X-ray Diffraction from Isolated and Strongly Aligned Gas-Phase Molecules with a Free-Electron Laser

DEFF Research Database (Denmark)

Küpper, Jochen; Stern, Stephan; Holmegaard, Lotte

2014-01-01

We report experimental results on x-ray diffraction of quantum-state-selected and strongly aligned ensembles of the prototypical asymmetric rotor molecule 2,5-diiodobenzonitrile using the Linac Coherent Light Source. The experiments demonstrate first steps toward a new approach to diffractive...... imaging of distinct structures of individual, isolated gas-phase molecules. We confirm several key ingredients of single molecule diffraction experiments: the abilities to detect and count individual scattered x-ray photons in single shot diffraction data, to deliver state-selected, e. g., structural......-isomer-selected, ensembles of molecules to the x-ray interaction volume, and to strongly align the scattering molecules. Our approach, using ultrashort x-ray pulses, is suitable to study ultrafast dynamics of isolated molecules....

Accessing the molecular frame through strong-field alignment of distributions of gas phase molecules

Science.gov (United States)

Reid, Katharine L.

2018-03-01

A rationale for creating highly aligned distributions of molecules is that it enables vector properties referenced to molecule-fixed axes (the molecular frame) to be determined. In the present work, the degree of alignment that is necessary for this to be achieved in practice is explored. Alignment is commonly parametrized in experiments by a single parameter, ?, which is insufficient to enable predictive calculations to be performed. Here, it is shown that, if the full distribution of molecular axes takes a Gaussian form, this single parameter can be used to determine the complete set of alignment moments needed to characterize the distribution. In order to demonstrate the degree of alignment that is required to approach the molecular frame, the alignment moments corresponding to a few chosen values of ? are used to project a model molecular frame photoelectron angular distribution into the laboratory frame. These calculations show that ? needs to approach 0.9 in order to avoid significant blurring to be caused by averaging. This article is part of the theme issue `Modern theoretical chemistry'.

Label-Free Alignment of Nonmagnetic Particles in a Small Uniform Magnetic Field.

Science.gov (United States)

Wang, Zhaomeng; Wang, Ying; Wu, Rui Ge; Wang, Z P; Ramanujan, R V

2018-01-01

Label-free manipulation of biological entities can minimize damage, increase viability and improve efficiency of subsequent analysis. Understanding the mechanism of interaction between magnetic and nonmagnetic particles in an inverse ferrofluid can provide a mechanism of label-free manipulation of such entities in a uniform magnetic field. The magnetic force, induced by relative magnetic susceptibility difference between nonmagnetic particles and surrounding magnetic particles as well as particle-particle interaction were studied. Label-free alignment of nonmagnetic particles can be achieved by higher magnetic field strength (Ba), smaller particle spacing (R), larger particle size (rp1), and higher relative magnetic permeability difference between particle and the surrounding fluid (Rμr). Rμr can be used to predict the direction of the magnetic force between both magnetic and nonmagnetic particles. A sandwich structure, containing alternate layers of magnetic and nonmagnetic particle chains, was studied. This work can be used for manipulation of nonmagnetic particles in lab-on-a-chip applications.

Mechanisms of two-color laser-induced field-free molecular orientation.

Science.gov (United States)

Spanner, Michael; Patchkovskii, Serguei; Frumker, Eugene; Corkum, Paul

2012-09-14

Two mechanisms of two-color (ω+2ω) laser-induced field-free molecular orientation, based on the hyperpolarizability and ionization depletion, are explored and compared. The CO molecule is used as a computational example. While the hyperpolarizability mechanism generates small amounts of orientation at intensities below the ionization threshold, ionization depletion quickly becomes the dominant mechanism as soon as ionizing intensities are reached. Only the ionization mechanism leads to substantial orientation (e.g., on the order of ≳0.1). For intensities typical of laser-induced molecular alignment and orientation experiments, the two mechanisms lead to robust, characteristic timings of the field-free orientation wave-packet revivals relative to the alignment revivals and the revival time. The revival timings can be used to detect the active orientation mechanism experimentally.

Spontaneous magnetic alignment behaviour in free-living lizards

Science.gov (United States)

Diego-Rasilla, Francisco J.; Pérez-Mellado, Valentín; Pérez-Cembranos, Ana

2017-04-01

Several species of vertebrates exhibit spontaneous longitudinal body axis alignment relative to the Earth's magnetic field (i.e., magnetic alignment) while they are performing different behavioural tasks. Since magnetoreception is still not fully understood, studying magnetic alignment provides evidence for magnetoreception and broadens current knowledge of magnetic sense in animals. Furthermore, magnetic alignment widens the roles of magnetic sensitivity in animals and may contribute to shed new light on magnetoreception. In this context, spontaneous alignment in two species of lacertid lizards ( Podarcis muralis and Podarcis lilfordi) during basking periods was monitored. Alignments in 255 P. muralis and 456 P. lilfordi were measured over a 5-year period. The possible influence of the sun's position (i.e., altitude and azimuth) and geomagnetic field values corresponding to the moment in which a particular lizard was observed on lizards' body axis orientation was evaluated. Both species exhibited a highly significant bimodal orientation along the north-northeast and south-southwest magnetic axis. The evidence from this study suggests that free-living lacertid lizards exhibit magnetic alignment behaviour, since their body alignments cannot be explained by an effect of the sun's position. On the contrary, lizard orientations were significantly correlated with geomagnetic field values at the time of each observation. We suggest that this behaviour might provide lizards with a constant directional reference while they are sun basking. This directional reference might improve their mental map of space to accomplish efficient escape behaviour. This study is the first to provide spontaneous magnetic alignment behaviour in free-living reptiles.

Elliptically polarized high-order harmonics from aligned molecules within the strong-field approximation

DEFF Research Database (Denmark)

Etches, Adam; Madsen, Christian Bruun; Madsen, Lars Bojer

A correction term is introduced in the stationary-point analysis on high-order harmonic generation (HHG) from aligned molecules. Arising from a multi-centre expansion of the electron wave function, this term brings our numerical calculations of the Lewenstein model into qualitative agreement...

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...

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.

Molecules in strong laser fields. In depth study of H2 molecule

International Nuclear Information System (INIS)

Awasthi, Manohar

2009-01-01

A method for solving the time-dependent Schroedinger equation (TDSE) describing the electronic motion of the molecules exposed to very short intense laser pulses has been developed. The time-dependent electronic wavefunction is expanded in terms of a superposition of field-free eigenstates. The field-free eigenstates are calculated in two ways. In the first approach, which is applicable to two electron systems like H 2 , fully correlated field-free eigenstates are obtained in complete dimensionality using configuration-interaction calculation where the one-electron basis functions are built from B splines. In the second approach, which is even applicable to larger molecules, the field-free eigenstates are calculated within the single-active-electron (SAE) approximation using density functional theory. In general, the method can be divided into two parts, in the first part the field-free eigenstates are calculated and then in the second part a time propagation for the laser pulse parameters is performed. The H 2 molecule is the testing ground for the implementation of both the methods. The reliability of the configuration interaction (CI) based method for the solution of TDSE (CI-TDSE) is tested by comparing results in the low-intensity regime to the prediction of lowest-order perturbation theory. Another test for the CI-TDSE method is in the united atom limit for the H 2 molecule. By selecting a very small value of the internuclear distance close to zero for the H 2 molecule, Helium atom is obtained. Once the functionality and the reliability of the method is established, it is used for obtaining accurate results for molecular hydrogen exposed to intense laser fields. The results for the standard 800 nm Titanium-Sapphire laser and its harmonics at 400 nm and 266 nm are shown. The results for a scan over a wide range of incident photon energies as well as dependence on the internuclear distance are presented. The photoelectron spectra including above

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)

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.

Molecules in strong laser fields. In depth study of H{sub 2} molecule

Energy Technology Data Exchange (ETDEWEB)

Awasthi, Manohar

2009-10-29

A method for solving the time-dependent Schroedinger equation (TDSE) describing the electronic motion of the molecules exposed to very short intense laser pulses has been developed. The time-dependent electronic wavefunction is expanded in terms of a superposition of field-free eigenstates. The field-free eigenstates are calculated in two ways. In the first approach, which is applicable to two electron systems like H{sub 2}, fully correlated field-free eigenstates are obtained in complete dimensionality using configuration-interaction calculation where the one-electron basis functions are built from B splines. In the second approach, which is even applicable to larger molecules, the field-free eigenstates are calculated within the single-active-electron (SAE) approximation using density functional theory. In general, the method can be divided into two parts, in the first part the field-free eigenstates are calculated and then in the second part a time propagation for the laser pulse parameters is performed. The H{sub 2} molecule is the testing ground for the implementation of both the methods. The reliability of the configuration interaction (CI) based method for the solution of TDSE (CI-TDSE) is tested by comparing results in the low-intensity regime to the prediction of lowest-order perturbation theory. Another test for the CI-TDSE method is in the united atom limit for the H{sub 2} molecule. By selecting a very small value of the internuclear distance close to zero for the H{sub 2} molecule, Helium atom is obtained. Once the functionality and the reliability of the method is established, it is used for obtaining accurate results for molecular hydrogen exposed to intense laser fields. The results for the standard 800 nm Titanium-Sapphire laser and its harmonics at 400 nm and 266 nm are shown. The results for a scan over a wide range of incident photon energies as well as dependence on the internuclear distance are presented. The photoelectron spectra including

Strong-field ionization of linear molecules by a bicircular laser field: Symmetry considerations

Science.gov (United States)

Gazibegović-Busuladžić, A.; Busuladžić, M.; Hasović, E.; Becker, W.; Milošević, D. B.

2018-04-01

Using the improved molecular strong-field approximation, we investigate (high-order) above-threshold ionization [(H)ATI] of various linear polyatomic molecules by a two-color laser field of frequencies r ω and s ω (with integer numbers r and s ) having coplanar counter-rotating circularly polarized components (a so-called bicircular field). Reflection and rotational symmetries for molecules aligned in the laser-field polarization plane, analyzed for diatomic homonuclear molecules in Phys. Rev. A 95, 033411 (2017), 10.1103/PhysRevA.95.033411, are now considered for diatomic heteronuclear molecules and symmetric and asymmetric linear triatomic molecules. There are additional rotational symmetries for (H)ATI spectra of symmetric linear molecules compared to (H)ATI spectra of the asymmetric ones. It is shown that these symmetries manifest themselves differently for r +s odd and r +s even. For example, HATI spectra for symmetric molecules with r +s even obey inversion symmetry. For ATI spectra of linear molecules, reflection symmetry appears only for certain molecular orientation angles ±90∘-j r 180∘/(r +s ) (j integer). For symmetric linear molecules, reflection symmetry appears also for the angles -j r 180∘/(r +s ) . For perpendicular orientation of molecules with respect to the laser-field polarization plane, the HATI spectra are very similar to those of the atomic targets, i.e., both spectra are characterized by the same type of the (r +s )-fold symmetry.

TMRG studies on spin alignment in molecule-based ferrimagnetics [rapid communication

Science.gov (United States)

Liu, Q. M.; Yao, K. L.; Liu, Z. L.

2005-05-01

A physical picture of spin alignment in organic molecule-based ferrimagnets is presented from studying the thermal effective magnetic moment of the sublattice by use of the transfer matrix renormalization group. We conclude that the classical antiparallel spin alignment is not the most stable state. The three-spin system tends to parallel alignment when the exchange interaction between the biradical and the monoradical molecules is much weaker than that within the biradical, which can result in the decrease of the effective magnetic moment upon lowering the temperature. More importantly, we give the theoretical evidence that even the antiparallel spin alignment in the biradical monoradical alternating chain does not necessarily lead to ferrimagnetic spin ordering due to the formation of the spin singlet pairs, which suppresses the ferrimagnetic spin alignment.

Fabrication and Characterization of Aligned Flexible Lead-Free Piezoelectric Nanofibers for Wearable Device Applications

Directory of Open Access Journals (Sweden)

Sang Hyun Ji

2018-03-01

Full Text Available Flexible lead-free piezoelectric nanofibers, based on BNT-ST (0.78Bi0.5Na0.5TiO3-0.22SrTiO3 ceramic and poly(vinylidene fluoride-trifluoroethylene (PVDF-TrFE copolymers, were fabricated by an electrospinning method and the effects of the degree of alignment in the nanofibers on the piezoelectric characteristics were investigated. The microstructure of the lead-free piezoelectric nanofibers was observed by field emission scanning electron microscope (FE-SEM and the orientation was analyzed by fast Fourier transform (FFT images. X-ray diffraction (XRD analysis confirmed that the phase was not changed by the electrospinning process and maintained a perovskite phase. Polarization-electric field (P-E loops and piezoresponse force microscopy (PFM were used to investigate the piezoelectric properties of the piezoelectric nanofibers, according to the degree of alignment—the well aligned piezoelectric nanofibers had higher piezoelectric properties. Furthermore, the output voltage of the aligned lead-free piezoelectric nanofibers was measured according to the vibration frequency and the bending motion and the aligned piezoelectric nanofibers with a collector rotation speed of 1500 rpm performed the best.

Efficient alignment-free DNA barcode analytics.

Science.gov (United States)

Kuksa, Pavel; Pavlovic, Vladimir

2009-11-10

In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). The methods use fixed-length representations (spectrum) for barcode sequences to measure similarities or dissimilarities between sequences coming from the same or different species. The spectrum-based representation not only allows for accurate and computationally efficient species classification, but also opens possibility for accurate clustering analysis of putative species barcodes and identification of critical within-barcode loci distinguishing barcodes of different sample groups. New alignment-free methods provide highly accurate and fast DNA barcode-based identification and classification of species with substantial improvements in accuracy and speed over state-of-the-art barcode analysis methods. We evaluate our methods on problems of species classification and identification using barcodes, important and relevant analytical tasks in many practical applications (adverse species movement monitoring, sampling surveys for unknown or pathogenic species identification, biodiversity assessment, etc.) On several benchmark barcode datasets, including ACG, Astraptes, Hesperiidae, Fish larvae, and Birds of North America, proposed alignment-free methods considerably improve prediction accuracy compared to prior results. We also observe significant running time improvements over the state-of-the-art methods. Our results show that newly developed alignment-free methods for DNA barcoding can efficiently and with high accuracy identify specimens by examining only few barcode features, resulting in increased scalability and interpretability of current computational approaches to barcoding.

Magnetic field-aligned particle precipitation

International Nuclear Information System (INIS)

Carlson, W.

1985-01-01

Magnetic field-aligned particle fluxes are a common auroral phenomenon. Precipitating field-aligned electrons are seen in the vicinity of auroral arcs as suprathermal bursts, as well as superimposed on the more isotropic inverted V electron precipitation. Electron distribution functions reveal two distinct source populations for the inverted V and field-aligned electron components, and also suggest possible acceleration mechanisms. The inverted V electrons are a hot, boundary plasma sheet population that gains the full parallel acceleration. The field-aligned component appears to originate from cold ionospheric electrons that may be distributed throughout the acceleration region. A turbulent parallel field might explain the apparent lifetime of cold electrons in the acceleration region

Aligned deposition and electrical measurements on single DNA molecules

International Nuclear Information System (INIS)

Eidelshtein, Gennady; Kotlyar, Alexander; Hashemi, Mohtadin; Gurevich, Leonid

2015-01-01

A reliable method of deposition of aligned individual dsDNA molecules on mica, silicon, and micro/nanofabricated circuits is presented. Complexes of biotinylated double stranded poly(dG)–poly(dC) DNA with avidin were prepared and deposited on mica and silicon surfaces in the absence of Mg 2+ ions. Due to its positive charge, the avidin attached to one end of the DNA anchors the complex to negatively charged substrates. Subsequent drying with a directional gas flow yields DNA molecules perfectly aligned on the surface. In the avidin–DNA complex only the avidin moiety is strongly and irreversibly bound to the surface, while the DNA counterpart interacts with the substrates much more weakly and can be lifted from the surface and realigned in any direction. Using this technique, avidin–DNA complexes were deposited across platinum electrodes on a silicon substrate. Electrical measurements on the deposited DNA molecules revealed linear IV-characteristics and exponential dependence on relative humidity. (paper)

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.

Photoelectron diffraction from single oriented molecules: Towards ultrafast structure determination of molecules using x-ray free-electron lasers

Science.gov (United States)

Kazama, Misato; Fujikawa, Takashi; Kishimoto, Naoki; Mizuno, Tomoya; Adachi, Jun-ichi; Yagishita, Akira

2013-06-01

We provide a molecular structure determination method, based on multiple-scattering x-ray photoelectron diffraction (XPD) calculations. This method is applied to our XPD data on several molecules having different equilibrium geometries. Then it is confirmed that, by our method, bond lengths and bond angles can be determined with a resolution of less than 0.1 Å and 10∘, respectively. Differently from any other scenario of ultrafast structure determination, we measure the two- or three-dimensional XPD of aligned or oriented molecules in the energy range from 100 to 200 eV with a 4π detection velocity map imaging spectrometer. Thanks to the intense and ultrashort pulse properties of x-ray free-electron lasers, our approach exhibits the most probable method for obtaining ultrafast real-time structural information on small to medium-sized molecules consisting of light elements, i.e., a “molecular movie.”

Hyperfine-Structure-Induced Depolarization of Impulsively Aligned I2 Molecules

Science.gov (United States)

Thomas, Esben F.; Søndergaard, Anders A.; Shepperson, Benjamin; Henriksen, Niels E.; Stapelfeldt, Henrik

2018-04-01

A moderately intense 450 fs laser pulse is used to create rotational wave packets in gas phase I2 molecules. The ensuing time-dependent alignment, measured by Coulomb explosion imaging with a delayed probe pulse, exhibits the characteristic revival structures expected for rotational wave packets but also a complex nonperiodic substructure and decreasing mean alignment not observed before. A quantum mechanical model attributes the phenomena to coupling between the rotational angular momenta and the nuclear spins through the electric quadrupole interaction. The calculated alignment trace agrees very well with the experimental results.

Alignment of symmetric top molecules by short laser pulses

DEFF Research Database (Denmark)

Hamilton, Edward; Seideman, Tamar; Ejdrup, Tine

2005-01-01

-resolved photofragment imaging. Using methyliodide and tert-butyliodide as examples, we calculate and measure the alignment dynamics, focusing on the temporal structure and intensity of the revival patterns, including their dependence on the pulse duration, and their behavior at long times, where centrifugal distortion......Nonadiabatic alignment of symmetric top molecules induced by a linearly polarized, moderately intense picosecond laser pulse is studied theoretically and experimentally. Our studies are based on the combination of a nonperturbative solution of the Schrodinger equation with femtosecond time...

Free and binary rotation of polyatomic molecules

International Nuclear Information System (INIS)

Konyukhov, V K

2003-01-01

A modification of the quantum-mechanical theory of rotation of polyatomic molecules (binary rotation) is proposed, which is based on the algebra and representations of the SO(4) group and allows the introduction of the concept of parity, as in atomic spectroscopy. It is shown that, if an asymmetric top molecule performing binary rotation finds itself in a spatially inhomogeneous electric field, its rotational levels acquire the additional energy due to the quadrupole moment. The existence of the rotational states of polyatomic molecules that cannot transfer to the free rotation state is predicted. In particular, the spin isomers of a water molecule, which corresponds to such states, can have different absolute values of the adsorption energy due to the quadrupole interaction of the molecule with a surface. The difference in the adsorption energies allows one to explain qualitatively the behaviour of the ortho- and para-molecules of water upon their adsorption on the surface of solids in accordance with experimental data. (laser applications and other topics in quantum electronics)

Importance of the alignment of polar π conjugated molecules inside carbon nanotubes in determining second-order non-linear optical properties.

Science.gov (United States)

Yumura, Takashi; Yamamoto, Wataru

2017-09-20

We employed density functional theory (DFT) calculations with dispersion corrections to investigate energetically preferred alignments of certain p,p'-dimethylaminonitrostilbene (DANS) molecules inside an armchair (m,m) carbon nanotube (n × DANS@(m,m)), where the number of inner molecules (n) is no greater than 3. Here, three types of alignments of DANS are considered: a linear alignment in a parallel fashion and stacking alignments in parallel and antiparallel fashions. According to DFT calculations, a threshold tube diameter for containing DANS molecules in linear or stacking alignments was found to be approximately 1.0 nm. Nanotubes with diameters smaller than 1.0 nm result in the selective formation of linearly aligned DANS molecules due to strong confinement effects within the nanotubes. By contrast, larger diameter nanotubes allow DANS molecules to align in a stacking and linear fashion. The type of alignment adopted by the DANS molecules inside a nanotube is responsible for their second-order non-linear optical properties represented by their static hyperpolarizability (β 0 values). In fact, we computed β 0 values of DANS assemblies taken from optimized n × DANS@(m,m) structures, and their values were compared with those of a single DANS molecule. DFT calculations showed that β 0 values of DANS molecules depend on their alignment, which decrease in the following order: linear alignment > parallel stacking alignment > antiparallel stacking alignment. In particular, a linear alignment has a β 0 value more significant than that of the same number of isolated molecules. Therefore, the linear alignment of DANS molecules, which is only allowed inside smaller diameter nanotubes, can strongly enhance their second-order non-linear optical properties. Since the nanotube confinement determines the alignment of DANS molecules, a restricted nanospace can be utilized to control their second-order non-linear optical properties. These DFT findings can assist in the

Theoretical analysis of bimetallic nanorod dimer biosensors for label-free molecule detection

Science.gov (United States)

Das, Avijit; Talukder, Muhammad Anisuzzaman

2018-02-01

In this work, we theoretically analyze a gold (Au) core within silver (Ag) shell (Au@Ag) nanorod dimer biosensor for label-free molecule detection. The incident light on an Au@Ag nanorod strongly couples to localized surface plasmon modes, especially around the tip region. The field enhancement around the tip of a nanorod or between the tips of two longitudinally aligned nanorods as in a dimer can be exploited for sensitive detection of biomolecules. We derive analytical expressions for the interactions of an Au@Ag nanorod dimer with the incident light. We also study the detail dynamics of an Au@Ag nanorod dimer with the incident light computationally using finite difference time domain (FDTD) technique when core-shell ratio, relative position of the nanorods, and angle of incidence of light change. We find that the results obtained using the developed analytical model match well with that obtained using FDTD simulations. Additionally, we investigate the sensitivity of the Au@Ag nanorod dimer, i.e., shift in the resonance wavelength, when a target biomolecule such as lysozyme (Lys), human serum albumin (HSA), anti-biotin (Abn), human catalase (CAT), and human fibrinogen (Fb) protein molecules are attached to the tips of the nanorods.

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).

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.

Controlling the branching ratio of photodissociation using aligned molecules

DEFF Research Database (Denmark)

Larsen, J.J.; Wendt-Larsen, I.; Stapelfeldt, H.

1999-01-01

Using a sample of iodine molecules, aligned by a strong, linearly polarized laser pulse, we control the branching ratio of the I+I and I+I* photodissociation channels by a factor of 26. The control relies on selective photoexcitation of two potential curves that each correlate adiabatically...

Tracing magnetic fields with aligned grains

International Nuclear Information System (INIS)

Lazarian, A.

