Supersonic free jet, molecular free regime

International Nuclear Information System (INIS)

Sanna, G.; Tomassetti, G.

1999-01-01

The structure of the free jet emitted by a converging nozzle as obtained by the method of characteristics by Ashkenas and Sherman is described in details. In particular the dependence of the field variable by the distance from the nozzle is given. The transition from continuum to molecular free regime is then considered and the sudden freeze approximation is introduced. The processing of monoatomic and polyatomic gasses is also considered [it

CHANGE OF MAGNETIC FIELD-GAS ALIGNMENT AT THE GRAVITY-DRIVEN ALFVÉNIC TRANSITION IN MOLECULAR CLOUDS: IMPLICATIONS FOR DUST POLARIZATION OBSERVATIONS

Energy Technology Data Exchange (ETDEWEB)

Chen, Che-Yu; King, Patrick K.; Li, Zhi-Yun [Department of Astronomy, University of Virginia, Charlottesville, VA 22901 (United States)

2016-10-01

Diffuse striations in molecular clouds are preferentially aligned with local magnetic fields, whereas dense filaments tend to be perpendicular to them. When and why this transition occurs remain uncertain. To explore the physics behind this transition, we compute the histogram of relative orientation (HRO) between the density gradient and the magnetic field in three-dimensional magnetohydrodynamic (MHD) simulations of prestellar core formation in shock-compressed regions within giant molecular clouds. We find that, in the magnetically dominated (sub-Alfvénic) post-shock region, the gas structure is preferentially aligned with the local magnetic field. For overdense sub-regions with super-Alfvénic gas, their elongation becomes preferentially perpendicular to the local magnetic field. The transition occurs when self-gravitating gas gains enough kinetic energy from the gravitational acceleration to overcome the magnetic support against the cross-field contraction, which results in a power-law increase of the field strength with density. Similar results can be drawn from HROs in projected two-dimensional maps with integrated column densities and synthetic polarized dust emission. We quantitatively analyze our simulated polarization properties, and interpret the reduced polarization fraction at high column densities as the result of increased distortion of magnetic field directions in trans- or super-Alfvénic gas. Furthermore, we introduce measures of the inclination and tangledness of the magnetic field along the line of sight as the controlling factors of the polarization fraction. Observations of the polarization fraction and angle dispersion can therefore be utilized in studying local magnetic field morphology in star-forming regions.

Three dimensional alignment of molecules using elliptically polarized laser fields

DEFF Research Database (Denmark)

Larsen, J.J.; Bjerre, N.; Hald, K.

2000-01-01

We demonstrate, theoretically and experimentally, that an intense, elliptically polarized, nonresonant laser field can simultaneously force all three axes of a molecule to align along given axes fixed in space, thus inhibiting the free rotation in all three Euler angles. Theoretically, the effect...

Magnetic Field Alignment of PS-P4VP: a Non-Liquid Crystalline Coil-Coil Block Copolymer

Science.gov (United States)

Rokhlenko, Yekaterina; Zhang, Kai; Larson, Steven; Gopalan, Padma; O'Hern, Corey; Osuji, Chinedum

2015-03-01

Magnetic fields provide the ability to control alignment of self-assembled soft materials such as block copolymers. Most prior work in this area has relied on the presence of ordered assemblies of anisotropic liquid crystalline species to ensure sufficient magnetic anisotropy to drive alignment. Recent experiments with poly(styrene-b-4-vinylpyridine), a non-liquid crystalline BCP, however, show field-induced alignment of a lamellar microstructure during cooling across the order-disorder transition. Using in situ x-ray scattering, we examine the roles of field strength and cooling rate on the alignment response of this low MW coil-coil BCP. Alignment is first observed at field strengths as low as 1 Tesla and improves markedly with both increasing field strength and slower cooling. We present a geometric argument to illustrate the origin of a finite, non-trivial magnetic susceptibility anisotropy for highly stretched surface-tethered polymer chains and corroborate this using coarse-grained molecular dynamics simulations. We rationalize the magnetic field response of the system in terms of the mobility afforded by the absence of entanglements, the intrinsic anisotropy resulting from the stretched polymer chains and sterically constrained conjugated rings, and the large grain size in these low molecular weight materials.

Analytical free energy gradient for the molecular Ornstein-Zernike self-consistent-field method

Directory of Open Access Journals (Sweden)

N.Yoshida

2007-09-01

Full Text Available An analytical free energy gradient for the molecular Ornstein-Zernike self-consistent-field (MOZ-SCF method is presented. MOZ-SCF theory is one of the theories to considering the solvent effects on the solute electronic structure in solution. [Yoshida N. et al., J. Chem. Phys., 2000, 113, 4974] Molecular geometries of water, formaldehyde, acetonitrile and acetone in water are optimized by analytical energy gradient formula. The results are compared with those from the polarizable continuum model (PCM, the reference interaction site model (RISM-SCF and the three dimensional (3D RISM-SCF.

Laser-induced field-free alignment of the OCS molecule

International Nuclear Information System (INIS)

Loriot, V; Tzallas, P; Benis, E P; Hertz, E; Lavorel, B; Charalambidis, D; Faucher, O

2007-01-01

We investigate the dynamical alignment of jet-cooled OCS molecules induced by a short laser pulse. The alignment is measured through the orientational contribution of the optical Kerr effect using a second weak laser pulse as a probe. Maximum alignment is observed at conditions close to saturation of ionization. The results are analysed with a quantum mechanical model solving for the rotational dynamics

Molecular-alignment dependence in the transfer excitation of H2

International Nuclear Information System (INIS)

Wang, Y.D.; McGuire, J.H.; Weaver, O.L.; Corchs, S.E.; Rivarola, R.D.

1993-01-01

Molecular-alignment effects in the transfer excitation of H 2 by high-velocity heavy ions are studied using a two-step mechanism with amplitudes evaluated from first-order perturbation theory. Two-electron transfer excitation is treated as a result of two independent collision processes (excitation and electron transfer). Cross sections for each one-electron subprocess as well as the combined two-electron process are calculated as functions of the molecular-alignment angle. Within the independent-electron approximation, the dynamic roles of electron excitation and transfer in conjunction with molecular alignment are explored. While both excitation and transfer cross sections may strongly depend on molecular alignment, it is electron transfer that is largely responsible for the molecular-alignment dependence in the transfer excitation process. Interpretation of some experimental observations based on this model will also be discussed

Impulsive Laser Induced Alignment of Molecules Dissolved in Helium Nanodroplets

DEFF Research Database (Denmark)

Pentlehner, Dominik; H. Nielsen, Jens; Slenczka, Alkwin

2013-01-01

We show that a 450 fs nonresonant, moderately intense, linearly polarized laser pulse can induce field-free molecular axis alignment of methyliodide (CH3I) molecules dissolved in a helium nanodroplet. Time-resolved measurements reveal rotational dynamics much slower than that of isolated molecules...

Theory of strong-field ionization of aligned CO₂

DEFF Research Database (Denmark)

Abu-Samha, Mahmoud; Madsen, Lars Bojer

2009-01-01

resonance states, and the alignment-dependent ionization yields do not follow the electron density of the initial states. The theory explains the breakdown of semianalytical theories, such as the molecular tunneling theory and strong-field approximation, where excited electronic structure is neglected....

Clustering of reads with alignment-free measures and quality values.

Science.gov (United States)

Comin, Matteo; Leoni, Andrea; Schimd, Michele

2015-01-01

The data volume generated by Next-Generation Sequencing (NGS) technologies is growing at a pace that is now challenging the storage and data processing capacities of modern computer systems. In this context an important aspect is the reduction of data complexity by collapsing redundant reads in a single cluster to improve the run time, memory requirements, and quality of post-processing steps like assembly and error correction. Several alignment-free measures, based on k-mers counts, have been used to cluster reads. Quality scores produced by NGS platforms are fundamental for various analysis of NGS data like reads mapping and error detection. Moreover future-generation sequencing platforms will produce long reads but with a large number of erroneous bases (up to 15 %). In this scenario it will be fundamental to exploit quality value information within the alignment-free framework. To the best of our knowledge this is the first study that incorporates quality value information and k-mers counts, in the context of alignment-free measures, for the comparison of reads data. Based on this principles, in this paper we present a family of alignment-free measures called D (q) -type. A set of experiments on simulated and real reads data confirms that the new measures are superior to other classical alignment-free statistics, especially when erroneous reads are considered. Also results on de novo assembly and metagenomic reads classification show that the introduction of quality values improves over standard alignment-free measures. These statistics are implemented in a software called QCluster (http://www.dei.unipd.it/~ciompin/main/qcluster.html).

Alignment engineering in liquid crystalline elastomers: Free-form microstructures with multiple functionalities

Energy Technology Data Exchange (ETDEWEB)

Zeng, Hao; Cerretti, Giacomo; Wiersma, Diederik S., E-mail: camilla.parmeggiani@lens.unifi.it, E-mail: wiersma@lens.unifi.it [European Laboratory for Non Linear Spectroscopy (LENS), University of Florence, via Nello Carrara 1, 50019 Sesto Fiorentino (Italy); Wasylczyk, Piotr [European Laboratory for Non Linear Spectroscopy (LENS), University of Florence, via Nello Carrara 1, 50019 Sesto Fiorentino (Italy); Faculty of Physics, Institute of Experimental Physics, University of Warsaw, ul. Hoza 69, Warszawa 00-681 (Poland); Martella, Daniele [European Laboratory for Non Linear Spectroscopy (LENS), University of Florence, via Nello Carrara 1, 50019 Sesto Fiorentino (Italy); Dipartimento di Chimica “Ugo Schiff,” University of Florence, via della Lastruccia 3-13, 50019 Sesto Fiorentino (Italy); Parmeggiani, Camilla, E-mail: camilla.parmeggiani@lens.unifi.it, E-mail: wiersma@lens.unifi.it [European Laboratory for Non Linear Spectroscopy (LENS), University of Florence, via Nello Carrara 1, 50019 Sesto Fiorentino (Italy); CNR-INO, via Nello Carrara 1, 50019 Sesto Fiorentino (Italy)

2015-03-16

We report a method to fabricate polymer microstructures with local control over the molecular orientation. Alignment control is achieved on molecular level in a structure of arbitrary form that can be from 1 to 100 μm in size, by fixing the local boundary conditions with micro-grating patterns. The method makes use of two-photon polymerization (Direct Laser Writing) and is demonstrated specifically in liquid-crystalline elastomers. This concept allows for the realization of free-form polymeric structures with multiple functionalities which are not possible to realize with existing techniques and which can be locally controlled by light in the micrometer scale.

Coma-free alignment of high resolution electron microscopes with the aid of optical diffractograms

International Nuclear Information System (INIS)

Zemlin, F.; Weiss, K.; Schiske, P.; Kunath, W.; Herrmann, K.-H.

1978-01-01

Alignment by means of current commutating and defocusing of the objective does not yield the desired rotational symmetry of the imaging pencils. This was found while aligning a transmission electron microscope with a single field condenser objective. A series of optical diffractograms of micrographs taken under the same tilted illumination yet under various azimuths have been arranged in a tableau, wherein strong asymmetry is exhibited. Quantitative evaluation yields the most important asymmetric aberration to be the axial coma, which becomes critical when a resolution better than 5 A 0 is obtained. The tableau also allows an assessment of the three-fold astigmatism. A procedure has been developed which aligns the microscope onto the coma-free and dispersion-free pencil axis and does not rely on current communication. The procedure demands equal appearance of astigmatic carbon film images produced under the same tilt yet diametrical azimuth. (Auth.)

Electric fields and field-aligned current generation in the magnetosphere

International Nuclear Information System (INIS)

Alexeev, I.I.; Belenkaya, E.S.; Kalegaev, V.V.; Lyutov, Yu.G.

1993-01-01

The authors present a calculation of the electric potential, field-aligned currents, and plasma convection caused by the penetration of the solar wind electric field into the magnetosphere. Ohm's law and the continuity equation of ionospheric currents are used. It is shown that the large-scale convection system is reversed in the plasma sheet flanks. In this region the plasma flow is antisunward earthward of the neutral line and sunward tailward of it. The interplanetary magnetic field (IMF) B z dependences on the dimension of the magnetopause open-quotes windowsclose quotes which are intersected by open field lines, on the potential drop across the polar cap, and on the distance to the neutral line are determined. Because of the IMF effect and the effect of seasonal or daily variations of the geomagnetic field which violate its symmetry relative to the equatorial plane, there may arise a potential drop along field lines which causes field-aligned currents. The values and directions of these currents, the field-aligned potential drop, and a self-consistent solution for the potential at the ionosphere level for high field-aligned conductivity have been determined. 41 refs., 7 figs

XUV ionization of aligned molecules

Energy Technology Data Exchange (ETDEWEB)

Kelkensberg, F.; Siu, W.; Gademann, G. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Rouzee, A.; Vrakking, M. J. J. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Max-Born-Institut, Max-Born Strasse 2A, D-12489 Berlin (Germany); Johnsson, P. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Department of Physics, Lund University, Post Office Box 118, SE-221 00 Lund (Sweden); Lucchini, M. [Department of Physics, Politecnico di Milano, Istituto di Fotonica e Nanotecnologie CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Lucchese, R. R. [Department of Chemistry, Texas A and M University, College Station, Texas 77843-3255 (United States)

2011-11-15

New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

XUV ionization of aligned molecules

International Nuclear Information System (INIS)

Kelkensberg, F.; Siu, W.; Gademann, G.; Rouzee, A.; Vrakking, M. J. J.; Johnsson, P.; Lucchini, M.; Lucchese, R. R.

2011-01-01

New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO 2 molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

No alignment of cattle along geomagnetic field lines found

OpenAIRE

Hert, J.; Jelinek, L.; Pekarek, L.; Pavlicek, A.

2011-01-01

This paper presents a study of the body orientation of domestic cattle on free pastures in several European states, based on Google satellite photographs. In sum, 232 herds with 3412 individuals were evaluated. Two independent groups participated in our study and came to the same conclusion that, in contradiction to the recent findings of other researchers, no alignment of the animals and of their herds along geomagnetic field lines could be found. Several possible reasons for this discrepanc...

Measurements of magnetic field alignment

International Nuclear Information System (INIS)

Kuchnir, M.; Schmidt, E.E.

1987-01-01

The procedure for installing Superconducting Super Collider (SSC) dipoles in their respective cryostats involves aligning the average direction of their field with the vertical to an accuracy of 0.5 mrad. The equipment developed for carrying on these measurements is described and the measurements performed on the first few prototypes SSC magnets are presented. The field angle as a function of position in these 16.6 m long magnets is a characteristic of the individual magnet with possible feedback information to its manufacturing procedure. A comparison of this vertical alignment characteristic with a magnetic field intensity (by NMR) characteristic for one of the prototypes is also presented. 5 refs., 7 figs

Prediction of molecular alignment of nucleic acids in aligned media

International Nuclear Information System (INIS)

Wu Bin; Petersen, Michael; Girard, Frederic; Tessari, Marco; Wijmenga, Sybren S.

2006-01-01

We demonstrate - using the data base of all deposited DNA and RNA structures aligned in Pf1-medium and RDC refined - that for nucleic acids in a Pf1-medium the electrostatic alignment tensor can be predicted reliably and accurately via a simple and fast calculation based on the gyration tensor spanned out by the phosphodiester atoms. The rhombicity is well predicted over its full range from 0 to 0.66, while the alignment tensor orientation is predicted correctly for rhombicities up to ca. 0.4, for larger rhombicities it appears to deviate somewhat more than expected based on structural noise and measurement error. This simple analytical approach is based on the Debye-Huckel approximation for the electrostatic interaction potential, valid at distances sufficiently far away from a poly-ionic charged surface, a condition naturally enforced when the charge of alignment medium and solute are of equal sign, as for nucleic acids in a Pf1-phage medium. For the usual salt strengths and nucleic acid sizes, the Debye-Huckel screening length is smaller than the nucleic acid size, but large enough for the collective of Debye-Huckel spheres to encompass the whole molecule. The molecular alignment is then purely electrostatic, but it's functional form is under these conditions similar to that for steric alignment. The proposed analytical expression allows for very fast calculation of the alignment tensor and hence RDCs from the conformation of the nucleic acid molecule. This information provides opportunities for improved structure determination of nucleic acids, including better assessment of dynamics in (multi-domain) nucleic acids and the possibility to incorporate alignment tensor prediction from shape directly into the structure calculation process. The procedures are incorporated into MATLAB scripts, which are available on request

On the field-induced switching of molecular organization in a biaxial nematic cell and its relaxation

Science.gov (United States)

Ricci, Matteo; Berardi, Roberto; Zannoni, Claudio

2015-08-01

We investigate the switching of a biaxial nematic filling a flat cell with planar homogeneous anchoring using a coarse-grained molecular dynamics simulation. We have found that an aligning field applied across the film, and acting on specific molecular axes, can drive the reorientation of the secondary biaxial director up to one order of magnitude faster than that for the principal director. While the π/2 switching of the secondary director does not affect the alignment of the long molecular axes, the field-driven reorientation of the principal director proceeds via a concerted rotation of the long and transversal molecular axes. More importantly, while upon switching off a (relatively) weak or intermediate field, the biaxial nematic liquid crystal is always able to relax to the initial surface aligned director state; this is not the case when using fields above a certain threshold. In that case, while the secondary director always recovers the initial state, the principal one remains, occasionally, trapped in a nonuniform director state due to the formation of domain walls.

Uni- and tridimensional alignment of molecules by femto-second laser pulse

International Nuclear Information System (INIS)

Rouzee, Arnaud

2007-01-01

This thesis is devoted to the study of the alignment of linear and asymmetric top molecules generated by an intense laser pulse. In the case of short pulses with respect to molecular rotation, periodic alignment appears in field-free conditions after the extinction of the field. We study theoretically and experimentally the effects of intensity, temperature and polarization of the electric field on produced alignment. If the field is linearly polarized, the interaction leads to the alignment of the most polarizable axis of the molecule. If the field is elliptically polarized, the pulse can generate a simultaneous alignment of the three principal axes of inertia of an asymmetric top molecule (3-D alignment). This alignment can be characterized experimentally using pump-probe techniques which exploit the optical properties of the medium. They require the use of a second pulse of low intensity temporally delayed. Three techniques were exploited during this thesis. The first technique measures a depolarization due to the birefringence of the medium when the molecules are aligned. The second is based on the defocusing of the pulse on a gradient of index created following the space variation of alignment with respect to the spatial profile of the field. The last involves the creation of a grading of index to the intersection of two intense pulses, which causes the diffraction of the probe. Finally, we show experimentally that the birefringence technique can be used to quantify the 3-D alignment of an asymmetric top molecule like ethylene. (author) [fr

Molecular stopwatches, cogwheels and ``spinflakes'': studying the dynamics of molecular superrotors

Science.gov (United States)

Korobenko, Aleksey; Milner, Alexander; Hepburn, John; Milner, Valery

2015-05-01

Using the technique of an optical centrifuge, we excite diatomic molecules to ultrafast synchronous rotation. Femtosecond velocity-map imaging allows us to visualize and study the coherent dynamics of molecular superrotors under field free conditions and in external magnetic field. We demonstrate that when the created rotational wave packet is narrow, its free evolution is nondispersing and follows the motion of a classically rotating dumbbell or a hand of the smallest natural stopwatch. For wider rotational distributions, we observe the breakdown of classical rotation, when a dumbbell shape changes to that of a ``quantum cogwheel'' - a molecular state simultaneously aligned along multiple direction. Our measurements in external magnetic field reveal other peculiar aspects of the rich dynamics of molecular superrotors. The rotation of a non-magnetic molecule interacts with the applied field only weakly, giving rise to slow precession of the molecular angular momentum around the field direction. In contrast, the electronic spin of a paramagnetic superrotor mediates this interaction, causing the initial disk-like angular distribution to split into several spatial components, each precessing with its own frequency determined by the spin projection.

Reliability of image-free navigation to monitor lower-limb alignment.

Science.gov (United States)

Pearle, Andrew D; Goleski, Patrick; Musahl, Volker; Kendoff, Daniel

2009-02-01

Proper alignment of the mechanical axis of the lower limb is the principal goal of a high tibial osteotomy. A well-accepted and relevant technical specification is the coronal plane lower-limb alignment. Target values for coronal plane alignment after high tibial osteotomy include 2 degrees of overcorrection, while tolerances for this specification have been established as 2 degrees to 4 degrees. However, the role of axial plane and sagittal plane realignment after high tibial osteotomy is poorly understood; consequently, targets and tolerance for this technical specification remain undefined. This article reviews the literature concerning the reliability and precision of navigation in monitoring the clinically relevant specification of lower-limb alignment in high tibial osteotomy. We conclude that image-free navigation registration may be clinically useful for intraoperative monitoring of the coronal plane only. Only fair and poor results for the axial and sagittal planes can be obtained by image-free navigation systems. In the future, combined image-based data, such as those from radiographs, magnetic resonance imaging, and gait analysis, may be used to help to improve the accuracy and reproducibility of quantitative intraoperative monitoring of lower-limb alignment.

Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer

Directory of Open Access Journals (Sweden)

Kujin Tang

2018-04-01

Full Text Available Horizontal gene transfer (HGT plays an important role in the evolution of microbial organisms including bacteria. Alignment-free methods based on single genome compositional information have been used to detect HGT. Currently, Manhattan and Euclidean distances based on tetranucleotide frequencies are the most commonly used alignment-free dissimilarity measures to detect HGT. By testing on simulated bacterial sequences and real data sets with known horizontal transferred genomic regions, we found that more advanced alignment-free dissimilarity measures such as CVTree and d2* that take into account the background Markov sequences can solve HGT detection problems with significantly improved performance. We also studied the influence of different factors such as evolutionary distance between host and donor sequences, size of sliding window, and host genome composition on the performances of alignment-free methods to detect HGT. Our study showed that alignment-free methods can predict HGT accurately when host and donor genomes are in different order levels. Among all methods, CVTree with word length of 3, d2* with word length 3, Markov order 1 and d2* with word length 4, Markov order 1 outperform others in terms of their highest F1-score and their robustness under the influence of different factors.

Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

Science.gov (United States)

Lee, M.W.; Meuwly, M.

2013-01-01

The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

Electric field-induced astrocyte alignment directs neurite outgrowth.

Science.gov (United States)

Alexander, John K; Fuss, Babette; Colello, Raymond J

2006-05-01

The extension and directionality of neurite outgrowth are key to achieving successful target connections during both CNS development and during the re-establishment of connections lost after neural trauma. The degree of axonal elongation depends, in large part, on the spatial arrangement of astrocytic processes rich in growth-promoting proteins. Because astrocytes in culture align their processes on exposure to an electrical field of physiological strength, we sought to determine the extent to which aligned astrocytes affect neurite outgrowth. To this end, dorsal root ganglia cells were seeded onto cultured rat astrocytes that were pre-aligned by exposure to an electric field of physiological strength (500 mV mm(-1)). Using confocal microscopy and digital image analysis, we found that neurite outgrowth at 24 hours and at 48 hours is enhanced significantly and directed consistently along the aligned astrocyte processes. Moreover, this directed neurite outgrowth is maintained when grown on fixed, aligned astrocytes. Collectively, these results indicate that endogenous electric fields present within the developing CNS might act to align astrocyte processes, which can promote and direct neurite growth. Furthermore, these results demonstrate a simple method to produce an aligned cellular substrate, which might be used to direct regenerating neurites.

Aligned Magnetic Field, Radiation, and Rotation Effects on Unsteady Hydromagnetic Free Convection Flow Past an Impulsively Moving Vertical Plate in a Porous Medium

Directory of Open Access Journals (Sweden)

Sandeep Naramgari

2014-01-01

Full Text Available We analyse the effects of aligned magnetic field, radiation, and rotation on unsteady hydromagnetic free convection flow of a viscous incompressible electrically conducting fluid past an impulsively moving vertical plate in a porous medium in presence of heat source. An exact solution of the governing equations in dimensionless form is obtained by Laplace transform technique in ramped temperature case. To compare the results obtained in this case with that of isothermal plate, the exact solution of the governing equations is also obtained for isothermal plate and results are discussed graphically in both ramped temperature and isothermal cases.

Electric-field-induced flow-aligning state in a nematic liquid crystal.

Science.gov (United States)

Fatriansyah, Jaka Fajar; Orihara, Hiroshi

2015-04-01

The response of shear stress to a weak ac electric field as a probe is measured in a nematic liquid crystal under shear flow and dc electric fields. Two states with different responses are clearly observed when the dc electric field is changed at a constant shear rate: the flow aligning and non-flow aligning states. The director lies in the shear plane in the flow aligning state and out of the plane in the non-flow aligning state. Through application of dc electric field, the non-flow aligning state can be changed to the flow aligning state. In the transition from the flow aligning state to the non-flow aligning state, it is found that the response increases and the relaxation time becomes longer. Here, the experimental results in the flow aligning state are discussed on the basis of the Ericksen-Leslie theory.

Field Emission of ITO-Coated Vertically Aligned Nanowire Array.

KAUST Repository

Lee, Changhwa

2010-04-29

An indium tin oxide (ITO)-coated vertically aligned nanowire array is fabricated, and the field emission characteristics of the nanowire array are investigated. An array of vertically aligned nanowires is considered an ideal structure for a field emitter because of its parallel orientation to the applied electric field. In this letter, a vertically aligned nanowire array is fabricated by modified conventional UV lithography and coated with 0.1-μm-thick ITO. The turn-on electric field intensity is about 2.0 V/μm, and the field enhancement factor, β, is approximately 3,078 when the gap for field emission is 0.6 μm, as measured with a nanomanipulator in a scanning electron microscope.

Field Emission of ITO-Coated Vertically Aligned Nanowire Array.

KAUST Repository

Lee, Changhwa; Lee, Seokwoo; Lee, Seung S

2010-01-01

An indium tin oxide (ITO)-coated vertically aligned nanowire array is fabricated, and the field emission characteristics of the nanowire array are investigated. An array of vertically aligned nanowires is considered an ideal structure for a field emitter because of its parallel orientation to the applied electric field. In this letter, a vertically aligned nanowire array is fabricated by modified conventional UV lithography and coated with 0.1-μm-thick ITO. The turn-on electric field intensity is about 2.0 V/μm, and the field enhancement factor, β, is approximately 3,078 when the gap for field emission is 0.6 μm, as measured with a nanomanipulator in a scanning electron microscope.

Generation of macroscopic magnetic-field-aligned electric fields by the convection surge ion acceleratiom mechanism

International Nuclear Information System (INIS)

Mauk, B.H.

1989-01-01

The ''convection surge'' computer model presented previously (concerning the dramatic, nonadiabatic, magnetic-field-aligned energization of ions near the Earth's geosynchronous orbit in the presence of strong, transient, magnetic-field-perpendicular inductive electric fields) has been extended to include the self-consistent generation of magnetic-field-aligned electric fields. The field-aligned electric potential is obtained by imposing the quasi-neutrality condition using approximated electron distribution forms. The ions are forced to respond self-consistently to this potential. It is found that field-aligned potential drops up to 1 to 10 kV can be generated depending on electron temperatures and on the mass species of the ions. During transient periods of the process, these large potential drops can be confined to a few degrees of magnetic latitude at positions close to the magnetic equator. Anomalous, sometimes dramatic, additional magnetic-field-aligned ion acceleration also occurs in part as a result of a quasi-resonance between the parallel velocities of some ions and the propagating electric potential fronts. It is speculated that the convection surge mechanism could be a key player in the transient, field-aligned electromagnetic processes observed to operate within the middle (e.g., geosynchronous) magnetosphere. copyright American Geophysical Union 1989

Adiabatic, diabatic field-free and dressed molecular bases in a semiclassical treatment of laser induced transitions near pseudocrossings

Energy Technology Data Exchange (ETDEWEB)

Errea, L.F.; Mendez, L.; Riera, A.

1986-07-15

We study the characteristics of charge exchange processes in ion--atom collisions, induced by a strong laser field whose wavelength is resonant to the splitting at a pseudocrossing of two molecular adiabatic energies, where the transition dipole has a sharp maximum. To calculate the charge exchange cross section we use a semiclassical approach and a molecular expansion for the electronic wave function. Using the formalism of Macias and Riera, and of Ho, Chu, and Laughlin, the properties and practical advantages of field-free and dressed molecular wave functions in that expansion are studied in detail. In practice we have found the former basis to be more advantageous from the computational point of view. A limitation of the Floquet approach of Ho et al. is obtained. As an illustration, we treat O/sup 8 +/+H(1s) charge exchange collisions in presence of a laser field whose frequency is quasiresonant with the energy splitting at the pseudocrossing between the 7isigma and the 6hsigma energy curves. The importance of the (usually neglected) diagonal ac Stark terms is stressed.

Adiabatic, diabatic field-free and dressed molecular bases in a semiclassical treatment of laser induced transitions near pseudocrossings

International Nuclear Information System (INIS)

Errea, L.F.; Mendez, L.; Riera, A.

1986-01-01

We study the characteristics of charge exchange processes in ion--atom collisions, induced by a strong laser field whose wavelength is resonant to the splitting at a pseudocrossing of two molecular adiabatic energies, where the transition dipole has a sharp maximum. To calculate the charge exchange cross section we use a semiclassical approach and a molecular expansion for the electronic wave function. Using the formalism of Macias and Riera, and of Ho, Chu, and Laughlin, the properties and practical advantages of field-free and dressed molecular wave functions in that expansion are studied in detail. In practice we have found the former basis to be more advantageous from the computational point of view. A limitation of the Floquet approach of Ho et al. is obtained. As an illustration, we treat O 8+ +H(1s) charge exchange collisions in presence of a laser field whose frequency is quasiresonant with the energy splitting at the pseudocrossing between the 7isigma and the 6hsigma energy curves. The importance of the (usually neglected) diagonal ac Stark terms is stressed

Alignment-free genome tree inference by learning group-specific distance metrics.

Science.gov (United States)

Patil, Kaustubh R; McHardy, Alice C

2013-01-01

Understanding the evolutionary relationships between organisms is vital for their in-depth study. Gene-based methods are often used to infer such relationships, which are not without drawbacks. One can now attempt to use genome-scale information, because of the ever increasing number of genomes available. This opportunity also presents a challenge in terms of computational efficiency. Two fundamentally different methods are often employed for sequence comparisons, namely alignment-based and alignment-free methods. Alignment-free methods rely on the genome signature concept and provide a computationally efficient way that is also applicable to nonhomologous sequences. The genome signature contains evolutionary signal as it is more similar for closely related organisms than for distantly related ones. We used genome-scale sequence information to infer taxonomic distances between organisms without additional information such as gene annotations. We propose a method to improve genome tree inference by learning specific distance metrics over the genome signature for groups of organisms with similar phylogenetic, genomic, or ecological properties. Specifically, our method learns a Mahalanobis metric for a set of genomes and a reference taxonomy to guide the learning process. By applying this method to more than a thousand prokaryotic genomes, we showed that, indeed, better distance metrics could be learned for most of the 18 groups of organisms tested here. Once a group-specific metric is available, it can be used to estimate the taxonomic distances for other sequenced organisms from the group. This study also presents a large scale comparison between 10 methods--9 alignment-free and 1 alignment-based.

Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer.

Directory of Open Access Journals (Sweden)

Raquel Bromberg

2016-06-01

Full Text Available Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz.

Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer

Science.gov (United States)

Grishin, Nick V.; Otwinowski, Zbyszek

2016-01-01

Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz. PMID:27336403

Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers.

Science.gov (United States)

Galpert, Deborah; Fernández, Alberto; Herrera, Francisco; Antunes, Agostinho; Molina-Ruiz, Reinaldo; Agüero-Chapin, Guillermin

2018-05-03

The development of new ortholog detection algorithms and the improvement of existing ones are of major importance in functional genomics. We have previously introduced a successful supervised pairwise ortholog classification approach implemented in a big data platform that considered several pairwise protein features and the low ortholog pair ratios found between two annotated proteomes (Galpert, D et al., BioMed Research International, 2015). The supervised models were built and tested using a Saccharomycete yeast benchmark dataset proposed by Salichos and Rokas (2011). Despite several pairwise protein features being combined in a supervised big data approach; they all, to some extent were alignment-based features and the proposed algorithms were evaluated on a unique test set. Here, we aim to evaluate the impact of alignment-free features on the performance of supervised models implemented in the Spark big data platform for pairwise ortholog detection in several related yeast proteomes. The Spark Random Forest and Decision Trees with oversampling and undersampling techniques, and built with only alignment-based similarity measures or combined with several alignment-free pairwise protein features showed the highest classification performance for ortholog detection in three yeast proteome pairs. Although such supervised approaches outperformed traditional methods, there were no significant differences between the exclusive use of alignment-based similarity measures and their combination with alignment-free features, even within the twilight zone of the studied proteomes. Just when alignment-based and alignment-free features were combined in Spark Decision Trees with imbalance management, a higher success rate (98.71%) within the twilight zone could be achieved for a yeast proteome pair that underwent a whole genome duplication. The feature selection study showed that alignment-based features were top-ranked for the best classifiers while the runners-up were

Molecular alignment dependent electron interference in attosecond ultraviolet photoionization

Directory of Open Access Journals (Sweden)

Kai-Jun Yuan

2015-01-01

Full Text Available We present molecular photoionization processes by intense attosecond ultraviolet laser pulses from numerical solutions of time-dependent Schrödinger equations. Simulations preformed on a single electron diatomic H2+ show minima in molecular photoelectron energy spectra resulting from two center interference effects which depend strongly on molecular alignment. We attribute such sensitivity to the spatial orientation asymmetry of the photoionization process from the two nuclei. A similar influence on photoelectron kinetic energies is also presented.

Molecular alignment dependent electron interference in attosecond ultraviolet photoionization

Science.gov (United States)

Yuan, Kai-Jun; Bandrauk, André D.

2015-01-01

We present molecular photoionization processes by intense attosecond ultraviolet laser pulses from numerical solutions of time-dependent Schrödinger equations. Simulations preformed on a single electron diatomic H2+ show minima in molecular photoelectron energy spectra resulting from two center interference effects which depend strongly on molecular alignment. We attribute such sensitivity to the spatial orientation asymmetry of the photoionization process from the two nuclei. A similar influence on photoelectron kinetic energies is also presented. PMID:26798785

STAR/SVT alignment within a finite magnetic field

International Nuclear Information System (INIS)

Barannikova, O.Yu.; Belaga, V.V.; Ososkov, G.A.; Panebrattsev, Yu.A.; Bellweid, R.K.; Pruneau, C.A.; Wilson, W.K.

1999-01-01

We report on the development of SVT (Silicon Vertex Tracker) software for the purpose of the SVT and TPC (Time Projection Chamber) relative alignment as well as the internal alignment of the SVT components. The alignment procedure described complements the internal SVT alignment procedure discussed in Star Note 356. It involves track reconstruction in both the Star TPC and SVT for the calibration of the SVT geometry in the presence of a finite magnetic field. This new software has been integrated under the package SAL already running under STAR. Both the implementation and the performance of the alignment algorithm are described. We find that the current software implementation in SAL should enable a very satisfactory internal SVT alignment as well as an excellent SVT to TPC relative alignment

K2 and K2*: efficient alignment-free sequence similarity measurement based on Kendall statistics.

Science.gov (United States)

Lin, Jie; Adjeroh, Donald A; Jiang, Bing-Hua; Jiang, Yue

2018-05-15

Alignment-free sequence comparison methods can compute the pairwise similarity between a huge number of sequences much faster than sequence-alignment based methods. We propose a new non-parametric alignment-free sequence comparison method, called K2, based on the Kendall statistics. Comparing to the other state-of-the-art alignment-free comparison methods, K2 demonstrates competitive performance in generating the phylogenetic tree, in evaluating functionally related regulatory sequences, and in computing the edit distance (similarity/dissimilarity) between sequences. Furthermore, the K2 approach is much faster than the other methods. An improved method, K2*, is also proposed, which is able to determine the appropriate algorithmic parameter (length) automatically, without first considering different values. Comparative analysis with the state-of-the-art alignment-free sequence similarity methods demonstrates the superiority of the proposed approaches, especially with increasing sequence length, or increasing dataset sizes. The K2 and K2* approaches are implemented in the R language as a package and is freely available for open access (http://community.wvu.edu/daadjeroh/projects/K2/K2_1.0.tar.gz). yueljiang@163.com. Supplementary data are available at Bioinformatics online.

Orbital free molecular dynamics; Approche sans orbitale des plasmas denses

Energy Technology Data Exchange (ETDEWEB)

Lambert, F

2007-08-15

The microscopic properties of hot and dense plasmas stay a field essentially studied thanks to classical theories like the One Component Plasma, models which rely on free parameters, particularly ionization. In order to investigate these systems, we have used, in this PhD work, a semi-classical model, without free parameters, that is based on coupling consistently classical molecular dynamics for the nuclei and orbital free density functional theory for the electrons. The electronic fluid is represented by a free energy entirely determined by the local density. This approximation was validated by a comparison with an ab initio technique, quantum molecular dynamics. This one is identical to the previous except for the description of the free energy that depends on a quantum-independent-particle model. Orbital free molecular dynamics was then used to compute equation of state of boron and iron plasmas in the hot and dense regime. Furthermore, comparisons with classical theories were performed on structural and dynamical properties. Finally, equation of state and transport coefficients mixing laws were studied by direct simulation of a plasma composed of deuterium and copper. (author)

Earle K. Plyler Prize Lecture: The Three Pillars of Ultrafast Molecular Science - Time, Phase, Intensity

Science.gov (United States)

Stolow, Albert

We discuss the probing and control of molecular wavepacket dynamics in the context of three main `pillars' of light-matter interaction: time, phase, intensity. Time: Using short, coherent laser pulses and perturbative matter-field interactions, we study molecular wavepackets with a focus on the ultrafast non-Born-Oppenheimer dynamics, that is, the coupling of electronic and nuclear motions. Time-Resolved Photoelectron Spectroscopy (TRPES) is a powerful ultrafast probe of these processes in polyatomic molecules because it is sensitive both electronic and vibrational dynamics. Ideally, one would like to observe these ultrafast processes from the molecule's point of view - the Molecular Frame - thereby avoiding loss of information due to orientational averaging. This can be achieved by Time-Resolved Coincidence Imaging Spectroscopy (TRCIS) which images 3D recoil vectors of both photofragments and photoelectrons, in coincidence and as a function of time, permitting direct Molecular Frame imaging of valence electronic dynamics during a molecular dynamics. Phase: Using intermediate strength non-perturbative interactions, we apply the second order (polarizability) Non-Resonant Dynamic Stark Effect (NRDSE) to control molecular dynamics without any net absorption of light. NRDSE is also the interaction underlying molecular alignment and applies to field-free 1D of linear molecules and field-free 3D alignment of general (asymmetric) molecules. Using laser alignment, we can transiently fix a molecule in space, yielding a more general approach to direct Molecular Frame imaging of valence electronic dynamics during a chemical reaction. Intensity: In strong (ionizing) laser fields, a new laser-matter physics emerges for polyatomic systems wherein both the single active electron picture and the adiabatic electron response, both implicit in the standard 3-step models, can fail dramatically. This has important consequences for all attosecond strong field spectroscopies of

First principles molecular dynamics without self-consistent field optimization

International Nuclear Information System (INIS)

Souvatzis, Petros; Niklasson, Anders M. N.

2014-01-01

We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations

Field emission from vertically aligned few-layer graphene

International Nuclear Information System (INIS)

Malesevic, Alexander; Kemps, Raymond; Vanhulsel, Annick; Chowdhury, Manish Pal; Volodin, Alexander; Van Haesendonck, Chris

2008-01-01

The electric field emission behavior of vertically aligned few-layer graphene was studied in a parallel plate-type setup. Few-layer graphene was synthesized in the absence of any metallic catalyst by microwave plasma enhanced chemical vapor deposition with gas mixtures of methane and hydrogen. The deposit consists of nanostructures that are several micrometers wide, highly crystalline stacks of four to six atomic layers of graphene, aligned vertically to the substrate surface in a high density network. The few-layer graphene is found to be a good field emitter, characterized by turn-on fields as low as 1 V/μm and field amplification factors up to several thousands. We observe a clear dependence of the few-layer graphene field emission behavior on the synthesis parameters: Hydrogen is identified as an efficient etchant to improve field emission, and samples grown on titanium show lower turn-on field values and higher amplification factors when compared to samples grown on silicon

GRAIN ALIGNMENT INDUCED BY RADIATIVE TORQUES: EFFECTS OF INTERNAL RELAXATION OF ENERGY AND COMPLEX RADIATION FIELD

International Nuclear Information System (INIS)

Hoang, Thiem; Lazarian, A.

2009-01-01

Earlier studies of grain alignment dealt mostly with interstellar grains that have strong internal relaxation of energy which aligns the grain axis of maximum moment of inertia (the axis of major inertia) with respect to the grain's angular momentum. In this paper, we study the alignment by radiative torques for large irregular grains, e.g., grains in accretion disks, for which internal relaxation is subdominant. We use both numerical calculations and the analytical model of a helical grain introduced by us earlier. We demonstrate that grains in such a regime exhibit more complex dynamics. In particular, if initially the grain axis of major inertia makes a small angle with angular momentum, then radiative torques can align the grain axis of major inertia with angular momentum, and both the axis of major inertia and angular momentum are aligned with the magnetic field when attractors with high angular momentum (high-J attractors) are available. For alignment without high-J attractors, beside the earlier studied attractors with low angular momentum (low-J attractors), there appear new low-J attractors. In addition, we also study the alignment of grains in the presence of strong internal relaxation, but induced not by a radiation beam as in earlier studies but instead induced by a complex radiation field that can be decomposed into dipole and quadrupole components. We found that in this situation the parameter space q max , for which high-J attractors exist in trajectory maps, is more extended, resulting in the higher degree of polarization expected. Our results are useful for modeling polarization arising from aligned dust grains in molecular clouds.

Merging of magnetic fields with field-aligned plasma flow components

International Nuclear Information System (INIS)

Mitchell, H.G. Jr.; Kan, J.R.

1978-01-01

The Sonnerup merging model for an incompressible plasma is extended to allow a flow component along the field lines in the inflow regions. Solutions are found to exist as long as the difference between the quantities B. V for the two inflow regions does not exceed a critical magnitude dependent on the inflow field magnitudes and plasma densities. All such solutions satisfy Vasyliunas' definition of merging, but some classes of solution have radically altered geometries, i.e. geometries in which the inflow regions are much smaller than the outflow regions. The necessary but not sufficient condition for these unusual geometries is that the field-aligned flow component in at least one inflow region be super-Alfvenic. A solution for the case of a vacuum field in one inflow region is obtained in which any flow velocity is allowed in the non-vacuum inflow region, although super-Alfvenic flow can still result in an unusual geometry. For symmetric configurations, the usual geometry, that of Petschek and Sonnerup, is retained as long as both field-aligned flow components in the inflow regions are less than twice the inflow Alfven speed. For the case of a vacuum field on one side and fields approximating the boundary between the solar wind and the earth's dayside magnetosphere, the usual geometry is retained for flow less than about 2.5 times the local Alfven speed. (author)

Multiorbital effects in strong-field ionization and dissociation of aligned polar molecules CH3I and CH3Br

Science.gov (United States)

Luo, Sizuo; Zhou, Shushan; Hu, Wenhui; Li, Xiaokai; Ma, Pan; Yu, Jiaqi; Zhu, Ruihan; Wang, Chuncheng; Liu, Fuchun; Yan, Bing; Liu, Aihua; Yang, Yujun; Guo, Fuming; Ding, Dajun

2017-12-01

Controlling the molecular axis offers additional ways to study molecular ionization and dissociation in strong laser fields. We measure the ionization and dissociation yields of aligned polar CH3X (X =I , Br) molecules in a linearly polarized femtosecond laser field. The current data show that maximum ionization occurs when the laser polarization is perpendicular to the molecular C -X axis, and dissociation prefers to occur at the laser polarization parallel to the C -X axis. The observed angular distributions suggest that the parent ions are generated by ionization from the HOMO. The angular distribution of fragment ions indicates that dissociation occurs mainly from an ionic excited state produced by ionization from the HOMO-1.

Acceleration of auroral particles by magnetic-field aligned electric fields

International Nuclear Information System (INIS)

Block, L.P.

1988-01-01

Measurements on the S3-3 and Viking satellites appear to show that at least a large fraction of magnetic field-aligned potential drops are made up of multiple double layers. Solitons and double layers in U-shaped potential structures give rise to spiky electric fields also perpendicular to the magnetic field in agreement with satellite measurements. The large scale potential structures associated with inverted V-events are built up of many similar short-lived structures on a small scale. Viking measurements indicate that electric fields parallel to the magnetic field are almost always directed upward

Vertically aligned carbon nanotube field-effect transistors

KAUST Repository

Li, Jingqi; Zhao, Chao; Wang, Qingxiao; Zhang, Qiang; Wang, Zhihong; Zhang, Xixiang; Abutaha, Anas I.; Alshareef, Husam N.

2012-01-01

Vertically aligned carbon nanotube field-effect transistors (CNTFETs) have been developed using pure semiconducting carbon nanotubes. The source and drain were vertically stacked, separated by a dielectric, and the carbon nanotubes were placed

Alfven Wave Reflection Model of Field-Aligned Currents at Mercury

Science.gov (United States)

Lyatsky, Wladislaw; Khazanov, George V.; Slavin, James

2010-01-01

An Alfven Wave Reflection (AWR) model is proposed that provides closure for strong field-aligned currents (FACs) driven by the magnetopause reconnection in the magnetospheres of planets having no significant ionospheric and surface electrical conductance. The model is based on properties of the Alfven waves, generated at high altitudes and reflected from the low-conductivity surface of the planet. When magnetospheric convection is very slow, the incident and reflected Alfven waves propagate along approximately the same path. In this case, the net field-aligned currents will be small. However, as the convection speed increases. the reflected wave is displaced relatively to the incident wave so that the incident and reflected waves no longer compensate each other. In this case, the net field-aligned current may be large despite the lack of significant ionospheric and surface conductivity. Our estimate shows that for typical solar wind conditions at Mercury, the magnitude of Region 1-type FACs in Mercury's magnetosphere may reach hundreds of kilo-Amperes. This AWR model of field-aligned currents may provide a solution to the long-standing problem of the closure of FACs in the Mercury's magnetosphere. c2009 Elsevier Inc. All rights reserved.

Generation mechanisms for magnetic-field-aligned electric fields in the magnetosphere

International Nuclear Information System (INIS)

Faelthammar, C.-G.

1977-09-01

Magnetic-field-aligned electric fields in the magnetosphere can be generated in several different ways, and in this review some possible mechanisms are presented. Observational data now available indicates that more than one of the mechanisms mentioned are operative in the magnetosphere but it is not yet possible to evaluate their relative importance. (author)

Alignment-free phylogeny of whole genomes using underlying subwords

Directory of Open Access Journals (Sweden)

Comin Matteo

2012-12-01

Full Text Available Abstract Background With the progress of modern sequencing technologies a large number of complete genomes are now available. Traditionally the comparison of two related genomes is carried out by sequence alignment. There are cases where these techniques cannot be applied, for example if two genomes do not share the same set of genes, or if they are not alignable to each other due to low sequence similarity, rearrangements and inversions, or more specifically to their lengths when the organisms belong to different species. For these cases the comparison of complete genomes can be carried out only with ad hoc methods that are usually called alignment-free methods. Methods In this paper we propose a distance function based on subword compositions called Underlying Approach (UA. We prove that the matching statistics, a popular concept in the field of string algorithms able to capture the statistics of common words between two sequences, can be derived from a small set of “independent” subwords, namely the irredundant common subwords. We define a distance-like measure based on these subwords, such that each region of genomes contributes only once, thus avoiding to count shared subwords a multiple number of times. In a nutshell, this filter discards subwords occurring in regions covered by other more significant subwords. Results The Underlying Approach (UA builds a scoring function based on this set of patterns, called underlying. We prove that this set is by construction linear in the size of input, without overlaps, and can be efficiently constructed. Results show the validity of our method in the reconstruction of phylogenetic trees, where the Underlying Approach outperforms the current state of the art methods. Moreover, we show that the accuracy of UA is achieved with a very small number of subwords, which in some cases carry meaningful biological information. Availability http://www.dei.unipd.it/∼ciompin/main/underlying.html

Beam alignment based on two-dimensional power spectral density of a near-field image.

Science.gov (United States)

Wang, Shenzhen; Yuan, Qiang; Zeng, Fa; Zhang, Xin; Zhao, Junpu; Li, Kehong; Zhang, Xiaolu; Xue, Qiao; Yang, Ying; Dai, Wanjun; Zhou, Wei; Wang, Yuanchen; Zheng, Kuixing; Su, Jingqin; Hu, Dongxia; Zhu, Qihua

2017-10-30

Beam alignment is crucial to high-power laser facilities and is used to adjust the laser beams quickly and accurately to meet stringent requirements of pointing and centering. In this paper, a novel alignment method is presented, which employs data processing of the two-dimensional power spectral density (2D-PSD) for a near-field image and resolves the beam pointing error relative to the spatial filter pinhole directly. Combining this with a near-field fiducial mark, the operation of beam alignment is achieved. It is experimentally demonstrated that this scheme realizes a far-field alignment precision of approximately 3% of the pinhole size. This scheme adopts only one near-field camera to construct the alignment system, which provides a simple, efficient, and low-cost way to align lasers.

Design of a magnetic field alignment diagnostic for the MFTF-B magnet system

International Nuclear Information System (INIS)

Deadrick, F.J.; House, P.A.; Frye, R.W.

1985-01-01

Magnet alignment in tandem mirror fusion machines plays a crucial role in achieving and maintaining plasma confinement. Various visual alignment tools have been described by Post et al. to align the Tara magnet system. We have designed and installed a remotely operated magnetic field alignment (MFA) diagnostic system as a part of the Mirror Fusion Test Facility (MFTF-B). It measures critical magnetic field alignment parameters of the MFTF-B coil set while under full-field operating conditions. The MFA diagnostic employs a pair of low-energy, electron beam guns on a remotely positionable probe to trace and map selected magnetic field lines. An array of precision electrical detector paddles locates the position of the electron beam, and thus the magnetic field line, at several critical points. The measurements provide a means to compute proper compensating currents to correct for mechanical misalignments of the magnets with auxiliary trim coils if necessary. This paper describes both the mechanical and electrical design of the MFA diagnostic hardware

Shape resonances in molecular fields

International Nuclear Information System (INIS)

Dehmer, J.L.

