer follows the tidal alignment prediction, likely reflecting nonlinear processes that must be considered when modeling IA on these scales. Finally, we discuss tidal alignment in the context of cosmic shear measurements.« less

Tidal alignment of galaxies

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

Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš, E-mail: blazek@berkeley.edu, E-mail: zvlah@stanford.edu, E-mail: useljak@berkeley.edu

We develop an analytic model for galaxy intrinsic alignments (IA) based on the theory of tidal alignment. We calculate all relevant nonlinear corrections at one-loop order, including effects from nonlinear density evolution, galaxy biasing, and source density weighting. Contributions from density weighting are found to be particularly important and lead to bias dependence of the IA amplitude, even on large scales. This effect may be responsible for much of the luminosity dependence in IA observations. The increase in IA amplitude for more highly biased galaxies reflects their locations in regions with large tidal fields. We also consider the impact ofmore » smoothing the tidal field on halo scales. We compare the performance of this consistent nonlinear model in describing the observed alignment of luminous red galaxies with the linear model as well as the frequently used 'nonlinear alignment model,' finding a significant improvement on small and intermediate scales. We also show that the cross-correlation between density and IA (the 'GI' term) can be effectively separated into source alignment and source clustering, and we accurately model the observed alignment down to the one-halo regime using the tidal field from the fully nonlinear halo-matter cross correlation. Inside the one-halo regime, the average alignment of galaxies with density tracers no longer follows the tidal alignment prediction, likely reflecting nonlinear processes that must be considered when modeling IA on these scales. Finally, we discuss tidal alignment in the context of cosmic shear measurements.« less

Level Alignment as Descriptor for Semiconductor/Catalyst Systems in Water Splitting: The Case of Hematite/Cobalt Hexacyanoferrate Photoanodes.

PubMed

Hegner, Franziska Simone; Cardenas-Morcoso, Drialys; Giménez, Sixto; López, Núria; Galan-Mascaros, Jose Ramon

2017-11-23

The realization of artificial photosynthesis may depend on the efficient integration of photoactive semiconductors and catalysts to promote photoelectrochemical water splitting. Many efforts are currently devoted to the processing of multicomponent anodes and cathodes in the search for appropriate synergy between light absorbers and active catalysts. No single material appears to combine both features. Many experimental parameters are key to achieve the needed synergy between both systems, without clear protocols for success. Herein, we show how computational chemistry can shed some light on this cumbersome problem. DFT calculations are useful to predict adequate energy-level alignment for thermodynamically favored hole transfer. As proof of concept, we experimentally confirmed the limited performance enhancement in hematite photoanodes decorated with cobalt hexacyanoferrate as a competent water-oxidation catalyst. Computational methods describe the misalignment of their energy levels, which is the origin of this mismatch. Photoelectrochemical studies indicate that the catalyst exclusively shifts the hematite surface state to lower potentials, which therefore reduces the onset for water oxidation. Although kinetics will still depend on interface architecture, our simple theoretical approach may identify and predict plausible semiconductor/catalyst combinations, which will speed up experimental work towards promising photoelectrocatalytic systems. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Homeotropic alignment of multiple bent-core liquid crystal phases using a polydimethylsiloxane alignment layer

NASA Astrophysics Data System (ADS)

Carlson, Eric D.; Foley, Lee M.; Guzman, Edward; Korblova, Eva D.; Visvanathan, Rayshan; Ryu, SeongHo; Gim, Min-Jun; Tuchband, Michael R.; Yoon, Dong Ki; Clark, Noel A.; Walba, David M.

2017-08-01

The control of the molecular orientation of liquid crystals (LCs) is important in both understanding phase properties and the continuing development of new LC technologies including displays, organic transistors, and electro-optic devices. Many techniques have been developed for successfully inducing alignment of calamitic LCs, though these techniques typically do not translate to the alignment of bent-core liquid crystals (BCLCs). Some techniques have been utilized to align various phases of BCLCs, but these techniques are often unsuccessful for general alignment of multiple materials and/or multiple phases. Here, we demonstrate that glass cells treated with polydimethylsiloxane (PDMS) thin films induce high quality homeotropic alignment of multiple mesophases of four BCLCs. On cooling to the lowest temperature phase the homeotropic alignment is lost, and spherulitic growth is seen in crystal and crystal-like phases including the dark conglomerate (DC) and helical nanofilament (HNF) phases. Evidence of homeotropic alignment is observed using polarized optical microscopy. We speculate that the methyl groups on the surface of the PDMS films strongly interact with the aliphatic tails of each mesogens, resulting in homeotropic alignment.

Energy Level Alignment at Aqueous GaN and ZnO Interfaces

NASA Astrophysics Data System (ADS)

Hybertsen, Mark S.; Kharche, Neerav; Muckerman, James T.

2014-03-01

Electronic energy level alignment at semiconductor-electrolyte interfaces is fundamental to electrochemical activity. Motivated in particular by the search for new materials that can be more efficient for photocatalysis, we develop a first principles method to calculate this alignment at aqueous interfaces and demonstrate it for the specific case of non-polar GaN and ZnO interfaces with water. In the first step, density functional theory (DFT) based molecular dynamics is used to sample the physical interface structure and to evaluate the electrostatic potential step at the interface. In the second step, the GW approach is used to evaluate the reference electronic energy level separately in the bulk semiconductor (valence band edge energy) and in bulk water (the 1b1 energy level), relative to the internal electrostatic energy reference. Use of the GW approach naturally corrects for errors inherent in the use of Kohn-Sham energy eigenvalues to approximate the electronic excitation energies in each material. With this predicted interface alignment, specific redox levels in water, with potentials known relative to the 1b1 level, can then be compared to the semiconductor band edge positions. Our results will be discussed in the context of experiments in which photoexcited GaN and ZnO drive the hydrogen evolution reaction. Research carried out at Brookhaven National Laboratory under Contract No. DE-AC02-98CH10886 with the U.S. Department of Energy.

Anomalous Debye-like dielectric relaxation of water in micro-sized confined polymeric systems.

PubMed

Colosi, C; Costantini, M; Barbetta, A; Cametti, C; Dentini, M

2013-12-14

While it is well known that spatial confinement on a nm scale affects the molecular dynamics of water resulting in a hindered dipolar reorientation, question of whether these effects could result at length scales larger than these, i.e., in confined regions of the order of μm or more, is still under debate. Here we use dielectric relaxation spectroscopy techniques to study the relaxation orientation dynamics of water entrapped in different polymeric matrices with pore sizes of the order of 100 μm, analyzing the frequency relaxation behaviour of the dielectric response. Our results show that, contrary to what has been generally thought, even in confinements which are not particularly high such as those realized here, regions typically hundred micrometers in size can affect the water structure, inducing a water phase with properties different from those of bulk water. In particular, we observe a dielectric dispersion centered in the range 10(5)-10(7) Hz, in between the one characteristic of ice (8.3 kHz at T = 0 °C) and the one of bulk water (19.2 GHz at T = 25 °C). The analysis of the dependence on temperature of the relaxation time of this unexpected contribution rules out the possibility that it can be attributed to an interfacial polarization (Maxwell-Wagner effect) and suggests a dipolar Debye-like origin due to a slow-down of the hydrogen-bonded network orientational polarization. Also at these scales, the confinement alters the structure of water, leading to a hindered reorientation. These properties imply that water confined within these polymeric porous matrices is more ordered than bulk water. These findings may be important in order to understand biological processes in cells and in different biological compartments, where water is physiologically confined.

High Temperature Ultrasonic Probe and Pulse-Echo Probe Mounting Fixture for Testing and Blind Alignment on Steam Pipes

NASA Technical Reports Server (NTRS)

Lih, Shyh-Shiuh (Inventor); Takano, Nobuyuki (Inventor); Lee, Hyeong Jae (Inventor); Bao, Xiaoqi (Inventor); Badescu, Mircea (Inventor); Bar-Cohen, Yoseph (Inventor); Sherrit, Stewart (Inventor); Ostlund, Patrick N. (Inventor)

2017-01-01

A high temperature ultrasonic probe and a mounting fixture for attaching and aligning the probe to a steam pipe using blind alignment. The high temperature ultrasonic probe includes a piezoelectric transducer having a high temperature. The probe provides both transmitting and receiving functionality. The mounting fixture allows the high temperature ultrasonic probe to be accurately aligned to the bottom external surface of the steam pipe so that the presence of liquid water in the steam pipe can be monitored. The mounting fixture with a mounted high temperature ultrasonic probe are used to conduct health monitoring of steam pipes and to track the height of condensed water through the wall in real-time.

Molecular dynamics and information on possible sites of interaction of intramyocellular metabolites in vivo from resolved dipolar couplings in localized 1H NMR spectra

NASA Astrophysics Data System (ADS)

Schröder, Leif; Schmitz, Christian; Bachert, Peter

2004-12-01

Proton NMR resonances of the endogenous metabolites creatine and phosphocreatine ((P)Cr), taurine (Tau), and carnosine (Cs, β-alanyl- L-histidine) were studied with regard to residual dipolar couplings and molecular mobility. We present an analysis of the direct 1H- 1H interaction that provides information on motional reorientation of subgroups in these molecules in vivo. For this purpose, localized 1H NMR experiments were performed on m. gastrocnemius of healthy volunteers using a 1.5-T clinical whole-body MR scanner. We evaluated the observable dipolar coupling strength SD0 ( S = order parameter) of the (P)Cr-methyl triplet and the Tau-methylene doublet by means of the apparent line splitting. These were compared to the dipolar coupling strength of the (P)Cr-methylene doublet. In contrast to the aliphatic protons of (P)Cr and Tau, the aromatic H2 ( δ = 8 ppm) and H4 ( δ = 7 ppm) protons of the imidazole ring of Cs exhibit second-order spectra at 1.5 T. This effect is the consequence of incomplete transition from Zeeman to Paschen-Back regime and allows a determination of SD0 from H2 and H4 of Cs as an alternative to evaluating the multiplet splitting which can be measured directly in high-resolution 1H NMR spectra. Experimental data showed striking differences in the mobility of the metabolites when the dipolar coupling constant D0 (calculated with the internuclear distance known from molecular geometry in the case of complete absence of molecular dynamics and motion) is used for comparison. The aliphatic signals involve very small order parameters S ≈ (1.4 - 3) × 10 -4 indicating rapid reorientation of the corresponding subgroups in these metabolites. In contrast, analysis of the Cs resonances yielded S ≈ (113 - 137) × 10 -4. Thus, the immobilization of the Cs imidazole ring owing to an anisotropic cellular substructure in human m. gastrocnemius is much more effective than for (P)Cr and Tau subgroups. Furthermore, 1H NMR experiments on aqueous model

Inference and Biogeochemical Response of Vertical Velocities inside a Mode Water Eddy

NASA Astrophysics Data System (ADS)

Barceló-Llull, B.; Pallas Sanz, E.; Sangrà, P.

2016-02-01

With the aim to study the modulation of the biogeochemical fluxes by the ageostrophic secondary circulation in anticyclonic mesoscale eddies, a typical eddy of the Canary Eddy Corridor was interdisciplinary surveyed on September 2014 in the framework of the PUMP project. The eddy was elliptical shaped, 4 month old, 110 km diameter and 400 m depth. It was an intrathermocline type often also referred as mode water eddy type. We inferred the mesoscale vertical velocity field resolving a generalized omega equation from the 3D density and ADCP velocity fields of a five-day sampled CTD-SeaSoar regular grid centred on the eddy. The grid transects where 10 nautical miles apart. Although complex, in average, the inferred omega velocity field (hereafter w) shows a dipolar structure with downwelling velocities upstream of the propagation path (west) and upwelling velocities downstream. The w at the eddy center was zero and maximum values were located at the periphery attaining ca. 6 m day-1. Coinciding with the occurrence of the vertical velocities cells a noticeable enhancement of phytoplankton biomass was observed at the eddy periphery respect to the far field. A corresponding upward diapycnal flux of nutrients was also observed at the periphery. As minimum velocities where reached at the eddy center, lineal Ekman pumping mechanism was discarded. Minimum values of phytoplankton biomass where also observed at the eddy center. The possible mechanisms for such dipolar w cell are still being investigated, but an analysis of the generalized omega equation forcing terms suggest that it may be a combination of horizontal deformation and advection of vorticity by the ageostrophic current (related to nonlinear Ekman pumping). As expected for Trades, the wind was rather constant and uniform with a speed of ca. 5 m s-1. Diagnosed nonlinear Ekman pumping leaded also to a dipolar cell that mirrors the omega w dipolar cell.

Connecting Interface Structure to Energy Level Alignment at Aqueous Semiconductor Interfaces

NASA Astrophysics Data System (ADS)

Hybertsen, Mark

Understanding structure-function relationships at aqueous semiconductor interfaces presents fundamental challenges, including the discovery of the key interface structure motifs themselves. Important examples include the alignment of electrochemical redox levels with the semiconductor band edges and the identification of catalytic active sites. We have developed a multistep approach, initially demonstrated for GaN, ZnO and their alloys, motivated by measured high efficiency for photocatalytic water oxidation. The interface structure is simulated using ab initio molecular dynamics (AIMD). The calculated, average interface dipole is combined with the GW approach from many-body perturbation theory to calculate the energy level alignment between the semiconductor band edges and the centroid of the occupied 1b1 energy level of water and thus, the electrochemical levels. Cluster models are used to study reaction pathways. The emergent interface motif is the full (GaN) or partial (ZnO) dissociated interface water layer. Here I will focus on the aqueous interfaces to the stable TiO2 anatase (101) and rutile (110) facets. The AIMD calculations reveal interface water dissociation and reassociation processes through distinct pathways: one direct at the interface and the other via a spectator water molecule from the hydration layer. Comparisons between the two interfaces shows that the energy landscape for these pathways depends on the local hydrogen bonding patterns and the interplay with the interface template. Combined results from different initial conditions and AIMD temperatures demonstrate a partially dissociated interface water layer in both cases. Specifically for rutile, structure and the GW-based analysis of the interface energy level alignment agree with experiment. Finally, hole localization at different interface structure motifs will be discussed. Work performed in collaboration with J. Lyons, N. Kharche, M. Ertem and J. Muckerman, done in part at the CFN, which

LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening.

PubMed

Hu, Jun; Liu, Zi; Yu, Dong-Jun; Zhang, Yang

2018-02-15

Sequence-order independent structural comparison, also called structural alignment, of small ligand molecules is often needed for computer-aided virtual drug screening. Although many ligand structure alignment programs are proposed, most of them build the alignments based on rigid-body shape comparison which cannot provide atom-specific alignment information nor allow structural variation; both abilities are critical to efficient high-throughput virtual screening. We propose a novel ligand comparison algorithm, LS-align, to generate fast and accurate atom-level structural alignments of ligand molecules, through an iterative heuristic search of the target function that combines inter-atom distance with mass and chemical bond comparisons. LS-align contains two modules of Rigid-LS-align and Flexi-LS-align, designed for rigid-body and flexible alignments, respectively, where a ligand-size independent, statistics-based scoring function is developed to evaluate the similarity of ligand molecules relative to random ligand pairs. Large-scale benchmark tests are performed on prioritizing chemical ligands of 102 protein targets involving 1,415,871 candidate compounds from the DUD-E (Database of Useful Decoys: Enhanced) database, where LS-align achieves an average enrichment factor (EF) of 22.0 at the 1% cutoff and the AUC score of 0.75, which are significantly higher than other state-of-the-art methods. Detailed data analyses show that the advanced performance is mainly attributed to the design of the target function that combines structural and chemical information to enhance the sensitivity of recognizing subtle difference of ligand molecules and the introduces of structural flexibility that help capture the conformational changes induced by the ligand-receptor binding interactions. These data demonstrate a new avenue to improve the virtual screening efficiency through the development of sensitive ligand structural alignments. http://zhanglab.ccmb.med.umich.edu/LS-align

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

Free energy and entropy of a dipolar liquid by computer simulations

NASA Astrophysics Data System (ADS)

Palomar, Ricardo; Sesé, Gemma

2018-02-01

Thermodynamic properties for a system composed of dipolar molecules are computed. Free energy is evaluated by means of the thermodynamic integration technique, and it is also estimated by using a perturbation theory approach, in which every molecule is modeled as a hard sphere within a square well, with an electric dipole at its center. The hard sphere diameter, the range and depth of the well, and the dipole moment have been calculated from properties easily obtained in molecular dynamics simulations. Connection between entropy and dynamical properties is explored in the liquid and supercooled states by using instantaneous normal mode calculations. A model is proposed in order to analyze translation and rotation contributions to entropy separately. Both contributions decrease upon cooling, and a logarithmic correlation between excess entropy associated with translation and the corresponding proportion of imaginary frequency modes is encountered. Rosenfeld scaling law between reduced diffusion and excess entropy is tested, and the origin of its failure at low temperatures is investigated.

Sensitivity-enhanced IPAP experiments for measuring one-bond 13C '- 13C α and 13C α- 1H α residual dipolar couplings in proteins

NASA Astrophysics Data System (ADS)

Ding, Keyang; Gronenborn, Angela M.

2004-04-01

Sensitivity-enhanced 2D IPAP experiments using the accordion principle for measuring one-bond 13C '- 13C α and 1H α- 13C α dipolar couplings in proteins are presented. The resolution of the resulting spectra is identical to that of the decoupled HSQC spectra and the sensitivity of the corresponding 1D acquisitions are only slightly lower than those obtained with 3D HNCO and 3D HN(COCA)HA pulse sequences due to an additional delay 2 Δ. For cases of limited resolution in the 2D 15N- 1H N HSQC spectrum the current pulse sequences can easily be modified into 3D versions by introducing a poorly digitized third dimension, if so desired. The experiments described here are a valuable addition to the suites available for determination of residual dipolar couplings in biological systems.

A generalized global alignment algorithm.

PubMed

Huang, Xiaoqiu; Chao, Kun-Mao

2003-01-22

Homologous sequences are sometimes similar over some regions but different over other regions. Homologous sequences have a much lower global similarity if the different regions are much longer than the similar regions. We present a generalized global alignment algorithm for comparing sequences with intermittent similarities, an ordered list of similar regions separated by different regions. A generalized global alignment model is defined to handle sequences with intermittent similarities. A dynamic programming algorithm is designed to compute an optimal general alignment in time proportional to the product of sequence lengths and in space proportional to the sum of sequence lengths. The algorithm is implemented as a computer program named GAP3 (Global Alignment Program Version 3). The generalized global alignment model is validated by experimental results produced with GAP3 on both DNA and protein sequences. The GAP3 program extends the ability of standard global alignment programs to recognize homologous sequences of lower similarity. The GAP3 program is freely available for academic use at http://bioinformatics.iastate.edu/aat/align/align.html.

Onorbit IMU alignment error budget

NASA Technical Reports Server (NTRS)

Corson, R. W.

1980-01-01

The Star Tracker, Crew Optical Alignment Sight (COAS), and Inertial Measurement Unit (IMU) from a complex navigation system with a multitude of error sources were combined. A complete list of the system errors is presented. The errors were combined in a rational way to yield an estimate of the IMU alignment accuracy for STS-1. The expected standard deviation in the IMU alignment error for STS-1 type alignments was determined to be 72 arc seconds per axis for star tracker alignments and 188 arc seconds per axis for COAS alignments. These estimates are based on current knowledge of the star tracker, COAS, IMU, and navigation base error specifications, and were partially verified by preliminary Monte Carlo analysis.

Precision alignment and mounting apparatus

NASA Technical Reports Server (NTRS)

Preston, Dennis R. (Inventor)

1993-01-01

An alignment and mounting apparatus for mounting two modules (10,12) includes a first portion having a cylindrical alignment pin (16) projecting normal to a module surface, a second portion having a three-stage alignment guide (18) including a shoehorn flange (34), a Y-slot (42) and a V-block (22) which sequentially guide the alignment pin (16) with successively finer precision and a third portion in the form of a spring-loaded captive fastener (20) for connecting the two modules after alignment is achieved.