2007-01-01

Magnetic fields play a crucial role in various astrophysical processes, including star formation, accretion of matter, transport processes (e.g., transport of heat), and cosmic rays. One of the easiest ways to determine the magnetic field direction is via polarization of radiation resulting from extinction or/and emission by aligned dust grains. Reliability of interpretation of the polarization maps in terms of magnetic fields depends on how well we understand the grain-alignment theory. Explaining what makes grains aligned has been one of the big issues of the modern astronomy. Numerous exciting physical effects have been discovered in the course of research undertaken in this field. As both the theory and observations matured, it became clear that the grain-alignment phenomenon is inherent not only in diffuse interstellar medium or molecular clouds but also is a generic property of the dust in circumstellar regions, interplanetary space and cometary comae. Currently the grain-alignment theory is a predictive one, and its results nicely match observations. Among its predictions is a subtle phenomenon of radiative torques. This phenomenon, after having stayed in oblivion for many years after its discovery, is currently viewed as the most powerful means of alignment. In this article, I shall review the basic physical processes involved in grain alignment, and the currently known mechanisms of alignment. I shall also discuss possible niches for different alignment mechanisms. I shall dwell on the importance of the concept of grain helicity for understanding of many properties of grain alignment, and shall demonstrate that rather arbitrarily shaped grains exhibit helicity when they interact with gaseous and radiative flows

Structures of water molecules in carbon nanotubes under electric fields

International Nuclear Information System (INIS)

Winarto,; Takaiwa, Daisuke; Yamamoto, Eiji; Yasuoka, Kenji

2015-01-01

Carbon nanotubes (CNTs) are promising for water transport through membranes and for use as nano-pumps. The development of CNT-based nanofluidic devices, however, requires a better understanding of the properties of water molecules in CNTs because they can be very different from those in the bulk. Using all-atom molecular dynamics simulations, we investigate the effect of axial electric fields on the structure of water molecules in CNTs having diameters ranging from (7,7) to (10,10). The water dipole moments were aligned parallel to the electric field, which increases the density of water inside the CNTs and forms ordered ice-like structures. The electric field induces the transition from liquid to ice nanotubes in a wide range of CNT diameters. Moreover, we found an increase in the lifetime of hydrogen bonds for water structures in the CNTs. Fast librational motion breaks some hydrogen bonds, but the molecular pairs do not separate and the hydrogen bonds reform. Thus, hydrogen bonds maintain the water structure in the CNTs, and the water molecules move collectively, decreasing the axial diffusion coefficient and permeation rate

Magnetic field modification of ultracold molecule-molecule collisions

International Nuclear Information System (INIS)

Tscherbul, T V; Suleimanov, Yu V; Aquilanti, V; Krems, R V

2009-01-01

We present an accurate quantum mechanical study of molecule-molecule collisions in the presence of a magnetic field. The work focuses on the analysis of elastic scattering and spin relaxation in collisions of O 2 ( 3 Σ g - ) molecules at cold (∼0.1 K) and ultracold (∼10 -6 K) temperatures. Our calculations show that magnetic spin relaxation in molecule-molecule collisions is extremely efficient except at magnetic fields below 1 mT. The rate constant for spin relaxation at T=0.1 K and a magnetic field of 0.1 T is found to be as large as 6.1x10 -11 cm -3 s -1 . The magnetic field dependence of elastic and inelastic scattering cross sections at ultracold temperatures is dominated by a manifold of Feshbach resonances with the density of ∼100 resonances per Tesla for collisions of molecules in the absolute ground state. This suggests that the scattering length of ultracold molecules in the absolute ground state can be effectively tuned in a very wide range of magnetic fields. Our calculations demonstrate that the number and properties of the magnetic Feshbach resonances are dramatically different for molecules in the absolute ground and excited spin states. The density of Feshbach resonances for molecule-molecule scattering in the low-field-seeking Zeeman state is reduced by a factor of 10.

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.)

Photoelectron angular distributions from strong-field ionization of oriented molecules

DEFF Research Database (Denmark)

Holmegaard, Lotte; Hansen, Jonas Lerche; Kalhøj, Line

2010-01-01

The combination of ultrafast light sources with detection of molecular-frame photoelectron angular distributions (MFPADs) is setting new standards for detailed interrogation of molecular dynamics. However, until recently measurement of MFPADs relied on determining the molecular orientation after...... ionization, which is limited to species and processes where ionization leads to fragmentation. An alternative is to fix the molecular frame before ionization. The only demonstrations of such spatial orientation involved aligned small linear nonpolar molecules. Here we extend these techniques to the general...... class of polar molecules. Carbonylsulphide and benzonitrile molecules, fixed in space by combined laser and electrostatic fields, are ionized with intense, circularly polarized 30-fs laser pulses. For carbonylsulphide and benzonitrile oriented in one dimension, the MFPADs exhibit pronounced anisotropies...

Nanofabricated racks of aligned and anchored DNA substrates for single-molecule imaging.

Science.gov (United States)

Gorman, Jason; Fazio, Teresa; Wang, Feng; Wind, Shalom; Greene, Eric C

2010-01-19

Single-molecule studies of biological macromolecules can benefit from new experimental platforms that facilitate experimental design and data acquisition. Here we develop new strategies to construct curtains of DNA in which the molecules are aligned with respect to one another and maintained in an extended configuration by anchoring both ends of the DNA to the surface of a microfluidic sample chamber that is otherwise coated with an inert lipid bilayer. This "double-tethered" DNA substrate configuration is established through the use of nanofabricated rack patterns comprised of two distinct functional elements: linear barriers to lipid diffusion that align DNA molecules anchored by one end to the bilayer and antibody-coated pentagons that provide immobile anchor points for the opposite ends of the DNA. These devices enable the alignment and anchoring of thousands of individual DNA molecules, which can then be visualized using total internal reflection fluorescence microscopy under conditions that do not require continuous application of buffer flow to stretch the DNA. This unique strategy offers the potential for studying protein-DNA interactions on large DNA substrates without compromising measurements through application of hydrodynamic force. We provide a proof-of-principle demonstration that double-tethered DNA curtains made with nanofabricated rack patterns can be used in a one-dimensional diffusion assay that monitors the motion of quantum dot-tagged proteins along DNA.

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

Three dimensional extrusion printing induces polymer molecule alignment and cell organization within engineered cartilage.

Science.gov (United States)

Guo, Ting; Ringel, Julia P; Lim, Casey G; Bracaglia, Laura G; Noshin, Maeesha; Baker, Hannah B; Powell, Douglas A; Fisher, John P

2018-04-16

Proper cell-material interactions are critical to remain cell function and thus successful tissue regeneration. Many fabrication processes have been developed to create microenvironments to control cell attachment and organization on a three-dimensional (3D) scaffold. However, these approaches often involve heavy engineering and only the surface layer can be patterned. We found that 3D extrusion based printing at high temperature and pressure will result an aligned effect on the polymer molecules, and this molecular arrangement will further induce the cell alignment and different differentiation capacities. In particular, articular cartilage tissue is known to have zonal collagen fiber and cell orientation to support different functions, where collagen fibers and chondrocytes align parallel, randomly, and perpendicular, respectively, to the surface of the joint. Therefore, cell alignment was evaluated in a cartilage model in this study. We used small angle X-ray scattering analysis to substantiate the polymer molecule alignment phenomenon. The cellular response was evaluated both in vitro and in vivo. Seeded mesenchymal stem cells (MSCs) showed different morphology and orientation on scaffolds, as a combined result of polymer molecule alignment and printed scaffold patterns. Gene expression results showed improved superficial zonal chondrogenic marker expression in parallel-aligned group. The cell alignment was successfully maintained in the animal model after 7 days with distinct MSC morphology between the casted and parallel printed scaffolds. This 3D printing induced polymer and cell alignment will have a significant impact on developing scaffold with controlled cell-material interactions for complex tissue engineering while avoiding complicated surface treatment, and therefore provides new concept for effective tissue repairing in future clinical applications. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2018. © 2018 Wiley Periodicals, Inc.

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.)

Effect of the R dependence of laser-induced polarizability on molecular dynamic alignment in an intense femtosecond laser field

International Nuclear Information System (INIS)

Chen Jianxin; Cui Xiaomei; Huang Bomin; Wu Hongchun; Zhuo Shuangmu

2006-01-01

In the rotation equation of the angle θ between the molecular axis and the laser polarization direction, the dependence of laser-induced polarizability on the molecular internuclear distance R is considered. The effect of the R dependence of laser-induced polarizability on molecular dynamic alignment in an intense femtosecond laser field is investigated with 20 and 100 fs laser pulses for N 2 molecules and with 60 and 100 fs laser pulses for Br 2 molecules at intensities of 5x10 14 W cm -2 and 5x10 15 W cm -2 . This effect exists and only occurs during the dissociative process after the molecule is ionized. It enhances the degrees of molecular dynamic alignment and is more significant in reorienting the angular distributions of molecules towards the laser polarization direction in the conditions of high laser intensity and short pulse length. Compared with the N 2 molecule, the effect of the R dependence of laser-induced polarizability on molecular dynamic alignment for Br 2 is stronger. The reasons are presented and discussed

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.

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

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.

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.

Self-consistent field theory of polymer-ionic molecule complexation.

Science.gov (United States)

Nakamura, Issei; Shi, An-Chang

2010-05-21

A self-consistent field theory is developed for polymers that are capable of binding small ionic molecules (adsorbates). The polymer-ionic molecule association is described by Ising-like binding variables, C(i) ((a))(kDelta)(=0 or 1), whose average determines the number of adsorbed molecules, n(BI). Polymer gelation can occur through polymer-ionic molecule complexation in our model. For polymer-polymer cross-links through the ionic molecules, three types of solutions for n(BI) are obtained, depending on the equilibrium constant of single-ion binding. Spinodal lines calculated from the mean-field free energy exhibit closed-loop regions where the homogeneous phase becomes unstable. This phase instability is driven by the excluded-volume interaction due to the single occupancy of ion-binding sites on the polymers. Moreover, sol-gel transitions are examined using a critical degree of conversion. A gel phase is induced when the concentration of adsorbates is increased. At a higher concentration of the adsorbates, however, a re-entrance from a gel phase into a sol phase arises from the correlation between unoccupied and occupied ion-binding sites. The theory is applied to a model system, poly(vinyl alcohol) and borate ion in aqueous solution with sodium chloride. Good agreement between theory and experiment is obtained.

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

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.

A practical strategy for the accurate measurement of residual dipolar couplings in strongly aligned small molecules

Science.gov (United States)

Liu, Yizhou; Cohen, Ryan D.; Martin, Gary E.; Williamson, R. Thomas

2018-06-01

Accurate measurement of residual dipolar couplings (RDCs) requires an appropriate degree of alignment in order to optimize data quality. An overly weak alignment yields very small anisotropic data that are susceptible to measurement errors, whereas an overly strong alignment introduces extensive anisotropic effects that severely degrade spectral quality. The ideal alignment amplitude also depends on the specific pulse sequence used for the coupling measurement. In this work, we introduce a practical strategy for the accurate measurement of one-bond 13C-1H RDCs up to a range of ca. -300 to +300 Hz, corresponding to an alignment that is an order of magnitude stronger than typically employed for small molecule structural elucidation. This strong alignment was generated in the mesophase of the commercially available poly-γ-(benzyl-L-glutamate) polymer. The total coupling was measured by the simple and well-studied heteronuclear two-dimensional J-resolved experiment, which performs well in the presence of strong anisotropic effects. In order to unequivocally determine the sign of the total coupling and resolve ambiguities in assigning total couplings in the CH2 group, coupling measurements were conducted at an isotropic condition plus two anisotropic conditions of different alignment amplitudes. Most RDCs could be readily extracted from these measurements whereas more complicated spectral effects resulting from strong homonuclear coupling could be interpreted either theoretically or by simulation. Importantly, measurement of these very large RDCs actually offers significantly improved data quality and utility for the structure determination of small organic molecules.

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

Fermi level alignment in molecular nanojunctions and its relation to charge transfer

DEFF Research Database (Denmark)

Stadler, Robert; Jacobsen, Karsten Wedel

2006-01-01

The alignment of the Fermi level of a metal electrode within the gap of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of a molecule is a key quantity in molecular electronics, which can vary the electron transparency of a single-molecule junction...... by orders of magnitude. We present a quantitative analysis of the relation between this level alignment (which can be estimated from charging free molecules) and charge transfer for bipyridine and biphenyl dithiolate (BPDT) molecules attached to gold leads based on density functional theory calculations...... end of the gap in the transmission function for bipyridine and at its lower end for BPDT....

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

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.

Molecular alignment effect on the photoassociation process via a pump-dump scheme

Science.gov (United States)

Wang, Bin-Bin; Han, Yong-Chang; Cong, Shu-Lin

2015-09-01

The photoassociation processes via the pump-dump scheme for the heternuclear (Na + H → NaH) and the homonuclear (Na + Na → Na2) molecular systems are studied, respectively, using the time-dependent quantum wavepacket method. For both systems, the initial atom pair in the continuum of the ground electronic state (X1Σ+) is associated into the molecule in the bound states of the excited state (A1Σ+) by the pump pulse. Then driven by a time-delayed dumping pulse, the prepared excited-state molecule can be transferred to the bound states of the ground electronic state. It is found that the pump process can induce a superposition of the rovibrational levels |v, j> on the excited state, which can lead to the field-free alignment of the excited-state molecule. The molecular alignment can affect the dumping process by varying the effective coupling intensity between the two electronic states or by varying the population transfer pathways. As a result, the final population transferred to the bound states of the ground electronic state varies periodically with the delay time of the dumping pulse.

Distilling two-center-interference information during tunneling of aligned molecules with orthogonally polarized two-color laser fields

Science.gov (United States)

Gao, F.; Chen, Y. J.; Xin, G. G.; Liu, J.; Fu, L. B.

2017-12-01

When electrons tunnel through a barrier formed by the strong laser field and the two-center potential of a diatomic molecule, a double-slit-like interference can occur. However, this interference effect can not be probed directly right now, as it is strongly coupled with other dynamical processes during tunneling. Here, we show numerically and analytically that orthogonally polarized two-color (OTC) laser fields are capable of resolving the interference effect in tunneling, while leaving clear footprints of this effect in photoelectron momentum distributions. Moreover, this effect can be manipulated by changing the relative field strength of OTC fields.

The importance of Rydberg orbitals in dissociative ionization of small hydrocarbon molecules in intense laser fields.

Science.gov (United States)

Jochim, Bethany; Siemering, R; Zohrabi, M; Voznyuk, O; Mahowald, J B; Schmitz, D G; Betsch, K J; Berry, Ben; Severt, T; Kling, Nora G; Burwitz, T G; Carnes, K D; Kling, M F; Ben-Itzhak, I; Wells, E; de Vivie-Riedle, R

2017-06-30

Much of our intuition about strong-field processes is built upon studies of diatomic molecules, which typically have electronic states that are relatively well separated in energy. In polyatomic molecules, however, the electronic states are closer together, leading to more complex interactions. A combined experimental and theoretical investigation of strong-field ionization followed by hydrogen elimination in the hydrocarbon series C 2 D 2 , C 2 D 4 and C 2 D 6 reveals that the photofragment angular distributions can only be understood when the field-dressed orbitals rather than the field-free orbitals are considered. Our measured angular distributions and intensity dependence show that these field-dressed orbitals can have strong Rydberg character for certain orientations of the molecule relative to the laser polarization and that they may contribute significantly to the hydrogen elimination dissociative ionization yield. These findings suggest that Rydberg contributions to field-dressed orbitals should be routinely considered when studying polyatomic molecules in intense laser fields.

Improved production of Br atoms near zero speed by photodissociating laser aligned Br2 molecules.

Science.gov (United States)

Deng, L Z; Yin, J P

2014-10-28

We theoretically investigated the improvement on the production rate of the decelerated bromine (Br) atoms near zero speed by photodissociating laser aligned Br2 precursors. Adiabatic alignment of Br2 precursors exposed to long laser pulses with duration on the order of nanoseconds was investigated by solving the time-dependent Schrödinger equation. The dynamical fragmentation of adiabatically aligned Br2 precursors was simulated and velocity distribution of the Br atoms produced was analyzed. Our study shows that the larger the degree of the precursor alignment, ⟨cos(2) θ⟩, the higher the production rate of the decelerated Br atoms near zero speed. For Br2 molecules with an initial rotational temperature of ~1 K, a ⟨cos(2) θ⟩ value of ~0.88 can result in an improvement factor of over ~20 on the production rate of the decelerated Br atoms near zero speed, requiring a laser intensity of only ~1 × 10(12) W/cm(2) for alignment.

Insertion of liquid crystal molecules into hydrocarbon monolayers

Energy Technology Data Exchange (ETDEWEB)

Popov, Piotr, E-mail: ppopov@kent.edu; Mann, Elizabeth K. [Department of Physics, Kent State University, Kent, Ohio 44242 (United States); Lacks, Daniel J. [Department of Chemical Engineering, Case Western Reserve University, Cleveland, Ohio 44106 (United States); Jákli, Antal [Liquid Crystal Institute, Kent State University, Kent, Ohio 44242-0001 (United States)

2014-08-07

Atomistic molecular dynamics simulations were carried out to investigate the molecular mechanisms of vertical surface alignment of liquid crystals. We study the insertion of nCB (4-Cyano-4{sup ′}-n-biphenyl) molecules with n = 0,…,6 into a bent-core liquid crystal monolayer that was recently found to provide good vertical alignment for liquid crystals. The results suggest a complex-free energy landscape for the liquid crystal within the layer. The preferred insertion direction of the nCB molecules (core or tail first) varies with n, which can be explained by entropic considerations. The role of the dipole moments was found to be negligible. As vertical alignment is the leading form of present day liquid crystal displays (LCD), these results will help guide improvement of the LCD technology, as well as lend insight into the more general problem of insertion of biological and other molecules into lipid and surfactant layers.

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

Simulation of a small molecule analogue of a lithium ionomer in an external electric field

Energy Technology Data Exchange (ETDEWEB)

Waters, Sara M.; McCoy, John D., E-mail: mccoy@nmt.edu; Brown, Jonathan R. [Department of Materials Engineering, New Mexico Institute of Mining and Technology, Socorro, New Mexico 87801 (United States); Frischknecht, Amalie L. [Sandia National Laboratories, Albuquerque, New Mexico 87185 (United States)

2014-01-07

We have investigated the ion dynamics in lithium-neutralized 2-pentylheptanoic acid, a small molecule analogue of a precise poly(ethylene-co-acrylic acid) lithium ionomer. Atomistic molecular dynamics simulations were performed in an external electric field. The electric field causes alignment of the ionic aggregates along the field direction. The energetic response of the system to an imposed oscillating electric field for a wide range of frequencies was tracked by monitoring the coulombic contribution to the energy. The susceptibility found in this manner is a component of the dielectric susceptibility typically measured experimentally. A dynamic transition is found and the frequency associated with this transition varies with temperature in an Arrhenius manner. The transition is observed to be associated with rearrangements of the ionic aggregates.

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)

Rapid parameterization of small molecules using the Force Field Toolkit.

Science.gov (United States)

Mayne, Christopher G; Saam, Jan; Schulten, Klaus; Tajkhorshid, Emad; Gumbart, James C

2013-12-15

The inability to rapidly generate accurate and robust parameters for novel chemical matter continues to severely limit the application of molecular dynamics simulations to many biological systems of interest, especially in fields such as drug discovery. Although the release of generalized versions of common classical force fields, for example, General Amber Force Field and CHARMM General Force Field, have posited guidelines for parameterization of small molecules, many technical challenges remain that have hampered their wide-scale extension. The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error-prone tasks, and graphical user interface design. Distributed as a VMD plugin, ffTK facilitates the traversal of a clear and organized workflow resulting in a complete set of CHARMM-compatible parameters. A variety of tools are provided to generate quantum mechanical target data, setup multidimensional optimization routines, and analyze parameter performance. Parameters developed for a small test set of molecules using ffTK were comparable to existing CGenFF parameters in their ability to reproduce experimentally measured values for pure-solvent properties (<15% error from experiment) and free energy of solvation (±0.5 kcal/mol from experiment). Copyright © 2013 Wiley Periodicals, Inc.

Single-active-electron potentials for molecules in intense laser fields

DEFF Research Database (Denmark)

Abu-Samha, Mahmoud; Madsen, Lars Bojer

2010-01-01

Single-active-electron potentials are computed for selected molecules, and molecular wave functions with the correct asymptotic behavior are produced. Asymptotic expansion coefficients are extracted from the wave functions and used to compute alignment-dependent ionization yields from molecular...

Quick synthesis of highly aligned or randomly oriented nanofibrous structures composed of C60 molecules via self-assembly

International Nuclear Information System (INIS)

Kurosu, Shunji; Fukuda, Takahiro; Maekawa, Toru

2013-01-01

Assemblies, which are composed of nanoparticles such as nanofibres, have been intensively studied in recent years. This has particularly been the case in the field of biomedicine, where the aim is to develop efficient methodologies for capturing and separating target biomolecules and cells and/or encouraging bio-chemical reactions, utilizing the extremely high surface area to volume ratio of assemblies. There is an urgent need for the development of a quick synthesis method of forming nanofibrous structures on the surface of biomedical microchips and devices for the investigation of the interactions between biomolecules/cells and the nanostructures. Here, we produce nanofibrous structures composed of C 60 molecules, which are aligned in one direction or randomly oriented, by dissolving C 60 molecules and sulphur in benzene and evaporating a droplet of the solution on a glass substrate under appropriate conditions. The synthesis time is as short as 30 s. Sulphur is extracted and nanofibres are crystallized by leaving them in supercritical carbon dioxide. (paper)

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, 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.

Free energy profiles from single-molecule pulling experiments.

Science.gov (United States)

Hummer, Gerhard; Szabo, Attila

2010-12-14

Nonequilibrium pulling experiments provide detailed information about the thermodynamic and kinetic properties of molecules. We show that unperturbed free energy profiles as a function of molecular extension can be obtained rigorously from such experiments without using work-weighted position histograms. An inverse Weierstrass transform is used to relate the system free energy obtained from the Jarzynski equality directly to the underlying molecular free energy surface. An accurate approximation for the free energy surface is obtained by using the method of steepest descent to evaluate the inverse transform. The formalism is applied to simulated data obtained from a kinetic model of RNA folding, in which the dynamics consists of jumping between linker-dominated folded and unfolded free energy surfaces.

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

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.

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.

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

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

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

Ellipticity and the offset angle of high harmonics generated by homonuclear diatomic molecules

International Nuclear Information System (INIS)

Odzak, S; Milosevic, D B

2011-01-01

In our recent paper (2010 Phys. Rev. A 82 023412) we introduced a theory of high-order harmonic generation by diatomic molecules exposed to an elliptically polarized laser field and have shown that the nth harmonic emission rate has contributions of the components of the T-matrix element in the direction of the laser-field polarization and in the direction perpendicular to it. Using both components of the T-matrix element we now develop a theoretical approach for calculating ellipticity and the offset angle of high harmonics. We show that the emitted harmonics generated by aligned molecules are elliptically polarized even if the applied field is linearly polarized. Using examples of N 2 , O 2 and Ar 2 molecules we show the existence of extrema and sudden changes of the harmonic ellipticity and the offset angle for particular molecular alignment and explain them by the destructive two-centre interference. Taking into account that the aligned molecules are an anisotropic medium for high harmonic generation, we introduce elliptic dichroism as a measure of this anisotropy, for both components of the T-matrix element. We propose that the measurement of the elliptic dichroism may reveal further information about the molecular structure.