1984-01-01

A shape resonance is a quasibound state in which a particle is temporarily trapped by a potential barrier (i.e., the shape of the potential), through which it may eventually tunnel and escape. This simple mechanism plays a prominent role in a variety of excitation processes in molecules, ranging from vibrational excitation by slow electrons to ionization of deep core levels by x-rays. Moreover, their localized nature makes shape resonances a unifying link between otherwise dissimilar circumstances. One example is the close connection between shape resonances in electron-molecule scattering and in molecular photoionization. Another is the frequent persistence of free-molecule shape resonant behavior upon adsorption on a surface or condensation into a molecular solid. The main focus of this article is a discussion of the basic properties of shape resonances in molecular fields, illustrated by the more transparent examples studied over the last ten years. Other aspects to be discussed are vibrational effects of shape resonances, connections between shape resonances in different physical settings, and examples of shape resonant behavior in more complex cases, which form current challenges in this field

Quality for quantum free fields

International Nuclear Information System (INIS)

Leyland, Pen; Roberts, John; Testard, Daniel; Centre National de la Recherche Scientifique, 13 - Marseille

1978-07-01

A proof is given concerning duality for the free neutral scalar boson field (abstract duality). Then real subspaces of a complex Hilbert space and the Von Neumann algebra associated with real subspaces are considered. Lastly duality for free fields (free electromagnetic field and free scalar field of any mass) is studied

Rabi oscillations in the dissociative continuum: Rotation and alignment effects

Science.gov (United States)

Granucci, Giovanni; Magnier, Sylvie; Persico, Maurizio

2002-01-01

We have simulated a set of experiments in which Rabi oscillations are induced in bound-free and free-free transitions of a diatomic molecule. Dissociative vibrational states belonging to different electronic terms are involved. We show analytically and confirm computationally that a simple relationship exists between the one-dimensional dynamics of a molecule with fixed orientation with respect to the polarization of the radiation field and the three-dimensional dynamics of a rotating system. It is demonstrated that sufficiently short laser pulses can induce oscillations in the probabilities of two coupled electronic states, and in the yields of the respective dissociation products, as functions of the radiation intensity. As a result of molecular rotation the oscillations are damped but not washed out. The initial thermal distribution on several rotational levels has a negligible effect on the photodissociation yields and other experimentally relevant quantities. Since the molecule undergoes a strong alignment along the polarization axis of the laser field, the ejection of atoms and ions is anisotropic. We have chosen the well known diatomic ion Na2+ as a convenient example.

Conductance of Conjugated Molecular Wires: Length Dependence, Anchoring Groups, and Band Alignment

DEFF Research Database (Denmark)

Peng, Guowen; Strange, Mikkel; Thygesen, Kristian Sommer

2009-01-01

, is not solely determined by the intrinsic band gap of the molecular wire but also depends on the anchoring group. This is because the alignment of the metal Fermi level with respect to the molecular levels is controlled by charge transfer and interface dipoles which in turn are determined by the local chemistry...

The role of magnetic-field-aligned electric fields in auroral acceleration

International Nuclear Information System (INIS)

Block, L.P.; Faelthammar, C.G.

1990-01-01

Electric field measurements on the Swedish satellite Viking have confirmed and extended earlier observations on S3-3 and provided further evidence of the role of dc electric fields in auroral acceleration processes. On auroral magnetic field lines the electric field is strongly fluctuating both transverse and parallel to the magnetic field. The significance of these fluctuations for the auroral acceleration process is discussed. A definition of dc electric fields is given in terms of their effects on charged particles. Fluctuations below several hertz are experienced as dc by typical auroral electrons if the acceleration length is a few thousand kilometers. For ions the same is true below about 0.1 Hz. The magnetic-field-aligned (as well as the transverse) component of the electric field fluctuations has a maximum below 1 Hz, in a frequency range that appears as dc to the electrons but not to the ions. This allows it to cause a selective acceleration, which may be important in explaining some of the observed characteristics of auroral particle distributions. The electric field observations on Viking support the conclusion that magnetic-field-aligned potential drops play an important role in auroral acceleration, in good agreement with particle observations boht on Viking and on the DE satellites. They also show that a large part, or even all, of the accelerating potential drop may be accounted for by numerous weak (about a volt) electric double layers, in agreement with earlier observations on the S3-3 satellite and with an early theoretical suggestion by L. Block

Free radicals. High-resolution spectroscopy and molecular structure

International Nuclear Information System (INIS)

Hirota, E.

1983-01-01

High-resolution, high-sensitivity spectroscopy using CW laser and microwave sources has been applied to free radicals and transient molecules to establish their existence and to explore their properties in detail. The radicals studied were mainly generated by discharge-induced reactions. A few molecules are used as typical examples to illustrate the results so far obtained. The molecular and electronic structures of free radicals, intramolecular motions of large amplitudes in some labile molecules, and metastable electronic states of carbenes are given special emphasis. The significance of the present spectroscopic results in other related fields such as astronomy and atmospheric chemistry is stressed. 4 figures, 3 tables

Correlation between Auroral kilometric radiation and field-aligned currents

International Nuclear Information System (INIS)

Green, J.L.; Saflekos, N.A.; Gurnett, D.A.; Potemra, T.A.

1982-01-01

Simultaneous observations of field-aligned currents (FAC) and auroral kilometric radiation (AKR) are compared from the polar-orbiting satellites Triad and Hawkeye. The Triad observations were restricted to the evening-to-midnight local time sector (1900 to 0100 hours magnetic local time) in the northern hemisphere. This is the region in which the most intense storms of AKR are believed to originate. The Hawkeye observations were restricted to when the satellite was in the AKR emission cone in the northern hemisphere and at radial distances > or =7R/sub E/ (earth radii) to avoid local propagation cutoff effects. A(R/7R/sub E/) 2 normalization to the power flux measurements of the kilometric radiation from Hawkeye is used to take into account the radial dependence of this radiation and to scale all intensity measurements so that they are independent of Hawkeye's position in the emission cone. Integrated field-aligned current intensities from Triad are determined from the observed transverse magnetic field disturbances. There appears to be a weak correlation between AKR intensity and the integrated current sheet intensity of field-aligned currents. In general, as the intensity of auroral kilometric radiation increases so does the integrated auroral zone current sheet intensity increase. Statistically, the linear correlation coefficient between the log of the AKR power flux and the log of the current sheet intensity is 0.57. During weak AKR bursts ( - 18 W m - 2 Hz - 1 ), Triad always observed weak FAC'S ( - 1 ), and when Triad observed large FAC's (> or =0.6 A m - 1 ), the AKR intensity from Hawkeye was moderately intense (10 - 5 to 10 - 14 W m - 2 Hz - 1 ) to intense (>10 - 14 W m - 2 Hz - 1 ). It is not clear from these preliminary results what the exact role is that auroral zone field-aligned currents play in the generation or amplification of auroral kilometric radiation

Molecular structure determination from x-ray scattering patterns of laser-aligned symmetric-top molecules

International Nuclear Information System (INIS)

Ho, P. J.; Starodub, D.; Saldin, D. K.; Shneerson, V. L.; Ourmazd, A.; Santra, R.

2009-01-01

We investigate the molecular structure information contained in the x-ray diffraction patterns of an ensemble of rigid CF 3 Br molecules aligned by an intense laser pulse at finite rotational temperature. The diffraction patterns are calculated at an x-ray photon energy of 20 keV to probe molecular structure at angstrom-scale resolution. We find that a structural reconstruction algorithm based on iterative phase retrieval fails to extract a reliable structure. However, the high atomic number of Br compared with C or F allows each diffraction pattern to be treated as a hologram. Using this approach, the azimuthal projection of the molecular electron density about the alignment axis may be retrieved.

Peptide Free Energy Landscapes Calibrated by Molecular Orbital Calculations

OpenAIRE

Ono, S.; Kuroda, M.; Higo, J.; Kamiya, N.; Nakajima, N.; Nakamura, H.

2002-01-01

Free energy landscapes of peptide conformations werecalibrated by ab initiomolecular orbital calculations, after enhancedconformational sampling using the multicanonical molecular dynamicssimulations. Three different potentials of mean force for an isolateddipeptide were individually obtained using the conventional force fields,AMBER parm94, AMBER parm96, and CHARMm22. Each potential ofmean force was calibrated based on the umbrella sampling algorithm fromthe adiabatic energy map that was cal...

Auroral streamers: characteristics of associated precipitation,convection and field-aligned currents

Directory of Open Access Journals (Sweden)

V. A. Sergeev

2004-01-01

Full Text Available During the long-duration steady convection activity on 11 December 1998, the development of a few dozen auroral streamers was monitored by Polar UVI instrument in the dark northern nightside ionosphere. On many occasions the DMSP spacecraft crossed the streamer-conjugate regions over the sunlit southern auroral oval, permitting the investigation of the characteristics of ion and electron precipitation, ionospheric convection and field-aligned currents associated with the streamers. We confirm the conjugacy of streamer-associated precipitation, as well as their association with ionospheric plasma streams having a substantial equatorward convection component. The observations display two basic types of streamer-associated precipitation. In its polewardmost half, the streamer-associated (field-aligned accelerated electron precipitation coincides with the strong (≥2–7μA/m² upward field-aligned currents on the westward flank of the convection stream, sometimes accompanied by enhanced proton precipitation in the adjacent region. In the equatorward portion of the streamer, the enhanced precipitation includes both electrons and protons, often without indication of field-aligned acceleration. Most of these characteristics are consistent with the model describing the generation of the streamer by the narrow plasma bubbles (bursty bulk flows which are contained on dipolarized field lines in the plasma sheet, although the mapping is strongly distorted which makes it difficult to quantitatively interprete the ionospheric image. The convective streams in the ionosphere, when well-resolved, had the maximal convection speeds ∼0.5–1km/s, total field-aligned currents of a few tenths of MA, thicknesses of a few hundreds km and a potential drop of a few kV across the stream. However, this might represent only a small part of the associated flux transport in the equatorial plasma sheet.

Key words. Ionosphere (electric fiels and

Theoretically informed Monte Carlo simulation of liquid crystals by sampling of alignment-tensor fields

Energy Technology Data Exchange (ETDEWEB)

Armas-Pérez, Julio C.; Londono-Hurtado, Alejandro [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637 (United States); Guzmán, Orlando [Departamento de Física, Universidad Autónoma Metropolitana, Iztapalapa, DF 09340, México (Mexico); Hernández-Ortiz, Juan P. [Departamento de Materiales y Minerales, Universidad Nacional de Colombia, Sede Medellín, Medellín (Colombia); Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637 (United States); Pablo, Juan J. de, E-mail: depablo@uchicago.edu [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637 (United States); Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)

2015-07-28

A theoretically informed coarse-grained Monte Carlo method is proposed for studying liquid crystals. The free energy functional of the system is described in the framework of the Landau-de Gennes formalism. The alignment field and its gradients are approximated by finite differences, and the free energy is minimized through a stochastic sampling technique. The validity of the proposed method is established by comparing the results of the proposed approach to those of traditional free energy minimization techniques. Its usefulness is illustrated in the context of three systems, namely, a nematic liquid crystal confined in a slit channel, a nematic liquid crystal droplet, and a chiral liquid crystal in the bulk. It is found that for systems that exhibit multiple metastable morphologies, the proposed Monte Carlo method is generally able to identify lower free energy states that are often missed by traditional approaches. Importantly, the Monte Carlo method identifies such states from random initial configurations, thereby obviating the need for educated initial guesses that can be difficult to formulate.

Theoretically informed Monte Carlo simulation of liquid crystals by sampling of alignment-tensor fields.

Energy Technology Data Exchange (ETDEWEB)

Armas-Perez, Julio C.; Londono-Hurtado, Alejandro; Guzman, Orlando; Hernandez-Ortiz, Juan P.; de Pablo, Juan J.

2015-07-27

A theoretically informed coarse-grained Monte Carlo method is proposed for studying liquid crystals. The free energy functional of the system is described in the framework of the Landau-de Gennes formalism. The alignment field and its gradients are approximated by finite differences, and the free energy is minimized through a stochastic sampling technique. The validity of the proposed method is established by comparing the results of the proposed approach to those of traditional free energy minimization techniques. Its usefulness is illustrated in the context of three systems, namely, a nematic liquid crystal confined in a slit channel, a nematic liquid crystal droplet, and a chiral liquid crystal in the bulk. It is found that for systems that exhibit multiple metastable morphologies, the proposed Monte Carlo method is generally able to identify lower free energy states that are often missed by traditional approaches. Importantly, the Monte Carlo method identifies such states from random initial configurations, thereby obviating the need for educated initial guesses that can be difficult to formulate.

On the role of neutral flow in field-aligned currents

Science.gov (United States)

Mannucci, Anthony J.; Verkhoglyadova, Olga P.; Meng, Xing; McGranaghan, Ryan

2018-01-01

In this brief note we explore the role of the neutral atmosphere in magnetosphere-ionosphere coupling. We analyze momentum balance in the ion rest frame to form hypotheses regarding the role of neutral momentum in the lower ionosphere during geomagnetic storms. Neutral momentum that appears in the ion rest frame is likely the result of momentum imparted to ionospheric ions by solar wind flow and the resultant magnetospheric dynamics. The resulting ion-neutral collisions lead to the existence of an electric field. Horizontal electron flow balances the momentum supplied by this electric field. We suggest a possible role played by the neutral atmosphere in generating field-aligned currents due to local auroral heating. Our physical interpretation suggests that thermospheric neutral dynamics plays a complementary role to the high-latitude field-aligned currents and electric fields resulting from magnetospheric dynamics.

The evening diffuse radio aurora, field-aligned currents and particle precipitation

International Nuclear Information System (INIS)

Unwin, R.S.

1980-01-01

The relationship of the afternoon/evening diffuse radio aurora, proton and electron precipitation and field-aligned currents is studied with data from the auroral radar at Slope Point, New Zealand, and the ISIS 2 satellite. It is shown that there is a very close association between the radio aurora and (primarily downward) field-aligned currents, which confirms and extends previous work, but that there is no clear relation with either proton or electron precipitation. (author)

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

Science.gov (United States)

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.

Controlling the alignment of neutral molecules by a strong laser field

DEFF Research Database (Denmark)

Sakai, H.; Hilligsøe, Karen Marie; Hald, K.

1999-01-01

by lowering the initial rotational energy of the molecules or by increasing the laser intensity. The alignment is measured by photodissociating the molecules with a femtosecond laser pulse and detecting the direction of the photofragments by imaging techniques. The strongest degree of alignment observed......A strong nonresonant nanosecond laser pulse is used to align neutral iodine molecules. The technique, applicable to both polar and nonpolar molecules, relies on the interaction between the strong laser field and the induced dipole moment of the molecules. The degree of alignment is enhanced...

The field-aligned currents observed by JIKIKEN

International Nuclear Information System (INIS)

Aoyama, I.; Toyama, F.; Takahashi, T.; Sakurai, T.; Tonegawa, Y.

1979-01-01

New substorm effects on field-aligned current which belongs to a magnetic shell at L asymptotically equals 6 are found in the records from the fluxgate magnetometer on board the scientific satellite, JIKIKEN. The deviation from base line in the magnetometer data seems to be enhanced associating with the substorm onset. (author)

Sequence comparison alignment-free approach based on suffix tree and L-words frequency.

Science.gov (United States)

Soares, Inês; Goios, Ana; Amorim, António

2012-01-01

The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions). In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L-L-words--in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

The influence of conductivities consistent with field-aligned currents on high-latitude convection patterns

International Nuclear Information System (INIS)

Blomberg, L.G.; Marklund, G.T.

1988-02-01

The influence on the high-latitude ionospheric convection of conductivities associated with upward field-aligned currents is investigated. Potential patterns are calculated from a given distribution of field-aligned currents and a conductivity model. The resulting patterns are shown to be modified considerably by including a coupling term between the conductivity and the field-aligned current in the conductivity model. The clockwise rotation of the entire potential pattern is reduced when the conductivity enhancement coincides with the regions of upward field-aligned current. Also, the electric field within these regions turns out to be rather insensitive to change in the magnitude of the current. In regions of downward current or when the current-dependent conductivity is excluded there is on the other hand an almost linear relationship between current and electric field. Although the particles producing the conductivity enhancement may not be the same as those carrying the major part of the field-aligned current it is clear from observations that there is a positive correlation between upward current conductivity. Therefore, the simple relationship used in this study is believed to reflect rather well the principal features of the current-conductivity coupling, which is of im- portance to the modelling of ionospheric electrodynamics. (With 26 refs.) (authors)

On the role of neutral flow in field-aligned currents

Directory of Open Access Journals (Sweden)

A. J. Mannucci

2018-01-01

Full Text Available In this brief note we explore the role of the neutral atmosphere in magnetosphere–ionosphere coupling. We analyze momentum balance in the ion rest frame to form hypotheses regarding the role of neutral momentum in the lower ionosphere during geomagnetic storms. Neutral momentum that appears in the ion rest frame is likely the result of momentum imparted to ionospheric ions by solar wind flow and the resultant magnetospheric dynamics. The resulting ion-neutral collisions lead to the existence of an electric field. Horizontal electron flow balances the momentum supplied by this electric field. We suggest a possible role played by the neutral atmosphere in generating field-aligned currents due to local auroral heating. Our physical interpretation suggests that thermospheric neutral dynamics plays a complementary role to the high-latitude field-aligned currents and electric fields resulting from magnetospheric dynamics.

Planar solar concentrator featuring alignment-free total-internal-reflection collectors and an innovative compound tracker.

Science.gov (United States)

Teng, Tun-Chien; Lai, Wei-Che

2014-12-15

This study proposed a planar solar concentrator featuring alignment-free total-internal-reflection (TIR) collectors and an innovative compound tracker. The compound tracker, combining a mechanical single-axis tracker and scrollable prism sheets, can achieve a performance on a par with dual-axis tracking while reducing the cost of the tracking system and increasing its robustness. The alignment-free TIR collectors are assembled on the waveguide without requiring alignment, so the planar concentrator is relatively easily manufactured and markedly increases the feasibility for use in large concentrators. Further, the identical TIR collector is applicable to various-sized waveguide slab without requiring modification, which facilitates flexibility regarding the size of the waveguide slab. In the simulation model, the thickness of the slab was 2 mm, and its maximal length reached 6 m. With an average angular tolerance of ±0.6°, and after considering both the Fresnel loss and the angular spread of the sun, the simulation indicates that the waveguide concentrator of a 1000-mm length provides the optical efficiencies of 62-77% at the irradiance concentrations of 387-688, and the one of a 2000-mm length provides the optical efficiencies of 52-64.5% at the irradiance concentrations of 645-1148. Alternatively, if a 100-mm horizontally staggered waveguide slab is collocated with the alignment-free TIR collectors, the optical efficiency would be greatly improved up to 91.5% at an irradiance concentration of 1098 (C(geo) = 1200X).

Short-term magnetic field alignment variations of equatorial ionospheric irregularities

International Nuclear Information System (INIS)

Johnson, A.L.

1988-01-01

The ionospheric irregularities that cause equatorial scintillation are elongated along the north-south magnetic field lines. During a 1981 field campaign at Ascension Island, 250-MHz receivers were spaced from 300 m to 1.6 km along the field lines, and the signals received from the Marisat satellite were cross correlated. Data collected during eight nights of fading showed a linear relationship between fading rate and cross correlation. The alignment of the antennas was adjusted to give a zero time lag between the widely spaced receivers with a measurement accuracy of 0.03 s. Since the average irregularity velocity was 125 m/s, this time accuracy translated to an angular measurement accuracy of 0.1 deg. During a 4-hour period of nightly fading, occasional differences in time of arrival were noted that corresponded to a tilt in the north-south alignment of + or - 1 deg. Data from several nights of fading were analyzed, and each night exhibited the same variance in the north-south irregularity alignment. It is postulated that the shift in the measured peak correlation may have been caused by patches of irregularities at different altitudes where the magnetic field lines have a slightly different direction. 13 references

Magnetic Alignment of Block Copolymer Microdomains by Intrinsic Chain Anisotropy.

Science.gov (United States)

Rokhlenko, Yekaterina; Gopinadhan, Manesh; Osuji, Chinedum O; Zhang, Kai; O'Hern, Corey S; Larson, Steven R; Gopalan, Padma; Majewski, Paweł W; Yager, Kevin G

2015-12-18

We examine the role of intrinsic chain susceptibility anisotropy in magnetic field directed self-assembly of a block copolymer using in situ x-ray scattering. Alignment of a lamellar mesophase is observed on cooling across the disorder-order transition with the resulting orientational order inversely proportional to the cooling rate. We discuss the origin of the susceptibility anisotropy, Δχ, that drives alignment and calculate its magnitude using coarse-grained molecular dynamics to sample conformations of surface-tethered chains, finding Δχ≈2×10^{-8}. From field-dependent scattering data, we estimate that grains of ≈1.2  μm are present during alignment. These results demonstrate that intrinsic anisotropy is sufficient to support strong field-induced mesophase alignment and suggest a versatile strategy for field control of orientational order in block copolymers.

Electron re-scattering from aligned linear molecules using the R-matrix method

International Nuclear Information System (INIS)

Harvey, A G; Tennyson, J

2009-01-01

Electron re-scattering in a strong laser field provides an important probe of molecular structure and processes. The laser field drives the ionization of the molecule, followed by acceleration and subsequent recollision of the electron with the parent molecular ion, the scattered electrons carry information about the nuclear geometry and electronic states of the molecular ion. It is advantageous in strong field experiments to work with aligned molecules, which introduces extra physics compared to the standard gas-phase, electron-molecule scattering problem. The formalism for scattering from oriented linear molecules is presented and applied to H 2 and CO 2 . Differential cross sections are presented for (re-)scattering by these systems concentrating on the most common, linear alignment. In H 2 these cross sections show significant angular structure which, particularly for a scattering angle of 90 deg., are predicted to vary significantly between re-collisions stimulated by an even or an odd number of photons. In CO 2 these cross sections are zero indicating the necessity of using non-parallel alignment with this molecule.

Waferscale assembly of Field-Aligned nanotube Networks (FANs)

DEFF Research Database (Denmark)

Dimaki, Maria; Bøggild, Peter

2006-01-01

We demonstrate the integration of nanotube networks on 512 individual devices on a full 4-inch wafer in less than 60 seconds with a roughly 80% yield using dielectrophoresis. We present here investigations of the morphology and electrical resistance of such field aligned networks for different fr...

Sequence Comparison Alignment-Free Approach Based on Suffix Tree and L-Words Frequency

Directory of Open Access Journals (Sweden)

Inês Soares

2012-01-01

Full Text Available The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions. In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L—L-words—in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

Field-aligned currents during northward interplanetary magnetic field: Morphology and causes

DEFF Research Database (Denmark)

Vennerstrøm, Susanne; Moretto, T.; Rastatter, L.

2005-01-01

[1] We present the results of a global MHD simulation of solar wind magnetosphere interaction during northward IMF. In particular, we emphasize the effect of the IMF By component on the reconnection geometry and the mapping along field lines to the polar ionosphere, through field-aligned currents....... We find that the existence and geometry of the polar cap is closely connected to the IMF By component. During strictly northward IMF the simulated magnetosphere can remain essentially closed because the solar wind field lines reconnect in both hemispheres, thereby creating newly reconnected closed...... both on open and closed field lines and are created by the shear of the newly reconnected field lines against the mantle field as they are convected tailward by the solar wind. When the IMF rotates from northward toward east, the magnetospheric mapping regions of the NBZ currents likewise rotates...

IMF By associated interhemispheric asymmetries in ionospheric convection and field-aligned currents

Science.gov (United States)

Kunduri, B.; Baker, J.; Ruohoniemi, J. M.; Clausen, L.; Ribeiro, A.

2012-12-01

The solar wind-magnetosphere interaction plays an important role in controlling the dynamics of ionospheric convection. It is widely known that the By component of IMF generates asymmetries in ionospheric convection between the northern and southern polar caps. Some studies show that IMF By-generated electric field penetrates into the closed magnetosphere producing differences in the high latitude ionospheric convection between hemispheres. The differences in convection were attributed to field-aligned potential drop between hemispheres resulting in flow of interhemispheric field aligned currents. In the current paper we present interhemispheric observations of high latitude ionospheric convection on closed field lines in the noon-dusk sector. The observations reveal that the convection is stronger in the northern (southern) hemisphere when IMF By is positive (negative) irrespective of season. The inter-hemispheric differences can be attributed to the flow of interhemispheric field aligned currents which support the existence of oppositely-directed zonal plasma flows in the closed field line regions, suppressing the convection in one hemisphere and aiding it in the other. We estimate the strength of these currents, analyze their characteristics and identify the various factors such as magnetic local time, magnetic latitude and ionospheric conductivity that impact them.

Field-aligned plasma-potential structure formed by local electron cyclotron resonance

International Nuclear Information System (INIS)

Hatakeyama, Rikizo; Kaneko, Toshiro; Sato, Noriyoshi

2001-01-01

The significance of basic experiments on field-aligned plasma-potential structure formed by local electron cyclotron resonance (ECR) is claimed based on the historical development of the investigation on electric double layer and electrostatic potential confinement of open-ended fusion-oriented plasmas. In the presence of a single ECR point in simple mirror-type configurations of magnetic field, a potential dip (thermal barrier) appears around this point, being followed by a subsequent potential hump (plug potential) along a collisionless plasma flow. The observed phenomenon gives a clear-cut physics to the formation of field-aligned plug potential with thermal barrier, which is closely related to the double layer formation triggered by a negative dip. (author)

Free-solution, label-free molecular interactions studied by back-scattering interferometry

DEFF Research Database (Denmark)

Bornhop, D.J.; Latham, J.C.; Kussrow, A.

2007-01-01

Free-solution, label-free molecular interactions were investigated with back-scattering interferometry in a simple optical train composed of a helium-neon laser, a microfluidic channel, and a position sensor. Molecular binding interactions between proteins, ions and protein, and small molecules...... and protein, were determined with high dynamic range dissociation constants (K-d spanning six decades) and unmatched sensitivity (picomolar K-d's and detection limits of 10,000s of molecules). With this technique, equilibrium dissociation constants were quantified for protein A and immunoglobulin G...

Effects of polar field-aligned currents on the distribution of the electric field and current in the middle and low latitudes ionosphere

International Nuclear Information System (INIS)

Maekawa, Koichiro

1978-01-01

According to the analysis of the magnetic records from the Triad satellite, it has been found that there are two regions of the field-aligned current of magnetospheric origin along the auroral oval; Region 1 in higher latitude and Region 2 in lower latitude. These currents seem to have important effect on the distribution of electric field and current in the ionosphere, in addition to the Sq electric field and current of ionospheric origin. The global current systems generated by the field-aligned current were calculated, using some simplified ionospheric models. The effect of the field-aligned current on the distribution of electric field and current of the ionosphere at middle and low latitudes was investigated. (Yoshimori, M.)

Magnetic-field-aligned characteristics of plasma bubbles in the nighttime equatorial ionosphere

International Nuclear Information System (INIS)

Tsunoda, R.T.

1980-01-01

Measurements of both incoherent-scatter (IS) and backscatter from field-aligned irregularities (FAI) were made in 1978 with ALTAIR, a fully-steerable high-power radar, to investigate the magnetic-field-aligned characteristics of equatorial plasma bubbles. By operating the radar in a latitude-scan IS mode it was possible to map the location and percentage depletion of plasma bubbles as a function of altitude. By showing that backscatter from FAI is spatially collocated with the upper wall of plasma bubbles it was possible to use the spatial displacement of a field aligned backscatter region to estimate the upward bubble velocity. Besides showing that plasma bubbles are indeed aligned along magnetic field lines, this data set is used to show that a plasma bubble with a percentage depletion of as much as 90% does not have as large an upward velocity as predicted by two-dimensional models. Instead, the inferred bubble velocity is shown to be in better agreement with the bubble velocity predicted by theoretical models using flux-integrated values of electron density and Pedersen conductivity. The need to use flux-tube-integrated values when comparing theory and observation is further stressed by the presence of a non-uniform latitudinal distribution of electron density (i.e. the equatorial anomaly) that was found in the latitude-scan data. (author)

An atomistic fingerprint algorithm for learning ab initio molecular force fields

Science.gov (United States)

Tang, Yu-Hang; Zhang, Dongkun; Karniadakis, George Em

2018-01-01

Molecular fingerprints, i.e., feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and interatomic force. In this paper, we present the density-encoded canonically aligned fingerprint algorithm, which is robust and efficient, for fitting per-atom scalar and vector quantities. The fingerprint is essentially a continuous density field formed through the superimposition of smoothing kernels centered on the atoms. Rotational invariance of the fingerprint is achieved by aligning, for each fingerprint instance, the neighboring atoms onto a local canonical coordinate frame computed from a kernel minisum optimization procedure. We show that this approach is superior over principal components analysis-based methods especially when the atomistic neighborhood is sparse and/or contains symmetry. We propose that the "distance" between the density fields be measured using a volume integral of their pointwise difference. This can be efficiently computed using optimal quadrature rules, which only require discrete sampling at a small number of grid points. We also experiment on the choice of weight functions for constructing the density fields and characterize their performance for fitting interatomic potentials. The applicability of the fingerprint is demonstrated through a set of benchmark problems.

Scattering of field-aligned beam ions upstream of Earth's bow shock

Directory of Open Access Journals (Sweden)

A. Kis

2007-03-01

Full Text Available Field-aligned beams are known to originate from the quasi-perpendicular side of the Earth's bow shock, while the diffuse ion population consists of accelerated ions at the quasi-parallel side of the bow shock. The two distinct ion populations show typical characteristics in their velocity space distributions. By using particle and magnetic field measurements from one Cluster spacecraft we present a case study when the two ion populations are observed simultaneously in the foreshock region during a high Mach number, high solar wind velocity event. We present the spatial-temporal evolution of the field-aligned beam ion distribution in front of the Earth's bow shock, focusing on the processes in the deep foreshock region, i.e. on the quasi-parallel side. Our analysis demonstrates that the scattering of field-aligned beam (FAB ions combined with convection by the solar wind results in the presence of lower-energy, toroidal gyrating ions at positions deeper in the foreshock region which are magnetically connected to the quasi-parallel bow shock. The gyrating ions are superposed onto a higher energy diffuse ion population. It is suggested that the toroidal gyrating ion population observed deep in the foreshock region has its origins in the FAB and that its characteristics are correlated with its distance from the FAB, but is independent on distance to the bow shock along the magnetic field.

Magnetic field alignment of coil-coil diblock copolymers and blends via intrinsic chain anisotropy

Science.gov (United States)

Rokhlenko, Yekaterina; Majewski, Pawel; Larson, Steven; Yager, Kevin; Gopalan, Padma; Avgeropoulos, Apostolos; Chan, Edwin; Osuji, Chinedum

Magnetic fields can control alignment of self-assembled soft materials such as block copolymers provided there is a suitably large magnetic susceptibility anisotropy present in the system. Recent results have highlighted the existence of a non-trivial intrinsic anisotropy in coil-coil diblock copolymers, specifically in lamellar-forming PS-b-P4VP, which enables alignment at field strengths of a few tesla in systems lacking mesogenic components. Alignment is predicated on correlation in the orientation of end-end vectors implied by the localization of block junctions at the microdomain interface and is observed on cooling across the order-disorder transition in the presence of the field. For appropriate combinations of field strength and grain size, we can leverage intrinsic chain anisotropy to magnetically direct self-assembly of many non-mesogenic systems, including other coil-coil BCPs like PS-b-PDMS and PS-b-PMMA, blends of BCPs of disparate morphologies and MWs, and blends of BCPs with homopolymers. This is noteworthy as blends of PS-b-P4VP with PEO provide a route to form functional materials such as nanoporous films by dissolution of PEO, or aligned ion conduction materials. We survey these various systems using TEM and in-situ X-ray scattering to study the phase behavior and temperature-, time- and field- dependent dynamics of alignment.

Alignment of Gold Nanoparticle-Decorated DNA Origami Nanotubes: Substrate Prepatterning versus Molecular Combing.

Science.gov (United States)

Teschome, Bezu; Facsko, Stefan; Gothelf, Kurt V; Keller, Adrian

2015-11-24

DNA origami has become an established technique for designing well-defined nanostructures with any desired shape and for the controlled arrangement of functional nanostructures with few nanometer resolution. These unique features make DNA origami nanostructures promising candidates for use as scaffolds in nanoelectronics and nanophotonics device fabrication. Consequently, a number of studies have shown the precise organization of metallic nanoparticles on various DNA origami shapes. In this work, we fabricated large arrays of aligned DNA origami decorated with a high density of gold nanoparticles (AuNPs). To this end, we first demonstrate the high-yield assembly of high-density AuNP arrangements on DNA origami adsorbed to Si surfaces with few unbound background nanoparticles by carefully controlling the concentrations of MgCl2 and AuNPs in the hybridization buffer and the hybridization time. Then, we evaluate two methods, i.e., hybridization to prealigned DNA origami and molecular combing in a receding meniscus, with respect to their potential to yield large arrays of aligned AuNP-decorated DNA origami nanotubes. Because of the comparatively low MgCl2 concentration required for the efficient immobilization of the AuNPs, the prealigned DNA origami become mobile and displaced from their original positions, thereby decreasing the alignment yield. This increased mobility, on the other hand, makes the adsorbed origami susceptible to molecular combing, and a total alignment yield of 86% is obtained in this way.

Fluorescence excitation studies of molecular photoionization in external electric fields

International Nuclear Information System (INIS)

Poliakoff, E.D.; Dehmer, J.L.; Parr, A.C.; Leroi, G.E.

1985-01-01

Using molecular nitrogen as an example, we show that fluorescence excitation spectroscopy can be used to measure partial photoionization cross sections of free molecules in external electric fields. The production of the N 2 + (B 2 Σ/sub u/ + ) state was studied and the threshold for this process was found to shift linearly with the square root of the applied field. This behavior is compared with the hydrogenic case and with previously studied systems

Alignment enhancement of a symmetric top molecule by two short laser pulses

DEFF Research Database (Denmark)

Bisgaard, Christer Z; Viftrup, Simon; Stapelfeldt, Henrik

2006-01-01

equation. It is shown that the strongest degree of one-dimensional (single axis) field-free alignment obtainable with a single pulse can be enhanced using the two-pulse sequence in a parallel polarization geometry. The conditions for alignment enhancement are: (1) The second pulse must be sent near...

Examining the Electric Fields of the Evening Equatorial Ionosphere When the Solar Terminator is Aligned and Not Aligned with the Magnetic Meridian

Science.gov (United States)

Eccles, J. V.

2014-12-01

The electric field structure of the equatorial ionosphere near sunset has implications on the development of plasma irregularities. The details of the development of the electric fields are examined using a global ionosphere-electrodynamics model. The results of simulations of simplified conditions show the influence of the arrangement of the solar terminator with the magnetic meridian. The relationships of the Curl-Free mechanism, the Hall Current Divergence mechanism, and the role of the Equatorial Electorjet region control the magnitude and timing of the Prereversal Enhancement of the zonal electric field as well as its altitude profile above the F region bottomside. Realistic conditions for 'equinox' and 'solstice' solar terminator arrangments are presented. The stability of the low-latitude ionosphere has a demonstrated relationship with the solar terminator alignment [Tsunoda, JGR, 1981]. The profile of the vertical and zonal electric field below the bottomside is then examined using the global model to explore the controlling elements of the electric field structure and the growth rates of the Rayleigh-Taylor instability and Collisional Shear instability.Tsunoda, R. T. (1985), Control of the seasonal and longitudinal occurrence of equatorial scintillations by the longitudinal gradient in integrated E region Pedersen conductivity, J. Geophys. Res., 90(A1),447-456, doi:10.1029/JA090iA01p00447.

GraphAlignment: Bayesian pairwise alignment of biological networks

Directory of Open Access Journals (Sweden)

Kolář Michal

2012-11-01

Full Text Available Abstract Background With increased experimental availability and accuracy of bio-molecular networks, tools for their comparative and evolutionary analysis are needed. A key component for such studies is the alignment of networks. Results We introduce the Bioconductor package GraphAlignment for pairwise alignment of bio-molecular networks. The alignment incorporates information both from network vertices and network edges and is based on an explicit evolutionary model, allowing inference of all scoring parameters directly from empirical data. We compare the performance of our algorithm to an alternative algorithm, Græmlin 2.0. On simulated data, GraphAlignment outperforms Græmlin 2.0 in several benchmarks except for computational complexity. When there is little or no noise in the data, GraphAlignment is slower than Græmlin 2.0. It is faster than Græmlin 2.0 when processing noisy data containing spurious vertex associations. Its typical case complexity grows approximately as O(N2.6. On empirical bacterial protein-protein interaction networks (PIN and gene co-expression networks, GraphAlignment outperforms Græmlin 2.0 with respect to coverage and specificity, albeit by a small margin. On large eukaryotic PIN, Græmlin 2.0 outperforms GraphAlignment. Conclusions The GraphAlignment algorithm is robust to spurious vertex associations, correctly resolves paralogs, and shows very good performance in identification of homologous vertices defined by high vertex and/or interaction similarity. The simplicity and generality of GraphAlignment edge scoring makes the algorithm an appropriate choice for global alignment of networks.

Thermal electron acceleration by electric field spikes in the outer radiation belt: generation of field-aligned pitch angle distributions

Science.gov (United States)

Vasko, I.; Agapitov, O. V.; Mozer, F.; Artemyev, A.

2015-12-01

Van Allen Probes observations in the outer radiation belt have demonstrated an abundance non-linear electrostatic stucture called Time Domain Structures (TDS). One of the type of TDS is electrostatic electron-acoustic double layers (DL). Observed DLs are frequently accompanied by field-aligned (bi-directional) pitch angle distributions (PAD) of electrons with energies from hundred eVs up to several keV (rarely up to tens of keV). We perform numerical simulations of the DL interaction with thermal electrons making use of the test particle approach. DL parameters assumed in the simulations are adopted from observations. We show that DLs accelerate thermal electrons parallel to the magnetic field via the electrostatic Fermi mechanism, i.e. due to reflections from DL potential humps. Due to this interaction some fraction of electrons is scattered into the loss cone. The electron energy gain is larger for larger DL scalar potential amplitudes and higher propagation velocities. In addition to the Fermi mechanism electrons can be trapped by DLs in their generation region and accelerated due to transport to higher latitudes. Both mechanisms result in formation of field-aligned PADs for electrons with energies comparable to those found in observations. The Fermi mechanism provides field-aligned PADs for <1 keV electrons, while the trapping mechanism extends field-aligned PADs to higher energy electrons.

Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

Science.gov (United States)

Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

2016-01-01

We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method. PMID:27025410

The sagittal stem alignment and the stem version clearly influence the impingement-free range of motion in total hip arthroplasty: a computer model-based analysis.

Science.gov (United States)

Müller, Michael; Duda, Georg; Perka, Carsten; Tohtz, Stephan

2016-03-01

The component alignment in total hip arthroplasty influences the impingement-free range of motion (ROM). While substantiated data is available for the cup positioning, little is known about the stem alignment. Especially stem rotation and the sagittal alignment influence the position of the cone in relation to the edge of the socket and thus the impingement-free functioning. Hence, the question arises as to what influence do these parameters have on the impingement-free ROM? With the help of a computer model the influence of the sagittal stem alignment and rotation on the impingement-free ROM were investigated. The computer model was based on the CT dataset of a patient with a non-cemented THA. In the model the stem version was set at 10°/0°/-10° and the sagittal alignment at 5°/0°/-5°, which resulted in nine alternative stem positions. For each position, the maximum impingement-free ROM was investigated. Both stem version and sagittal stem alignment have a relevant influence on the impingement-free ROM. In particular, flexion and extension as well as internal and external rotation capability present evident differences. In the position intervals of 10° sagittal stem alignment and 20° stem version a difference was found of about 80° in the flexion and 50° in the extension capability. Likewise, differences were evidenced of up to 72° in the internal and up to 36° in the external rotation. The sagittal stem alignment and the stem torsion have a relevant influence on the impingement-free ROM. To clarify the causes of an impingement or accompanying problems, both parameters should be examined and, if possible, a combined assessment of these factors should be made.

Effect of upflowing field-aligned electron beams on the electron ...

Indian Academy of Sciences (India)

The role of low density upflowing field-aligned electron beams (FEBs) on the growth rate of the electron cyclotron waves at the frequencies r < e, propagating downward in the direction of the Earth's magnetic field, has been analysed in the auroral region at e/e < 1 where e is the plasma frequency and e is the ...

New theoretical approaches to atomic and molecular dynamics triggered by ultrashort light pulses on the atto- to picosecond time scale

International Nuclear Information System (INIS)

Pabst, Stefan Ulf

2013-04-01

The concept of atoms as the building blocks of matter has existed for over 3000 years. A revolution in the understanding and the description of atoms and molecules has occurred in the last century with the birth of quantum mechanics. After the electronic structure was understood, interest in studying the dynamics of electrons, atoms, and molecules increased. However, time-resolved investigations of these ultrafast processes were not possible until recently. The typical time scale of atomic and molecular processes is in the picosecond to attosecond realm. Tremendous technological progress in recent years makes it possible to generate light pulses on these time scales. With such ultrashort pulses, atomic and molecular dynamics can be triggered, watched, and controlled. Simultaneously, the need rises for theoretical models describing the underlying mechanisms. This doctoral thesis focuses on the development of theoretical models which can be used to study the dynamical behavior of electrons, atoms, and molecules in the presence of ultrashort light pulses. Several examples are discussed illustrating how light pulses can trigger and control electronic, atomic, and molecular motions. In the first part of this work, I focus on the rotational motion of asymmetric molecules, which happens on picosecond and femtosecond time scales. Here, the aim is to align all three axes of the molecule as well as possible. To investigate theoretically alignment dynamics, I developed a program that can describe alignment motion ranging from the impulsive to the adiabatic regime. The asymmetric molecule SO 2 is taken as an example to discuss strategies of optimizing 3D alignment without the presence of an external field (i.e., field-free alignment). Field-free alignment is particularly advantageous because subsequent experiments on the aligned molecule are not perturbed by the aligning light pulse. Wellaligned molecules in the gas phase are suitable for diffraction experiments. From the

New theoretical approaches to atomic and molecular dynamics triggered by ultrashort light pulses on the atto- to picosecond time scale

Energy Technology Data Exchange (ETDEWEB)

Pabst, Stefan Ulf

2013-04-15

The concept of atoms as the building blocks of matter has existed for over 3000 years. A revolution in the understanding and the description of atoms and molecules has occurred in the last century with the birth of quantum mechanics. After the electronic structure was understood, interest in studying the dynamics of electrons, atoms, and molecules increased. However, time-resolved investigations of these ultrafast processes were not possible until recently. The typical time scale of atomic and molecular processes is in the picosecond to attosecond realm. Tremendous technological progress in recent years makes it possible to generate light pulses on these time scales. With such ultrashort pulses, atomic and molecular dynamics can be triggered, watched, and controlled. Simultaneously, the need rises for theoretical models describing the underlying mechanisms. This doctoral thesis focuses on the development of theoretical models which can be used to study the dynamical behavior of electrons, atoms, and molecules in the presence of ultrashort light pulses. Several examples are discussed illustrating how light pulses can trigger and control electronic, atomic, and molecular motions. In the first part of this work, I focus on the rotational motion of asymmetric molecules, which happens on picosecond and femtosecond time scales. Here, the aim is to align all three axes of the molecule as well as possible. To investigate theoretically alignment dynamics, I developed a program that can describe alignment motion ranging from the impulsive to the adiabatic regime. The asymmetric molecule SO{sub 2} is taken as an example to discuss strategies of optimizing 3D alignment without the presence of an external field (i.e., field-free alignment). Field-free alignment is particularly advantageous because subsequent experiments on the aligned molecule are not perturbed by the aligning light pulse. Wellaligned molecules in the gas phase are suitable for diffraction experiments. From the

Quantitative analysis of gold nanorod alignment after electric field assisted deposition

NARCIS (Netherlands)

Ahmed, W.; Ahmed, Waqqar; Kooij, Ernst S.; van Silfhout, Arend; Poelsema, Bene

2009-01-01

We have studied the alignment of colloidal gold nanorods, deposited from solution onto well-defined substrates in the presence of an AC electric field generated by micrometer spaced electrodes. The field strengths employed in our experiments are sufficiently large to overcome Brownian motion and

Markov random field based automatic image alignment for electron tomography.

Science.gov (United States)

Amat, Fernando; Moussavi, Farshid; Comolli, Luis R; Elidan, Gal; Downing, Kenneth H; Horowitz, Mark

2008-03-01

We present a method for automatic full-precision alignment of the images in a tomographic tilt series. Full-precision automatic alignment of cryo electron microscopy images has remained a difficult challenge to date, due to the limited electron dose and low image contrast. These facts lead to poor signal to noise ratio (SNR) in the images, which causes automatic feature trackers to generate errors, even with high contrast gold particles as fiducial features. To enable fully automatic alignment for full-precision reconstructions, we frame the problem probabilistically as finding the most likely particle tracks given a set of noisy images, using contextual information to make the solution more robust to the noise in each image. To solve this maximum likelihood problem, we use Markov Random Fields (MRF) to establish the correspondence of features in alignment and robust optimization for projection model estimation. The resulting algorithm, called Robust Alignment and Projection Estimation for Tomographic Reconstruction, or RAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as good as the manual approach by an expert user. We are able to automatically map complete and partial marker trajectories and thus obtain highly accurate image alignment. Our method has been applied to challenging cryo electron tomographic datasets with low SNR from intact bacterial cells, as well as several plastic section and X-ray datasets.

Transient, Small-Scale Field-Aligned Currents in the Plasma Sheet Boundary Layer During Storm Time Substorms

Science.gov (United States)

Nakamura, R.; Sergeev, V. A.; Baumjohann, W.; Plaschke, F.; Magnes, W.; Fischer, D.; Varsani, A.; Schmid, D.; Nakamura, T. K. M.; Russell, C. T.;

Effect of upflowing field-aligned electron beams on the electron ...

Indian Academy of Sciences (India)

Abstract. The role of low density upflowing field-aligned electron beams (FEBs) on the growth rate of the electron cyclotron waves at the frequencies ωr < Ωe, propagating downward in the direction of the Earth's magnetic field, has been analysed in the auroral region at ωe/Ωe < 1 where ωe is the plasma frequency and Ωe is ...

High-order-harmonic generation from H2+ molecular ions near plasmon-enhanced laser fields

Science.gov (United States)

Yavuz, I.; Tikman, Y.; Altun, Z.

2015-08-01

Simulations of plasmon-enhanced high-order-harmonic generation are performed for a H2+ molecular cation near the metallic nanostructures. We employ the numerical solution of the time-dependent Schrödinger equation in reduced coordinates. We assume that the main axis of H2+ is aligned perfectly with the polarization direction of the plasmon-enhanced field. We perform systematic calculations on plasmon-enhanced harmonic generation based on an infinite-mass approximation, i.e., pausing nuclear vibrations. Our simulations show that molecular high-order-harmonic generation from plasmon-enhanced laser fields is possible. We observe the dispersion of a plateau of harmonics when the laser field is plasmon enhanced. We find that the maximum kinetic energy of the returning electron follows 4 Up . We also find that when nuclear vibrations are enabled, the efficiency of the harmonics is greatly enhanced relative to that of static nuclei. However, the maximum kinetic energy 4 Up is largely maintained.

Energy level alignment and molecular conformation at rubrene/Ag interfaces: Impact of contact contaminations on the interfaces

Energy Technology Data Exchange (ETDEWEB)

Sinha, Sumona, E-mail: sumona.net.09@gmail.com [Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064 (India); Wang, C.-H. [National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan (China); Mukherjee, M. [Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064 (India)

2017-07-01

Highlights: • Impact of contact contaminations on the energy level alignment and molecular conformation at rubrene/Ag interfaces. • Adventitious contamination layer was acted as a spacer layer between Ag substrate surface and rubrene molecular layer. • Hole injection barrier height and interface dipole at rubrene/Ag interfaces depend on the cleanliness of Ag substrate. • Molecular conformation as well as orientation controlled by the cleanliness of Ag surface. • Resulted different surface morphology of rubrene thin films on unclean and clean Ag substrate. - Abstract: This paper addresses the impact of electrode contaminations on the interfacial energy level alignment, the molecular conformation, orientation and surface morphology deposited organic film at organic semiconductor/noble metal interfaces by varying of film thickness from sub-monolayer to multilayer, which currently draws significant attention with regard to its application in organic electronics. The UHV clean Ag and unclean Ag were employed as substrate whereas rubrene was used as an organic semiconducting material. The photoelectron spectroscopy (XPS and UPS) was engaged to investigate the evolution of interfacial energetics; polarization dependent near edge x-ray absorption fine structure spectroscopy (NEXAFS) was employed to understand the molecular conformation as well as orientation whereas atomic force microscopy (AFM) was used to investigate the surface morphologies of the films. The adventitious contamination layer was acted as a spacer layer between clean Ag substrate surface and rubrene molecular layer. As a consequence, hole injection barrier height, interface dipole as well as molecular-conformation, molecular-orientation and surface morphology of rubrene thin films were found to depend on the cleanliness of Ag substrate. The results have important inferences about the understanding of the impact of substrate contamination on the energy level alignment, the molecular conformation

A numerical model of ionospheric convection derived from field-aligned currents and the corresponding conductivity

International Nuclear Information System (INIS)

Blomberg, L.G.; Marklund, G.T.

1991-08-01

A numerical model for the calculation of ionospheric convection patterns from given distributions of field-aligned current and ionospheric conductivity is described. The model includes a coupling between the conductivity and the field-aligned current, so that the conductivity peaks in regions of upward current, as is usually observed by measurements. The model is very flexible in that the input distributions, the field-aligned current and the conductivity, have been parametrized in a convenient way. From the primary model output, namely the ionospheric electrostatic potential (or convection) in the corotating frame, a number of other quantities can be computed. These include; the potential in the inertial frame (the transformation takes into account the non-alignment of the Earths magnetic and geographic axes), the potential in the magnetospheric equatorial plane (projected using either a dipole magnetic field model or the Tsyganenko-Usmanov model, and the assumption of either vanishing parallel electric field or a proportionality between parallel potential and upward field-aligned current), the distribution of ionospheric (horizontal) current, and the Joule heating in the ionosphere. This model has been used together with a new snapshot technique to calculate the high-latitude potential distribution prevailing during a particular event by combining information from global auroral images and local measurements of fields and particles. The model potential variation along the satellite orbit was found to be in excellent agreement with that calculated from the measured electric field. The model has also been used to study some fundamental properties of the electrodynamics of the high-latitude ionosphere. The results of these different applications of the model have been published separately. (au) (39 refs.)

Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria.

Science.gov (United States)

Padial, José M; Grant, Taran; Frost, Darrel R

2014-06-26

Brachycephaloidea is a monophyletic group of frogs with more than 1000 species distributed throughout the New World tropics, subtropics, and Andean regions. Recently, the group has been the target of multiple molecular phylogenetic analyses, resulting in extensive changes in its taxonomy. Here, we test previous hypotheses of phylogenetic relationships for the group by combining available molecular evidence (sequences of 22 genes representing 431 ingroup and 25 outgroup terminals) and performing a tree-alignment analysis under the parsimony optimality criterion using the program POY. To elucidate the effects of alignment and optimality criterion on phylogenetic inferences, we also used the program MAFFT to obtain a similarity-alignment for analysis under both parsimony and maximum likelihood using the programs TNT and GARLI, respectively. Although all three analytical approaches agreed on numerous points, there was also extensive disagreement. Tree-alignment under parsimony supported the monophyly of the ingroup and the sister group relationship of the monophyletic marsupial frogs (Hemiphractidae), while maximum likelihood and parsimony analyses of the MAFFT similarity-alignment did not. All three methods differed with respect to the position of Ceuthomantis smaragdinus (Ceuthomantidae), with tree-alignment using parsimony recovering this species as the sister of Pristimantis + Yunganastes. All analyses rejected the monophyly of Strabomantidae and Strabomantinae as originally defined, and the tree-alignment analysis under parsimony further rejected the recently redefined Craugastoridae and Pristimantinae. Despite the greater emphasis in the systematics literature placed on the choice of optimality criterion for evaluating trees than on the choice of method for aligning DNA sequences, we found that the topological differences attributable to the alignment method were as great as those caused by the optimality criterion. Further, the optimal tree-alignment indicates

Calculation of molecular free energies in classical potentials

International Nuclear Information System (INIS)

Farhi, Asaf; Singh, Bipin

2016-01-01

Free energies of molecules can be calculated by quantum chemistry computations or by normal mode classical calculations. However, the first can be computationally impractical for large molecules and the second is based on the assumption of harmonic dynamics. We present a novel, accurate and complete calculation of molecular free energies in standard classical potentials. In this method we transform the molecule by relaxing potential terms which depend on the coordinates of a group of atoms in that molecule and calculate the free energy difference associated with the transformation. Then, since the transformed molecule can be treated as non-interacting systems, the free energy associated with these atoms is analytically or numerically calculated. This two-step calculation can be applied to calculate free energies of molecules or free energy difference between (possibly large) molecules in a general environment. We demonstrate the method in free energy calculations for methanethiol and butane molecules in vacuum and solvent. We suggest the potential application of free energy calculation of chemical reactions in classical molecular simulations. (paper)

Linear Response of Field-Aligned Currents to the Interplanetary Electric Field

DEFF Research Database (Denmark)

Weimer, D. R.; R. Edwards, T.; Olsen, Nils

2017-01-01

Many studies that have shown that the ionospheric, polar cap electric potentials (PCEP) exhibit a “saturation” behavior in response to the level of the driving by the solar wind. As the magnitude of the interplanetary magnetic field (IMF) and electric field (IEF) increase, the PCEP response...... of the field-aligned currents (FAC) with the solar wind/magnetosphere/ionosphere system has a role. As the FAC are more difficult to measure, their behavior in response to the level of the IEF has not been investigated as thoroughly. In order to resolve the question of whether or not the FAC also exhibit...... saturation, we have processed the magnetic field measurements from the Ørsted, CHAMP, and Swarm missions, spanning more than a decade. As the amount of current in each region needs to be known, a new technique is used to separate and sum the current by region, widely known as R0, R1, and R2. These totals...

Field-Aligned Current Response to Solar Indices

DEFF Research Database (Denmark)

R. Edwards, Thom; Weimer, D. R.; Tobiska, W. K.

2017-01-01

Magnetometer data from three satellite missions have been used to analyze and identify the effects of varying solar radiation on the magnitudes and locations of field-aligned currents in the Earth's upper atmosphere. Data from the CHAMP, Ørsted, and Swarm satellite missions have been bought...... together to provide a database spanning a 15 year period. The extensive time frame has been augmented by data from the ACE satellite, as well as a number of indices of solar radiation. This data set has been sorted by a number of solar wind, interplanetary magnetic field, and solar radiation indices...... to evaluate the effects of variations in four different solar indices on the total current in different regions of the polar cap. While the solar indices do not have major influence on the total current of the polar cap when compared to solar wind and interplanetary magnetic field parameters it does appear...

Alignment of Duke free electron laser storage ring and optical beam delivery system

International Nuclear Information System (INIS)

Emamian, M.; Hower, N.

1999-01-01

Duke Free Electron Laser Laboratory (DFELL) hosts a 1.1 GeV electron beam storage ring facility which is capable of generating beams in the range of nearly monochromatic gamma rays to high peak power infra red (IR) laser. In this report specifications and procedures for alignment of OK-4 /Duke storage ring FEL wiggler and optical cavity mirrors will be discussed. The OK-4 FEL lasing has demonstrated a series of world record in the last few years. In August of this year the OK-4 FEL successfully commissioned to laser at 193.7 nm. Also in this article, alignment of the γ-ray and UV optical beam delivery system that is currently in progress will be described. (authors)

Facilitating Constructive Alignment in Power Systems Engineering Education Using Free and Open-Source Software

Science.gov (United States)

Vanfretti, L.; Milano, F.

2012-01-01

This paper describes how the use of free and open-source software (FOSS) can facilitate the application of constructive alignment theory in power systems engineering education by enabling the deep learning approach in power system analysis courses. With this aim, this paper describes the authors' approach in using the Power System Analysis Toolbox…

Flexible Piezoelectric Touch Sensor by Alignment of Lead-Free Alkaline Niobate Microcubes in PDMS

NARCIS (Netherlands)

Deutz, D.B.; Mascarenhas, N.T.; Schelen, J.B.J.; de Leeuw, D.M.; van der Zwaag, S.; Groen, W.A.

2017-01-01

A highly sensitive, lead-free, and flexible piezoelectric touch sensor is reported based on composite films of alkaline niobate K_0.485Na_0.485Li_0.03NbO₃ (KNLN) powders aligned in a polydimethylsiloxane (PDMS) matrix. KNLN powder is fabricated by

Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase.

Science.gov (United States)

De Beer, Stephanie B A; Glättli, Alice; Hutzler, Johannes; Vermeulen, Nico P E; Oostenbrink, Chris

2011-07-30

4-Hydroxyphenylpyruvate dioxygenase is a relevant target in both pharmaceutical and agricultural research. We report on molecular dynamics simulations and free energy calculations on this enzyme, in complex with 12 inhibitors for which experimental affinities were determined. We applied the thermodynamic integration approach and the more efficient one-step perturbation. Even though simulations seem well converged and both methods show excellent agreement between them, the correlation with the experimental values remains poor. We investigate the effect of slight modifications on the charge distribution of these highly conjugated systems and find that accurate models can be obtained when using improved force field parameters. This study gives insight into the applicability of free energy methods and current limitations in force field parameterization. Copyright © 2011 Wiley Periodicals, Inc.

High-performance field emission device utilizing vertically aligned carbon nanotubes-based pillar architectures

Science.gov (United States)

Gupta, Bipin Kumar; Kedawat, Garima; Gangwar, Amit Kumar; Nagpal, Kanika; Kashyap, Pradeep Kumar; Srivastava, Shubhda; Singh, Satbir; Kumar, Pawan; Suryawanshi, Sachin R.; Seo, Deok Min; Tripathi, Prashant; More, Mahendra A.; Srivastava, O. N.; Hahm, Myung Gwan; Late, Dattatray J.

2018-01-01

The vertical aligned carbon nanotubes (CNTs)-based pillar architectures were created on laminated silicon oxide/silicon (SiO2/Si) wafer substrate at 775 °C by using water-assisted chemical vapor deposition under low pressure process condition. The lamination was carried out by aluminum (Al, 10.0 nm thickness) as a barrier layer and iron (Fe, 1.5 nm thickness) as a catalyst precursor layer sequentially on a silicon wafer substrate. Scanning electron microscope (SEM) images show that synthesized CNTs are vertically aligned and uniformly distributed with a high density. The CNTs have approximately 2-30 walls with an inner diameter of 3-8 nm. Raman spectrum analysis shows G-band at 1580 cm-1 and D-band at 1340 cm-1. The G-band is higher than D-band, which indicates that CNTs are highly graphitized. The field emission analysis of the CNTs revealed high field emission current density (4mA/cm2 at 1.2V/μm), low turn-on field (0.6 V/μm) and field enhancement factor (6917) with better stability and longer lifetime. Emitter morphology resulting in improved promising field emission performances, which is a crucial factor for the fabrication of pillared shaped vertical aligned CNTs bundles as practical electron sources.

High-performance field emission device utilizing vertically aligned carbon nanotubes-based pillar architectures

Directory of Open Access Journals (Sweden)

Bipin Kumar Gupta

2018-01-01

Full Text Available The vertical aligned carbon nanotubes (CNTs-based pillar architectures were created on laminated silicon oxide/silicon (SiO2/Si wafer substrate at 775 °C by using water-assisted chemical vapor deposition under low pressure process condition. The lamination was carried out by aluminum (Al, 10.0 nm thickness as a barrier layer and iron (Fe, 1.5 nm thickness as a catalyst precursor layer sequentially on a silicon wafer substrate. Scanning electron microscope (SEM images show that synthesized CNTs are vertically aligned and uniformly distributed with a high density. The CNTs have approximately 2–30 walls with an inner diameter of 3–8 nm. Raman spectrum analysis shows G-band at 1580 cm−1 and D-band at 1340 cm−1. The G-band is higher than D-band, which indicates that CNTs are highly graphitized. The field emission analysis of the CNTs revealed high field emission current density (4mA/cm2 at 1.2V/μm, low turn-on field (0.6 V/μm and field enhancement factor (6917 with better stability and longer lifetime. Emitter morphology resulting in improved promising field emission performances, which is a crucial factor for the fabrication of pillared shaped vertical aligned CNTs bundles as practical electron sources.

Radiation chemistry in high pressure paying attention to molecular motion and alignment

International Nuclear Information System (INIS)

Sasuga, Tsuneo

1978-01-01

Effects of high pressure or radiation-induced cross-linking of synthetic rubbers and polymerization of methacrylates and acrylonitrile (AN) have been studied paying attention to molecular motion and alignment. The following were revealed from radiation-induced crosslinking reaction, pressure-volume-temperature (P-V-T) measurement and chemical relaxation of polymer crosslinked at high pressure: (1) The rate of crosslinking is increased in compression especially in polymers containing double bonds, due to chain reaction through double bonds. (2) Crosslinking points of the polymer with double bonds crosslinked at high pressure are dispersed as cluster. (3) Crosslinking reaction is intimately related with change of the molecular motion in a polymer under pressure. Van't Hoff plots of methacrylates and AN breaked at a pressure depending on the monomer. The pressure giving the breaks depends on length of methacrylate. P-V curves of the polymer-monomer coexistence system as-polymerized exhibit peculiar behavior at the pressure giving the breaks. AN exhibits complicated polymerization behavior at a pressure changing compressibility of the monomer. From above results etc. it is concluded that monomer molecules are aligned in short range at a pressure corresponding to geometrical structure of the monomer molecules. (auth.)

Magnetic field alignment for a 20 MeV linear induction accelerator

International Nuclear Information System (INIS)

Zhang Wenwei; Pan Haifeng; Li Hong; Liu Yunlong; Zhang Linwen

2002-01-01

'Dragon-1' accelerator now is being constructed in CAEP. It will produce high current pulse electron beams. The main components of the accelerator include 72 induction accelerating cells and 18 connection cells with ports for beam di gnostic hardware and vacuum pump. In order to acquire high quality beams, a lot of problems have to be addressed such as to reduce the emittance, to control the increase of corkscrew and so on. The alignment of the focus magnetic field is the most concerned. A laser track has been used for mechanical alignment, magnetic alignment is performed by using pulsed-wire technique, and the natural tilt errors is corrected by a pair of steering coil, which is located inside the cell

Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method.

Science.gov (United States)

König, Gerhard; Mei, Ye; Pickard, Frank C; Simmonett, Andrew C; Miller, Benjamin T; Herbert, John M; Woodcock, H Lee; Brooks, Bernard R; Shao, Yihan

2016-01-12

A recently developed MESS-E-QM/MM method (multiple-environment single-system quantum mechanical molecular/mechanical calculations with a Roothaan-step extrapolation) is applied to the computation of hydration free energies for the blind SAMPL4 test set and for 12 small molecules. First, free energy simulations are performed with a classical molecular mechanics force field using fixed-geometry solute molecules and explicit TIP3P solvent, and then the non-Boltzmann-Bennett method is employed to compute the QM/MM correction (QM/MM-NBB) to the molecular mechanical hydration free energies. For the SAMPL4 set, MESS-E-QM/MM-NBB corrections to the hydration free energy can be obtained 2 or 3 orders of magnitude faster than fully converged QM/MM-NBB corrections, and, on average, the hydration free energies predicted with MESS-E-QM/MM-NBB fall within 0.10-0.20 kcal/mol of full-converged QM/MM-NBB results. Out of five density functionals (BLYP, B3LYP, PBE0, M06-2X, and ωB97X-D), the BLYP functional is found to be most compatible with the TIP3P solvent model and yields the most accurate hydration free energies against experimental values for solute molecules included in this study.

Magnetohydrodynamic Ekman layers with field-aligned flow

Energy Technology Data Exchange (ETDEWEB)

Nunez, Manuel, E-mail: mnjmhd@am.uva.es [Departamento de Analisis Matematico, Universidad de Valladolid, 47005 Valladolid (Spain)

2011-05-01

The Ekman layer in a conducting fluid with constant angular velocity, provided with a magnetic field aligned with the flow, is studied here. The existence of solutions to the magnetohydrodynamic linearized equations depends on the balance between viscosity and resistivity, on the one hand, and the angular and Alfven velocities, on the other. In most cases, exponentially decreasing solutions exist, although their longitudinal oscillations do not need to be periodic. One of the instances without a solution is explained by the presence of Alfven waves traveling backwards along the streamlines.

Shock aurora: Field-aligned discrete structures moving along the dawnside oval

Science.gov (United States)

Zhou, Xiaoyan; Haerendel, Gerhard; Moen, Jøran I.; Trondsen, Espen; Clausen, Lasse; Strangeway, Robert J.; Lybekk, Bjørn; Lorentzen, Dag A.

2017-03-01

Generated by interplanetary shocks or solar wind pressure pulses, shock aurora has transient, global, and dynamic significances and provides a direct manifestation of the solar wind-magnetosphere-ionosphere interaction. As a part of a series of studies of the shock aurora, this paper focuses on the interaction at the morning magnetopause and its auroral manifestation at 06 magnetic local time, where the velocity and magnetic field shears dominate the interaction. Flow shears can generate wave-like structures inside a viscous boundary layer or even larger-scale vortices. These structures couple to the ionosphere via quasi-static field-aligned currents or via kinetic Alfvén waves. Potential drops along field-aligned filaments may be generated accelerating electrons to form auroral manifestations of the structures. A shock aurora event at dawnside is used to test this scenario. The findings include moving auroral streaks/rays that have a vertical profile from red (at 250 km altitude) to purple (at 100 km). The streaks moved antisunward along the poleward boundary of the oval at an ionospheric speed of 3 km s-1. It was mapped to the magnetopause flank at 133 km s-1, which was consistent with the observed speed of the magnetopause surface waves generated by the Kelvin-Helmholtz instability. The calculated field-aligned potential drop using Haerendel's analytic model was 5 kV that reasonably explained the observations. The results support the above scenario and reveal that magnetic and velocity shears at the flanks of the magnetospause may be the main cause of the fast moving shock aurora streaks.

Electric field-induced astrocyte alignment directs neurite outgrowth

OpenAIRE

ALEXANDER, JOHN K.; FUSS, BABETTE; COLELLO, RAYMOND J.

2006-01-01

The extension and directionality of neurite outgrowth are key to achieving successful target connections during both CNS development and during the re-establishment of connections lost after neural trauma. The degree of axonal elongation depends, in large part, on the spatial arrangement of astrocytic processes rich in growth-promoting proteins. Because astrocytes in culture align their processes on exposure to an electrical field of physiological strength, we sought to determine the extent t...

Magnetosphere-ionosphere coupling currents in Jupiter's middle magnetosphere: effect of magnetosphere-ionosphere decoupling by field-aligned auroral voltages

Directory of Open Access Journals (Sweden)

J. D. Nichols

2005-03-01

Full Text Available We consider the effect of field-aligned voltages on the magnetosphere-ionosphere coupling current system associated with the breakdown of rigid corotation of equatorial plasma in Jupiter's middle magnetosphere. Previous analyses have assumed perfect mapping of the electric field and flow along equipotential field lines between the equatorial plane and the ionosphere, whereas it has been shown that substantial field-aligned voltages must exist to drive the field-aligned currents associated with the main auroral oval. The effect of these field-aligned voltages is to decouple the flow of the equatorial and ionospheric plasma, such that their angular velocities are in general different from each other. In this paper we self-consistently include the field-aligned voltages in computing the plasma flows and currents in the system. A third order differential equation is derived for the ionospheric plasma angular velocity, and a power series solution obtained which reduces to previous solutions in the limit that the field-aligned voltage is small. Results are obtained to second order in the power series, and are compared to the original zeroth order results with no parallel voltage. We find that for system parameters appropriate to Jupiter the effect of the field-aligned voltages on the solutions is small, thus validating the results of previously-published analyses.

Convection and field-aligned currents, related to polar cap arcs, during strongly northward IMF (11 January 1983)

International Nuclear Information System (INIS)

Israelevich, P.L.; Podgorny, I.M.; Kuzmin, A.K.; Nikolaeva, N.S.; Dubinin, E.M.

1988-01-01

Electric and magnetic fields and auroral emissions have been measured by the Intercosmos-Bulgaria-1300 satellite on 10-11 January 1983. The measured distributions of the plasma drift velocity show that viscous convection is diminished in the evening sector under IMF B y y > 0. A number of sun-aligned polar cap arcs were observed at the beginning of the period of strongly northward IMF and after a few hours a θ-aurora appeared. The intensity of ionized oxygen emission increased significantly reaching up to several kilo-Rayleighs in the polar cap arc. A complicated pattern of convection and field-aligned currents existed in the nightside polar cap which differed from the four-cell model of convection and NBZ field-aligned current system. This pattern was observed during 12 h and could be interpreted as six large scale field-aligned current sheets and three convective vortices inside the polar cap. Sun-aligned polar cap arcs may be located in regions both of sunward and anti-sunward convection. Structures of smaller spatial scale-correspond to the boundaries of hot plasma regions related to polar cap arcs. Obviously these structures are due to S-shaped distributions of electric potential. Parallel electric fields in these S-structures provide electron acceleration up to 1 keV at the boundaries of polar cap arcs. The pairs of field-aligned currents correspond to those S-structures: a downward current at the external side of the boundary and an upward current at the internal side of it. (author)

A comparison of field-aligned current signatures simultaneously observed by the MAGSAT and TIROS/NOAA spacecraft

International Nuclear Information System (INIS)

Kamide, Y.; Evans, D.S.; Cain, J.C.

1984-01-01

In order to examine the relative locations of auroral particle fluxes and field-aligned currents and to identify the main charge carriers of the field-aligned currents at auroral latitudes, nearly simultaneous data from the vector magnetometers on MAGSAT and of precipitating electrons with energies between 300 eV and 20 keV observed by TIROS-N and NOAA-6 are compared. For more than fifty cases, MAGSAT and TIROS and/or NOAA orbits occurred within two minutes (mostly within one minute) of each other in the dawn/dusk sectors, during the time the IMS meridian chains of ground magnetometers were operating from November, 1979 through January, 1980. The latitudinal boundaries of precipitating electrons are found to line up within 1 0 with those of the field-aligned current region. Major portions of the upward field-aligned currents in the poleward half of the evening-sector auroral oval and in the equatorward half of the morining-sector auroral oval appear to be carried by the precipitating keV electrons. (author)

Relationship between PC index and magnetospheric field-aligned currents measured by Swarm satellites

DEFF Research Database (Denmark)

Troshichev, О.; Sormakov, D.; Behlke, R.

2018-01-01

Abstract The relationship between the magnetospheric field-aligned currents (FAC) monitored by the Swarm satellites and the magnetic activity PC index (which is a proxy of the solar wind energy incoming into the magnetosphere) is examined. It is shown that current intensities measured in the R1...... between the PC index and the intensity of field-aligned currents in the R1 dawn and dusk layers: increase of FAC intensity in the course of substorm development is accompanied by increasing the PC index values. Correlation between PC and FAC intensities in the R2 dawn and dusk layers is also observed...

Field-aligned currents' scale analysis performed with the Swarm constellation

DEFF Research Database (Denmark)

Lühr, Hermann; Park, Jaeheung; Gjerløv, Jesper Wittendorff

2015-01-01

We present a statistical study of the temporal- and spatial-scale characteristics of different field-aligned current (FAC) types derived with the Swarm satellite formation. We divide FACs into two classes: small-scale, up to some 10 km, which are carried predominantly by kinetic Alfve´n waves...

Initial alignment method for free space optics laser beam

Science.gov (United States)

Shimada, Yuta; Tashiro, Yuki; Izumi, Kiyotaka; Yoshida, Koichi; Tsujimura, Takeshi

2016-08-01

The authors have newly proposed and constructed an active free space optics transmission system. It is equipped with a motor driven laser emitting mechanism and positioning photodiodes, and it transmits a collimated thin laser beam and accurately steers the laser beam direction. It is necessary to introduce the laser beam within sensible range of the receiver in advance of laser beam tracking control. This paper studies an estimation method of laser reaching point for initial laser beam alignment. Distributed photodiodes detect laser luminescence at respective position, and the optical axis of laser beam is analytically presumed based on the Gaussian beam optics. Computer simulation evaluates the accuracy of the proposed estimation methods, and results disclose that the methods help us to guide the laser beam to a distant receiver.

Automatic alignment device for focal spot measurements in the center of the field for mammography

International Nuclear Information System (INIS)

Vieira, Marcelo A.C.; Watanabe, Alex O.; Oliveira Junior, Paulo D.; Schiabel, Homero

2010-01-01

Some quality control procedures used for mammography, such as focal spot evaluation, requires previous alignment of the measurement equipment with the X-ray central beam. However, alignment procedures are, in general, the most difficult task and the one that needs more time to be performed. Moreover, the operator sometimes is exposed to radiation during this procedure. This work presents an automatic alignment system for mammographic equipment that allows locating the central ray of the radiation beam and, immediately, aligns with it by dislocating itself automatically along the field. The system consists on a bidirectional moving device, connected to a CCD sensor for digital radiographic image acquisition. A computational analysis of a radiographic image, acquired at any position on the field, is performed in order to determine its positioning under the X-ray beam. Finally, a mechanical system for two moving directions, electronically controlled by a microcontroller under USB communication, makes the system to align automatically with the radiation beam central ray. The alignment process is fully automatic, fast and accurate, with no operator exposure to radiation, which allows a considerable time saving for quality control procedures achievement for mammography. (author)

Measurement of the attosecond emission from aligned molecules

International Nuclear Information System (INIS)

Boutu, W.; Merdji, H.; Fitour, R.; Monchicourt, P.; Breger, P.; Carre, B.; Salieres, P.

2006-01-01

Complete test of publication follows. Recently, a number of papers have demonstrated the interest of high-order harmonic generation (HHG) from molecules aligned with respect to the laser polarization. Itatani et al. (Nature 432, 867 (2004)) have shown that a precise characterization of the harmonic emission allows performing a tomographic reconstruction of the molecular orbitals that radiate. Kanai et al. (Nature 435, 470 (2005)) have evidenced quantum interferences in the recombination process of HHG that are directly related to the molecular structure. In all of these papers, only the HHG intensity was measured. The relative harmonic phase, though more difficult to measure, contains important information on the interference process, and is needed for an ab initio tomographic reconstruction. Finally, while the attosecond emission from atoms has been thoroughly studied, in particular by our group (Mairesse et al., Science (302, 1540 (2003)), it has not been investigated in molecules. In a first experiment (Wabnitz et al., EPJD (2006)), we measured the amplitude and relative phase of harmonics radiated by un-aligned nitrogen molecules. Small but reproducible deviations from the phase of harmonics generated in argon (same ionization potential as nitrogen) were measured for low orders. In a recent experiment, we have measured, up to high order, the harmonic amplitude and relative phase for aligned molecules (N 2 and CO 2 ). In order to align the molecules, we used the so-called nonadiabatic technique: a rotational wavepacket is created by a strong enough and short aligning pulse, so that a field-free alignment is obtained at the revival (a few ps after the aligning pulse). The measurement of phase locking between neighboring harmonics was performed through the photoionization of a target gas by the harmonic beam in presence of a sufficiently intense 'dressing' laser beam (RABITT technique). The harmonic phase measured when the CO 2 molecules are aligned parallel to

Laboratory investigation of physical mechanisms of auroral charged particle acceleration in the field-aligned currents layers

Science.gov (United States)

Gavrilov, B.; Zetzer, J.; Sobyanin, D.; Podgorny, I.

One of the major topics of space weather research is to understand auroral structure and the processes that guide, accelerate, and otherwise control particle precipitation and produce auroral substorms. Navigation, communications and radars in the high latitude regions are severely affected through the effects on the ionosphere. It has long been recognized that the direct cause of the aurora is the precipitation of energetic electrons and ions into the atmosphere leading to excitation of the ambient atmospheric gases. Observations of the ionospheric ionization profiles and auroral precipitation characteristics have shown that field-aligned potential drops are formed to create this effect. The problem is that it is not clear the structure of the regions of magnetic field-aligned electric fields and how they are supported in the magnetospheric plasma. The objective of this research is to study the physical mechanisms of these phenomena in a laboratory experiment. It should be achieved by simulating the charged particle acceleration due to field-aligned electrical field generation in all totality of the interconnected events: generation of a plasma flow, its evolution in the magnetic field, polarization of plasma, generation of the field-aligned currents, development of instabilities in the plasma and current layers, double layers or anomalous resistance regions appearance, electrons acceleration. Parameters of the laboratory simulation and preliminary results of the experiment are discussed.

A flexible statistical model for alignment of label-free proteomics data--incorporating ion mobility and product ion information.

Science.gov (United States)

Benjamin, Ashlee M; Thompson, J Will; Soderblom, Erik J; Geromanos, Scott J; Henao, Ricardo; Kraus, Virginia B; Moseley, M Arthur; Lucas, Joseph E

2013-12-16

The goal of many proteomics experiments is to determine the abundance of proteins in biological samples, and the variation thereof in various physiological conditions. High-throughput quantitative proteomics, specifically label-free LC-MS/MS, allows rapid measurement of thousands of proteins, enabling large-scale studies of various biological systems. Prior to analyzing these information-rich datasets, raw data must undergo several computational processing steps. We present a method to address one of the essential steps in proteomics data processing--the matching of peptide measurements across samples. We describe a novel method for label-free proteomics data alignment with the ability to incorporate previously unused aspects of the data, particularly ion mobility drift times and product ion information. We compare the results of our alignment method to PEPPeR and OpenMS, and compare alignment accuracy achieved by different versions of our method utilizing various data characteristics. Our method results in increased match recall rates and similar or improved mismatch rates compared to PEPPeR and OpenMS feature-based alignment. We also show that the inclusion of drift time and product ion information results in higher recall rates and more confident matches, without increases in error rates. Based on the results presented here, we argue that the incorporation of ion mobility drift time and product ion information are worthy pursuits. Alignment methods should be flexible enough to utilize all available data, particularly with recent advancements in experimental separation methods.

Radar observations of artificial E-region field-aligned irregularities

Directory of Open Access Journals (Sweden)

E. Nossa

2009-07-01

Full Text Available Artificial E region field aligned plasma density irregularities (FAIs were generated using HAARP in four different experimental modes and observed with a coherent scatter radar imager located 450 km to the southwest where it could detect field-aligned backscatter. The experiments were conducted in July of 2008, during the Polar Aeronomy and Radio Science Summer School (PARS, during quiet conditions in the daytime when the E layer was dense and absorption was modest. The echoes observed during zenith and magnetic zenith heating experiments were deflected from their nominally anticipated horizontal positions toward the midpoint position. The occurrence of hysteresis when heating with amplitude modulated pulses implied the development of the resonance instability, although the threshold for the onset of instability appeared to be higher than what has been predicted theoretically. Heating experiments involving pump frequencies slightly above and below the second electron gyroharmonic frequency produced no significant differences in the observed echoes. Finally, heating with a pump frequency slightly above the E region critical frequency appears to have produced FAIs at two distinct altitudes where the upper-hybrid resonance condition could be satisfied.

Field-aligned currents during northward IMF: Morphology and causes

DEFF Research Database (Denmark)

Vennerstrøm, Susanne; Moretto, T.; Rastätter, L.

2005-01-01

We present the results of a global MHD simulation of solar wind magnetosphere interaction during northward IMF. In particular, we emphasize the effect of the IMF B y component on the reconnection geometry and the mapping along field lines to the polar ionosphere, through field-aligned currents. We...... find that the existence and geometry of the polar cap is closely connected to the IMF B y component. During strictly northward IMF the simulated magnetosphere can remain essentially closed because the solar wind field lines reconnect in both hemispheres, thereby creating newly reconnected closed...... exist both on open and closed field lines and are created by the shear of the newly reconnected field lines against the mantle field as they are convected tailward by the solar wind. When the IMF rotates from northward toward east, the magnetospheric mapping regions of the NBZ currents likewise rotates...

Positioning and aligning CNTs by external magnetic field to assist localised epoxy cure

Directory of Open Access Journals (Sweden)

Ariu G.

2016-01-01

Full Text Available This work focuses on the generation of conductive networks through the localised alignment of nano fillers, such as multi-walled carbon nanotubes (MWCNTs. The feasibility of alignment and positioning of functionalised MWCNTs by external DC magnetic fields was investigated. The aim of this manipulation is to enhance resin curing through AC induction heating due to hysteresis losses from the nanotubes. Experimental analyses focused on in-depth assessment of the nanotube functionalisation, processing and characterisation of magnetic, rheological and cure kinetics properties of the MWCNT solution. The study has shown that an external magnetic field has great potential for positioning and alignment of CNTs. The study demonstrated potential for creating well-ordered architectures with an unprecedented level of control of network geometry. Magnetic characterisation indicated cobalt-plated nanotubes to be the most suitable candidate for magnetic alignment due to their high magnetic sensitivity. Epoxy/metal-plated CNT nanocomposite systems were validated by thermal analysis as induction heating mediums. The curing process could therefore be optimised by the use of dielectric resins. This study offers a first step towards the proof of concept of this technique as a novel repair technology.

Positioning and aligning CNTs by external magnetic field to assist localised epoxy cure

Science.gov (United States)

Ariu, G.; Hamerton, I.; Ivanov, D.

2016-01-01

This work focuses on the generation of conductive networks through the localised alignment of nano fillers, such as multi-walled carbon nanotubes (MWCNTs). The feasibility of alignment and positioning of functionalised MWCNTs by external DC magnetic fields was investigated. The aim of this manipulation is to enhance resin curing through AC induction heating due to hysteresis losses from the nanotubes. Experimental analyses focused on in-depth assessment of the nanotube functionalisation, processing and characterisation of magnetic, rheological and cure kinetics properties of the MWCNT solution. The study has shown that an external magnetic field has great potential for positioning and alignment of CNTs. The study demonstrated potential for creating well-ordered architectures with an unprecedented level of control of network geometry. Magnetic characterisation indicated cobalt-plated nanotubes to be the most suitable candidate for magnetic alignment due to their high magnetic sensitivity. Epoxy/metal-plated CNT nanocomposite systems were validated by thermal analysis as induction heating mediums. The curing process could therefore be optimised by the use of dielectric resins. This study offers a first step towards the proof of concept of this technique as a novel repair technology.

Galactic cosmic ray gradients, field-aligned and latitudinal, among Voyagers 1/2 and IMP-8

Science.gov (United States)

Roelof, E. C.; Decker, R. B.; Krimigis, S. M.; Venkatesan, D.; Lazarus, A. J.

1982-01-01

The present investigation represents a summary of a comprehensive analysis of the same subject conducted by Roelof et al. (1981). It is pointed out that the tandem earth-Jupiter trajectories of the Voyager 1/2 spacecraft, combined with baseline measurements from the earth-orbiting IMP 7/8 spacecraft, provide the first opportunity for unambiguously separating latitude from radial or field-aligned effects in galactic cosmic ray gradients. Attention is given to the method of data analysis, and the separation of field-aligned and latitudinal gradients. It is found that latitudinal gradients approximately equal to or greater than 1 percent per deg in the cosmic ray intensity were a common feature of the interplanetary medium between 1 and 5 AU in 1977-78. Except in the most disturbed periods, cosmic ray intensities are well-ordered in field-aligned structures.

Grain alignment in starless cores

International Nuclear Information System (INIS)

Jones, T. J.; Bagley, M.; Krejny, M.; Andersson, B.-G.; Bastien, P.

2015-01-01

We present near-IR polarimetry data of background stars shining through a selection of starless cores taken in the K band, probing visual extinctions up to A V ∼48. We find that P K /τ K continues to decline with increasing A V with a power law slope of roughly −0.5. Examination of published submillimeter (submm) polarimetry of starless cores suggests that by A V ≳20 the slope for P versus τ becomes ∼−1, indicating no grain alignment at greater optical depths. Combining these two data sets, we find good evidence that, in the absence of a central illuminating source, the dust grains in dense molecular cloud cores with no internal radiation source cease to become aligned with the local magnetic field at optical depths greater than A V ∼20. A simple model relating the alignment efficiency to the optical depth into the cloud reproduces the observations well.

Grain alignment in starless cores

Energy Technology Data Exchange (ETDEWEB)

Jones, T. J.; Bagley, M. [Minnesota Institute for Astrophysics, University of Minnesota, Minneapolis, MN 55455 (United States); Krejny, M. [Cree Inc., 4600 Silicon Dr., Durham, NC (United States); Andersson, B.-G. [SOFIA Science Center, USRA, Moffett Field, CA (United States); Bastien, P., E-mail: tjj@astro.umn.edu [Centre de recherche en astrophysique du Québec and Départment de Physique, Université de Montréal, Montréal (Canada)

2015-01-01

We present near-IR polarimetry data of background stars shining through a selection of starless cores taken in the K band, probing visual extinctions up to A{sub V}∼48. We find that P{sub K}/τ{sub K} continues to decline with increasing A{sub V} with a power law slope of roughly −0.5. Examination of published submillimeter (submm) polarimetry of starless cores suggests that by A{sub V}≳20 the slope for P versus τ becomes ∼−1, indicating no grain alignment at greater optical depths. Combining these two data sets, we find good evidence that, in the absence of a central illuminating source, the dust grains in dense molecular cloud cores with no internal radiation source cease to become aligned with the local magnetic field at optical depths greater than A{sub V}∼20. A simple model relating the alignment efficiency to the optical depth into the cloud reproduces the observations well.

Identifications of the polar cap boundary and the auroral belt in the high-altitude magnetosphere: a model for field-aligned currents

International Nuclear Information System (INIS)

Sugiura, M.

1975-01-01

By means of the Ogo 5 Goddard Space Flight Center fluxgate magnetometer data the polar cap boundary is identified in the high-altitude magnetosphere by a sudden transition from a dipolar field to a more taillike configuration. It is inferred that there exists a field-aligned-current layer at the polar cap boundary. In the night side magnetosphere the polar cap boundary is identified as the high-latitude boundary of the plasma sheet. The field-aligned current flows downward to the ionosphere on the morning side of the magnetosphere and upward from the ionosphere on the afternoon side. The basic pattern of the magnetic field variations observed during the satellite's traversal of the auroral belt is presented. Currents flow in opposite directions in the two field-aligned-current layers. The current directions in these layers as observed by Ogo 5 in the high-altitude magnetosphere are the same as those observed at low altitudes by the polar-orbiting Triad satellite (Armstrong and Zmuda, 1973). The magnetic field in the region where the lower-latitude field-aligned-current layer is situated is essentially meridional. A model is presented in which two field-aligned-current systems, one at the polar cap boundary and the other on the low-latitude part of the auroral belt, are main []y connected by ionospheric currents flowing across the auroral belt. The existence of field-aligned currents deduced from the Ogo 5 observations is a permanent feature of the magnetosphere. Intensifications of the field-aligned currents and occurrences of multiple pairs of field-aligned-current layers characterize the disturbed conditions of these regions

An additional reference axis improves femoral rotation alignment in image-free computer navigation assisted total knee arthroplasty.

Science.gov (United States)

Inui, Hiroshi; Taketomi, Shuji; Nakamura, Kensuke; Sanada, Takaki; Tanaka, Sakae; Nakagawa, Takumi

2013-05-01

Few studies have demonstrated improvement in accuracy of rotational alignment using image-free navigation systems mainly due to the inconsistent registration of anatomical landmarks. We have used an image-free navigation for total knee arthroplasty, which adopts the average algorithm between two reference axes (transepicondylar axis and axis perpendicular to the Whiteside axis) for femoral component rotation control. We hypothesized that addition of another axis (condylar twisting axis measured on a preoperative radiograph) would improve the accuracy. One group using the average algorithm (double-axis group) was compared with the other group using another axis to confirm the accuracy of the average algorithm (triple-axis group). Femoral components were more accurately implanted for rotational alignment in the triple-axis group (ideal: triple-axis group 100%, double-axis group 82%, P<0.05). Copyright © 2013 Elsevier Inc. All rights reserved.

RV-Typer: A Web Server for Typing of Rhinoviruses Using Alignment-Free Approach.

Directory of Open Access Journals (Sweden)

Pandurang S Kolekar

Full Text Available Rhinoviruses (RV are increasingly being reported to cause mild to severe infections of respiratory tract in humans. RV are antigenically the most diverse species of the genus Enterovirus and family Picornaviridae. There are three species of RV (RV-A, -B and -C, with 80, 32 and 55 serotypes/types, respectively. Antigenic variation is the main limiting factor for development of a cross-protective vaccine against RV.Serotyping of Rhinoviruses is carried out using cross-neutralization assays in cell culture. However, these assays become laborious and time-consuming for the large number of strains. Alternatively, serotyping of RV is carried out by alignment-based phylogeny of both protein and nucleotide sequences of VP1. However, serotyping of RV based on alignment-based phylogeny is a multi-step process, which needs to be repeated every time a new isolate is sequenced. In view of the growing need for serotyping of RV, an alignment-free method based on "return time distribution" (RTD of amino acid residues in VP1 protein has been developed and implemented in the form of a web server titled RV-Typer. RV-Typer accepts nucleotide or protein sequences as an input and computes return times of di-peptides (k = 2 to assign serotypes. The RV-Typer performs with 100% sensitivity and specificity. It is significantly faster than alignment-based methods. The web server is available at http://bioinfo.net.in/RV-Typer/home.html.

Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

Science.gov (United States)

Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

2018-06-01

We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

Scattering of field-aligned beam ions upstream of Earth's bow shock

Directory of Open Access Journals (Sweden)

A. Kis

2007-03-01

Full Text Available Field-aligned beams are known to originate from the quasi-perpendicular side of the Earth's bow shock, while the diffuse ion population consists of accelerated ions at the quasi-parallel side of the bow shock. The two distinct ion populations show typical characteristics in their velocity space distributions. By using particle and magnetic field measurements from one Cluster spacecraft we present a case study when the two ion populations are observed simultaneously in the foreshock region during a high Mach number, high solar wind velocity event. We present the spatial-temporal evolution of the field-aligned beam ion distribution in front of the Earth's bow shock, focusing on the processes in the deep foreshock region, i.e. on the quasi-parallel side. Our analysis demonstrates that the scattering of field-aligned beam (FAB ions combined with convection by the solar wind results in the presence of lower-energy, toroidal gyrating ions at positions deeper in the foreshock region which are magnetically connected to the quasi-parallel bow shock. The gyrating ions are superposed onto a higher energy diffuse ion population. It is suggested that the toroidal gyrating ion population observed deep in the foreshock region has its origins in the FAB and that its characteristics are correlated with its distance from the FAB, but is independent on distance to the bow shock along the magnetic field.

Free energy from molecular dynamics with multiple constraints

NARCIS (Netherlands)

den Otter, Wouter K.; Briels, Willem J.

2000-01-01

In molecular dynamics simulations of reacting systems, the key step to determining the equilibrium constant and the reaction rate is the calculation of the free energy as a function of the reaction coordinate. Intuitively the derivative of the free energy is equal to the average force needed to

Comprehensive simulation study on local and global development of auroral arcs and field-aligned potentials

International Nuclear Information System (INIS)

Watanabe, Tomohiko; Oya, Hiroshi; Watanabe, Kunihiko; Sato, Tetsuya.

1992-10-01

Extensive three-dimensional computer simulations of the magnetosphere-ionosphere (M-I) coupling are performed to study self-excitation of auroral arcs with special emphasis on 1) nonlinear evolution of the feedback instability in the M-I coupling system, 2) controlling mechanisms of the auroral arc structure, 3) formation of a field-aligned electric potential structure in association with the development of the feedback instability, and 4) effects of the parallel potential generation on auroral arc development. It is reconfirmed that the feedback instability produces a longitudinally elongated, latitudinally striated structure where the upward field-aligned current and the ionospheric density are locally enhanced. The following important new features are revealed. 1) The global distribution of the striation structure is primarily governed by the magnetospheric convection pattern and the ionospheric density distribution. 2) There appears a significant dawn-dusk asymmetry in the auroral arc formation, even though the apparent geometrical relationship is symmetric. 3) The recombination effect plays a significant role in the global, as well as local, development of the auroral arc structure. The nonlinearity of recombination, in conjunction with the closure of an arc-associated local field-aligned current system, acts to destroy an old arc and creates a new arc in a different but adjacent position. 4) A V-shaped field aligned potential structure is created in association with an auroral arc. Rapid increase in the electron density and the local upward field-aligned current of an arc arises as a result of enhanced ionization by precipitating electrons accelerated by the parallel potential. 5) A drastic oscillatory behavior of appearance and disappearance of auroral arcs is obtained when the ionization effect is strong. The period is primarily given by the Alfven bounce time. (J.P.N.)

Instantaneous flow field above the free end of finite-height cylinders and prisms

International Nuclear Information System (INIS)

Rostamy, N.; Sumner, D.; Bergstrom, D.J.; Bugg, J.D.

2013-01-01

Highlights: • PIV measurements of the flow above the free end of finite-height bodies. • Effect of cross-sectional shape of the models on the instantaneous flow. • Small-scale structures generated by the separated shear layer were revealed. • Effect of aspect ratio on the reattachment of the separated flow on the free end. -- Abstract: The flow above the free ends of surface-mounted finite-height circular cylinders and square prisms was studied experimentally using particle image velocimetry (PIV). Cylinders and prisms with aspect ratios of AR = 9, 7, 5, and 3 were tested at a Reynolds number of Re = 4.2 × 10 4 . The bodies were mounted normal to a ground plane and were partially immersed in a turbulent zero-pressure-gradient boundary layer, where the boundary layer thickness relative to the body width was δ/D = 1.6. PIV measurements were made above the free ends of the bodies in a vertical plane aligned with the flow centreline. The present PIV results provide insight into the effects of aspect ratio and body shape on the instantaneous flow field. The recirculation zone under the separated shear layer is larger for the square prism of AR = 3 compared to the more slender prism of AR = 9. Also, for a square prism with low aspect ratio (AR = 3), the influence of the reverse flow over the free end surface becomes more significant compared to that for a higher aspect ratio (AR = 9). For the circular cylinder, a cross-stream vortex forms within the recirculation zone. As the aspect ratio of the cylinder decreases, the reattachment point of the separated flow on the free end surface moves closer to the trailing edge. For both the square prism and circular cylinder cases, the instantaneous velocity vector field and associated in-plane vorticity field revealed small-scale structures mostly generated by the separated shear layer

Enhanced field emission properties of vertically aligned double-walled carbon nanotube arrays

International Nuclear Information System (INIS)

Chen, Guohai; Shin, Dong Hoon; Lee, Cheol Jin; Iwasaki, Takayuki; Kawarada, Hiroshi

2008-01-01

Vertically aligned double-walled carbon nanotube (VA-DWCNT) arrays were synthesized by point-arc microwave plasma chemical vapor deposition on Cr/n-Si and SiO 2 /n-Si substrates. The outer tube diameters of VA-DWCNTs are in the range of 2.5-3.8 nm, and the average interlayer spacing is approximately 0.42 nm. The field emission properties of these VA-DWCNTs were studied. It was found that a VA-DWCNT array grown on a Cr/n-Si substrate had better field emission properties as compared with a VA-DWCNT array grown on a SiO 2 /n-Si substrate and randomly oriented DWCNTs, showing a turn-on field of about 0.85 V μm -1 at the emission current density of 0.1 μA cm -2 and a threshold field of 1.67 V μm -1 at the emission current density of 1.0 mA cm -2 . The better field emission performance of the VA-DWCNT array was mainly attributed to the vertical alignment of DWCNTs on the Cr/n-Si substrate and the low contact resistance between CNTs and the Cr/n-Si substrate

Can primordial magnetic fields seeded by electroweak strings cause an alignment of quasar axes on cosmological scales?

Science.gov (United States)

Poltis, Robert; Stojkovic, Dejan

2010-10-15

The decay of nontopological electroweak strings may leave an observable imprint in the Universe today in the form of primordial magnetic fields. Protogalaxies preferentially tend to form with their axis of rotation parallel to an external magnetic field, and, moreover, an external magnetic field produces torque which tends to align the galaxy axis with the magnetic field. We demonstrate that the shape of a magnetic field left over from two looped electroweak strings can explain the observed nontrivial alignment of quasar polarization vectors and make predictions for future observations.

Small-scale field-aligned currents observed by the AKEBONO (EXOS-D) satellite

International Nuclear Information System (INIS)

Fukunishi, H.; Oya, H.; Kokubun, S.; Tohyama, F.; Mukai, T.; Fujii, R.

1991-01-01

The EXOS-D fluxgate magnetometer data obtained at 3,000-10,000 km altitude have shown that small-scale field-aligned currents always exist in large-scale region 1, region 2, cusp and polar cap current systems. Assuming that these small-scale field-aligned currents have current sheet structure, the width of current sheet is estimated to be 5-20 km at ionospheric altitude. By comparing the magnetometer data with charged particle and high frequency plasma wave data simultaneously obtained from EXOS-D, it is found that small-scale currents have one-to-one correspondence with localized electron precipitation events characterized by flux enhancement over a wide energy range from 10 eV to several keV and broadband electrostatic bursts occasionally extending above local plasma frequencies or electron cyclotron frequencies

Energy buildup in sheared force-free magnetic fields

Science.gov (United States)

Wolfson, Richard; Low, Boon C.

1992-01-01

Photospheric displacement of the footpoints of solar magnetic field lines results in shearing and twisting of the field, and consequently in the buildup of electric currents and magnetic free energy in the corona. The sudden release of this free energy may be the origin of eruptive events like coronal mass ejections, prominence eruptions, and flares. An important question is whether such an energy release may be accompanied by the opening of magnetic field lines that were previously closed, for such open field lines can provide a route for matter frozen into the field to escape the sun altogether. This paper presents the results of numerical calculations showing that opening of the magnetic field is permitted energetically, in that it is possible to build up more free energy in a sheared, closed, force-free magnetic field than is in a related magnetic configuration having both closed and open field lines. Whether or not the closed force-free field attains enough energy to become partially open depends on the form of the shear profile; the results presented compare the energy buildup for different shear profiles. Implications for solar activity are discussed briefly.

Field-aligned currents near the magnetosphere boundary

International Nuclear Information System (INIS)

Hones, E.W. Jr.

1984-01-01

This paper describes present thinking about the structure of magnetospheric boundary layers and their roles in the generation of the field-aligned currents that are observed in the polar regions. A principal effect of the momentum loss by magnetosheath plasma to the magnetosphere boundary regions just within the magnetopause, whether it be by a diffusive process or by magnetic reconnection, is the tailward pulling of the surface flux tubes relative to those deeper below the surface. The dayside region 1 currents at low altitudes flow along field lines in the resulting regions of magnetic shear. The direction of the shear and its magnitude, actually measured in the boundary region, confirm that the polarities and intensities of the dayside region 1 currents can be accounted for by this process. The low latitude boundary layer, formerly thought to be threaded entirely by closed field lines, now appears to contain at least some open field lines, newly reconnected, that are in the process of being swept into the high latitude tail to form the plasma mantle. The open flux tubes of the flux transfer events, thought to be the product of patchy reconnection have a spiral magnetic structure whose helicity is such as to suggest currents having the polarities of the region 1 currents. 13 references

Field-aligned currents near the magnetosphere boundary

International Nuclear Information System (INIS)

Hones, E.W. Jr.

1983-01-01

This paper reviews present thinking about the structure of magnetospheric boundary layers and their roles in the generation of the field-aligned currents that are observed in the polar regions. A principal effect of the momentum loss by magnetosheath plasma to the magnetosphere boundary regions just within the magnetopause, whether it be by a diffusive process or by magnetic reconnection, is the tailward pulling of surface flux tubes relative to those deeper below the surface. The dayside region 1 currents at low altitudes flow along field lines in the resulting regions of magnetic shear. The direction of the shear and its magnitude, measured in the boundary region, confirm tht the polarities and intensities of the dayside region 1 currents can be accounted for by this process. The low latitude boundary layer, formerly thought to be threaded entirely by closed field lines, now appears to contain at least some open field lines, newly reconnected, that are in the process of being swept into the high latitude tail to form the plasma mantle. The open flux tubes of the flux transfer events, thought to be the product of patchy reconnection have a spiral magnetic structure whose helicity is such as to suggest currents having the polarities of the region 1 currents

The use of the empirical mode decomposition for the identification of mean field aligned reference frames

Directory of Open Access Journals (Sweden)

Mauro Regi

2017-01-01

Full Text Available The magnetic field satellite data are usually referred to geocentric coordinate reference frame. Conversely, the magnetohydrodynamic waves modes in magnetized plasma depend on the ambient magnetic field, and is then useful to rotate the magnetic field measurements into the mean field aligned (MFA coordinate system. This reference frame is useful to study the ultra low frequency magnetic field variations along the direction of the mean field and perpendicularly to it. In order to identify the mean magnetic field the classical moving average (MAVG approach is usually adopted but, under particular conditions, this procedure induces undesired features, such as spectral alteration in the rotated components. We discuss these aspects promoting an alternative and more efficient method for mean field aligned projection, based on the empirical mode decomposition (EMD.