Hydrodynamic alignment and assembly of nanofibrils resulting in strong cellulose filaments

PubMed Central

Håkansson, Karl M. O.; Fall, Andreas B.; Lundell, Fredrik; Yu, Shun; Krywka, Christina; Roth, Stephan V.; Santoro, Gonzalo; Kvick, Mathias; Prahl Wittberg, Lisa; Wågberg, Lars; Söderberg, L. Daniel

2014-01-01

Cellulose nanofibrils can be obtained from trees and have considerable potential as a building block for biobased materials. In order to achieve good properties of these materials, the nanostructure must be controlled. Here we present a process combining hydrodynamic alignment with a dispersion–gel transition that produces homogeneous and smooth filaments from a low-concentration dispersion of cellulose nanofibrils in water. The preferential fibril orientation along the filament direction can be controlled by the process parameters. The specific ultimate strength is considerably higher than previously reported filaments made of cellulose nanofibrils. The strength is even in line with the strongest cellulose pulp fibres extracted from wood with the same degree of fibril alignment. Successful nanoscale alignment before gelation demands a proper separation of the timescales involved. Somewhat surprisingly, the device must not be too small if this is to be achieved. PMID:24887005

A UNIFIED MODEL OF GRAIN ALIGNMENT: RADIATIVE ALIGNMENT OF INTERSTELLAR GRAINS WITH MAGNETIC INCLUSIONS

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

Hoang, Thiem; Lazarian, A.

The radiative torque (RAT) alignment of interstellar grains with ordinary paramagnetic susceptibilities has been supported by earlier studies. The alignment of such grains depends on the so-called RAT parameter q {sup max}, which is determined by the grain shape. In this paper, we elaborate on our model of RAT alignment for grains with enhanced magnetic susceptibility due to iron inclusions, such that RAT alignment is magnetically enhanced, which we term the MRAT mechanism. Such grains can be aligned with high angular momentum at the so-called high- J attractor points, achieving a high degree of alignment. Using our analytical model ofmore » RATs, we derive the critical value of the magnetic relaxation parameter δ {sub m} to produce high- J attractor points as functions of q {sup max} and the anisotropic radiation angle relative to the magnetic field ψ . We find that if about 10% of the total iron abundance present in silicate grains is forming iron clusters, this is sufficient to produce high- J attractor points for all reasonable values of q {sup max}. To calculate the degree of grain alignment, we carry out numerical simulations of MRAT alignment by including stochastic excitations from gas collisions and magnetic fluctuations. We show that large grains can achieve perfect alignment when the high- J attractor point is present, regardless of the values of q {sup max}. Our obtained results pave the way for the physical modeling of polarized thermal dust emission as well as magnetic dipole emission. We also find that millimeter-sized grains in accretion disks may be aligned with the magnetic field if they are incorporated with iron nanoparticles.« less

Composite-pulse and partially dipolar dephased multiCP for improved quantitative solid-state 13C NMR

NASA Astrophysics Data System (ADS)

Duan, Pu; Schmidt-Rohr, Klaus

2017-12-01

Improved multiple cross polarization (multiCP) pulse sequences for quickly acquiring quantitative 13C NMR spectra of organic solids are presented. Loss of 13C magnetization due to imperfect read-out and storage pulses in multiCP has been identified as a significant mechanism limiting polarization enhancement for 13C sites with weak couplings to 1H. This problem can be greatly reduced by composite 90° pulses with non-orthogonal phases that flip the magnetization onto the spin-lock field and back to the longitudinal direction for the 1H repolarization period; the observed loss is <3% for over ±10 kHz resonance offset and up to 20% flip-angle error. This composite-pulse multiCP (ComPmultiCP) sequence consistently provides performance superior to that of conventional multiCP, without any trade-off. The longer total CP time enabled by the composite pulses allows for a wider amplitude ramp during CP, which decreases the sensitivity to Hartmann-Hahn mismatch by a factor of two, with a <7% root-mean-square deviation within a 1-dB range for Boc-alanine. In samples with very short T1ρ, under-polarization of non-protonated carbons can be compensated by slight dipolar dephasing of CHn signals resulting from relatively weak decoupling during the Hahn spin echo period before detection. Quantitative spectra have been obtained by ComPmultiCP for low-crystallinity branched polyethylene at 4.5 kHz MAS, and in combination with partial dipolar dephasing for soil organic matter at 14 kHz MAS.

Multiple-quantum spin counting in magic-angle-spinning NMR via low-power symmetry-based dipolar recoupling

NASA Astrophysics Data System (ADS)

Teymoori, Gholamhasan; Pahari, Bholanath; Viswanathan, Elumalai; Edén, Mattias

2013-11-01

By using a symmetry-based R281R28-1 double-quantum (2Q) dipolar recoupling sequence, we demonstrate high-order multiple-quantum coherence (MQC) excitation at fast magic-angle spinning (MAS) frequencies up to 34 kHz. This scheme combines several attractive features, such as a relatively high dipolar scaling factor, good compensation to rf-errors, isotropic and anisotropic chemical shifts, as well as an ultra-low radio-frequency (rf) power requirement. The latter translates into nutation frequencies below 30 kHz for MAS rates up to 60 kHz, thereby permitting rf application for very long excitation periods without risk of damaging the NMR probehead or sample, while the compensation to chemical shifts improves as the MAS rate increases. 31P MQC spin counting is demonstrated on powders of calcium hydroxyapatite (Ca5(PO4)3OH) and anhydrous sodium diphosphate (Na4P2O7), from which all even coherence orders up to 30 and 14 were detected, respectively, over the respective MAS ranges of 15-24 kHz and 20-34 kHz. The amplitude distributions among the 31P MQC orders depend on the precise nutation frequency during recoupling, despite that the highest detected order was relatively insensitive to this parameter. An observed gradual transition from a Gaussian to exponential functionality of the MQC amplitude-profile is discussed in relation to the prevailing approach to derive spin-cluster sizes by fitting the MQC amplitude-distribution to a Gaussian decay, where minor systematic deviations between the model and experimental data are frequently reported.

Influence of dipolar interactions on the superparamagnetic relaxation time of γ-Fe2O3

NASA Astrophysics Data System (ADS)

Labzour, A.; Housni, A.; Limame, K.; Essahlaoui, A.; Sayouri, S.

2017-03-01

Influence of dipolar interactions on the Néel superparamagnetic relaxation time, τ , of an assembly of ultrafine ferromagnetic particles (γ-Fe2O3 ) with uniaxial anisotropy and of different sizes has been widely studied using Mössbauer technique. These studies, based on different analytical approaches, have shown that τ decreases with increasing interactions between particles. To interpret these results, we propose a model where interaction effects are considered as being due to a constant and external randomly oriented magnetic field B(Ψ, ϕ). The model is based on the resolution of the Fokker-Planck equation (FPE), generalizes previous calculations and gives satisfactory interpretation of the relaxation phenomenon in such systems.

Complete devil's staircase and crystal-superfluid transitions in a dipolar XXZ spin chain: a trapped ion quantum simulation

NASA Astrophysics Data System (ADS)

Hauke, Philipp; Cucchietti, Fernando M.; Müller-Hermes, Alexander; Bañuls, Mari-Carmen; Cirac, J. Ignacio; Lewenstein, Maciej

2010-11-01

Systems with long-range interactions show a variety of intriguing properties: they typically accommodate many metastable states, they can give rise to spontaneous formation of supersolids, and they can lead to counterintuitive thermodynamic behavior. However, the increased complexity that comes with long-range interactions strongly hinders theoretical studies. This makes a quantum simulator for long-range models highly desirable. Here, we show that a chain of trapped ions can be used to quantum simulate a one-dimensional (1D) model of hard-core bosons with dipolar off-site interaction and tunneling, equivalent to a dipolar XXZ spin-1/2 chain. We explore the rich phase diagram of this model in detail, employing perturbative mean-field theory, exact diagonalization and quasi-exact numerical techniques (density-matrix renormalization group and infinite time-evolving block decimation). We find that the complete devil's staircase—an infinite sequence of crystal states existing at vanishing tunneling—spreads to a succession of lobes similar to the Mott lobes found in Bose-Hubbard models. Investigating the melting of these crystal states at increased tunneling, we do not find (contrary to similar 2D models) clear indications of supersolid behavior in the region around the melting transition. However, we find that inside the insulating lobes there are quasi-long-range (algebraic) correlations, as opposed to models with nearest-neighbor tunneling, that show exponential decay of correlations.

Nuclear reactor internals alignment configuration

DOEpatents

Gilmore, Charles B [Greensburg, PA; Singleton, Norman R [Murrysville, PA

2009-11-10

An alignment system that employs jacking block assemblies and alignment posts around the periphery of the top plate of a nuclear reactor lower internals core shroud to align an upper core plate with the lower internals and the core shroud with the core barrel. The distal ends of the alignment posts are chamfered and are closely received within notches machined in the upper core plate at spaced locations around the outer circumference of the upper core plate. The jacking block assemblies are used to center the core shroud in the core barrel and the alignment posts assure the proper orientation of the upper core plate. The alignment posts may alternately be formed in the upper core plate and the notches may be formed in top plate.

BAYESIAN PROTEIN STRUCTURE ALIGNMENT.

PubMed

Rodriguez, Abel; Schmidler, Scott C

The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key "gap" parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence-structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples.

Galaxy Alignments: Theory, Modelling & Simulations

NASA Astrophysics Data System (ADS)

Kiessling, Alina; Cacciato, Marcello; Joachimi, Benjamin; Kirk, Donnacha; Kitching, Thomas D.; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Brown, Michael L.; Rassat, Anais

2015-11-01

The shapes of galaxies are not randomly oriented on the sky. During the galaxy formation and evolution process, environment has a strong influence, as tidal gravitational fields in the large-scale structure tend to align nearby galaxies. Additionally, events such as galaxy mergers affect the relative alignments of both the shapes and angular momenta of galaxies throughout their history. These "intrinsic galaxy alignments" are known to exist, but are still poorly understood. This review will offer a pedagogical introduction to the current theories that describe intrinsic galaxy alignments, including the apparent difference in intrinsic alignment between early- and late-type galaxies and the latest efforts to model them analytically. It will then describe the ongoing efforts to simulate intrinsic alignments using both N-body and hydrodynamic simulations. Due to the relative youth of this field, there is still much to be done to understand intrinsic galaxy alignments and this review summarises the current state of the field, providing a solid basis for future work.

Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search

NASA Technical Reports Server (NTRS)

Wheeler, Ward C.

2003-01-01

A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These "lines of correspondence" link ancestor-descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion-deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

Relation between film character and wafer alignment: critical alignment issues on HV device for VLSI manufacturing

NASA Astrophysics Data System (ADS)

Lo, Yi-Chuan; Lee, Chih-Hsiung; Lin, Hsun-Peng; Peng, Chiou-Shian

1998-06-01

Several continuous splits for wafer alignment target topography conditions to improve epitaxy film alignment were applied. The alignment evaluation among former layer pad oxide thickness (250 angstrom - 500 angstrom), drive oxide thickness (6000 angstrom - 10000 angstrom), nitride film thickness (600 angstrom - 1500 angstrom), initial oxide etch (fully wet etch, fully dry etch and dry plus wet etch) will be split to this experiment. Also various epitaxy deposition recipe such as: epitaxy source (SiHCl2 or SiCHCl3) and growth rate (1.3 micrometer/min approximately 2.0 micrometer/min) will be used to optimize the process window for alignment issue. All the reflectance signal and cross section photography of alignment target during NIKON stepper alignment process will be examined. Experimental results show epitaxy recipe plays an important role to wafer alignment. Low growth rate with good performance conformity epitaxy lead to alignment target avoid washout, pattern shift and distortion. All the results (signal monitor and film character) combined with NIKON's stepper standard laser scanning alignment system will be discussed in this paper.

Pairwise Sequence Alignment Library

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

Jeff Daily, PNNL

2015-05-20

Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, amore » novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.« less

Antares alignment gimbal positioner

NASA Astrophysics Data System (ADS)

Day, R. D.; Viswanathan, V. K.; Saxman, A. C.; Lujan, R. E.; Woodfin, W. C.; Sweatt, W. C.

Antares is a 24-beam 40-TW carbon dioxide (CO2) laser fusion system currently under construction at the Los Alamos National Laboratory. The Antares alignment gimbal positioner (AGP) is an optomechanical instrument that will be used for target alignment and alignment of the 24 laser beams, as well as beam quality assessments. The AGP will be capable of providing pointing, focusing, an wavefront optical path difference, as well as aberration information at both helium neon (He-Ne) and CO2 wavelengths. It is designed to allow the laser beams to be aligned to any position within a 1 cm cube to a tolerance of 10 micrometers.

Antares Alignment Gimbal Positioner

NASA Astrophysics Data System (ADS)

Day, R. D.; Viswanathan, V. K.; Saxman, A. C.; Lujan, R. E.; Woodfin, G. L.; Sweatt, W. C.

1981-12-01

Antares is a 24-beam 40-TW carbon-dioxide (CO2) laser fusion system currently under construction at the Los Alamos National Laboratory. The Antares alignment gimbal positioner (AGP) is an optomechanical instrument that will be used for target alignment and alignment of the 24 laser beams, as well as beam quality assessments. The AGP will be capable of providing pointing, focusing, and wavefront optical path difference, as well as aberration information at both helium-neon (He-Ne) and CO2 wavelengths. It is designed to allow the laser beams to be aligned to any position within a 1-cm cube to a tolerance of 10 μm.

A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments.

PubMed

Rajan, Vaibhav

2013-03-01

Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common practice in phylogenetic analysis. Although masking is often done manually, automated methods are necessary to handle the much larger data sets being prepared today. In this study, we introduce the concept of subsplits and demonstrate their use in extracting phylogenetic signal from alignments. We design a clustering approach for alignment masking where each cluster contains similar columns-similarity being defined on the basis of compatible subsplits; our approach then identifies noisy clusters and eliminates them. Trees inferred from the columns in the retained clusters are found to be topologically closer to the reference trees. We test our method on numerous standard benchmarks (both synthetic and biological data sets) and compare its performance with other methods of alignment masking. We find that our method can eliminate sites more accurately than other methods, particularly on divergent data, and can improve the topologies of the inferred trees in likelihood-based analyses. Software available upon request from the author.

Interfacial Engineering of Nanoporous Architectures in Ga2O3 Film toward Self-Aligned Tubular Nanostructure with an Enhanced Photocatalytic Activity on Water Splitting.

PubMed

Shrestha, Nabeen K; Bui, Hoa Thi; Lee, Taegweon; Noh, Yong-Young

2018-04-17

The present work demonstrates the formation of self-aligned nanoporous architecture of gallium oxide by anodization of gallium metal film controlled at -15 °C in aqueous electrolyte consisting of phosphoric acid. SEM examination of the anodized film reveals that by adding ethylene glycol to the electrolyte and optimizing the ratio of phosphoric acid and water, chemical etching at the oxide/electrolyte interfaces can be controlled, leading to the formation of aligned nanotubular oxide structures with closed bottom. XPS analysis confirms the chemical composition of the oxide film as Ga 2 O 3 . Further, XRD and SAED examination reveals that the as-synthesized nanotubular structure is amorphous, and can be crystallized to β-Ga 2 O 3 phase by annealing the film at 600 °C. The nanotubular structured film, when used as photoanode for photoelectrochemical splitting of water, achieved a higher photocurrent of about two folds than that of the nanoporous film, demonstrating the rewarding effect of the nanotubular structure. In addition, the work also demonstrates the formation of highly organized nonporous Ga 2 O 3 structure on a nonconducting glass substrate coated with thin film of Ga-metal, highlighting that the current approach can be extended for the formation of self-organized nanoporous Ga 2 O 3 thin film even on nonconducting flexible substrates.

Iterative non-sequential protein structural alignment.

PubMed

Salem, Saeed; Zaki, Mohammed J; Bystroff, Christopher

2009-06-01

Structural similarity between proteins gives us insights into their evolutionary relationships when there is low sequence similarity. In this paper, we present a novel approach called SNAP for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process consisting of a superposition step and an alignment step, until convergence. We propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of SNAP alignments were assessed by comparing against the manually curated reference alignments in the challenging SISY and RIPC datasets. Moreover, when applied to a dataset of 4410 protein pairs selected from the CATH database, SNAP produced longer alignments with lower rmsd than several state-of-the-art alignment methods. Classification of folds using SNAP alignments was both highly sensitive and highly selective. The SNAP software along with the datasets are available online at http://www.cs.rpi.edu/~zaki/software/SNAP.

Nonideality in diffusion of ionic and hydrophobic solutes and pair dynamics in water-acetone mixtures of varying composition.

PubMed

Gupta, Rini; Chandra, Amalendu

2007-07-14

We have performed a series of molecular dynamics simulations of water-acetone mixtures containing either an ionic solute or a neutral hydrophobic solute to study the extent of nonideality in the dynamics of these solutes with variation of composition of the mixtures. The diffusion coefficients of the charged solutes, both cationic and anionic, are found to change nonmonotonically with the composition of the mixtures showing strong nonideality of their dynamics. Also, the extent of nonideality in the diffusion of these charged solutes is found to be similar to the nonideality that is observed for the diffusion and orientational relaxation of water and acetone molecules in these mixtures which show a somewhat similar changes in the solvation characteristics of charged and dipolar solutes with changes of composition of water-acetone mixtures. The diffusion of the hydrophobic solute, however, shows a monotonic increase with increase of acetone concentration showing its different solvation characteristics as compared to the charged and dipolar solutes. The links between the nonideality in diffusion and solvation structures are further confirmed through calculations of the relevant solute-solvent and solvent-solvent radial distribution functions for both ionic and hydrophobic solutes. We have also calculated various pair dynamical properties such as the relaxation of water-water and acetone-water hydrogen bonds and residence dynamics of water molecules in water and acetone hydration shells. The lifetimes of both water-water and acetone-water hydrogen bonds and also the residence times of water molecules are found to increase steadily with increase in acetone concentration. No maximum or minimum was found in the composition dependence of these pair dynamical quantities. The lifetimes of water-water hydrogen bonds are always found to be longer than that of acetone-water hydrogen bonds in these mixtures. The residence times of water molecules are also found to follow a

Desorption Kinetics of Methanol, Ethanol, and Water from Graphene

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

Smith, R. Scott; Matthiesen, Jesper; Kay, Bruce D.

2014-09-18

The desorption kinetics of methanol, ethanol, and water from graphene covered Pt(111) are investigated. The temperature programmed desorption (TPD) spectra for both methanol and ethanol have well-resolved first, second, third, and multilayer layer desorption peaks. The alignment of the leading edges is consistent with zero-order desorption kinetics from all layers. In contrast, for water the first and second layers are not resolved. At low water coverages (< 1 ML) the initial desorption leading edges are aligned but then fall out of alignment at higher temperatures. For thicker water layers (10 to 100 ML), the desorption leading edges are in alignmentmore » throughout the desorption of the film. The coverage dependence of the desorption behavoir suggests that at low water coverages the non-alignment of the desorption leading edges is due to water dewetting from the graphene substrate. Kinetic simulations reveal that the experimental results are consistent with zero-order desorption. The simulations also show that fractional order desorption kinetics would be readily apparent in the experimental TPD spectra.« less

Desorption kinetics of methanol, ethanol, and water from graphene.

PubMed

Smith, R Scott; Matthiesen, Jesper; Kay, Bruce D

2014-09-18

The desorption kinetics of methanol, ethanol, and water from graphene covered Pt(111) are investigated. The temperature programmed desorption (TPD) spectra for both methanol and ethanol have well-resolved first, second, third, and multilayer layer desorption peaks. The alignment of the leading edges is consistent with zero-order desorption kinetics from all layers. In contrast, for water, the first and second layers are not resolved. At low water coverages (<1 monolayer (ML)) the initial desorption leading edges are aligned but then fall out of alignment at higher temperatures. For thicker water layers (10-100 ML), the desorption leading edges are in alignment throughout the desorption of the film. The coverage dependence of the desorption behavoir suggests that at low water coverages the nonalignment of the desorption leading edges is due to water dewetting from the graphene substrate. Kinetic simulations reveal that the experimental results are consistent with zero-order desorption. The simulations also show that fractional order desorption kinetics would be readily apparent in the experimental TPD spectra.