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

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

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

Angular momentum alignment in molecular beam scattering

International Nuclear Information System (INIS)

Treffers, M.A.

1985-01-01

It is shown how the angular momentum alignment in a molecular beam can be determined using laser-induced fluorescence in combination with precession of the angular momenta in a magnetic field. After a general analysis of the method, some results are presented to illustrate the possibilities of the method. Experimental data are presented on the alignment production for Na 2 molecules that made a collision induced angular momentum transition. Magnitude as well as direction of the alignment have been determined for scattering with several scattering partners and for a large number of scattering angles and transitions. The last chapter deals with the total alignment production in a final J-state, i.e. without state selection of the initial rotational state. (orig.)

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.

Free molecule flow analysis of the interaction of skimming hardware components and background gas with free jets

International Nuclear Information System (INIS)

Raghuraman, P.; Bossel, U.

1974-01-01

Under conditions typical for the extraction of nozzle beams from free jets the rarefied flow pattern in the expansion chamber containing skimming hardware components and background gas is studied using a free molecule solution to the Boltzmann equation

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)

Alignment of paired molecules of C60 within a hexagonal platform networked through hydrogen-bonds.

Science.gov (United States)

Hisaki, Ichiro; Nakagawa, Shoichi; Sato, Hiroyasu; Tohnai, Norimitsu

2016-07-28

We demonstrate, for the first time, that a hydrogen-bonded low-density organic framework can be applied as a platform to achieve periodic alignment of paired molecules of C60, which is the smallest example of a finite-numbered cluster of C60. The framework is a layered assembly of a hydrogen-bonded 2D hexagonal network (LA-H-HexNet) composed of dodecadehydrotribenzo[18]annulene derivatives.

High-Mobility Aligned Pentacene Films Grown by Zone-Casting

DEFF Research Database (Denmark)

Duffy, Claudia M.; Andreasen, Jens Wenzel; Breiby, Dag W.

2008-01-01

We investigate the growth and field-effect transistor performance of aligned pentacene thin films deposited by zone-casting from a solution of unsubstituted pentacene molecules in a chlorinated solvent. Polarized optical microscopy shows that solution processed pentacene films grow as large...

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)

Constrained-DFT method for accurate energy-level alignment of metal/molecule interfaces

KAUST Repository

Souza, A. M.

2013-10-07

We present a computational scheme for extracting the energy-level alignment of a metal/molecule interface, based on constrained density functional theory and local exchange and correlation functionals. The method, applied here to benzene on Li(100), allows us to evaluate charge-transfer energies, as well as the spatial distribution of the image charge induced on the metal surface. We systematically study the energies for charge transfer from the molecule to the substrate as function of the molecule-substrate distance, and investigate the effects arising from image-charge confinement and local charge neutrality violation. For benzene on Li(100) we find that the image-charge plane is located at about 1.8 Å above the Li surface, and that our calculated charge-transfer energies compare perfectly with those obtained with a classical electrostatic model having the image plane located at the same position. The methodology outlined here can be applied to study any metal/organic interface in the weak coupling limit at the computational cost of a total energy calculation. Most importantly, as the scheme is based on total energies and not on correcting the Kohn-Sham quasiparticle spectrum, accurate results can be obtained with local/semilocal exchange and correlation functionals. This enables a systematic approach to convergence.

Constrained-DFT method for accurate energy-level alignment of metal/molecule interfaces

KAUST Repository

Souza, A. M.; Rungger, I.; Pemmaraju, C. D.; Schwingenschlö gl, Udo; Sanvito, S.

2013-01-01

We present a computational scheme for extracting the energy-level alignment of a metal/molecule interface, based on constrained density functional theory and local exchange and correlation functionals. The method, applied here to benzene on Li(100), allows us to evaluate charge-transfer energies, as well as the spatial distribution of the image charge induced on the metal surface. We systematically study the energies for charge transfer from the molecule to the substrate as function of the molecule-substrate distance, and investigate the effects arising from image-charge confinement and local charge neutrality violation. For benzene on Li(100) we find that the image-charge plane is located at about 1.8 Å above the Li surface, and that our calculated charge-transfer energies compare perfectly with those obtained with a classical electrostatic model having the image plane located at the same position. The methodology outlined here can be applied to study any metal/organic interface in the weak coupling limit at the computational cost of a total energy calculation. Most importantly, as the scheme is based on total energies and not on correcting the Kohn-Sham quasiparticle spectrum, accurate results can be obtained with local/semilocal exchange and correlation functionals. This enables a systematic approach to convergence.

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).

Toward atomic resolution diffractive imaging of isolated molecules with x-ray free-electron lasers

DEFF Research Database (Denmark)

Stern, Stephan; Holmegaard, Lotte; Filsinger, Frank

2014-01-01

We give a detailed account of the theoretical analysis and the experimental results of an x-ray-diffraction experiment on quantum-state selected and strongly laser-aligned gas-phase ensembles of the prototypical large asymmetric rotor molecule 2,5-diiodobenzonitrile, performed at the Linac Cohere...

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

Effect of oscillation mode on the free-molecule squeeze-film air damping

KAUST Repository

Gang Hong,

2010-01-01

A 3D Monte Carlo (MC) simulation approach is developed and employed to study the effect of the oscillation mode on the squeeze-film air damping in the free-molecule regime. By tracking individual gas molecule\\'s motion and its interaction with the resonator, the MC approach is by far the most accurate modeling approach for the modeling of squeeze-film damping in the free-molecule regime. The accuracy of this approach is demonstrated on several cases in which either analytical solutions or experimental measurements are available. It has been found that unlike the case when resonators oscillate in an unbounded domain, squeeze film damping is very sensitive to the mode shape, which implies that some of the existing modeling approaches based on rigid-resonator assumption may not be accurate when applied to model resonators oscillating at their deformed shape. ©2010 IEEE.

Effect of oscillation mode on the free-molecule squeeze-film air damping

KAUST Repository

Gang Hong,; Wenjing Ye,

2010-01-01

A 3D Monte Carlo (MC) simulation approach is developed and employed to study the effect of the oscillation mode on the squeeze-film air damping in the free-molecule regime. By tracking individual gas molecule's motion and its interaction

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.

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.

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.

Polarization and ellipticity of high-order harmonics from aligned molecules generated by linearly polarized intense laser pulses

International Nuclear Information System (INIS)

Le, Anh-Thu; Lin, C. D.; Lucchese, R. R.

2010-01-01

We present theoretical calculations for polarization and ellipticity of high-order harmonics from aligned N 2 , CO 2 , and O 2 molecules generated by linearly polarized lasers. Within the rescattering model, the two polarization amplitudes of the harmonics are determined by the photo-recombination amplitudes for photons emitted with polarization parallel or perpendicular to the direction of the same returning electron wave packet. Our results show clear species-dependent polarization states, in excellent agreement with experiments. We further note that the measured polarization ellipse of the harmonic furnishes the needed parameters for a 'complete' experiment in molecules.

Probabilistic biological network alignment.

Science.gov (United States)

Todor, Andrei; Dobra, Alin; Kahveci, Tamer

2013-01-01

Interactions between molecules are probabilistic events. An interaction may or may not happen with some probability, depending on a variety of factors such as the size, abundance, or proximity of the interacting molecules. In this paper, we consider the problem of aligning two biological networks. Unlike existing methods, we allow one of the two networks to contain probabilistic interactions. Allowing interaction probabilities makes the alignment more biologically relevant at the expense of explosive growth in the number of alternative topologies that may arise from different subsets of interactions that take place. We develop a novel method that efficiently and precisely characterizes this massive search space. We represent the topological similarity between pairs of aligned molecules (i.e., proteins) with the help of random variables and compute their expected values. We validate our method showing that, without sacrificing the running time performance, it can produce novel alignments. Our results also demonstrate that our method identifies biologically meaningful mappings under a comprehensive set of criteria used in the literature as well as the statistical coherence measure that we developed to analyze the statistical significance of the similarity of the functions of the aligned protein pairs.

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)

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)

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.

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.

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.

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.

JSME: a free molecule editor in JavaScript.

Science.gov (United States)

Bienfait, Bruno; Ertl, Peter

2013-01-01

A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. Today, when a web browser has become the universal scientific user interface, a tool to edit molecules directly within the web browser is essential. One of the most popular tools for molecular structure input on the web is the JME applet. Since its release nearly 15 years ago, however the web environment has changed and Java applets are facing increasing implementation hurdles due to their maintenance and support requirements, as well as security issues. This prompted us to update the JME editor and port it to a modern Internet programming language - JavaScript. The actual molecule editing Java code of the JME editor was translated into JavaScript with help of the Google Web Toolkit compiler and a custom library that emulates a subset of the GUI features of the Java runtime environment. In this process, the editor was enhanced by additional functionalities including a substituent menu, copy/paste, drag and drop and undo/redo capabilities and an integrated help. In addition to desktop computers, the editor supports molecule editing on touch devices, including iPhone, iPad and Android phones and tablets. In analogy to JME the new editor is named JSME. This new molecule editor is compact, easy to use and easy to incorporate into web pages. A free molecule editor written in JavaScript was developed and is released under the terms of permissive BSD license. The editor is compatible with JME, has practically the same user interface as well as the web application programming interface. The JSME editor is available for download from the project web page http://peter-ertl.com/jsme/

Multiple ionization dynamics of molecules in intense laser fields

International Nuclear Information System (INIS)

Ichimura, Atsushi; Ohyama-Yamaguchi, Tomoko

2005-01-01

A classical field-ionization model is developed for sequential multiple ionization of diatomic and linear triatomic molecules exposed to intense (∼ 10 15 W/cm 2 ) laser fields. The distance R ion of Coulomb explosion is calculated for a combination of fragment charges, by considering nonadiabatic excitation followed by field ionization associated with the inner and outer saddle points. For diatomic molecules (N 2 , NO, and I 2 ), the model explains behaviors observed in experiments, as R ion (21→31) ion (21→22) between competing charge-asymmetric and symmetric channels, and even-odd fluctuation along a principal pathway. For a triatomic molecule CO 2 , a comparison of the model with an experiment suggests that charge-symmetric (or nearly symmetric) channels are dominantly populated. (author)

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 ...

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.

High-harmonic spectroscopy of oriented OCS molecules: emission of even and odd harmonics.

Science.gov (United States)

Kraus, P M; Rupenyan, A; Wörner, H J

2012-12-07

We study the emission of even and odd high-harmonic orders from oriented OCS molecules. We use an intense, nonresonant femtosecond laser pulse superimposed with its phase-controlled second harmonic field to impulsively align and orient a dense sample of molecules from which we subsequently generate high-order harmonics. The even harmonics appear around the full revivals of the rotational dynamics. We demonstrate perfect coherent control over their intensity through the subcycle delay of the two-color fields. The odd harmonics are insensitive to the degree of orientation, but modulate with the degree of axis alignment, in agreement with calculated photorecombination dipole moments. We further compare the shape of the even and odd harmonic spectra with our calculations and determine the degree of orientation.

Self-consistent field theory of polymer-ionic molecule complexation

OpenAIRE

Nakamura, Issei; Shi, An-Chang

2010-01-01

A self-consistent field theory is developed for polymers that are capable of binding small ionic molecules (adsorbates). The polymer-ionic molecule association is described by Ising-like binding variables, C_(i)^(a)(kΔ)(= 0 or 1), whose average determines the number of adsorbed molecules, nBI. Polymer gelation can occur through polymer-ionic molecule complexation in our model. For polymer-polymer cross-links through the ionic molecules, three types of solutions for nBI are obtained, depending...

Free radicals trapped in polyethylene matrix

International Nuclear Information System (INIS)

Shimada, S.; Maeda, M.; Hori, Y.; Kashiwabara, H.

1977-01-01

Two types of alkyl radicals were found to be trapped in irradiated crystals grown from polyethylene solution. One of them corresponds to the broad sextet pattern of the e.s.r. spectrum and the other corresponds to the sharp sextet pattern. The free radicals attributed to the broad sextet began to disappear at a lower temperature than the temperature at which the free radicals attributed to the sharp sextet disappeared. When butadiene molecules were brought into contact with the specimen, the decay of the free radicals corresponding to the broad sextet was accelerated. When the specimen was subjected to fuming nitric acid treatment, no broad sextet was observed. The mat of the crystals was aligned so that the c-axes of its crystallites were perpendicular to its surface. The broad sextet showed no anisotropy when the angle between the direction of applied magnetic field and that of the c-axis of the crystallite was varied. On the other hand, the sharp component of the spectrum showed apparent anisotropy. It can be concluded that the broad component comes from the free radicals trapped in the lamellar surface and the sharp component is attributed to the free radicals trapped in the inner part of the crystallite. (author)

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.

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 ...

Optimized Free Energies from Bidirectional Single-Molecule Force Spectroscopy

Science.gov (United States)

Minh, David D. L.; Adib, Artur B.

2008-05-01

An optimized method for estimating path-ensemble averages using data from processes driven in opposite directions is presented. Based on this estimator, bidirectional expressions for reconstructing free energies and potentials of mean force from single-molecule force spectroscopy—valid for biasing potentials of arbitrary stiffness—are developed. Numerical simulations on a model potential indicate that these methods perform better than unidirectional strategies.

Theoretical studies on nuclear spin selective quantum dynamics of non-linear molecules; Theoretische Untersuchung zur Quantendynamik der Kernspinisomere nicht-linearer Molekuele

Energy Technology Data Exchange (ETDEWEB)

Grohmann, Thomas

2012-05-31

In this thesis the wave packet dynamics of nuclear spin isomers of polyatomic molecules after interaction with static and time-dependent magnetic fields and moderate intense nonresonant laser pulses is investigated. In particular, the process of inducing (internal) molecular rotation as well as alignment of molecules by manipulating their rotational or rotational-torsional degrees of freedom is studied. In the first part of the thesis all theoretical concepts for identifying nuclear spin isomers and for describing their quantum dynamics will be discussed. Especially the symmetrization postulate and themolecular symmetry group will be introduced and illustrated for some examples of molecules. These concepts will be extended to the case of identifying nuclear spin isomers in the presence of an external field. In the second part it is shown for nitromethane that magnetic fields are able to induce unidirectional rotations in opposite directions for different nuclear spin isomers of molecules containing methyl groups if the dipolar interaction is included. Additionally, it is demonstrated that different nuclear spin isomers of a chemical compound may show different alignment after the interaction with a moderate intense laser pulse. As shown for the rigid symmetric top propadien and the rigid asymmetric tops ethene and analogues, distinct pairs of nuclear spin isomers show at certain points in time a complementary behavior: while one isomer is showing alignment the partner isomer is showing anti-alignment. Moreover, it is illustrated that not every nuclear spin isomer can be aligned equally efficient. The alignment of non-rigid molecules is considered as well. As an example for a molecule with feasible torsion in the electronic ground state, the alignment of diboron tetrafluoride is investigated. It becomes apparent that not only rotational but also the torsional dynamics of the molecules is nuclear spin selective; different nuclear spin isomers have at distinct points

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.)

Supersonic pulsed free-jet of atoms and molecules of refractory metals: laser induced fluorescence spectroscopic studies on zirconium atoms and zirconium oxide molecules

International Nuclear Information System (INIS)

Nakhale, S.G.

2004-11-01

The experimental setup for generating supersonic pulsed free-jet containing atoms and molecules of refractory nature has been built. The technique of laser vaporization in conjunction with supersonic cooling is used to generate these species. The cooled atoms and molecules in supersonic free-jet are probed by laser induced fluorescence spectroscopy. In particular, the technique has been used to perform low-resolution laser induced fluorescence spectroscopy, limited by laser linewidth, on cold Zr atoms and ZrO molecules. The translational temperatures of ∼ 26.5 K and the rotational temperatures of ∼ 81 K have been achieved. It is possible to achieve the Doppler width of few tens of MHz allowing it to perform high-resolution spectroscopy on these atomic and molecular species. Also because of low rotational temperature of molecules the spectral congestion is greatly reduced. In general, this technique can be applied to perform spectroscopy on atoms and molecules of refractory nature. (author)

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...

Imaging Molecular Structure through Femtosecond Photoelectron Diffraction on Aligned and Oriented Gas-Phase Molecules

DEFF Research Database (Denmark)

Boll, Rebecca; Rouzee, Arnaud; Adolph, Marcus

2014-01-01

This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray Free-Electron Laser. We present results of two experiments aimed at measuring photoelectron angular...

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)

Controlling translational motion of neutral molecules in inhomogeneous electric fields

International Nuclear Information System (INIS)

Yamakita, Yoshihiro

2006-01-01

Hydrogen molecules are excited to Rydberg states with n=16, 17 in the presence of inhomogeneous field of an electric dipole by a vacuum ultraviolet-ultraviolet double resonance scheme. The large dipole moment produced in Stark eigenstates leads to strong forces on the molecules in the inhomogeneous electric field. Deflection and deceleration are demonstrated for a pulsed supersonic beam containing the H 2 molecules in the n=16, 17, N + =2, M J =0 Rydberg states. The Rydberg states are found to survive for over 100 μs after the dipole field is switched off. The Rydberg states have a special stability with respect to decay by predissociation. Complete deceleration to the zero mean velocity is numerically demonstrated for H 2 molecules in the higher linear low-field-seeking n=16, M J =0 Rydberg states by using a symplectic integrator of the fourth order. The calculations show that the initial velocity of 900 ms -1 with translational temperature 1 K is decelerated to 0 ms -1 with 13 mK. (author)

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

Femtosecond x-ray photoelectron diffraction on gas-phase dibromobenzene molecules

International Nuclear Information System (INIS)

Rolles, D; Boll, R; Epp, S W; Erk, B; Foucar, L; Hömke, A; Adolph, M; Gorkhover, T; Aquila, A; Chapman, H N; Coppola, N; Delmas, T; Gumprecht, L; Holmegaard, L; Bostedt, C; Bozek, J D; Coffee, R; Decleva, P; Filsinger, F; Johnsson, P

2014-01-01

We present time-resolved femtosecond photoelectron momentum images and angular distributions of dissociating, laser-aligned 1,4-dibromobenzene (C 6 H 4 Br 2 ) molecules measured in a near-infrared pump, soft-x-ray probe experiment performed at an x-ray free-electron laser. The observed alignment dependence of the bromine 2p photoelectron angular distributions is compared to density functional theory calculations and interpreted in terms of photoelectron diffraction. While no clear time-dependent effects are observed in the angular distribution of the Br(2p) photoelectrons, other, low-energy electrons show a pronounced dependence on the time delay between the near-infrared laser and the x-ray pulse. (paper)

Single-molecule tracking studies of flow-induced microdomain alignment in cylinder-forming polystyrene-poly(ethylene oxide) diblock copolymer films.

Science.gov (United States)

Tran-Ba, Khanh-Hoa; Higgins, Daniel A; Ito, Takashi

2014-09-25

Flow-based approaches are promising routes to preparation of aligned block copolymer microdomains within confined spaces. An in-depth characterization of such nanoscale morphologies within macroscopically nonuniform materials under ambient conditions is, however, often challenging. In this study, single-molecule tracking (SMT) methods were employed to probe the flow-induced alignment of cylindrical microdomains (ca. 22 nm in diameter) in polystyrene-poly(ethylene oxide) diblock copolymer (PS-b-PEO) films. Films of micrometer-scale thicknesses were prepared by overlaying a benzene solution droplet on a glass coverslip with a rectangular glass plate, followed by solvent evaporation under a nitrogen atmosphere. The microdomain alignment was quantitatively assessed from SMT data exhibiting the diffusional motions of individual sulforhodamine B fluorescent probes that preferentially partitioned into cylindrical PEO microdomains. Better overall microdomain orientation along the flow direction was observed near the substrate interface in films prepared at a higher flow rate, suggesting that the microdomain alignment was primarily induced by shear flow. The SMT data also revealed the presence of micrometer-scale grains consisting of highly ordered microdomains with coherent orientation. The results of this study provide insights into shear-based preparation of aligned cylindrical microdomains in block copolymer films from solutions within confined spaces.

Inducing elliptically polarized high-order harmonics from aligned molecules with linearly polarized femtosecond pulses

DEFF Research Database (Denmark)

Etches, Adam; Madsen, Christian Bruun; Madsen, Lars Bojer

2010-01-01

A recent paper reported elliptically polarized high-order harmonics from aligned N2 using a linearly polarized driving field [X. Zhou et al., Phys. Rev. Lett. 102, 073902 (2009)]. This observation cannot be explained in the standard treatment of the Lewenstein model and has been ascribed to many...

Nonadiabatic laser-induced alignment of molecules: Reconstructing ⟨ θ⟩ directly from ⟨ θ2D⟩ by Fourier analysis.

Science.gov (United States)

Søndergaard, Anders Aspegren; Shepperson, Benjamin; Stapelfeldt, Henrik

2017-07-07

We present an efficient, noise-robust method based on Fourier analysis for reconstructing the three-dimensional measure of the alignment degree, ⟨cos 2 θ⟩, directly from its two-dimensional counterpart, ⟨cos 2 θ 2D ⟩. The method applies to nonadiabatic alignment of linear molecules induced by a linearly polarized, nonresonant laser pulse. Our theoretical analysis shows that the Fourier transform of the time-dependent ⟨cos 2 θ 2D ⟩ trace over one molecular rotational period contains additional frequency components compared to the Fourier transform of ⟨cos 2 θ⟩. These additional frequency components can be identified and removed from the Fourier spectrum of ⟨cos 2 θ 2D ⟩. By rescaling of the remaining frequency components, the Fourier spectrum of ⟨cos 2 θ⟩ is obtained and, finally, ⟨cos 2 θ⟩ is reconstructed through inverse Fourier transformation. The method allows the reconstruction of the ⟨cos 2 θ⟩ trace from a measured ⟨cos 2 θ 2D ⟩ trace, which is the typical observable of many experiments, and thereby provides direct comparison to calculated ⟨cos 2 θ⟩ traces, which is the commonly used alignment metric in theoretical descriptions. We illustrate our method by applying it to the measurement of nonadiabatic alignment of I 2 molecules. In addition, we present an efficient algorithm for calculating the matrix elements of cos 2 θ 2D and any other observable in the symmetric top basis. These matrix elements are required in the rescaling step, and they allow for highly efficient numerical calculation of ⟨cos 2 θ 2D ⟩ and ⟨cos 2 θ⟩ in general.

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.

Complexation of Polyelectrolytes with Hydrophobic Drug Molecules in Salt-Free Solution: Theory and Simulations.

Science.gov (United States)

Lei, Qun-Li; Hadinoto, Kunn; Ni, Ran

2017-04-18

The delivery and dissolution of poorly soluble drugs is challenging in the pharmaceutical industry. One way to significantly improve the delivery efficiency is to incorporate these hydrophobic small molecules into a colloidal polyelectrolyes(PE)-drug complex in their ionized states. Despite its huge application value, the general mechanism of PE collapse and complex formation in this system has not been well understood. In this work, by combining a mean-field theory with extensive molecular simulations, we unveil the phase behaviors of the system under dilute and salt-free conditions. We find that the complexation is a first-order-like phase transition triggered by the hydrophobic attraction between the drug molecules. Importantly, the valence ratio between the drug molecule and PE monomer plays a crucial role in determining the stability and morphology of the complex. Moreover, the sign of the zeta potential and the net charge of the complex are found to be inverted as the hydrophobicity of the drug molecules increases. Both theory and simulation indicate that the complexation point and complex morphology and the electrostatic properties of the complex have a weak dependence on chain length. Finally, the dynamics aspect of PE-drug complexation is also explored, and it is found that the complex can be trapped into a nonequilibrium glasslike state when the hydropobicity of the drug molecule is too strong. Our work gives a clear physical picture behind the PE-drug complexation phenomenon and provides guidelines to fabricate the colloidal PE-drug complex with the desired physical characteristics.