Polarization effects in molecular mechanical force fields

Energy Technology Data Exchange (ETDEWEB)

Cieplak, Piotr [Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92120 (United States); Dupradeau, Francois-Yves [UMR CNRS 6219-Faculte de Pharmacie, Universite de Picardie Jules Verne, 1 rue des Louvels, F-80037 Amiens (France); Duan, Yong [Genome Center and Department of Applied Science, University of California, Davis, One Shields Avenue, Davis, CA 95616 (United States); Wang Junmei, E-mail: pcieplak@burnham.or [Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Boulevard, ND9.136, Dallas, TX 75390-9050 (United States)

2009-08-19

The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component-polarization energy-and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations. (topical review)

Far-field and Fresnel Liquid Crystal Geometric Phase Holograms via Direct-Write Photo-Alignment

Directory of Open Access Journals (Sweden)

Xiao Xiang

2017-12-01

Full Text Available We study computer-generated geometric-phase holograms (GPHs realized by photo-aligned liquid crystals, in both simulation and experiment. We demonstrate both far-field and Fresnel holograms capable of producing far-field and near-field images with preserved fidelity for all wavelengths. The GPHs are fabricated by patterning a photo-alignment layer (PAL using a direct-write laser scanner and coating the surface with a polymerizable liquid crystal (i.e., a reactive mesogen. We study various recording pixel sizes, down to 3 μm, that are easily recorded in the PAL. We characterize the fabricated elements and find good agreement with theory and numerical simulation. Because of the wavelength independent geometric phase, the (phase fidelity of the replay images is preserved for all wavelengths, unlike conventional dynamic phase holograms. However, governed by the diffraction equation, the size and location of a reconstructed image depends on the replay wavelength for far-field and near-field GPHs, respectively. These offer interesting opportunities for white-light holography.

Planck intermediate results XXXV. Probing the role of the magnetic field in the formation of structure in molecular clouds

DEFF Research Database (Denmark)

Ade, P. A. R.; Aghanim, N.; Alves, M. I. R.

2016-01-01

emission observed by Planck at 353 GHz is representative of the projected morphology of the magnetic field in each region, i.e., we assume a constant dust grain alignment efficiency, independent of the local environment. Within most clouds we find that the relative orientation changes progressively...... for the gas dynamics at the scales probed by Planck. We compare the deduced magnetic field strength with estimates we obtain from other methods and discuss the implications of the Planck observations for the general picture of molecular cloud formation and evolution....

Vertically aligned carbon nanotube field-effect transistors

KAUST Repository

Li, Jingqi

2012-10-01

Vertically aligned carbon nanotube field-effect transistors (CNTFETs) have been developed using pure semiconducting carbon nanotubes. The source and drain were vertically stacked, separated by a dielectric, and the carbon nanotubes were placed on the sidewall of the stack to bridge the source and drain. Both the effective gate dielectric and gate electrode were normal to the substrate surface. The channel length is determined by the dielectric thickness between source and drain electrodes, making it easier to fabricate sub-micrometer transistors without using time-consuming electron beam lithography. The transistor area is much smaller than the planar CNTFET due to the vertical arrangement of source and drain and the reduced channel area. © 2012 Elsevier Ltd. All rights reserved.

Electronic properties of field aligned CrO2 powders

International Nuclear Information System (INIS)

Tripathy, D.; Adeyeye, A.O.

2005-01-01

We have investigated in detail the electronic transport properties of half metallic CrO 2 powder-based devices, fabricated using optical lithography and field alignment technique. A transition in the conduction mechanism from spin-dependent intergranular tunneling to inelastic hopping was observed at 215 K. This transition temperature shifts to 230 K in the presence of 10 kOe field cooling due to reduction of the spin-independent hopping conductance channel. I-V characteristics exhibit strong temperature dependence and are non-linear even at room temperature. Our experimental results are in good agreement with a simple theoretical model. A novel 'double switching' phenomenon was observed in the I-V curves below the transition temperature

Aqueous electrolyte surfaces in strong electric fields: molecular insight into nanoscale jets and bridges

Science.gov (United States)

Jirsák, Jan; Moučka, Filip; Škvor, Jiří; Nezbeda, Ivo

2015-04-01

Exposing aqueous surfaces to a strong electric field gives rise to interesting phenomena, such as formation of a floating water bridge or an eruption of a jet in electrospinning. In an effort to account for the phenomena at the molecular level, we performed molecular dynamics simulations using several protocols on both pure water and aqueous solutions of sodium chloride subjected to an electrostatic field. All simulations consistently point to the same mechanisms which govern the rearrangement of the originally planar surface. The results show that the phenomena are primarily governed by an orientational reordering of the water molecules driven by the applied field. It is demonstrated that, for pure water, a sufficiently strong field yields a columnar structure parallel to the field with an anisotropic arrangement of the water molecules with their dipole moments aligned along the applied field not only in the surface layer but over the entire cross section of the column. Nonetheless, the number of hydrogen bonds per molecule does not seem to be affected by the field regardless of its strength and molecule's orientation. In the electrolyte solutions, the ionic charge is able to overcome the effect of the external field tending to arrange the water molecules radially in the first coordination shell of an ion. The ion-water interaction interferes thus with the water-electric field interaction, and the competition between these two forces (i.e., strength of the field versus concentration) provides the key mechanism determining the stability of the observed structures.

Shape, size, velocity and field-aligned currents of dayside plasma injections: a multi-altitude study

Directory of Open Access Journals (Sweden)

A. Marchaudon

2009-03-01

Full Text Available On 20 February 2005, Cluster in the outer magnetosphere and Double Star-2 (TC-2 at mid-altitude are situated in the vicinity of the northern cusp/mantle, with Cluster moving sunward and TC-2 anti-sunward. Their magnetic footprints come very close together at about 15:28 UT, over the common field-of-view of SuperDARN radars. Thanks to this conjunction, we determine the velocity, the transverse sizes, perpendicular and parallel to this velocity, and the shape of three magnetic flux tubes of magnetosheath plasma injection. The velocity of the structures determined from the Cluster four-spacecraft timing analysis is almost purely antisunward, in contrast with the antisunward and duskward convection velocity inside the flux tubes. The transverse sizes are defined from the Cluster-TC-2 separation perpendicular to the magnetic field, and from the time spent by a Cluster spacecraft in one structure; they are comprised between 0.6 and 2 RE in agreement with previous studies. Finally, using a comparison between the eigenvectors deduced from a variance analysis of the magnetic perturbation at the four Cluster and at TC-2, we show that the upstream side of the injection flux tubes is magnetically well defined, with even a concave front for the third one giving a bean-like shape, whereas the downstream side is far more turbulent. We also realise the first quantitative comparison between field-aligned currents at Cluster calculated with the curlometer technique and with the single-spacecraft method, assuming infinite parallel current sheets and taking into account the velocity of the injection flux tubes. The results agree nicely, confirming the validity of both methods. Finally, we compare the field-aligned current distribution of the three injection flux tubes at the altitudes of Cluster and TC-2. Both profiles are fairly similar, with mainly a pair of opposite field-aligned currents, upward at low-latitude and downward at high-latitude. In terms of

Growth of vertically aligned arrays of carbon nanotubes for high field emission

International Nuclear Information System (INIS)

Kim, D.; Lim, S.H.; Guilley, A.J.; Cojocaru, C.S.; Bouree, J.E.; Vila, L.; Ryu, J.H.; Park, K.C.; Jang, J.

2008-01-01

Vertically aligned multi-walled carbon nanotubes have been grown on Ni-coated silicon substrates, by using either direct current diode or triode plasma-enhanced chemical vapor deposition at low temperature (around 620 deg. C). Acetylene gas has been used as the carbon source while ammonia and hydrogen have been used for etching. However densely packed (∼ 10 9 cm -2 ) CNTs were obtained when the pressure was ∼ 100 Pa. The alignment of nanotubes is a necessary, but not a sufficient condition in order to get an efficient electron emission: the growth of nanotubes should be controlled along regular arrays, in order to minimize the electrostatic interactions between them. So a three dimensional numerical simulation has been developed to calculate the local electric field in the vicinity of the tips for a finite square array of nanotubes and thus to calculate the maximum of the electron emission current density as a function of the spacing between nanotubes. Finally the triode plasma-enhanced process combined with pre-patterned catalyst films (using different lithography techniques) has been chosen in order to grow regular arrays of aligned CNTs with different pitches in the micrometer range. The comparison between the experimental and the simulation data permits to define the most efficient CNT-based electron field emitters

Image stack alignment in full-field X-ray absorption spectroscopy using SIFT_PyOCL.

Science.gov (United States)

Paleo, Pierre; Pouyet, Emeline; Kieffer, Jérôme

2014-03-01

Full-field X-ray absorption spectroscopy experiments allow the acquisition of millions of spectra within minutes. However, the construction of the hyperspectral image requires an image alignment procedure with sub-pixel precision. While the image correlation algorithm has originally been used for image re-alignment using translations, the Scale Invariant Feature Transform (SIFT) algorithm (which is by design robust versus rotation, illumination change, translation and scaling) presents an additional advantage: the alignment can be limited to a region of interest of any arbitrary shape. In this context, a Python module, named SIFT_PyOCL, has been developed. It implements a parallel version of the SIFT algorithm in OpenCL, providing high-speed image registration and alignment both on processors and graphics cards. The performance of the algorithm allows online processing of large datasets.

Force-free field model of ball lightning

International Nuclear Information System (INIS)

Tsui, K.H.

2001-01-01

Due to the nature that the force-free magnetic field, whose current carried by the conducting plasma is everywhere parallel to the magnetic field it generates, is the minimum energy configuration under the constraint of magnetic helicity conservation, ball lightning is considered as a self-organized phenomenon with a plasma fireball immersed in a spherical force-free magnetic field. Since this field does not exert force on the plasma, the plasma pressure, by itself, is in equilibrium with the surrounding environment, and the force-free magnetic field can take on any value without affecting the plasma. Due to this second feature, singular solutions of the magnetic field that are otherwise excluded are allowed, which enable a large amount of energy to be stored to sustain the ball lightning. The singularity is truncated only by the physical limit of current density that a plasma can carry. Scaling the customary soccer-size fireball to larger dimensions could account for day and night sightings of luminous objects in the sky

Morphologically Aligned Cation-Exchange Membranes by a Pulsed Electric Field for Reverse Electrodialysis.

Science.gov (United States)

Lee, Ju-Young; Kim, Jae-Hun; Lee, Ju-Hyuk; Kim, Seok; Moon, Seung-Hyeon

2015-07-21

A low-resistance ion-exchange membrane is essential to achieve the high-performance energy conversion or storage systems. The formation methods for low-resistance membranes are various; one of the methods is the ion channel alignment of an ion-exchange membrane under a direct current (DC) electric field. In this study, we suggest a more effective alignment method than the process with the DC electric field. First, an ion-exchange membrane was prepared under a pulsed electric field [alternating current (AC) mode] to enhance the effectiveness of the alignment. The membrane properties and the performance in reverse electrodialysis (RED) were then examined to assess the membrane resistance and ion selectivity. The results show that the membrane electrical resistance (MER) had a lower value of 0.86 Ω cm(2) for the AC membrane than 2.13 Ω cm(2) observed for the DC membrane and 4.30 Ω cm(2) observed for the pristine membrane. Furthermore, RED achieved 1.34 W/m(2) of maximum power density for the AC membrane, whereas that for the DC membrane was found to be 1.14 W/m(2) [a RED stack assembled with CMX, used as a commercial cation-exchange membrane (CEM), showed 1.07 W/m(2)]. Thereby, the novel preparation process for a remarkable low-resistance membrane with high ion selectivity was demonstrated.

An alignment-free method to find similarity among protein sequences via the general form of Chou's pseudo amino acid composition.

Science.gov (United States)

Gupta, M K; Niyogi, R; Misra, M

2013-01-01

In this paper, we propose a method to create the 60-dimensional feature vector for protein sequences via the general form of pseudo amino acid composition. The construction of the feature vector is based on the contents of amino acids, total distance of each amino acid from the first amino acid in the protein sequence and the distribution of 20 amino acids. The obtained cosine distance metric (also called the similarity matrix) is used to construct the phylogenetic tree by the neighbour joining method. In order to show the applicability of our approach, we tested it on three proteins: 1) ND5 protein sequences from nine species, 2) ND6 protein sequences from eight species, and 3) 50 coronavirus spike proteins. The results are in agreement with known history and the output from the multiple sequence alignment program ClustalW, which is widely used. We have also compared our phylogenetic results with six other recently proposed alignment-free methods. These comparisons show that our proposed method gives a more consistent biological relationship than the others. In addition, the time complexity is linear and space required is less as compared with other alignment-free methods that use graphical representation. It should be noted that the multiple sequence alignment method has exponential time complexity.

Molecular dynamics in high electric fields

International Nuclear Information System (INIS)

Apostol, M.; Cune, L.C.

2016-01-01

Highlights: • New method for rotation molecular spectra in high electric fields. • Parametric resonances – new features in spectra. • New elementary excitations in polar solids from dipolar interaction (“dipolons”). • Discussion about a possible origin of the ferroelectricity from dipolar interactions. - Abstract: Molecular rotation spectra, generated by the coupling of the molecular electric-dipole moments to an external time-dependent electric field, are discussed in a few particular conditions which can be of some experimental interest. First, the spherical-pendulum molecular model is reviewed, with the aim of introducing an approximate method which consists in the separation of the azimuthal and zenithal motions. Second, rotation spectra are considered in the presence of a static electric field. Two particular cases are analyzed, corresponding to strong and weak fields. In both cases the classical motion of the dipoles consists of rotations and vibrations about equilibrium positions; this motion may exhibit parametric resonances. For strong fields a large macroscopic electric polarization may appear. This situation may be relevant for polar matter (like pyroelectrics, ferroelectrics), or for heavy impurities embedded in a polar solid. The dipolar interaction is analyzed in polar condensed matter, where it is shown that new polarization modes appear for a spontaneous macroscopic electric polarization (these modes are tentatively called “dipolons”); one of the polarization modes is related to parametric resonances. The extension of these considerations to magnetic dipoles is briefly discussed. The treatment is extended to strong electric fields which oscillate with a high frequency, as those provided by high-power lasers. It is shown that the effect of such fields on molecular dynamics is governed by a much weaker, effective, renormalized, static electric field.

Intense auroral field-aligned currents and electrojets detected by rocket-borne fluxgate magnetometer

International Nuclear Information System (INIS)

Tohyama, Fumio; Fukunishi, Hiroshi; Takahashi, Takao; Kokubun, Susumu; Fujii, Ryoichi; Yamagishi, Hisao.

1988-01-01

The S-310JA-11 and S-310JA-12 rockets, having a vector magnetometer with high sensitivity (1.8 nT) and high sampling frequency (100 Hz), were launched into the aurora on May 29 and July 12, 1985, from Syowa Station, Antarctica. The S-310JA-11 rocket penetrated twice quiet arcs, while the S-310JA-12 rocket traversed across intense and active auroral arcs during a large magnetic substorm. In the S-310JA-12 rocket experiment, intense field-aligned currents of 400 - 600 nT were observed when the rocket penetrated an active arc during the descending flight. The magnetometer on board the S-310JA-12 rocket also detected intense electrojet currents with a center at 110 km on the upward leg and at 108 km on the downward leg. The magnetometer data of the S-310JA-11 rocket showed no distinguished magnetic field variation due to field-aligned current and electrojet. (author)

CAFE: aCcelerated Alignment-FrEe sequence analysis.

Science.gov (United States)

Lu, Yang Young; Tang, Kujin; Ren, Jie; Fuhrman, Jed A; Waterman, Michael S; Sun, Fengzhu

2017-07-03

Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, $d_2^*$ and $d_2^S$ are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures. CAFE allows for both assembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standard PHYLIP format. In downstream analyses, CAFE can also be used to visualize the pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. CAFE serves as a general k-mer based alignment-free analysis platform for studying the relationships among genomes and metagenomes, and is freely available at https://github.com/younglululu/CAFE. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

BinAligner: a heuristic method to align biological networks.

Science.gov (United States)

Yang, Jialiang; Li, Jun; Grünewald, Stefan; Wan, Xiu-Feng

2013-01-01

The advances in high throughput omics technologies have made it possible to characterize molecular interactions within and across various species. Alignments and comparison of molecular networks across species will help detect orthologs and conserved functional modules and provide insights on the evolutionary relationships of the compared species. However, such analyses are not trivial due to the complexity of network and high computational cost. Here we develop a mixture of global and local algorithm, BinAligner, for network alignments. Based on the hypotheses that the similarity between two vertices across networks would be context dependent and that the information from the edges and the structures of subnetworks can be more informative than vertices alone, two scoring schema, 1-neighborhood subnetwork and graphlet, were introduced to derive the scoring matrices between networks, besides the commonly used scoring scheme from vertices. Then the alignment problem is formulated as an assignment problem, which is solved by the combinatorial optimization algorithm, such as the Hungarian method. The proposed algorithm was applied and validated in aligning the protein-protein interaction network of Kaposi's sarcoma associated herpesvirus (KSHV) and that of varicella zoster virus (VZV). Interestingly, we identified several putative functional orthologous proteins with similar functions but very low sequence similarity between the two viruses. For example, KSHV open reading frame 56 (ORF56) and VZV ORF55 are helicase-primase subunits with sequence identity 14.6%, and KSHV ORF75 and VZV ORF44 are tegument proteins with sequence identity 15.3%. These functional pairs can not be identified if one restricts the alignment into orthologous protein pairs. In addition, BinAligner identified a conserved pathway between two viruses, which consists of 7 orthologous protein pairs and these proteins are connected by conserved links. This pathway might be crucial for virus packing and

Hamiltonian representation of divergence-free fields

International Nuclear Information System (INIS)

Boozer, A.H.

1984-11-01

Globally divergence-free fields, such as the magnetic field and the vorticity, can be described by a two degree of freedom Hamiltonian. The Hamiltonian function provides a complete topological description of the field lines. The formulation also separates the dissipative and inertial time scale evolution of the magnetic and the vorticity fields

Graphene nanoribbon field-effect transistors fabricated by etchant-free transfer from Au(788)

Science.gov (United States)

Ohtomo, Manabu; Sekine, Yoshiaki; Hibino, Hiroki; Yamamoto, Hideki

2018-01-01

We report etching-free and iodine-free transfer of highly aligned array of armchair-edge graphene nanoribbons (ACGNRs) and their field-effect transistor (FET) characteristics. They were prepared by on-surface polymerization on Au(788) templates. The ACGNRs were mechanically delaminated and transferred onto insulating substrates with the aid of a nano-porous support layer composed of hydrogen silsesquioxane (HSQ). The key process in the mechanical delamination is the intercalation of octanethiol self-assembled monolayers (SAMs), which penetrate the HSQ layer and intercalate between the ACGNRs and Au(788). After the transfer, the octanethiol SAMs were removed with Piranha solution, enabling the reuse of the Au single crystals. The FETs fabricated with the transferred ACGNR array showed ambipolar behavior when the channel length was as long as 60 nm. Quasi-one-dimensional conductivity was observed, which implies a good alignment of GNRs after the transfer. In contrast, short-channel ACGNR FETs (channel length ˜20 nm) suffer from a geometry-dependent short-channel effect. This effect is more severe in the FETs with ACGNRs parallel to the channel, which is an ideal geometry, than in ones perpendicular to the channel. Since the ID-VD curve is well fitted by the power-law model, the short-channel effect likely stems from the space-charge limited current effect, while the wide charge-transfer region in the GNR channel can be another possible cause for the short-channel effect. These results provide us with important insights into the designing short-channel GNR-FETs with improved performance.

A numerical model of ionospheric convection derived from field-aligned current and the corresponding conductivity

International Nuclear Information System (INIS)

Blomberg, L.G.; Marklund, G.T.

1988-03-01

A numerical model for the calculation of ionospheric convection patterns from given distributions of field-aligned current and ionospheric conductivity is described. The model includes a coupling between the conductivity and the field-aligned current, so that the conductivity peaks in regions of upward current, as usually observed by measurements. The model is very flexible in that the input distributions, the field-aligned current and the conductivity, have been parameterized in a convenient way. From the primary model output, namely the ionospheric electrostatic potential (or convection) in the corotating frame, a number of other quantities can be computed. These include: the potential in a Sun-fixed frame, the distribution of ionospheric (horizontal) current, and the Joule heating in the ionosphere. This model has been used together with input data inferred from satellite measurements to calculate the high-latitude potential distribution prevailing during a particular event. The model potential variation along the satellite orbit was found to be in excellent agreement with the measured electric field. The model has also been used to study some fundamental properties of the electrodynamics of the high-latitude ionosphere. The results of these different applications of the model have been published separately. (With 23 refs.) (authors)

Galactic cosmic ray gradients, field-aligned and latitudinal, among Voyagers 1/2 and IMP-8

International Nuclear Information System (INIS)

Roelof, E.C.; Decker, R.B.; Krimigis, S.M.; Venkatesan, D.; Lazarus, A.J.

1982-01-01

The tandem Earth-Jupiter trajectories of the Voyager 1/2 spacecraft, combined with baseline measurements from the earth-orbiting IMP-7/8 spacecraft, provide the first opportunity for unambiguously separating latitude from radial or field-aligned effects in galactic cosmic ray gradients. Anti-coincidence solid-state detectors on the Voyager 1/2 LECP experiment measure nucleons > or approximately 20 MeV/nuc with large (28 cm 2 ) omnidirectional geometry factors. Anti-coincidence scintillators on the IMP-7/8 CPME with omnidirectional geometry factors comparable to those on Voyager measure nucleons > or approximately 35 MeV/nuc. Because the Voyagers are well-connected via the interplanetary magnetic field (IMF) to the near-Earth vicinity throughout their transit from 1-5 AU (September 1977 - February 1979), we obtained the first direct measurement of field-aligned gradients, i.e., those that do not depend upon ''corotation'' from one spacecraft to another over many days. Another new result is the unambiguous identification of nonuniform latitudinal gradients approximately 2-5% degree -1 in structures lasting 10-30 days. There is additional evidence for somewhat smaller latitudinal gradients, north to south and probably mixed with small field-aligned gradients -1 , which persist for several solar rotations

Molecular alignment and orientation in short pulse laser fields

DEFF Research Database (Denmark)

Henriksen, Niels Engholm

1999-01-01

An analytical expression for the propagator associated with impulsive excitation is derived based on the Magnus expansion. We apply this expression to the excitation of angular motion out of a rotational eigenstate for a linear polar molecule in a plane polarized electromagnetic field. We show...

Supersonic free jet, molecular free regime; Fondamenti fisici dei fasci molecolari supersonici. Parte 7. Il getto libero supersonico

Energy Technology Data Exchange (ETDEWEB)

Sanna, G. [ENEA, Centro Ricerche Frascati, Rome (Italy). Dipt. Innovazione; Tomassetti, G. [L' Aquila Univ., L' Aquila (Italy). Dipt. di Fisica

1999-07-01

The structure of the free jet emitted by a converging nozzle as obtained by the method of characteristics by Ashkenas e Sherman is described in details. In particular the dependence of the field variable by the distance from the nozzle is given. The transition from continuum to molecular free regime is then considered and the sudden freeze approximation is introduced. The processing of monoatomic and polyatomic gasses is also considered. [Italian] Le caratteristiche del campo di flusso in regime continuo di un getto libero supersonico ottenute col metodo delle caratteristiche da Ashekanas e Sherman sono messe in evidenza. In paricolare le relazioni analitiche per i parametri di flusso in funzione della distanza dal nozzle sono riportate. Viene poi considerata la transizione al regime molecolare ed e' introdotta la sudden freeze approximation. Vengono anche considerate le situazioni di non equilibrio tra gradi di liberta' interni ed esterni.

Field-free orientation of molecules

DEFF Research Database (Denmark)

Machholm, Mette; Henriksen, Niels Engholm

2001-01-01

The excitation of angular motion, in particular, the creation of a wave packet in the angular degrees of freedom via short-pulse, off-resonant excitation with respect to rotational transitions, was examined. The key result was that field-free time-dependent orientation for a molecule like LiH can...... be generated after the turn-off of a state-of-the-art electromagnetic half-cycle pulse.......The excitation of angular motion, in particular, the creation of a wave packet in the angular degrees of freedom via short-pulse, off-resonant excitation with respect to rotational transitions, was examined. The key result was that field-free time-dependent orientation for a molecule like LiH can...

Field-aligned current density versus electric potential characteristics for magnetospheric flux tubes

International Nuclear Information System (INIS)

Lemaire, J.; Scherer, M.

1983-01-01

The field-aligned current density (Jsub(tot)) is a non-linear function of the applied potential difference (phi) between the ionosphere and the magnetosphere. This nonlinear function has been calculated for plasma boundary conditions typical in a dayside cusp magnetic flux tube. The J-characteristic of such a flux tube changes when the temperatures of the warm magnetospheric electrons and of the cold ionospheric electrons are modified; it changes also when the relative density of the warm plasma is modified; the presence of trapped secondary electrons changes also the J-characteristic. The partial currents contributed by the warm and cold electrons, and by warm and cold ions are illustrated. The dynamic characteristic of an electric circuit depends on the static characteristic of each component of the sytem: i.e. the resistive ionosphere, the return current region, and the region of particle precipitation whose field-aligned current/voltage characteristics have been studied in this article

Effects of atmospheric oscillations on the field-aligned ion motions in the polar F-region

Directory of Open Access Journals (Sweden)

S. Oyama

Full Text Available The field-aligned neutral oscillations in the F-region (altitudes between 165 and 275 km were compared using data obtained simultaneously with two independent instruments: the European Incoherent Scatter (EISCAT UHF radar and a scanning Fabry-Perot interferometer (FPI. During the night of February 8, 1997, simultaneous observations with these instruments were conducted at Tromsø, Norway. Theoretically, the field-aligned neutral wind velocity can be obtained from the field-aligned ion velocity and by diffusion and ambipolar diffusion velocities. We thus derived field-aligned neutral wind velocities from the plasma velocities in EISCAT radar data. They were compared with those observed with the FPI (λ=630.0 nm, which are assumed to be weighted height averages of the actual neutral wind. The weighting function is the normalized height dependent emission rate. We used two model weighting functions to derive the neutral wind from EISCAT data. One was that the neutral wind velocity observed with the FPI is velocity integrated over the entire emission layer and multiplied by the theoretical normalized emission rate. The other was that the neutral wind velocity observed with the FPI corresponds to the velocity only around an altitude where the emission rate has a peak. Differences between the two methods were identified, but not completely clarified. However, the neutral wind velocities from both instruments had peak-to-peak correspondences at oscillation periods of about 10–40 min, shorter than that for the momentum transfer from ions to neutrals, but longer than from neutrals to ions. The synchronizing motions in the neutral wind velocities suggest that the momentum transfer from neutrals to ions was thought to be dominant for the observed field-aligned oscillations rather than the transfer from ions to neutrals. It is concluded that during the observation, the plasma oscillations observed with the EISCAT radar at different altitudes

Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer.

Science.gov (United States)

Bernard, Guillaume; Chan, Cheong Xin; Ragan, Mark A

2016-07-01

Alignment-free (AF) approaches have recently been highlighted as alternatives to methods based on multiple sequence alignment in phylogenetic inference. However, the sensitivity of AF methods to genome-scale evolutionary scenarios is little known. Here, using simulated microbial genome data we systematically assess the sensitivity of nine AF methods to three important evolutionary scenarios: sequence divergence, lateral genetic transfer (LGT) and genome rearrangement. Among these, AF methods are most sensitive to the extent of sequence divergence, less sensitive to low and moderate frequencies of LGT, and most robust against genome rearrangement. We describe the application of AF methods to three well-studied empirical genome datasets, and introduce a new application of the jackknife to assess node support. Our results demonstrate that AF phylogenomics is computationally scalable to multi-genome data and can generate biologically meaningful phylogenies and insights into microbial evolution.

Free fields on the Poincare group

Energy Technology Data Exchange (ETDEWEB)

Toller, M; Vanzo, L [Dipartimento di Matematica e Fisica della Libera Universita di Trento, Italy

1978-07-01

Using a general formalism the tensor and spinor free fields as fields defined on the Poincare group manifold is treated. From an action principle it is deduced, besides the usual Klein-Gordon or Dirac equations, also the equations which describe the transformation properties of the fields under proper Lorentz transformations.

Direct spectroscopic evidence for competition between thermal molecular agitation and magnetic field in a tetrameric protein in aqueous solution

Science.gov (United States)

Calabrò, Emanuele; Magazù, Salvatore

2018-05-01

Samples of a typical tetrameric protein, the hemoglobin, at the concentration of 150 mg/ml in bidistilled water solution, were exposed to a uniform magnetic field at 200 mT at different temperatures of 15∘C, 40∘C and 65∘C. Fourier Transform Infrared Spectroscopy was used to analyze the response of the secondary structure of the protein to both stress agents, heating and static magnetic field. The most relevant result which was observed was the significant increasing in intensity of the Amide I band after exposure to the uniform magnetic field at the room temperature of 15∘C. This result can be explained assuming that protein's α-helices aligned along the direction of the applied magnetic field due to their large dipole moment, inducing the alignment of the entire protein. Increasing of temperature up to 40∘C and 65∘C induced a significant reduction of the increasing in intensity of the Amide I band. This effect may be easily explained assuming that Brownian motion of the protein in water solution caused by thermal molecular agitation increased with increasing of temperature, contrasting the effect of the torque of the magnetic field applied to the protein in water solution.

Tuning vertical alignment and field emission properties of multi-walled carbon nanotube bundles

Science.gov (United States)

Sreekanth, M.; Ghosh, S.; Srivastava, P.

2018-01-01

We report the growth of vertically aligned carbon nanotube bundles on Si substrate by thermal chemical vapor deposition technique. Vertical alignment was achieved without any carrier gas or lithography-assisted deposition. Growth has been carried out at 850 °C for different quantities of solution of xylene and ferrocene ranging from 2.25 to 3.00 ml in steps of 0.25 ml at a fixed concentration of 0.02 gm (ferrocene) per ml. To understand the growth mechanism, deposition was carried out for different concentrations of the solution by changing only the ferrocene quantity, ranging from 0.01 to 0.03 gm/ml. A tunable vertical alignment of multi-walled carbon nanotubes (CNTs) has been achieved by this process and examined by scanning and transmission electron microscopic techniques. Micro-crystalline structural analysis has been done using Raman spectroscopy. A systematic variation in field emission (FE) current density has been observed. The highest FE current density is seen for the film grown with 0.02 gm/ml concentration, which is attributed to the better alignment of CNTs, less structural disorder and less entanglement of CNTs on the surface. The alignment of CNTs has been qualitatively understood on the basis of self-assembled catalytic particles.

Radiation-induced microenvironments - The molecular basis for free flap complications in the pre-irradiated field?

International Nuclear Information System (INIS)

Mueller, Cornelia Katharina; Schultze-Mosgau, Stefan

2009-01-01

Background and purpose: The effect of preoperative radio- or radiochemotherapy on the survival of free flaps used for head and neck reconstruction is reported in a contradictory way. Although there is a lot of knowledge on radiation-induced wound healing disorders from animal models there are no investigations on human patients so far. Our prospective study aimed at clarifying the effect of radiotherapy on clinically apparent free flap complications and on correlating them with radiation-induced extracellular matrix (ECM) remodeling. Materials and methods: Healing of 114 free flaps was monitored in a prospective study and correlated with different anamnestic features, such as diabetes and radio- or radiochemotherapy using multivariate regression. During the operation connective tissue biopsies were harvested from the graft beds and analyzed for Transforming Growth Factor (TGF)-β 1 -expression by means of Western blotting as well as Tissue Inhibitor of Matrix-Metallo-Proteinase (TIMP)-1 and Matrix-Metallo-Proteinase (MMP)-1 by immunohistochemistry. Results: History of radio- or radiochemotherapy was the only factor significantly predicting free flap complications. Radiochemotherapy resulted in a significant increase in TGF-β 1 - and TIMP-1-expression, while MMP-1-expression was not significantly altered. Radiotherapy alone significantly increased TIMP-1-expression without detectable effects on TGF-β 1 and MMP-1. Conclusions: Radio- and radiochemotherapy alter graft bed ECM organization prior to surgery. This alteration impacts significantly on free flap survival in the pre-irradiated field.

Self-propelled in-tube shuttle and control system for automated measurements of magnetic field alignment

International Nuclear Information System (INIS)

Boroski, W.N.; Nicol, T.H.; Pidcoe, S.V.

1990-03-01

A magnetic field alignment gauge is used to measure the field angle as a function of axial position in each of the magnets for the Superconducting Super Collider (SSC). Present measurements are made by manually pushing the through the magnet bore tube and stopping at intervals to record field measurements. Gauge location is controlled through graduation marks and alignment pins on the push rods. Field measurements are recorded on a logging multimeter with tape output. Described is a computerized control system being developed to replace the manual procedure for field alignment measurements. The automated system employs a pneumatic walking device to move the measurement gauge through the bore tube. Movement of the device, called the Self-Propelled In-Tube Shuttle (SPITS), is accomplished through an integral, gas driven, double-acting cylinder. The motion of the SPITS is transferred to the bore tube by means of a pair of controlled, retractable support feet. Control of the SPITS is accomplished through an RS-422 interface from an IBM-compatible computer to a series of solenoid-actuated air valves. Direction of SPITS travel is determined by the air-valve sequence, and is managed through the control software. Precise axial position of the gauge within the magnet is returned to the control system through an optically-encoded digital position transducer attached to the shuttle. Discussed is the performance of the transport device and control system during preliminary testing of the first prototype shuttle. 1 ref., 7 figs

Galaxy Alignments: Theory, Modelling & Simulations

Science.gov (United States)

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.

Progress in ETA-II magnetic field alignment using stretched wire and low energy electron beam techniques

International Nuclear Information System (INIS)

Griffith, L.V.; Deadrick, F.J.

1991-01-01

Flux line alignment of the solenoidal focus magnets used on the ETA-II linear induction accelerator is a key element leading to a reduction of beam corkscrew motion. Two techniques have been used on the ETA-II accelerator to measure and establish magnet alignment. A low energy electron beam has been used to directly map magnetic field lines, and recent work has utilized a pulsed stretched wire technique to measure magnet tilts and offsets with respect to a reference axis. This paper reports on the techniques used in the ETA-II accelerator alignment, and presents results from those measurements which show that accelerator is magnetically aligned to within ∼ ± 200 microns

Aligned Layers of Silver Nano-Fibers

Directory of Open Access Journals (Sweden)

Andrii B. Golovin

2012-02-01

Full Text Available 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.

Applications of free-jet, molecular beam, mass spectrometric sampling: Proceedings

Energy Technology Data Exchange (ETDEWEB)

Milne, T. [ed.

1995-03-01

Over the past 35 years, the study of die behavior and uses of free-jet expansions for laboratory experiments has greatly expanded and matured. Not the least of these uses of free-jet expansions, is that of extractive sampling from high temperature, reactive systems. The conversion of the free-jet expanded gases to molecular flow for direct introduction into the ion source of a mass spectrometer offers several advantages, to be illustrated in these pages. Two meetings on this subject were held in 1965 and 1972 in Missouri, sponsored by the Office of Naval Research and Midwest Research Institute. At these meetings rarefied gas dynamicists came together with scientists using free-jet sampling for analytical purposes. After much too long a time, this workshop was convened to bring together modem practitioners of FJMBS (Free-jet, Molecular-beam, mass spectrometry) and long time students of the free-jet process itself, to assess the current state of the art and to forge a community that can foster the development of this novel analytical approach. This proceedings is comprised of 38 individually submitted papers. Individual papers are indexed separately on the Energy Data Base.

Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains.

Science.gov (United States)

Liao, Weinan; Ren, Jie; Wang, Kun; Wang, Shun; Zeng, Feng; Wang, Ying; Sun, Fengzhu

2016-11-23

The comparison between microbial sequencing data is critical to understand the dynamics of microbial communities. The alignment-based tools analyzing metagenomic datasets require reference sequences and read alignments. The available alignment-free dissimilarity approaches model the background sequences with Fixed Order Markov Chain (FOMC) yielding promising results for the comparison of microbial communities. However, in FOMC, the number of parameters grows exponentially with the increase of the order of Markov Chain (MC). Under a fixed high order of MC, the parameters might not be accurately estimated owing to the limitation of sequencing depth. In our study, we investigate an alternative to FOMC to model background sequences with the data-driven Variable Length Markov Chain (VLMC) in metatranscriptomic data. The VLMC originally designed for long sequences was extended to apply to high-throughput sequencing reads and the strategies to estimate the corresponding parameters were developed. The flexible number of parameters in VLMC avoids estimating the vast number of parameters of high-order MC under limited sequencing depth. Different from the manual selection in FOMC, VLMC determines the MC order adaptively. Several beta diversity measures based on VLMC were applied to compare the bacterial RNA-Seq and metatranscriptomic datasets. Experiments show that VLMC outperforms FOMC to model the background sequences in transcriptomic and metatranscriptomic samples. A software pipeline is available at https://d2vlmc.codeplex.com.

Combined CT-based and image-free navigation systems in TKA reduces postoperative outliers of rotational alignment of the tibial component.

Science.gov (United States)

Mitsuhashi, Shota; Akamatsu, Yasushi; Kobayashi, Hideo; Kusayama, Yoshihiro; Kumagai, Ken; Saito, Tomoyuki

2018-02-01

Rotational malpositioning of the tibial component can lead to poor functional outcome in TKA. Although various surgical techniques have been proposed, precise rotational placement of the tibial component was difficult to accomplish even with the use of a navigation system. The purpose of this study is to assess whether combined CT-based and image-free navigation systems replicate accurately the rotational alignment of tibial component that was preoperatively planned on CT, compared with the conventional method. We compared the number of outliers for rotational alignment of the tibial component using combined CT-based and image-free navigation systems (navigated group) with those of conventional method (conventional group). Seventy-two TKAs were performed between May 2012 and December 2014. In the navigated group, the anteroposterior axis was prepared using CT-based navigation system and the tibial component was positioned under control of the navigation. In the conventional group, the tibial component was placed with reference to the Akagi line that was determined visually. Fisher's exact probability test was performed to evaluate the results. There was a significant difference between the two groups with regard to the number of outliers: 3 outliers in the navigated group compared with 12 outliers in the conventional group (P image-free navigation systems decreased the number of rotational outliers of tibial component, and was helpful for the replication of the accurate rotational alignment of the tibial component that was preoperatively planned.

Tidal alignment of galaxies

Energy Technology Data Exchange (ETDEWEB)

Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš

2015-08-01

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 of 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.

Vertically aligned carbon nanotubes/diamond double-layered structure for improved field electron emission stability

Energy Technology Data Exchange (ETDEWEB)

Yang, L., E-mail: qiaoqin.yang@mail.usask.ca; Yang, Q.; Zhang, C.; Li, Y.S.

2013-12-31

A double-layered nanostructure consisting of a layer of vertically aligned Carbon Nanotubes (CNTs) and a layer of diamond beneath has been synthesized on silicon substrate by Hot Filament Chemical Vapor Deposition. The synthesis was achieved by first depositing a layer of diamond on silicon and then depositing a top layer of vertically aligned CNTs by applying a negative bias on the substrate holder. The growth of CNTs was catalyzed by a thin layer of spin-coated iron nitride. The surface morphology and structure of the CNTs/diamond double-layered structure were characterized by Scanning Electron Microscope, Energy Dispersive X-ray spectrum, and Raman Spectroscopy. Their field electron emission (FEE) properties were measured by KEITHLEY 237 high voltage measurement unit, showing much higher FEE current stability than single layered CNTs. - Highlights: • A new double-layered nanostructure consisting of a layer of vertically aligned CNTs and a layer of diamond beneath has been synthesized by hot filament chemical vapor deposition. • This double-layered structure exhibits superior field electron emission stability. • The improvement of emission stability is due to the combination of the unique properties of diamond and CNTs.

Molecular orientation in aligned electrospun polyimide nanofibers by polarized FT-IR spectroscopy.

Science.gov (United States)

Yang, Haoqi; Jiang, Shaohua; Fang, Hong; Hu, Xiaowu; Duan, Gaigai; Hou, Haoqing

2018-07-05

Quantitative explanation on the improved mechanical properties of aligned electrospun polyimide (PI) nanofibers as the increased imidization temperatures is highly required. In this work, polarized FT-IR spectroscopy is applied to solve this problem. Based on the polarized FT-IR spectroscopy and the molecular model in the fibers, the length of the repeat unit of PI molecule, the angle between the fiber axis and the symmetric stretching direction of carbonyl group on the imide ring, and the angle between the PI molecular axis and fiber axis are all investigated. The Mark-Howink equation is used to calculate the number-average molar mass of PI molecules. The orientation states of PI molecules in the electrospun nanofibers are studied from the number-average molar mass of PI molecules and the average fiber diameter. Quantitative analysis of the orientation factor of PI molecules in the electrospun nanofibers is performed by polarized FT-IR spectroscopy. Copyright © 2018 Elsevier B.V. All rights reserved.

Thermal Analysis of NR Composite with MWCNTs Aligned in a Magnetic Field

Directory of Open Access Journals (Sweden)

Jin Xu

2015-01-01

Full Text Available We got the aligned carbon tube in the rubber matrix through magnetic field. TEM shows that Fe3O4 is symmetrically coated on the outer surface of MWCNTs. Diffraction peaks corresponding to Fe3O4 cubic crystal also appeared in the X-ray diffraction spectra. Thermal conductivity of composites increases by filling the appropriate content of carbon tube. If the magnetic field is larger and the direction time is longer, a greater thermal conductivity of composites can be obtained.

Free bosonic string field theory without supplementary fields

International Nuclear Information System (INIS)

Embacher, F.

1987-01-01

A covariant local action for free bosonic string fields is constructed without the use of supplementary fields. The open string case is treated in detail. Up to a mathematical conjecture which is likely to hold it is shown that the Virasoro constraints arise as a special choice of gauge. The kinetic operator turns out to be extremely simple, the gauge transformation law arising rather implicitly. The case of closed strings is briefly discussed. 25 refs. (Author)

Fabrication and characterization of a solid-state nanopore with self-aligned carbon nanoelectrodes for molecular detection

International Nuclear Information System (INIS)

Spinney, Patrick S; Collins, Scott D; Smith, Rosemary L; Howitt, David G

2012-01-01

Stochastic molecular sensors based on resistive pulse nanopore modalities are envisioned as facile DNA sequencers. However, recent advances in nanotechnology fabrication have highlighted promising alternative detection mechanisms with higher sensitivity and potential single-base resolution. In this paper we present the novel self-aligned fabrication of a solid-state nanopore device with integrated transverse graphene-like carbon nanoelectrodes for polyelectrolyte molecular detection. The electrochemical transduction mechanism is characterized and found to result primarily from thermionic emission between the two transverse electrodes. Response of the nanopore to Lambda dsDNA and short (16-mer) ssDNA is demonstrated and distinguished. (paper)

Design and fabrication of advanced fiber alignment structures for field-installable fiber connectors

Science.gov (United States)

Van Erps, Jürgen; Vervaeke, Michael; Sánchez Martínez, Alberto; Beri, Stefano; Debaes, Christof; Watté, Jan; Thienpont, Hugo

2012-06-01

Fiber-To-The-Home (FTTH) networks have been adopted as a potential replacement of traditional electrical connections for the 'last mile' transmission of information at bandwidths over 1Gb/s. However, the success and adoption of optical access networks critically depend on the quality and reliability of connections between optical fibers. In particular a further reduction of insertion loss of field-installable connectors must be achieved without a significant increase in component cost. This requires precise alignment of fibers that can differ in terms of ellipticity, eccentricity or diameter and seems hardly achievable using today's widespread ferrule-based alignment systems. Novel low-cost structures for bare fiber alignment with outstanding positioning accuracies are strongly desired as they would allow reducing loss beyond the level achievable with ferrule-bore systems. However, the realization of such alignment system is challenging as it should provide sufficient force to position the fiber with sub-micron accuracy required in positioning the fiber. In this contribution we propose, design and prototype a bare-fiber alignment system which makes use of deflectable/compressible micro-cantilevers. Such cantilevers behave as springs and provide self-centering functionality to the structure. Simulations of the mechanical properties of the cantilevers are carried out in order to get an analytical approximation and a mathematical model of the spring constant and stress in the structure. Elastic constants of the order of 104 to 105N/m are found out to be compatible with a proof stress of 70 MPa. Finally a first self-centering structure is prototyped in PMMA using our Deep Proton Writing technology. The spring constants of the fabricated cantilevers are in the range of 4 to 6 × 104N/m and the stress is in the range 10 to 20 MPa. These self-centering structures have the potential to become the basic building blocks for a new generation of field-installable connectors.

Equation of state of dense plasmas: Orbital-free molecular dynamics as the limit of quantum molecular dynamics for high-Z elements

Energy Technology Data Exchange (ETDEWEB)

Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M. [CEA, DAM, DIF, 91297 Arpajon (France)

2014-10-15

The applicability of quantum molecular dynamics to the calculation of the equation of state of a dense plasma is limited at high temperature by computational cost. Orbital-free molecular dynamics, based on a semiclassical approximation and possibly on a gradient correction, is a simulation method available at high temperature. For a high-Z element such as lutetium, we examine how orbital-free molecular dynamics applied to the equation of state of a dense plasma can be regarded as the limit of quantum molecular dynamics at high temperature. For the normal mass density and twice the normal mass density, we show that the pressures calculated with the quantum approach converge monotonically towards those calculated with the orbital-free approach; we observe a faster convergence when the orbital-free approach includes the gradient correction. We propose a method to obtain an equation of state reproducing quantum molecular dynamics results up to high temperatures where this approach cannot be directly implemented. With the results already obtained for low-Z plasmas, the present study opens the way for reproducing the quantum molecular dynamics pressure for all elements up to high temperatures.

Three-dimensional MHD simulation of the interaction of the solar wind with the earth's magnetosphere: The generation of field-aligned currents

International Nuclear Information System (INIS)

Ogino, T.

1986-01-01

A global computer simulation of the interaction of the solar wind with the earth's magnetosphere was executed by using a three-dimensional magnetohydrodynamic model. As a result, we were able to reproduce quasi-steady-state magnetospheric configurations and a Birkeland field-aligned current system which depend on the polarity of the z component of the interplanetary magnetic field (IMF). Twin convection cells and a dawn to dusk electric potential of 30--100 kV appeared at the equator in the magnetosphere. Four types of field-aligned currents were observed. Region 1 and 2 field-aligned currents generated for all IMF conditions were 0.6--1.0 x 10 6 A and 0.15--0.61 x 10 6 A, respectively, in the total current. Region 1 currents at high latitudes are generated from the field-aligned vorticity at the flanks through a viscous interaction and are strengthened by a twisting of open magnetic field lines in the tail region for southward IMF. On the other hand, the low-latitude region 2 currents probably are generated mainly from the inner pressure gradient of the plasma sheet. The region 1 current obtained from the simulation was in good agreement with an estimate from our theoretical analysis of the localized Alfven mode. The other two types of field-aligned currents are the dayside magnetopause currents in the dayside cusp region, which increase for northward IMF, and the dayside cusp currents for southward IMF. The cusp currents are associated with a twisting of open magnetic field lines in the magnetopause region

Assessment of acetabulum anteversion aligned with the transverse acetabulum ligament: cadaveric study using image-free navigation system

Directory of Open Access Journals (Sweden)

Tomokazu Fukui

2013-02-01

Full Text Available The transverse acetabulum ligament (TAL has been used as an intraoperative anatomical landmark to position the acetabulum cup in total hip arthroplasty (THA. However, the validity of the use of TAL has not been clarified. The purpose of this study was to examine the orientation of the cup component aligned with the TAL in cadaveric study. The 31 hips in 25 whole-body embalmed cadavers were examined. The donors were 12 men and 13 women. Simulated THA procedure using image-free navigation system was performed and a trial cup with a diameter of approximately 2 mm less than the size of the acetabulum were inserted and snugly fitted on the TAL through the posterior wall of acetabulum. The orientation of the cup component was measured using an image-free THA navigation system. The measured radiographic anteversion and inclination angles averaged 18.2±7.2° (range: 2.0-33.2° and 43.5±4.2° (range: 33.1-51.0° respectively. Based on the Lewinnek’s safe zone criteria, 26 hips (80.6% were judged to be within the. Moreover, in the analysis of the gender difference of TAL angles, the average anteversion angle was shown to be significant larger in female than male population. The TAL can be effectively used an intraoperative landmark to align the acetabulum component helping reduce the risk of dislocation after surgery. In the intraoperative judgment, a gender difference in the alignment of the TAL should be taken into consideration.

Oxygen plasma assisted end-opening and field emission enhancement in vertically aligned multiwall carbon nanotubes

International Nuclear Information System (INIS)

Mathur, A.; Roy, S.S.; Hazra, K.S.; Wadhwa, S.; Ray, S.C.; Mitra, S.K.; Misra, D.S.; McLaughlin, J.A.

2012-01-01

Highlights: ► We showed Ar/O 2 plasma can be effective for the end opening of aligned CNTs. ► The field emission property was dramatically enhanced after plasma modification. ► Microstructures were clearly understood by Raman and SEM analysis. ► Surface wet-ability at various functionalised conditions was studied. - Abstract: This paper highlights the changes in micro-structural and field emission properties of vertically aligned carbon nanotubes (VACNTs) via oxygen plasma treatment. We find that exposure of very low power oxygen plasma (6 W) at 13.56 MHz for 15–20 min, opens the tip of vertically aligned CNTs. Scanning electron microscopy and transmission electron microscopy images were used to identify the quality and micro-structural changes of the nanotube morphology and surfaces. Raman spectra showed that the numbers of defects were increased throughout the oxygen plasma treatment process. In addition, the hydrophobic nature of the VACNTs is altered significantly and the contact angle decreases drastically from 110° to 40°. It was observed that the electron field emission (EFE) characteristics are significantly enhanced. The turn-on electric field (ETOE) of CNTs decreased from ∼0.80 V μm −1 (untreated) to ∼0.60 V μm −1 (oxygen treated). We believe that the open ended VACNTs would be immensely valuable for applications such as micro/nanofluidic based filtering elements and display devices.