Kinematic alignment is a possible alternative to mechanical alignment in total knee arthroplasty.

PubMed

Lee, Yong Seuk; Howell, Stephen M; Won, Ye-Yeon; Lee, O-Sung; Lee, Seung Hoon; Vahedi, Hamed; Teo, Seow Hui

2017-11-01

A systematic review was conducted to answer the following questions: (1) Does kinematically aligned (KA) total knee arthroplasty (TKA) achieve clinical outcomes comparable to those of mechanically aligned (MA) TKA? (2) How do the limb, knee, and component alignments differ between KA and MA TKA? (3) How is joint line orientation angle (JLOA) changed from the native knee in KA TKA compared to that in MA TKA? Nine full-text articles in English that reported the clinical and radiological outcomes of KA TKA were included. Five studies had a control group of patients who underwent MA TKA. Data on patient demographics, clinical scores, and radiological results were extracted. There were two level I, one level II, three level III, and three level IV studies. Six of the nine studies used patient-specific instrumentation, one study used computer navigation, and two studies used manual instrumentation. The clinical outcomes of KA TKA were comparable or superior to those of MA TKA with a minimum 2-year follow-up. Limb and knee alignment in KA TKA was similar to those in MA TKA, and component alignment showed slightly more varus in the tibial component and slightly more valgus in the femoral component. The JLOA in KA TKA was relatively parallel to the floor compared to that in the native knee and not oblique (medial side up and lateral side down) compared to that in MA TKA. The implant survivorship and complication rate of the KA TKA were similar to those of the MA TKA. Similar or better clinical outcomes were produced by using a KA TKA at early-term follow-up and the component alignment differed from that of MA TKA. KA TKA seemed to restore function without catastrophic failure regardless of the alignment category up to midterm follow-up. The JLOA in KA TKA was relatively parallel to the floor similar to the native knee compared to that in MA TKA. The present review of nine published studies suggests that relatively new kinematic alignment is an acceptable and alternative

The Dynamic Surface Tension of Water

PubMed Central

2017-01-01

The surface tension of water is an important parameter for many biological or industrial processes, and roughly a factor of 3 higher than that of nonpolar liquids such as oils, which is usually attributed to hydrogen bonding and dipolar interactions. Here we show by studying the formation of water drops that the surface tension of a freshly created water surface is even higher (∼90 mN m–1) than under equilibrium conditions (∼72 mN m–1) with a relaxation process occurring on a long time scale (∼1 ms). Dynamic adsorption effects of protons or hydroxides may be at the origin of this dynamic surface tension. However, changing the pH does not significantly change the dynamic surface tension. It also seems unlikely that hydrogen bonding or dipole orientation effects play any role at the relatively long time scale probed in the experiments. PMID:28301160

The Dynamic Surface Tension of Water.

PubMed

Hauner, Ines M; Deblais, Antoine; Beattie, James K; Kellay, Hamid; Bonn, Daniel

2017-04-06

The surface tension of water is an important parameter for many biological or industrial processes, and roughly a factor of 3 higher than that of nonpolar liquids such as oils, which is usually attributed to hydrogen bonding and dipolar interactions. Here we show by studying the formation of water drops that the surface tension of a freshly created water surface is even higher (∼90 mN m -1 ) than under equilibrium conditions (∼72 mN m -1 ) with a relaxation process occurring on a long time scale (∼1 ms). Dynamic adsorption effects of protons or hydroxides may be at the origin of this dynamic surface tension. However, changing the pH does not significantly change the dynamic surface tension. It also seems unlikely that hydrogen bonding or dipole orientation effects play any role at the relatively long time scale probed in the experiments.

Orbit Alignment in Triple Stars

NASA Astrophysics Data System (ADS)

Tokovinin, Andrei

2017-08-01

The statistics of the angle Φ between orbital angular momenta in hierarchical triple systems with known inner visual or astrometric orbits are studied. A correlation between apparent revolution directions proves the partial orbit alignment known from earlier works. The alignment is strong in triples with outer projected separation less than ˜50 au, where the average Φ is about 20^\\circ . In contrast, outer orbits wider than 1000 au are not aligned with the inner orbits. It is established that the orbit alignment decreases with the increasing mass of the primary component. The average eccentricity of inner orbits in well-aligned triples is smaller than in randomly aligned ones. These findings highlight the role of dissipative interactions with gas in defining the orbital architecture of low-mass triple systems. On the other hand, chaotic dynamics apparently played a role in shaping more massive hierarchies. The analysis of projected configurations and triples with known inner and outer orbits indicates that the distribution of Φ is likely bimodal, where 80% of triples have {{Φ }}< 70^\\circ and the remaining ones are randomly aligned.

Measurement of untruncated nuclear spin interactions via zero- to ultralow-field nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Blanchard, J. W.; Sjolander, T. F.; King, J. P.; Ledbetter, M. P.; Levine, E. H.; Bajaj, V. S.; Budker, D.; Pines, A.

2015-12-01

Zero- to ultralow-field nuclear magnetic resonance (ZULF NMR) provides a new regime for the measurement of nuclear spin-spin interactions free from the effects of large magnetic fields, such as truncation of terms that do not commute with the Zeeman Hamiltonian. One such interaction, the magnetic dipole-dipole coupling, is a valuable source of spatial information in NMR, though many terms are unobservable in high-field NMR, and the coupling averages to zero under isotropic molecular tumbling. Under partial alignment, this information is retained in the form of so-called residual dipolar couplings. We report zero- to ultralow-field NMR measurements of residual dipolar couplings in acetonitrile-2-13C aligned in stretched polyvinyl acetate gels. This permits the investigation of dipolar couplings as a perturbation on the indirect spin-spin J coupling in the absence of an applied magnetic field. As a consequence of working at zero magnetic field, we observe terms of the dipole-dipole coupling Hamiltonian that are invisible in conventional high-field NMR. This technique expands the capabilities of zero- to ultralow-field NMR and has potential applications in precision measurement of subtle physical interactions, chemical analysis, and characterization of local mesoscale structure in materials.

Functional Alignment of Metabolic Networks.

PubMed

Mazza, Arnon; Wagner, Allon; Ruppin, Eytan; Sharan, Roded

2016-05-01

Network alignment has become a standard tool in comparative biology, allowing the inference of protein function, interaction, and orthology. However, current alignment techniques are based on topological properties of networks and do not take into account their functional implications. Here we propose, for the first time, an algorithm to align two metabolic networks by taking advantage of their coupled metabolic models. These models allow us to assess the functional implications of genes or reactions, captured by the metabolic fluxes that are altered following their deletion from the network. Such implications may spread far beyond the region of the network where the gene or reaction lies. We apply our algorithm to align metabolic networks from various organisms, ranging from bacteria to humans, showing that our alignment can reveal functional orthology relations that are missed by conventional topological alignments.

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

PubMed

Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

2013-07-01

The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.

Aligned Layers of Silver Nano-Fibers.

PubMed

Golovin, Andrii B; Stromer, Jeremy; Kreminska, Liubov

2012-02-01

We describe a new dichroic polarizers made by ordering silver nano-fibers to aligned layers. The aligned layers consist of nano-fibers and self-assembled molecular aggregates of lyotropic liquid crystals. Unidirectional alignment of the layers is achieved by means of mechanical shearing. Aligned layers of silver nano-fibers are partially transparent to a linearly polarized electromagnetic radiation. The unidirectional alignment and density of the silver nano-fibers determine degree of polarization of transmitted light. The aligned layers of silver nano-fibers might be used in optics, microwave applications, and organic electronics.

Antares alignment gimbal positioner

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

Day, R.D.; Viswanathan, V.K.; Saxman, A.C.

1981-01-01

Antares is a 24-beam 40-TW carbon-dioxide (CO/sub 2/) laser fusion system currently under construction at the Los Alamos National Laboratory. The Antares alignment gimbal positioner (AGP) is an optomechanical instrument that will be used for target alignment and alignment of the 24 laser beams, as well as beam quality assessments. The AGP will be capable of providing pointing, focusing, and wavefront optical path difference, as well as aberration information at both helium-neon (He-Ne) and CO/sub 2/ wavelengths. It is designed to allow the laser beams to be aligned to any position within a 1-cm cube to a tolerance of 10more » ..mu..m.« less

Precision alignment device

DOEpatents

Jones, Nelson E.

1990-01-01

Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam.

One-Shot Determination of Residual Dipolar Couplings: Application to the Structural Discrimination of Small Molecules Containing Multiple Stereocenters.

PubMed

Castañar, Laura; Garcia, Manuela; Hellemann, Erich; Nolis, Pau; Gil, Roberto R; Parella, Teodor

2016-11-18

A novel approach for the fast and efficient structural discrimination of molecules containing multiple stereochemical centers is described. A robust J-resolved HSQC experiment affording highly resolved 1 J CH / 1 T CH splittings along the indirect dimension and homodecoupled 1 H signals in the detected dimension is proposed. The experiment enables in situ distinction of both isotropic and anisotropic components of molecules dissolved in compressed PMMA gels, allowing a rapid and direct one-shot determination of accurate residual dipolar coupling constants from a single NMR spectrum.

Physician-Hospital Alignment in Orthopedic Surgery.

PubMed

Bushnell, Brandon D

2015-09-01

The concept of "alignment" between physicians and hospitals is a popular buzzword in the age of health care reform. Despite their often tumultuous histories, physicians and hospitals find themselves under increasing pressures to work together toward common goals. However, effective alignment is more than just simple cooperation between parties. The process of achieving alignment does not have simple, universal steps. Alignment will differ based on individual situational factors and the type of specialty involved. Ultimately, however, there are principles that underlie the concept of alignment and should be a part of any physician-hospital alignment efforts. In orthopedic surgery, alignment involves the clinical, administrative, financial, and even personal aspects of a surgeon's practice. It must be based on the principles of financial interest, clinical authority, administrative participation, transparency, focus on the patient, and mutual necessity. Alignment can take on various forms as well, with popular models consisting of shared governance and comanagement, gainsharing, bundled payments, accountable care organizations, and other methods. As regulatory and financial pressures continue to motivate physicians and hospitals to develop alignment relationships, new and innovative methods of alignment will also appear. Existing models will mature and evolve, with individual variability based on local factors. However, certain trends seem to be appearing as time progresses and alignment relationships deepen, including regional and national collaboration, population management, and changes in the legal system. This article explores the history, principles, and specific methods of physician-hospital alignment and its critical importance for the future of health care delivery. Copyright 2015, SLACK Incorporated.

Multiple network alignment via multiMAGNA+.

PubMed

Vijayan, Vipin; Milenkovic, Tijana

2017-08-21

Network alignment (NA) aims to find a node mapping that identifies topologically or functionally similar network regions between molecular networks of different species. Analogous to genomic sequence alignment, NA can be used to transfer biological knowledge from well- to poorly-studied species between aligned network regions. Pairwise NA (PNA) finds similar regions between two networks while multiple NA (MNA) can align more than two networks. We focus on MNA. Existing MNA methods aim to maximize total similarity over all aligned nodes (node conservation). Then, they evaluate alignment quality by measuring the amount of conserved edges, but only after the alignment is constructed. Directly optimizing edge conservation during alignment construction in addition to node conservation may result in superior alignments. Thus, we present a novel MNA method called multiMAGNA++ that can achieve this. Indeed, multiMAGNA++ outperforms or is on par with existing MNA methods, while often completing faster than existing methods. That is, multiMAGNA++ scales well to larger network data and can be parallelized effectively. During method evaluation, we also introduce new MNA quality measures to allow for more fair MNA method comparison compared to the existing alignment quality measures. MultiMAGNA++ code is available on the method's web page at http://nd.edu/~cone/multiMAGNA++/.

Lexical alignment in triadic communication

PubMed Central

Foltz, Anouschka; Gaspers, Judith; Thiele, Kristina; Stenneken, Prisca; Cimiano, Philipp

2015-01-01

Lexical alignment refers to the adoption of one’s interlocutor’s lexical items. Accounts of the mechanisms underlying such lexical alignment differ (among other aspects) in the role assigned to addressee-centered behavior. In this study, we used a triadic communicative situation to test which factors may modulate the extent to which participants’ lexical alignment reflects addressee-centered behavior. Pairs of naïve participants played a picture matching game and received information about the order in which pictures were to be matched from a voice over headphones. On critical trials, participants did or did not hear a name for the picture to be matched next over headphones. Importantly, when the voice over headphones provided a name, it did not match the name that the interlocutor had previously used to describe the object. Participants overwhelmingly used the word that the voice over headphones provided. This result points to non-addressee-centered behavior and is discussed in terms of disrupting alignment with the interlocutor as well as in terms of establishing alignment with the voice over headphones. In addition, the type of picture (line drawing vs. tangram shape) independently modulated lexical alignment, such that participants showed more lexical alignment to their interlocutor for (more ambiguous) tangram shapes compared to line drawings. Overall, the results point to a rather large role for non-addressee-centered behavior during lexical alignment. PMID:25762955

Dipolar bright solitons and solitary vortices in a radial lattice

NASA Astrophysics Data System (ADS)

Huang, Chunqing; Lyu, Lin; Huang, Hao; Chen, Zhaopin; Fu, Shenhe; Tan, Haishu; Malomed, Boris A.; Li, Yongyao

2017-11-01

Stabilizing vortex solitons with high values of the topological charge S is a challenging issue in optics, studies of Bose-Einstein condensates (BECs), and other fields. To develop an approach to the solution of this problem, we consider a two-dimensional dipolar BEC under the action of an axisymmetric radially periodic lattice potential, V (r )˜cos(2 r +δ ) , with dipole moments polarized perpendicular to the system's plane, which gives rise to isotropic repulsive dipole-dipole interactions. Two radial lattices are considered, with δ =0 and π , i.e., a potential maximum or minimum at r =0 , respectively. Families of vortex gap soliton (GSs) with S =1 and S ≥2 , the latter ones often being unstable in other settings, are completely stable in the present system (at least up to S =11 ), being trapped in different annular troughs of the radial potential. The vortex solitons with different S may stably coexist in sufficiently far separated troughs. Fundamental GSs, with S =0 , are found too. In the case of δ =0 , the fundamental solitons are ring-shaped modes, with a local minimum at r =0 . At δ =π , they place a density peak at the center.

Double-quantum homonuclear rotary resonance: Efficient dipolar recovery in magic-angle spinning nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Nielsen, N. C.; Bildsøe, H.; Jakobsen, H. J.; Levitt, M. H.

1994-08-01

We describe an efficient method for the recovery of homonuclear dipole-dipole interactions in magic-angle spinning NMR. Double-quantum homonuclear rotary resonance (2Q-HORROR) is established by fulfilling the condition ωr=2ω1, where ωr is the sample rotation frequency and ω1 is the nutation frequency around an applied resonant radio frequency (rf) field. This resonance can be used for double-quantum filtering and measurement of homonuclear dipolar interactions in the presence of magic-angle spinning. The spin dynamics depend only weakly on crystallite orientation allowing good performance for powder samples. Chemical shift effects are suppressed to zeroth order. The method is demonstrated for singly and doubly 13C labeled L-alanine.

Aligning Plasma-Arc Welding Oscillations

NASA Technical Reports Server (NTRS)

Norris, Jeff; Fairley, Mike

1989-01-01

Tool aids in alignment of oscillator probe on variable-polarity plasma-arc welding torch. Probe magnetically pulls arc from side to side as it moves along joint. Tensile strength of joint depends on alignment of weld bead and on alignment of probe. Operator installs new tool on front of torch body, levels it with built-in bubble glass, inserts probe in slot on tool, and locks probe in place. Procedure faster and easier and resulting alignment more accurate and repeatable.

Alignment as a Teacher Variable

ERIC Educational Resources Information Center

Porter, Andrew C.; Smithson, John; Blank, Rolf; Zeidner, Timothy

2007-01-01

With the exception of the procedures developed by Porter and colleagues (Porter, 2002), other methods of defining and measuring alignment are essentially limited to alignment between tests and standards. Porter's procedures have been generalized to investigating the alignment between content standards, tests, textbooks, and even classroom…

Unified Alignment of Protein-Protein Interaction Networks.

PubMed

Malod-Dognin, Noël; Ban, Kristina; Pržulj, Nataša

2017-04-19

Paralleling the increasing availability of protein-protein interaction (PPI) network data, several network alignment methods have been proposed. Network alignments have been used to uncover functionally conserved network parts and to transfer annotations. However, due to the computational intractability of the network alignment problem, aligners are heuristics providing divergent solutions and no consensus exists on a gold standard, or which scoring scheme should be used to evaluate them. We comprehensively evaluate the alignment scoring schemes and global network aligners on large scale PPI data and observe that three methods, HUBALIGN, L-GRAAL and NATALIE, regularly produce the most topologically and biologically coherent alignments. We study the collective behaviour of network aligners and observe that PPI networks are almost entirely aligned with a handful of aligners that we unify into a new tool, Ulign. Ulign enables complete alignment of two networks, which traditional global and local aligners fail to do. Also, multiple mappings of Ulign define biologically relevant soft clusterings of proteins in PPI networks, which may be used for refining the transfer of annotations across networks. Hence, PPI networks are already well investigated by current aligners, so to gain additional biological insights, a paradigm shift is needed. We propose such a shift come from aligning all available data types collectively rather than any particular data type in isolation from others.

Some aspects of SR beamline alignment

NASA Astrophysics Data System (ADS)

Gaponov, Yu. A.; Cerenius, Y.; Nygaard, J.; Ursby, T.; Larsson, K.

2011-09-01

Based on the Synchrotron Radiation (SR) beamline optical element-by-element alignment with analysis of the alignment results an optimized beamline alignment algorithm has been designed and developed. The alignment procedures have been designed and developed for the MAX-lab I911-4 fixed energy beamline. It has been shown that the intermediate information received during the monochromator alignment stage can be used for the correction of both monochromator and mirror without the next stages of alignment of mirror, slits, sample holder, etc. Such an optimization of the beamline alignment procedures decreases the time necessary for the alignment and becomes useful and helpful in the case of any instability of the beamline optical elements, storage ring electron orbit or the wiggler insertion device, which could result in the instability of angular and positional parameters of the SR beam. A general purpose software package for manual, semi-automatic and automatic SR beamline alignment has been designed and developed using the developed algorithm. The TANGO control system is used as the middle-ware between the stand-alone beamline control applications BLTools, BPMonitor and the beamline equipment.

Precision alignment device

DOEpatents

Jones, N.E.

1988-03-10

Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam. 5 figs.

Analyzing the Curriculum Alignment of Teachers

ERIC Educational Resources Information Center

Turan-Özpolat, Esen; Bay, Erdal

2017-01-01

The purpose of this research was to analyze the curriculum alignment of teachers in secondary education 5th grade Science course. Alignment levels of teachers in dimensions of acquisition, content, teaching methods and techniques, activity, material and measurement - assessment, and the reasons for their alignment/non-alignment to the curriculum…

Efficient creation of dipolar coupled nitrogen-vacancy spin qubits in diamond

NASA Astrophysics Data System (ADS)

Jakobi, I.; Momenzadeh, S. A.; Fávaro de Oliveira, F.; Michl, J.; Ziem, F.; Schreck, M.; Neumann, P.; Denisenko, A.; Wrachtrup, J.