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

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.

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

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.

Controlling single-molecule junction conductance by molecular interactions

Science.gov (United States)

Kitaguchi, Y.; Habuka, S.; Okuyama, H.; Hatta, S.; Aruga, T.; Frederiksen, T.; Paulsson, M.; Ueba, H.

2015-01-01

For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment. PMID:26135251

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.

Highly Enhanced Gas Adsorption Properties in Vertically Aligned MoS2 Layers.

Science.gov (United States)

Cho, Soo-Yeon; Kim, Seon Joon; Lee, Youhan; Kim, Jong-Seon; Jung, Woo-Bin; Yoo, Hae-Wook; Kim, Jihan; Jung, Hee-Tae

2015-09-22

In this work, we demonstrate that gas adsorption is significantly higher in edge sites of vertically aligned MoS2 compared to that of the conventional basal plane exposed MoS2 films. To compare the effect of the alignment of MoS2 on the gas adsorption properties, we synthesized three distinct MoS2 films with different alignment directions ((1) horizontally aligned MoS2 (basal plane exposed), (2) mixture of horizontally aligned MoS2 and vertically aligned layers (basal and edge exposed), and (3) vertically aligned MoS2 (edge exposed)) by using rapid sulfurization method of CVD process. Vertically aligned MoS2 film shows about 5-fold enhanced sensitivity to NO2 gas molecules compared to horizontally aligned MoS2 film. Vertically aligned MoS2 has superior resistance variation compared to horizontally aligned MoS2 even with same surface area exposed to identical concentration of gas molecules. We found that electrical response to target gas molecules correlates directly with the density of the exposed edge sites of MoS2 due to high adsorption of gas molecules onto edge sites of vertically aligned MoS2. Density functional theory (DFT) calculations corroborate the experimental results as stronger NO2 binding energies are computed for multiple configurations near the edge sites of MoS2, which verifies that electrical response to target gas molecules (NO2) correlates directly with the density of the exposed edge sites of MoS2 due to high adsorption of gas molecules onto edge sites of vertically aligned MoS2. We believe that this observation extends to other 2D TMD materials as well as MoS2 and can be applied to significantly enhance the gas sensor performance in these materials.

Coherent control of atto-second emission from aligned molecules

Energy Technology Data Exchange (ETDEWEB)

Boutu, W; Haessler, S; Merdji, H; Breger, P; Monchicourt, P; Carre, B; Salieres, P [CEA Saclay, DSM, Serv Photons Atomes Mol, F-91191 Gif Sur Yvette, (France); Waters, G [Univ Reading, JJ Thomson Phys Lab, Reading RG6 6AF, Berks, (United Kingdom); Stankiewicz, M [Jagiellonian Univ, Inst Phys, PL-30059 Krakow, (Poland); Frasinski, L J [Univ London Imperial Coll Sci Technol and Med, Blackett Lab, London SW7 2BW, (United Kingdom); Taieb, R; Caillat, J; Maquet, A [Univ Paris 06, UMR 7614, Lab Chim Phys Matiere Rayonnement, F-75231 Paris 05, (France); Taieb, R; Caillat, J; Maquet, A [LCPMR, UMR 7614, CNRS, F-75005 Paris, (France)

2008-07-01

Controlling atto-second electron wave packets and soft X-ray pulses represents a formidable challenge of general implication to many areas of science. A strong laser field interacting with atoms or molecules drives ultrafast intra-atomic/molecular electron wave packets on a sub femtosecond timescale, resulting in the emission of atto-second bursts of extreme-ultraviolet light. Controlling the intra-atomic/molecular electron dynamics enables steering of the atto-second emission. Here, we carry out a coherent control in linear molecules, where the interaction of the laser-driven electron wave packet with the core leads to quantum interferences. We demonstrate that these interferences can be finely controlled by turning the molecular axis relative to the laser polarization, that is, changing the electron re-collision angle. The wave-packet coulombic distortion modifies the spectral phase jump measured in the extreme-ultraviolet emission. Our atto-second control of the interference results in atto-second pulse shaping, useful for future applications in ultrafast coherent control of atomic and molecular processes. (authors)

Molecules in the cold environment of a supersonic free-jet beam: from spectroscopy of neutral-neutral interactions to a test of Bell's inequality

International Nuclear Information System (INIS)

Koperski, J; Fry, E S

2006-01-01

The supersonic free-jet expansion technique has been used in different fields of research in physics, physical chemistry and chemistry to study vibrational and rotational molecular structures in ground and excited electronic energy states as well as in cold chemistry to study chemical reactions in a unique environment. The supersonic beam technique, as a widely used method in laser spectroscopy of molecules, exploits a source of monokinetic, rotationally and vibrationally cold molecules, that are very weakly bound in their ground electronic states (van der Waals molecules). In experiments at Jagiellonian University the supersonic free-jet beam serves as a source of ground-state van der Waals objects in studies of neutral-neutral interactions between group 12 metal (M = Zn, Cd, Hg) and noble gas (NG) atoms. Recently, the method has been applied as a source of entangled 199 Hg atom pairs in order to test Bell's inequality in an experiment at Texas A and M University

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.

Electric-field-modified Feshbach resonances in ultracold atom–molecule collision

International Nuclear Information System (INIS)

Cheng Dong; Li Ya; Feng Eryin; Huang Wuying

2017-01-01

We present a detailed analysis of near zero-energy Feshbach resonances in ultracold collisions of atom and molecule, taking the He–PH system as an example, subject to superimposed electric and magnetic static fields. We find that the electric field can induce Feshbach resonance which cannot occur when only a magnetic field is applied, through couplings of the adjacent rotational states of different parities. We show that the electric field can shift the position of the magnetic Feshbach resonance, and change the amplitude of resonance significantly. Finally, we demonstrate that, for narrow magnetic Feshbach resonance as in most cases of ultracold atom–molecule collision, the electric field may be used to modulate the resonance, because the width of resonance in electric field scale is relatively larger than that in magnetic field scale. (paper)

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)

Local-global alignment for finding 3D similarities in protein structures

Science.gov (United States)

Zemla, Adam T [Brentwood, CA

2011-09-20

A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

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 macromodel for squeeze-film air damping in the free-molecule regime

KAUST Repository

Hong, Gang; Ye, Wenjing

2010-01-01

A three-dimensional Monte Carlo(MC) simulation approach is developed for the accurate prediction of the squeeze-film air damping on microresonators in the free-molecule gas regime. Based on the MC simulations and the analytical traveling

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

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.

Comparative assessment of computational methods for the determination of solvation free energies in alcohol-based molecules.

Science.gov (United States)

Martins, Silvia A; Sousa, Sergio F

2013-06-05

The determination of differences in solvation free energies between related drug molecules remains an important challenge in computational drug optimization, when fast and accurate calculation of differences in binding free energy are required. In this study, we have evaluated the performance of five commonly used polarized continuum model (PCM) methodologies in the determination of solvation free energies for 53 typical alcohol and alkane small molecules. In addition, the performance of these PCM methods, of a thermodynamic integration (TI) protocol and of the Poisson-Boltzmann (PB) and generalized Born (GB) methods, were tested in the determination of solvation free energies changes for 28 common alkane-alcohol transformations, by the substitution of an hydrogen atom for a hydroxyl substituent. The results show that the solvation model D (SMD) performs better among the PCM-based approaches in estimating solvation free energies for alcohol molecules, and solvation free energy changes for alkane-alcohol transformations, with an average error below 1 kcal/mol for both quantities. However, for the determination of solvation free energy changes on alkane-alcohol transformation, PB and TI yielded better results. TI was particularly accurate in the treatment of hydroxyl groups additions to aromatic rings (0.53 kcal/mol), a common transformation when optimizing drug-binding in computer-aided drug design. Copyright © 2013 Wiley Periodicals, Inc.

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.

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.

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....

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

Encaged molecules in external electric fields: A molecular "tug-of-war"

Science.gov (United States)

Gurav, Nalini D.; Gejji, Shridhar P.; Bartolotti, Libero J.; Pathak, Rajeev K.

2016-08-01

Response of polar molecules CH3OH and H2O2 and a non-polar molecule, CO2, as "guests" encapsulated in the dodecahedral water cage (H2O)20 "host," to an external, perturbative electric field is investigated theoretically. We employ the hybrid density-functionals M06-2X and ωB97X-D incorporating the effects of damped dispersion, in conjunction with the maug-cc-pVTZ basis set, amenable for a hydrogen bonding description. While the host cluster (cage) tends to confine the embedded guest molecule through cooperative hydrogen bonding, the applied electric field tends to rupture the cluster-composite by stretching it; these two competitive effects leading to a molecular "tug-of-war." The composite remains stable up to a maximal sustainable threshold electric field, beyond which, concomitant with the vanishing of the HOMO-LUMO gap, the field wins over and the cluster breaks down. The electric-field effects are gauged in terms of the changes in the molecular geometry of the confined species, interaction energy, molecular electrostatic potential surfaces, and frequency shifts of characteristic normal vibrations in the IR regime. Interestingly, beyond the characteristic threshold electric field, the labile, distorted host cluster fragmentizes, and the guest molecule still tethered to a remnant fragment, an effect attributed to the underlying hydrogen-bonded networks.

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.

Exotic behavior of molecules in intense laser light fields. New research directions

Energy Technology Data Exchange (ETDEWEB)

Yamanouchi, Kaoru [Tokyo Univ., Department of Chemistry, Tokyo (Japan)

2002-08-01

The recent investigation of the dynamical behavior of molecules and clusters in intense laser fields has afforded us invaluable opportunities to understand fundamentals of the interaction between molecular species and light fields as well as to manipulate molecules and their dynamical pathways by taking advantage of characteristics of coherent ultrashort laser light fields. In the present report, new directions of this rapidly growing interdisciplinary research fields called molecular science in intense laser fields are discussed by referring to our recent studies. (author)

Real-time monitoring and manipulation of single bio-molecules in free solution

Energy Technology Data Exchange (ETDEWEB)

Li, Hung-Wing [Iowa State Univ., Ames, IA (United States)

2005-01-01

The observation and manipulation of single biomolecules allow their dynamic behaviors to be studied to provide insight into molecular genetics, biochip assembly, biosensor design, DNA biophysics. In a PDMS/glass microchannel, a nonuniform electroosmotic flow (EOF) was created. By using a scanning confocal fluorescence microscope and total internal-reflection fluorescence microscope (TIRFM), we demonstrated that negatively charged DNA molecules were focused by the nonuniform EOF into a thin layer at the glass surface. This phenomenon was applied to selectively detect target DNA molecules without requiring the separation of excessive probes and can be applied continuously to achieve high throughput. A variable-angle-TIRFM was constructed for imaging single DNA molecule dynamics at a solid/liquid interface. Implications we have are that the measured intensities cannot be used directly to determine the distances of molecules from the surface and the experimental counting results depict the distance-dependent dynamics of molecules near the surface; Molecules at low ionic strengths experience electrostatic repulsion at distances much further away from the surface than the calculated thickness of the electrical double layer. {delta}-DNA was employed as a nanoprobe for different functionalized surfaces to elucidate adsorption in chromatography. The 12-base unpaired ends of this DNA provide exposed purine and pyrimidine groups for adsorption. Patterns of self-assembled monolayers (SAMs) and patterns of metal oxides are generated. By recording the real-time dynamic motion of DNA molecules at the SAMs/aqueous interface, the various parameters governing the retention of an analyte during chromatographic separation can be studied. Even subtle differences among adsorptive forces can be revealed. Dynamic conformational changes of the prosthetic group, flavin adenine dinucleotide (FAD), in flavoprotein NADH peroxidase, in thioredoxin reductase, and in free solution were monitored

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

A high-yield, one-step synthesis of surfactant-free gold nanostars and numerical study for single-molecule SERS application

Energy Technology Data Exchange (ETDEWEB)

Chatterjee, S.; Ringane, A. B.; Arya, A.; Das, G. M.; Dantham, V. R., E-mail: dantham@iitp.ac.in; Laha, R. [Indian Institute of Technology Patna, Department of Physics (India); Hussian, S. [Indian Institute of Technology Patna, Department of Chemistry (India)

2016-08-15

We report a high-yield synthesis of star-shaped gold nanostructures in one step, using a new surfactant-free wet chemistry method. Compared to the existing reports, these nanostars were found to have longer and sharper spikes anchored uniformly on the surface of the spherical core, allowing at least a few hot spots irrespective of the incident light polarization. The average experimental values of core radius and spike length were found to be 88.5 and 72 nm, respectively. Using these values in numerical simulations, the local electric field enhancement (η) and localized surface plasmon resonance (LSPR) spectrum were obtained. Moreover, the single-molecule surface-enhanced Raman scattering (SERS) enhancement factor was found to vary from 10{sup 10} to 10{sup 13} depending on the excitation wavelengths. Our theoretical calculations suggest that these nanostructures can be used to fabricate efficient SERS-based biosensors for the detection of single molecules in real time and for predicting structural information of single molecules.

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.

Photodissociation from a manifold of rovibrational states and free-free absorption by a diatomic molecule

International Nuclear Information System (INIS)

Lebedev, V S; Presnyakov, L P

2002-01-01

An analytical approach for the description of photoabsorption by a gas or plasma medium containing atomic and molecular components in thermodynamic equilibrium is developed. Continuous absorption of radiation is due to the photodissociation of a diatomic molecule from a manifold of excited rovibrational states and free-free transitions between the two electronic terms of a quasimolecule temporarily formed during a collision of atomic particles. The formulae are obtained for individual photodissociation cross sections from a given rovibrational state and for the Boltzmann-averaged cross section. Particular attention is paid to the derivation of a general analytical expression for the total absorption coefficient including the integral contribution of bound-free and free-free radiative transitions. The consideration is based on the theory of nonadiabatic transitions combined with the approximation of a quasicontinuum for rovibrational states. The theory is applied to the investigation of photoabsorption by the H 2 + ion in the IR, visible and UV spectral regions. It is shown that our results are in good agreement with available ab initio quantal calculations of photodissociation cross sections and with semiclassical calculations of absorption coefficients. Special attention is paid to the investigation of the relative contributions of the H 2 + and H - ions to the total absorption in a wide range of wavelengths and temperatures

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

Study of the In2O3 molecule in the free state and in the crystal

Science.gov (United States)

Kaplan, Ilya G.; Miranda, Ulises; Trakhtenberg, Leonid I.

2018-03-01

The nanomaterials based on the In2O3 molecule are widely used as catalysts and sensors among other applications. In the present study, we discuss the possibility of using nanoclusters of In2O3 as molecular photomotors. A comparative analysis of the electronic structure of the In2O3 molecule in the free state and in the crystal is performed. For the free In2O3 molecule the geometry of its lowest structures, V-shape and linear, was optimised at the CCSD(T) level, which is the most precise computational method applied up to date to study In2O3. Using experimental crystallographic data, we determined the geometry of In2O3 in the crystal. It has a zigzag, not symmetric structure and possesses a dipole moment with magnitude slightly smaller than that of the V-structure of the free molecule (the linear structure due to its symmetry has no dipole moment). According to the Natural Atomic population analysis, the chemical structure of the linear In2O3 can be represented as O = In-O-In = O; the V-shaped molecule has the similar double- and single-bond structure. The construction of nanoclusters from ´bricksʼ of In2O3 with geometry extracted from crystal (or nanoclusters extracted directly from crystal) and their use as photo-driven molecular motors are discussed.

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.

Structural Design Principle of Small-Molecule Organic Semiconductors for Metal-Free, Visible-Light-Promoted Photocatalysis.

Science.gov (United States)

Wang, Lei; Huang, Wei; Li, Run; Gehrig, Dominik; Blom, Paul W M; Landfester, Katharina; Zhang, Kai A I

2016-08-08

Herein, we report on the structural design principle of small-molecule organic semiconductors as metal-free, pure organic and visible light-active photocatalysts. Two series of electron-donor and acceptor-type organic semiconductor molecules were synthesized to meet crucial requirements, such as 1) absorption range in the visible region, 2) sufficient photoredox potential, and 3) long lifetime of photogenerated excitons. The photocatalytic activity was demonstrated in the intermolecular C-H functionalization of electron-rich heteroaromates with malonate derivatives. A mechanistic study of the light-induced electron transport between the organic photocatalyst, substrate, and the sacrificial agent are described. With their tunable absorption range and defined energy-band structure, the small-molecule organic semiconductors could offer a new class of metal-free and visible light-active photocatalysts for chemical reactions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sequential nonadiabatic excitation of large molecules and ions driven by strong laser fields

International Nuclear Information System (INIS)

Markevitch, Alexei N.; Levis, Robert J.; Romanov, Dmitri A.; Smith, Stanley M.; Schlegel, H. Bernhard; Ivanov, Misha Yu.

2004-01-01

Electronic processes leading to dissociative ionization of polyatomic molecules in strong laser fields are investigated experimentally, theoretically, and numerically. Using time-of-flight ion mass spectroscopy, we study the dependence of fragmentation on laser intensity for a series of related molecules and report regular trends in this dependence on the size, symmetry, and electronic structure of a molecule. Based on these data, we develop a model of dissociative ionization of polyatomic molecules in intense laser fields. The model is built on three elements: (i) nonadiabatic population transfer from the ground electronic state to the excited-state manifold via a doorway (charge-transfer) transition; (ii) exponential enhancement of this transition by collective dynamic polarization of all electrons, and (iii) sequential energy deposition in both neutral molecules and resulting molecular ions. The sequential nonadiabatic excitation is accelerated by a counterintuitive increase of a large molecule's polarizability following its ionization. The generic theory of sequential nonadiabatic excitation forms a basis for quantitative description of various nonlinear processes in polyatomic molecules and ions in strong laser fields

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.

Enzyme Molecules in Solitary Confinement

Directory of Open Access Journals (Sweden)

Raphaela B. Liebherr

2014-09-01

Full Text Available Large arrays of homogeneous microwells each defining a femtoliter volume are a versatile platform for monitoring the substrate turnover of many individual enzyme molecules in parallel. The high degree of parallelization enables the analysis of a statistically representative enzyme population. Enclosing individual enzyme molecules in microwells does not require any surface immobilization step and enables the kinetic investigation of enzymes free in solution. This review describes various microwell array formats and explores their applications for the detection and investigation of single enzyme molecules. The development of new fabrication techniques and sensitive detection methods drives the field of single molecule enzymology. Here, we introduce recent progress in single enzyme molecule analysis in microwell arrays and discuss the challenges and opportunities.

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

Rydberg excitation of neutral nitric oxide molecules in strong UV and near-IR laser fields

International Nuclear Information System (INIS)

Lv Hang; Zhang Jun-Feng; Zuo Wan-Long; Xu Hai-Feng; Jin Ming-Xing; Ding Da-Jun

2015-01-01

Rydberg state excitations of neutral nitric oxide molecules are studied in strong ultraviolet (UV) and near-infra-red (IR) laser fields using a linear time-of-flight (TOF) mass spectrometer with the pulsed electronic field ionization method. The yield of Rydberg molecules is measured as a function of laser intensity and ellipticity, and the results in UV laser fields are compared with those in near-IR laser fields. The present study provides the first experimental evidence of neutral Rydberg molecules surviving in a strong laser field. The results indicate that a rescattering-after-tunneling process is the main contribution to the formation of Rydberg molecules in strong near-IR laser fields, while multi-photon excitation may play an important role in the strong UV laser fields. (paper)

Effects of microwave electric fields on the translational diffusion of dipolar molecules in surface potential: A simulation study

Science.gov (United States)

Kapranov, Sergey V.; Kouzaev, Guennadi A.

2018-01-01

Variations of effective diffusion coefficient of polar molecules exposed to microwave electric fields in a surface potential are studied by solving coupled stochastic differential equations of motion with a deterministic component of the surface force. Being an essential tool for the simulation interpretation, a theoretical approach to effective diffusion in surface potential is first developed. The effective diffusion coefficient is represented as the product of the normal diffusion coefficient and potential-dependent correction function, whose temperature dependence is close to the Arrhenius form. The analytically found zero-diffusion condition defines the state of thermal equilibrium at the surface. The diffusion of a water-like dipole molecule in the potential of graphite surface is simulated in the field-free conditions and in the presence of the alternating electric fields of various magnitude intensities and frequencies. Temperature dependence of the correction function exhibits field-induced variations of the effective Lennard-Jones energy parameter. It demonstrates maximum departure from the zero-field value at certain frequencies and intensities, which is associated with variations in the rotational dynamics. A concept of the amplitude-frequency resonance put forward to interpret the simulation results is explained using a heuristic reasoning and is corroborated by semi-quantitative considerations in terms of the Dissado-Hill cluster theory of dielectric relaxation.

Finding optimal interaction interface alignments between biological complexes

KAUST Repository

Cui, Xuefeng

2015-06-13

Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which are keys to understanding their evolutionary histories and functions. Although various structure alignment methods have been developed to successfully access the similarities of protein structures or certain types of interaction interfaces, existing alignment tools cannot directly align arbitrary types of interfaces formed by protein, DNA or RNA molecules. Specifically, they require a \\'blackbox preprocessing\\' to standardize interface types and chain identifiers. Yet their performance is limited and sometimes unsatisfactory. Results: Here we introduce a novel method, PROSTA-inter, that automatically determines and aligns interaction interfaces between two arbitrary types of complex structures. Our method uses sequentially remote fragments to search for the optimal superimposition. The optimal residue matching problem is then formulated as a maximum weighted bipartite matching problem to detect the optimal sequence order-independent alignment. Benchmark evaluation on all non-redundant protein-DNA complexes in PDB shows significant performance improvement of our method over TM-align and iAlign (with the \\'blackbox preprocessing\\'). Two case studies where our method discovers, for the first time, structural similarities between two pairs of functionally related protein-DNA complexes are presented. We further demonstrate the power of our method on detecting structural similarities between a protein-protein complex and a protein-RNA complex, which is biologically known as a protein-RNA mimicry case. © The Author 2015. Published by Oxford University Press.

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.

Interference effects in double ionization of spatially aligned hydrogen molecules by fast highly charged ions

International Nuclear Information System (INIS)

Landers, A.L.; Alnaser, A.S.; Tanis, J.A.; Wells, E.; Osipov, T.; Carnes, K.D.; Ben-Itzhak, I.; Cocke, C.L.; McGuire, J.H.

2004-01-01

Cross sections differential in target orientation angle were measured for 19 MeV F 8+ +D 2 collisions. Multihit position-sensitive detectors were used to isolate the double-ionization channel and determine a posteriori the full momentum vectors of both ejected D + fragments. A strong dependence of the double ionization cross section on the angle between the incident ion direction and the target molecular axis is observed with a ≅3.5:1 enhancement for molecules aligned perpendicular to the projectile axis. This clear asymmetry is attributed to interference effects, analogous to Young's two-slit experiment, arising from coherent contributions to the ionization from both atomic centers. The data are compared to a simple scattering model based on two center interference

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.

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.

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...

Molecules with an induced dipole moment in a stochastic electric field.