Oxygen plasma assisted end-opening and field emission enhancement in vertically aligned multiwall carbon nanotubes

Energy Technology Data Exchange (ETDEWEB)

Mathur, A. [NIBEC, School of Engineering, University of Ulster, Jordanstown, BT37 0QB (United Kingdom); Roy, S.S., E-mail: sinharoy@ualberta.ca [Department of Mechanical Engineering, University of Alberta, Edmonton, T6T 2G8 (Canada); Hazra, K.S. [Department of Physics, IIT Bombay, Powai, Mumbai-400076 (India); Wadhwa, S. [NIBEC, School of Engineering, University of Ulster, Jordanstown, BT37 0QB (United Kingdom); Ray, S.C. [School of Physics, University of the Witwatersrand, WITS 2050, Johannesburg (South Africa); Mitra, S.K. [Department of Mechanical Engineering, University of Alberta, Edmonton, T6T 2G8 (Canada); Misra, D.S. [Department of Physics, IIT Bombay, Powai, Mumbai-400076 (India); McLaughlin, J.A. [NIBEC, School of Engineering, University of Ulster, Jordanstown, BT37 0QB (United Kingdom)

2012-05-15

Highlights: Black-Right-Pointing-Pointer We showed Ar/O{sub 2} plasma can be effective for the end opening of aligned CNTs. Black-Right-Pointing-Pointer The field emission property was dramatically enhanced after plasma modification. Black-Right-Pointing-Pointer Microstructures were clearly understood by Raman and SEM analysis. Black-Right-Pointing-Pointer Surface wet-ability at various functionalised conditions was studied. - Abstract: This paper highlights the changes in micro-structural and field emission properties of vertically aligned carbon nanotubes (VACNTs) via oxygen plasma treatment. We find that exposure of very low power oxygen plasma (6 W) at 13.56 MHz for 15-20 min, opens the tip of vertically aligned CNTs. Scanning electron microscopy and transmission electron microscopy images were used to identify the quality and micro-structural changes of the nanotube morphology and surfaces. Raman spectra showed that the numbers of defects were increased throughout the oxygen plasma treatment process. In addition, the hydrophobic nature of the VACNTs is altered significantly and the contact angle decreases drastically from 110 Degree-Sign to 40 Degree-Sign . It was observed that the electron field emission (EFE) characteristics are significantly enhanced. The turn-on electric field (ETOE) of CNTs decreased from {approx}0.80 V {mu}m{sup -1} (untreated) to {approx}0.60 V {mu}m{sup -1} (oxygen treated). We believe that the open ended VACNTs would be immensely valuable for applications such as micro/nanofluidic based filtering elements and display devices.

Free-Molecular Gas Flow in Narrow (Nanoscale) Channel

Czech Academy of Sciences Publication Activity Database

Levdansky, V.V.; Roldugin, V.I.; Žďanov, V.M.; Ždímal, Vladimír

2014-01-01

Roč. 87, č. 4 (2014), s. 802-814 ISSN 1062-0125 Grant - others:BRFFI(BY) T12P-018; RFBR(RU) 12-08-90009 Institutional support: RVO:67985858 Keywords : narrow channels * free-molecular gas flow * surface diffusion Subject RIV: CF - Physical ; Theoretical Chemistry

Enhancement of electron field emission of vertically aligned carbon nanotubes by nitrogen plasma treatment

Energy Technology Data Exchange (ETDEWEB)

Wang, B.B. [College of Chemistry and Chemical Engineering, Chongqing University of Technology, 69 Hongguang Rd, Lijiatuo, Banan District, Chongqing 400054 (China); Plasma Nanoscience Centre Australia (PNCA), CSIRO Materials Science and Engineering, P.O. Box 218, Lindfield, NSW 2070 (Australia); Cheng, Q.J. [Plasma Nanoscience Centre Australia (PNCA), CSIRO Materials Science and Engineering, P.O. Box 218, Lindfield, NSW 2070 (Australia); Plasma Nanoscience, School of Physics, University of Sydney, Sydney, NSW 2006 (Australia); Chen, X. [College of Materials Science and Engineering, Chongqing University, Chongqing 400044 (China); Ostrikov, K., E-mail: kostya.ostrikov@csiro.au [Plasma Nanoscience Centre Australia (PNCA), CSIRO Materials Science and Engineering, P.O. Box 218, Lindfield, NSW 2070 (Australia); Plasma Nanoscience, School of Physics, University of Sydney, Sydney, NSW 2006 (Australia)

2011-09-22

Highlights: > A new and custom-designed bias-enhanced hot-filament chemical vapor deposition system is developed to synthesize vertically aligned carbon nanotubes. > The carbon nanotubes are later treated with nitrogen plasmas. > The electron field emission characteristics of the carbon nanotubes are significantly improved after the nitrogen plasma treatment. > A new physical mechanism is proposed to interpret the improvement of the field emission characteristics. - Abstract: The electron field emission (EFE) characteristics from vertically aligned carbon nanotubes (VACNTs) without and with treatment by the nitrogen plasma are investigated. The VACNTs with the plasma treatment showed a significant improvement in the EFE property compared to the untreated VACNTs. The morphological, structural, and compositional properties of the VACNTs are extensively examined by scanning electron microscopy, transmission electron microscopy, Raman spectroscopy, and energy dispersive X-ray spectroscopy. It is shown that the significant EFE improvement of the VACNTs after the nitrogen plasma treatment is closely related to the variation of the morphological and structural properties of the VACNTs. The high current density (299.6 {mu}A/cm{sup 2}) achieved at a low applied field (3.50 V/{mu}m) suggests that the VACNTs after nitrogen plasma treatment can serve as effective electron field emission sources for numerous applications.

Enhancement of electron field emission of vertically aligned carbon nanotubes by nitrogen plasma treatment

International Nuclear Information System (INIS)

Wang, B.B.; Cheng, Q.J.; Chen, X.; Ostrikov, K.

2011-01-01

Highlights: → A new and custom-designed bias-enhanced hot-filament chemical vapor deposition system is developed to synthesize vertically aligned carbon nanotubes. → The carbon nanotubes are later treated with nitrogen plasmas. → The electron field emission characteristics of the carbon nanotubes are significantly improved after the nitrogen plasma treatment. → A new physical mechanism is proposed to interpret the improvement of the field emission characteristics. - Abstract: The electron field emission (EFE) characteristics from vertically aligned carbon nanotubes (VACNTs) without and with treatment by the nitrogen plasma are investigated. The VACNTs with the plasma treatment showed a significant improvement in the EFE property compared to the untreated VACNTs. The morphological, structural, and compositional properties of the VACNTs are extensively examined by scanning electron microscopy, transmission electron microscopy, Raman spectroscopy, and energy dispersive X-ray spectroscopy. It is shown that the significant EFE improvement of the VACNTs after the nitrogen plasma treatment is closely related to the variation of the morphological and structural properties of the VACNTs. The high current density (299.6 μA/cm 2 ) achieved at a low applied field (3.50 V/μm) suggests that the VACNTs after nitrogen plasma treatment can serve as effective electron field emission sources for numerous applications.

Construction of theoretical F-spread ionogams from scattering in the HF band from field-aligned irregularities

International Nuclear Information System (INIS)

Powers, W.J.

1985-01-01

The scattering and propagation of electromagnetic fields in the ionosphere for the HF band is considered. Particular attention is given to scattering at the geomagnetic equator from irregularities of ionization density that are aligned along the earth's magnetic field and that have lengths that are much greater than a Fresnel scale. Perpendicular to the earth's magnetic field the irregularities are assumed to be isotropic with scale lengths (wavelengths /(2π)) extending from an inner scale equal to the ionic gyroradius to an outer scale on the order of the scale height of the ionosphere. Primary emphasis is placed on the weak scattering of pulses from field-aligned irregularities embedded in the night time F-layer, with application to explaining F-spread ionograms. The average ionization density of the night time F-layer is assumed to be well modeled by a parabolic layer. Assuming that the effects of the earth's magnetic field and collisions can be neglected, an approximate dyadic Green's function is derived and utilized in the determination of the incident and singly scattered fields

Topological and statistical properties of nonlinear force-free fields

Science.gov (United States)

Mangalam, A.; Prasad, A.

2018-01-01

We use our semi-analytic solution of the nonlinear force-free field equation to construct three-dimensional magnetic fields that are applicable to the solar corona and study their statistical properties for estimating the degree of braiding exhibited by these fields. We present a new formula for calculating the winding number and compare it with the formula for the crossing number. The comparison is shown for a toy model of two helices and for realistic cases of nonlinear force-free fields; conceptually the formulae are nearly the same but the resulting distributions calculated for a given topology can be different. We also calculate linkages, which are useful topological quantities that are independent measures of the contribution of magnetic braiding to the total free energy and relative helicity of the field. Finally, we derive new analytical bounds for the free energy and relative helicity for the field configurations in terms of the linking number. These bounds will be of utility in estimating the braided energy available for nano-flares or for eruptions.

Modelling dust polarization observations of molecular clouds through MHD simulations

Science.gov (United States)

King, Patrick K.; Fissel, Laura M.; Chen, Che-Yu; Li, Zhi-Yun

2018-03-01

The BLASTPol observations of Vela C have provided the most detailed characterization of the polarization fraction p and dispersion in polarization angles S for a molecular cloud. We compare the observed distributions of p and S with those obtained in synthetic observations of simulations of molecular clouds, assuming homogeneous grain alignment. We find that the orientation of the mean magnetic field relative to the observer has a significant effect on the p and S distributions. These distributions for Vela C are most consistent with synthetic observations where the mean magnetic field is close to the line of sight. Our results point to apparent magnetic disorder in the Vela C molecular cloud, although it can be due to either an inclination effect (i.e. observing close to the mean field direction) or significant field tangling from strong turbulence/low magnetization. The joint correlations of p with column density and of S with column density for the synthetic observations generally agree poorly with the Vela C joint correlations, suggesting that understanding these correlations requires a more sophisticated treatment of grain alignment physics.

Strong-field Photoionization of Sputtered Neutral Molecules for Molecular Depth Profiling

Science.gov (United States)

Willingham, D; Brenes, D. A.; Wucher, A

2009-01-01

Molecular depth profiles of an organic thin film of guanine vapor deposited onto a Ag substrate are obtained using a 40 keV C60 cluster ion beam in conjunction with time-of-flight secondary ion mass spectrometric (ToF-SIMS) detection. Strong-field, femtosecond photoionization of intact guanine molecules is used to probe the neutral component of the profile for direct comparison with the secondary ion component. The ability to simultaneously acquire secondary ions and photoionized neutral molecules reveals new fundamental information about the factors that influence the properties of the depth profile. Results show that there is an increased ionization probability for protonated molecular ions within the first 10 nm due to the generation of free protons within the sample. Moreover, there is a 50% increase in fragment ion signal relative to steady state values 25 nm before reaching the guanine/Ag interface as a result of interfacial chemical damage accumulation. An altered layer thickness of 20 nm is observed as a consequence of ion beam induced chemical mixing. In general, we show that the neutral component of a molecular depth profile using the strong-field photoionization technique can be used to elucidate the effects of variations in ionization probability on the yield of molecular ions as well as to aid in obtaining accurate information about depth dependent chemical composition that cannot be extracted from TOF-SIMS data alone. PMID:20495665

Response to perturbations of the force-free aligned pulsar atmosphere

International Nuclear Information System (INIS)

Jackson, E.A.

1978-01-01

To clarify the likely structure of the pulsar atmosphere, the response of various plasma configurations near a rotating neutron star with aligned rotational and dipole magnetic axes is investigated. These configurations represent both general infinitesimal perturbations along B of the force-free (E.B = O) atmosphere, as well as a heuristic class of finite perturbations (shell atmospheres). It is shown that the general infinitesimal perturbations along B which preserve spatial ordering involve regions of both negative and positive work, whose boundaries are at the surfaces E.B = O(E is not equal to O) and those of zero charge density (cos 2 theta = 1/3). At the latter surfaces, and on one side of the system will produce mixing of charges of opposite sign. The intersecting E.B=O surface, the response of the recombination of these charges, and their removal by gravity, shows that the force-free atmosphere is physically unstable, favouring a lower density at mid-latitude. The response of various plasma shell atmospheres is also examined and confirms the likelihood of the plasma atmosphere previously predicted from a near-vacuum analysis, provided the density is not too large. Larger density shells are found to break up into 'striated' configurations, containing two electron and one or two ion groups, which however may not develop into stable configurations. Criteria on the plasma density related to this and other responses of the plasma shells are discussed. (author)

Magneto-plasmonic study of aligned Ni, Co and Ni/Co multilayer in polydimethylsiloxane as magnetic field sensor

Energy Technology Data Exchange (ETDEWEB)

Hamidi, Seyedeh Mehri, E-mail: M_hamidi@sbu.ac.ir [Magneto-plasmonic Lab, Laser and Plasma Research Institute, Shahid Beheshti University, Tehran (Iran, Islamic Republic of); Mosaeii, Babak; Afsharnia, Mina [Magneto-plasmonic Lab, Laser and Plasma Research Institute, Shahid Beheshti University, Tehran (Iran, Islamic Republic of); Aftabi, Ali [Physics Department, Shahid Beheshti University, Tehran (Iran, Islamic Republic of); Najafi, Mojgan [Department of Materials Engineering, Hamedan University of Technology, Hamedan (Iran, Islamic Republic of)

2016-11-01

We report the magneto-optical properties of aligned cobalt, Nickel and nickel/ Cobalt multilayer nanowires embedded in polydimethylsiloxane matrix. The NWs prepared by electrodeposition method in anodic alumina template and then dispersed in ethanol and placed in a heater to evaporate the ethanol and finally dispersed in polydimethylsiloxane matrix to reach to the composite. The used external magnetic field arranges the nanowires and our aligned nanowires were investigated by magneto-optical surface plasmon resonance techniques in two easy and hard axis configurations. Our results show the sufficient sensitivity in magneto-optical surface plasmon resonance of Nickel and cobalt arrays nanowires and because the different modulation mechanism in Ni and Co nanodisks, in Ni/Co multilayer we see the magnetization modulation of the excitation angle in accordance with magnetic field modulation of the SPP wave vector in each nanodisk. Finally, we show that the Ni/Co multilayer aligned nanowires can be used as efficient magnetic field sensor. - Highlights: • The magneto-optical properties of aligned multilayer nanowires has been investigated. • We see the sufficient sensitivity in magneto-optical surface plasmon resonance of Ni and Co nanowires. • The magnetic modulation mechanism in Ni/Co multilayer has been changed by angular modulation. • The magnetization modulation of the excitation angle accompanying the SPP wave vector modulation takes place in each nanodisk of multilayer.

Molecular dynamics simulations and free energy profile of ...

Indian Academy of Sciences (India)

aDepartment of Chemical Engineering, bDepartment of Chemistry, Amirkabir University of Technology,. 15875-4413 ... Lipid bilayers; Paracetamol; free energy; molecular dynamics simulation; membrane. 1. ..... bilayer is less favourable due to the hydrophobic nature .... Orsi M and Essex J W 2010 Soft Matter 6 3797. 54.

Do field-free electromagnetic potentials play a role in biology?

Science.gov (United States)

Szasz, A; Vincze, G; Andocs, G; Szasz, O

2009-01-01

All bio-systems are imperfect dielectrics. Their general properties however cannot be described by conventional simple electrodynamics; the system is more complex. A central question in our present paper is centered on a controversial debate of the possible effect of the zero fields (only potentials exist). We show that the identical use of the "field-free," "curl-free," and "force-free" terminologies is incorrect, there have definitely different meanings. It is shown that the effective electro-dynamical parameters that describe and modify living systems are the potentials and not the fields. We discuss how the potentials have a role in biological processes even in field-free cases.

The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine

DEFF Research Database (Denmark)

Li, Xiaozhou; Neumann, Marcus A.; van de Streek, Jacco

2017-01-01

of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base...

S-matrix analysis of vibrational and alignment effects in intense-field multiphoton ionization of molecules

International Nuclear Information System (INIS)

Requate, A.

2007-03-01

Theoretical analysis of the vibrational excitation of small molecules during multiphoton ionization in intense laser fields of optical and infrared frequencies. Analysis of the alignment dependence of the electron impact ionization of diatomic molecules in the presence of an intense laser field as the final step in the process of Nonsequential Double Ionization. Quantum mechanical description using S-matrix theory in Strong Field Approximation (SFA), i.e. beyond perturbation theory. (orig.)

S-matrix analysis of vibrational and alignment effects in intense-field multiphoton ionization of molecules

Energy Technology Data Exchange (ETDEWEB)

Requate, A

2007-03-15

Theoretical analysis of the vibrational excitation of small molecules during multiphoton ionization in intense laser fields of optical and infrared frequencies. Analysis of the alignment dependence of the electron impact ionization of diatomic molecules in the presence of an intense laser field as the final step in the process of Nonsequential Double Ionization. Quantum mechanical description using S-matrix theory in Strong Field Approximation (SFA), i.e. beyond perturbation theory. (orig.)

Superstructure of self-aligned hexagonal GaN nanorods formed on nitrided Si(111) surface

Energy Technology Data Exchange (ETDEWEB)

Kumar, Praveen; Tuteja, Mohit; Kesaria, Manoj; Waghmare, U. V.; Shivaprasad, S. M. [Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560 064 (India)

2012-09-24

We present here the spontaneous formation of catalyst-free, self-aligned crystalline (wurtzite) nanorods on Si(111) surfaces modified by surface nitridation. Nanorods grown by molecular beam epitaxy on bare Si(111) and non-stoichiometric silicon nitride interface are found to be single crystalline but disoriented. Those grown on single crystalline Si{sub 3}N{sub 4} intermediate layer are highly dense c-oriented hexagonal shaped nanorods. The morphology and the self-assembly of the nanorods shows an ordered epitaxial hexagonal superstructure, suggesting that they are nucleated at screw dislocations at the interface and grow spirally in the c-direction. The aligned nanorod assembly shows high-quality structural and optical emission properties.

Self-centering fiber alignment structures for high-precision field installable single-mode fiber connectors

Science.gov (United States)

Van Erps, Jürgen; Ebraert, Evert; Gao, Fei; Vervaeke, Michael; Berghmans, Francis; Beri, Stefano; Watté, Jan; Thienpont, Hugo

2014-05-01

There is a steady increase in the demand for internet bandwidth, primarily driven by cloud services and high-definition video streaming. Europe's Digital Agenda states the ambitious objective that by 2020 all Europeans should have access to internet at speeds of 30Mb/s or above, with 50% or more of households subscribing to connections of 100Mb/s. Today however, internet access in Europe is mainly based on the first generation of broadband, meaning internet accessed over legacy telephone copper and TV cable networks. In recent years, Fiber-To-The-Home (FTTH) networks have been adopted as a replacement of traditional electrical connections for the `last mile' transmission of information at bandwidths over 1Gb/s. However, FTTH penetration is still very low (economies. The main reason for this is the high deployment cost of FTTH networks. Indeed, the success and adoption of optical access networks critically depend on the quality and reliability of connections between optical fibers. In particular a further reduction of insertion loss of field- installable connectors must be achieved without a significant increase in component cost. This requires precise alignment of fibers that can differ in terms of ellipticity, eccentricity or diameter and seems hardly achievable using today's widespread ferrule-based alignment systems. In this paper, we present a field-installable connector based on deflectable/compressible spring structures, providing a self-centering functionality for the fiber. This way, it can accommodate for possible fiber cladding diameter variations (the tolerance on the cladding diameter of G.652 fiber is typically +/-0.7μm). The mechanical properties of the cantilever are derived through an analytical approximation and a mathematical model of the spring constant, and finite element-based simulations are carried out to find the maximum first principal stress as well as the stress distribution distribution in the fiber alignment structure. Elastic

Free-Free Transitions in the Presence of Laser Fields at Very Low Incident Electron Energy

Science.gov (United States)

Bhatia, A. K.; Sinha, Chandana

2010-01-01

We study the free-free transition in electron-hydrogenic systems in ground state in presence of an external laser field at very loud incident energies. The laser field is treated classically while the collision dynamics is treated quantum mechanically. The laser field is chosen to be monochromatic, linearly polarized and homogeneous. The incident electron is considered to be dressed by the laser in a nonperturbative manner by choosing a Volkov wave function for it. The scattering weave function for the electron is solved numerically by taking into account the effect of the electron exchange, short-range as well as of the long-range interactions to get the S and P wave phase shifts while for the higher angular momentum phase shifts the exchange approximation has only been considered. We calculate the laser assisted differential cross sections (LADCS) for the aforesaid free-free transition process for single photon absorption/emission. The laser intensity is chosen to be much less than the atomic field intensity. A strong suppression is noted in the LADCS as compared to the field free (FF) cross sections. Unlike the FF ones, the LADCS exhibit some oscillations having a distinct maximum at a low value of the scattering angle depending on the laser parameters as well as on the incident energies.

Free energy landscape and molecular pathways of gas hydrate nucleation

Energy Technology Data Exchange (ETDEWEB)

Bi, Yuanfei; Porras, Anna; Li, Tianshu, E-mail: tsli@gwu.edu [Department of Civil and Environmental Engineering, George Washington University, Washington DC 20052 (United States)

2016-12-07

Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p{sub B} histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p{sub B} histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.

Free energy landscape and molecular pathways of gas hydrate nucleation

International Nuclear Information System (INIS)

Bi, Yuanfei; Porras, Anna; Li, Tianshu

2016-01-01

Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p B histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p B histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.

Free energy landscape and molecular pathways of gas hydrate nucleation.

Science.gov (United States)

Bi, Yuanfei; Porras, Anna; Li, Tianshu

2016-12-07

Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p B histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p B histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.

Molecular gyroscopes and biological effects of weak extremely low-frequency magnetic fields

International Nuclear Information System (INIS)

Binhi, V.N.; Savin, A.V.

2002-01-01

Extremely low-frequency magnetic fields are known to affect biological systems. In many cases, biological effects display 'windows' in biologically effective parameters of the magnetic fields: most dramatic is the fact that the relatively intense magnetic fields sometimes do not cause appreciable effect, while smaller fields of the order of 10-100 μT do. Linear resonant physical processes do not explain the frequency windows in this case. Amplitude window phenomena suggest a nonlinear physical mechanism. Such a nonlinear mechanism has been proposed recently to explain those 'windows'. It considers the quantum-interference effects on the protein-bound substrate ions. Magnetic fields cause an interference of ion quantum states and change the probability of ion-protein dissociation. This ion-interference mechanism predicts specific magnetic-field frequency and amplitude windows within which the biological effects occur. It agrees with a lot of experiments. However, according to the mechanism, the lifetime Γ -1 of ion quantum states within a protein cavity should be of unrealistic value, more than 0.01 s for frequency band 10-100 Hz. In this paper, a biophysical mechanism has been proposed, which (i) retains the attractive features of the ion interference mechanism, i.e., predicts physical characteristics that might be experimentally examined and (ii) uses the principles of gyroscopic motion and removes the necessity to postulate large lifetimes. The mechanism considers the dynamics of the density matrix of the molecular groups, which are attached to the walls of protein cavities by two covalent bonds, i.e., molecular gyroscopes. Numerical computations have shown almost free rotations of the molecular gyroscopes. The relaxation time due to van der Waals forces was about 0.01 s for the cavity size of 28 Aa

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G.Gomez

Since September, the muon alignment system shifted from a mode of hardware installation and commissioning to operation and data taking. All three optical subsystems (Barrel, Endcap and Link alignment) have recorded data before, during and after CRAFT, at different magnetic fields and during ramps of the magnet. This first data taking experience has several interesting goals: •    study detector deformations and movements under the influence of the huge magnetic forces; •    study the stability of detector structures and of the alignment system over long periods, •    study geometry reproducibility at equal fields (specially at 0T and 3.8T); •    reconstruct B=0T geometry and compare to nominal/survey geometries; •    reconstruct B=3.8T geometry and provide DT and CSC alignment records for CMSSW. However, the main goal is to recons...

Rotational Coherence Encoded in an “Air-Laser” Spectrum of Nitrogen Molecular Ions in an Intense Laser Field

Directory of Open Access Journals (Sweden)

Haisu Zhang

2013-10-01

Full Text Available We investigate lasing action in aligned nitrogen molecular ions (N_{2}^{+} produced in an intense laser field. We find that, besides the population inversion between the B^{2}Σ_{u}^{+}-X^{2}Σ_{g}^{+} states, which is responsible for the observed simulated amplification of a seed pulse, a rotational wave packet in the ground vibrational state (v=0 of the excited electronic B^{2}Σ_{u}^{+} state has been created in N_{2}^{+}. The rotational coherence can faithfully encode its characteristics into the amplified seed pulses, enabling reconstruction of rotational wave packets of molecules in a single-shot detection manner from the frequency-resolved laser spectrum. Our results suggest that the air laser can potentially provide a promising tool for remote characterization of coherent molecular rotational wave packets.

Auroral electron fluxes induced by static magnetic field aligned electric field and plasma wave turbulence

International Nuclear Information System (INIS)

Assis, A.S. de; Silva, C.E. da; Dias Tavares, A. Jr.; Leubner, C.; Kuhn, S.

2001-07-01

We have studied the formation of auroral electron fluxes induced by a field aligned dc electric field in the presence of plasma wave turbulence. The effect of the wave spectral shape on the production rate has been considered. This acceleration scheme was modelled by the weak turbulence approach. The electron fluxes for narrow and broad band spectra, in the case of low and high phase velocities, are calculated, and it is found as a general feature, for all modes, that their enhancement is larger the weaker the background electric field, while for its absolute enhancement it is just the opposite. The electron fluxes are enhanced by many orders of magnitude over that without turbulence. It is also shown that the modes enhance the runaway production rate via their Cherenkov dissipation, and that a synergetic effect occurs in the enhancement when more than one mode turbulent is present in the acceleration region. (author)

Quencher-free molecular beacon tethering 7-hydroxycoumarin detects targets through protonation/deprotonation.

Science.gov (United States)

Kashida, Hiromu; Yamaguchi, Kyohei; Hara, Yuichi; Asanuma, Hiroyuki

2012-07-15

In this study, we synthesized a simple but efficient quencher-free molecular beacon tethering 7-hydroxycoumarin on D-threoninol based on its pK(a) change. The pK(a) of 7-hydroxycoumarin in a single strand was determined as 8.8, whereas that intercalated in the duplex was over 10. This large pK(a) shift (more than 1.2) upon hybridization could be attributed to the anionic and hydrophobic microenvironment inside the DNA duplex. Because 7-hydroxycoumarin quenches its fluorescence upon protonation, the emission intensity of the duplex at pH 8.5 was 1/15 that of the single strand. We applied this quenching mechanism to the preparation of a quencher-free molecular beacon by introducing the dye into the middle of the stem part. In the absence of the target, the stem region formed a duplex and fluorescence was quenched. However, when the target was added, the molecular beacon opened and the dye was deprotonated. As a result, the emission intensity of the molecular beacon with the target was 10 times higher than that without the target. Accordingly, a quencher-free molecular beacon utilizing the pK(a) change was successfully developed. Copyright © 2012 Elsevier Ltd. All rights reserved.

Improved accuracy of component alignment with the implementation of image-free navigation in total knee arthroplasty.

Science.gov (United States)

Rosenberger, Ralf E; Hoser, Christian; Quirbach, Sebastian; Attal, Rene; Hennerbichler, Alfred; Fink, Christian

2008-03-01

Accuracy of implant positioning and reconstruction of the mechanical leg axis are major requirements for achieving good long-term results in total knee arthroplasty (TKA). The purpose of the present study was to determine whether image-free computer navigation technology has the potential to improve the accuracy of component alignment in TKA cohorts of experienced surgeons immediately and constantly. One hundred patients with primary arthritis of the knee underwent the unilateral total knee arthroplasty. The cohort of 50 TKAs implanted with conventional instrumentation was directly followed by the cohort of the very first 50 computer-assisted TKAs. All surgeries were performed by two senior surgeons. All patients received the Zimmer NexGen total knee prosthesis (Zimmer Inc., Warsaw, IN, USA). There was no variability regarding surgeons or surgical technique, except for the use of the navigation system (StealthStation) Treon plus Medtronic Inc., Minnesota, MI, USA). Accuracy of implant positioning was measured on postoperative long-leg standing radiographs and standard lateral X-rays with regard to the valgus angle and the coronal and sagittal component angles. In addition, preoperative deformities of the mechanical leg axis, tourniquet time, age, and gender were correlated. Statistical analyses were performed using the SPSS 15.0 (SPSS Inc., Chicago, IL, USA) software package. Independent t-tests were used, with significance set at P alignment between the two cohorts. To compute the rate of optimally implanted prostheses between the two groups we used the chi(2) test. The average postoperative radiological frontal mechanical alignment was 1.88 degrees of varus (range 6.1 degrees of valgus-10.1 degrees of varus; SD 3.68 degrees ) in the conventional cohort and 0.28 degrees of varus (range 3.7 degrees -6.0 degrees of varus; SD 1.97 degrees ) in the navigated cohort. Including all criteria for optimal implant alignment, 16 cases (32%) in the conventional cohort and 31

Fundamental Insights into Proton-Coupled Electron Transfer in Soybean Lipoxygenase from Quantum Mechanical/Molecular Mechanical Free Energy Simulations.

Science.gov (United States)

Li, Pengfei; Soudackov, Alexander V; Hammes-Schiffer, Sharon

2018-02-28

The proton-coupled electron transfer (PCET) reaction catalyzed by soybean lipoxygenase has served as a prototype for understanding hydrogen tunneling in enzymes. Herein this PCET reaction is studied with mixed quantum mechanical/molecular mechanical (QM/MM) free energy simulations. The free energy surfaces are computed as functions of the proton donor-acceptor (C-O) distance and the proton coordinate, and the potential of mean force is computed as a function of the C-O distance, inherently including anharmonicity. The simulation results are used to calculate the kinetic isotope effects for the wild-type enzyme (WT) and the L546A/L754A double mutant (DM), which have been measured experimentally to be ∼80 and ∼700, respectively. The PCET reaction is found to be exoergic for WT and slightly endoergic for the DM, and the equilibrium C-O distance for the reactant is found to be ∼0.2 Å greater for the DM than for WT. The larger equilibrium distance for the DM, which is due mainly to less optimal substrate binding in the expanded binding cavity, is primarily responsible for its higher kinetic isotope effect. The calculated potentials of mean force are anharmonic and relatively soft at shorter C-O distances, allowing efficient thermal sampling of the shorter distances required for effective hydrogen tunneling. The primarily local electrostatic field at the transferring hydrogen is ∼100 MV/cm in the direction to facilitate proton transfer and increases dramatically as the C-O distance decreases. These simulations suggest that the overall protein environment is important for conformational sampling of active substrate configurations aligned for proton transfer, but the PCET reaction is influenced primarily by local electrostatic effects that facilitate conformational sampling of shorter proton donor-acceptor distances required for effective hydrogen tunneling.

Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method

International Nuclear Information System (INIS)

Zeng Xiancheng; Hu Hao; Hu Xiangqian; Yang Weitao

2009-01-01

A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids 'on-the-fly' QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.

Theory and observations of upward field-aligned currents at the magnetopause boundary layer.

Science.gov (United States)

Wing, Simon; Johnson, Jay R

2015-11-16

The dependence of the upward field-aligned current density ( J ‖ ) at the dayside magnetopause boundary layer is well described by a simple analytic model based on a velocity shear generator. A previous observational survey confirmed that the scaling properties predicted by the analytical model are applicable between 11 and 17 MLT. We utilize the analytic model to predict field-aligned currents using solar wind and ionospheric parameters and compare with direct observations. The calculated and observed parallel currents are in excellent agreement, suggesting that the model may be useful to infer boundary layer structures. However, near noon, where velocity shear is small, the kinetic pressure gradients and thermal currents, which are not included in the model, could make a small but significant contribution to J ‖ . Excluding data from noon, our least squares fit returns log( J ‖,max_cal ) = (0.96 ± 0.04) log( J ‖_obs ) + (0.03 ± 0.01) where J ‖,max_cal = calculated J ‖,max and J ‖_obs = observed J ‖ .

Energy of Force-Free Magnetic Fields in Relation to Coronal Mass Ejections

International Nuclear Information System (INIS)

Choe, G.S.; Cheng, C.Z.

2002-01-01

In typical observations of coronal mass ejections (CMEs), a magnetic structure of a helmet-shaped closed configuration bulges out and eventually opens up. However, a spontaneous transition between these field configurations has been regarded to be energetically impossible in force-free fields according to the Aly-Sturrock theorem. The theorem states that the maximum energy state of force-free fields with a given boundary normal field distribution is the open field. The theorem implicitly assumes the existence of the maximum energy state, which may not be taken for granted. In this study, we have constructed force-free fields containing tangential discontinuities in multiple flux systems. These force-free fields can be generated from a potential field by footpoint motions that do not conserve the boundary normal field distribution. Some of these force-free fields are found to have more magnetic energy than the corresponding open fields. The constructed force-free configurations are compared with observational features of CME-bearing active regions. Possible mechanisms of CMEs are also discussed

Intradomain phase transitions in flexible block copolymers with self-aligning segments

Science.gov (United States)

Burke, Christopher J.; Grason, Gregory M.

2018-05-01

We study a model of flexible block copolymers (BCPs) in which there is an enlthalpic preference for orientational order, or local alignment, among like-block segments. We describe a generalization of the self-consistent field theory of flexible BCPs to include inter-segment orientational interactions via a Landau-de Gennes free energy associated with a polar or nematic order parameter for segments of one component of a diblock copolymer. We study the equilibrium states of this model numerically, using a pseudo-spectral approach to solve for chain conformation statistics in the presence of a self-consistent torque generated by inter-segment alignment forces. Applying this theory to the structure of lamellar domains composed of symmetric diblocks possessing a single block of "self-aligning" polar segments, we show the emergence of spatially complex segment order parameters (segment director fields) within a given lamellar domain. Because BCP phase separation gives rise to spatially inhomogeneous orientation order of segments even in the absence of explicit intra-segment aligning forces, the director fields of BCPs, as well as thermodynamics of lamellar domain formation, exhibit a highly non-linear dependence on both the inter-block segregation (χN) and the enthalpy of alignment (ɛ). Specifically, we predict the stability of new phases of lamellar order in which distinct regions of alignment coexist within the single mesodomain and spontaneously break the symmetries of the lamella (or smectic) pattern of composition in the melt via in-plane tilt of the director in the centers of the like-composition domains. We further show that, in analogy to Freedericksz transition confined nematics, the elastic costs to reorient segments within the domain, as described by the Frank elasticity of the director, increase the threshold value ɛ needed to induce this intra-domain phase transition.

Growth and field emission properties of one-dimensional carbon composite structure consisting of vertically aligned carbon nanotubes and nanocones

International Nuclear Information System (INIS)

Zhang Hongxin; Feng, Peter X; Fonseca, Luis; Morell, Gerardo; Makarov, Vladimir I; Weiner, Brad R

2009-01-01

A simple approach is demonstrated for quickly growing a large-area aligned carbon composite nanostructure consisting of vertically aligned nanotubes and nanocones by the catalyst-assisted pulsed laser deposition techniques. The pyrolytic graphite was used as carbon source. The carbon nanocones were first grown on the molybdenum substrate with Ni catalysts. The carbon nanotubes have a uniform shape and length, aligned vertically on carbon nanocones, and the average diameter is about 7 nm. The special carbon composite arrays exhibit excellent field emission behaviours. The long-term field emission current stability of the one-dimensioned carbon nanostructure has also been investigated. No obvious current density decay was observed after a 10-day continuous experiment, indicating the super stability of the sample as cathode material.

MUON DETECTORS: ALIGNMENT

CERN Multimedia

Gervasio Gomez

The main progress of the muon alignment group since March has been in the refinement of both the track-based alignment for the DTs and the hardware-based alignment for the CSCs. For DT track-based alignment, there has been significant improvement in the internal alignment of the superlayers inside the DTs. In particular, the distance between superlayers is now corrected, eliminating the residual dependence on track impact angles, and good agreement is found between survey and track-based corrections. The new internal geometry has been approved to be included in the forthcoming reprocessing of CRAFT samples. The alignment of DTs with respect to the tracker using global tracks has also improved significantly, since the algorithms use the latest B-field mapping, better run selection criteria, optimized momentum cuts, and an alignment is now obtained for all six degrees of freedom (three spatial coordinates and three rotations) of the aligned DTs. This work is ongoing and at a stage where we are trying to unders...

IDENTIFICATION OF FREE-FIELD SOIL PROPERTIES USING NUPEC RECORDED GROUND MOTIONS

International Nuclear Information System (INIS)

Xu, J.; Costantino, C.; Hofmayer, C.; Murphy, A.; Chokshi, N.; Kitada, Y.

2001-01-01

Over the past twenty years, the Nuclear Power Engineering Corporation (NUPEC) of Japan has conducted a series of field model test programs to investigate various aspects of soil-structure interaction (SSI) effects on nuclear power plant structures, including embedment and dynamic structure-soil-structure interaction (SSSI) effects. As part of a collaborative agreement between the US Nuclear Regulatory Commission (NRC) and NUPEC, Brookhaven National Laboratory (BNL) performed a numerical analysis to predict the free field soil profile using industry standard methods and the recorded free field responses to actual earthquake events. This paper describes the BNL free-field analyses, including the methods and the analysis results and their comparison to recorded data in the free field. The free-field soil profiles determined from the BNL analyses are being used for both the embedment and SSSI studies, the results of which will be made available upon their completion

An Alignment-Free Algorithm in Comparing the Similarity of Protein Sequences Based on Pseudo-Markov Transition Probabilities among Amino Acids.

Science.gov (United States)

Li, Yushuang; Song, Tian; Yang, Jiasheng; Zhang, Yi; Yang, Jialiang

2016-01-01

In this paper, we have proposed a novel alignment-free method for comparing the similarity of protein sequences. We first encode a protein sequence into a 440 dimensional feature vector consisting of a 400 dimensional Pseudo-Markov transition probability vector among the 20 amino acids, a 20 dimensional content ratio vector, and a 20 dimensional position ratio vector of the amino acids in the sequence. By evaluating the Euclidean distances among the representing vectors, we compare the similarity of protein sequences. We then apply this method into the ND5 dataset consisting of the ND5 protein sequences of 9 species, and the F10 and G11 datasets representing two of the xylanases containing glycoside hydrolase families, i.e., families 10 and 11. As a result, our method achieves a correlation coefficient of 0.962 with the canonical protein sequence aligner ClustalW in the ND5 dataset, much higher than those of other 5 popular alignment-free methods. In addition, we successfully separate the xylanases sequences in the F10 family and the G11 family and illustrate that the F10 family is more heat stable than the G11 family, consistent with a few previous studies. Moreover, we prove mathematically an identity equation involving the Pseudo-Markov transition probability vector and the amino acids content ratio vector.

Hamiltonian mechanics and divergence-free fields

International Nuclear Information System (INIS)

Boozer, A.H.

1986-08-01

The field lines, or integral curves, of a divergence-free field in three dimensions are shown to be topologically equivalent to the trajectories of a Hamiltonian with two degrees of freedom. The consideration of fields that depend on a parameter allow the construction of a canonical perturbation theory which is valid even if the perturbation is large. If the parametric dependence of the magnetic, or the vorticity field is interpreted as time dependence, evolution equations are obtained which give Kelvin's theorem or the flux conservation theorem for ideal fluids and plasmas. The Hamiltonian methods prove especially useful for study of fields in which the field lines must be known throughout a volume of space

Dynamics of solar magnetic fields. VI. Force-free magnetic fields and motions of magnetic foot-points

International Nuclear Information System (INIS)

Low, B.C.; Nakagawa, Y.

1975-01-01

A mathematical model is developed to consider the evolution of force-free magnetic fields in relation to the displacements of their foot-points. For a magnetic field depending on only two Cartesian coordinates and time, the problem reduces to solving a nonlinear elliptic partial differential equation. As illustration of the physical process, two specific examples of evolving force-free magnetic fields are examined in detail, one evolving with rising and the other with descending field lines. It is shown that these two contrasting behaviors of the field lines correspond to sheared motions of their foot-points of quite different characters. The physical implications of these two examples of evolving force-free magnetic fields are discussed. (auth)

Atomic wavefunctions probed through strong-field light-matter interaction

Energy Technology Data Exchange (ETDEWEB)

Mairesse, Y; Villeneuve, D M; Corkum, P B; Dudovich, N [Natl Res Council Canada, Ottawa, ON K1A 0R6 (Canada); Shafir, D; Dudovich, N [Weizmann Inst Sci, Dept Phys Complex Syst, IL-76100 Rehovot, (Israel); Mairesse, Y [Univ Bordeaux 1, CELIA, CNRS, UMR 5107, CEA, F-33405 Talence (France)

2009-07-01

Strong-field light-matter interactions can encode the spatial properties of the electronic wavefunctions that contribute to the process. In particular, the broadband harmonic spectra, measured for a series of molecular alignments, can be used to create a tomographic reconstruction of molecular orbitals. Here, we present an extension of the tomography approach to systems that cannot be naturally aligned. We demonstrate this ability by probing the two-dimensional properties of atomic wavefunctions. By manipulating an electron-ion re-collision process, we are able to resolve the symmetry of the atomic wavefunction with high contrast. (authors)

Genomic signal processing methods for computation of alignment-free distances from DNA sequences.

Science.gov (United States)

Borrayo, Ernesto; Mendizabal-Ruiz, E Gerardo; Vélez-Pérez, Hugo; Romo-Vázquez, Rebeca; Mendizabal, Adriana P; Morales, J Alejandro

2014-01-01

Genomic signal processing (GSP) refers to the use of digital signal processing (DSP) tools for analyzing genomic data such as DNA sequences. A possible application of GSP that has not been fully explored is the computation of the distance between a pair of sequences. In this work we present GAFD, a novel GSP alignment-free distance computation method. We introduce a DNA sequence-to-signal mapping function based on the employment of doublet values, which increases the number of possible amplitude values for the generated signal. Additionally, we explore the use of three DSP distance metrics as descriptors for categorizing DNA signal fragments. Our results indicate the feasibility of employing GAFD for computing sequence distances and the use of descriptors for characterizing DNA fragments.

Label-free detection of DNA hybridization using carbon nanotube network field-effect transistors

Science.gov (United States)

Star, Alexander; Tu, Eugene; Niemann, Joseph; Gabriel, Jean-Christophe P.; Joiner, C. Steve; Valcke, Christian

2006-01-01

We report carbon nanotube network field-effect transistors (NTNFETs) that function as selective detectors of DNA immobilization and hybridization. NTNFETs with immobilized synthetic oligonucleotides have been shown to specifically recognize target DNA sequences, including H63D single-nucleotide polymorphism (SNP) discrimination in the HFE gene, responsible for hereditary hemochromatosis. The electronic responses of NTNFETs upon single-stranded DNA immobilization and subsequent DNA hybridization events were confirmed by using fluorescence-labeled oligonucleotides and then were further explored for label-free DNA detection at picomolar to micromolar concentrations. We have also observed a strong effect of DNA counterions on the electronic response, thus suggesting a charge-based mechanism of DNA detection using NTNFET devices. Implementation of label-free electronic detection assays using NTNFETs constitutes an important step toward low-cost, low-complexity, highly sensitive and accurate molecular diagnostics. hemochromatosis | SNP | biosensor

GraphAlignment: Bayesian pairwise alignment of biological networks

Czech Academy of Sciences Publication Activity Database

Kolář, Michal; Meier, J.; Mustonen, V.; Lässig, M.; Berg, J.

2012-01-01

Roč. 6, November 21 (2012) ISSN 1752-0509 Grant - others:Deutsche Forschungsgemeinschaft(DE) SFB 680; Deutsche Forschungsgemeinschaft(DE) SFB-TR12; Deutsche Forschungsgemeinschaft(DE) BE 2478/2-1 Institutional research plan: CEZ:AV0Z50520514 Keywords : Graph alignment * Biological networks * Parameter estimation * Bioconductor Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.982, year: 2012

Transient molecular orientation and rheology in flow aligning thermotropic liquid crystalline polymers

International Nuclear Information System (INIS)

Ugaz, Victor M.; Burghardt, Wesley R.; Zhou, Weijun; Kornfield, Julia A.

2001-01-01

Quantitative measurements of molecular orientation and rheology are reported for various transient shear flows of a nematic semiflexible copolyether. Unlike the case of lyotropic liquid crystalline polymers (LCPs), whose structure and rheology in shear are dominated by director tumbling, this material exhibits flow aligning behavior. The observed behavior is quite similar to that seen in a copolyester that we have recently studied [Ugaz and Burghardt (1998)], suggesting that flow aligning dynamics may predominate in main-chain thermotropes that incorporate significant chain flexibility. Since the flow aligning regime has received little attention in previous attempts to model the rheology of textured, polydomain LCPs, we attempt to determine whether available models are capable of predicting the orientation and stress response of this class of LCP. We first examine the predictions of the polydomain Ericksen model, an adaptation of Ericksen's transversely isotropic fluid model which accounts for the polydomain distribution of director orientation while neglecting distortional elasticity. This simple model captures a number of qualitative and quantitative features associated with the evolution of orientation and stress during shear flow inception, but cannot cope with reversing flows. To consider the possible role of distortional elasticity in the re-orientation dynamics upon reversal, we evaluate the mesoscopically averaged domain theory of Larson and Doi [Larson and Doi (1991)], which incorporates a phenomenological description of distortional elastic effects. To date, their approach to account for polydomain structure has only been applied to describe tumbling LCPs. We find that it captures the qualitative transient orientation response to flow reversals, but is less successful in describing the evolution of stresses. This is linked to the decoupling approximation adopted during the model's development. Finally, a modified polydomain Ericksen model is introduced

The Weiss molecular field and the local molecular field; Le champ moleculaire de Weiss et le champ moleculaire local

Energy Technology Data Exchange (ETDEWEB)

Neel, L [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires; Faculte des Sciences de Grenoble, 38 (France)

1959-07-01

Initially, the present report outlines the work done by P. Weiss in the molecular field and spontaneous magnetization theory. It then stresses the success of the theory in the interpretation of the magnetic and energetic properties of ferro-magnetic bodies, and indicates recent progress: 'the energetic molecular field, and the corrective molecular field of the equation of state'. In the second part, the author reviews the difficulties encountered by the theory, and shows how they were overcome by the introduction of the notion of the 'local molecular field', thus supplying the key to the properties of anti-ferro and ferri-magnetic bodies. The present level of progress in the interpretation of the magnetic properties of pyrrhotite, which played a major part in the molecular field discoveries, is also discussed in paragraph 4 and appendices. (author) [French] Dans une premiere partie, l'auteur retrace l'historique des travaux de P. Weiss sur la theorie du champ moleculaire et l'aimantation spontanee; il en souligne les succes dans l'interpretation des proprietes magnetiques et energetiques des corps ferro-magnetiques et les perfectionnements ultimes: champ moleculaire energetique et champ moleculaire correctif de l'equation d'etat. Dans une deuxieme partie, apres avoir examine les difficultes auxquelles se heurtait la theorie, l'auteur montre qu'elles ont ete resolues en introduisant la notion de champ moleculaire local et en donnant ainsi la cle des proprietes des corps antiferro-et ferri-magnetiques. II etudie egalement (paragraphe 4 et Appendice) l'etat actuel de l'interpretation des proprietes magnetiques de la pyrrhotine qui a joue un grand role dans l'histoire du champ moleculaire. (auteur)

Modulating the Electron-Hole Interaction in a Hybrid Lead Halide Perovskite with an Electric Field.

Science.gov (United States)

Leijtens, Tomas; Srimath Kandada, Ajay Ram; Eperon, Giles E; Grancini, Giulia; D'Innocenzo, Valerio; Ball, James M; Stranks, Samuel D; Snaith, Henry J; Petrozza, Annamaria

2015-12-16

Despite rapid developments in both photovoltaic and light-emitting device performance, the understanding of the optoelectronic properties of hybrid lead halide perovskites is still incomplete. In particular, the polarizability of the material, the presence of molecular dipoles, and their influence on the dynamics of the photoexcitations remain an open issue to be clarified. Here, we investigate the effect of an applied external electric field on the photoexcited species of CH3NH3PbI3 thin films, both at room temperature and at low temperature, by monitoring the photoluminescence (PL) yield and PL decays. At room temperature we find evidence for electric-field-induced reduction of radiative bimolecular carrier recombination together with motion of charged defects that affects the nonradiative decay rate of the photoexcited species. At low temperature (190 K), we observe a field-induced enhancement of radiative free carrier recombination rates that lasts even after the removal of the field. We assign this to field-induced alignment of the molecular dipoles, which reduces the vibrational freedom of the lattice and the associated local screening and hence results in a stronger electron-hole interaction.

Analysis of the Numerical Diffusion in Anisotropic Mediums: Benchmarks for Magnetic Field Aligned Meshes in Space Propulsion Simulations

Directory of Open Access Journals (Sweden)

Daniel Pérez-Grande

2016-11-01

Full Text Available This manuscript explores numerical errors in highly anisotropic diffusion problems. First, the paper addresses the use of regular structured meshes in numerical solutions versus meshes aligned with the preferential directions of the problem. Numerical diffusion in structured meshes is quantified by solving the classical anisotropic diffusion problem; the analysis is exemplified with the application to a numerical model of conducting fluids under magnetic confinement, where rates of transport in directions parallel and perpendicular to a magnetic field are quite different. Numerical diffusion errors in this problem promote the use of magnetic field aligned meshes (MFAM. The generation of this type of meshes presents some challenges; several meshing strategies are implemented and analyzed in order to provide insight into achieving acceptable mesh regularity. Second, Gradient Reconstruction methods for magnetically aligned meshes are addressed and numerical errors are compared for the structured and magnetically aligned meshes. It is concluded that using the latter provides a more correct and straightforward approach to solving problems where anisotropicity is present, especially, if the anisotropicity level is high or difficult to quantify. The conclusions of the study may be extrapolated to the study of anisotropic flows different from conducting fluids.