2016-09-01

Coherently coupled pairs or multimers of nitrogen-vacancy defect electron spins in diamond have many promising applications especially in quantum information processing (QIP) but also in nanoscale sensing applications. Scalable registers of spin qubits are essential to the progress of QIP. Ion implantation is the only known technique able to produce defect pairs close enough to allow spin coupling via dipolar interaction. Although several competing methods have been proposed to increase the resulting resolution of ion implantation, the reliable creation of working registers is still to be demonstrated. The current limitation are residual radiation-induced defects, resulting in degraded qubit performance as trade-off for positioning accuracy. Here we present an optimized estimation of nanomask implantation parameters that are most likely to produce interacting qubits under standard conditions. We apply our findings to a well-established technique, namely masks written in electron-beam lithography, to create coupled defect pairs with a reasonable probability. Furthermore, we investigate the scaling behavior and necessary improvements to efficiently engineer interacting spin architectures.

Alignment of dynamic networks

PubMed Central

Vijayan, V.; Critchlow, D.; Milenković, T.

2017-01-01

Abstract Motivation: Network alignment (NA) aims to find a node mapping that conserves similar regions between compared networks. NA is applicable to many fields, including computational biology, where NA can guide the transfer of biological knowledge from well- to poorly-studied species across aligned network regions. Existing NA methods can only align static networks. However, most complex real-world systems evolve over time and should thus be modeled as dynamic networks. We hypothesize that aligning dynamic network representations of evolving systems will produce superior alignments compared to aligning the systems’ static network representations, as is currently done. Results: For this purpose, we introduce the first ever dynamic NA method, DynaMAGNA ++. This proof-of-concept dynamic NA method is an extension of a state-of-the-art static NA method, MAGNA++. Even though both MAGNA++ and DynaMAGNA++ optimize edge as well as node conservation across the aligned networks, MAGNA++ conserves static edges and similarity between static node neighborhoods, while DynaMAGNA++ conserves dynamic edges (events) and similarity between evolving node neighborhoods. For this purpose, we introduce the first ever measure of dynamic edge conservation and rely on our recent measure of dynamic node conservation. Importantly, the two dynamic conservation measures can be optimized with any state-of-the-art NA method and not just MAGNA++. We confirm our hypothesis that dynamic NA is superior to static NA, on synthetic and real-world networks, in computational biology and social domains. DynaMAGNA++ is parallelized and has a user-friendly graphical interface. Availability and implementation: http://nd.edu/∼cone/DynaMAGNA++/. Contact: tmilenko@nd.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28881980

Alignment method for solar collector arrays

DOEpatents

Driver, Jr., Richard B

2012-10-23

The present invention is directed to an improved method for establishing camera fixture location for aligning mirrors on a solar collector array (SCA) comprising multiple mirror modules. The method aligns the mirrors on a module by comparing the location of the receiver image in photographs with the predicted theoretical receiver image location. To accurately align an entire SCA, a common reference is used for all of the individual module images within the SCA. The improved method can use relative pixel location information in digital photographs along with alignment fixture inclinometer data to calculate relative locations of the fixture between modules. The absolute locations are determined by minimizing alignment asymmetry for the SCA. The method inherently aligns all of the mirrors in an SCA to the receiver, even with receiver position and module-to-module alignment errors.

Regio- and Stereoselective Cascades via Aldol Condensation and 1,3-Dipolar Cycloaddition for Construction of Functional Pyrrolizidine Derivatives.

PubMed

Mao, Zhuo-Ya; Liu, Yi-Wen; Han, Pan; Dong, Han-Qing; Si, Chang-Mei; Wei, Bang-Guo; Lin, Guo-Qiang

2018-02-16

An efficient and step-economical approach to access functionalized pyrrolizidine derivatives by a one-pot tandem sequence, including an aldol condensation and subsequent 1,3-dipolar cycloaddition process, has been developed, starting from acetone, aldehyde, and proline. A number of substituted aromatic aldehydes were amenable to this transformation, and the desired products, racemic 7a-7w and chiral 9a-9m, were obtained with excellent regioselectivities and outstanding diastereoselectivities. Moreover, in situ NMR studies revealed MgSO 4 could effectively promote the aldol condensation pathway in this tandem process.

Intramolecular Hydrogen Bond Activation: Thiourea-Organocatalyzed Enantioselective 1,3-Dipolar Cycloaddition of Salicylaldehyde-Derived Azomethine Ylides with Nitroalkenes.

PubMed

Esteban, Francisco; Cieślik, Wioleta; Arpa, Enrique M; Guerrero-Corella, Andrea; Díaz-Tendero, Sergio; Perles, Josefina; Fernández-Salas, José A; Fraile, Alberto; Alemán, José

2018-03-02

An organocatalytic strategy for the synthesis of tetrasubstituted pyrrolidines with monoactivated azomethine ylides in high enantiomeric excess and excellent exo/endo selectivity is presented. The key to success is the intramolecular activation via hydrogen bonding through an o -hydroxy group, which allows the dipolar cycloaddition to take place in the presence of azomethine ylides bearing only one activating group. The intramolecular hydrogen bond in the azomethine ylide and the intermolecular hydrogen bond with the catalyst have been demonstrated by DFT calculations and mechanistic proofs to be crucial for the reaction to proceed.

DR-TAMAS: Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures

PubMed Central

Irfanoglu, M. Okan; Nayak, Amritha; Jenkins, Jeffrey; Hutchinson, Elizabeth B.; Sadeghi, Neda; Thomas, Cibu P.; Pierpaoli, Carlo

2016-01-01

In this work, we propose DR-TAMAS (Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures), a novel framework for intersubject registration of Diffusion Tensor Imaging (DTI) data sets. This framework is optimized for brain data and its main goal is to achieve an accurate alignment of all brain structures, including white matter (WM), gray matter (GM), and spaces containing cerebrospinal fluid (CSF). Currently most DTI-based spatial normalization algorithms emphasize alignment of anisotropic structures. While some diffusion-derived metrics, such as diffusion anisotropy and tensor eigenvector orientation, are highly informative for proper alignment of WM, other tensor metrics such as the trace or mean diffusivity (MD) are fundamental for a proper alignment of GM and CSF boundaries. Moreover, it is desirable to include information from structural MRI data, e.g., T1-weighted or T2-weighted images, which are usually available together with the diffusion data. The fundamental property of DR-TAMAS is to achieve global anatomical accuracy by incorporating in its cost function the most informative metrics locally. Another important feature of DR-TAMAS is a symmetric time-varying velocity-based transformation model, which enables it to account for potentially large anatomical variability in healthy subjects and patients. The performance of DR-TAMAS is evaluated with several data sets and compared with other widely-used diffeomorphic image registration techniques employing both full tensor information and/or DTI-derived scalar maps. Our results show that the proposed method has excellent overall performance in the entire brain, while being equivalent to the best existing methods in WM. PMID:26931817

Aligning Greek-English parallel texts

NASA Astrophysics Data System (ADS)

Galiotou, Eleni; Koronakis, George; Lazari, Vassiliki

2015-02-01

In this paper, we discuss issues concerning the alignment of parallel texts written in languages with different alphabets based on an experiment of aligning texts from the proceedings of the European Parliament in Greek and English. First, we describe our implementation of the k-vec algorithm and its application to the bilingual corpus. Then the output of the algorithm is used as a starting point for an alignment procedure at a sentence level which also takes into account mark-ups of meta-information. The results of the implementation are compared to those of the application of the Church and Gale alignment algorithm on the Europarl corpus. The conclusions of this comparison can give useful insights as for the efficiency of alignment algorithms when applied to the particular bilingual corpus.

AlignNemo: a local network alignment method to integrate homology and topology.

PubMed

Ciriello, Giovanni; Mina, Marco; Guzzi, Pietro H; Cannataro, Mario; Guerra, Concettina

2012-01-01

Local network alignment is an important component of the analysis of protein-protein interaction networks that may lead to the identification of evolutionary related complexes. We present AlignNemo, a new algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that relate in biological function and topology of interactions. The discovered conserved subnetworks have a general topology and need not to correspond to specific interaction patterns, so that they more closely fit the models of functional complexes proposed in the literature. The algorithm is able to handle sparse interaction data with an expansion process that at each step explores the local topology of the networks beyond the proteins directly interacting with the current solution. To assess the performance of AlignNemo, we ran a series of benchmarks using statistical measures as well as biological knowledge. Based on reference datasets of protein complexes, AlignNemo shows better performance than other methods in terms of both precision and recall. We show our solutions to be biologically sound using the concept of semantic similarity applied to Gene Ontology vocabularies. The binaries of AlignNemo and supplementary details about the algorithms and the experiments are available at: sourceforge.net/p/alignnemo.

Amide proton spin-lattice relaxation in polypeptides. A field-dependence study of the proton and nitrogen dipolar interactions in alumichrome.

PubMed

Llinás, M; Klein, M P; Wüthrich, K

1978-12-01

The proton nuclear magnetic resonance (NMR) spin-lattice relaxation of all six amides of deferriferrichrome and of various alumichromes dissolved in hexadeutero-dimethylsulfoxide have been investigated at 100, 220, and 360 MHz. We find that, depending on the type of residue (glycyl or ornithyl), the amide proton relaxation rates are rather uniform in the metal-free cyclohexapeptide. In contrast, the (1)H spinlattice relaxation times (T(1)'s) are distinct in the Al(3+)-coordination derivative. Similar patterns are observed in a number of isomorphic alumichrome homologues that differ in single-site residue substitutions, indicating that the spin-lattice relaxation rate is mainly determined by dipole-dipole interactions within a rigid molecular framework rather than by the specific primary structures. Analysis of the data in terms of (1)H-(1)H distances (r) calculated from X-ray coordinates yields a satisfactory linear fit between T(1) (-1) and Sigmar(-6) at the three magnetic fields. Considering the very sensitive r-dependence of T(1), the agreement gives confidence, at a quantitative level, both on the fitness of the crystallographic model to represent the alumichromes' solution conformation and on the validity of assuming isotropic rotational motion for the globular metallopeptides. An extra contribution to the amide proton T(1) (-1) is proposed to mainly originate from the (1)H-(14)N dipolar interaction: this was supported by comparison with measurements on an (15)N-enriched peptide. The nitrogen dipolar contribution to the peptide proton relaxation is discussed in the context of {(1)H}-(1)H nuclear Overhauser enhancement (NOE) studies because, especially at high fields, it can be dominant in determining the amide proton relaxation rates and hence result in a decreased effectiveness for the (1)H-(1)H dipolar mechanism to cause NOE's. From the slope and intersect values of T(1) (-1) vs. Sigmar(-6) linear plots, a number of independent estimates of tau(r), the

mTM-align: a server for fast protein structure database search and multiple protein structure alignment.

PubMed

Dong, Runze; Pan, Shuo; Peng, Zhenling; Zhang, Yang; Yang, Jianyi

2018-05-21

With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop algorithms for efficient protein structure comparisons. In this article, we present the mTM-align server, which consists of two closely related modules: one for structure database search and the other for multiple structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization of the structures in the database. The multiple structure alignment is performed using the recently developed algorithm mTM-align. Benchmark tests demonstrate that our algorithms outperform other peering methods for both modules, in terms of speed and accuracy. One of the unique features for the server is the interplay between database search and multiple structure alignment. The server provides service not only for performing fast database search, but also for making accurate multiple structure alignment with the structures found by the search. For the database search, it takes about 2-5 min for a structure of a medium size (∼300 residues). For the multiple structure alignment, it takes a few seconds for ∼10 structures of medium sizes. The server is freely available at: http://yanglab.nankai.edu.cn/mTM-align/.

Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences.

PubMed

Hartman, Amber L; Riddle, Sean; McPhillips, Timothy; Ludäscher, Bertram; Eisen, Jonathan A

2010-06-12

For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly. We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform. By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable

Alignment method for parabolic trough solar concentrators

DOEpatents

Diver, Richard B [Albuquerque, NM

2010-02-23

A Theoretical Overlay Photographic (TOP) alignment method uses the overlay of a theoretical projected image of a perfectly aligned concentrator on a photographic image of the concentrator to align the mirror facets of a parabolic trough solar concentrator. The alignment method is practical and straightforward, and inherently aligns the mirror facets to the receiver. When integrated with clinometer measurements for which gravity and mechanical drag effects have been accounted for and which are made in a manner and location consistent with the alignment method, all of the mirrors on a common drive can be aligned and optimized for any concentrator orientation.

Alignment of dynamic networks.

PubMed

Vijayan, V; Critchlow, D; Milenkovic, T

2017-07-15

Network alignment (NA) aims to find a node mapping that conserves similar regions between compared networks. NA is applicable to many fields, including computational biology, where NA can guide the transfer of biological knowledge from well- to poorly-studied species across aligned network regions. Existing NA methods can only align static networks. However, most complex real-world systems evolve over time and should thus be modeled as dynamic networks. We hypothesize that aligning dynamic network representations of evolving systems will produce superior alignments compared to aligning the systems' static network representations, as is currently done. For this purpose, we introduce the first ever dynamic NA method, DynaMAGNA ++. This proof-of-concept dynamic NA method is an extension of a state-of-the-art static NA method, MAGNA++. Even though both MAGNA++ and DynaMAGNA++ optimize edge as well as node conservation across the aligned networks, MAGNA++ conserves static edges and similarity between static node neighborhoods, while DynaMAGNA++ conserves dynamic edges (events) and similarity between evolving node neighborhoods. For this purpose, we introduce the first ever measure of dynamic edge conservation and rely on our recent measure of dynamic node conservation. Importantly, the two dynamic conservation measures can be optimized with any state-of-the-art NA method and not just MAGNA++. We confirm our hypothesis that dynamic NA is superior to static NA, on synthetic and real-world networks, in computational biology and social domains. DynaMAGNA++ is parallelized and has a user-friendly graphical interface. http://nd.edu/∼cone/DynaMAGNA++/ . tmilenko@nd.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Thermalization near Integrability in a Dipolar Quantum Newton's Cradle

NASA Astrophysics Data System (ADS)

Tang, Yijun; Kao, Wil; Li, Kuan-Yu; Seo, Sangwon; Mallayya, Krishnanand; Rigol, Marcos; Gopalakrishnan, Sarang; Lev, Benjamin L.

2018-04-01

Isolated quantum many-body systems with integrable dynamics generically do not thermalize when taken far from equilibrium. As one perturbs such systems away from the integrable point, thermalization sets in, but the nature of the crossover from integrable to thermalizing behavior is an unresolved and actively discussed question. We explore this question by studying the dynamics of the momentum distribution function in a dipolar quantum Newton's cradle consisting of highly magnetic dysprosium atoms. This is accomplished by creating the first one-dimensional Bose gas with strong magnetic dipole-dipole interactions. These interactions provide tunability of both the strength of the integrability-breaking perturbation and the nature of the near-integrable dynamics. We provide the first experimental evidence that thermalization close to a strongly interacting integrable point occurs in two steps: prethermalization followed by near-exponential thermalization. Exact numerical calculations on a two-rung lattice model yield a similar two-timescale process, suggesting that this is generic in strongly interacting near-integrable models. Moreover, the measured thermalization rate is consistent with a parameter-free theoretical estimate, based on identifying the types of collisions that dominate thermalization. By providing tunability between regimes of integrable and nonintegrable dynamics, our work sheds light on the mechanisms by which isolated quantum many-body systems thermalize and on the temporal structure of the onset of thermalization.

Testing physical models for dipolar asymmetry with CMB polarization

NASA Astrophysics Data System (ADS)

Contreras, D.; Zibin, J. P.; Scott, D.; Banday, A. J.; Górski, K. M.

2017-12-01

The cosmic microwave background (CMB) temperature anisotropies exhibit a large-scale dipolar power asymmetry. To determine whether this is due to a real, physical modulation or is simply a large statistical fluctuation requires the measurement of new modes. Here we forecast how well CMB polarization data from Planck and future experiments will be able to confirm or constrain physical models for modulation. Fitting several such models to the Planck temperature data allows us to provide predictions for polarization asymmetry. While for some models and parameters Planck polarization will decrease error bars on the modulation amplitude by only a small percentage, we show, importantly, that cosmic-variance-limited (and in some cases even Planck) polarization data can decrease the errors by considerably better than the expectation of √{2 } based on simple ℓ-space arguments. We project that if the primordial fluctuations are truly modulated (with parameters as indicated by Planck temperature data) then Planck will be able to make a 2 σ detection of the modulation model with 20%-75% probability, increasing to 45%-99% when cosmic-variance-limited polarization is considered. We stress that these results are quite model dependent. Cosmic variance in temperature is important: combining statistically isotropic polarization with temperature data will spuriously increase the significance of the temperature signal with 30% probability for Planck.

Probabilistic biological network alignment.

PubMed

Todor, Andrei; Dobra, Alin; Kahveci, Tamer

2013-01-01

Interactions between molecules are probabilistic events. An interaction may or may not happen with some probability, depending on a variety of factors such as the size, abundance, or proximity of the interacting molecules. In this paper, we consider the problem of aligning two biological networks. Unlike existing methods, we allow one of the two networks to contain probabilistic interactions. Allowing interaction probabilities makes the alignment more biologically relevant at the expense of explosive growth in the number of alternative topologies that may arise from different subsets of interactions that take place. We develop a novel method that efficiently and precisely characterizes this massive search space. We represent the topological similarity between pairs of aligned molecules (i.e., proteins) with the help of random variables and compute their expected values. We validate our method showing that, without sacrificing the running time performance, it can produce novel alignments. Our results also demonstrate that our method identifies biologically meaningful mappings under a comprehensive set of criteria used in the literature as well as the statistical coherence measure that we developed to analyze the statistical significance of the similarity of the functions of the aligned protein pairs.

Alignment telescope for Antares

NASA Astrophysics Data System (ADS)

Appert, Q. D.; Swann, T. A.; Ward, J. H.; Hardesty, C.; Wright, L.

The Antares Automatic Alignment System employs a specially designed telescope for alignment of its laser beamlines. There are two telescopes in the system, and since each telescope is a primary alignment reference, stringent boresight accuracy and stability over the focus range were required. Optical and mechanical designs, which meet this requirements as well as that of image quality over a wide wavelength band, are described. Special test techniques for initial assembly and alignment of the telescope are also presented. The telescope, which has a 180-mm aperture FK51-KZF2 type glass doublet objective, requires a boresight accuracy of 2.8 (SIGMA)rad at two focal lengths, and object distances between 11 meters and infinity. Travel of a smaller secondary doublet provides focus from 11 m to infinity with approximately 7.8 m effective focal length. By flipping in a third doublet, the effective focal length is reduced to 2.5 m. Telescope alignment was accomplished by using a rotary air bearing to establish an axis in front of the system and placing the focus of a Laser Unequal Path Interferometer (LUPI) at the image plane.

Alignment Telescope For Antares

NASA Astrophysics Data System (ADS)

Appert, Q. D.; Swann, T. A.; Ward, J. H.; Hardesty, C.; Wrignt, L.

1983-11-01

The Antares Automatic Alignment System employs a specially designed telescope for alignment of its laser beamlines. There are two telescopes in the system, and since eacn telescope is a primary alignment reference, stringent boresight accuracy and stability over the focus range were required. Optical and mechanical designs, which meet this requirement as well as that of image quality over a wide wavelength band, are described. Special test techniques for initial assembly and alignment of the telescope are also presented. The telescope, which has a 180-mm aperture FK51-KZF2 type glass doublet objective, requires a boresight accuracy of 2.8 prad at two focal lengths, and object distances between 11 meters and infinity. Travel of a smaller secondary doublet provides focus from 11 m to infinity with approximately 7.8 m effective focal length. By flipping in a third doublet, the effective focal length is reduced to 2.5 m. Telescope alignment was accomplished by using a rotary air bearing to establish an axis in front of the system and placing the focus of a Laser Unequal Path Interferometer (LUPI) at the image plane.