Science.gov (United States)

Band, Y B; Ben-Shimol, Y

2013-10-01

The mean-field dynamics of a molecule with an induced dipole moment (e.g., a homonuclear diatomic molecule) in a deterministic and a stochastic (fluctuating) electric field is solved to obtain the decoherence properties of the system. The average (over fluctuations) electric dipole moment and average angular momentum as a function of time for a Gaussian white noise electric field are determined via perturbative and nonperturbative solutions in the fluctuating field. In the perturbative solution, the components of the average electric dipole moment and the average angular momentum along the deterministic electric field direction do not decay to zero, despite fluctuations in all three components of the electric field. This is in contrast to the decay of the average over fluctuations of a magnetic moment in a Gaussian white noise magnetic field. In the nonperturbative solution, the component of the average electric dipole moment and the average angular momentum in the deterministic electric field direction also decay to zero.

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

Single-Molecule Imaging with X-Ray Free-Electron Lasers: Dream or Reality?

KAUST Repository

Fratalocchi, Andrea

2011-03-09

X-ray free-electron lasers (XFEL) are revolutionary photon sources, whose ultrashort, brilliant pulses are expected to allow single-molecule diffraction experiments providing structural information on the atomic length scale of nonperiodic objects. This ultimate goal, however, is currently hampered by several challenging questions basically concerning sample damage, Coulomb explosion, and the role of nonlinearity. By employing an original ab initio approach, we address these issues showing that XFEL-based single-molecule imaging will be only possible with a few-hundred long attosecond pulses, due to significant radiation damage and the formation of preferred multisoliton clusters which reshape the overall electronic density of the molecular system at the femtosecond scale.

Single-Molecule Imaging with X-Ray Free-Electron Lasers: Dream or Reality?

KAUST Repository

Fratalocchi, Andrea; Ruocco, G.

2011-01-01

X-ray free-electron lasers (XFEL) are revolutionary photon sources, whose ultrashort, brilliant pulses are expected to allow single-molecule diffraction experiments providing structural information on the atomic length scale of nonperiodic objects. This ultimate goal, however, is currently hampered by several challenging questions basically concerning sample damage, Coulomb explosion, and the role of nonlinearity. By employing an original ab initio approach, we address these issues showing that XFEL-based single-molecule imaging will be only possible with a few-hundred long attosecond pulses, due to significant radiation damage and the formation of preferred multisoliton clusters which reshape the overall electronic density of the molecular system at the femtosecond scale.

Finding optimal interaction interface alignments between biological complexes

KAUST Repository

Cui, Xuefeng; Naveed, Hammad; Gao, Xin

2015-01-01

Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which

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.

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.

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

Dynamics of photoprocesses induced by femtosecond infrared radiation in free molecules and clusters of iron pentacarbonyl

International Nuclear Information System (INIS)

Kompanets, V. O.; Lokhman, V. N.; Poydashev, D. G.; Chekalin, S. V.; Ryabov, E. A.

2016-01-01

The dynamics of photoprocesses induced by femtosecond infrared radiation in free Fe(CO) 5 molecules and their clusters owing to the resonant excitation of vibrations of CO bonds in the 5-μm range has been studied. The technique of infrared excitation and photoionization probing (λ = 400 nm) by femtosecond pulses has been used in combination with time-of-flight mass spectrometry. It has been found that an infrared pulse selectively excites vibrations of CO bonds in free molecules, which results in a decrease in the yield of the Fe(CO) 5 + molecular ion. Subsequent relaxation processes have been analyzed and the results have been interpreted. The time of the energy transfer from excited vibrations to other vibrations of the molecule owing to intramolecular relaxation has been measured. The dynamics of dissociation of [Fe(CO) 5 ] n clusters irradiated by femtosecond infrared radiation has been studied. The time dependence of the yield of free molecules has been measured under different infrared laser excitation conditions. We have proposed a model that well describes the results of the experiment and makes it possible, in particular, to calculate the profile of variation of the temperature of clusters within the “evaporation ensemble” concept. The intramolecular and intracluster vibrational relaxation rates in [Fe(CO) 5 ] n clusters have been estimated.

The ITO-capped WO3 nanowires biosensor based on field-effect transistor in label-free protein sensing

International Nuclear Information System (INIS)

Shariati, Mohsen

2017-01-01

The fabrication of ITO-capped WO 3 nanowires associated with their bio-sensing properties in field-effect transistor diagnostics basis as a biosensor has been reported. The bio-sensing property for manipulated nanowires elucidated that the grown nanostructures were very sensitive to protein. The ITO-capped WO 3 nanowires biosensor showed an intensive bio-sensing activity against reliable protein. Polylysine strongly charged bio-molecule was applied as model system to demonstrate the implementation of materialized biosensor. The employed sensing mechanism was 'label-free' and depended on bio-molecule's intrinsic charge. For nanowires synthesis, the vapor-liquid-solid mechanism was used. Nanowires were beyond a few hundred nanometers in lengths and around 15-20 nm in diameter, while the globe cap's size on the nanowires was around 15-25 nm. The indium tin oxide (ITO) played as catalyst in nanofabrication for WO 3 nanowires growth and had outstanding role in bio-sensing especially for bio-molecule adherence. In applied electric field presence, the fabricated device showed the great potential to enhance medical diagnostics. (orig.)

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.

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

Relativistic four-component multiconfigurational self-consistent-field theory for molecules

DEFF Research Database (Denmark)

Jensen, Hans Jørgen Aa; Dyall, Kenneth G.; Saue, Trond

1996-01-01

A formalism for relativistic four-component multiconfigurational self-consistent-field calculations on molecules is presented. The formalism parallels a direct second-order restricted-step algorithm developed for nonrelativistic molecular calculations. The presentation here focuses on the differe......A formalism for relativistic four-component multiconfigurational self-consistent-field calculations on molecules is presented. The formalism parallels a direct second-order restricted-step algorithm developed for nonrelativistic molecular calculations. The presentation here focuses...... the memory used by the largest nonrelativistic calculation in the equivalent basis, due to the complex arithmetic. The feasibility of the calculations is then determined more by the disk space for storage of integrals and N-particle expansion vectors....

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.

Stereoselectivity in catalytic reactions: CO oxidation on Pd(100) by rotationally aligned O2 molecules

Science.gov (United States)

Vattuone, L.; Gerbi, A.; Savio, L.; Cappelletti, D.; Pirani, F.; Rocca, M.

2010-05-01

We report on stereodynamical effects in heterogeneous catalytic reactions as measured by molecular beam-surface experiments. Specifically for CO oxidation on Pd(100) we find that the rotational alignment of the incoming O2 at low (Θ = 0.04 ML) and at intermediate (ΘCO = 0.17 ML) CO pre-coverage, causes a higher reactivity of molecules in high and in low helicity states, respectively (corresponding to helicoptering and cartwheeling motion of O2). In first approximation, at low CO pre-coverage the difference in reactivity is determined by the different location of the O atoms generated in the dissociation process by the different parent molecules, while at intermediate CO pre-coverage the reactivity is influenced also by the different ability of cartwheeling and helicoptering O2 to penetrate through the CO adlayer. In accord with this the total amount of CO2 produced is always largest for helicopters which generate supersurface O atoms at least in the low CO pre-coverage limit. A deeper inspection of the data indicates, however, that the dynamics is more complex, two different pathways being present for the reaction with O generated by helicopters and one for O generated by cartwheels. Moreover, cartwheels generated oxygen influences the reactivity of subsequently arriving helicopters.

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.

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

RNA structure alignment by a unit-vector approach.

Science.gov (United States)

Capriotti, Emidio; Marti-Renom, Marc A

2008-08-15

The recent discovery of tiny RNA molecules such as microRNAs and small interfering RNA are transforming the view of RNA as a simple information transfer molecule. Similar to proteins, the native three-dimensional structure of RNA determines its biological activity. Therefore, classifying the current structural space is paramount for functionally annotating RNA molecules. The increasing numbers of RNA structures deposited in the PDB requires more accurate, automatic and benchmarked methods for RNA structure comparison. In this article, we introduce a new algorithm for RNA structure alignment based on a unit-vector approach. The algorithm has been implemented in the SARA program, which results in RNA structure pairwise alignments and their statistical significance. The SARA program has been implemented to be of general applicability even when no secondary structure can be calculated from the RNA structures. A benchmark against the ARTS program using a set of 1275 non-redundant pairwise structure alignments results in inverted approximately 6% extra alignments with at least 50% structurally superposed nucleotides and base pairs. A first attempt to perform RNA automatic functional annotation based on structure alignments indicates that SARA can correctly assign the deepest SCOR classification to >60% of the query structures. The SARA program is freely available through a World Wide Web server http://sgu.bioinfo.cipf.es/services/SARA/. Supplementary data are available at Bioinformatics online.

NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction

Directory of Open Access Journals (Sweden)

Lund Ole

2009-09-01

Full Text Available Abstract Background The major histocompatibility complex (MHC molecule plays a central role in controlling the adaptive immune response to infections. MHC class I molecules present peptides derived from intracellular proteins to cytotoxic T cells, whereas MHC class II molecules stimulate cellular and humoral immunity through presentation of extracellularly derived peptides to helper T cells. Identification of which peptides will bind a given MHC molecule is thus of great importance for the understanding of host-pathogen interactions, and large efforts have been placed in developing algorithms capable of predicting this binding event. Results Here, we present a novel artificial neural network-based method, NN-align that allows for simultaneous identification of the MHC class II binding core and binding affinity. NN-align is trained using a novel training algorithm that allows for correction of bias in the training data due to redundant binding core representation. Incorporation of information about the residues flanking the peptide-binding core is shown to significantly improve the prediction accuracy. The method is evaluated on a large-scale benchmark consisting of six independent data sets covering 14 human MHC class II alleles, and is demonstrated to outperform other state-of-the-art MHC class II prediction methods. Conclusion The NN-align method is competitive with the state-of-the-art MHC class II peptide binding prediction algorithms. The method is publicly available at http://www.cbs.dtu.dk/services/NetMHCII-2.0.

Core excitation and de-excitation spectroscopies of free atoms and molecules

International Nuclear Information System (INIS)

Ueda, Kiyoshi

2006-01-01

This article provides a review of the current status of core excitation and de-excitation spectroscopy studies of free atoms molecules using a high-resolution soft X-ray monochromator and a high-resolution electron energy analyzer, installed in the soft X-ray photochemistry beam line at SPring-8. Experimental results are discussed for 1s excitation of Ne, O 1s excitation of CO and H 2 O, and F 1s excitation of CF 4 . (author)

The ITO-capped WO{sub 3} nanowires biosensor based on field-effect transistor in label-free protein sensing

Energy Technology Data Exchange (ETDEWEB)

Shariati, Mohsen [Sharif University of Technology, Institute for Nanoscience and Nanotechnology, Tehran (Iran, Islamic Republic of)

2017-05-15

The fabrication of ITO-capped WO{sub 3} nanowires associated with their bio-sensing properties in field-effect transistor diagnostics basis as a biosensor has been reported. The bio-sensing property for manipulated nanowires elucidated that the grown nanostructures were very sensitive to protein. The ITO-capped WO{sub 3} nanowires biosensor showed an intensive bio-sensing activity against reliable protein. Polylysine strongly charged bio-molecule was applied as model system to demonstrate the implementation of materialized biosensor. The employed sensing mechanism was 'label-free' and depended on bio-molecule's intrinsic charge. For nanowires synthesis, the vapor-liquid-solid mechanism was used. Nanowires were beyond a few hundred nanometers in lengths and around 15-20 nm in diameter, while the globe cap's size on the nanowires was around 15-25 nm. The indium tin oxide (ITO) played as catalyst in nanofabrication for WO{sub 3} nanowires growth and had outstanding role in bio-sensing especially for bio-molecule adherence. In applied electric field presence, the fabricated device showed the great potential to enhance medical diagnostics. (orig.)

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.

Equilibrium distributions of free charged particles and molecules in systems with non-plane boundaries

International Nuclear Information System (INIS)

Usenko, A.S.

1995-01-01

The equilibrium space-inhomogeneous distributions of free and pair bound charged particles are calculated in the dipole approximation for the plasma-molecular cylinder and sphere. It is shown that the space and orientational distributions of charged particles and molecules in these systems are similar to those in the cases of plasma-molecular system restricted by one or two parallel planes. The influence of the parameters of outer medium and a plasma-molecular system on the space and orientational distributions of charged particles and molecules is studied in detail

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.

Classical study of the rovibrational dynamics of a polar diatomic molecule in static electric fields

Energy Technology Data Exchange (ETDEWEB)

Inarrea, Manuel, E-mail: manuel.inarrea@unirioja.e [Area de Fisica, Universidad de la Rioja, E-26006 Logrono (Spain); Salas, J. Pablo [Area de Fisica, Universidad de la Rioja, E-26006 Logrono (Spain); Gonzalez-Ferez, Rosario [Instituto ' Carlos I' de Fisica Teorica y Computacional, Universidad de Granada, E-18071 Granada (Spain); Departamento de Fisica Atomica, Molecular y Nuclear, Universidad de Granada, E-18071 Granada (Spain); Schmelcher, Peter [Theoretische Chemie, Physikalisch-Chemisches Institut, D-69120 Heidelberg (Germany); Physikalisches Institut, Universitaet Heidelberg, D-69120 Heidelberg (Germany)

2010-01-04

We study the classical dynamics of a polar diatomic molecule in the presence of a strong static homogeneous electric field. Our full rovibrational investigation includes the interaction with the field due to the permanent electric dipole moment and the polarizability of the molecule. Using the LiCs molecule as a prototype, we explore the stability of the equilibrium points and their bifurcations as the field strength is increased. The phase space structure and its dependence on the energy and field strength are analyzed in detail. We demonstrate that depending on the field strength and on the energy, the phase space is characterized either by regular features or by small stochastic layers of chaotic motion.

Effects of molecular orientation in the laser ionization of molecules

International Nuclear Information System (INIS)

Xinhua Xie; Gerald Jordan; Christopher Ede; Armin Scrinzi

2006-01-01

Complete test of publication follows. Time-dependent electron momentum distributions are calculated during ionization of linear molecules by a strong laser pulse and upon recollision. For typical experimental laser parameters, we find a strong influence of molecular orientation and initial state symmetry on the total ionization rates and also on momentum distributions, compared to which the effect of electron correlation is less important for simple molecules. The dynamics of electron release and subsequent recollision with the parent ion largely determines the time-frequency structure of harmonic radiation, which underlies the generation of attosecond XUV pulses and the time-resolved imaging techniques for the electronic structure of molecules. In the present work, the effects of orientation and initial orbital symmetry are investigated by solving the time-dependent Schroedinger equation for a two-dimensional diatomic molecule in the single-active electron approximation. As in the presence of strong external fields recolliding electrons cannot be easily separated from bound electrons, the electron wave packet is probed at some distance from where all electrons can be safety considered as detached. We find that momentum distributions strongly depend on molecular size, orientation of the molecular axis, and node structure of the initial state. In order to determine the momentum spectra at the time of electron release and upon recollision, we classically propagate the Wigner distributions of probed wavepackets backward and forward in time, respectively. We find that the times of peak recollision current can vary strongly with the orientation of the molecule. Moreover, correlation effects on the electron spectra are included using the multi-configuration time-dependent Hartree-Fock method. The calculations are performed in three spatial dimensions with the restriction to cylindrical symmetry, where the molecule is aligned with the laser field. Correlation is studied

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)

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.

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.

Minimizing pulling geometry errors in atomic force microscope single molecule force spectroscopy.

Science.gov (United States)

Rivera, Monica; Lee, Whasil; Ke, Changhong; Marszalek, Piotr E; Cole, Daniel G; Clark, Robert L

2008-10-01

In atomic force microscopy-based single molecule force spectroscopy (AFM-SMFS), it is assumed that the pulling angle is negligible and that the force applied to the molecule is equivalent to the force measured by the instrument. Recent studies, however, have indicated that the pulling geometry errors can drastically alter the measured force-extension relationship of molecules. Here we describe a software-based alignment method that repositions the cantilever such that it is located directly above the molecule's substrate attachment site. By aligning the applied force with the measurement axis, the molecule is no longer undergoing combined loading, and the full force can be measured by the cantilever. Simulations and experimental results verify the ability of the alignment program to minimize pulling geometry errors in AFM-SMFS studies.

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.

Gauge-invariant expectation values of the energy of a molecule in an electromagnetic field

International Nuclear Information System (INIS)

Mandal, Anirban; Hunt, Katharine L. C.

2016-01-01

In this paper, we show that the full Hamiltonian for a molecule in an electromagnetic field can be separated into a molecular Hamiltonian and a field Hamiltonian, both with gauge-invariant expectation values. The expectation value of the molecular Hamiltonian gives physically meaningful results for the energy of a molecule in a time-dependent applied field. In contrast, the usual partitioning of the full Hamiltonian into molecular and field terms introduces an arbitrary gauge-dependent potential into the molecular Hamiltonian and leaves a gauge-dependent form of the Hamiltonian for the field. With the usual partitioning of the Hamiltonian, this same problem of gauge dependence arises even in the absence of an applied field, as we show explicitly by considering a gauge transformation from zero applied field and zero external potentials to zero applied field, but non-zero external vector and scalar potentials. We resolve this problem and also remove the gauge dependence from the Hamiltonian for a molecule in a non-zero applied field and from the field Hamiltonian, by repartitioning the full Hamiltonian. It is possible to remove the gauge dependence because the interaction of the molecular charges with the gauge potential cancels identically with a gauge-dependent term in the usual form of the field Hamiltonian. We treat the electromagnetic field classically and treat the molecule quantum mechanically, but nonrelativistically. Our derivation starts from the Lagrangian for a set of charged particles and an electromagnetic field, with the particle coordinates, the vector potential, the scalar potential, and their time derivatives treated as the variables in the Lagrangian. We construct the full Hamiltonian using a Lagrange multiplier method originally suggested by Dirac, partition this Hamiltonian into a molecular term H m and a field term H f , and show that both H m and H f have gauge-independent expectation values. Any gauge may be chosen for the calculations; but

Dipolar molecules inside C-70: an electric field-driven room-temperature single-molecule switch

Czech Academy of Sciences Publication Activity Database

Foroutan-Nejad, C.; Andrushchenko, Valery; Straka, Michal

2016-01-01

Roč. 18, č. 48 (2016), s. 32673-32677 ISSN 1463-9076 R&D Projects: GA ČR(CZ) GA14-03564S Institutional support: RVO:61388963 Keywords : room-temperature single-molecule switch * electric field * endohedral fullerene * density functional calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.123, year: 2016 http://pubs.rsc.org/en/content/articlepdf/2016/cp/c6cp06986j

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.

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson–Boltzmann electrostatics

Science.gov (United States)

Sun, Hui; Wen, Jiayi; Zhao, Yanxiang; Li, Bo; McCammon, J. Andrew

2015-01-01

Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson–Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum–Chandler–Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods. PMID:26723595

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics.

Science.gov (United States)

Sun, Hui; Wen, Jiayi; Zhao, Yanxiang; Li, Bo; McCammon, J Andrew

2015-12-28

Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson-Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum-Chandler-Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods.

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.

Nanodevices for generating power from molecules and batteryless sensing

Energy Technology Data Exchange (ETDEWEB)

Wang, Yinmin; Wang, Xianying; Hamza, Alex V.

2017-01-03

A nanoconverter or nanosensor is disclosed capable of directly generating electricity through physisorption interactions with molecules that are dipole containing organic species in a molecule interaction zone. High surface-to-volume ratio semiconductor nanowires or nanotubes (such as ZnO, silicon, carbon, etc.) are grown either aligned or randomly-aligned on a substrate. Epoxy or other nonconductive polymers are used to seal portions of the nanowires or nanotubes to create molecule noninteraction zones. By correlating certain molecule species to voltages generated, a nanosensor may quickly identify which species is detected. Nanoconverters in a series parallel arrangement may be constructed in planar, stacked, or rolled arrays to supply power to nano- and micro-devices without use of external batteries. In some cases breath, from human or other life forms, contain sufficient molecules to power a nanoconverter. A membrane permeable to certain molecules around the molecule interaction zone increases specific molecule nanosensor selectivity response.

The spontaneous synchronized dance of pairs of water molecules

Energy Technology Data Exchange (ETDEWEB)

Roncaratti, Luiz F. [Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia (Italy); Instituto de Física, Universidade de Brasília, 70910-900 Brasília (Brazil); Cappelletti, David, E-mail: david.cappelletti@unipg.it; Pirani, Fernando [Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia (Italy)

2014-03-28

Molecular beam scattering experiments have been performed to study the effect of long-range anisotropic forces on the collision dynamics of two small polar molecules. The main focus of this paper is on water, but also ammonia and hydrogen sulphide molecules have been investigated, and some results will be anticipated. The intermolecular distances mainly probed are of the order of 1 nm and therefore much larger than the molecular dimensions. In particular, we have found that the natural electric field gradient, generated by different spatial orientations of the permanent electric dipoles, is able to promote the transformation of free rotations into coupled pendular states, letting the molecular partners involved in the collision complex swinging to and fro around the field direction. This long-ranged concerted motion manifested itself as large increases of the magnitude of the total integral cross section. The experimental findings and the theoretical treatment developed to shed light on the details of the process suggest that the transformation from free rotations to pendular states depends on the rotational level of both molecules, on the impact parameter, on the relative collision velocity, on the dipole moment product and occurs in the time scale of picoseconds. The consequences of this intriguing phenomenon may be important for the interpretation and, in perspective, for the control of elementary chemical and biological processes, given by polar molecules, ions, and free radicals, occurring in several environments under various conditions.

The spontaneous synchronized dance of pairs of water molecules

International Nuclear Information System (INIS)

Roncaratti, Luiz F.; Cappelletti, David; Pirani, Fernando

2014-01-01

Molecular beam scattering experiments have been performed to study the effect of long-range anisotropic forces on the collision dynamics of two small polar molecules. The main focus of this paper is on water, but also ammonia and hydrogen sulphide molecules have been investigated, and some results will be anticipated. The intermolecular distances mainly probed are of the order of 1 nm and therefore much larger than the molecular dimensions. In particular, we have found that the natural electric field gradient, generated by different spatial orientations of the permanent electric dipoles, is able to promote the transformation of free rotations into coupled pendular states, letting the molecular partners involved in the collision complex swinging to and fro around the field direction. This long-ranged concerted motion manifested itself as large increases of the magnitude of the total integral cross section. The experimental findings and the theoretical treatment developed to shed light on the details of the process suggest that the transformation from free rotations to pendular states depends on the rotational level of both molecules, on the impact parameter, on the relative collision velocity, on the dipole moment product and occurs in the time scale of picoseconds. The consequences of this intriguing phenomenon may be important for the interpretation and, in perspective, for the control of elementary chemical and biological processes, given by polar molecules, ions, and free radicals, occurring in several environments under various conditions

Flow-alignment of bicellar lipid mixtures: orientations of probe molecules and membrane-associated biomacromolecules in lipid membranes studied with polarized light

KAUST Repository

Kogan, Maxim; Beke-Somfai, Tamá s; Nordé n, Bengt

2011-01-01

Bicelles are excellent membrane-mimicking hosts for a dynamic and structural study of solutes with NMR, but the magnetic fields required for their alignment are hard to apply to optical conditions. Here we demonstrate that bicellar mixtures can be aligned by shear forces in a Couette flow cell, to provide orientation of membrane-bound retinoic acid, pyrene and cytochrome c (cyt c) protein, conveniently studied with linear dichroism spectroscopy. © 2011 The Royal Society of Chemistry.