Polarization properties of below-threshold harmonics from aligned molecules H2+ in linearly polarized laser fields.

Science.gov (United States)

Dong, Fulong; Tian, Yiqun; Yu, Shujuan; Wang, Shang; Yang, Shiping; Chen, Yanjun

2015-07-13

We investigate the polarization properties of below-threshold harmonics from aligned molecules in linearly polarized laser fields numerically and analytically. We focus on lower-order harmonics (LOHs). Our simulations show that the ellipticity of below-threshold LOHs depends strongly on the orientation angle and differs significantly for different harmonic orders. Our analysis reveals that this LOH ellipticity is closely associated with resonance effects and the axis symmetry of the molecule. These results shed light on the complex generation mechanism of below-threshold harmonics from aligned molecules.

Two-dimensional dynamics of a free molecular chain with a secondary structure

DEFF Research Database (Denmark)

Zolotaryuk, Alexander; Christiansen, Peter Leth; Savin, A.V.

1996-01-01

A simple two-dimensional (2D) model of an isolated (free) molecular chain with primary and secondary structures has been suggested and investigated both analytically and numerically. This model can be considered as the simplest generalization of the well-known Fermi-Pasta-Ulam model of an anharmo......A simple two-dimensional (2D) model of an isolated (free) molecular chain with primary and secondary structures has been suggested and investigated both analytically and numerically. This model can be considered as the simplest generalization of the well-known Fermi-Pasta-Ulam model...

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G. Gomez

Since December, the muon alignment community has focused on analyzing the data recorded so far in order to produce new DT and CSC Alignment Records for the second reprocessing of CRAFT data. Two independent algorithms were developed which align the DT chambers using global tracks, thus providing, for the first time, a relative alignment of the barrel with respect to the tracker. These results are an important ingredient for the second CRAFT reprocessing and allow, for example, a more detailed study of any possible mis-modelling of the magnetic field in the muon spectrometer. Both algorithms are constructed in such a way that the resulting alignment constants are not affected, to first order, by any such mis-modelling. The CSC chambers have not yet been included in this global track-based alignment due to a lack of statistics, since only a few cosmics go through the tracker and the CSCs. A strategy exists to align the CSCs using the barrel as a reference until collision tracks become available. Aligning the ...

Dynamics of molecular superrotors in an external magnetic field

Science.gov (United States)

Korobenko, Aleksey; Milner, Valery

2015-08-01

We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin-rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.

Seasonal and interplanetary magnetic field dependence of the field-aligned currents for both Northern and Southern Hemispheres

Directory of Open Access Journals (Sweden)

D. L. Green

2009-04-01

Full Text Available The configuration of the Earth's magnetosphere under various Interplanetary Magnetic Field (IMF and solar wind conditions alters the global distribution of Field-Aligned Currents (FACs at the high latitude ionospheres. We use magnetic field data obtained from the Iridium constellation to extend recent studies that infer the dependence of the global FAC configuration on IMF direction and magnitude, hemisphere and season. New results are a reduced IMF By influence on the FAC configuration for the winter hemisphere and a redistribution of FAC to the nightside for winter relative to the summer hemisphere. These effects are linked to the winter ionosphere conductance distribution being dominated by localised nightside enhancement associated with ionisation from energetic particle precipitation. A comparison of an estimated open-closed field line boundary (OCFLB with the Region 1 FAC locations shows reasonable agreement for summer FAC configurations. However, the OCFLB location is decoupled from the Region 1 FACs in winter, especially for IMF Bz>0.

Molecular structure and motion in zero field magnetic resonance

International Nuclear Information System (INIS)

Jarvie, T.P.

1989-10-01

Zero field magnetic resonance is well suited for the determination of molecular structure and the study of motion in disordered materials. Experiments performed in zero applied magnetic field avoid the anisotropic broadening in high field nuclear magnetic resonance (NMR) experiments. As a result, molecular structure and subtle effects of motion are more readily observed

Finite-temperature orbital-free DFT molecular dynamics: Coupling PROFESS and QUANTUM ESPRESSO

Science.gov (United States)

Karasiev, Valentin V.; Sjostrom, Travis; Trickey, S. B.

2014-12-01

Implementation of orbital-free free-energy functionals in the PROFESS code and the coupling of PROFESS with the QUANTUM ESPRESSO code are described. The combination enables orbital-free DFT to drive ab initio molecular dynamics simulations on the same footing (algorithms, thermostats, convergence parameters, etc.) as for Kohn-Sham (KS) DFT. All the non-interacting free-energy functionals implemented are single-point: the local density approximation (LDA; also known as finite-T Thomas-Fermi, ftTF), the second-order gradient approximation (SGA or finite-T gradient-corrected TF), and our recently introduced finite-T generalized gradient approximations (ftGGA). Elimination of the KS orbital bottleneck via orbital-free methodology enables high-T simulations on ordinary computers, whereas those simulations would be costly or even prohibitively time-consuming for KS molecular dynamics (MD) on very high-performance computer systems. Example MD simulations on H over a temperature range 2000 K ≤ T ≤4,000,000 K are reported, with timings on small clusters (16-128 cores) and even laptops. With respect to KS-driven calculations, the orbital-free calculations are between a few times through a few hundreds of times faster.

Parallel and Perpendicular Alignment of Anisotropic Particles in Free Liquid Microjets and Emerging Microdroplets.

Science.gov (United States)

Schlenk, Mathias; Hofmann, Eddie; Seibt, Susanne; Rosenfeldt, Sabine; Schrack, Lukas; Drechsler, Markus; Rothkirch, Andre; Ohm, Wiebke; Breu, Josef; Gekle, Stephan; Förster, Stephan

2018-04-24

Liquid microjets play a key role in fiber spinning, inkjet printing, and coating processes. In all of these applications, the liquid jets carry dispersed particles whose spatial and orientational distributions within the jet critically influence the properties of the fabricated structures. Despite its importance, there is currently no knowledge about the orientational distribution of particles within microjets and droplets. Here, we demonstrate a microfluidic device that allows to determine the local particle distribution and orientation by X-ray scattering. Using this methodology, we discovered unexpected changes in the particle orientation upon exiting the nozzle to form a free jet, and upon jet break-up into droplets, causing an unusual biaxial particle orientation. We show how flow and aspect ratio determine the flow orientation of anisotropic particles. Furthermore, we demonstrate that the observed phenomena are a general characteristic of anisotropic particles. Our findings greatly enhance our understanding of particle orientation in free jets and droplets and provide a rationale for controlling particle alignment in liquid jet-based fabrication methodologies.

Three-dimensional equilibria for the extended magnetotail and the generation of field-aligned current sheets

International Nuclear Information System (INIS)

Birn, J.

1989-01-01

Using the magnetotail equilibrium theory and a solution method outlined by Birn (1987), we have constructed self-consistent three-dimensional models for the quiet average magnetotail beyond about 20 R/sub E/ distance but earthward of a potential distant neutral line, which take into account the decrease of the tail flaring with distance. We find that this effect is coupled with the presence of magnetic shear and thus with field-aligned electric currents. These currents have the signature of region 1 currents, toward the Earth on the dawnside and away on the duskside, and contribute about 5 x 10 5 A to the total Birkeland current. They are strongly concentrated near the plasma sheet-lobe boundary and increase toward the flanks of the tail. Associated with the field-aligned currents and the corresponding magnetic field shear there is a bulging effect that tends to deform a circular cross section of the tail near the Earth into one that has bulges in the low-latitude boundary region. We argue that this effect may be the cause for increased interaction with the solar wind in these regions, producing interconnected fields and tailward flowing plasma on magnetospheric-like fields in the low-latitude boundary layer, and deforming this boundary region into the observed dog bone shape of the plasma sheet cross section. copyright American Geophysical Union 1989

Dynamics of molecular superrotors in an external magnetic field

International Nuclear Information System (INIS)

Korobenko, Aleksey; Milner, Valery

2015-01-01

We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin–rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation. (paper)

Energy of Force-Free Magnetic Fields in Relation to Coronal Mass Ejections; TOPICAL

International Nuclear Information System (INIS)

G.S. Choe; C.Z. Cheng

2002-01-01

In typical observations of coronal mass ejections (CMEs), a magnetic structure of a helmet-shaped closed configuration bulges out and eventually opens up. However, a spontaneous transition between these field configurations has been regarded to be energetically impossible in force-free fields according to the Aly-Sturrock theorem. The theorem states that the maximum energy state of force-free fields with a given boundary normal field distribution is the open field. The theorem implicitly assumes the existence of the maximum energy state, which may not be taken for granted. In this study, we have constructed force-free fields containing tangential discontinuities in multiple flux systems. These force-free fields can be generated from a potential field by footpoint motions that do not conserve the boundary normal field distribution. Some of these force-free fields are found to have more magnetic energy than the corresponding open fields. The constructed force-free configurations are compared with observational features of CME-bearing active regions. Possible mechanisms of CMEs are also discussed

Study on orientation mechanisms of poly(vinylidenefluoride-trifluoroethylene) molecules aligned by atomic force microscopy

International Nuclear Information System (INIS)

Kimura, Kuniko; Kobayashi, Kei; Yamada, Hirofumi; Horiuchi, Toshihisa; Ishida, Kenji; Matsushige, Kazumi

2006-01-01

We have developed a molecular orientation control technique for polymers utilizing contact-mode atomic force microscopy (AFM). In this paper, we studied the molecular alignment mechanism of this technique by applying it to poly(vinylidenefluoride-trifluoroethylene) (P(VDF-TrFE)). The resultant alignment and formed crystal size were strongly dependent on the temperature during the modification. They also depended on the scan line spacing of the modification. These results made the alignment mechanism clear. The obtained molecular alignment was stable against the heat treatment even at the temperatures just below T m

Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory

International Nuclear Information System (INIS)

Mrugalla, Florian; Kast, Stefan M

2016-01-01

Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute–solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute–solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems. (paper)

Optimization of bicelle lipid composition and temperature for EPR spectroscopy of aligned membranes.

Science.gov (United States)

McCaffrey, Jesse E; James, Zachary M; Thomas, David D

2015-01-01

We have optimized the magnetic alignment of phospholipid bilayered micelles (bicelles) for EPR spectroscopy, by varying lipid composition and temperature. Bicelles have been extensively used in NMR spectroscopy for several decades, in order to obtain aligned samples in a near-native membrane environment and take advantage of the intrinsic sensitivity of magnetic resonance to molecular orientation. Recently, bicelles have also seen increasing use in EPR, which offers superior sensitivity and orientational resolution. However, the low magnetic field strength (less than 1 T) of most conventional EPR spectrometers results in homogeneously oriented bicelles only at a temperature well above physiological. To optimize bicelle composition for magnetic alignment at reduced temperature, we prepared bicelles containing varying ratios of saturated (DMPC) and unsaturated (POPC) phospholipids, using EPR spectra of a spin-labeled fatty acid to assess alignment as a function of lipid composition and temperature. Spectral analysis showed that bicelles containing an equimolar mixture of DMPC and POPC homogeneously align at 298 K, 20 K lower than conventional DMPC-only bicelles. It is now possible to perform EPR studies of membrane protein structure and dynamics in well-aligned bicelles at physiological temperatures and below. Copyright © 2014 Elsevier Inc. All rights reserved.

Orientation of KRb molecules in a switched electrostatic field

International Nuclear Information System (INIS)

Huang Yun-Xia; Xu Shu-Wu; Yang Xiao-Hua

2013-01-01

We theoretically investigate the orientation of the cold KRb molecules induced in a switched electrostatic field by numerically solving the full time-dependent Schrödinger equation. The results show that the periodic field-free molecular orientation can be realized for the KRb molecules by rapidly switching off the electrostatic field. Meanwhile, by varying the switching times of the electrostatic field, the adiabatic and nonadiabatic interactions of the molecules with the applied field can be realized. Moreover, the influences of the electrostatic field strength and the rotational temperature to the degree of the molecular orientation are studied. The investigations show that increasing the electrostatic field will increase the degree of the molecular orientation, both in the constant-field regime and in the field-free regime, while the increasing of the rotational temperature of the cold molecules will greatly decrease the degree of the molecular orientation. (atomic and molecular physics)

Effects of fluctuations and noise on the neutron monitor diurnal anisotropy. II. Non-field-aligned diffusion

International Nuclear Information System (INIS)

Owens, A.J.

1977-01-01

The effects of non-field-aligned diffusion (i.e., terms in the diffusion tensor proportional to the antisymmetric coefficient kappa/sub A/) on the observed day-to-day deviation of the diffusive diurnal anisotropy from the daily average magnetic field direction are considered. Using reasonable parameters for the diffusion of cosmic rays in interplanetary space, I show that these terms give a natural explanation for the angular difference between the anisotropy and field directions during normal quiet interplanetary epochs

Dependence of Interaction Free Energy between Solutes on an External Electrostatic Field

Directory of Open Access Journals (Sweden)

Pei-Kun Yang

2013-07-01

Full Text Available To explore the athermal effect of an external electrostatic field on the stabilities of protein conformations and the binding affinities of protein-protein/ligand interactions, the dependences of the polar and hydrophobic interactions on the external electrostatic field, −Eext, were studied using molecular dynamics (MD simulations. By decomposing Eext into, along, and perpendicular to the direction formed by the two solutes, the effect of Eext on the interactions between these two solutes can be estimated based on the effects from these two components. Eext was applied along the direction of the electric dipole formed by two solutes with opposite charges. The attractive interaction free energy between these two solutes decreased for solutes treated as point charges. In contrast, the attractive interaction free energy between these two solutes increased, as observed by MD simulations, for Eext = 40 or 60 MV/cm. Eext was applied perpendicular to the direction of the electric dipole formed by these two solutes. The attractive interaction free energy was increased for Eext = 100 MV/cm as a result of dielectric saturation. The force on the solutes along the direction of Eext computed from MD simulations was greater than that estimated from a continuum solvent in which the solutes were treated as point charges. To explore the hydrophobic interactions, Eext was applied to a water cluster containing two neutral solutes. The repulsive force between these solutes was decreased/increased for Eext along/perpendicular to the direction of the electric dipole formed by these two solutes.

The value of cell-free DNA for molecular pathology.

Science.gov (United States)

Stewart, Caitlin M; Kothari, Prachi D; Mouliere, Florent; Mair, Richard; Somnay, Saira; Benayed, Ryma; Zehir, Ahmet; Weigelt, Britta; Dawson, Sarah-Jane; Arcila, Maria E; Berger, Michael F; Tsui, Dana Wy

2018-04-01

Over the past decade, advances in molecular biology and genomics techniques have revolutionized the diagnosis and treatment of cancer. The technological advances in tissue profiling have also been applied to the study of cell-free nucleic acids, an area of increasing interest for molecular pathology. Cell-free nucleic acids are released from tumour cells into the surrounding body fluids and can be assayed non-invasively. The repertoire of genomic alterations in circulating tumour DNA (ctDNA) is reflective of both primary tumours and distant metastatic sites, and ctDNA can be sampled multiple times, thereby overcoming the limitations of the analysis of single biopsies. Furthermore, ctDNA can be sampled regularly to monitor response to treatment, to define the evolution of the tumour genome, and to assess the acquisition of resistance and minimal residual disease. Recently, clinical ctDNA assays have been approved for guidance of therapy, which is an exciting first step in translating cell-free nucleic acid research tests into clinical use for oncology. In this review, we discuss the advantages of cell-free nucleic acids as analytes in different body fluids, including blood plasma, urine, and cerebrospinal fluid, and their clinical applications in solid tumours and haematological malignancies. We will also discuss practical considerations for clinical deployment, such as preanalytical factors and regulatory requirements. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Aligned Magnetic Field Effects on Flow and Heat Transfer of the Upper-Convected Maxwell Fluid over a Stretching/Shrinking Sheet

Directory of Open Access Journals (Sweden)

Waini Iskandar

2017-01-01

Full Text Available In this paper, the effect of aligned magnetic field towards the flow and heat transfer of the upper-convected Maxwell (UCM fluid over a stretching/shrinking sheet is numerically studied. The governing partial differential equations are reduced into a system of ordinary differential equations using a similarity transformation, which are then solved numerically using the shooting method. The skin friction and heat transfer coefficients, the velocity, as well as the temperature profiles of the fluid are presented and discussed. Results indicate that an increase in the aligned angle strengthens the applied magnetic field which decrease the velocity and increase the temperature profiles of the fluid. This implies that an increase in the aligned angle increases the skin friction coefficient and decreases the heat transfer coefficients.

Minerals and aligned collagen fibrils in tilapia fish scales: structural analysis using dark-field and energy-filtered transmission electron microscopy and electron tomography.

Science.gov (United States)

Okuda, Mitsuhiro; Ogawa, Nobuhiro; Takeguchi, Masaki; Hashimoto, Ayako; Tagaya, Motohiro; Chen, Song; Hanagata, Nobutaka; Ikoma, Toshiyuki

2011-10-01

The mineralized structure of aligned collagen fibrils in a tilapia fish scale was investigated using transmission electron microscopy (TEM) techniques after a thin sample was prepared using aqueous techniques. Electron diffraction and electron energy loss spectroscopy data indicated that a mineralized internal layer consisting of aligned collagen fibrils contains hydroxyapatite crystals. Bright-field imaging, dark-field imaging, and energy-filtered TEM showed that the hydroxyapatite was mainly distributed in the hole zones of the aligned collagen fibrils structure, while needle-like materials composed of calcium compounds including hydroxyapatite existed in the mineralized internal layer. Dark-field imaging and three-dimensional observation using electron tomography revealed that hydroxyapatite and needle-like materials were mainly found in the matrix between the collagen fibrils. It was observed that hydroxyapatite and needle-like materials were preferentially distributed on the surface of the hole zones in the aligned collagen fibrils structure and in the matrix between the collagen fibrils in the mineralized internal layer of the scale.

Torsional structural response from free-field ground motion

International Nuclear Information System (INIS)

Lam, P.C.; Scavuzzo, R.J.

1979-01-01

Torsional response of structures subjected to the action of both the free-field torsional inputs and external torque is investigated. By expanding the work of Scanlan, both lateral and torsional foundation inputs due to a travelling shear wave are derived from the free-field point motion. These free-field torsional motions are used as the basis of numerical studies. Response for different soil stiffness and structural characteristics are studied, as well as different dynamic models. In one dynamic model the structure is coupled to the soil using a compliance spring matrix and in the second model the structure coupled to an elastic half-space. Results of these two basic models are compared and found to be in good agreement. Finally, torsional structural response caused by torsional inputs is compared with lateral response caused by modified lateral inputs to determine the significance of torsional excitation on the seismic response of building structures. Numerical results show that these torsional seismic loads are as large or larger than those from modified lateral inputs. (orig.)

Simulation of enhanced deposition due to magnetic field alignment of ellipsoidal particles in a lung bifurcation.

Science.gov (United States)

Martinez, R C; Roshchenko, A; Minev, P; Finlay, W H

2013-02-01

Aerosolized chemotherapy has been recognized as a potential treatment for lung cancer. The challenge of providing sufficient therapeutic effects without reaching dose-limiting toxicity levels hinders the development of aerosolized chemotherapy. This could be mitigated by increasing drug-delivery efficiency with a noninvasive drug-targeting delivery method. The purpose of this study is to use direct numerical simulations to study the resulting local enhancement of deposition due to magnetic field alignment of high aspect ratio particles. High aspect ratio particles were approximated by a rigid ellipsoid with a minor diameter of 0.5 μm and fluid particle density ratio of 1,000. Particle trajectories were calculated by solving the coupled fluid particle equations using an in-house micro-macro grid finite element algorithm based on a previously developed fictitious domain approach. Particle trajectories were simulated in a morphologically realistic geometry modeling a symmetrical terminal bronchiole bifurcation. Flow conditions were steady inspiratory air flow due to typical breathing at 18 L/min. Deposition efficiency was estimated for two different cases: [1] particles aligned with the streamlines and [2] particles with fixed angular orientation simulating the magnetic field alignment of our previous in vitro study. The local enhancement factor defined as the ratio between deposition efficiency of Case [1] and Case [2] was found to be 1.43 and 3.46 for particles with an aspect ratio of 6 and 20, respectively. Results indicate that externally forcing local alignment of high aspect ratio particles can increase local deposition considerably.

Controlling the diameters and field emission properties of vertically aligned carbon nanotubes synthesized by thermal chemical vapor deposition

International Nuclear Information System (INIS)

Choi, Sung Yool; Kang, Young Il; Cho, Kyoung Ik; Choi, Kyu Seok; Kim, Do Jin

2001-01-01

We report here the synthesis of vertically well-aligned carbon nanotubes and the effect of catalytic metal layer on the diameter of grown carbon nanotubes and the field emission characteristics of them, The carbon nanotubes were grown by thermal chemical vapor deposition at temperatures below 900 .deg. C on Fe metal catalytic layer, deposited by sputtering process on a Si substrate and pretreated by heat and NH 3 gas. We found that the thickness of metal layers could be an important parameter in controlling the diameters of carbon nanotubes. With varying the thickness of the metal layers the grain sizes of them also vary so that the diameters of the nanotubes could be controlled. Field emission measurement has been made on the carbon nanotube field emitters at room temperature in a vacuum chamber below 10 -6 Torr. Our vertically aligned carbon nanotube field emitter of the smallest diameter emits a current density about 10 mA/cm 2 at 7.2 V/μm. The field emission property of the carbon nanotubes shows strong dependence on the nanotube diameters as expected

The connexion of duality and causal properties for generalized free fields

International Nuclear Information System (INIS)

Garber, W.D.

1975-01-01

It is shown that the time-slice axiom and the diamond property are equivalent for the generalized free field. If, in addition, there is a mass gap, duality is equivalent to either causality requirement. It is further shown that the local rings associated with certain space-time regions are factors in the case of causal generalized free fields with mass gap. Necessary and sufficient conditions for causality and duality and some examples for causal and acausal generalized free fields are also given. (orig.) [de

Active manipulation of the selective alignment by two laser pulses

International Nuclear Information System (INIS)

Zeng-Qiang, Yang; Zhi-Rong, Guo; Gui-Xian, Ge

2010-01-01

This paper solves numerically the full time-dependent Schrödinger equation based on the rigid rotor model, and proposes a novel strategy to determine the optimal time delay of the two laser pulses to manipulate the molecular selective alignment. The results illustrate that the molecular alignment generated by the first pulse can be suppressed or enhanced selectively, the relative populations of even and odd rotational states in the final rotational wave packet can be manipulated selectively by precisely inserting the peak of the second laser pulse at the time when the slope for the alignment parameter by the first laser locates a local maximum for the even rotational states and a local minimum for the odds, and vice versa. The selective alignment can be further optimised by selecting the intensity ratio of the two laser pulses on the condition that the total laser intensity and pulse duration are kept constant. (atomic and molecular physics)

Planck intermediate results: XXXV. Probing the role of the magnetic field in the formation of structure in molecular clouds

International Nuclear Information System (INIS)

Ade, P. A. R.; Aghanim, N.; Alves, M. I. R.; Arnaud, M.; Arzoumanian, D.

2016-01-01

Within ten nearby (d < 450 pc) Gould belt molecular clouds we evaluate in this paper statistically the relative orientation between the magnetic field projected on the plane of sky, inferred from the polarized thermal emission of Galactic dust observed by Planck at 353 GHz, and the gas column density structures, quantified by the gradient of the column density, N_H. The selected regions, covering several degrees in size, are analysed at an effective angular resolution of 10' FWHM, thus sampling physical scales from 0.4 to 40 pc in the nearest cloud. The column densities in the selected regions range from N_H≈ 10"2"1 to10"2"3 cm"-"2, and hence they correspond to the bulk of the molecular clouds. The relative orientation is evaluated pixel by pixel and analysed in bins of column density using the novel statistical tool called “histogram of relative orientations”. Throughout this study, we assume that the polarized emission observed by Planck at 353 GHz is representative of the projected morphology of the magnetic field in each region, i.e., we assume a constant dust grain alignment efficiency, independent of the local environment. Within most clouds we find that the relative orientation changes progressively with increasing N_H, from mostly parallel or having no preferred orientation to mostly perpendicular. In simulations of magnetohydrodynamic turbulence in molecular clouds this trend in relative orientation is a signature of Alfvénic or sub-Alfvénic turbulence, implying that the magnetic field is significant for the gas dynamics at the scales probed by Planck. Finally, we compare the deduced magnetic field strength with estimates we obtain from other methods and discuss the implications of the Planck observations for the general picture of molecular cloud formation and evolution.

Beam-Based Alignment of Magnetic Field in the Fermilab Electron Cooler Cooling Section

International Nuclear Information System (INIS)

Seletskiy, S. M.; Tupikov, V.

2006-01-01

The Fermilab Electron Cooling Project requires low effective anglular spread of electrons in the cooling section. One of the main components of the effective electron angles is an angle of electron beam centroid with respect to antiproton beam. This angle is caused by the poor quality of magnetic field in the 20 m long cooling section solenoid and by the mismatch of the beam centroid to the entrance of the cooling section. This paper focuses on the beam-based procedure of the alignment of the cooling section field and beam centroid matching. The discussed procedure allows to suppress the beam centroid angles below the critical value of 0.1 mrad

Free-Free Transitions in the Presence of Laser Fields and Debye Potential at Very Low Incident Electron Energies

Science.gov (United States)

Bhatia, Anand

2012-01-01

We study the free-free transition in electron-helium ion in the ground state and embedded in a Debye potential in the presence of an external laser field at very low incident electron energies. The laser field is treated classically while the collision dynamics is treated quantum mechanically. The laser field is chosen as monochromatic, linearly polarized and homogeneous. The incident electron is considered to be dressed by the laser field in a nonperturbative manner by choosing Volkov wave function for it. The scattering wave function for the incident electron on the target embedded in a Debye potential is solved numerically by taking into account the effect of electron exchange. We calculate the laser-assisted differential and total cross sections for free-free transition for absorption/emission of a single photon or no photon exchange. The results will be presented at the conference.

Retardative chain transfer in free radical free-radical polymerisations of vinyl neo-decanoate in low molecular weight polyisoprene and toluene

NARCIS (Netherlands)

Monteiro, M.J.; Subramaniam, N.; Taylor, J.R.; Pham, B.T.T.; Tonge, M.P.; Gilbert, R.G.

2001-01-01

The kinetics of free-radical polymerisation of vinyl neo-decanoate (VneoD) and the molecular weight distributions (MWDs) of the polymers formed in the presence and absence of low molecular weight polyisoprene at 50°C under a variety of conditions were investigated. The bulk reaction was successfully

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

Energy Technology Data Exchange (ETDEWEB)

Hoang, Thiem [Canadian Institute for Theoretical Astrophysics, University of Toronto, 60 St. George Street, Toronto, ON M5S 3H8 (Canada); Lazarian, A. [Department of Astronomy, University of Wisconsin-Madison (United States)

2016-11-10

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 of 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.

Compositions for directed alignment of conjugated polymers

Science.gov (United States)

Kim, Jinsang; Kim, Bong-Gi; Jeong, Eun Jeong

2016-04-19

Conjugated polymers (CPs) achieve directed alignment along an applied flow field and a dichroic ratio of as high as 16.67 in emission from well-aligned thin films and fully realized anisotropic optoelectronic properties of CPs in field-effect transistor (FET).

Alignment system for SGII-Up laser facility

Science.gov (United States)

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.

DNA Translator and Aligner: HyperCard utilities to aid phylogenetic analysis of molecules.

Science.gov (United States)

Eernisse, D J

1992-04-01

DNA Translator and Aligner are molecular phylogenetics HyperCard stacks for Macintosh computers. They manipulate sequence data to provide graphical gene mapping, conversions, translations and manual multiple-sequence alignment editing. DNA Translator is able to convert documented GenBank or EMBL documented sequences into linearized, rescalable gene maps whose gene sequences are extractable by clicking on the corresponding map button or by selection from a scrolling list. Provided gene maps, complete with extractable sequences, consist of nine metazoan, one yeast, and one ciliate mitochondrial DNAs and three green plant chloroplast DNAs. Single or multiple sequences can be manipulated to aid in phylogenetic analysis. Sequences can be translated between nucleic acids and proteins in either direction with flexible support of alternate genetic codes and ambiguous nucleotide symbols. Multiple aligned sequence output from diverse sources can be converted to Nexus, Hennig86 or PHYLIP format for subsequent phylogenetic analysis. Input or output alignments can be examined with Aligner, a convenient accessory stack included in the DNA Translator package. Aligner is an editor for the manual alignment of up to 100 sequences that toggles between display of matched characters and normal unmatched sequences. DNA Translator also generates graphic displays of amino acid coding and codon usage frequency relative to all other, or only synonymous, codons for approximately 70 select organism-organelle combinations. Codon usage data is compatible with spreadsheet or UWGCG formats for incorporation of additional molecules of interest. The complete package is available via anonymous ftp and is free for non-commercial uses.

Invariant gauge families inherent in Abelian-gauge field theory. [Scalar dipole ghost field, free-field equations

Energy Technology Data Exchange (ETDEWEB)

Yokoyama, Kan-ichi; Kubo, Reijiro

1974-12-01

The framework of the Nakanishi-Lautrup formalism should be enlarged by introducing a scalar dipole ghost field B(x), which is called gauge on field, together with its pair field. By taking free Lagrangian density, Free-field equations can be described. The vacuum is defined by using a neutral vector field U..mu..(x). The state-vector space is generated by the adjoining conjugates of U..mu..sup((+))(x), and auxiliary fields B(x), B/sub 1/(x) and B/sub 2/(x), which were introduced in the form of the Lagrangian density. The physical states can be defined by the supplementary conditions of the form B/sub 1/sup((+))(x) 1 phys>=B/sub 2/sup((+))(x) 1 phys>=0. It is seen that all the field equations and all the commutators are kept form-invariant, and that the gauge parameter ..cap alpha.. is transformed into ..cap alpha..' given by ..cap alpha..'=..cap alpha..+lambda, with epsilon unchanged. The Lagrangian density is specified only by the gauge invariant parameter epsilon. The gauge structure of theory has universal meaning over whole Abelian-gauge field. C-number gauge transformation and the gauge structure in the presence of interaction are also discussed.

Dispersion equations for field-aligned cyclotron waves in axisymmetric magnetospheric plasmas

Directory of Open Access Journals (Sweden)

N. I. Grishanov

2006-03-01

Full Text Available In this paper, we derive the dispersion equations for field-aligned cyclotron waves in two-dimensional (2-D magnetospheric plasmas with anisotropic temperature. Two magnetic field configurations are considered with dipole and circular magnetic field lines. The main contribution of the trapped particles to the transverse dielectric permittivity is estimated by solving the linearized Vlasov equation for their perturbed distribution functions, accounting for the cyclotron and bounce resonances, neglecting the drift effects, and assuming the weak connection of the left-hand and right-hand polarized waves. Both the bi-Maxwellian and bi-Lorentzian distribution functions are considered to model the ring current ions and electrons in the dipole magnetosphere. A numerical code has been developed to analyze the dispersion characteristics of electromagnetic ion-cyclotron waves in an electron-proton magnetospheric plasma with circular magnetic field lines, assuming that the steady-state distribution function of the energetic protons is bi-Maxwellian. As in the uniform magnetic field case, the growth rate of the proton-cyclotron instability (PCI in the 2-D magnetospheric plasmas is defined by the contribution of the energetic ions/protons to the imaginary part of the transverse permittivity elements. We demonstrate that the PCI growth rate in the 2-D axisymmetric plasmasphere can be significantly smaller than that for the straight magnetic field case with the same macroscopic bulk parameters.

JavaScript DNA translator: DNA-aligned protein translations.

Science.gov (United States)

Perry, William L

2002-12-01

There are many instances in molecular biology when it is necessary to identify ORFs in a DNA sequence. While programs exist for displaying protein translations in multiple ORFs in alignment with a DNA sequence, they are often expensive, exist as add-ons to software that must be purchased, or are only compatible with a particular operating system. JavaScript DNA Translator is a shareware application written in JavaScript, a scripting language interpreted by the Netscape Communicator and Internet Explorer Web browsers, which makes it compatible with several different operating systems. While the program uses a familiar Web page interface, it requires no connection to the Internet since calculations are performed on the user's own computer. The program analyzes one or multiple DNA sequences and generates translations in up to six reading frames aligned to a DNA sequence, in addition to displaying translations as separate sequences in FASTA format. ORFs within a reading frame can also be displayed as separate sequences. Flexible formatting options are provided, including the ability to hide ORFs below a minimum size specified by the user. The program is available free of charge at the BioTechniques Software Library (www.Biotechniques.com).

Molecular bond formation in Na* + N2 energy transfer: Crossed beam study of atomic alignment and orientation

International Nuclear Information System (INIS)

Reiland, W.; Jamieson, G.; Tittes, U.; Hertel, I.V.

1982-01-01

We report the first full analysis of collisionally induced atomic alignment and orientation for a molecular collision process. In an experiment with crossed supersonic beams of N 2 and laser excited Na(3 2 Psub(3/2)) we have studied the dependence of angular and energy resolved differential quenching cross sections as a function of the linear and circular polarization of the exciting laser light. The ansisotropies observed in the linear polarization data range up to 2:1 when corrected for electron and nuclear spin relaxation. The maximum effect is found at small scattering angles and intermediate energy transfer where the cross section is also largest. The atomic alignment angle most favourable for quenching relates to the scattering angle and can be understood in a model picture in such a way that the (NaN 2 )* molecular system is formed at internuclear distances as low as R = 10a 0 . The circular asymmetry is small but with significant structure and is attributed to interaction on different potential surfaces at R > 10a 0 . Full analysis of the four measurable parameter is given in terms of the density matrix in a frame with z-axis perpendicular to collision plane which allows a clear understanding of the properties of atomic reflection symmetry and coherence of the scattering process. (orig.)

Accuracy of field alignment in abdominal radiation therapy

International Nuclear Information System (INIS)

Kortmann, R. D.; Hess, C. F.; Meisner, C.; Schmidberger, H.; Bamberg, M.

1996-01-01

Purpose: To assess the accuracy of field alignment in a homogeneous group of patients undergoing radiotherapy of the abdomen (adjuvant treatment of the paraaortic region in Stage I testicular seminoma). To evaluate the predictive value of the first verification on field placement errors during subsequent treatment delivery. Methods and Materials: In 45 patients, linear and rotational discrepancies were measured between simulation and first check and between 10 consecutive verification films. Results: For the total group of patients, the distribution of all deviations showed mean values between 2.3 mm and -2.7 mm with standard deviations of 3.9 mm to 4.7 mm for linear discrepancies, and -0.5 deg. to 0.3 deg. with standard deviations of 1.2 deg. to 2.1 deg. for rotational discrepancies, respectively. For all patients, deviations for the transition from simulator to the treatment machine were similar to deviations during subsequent treatment delivery, with 95% of all absolute deviations < 10.0 mm and 4 deg. , respectively. When performing correlation analysis between deviations at first check and during treatment delivery, a correlation for lateral displacements and a borderline correlation for caudal displacements could be found. There was no correlation for cranial and rotational displacements. Conclusions: Although a trend of deviations for subsequent treatment delivery may be shown at first check, our analysis indicates that the first verification cannot reliably predict inaccuracies during treatment delivery. Random fluctuations of field displacements of up to 1.0 cm prevail. They must be considered when prescribing the safety margins of the planned target volume and determining cutoff points for corrective actions in abdominal radiation therapy

Isotope-selective ionization using four-pulse alignment

International Nuclear Information System (INIS)

Akagi, Hiroshi; Kasajima, Tatsuya; Kumada, Takayuki; Itakura, Ryuji; Yokoyama, Atsushi; Hasegawa, Hirokazu; Ohshima, Yasuhiro

2013-01-01

We have proposed a laser isotope separation method utilizing molecular alignment and non-resonant multiphoton ionization, and demonstrated isotope-selective ionization of 14 N 2 and 15 N 2 isotopomers, using one-pulse alignment. In the present work, we used a train of four identical pulses, instead of one pulse, to obtain the higher selectivity. (author)

EVIDENCE FOR H{sub 2} FORMATION DRIVEN DUST GRAIN ALIGNMENT IN IC 63

Energy Technology Data Exchange (ETDEWEB)

Andersson, B-G; De Buizer, J.; Charcos-Llorens, M. [SOFIA Science Center, USRA, NASA Ames Research Center, M.S. N211-3 Moffett Field, CA 94035 (United States); Piirola, V. [Finnish Centre for Astronomy with ESO, University of Turku, Väisäläntie 20, FI-21500 Piikkiö (Finland); Clemens, D. P. [Institute for Astrophysical Research, Boston University, Boston, MA 02215 (United States); Uomoto, A. [Observatories of the Carnegie Institution, 813 Santa Barbara Street, Pasadena, CA 91101 (United States); Geballe, T. R. [Gemini Observatory, Northern Operations Center, 670 N. A' ohoku Place, Hilo, HI 96720 (United States); Lazarian, A.; Hoang, T. [Department of Astronomy, University of Wisconsin, 475 North Charter Street, Madison, WI 53706 (United States); Vornanen, T., E-mail: bg@sofia.usra.edu [Tuorla Observatory, University of Turku, Väisäläntie 20, FI-21500 Piikkiö (Finland)

2013-10-01

In the interstellar medium (ISM), molecular hydrogen is expected to form almost exclusively on the surfaces of dust grains. Due to that molecule's large formation energy (–4.5 eV), several dynamical effects are likely associated with the process, including the alignment of asymmetric dust grains with the ambient magnetic field. Such aligned dust grains are, in turn, believed to cause the broadband optical/infrared polarization observed in the ISM. Here, we present the first observational evidence for grain alignment driven by H{sub 2} formation, by showing that the polarization of the light from stars behind the reflection nebula IC 63 appears to correlate with the intensity of H{sub 2} fluorescence. While our results strongly suggest a role for 'Purcell rockets' in grain alignment, additional observations are needed to conclusively confirm their role. By showing a direct connection between H{sub 2} formation and a probe of the dust characteristics, these results also provide one of the first direct confirmations of the grain-surface formation of H{sub 2}. We compare our observations to ab initio modeling based on Radiative Torque Alignment (RAT) theory.

Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome.

Science.gov (United States)

Rzhetsky, A; Gomez, S M

2001-10-01

Current growth in the field of genomics has provided a number of exciting approaches to the modeling of evolutionary mechanisms within the genome. Separately, dynamical and statistical analyses of networks such as the World Wide Web and the social interactions existing between humans have shown that these networks can exhibit common fractal properties-including the property of being scale-free. This work attempts to bridge these two fields and demonstrate that the fractal properties of molecular networks are linked to the fractal properties of their underlying genomes. We suggest a stochastic model capable of describing the evolutionary growth of metabolic or signal-transduction networks. This model generates networks that share important statistical properties (so-called scale-free behavior) with real molecular networks. In particular, the frequency of vertices connected to exactly k other vertices follows a power-law distribution. The shape of this distribution remains invariant to changes in network scale: a small subgraph has the same distribution as the complete graph from which it is derived. Furthermore, the model correctly predicts that the frequencies of distinct DNA and protein domains also follow a power-law distribution. Finally, the model leads to a simple equation linking the total number of different DNA and protein domains in a genome with both the total number of genes and the overall network topology. MatLab (MathWorks, Inc.) programs described in this manuscript are available on request from the authors. ar345@columbia.edu.

Electrostatically Induced Carbon Nanotube Alignment for Polymer Composite Applications

Science.gov (United States)

Chapkin, Wesley Aaron

We have developed a non-invasive technique utilizing polarized Raman spectroscopy to measure changes in carbon nanotube (CNT) alignment in situ and in real time in a polymer matrix. With this technique, we have confirmed the prediction of faster alignment for CNTs in higher electric fields. Real-time polarized Raman spectroscopy also allows us to demonstrate the loss of CNT alignment that occurs after the electric field is removed, which reveals the need for fast polymerization steps or the continued application of the aligning force during polymerization to lock in CNT alignment. Through a study on the effect of polymer viscosity on the rate of CNT alignment, we have determined that shear viscosity serves as the controlling mechanism for CNT rotation. This finding matches literature modeling of rigid rod mobility in a polymer melt and demonstrates that the rotational mobility of CNTs can be explained by a continuum model even though the diameters of single-walled CNTs are 1-2 nm. The viscosity dependence indicates that the manipulation of temperature (and indirectly viscosity) will have a direct effect on the rate of CNT alignment, which could prove useful in expediting the manufacturing of CNT-reinforced composites cured at elevated temperatures. Using real-time polarized Raman spectroscopy, we also demonstrate that electric fields of various strengths lead not only to different speeds of CNT rotation but also to different degrees of alignment. We hypothesize that this difference in achievable alignment results from discrete populations of nanotubes based on their length. The results are then explained by balancing the alignment energy for a given electric field strength with the randomizing thermal energy of the system. By studying the alignment dynamics of different CNT length distributions, we show that different degrees of alignment achieved as a function of the applied electric field strength are directly related to the square of the nanotube length. This

An investigation of the field-aligned currents associated with a large-scale ULF wave using data from CUTLASS and FAST

Directory of Open Access Journals (Sweden)

H. C. Scoffield

2005-02-01

Full Text Available On 14 December 1999, a large-scale ULF wave event was observed by the Hankasalmi radar of the SuperDARN chain. Simultaneously, the FAST satellite passed through the Hankasalmi field-of-view, measuring the magnetic field oscillations of the wave at around 2000km altitude, along with the precipitating ion and electron populations associated with these fields. A simple field line resonance model of the wave has been created and scaled using the wave's spatial and temporal characteristics inferred from SuperDARN and IMAGE magnetometer data. Here the model calculated field-aligned current is compared with field-aligned currents derived from the FAST energetic particle spectra and magnetic field measurements. This comparison reveals the small-scale structuring and energies of the current carriers in a large-scale Alfvén wave, a topic, which at present, is of considerable theoretical interest. When FAST traverses a region of the wave involving low upward field-aligned current densities, the current appears to be carried by unstructured downgoing electrons of energies less than 30eV. A downward current region appears to be carried partially by upgoing electrons below the FAST energy detection threshold, but also consists of a mixture of hotter downgoing magnetospheric electrons and upgoing ionospheric electrons of energies <30eV, with the hotter upgoing electrons presumably representing those upgoing electrons which have been accelerated by the wave field above the low energy detection threshold of FAST. A stronger interval of upward current shows that small-scale structuring of scale ~50km has been imposed on the current carriers, which are downgoing magnetospheric electrons of energy 0-500eV.

Effect of magnetic field-aligned currents on VLF emissions in the magnetosphere

International Nuclear Information System (INIS)

Kulkarni, V.H.

1988-01-01

The dispersion relation for the electromagnetic electron cyclotron waves in the presence of magnetic field-aligned currents has been obtained. The kinetic distribution of electrons for the main body of plasma with a temperature anisotropy and a loss cone distribution have been considered. In general, it has been seen that the current moving along the direction of resonant electrons reduce the growth rate. This effect has been analysed in the case of magnetospheric plasma to suggest possible correlations between the Birkeland currents and the emissions of very low frequency (VLF) electromagnetic waves. (author). 19 refs

Alignment of SWNTs by protein-ligand interaction of functionalized magnetic particles under low magnetic fields.

Science.gov (United States)

Park, Tae Jung; Park, Jong Pil; Lee, Seok Jae; Jung, Dae-Hwan; Ko, Young Koan; Jung, Hee-Tae; Lee, Sang Yup

2011-05-01

Carbon nanotubes (CNTs) have attracted considerable attention for applications using their superior mechanical, thermal and electrical properties. A simple method to controllably align single-walled CNTs (SWNTs) by using magnetic particles embedded with superparamagnetic iron oxide as an accelerator under the magnetic field was developed. The functionalization of SWNTs using biotin, interacted with streptavidin-coupled magnetic particles (micro-to-nano in diameter), and layer-by-layer assembly were performed for the alignment of a particular direction onto the clean silicon and the gold substrate at very low magnetic forces (0.02-0.89 T) at room temperature. The successful alignment of the SWNTs with multi-layer film was observed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). By changing the orientation and location of the substrates, crossed-networks of SWNTs-magnetic particle complex could easily be fabricated. We suggest that this approach, which consists of a combination of biological interaction among streptavidin-biotin and magnetite particles, should be useful for lateral orientation of individual SWNTs with controllable direction.

Beyond the Floquet theorem: generalized Floquet formalisms and quasienergy methods for atomic and molecular multiphoton processes in intense laser fields

International Nuclear Information System (INIS)

Chu, S.-I.; Telnov, D.A.

2004-01-01

The advancement of high-power and short-pulse laser technology in the past two decades has generated considerable interest in the study of multiphoton and very high-order nonlinear optical processes of atomic and molecular systems in intense and superintense laser fields, leading to the discovery of a host of novel strong-field phenomena which cannot be understood by the conventional perturbation theory. The Floquet theorem and the time-independent Floquet Hamiltonian method are powerful theoretical framework for the study of bound-bound multiphoton transitions driven by periodically time-dependent fields. However, there are a number of significant strong-field processes cannot be directly treated by the conventional Floquet methods. In this review article, we discuss several recent developments of generalized Floquet theorems, formalisms, and quasienergy methods, beyond the conventional Floquet theorem, for accurate nonperturbative treatment of a broad range of strong-field atomic and molecular processes and phenomena of current interests. Topics covered include (a) artificial intelligence (AI)-most-probable-path approach (MPPA) for effective treatment of ultralarge Floquet matrix problem; (b) non-Hermitian Floquet formalisms and complex quasienergy methods for nonperturbative treatment of bound-free and free-free processes such as multiphoton ionization (MPI) and above-threshold ionization (ATI) of atoms and molecules, multiphoton dissociation (MPD) and above-threshold dissociation (ATD) of molecules, chemical bond softening and hardening, charge-resonance enhanced ionization (CREI) of molecular ions, and multiple high-order harmonic generation (HHG), etc.; (c) many-mode Floquet theorem (MMFT) for exact treatment of multiphoton processes in multi-color laser fields with nonperiodic time-dependent Hamiltonian; (d) Floquet-Liouville supermatrix (FLSM) formalism for exact nonperturbative treatment of time-dependent Liouville equation (allowing for relaxations and

Beyond the Floquet theorem: generalized Floquet formalisms and quasienergy methods for atomic and molecular multiphoton processes in intense laser fields

Science.gov (United States)

Chu, Shih-I.; Telnov, Dmitry A.

2004-02-01

The advancement of high-power and short-pulse laser technology in the past two decades has generated considerable interest in the study of multiphoton and very high-order nonlinear optical processes of atomic and molecular systems in intense and superintense laser fields, leading to the discovery of a host of novel strong-field phenomena which cannot be understood by the conventional perturbation theory. The Floquet theorem and the time-independent Floquet Hamiltonian method are powerful theoretical framework for the study of bound-bound multiphoton transitions driven by periodically time-dependent fields. However, there are a number of significant strong-field processes cannot be directly treated by the conventional Floquet methods. In this review article, we discuss several recent developments of generalized Floquet theorems, formalisms, and quasienergy methods, beyond the conventional Floquet theorem, for accurate nonperturbative treatment of a broad range of strong-field atomic and molecular processes and phenomena of current interests. Topics covered include (a) artificial intelligence (AI)-most-probable-path approach (MPPA) for effective treatment of ultralarge Floquet matrix problem; (b) non-Hermitian Floquet formalisms and complex quasienergy methods for nonperturbative treatment of bound-free and free-free processes such as multiphoton ionization (MPI) and above-threshold ionization (ATI) of atoms and molecules, multiphoton dissociation (MPD) and above-threshold dissociation (ATD) of molecules, chemical bond softening and hardening, charge-resonance enhanced ionization (CREI) of molecular ions, and multiple high-order harmonic generation (HHG), etc.; (c) many-mode Floquet theorem (MMFT) for exact treatment of multiphoton processes in multi-color laser fields with nonperiodic time-dependent Hamiltonian; (d) Floquet-Liouville supermatrix (FLSM) formalism for exact nonperturbative treatment of time-dependent Liouville equation (allowing for relaxations and

Atomic and free electrons in a strong light field

CERN Document Server

Fedorov, Mikhail V

1997-01-01

This book presents and describes a series of unusual and striking strong-field phenomena concerning atoms and free electrons. Some of these phenomena are: multiphoton stimulated bremsstrahlung, free-electron lasers, wave-packet physics, above-threshold ionization, and strong-field stabilization in Rydberg atoms. The theoretical foundations and causes of the phenomena are described in detail, with all the approximations and derivations discussed. All the known and relevant experiments are described too, and their results are compared with those of the existing theoretical models.An extensive ge

Controlled molecules for X-ray diffraction experiments at free-electron lasers

International Nuclear Information System (INIS)

Stern, Stephan

2013-12-01

performed on a gas-phase ensemble of the prototypical molecule 2,5-diiodobenzonitrile (C 7 H 3 I 2 N, DIBN) at the X-ray free-electron laser LCLS. The target molecules were laser-aligned along a common axis in the laboratory frame by a Nd:YAG laser. Reaching a strong degree of molecular alignment, was an important step in this experiment. Therefore, a significant part of the work was dedicated to gaining control of the molecular degrees of freedom. In order to reach a high degree of alignment, the target molecules were prepared in low rotational quantum states by means of efficient cooling in a supersonic expansion from a pulsed valve followed by spatial quantum-state selection in an electrostatic deflector. Utilization of the deflector significantly improved alignment of the DIBN molecules. Further applications of the deection technique such as, e.g., the spatial separation of several species of molecular complexes/clusters are presented in this thesis as well. The quantum-state selected and strongly laser-aligned samples were probed by the X-ray pulses of LCLS and the obtained diffraction patterns show a significant difference when comparing diffraction from aligned and isotropically-distributed DIBN which agrees well with theory. The results represent an important step in the effort of pushing diffractive imaging of non-crystalline samples at XFELs towards the single-molecule limit. Concepts and experimental requirements for future experiments of this kind are discussed, involving, e.g., the step towards imaging of laser-aligned large (bio)macromolecules or imaging of ultrafast fragmentation dynamics in femtosecond pump-probe experiments at XFELs.