Align-and-shine photolithography

NASA Astrophysics Data System (ADS)

Petrusis, Audrius; Rector, Jan H.; Smith, Kristen; de Man, Sven; Iannuzzi, Davide

2009-10-01

At the beginning of 2009, our group has introduced a new technique that allows fabrication of photolithographic patterns on the cleaved end of an optical fibre: the align-and-shine photolithography technique (see A. Petrušis et al., "The align-and-shine technique for series production of photolithography patterns on optical fibres", J. Micromech. Microeng. 19, 047001, 2009). Align-and-shine photolithography combines standard optical lithography with imagebased active fibre alignment processes. The technique adapts well to series production, opening the way to batch fabrication of fibre-top devices (D. Iannuzzi et al., "Monolithic fibre-top cantilever for critical environments and standard applications", Appl. Phys. Lett. 88, 053501, 2006) and all other devices that rely on suitable machining of engineered parts on the tip of a fibre. In this paper we review our results and briefly discuss its potential applications.

Spatio-temporal alignment of multiple sensors

NASA Astrophysics Data System (ADS)

Zhang, Tinghua; Ni, Guoqiang; Fan, Guihua; Sun, Huayan; Yang, Biao

2018-01-01

Aiming to achieve the spatio-temporal alignment of multi sensor on the same platform for space target observation, a joint spatio-temporal alignment method is proposed. To calibrate the parameters and measure the attitude of cameras, an astronomical calibration method is proposed based on star chart simulation and collinear invariant features of quadrilateral diagonal between the observed star chart. In order to satisfy a temporal correspondence and spatial alignment similarity simultaneously, the method based on the astronomical calibration and attitude measurement in this paper formulates the video alignment to fold the spatial and temporal alignment into a joint alignment framework. The advantage of this method is reinforced by exploiting the similarities and prior knowledge of velocity vector field between adjacent frames, which is calculated by the SIFT Flow algorithm. The proposed method provides the highest spatio-temporal alignment accuracy compared to the state-of-the-art methods on sequences recorded from multi sensor at different times.

Projected power iteration for network alignment

NASA Astrophysics Data System (ADS)

Onaran, Efe; Villar, Soledad

2017-08-01

The network alignment problem asks for the best correspondence between two given graphs, so that the largest possible number of edges are matched. This problem appears in many scientific problems (like the study of protein-protein interactions) and it is very closely related to the quadratic assignment problem which has graph isomorphism, traveling salesman and minimum bisection problems as particular cases. The graph matching problem is NP-hard in general. However, under some restrictive models for the graphs, algorithms can approximate the alignment efficiently. In that spirit the recent work by Feizi and collaborators introduce EigenAlign, a fast spectral method with convergence guarantees for Erd-s-Renyí graphs. In this work we propose the algorithm Projected Power Alignment, which is a projected power iteration version of EigenAlign. We numerically show it improves the recovery rates of EigenAlign and we describe the theory that may be used to provide performance guarantees for Projected Power Alignment.

Hybrid vehicle motor alignment

DOEpatents

Levin, Michael Benjamin

2001-07-03

A rotor of an electric motor for a motor vehicle is aligned to an axis of rotation for a crankshaft of an internal combustion engine having an internal combustion engine and an electric motor. A locator is provided on the crankshaft, a piloting tool is located radially by the first locator to the crankshaft. A stator of the electric motor is aligned to a second locator provided on the piloting tool. The stator is secured to the engine block. The rotor is aligned to the crankshaft and secured thereto.

STELLAR: fast and exact local alignments

PubMed Central

2011-01-01

Background Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast, but heuristic, and hence sometimes miss significant matches. Results We present here the local pairwise aligner STELLAR that has full sensitivity for ε-alignments, i.e. guarantees to report all local alignments of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. We apply the SWIFT algorithm for lossless filtering, and have developed a new verification strategy that we prove to be exact. Our results on simulated and real genomic data confirm and quantify the conjecture that heuristic tools like BLAST or BLAT miss a large percentage of significant local alignments. Conclusions STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar. The source code is freely distributed with the SeqAn C++ library version 1.3 and later at http://www.seqan.de. PMID:22151882

The aluminum ordering in aluminosilicates: a dipolar 27Al NMR spectroscopy study.

PubMed

Gee, Becky A

2004-01-01

The spatial ordering of aluminum atoms in CsAl(SiO3)2 and 3Al2O3.2SiO2 was probed by 27Al dipolar solid-state NMR spectroscopy. The 27Al response to a Hahn spin-echo pulse sequence in a series of aluminum-containing model crystalline compounds demonstrates that quantitative 27Al homonuclear dipolar second moments can be obtained to within +/-20% of the theoretical values, if evaluation of the spin-echo response curve is limited to short evolution periods (2t1 < or = 0.10 ms). Additionally, selective excitation of the central transition m = 1/2 --> -1/2 is necessary in order to ensure quantitative results. Restriction of spin exchange affecting the dephasing of the magnetization may decelerate the spin-echo decay at longer evolution periods. Considering these restraints, the method was used to probe the spatial distribution of aluminum atoms among the tetrahedral sites in two aluminosilicate materials. Experimental 27Al spin-echo response data for the aluminosilicates CsAl(SiO3)2 (synthetic pollucite) and 3Al2O3.2SiO2 (mullite) are compared with theoretical data based on (I) various degrees of aluminum-oxygen-aluminum bond formation among tetrahedrally coordinated aluminum atoms (Al(T(d) )-O-Al(T(d) )) and (II) the maximum avoidance of Al(T(d) )-O-Al(T(d) ) bonding. Analysis of the second moment values and resulting echo decay responses suggests that partial suppression of spin exchange among aluminum atoms in crystallographically distinct sites may contribute to the 27Al spin echo decay in 3Al2O3.2SiO2, thus complicating quantitative analysis of the data. Silicon-29 and aluminum-27 magic angle spinning (MAS) NMR spectra of 3Al2O3.2SiO2 are consistent with those previously reported. The experimental 27Al spin-echo response behavior of CsAl(SiO3)2 differs from the theoretical response behavior based on the maximum avoidance of Al-O-Al bonding between tetrahedral aluminum sites in CsAl(SiO3)2. A single unresolved resonance is observed in both the silicon-29 and

Forced Alignment for Understudied Language Varieties: Testing Prosodylab-Aligner with Tongan Data

ERIC Educational Resources Information Center

Johnson, Lisa M.; Di Paolo, Marianna; Bell, Adrian

2018-01-01

Automated alignment of transcriptions to audio files expedites the process of preparing data for acoustic analysis. Unfortunately, the benefits of auto-alignment have generally been available only to researchers studying majority languages, for which large corpora exist and for which acoustic models have been created by large-scale research…

Jig Aligns Shadow Mask On CCD

NASA Technical Reports Server (NTRS)

Matus, Carlos V.

1989-01-01

Alignment viewed through microscope. Alignment jig positions shadow mask on charge-coupled device (CCD) so metal film deposited on it precisely. Allows CCD package to be inserted and removed without disturbing alignment of mask. Holds CCD packages securely and isolates it electrostatically while providing electrical contact to each of its pins. When alignment jig assembled with CCD, used to move mask under micrometer control.

libgapmis: extending short-read alignments

PubMed Central

2013-01-01

Background A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy. These tools allow for a small number of mismatches in the alignment; however, their ability to allow for gaps varies greatly, with many performing poorly or not allowing them at all. The seed-and-extend strategy is applied in most short-read alignment programmes. After aligning a substring of the reference sequence against the high-quality prefix of a short read--the seed--an important problem is to find the best possible alignment between a substring of the reference sequence succeeding and the remaining suffix of low quality of the read--extend. The fact that the reads are rather short and that the gap occurrence frequency observed in various studies is rather low suggest that aligning (parts of) those reads with a single gap is in fact desirable. Results In this article, we present libgapmis, a library for extending pairwise short-read alignments. Apart from the standard CPU version, it includes ultrafast SSE- and GPU-based implementations. libgapmis is based on an algorithm computing a modified version of the traditional dynamic-programming matrix for sequence alignment. Extensive experimental results demonstrate that the functions of the CPU version provided in this library accelerate the computations by a factor of 20 compared to other programmes. The analogous SSE- and GPU-based implementations accelerate the computations by a factor of 6 and 11, respectively, compared to the CPU version. The library also provides the user the flexibility to split the read into fragments, based on the observed gap occurrence frequency and the length of the read, thereby allowing for a variable, but bounded, number of gaps in the alignment. Conclusions We present libgapmis, a library for extending

Using automatic alignment to analyze endangered language data: Testing the viability of untrained alignment

PubMed Central

DiCanio, Christian; Nam, Hosung; Whalen, Douglas H.; Timothy Bunnell, H.; Amith, Jonathan D.; García, Rey Castillo

2013-01-01

While efforts to document endangered languages have steadily increased, the phonetic analysis of endangered language data remains a challenge. The transcription of large documentation corpora is, by itself, a tremendous feat. Yet, the process of segmentation remains a bottleneck for research with data of this kind. This paper examines whether a speech processing tool, forced alignment, can facilitate the segmentation task for small data sets, even when the target language differs from the training language. The authors also examined whether a phone set with contextualization outperforms a more general one. The accuracy of two forced aligners trained on English (hmalign and p2fa) was assessed using corpus data from Yoloxóchitl Mixtec. Overall, agreement performance was relatively good, with accuracy at 70.9% within 30 ms for hmalign and 65.7% within 30 ms for p2fa. Segmental and tonal categories influenced accuracy as well. For instance, additional stop allophones in hmalign's phone set aided alignment accuracy. Agreement differences between aligners also corresponded closely with the types of data on which the aligners were trained. Overall, using existing alignment systems was found to have potential for making phonetic analysis of small corpora more efficient, with more allophonic phone sets providing better agreement than general ones. PMID:23967953

Using automatic alignment to analyze endangered language data: testing the viability of untrained alignment.

PubMed

DiCanio, Christian; Nam, Hosung; Whalen, Douglas H; Bunnell, H Timothy; Amith, Jonathan D; García, Rey Castillo

2013-09-01

While efforts to document endangered languages have steadily increased, the phonetic analysis of endangered language data remains a challenge. The transcription of large documentation corpora is, by itself, a tremendous feat. Yet, the process of segmentation remains a bottleneck for research with data of this kind. This paper examines whether a speech processing tool, forced alignment, can facilitate the segmentation task for small data sets, even when the target language differs from the training language. The authors also examined whether a phone set with contextualization outperforms a more general one. The accuracy of two forced aligners trained on English (hmalign and p2fa) was assessed using corpus data from Yoloxóchitl Mixtec. Overall, agreement performance was relatively good, with accuracy at 70.9% within 30 ms for hmalign and 65.7% within 30 ms for p2fa. Segmental and tonal categories influenced accuracy as well. For instance, additional stop allophones in hmalign's phone set aided alignment accuracy. Agreement differences between aligners also corresponded closely with the types of data on which the aligners were trained. Overall, using existing alignment systems was found to have potential for making phonetic analysis of small corpora more efficient, with more allophonic phone sets providing better agreement than general ones.

Modified alignment CGHs for aspheric surface test

NASA Astrophysics Data System (ADS)

Song, Jae-Bong; Yang, Ho-Soon; Rhee, Hyug-Gyo; Lee, Yun-Woo

2009-08-01

Computer Generated Holograms (CGH) for optical test are commonly consisted of one main pattern for testing aspheric surface and some alignment patterns for aligning the interferometer, CGH, and the test optics. To align the CGH plate and the test optics, we designed the alignment CGHs modified from the cat's eye alignment method, which are consisted of a couple of CGH patterns. The incident beam passed through the one part of the alignment CGH pattern is focused onto the one radius position of the test aspheric surface, and is reflected to the other part, and vice versa. This method has several merits compared to the conventional cat's eye alignment method. First, this method can be used in testing optics with a center hole, and the center part of CGH plate can be assigned to the alignment pattern. Second, the alignment pattern becomes a concentric circular arc pattern. The whole CGH patterns including the main pattern and alignment patterns are consisted of only concentric circular fringes. This concentric circular pattern can be easily made by the polar coordinated writer with circular scanning. The required diffraction angle becomes relatively small, so the 1st order diffraction beams instead of the 3rd order diffraction beam can be used as alignment beams, and the visibility can be improved. This alignment method also is more sensitive to the tilt and the lateral shift of the test aspheric surface. Using this alignment pattern, a 200 mm diameter F/0.5 aspheric mirror and a 600 mm diameter F/0.9 mirror were tested.

Laser beam alignment apparatus and method

DOEpatents

Gruhn, C.R.; Hammond, R.B.

The disclosure related to an apparatus and method for laser beam alignment. Thermoelectric properties of a disc in a laser beam path are used to provide an indication of beam alignment and/or automatic laser alignment.

Laser beam alignment apparatus and method

DOEpatents

Gruhn, Charles R.; Hammond, Robert B.

1981-01-01

The disclosure relates to an apparatus and method for laser beam alignment. Thermoelectric properties of a disc in a laser beam path are used to provide an indication of beam alignment and/or automatic laser alignment.

ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces.

PubMed

Sadygov, Rovshan G; Maroto, Fernando Martin; Hühmer, Andreas F R

2006-12-15

We present an algorithmic approach to align three-dimensional chromatographic surfaces of LC-MS data of complex mixture samples. The approach consists of two steps. In the first step, we prealign chromatographic profiles: two-dimensional projections of chromatographic surfaces. This is accomplished by correlation analysis using fast Fourier transforms. In this step, a temporal offset that maximizes the overlap and dot product between two chromatographic profiles is determined. In the second step, the algorithm generates correlation matrix elements between full mass scans of the reference and sample chromatographic surfaces. The temporal offset from the first step indicates a range of the mass scans that are possibly correlated, then the correlation matrix is calculated only for these mass scans. The correlation matrix carries information on highly correlated scans, but it does not itself determine the scan or time alignment. Alignment is determined as a path in the correlation matrix that maximizes the sum of the correlation matrix elements. The computational complexity of the optimal path generation problem is reduced by the use of dynamic programming. The program produces time-aligned surfaces. The use of the temporal offset from the first step in the second step reduces the computation time for generating the correlation matrix and speeds up the process. The algorithm has been implemented in a program, ChromAlign, developed in C++ language for the .NET2 environment in WINDOWS XP. In this work, we demonstrate the applications of ChromAlign to alignment of LC-MS surfaces of several datasets: a mixture of known proteins, samples from digests of surface proteins of T-cells, and samples prepared from digests of cerebrospinal fluid. ChromAlign accurately aligns the LC-MS surfaces we studied. In these examples, we discuss various aspects of the alignment by ChromAlign, such as constant time axis shifts and warping of chromatographic surfaces.

Text-image alignment for historical handwritten documents

NASA Astrophysics Data System (ADS)

Zinger, S.; Nerbonne, J.; Schomaker, L.

2009-01-01

We describe our work on text-image alignment in context of building a historical document retrieval system. We aim at aligning images of words in handwritten lines with their text transcriptions. The images of handwritten lines are automatically segmented from the scanned pages of historical documents and then manually transcribed. To train automatic routines to detect words in an image of handwritten text, we need a training set - images of words with their transcriptions. We present our results on aligning words from the images of handwritten lines and their corresponding text transcriptions. Alignment based on the longest spaces between portions of handwriting is a baseline. We then show that relative lengths, i.e. proportions of words in their lines, can be used to improve the alignment results considerably. To take into account the relative word length, we define the expressions for the cost function that has to be minimized for aligning text words with their images. We apply right to left alignment as well as alignment based on exhaustive search. The quality assessment of these alignments shows correct results for 69% of words from 100 lines, or 90% of partially correct and correct alignments combined.

Method for alignment of microwires

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

Beardslee, Joseph A.; Lewis, Nathan S.; Sadtler, Bryce

2017-01-24

A method of aligning microwires includes modifying the microwires so they are more responsive to a magnetic field. The method also includes using a magnetic field so as to magnetically align the microwires. The method can further include capturing the microwires in a solid support structure that retains the longitudinal alignment of the microwires when the magnetic field is not applied to the microwires.

Algorithms for Automatic Alignment of Arrays

NASA Technical Reports Server (NTRS)

Chatterjee, Siddhartha; Gilbert, John R.; Oliker, Leonid; Schreiber, Robert; Sheffler, Thomas J.

1996-01-01

Aggregate data objects (such as arrays) are distributed across the processor memories when compiling a data-parallel language for a distributed-memory machine. The mapping determines the amount of communication needed to bring operands of parallel operations into alignment with each other. A common approach is to break the mapping into two stages: an alignment that maps all the objects to an abstract template, followed by a distribution that maps the template to the processors. This paper describes algorithms for solving the various facets of the alignment problem: axis and stride alignment, static and mobile offset alignment, and replication labeling. We show that optimal axis and stride alignment is NP-complete for general program graphs, and give a heuristic method that can explore the space of possible solutions in a number of ways. We show that some of these strategies can give better solutions than a simple greedy approach proposed earlier. We also show how local graph contractions can reduce the size of the problem significantly without changing the best solution. This allows more complex and effective heuristics to be used. We show how to model the static offset alignment problem using linear programming, and we show that loop-dependent mobile offset alignment is sometimes necessary for optimum performance. We describe an algorithm with for determining mobile alignments for objects within do loops. We also identify situations in which replicated alignment is either required by the program itself or can be used to improve performance. We describe an algorithm based on network flow that replicates objects so as to minimize the total amount of broadcast communication in replication.

DNAAlignEditor: DNA alignment editor tool

PubMed Central

Sanchez-Villeda, Hector; Schroeder, Steven; Flint-Garcia, Sherry; Guill, Katherine E; Yamasaki, Masanori; McMullen, Michael D

2008-01-01

Background With advances in DNA re-sequencing methods and Next-Generation parallel sequencing approaches, there has been a large increase in genomic efforts to define and analyze the sequence variability present among individuals within a species. For very polymorphic species such as maize, this has lead to a need for intuitive, user-friendly software that aids the biologist, often with naïve programming capability, in tracking, editing, displaying, and exporting multiple individual sequence alignments. To fill this need we have developed a novel DNA alignment editor. Results We have generated a nucleotide sequence alignment editor (DNAAlignEditor) that provides an intuitive, user-friendly interface for manual editing of multiple sequence alignments with functions for input, editing, and output of sequence alignments. The color-coding of nucleotide identity and the display of associated quality score aids in the manual alignment editing process. DNAAlignEditor works as a client/server tool having two main components: a relational database that collects the processed alignments and a user interface connected to database through universal data access connectivity drivers. DNAAlignEditor can be used either as a stand-alone application or as a network application with multiple users concurrently connected. Conclusion We anticipate that this software will be of general interest to biologists and population genetics in editing DNA sequence alignments and analyzing natural sequence variation regardless of species, and will be particularly useful for manual alignment editing of sequences in species with high levels of polymorphism. PMID:18366684

MEMS Integrated Submount Alignment for Optoelectronics

NASA Astrophysics Data System (ADS)

Shakespeare, W. Jeffrey; Pearson, Raymond A.; Grenestedt, Joachim L.; Hutapea, Parsaoran; Gupta, Vikas

2005-02-01

One of the most expensive and time-consuming production processes for single-mode fiber-optic components is the alignment of the photonic chip or waveguide to the fiber. The alignment equipment is capital intensive and usually requires trained technicians to achieve desired results. Current technology requires active alignment since tolerances are only ~0.2 μ m or less for a typical laser diode. This is accomplished using piezoelectric actuated stages and active optical feedback. Joining technologies such as soldering, epoxy bonding, or laser welding may contribute significant postbond shift, and final coupling efficiencies are often less than 80%. This paper presents a method of adaptive optical alignment to freeze in place directly on an optical submount using a microelectromechanical system (MEMS) shape memory alloy (SMA) actuation technology. Postbond shift is eliminated since the phase change is the alignment actuation. This technology is not limited to optical alignment but can be applied to a variety of MEMS actuations, including nano-actuation and nano-alignment for biomedical applications. Experimental proof-of-concept results are discussed, and a simple analytical model is proposed to predict the stress strain behavior of the optical submount. Optical coupling efficiencies and alignment times are compared with traditional processes. The feasibility of this technique in high-volume production is discussed.

Poly(hydroxybutyrate)/chitosan Aligned Electrospun Scaffold as a Novel Substrate for Nerve Tissue Engineering.