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.

Theoretical femtosecond physics atoms and molecules in strong laser fields

CERN Document Server

Grossmann, Frank

2018-01-01

This textbook extends from the basics of femtosecond physics all the way to some of the latest developments in the field. In this updated edition, the chapter on laser-driven atoms is augmented by the discussion of two-electron atoms interacting with strong and short laser pulses, as well as by a review of ATI rings and low energy structures in photo-electron spectra. In the chapter on laser-driven molecules a discussion of 2D infrared spectroscopy is incorporated. Theoretical investigations of atoms and molecules interacting with pulsed lasers up to atomic field strengths on the order of 10^16 W/cm² are leading to an understanding of many challenging experimental discoveries. The presentation starts with a brief introduction to pulsed laser physics. The basis for the non-perturbative treatment of laser-matter interaction in the book is the time-dependent Schrödinger equation. Its analytical as well as numerical solution are laid out in some detail. The light field is treated classically and different possi...

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

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...

Toward Additive-Free Small-Molecule Organic Solar Cells: Roles of the Donor Crystallization Pathway and Dynamics

KAUST Repository

Abdelsamie, Maged

2015-09-29

The ease with which small-molecule donors crystallize during solution processing is directly linked to the need for solvent additives. Donor molecules that get trapped in disordered (H1) or liquid crystalline (T1) mesophases require additive processing to promote crystallization, phase separation, and efficient light harvesting. A donor material (X2) that crystallizes directly from solution yields additive-free solar cells with an efficiency of 7.6%. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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)

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

Label-free electrochemical biosensing of small-molecule inhibition on O-GlcNAc glycosylation.

Science.gov (United States)

Yang, Yu; Gu, Yuxin; Wan, Bin; Ren, Xiaomin; Guo, Liang-Hong

2017-09-15

O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT) plays a critical role in modulating protein function in many cellular processes and human diseases such as Alzheimer's disease and type II diabetes, and has emerged as a promising new target. Specific inhibitors of OGT could be valuable tools to probe the biological functions of O-GlcNAcylation, but a lack of robust nonradiometric assay strategies to detect glycosylation, has impeded efforts to identify such compounds. Here we have developed a novel label-free electrochemical biosensor for the detection of peptide O-GlcNAcylation using protease-protection strategy and electrocatalytic oxidation of tyrosine mediated by osmium bipyridine as a signal reporter. There is a large difference in the abilities of proteolysis of the glycosylated and the unglycosylated peptides by protease, thus providing a sensing mechanism for OGT activity. When the O-GlcNAcylation is achieved, the glycosylated peptides cannot be cleaved by proteinase K and result in a high current response on indium tin oxide (ITO) electrode. However, when the O-GlcNAcylation is successfully inhibited using a small molecule, the unglycosylated peptides can be cleaved easily and lead to low current signal. Peptide O-GlcNAcylation reaction was performed in the presence of a well-defined small-molecule OGT inhibitor. The results indicated that the biosensor could be used to screen the OGT inhibitors effectively. Our label-free electrochemical method is a promising candidate for protein glycosylation pathway research in screening small-molecule inhibitors of OGT. Copyright © 2017 Elsevier B.V. All rights reserved.

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 ‖ .

Sum-frequency spectroscopic studies: I. Surface melting of ice, II. Surface alignment of polymers

Energy Technology Data Exchange (ETDEWEB)

Wei, Xing [Univ. of California, Berkeley, CA (United States)

2000-01-01

Surface vibrational spectroscopy via infrared-visible sum-frequency generation (SFG) has been established as a useful tool to study the structures of different kinds of surfaces and interfaces. This technique was used to study the (0001) face of hexagonal ice (Ih). SFG spectra in the O-H stretch frequency range were obtained at various sample temperatures. For the vapor(air)/ice interface, the degree of orientational order of the dangling OH bonds at the surface was measured as a function of temperature. Disordering sets in around 200 K and increases dramatically with temperature, which is strong evidence of surface melting of ice. For the other ice interfaces (silica/OTS/ice and silica/ice), a similar temperature dependence of the hydrogen bonded OH stretch peak was observed; the free OH stretch mode, however, appears to be different from that of the vapor (air)/ice interface due to interactions at the interfaces. The technique was also used to measure the orientational distributions of the polymer chains on a rubbed polyvinyl alcohol surface. Results show that the polymer chains at the surface appear to be well aligned by rubbing, and the adsorbed liquid crystal molecules are aligned, in turn, by the surface polymer chains. A strong correlation exists between the orientational distributions of the polymer chains and the liquid crystal molecules, indicating that the surface-induced bulk alignment of a liquid crystal film by rubbed polymer surfaces is via an orientational epitaxy-like mechanism. This thesis also contains studies on some related issues that are crucial to the above applications. An experiment was designed to measure SFG spectra in both reflection and transmission. The result confirms that SFG in reflection is generally dominated by the surface contribution. Another issue is the motional effect due to fast orientational motion of molecules at a surface or interface. Calculations show that the effect is significant if the molecular orientation varies

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.

Electric-Field Control of Interfering Transport Pathways in a Single-Molecule Anthraquinone Transistor

NARCIS (Netherlands)

Koole, Max; Thijssen, Jos M.; Valkenier, Hennie; Hummelen, Jan C.; van der Zant, Herre S. J.

It is understood that molecular conjugation plays an important role in charge transport through single-molecule junctions. Here, we investigate electron transport through an anthraquinone based single-molecule three-terminal device. With the use of an electric-field induced by a gate electrode, the

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.

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.

Fractionation of hydrogen and oxygen isotopes between hydrated and free water molecules in aqueous urea solution

International Nuclear Information System (INIS)

Kakiuchi, M.; Matsuo, S.

1985-01-01

Ratios of D/H and 18 O/ 16 O in the vapor phase in equilibrium with aqueous urea solution with different urea molalities were measured at 15 and 25 0 C. Under the assumption that urea solutions consist of two species, i.e., the urea-water cluster and free water, the results are interpreted to give the average hydration number, i.e., the number of water molecules per urea molecule in the urea-water cluster. Good agreement was obtained for the hydration number estimated independently from hydrogen and oxygen isotopic fractions. On the basis of hydrogen isotopic data at 25 0 C, the average hydration number of urea in the cluster is 6.3 +/- 0.8 at 2.1 m and 2.75 +/- 0.08 at saturation (20.15 m). The corresponding average hydration numbers based on oxygen isotopic data were calculated to be 6.7 +/- 2.4 at 2.1 m and 2.75 +/- 0.25 at urea saturation. HD 16 O is enriched in the urea-water cluster and H 2 18 O is enriched in free water. Isotopic partitioning between the cluster and free water is markedly different from those between hydration spheres and free water in aqueous electrolyte solutions. 29 references, 6 figures, 5 tables

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

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

A rapid and sensitive method for the simultaneous analysis of aliphatic and polar molecules containing free carboxyl groups in plant extracts by LC-MS/MS

Directory of Open Access Journals (Sweden)

Bonaventure Gustavo

2009-11-01

Full Text Available Abstract Background Aliphatic molecules containing free carboxyl groups are important intermediates in many metabolic and signalling reactions, however, they accumulate to low levels in tissues and are not efficiently ionized by electrospray ionization (ESI compared to more polar substances. Quantification of aliphatic molecules becomes therefore difficult when small amounts of tissue are available for analysis. Traditional methods for analysis of these molecules require purification or enrichment steps, which are onerous when multiple samples need to be analyzed. In contrast to aliphatic molecules, more polar substances containing free carboxyl groups such as some phytohormones are efficiently ionized by ESI and suitable for analysis by LC-MS/MS. Thus, the development of a method with which aliphatic and polar molecules -which their unmodified forms differ dramatically in their efficiencies of ionization by ESI- can be simultaneously detected with similar sensitivities would substantially simplify the analysis of complex biological matrices. Results A simple, rapid, specific and sensitive method for the simultaneous detection and quantification of free aliphatic molecules (e.g., free fatty acids (FFA and small polar molecules (e.g., jasmonic acid (JA, salicylic acid (SA containing free carboxyl groups by direct derivatization of leaf extracts with Picolinyl reagent followed by LC-MS/MS analysis is presented. The presence of the N atom in the esterified pyridine moiety allowed the efficient ionization of 25 compounds tested irrespective of their chemical structure. The method was validated by comparing the results obtained after analysis of Nicotiana attenuata leaf material with previously described analytical methods. Conclusion The method presented was used to detect 16 compounds in leaf extracts of N. attenuata plants. Importantly, the method can be adapted based on the specific analytes of interest with the only consideration that the

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)

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.

Notes on free radicals in the field of human and environmental protection against ionizing radiations

International Nuclear Information System (INIS)

Bittel, R.

It is well known that ionizing radiations, in vitro and in vivo produce, free radicals which may be considered as mediators between physical agents and biological targets. Some aspects of this vast problem are accentuated. Ionizing radiations act either directly on the organic molecules of tissues or indirectly by creating, in the surroundings and in tissular water, inorganic free radicals which act on biochemical molecules to gives new radicals. Analysis of the free radical initiation phenomenon in vivo shows that many initiating agents exist, ionizing radiations representing only one group. The role of oxydants, especially oxydising polluants, and the part played by various enzyme systems (super-oxide dismutase, oxydases etc...) are emphasized. After propagation the chain reactions end in combinations between radicals are stopped by certain organic molecules (radical scavengers). Examples are given (free radical formation from compounds of great biological importance: puric and pyrimidic bases, nucleic acids in particular). These aspects are discussed from the viewpoint of their effects on human and environmental protection against both ionizing radiations and certain chemical pollution [fr

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

Control of magnetism in dilute magnetic semiconductor (Ga,Mn)As films by surface decoration of molecules

Science.gov (United States)

Wang, Hailong; Wang, Xiaolei; Xiong, Peng; Zhao, Jianhua

2016-03-01

The responses of magnetic moments to external stimuli such as magnetic-field, heat, light and electric-field have been utilized to manipulate the magnetism in magnetic semiconductors, with many of the novel ideas applied even to ferromagnetic metals. Here, we review a new experimental development on the control of magnetism in (Ga,Mn)As thin films by surface decoration of organic molecules: Molecules deposited on the surface of (Ga,Mn)As thin films are shown to be capable of significantly modulating their saturation magnetization and Curie temperature. These phenomena are shown to originate from the carrier-mediated ferromagnetism in (Ga,Mn)As and the surface molecules acting as acceptors or donors depending on their highest occupied molecular orbitals, resembling the charge transfer mechanism in a pn junction in which the equilibrium state is reached on the alignment of Fermi levels.

Control of magnetism in dilute magnetic semiconductor (Ga,MnAs films by surface decoration of molecules

Directory of Open Access Journals (Sweden)

Hailong eWang

2016-03-01

Full Text Available The responses of magnetic moments to external stimuli such as magnetic-field, heat, light and electric-field have been utilized to manipulate the magnetism in magnetic semiconductors, with many of the novel ideas applied even to ferromagnetic metals. Here, we review a new experimental development on the control of magnetism in (Ga,MnAs thin films by surface decoration of organic molecules: Molecules deposited on the surface of (Ga,MnAs thin films are shown to be capable of significantly modulating their saturation magnetization and Curie temperature. These phenomena are shown to originate from the carrier-mediated ferromagnetism in (Ga,MnAs and the surface molecules acting as acceptors or donors depending on their highest occupied molecular orbitals, resembling the charge transfer mechanism in a pn junction in which the equilibrium state is reached on the alignment of Fermi levels.

Theoretical femtosecond physics atoms and molecules in strong laser fields

CERN Document Server

Grossmann, Frank

2013-01-01

Theoretical investigations of atoms and molecules interacting with pulsed or continuous wave lasers up to atomic field strengths on the order of 10^16 W/cm² are leading to an understanding of many challenging experimental discoveries. This book deals with the basics of femtosecond physics and goes up to the latest applications of new phenomena. The book presents an introduction to laser physics with mode-locking and pulsed laser operation. The solution of the time-dependent Schrödinger equation is discussed both analytically and numerically. The basis for the non-perturbative treatment of laser-matter interaction in the book is the numerical solution of the time-dependent Schrödinger equation. The light field is treated classically, and different possible gauges are discussed. Physical phenonema, ranging from Rabi-oscillations in two-level systems to the ionization of atoms, the generation of high harmonics, the ionization and dissociation of molecules as well as the control of chemical reactions are pre...

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.

Probing strong-field electron-nuclear dynamics of polyatomic molecules using proton motion

International Nuclear Information System (INIS)

Markevitch, Alexei N.; Smith, Stanley M.; Levis, Robert J.; Romanov, Dmitri A.

2007-01-01

Proton ejection during Coulomb explosion is studied for several structure-related organic molecules (anthracene, anthraquinone, and octahydroanthracene) subjected to 800 nm, 60 fs laser pulses at intensities from 0.50 to 4.0x10 14 W cm -2 . The proton kinetic energy distributions are found to be markedly structure specific. The distributions are bimodal for anthracene and octahydroanthracene and trimodal for anthraquinone. Maximum (cutoff) energies of the distributions range from 50 eV for anthracene to 83 eV for anthraquinone. The low-energy mode (∼10 eV) is most pronounced in octahydroanthracene. The dependence of the characteristic features of the distributions on the laser intensity provides insights into molecular specificity of such strong-field phenomena as (i) nonadiabatic charge localization and (ii) field-mediated restructuring of polyatomic molecules polarized by a strong laser field

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 ...

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.

High Throughput, Label-free Screening Small Molecule Compound Libraries for Protein-Ligands using Combination of Small Molecule Microarrays and a Special Ellipsometry-based Optical Scanner.

Science.gov (United States)

Landry, James P; Fei, Yiyan; Zhu, X D

2011-12-01

Small-molecule compounds remain the major source of therapeutic and preventative drugs. Developing new drugs against a protein target often requires screening large collections of compounds with diverse structures for ligands or ligand fragments that exhibit sufficiently affinity and desirable inhibition effect on the target before further optimization and development. Since the number of small molecule compounds is large, high-throughput screening (HTS) methods are needed. Small-molecule microarrays (SMM) on a solid support in combination with a suitable binding assay form a viable HTS platform. We demonstrate that by combining an oblique-incidence reflectivity difference optical scanner with SMM we can screen 10,000 small-molecule compounds on a single glass slide for protein ligands without fluorescence labeling. Furthermore using such a label-free assay platform we can simultaneously acquire binding curves of a solution-phase protein to over 10,000 immobilized compounds, thus enabling full characterization of protein-ligand interactions over a wide range of affinity constants.

Electric-Field Control of Interfering Transport Pathways in a Single-Molecule Anthraquinone Transistor

Science.gov (United States)

Koole, Max; Thijssen, Jos M.; Valkenier, Hennie; Hummelen, Jan C.; Zant, Herre S. J. van der

2015-08-01

It is understood that molecular conjugation plays an important role in charge transport through single-molecule junctions. Here, we investigate electron transport through an anthraquinone based single-molecule three-terminal device. With the use of an electric-field induced by a gate electrode, the molecule is reduced resulting into a ten-fold increase in the off-resonant differential conductance. Theoretical calculations link the change in differential conductance to a reduction-induced change in conjugation, thereby lifting destructive interference of transport pathways.

Isotope-selective high-order interferometry with large organic molecules in free fall

Science.gov (United States)

Rodewald, Jonas; Dörre, Nadine; Grimaldi, Andrea; Geyer, Philipp; Felix, Lukas; Mayor, Marcel; Shayeghi, Armin; Arndt, Markus

2018-03-01

Interferometry in the time domain has proven valuable for matter-wave based measurements. This concept has recently been generalized to cold molecular clusters using short-pulse standing light waves which realized photo-depletion gratings, arranged in a time-domain Talbot–Lau interferometer (OTIMA). Here we extend this idea further to large organic molecules and demonstrate a new scheme to scan the emerging molecular interferogram in position space. The capability of analyzing different isotopes of the same monomer under identical conditions opens perspectives for studying the interference fringe shift as a function of time in gravitational free fall. The universality of OTIMA interferometry allows one to handle a large variety of particles. In our present work, quasi-continuous laser evaporation allows transferring fragile organic molecules into the gas phase, covering more than an order of magnitude in mass between 614 amu and 6509 amu, i.e. 300% more massive than in previous OTIMA experiments. For all masses, we find about 30% fringe visibility.

Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology

Energy Technology Data Exchange (ETDEWEB)

Taylor, Ronald C. [Case Western Reserve Univ., Cleveland, OH (United States)

1991-11-01

This thesis involved the construction of (1) a grammar that incorporates knowledge on base invariancy and secondary structure in a molecule and (2) a parser engine that uses the grammar to position bases into the structural subunits of the molecule. These concepts were combined with a novel pinning technique to form a tool that semi-automates insertion of a new species into the alignment for the 16S rRNA molecule (a component of the ribosome) maintained by Dr. Carl Woese`s group at the University of Illinois at Urbana. The tool was tested on species extracted from the alignment and on a group of entirely new species. The results were very encouraging, and the tool should be substantial aid to the curators of the 16S alignment. The construction of the grammar was itself automated, allowing application of the tool to alignments for other molecules. The logic programming language Prolog was used to construct all programs involved. The computational linguistics approach used here was found to be a useful way to attach the problem of insertion into an alignment.

Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology

Energy Technology Data Exchange (ETDEWEB)

Taylor, R.C.

1991-11-01

This thesis involved the construction of (1) a grammar that incorporates knowledge on base invariancy and secondary structure in a molecule and (2) a parser engine that uses the grammar to position bases into the structural subunits of the molecule. These concepts were combined with a novel pinning technique to form a tool that semi-automates insertion of a new species into the alignment for the 16S rRNA molecule (a component of the ribosome) maintained by Dr. Carl Woese's group at the University of Illinois at Urbana. The tool was tested on species extracted from the alignment and on a group of entirely new species. The results were very encouraging, and the tool should be substantial aid to the curators of the 16S alignment. The construction of the grammar was itself automated, allowing application of the tool to alignments for other molecules. The logic programming language Prolog was used to construct all programs involved. The computational linguistics approach used here was found to be a useful way to attach the problem of insertion into an alignment.

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

Effects of Electric Field on the Valence-Bond Property of an Electron in a Quantum-Dot Molecule

Institute of Scientific and Technical Information of China (English)

王立民; 罗莹; 马本堃

2002-01-01

The electronic structure of the quantum-dot molecules in an electric field is investigated by the finite element method with the effective mass approximation. The numerical calculation results show that the valence bond of the quantum-dot molecule alternates between covalent bonds and ionic bonds as the electric field increases. The valence-bond property can be reflected by the oscillator strength of the intraband transition. The bound state with the highest energy level in the quantum-dot molecule gradually changes into a quasibound state when the electric field increases.

Influence of thermocleavable functionality on organic field-effect transistor performance of small molecules

Science.gov (United States)

Mahale, Rajashree Y.; Dharmapurikar, Satej S.; Chini, Mrinmoy Kumar; Venugopalan, Vijay

2017-06-01

Diketopyrrolopyrrole based donor-acceptor-donor conjugated small molecules using ethylene dioxythiophene as a donor was synthesized. Electron deficient diketopyrrolopyrrole unit was substituted with thermocleavable (tert-butyl acetate) side chains. The thermal treatment of the molecules at 160 °C eliminated the tert-butyl ester group results in the formation of corresponding acid. Optical and theoretical studies revealed that the molecules adopted a change in molecular arrangement after thermolysis. The conjugated small molecules possessed p-channel charge transport characteristics in organic field effect transistors. The charge carrier mobility was increased after thermolysis of tert-butyl ester group to 5.07 × 10-5 cm2/V s.

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

Heat transfer and forces on concave surfaces in free molecule flow.

Science.gov (United States)

Fan, C.

1971-01-01

A Monte Carlo modeling technique is described for mathematically simulating free molecular flows over a concave spherical surface and a concave cylindrical surface of finite length. The half-angle of the surfaces may vary from 0 to 90 degrees, and the incident flow may have an arbitrary speed ratio and an arbitrary angle of attack. Partial diffuse reflection and imperfect energy accommodation for molecules colliding with the surfaces are also considered. Results of heat transfer, drag and lift coefficients are presented for a variety of flow conditions. The present Monte Carlo results are shown to be in very good agreement with certain available theoretical solutions.

Free energy minimization to predict RNA secondary structures and computational RNA design.

Science.gov (United States)

Churkin, Alexander; Weinbrand, Lina; Barash, Danny

2015-01-01

Determining the RNA secondary structure from sequence data by computational predictions is a long-standing problem. Its solution has been approached in two distinctive ways. If a multiple sequence alignment of a collection of homologous sequences is available, the comparative method uses phylogeny to determine conserved base pairs that are more likely to form as a result of billions of years of evolution than by chance. In the case of single sequences, recursive algorithms that compute free energy structures by using empirically derived energy parameters have been developed. This latter approach of RNA folding prediction by energy minimization is widely used to predict RNA secondary structure from sequence. For a significant number of RNA molecules, the secondary structure of the RNA molecule is indicative of its function and its computational prediction by minimizing its free energy is important for its functional analysis. A general method for free energy minimization to predict RNA secondary structures is dynamic programming, although other optimization methods have been developed as well along with empirically derived energy parameters. In this chapter, we introduce and illustrate by examples the approach of free energy minimization to predict RNA secondary structures.

Relation of high harmonic spectra to electronic structure in N2

International Nuclear Information System (INIS)

Farrell, J.P.; McFarland, B.K.; Guehr, M.; Bucksbaum, P.H.

2009-01-01

High harmonics of N 2 exhibit a number of features that are related to the electronic structure and sub-femtosecond dynamics of the molecule. Through measurements and simulations, we show how the harmonic spectral shape, spectral phase, alignment angle dependence, and intensity dependence can be related to the strong-field ionization and recombination dynamics of the HOMO and HOMO-1 electron orbitals. A field-free static model of the molecule is insufficient to explain the observations.

Separation of large DNA molecules by applying pulsed electric field to size exclusion chromatography-based microchip

Science.gov (United States)

Azuma, Naoki; Itoh, Shintaro; Fukuzawa, Kenji; Zhang, Hedong

2018-02-01

Through electrophoresis driven by a pulsed electric field, we succeeded in separating large DNA molecules with an electrophoretic microchip based on size exclusion chromatography (SEC), which was proposed in our previous study. The conditions of the pulsed electric field required to achieve the separation were determined by numerical analyses using our originally proposed separation model. From the numerical results, we succeeded in separating large DNA molecules (λ DNA and T4 DNA) within 1600 s, which was approximately half of that achieved under a direct electric field in our previous study. Our SEC-based electrophoresis microchip will be one of the effective tools to meet the growing demand of faster and more convenient separation of large DNA molecules, especially in the field of epidemiological research of infectious diseases.

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

Spectral analysis for systems of atoms and molecules coupled to the quantized radiation field

International Nuclear Information System (INIS)

Bach, V.; Sigal, I.M.

1999-01-01

We consider systems of static nuclei and electrons - atoms and molecules - coupled to the quantized radiation field. The interactions between electrons and the soft modes of the quantized electromagnetic field are described by minimal coupling, p→p-eA(x), where A(x) is the electromagnetic vector potential with an ultraviolet cutoff. If the interactions between the electrons and the quantized radiation field are turned off, the atom or molecule is assumed to have at least one bound state. We prove that, for sufficiently small values of the fine structure constant α, the interacting system has a ground state corresponding to the bottom of its energy spectrum. For an atom, we prove that its excited states above the ground state turn into metastable states whose life-times we estimate. Furthermore the energy spectrum is absolutely continuous, except, perhaps,in a small interval above the ground state energy and around the threshold energies of the atom or molecule. (orig.)