Controlled molecules for X-ray diffraction experiments at free-electron lasers

Energy Technology Data Exchange (ETDEWEB)

Stern, Stephan

2013-12-15

performed on a gas-phase ensemble of the prototypical molecule 2,5-diiodobenzonitrile (C{sub 7}H{sub 3}I{sub 2}N, DIBN) at the X-ray free-electron laser LCLS. The target molecules were laser-aligned along a common axis in the laboratory frame by a Nd:YAG laser. Reaching a strong degree of molecular alignment, was an important step in this experiment. Therefore, a significant part of the work was dedicated to gaining control of the molecular degrees of freedom. In order to reach a high degree of alignment, the target molecules were prepared in low rotational quantum states by means of efficient cooling in a supersonic expansion from a pulsed valve followed by spatial quantum-state selection in an electrostatic deflector. Utilization of the deflector significantly improved alignment of the DIBN molecules. Further applications of the deection technique such as, e.g., the spatial separation of several species of molecular complexes/clusters are presented in this thesis as well. The quantum-state selected and strongly laser-aligned samples were probed by the X-ray pulses of LCLS and the obtained diffraction patterns show a significant difference when comparing diffraction from aligned and isotropically-distributed DIBN which agrees well with theory. The results represent an important step in the effort of pushing diffractive imaging of non-crystalline samples at XFELs towards the single-molecule limit. Concepts and experimental requirements for future experiments of this kind are discussed, involving, e.g., the step towards imaging of laser-aligned large (bio)macromolecules or imaging of ultrafast fragmentation dynamics in femtosecond pump-probe experiments at XFELs.

Detecting the limits of regulatory element conservation anddivergence estimation using pairwise and multiple alignments

Energy Technology Data Exchange (ETDEWEB)

Pollard, Daniel A.; Moses, Alan M.; Iyer, Venky N.; Eisen,Michael B.

2006-08-14

Background: Molecular evolutionary studies of noncodingsequences rely on multiple alignments. Yet how multiple alignmentaccuracy varies across sequence types, tree topologies, divergences andtools, and further how this variation impacts specific inferences,remains unclear. Results: Here we develop a molecular evolutionsimulation platform, CisEvolver, with models of background noncoding andtranscription factor binding site evolution, and use simulated alignmentsto systematically examine multiple alignment accuracy and its impact ontwo key molecular evolutionary inferences: transcription factor bindingsite conservation and divergence estimation. We find that the accuracy ofmultiple alignments is determined almost exclusively by the pairwisedivergence distance of the two most diverged species and that additionalspecies have a negligible influence on alignment accuracy. Conservedtranscription factor binding sites align better than surroundingnoncoding DNA yet are often found to be misaligned at relatively shortdivergence distances, such that studies of binding site gain and losscould easily be confounded by alignment error. Divergence estimates frommultiple alignments tend to be overestimated at short divergencedistances but reach a tool specific divergence at which they cease toincrease, leading to underestimation at long divergences. Our moststriking finding was that overall alignment accuracy, binding sitealignment accuracy and divergence estimation accuracy vary greatly acrossbranches in a tree and are most accurate for terminal branches connectingsister taxa and least accurate for internal branches connectingsub-alignments. Conclusions: Our results suggest that variation inalignment accuracy can lead to errors in molecular evolutionaryinferences that could be construed as biological variation. Thesefindings have implications for which species to choose for analyses, whatkind of errors would be expected for a given set of species and howmultiple alignment tools and

Interacting massless scalar and source-free electromagnetic fields

International Nuclear Information System (INIS)

Ayyangar, B.R.N.; Mohanty, G.

1985-01-01

The relativistic field equations for interacting massless attractive scalar and source-free electromagnetic fields in a cylindrically symmetric spacetime of one degree of freedom with reflection symmetry have been reduced to a first order implicit differential equation depending on time which enables one to generate a class of solution to the field equations. The nature of the scalar and electromagnetic fields is discussed. It is shown that the geometry of the spacetime admits of an irrotational stiff fluid distribution without prejudice to the interacting electromagnetic fields. 10 refs. (author)

Characterization and performance of a field aligned ion cyclotron range of frequency antenna in Alcator C-Moda)

Science.gov (United States)

Wukitch, S. J.; Garrett, M. L.; Ochoukov, R.; Terry, J. L.; Hubbard, A.; Labombard, B.; Lau, C.; Lin, Y.; Lipschultz, B.; Miller, D.; Reinke, M. L.; Whyte, D.; Alcator C-Mod Team

2013-05-01

Ion cyclotron range of frequency (ICRF) heating is expected to provide auxiliary heating for ITER and future fusion reactors where high Z metallic plasma facing components (PFCs) are being considered. Impurity contamination linked to ICRF antenna operation remains a major challenge particularly for devices with high Z metallic PFCs. Here, we report on an experimental investigation to test whether a field aligned (FA) antenna can reduce impurity contamination and impurity sources. We compare the modification of the scrape of layer (SOL) plasma potential of the FA antenna to a conventional, toroidally aligned (TA) antenna, in order to explore the underlying physics governing impurity contamination linked to ICRF heating. The FA antenna is a 4-strap ICRF antenna where the current straps and antenna enclosure sides are perpendicular to the total magnetic field while the Faraday screen rods are parallel to the total magnetic field. In principle, alignment with respect to the total magnetic field minimizes integrated E|| (electric field along a magnetic field line) via symmetry. A finite element method RF antenna model coupled to a cold plasma model verifies that the integrated E|| should be reduced for all antenna phases. Monopole phasing in particular is expected to have the lowest integrated E||. Consistent with expectations, we observed that the impurity contamination and impurity source at the FA antenna are reduced compared to the TA antenna. In both L and H-mode discharges, the radiated power is 20%-30% lower for a FA-antenna heated discharge than a discharge heated with the TA-antennas. However, inconsistent with expectations, we observe RF induced plasma potentials (via gas-puff imaging and emissive probes to be nearly identical for FA and TA antennas when operated in dipole phasing). Moreover, the highest levels of RF-induced plasma potentials are observed using monopole phasing with the FA antenna. Thus, while impurity contamination and sources are indeed

Progresses in organic field-effect transistors and molecular electronics

Institute of Scientific and Technical Information of China (English)

Wu Weiping; Xu Wei; Hu Wenping; Liu Yunqi; Zhu Daoben

2006-01-01

In the past years,organic semiconductors have been extensively investigated as electronic materials for organic field-effect transistors (OFETs).In this review,we briefly summarize the current status of organic field-effect transistors including materials design,device physics,molecular electronics and the applications of carbon nanotubes in molecular electronics.Future prospects and investigations required to improve the OFET performance are also involved.

Shuttlecock-Shaped Molecular Rectifier: Asymmetric Electron Transport Coupled with Controlled Molecular Motion.

Science.gov (United States)

Ryu, Taekhee; Lansac, Yves; Jang, Yun Hee

2017-07-12

A fullerene derivative with five hydroxyphenyl groups attached around a pentagon, (4-HOC 6 H 4 ) 5 HC 60 (1), has shown an asymmetric current-voltage (I-V) curve in a conducting atomic force microscopy experiment on gold. Such molecular rectification has been ascribed to the asymmetric distribution of frontier molecular orbitals over its shuttlecock-shaped structure. Our nonequilibrium Green's function (NEGF) calculations based on density functional theory (DFT) indeed exhibit an asymmetric I-V curve for 1 standing up between two Au(111) electrodes, but the resulting rectification ratio (RR ∼ 3) is insufficient to explain the wide range of RR observed in experiments performed under a high bias voltage. Therefore, we formulate a hypothesis that high RR (>10) may come from molecular orientation switching induced by a strong electric field applied between two electrodes. Indeed, molecular dynamics simulations of a self-assembled monolayer of 1 on Au(111) show that the orientation of 1 can be switched between standing-up and lying-on-the-side configurations in a manner to align its molecular dipole moment with the direction of the applied electric field. The DFT-NEGF calculations taking into account such field-induced reorientation between up and side configurations indeed yield RR of ∼13, which agrees well with the experimental value obtained under a high bias voltage.

Environmental coefficients of the free-field sensitivity of measurement microphones

DEFF Research Database (Denmark)

Barrera Figueroa, Salvador; Cutanda Henriquez, Vicente; Torras-Rosell, Antoni

2017-01-01

The sensitivity of measurement microphones, both pressure and free field, is affected by changes in the environmental conditions, mainly temperature and static pressure. Static pressure and temperature coefficients for the pressure sensitivity have been the object of previous studies focused...... on Laboratory Standard microphones and few working standard microphones. The literature describes frequency dependent values for these coefficients which are used for calibration purposes. However, there is no description of the environmental coefficients of the free-field sensitivity though there have been...... some implementations that attempt to take care of the differences between the coefficients for the two types of sensitivities. Measuring the coefficients in a free field poses some challeng; it is not so easy to change neither the static pressure nor the temperature inside anechoic room within...

Thermal characterization of magnetically aligned carbonyl iron/agar composites.

Science.gov (United States)

Diaz-Bleis, D; Vales-Pinzón, C; Freile-Pelegrín, Y; Alvarado-Gil, J J

2014-01-01

Composites of magnetic particles into polymeric matrices have received increasing research interest due to their capacity to respond to external magnetic or electromagnetic fields. In this study, agar from Gelidium robustum has been chosen as natural biocompatible polymer to build the matrix of the magnetic carbonyl iron particles (CIP) for their uses in biomedical fields. Heat transfer behavior of the CIP-agar composites containing different concentrations (5, 10, 15, 20, 25 and 30% w/w) of magnetically aligned and non-aligned CIP in the agar matrix was studied using photothermal radiometry (PTR) in the back-propagation emission configuration. The morphology of the CIP-agar composites with aligned and non-aligned CIP under magnetic field was also evaluated by scanning electron microscopy (SEM). The results revealed a dominant effect of CIP concentration over the alignment patterns induced by the magnetic field, which agrees with the behavior of the thermal diffusivity and thermal conductivity. Agar served as a perfect matrix to be used with CIP, and CIP-agar composites magnetically aligned at 20% CIP concentration can be considered as promising 'smart' material for hyperthermia treatments in the biomedical field. Copyright © 2013 Elsevier Ltd. All rights reserved.

Synthesis and assessment methods for an edge-alignment-free hybrid image

Science.gov (United States)

Sripian, Peeraya; Yamaguchi, Yasushi

2017-07-01

A hybrid image allows multiple image interpretations to be modulated by the viewing distance. It can be constructed on the basis of the multiscale perceptual mechanisms of the human visual system by combining the low and high spatial frequencies of two different images. The hybrid image was introduced as an experimental tool for visual recognition study in terms of spatial frequency perception. To produce a compelling hybrid image, the original hybrid image synthesis method could only use similar shapes of source images that were aligned in the edges. If any two different images can be hybrid, it would be beneficial as a new experimental tool. In addition, there is no measure for the actual perception of spatial frequency, whether a single spatial frequency or both spatial frequencies are perceived from the hybrid stimulus. This paper describes two methods for synthesizing a hybrid image from dissimilar shape images or unaligned images; this hybrid image is known as an "edge-alignment-free hybrid image." A noise-inserted method can be done by intentionally inserting and enhancing noises into the high-frequency image. With this method, the low-frequency blobs are covered with high-frequency noises when viewed up close. A color-inserted method uses complementary color gratings in the background of the high-frequency image to emphasize the high-frequency image when viewed up close, whereas the gratings disappear when viewed from far away. To ascertain that our approach successfully separates the spatial frequency at each viewing distance, we measured this property using our proposed assessment method. Our proposed method allows the experimenter to quantify the probability of perceiving both spatial frequencies and a single spatial frequency in a hybrid image. The experimental results confirmed that our proposed synthesis methods successfully hid the low-frequency image and emphasized the high-frequency image at a close viewing distance. At the same time, the

Effect of multi-dimensional ultraviolet light exposure on the growth of pentacene film and application to organic field-effect transistors.

Science.gov (United States)

Bae, Jin-Hyuk; Lee, Sin-Doo; Choi, Jong Sun; Park, Jaehoon

2012-05-01

We report on the multi-dimensional alignment of pentacene molecules on a poly(methyl methacrylate)-based photosensitive polymer (PMMA-polymer) and its effect on the electrical performance of the pentacene-based field-effect transistor (FET). Pentacene molecules are shown to be preferentially aligned on the linearly polarized ultraviolet (LPUV)-exposed PMMA-polymer layer, which is contrast to an isotropic alignment on the bare PMMA-polymer layer. Multi-dimensional alignment of pentacene molecules in the film could be achieved by adjusting the direction of LPUV exposed to the PMMA-polymer. The control of pentacene molecular alignment is found to be promising for the field-effect mobility enhancement in the pentacene FET.

Free massless scalar fields in two dimensions

International Nuclear Information System (INIS)

Hadjiivanov, L.K.

1980-01-01

A common Fock space for two free massless scalar fields, nonlocal with respect to each other, is constructed. The operators corresponding to the two formal charges are correctly defined and it is shown that they generate translationally invariant states from the vacuum

Generation of hydrogen free radicals from water for fuels by electric field induction

International Nuclear Information System (INIS)

Nong, Guangzai; Chen, Yiyi; Li, Ming; Zhou, Zongwen

2015-01-01

Highlights: • Hydrogen free radicals are generated from water splitting. • Hydrogen fuel is generated from water by electric field induction. • Hydrocarbon fuel is generated from CO_2 and water by electric field induction. - Abstract: Water is the most abundant resource for generating hydrogen fuel. In addition to dissociating H"+ and "−OH ions, certain water molecules dissociate to radicals under an electric field are considered. Therefore, an electric field inducing reactor is constructed and operated to generate hydrogen free radicals in this paper. Hydrogen free radicals begin to be generated under a 1.0 V electric field, and increasing the voltage and temperature increases the number of hydrogen free radicals. The production rate of hydrogen free radicals is 0.245 mmol/(L h) at 5.0 V and room temperature. The generated hydrogen free radicals are converted to polymer fuel and hydrogen fuel at production rates of 0.0093 mmol/(L h) and 0.0038 mmol/(L h) respectively, under 5.0 V and 0.25 mA. The results provide a way to generate hydrogen free radicals, which might be used to generate hydrocarbon fuel in industrial manufacture.

Optimal design of an alignment-free two-DOF rehabilitation robot for the shoulder complex.

Science.gov (United States)

Galinski, Daniel; Sapin, Julien; Dehez, Bruno

2013-06-01

This paper presents the optimal design of an alignment-free exoskeleton for the rehabilitation of the shoulder complex. This robot structure is constituted of two actuated joints and is linked to the arm through passive degrees of freedom (DOFs) to drive the flexion-extension and abduction-adduction movements of the upper arm. The optimal design of this structure is performed through two steps. The first step is a multi-objective optimization process aiming to find the best parameters characterizing the robot and its position relative to the patient. The second step is a comparison process aiming to select the best solution from the optimization results on the basis of several criteria related to practical considerations. The optimal design process leads to a solution outperforming an existing solution on aspects as kinematics or ergonomics while being more simple.

Electrical alignment of antenna coordinate system in a planar near-field setup

DEFF Research Database (Denmark)

Mynster, Anders P.; Nielsen, Jeppe Majlund; Pivnenko, Sergey

2011-01-01

In this paper, a simple and efficient electrical alignment procedure known as flip-test is adapted and applied to check and correct two errors in the mechanical setup of a planar near-field system: the mis-pointing of the z-axis of the antenna coordinate system with respect to the scan plane...... and the displacement of the center point of the scan plane with respect to the z-axis of the antenna coordinate system. Simulations of the errors and their correction algorithms were carried out with different models of antennas composed of Hertzian dipoles and an optimum algorithm was then selected. The proposed...

Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges.

Science.gov (United States)

Lara, A; Riquelme, M; Vöhringer-Martinez, E

2018-05-11

Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases, the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account, and when the energy needed to polarize the electron density of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogs. Comparison of the two partitioning methods, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS), revealed some deficiencies in the Hirshfeld-I method related to the unstable isolated anionic nitrogen pro-atom used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model

Experiments in Molecular Optics - Final Report

International Nuclear Information System (INIS)

Gordon, Robert J.

2009-01-01

A combined experimental and theoretical study of the manipulation of molecules with laser light is reported. It is shown that the dipole force produced by the electric field of a focused laser may be used to deflect, align, and orient molecules in a collision free environment. The feasibility of applying these techniques to nanolithography is explored, and a scheme for orienting molecules in space is developed

Free-field correction values for Interacoustics DD 45 supra-aural audiometric earphones

DEFF Research Database (Denmark)

Poulsen, Torben

2010-01-01

This paper report free-field correction values for the Interacoustics DD 45 audiometric earphones. The free-field correction values for earphones provide the loudness based equivalence to loudspeaker presentation. Correction values are especially used for the calibration of audiometric equipment...... for the acoustic coupler IEC 60318-3 (NBS 9-A) and for the ear simulator IEC 60318-1. The results are in good agreement with the results of another independent investigation. The reported free-field correction values may be used as part of the basis for future standardization of the DD 45 earphone....

OBSERVATIONS OF ENHANCED RADIATIVE GRAIN ALIGNMENT NEAR HD 97300

International Nuclear Information System (INIS)

Andersson, B-G; Potter, S. B.

2010-01-01

We have obtained optical multi-band polarimetry toward sightlines through the Chamaeleon I cloud, particularly in the vicinity of the young B9/A0 star HD 97300. We show, in agreement with earlier studies, that the radiation field impinging on the cloud in the projected vicinity of the star is dominated by the flux from the star, as evidenced by a local enhancement in the grain heating. By comparing the differential grain heating with the differential change in the location of the peak of the polarization curve, we show that the grain alignment is enhanced by the increase in the radiation field. We also find a weak, but measurable, variation in the grain alignment with the relative angle between the radiation field anisotropy and the magnetic field direction. Such an anisotropy in the grain alignment is consistent with a unique prediction of modern radiative alignment torque theory and provides direct support for radiatively driven grain alignment.

Electrospinning of aligned fibers with adjustable orientation using auxiliary electrodes

International Nuclear Information System (INIS)

Arras, Matthias M L; Grasl, Christian; Schima, Heinrich; Bergmeister, Helga

2012-01-01

A conventional electrospinning setup was upgraded by two turnable plate-like auxiliary high-voltage electrodes that allowed aligned fiber deposition in adjustable directions. Fiber morphology was analyzed by scanning electron microscopy and attenuated total reflection Fourier transform infrared spectroscopy (FTIR-ATR). The auxiliary electric field constrained the jet bending instability and the fiber deposition became controllable. At target speeds of 0.9 m s −1 90% of the fibers had aligned within 2°, whereas the angular spread was 70° without the use of auxiliary electrodes. It was even possible to orient fibers perpendicular to the rotational direction of the target. The fiber diameter became smaller and its distribution narrower, while according to the FTIR-ATR measurement the molecular orientation of the polymer was unaltered. This study comprehensively documents the feasibility of directed fiber deposition and offers an easy upgrade to existing electrospinning setups. (paper)

Transient reflectivity on vertically aligned single-wall carbon nanotubes

Energy Technology Data Exchange (ETDEWEB)

Galimberti, Gianluca; Ponzoni, Stefano; Ferrini, Gabriele [Interdisciplinary Laboratory for Advanced Materials Physics (i-LAMP) and Dipartimento di Matematica e Fisica, Università Cattolica del Sacro Cuore, I-25121 Brescia (Italy); Hofmann, Stephan [Department of Engineering, University of Cambridge, Cambridge CB3 0FA (United Kingdom); Arshad, Muhammad [Zernike Institute for Advanced Materials, University of Groningen (Netherlands); ICTP, Strada Costiera 11, I-34151 Trieste (Italy); National Centre for Physics Quaid-i-Azam University Islamabad (Pakistan); Cepek, Cinzia [Istituto Officina dei Materiali — CNR, Laboratorio TASC, Area Science Park, Basovizza, I-34149 Trieste (Italy); Pagliara, Stefania, E-mail: pagliara@dmf.unicatt.it [Interdisciplinary Laboratory for Advanced Materials Physics (i-LAMP) and Dipartimento di Matematica e Fisica, Università Cattolica del Sacro Cuore, I-25121 Brescia (Italy)

2013-09-30

One-color transient reflectivity measurements are carried out on two different samples of vertically aligned single-wall carbon nanotube bundles and compared with the response recently published on unaligned bundles. The negative sign of the optical response for both samples indicates that the free electron character revealed on unaligned bundles is only due to the intertube interactions favored by the tube bending. Neither the presence of bundles nor the existence of structural defects in aligned bundles is able to induce a free-electron like behavior of the photoexcited carriers. This result is also confirmed by the presence of non-linear excitonic effects in the transient response of the aligned bundles. - Highlights: • Transient reflectivity measurements on two aligned carbon nanotube samples • Relationship between unalignment and/or bundling and intertube interaction • The bundling is not able to modify the intertube interactions • The presence of structural defects does not affect the intertube interactions • A localized exciton-like behavior has been revealed in these samples.

On quantization of free fields in stationary space-times

International Nuclear Information System (INIS)

Moreno, C.

1977-01-01

In Section 1 the structure of the infinite-dimensional Hamiltonian system described by the Klein-Gordon equation (free real scalar field) in stationary space-times with closed space sections, is analysed, an existence and uniqueness theorem is given for the Lichnerowicz distribution kernel G 1 together with its proper Fourier expansion, and the Hilbert spaces of frequency-part solutions defined by means of G 1 are constructed. In Section 2 an analysis, a theorem and a construction similar to the above are formulated for the free real field spin 1, mass m>0, in one kind of static space-times. (Auth.)

Field emission from carbon nanotube bundle arrays grown on self-aligned ZnO nanorods

International Nuclear Information System (INIS)

Li Chun; Fang Guojia; Yuan Longyan; Liu Nishuang; Ai Lei; Xiang Qi; Zhao Dongshan; Pan Chunxu; Zhao Xingzhong

2007-01-01

The field emission (FE) properties of carbon nanotube (CNT) bundle arrays grown on vertically self-aligned ZnO nanorods (ZNRs) are reported. The ZNRs were first synthesized on ZnO-seed-coated Si substrate by the vapour phase transport method, and then the radically grown CNTs were grown directly on the surface of the ZNRs from ethanol flames. The CNT/ZNR composite showed a turn-on field of 1.5 V μm -1 (at 0.1 μA cm -2 ), a threshold field of 4.5 V μm -1 (at 1 mA cm -2 ) and a stable emission current with fluctuations of 5%, demonstrating significantly enhanced FE of ZNRs due to the low work function and high aspect ratio of the CNTs, and large surface-to-volume ratio of the underlying ZNRs

Equations of motion of higher-spin gauge fields as a free differential algebra

International Nuclear Information System (INIS)

Vasil'ev, M.A.

1988-01-01

It is shown that the introduction of auxiliary dynamical variables that generalize the gravitational Weyl tensor permits one to reduce the equations of motion of free massless fields of all spins in the anti-de Sitter O(3,2) space to a form characteristic of free differential algebras. The equations of motion of auxiliary gauge fields introduced previously are modified analogously. Arguments are presented to the effect that the equations of motion of interacting massless fields of all spins should be described in terms of a free differential algebra which is a deformation of a known free differential algebra generated by 1- and 0-forms in the adjoint representation of a nonabelian superalgebra of higher spins and auxiliary fields

Fast Computation of Solvation Free Energies with Molecular Density Functional Theory: Thermodynamic-Ensemble Partial Molar Volume Corrections.

Science.gov (United States)

Sergiievskyi, Volodymyr P; Jeanmairet, Guillaume; Levesque, Maximilien; Borgis, Daniel

2014-06-05

Molecular density functional theory (MDFT) offers an efficient implicit-solvent method to estimate molecule solvation free-energies, whereas conserving a fully molecular representation of the solvent. Even within a second-order approximation for the free-energy functional, the so-called homogeneous reference fluid approximation, we show that the hydration free-energies computed for a data set of 500 organic compounds are of similar quality as those obtained from molecular dynamics free-energy perturbation simulations, with a computer cost reduced by 2-3 orders of magnitude. This requires to introduce the proper partial volume correction to transform the results from the grand canonical to the isobaric-isotherm ensemble that is pertinent to experiments. We show that this correction can be extended to 3D-RISM calculations, giving a sound theoretical justification to empirical partial molar volume corrections that have been proposed recently.

Relaxing the electrostatic screening effect by patterning vertically-aligned silicon nanowire arrays into bundles for field emission application

Energy Technology Data Exchange (ETDEWEB)

Hung, Yung-Jr, E-mail: yungjrhung@gmail.com [Department of Electronic Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Department of Photonics, National Sun Yat-sen University, No. 70, Lienhai Rd., Kaohsiung 80424, Taiwan, ROC (China); Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Lee, San-Liang [Department of Electronic Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Beng, Looi Choon [Faculty of Engineering, Multimedia University, Jalan Multimedia, 63100 Cyberjaya, Selangor (Malaysia); Chang, Hsuan-Chen [Department of Electronic Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Huang, Yung-Jui [Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Lee, Kuei-Yi; Huang, Ying-Sheng [Department of Electronic Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China)

2014-04-01

Top-down fabrication strategies are proposed and demonstrated to realize arrays of vertically-aligned silicon nanowire bundles and bundle arrays of carbon nanotube–silicon nanowire (CNT–SiNW) heterojunctions, aiming for releasing the electrostatic screening effect and improving the field emission characteristics. The trade-off between the reduction in the electrostatic screening effect and the decrease of emission sites leads to an optimal SiNW bundle arrangement which enables the lowest turn-on electric field of 1.4 V/μm and highest emission current density of 191 μA/cm{sup 2} among all testing SiNW samples. Benefiting from the superior thermal and electrical properties of CNTs and the flexible patterning technologies available for SiNWs, bundle arrays of CNT–SiNW heterojunctions show improved and highly-uniform field emission with a lower turn-on electric field of 0.9 V/μm and higher emission current density of 5.86 mA/cm{sup 2}. The application of these materials and their corresponding fabrication approaches is not limited to the field emission but can be used for a variety of emerging fields like nanoelectronics, lithium-ion batteries, and solar cells. - Highlights: • Aligned silicon nanowire (SiNW) bundle arrays are realized with top-down methods. • Growing carbon nanotubes atop SiNW bundle arrays enable uniform field emission. • A turn-on field of 0.9 V/μm and an emission current of > 5 mA/cm{sup 2} are achieved.

ON THE GLOBAL STRUCTURE OF PULSAR FORCE-FREE MAGNETOSPHERE

International Nuclear Information System (INIS)

Petrova, S. A.

2013-01-01

The dipolar magnetic field structure of a neutron star is modified by the plasma originating in the pulsar magnetosphere. In the simplest case of a stationary axisymmetric force-free magnetosphere, a self-consistent description of the fields and currents is given by the well-known pulsar equation. Here we revise the commonly used boundary conditions of the problem in order to incorporate the plasma-producing gaps and to provide a framework for a truly self-consistent treatment of the pulsar magnetosphere. A generalized multipolar solution of the pulsar equation is found, which, as compared to the customary split monopole solution, is suggested to better represent the character of the dipolar force-free field at large distances. In particular, the outer gap location entirely inside the light cylinder implies that beyond the light cylinder the null and critical lines should be aligned and become parallel to the equator at a certain altitude. Our scheme of the pulsar force-free magnetosphere, which will hopefully be followed by extensive analytic and numerical studies, may have numerous implications for different fields of pulsar research.

Phase Structure of Strong-Field Tunneling Wave Packets from Molecules.

Science.gov (United States)

Liu, Ming-Ming; Li, Min; Wu, Chengyin; Gong, Qihuang; Staudte, André; Liu, Yunquan

2016-04-22

We study the phase structure of the tunneling wave packets from strong-field ionization of molecules and present a molecular quantum-trajectory Monte Carlo model to describe the laser-driven dynamics of photoelectron momentum distributions of molecules. Using our model, we reproduce and explain the alignment-dependent molecular frame photoelectron spectra of strong-field tunneling ionization of N_{2} reported by M. Meckel et al. [Nat. Phys. 10, 594 (2014)]. In addition to modeling the low-energy photoelectron angular distributions quantitatively, we extract the phase structure of strong-field molecular tunneling wave packets, shedding light on its physical origin. The initial phase of the tunneling wave packets at the tunnel exit depends on both the initial transverse momentum distribution and the molecular internuclear distance. We further show that the ionizing molecular orbital has a critical effect on the initial phase of the tunneling wave packets. The phase structure of the photoelectron wave packet is a key ingredient for modeling strong-field molecular photoelectron holography, high-harmonic generation, and molecular orbital imaging.

Polymer chain alignment and transistor properties of nanochannel-templated poly(3-hexylthiophene) nanowires

Science.gov (United States)

Oh, Seungjun; Hayakawa, Ryoma; Pan, Chengjun; Sugiyasu, Kazunori; Wakayama, Yutaka

2016-08-01

Nanowires of semiconducting poly(3-hexylthiophene) (P3HT) were produced by a nanochannel-template technique. Polymer chain alignment in P3HT nanowires was investigated as a function of nanochannel widths (W) and polymer chain lengths (L). We found that the ratio between chain length and channel width (L/W) was a key parameter as regards promoting polymer chain alignment. Clear dichroism was observed in polarized ultraviolet-visible (UV-Vis) absorption spectra only at a ratio of approximately L/W = 2, indicating that the L/W ratio must be optimized to achieve uniaxial chain alignment in the nanochannel direction. We speculate that an appropriate L/W ratio is effective in confining the geometries and conformations of polymer chains. This discussion was supported by theoretical simulations based on molecular dynamics. That is, the geometry of the polymer chains, including the distance and tilting angles of the chains in relation to the nanochannel surface, was dominant in determining the longitudinal alignment along the nanochannels. Thus prepared highly aligned polymer nanowire is advantageous for electrical carrier transport and has great potential for improving the device performance of field-effect transistors. In fact, a one-order improvement in carrier mobility was observed in a P3HT nanowire transistor.

Atomic and Free Electrons in a Strong Light Field

International Nuclear Information System (INIS)

Fedorov, Mikhail V.

1998-02-01

This book presents and describes a series of unusual and striking strong-field phenomena concerning atoms and free electrons. Some of these phenomena are: multiphoton stimulated Bremsstrahlung, free-electron lasers, ave-packet physics, above-threshold ionization, and strong-field stabilization in Rydberg atoms. The theoretical foundations and causes of the phenomena are described in detail, with all the approximations and derivations discussed. All the known and relevant experiments are described oo, and their results are compared with those of the existing theoretical models. An extensive general theoretical introduction gives a good basis for subsequent parts of the book and is an independent and self-sufficient description of the most efficient theoretical methods of the strong-field and multiphoton physics. This book can serve as a textbook for graduate students

Low temperature superconductor and aligned high temperature superconductor magnetic dipole system and method for producing high magnetic fields

Science.gov (United States)

Gupta, Ramesh; Scanlan, Ronald; Ghosh, Arup K.; Weggel, Robert J.; Palmer, Robert; Anerella, Michael D.; Schmalzle, Jesse

2017-10-17

A dipole-magnet system and method for producing high-magnetic-fields, including an open-region located in a radially-central-region to allow particle-beam transport and other uses, low-temperature-superconducting-coils comprised of low-temperature-superconducting-wire located in radially-outward-regions to generate high magnetic-fields, high-temperature-superconducting-coils comprised of high-temperature-superconducting-tape located in radially-inward-regions to generate even higher magnetic-fields and to reduce erroneous fields, support-structures to support the coils against large Lorentz-forces, a liquid-helium-system to cool the coils, and electrical-contacts to allow electric-current into and out of the coils. The high-temperature-superconducting-tape may be comprised of bismuth-strontium-calcium-copper-oxide or rare-earth-metal, barium-copper-oxide (ReBCO) where the rare-earth-metal may be yttrium, samarium, neodymium, or gadolinium. Advantageously, alignment of the large-dimension of the rectangular-cross-section or curved-cross-section of the high-temperature-superconducting-tape with the high-magnetic-field minimizes unwanted erroneous magnetic fields. Alignment may be accomplished by proper positioning, tilting the high-temperature-superconducting-coils, forming the high-temperature-superconducting-coils into a curved-cross-section, placing nonconducting wedge-shaped-material between windings, placing nonconducting curved-and-wedge-shaped-material between windings, or by a combination of these techniques.

Quasiparticle Level Alignment for Photocatalytic Interfaces.

Science.gov (United States)

Migani, Annapaoala; Mowbray, Duncan J; Zhao, Jin; Petek, Hrvoje; Rubio, Angel

2014-05-13

Electronic level alignment at the interface between an adsorbed molecular layer and a semiconducting substrate determines the activity and efficiency of many photocatalytic materials. Standard density functional theory (DFT)-based methods have proven unable to provide a quantitative description of this level alignment. This requires a proper treatment of the anisotropic screening, necessitating the use of quasiparticle (QP) techniques. However, the computational complexity of QP algorithms has meant a quantitative description of interfacial levels has remained elusive. We provide a systematic study of a prototypical interface, bare and methanol-covered rutile TiO2(110) surfaces, to determine the type of many-body theory required to obtain an accurate description of the level alignment. This is accomplished via a direct comparison with metastable impact electron spectroscopy (MIES), ultraviolet photoelectron spectroscopy (UPS), and two-photon photoemission (2PP) spectroscopy. We consider GGA DFT, hybrid DFT, and G0W0, scQPGW1, scQPGW0, and scQPGW QP calculations. Our results demonstrate that G0W0, or our recently introduced scQPGW1 approach, are required to obtain the correct alignment of both the highest occupied and lowest unoccupied interfacial molecular levels (HOMO/LUMO). These calculations set a new standard in the interpretation of electronic structure probe experiments of complex organic molecule/semiconductor interfaces.

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

Energy Technology Data Exchange (ETDEWEB)

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

2017-06-01

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) 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.

En route to surface-bound electric field-driven molecular motors.

Science.gov (United States)

Jian, Huahua; Tour, James M

2003-06-27

Four caltrop-shaped molecules that might be useful as surface-bound electric field-driven molecular motors have been synthesized. The caltrops are comprised of a pair of electron donor-acceptor arms and a tripod base. The molecular arms are based on a carbazole or oligo(phenylene ethynylene) core with a strong net dipole. The tripod base uses a silicon atom as its core. The legs of the tripod bear sulfur-tipped bonding units, as acetyl-protected benzylic thiols, for bonding to a gold surface. The geometry of the tripod base allows the caltrop to project upward from a metallic surface after self-assembly. Ellipsometric studies show that self-assembled monolayers of the caltrops are formed on Au surfaces with molecular thicknesses consistent with the desired upright-shaft arrangement. As a result, the zwitterionic molecular arms might be controllable when electric fields are applied around the caltrops, thereby constituting field-driven motors.

Anomalous foreshock field-aligned beams observed by Cluster

Directory of Open Access Journals (Sweden)

K. Meziane

2011-10-01

Full Text Available We report occasional observations of two simultaneously distinct ion foreshock components recorded by the Cluster spacecraft upstream of the Earth's bow shock. In most occurrences, the lower-energy population originates as a field-aligned beam (FAB associated with quasi-perpendicular regions, which loses energy as the IMF rotates into oblique geometries. A second beam, with energies in excess of ~10 keV, appears sometimes in association with the onset of ultra-low frequency (ULF waves, and sometimes ahead of the appearance of the latter. Measurements from the mass spectrometer indicate that both beams consist of protons. While the lower-speed beam is well-accounted for by a known reflection mechanism, the non-radial IMF orientations as well as other arguments seem to rule out magnetosheath or magnetospheric sources for the higher energy component. The wave characteristics are typical of the oblique foreshock and we have found that they are in cyclotron-resonance with the low speed beam (FAB. These observations constitute a theoretical challenge since conventional mechanisms described in the literature cannot account for the production of beams at two different energies.

Field aligned current study during the solar declining- extreme minimum of 23 solar cycle

Science.gov (United States)

Nepolian, Jeni Victor; Kumar, Anil; C, Panneerselvam

Field Aligned Current (FAC) density study has been carried out during the solar declining phase from 2004 to 2006 of the 23rd solar cycle and the ambient terrestrial magnetic field of the extended minimum period of 2008 and 2009. We mainly depended on CHAMP satellite data (http://isdc.gfz-potsdam.de/) for computing the FAC density with backup of IGRF-10 model. The study indicates that, the FAC is controlled by quasi-viscous processes occurring at the flank of the earth’s magnetosphere. The dawn-dusk conventional pattern enhanced during disturbed days. The intensity of R1 current system is higher than the R2 current system. Detailed results will be discussed in the conference.

General equilibrium second-order hydrodynamic coefficients for free quantum fields

Science.gov (United States)

Buzzegoli, M.; Grossi, E.; Becattini, F.

2017-10-01

We present a systematic calculation of the corrections of the stress-energy tensor and currents of the free boson and Dirac fields up to second order in thermal vorticity, which is relevant for relativistic hydrodynamics. These corrections are non-dissipative because they survive at general thermodynamic equilibrium with non vanishing mean values of the conserved generators of the Lorentz group, i.e. angular momenta and boosts. Their equilibrium nature makes it possible to express the relevant coefficients by means of correlators of the angular-momentum and boost operators with stress-energy tensor and current, thus making simpler to determine their so-called "Kubo formulae". We show that, at least for free fields, the corrections are of quantum origin and we study several limiting cases and compare our results with previous calculations. We find that the axial current of the free Dirac field receives corrections proportional to the vorticity independently of the anomalous term.

Fantastic Striations and Where to Find Them: The Origin of Magnetically Aligned Striations in Interstellar Clouds

Energy Technology Data Exchange (ETDEWEB)

Chen, Che-Yu; Li, Zhi-Yun; King, Patrick K. [Department of Astronomy, University of Virginia, Charlottesville, VA 22904 (United States); Fissel, Laura M. [National Radio Astronomy Observatory, Charlottesville, VA 22904 (United States)

2017-10-01

Thin, magnetically aligned striations of relatively moderate contrast with the background are commonly observed in both atomic and molecular clouds. They are also prominent in MHD simulations with turbulent converging shocks. The simulated striations develop within a dense, stagnated sheet in the midplane of the post-shock region where magnetically induced converging flows collide. We show analytically that the secondary flows are an inevitable consequence of the jump conditions of oblique MHD shocks. They produce the stagnated, sheet-like sub-layer through a secondary shock when, roughly speaking, the Alfvénic speed in the primary converging flows is supersonic, a condition that is relatively easy to satisfy in interstellar clouds. The dense sub-layer is naturally threaded by a strong magnetic field that lies close to the plane of the sub-layer. The substantial magnetic field makes the sheet highly anisotropic, which is the key to the striation formation. Specifically, perturbations of the primary inflow that vary spatially perpendicular to the magnetic field can easily roll up the sheet around the field lines without bending them, creating corrugations that appear as magnetically aligned striations in column density maps. On the other hand, perturbations that vary spatially along the field lines curve the sub-layer and alter its orientation relative to the magnetic field locally, seeding special locations that become slanted overdense filaments and prestellar cores through enhanced mass accumulation along field lines. In our scenario, the dense sub-layer, which is unique to magnetized oblique shocks, is the birthplace for both magnetically aligned diffuse striations and massive star-forming structures.

Molecular orientation and electronic structure at organic heterojunction interfaces

Energy Technology Data Exchange (ETDEWEB)

Zhong, Shu [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Zhong, Jian Qiang; Wee, Andrew T.S. [Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); Chen, Wei, E-mail: phycw@nus.edu.sg [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); National University of Singapore (Suzhou) Research Institute, Suzhou (China)

2015-10-01

Highlights: • Molecular orientation at the organic heterojunction interfaces. • Energy level alignments at the organic heterojunction interfaces. • Gap-states mediated interfacial energy level alignment. - Abstract: Due to the highly anisotropic nature of π-conjugated molecules, the molecular orientation in organic thin films can significantly affect light absorption, charge transport, energy level alignment (ELA) and hence device performance. Synchrotron-based near-edge X-ray absorption fine structure (NEXAFS) spectroscopy represents a powerful technique for probing molecular orientation. The aim of this review paper is to provide a balanced assessment on the investigation of molecular orientation at the organic–organic heterojunction (OOH) interface by NEXAFS, as well as the gap-states mediated orientation dependent energy level alignment at OOH interfaces. We highlight recent progress in elucidating molecular orientation at OOH interfaces dominated by various interfacial interactions, gap-states controlled orientation dependent energy level alignments at OOH interfaces, and the manipulations of molecular orientation and ELA in OOH.

A model of lipid-free apolipoprotein A-I revealed by iterative molecular dynamics simulation.

Directory of Open Access Journals (Sweden)

Xing Zhang

Full Text Available Apolipoprotein A-I (apo A-I, the major protein component of high-density lipoprotein, has been proven inversely correlated to cardiovascular risk in past decades. The lipid-free state of apo A-I is the initial stage which binds to lipids forming high-density lipoprotein. Molecular models of lipid-free apo A-I have been reported by methods like X-ray crystallography and chemical cross-linking/mass spectrometry (CCL/MS. Through structural analysis we found that those current models had limited consistency with other experimental results, such as those from hydrogen exchange with mass spectrometry. Through molecular dynamics simulations, we also found those models could not reach a stable equilibrium state. Therefore, by integrating various experimental results, we proposed a new structural model for lipid-free apo A-I, which contains a bundled four-helix N-terminal domain (1-192 that forms a variable hydrophobic groove and a mobile short hairpin C-terminal domain (193-243. This model exhibits an equilibrium state through molecular dynamics simulation and is consistent with most of the experimental results known from CCL/MS on lysine pairs, fluorescence resonance energy transfer and hydrogen exchange. This solution-state lipid-free apo A-I model may elucidate the possible conformational transitions of apo A-I binding with lipids in high-density lipoprotein formation.

Alignment, orientation, and Coulomb explosion of difluoroiodobenzene studied with the pixel imaging mass spectrometry (PImMS) camera.

Science.gov (United States)

Amini, Kasra; Boll, Rebecca; Lauer, Alexandra; Burt, Michael; Lee, Jason W L; Christensen, Lauge; Brauβe, Felix; Mullins, Terence; Savelyev, Evgeny; Ablikim, Utuq; Berrah, Nora; Bomme, Cédric; Düsterer, Stefan; Erk, Benjamin; Höppner, Hauke; Johnsson, Per; Kierspel, Thomas; Krecinic, Faruk; Küpper, Jochen; Müller, Maria; Müller, Erland; Redlin, Harald; Rouzée, Arnaud; Schirmel, Nora; Thøgersen, Jan; Techert, Simone; Toleikis, Sven; Treusch, Rolf; Trippel, Sebastian; Ulmer, Anatoli; Wiese, Joss; Vallance, Claire; Rudenko, Artem; Stapelfeldt, Henrik; Brouard, Mark; Rolles, Daniel

2017-07-07

Laser-induced adiabatic alignment and mixed-field orientation of 2,6-difluoroiodobenzene (C 6 H 3 F 2 I) molecules are probed by Coulomb explosion imaging following either near-infrared strong-field ionization or extreme-ultraviolet multi-photon inner-shell ionization using free-electron laser pulses. The resulting photoelectrons and fragment ions are captured by a double-sided velocity map imaging spectrometer and projected onto two position-sensitive detectors. The ion side of the spectrometer is equipped with a pixel imaging mass spectrometry camera, a time-stamping pixelated detector that can record the hit positions and arrival times of up to four ions per pixel per acquisition cycle. Thus, the time-of-flight trace and ion momentum distributions for all fragments can be recorded simultaneously. We show that we can obtain a high degree of one-and three-dimensional alignment and mixed-field orientation and compare the Coulomb explosion process induced at both wavelengths.

Multiscale equation-free algorithms for molecular dynamics

Science.gov (United States)

Abi Mansour, Andrew

Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.

From free fields to AdS space. II

International Nuclear Information System (INIS)

Gopakumar, Rajesh

2004-01-01

We continue with the program of paper I [Phys. Rev. D 70, 025009 (2004)] to implement open-closed string duality on free gauge field theory (in the large-N limit). In this paper we consider correlators such as i=1 n TrΦ J i (x i )>. The Schwinger parametrization of this n-point function exhibits a partial gluing up into a set of basic skeleton graphs. We argue that the moduli space of the planar skeleton graphs is exactly the same as the moduli space of genus zero Riemann surfaces with n holes. In other words, we can explicitly rewrite the n-point (planar) free-field correlator as an integral over the moduli space of a sphere with n holes. A preliminary study of the integrand also indicates compatibility with a string theory on AdS space. The details of our argument are quite insensitive to the specific form of the operators and generalize to diagrams of a higher genus as well. We take this as evidence of the field theory's ability to reorganize itself into a string theory

Dynamical formation of spatially localized arrays of aligned nanowires in plastic films with magnetic anisotropy.

Science.gov (United States)

Fragouli, Despina; Buonsanti, Raffaella; Bertoni, Giovanni; Sangregorio, Claudio; Innocenti, Claudia; Falqui, Andrea; Gatteschi, Dante; Cozzoli, Pantaleo Davide; Athanassiou, Athanassia; Cingolani, Roberto

2010-04-27

We present a simple technique for magnetic-field-induced formation, assembling, and positioning of magnetic nanowires in a polymer film. Starting from a polymer/iron oxide nanoparticle casted solution that is allowed to dry along with the application of a weak magnetic field, nanocomposite films incorporating aligned nanocrystal-built nanowire arrays are obtained. The control of the dimensions of the nanowires and of their localization across the polymer matrix is achieved by varying the duration of the applied magnetic field, in combination with the evaporation dynamics. These multifunctional anisotropic free-standing nanocomposite films, which demonstrate high magnetic anisotropy, can be used in a wide field of technological applications, ranging from sensors to microfluidics and magnetic devices.

Formation of Negative Metal Ions in a Field-Free Plasma

Energy Technology Data Exchange (ETDEWEB)

Larsson, E

1969-02-15

A field-free and homogeneous plasma of a large volume is formed by neutron irradiation of {sup 3}He at a density corresponding to NTP and at gas temperatures in the range 300-1600 deg K. The accuracy and ease by which the source density of free electrons can be varied and controlled offers special possibilities to study recombination and attachment phenomena in the absence of diffusion. These possibilities are described and utilized for the study of the effects of mixing the helium gas with metal vapours. Attachment of electrons to neutral metal atoms is found to be the dominant cause of electron removal for metal concentrations above certain limits. Negative metal ions are formed and the rate of their formation was determined to be about 10{sup -13} cm{sup 3}/s. Evidence is also presented, that for such conditions where formation of negative metal ions does not occur, the electrons are lost in electron-ion recombinations, in which the third body is not an electron. No molecular helium spectrum is observed from the plasma when it is very close to spectroscopic purity. Instead, between 3,000-7,000 A only one atomic helium line at 5875 A is observed. The recombination of He{sup +}{sub 2} may therefore be dissociative. A difference in recombination behaviour between {sup 3}He and {sup 4}He at high pressures may therefore exist considering results from previous work on {sup 4}He.

Formation of Negative Metal Ions in a Field-Free Plasma

International Nuclear Information System (INIS)

Larsson, E.

1969-02-01

A field-free and homogeneous plasma of a large volume is formed by neutron irradiation of 3 He at a density corresponding to NTP and at gas temperatures in the range 300-1600 deg K. The accuracy and ease by which the source density of free electrons can be varied and controlled offers special possibilities to study recombination and attachment phenomena in the absence of diffusion. These possibilities are described and utilized for the study of the effects of mixing the helium gas with metal vapours. Attachment of electrons to neutral metal atoms is found to be the dominant cause of electron removal for metal concentrations above certain limits. Negative metal ions are formed and the rate of their formation was determined to be about 10 -13 cm 3 /s. Evidence is also presented, that for such conditions where formation of negative metal ions does not occur, the electrons are lost in electron-ion recombinations, in which the third body is not an electron. No molecular helium spectrum is observed from the plasma when it is very close to spectroscopic purity. Instead, between 3,000-7,000 A only one atomic helium line at 5875 A is observed. The recombination of He + 2 may therefore be dissociative. A difference in recombination behaviour between 3 He and 4 He at high pressures may therefore exist considering results from previous work on 4 He

First Use of Synoptic Vector Magnetograms for Global Nonlinear, Force-Free Coronal Magnetic Field Models

Science.gov (United States)

Tadesse, T.; Wiegelmann, T.; Gosain, S.; MacNeice, P.; Pevtsov, A. A.

2014-01-01

Context. The magnetic field permeating the solar atmosphere is generally thought to provide the energy for much of the activity seen in the solar corona, such as flares, coronal mass ejections (CMEs), etc. To overcome the unavailability of coronal magnetic field measurements, photospheric magnetic field vector data can be used to reconstruct the coronal field. Currently, there are several modelling techniques being used to calculate three-dimensional field lines into the solar atmosphere. Aims. For the first time, synoptic maps of a photospheric-vector magnetic field synthesized from the vector spectromagnetograph (VSM) on Synoptic Optical Long-term Investigations of the Sun (SOLIS) are used to model the coronal magnetic field and estimate free magnetic energy in the global scale. The free energy (i.e., the energy in excess of the potential field energy) is one of the main indicators used in space weather forecasts to predict the eruptivity of active regions. Methods. We solve the nonlinear force-free field equations using an optimization principle in spherical geometry. The resulting threedimensional magnetic fields are used to estimate the magnetic free energy content E(sub free) = E(sub nlfff) - E(sub pot), which is the difference of the magnetic energies between the nonpotential field and the potential field in the global solar corona. For comparison, we overlay the extrapolated magnetic field lines with the extreme ultraviolet (EUV) observations by the atmospheric imaging assembly (AIA) on board the Solar Dynamics Observatory (SDO). Results. For a single Carrington rotation 2121, we find that the global nonlinear force-free field (NLFFF) magnetic energy density is 10.3% higher than the potential one. Most of this free energy is located in active regions.

The force-free configuration of flux ropes in geomagnetotail: Cluster observations

Science.gov (United States)

Yang, Y. Y.; Shen, C.; Zhang, Y. C.; Rong, Z. J.; Li, X.; Dunlop, M.; Ma, Y. H.; Liu, Z. X.; Carr, C. M.; Rème, H.

2014-08-01

Unambiguous knowledge of magnetic field structure and the electric current distribution is critical for understanding the origin, evolution, and related dynamic properties of magnetic flux ropes (MFRs). In this paper, a survey of 13 MFRs in the Earth's magnetotail are conducted by Cluster multipoint analysis, so that their force-free feature, i.e., the kind of magnetic field structure satisfying J × B = 0, can be probed directly. It is showed that the selected flux ropes with the bipolar signature of the south-north magnetic field component generally lie near the equatorial plane, as expected, and that the magnetic field gradient is rather weak near the axis center, where the curvature radius is large. The current density (up to several tens of nA/m2) reaches their maximum values as the center is approached. It is found that the stronger the current density, the smaller the angles between the magnetic field and current in MFRs. The direct observations show that only quasi force-free structure is observed, and it tends to appear in the low plasma beta regime (in agreement with the theoretic results). The quasi force-free region is generally found to be embedded in the central portion of the MFRs, where the current is approximately field aligned and proportional to the strength of core field. It is shown that ~60% of surveyed MFRs can be globally approximated as force free. The force-free factor α is found to be nonconstantly varied through the quasi force-free MFR, suggesting that the force-free structure is nonlinear.