PubMed

Karimi, Afarin; Karbasi, Saeed; Razavi, Shahnaz; Zargar, Elham Naghash

2018-01-01

Reconstruction of nervous system is a great challenge in the therapeutic medical field. Nerve tissue engineering is a novel method to regenerate nervous system in human health care. Tissue engineering has introduced novel approaches to promote and guide peripheral nerve regeneration using submicron and nanoscale fibrous scaffolds. In this study, 9 wt% poly(3-hydroxybutyrate) (PHB) solutions with two different ratios of chitosan (CTS) (15%, and 20%) were mixed in trifluoroacetic acid as a cosolvent. Thereafter, random and aligned PHB/CTS scaffolds were fabricated by electrospinning method in an appropriate condition. Average diameters for aligned PHB, PHB/CTS 85:15 and PHB/CTS 80:20 were obtained as 675 nm, 740.3 nm, and 870.74 nm, which was lesser than random fibers. The solution components entity authenticity was approved by Fourier transform infrared. The addition of CTS decreased both water droplet contact angle from 124.79° to 43.14° in random and 110.87° to 33.49° in aligned PHB/CTS fibrous scaffold. Moreover, alignment of fibers causes tremendous increase in hydrophilicity of fibrous PHB/CTS substrate. Tensile strength increased from 6.41 MPa for random to 8.73 MPa for aligned PHB/CTS 85:15. Our results indicated that aligned PHB/CTS 85:15 nanofibers are the desired scaffold than the random PHB/CTS nanofibers for application in nerve tissue regeneration.

Alignment system for SGII-Up laser facility

NASA Astrophysics Data System (ADS)

Gao, Yanqi; Cui, Yong; Li, Hong; Gong, Lei; Lin, Qiang; Liu, Daizhong; Zhu, Baoqiang; Ma, Weixin; Zhu, Jian; Lin, Zunqi

2018-03-01

The SGII-Up laser facility in Shanghai is one of the most important high-power laser facilities in China. It is designed to obtain 24 kJ (3ω) of energy with a square pulse of 3 ns using eight laser beams (two bundles). To satisfy the requirements for the safety, efficiency, and quality, an alignment system is developed for this facility. This alignment system can perform automatic alignment of the preamplifier system, main amplifier system, and harmonic conversion system within 30 min before every shot during the routine operation of the facility. In this article, an overview of the alignment system is first presented. Then, its alignment characteristics are discussed, along with the alignment process. Finally, experimental results, including the alignment results and the facility performance, are reported. The results show that the far-field beam pointing alignment accuracy is better than 3 μrad, and the alignment error of the near-field beam centering is no larger than 1 mm. These satisfy the design requirements very well.

13C-13C dipolar recoupling under very fast magic angle spinning in solid-state nuclear magnetic resonance: Applications to distance measurements, spectral assignments, and high-throughput secondary-structure determination

NASA Astrophysics Data System (ADS)

Ishii, Yoshitaka

2001-05-01

A technique is presented to recouple homonuclear dipolar couplings between dilute spin pairs such as 13C-13C systems under very fast magic angle spinning (MAS) in solid-state nuclear magnetic resonance (NMR) spectroscopy. The presented technique, finite pulse rf driven recoupling (fpRFDR), restores homonuclear dipolar interactions based on constructive usage of finite pulse-width effects in a phase- and symmetry-cycled π-pulse train in which a rotor-synchronous π pulse is applied every rotation period. The restored effective dipolar interaction has the form of a zero-quantum dipolar Hamiltonian for static solids, whose symmetry in spin space is different from that obtained by conventional rf driven recoupling (RFDR) techniques. It is demonstrated that the efficiency of recoupling by fpRFDR is not strongly dependent on chemical shift differences or resonance offsets in contrast to previous recoupling methods under very fast MAS. To realize distance measurements without effects of spin relaxation, a constant-time version of fpRFDR (CT-fpRFDR) is introduced, in which the effective evolution period is varied by refocusing dipolar evolution with a rotor-synchronized solid echo while the total recoupling period is kept constant. From CT-fpRFDR experiments at a spinning speed of 30.3 kHz in a field of 17.6 T, the 13C-13C distance of [1-13C]Ala-[1-13C]Gly-Gly was determined to be 3.27 Å, which agrees well with the value of 3.20 Å obtained by x-ray diffraction. Also, two-dimensional (2D) 13C/13C chemical-shift correlation NMR spectrum in a field of 9.4 T was obtained with fpRFDR for fibrils of the segmentally 13C- and 15N-labeled Alzheimer's β-Amyloid fragments, Aβ16-22 (residues 16-22 taken from the 40-residue Aβ peptide) in which Leu-17 through Ala-21 are uniformly 13C- and 15N-labeled. Most 13C resonances for the main chain as well as for the side chains are assigned based on 2D 13C/13C chemical-shift correlation patterns specific to amino-acid types. Examination

Simultaneous phylogeny reconstruction and multiple sequence alignment

PubMed Central

Yue, Feng; Shi, Jian; Tang, Jijun

2009-01-01

Background A phylogeny is the evolutionary history of a group of organisms. To date, sequence data is still the most used data type for phylogenetic reconstruction. Before any sequences can be used for phylogeny reconstruction, they must be aligned, and the quality of the multiple sequence alignment has been shown to affect the quality of the inferred phylogeny. At the same time, all the current multiple sequence alignment programs use a guide tree to produce the alignment and experiments showed that good guide trees can significantly improve the multiple alignment quality. Results We devise a new algorithm to simultaneously align multiple sequences and search for the phylogenetic tree that leads to the best alignment. We also implemented the algorithm as a C program package, which can handle both DNA and protein data and can take simple cost model as well as complex substitution matrices, such as PAM250 or BLOSUM62. The performance of the new method are compared with those from other popular multiple sequence alignment tools, including the widely used programs such as ClustalW and T-Coffee. Experimental results suggest that this method has good performance in terms of both phylogeny accuracy and alignment quality. Conclusion We present an algorithm to align multiple sequences and reconstruct the phylogenies that minimize the alignment score, which is based on an efficient algorithm to solve the median problems for three sequences. Our extensive experiments suggest that this method is very promising and can produce high quality phylogenies and alignments. PMID:19208110

Whole-genome alignment.

PubMed

Dewey, Colin N

2012-01-01

Whole-genome alignment (WGA) is the prediction of evolutionary relationships at the nucleotide level between two or more genomes. It combines aspects of both colinear sequence alignment and gene orthology prediction, and is typically more challenging to address than either of these tasks due to the size and complexity of whole genomes. Despite the difficulty of this problem, numerous methods have been developed for its solution because WGAs are valuable for genome-wide analyses, such as phylogenetic inference, genome annotation, and function prediction. In this chapter, we discuss the meaning and significance of WGA and present an overview of the methods that address it. We also examine the problem of evaluating whole-genome aligners and offer a set of methodological challenges that need to be tackled in order to make the most effective use of our rapidly growing databases of whole genomes.

Photocatalysis-assisted water filtration: using TiO2-coated vertically aligned multi-walled carbon nanotube array for removal of Escherichia coli O157:H7.

PubMed

Oza, Goldie; Pandey, Sunil; Gupta, Arvind; Shinde, Sachin; Mewada, Ashmi; Jagadale, Pravin; Sharon, Maheshwar; Sharon, Madhuri

2013-10-01

A porous ceramic was coated with vertically aligned multi-walled carbon nanotubes (MWCNTs) by spray pyrolysis. Titanium dioxide (TiO2) nanoparticles were then coated onto this densely aligned MWCNT. The presence of TiO2/MWCNT interfacial arrays was confirmed by X-ray diffraction (XRD), scanning electron microscope-energy dispersive analysis of X-ray (SEM-EDAX) and transmission electron microscope (TEM). This is a novel report in which water loaded with a most dreadful enterohemorrhagic pathogenic strain of Escherichia coli O157:H7 was filtered through TiO2/MWCNT coated porous ceramic filter and then analysed. Bacterial removal performance was found to be significantly lower in control i.e. plain porous ceramic (P<0.05) as compared to TiO2/MWCNT coated ceramic. The photocatalytic killing rate constant for TiO2-ceramic and MWCNT/TiO2-ceramic under fluorescent light was found be 1.45×10(-2) min(-1) and 2.23×10(-2) min(-1) respectively. Further, when I-V characteristics were performed for TiO2/MWCNT composite, it was corroborated that the current under light irradiation is comparatively higher than that in dark, thus proving it to be photocatalytically efficient system. The enhanced photocatalysis may be a contribution of increased surface area and charge transfer rate as a consequence of aligned MWCNT network. © 2013 Elsevier B.V. All rights reserved.

Heuristics for multiobjective multiple sequence alignment.

PubMed

Abbasi, Maryam; Paquete, Luís; Pereira, Francisco B

2016-07-15

Aligning multiple sequences arises in many tasks in Bioinformatics. However, the alignments produced by the current software packages are highly dependent on the parameters setting, such as the relative importance of opening gaps with respect to the increase of similarity. Choosing only one parameter setting may provide an undesirable bias in further steps of the analysis and give too simplistic interpretations. In this work, we reformulate multiple sequence alignment from a multiobjective point of view. The goal is to generate several sequence alignments that represent a trade-off between maximizing the substitution score and minimizing the number of indels/gaps in the sum-of-pairs score function. This trade-off gives to the practitioner further information about the similarity of the sequences, from which she could analyse and choose the most plausible alignment. We introduce several heuristic approaches, based on local search procedures, that compute a set of sequence alignments, which are representative of the trade-off between the two objectives (substitution score and indels). Several algorithm design options are discussed and analysed, with particular emphasis on the influence of the starting alignment and neighborhood search definitions on the overall performance. A perturbation technique is proposed to improve the local search, which provides a wide range of high-quality alignments. The proposed approach is tested experimentally on a wide range of instances. We performed several experiments with sequences obtained from the benchmark database BAliBASE 3.0. To evaluate the quality of the results, we calculate the hypervolume indicator of the set of score vectors returned by the algorithms. The results obtained allow us to identify reasonably good choices of parameters for our approach. Further, we compared our method in terms of correctly aligned pairs ratio and columns correctly aligned ratio with respect to reference alignments. Experimental results show

Van Allen Probes observations of intense parallel Poynting flux associated with magnetic dipolarization, conjugate discrete auroral arcs, and energetic particle injection

NASA Astrophysics Data System (ADS)

Wygant, J. R.; Thaller, S. A.; Breneman, A. W.; Tian, S.; Cattell, C. A.; Chaston, C. C.; Mozer, F.; Bonnell, J. W.; Kistler, L. M.; Mouikis, C.; Hudson, M. K.; Claudepierre, S. G.; Fennell, J. F.; Reeves, G. D.; Baker, D. N.; Donovan, E.; Spanswick, E.; Kletzing, C.

2015-12-01

We present measurements from the Van Allen Probes, in the near Earth tail, at the outer boundary of the plasma sheet, of a magnetic dipolarization/injection event characterized by unusually strong earthward poynting flux flowing along magnetic field lines with amplitudes of 200 mW/m2 lasting ~ 1 minute. The Poynting flux was conjugate to a 30 km wide discrete auroral arc observed by the THEMIS auroral array. The observations were obtained at 5.8 Re in the pre-midnight sector during the main phase of a geomagnetic storm on 5/01/2013. This brief interval transferred more electromagnetic energy (at the spacecraft position) than that transferred during entire remainder of the main phase of the storm. The parallel Poynting flux coincided with a local section of the "cross tail current sheet" which generated the dipolarization signature. The latitudinal width of the arc, mapped along magnetic field lines, provides an estimate of the spatial scale of the Poynting flux, the electric fields, and the current sheets (parallel and perpendicular). It is estimated that the latitudinal width of the Poynting flux "sheet" was ~600 km or ~1-2 H+ inertial lengths. An estimate of the ∫E·dl across the current sheet along the direction normal to the plasma sheet is ~20-40 kilovolts. The "normal" to the plasma sheet component of the electric field (~70 mV/m) strongly dominated the azimuthal component(which is reponsible for drift energetization). The dipolarization event resulted in the local dispersion-less injection of electrons between 50 keV and ~2 MeV at the Van Allen Probe position. The injection event involved brief (factor of two) local spike in ~2 MeV electron fluxes. Measurements from the Los Alamos geosynchronous spacecraft, displaced eastward from the Van Allen probes, provided evidence for dispersive energy-time electron signatures consistent with injection and energization at the RBSP position. The Poynting flux also coincided with the energy peak in the up

SU-E-J-33: Comparison Between Soft Tissue Alignment and Bony Alignment for Pancreatic Cancer Radiotherapy

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

Suh, Y; Crane, C; Krishnan, S

Purpose An IGRT modality for pancreatic cancer treatment with dose escalation at our institution is in-room daily CT imaging. The purpose of this study is to assess the difference between soft tissue alignment and bony alignment for pancreatic tumor localization. Methods Eighteen patients with pancreatic tumors who underwent IMRT treatment with an inspiration breath-hold technique between July 2012 and February 2015 are included in this study. Prior to each treatment, a CT scan was acquired. The CT image guidance started with auto-alignment to either the bony anatomy (vertebral bodies) or fiducials (for the six patients with the stent in/near themore » tumor) and then, when necessary, manual adjustments were made based on soft tissue alignment using clinical software (CT-Assisted Targeting system). The difference between soft tissue alignment and bony/fiducial alignment was evaluated. Results Of all 380 treatments, manual adjustment was made in 225 treatments, ranging from 11% (3 treatments out of 28) to 96% (27 treatments out of 28) per patient. The mean of the difference between soft tissue alignment and bony/fiducial alignment per patient ranged from −3.6 to 0.3 mm, −1.5 to 2.8 mm, and −3.3 to 3.4 mm in the AP, SI, and RL directions, respectively. The maximum difference over all treatments was −9.5, −14.6, and −14.6 mm in the AP, SI, and RL directions, respectively. Conclusion About 60% of the time, manual adjustment based on soft tissue alignment was required. The extent of manual adjustment was usually small but varied significantly from patient to patient. The ultimate goal of the IGRT modality using daily CT imaging is not to fully cover the target but to spare organs-at-risk as much as possible to avoid them moving into higher dose gradients than accepted in the treatment plan. To this end, manual adjustment based on soft tissue alignment is critically important.« less

Water Cooled Mirror Design

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

Dale, Gregory E.; Holloway, Michael Andrew; Pulliam, Elias Noel

2015-03-30

This design is intended to replace the current mirror setup being used for the NorthStar Moly 99 project in order to monitor the target coupon. The existing setup has limited movement for camera alignment and is difficult to align properly. This proposed conceptual design for a water cooled mirror will allow for greater thermal transfer between the mirror and the water block. It will also improve positioning of the mirror by using flexible vacuum hosing and a ball head joint capable of a wide range of motion. Incorporating this design into the target monitoring system will provide more efficient coolingmore » of the mirror which will improve the amount of diffraction caused by the heating of the mirror. The process of aligning the mirror for accurate position will be greatly improved by increasing the range of motion by offering six degrees of freedom.« less

SIM Lite: Ground Alignment of the Instrument

NASA Technical Reports Server (NTRS)

Dekens, Frank G.; Goullioud, Renaud; Nicaise, Fabien; Kuan, Gary; Morales, Mauricio

2010-01-01

We present the start of the ground alignment plan for the SIM Lite Instrument. We outline the integration and alignment of the individual benches on which all the optics are mounted, and then the alignment of the benches to form the Science and Guide interferometers. The Instrument has a guide interferometer with only a 40 arc-seconds field of regard, and 200 arc-seconds of alignment adjustability. This requires each sides of the interferometer to be aligned to a fraction of that, while at the same time be orthogonal to the baseline defined by the External Metrology Truss. The baselines of the Science and Guide interferometers must also be aligned to be parallel. The start of these alignment plans is captured in a SysML Instrument System model, in the form of activity diagrams. These activity diagrams are then related to the hardware design and requirements. We finish with future plans for the alignment and integration activities and requirements.

SIM Lite: ground alignment of the instrument

NASA Astrophysics Data System (ADS)

Dekens, Frank G.; Goullioud, Renaud; Nicaise, Fabien; Kuan, Gary; Morales, Mauricio

2010-07-01

We present the start of the ground alignment plan for the SIM Lite Instrument. We outline the integration and alignment of the individual benches on which all the optics are mounted, and then the alignment of the benches to form the Science and Guide interferometers. The Instrument has a guide interferometer with only a 40 arc-seconds field of regard, and 200 arc-seconds of alignment adjustability. This requires each sides of the interferometer to be aligned to a fraction of that, while at the same time be orthogonal to the baseline defined by the External Metrology Truss. The baselines of the Science and Guide interferometers must also be aligned to be parallel. The start of these alignment plans is captured in a SysML Instrument System model, in the form of activity diagrams. These activity diagrams are then related to the hardware design and requirements. We finish with future plans for the alignment and integration activities and requirements.

Image alignment

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

Dowell, Larry Jonathan

Disclosed is a method and device for aligning at least two digital images. An embodiment may use frequency-domain transforms of small tiles created from each image to identify substantially similar, "distinguishing" features within each of the images, and then align the images together based on the location of the distinguishing features. To accomplish this, an embodiment may create equal sized tile sub-images for each image. A "key" for each tile may be created by performing a frequency-domain transform calculation on each tile. A information-distance difference between each possible pair of tiles on each image may be calculated to identify distinguishingmore » features. From analysis of the information-distance differences of the pairs of tiles, a subset of tiles with high discrimination metrics in relation to other tiles may be located for each image. The subset of distinguishing tiles for each image may then be compared to locate tiles with substantially similar keys and/or information-distance metrics to other tiles of other images. Once similar tiles are located for each image, the images may be aligned in relation to the identified similar tiles.« less

Role of lower hybrid waves in ion heating at dipolarization fronts

NASA Astrophysics Data System (ADS)

Greco, A.; Artemyev, A.; Zimbardo, G.; Angelopoulos, V.; Runov, A.

2017-05-01

One of the important sources of hot ions in the magnetotail is the bursty bulk flows propagating away from the reconnection region and heating the ambient plasma. Charged particles interact with nonlinear magnetic field pulses (dipolarization fronts, DFs) embedded into these flows. The convection electric fields associated with DF propagation are known to reflect and accelerate ambient ions. Moreover, a wide range of waves is observed within/near these fronts, the electric field fluctuations being dominated by the lower hybrid drift (LHD) instability. Here we investigate the potential role of these waves in the further acceleration of ambient ions. We use a LHD wave emission profile superimposed on the leading edge of a two-dimensional model profile of a DF and a test particle approach. We show that LHD waves with realistic amplitudes can significantly increase the upper limit of energies gained by ions. Wave-particle interaction near the front is more effective in producing superthermal ions than in increasing the flux of thermal ions. Comparison of test particle simulations and Time History of Events and Macroscale Interactions during Substorms observations show that ion acceleration by LHD waves is more important for slower DFs.

Atomic-scale sensing of the magnetic dipolar field from single atoms

NASA Astrophysics Data System (ADS)

Choi, Taeyoung; Paul, William; Rolf-Pissarczyk, Steffen; MacDonald, Andrew J.; Natterer, Fabian D.; Yang, Kai; Willke, Philip; Lutz, Christopher P.; Heinrich, Andreas J.

2017-05-01

Spin resonance provides the high-energy resolution needed to determine biological and material structures by sensing weak magnetic interactions. In recent years, there have been notable achievements in detecting and coherently controlling individual atomic-scale spin centres for sensitive local magnetometry. However, positioning the spin sensor and characterizing spin-spin interactions with sub-nanometre precision have remained outstanding challenges. Here, we use individual Fe atoms as an electron spin resonance (ESR) sensor in a scanning tunnelling microscope to measure the magnetic field emanating from nearby spins with atomic-scale precision. On artificially built assemblies of magnetic atoms (Fe and Co) on a magnesium oxide surface, we measure that the interaction energy between the ESR sensor and an adatom shows an inverse-cube distance dependence (r-3.01±0.04). This demonstrates that the atoms are predominantly coupled by the magnetic dipole-dipole interaction, which, according to our observations, dominates for atom separations greater than 1 nm. This dipolar sensor can determine the magnetic moments of individual adatoms with high accuracy. The achieved atomic-scale spatial resolution in remote sensing of spins may ultimately allow the structural imaging of individual magnetic molecules, nanostructures and spin-labelled biomolecules.