Energy levels of mesic molecules ddμ and dt μ in a homogeneous magnetic field

International Nuclear Information System (INIS)

Choi Nam Chol.

1990-01-01

The energy levels of mesic molecules ddμ and dtμ in a homogeneous magnetic field 0-10 8 Gs have been calculated. Calculations are carried out in the adiabatic representation of three-body problem. It is shown that in really existing fields ( 5 Gs) the shifts of energy levels produce no considerable effect on the process of resonant production of mesic molecules. 13 refs.; 3 figs.; 2 tabs

Gibbs Free Energy of Hydrolytic Water Molecule in Acyl-Enzyme Intermediates of a Serine Protease: A Potential Application for Computer-Aided Discovery of Mechanism-Based Reversible Covalent Inhibitors.

Science.gov (United States)

Masuda, Yosuke; Yamaotsu, Noriyuki; Hirono, Shuichi

2017-01-01

In order to predict the potencies of mechanism-based reversible covalent inhibitors, the relationships between calculated Gibbs free energy of hydrolytic water molecule in acyl-trypsin intermediates and experimentally measured catalytic rate constants (k cat ) were investigated. After obtaining representative solution structures by molecular dynamics (MD) simulations, hydration thermodynamics analyses using WaterMap™ were conducted. Consequently, we found for the first time that when Gibbs free energy of the hydrolytic water molecule was lower, logarithms of k cat were also lower. The hydrolytic water molecule with favorable Gibbs free energy may hydrolyze acylated serine slowly. Gibbs free energy of hydrolytic water molecule might be a useful descriptor for computer-aided discovery of mechanism-based reversible covalent inhibitors of hydrolytic enzymes.

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.

Helium atoms and molecules in strong magnetic fields

Science.gov (United States)

Mori, K.

Recent theoretical studies have shown that the neutron star surface may be composed of helium or heavier elements as hydrogen may be quickly depleted by diffuse nuclear burning Chang Bildsten However while Hydrogen atmospheres have been studied in great details atomic data for helium is available only for He ion Pavlov Bezchastnov 2005 We performed Hartree-Fock type calculation for Helium atom and molecules and computed their binding ionization and dissociation energies in strong magnetic fields B sim10 12 -- 10 15 G We will present ionization balance of Helium atmospheres at typical magnetic field strengths and temperatures to radio-quiet neutron stars and AXPs We will also discuss several implications of helium atmosphere to X-ray data of isolated neutron stars focusing on the detected spectral features

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.

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

Measurement and statistical analysis of single-molecule current-voltage characteristics, transition voltage spectroscopy, and tunneling barrier height.

Science.gov (United States)

Guo, Shaoyin; Hihath, Joshua; Díez-Pérez, Ismael; Tao, Nongjian

2011-11-30

We report on the measurement and statistical study of thousands of current-voltage characteristics and transition voltage spectra (TVS) of single-molecule junctions with different contact geometries that are rapidly acquired using a new break junction method at room temperature. This capability allows one to obtain current-voltage, conductance voltage, and transition voltage histograms, thus adding a new dimension to the previous conductance histogram analysis at a fixed low-bias voltage for single molecules. This method confirms the low-bias conductance values of alkanedithiols and biphenyldithiol reported in literature. However, at high biases the current shows large nonlinearity and asymmetry, and TVS allows for the determination of a critically important parameter, the tunneling barrier height or energy level alignment between the molecule and the electrodes of single-molecule junctions. The energy level alignment is found to depend on the molecule and also on the contact geometry, revealing the role of contact geometry in both the contact resistance and energy level alignment of a molecular junction. Detailed statistical analysis further reveals that, despite the dependence of the energy level alignment on contact geometry, the variation in single-molecule conductance is primarily due to contact resistance rather than variations in the energy level alignment.

Immobilization of sericin molecules via amorphous carbon plasma modified-polystyrene dish for serum-free culture

International Nuclear Information System (INIS)

Tunma, Somruthai; Song, Doo-Hoon; Kim, Si-Eun; Kim, Kyoung-Nam; Han, Jeon-Geon; Boonyawan, Dheerawan

2013-01-01

In this study, we focused on sericin hydrolysates, originating from silkworm used in serum-free human bone marrow-derived mesenchymal stem cells (hBM-MSCs) culture. We reported the effect of a covalent linkage between a bioactive protein molecule and polystyrene dish surface via a carbon intermediate layer which can slow down the release rate of protein compounds into the phosphate buffer saline (PBS) solution. Films of amorphous carbon (a-C) and functionalized-carbon were deposited on PS culture dish surfaces by using a DC magnetron sputtering system and RF PECVD system. We found that a-C based-films can increase the hydrophilicity and biocompatibility of polystyrene (PS) dishes, especially a-C films and a-C:N 2 films showed good attachment of hBM-MSCs at 24 h. However, in the case of silica surface (a-C:SiO x films), the cells showed a ragged and unattached boundary resulting from the presence of surface silanol groups. For the UV–vis absorbance, all carbon modified-PS dishes showed a lower release rate of sericin molecules into PBS solution than PS control. This revealed that the functionalized carbon could be enhanced by specific binding properties with given molecules. The carbon-coated PS dishes grafting with sericin protein were used in a serum-free condition. We also found that hBM-MSCs have higher percentage of proliferated cells at day 7 for the modified dishes with carbon films and coated with sericin than the PS control coated with sericin. The physical film properties were measured by atomic force microscopy (AFM), scanning electron microscope (SEM) and contact angle measurement. The presence of -NH 2 groups of sericin compounds on the PS dish was revealed by Fourier transform infrared spectroscopy (FTIR). The stability of covalent bonds of sericin molecules after washing out ungrafted sericin was confirmed by X-ray photoelectron spectroscopy (XPS).

Immobilization of sericin molecules via amorphous carbon plasma modified-polystyrene dish for serum-free culture

Science.gov (United States)

Tunma, Somruthai; Song, Doo-Hoon; Kim, Si-Eun; Kim, Kyoung-Nam; Han, Jeon-Geon; Boonyawan, Dheerawan

2013-10-01

In this study, we focused on sericin hydrolysates, originating from silkworm used in serum-free human bone marrow-derived mesenchymal stem cells (hBM-MSCs) culture. We reported the effect of a covalent linkage between a bioactive protein molecule and polystyrene dish surface via a carbon intermediate layer which can slow down the release rate of protein compounds into the phosphate buffer saline (PBS) solution. Films of amorphous carbon (a-C) and functionalized-carbon were deposited on PS culture dish surfaces by using a DC magnetron sputtering system and RF PECVD system. We found that a-C based-films can increase the hydrophilicity and biocompatibility of polystyrene (PS) dishes, especially a-C films and a-C:N2 films showed good attachment of hBM-MSCs at 24 h. However, in the case of silica surface (a-C:SiOx films), the cells showed a ragged and unattached boundary resulting from the presence of surface silanol groups. For the UV-vis absorbance, all carbon modified-PS dishes showed a lower release rate of sericin molecules into PBS solution than PS control. This revealed that the functionalized carbon could be enhanced by specific binding properties with given molecules. The carbon-coated PS dishes grafting with sericin protein were used in a serum-free condition. We also found that hBM-MSCs have higher percentage of proliferated cells at day 7 for the modified dishes with carbon films and coated with sericin than the PS control coated with sericin. The physical film properties were measured by atomic force microscopy (AFM), scanning electron microscope (SEM) and contact angle measurement. The presence of sbnd NH2 groups of sericin compounds on the PS dish was revealed by Fourier transform infrared spectroscopy (FTIR). The stability of covalent bonds of sericin molecules after washing out ungrafted sericin was confirmed by X-ray photoelectron spectroscopy (XPS).

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

Observation of Coherent and Incoherent Dissociation Mechanisms in the Angular Distribution of Atomic Photofragment Alignment

International Nuclear Information System (INIS)

Bracker, A.S.; Lee, Y.T.; Bracker, A.S.; Wouters, E.R.; Suits, A.G.; Lee, Y.T.; Lee, Y.T.; Vasyutinskii, O.S.

1998-01-01

We have analyzed the recoil angle dependence of chlorine atom angular momentum alignment for the dissociation of chlorine molecules at 355nm. This angular distribution was isolated from ion image measurements, which map a three-dimensional velocity vector distribution of state-selectively-ionized photofragments into a two-dimensional spatial distribution. Using a general quantum mechanical method to simulate the alignment angular distribution, we show that there are clear contributions to alignment from both incoherent and coherent components of a perpendicular optical transition in the molecule. copyright 1998 The American Physical Society

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

Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces

KAUST Repository

Cui, Xuefeng

2015-09-09

To detect and evaluate the similarities between the three-dimensional (3D) structures of two molecules, various kinds of methods have been proposed for the pairwise structure alignment problem [6, 9, 7, 11]. The problem plays important roles when studying the function and the evolution of biological molecules. Recently, pairwise structure alignment methods have been extended and applied on surface pocket structures [10, 3, 5] and interaction interface structures [8, 4]. The results show that, even when there are no global similarities discovered between the global sequences and the global structures, biological molecules or complexes could share similar functions because of well conserved pockets and interfaces. Thus, pairwise pocket and interface structure alignments are promising to unveil such shared functions that cannot be discovered by the well-studied global sequence and global structure alignments. State-of-the-art methods for pairwise pocket and interface structure alignments [4, 5] are direct extensions of the classic pairwise protein structure alignment methods, and thus such methods share a few limitations. First, the goal of the classic protein structure alignment methods is to align single-chain protein structures (i.e., a single fragment of residues connected by peptide bonds). However, we observed that pockets and interfaces tend to consist of tens of extremely short backbone fragments (i.e., three or fewer residues connected by peptide bonds). Thus, existing pocket and interface alignment methods based on the protein structure alignment methods still rely on the existence of long-enough backbone fragments, and the fragmentation issue of pockets and interfaces rises the risk of missing the optimal alignments. Moreover, existing interface structure alignment methods focus on protein-protein interfaces, and require a "blackbox preprocessing" before aligning protein-DNA and protein-RNA interfaces. Therefore, we introduce the PROtein STucture Alignment

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.

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.

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

Science.gov (United States)

Huang, Jing; Mei, Ye; König, Gerhard; Simmonett, Andrew C; Pickard, Frank C; Wu, Qin; Wang, Lee-Ping; MacKerell, Alexander D; Brooks, Bernard R; Shao, Yihan

2017-02-14

In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

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.

Fabrication of Vertically Aligned Carbon Nanotube or Zinc Oxide Nanorod Arrays for Optical Diffraction Gratings.

Science.gov (United States)

Kim, Jeong; Kim, Sun Il; Cho, Seong-Ho; Hwang, Sungwoo; Lee, Young Hee; Hur, Jaehyun

2015-11-01

We report on new fabrication methods for a transparent, hierarchical, and patterned electrode comprised of either carbon nanotubes or zinc oxide nanorods. Vertically aligned carbon nanotubes or zinc oxide nanorod arrays were fabricated by either chemical vapor deposition or hydrothermal growth, in combination with photolithography. A transparent conductive graphene layer or zinc oxide seed layer was employed as the transparent electrode. On the patterned surface defined using photoresist, the vertically grown carbon nanotubes or zinc oxides could produce a concentrated electric field under applied DC voltage. This periodic electric field was used to align liquid crystal molecules in localized areas within the optical cell, effectively modulating the refractive index. Depending on the material and morphology of these patterned electrodes, the diffraction efficiency presented different behavior. From this study, we established the relationship between the hierarchical structure of the different electrodes and their efficiency for modulating the refractive index. We believe that this study will pave a new path for future optoelectronic applications.

Ligandbook: an online repository for small and drug-like molecule force field parameters.

Science.gov (United States)

Domanski, Jan; Beckstein, Oliver; Iorga, Bogdan I

2017-06-01

Ligandbook is a public database and archive for force field parameters of small and drug-like molecules. It is a repository for parameter sets that are part of published work but are not easily available to the community otherwise. Parameter sets can be downloaded and immediately used in molecular dynamics simulations. The sets of parameters are versioned with full histories and carry unique identifiers to facilitate reproducible research. Text-based search on rich metadata and chemical substructure search allow precise identification of desired compounds or functional groups. Ligandbook enables the rapid set up of reproducible molecular dynamics simulations of ligands and protein-ligand complexes. Ligandbook is available online at https://ligandbook.org and supports all modern browsers. Parameters can be searched and downloaded without registration, including access through a programmatic RESTful API. Deposition of files requires free user registration. Ligandbook is implemented in the PHP Symfony2 framework with TCL scripts using the CACTVS toolkit. oliver.beckstein@asu.edu or bogdan.iorga@cnrs.fr ; contact@ligandbook.org . Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Exact results in nonequilibrium statistical mechanics: Formalism and applications in chemical kinetics and single-molecule free energy estimation

Science.gov (United States)

Adib, Artur B.

In the last two decades or so, a collection of results in nonequilibrium statistical mechanics that departs from the traditional near-equilibrium framework introduced by Lars Onsager in 1931 has been derived, yielding new fundamental insights into far-from-equilibrium processes in general. Apart from offering a more quantitative statement of the second law of thermodynamics, some of these results---typified by the so-called "Jarzynski equality"---have also offered novel means of estimating equilibrium quantities from nonequilibrium processes, such as free energy differences from single-molecule "pulling" experiments. This thesis contributes to such efforts by offering three novel results in nonequilibrium statistical mechanics: (a) The entropic analog of the Jarzynski equality; (b) A methodology for estimating free energies from "clamp-and-release" nonequilibrium processes; and (c) A directly measurable symmetry relation in chemical kinetics similar to (but more general than) chemical detailed balance. These results share in common the feature of remaining valid outside Onsager's near-equilibrium regime, and bear direct applicability in protein folding kinetics as well as in single-molecule free energy estimation.

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.

Energy and spectrum of BeO molecule under the electric field from different directions

NARCIS (Netherlands)

Jiang, M.; Guo, F. J.; Yan, A. Y.; Zhang, C. W.; Miao, F.

2010-01-01

Based on the density functional theory DFT/ B3LYP at 6-311g level, the ground states of BeO molecule are optimized. The effects of electric field on the bond length, the system energy, the charge distribution, the energy levels, the HOMO-LUMO gaps and the infrared spectrum of BeO molecule are

Effects of Magnetic Field on the Valence Bond Property of the Double-Quantum-Dot Molecule

Institute of Scientific and Technical Information of China (English)

王立民; 罗莹; 马本堃

2002-01-01

The effects of the magnetic field on the valence bond property of the double-quantum-dot molecule are numerically studied by the finite element method and perturbation approach because of the absence of cylindrical symmetry in the horizontally coupled dots. The calculation results show that the energy value of the ground state changes differently from that of the first excited state with increasing magnetic field strength, and they cross under a certain magnetic field. The increasing magnetic field makes the covalent bond state change into an ionic bond state, which agrees qualitatively with experimental results and makes ionic bond states remain. The oscillator strength of transition between covalent bond states decreases distinctly with the increasing magnetic field strength, when the molecule is irradiated by polarized light. Such a phenomenon is possibly useful for actual applications.

Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method.

Science.gov (United States)

Nielsen, Morten; Lundegaard, Claus; Lund, Ole

2007-07-04

Antigen presenting cells (APCs) sample the extra cellular space and present peptides from here to T helper cells, which can be activated if the peptides are of foreign origin. The peptides are presented on the surface of the cells in complex with major histocompatibility class II (MHC II) molecules. Identification of peptides that bind MHC II molecules is thus a key step in rational vaccine design and developing methods for accurate prediction of the peptide:MHC interactions play a central role in epitope discovery. The MHC class II binding groove is open at both ends making the correct alignment of a peptide in the binding groove a crucial part of identifying the core of an MHC class II binding motif. Here, we present a novel stabilization matrix alignment method, SMM-align, that allows for direct prediction of peptide:MHC binding affinities. The predictive performance of the method is validated on a large MHC class II benchmark data set covering 14 HLA-DR (human MHC) and three mouse H2-IA alleles. The predictive performance of the SMM-align method was demonstrated to be superior to that of the Gibbs sampler, TEPITOPE, SVRMHC, and MHCpred methods. Cross validation between peptide data set obtained from different sources demonstrated that direct incorporation of peptide length potentially results in over-fitting of the binding prediction method. Focusing on amino terminal peptide flanking residues (PFR), we demonstrate a consistent gain in predictive performance by favoring binding registers with a minimum PFR length of two amino acids. Visualizing the binding motif as obtained by the SMM-align and TEPITOPE methods highlights a series of fundamental discrepancies between the two predicted motifs. For the DRB1*1302 allele for instance, the TEPITOPE method favors basic amino acids at most anchor positions, whereas the SMM-align method identifies a preference for hydrophobic or neutral amino acids at the anchors. The SMM-align method was shown to outperform other

Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

Directory of Open Access Journals (Sweden)

Lund Ole

2007-07-01

Full Text Available Abstract Background Antigen presenting cells (APCs sample the extra cellular space and present peptides from here to T helper cells, which can be activated if the peptides are of foreign origin. The peptides are presented on the surface of the cells in complex with major histocompatibility class II (MHC II molecules. Identification of peptides that bind MHC II molecules is thus a key step in rational vaccine design and developing methods for accurate prediction of the peptide:MHC interactions play a central role in epitope discovery. The MHC class II binding groove is open at both ends making the correct alignment of a peptide in the binding groove a crucial part of identifying the core of an MHC class II binding motif. Here, we present a novel stabilization matrix alignment method, SMM-align, that allows for direct prediction of peptide:MHC binding affinities. The predictive performance of the method is validated on a large MHC class II benchmark data set covering 14 HLA-DR (human MHC and three mouse H2-IA alleles. Results The predictive performance of the SMM-align method was demonstrated to be superior to that of the Gibbs sampler, TEPITOPE, SVRMHC, and MHCpred methods. Cross validation between peptide data set obtained from different sources demonstrated that direct incorporation of peptide length potentially results in over-fitting of the binding prediction method. Focusing on amino terminal peptide flanking residues (PFR, we demonstrate a consistent gain in predictive performance by favoring binding registers with a minimum PFR length of two amino acids. Visualizing the binding motif as obtained by the SMM-align and TEPITOPE methods highlights a series of fundamental discrepancies between the two predicted motifs. For the DRB1*1302 allele for instance, the TEPITOPE method favors basic amino acids at most anchor positions, whereas the SMM-align method identifies a preference for hydrophobic or neutral amino acids at the anchors. Conclusion

Exploring the alignment of carbon nanotubes dispersed in a liquid crystal matrix using coplanar electrodes

International Nuclear Information System (INIS)

Volpati, D.; Massey, M. K.; Kotsialos, A.; Qaiser, F.; Pearson, C.; Tiburzi, G.; Zeze, D. A.; Petty, M. C.; Johnson, D. W.; Coleman, K. S.

2015-01-01

We report on the use of a liquid crystalline host medium to align single-walled carbon nanotubes in an electric field using an in-plane electrode configuration. Electron microscopy reveals that the nanotubes orient in the field with a resulting increase in the DC conductivity in the field direction. Current versus voltage measurements on the composite show a nonlinear behavior, which was modelled by using single-carrier space-charge injection. The possibility of manipulating the conductivity pathways in the same sample by applying the electrical field in different (in-plane) directions has also been demonstrated. Raman spectroscopy indicates that there is an interaction between the nanotubes and the host liquid crystal molecules that goes beyond that of simple physical mixing

Observation of rotational revivals for iodine molecules in helium droplets using a near-adiabatic laser pulse

Science.gov (United States)

Shepperson, Benjamin; Chatterley, Adam S.; Christiansen, Lars; Søndergaard, Anders A.; Stapelfeldt, Henrik

2018-01-01

A 160-ps near-Gaussian, linearly polarized laser pulse is used to align iodine (I2) molecules embedded in helium nanodroplets. The rise time of the laser pulse is sufficiently long and smooth that the alignment, characterized by , behaves adiabatically during the pulse turnon. However, after the laser pulse has turned off stays above 0.50 and a recurrence structure occurs ˜650 ps later. Measurements on isolated (I2) molecules with identical laser pulses are used to identify, through analysis of the observed half- and full-rotational revivals, that the nonadiabatic postpulse alignment dynamics results from a mild truncation of the trailing edge of the laser pulse. This truncation establishes a well-defined starting time for coherent rotation, which leads to the revival structures observed both for isolated molecules and molecules in He droplets. In the latter case the time-dependent trace recorded here is compared to that obtained previously for a 450-fs alignment pulse. It is found that the observed revivals are very similar.

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

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

Cold guided beams of polar molecules

International Nuclear Information System (INIS)

Motsch, Michael

2010-01-01

spectroscopy of formaldehyde. First, ultraviolet absorption spectroscopy of the A 1 A 2 1 A 1 transition of formaldehyde is performed in a room-temperature gas to extract molecular constants. These findings are used to address single rotational states of guided molecules. Since the formaldehyde molecules dissociate upon ultraviolet excitation, the laser-frequency-dependent decrease in the number of guided molecules allows to extract the population of individual rotational states in the beam. With the source temperature set to 155 K, populations of rotational states exceeding 10% are observed, which validates the theoretical model of velocity filtering. Finally, Rayleigh scattering into an optical cavity is investigated as an alternative, non-destructive detection method for cold molecules. Comparing the rate of scattering into the fundamental cavity mode to that into the same mode under free-space conditions, an enhancement by a factor of up to 38 is observed for room-temperature gases. This Purcell-like enhancement is explained by interference of electromagnetic fields scattered by a classical driven dipole oscillator in the resonator. (orig.)

Monte Carlo calculations of the free-molecule drag on chains of uniform spheres

International Nuclear Information System (INIS)

Dahneke, B.; Chan, P.

1980-01-01

Monte Carlo calculations of the free-molecule drag on straight chains of uniform spheres are presented. The drag on a long chain is expressed in terms of the drag on a basic chain unit (two hemispheres touching at their poles) multiplied by the number of spheres in the chain. Since there is no interaction between the basic chain units, it is argued that the results also apply as a good approximation to the drag on kinked and branched chains covering a broad range of geometries. Experimental data are cited which support this claim

Dissociative multiple ionization of diatomic molecules by extreme-ultraviolet free-electron-laser pulses

DEFF Research Database (Denmark)

Madsen, Lars Bojer; Leth, Henriette Astrup

2011-01-01

Nuclear dynamics in dissociative multiple ionization processes of diatomic molecules exposed to extreme-ultraviolet free-electron-laser pulses is studied theoretically using the Monte Carlo wave packet approach. By simulated detection of the emitted electrons, the model reduces a full propagation...... of the system to propagations of the nuclear wave packet in one specific electronic charge state at a time. Suggested ionization channels can be examined, and kinetic energy release spectra for the nuclei can be calculated and compared with experiments. Double ionization of O2 is studied as an example, and good...

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.

Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase.