FENICIA: a generic plasma simulation code using a flux-independent field-aligned coordinate approach

International Nuclear Information System (INIS)

Hariri, Farah

2013-01-01

The primary thrust of this work is the development and implementation of a new approach to the problem of field-aligned coordinates in magnetized plasma turbulence simulations called the FCI approach (Flux-Coordinate Independent). The method exploits the elongated nature of micro-instability driven turbulence which typically has perpendicular scales on the order of a few ion gyro-radii, and parallel scales on the order of the machine size. Mathematically speaking, it relies on local transformations that align a suitable coordinate to the magnetic field to allow efficient computation of the parallel derivative. However, it does not rely on flux coordinates, which permits discretizing any given field on a regular grid in the natural coordinates such as (x, y, z) in the cylindrical limit. The new method has a number of advantages over methods constructed starting from flux coordinates, allowing for more flexible coding in a variety of situations including X-point configurations. In light of these findings, a plasma simulation code FENICIA has been developed based on the FCI approach with the ability to tackle a wide class of physical models. The code has been verified on several 3D test models. The accuracy of the approach is tested in particular with respect to the question of spurious radial transport. Tests on 3D models of the drift wave propagation and of the Ion Temperature Gradient (ITG) instability in cylindrical geometry in the linear regime demonstrate again the high quality of the numerical method. Finally, the FCI approach is shown to be able to deal with an X-point configuration such as one with a magnetic island with good convergence and conservation properties. (author) [fr

Limit sets and global dynamic for 2-D divergence-free vector fields

International Nuclear Information System (INIS)

Marzougui, H.

2004-08-01

T. Ma and S. Wang studied the global structure of regular divergence-free vector fields on compact surfaces with or without boundary. This paper extends their study to the general case of divergence-free vector fields (regular or not) on closed surfaces and gives as a consequence a simple proof of their results. (author)

THE ATLAS INNER DETECTOR TRACK BASED ALIGNMENT

CERN Document Server

Marti i Garcia, Salvador; The ATLAS collaboration

2018-01-01

The alignment of the ATLAS Inner Detector is performed with a track-based alignment algorithm. Its goal is to provide an accurate description of the detector geometry such that track parameters are accurately determined and free from biases. Its software implementation is modular and configurable, with a clear separation of the alignment algorithm from the detector system specifics and the database handling. The alignment must cope with the rapid movements of the detector as well as with the slow drift of the different mechanical units. Prompt alignment constants are derived for every run at the calibration stage. These sets of constants are then dynamically split from the beginning of the run in many chunks, allowing to describe the tracker geometry as it evolves with time. The alignment of the Inner Detector is validated and improved by studying resonance decays (Z and J/psi to mu+mu-), as well as using information from the calorimeter system with the E/p method with electrons. A detailed study of these res...

A self-consistent two-dimensional resistive fluid theory of field-aligned potential structures including charge separation and magnetic and velocity shear

International Nuclear Information System (INIS)

Hesse, M.; Birn, J.; Schindler, K.

1990-01-01

A self-consistent two-fluid theory that includes the magnetic field and shear patterns therein is developed to model stationary electrostatic structures with field-aligned potential drops. Shear flow is also included in the theory since this seems to be a prominent feature of the structures of interest. In addition, Ohmic dissipation, a Hall term and pressure gradients in a generalized Ohm's law, modified for cases without quasi-neutrality are included. In the analytic theory, the electrostatic force is balanced by field-aligned pressure gradients, i.e., thermal effects in the direction of the magnetic field, and by pressure gradients and magnetic stresses in the perpendicular direction. Within this theory simple examples of applications are presented to demonstrate the kind of solutions resulting from the model. The results show how the effects of charge separation and shear in the magnetic field and the velocity can be combined to form self-consistent structures such as are found to exist above the aurora, suggested also in association with solar flares

A geometrical approach to free-field quantization

International Nuclear Information System (INIS)

Tabensky, R.; Valle, J.W.F.

1977-01-01

A geometrical approach to the quantization of free relativistic fields is given. Complex probability amplitudes are assigned to the solutions of the classical evolution equation. It is assumed that the evolution is stricly classical, according to the scalar unitary representation of the Poincare group in a functional space. The theory is equivalent to canonical quantization [pt

Large-scale aligned silicon carbonitride nanotube arrays: Synthesis, characterization, and field emission property

International Nuclear Information System (INIS)

Liao, L.; Xu, Z.; Liu, K. H.; Wang, W. L.; Liu, S.; Bai, X. D.; Wang, E. G.; Li, J. C.; Liu, C.

2007-01-01

Large-scale aligned silicon carbonitride (SiCN) nanotube arrays have been synthesized by microwave-plasma-assisted chemical vapor deposition using SiH 4 , CH 4 , and N 2 as precursors. The three elements of Si, C, and N are chemically bonded with each other and the nanotube composition can be adjusted by varying the SiH 4 concentration, as revealed by electron energy loss spectroscopy and x-ray photoelectron spectroscopy. The evolution of microstructure of the SiCN nanotubes with different Si concentrations was characterized by high-resolution transmission electron microscopy and Raman spectroscopy. The dependence of field emission characteristics of the SiCN nanotubes on the composition has been investigated. With the increasing Si concentration, the SiCN nanotube exhibits more favorable oxidation resistance, which suggests that SiCN nanotube is a promising candidate as stable field emitter

Method of making a self-aligned schottky metal semi-conductor field effect transistor with buried source and drain

International Nuclear Information System (INIS)

Bol, I.

1984-01-01

A semi-conductor structure and particularly a high speed VLSI Self-Aligned Schottky Metal Semi-Conductor Field Effect Transistor with buried source and drain, fabricated by the ion implantation of source and drain areas at a predetermined range of depths followed by very localized laser annealing to electrically reactivate the amorphous buried source and drain areas thereby providing effective vertical separation of the channel from the buried source and drain respectively. Accordingly, spatial separations between the self-aligned gate-to-drain, and gate-to-source can be relatively very closely controlled by varying the doping intensity and duration of the implantation thereby reducing the series resistance and increasing the operating speed

On the origin of field-aligned beams at the quasi-perpendicular bow shock: multi-spacecraft observations by Cluster

Directory of Open Access Journals (Sweden)

H. Kucharek

2004-07-01

Full Text Available Two distinct populations of reflected and accelerated ions are known to originate from quasi-perpendicular shocks, gyrating ions and reflected ion beams. Recent observations under such bow shock conditions with Cluster have shown strong evidence that both particle distributions appear to emerge from the same reflection process. In this paper the basic production mechanism of field-aligned beams has been investigated by using CLUSTER multi-spacecraft measurements. We have analyzed several quasi-perpendicular shocks with the Cluster Ion Spectrometry experiment (CIS and followed the spatial and temporal evolution of the reflected and transmitted ion populations across the shock. These observations show that the field-aligned beams most likely result from effective scattering in pitch angle during reflection in the shock ramp. Investigating a low Mach number shock, leakage of a fraction of the thermalized ion distribution in the downstream region does not appear to be the source as the volume in phase space occupied by beam ions is empty downstream of the shock ramp.

Assembly and Alignment of Ship Power Plants in Modern Shipbuilding

OpenAIRE

A. O. Mikhailov; K. N. Morozov

2013-01-01

Fine alignment of main ship power plants mechanisms and shaft lines provides long-term and failure-free performance of propulsion system while fast and high-quality installation of mechanisms and shaft lines decreases common labor intensity. For checking shaft line allowed stress and setting its alignment it is required to perform calculations considering various stages of life cycle. In 2012 JSC SSTC developed special software complex “Shaftline” for calculation of align...

Field aligned flows driven by neutral puffing at MAST

Science.gov (United States)

Waters, I.; Frerichs, H.; Silburn, S.; Feng, Y.; Harrison, J.; Kirk, A.; Schmitz, O.

2018-06-01

Neutral deuterium gas puffing at the high field side of the mega ampere spherical tokamak (MAST) is shown to drive carbon impurity flows that are aligned with the trajectory of the magnetic field lines in the plasma scrape-off-layer. These impurity flows were directly imaged with emissions from C2+ ions at MAST by coherence imaging spectroscopy and were qualitatively reproduced in deuterium plasmas by modeling with the EMC3-EIRENE plasma edge fluid and kinetic neutral transport code. A reduced one-dimensional momentum and particle balance shows that a localized increase in the static plasma pressure in front of the neutral gas puff yields an acceleration of the plasma due to local ionization. Perpendicular particle transport yields a decay from which a parallel length scale can be determined. Parameter scans in EMC3-EIRENE were carried out to determine the sensitivity of the deuterium plasma flow phenomena to local fueling and diffusion parameters and it is found that these flows robustly form across a wide variety of plasma conditions. Finally, efforts to couple this behavior in the background plasma directly to the impurity flows observed experimentally in MAST using a trace impurity model are discussed. These results provide insight into the fueling and exhaust features at this pivotal point of the radial and parallel particle flux balance, which is a major part of the plasma fueling and exhaust characteristics in a magnetically confined fusion device.

Stress fields around a crack lying parallel to a free surface

International Nuclear Information System (INIS)

Higashida, Yutaka; Kamada, K.

1980-12-01

A method of stress analysis for a two dimentional crack, which is subjected to internal gas pressure, and situated parallel to a free surface of a material, is presented. It is based on the concept of continuously distributed edge dislocations of two kinds, i.e. one with Burgers vector normal to the free surface and the other with parallel to it. Stress fields of individual dislocations are chosen so as to satisfy stress free boundary conditions at the free surface, by taking account of image dislocations. Distributions of the both kinds of dislocations in the crack are derived so as to give the internal gas pressure and, at the same time, to satisfy shear stress free boundary condition on the crack surface. Stress fields σsub(xx), σsub(yy) and σsub(xy) in the sub-surface layer are then determined from them. They have square root singularities at the crack-tip. (author)

Correlation of ICME Magnetic Fields at Radially Aligned Spacecraft

Science.gov (United States)

Good, S. W.; Forsyth, R. J.; Eastwood, J. P.; Möstl, C.

2018-03-01

The magnetic field structures of two interplanetary coronal mass ejections (ICMEs), each observed by a pair of spacecraft close to radial alignment, have been analysed. The ICMEs were observed in situ by MESSENGER and STEREO-B in November 2010 and November 2011, while the spacecraft were separated by more than 0.6 AU in heliocentric distance, less than 4° in heliographic longitude, and less than 7° in heliographic latitude. Both ICMEs took approximately two days to travel between the spacecraft. The ICME magnetic field profiles observed at MESSENGER have been mapped to the heliocentric distance of STEREO-B and compared directly to the profiles observed by STEREO-B. Figures that result from this mapping allow for easy qualitative assessment of similarity in the profiles. Macroscale features in the profiles that varied on timescales of one hour, and which corresponded to the underlying flux rope structure of the ICMEs, were well correlated in the solar east-west and north-south directed components, with Pearson's correlation coefficients of approximately 0.85 and 0.95, respectively; microscale features with timescales of one minute were uncorrelated. Overall correlation values in the profiles of one ICME were increased when an apparent change in the flux rope axis direction between the observing spacecraft was taken into account. The high degree of similarity seen in the magnetic field profiles may be interpreted in two ways. If the spacecraft sampled the same region of each ICME ( i.e. if the spacecraft angular separations are neglected), the similarity indicates that there was little evolution in the underlying structure of the sampled region during propagation. Alternatively, if the spacecraft observed different, nearby regions within the ICMEs, it indicates that there was spatial homogeneity across those different regions. The field structure similarity observed in these ICMEs points to the value of placing in situ space weather monitors well upstream of the

Energy level alignment at hybridized organic-metal interfaces from a GW projection approach

Science.gov (United States)

Chen, Yifeng; Tamblyn, Isaac; Quek, Su Ying

Energy level alignments at organic-metal interfaces are of profound importance in numerous (opto)electronic applications. Standard density functional theory (DFT) calculations generally give incorrect energy level alignments and missing long-range polarization effects. Previous efforts to address this problem using the many-electron GW method have focused on physisorbed systems where hybridization effects are insignificant. Here, we use state-of-the-art GW methods to predict the level alignment at the amine-Au interface, where molecular levels do hybridize with metallic states. This non-trivial hybridization implies that DFT result is a poor approximation to the quasiparticle states. However, we find that the self-energy operator is approximately diagonal in the molecular basis, allowing us to use a projection approach to predict the level alignments. Our results indicate that the metallic substrate reduces the HOMO-LUMO gap by 3.5 4.0 eV, depending on the molecular coverage/presence of Au adatoms. Our GW results are further compared with those of a simple image charge model that describes the level alignment in physisorbed systems. Syq and YC acknowledge Grant NRF-NRFF2013-07 and the medium-sized centre program from the National Research Foundation, Singapore.

Role of intrinsic molecular dipole in energy level alignment at organic interfaces

NARCIS (Netherlands)

Lindell, L.; Cakir, Deniz; Brocks, G.; Fahlman, M.; Braun, S.

2013-01-01

The energy level alignment in metal-organic and organic-organic junctions of the widely used materials tris-(8-hydroxyquinoline)aluminum (Alq3) and 1,4,5,8-naphthalenetetracarboxylic dianhydride (NTCDA) is investigated. The measured alignment schemes for single and bilayer films of Alq3 and NTCDA

Energy-level alignment at interfaces between manganese phthalocyanine and C60

Directory of Open Access Journals (Sweden)

Daniel Waas

2017-04-01

Full Text Available We have used photoelectron spectroscopy to determine the energy-level alignment at organic heterojunctions made of manganese phthalocyanine (MnPc and the fullerene C60. We show that this energy-level alignment depends upon the preparation sequence, which is explained by different molecular orientations. Moreover, our results demonstrate that MnPc/C60 interfaces are hardly suited for application in organic photovoltaic devices, since the energy difference of the two lowest unoccupied molecular orbitals (LUMOs is rather small.

The Influence of Morphology on High-Performance Polymer Field-Effect Transistors

DEFF Research Database (Denmark)

Tsao, Hoi Nok; Cho, Don; Andreasen, Jens Wenzel

2009-01-01

The influence of molecular packing on the performance of polymer organic field-effect transistors is illustrated in this work. Both close -stacking distance and long-range order are important for achieving high mobilities. By aligning the polymers from solution, long-range order is induced...

Axisymmetric Compression of a Mohr-Coulomb Medium with Arbitrary Dilatancy, Including Free-Field Yielding

National Research Council Canada - National Science Library

Kendall, David

1997-01-01

.... It also extends the solution to include cases where particular combinations of friction angle, elastic properties, and free-field pressure cause the free field to yield before significant deformation...

The generalized Fenyes-Nelson model for free scalar field theory

International Nuclear Information System (INIS)

Davidson, M.

1980-01-01

The generalized Fenyes-Nelson model of quantum mechanics is applied to the free scalar field. The resulting Markov field is equivalent to the Euclidean Markov field with the times scaled by a common factor which depends on the diffusion parameter. This result is consistent with Guerra's earlier work on stochastic quantization of scalar fields. It suggests a deep connection between Euclidean field theory and the stochastic interpretation of quantum mechanics. The question of Lorentz covariance is also discussed. (orig.)

Maxwell fields and shear-free null geodesic congruences

International Nuclear Information System (INIS)

Newman, Ezra T

2004-01-01

We study and report on the class of vacuum Maxwell fields in Minkowski space that possess a non-degenerate, diverging, principal null vector field (null eigenvector field of the Maxwell tensor) that is tangent to a shear-free null geodesics congruence. These congruences can be either surface forming (the tangent vectors being proportional to gradients) or not, i.e., the twisting congruences. In the non-twisting case, the associated Maxwell fields are precisely the Lienard-Wiechert fields, i.e., those Maxwell fields arising from an electric monopole moving on an arbitrary worldline. The null geodesic congruence is given by the generators of the light-cones with apex on the worldline. The twisting case is much richer, more interesting and far more complicated. In a twisting subcase, where our main interests lie, the following strange interpretation can be given. If we allow the real Minkowski space to be complexified so that the real Minkowski coordinates x a take complex values, i.e., x a → z a = x a + iy a with complex metric g η ab dz a dz b , the real vacuum Maxwell equations can be extended into the complex space and rewritten as curl W=i W radical, div W=0 with W=E+iB. This subcase of Maxwell fields can then be extended into the complex space so as to have as source, a complex analytic worldline, i.e., to now become complex Lienard-Wiechart fields. When viewed as real fields on the real Minkowski space (z a = x a ), they possess a real principal null vector that is shear-free but twisting and diverging. The twist is a measure of how far the complex worldline is from the real 'slice'. Most Maxwell fields in this subcase are asymptotically flat with a time-varying set of electric and magnetic moments, all depending on the complex displacements and the complex velocities

MODELING MAGNETIC FIELD STRUCTURE OF A SOLAR ACTIVE REGION CORONA USING NONLINEAR FORCE-FREE FIELDS IN SPHERICAL GEOMETRY

International Nuclear Information System (INIS)

Guo, Y.; Ding, M. D.; Liu, Y.; Sun, X. D.; DeRosa, M. L.; Wiegelmann, T.

2012-01-01

We test a nonlinear force-free field (NLFFF) optimization code in spherical geometry using an analytical solution from Low and Lou. Several tests are run, ranging from idealized cases where exact vector field data are provided on all boundaries, to cases where noisy vector data are provided on only the lower boundary (approximating the solar problem). Analytical tests also show that the NLFFF code in the spherical geometry performs better than that in the Cartesian one when the field of view of the bottom boundary is large, say, 20° × 20°. Additionally, we apply the NLFFF model to an active region observed by the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory (SDO) both before and after an M8.7 flare. For each observation time, we initialize the models using potential field source surface (PFSS) extrapolations based on either a synoptic chart or a flux-dispersal model, and compare the resulting NLFFF models. The results show that NLFFF extrapolations using the flux-dispersal model as the boundary condition have slightly lower, therefore better, force-free, and divergence-free metrics, and contain larger free magnetic energy. By comparing the extrapolated magnetic field lines with the extreme ultraviolet (EUV) observations by the Atmospheric Imaging Assembly on board SDO, we find that the NLFFF performs better than the PFSS not only for the core field of the flare productive region, but also for large EUV loops higher than 50 Mm.

Machine learning of accurate energy-conserving molecular force fields

Science.gov (United States)

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E.; Poltavsky, Igor; Schütt, Kristof T.; Müller, Klaus-Robert

2017-01-01

Using conservation of energy—a fundamental property of closed classical and quantum mechanical systems—we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol−1 for energies and 1 kcal mol−1 Å̊−1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods. PMID:28508076

The GEM Detector projective alignment simulation system

International Nuclear Information System (INIS)

Wuest, C.R.; Belser, F.C.; Holdener, F.R.; Roeben, M.D.; Paradiso, J.A.; Mitselmakher, G.; Ostapchuk, A.; Pier-Amory, J.

1993-01-01

Precision position knowledge (< 25 microns RMS) of the GEM Detector muon system at the Superconducting Super Collider Laboratory (SSCL) is an important physics requirement necessary to minimize sagitta error in detecting and tracking high energy muons that are deflected by the magnetic field within the GEM Detector. To validate the concept of the sagitta correction function determined by projective alignment of the muon detectors (Cathode Strip Chambers or CSCs), the basis of the proposed GEM alignment scheme, a facility, called the ''Alignment Test Stand'' (ATS), is being constructed. This system simulates the environment that the CSCs and chamber alignment systems are expected to experience in the GEM Detector, albeit without the 0.8 T magnetic field and radiation environment. The ATS experimental program will allow systematic study and characterization of the projective alignment approach, as well as general mechanical engineering of muon chamber mounting concepts, positioning systems and study of the mechanical behavior of the proposed 6 layer CSCs. The ATS will consist of a stable local coordinate system in which mock-ups of muon chambers (i.e., non-working mechanical analogs, representing the three superlayers of a selected barrel and endcap alignment tower) are implemented, together with a sufficient number of alignment monitors to overdetermine the sagitta correction function, providing a self-consistency check. This paper describes the approach to be used for the alignment of the GEM muon system, the design of the ATS, and the experiments to be conducted using the ATS

Ab initio molecular dynamics in a finite homogeneous electric field.

Science.gov (United States)

Umari, P; Pasquarello, Alfredo

2002-10-07

We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.

Field emission characteristics of vertically aligned carbon nanotubes with honeycomb configuration grown onto glass substrate with titanium coating

Energy Technology Data Exchange (ETDEWEB)

Huang, Yung-Jui [Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan (China); Chang, Hsin-Yueh; Chang, Hsuan-Chen [Department of Electronic and computer Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan (China); Shih, Yi-Ting; Su, Wei-Jhih [Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan (China); Ciou, Chen-Hong [Department of Electronic and computer Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan (China); Chen, Yi-Ling [Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan (China); Honda, Shin-ichi [Graduate School of Engineering, University of Hyogo, Himeji, Hyogo 671-2280 (Japan); Huang, Ying-Sheng [Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan (China); Department of Electronic and computer Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan (China); Lee, Kuei-Yi, E-mail: kylee@mail.ntust.edu.tw [Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan (China); Department of Electronic and computer Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan (China)

2014-03-15

Highlights: • We have successfully designed the honeycomb patterns on glass substrate by photolithography technique. • Honeycomb-VACNTs were synthesized successfully onto glass substrate by using thermal CVD and covered different Ti films on VACNTs by e-beam evaporation. • After coating the Ti films, the current density reached 7 mA/cm{sup 2} when the electric field was 2.5 V/μm. • The fluorescence of VACNTs with Ti 15 nm films exhibits the high brightness screen and emission uniformity. -- Abstract: Carbon nanotubes (CNTs) were grown successfully onto a glass substrate using thermal chemical vapor deposition (TCVD) with C{sub 2}H{sub 2} gas at 700 °C. The synthesized CNTs exhibited good crystallinity and a vertically aligned morphology. The vertically aligned CNTs (VACNTs) were patterned with a honeycomb configuration using photolithography and characterized using field emission (FE) applications. Owing to the electric field concentration, the FE current density of VACNTs with honeycomb configuration was higher than that of the un-patterned VACNTs. Ti was coated onto the VACNT surface utilizing the relatively lower work function property to enhance the FE current density. The FE current density reached up to 7.0 mA/cm{sup 2} at an applied electric field of 2.5 V/μm. A fluorescent screen was monitored to demonstrate uniform FE VACNTs with a honeycomb configuration. The designed field emitter provided an admirable example for FE applications.

Self-field effects on electron dynamics in free-electron lasers with axial magnetic field

International Nuclear Information System (INIS)

Mirzanejhad, S.; Maraghechi, B.; Mohsenpour, T.

2004-01-01

A self-consistent method for the analysis of self-magnetic field for a free-electron laser with a one-dimensional helical wiggler and an axial guide magnetic field is presented. The equilibrium orbits and their stability, under the influence of self-electric and self-magnetic fields, are analyzed. New unstable orbits, in the first part of the Group I orbits and in the resonance region of the Group II orbits, are found. It is shown that an increase in the defocusing effect of self-fields will widen the unstable orbits. An anomalous self-field regime is found where an increase in the defocusing effect of self-fields can have stabilizing effect on the resonance region

Magnetohydrodynamic free convection in a strong cross field

NARCIS (Netherlands)

Kuiken, H.K.

1970-01-01

The problem of magnetohydrodynamic free convection of an electrically conducting fluid in a strong cross field is investigated. It is solved by using a singular perturbation technique. The solutions presented cover the range of Prandtl numbers from zero to order one. This includes both the important

Observations of field-aligned energetic electron and ion distributions near the magnetopause at geosynchronous orbit

International Nuclear Information System (INIS)

Korth, A.; Kremser, G.; Daly, P.W.; Amata, E.

1982-01-01

On August 28, 1978, the dayside magnetopause crossed the geosynchronous satellite GEOS 2 several times during a geomagnetically disturbed period, and clear signatures of the interconnection of field lines through the magnetopause were observed. The MPAE particle spectrometer provided high time resolution observations of the distribution of energetic electrons (E>22 keV) and ions (E>27 keV). Magnetometer data were used to determine the location of GEOS 2 relative to the magnetopause. The pitch angle distributions of ions and electrons were found to be strongly asymmetric with respect to 90 0 , and the asymmetries have been interpreted in terms of field-aligned particle streaming. Evidence is provided for the first time for electron streaming inside the magnetopause which continues for many bounce periods. It is concluded that magnetospheric field lines opened, at least for brief time intervals, as a consequence of interconnection with magnetosheath field lines. Comparisons of electron spectra provide evidence that the streaming electrons observed in the magnetosheath originate in the magnetosphere

Molecular dynamics simulations of liquid crystals at interfaces

International Nuclear Information System (INIS)

Shield, Mark

2002-01-01

Molecular dynamics simulations of an atomistic model of 4-n-octyl-4'-cyanobiphenyl (8CB) were performed for thin films of 8CB on solid substrates (a pseudopotential representation of the molecular topography of the (100) crystal surface of polyethylene (PE), a highly ordered atomistic model of a pseudo-crystalline PE surface and an atomistic model of a partially orientated film of PE), free standing thin films of 8CB and 8CB droplets in a hexagonal pit. The systems showed strong homeotropic anchoring at the free volume interface and planar anchoring at the solid interface whose strength was dependent upon the surface present. The free volume interface also demonstrated weak signs of smectic wetting of the bulk. Simulations of thin free standing films of liquid crystals showed the ordered nature of the liquid crystals at the two free volume interfaces can be adopted by the region of liquid crystal molecules between the homeotropic layer at each interface only if there is a certain number of liquid crystal molecules present. The perpendicular anchoring imposed by the free volume interface and the solid interface for the thin films on the solid substrates resulted in some evidence for the liquid crystal director undergoing a continual rotation at low temperatures and a definite discontinuous change at higher temperatures. The liquid crystal alignment imparted by these substrates was found to depend upon the topography of the surface and not the direction of the polymer chains in the substrate. The liquid crystal was found to order via an epitaxy-like mechanism. The perpendicular anchoring results in a drop in the order - disorder transition temperature for the molecules in the region between the homeotropic layer at the free volume interface and the planar layers at the solid interface. An increase in the size of this region does not alter the transition temperature. The shape of the liquid crystal molecules is dependent upon the degree of order and thus the nematic

The free Maxwell field in curved spacetime

International Nuclear Information System (INIS)

Kueskue, M.

2001-09-01

The aim of this thesis is to discuss quantizations of the free Maxwell field in flat and curved spacetimes. First we introduce briefly some notions from tensor analysis and the causal structure of spacetime. As an introduction to the main topic, we review some aspects of the two axiomatic quantum field theories, Wightman theory and algebraic quantum field theory. We also give an introduction into concepts of the quantization of fields on curved spacetime backgrounds. Then the wave equation and quantization of the Maxwell field in flat spacetimes is discussed. It follows a review of J. Dimock's quantization of the Maxwell field on curved spacetimes and then we come to our main result: We show explicitly that the Maxwell field, defined by dF=0 and δF=0, has a well posed initial value formulation on arbitrary globally hyperbolic spacetime manifolds. We prove the existence and uniqueness of fundamental solutions without employing a vector potential. Thus our solution is also applicable to spacetimes not satisfying the Poincare lemma and should lead to a quantization of the Maxwell field on non-trivial spacetime backgrounds. This in turn provides the opportunity to investigate physical states on non-trivial spacetime-topologies and could lead to the discovery of new quantum phenomena. (orig.)

Iridium catalyzed growth of vertically aligned CNTs by APCVD

International Nuclear Information System (INIS)

Sahoo, R.K.; Jacob, C.

2014-01-01

Highlights: • Growth of uniform-diameter vertically-aligned multi-walled CNTs by APCVD. • Use of high melting point low carbon solubility iridium nanoparticles as catalyst. • Optimization of growth time for uniform sized, uniformly aligned CNTs. • Growth model for the various features in the vertically aligned CNTs is proposed. - Abstract: Vertically aligned carbon nanotubes (VA-CNTs) have been synthesized using high temperature catalyst nanoparticles of iridium. The catalyst layer was prepared by DC sputtering. Particle density, circularity and average particle size of the catalyst were analyzed using field emission scanning electron microscopy. The alignment, morphology and the length of the as-grown CNTs were analyzed using field-emission scanning electron microscopy. High resolution transmission electron microscopy was carried out to observe the layers of graphitic stacking which form the carbon nanotubes. Micro Raman measurement was used for the analysis of the graphitic crystallinity of the as-grown carbon nano structures. Effects of growth time variation on growth morphology and alignment have been studied. The alignment has been explained on the basis of the crowding effect of the neighboring nanoparticles

Iridium catalyzed growth of vertically aligned CNTs by APCVD

Energy Technology Data Exchange (ETDEWEB)

Sahoo, R.K.; Jacob, C., E-mail: cxj14_holiday@yahoo.com

2014-07-01

Highlights: • Growth of uniform-diameter vertically-aligned multi-walled CNTs by APCVD. • Use of high melting point low carbon solubility iridium nanoparticles as catalyst. • Optimization of growth time for uniform sized, uniformly aligned CNTs. • Growth model for the various features in the vertically aligned CNTs is proposed. - Abstract: Vertically aligned carbon nanotubes (VA-CNTs) have been synthesized using high temperature catalyst nanoparticles of iridium. The catalyst layer was prepared by DC sputtering. Particle density, circularity and average particle size of the catalyst were analyzed using field emission scanning electron microscopy. The alignment, morphology and the length of the as-grown CNTs were analyzed using field-emission scanning electron microscopy. High resolution transmission electron microscopy was carried out to observe the layers of graphitic stacking which form the carbon nanotubes. Micro Raman measurement was used for the analysis of the graphitic crystallinity of the as-grown carbon nano structures. Effects of growth time variation on growth morphology and alignment have been studied. The alignment has been explained on the basis of the crowding effect of the neighboring nanoparticles.

The Martini Coarse-Grained Force Field

NARCIS (Netherlands)

Periole, X.; Marrink, S.J.; Monticelli, Luca; Salonen, Emppu

2013-01-01

The Martini force field is a coarse-grained force field suited for molecular dynamics simulations of biomolecular systems. The force field has been parameterized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical

Orbital alignment effects in near-resonant Rydberg atoms-rare gas collisions

International Nuclear Information System (INIS)

Isaacs, W.A.; Morrison, M.A.

1993-01-01

Recent experimental and theoretical studies of near-resonant energy transfer collisions involving rare-gas atoms and alkali or alkaline earth atoms which have been initially excited to an aligned state via one or more linearly polarized rasters have yielded a wealth of insight into orbital alignment and related effects. We have extended this inquiry to initially aligned Rydberg states, examining state-to-state and alignment-selected cross sections using quantum collision theory augmented by approximations appropriate to the special characteristics of the Rydberg state (e.g., the quasi-free-electron model and the impulse approximation)

An investigation of methods for free-field comparison calibration of measurement microphones

DEFF Research Database (Denmark)

Barrera-Figueroa, Salvador; Moreno Pescador, Guillermo; Jacobsen, Finn

2010-01-01

Free-field comparison calibration of measurement microphones requires that a calibrated reference microphone and a test microphone are exposed to the same sound pressure in a free field. The output voltages of the microphones can be measured either sequentially or simultaneously. The sequential...... method requires the sound field to have good temporal stability. The simultaneous method requires instead that the sound pressure is the same in the positions where the microphones are placed. In this paper the results of the application of the two methods are compared. A third combined method...

Molecular dynamics study of charged dendrimers in salt-free solution : effect of counterions

NARCIS (Netherlands)

Gurtovenko, A.A.; Lyulin, S.V.; Karttunen, M.E.J.; Vattulainen, I.

2006-01-01

Polyamidoamine dendrimers, being protonated under physiological conditions, represent a promising class of nonviral, nanosized vectors for drug and gene delivery. We performed extensive molecular dynamics simulations of a generic model dendrimer in a salt-free solution with dendrimer’s terminal

Alignment methods: strategies, challenges, benchmarking, and comparative overview.

Science.gov (United States)

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.

New twistorial integral formulas for massless free fields of arbitrary spin

International Nuclear Information System (INIS)

Cardoso, J.G.

1991-01-01

A manifestly scaling-invariant version of the Kirchoff-D'Adhemar-Penrose field integrals is presented. The invariant integral expressions for the spinning massless free fields are directly transcribed into the framework of twistor theory. It is then shown that the resulting twistorial field integrals can be thought of as being equivalent to the universal Penrose contour integral formulas for these fields

MATCH: An Atom- Typing Toolset for Molecular Mechanics Force Fields

Science.gov (United States)

Yesselman, Joseph D.; Price, Daniel J.; Knight, Jennifer L.; Brooks, Charles L.

2011-01-01

We introduce a toolset of program libraries collectively titled MATCH (Multipurpose Atom-Typer for CHARMM) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion from multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges and force field parameters is achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In the present work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM CGENFF force field (Vanommeslaeghe, et al., JCC., 2010, 31, 671–690), one million molecules from the PubChem database of small molecules are typed, parameterized and minimized. PMID:22042689

Characteristics of electron cyclotron waves creating field-aligned and transverse plasma-potential structures

International Nuclear Information System (INIS)

Takahashi, K; Kaneko, T; Hatakeyama, R; Fukuyama, A

2009-01-01

Characteristics of electromagnetic waves of azimuthal mode number m = ±1 are investigated experimentally, analytically and numerically when the waves triggering the field-aligned and transverse plasma-potential structure modification near an electron cyclotron resonance (ECR) point are injected into an inhomogeneously magnetized plasma with high-speed ion flow. The waves of m = +1 and -1 modes generate an electric double layer near the ECR point at the radially central and peripheral areas of the plasma column, respectively, and the transverse electric fields are consequently formed. At these areas the waves have a right-handed polarization and are absorbed through the ECR mechanism, where the experimental and analytical results do show the polarization reversal along the radial axis. The numerical results by plasma analysis by finite element method (FEM)/wave analysis by FEM (PAF/WF) code show that the wave-absorption area is localized at the radially central and peripheral areas for m = +1 and -1 mode waves, respectively, being consistent with the experimental and analytical ones.

Neutron Reference Benchmark Field Specification: ACRR Free-Field Environment (ACRR-FF-CC-32-CL).

Energy Technology Data Exchange (ETDEWEB)

Vega, Richard Manuel [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Parma, Edward J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Griffin, Patrick J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Vehar, David W. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2015-07-01

This report was put together to support the International Atomic Energy Agency (IAEA) REAL- 2016 activity to validate the dosimetry community’s ability to use a consistent set of activation data and to derive consistent spectral characterizations. The report captures details of integral measurements taken in the Annular Core Research Reactor (ACRR) central cavity free-field reference neutron benchmark field. The field is described and an “a priori” calculated neutron spectrum is reported, based on MCNP6 calculations, and a subject matter expert (SME) based covariance matrix is given for this “a priori” spectrum. The results of 31 integral dosimetry measurements in the neutron field are reported.

Deep molecular responses for treatment-free remission in chronic myeloid leukemia.

Science.gov (United States)

Dulucq, Stéphanie; Mahon, Francois-Xavier

2016-09-01

Several clinical trials have demonstrated that some patients with chronic myeloid leukemia in chronic phase (CML-CP) who achieve sustained deep molecular responses on tyrosine kinase inhibitor (TKI) therapy can safely suspend therapy and attempt treatment-free remission (TFR). Many TFR studies to date have enrolled imatinib-treated patients; however, the feasibility of TFR following nilotinib or dasatinib has also been demonstrated. In this review, we discuss available data from TFR trials and what these data reveal about the molecular biology of TFR. With an increasing number of ongoing TFR clinical trials, TFR may become an achievable goal for patients with CML-CP. © 2016 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

Exact results for integrable asymptotically-free field theories

CERN Document Server

Evans, J M; Evans, Jonathan M; Hollowood, Timothy J

1995-01-01

An account is given of a technique for testing the equivalence between an exact factorizable S-matrix and an asymptotically-free Lagrangian field theory in two space-time dimensions. The method provides a way of resolving CDD ambiguities in the S-matrix and it also allows for an exact determination of the physical mass in terms of the Lambda parameter of perturbation theory. The results for various specific examples are summarized. (To appear in the Proceedings of the Conference on Recent Developments in Quantum Field Theory and Statistical Mechanics, ICTP, Trieste, Easter 1995).

A dark-field microscope for background-free detection of resonance fluorescence from single semiconductor quantum dots operating in a set-and-forget mode.

Science.gov (United States)

Kuhlmann, Andreas V; Houel, Julien; Brunner, Daniel; Ludwig, Arne; Reuter, Dirk; Wieck, Andreas D; Warburton, Richard J

2013-07-01

Optically active quantum dots, for instance self-assembled InGaAs quantum dots, are potentially excellent single photon sources. The fidelity of the single photons is much improved using resonant rather than non-resonant excitation. With resonant excitation, the challenge is to distinguish between resonance fluorescence and scattered laser light. We have met this challenge by creating a polarization-based dark-field microscope to measure the resonance fluorescence from a single quantum dot at low temperature. We achieve a suppression of the scattered laser exceeding a factor of 10(7) and background-free detection of resonance fluorescence. The same optical setup operates over the entire quantum dot emission range (920-980 nm) and also in high magnetic fields. The major development is the outstanding long-term stability: once the dark-field point has been established, the microscope operates for days without alignment. The mechanical and optical designs of the microscope are presented, as well as exemplary resonance fluorescence spectroscopy results on individual quantum dots to underline the microscope's excellent performance.

A dark-field microscope for background-free detection of resonance fluorescence from single semiconductor quantum dots operating in a set-and-forget mode

International Nuclear Information System (INIS)

Kuhlmann, Andreas V.; Houel, Julien; Warburton, Richard J.; Brunner, Daniel; Ludwig, Arne; Reuter, Dirk; Wieck, Andreas D.

2013-01-01

Optically active quantum dots, for instance self-assembled InGaAs quantum dots, are potentially excellent single photon sources. The fidelity of the single photons is much improved using resonant rather than non-resonant excitation. With resonant excitation, the challenge is to distinguish between resonance fluorescence and scattered laser light. We have met this challenge by creating a polarization-based dark-field microscope to measure the resonance fluorescence from a single quantum dot at low temperature. We achieve a suppression of the scattered laser exceeding a factor of 10 7 and background-free detection of resonance fluorescence. The same optical setup operates over the entire quantum dot emission range (920–980 nm) and also in high magnetic fields. The major development is the outstanding long-term stability: once the dark-field point has been established, the microscope operates for days without alignment. The mechanical and optical designs of the microscope are presented, as well as exemplary resonance fluorescence spectroscopy results on individual quantum dots to underline the microscope's excellent performance

Stability estimate for the aligned magnetic field in a periodic quantum waveguide from Dirichlet-to-Neumann map

Energy Technology Data Exchange (ETDEWEB)

Mejri, Youssef, E-mail: josef-bizert@hotmail.fr [Aix Marseille Universite, Toulon Universite, CNRS, CPT, Marseille (France); Dép. des Mathématiques, Faculté des Sciences de Bizerte, 7021 Jarzouna (Tunisia); Laboratoire de Modélisation Mathématique et Numérique dans les Sciences de l’Ingénieur, ENIT BP 37, Le Belvedere, 1002 Tunis (Tunisia)

2016-06-15

In this article, we study the boundary inverse problem of determining the aligned magnetic field appearing in the magnetic Schrödinger equation in a periodic quantum cylindrical waveguide, by knowledge of the Dirichlet-to-Neumann map. We prove a Hölder stability estimate with respect to the Dirichlet-to-Neumann map, by means of the geometrical optics solutions of the magnetic Schrödinger equation.

Patterned growth of carbon nanotubes over vertically aligned silicon nanowire bundles for achieving uniform field emission.

Science.gov (United States)

Hung, Yung-Jr; Huang, Yung-Jui; Chang, Hsuan-Chen; Lee, Kuei-Yi; Lee, San-Liang

2014-01-01

A fabrication strategy is proposed to enable precise coverage of as-grown carbon nanotube (CNT) mats atop vertically aligned silicon nanowire (VA-SiNW) bundles in order to realize a uniform bundle array of CNT-SiNW heterojunctions over a large sample area. No obvious electrical degradation of as-fabricated SiNWs is observed according to the measured current-voltage characteristic of a two-terminal single-nanowire device. Bundle arrangement of CNT-SiNW heterojunctions is optimized to relax the electrostatic screening effect and to maximize the field enhancement factor. As a result, superior field emission performance and relatively stable emission current over 12 h is obtained. A bright and uniform fluorescent radiation is observed from CNT-SiNW-based field emitters regardless of its bundle periodicity, verifying the existence of high-density and efficient field emitters on the proposed CNT-SiNW bundle arrays.

Characterization of surfactant liquid crystal phases suitable for molecular alignment and measurement of dipolar couplings

International Nuclear Information System (INIS)

Barrientos, Laura G.; Dolan, Caroline; Gronenborn, Angela M.

2000-01-01

Media employed for imparting partial alignment onto solute molecules have recently attracted considerable attention, since they permit the measurement of NMR parameters for solute biomolecules commonly associated with solid state NMR. Here we characterize a medium which is based on a quasi-ternary surfactant system comprising cetylpyridinium bromide/hexanol/sodium bromide. We demonstrate that dilute solutions of this system can exist in liquid crystalline phases which orient in the magnetic field and allow the measurement of residual dipolar couplings under a variety of conditions. The present system is extremely versatile and robust, tolerating different buffer conditions, temperature ranges and concentrations

Studies on in situ magnetic alignment of bonded anisotropic Nd-Fe-B alloy powders

Energy Technology Data Exchange (ETDEWEB)

Nlebedim, I.C. [Ames Laboratory, Ames, IA 50011 (United States); Ucar, Huseyin; Hatter, Christine B. [Oak Ridge National Laboratory, Oak Ridge, TN 37831 (United States); McCallum, R.W. [Ames Laboratory, Ames, IA 50011 (United States); McCall, Scott K. [Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Kramer, M.J. [Ames Laboratory, Ames, IA 50011 (United States); Paranthaman, M. Parans [Oak Ridge National Laboratory, Oak Ridge, TN 37831 (United States)

2017-01-15

Considerations for achieving high degree of alignment in polymer bonded permanent magnets are presented via the results of a study on in situ magnetic alignment of anisotropic Nd-Fe-B magnet powders. Contributions from effect of the alignment temperature, alignment magnetic field and the properties of the polymer on the hard magnetic properties of the bonded magnet were considered. The thermo-rheological properties of the polymer and the response of the magnet powders to the applied magnetic field indicate that hard magnetic properties were optimized at an alignment temperature just above the melting temperature of the EVA co-polymer. This agrees with an observed correlation between the change in magnetization due to improved magnetic alignment of the anisotropic powders and the change in viscosity of the binder. Manufacturing cost can be minimized by identifying optimum alignment temperatures and magnetic field strengths. - Highlights: • Optimum alignment of anisotropic magnet powders can enable high performance bonded magnets. • The viscoelastic state of polymer binders determines the dominating coercivity mechanism. • The minimum deviation in coercivity and remanence, with magnetic field, can occur at different temperatures. • Melting characteristics of polymer binders and the change in magnetization during alignment can be correlated.

Studies on in situ magnetic alignment of bonded anisotropic Nd-Fe-B alloy powders

International Nuclear Information System (INIS)

Nlebedim, I.C.; Ucar, Huseyin; Hatter, Christine B.; McCallum, R.W.; McCall, Scott K.; Kramer, M.J.; Paranthaman, M. Parans

2017-01-01

Considerations for achieving high degree of alignment in polymer bonded permanent magnets are presented via the results of a study on in situ magnetic alignment of anisotropic Nd-Fe-B magnet powders. Contributions from effect of the alignment temperature, alignment magnetic field and the properties of the polymer on the hard magnetic properties of the bonded magnet were considered. The thermo-rheological properties of the polymer and the response of the magnet powders to the applied magnetic field indicate that hard magnetic properties were optimized at an alignment temperature just above the melting temperature of the EVA co-polymer. This agrees with an observed correlation between the change in magnetization due to improved magnetic alignment of the anisotropic powders and the change in viscosity of the binder. Manufacturing cost can be minimized by identifying optimum alignment temperatures and magnetic field strengths. - Highlights: • Optimum alignment of anisotropic magnet powders can enable high performance bonded magnets. • The viscoelastic state of polymer binders determines the dominating coercivity mechanism. • The minimum deviation in coercivity and remanence, with magnetic field, can occur at different temperatures. • Melting characteristics of polymer binders and the change in magnetization during alignment can be correlated.

Stochastic sampling of the RNA structural alignment space.

Science.gov (United States)

Harmanci, Arif Ozgun; Sharma, Gaurav; Mathews, David H

2009-07-01

A novel method is presented for predicting the common secondary structures and alignment of two homologous RNA sequences by sampling the 'structural alignment' space, i.e. the joint space of their alignments and common secondary structures. The structural alignment space is sampled according to a pseudo-Boltzmann distribution based on a pseudo-free energy change that combines base pairing probabilities from a thermodynamic model and alignment probabilities from a hidden Markov model. By virtue of the implicit comparative analysis between the two sequences, the method offers an improvement over single sequence sampling of the Boltzmann ensemble. A cluster analysis shows that the samples obtained from joint sampling of the structural alignment space cluster more closely than samples generated by the single sequence method. On average, the representative (centroid) structure and alignment of the most populated cluster in the sample of structures and alignments generated by joint sampling are more accurate than single sequence sampling and alignment based on sequence alone, respectively. The 'best' centroid structure that is closest to the known structure among all the centroids is, on average, more accurate than structure predictions of other methods. Additionally, cluster analysis identifies, on average, a few clusters, whose centroids can be presented as alternative candidates. The source code for the proposed method can be downloaded at http://rna.urmc.rochester.edu.

Kinematically complete study on electron impact ionisation of aligned hydrogen molecules

Energy Technology Data Exchange (ETDEWEB)

Senftleben, Arne

2009-10-28

Within the work presented here, single ionisation of spatially aligned hydrogen molecules by 200 eV electrons was studied in a kinematically complete experiment. For the first time, a comprehensive set of fully differential cross sections (FDCS) was obtained for this process on a molecular target. The direction of the internuclear axis was derived from the fragment emission of post-collision dissociation of the residual H{sub 2}{sup +} ion. Therefore, a protonic fragment was detected in coincidence with the two final-state electrons using a dedicated reaction microscope and sophisticated data analysis. For direct ionisation into the ionic ground state, existing theoretical cross sections for aligned molecules were tested. Additionally, we observed molecular frame angular distributions of Auger electrons emitted through dissociative autoionisation of H{sub 2}. Earlier findings of kinematically incomplete experiments were reproduced, but the FDCS reveal structures so far unknown. Furthermore, for random alignment, differential cross sections at two distinct values of the mean internuclear distance were obtained, providing new arguments in the current discussion on the nature of discrepancies observed between atomic and molecular collisions. (orig.)

Finite size effects in the thermodynamics of a free neutral scalar field

Science.gov (United States)

Parvan, A. S.

2018-04-01

The exact analytical lattice results for the partition function of the free neutral scalar field in one spatial dimension in both the configuration and the momentum space were obtained in the framework of the path integral method. The symmetric square matrices of the bilinear forms on the vector space of fields in both configuration space and momentum space were found explicitly. The exact lattice results for the partition function were generalized to the three-dimensional spatial momentum space and the main thermodynamic quantities were derived both on the lattice and in the continuum limit. The thermodynamic properties and the finite volume corrections to the thermodynamic quantities of the free real scalar field were studied. We found that on the finite lattice the exact lattice results for the free massive neutral scalar field agree with the continuum limit only in the region of small values of temperature and volume. However, at these temperatures and volumes the continuum physical quantities for both massive and massless scalar field deviate essentially from their thermodynamic limit values and recover them only at high temperatures or/and large volumes in the thermodynamic limit.

Full Alignment of Molecules Using Elliptically Polarized Light

DEFF Research Database (Denmark)

Larsen, Jakob Juul; Hald, Kasper; Seideman, Tamar

When a molecule with an anisotropic polarizability is placed in a strong nonresonant laser field the interaction occurs through the induced dipole moment. The outcome is that the molecule experiences an angular dependent potential energy. It is now well established that a linearly polarized laser...... field can be used to align molecules along their axis of highest polarizability. Here we demonstrate, theoretically and experimentally, that an elliptically polarized laser field can be used to simultaneously force two axes of a molecule into alignment through the same mechanism. Due to the rigidity...

quality of corn-field bean gluten-free pasta

Directory of Open Access Journals (Sweden)

Dib Ahlem

2018-01-01

Full Text Available Corn semolina supplemented by field bean semolina in ratio of 2/1 (w/w were used for obtaining protein and fiber enriched gluten-free pasta. The effect of hydrothermal treatment of corn flour on its applicability as gluten-free pasta improver was tested. A central composite design involving water hydration level and the amount of hydrothermal treated corn flour were used. Instrumental analyses of pasta (cooking loss, water absorption capacity, hydration and pasting properties, textural parameters and microstructure were carried out to assess the impact of experimental factors. Results showed that hydrothermal treatment of corn flour affected in different extent on pasta properties, improving cooking and textural characteristics of pasta. The optimum formulation of corn-field bean contained 7.41 g of treated corn flour and 77.26 mL of water was selected on the base of desirability function approach with value of 0.825 which showed the best pasta properties. Obtained results showed also that addition of treated flour induced significant differences (p < 0.05 in all parameters in comparison with control pasta.

Fan texture of the compound Ba3Co2Fe244O41 pre-aligned in a magnetic field

NARCIS (Netherlands)

Huijser-Gerits, E.M.C.; Rieck, G.D.; Vogel, D.L.

1970-01-01

Samples of the ferrimagnetic material Ba3Co2Fe24O41, pre-aligned in a magnetic field and sintered at various temps., have been examd. for preferred orientation. Schulz's reflection technique and the standardizing method of Holland were used to det. quant. pole figures of several lattice planes. The

Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.

Science.gov (United States)

Peng, Xiangda; Zhang, Yuebin; Chu, Huiying; Li, Guohui

2016-03-05