MUSE optical alignment procedure

NASA Astrophysics Data System (ADS)

Laurent, Florence; Renault, Edgard; Loupias, Magali; Kosmalski, Johan; Anwand, Heiko; Bacon, Roland; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dubois, Jean-Pierre; Dupuy, Christophe; Kelz, Andreas; Lizon, Jean-Louis; Nicklas, Harald; Parès, Laurent; Remillieux, Alban; Seifert, Walter; Valentin, Hervé; Xu, Wenli

2012-09-01

MUSE (Multi Unit Spectroscopic Explorer) is a second generation VLT integral field spectrograph (1x1arcmin² Field of View) developed for the European Southern Observatory (ESO), operating in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently assembling and testing MUSE in the Integration Hall of the Observatoire de Lyon for the Preliminary Acceptance in Europe, scheduled for 2013. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic instrument mechanical structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2011, all MUSE subsystems were integrated, aligned and tested independently in each institute. After validations, the systems were shipped to the P.I. institute at Lyon and were assembled in the Integration Hall This paper describes the end-to-end optical alignment procedure of the MUSE instrument. The design strategy, mixing an optical alignment by manufacturing (plug and play approach) and few adjustments on key components, is presented. We depict the alignment method for identifying the optical axis using several references located in pupil and image planes. All tools required to perform the global alignment between each subsystem are described. The success of this alignment approach is demonstrated by the good results for the MUSE image quality. MUSE commissioning at the VLT (Very Large Telescope) is planned for 2013.

Alignment methods: strategies, challenges, benchmarking, and comparative overview.

PubMed

Löytynoja, Ari

2012-01-01

Comparative evolutionary analyses of molecular sequences are solely based on the identities and differences detected between homologous characters. Errors in this homology statement, that is errors in the alignment of the sequences, are likely to lead to errors in the downstream analyses. Sequence alignment and phylogenetic inference are tightly connected and many popular alignment programs use the phylogeny to divide the alignment problem into smaller tasks. They then neglect the phylogenetic tree, however, and produce alignments that are not evolutionarily meaningful. The use of phylogeny-aware methods reduces the error but the resulting alignments, with evolutionarily correct representation of homology, can challenge the existing practices and methods for viewing and visualising the sequences. The inter-dependency of alignment and phylogeny can be resolved by joint estimation of the two; methods based on statistical models allow for inferring the alignment parameters from the data and correctly take into account the uncertainty of the solution but remain computationally challenging. Widely used alignment methods are based on heuristic algorithms and unlikely to find globally optimal solutions. The whole concept of one correct alignment for the sequences is questionable, however, as there typically exist vast numbers of alternative, roughly equally good alignments that should also be considered. This uncertainty is hidden by many popular alignment programs and is rarely correctly taken into account in the downstream analyses. The quest for finding and improving the alignment solution is complicated by the lack of suitable measures of alignment goodness. The difficulty of comparing alternative solutions also affects benchmarks of alignment methods and the results strongly depend on the measure used. As the effects of alignment error cannot be predicted, comparing the alignments' performance in downstream analyses is recommended.

SU-D-210-07: The Dependence On Acoustic Velocity of Medium On the Needle Template and Electronic Grid Alignment in Ultrasound QA for Prostate Brachytherapy

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

Kapoor, P; Kapoor, R; Curran, B

Purpose: To analyze the impact on acoustic velocity (AV) of two different media (water and milk) using the needle template/electronic grid alignment test. Water, easily available, makes a good material to test the alignment of the template and grid although water’s AV (1498 m/s at 25°C) is significantly different from tissue (1540 m/s). Milk, with an AV much closer (1548 m/s) to prostate tissue, may be a good substitute for water in ultrasound quality assurance testing. Methods: Tests were performed using a Hitachi ultrasound unit with a mechanical arrangement designed to position needles parallel to the transducer. In this work,more » two materials – distilled water and homogenized whole milk (AVs of 1498 and 1548 m/s at 25°C) were used in a phantom to test ultrasound needle/grid alignment. The images were obtained with both materials and analyzed for their placement accuracy. Results: The needle template/electronic grid alignment tests showed displacement errors between measured and calculated values. The measurements showed displacements of 2.3mm (water) and 0.4mm (milk), and 1.6mm (water) and 0.3mm (milk) at depths of 7cm and 5cm respectively from true needle positions. The calculated results showed a displacement of 2.36 mm (water); 0.435mm (milk), and 1.66mm (water) and 0.31mm (milk) at a depth of 7cm and 5cm respectively. The displacements in the X and Y directions were also calculated. At depths of 7cm and 5cm, the (ΔX,ΔY) displacements in water were (0.829mm, 2.21mm) and (0.273mm, 1.634mm) and for milk were (0.15mm, 0.44mm) and (0.05mm, 0.302mm) respectively. Conclusion: The measured and calculated values were in good agreement for all tests. They show that milk provides superior results when performing needle template and electronic grid alignment tests for ultrasound units used in prostate brachytherapy.« less

System alignment using the Talbot effect

NASA Astrophysics Data System (ADS)

Chevallier, Raymond; Le Falher, Eric; Heggarty, Kevin

1990-08-01

The Talbot effect is utilized to correct an alignment problem related to a neural network used for image recognition, which required the alignment of a spatial light modulator (SLM) with the input module. A mathematical model which employs the Fresnel diffraction theory is presented to describe the method. The calculation of the diffracted amplitude describes the wavefront sphericity and the original object transmittance function in order to qualify the lateral shift of the Talbot image. Another explanation is set forth in terms of plane-wave illumination in the neural network. Using a Fourier series and by describing planes where all the harmonics are in phase, the reconstruction of Talbot images is explained. The alignment is effective when the lenslet array is aligned on the even Talbot images of the SLM pixels and the incident wave is a plane wave. The alignment is evaluated in terms of source and periodicity errors, tilt of the incident plane waves, and finite object dimensions. The effects of the error sources are concluded to be negligible, the lenslet array is shown to be successfully aligned with the SLM, and other alignment applications are shown to be possible.

The twilight zone of cis element alignments.

PubMed

Sebastian, Alvaro; Contreras-Moreira, Bruno

2013-02-01

Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein-DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein-DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments.

Observation of discrete time-crystalline order in a disordered dipolar many-body system

NASA Astrophysics Data System (ADS)

Choi, Soonwon; Choi, Joonhee; Landig, Renate; Kucsko, Georg; Zhou, Hengyun; Isoya, Junichi; Jelezko, Fedor; Onoda, Shinobu; Sumiya, Hitoshi; Khemani, Vedika; von Keyserlingk, Curt; Yao, Norman; Demler, Eugene; Lukin, Mikhail

2017-04-01

The interplay of periodic driving, disorder, and strong interactions has recently been predicted to result in exotic ``time crystalline'' phases, which spontaneously break the discrete time translation symmetry of the underlying drive. Here, we report the experimental observation of such discrete time crystalline order in a driven, disordered ensemble of dipolar spin impurities in diamond at room temperature. We observe long lived temporal correlations at integer multiples of the fundamental driving period, experimentally identify the phase boundary and find that the temporal order is protected by strong interactions; this order is remarkably stable against perturbations, even in the presence of slow thermalization. We provide a theoretical description of approximate Floquet eigenstates of the system based on product state ansatz and predict the phase boundary, which is in qualitative agreement with our observations. Our work opens the door to exploring dynamical phases of matter and controlling interacting, disordered many body systems. NSF, CUA, NSSEFF, ARO MURI, Moore Foundation.

System and method for 2D workpiece alignment

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

Weaver, William T.; Carlson, Charles T.; Smith, Scott A.

2015-07-14

A carrier capable of holding one or more workpieces is disclosed. The carrier includes movable projections located along the sides of each cell in the carrier. This carrier, in conjunction with a separate alignment apparatus, aligns each workpiece within its respective cell against several alignment pins, using a multiple step alignment process to guarantee proper positioning of the workpiece in the cell. First, the workpieces are moved toward one side of the cell. Once the workpieces have been aligned against this side, the workpieces are then moved toward an adjacent orthogonal side such that the workpieces are aligned to twomore » sides of the cell. Once aligned, the workpiece is held in place by the projections located along each side of each cell. In addition, the alignment pins are also used to align the associated mask, thereby guaranteeing that the mask is properly aligned to the workpiece.« less

Dipolar modulation in the size of galaxies: the effect of Doppler magnification

NASA Astrophysics Data System (ADS)

Bonvin, Camille; Andrianomena, Sambatra; Bacon, David; Clarkson, Chris; Maartens, Roy; Moloi, Teboho; Bull, Philip

2017-12-01

Objects falling into an overdensity appear larger on its near side and smaller on its far side than other objects at the same redshift. This produces a dipolar pattern of magnification, primarily as a consequence of the Doppler effect. At low redshift, this Doppler magnification completely dominates the usual integrated gravitational lensing contribution to the lensing magnification. We show that one can optimally observe this pattern by extracting the dipole in the cross-correlation of number counts and galaxy sizes. This dipole allows us to almost completely remove the contribution from gravitational lensing up to redshift ≲0.5, and even at high redshift z ≃ 1, the dipole picks up the Doppler magnification predominantly. Doppler magnification should be easily detectable in current and upcoming optical and radio surveys; by forecasting for telescopes such as the SKA, we show that this technique is competitive with using peculiar velocities via redshift-space distortions to constrain dark energy. It produces similar yet complementary constraints on the cosmological model to those found using measurements of the cosmic shear.

ARYANA: Aligning Reads by Yet Another Approach

PubMed Central

2014-01-01

Motivation Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $106 prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. Contribution We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. Availability ARYANA with complete source code can be obtained from http://github.com/aryana-aligner PMID:25252881

ARYANA: Aligning Reads by Yet Another Approach.

PubMed

Gholami, Milad; Arbabi, Aryan; Sharifi-Zarchi, Ali; Chitsaz, Hamidreza; Sadeghi, Mehdi

2014-01-01

Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $10(6) prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. ARYANA with complete source code can be obtained from http://github.com/aryana-aligner.

AQUASOL: An efficient solver for the dipolar Poisson–Boltzmann–Langevin equation

PubMed Central

Koehl, Patrice; Delarue, Marc

2010-01-01

The Poisson–Boltzmann (PB) formalism is among the most popular approaches to modeling the solvation of molecules. It assumes a continuum model for water, leading to a dielectric permittivity that only depends on position in space. In contrast, the dipolar Poisson–Boltzmann–Langevin (DPBL) formalism represents the solvent as a collection of orientable dipoles with nonuniform concentration; this leads to a nonlinear permittivity function that depends both on the position and on the local electric field at that position. The differences in the assumptions underlying these two models lead to significant differences in the equations they generate. The PB equation is a second order, elliptic, nonlinear partial differential equation (PDE). Its response coefficients correspond to the dielectric permittivity and are therefore constant within each subdomain of the system considered (i.e., inside and outside of the molecules considered). While the DPBL equation is also a second order, elliptic, nonlinear PDE, its response coefficients are nonlinear functions of the electrostatic potential. Many solvers have been developed for the PB equation; to our knowledge, none of these can be directly applied to the DPBL equation. The methods they use may adapt to the difference; their implementations however are PBE specific. We adapted the PBE solver originally developed by Holst and Saied [J. Comput. Chem. 16, 337 (1995)] to the problem of solving the DPBL equation. This solver uses a truncated Newton method with a multigrid preconditioner. Numerical evidences suggest that it converges for the DPBL equation and that the convergence is superlinear. It is found however to be slow and greedy in memory requirement for problems commonly encountered in computational biology and computational chemistry. To circumvent these problems, we propose two variants, a quasi-Newton solver based on a simplified, inexact Jacobian and an iterative self-consistent solver that is based directly on

AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation.

PubMed

Koehl, Patrice; Delarue, Marc

2010-02-14

The Poisson-Boltzmann (PB) formalism is among the most popular approaches to modeling the solvation of molecules. It assumes a continuum model for water, leading to a dielectric permittivity that only depends on position in space. In contrast, the dipolar Poisson-Boltzmann-Langevin (DPBL) formalism represents the solvent as a collection of orientable dipoles with nonuniform concentration; this leads to a nonlinear permittivity function that depends both on the position and on the local electric field at that position. The differences in the assumptions underlying these two models lead to significant differences in the equations they generate. The PB equation is a second order, elliptic, nonlinear partial differential equation (PDE). Its response coefficients correspond to the dielectric permittivity and are therefore constant within each subdomain of the system considered (i.e., inside and outside of the molecules considered). While the DPBL equation is also a second order, elliptic, nonlinear PDE, its response coefficients are nonlinear functions of the electrostatic potential. Many solvers have been developed for the PB equation; to our knowledge, none of these can be directly applied to the DPBL equation. The methods they use may adapt to the difference; their implementations however are PBE specific. We adapted the PBE solver originally developed by Holst and Saied [J. Comput. Chem. 16, 337 (1995)] to the problem of solving the DPBL equation. This solver uses a truncated Newton method with a multigrid preconditioner. Numerical evidences suggest that it converges for the DPBL equation and that the convergence is superlinear. It is found however to be slow and greedy in memory requirement for problems commonly encountered in computational biology and computational chemistry. To circumvent these problems, we propose two variants, a quasi-Newton solver based on a simplified, inexact Jacobian and an iterative self-consistent solver that is based directly on the PBE

Mutual capture of dipolar molecules at low and very low energies. I. Approximate analytical treatment.

PubMed

Nikitin, E E; Troe, J

2010-09-16

Approximate analytical expressions are derived for the low-energy rate coefficients of capture of two identical dipolar polarizable rigid rotors in their lowest nonresonant (j(1) = 0 and j(2) = 0) and resonant (j(1) = 0,1 and j(2) = 1,0) states. The considered range extends from the quantum, ultralow energy regime, characterized by s-wave capture, to the classical regime described within fly wheel and adiabatic channel approaches, respectively. This is illustrated by the table of contents graphic (available on the Web) that shows the scaled rate coefficients for the mutual capture of rotors in the resonant state versus the reduced wave vector between the Bethe zero-energy (left arrows) and classical high-energy (right arrow) limits for different ratios δ of the dipole-dipole to dispersion interaction.

Energetic Electrons in Dipolarization Events: Spatial Properties and Anisotropy

NASA Technical Reports Server (NTRS)

Birn, J.; Runov, A.; Hesse, M.

2014-01-01

Using the electromagnetic fields of an MHD simulation of magnetotail reconnection, flow bursts, and dipolarization, we further investigate the acceleration of electrons to suprathermal energies. Particular emphasis is on spatial properties and anisotropies as functions of energy and time. The simulation results are compared with Time History of Events and Macroscale Interactions during Substorms observations. The test particle approach successfully reproduces several observed injection features and puts them into a context of spatial maps of the injection region(s): a dominance of perpendicular anisotropies farther down the tail and closer to the equatorial plane, an increasing importance of parallel anisotropy closer to Earth and at higher latitudes, a drop in energy fluxes at energies below approximately 10 keV, coinciding with the plasma density drop, together with increases at higher energy, a triple peak structure of flux increases near 0 deg, 90 deg, and 180 deg, and a tendency of flux increases to extend to higher energy closer to Earth and at lower latitudes. We identified the plasma sheet boundary layers and adjacent lobes as a main source region for both increased and decreased energetic electron fluxes, related to the different effects of adiabatic acceleration at high and low energies. The simulated anisotropies tend to exceed the observed ones, particularly for perpendicular fluxes at high energies. The most plausible reason is that the MHD simulation lacks the effects of anisotropy-driven microinstabilities and waves, which would reduce anisotropies.

RF Jitter Modulation Alignment Sensing

NASA Astrophysics Data System (ADS)

Ortega, L. F.; Fulda, P.; Diaz-Ortiz, M.; Perez Sanchez, G.; Ciani, G.; Voss, D.; Mueller, G.; Tanner, D. B.

2017-01-01

We will present the numerical and experimental results of a new alignment sensing scheme which can reduce the complexity of alignment sensing systems currently used, while maintaining the same shot noise limited sensitivity. This scheme relies on the ability of electro-optic beam deflectors to create angular modulation sidebands in radio frequency, and needs only a single-element photodiode and IQ demodulation to generate error signals for tilt and translation degrees of freedom in one dimension. It distances itself from current techniques by eliminating the need for beam centering servo systems, quadrant photodetectors and Gouy phase telescopes. RF Jitter alignment sensing can be used to reduce the complexity in the alignment systems of many laser optical experiments, including LIGO and the ALPS experiment.

Fixture for aligning motor assembly

DOEpatents

Shervington, Roger M.; Vaghani, Vallabh V.; Vanek, Laurence D.; Christensen, Scott A.

2009-12-08

An alignment fixture includes a rotor fixture, a stator fixture and a sensor system which measures a rotational displacement therebetween. The fixture precisely measures rotation of a generator stator assembly away from a NULL position referenced by a unique reference spline on the rotor shaft. By providing an adjustable location of the stator assembly within the housing, the magnetic axes within each generator shall be aligned to a predetermined and controlled tolerance between the generator interface mounting pin and the reference spline on the rotor shaft. Once magnetically aligned, each generator is essentially a line replaceable unit which may be readily mounted to any input of a multi-generator gearbox assembly with the assurance that the magnetic alignment will be within a predetermined tolerance.

Ultralight anisotropic foams from layered aligned carbon nanotube sheets

NASA Astrophysics Data System (ADS)

Faraji, Shaghayegh; L. Stano, Kelly; Yildiz, Ozkan; Li, Ang; Zhu, Yuntian; Bradford, Philip D.

2015-10-01

In this work, we present large scale, ultralight aligned carbon nanotube (CNT) structures which have densities an order of magnitude lower than CNT arrays, have tunable properties and exhibit resiliency after compression. By stacking aligned sheets of carbon nanotubes and then infiltrating with a pyrolytic carbon (PyC), resilient foam-like materials were produced that exhibited complete recovery from 90% compressive strain. With density as low as 3.8 mg cm-3, the foam structure is over 500 times less dense than bulk graphite. Microscopy revealed that PyC coated the junctions among CNTs, and also increased CNT surface roughness. These changes in the morphology explain the transition from inelastic behavior to foam-like recovery of the layered CNT sheet structure. Mechanical and thermal properties of the foams were tuned for different applications through variation of PyC deposition duration while dynamic mechanical analysis showed no change in mechanical properties over a large temperature range. Observation of a large and linear electrical resistance change during compression of the aligned CNT/carbon (ACNT/C) foams makes strain/pressure sensors a relevant application. The foams have high oil absorption capacities, up to 275 times their own weight, which suggests they may be useful in water treatment and oil spill cleanup. Finally, the ACNT/C foam's high porosity, surface area and stability allow for demonstration of the foams as catalyst support structures.In this work, we present large scale, ultralight aligned carbon nanotube (CNT) structures which have densities an order of magnitude lower than CNT arrays, have tunable properties and exhibit resiliency after compression. By stacking aligned sheets of carbon nanotubes and then infiltrating with a pyrolytic carbon (PyC), resilient foam-like materials were produced that exhibited complete recovery from 90% compressive strain. With density as low as 3.8 mg cm-3, the foam structure is over 500 times less dense than

Vane segment support and alignment device

DOEpatents

McLaurin, Leroy Dixon; Sizemore, John Derek

1999-01-01

A support and alignment assembly for supporting and aligning a vane segment is provided. The support and alignment assembly comprises a torque plate which defines an opening for receiving an eccentric pin and a locking end member for receiving a lock socket member. An eccentric pin adjustably supported by the torque plate opening for supporting and aligning a vane segment is provided. A lock socket member adapted to securely receive the eccentric pin and rotated therewith, and adjustably engage the torque plate locking end is provided. The lock socket member receives the eccentric pin, such that when the eccentric pin is adjusted to align the vane segment, the lock socket member engages the torque plate locking end to secure the vane segment in the desired position.