Science.gov (United States)

Woods, Christopher J; Shaw, Katherine E; Mulholland, Adrian J

2015-01-22

The applicability of combined quantum mechanics/molecular mechanics (QM/MM) methods for the calculation of absolute binding free energies of conserved water molecules in protein/ligand complexes is demonstrated. Here, we apply QM/MM Monte Carlo simulations to investigate binding of water molecules to influenza neuraminidase. We investigate five different complexes, including those with the drugs oseltamivir and peramivir. We investigate water molecules in two different environments, one more hydrophobic and one hydrophilic. We calculate the free-energy change for perturbation of a QM to MM representation of the bound water molecule. The calculations are performed at the BLYP/aVDZ (QM) and TIP4P (MM) levels of theory, which we have previously demonstrated to be consistent with one another for QM/MM modeling. The results show that the QM to MM perturbation is significant in both environments (greater than 1 kcal mol(-1)) and larger in the more hydrophilic site. Comparison with the same perturbation in bulk water shows that this makes a contribution to binding. The results quantify how electronic polarization differences in different environments affect binding affinity and also demonstrate that extensive, converged QM/MM free-energy simulations, with good levels of QM theory, are now practical for protein/ligand complexes.

Theory of tunneling ionization of molecules: Weak-field asymptotics including dipole effects

DEFF Research Database (Denmark)

Tolstikhin, Oleg I.; Morishita, Toru; Madsen, Lars Bojer

2011-01-01

The formulation of the parabolic adiabatic expansion approach to the problem of ionization of atomic systems in a static electric field, originally developed for the axially symmetric case [ Phys. Rev. A 82 023416 (2010)], is generalized to arbitrary potentials. This approach is used to rederive...... the asymptotic theory of tunneling ionization in the weak-field limit. In the atomic case, the resulting formulas for the ionization rate coincide with previously known results. In addition, the present theory accounts for the possible existence of a permanent dipole moment of the unperturbed system and, hence......, applies to polar molecules. Accounting for dipole effects constitutes an important difference of the present theory from the so-called molecular Ammosov-Delone-Krainov theory. The theory is illustrated by comparing exact and asymptotic results for a set of model polar molecules and a realistic molecular...

Ion yields of laser aligned CH3I and CH3Br from multiple orbitals

NARCIS (Netherlands)

He, Lanhai; Pan, Yun; Yang, Yujun; Luo, Sizuo; Lu, Chunjing; Zhao, Huifang; Li, Dongxu; Song, Lele; Stolte, Steven; Ding, Dajun; Roeterdink, Wim G.

2016-01-01

We have measured the alignment influence on ion yields of CH3I and CH3Br molecules in the laser intensity regime from 1013 W/cm2 to 1015 W/cm2. The hexapole state-selection technique combined with laser induced alignment has been employed to obtain aligned (〈P2(cosθ)〉=0.7) and anti-aligned

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

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

Inkjet-Printed Small-Molecule Organic Light-Emitting Diodes: Halogen-Free Inks, Printing Optimization, and Large-Area Patterning.

Science.gov (United States)

Zhou, Lu; Yang, Lei; Yu, Mengjie; Jiang, Yi; Liu, Cheng-Fang; Lai, Wen-Yong; Huang, Wei

2017-11-22

Manufacturing small-molecule organic light-emitting diodes (OLEDs) via inkjet printing is rather attractive for realizing high-efficiency and long-life-span devices, yet it is challenging. In this paper, we present our efforts on systematical investigation and optimization of the ink properties and the printing process to enable facile inkjet printing of conjugated light-emitting small molecules. Various factors on influencing the inkjet-printed film quality during the droplet generation, the ink spreading on the substrates, and its solidification processes have been systematically investigated and optimized. Consequently, halogen-free inks have been developed and large-area patterning inkjet printing on flexible substrates with efficient blue emission has been successfully demonstrated. Moreover, OLEDs manufactured by inkjet printing the light-emitting small molecules manifested superior performance as compared with their corresponding spin-cast counterparts.

Photo polymerization-induced vertical phase separation and homeotropic alignment in liquid crystal and polymer mixtures

International Nuclear Information System (INIS)

Kang, Hyo; Joo, Sangwoo; Kang, Daeseung

2012-01-01

We presented a novel method for the homeotropic alignment of LC by using the irradiation of UV light on the LC/NOA65 mixture cell, in which the photo-initiated-polymerization-induced phase separation lowers the surface energy. When the amount of polymer content is sufficiently small, the gravel and network patterns were formed at the substrates via the vertical phase separation. We found that surface roughness plays an important role in the formation of the homeotropic alignment of LC. We also observed the alignment transition of the cells by varying the mixing ratio of LC/NOA65 or the UV radiation time. Furthermore, the present proposed method has great potential for application in display devices. For decades, studies on the alignment of liquid crystal (LC) molecules have been of significant interest due to their immediate applications for display devices and the intriguing physiochemical properties they exhibit at the surface of mixtures. Usually, homeotropic (or vertical) alignment, in which the long axes of the LC molecules are oriented in a direction perpendicular to the surface, is achieved by using surfactants such as lecithin, silanes or polyimide. Recently homeotropic alignment of liquid crystal molecules was achieved by irradiating photosensitive polymers, by doping nanoparticles into LC, by utilizing nano/micro patterns, or by incorporating self-assembled monolayers (SAMs). However, a clear understanding about the alignment mechanism is still elusive. In this paper, we report a novel method for homeotropic alignment of LC by utilizing the phase separation of LC/polymer mixtures

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...

Generation of atto-second pulses in atoms and molecules

International Nuclear Information System (INIS)

Haessler, St.

2009-12-01

When a low-frequency laser pulse is focused to a high intensity into a gas, the electric field of the laser light may become of comparable strength to that felt by the electrons bound in an atom or molecule. A valence electron can then be 'freed' by tunnel ionization, accelerated by the strong oscillating laser field and can eventually re-collide and recombine with the ion. The gained kinetic energy is then released as a burst of coherent X-UV light and the macroscopic gas medium then becomes a source of X-UV light pulses of atto-second (1 as equals 10 -18 s) duration. This is the natural time-scale of electron dynamics in atoms and molecules. The largest part of this thesis deals with experiments where molecules are the harmonic generation medium and the re-colliding electron wave packet acts as a 'self-probe'. In several experiments, we demonstrate the potential of this scheme to observe or image ultra-fast intra-molecular electronic and nuclear dynamics. In particular, we have performed the first phase measurements of the high harmonic emission from aligned molecules and we have extracted the recombination dipole matrix element. This observable contains signatures of quantum interference between the continuum and bound parts of the total electronic wavefunction. It is shown how this quantum interference can be utilized to shape the atto-second light emission from the molecules. In a second part of this thesis, we use the well characterized coherent X-UV light emitted by rare gas atoms to photo-ionize molecules. Measuring the ejected photoelectron wave packet then allows to extract information on the photoionization process itself, and possibly about the initial bound and final continuum states of the electron. The last chapter of this manuscript describes studies of high harmonic and atto-second light pulse generation in a different medium: ablation plasmas. (author)

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

Micropatterning stretched and aligned DNA for sequence-specific nanolithography

Science.gov (United States)

Petit, Cecilia Anna Paulette

Techniques for fabricating nanostructured materials can be categorized as either "top-down" or "bottom-up". Top-down techniques use lithography and contact printing to create patterned surfaces and microfluidic channels that can corral and organize nanoscale structures, such as molecules and nanorods in contrast; bottom-up techniques use self-assembly or molecular recognition to direct the organization of materials. A central goal in nanotechnology is the integration of bottom-up and top-down assembly strategies for materials development, device design; and process integration. With this goal in mind, we have developed strategies that will allow this integration by using DNA as a template for nanofabrication; two top-down approaches allow the placement of these templates, while the bottom-up technique uses the specific sequence of bases to pattern materials along each strand of DNA. Our first top-down approach, termed combing of molecules in microchannels (COMMIC), produces microscopic patterns of stretched and aligned molecules of DNA on surfaces. This process consists of passing an air-water interface over end adsorbed molecules inside microfabricated channels. The geometry of the microchannel directs the placement of the DNA molecules, while the geometry of the airwater interface directs the local orientation and curvature of the molecules. We developed another top-down strategy for creating micropatterns of stretched and aligned DNA using surface chemistry. Because DNA stretching occurs on hydrophobic surfaces, this technique uses photolithography to pattern vinyl-terminated silanes on glass When these surface-, are immersed in DNA solution, molecules adhere preferentially to the silanized areas. This approach has also proven useful in patterning protein for cell adhesion studies. Finally, we describe the use of these stretched and aligned molecules of DNA as templates for the subsequent bottom-up construction of hetero-structures through hybridization

A Method for Extracting the Free Energy Surface and Conformational Dynamics of Fast-Folding Proteins from Single Molecule Photon Trajectories

Science.gov (United States)

2015-01-01

Single molecule fluorescence spectroscopy holds the promise of providing direct measurements of protein folding free energy landscapes and conformational motions. However, fulfilling this promise has been prevented by technical limitations, most notably, the difficulty in analyzing the small packets of photons per millisecond that are typically recorded from individual biomolecules. Such limitation impairs the ability to accurately determine conformational distributions and resolve sub-millisecond processes. Here we develop an analytical procedure for extracting the conformational distribution and dynamics of fast-folding proteins directly from time-stamped photon arrival trajectories produced by single molecule FRET experiments. Our procedure combines the maximum likelihood analysis originally developed by Gopich and Szabo with a statistical mechanical model that describes protein folding as diffusion on a one-dimensional free energy surface. Using stochastic kinetic simulations, we thoroughly tested the performance of the method in identifying diverse fast-folding scenarios, ranging from two-state to one-state downhill folding, as a function of relevant experimental variables such as photon count rate, amount of input data, and background noise. The tests demonstrate that the analysis can accurately retrieve the original one-dimensional free energy surface and microsecond folding dynamics in spite of the sub-megahertz photon count rates and significant background noise levels of current single molecule fluorescence experiments. Therefore, our approach provides a powerful tool for the quantitative analysis of single molecule FRET experiments of fast protein folding that is also potentially extensible to the analysis of any other biomolecular process governed by sub-millisecond conformational dynamics. PMID:25988351

Effect of an improved molecular potential on strong-field tunneling ionization of molecules

International Nuclear Information System (INIS)

Zhao Songfeng; Jin Cheng; Le, Anh-Thu; Lin, C. D.

2010-01-01

We study the effect of one-electron model potentials on the tunneling ionization rates of molecules in strong fields. By including electron correlation using the modified Leeuwen-Baerends (LB α) model, the binding energies of outer shells of molecules are significantly improved. However, we show that the tunneling ionization rates from the LB α do not differ much from the earlier calculations [Phys. Rev. A 81, 033423 (2010)], in which the local correlation potential was neglected.

Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field.

Science.gov (United States)

Kim, Seonah; Orendt, Anita M; Ferraro, Marta B; Facelli, Julio C

2009-10-01

This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. Copyright 2009 Wiley Periodicals, Inc.

Immobilization of sericin molecules via amorphous carbon plasma modified-polystyrene dish for serum-free culture

Energy Technology Data Exchange (ETDEWEB)

Tunma, Somruthai [The Graduate School, Chiang Mai University, 239 Huay Kaew Road, Muang District, Chiang Mai 50200 (Thailand); Thailand Center of Excellence in Physics (ThEP), 239 Huay Kaew Road, Muang District, Chiang Mai 50200 (Thailand); Song, Doo-Hoon [Research Center for Orofacial Hard Tissue Regeneration, College of Dentistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752 (Korea, Republic of); Kim, Si-Eun; Kim, Kyoung-Nam [Research Center for Orofacial Hard Tissue Regeneration, College of Dentistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752 (Korea, Republic of); Department and Research Institute of Dental Biomaterials and Bioengineering, College of Dentistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752 (Korea, Republic of); Han, Jeon-Geon [Center for Advanced Plasma Surface Technology, Sungkyunkwan University, 300 Chunchun-dong, Jangan-gu, Suwon 440-746 (Korea, Republic of); Boonyawan, Dheerawan [Thailand Center of Excellence in Physics (ThEP), 239 Huay Kaew Road, Muang District, Chiang Mai 50200 (Thailand); Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Muang District, Chiang Mai 50200 (Thailand)

2013-10-15

In this study, we focused on sericin hydrolysates, originating from silkworm used in serum-free human bone marrow-derived mesenchymal stem cells (hBM-MSCs) culture. We reported the effect of a covalent linkage between a bioactive protein molecule and polystyrene dish surface via a carbon intermediate layer which can slow down the release rate of protein compounds into the phosphate buffer saline (PBS) solution. Films of amorphous carbon (a-C) and functionalized-carbon were deposited on PS culture dish surfaces by using a DC magnetron sputtering system and RF PECVD system. We found that a-C based-films can increase the hydrophilicity and biocompatibility of polystyrene (PS) dishes, especially a-C films and a-C:N{sub 2} films showed good attachment of hBM-MSCs at 24 h. However, in the case of silica surface (a-C:SiO{sub x} films), the cells showed a ragged and unattached boundary resulting from the presence of surface silanol groups. For the UV–vis absorbance, all carbon modified-PS dishes showed a lower release rate of sericin molecules into PBS solution than PS control. This revealed that the functionalized carbon could be enhanced by specific binding properties with given molecules. The carbon-coated PS dishes grafting with sericin protein were used in a serum-free condition. We also found that hBM-MSCs have higher percentage of proliferated cells at day 7 for the modified dishes with carbon films and coated with sericin than the PS control coated with sericin. The physical film properties were measured by atomic force microscopy (AFM), scanning electron microscope (SEM) and contact angle measurement. The presence of -NH{sub 2} groups of sericin compounds on the PS dish was revealed by Fourier transform infrared spectroscopy (FTIR). The stability of covalent bonds of sericin molecules after washing out ungrafted sericin was confirmed by X-ray photoelectron spectroscopy (XPS).

Effect of substrate thickness on ejection of phenylalanine molecules adsorbed on free-standing graphene bombarded by 10 keV C{sub 60}

Energy Technology Data Exchange (ETDEWEB)

Golunski, M. [Institute of Physics, Jagiellonian University, ul. Lojasiewicza 11, 30-348 Krakow (Poland); Verkhoturov, S.V.; Verkhoturov, D.S.; Schweikert, E.A. [Department of Chemistry, Texas A& M University, College Station, TX 77840 (United States); Postawa, Z., E-mail: zbigniew.postawa@uj.edu.pl [Institute of Physics, Jagiellonian University, ul. Lojasiewicza 11, 30-348 Krakow (Poland)

2017-02-15

Highlights: • Substrate thickness has a prominent effect on the molecular ejection mechanism. • Collisions with projectile atoms leads to molecular ejection at thin substrates. • Interactions with deforming graphene sheet ejects molecules from thicker substrates. • Probability of fragmentation process decreases with the graphene substrate thickness. - Abstract: Molecular dynamics computer simulations have been employed to investigate the effect of substrate thickness on the ejection mechanism of phenylalanine molecules deposited on free-standing graphene. The system is bombarded from the graphene side by 10 keV C{sub 60} projectiles at normal incidence and the ejected particles are collected both in transmission and reflection directions. It has been found that the ejection mechanism depends on the substrate thickness. At thin substrates mostly organic fragments are ejected by direct collisions between projectile atoms and adsorbed molecules. At thicker substrates interaction between deforming topmost graphene sheet and adsorbed molecules becomes more important. As this process is gentle and directionally correlated, it leads predominantly to ejection of intact molecules. The implications of the results to a novel analytical approach in Secondary Ion Mass Spectrometry based on ultrathin free-standing graphene substrates and a transmission geometry are discussed.

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

Massively Parallel Single-Molecule Manipulation Using Centrifugal Force

Science.gov (United States)

Wong, Wesley; Halvorsen, Ken

2011-03-01

Precise manipulation of single molecules has led to remarkable insights in physics, chemistry, biology, and medicine. However, two issues that have impeded the widespread adoption of these techniques are equipment cost and the laborious nature of making measurements one molecule at a time. To meet these challenges, we have developed an approach that enables massively parallel single- molecule force measurements using centrifugal force. This approach is realized in the centrifuge force microscope, an instrument in which objects in an orbiting sample are subjected to a calibration-free, macroscopically uniform force- field while their micro-to-nanoscopic motions are observed. We demonstrate high- throughput single-molecule force spectroscopy with this technique by performing thousands of rupture experiments in parallel, characterizing force-dependent unbinding kinetics of an antibody-antigen pair in minutes rather than days. Currently, we are taking steps to integrate high-resolution detection, fluorescence, temperature control and a greater dynamic range in force. With significant benefits in efficiency, cost, simplicity, and versatility, single-molecule centrifugation has the potential to expand single-molecule experimentation to a wider range of researchers and experimental systems.

High-fidelity target sequencing of individual molecules identified using barcode sequences: de novo detection and absolute quantitation of mutations in plasma cell-free DNA from cancer patients.

Science.gov (United States)

Kukita, Yoji; Matoba, Ryo; Uchida, Junji; Hamakawa, Takuya; Doki, Yuichiro; Imamura, Fumio; Kato, Kikuya

2015-08-01

Circulating tumour DNA (ctDNA) is an emerging field of cancer research. However, current ctDNA analysis is usually restricted to one or a few mutation sites due to technical limitations. In the case of massively parallel DNA sequencers, the number of false positives caused by a high read error rate is a major problem. In addition, the final sequence reads do not represent the original DNA population due to the global amplification step during the template preparation. We established a high-fidelity target sequencing system of individual molecules identified in plasma cell-free DNA using barcode sequences; this system consists of the following two steps. (i) A novel target sequencing method that adds barcode sequences by adaptor ligation. This method uses linear amplification to eliminate the errors introduced during the early cycles of polymerase chain reaction. (ii) The monitoring and removal of erroneous barcode tags. This process involves the identification of individual molecules that have been sequenced and for which the number of mutations have been absolute quantitated. Using plasma cell-free DNA from patients with gastric or lung cancer, we demonstrated that the system achieved near complete elimination of false positives and enabled de novo detection and absolute quantitation of mutations in plasma cell-free DNA. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Simulations of the Static Friction Due to Adsorbed Molecules

OpenAIRE

He, Gang; Robbins, Mark O.

2001-01-01

The static friction between crystalline surfaces separated by a molecularly thin layer of adsorbed molecules is calculated using molecular dynamics simulations. These molecules naturally lead to a finite static friction that is consistent with macroscopic friction laws. Crystalline alignment, sliding direction, and the number of adsorbed molecules are not controlled in most experiments and are shown to have little effect on the friction. Temperature, molecular geometry and interaction potenti...

Application of the weak-field asymptotic theory to the analysis of tunneling ionization of linear molecules

DEFF Research Database (Denmark)

Madsen, Lars Bojer; Tolstikhin, Oleg I.; Morishita, Toru

2012-01-01

The recently developed weak-field asymptotic theory [ Phys. Rev. A 84 053423 (2011)] is applied to the analysis of tunneling ionization of a molecular ion (H2+), several homonuclear (H2, N2, O2) and heteronuclear (CO, HF) diatomic molecules, and a linear triatomic molecule (CO2) in a static...... electric field. The dependence of the ionization rate on the angle between the molecular axis and the field is determined by a structure factor for the highest occupied molecular orbital. This factor is calculated using a virtually exact discrete variable representation wave function for H2+, very accurate...... Hartree-Fock wave functions for the diatomics, and a Hartree-Fock quantum chemistry wave function for CO2. The structure factors are expanded in terms of standard functions and the associated structure coefficients, allowing the determination of the ionization rate for any orientation of the molecule...

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...

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

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.

Control of unidirectional transport of single-file water molecules through carbon nanotubes in an electric field.

Science.gov (United States)

Su, Jiaye; Guo, Hongxia

2011-01-25

The transport of water molecules through nanopores is not only crucial to biological activities but also useful for designing novel nanofluidic devices. Despite considerable effort and progress that has been made, a controllable and unidirectional water flow is still difficult to achieve and the underlying mechanism is far from being understood. In this paper, using molecular dynamics simulations, we systematically investigate the effects of an external electric field on the transport of single-file water molecules through a carbon nanotube (CNT). We find that the orientation of water molecules inside the CNT can be well-tuned by the electric field and is strongly coupled to the water flux. This orientation-induced water flux is energetically due to the asymmetrical water-water interaction along the CNT axis. The wavelike water density profiles are disturbed under strong field strengths. The frequency of flipping for the water dipoles will decrease as the field strength is increased, and the flipping events vanish completely for the relatively large field strengths. Most importantly, a critical field strength E(c) related to the water flux is found. The water flux is increased as E is increased for E ≤ E(c), while it is almost unchanged for E > E(c). Thus, the electric field offers a level of governing for unidirectional water flow, which may have some biological applications and provides a route for designing efficient nanopumps.

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set.

Science.gov (United States)

Horta, Bruno A C; Merz, Pascal T; Fuchs, Patrick F J; Dolenc, Jozica; Riniker, Sereina; Hünenberger, Philippe H

2016-08-09

This article reports on the calibration and validation of a new GROMOS-compatible parameter set 2016H66 for small organic molecules in the condensed phase. The calibration is based on 62 organic molecules spanning the chemical functions alcohol, ether, aldehyde, ketone, carboxylic acid, ester, amine, amide, thiol, sulfide, and disulfide, as well as aromatic compounds and nucleic-acid bases. For 57 organic compounds, the calibration targets are the experimental pure-liquid density ρliq and the vaporization enthalpy ΔHvap, as well as the hydration free energy ΔGwat and the solvation free energy ΔGche in cyclohexane, at atmospheric pressure and at (or close to) room temperature. The final root-mean-square deviations (RMSD) for these four quantities over the set of compounds are 32.4 kg m(-3), 3.5 kJ mol(-1), 4.1 kJ mol(-1), and 2.1 kJ mol(-1), respectively, and the corresponding average deviations (AVED) are 1.0 kg m(-3), 0.2 kJ mol(-1), 2.6 kJ mol(-1), and 1.0 kJ mol(-1), respectively. For the five nucleic-acid bases, the parametrization is performed by transferring the final 2016H66 parameters from analogous organic compounds followed by a slight readjustment of the charges to reproduce the experimental water-to-chloroform transfer free energies ΔGtrn. The final RMSD for this quantity over the five bases is 1.7 kJ mol(-1), and the corresponding AVED is 0.8 kJ mol(-1). As an initial validation of the 2016H66 set, seven additional thermodynamic, transport, and dielectric properties are calculated for the 57 organic compounds in the liquid phase. The agreement with experiment in terms of these additional properties is found to be reasonable, with significant deviations typically affecting either a specific chemical function or a specific molecule. This suggests that in most cases, a classical force-field description along with a careful parametrization against ρliq, ΔHvap, ΔGwat, and ΔGche results in a model that appropriately describes the liquid in terms of

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

The effective crystal field potential

CERN Document Server

Mulak, J

2000-01-01

As it results from the very nature of things, the spherical symmetry of the surrounding of a site in a crystal lattice or an atom in a molecule can never occur. Therefore, the eigenfunctions and eigenvalues of any bound ion or atom have to differ from those of spherically symmetric respective free ions. In this way, the most simplified concept of the crystal field effect or ligand field effect in the case of individual molecules can be introduced. The conventional notion of the crystal field potential is narrowed to its non-spherical part only through ignoring the dominating spherical part which produces only a uniform energy shift of gravity centres of the free ion terms. It is well understood that the non-spherical part of the effective potential "seen" by open-shell electrons localized on a metal ion plays an essential role in most observed properties. Light adsorption, electron paramagnetic resonance, inelastic neutron scattering and basic characteristics derived from magnetic and thermal measurements, ar...

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