Superporous thermo-responsive hydrogels by combination of cellulose fibers and aligned micropores.

PubMed

Halake, Kantappa S; Lee, Jonghwi

2014-05-25

In the area of artificial hydrogels, simultaneous engineering of the volume transition characteristics and mechanical properties of stimuli-responsive hydrogels is an important subject. By unrestricted architecting of hierarchical structures, natural hydrogels are able to provide a wide range of swelling and mechanical properties, beyond the limits of artificial hydrogels. Herein, a combination of nanostructures and microstructures was developed to construct superporous hydrogels. Fibers of microfibrillated cellulose (MFC), an eco-friendly reinforcing material, were used as nanostructures, aligned micropores were used as microstructures, and in situ photopolymerization was used to immobilize the two structures together within the gel networks of poly(N-isopropyl acrylamide) (PNIPAm). The introduction of MFC distinctly enhanced volume transition, mainly by decreasing the swelling ratios above the transition. The introduction of directional micropores increased the swelling ratio below the transition and decreased the swelling ratio above the transition, thereby also enhancing the volume transition. Additionally, the formation of aligned micropores achieved fast water infiltration, which is beneficial for superabsorbent applications. The introduction of aligned micropores reduced the elastic modulus, but this could partially be compensated for by reinforcement with MFC. This combination of crystalline nanofibers and aligned micropores has great potential for the development of stimuli-responsive superporous hydrogels outperforming current artificial hydrogels. Copyright © 2014 Elsevier Ltd. All rights reserved.

The twilight zone of cis element alignments

PubMed Central

Sebastian, Alvaro; Contreras-Moreira, Bruno

2013-01-01

Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein–DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein–DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments. PMID:23268451

Sparse alignment for robust tensor learning.

PubMed

Lai, Zhihui; Wong, Wai Keung; Xu, Yong; Zhao, Cairong; Sun, Mingming

2014-10-01

Multilinear/tensor extensions of manifold learning based algorithms have been widely used in computer vision and pattern recognition. This paper first provides a systematic analysis of the multilinear extensions for the most popular methods by using alignment techniques, thereby obtaining a general tensor alignment framework. From this framework, it is easy to show that the manifold learning based tensor learning methods are intrinsically different from the alignment techniques. Based on the alignment framework, a robust tensor learning method called sparse tensor alignment (STA) is then proposed for unsupervised tensor feature extraction. Different from the existing tensor learning methods, L1- and L2-norms are introduced to enhance the robustness in the alignment step of the STA. The advantage of the proposed technique is that the difficulty in selecting the size of the local neighborhood can be avoided in the manifold learning based tensor feature extraction algorithms. Although STA is an unsupervised learning method, the sparsity encodes the discriminative information in the alignment step and provides the robustness of STA. Extensive experiments on the well-known image databases as well as action and hand gesture databases by encoding object images as tensors demonstrate that the proposed STA algorithm gives the most competitive performance when compared with the tensor-based unsupervised learning methods.

Study of the growth and pyroelectric properties of TGS crystals doped with aniline-family dipolar molecules

NASA Astrophysics Data System (ADS)

Zhang, Kecong; Song, Jiancheng; Wang, Min; Fang, Changshui; Lu, Mengkai

1987-04-01

TGS crystals doped with aniline-family dipolar molecules (aniline, 2-aminobenzoic acid, 3-aminobenzoic acid, 3-aminobenzene-sulphonic acid, 4-aminobenzenesulphonic acid and 4-nitroraniline) have been grown by the slow-cooling solution method. The influence of these dopants on the growth habits, crystal morphology pyroelectric properties, and structure parameters of TGS crystals has been systematically investigated. The effects of the domain structure of the seed crystal on the pyroelectric properties of the doped crystals have been studied. It is found that the spontaneous polarization (P), pyroelectric coefficient (lambda), and internal bias field of the doped crystals are slightly higher than those of the pure TGS, and the larger the dipole moment of the dopant molecule, the higher the P and lambda of the doped TGS crystal.

ALIGNING JIG

DOEpatents

Culver, J.S.; Tunnell, W.C.

1958-08-01

A jig or device is described for setting or aligning an opening in one member relative to another member or structure, with a predetermined offset, or it may be used for measuring the amount of offset with which the parts have previously been sct. This jig comprises two blocks rabbeted to each other, with means for securing thc upper block to the lower block. The upper block has fingers for contacting one of the members to be a1igmed, the lower block is designed to ride in grooves within the reference member, and calibration marks are provided to determine the amount of offset. This jig is specially designed to align the collimating slits of a mass spectrometer.

Fast responses from slowly relaxing'' liquids: A comparative study of the femtosecond dynamics of triacetin, ethylene glycol, and water

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

Chang, Y.J.; Castner, E.W. Jr.

1993-11-15

We have measured the ultrafast solvent relaxation of liquid ethylene glycol, triacetin, and water by means of femtosecond polarization spectroscopy, using optical-heterodyne-detected Raman-induced Kerr-effect spectroscopy. In the viscous liquids triacetin and ethylene glycol, femtosecond relaxation processes were resolved. Not surprisingly, the femtosecond nonlinear optical response of ethylene glycol is quite similar to that of water. Using the theory of Maroncelli, Kumar, and Papazyan, we transform the pure-nuclear solvent response into a dipolar-solvation correlation function for comparison with ultrafast electron-transfer reaction rates.

Fast responses from ``slowly relaxing'' liquids: A comparative study of the femtosecond dynamics of triacetin, ethylene glycol, and water

NASA Astrophysics Data System (ADS)

Chang, Yong Joon; Castner, Edward W., Jr.

1993-11-01

We have measured the ultrafast solvent relaxation of liquid ethylene glycol, triacetin, and water by means of femtosecond polarization spectroscopy, using optical-heterodyne-detected Raman-induced Kerr-effect spectroscopy. In the viscous liquids triacetin and ethylene glycol, femtosecond relaxation processes were resolved. Not surprisingly, the femtosecond nonlinear optical response of ethylene glycol is quite similar to that of water. Using the theory of Maroncelli, Kumar, and Papazyan, we transform the pure-nuclear solvent response into a dipolar-solvation correlation function for comparison with ultrafast electron-transfer reaction rates.

Poly(hydroxybutyrate)/chitosan Aligned Electrospun Scaffold as a Novel Substrate for Nerve Tissue Engineering

PubMed Central

Karimi, Afarin; Karbasi, Saeed; Razavi, Shahnaz; Zargar, Elham Naghash

2018-01-01

Background: Reconstruction of nervous system is a great challenge in the therapeutic medical field. Nerve tissue engineering is a novel method to regenerate nervous system in human health care. Tissue engineering has introduced novel approaches to promote and guide peripheral nerve regeneration using submicron and nanoscale fibrous scaffolds. Materials and Methods: In this study, 9 wt% poly(3-hydroxybutyrate) (PHB) solutions with two different ratios of chitosan (CTS) (15%, and 20%) were mixed in trifluoroacetic acid as a cosolvent. Thereafter, random and aligned PHB/CTS scaffolds were fabricated by electrospinning method in an appropriate condition. Results: Average diameters for aligned PHB, PHB/CTS 85:15 and PHB/CTS 80:20 were obtained as 675 nm, 740.3 nm, and 870.74 nm, which was lesser than random fibers. The solution components entity authenticity was approved by Fourier transform infrared. The addition of CTS decreased both water droplet contact angle from 124.79° to 43.14° in random and 110.87° to 33.49° in aligned PHB/CTS fibrous scaffold. Moreover, alignment of fibers causes tremendous increase in hydrophilicity of fibrous PHB/CTS substrate. Tensile strength increased from 6.41 MPa for random to 8.73 MPa for aligned PHB/CTS 85:15. Conclusions: Our results indicated that aligned PHB/CTS 85:15 nanofibers are the desired scaffold than the random PHB/CTS nanofibers for application in nerve tissue regeneration. PMID:29657929

Temperature- and pressure-dependent infrared spectroscopy of 1-butyl-3-methylimidazolium trifluoromethanesulfonate: A dipolar coupling theory analysis

NASA Astrophysics Data System (ADS)

Burba, Christopher M.; Chang, Hai-Chou

2018-03-01

Continued growth and development of ionic liquids requires a thorough understanding of how cation and anion molecular structure defines the liquid structure of the materials as well as the various properties that make them technologically useful. Infrared spectroscopy is frequently used to assess molecular-level interactions among the cations and anions of ionic liquids because the intramolecular vibrational modes of the ions are sensitive to the local potential energy environments in which they reside. Thus, different interaction modes among the ions may lead to different spectroscopic signatures in the vibrational spectra. Charge organization present in ionic liquids, such as 1-butyl-3-methylimidazolium trifluoromethanesulfonate ([C4mim]CF3SO3), is frequently modeled in terms of a quasicrystalline structure. Highly structured quasilattices enable the dynamic coupling of vibrationally-induced dipole moments to produce optical dispersion and transverse optical-longitudinal optical (TO-LO) splitting of vibrational modes of the ionic liquid. According to dipolar coupling theory, the degree of TO-LO splitting is predicted to have a linear dependence on the number density of the ionic liquid. Both temperature and pressure will affect the number density of the ionic liquid and, therefore, the amount of TO-LO splitting for this mode. Therefore, we test these relationships through temperature- and pressure-dependent FT-IR spectroscopic studies of [C4mim]CF3SO3, focusing on the totally symmetric Ssbnd O stretching mode for the anion, νs(SO3). Increased temperature decreases the amount of TO-LO splitting for νs(SO3), whereas elevated pressure is found to increase the amount of band splitting. In both cases, the experimental observations follow the general predictions of dipolar coupling theory, thereby supporting the quasilattice model for this ionic liquid.

Vane segment support and alignment device

DOEpatents

McLaurin, L.D.; Sizemore, J.D.

1999-07-13

A support and alignment assembly for supporting and aligning a vane segment is provided. The support and alignment assembly comprises a torque plate which defines an opening for receiving an eccentric pin and a locking end member for receiving a lock socket member. An eccentric pin adjustably supported by the torque plate opening for supporting and aligning a vane segment is provided. A lock socket member adapted to securely receive the eccentric pin and rotated therewith, and adjustably engage the torque plate locking end is provided. The lock socket member receives the eccentric pin, such that when the eccentric pin is adjusted to align the vane segment, the lock socket member engages the torque plate locking end to secure the vane segment in the desired position. 5 figs.

Vane segment support and alignment device

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

McLaurin, L.D.; Sizemore, J.D.

1999-07-13

A support and alignment assembly for supporting and aligning a vane segment is provided. The support and alignment assembly comprises a torque plate which defines an opening for receiving an eccentric pin and a locking end member for receiving a lock socket member. An eccentric pin adjustably supported by the torque plate opening for supporting and aligning a vane segment is provided. A lock socket member adapted to securely receive the eccentric pin and rotated therewith, and adjustably engage the torque plate locking end is provided. The lock socket member receives the eccentric pin, such that when the eccentric pinmore » is adjusted to align the vane segment, the lock socket member engages the torque plate locking end to secure the vane segment in the desired position. 5 figs.« less

Docking alignment system

NASA Technical Reports Server (NTRS)

Monford, Leo G. (Inventor)

1990-01-01

Improved techniques are provided for alignment of two objects. The present invention is particularly suited for three-dimensional translation and three-dimensional rotational alignment of objects in outer space. A camera 18 is fixedly mounted to one object, such as a remote manipulator arm 10 of the spacecraft, while the planar reflective surface 30 is fixed to the other object, such as a grapple fixture 20. A monitor 50 displays in real-time images from the camera, such that the monitor displays both the reflected image of the camera and visible markings on the planar reflective surface when the objects are in proper alignment. The monitor may thus be viewed by the operator and the arm 10 manipulated so that the reflective surface is perpendicular to the optical axis of the camera, the roll of the reflective surface is at a selected angle with respect to the camera, and the camera is spaced a pre-selected distance from the reflective surface.

Optics Alignment Panel

NASA Technical Reports Server (NTRS)

Schroeder, Daniel J.

1992-01-01

The Optics Alignment Panel (OAP) was commissioned by the HST Science Working Group to determine the optimum alignment of the OTA optics. The goal was to find the position of the secondary mirror (SM) for which there is no coma or astigmatism in the camera images due to misaligned optics, either tilt or decenter. The despace position was reviewed of the SM and the optimum focus was sought. The results of these efforts are as follows: (1) the best estimate of the aligned position of the SM in the notation of HDOS is (DZ,DY,TZ,TY) = (+248 microns, +8 microns, +53 arcsec, -79 arcsec), and (2) the best focus, defined to be that despace which maximizes the fractional energy at 486 nm in a 0.1 arcsec radius of a stellar image, is 12.2 mm beyond paraxial focus. The data leading to these conclusions, and the estimated uncertainties in the final results, are presented.

Photoresist thin-film effects on alignment process capability

NASA Astrophysics Data System (ADS)

Flores, Gary E.; Flack, Warren W.

1993-08-01

Two photoresists were selected for alignment characterization based on their dissimilar coating properties and observed differences on alignment capability. The materials are Dynachem OFPR-800 and Shipley System 8. Both photoresists were examined on two challenging alignment levels in a submicron CMOS process, a nitride level and a planarized second level metal. An Ultratech Stepper model 1500 which features a darkfield alignment system with a broadband green light for alignment signal detection was used for this project. Initially, statistically designed linear screening experiments were performed to examine six process factors for each photoresist: viscosity, spin acceleration, spin speed, spin time, softbake time, and softbake temperature. Using the results derived from the screening experiments, a more thorough examination of the statistically significant process factors was performed. A full quadratic experimental design was conducted to examine viscosity, spin speed, and spin time coating properties on alignment. This included a characterization of both intra and inter wafer alignment control and alignment process capability. Insight to the different alignment behavior is analyzed in terms of photoresist material properties and the physical nature of the alignment detection system.

Well-pump alignment system

DOEpatents

Drumheller, Douglas S.

1998-01-01

An improved well-pump for geothermal wells, an alignment system for a well-pump, and to a method for aligning a rotor and stator within a well-pump, wherein the well-pump has a whistle assembly formed at a bottom portion thereof, such that variations in the frequency of the whistle, indicating misalignment, may be monitored during pumping.

Electric alignment of plate shaped clay aggregates in oils

NASA Astrophysics Data System (ADS)

Castberg, Rene; Rozynek, Zbigniew; Måløy, Knut Jørgen; Flekkøy, Eirik

2016-01-01

We experimentally investigate the rotation of plate shaped aggregates of clay mineral particles immersed in silicone oil. The rotation is induced by an external electric field. The rotation time is measured as a function of the following parameters: electric field strength, the plate geometry (length and width) and the dielectric properties of the plates. We find that the plates always align with their longest axis parallel to the direction of the electric field (E), independently of the arrangement of individual clay -2 mineral particles within the plate. The rotation time is found to scale as E and is proportional to the viscosity (μ), which coincides well with a model that describes orientation of dipoles in electric fields. As the length of the plate is increased we quantify a difference between the longitudinal and transverse polarisability. Finally, we show that moist plates align faster. We attribute this to the change of the dielectric properties of the plate due to the presence of water.

Band alignment of rutile and anatase TiO2

NASA Astrophysics Data System (ADS)

Scanlon, David O.; Dunnill, Charles W.; Buckeridge, John; Shevlin, Stephen A.; Logsdail, Andrew J.; Woodley, Scott M.; Catlow, C. Richard A.; Powell, Michael. J.; Palgrave, Robert G.; Parkin, Ivan P.; Watson, Graeme W.; Keal, Thomas W.; Sherwood, Paul; Walsh, Aron; Sokol, Alexey A.

2013-09-01

The most widely used oxide for photocatalytic applications owing to its low cost and high activity is TiO2. The discovery of the photolysis of water on the surface of TiO2 in 1972 launched four decades of intensive research into the underlying chemical and physical processes involved. Despite much collected evidence, a thoroughly convincing explanation of why mixed-phase samples of anatase and rutile outperform the individual polymorphs has remained elusive. One long-standing controversy is the energetic alignment of the band edges of the rutile and anatase polymorphs of TiO2 (ref. ). We demonstrate, through a combination of state-of-the-art materials simulation techniques and X-ray photoemission experiments, that a type-II, staggered, band alignment of ~ 0.4 eV exists between anatase and rutile with anatase possessing the higher electron affinity, or work function. Our results help to explain the robust separation of photoexcited charge carriers between the two phases and highlight a route to improved photocatalysts.

HSA: a heuristic splice alignment tool.

PubMed

Bu, Jingde; Chi, Xuebin; Jin, Zhong

2013-01-01

RNA-Seq methodology is a revolutionary transcriptomics sequencing technology, which is the representative of Next generation Sequencing (NGS). With the high throughput sequencing of RNA-Seq, we can acquire much more information like differential expression and novel splice variants from deep sequence analysis and data mining. But the short read length brings a great challenge to alignment, especially when the reads span two or more exons. A two steps heuristic splice alignment tool is generated in this investigation. First, map raw reads to reference with unspliced aligner--BWA; second, split initial unmapped reads into three equal short reads (seeds), align each seed to the reference, filter hits, search possible split position of read and extend hits to a complete match. Compare with other splice alignment tools like SOAPsplice and Tophat2, HSA has a better performance in call rate and efficiency, but its results do not as accurate as the other software to some extent. HSA is an effective spliced aligner of RNA-Seq reads mapping, which is available at https://github.com/vlcc/HSA.

Theory of grain alignment in molecular clouds

NASA Technical Reports Server (NTRS)

Roberge, Wayne G.

1993-01-01

Research accomplishments are presented and include the following: (1) mathematical theory of grain alignment; (2) super-paramagnetic alignment of molecular cloud grains; and (3) theory of grain alignment by ambipolar diffusion.

Heparin/collagen encapsulating nerve growth factor multilayers coated aligned PLLA nanofibrous scaffolds for nerve tissue engineering.

PubMed

Zhang, Kuihua; Huang, Dianwu; Yan, Zhiyong; Wang, Chunyang

2017-07-01

Biomimicing topological structure of natural nerve tissue to direct axon growth and controlling sustained release of moderate neurotrophic factors are extremely propitious to the functional recovery of damaged nervous systems. In this study, the heparin/collagen encapsulating nerve growth factor (NGF) multilayers were coated onto the aligned poly-L-lactide (PLLA) nanofibrous scaffolds via a layer-by-layer (LbL) self-assembly technique to combine biomolecular signals, and physical guidance cues for peripheral nerve regeneration. Scanning electronic microscopy (SEM) revealed that the surface of aligned PLLA nanofibrous scaffolds coated with heparin/collagen multilayers became rougher and appeared some net-like filaments and protuberances in comparison with PLLA nanofibrous scaffolds. The heparin/collagen multilayers did not destroy the alignment of nanofibers. X-ray photoelectron spectroscopy and water contact angles displayed that heparin and collagen were successfully coated onto the aligned PLLA nanofibrous scaffolds and improved its hydrophilicity. Three-dimensional (3 D) confocal microscopy images further demonstrated that collagen, heparin, and NGF were not only coated onto the surface of aligned PLLA nanofibrous scaffolds but also permeated into the inner of scaffolds. Moreover, NGF presented a sustained release for 2 weeks from aligned nanofibrous scaffolds coated with 5.5 bilayers or above and remained good bioactivity. The heparin/collagen encapsulating NGF multilayers coated aligned nanofibrous scaffolds, in particular 5.5 bilayers or above, was more beneficial to Schwann cells (SCs) proliferation and PC12 cells differentiation as well as the SC cytoskeleton and neurite growth along the direction of nanofibrous alignment compared to the aligned PLLA nanofibrous scaffolds. This novel scaffolds combining sustained release of bioactive NGF and aligned nanofibrous topography presented an excellent potential in peripheral nerve regeneration. © 2016 Wiley