Preferred Azimuthal Orientation Research Articles

Pore Ordering in Anodic Aluminum Oxide: Interplay between the Pattern of Pore Nuclei and the Crystallographic Orientation of Aluminum.

Anodization of aluminum with a pre-patterned surface is a promising approach for preparing anodic aluminum oxide (AAO) films with defect-free pore arrangement. Although pronounced effects of crystallographic orientation of Al on the AAO structure have been demonstrated, all current studies on the anodization of pre-patterned aluminum consider the substrate as an isotropic medium and, thus, do not consider the azimuthal orientation of the pattern relative to the basis vectors of the Al unit cell. Here, we investigate the interplay between the azimuthal alignment of the pore nuclei array and the crystallographic orientation of aluminum. Al(100) and Al(111) single-crystal substrates were pre-patterned by a Ga focused ion beam and then anodized under self-ordering conditions. The thickness-dependent degree of pore ordering in AAO was quantified using statistical analysis of scanning electron microscopy images. The observed trends demonstrate that the preferred azimuthal orientation of pore nuclei rows coincides with the <110> directions in the Al unit cell, which is favorable for creating AAO with a high degree of pore ordering. In the case of an unspecified azimuthal orientation of the pore nuclei array, crystallography-affected disorder within the AAO structure occurs with increasing film thickness. Our findings have important implications for preparing defect-free porous films over 100 µm in thickness that are crucial for a variety of AAO applications, e.g., creating metamaterials and 2D/3D photonic crystals.

Reynolds numbers and the elliptic approximation near the ultimate state of turbulent Rayleigh–Bénard convection

We report results of Reynolds-number measurements, based on multi-point temperature measurements and the elliptic approximation (EA) of He and Zhang (2006 Phys. Rev. E 73 055303), Zhao and He (2009 Phys. Rev. E 79 046316) for turbulent Rayleigh–Bénard convection (RBC) over the Rayleigh-number range and for a Prandtl number Pr ≃ 0.8. The sample was a right-circular cylinder with the diameter D and the height L both equal to 112 cm. The Reynolds numbers ReU and ReV were obtained from the mean-flow velocity U and the root-mean-square fluctuation velocity V, respectively. Both were measured approximately at the mid-height of the sample and near (but not too near) the side wall close to a maximum of ReU. A detailed examination, based on several experimental tests, of the applicability of the EA to turbulent RBC in our parameter range is provided. The main contribution to ReU came from a large-scale circulation in the form of a single convection roll with the preferred azimuthal orientation of its down flow nearly coinciding with the location of the measurement probes. First we measured time sequences of ReU(t) and ReV(t) from short (10 s) segments which moved along much longer sequences of many hours. The corresponding probability distributions of ReU(t) and ReV(t) had single peaks and thus did not reveal significant flow reversals. The two averaged Reynolds numbers determined from the entire data sequences were of comparable size. For both ReU and ReV could be described by a power-law dependence on Ra with an exponent ζ close to 0.44. This exponent is consistent with several other measurements for the classical RBC state at smaller Ra and larger Pr and with the Grossmann–Lohse (GL) prediction for ReU (Grossmann and Lohse 2000 J. Fluid. Mech. 407 27; Grossmann and Lohse 2001 86 3316; Grossmann and Lohse 2002 66 016305) but disagrees with the prediction by GL (Grossmann and Lohse 2004 Phys. Fluids 16 4462) for ReV. At the dependence of ReV on Ra changed, and for larger Ra , consistent with the prediction for ReU (Grossmann and Lohse 2000 J. Fluid. Mech. 407 27; Grossmann and Lohse Phys. Rev. Lett. 2001 86 3316; Grossmann and Lohse Phys. Rev. E 2002 66 016305; Grossmann and Lohse 2012 Phys. Fluids 24 125103) in the ultimate state of RBC.

The Physics of DNA in Confinement

Throughout all kingdoms of life, DNA is found to form compact structures. DNA is neatly wound inside a viral capsid, DNA forms hierarchical structures in cell nuclei, DNA could even be woven into complex 3D structures known as DNA origami. Such a ubiquitous compaction is surprising, as it contradicts, at the first look, the very basic physical properties of DNA: the high electrostatic charge and resistance to bending at the scale of 50 nm or less. Experimental work has shown that counterions surrounding DNA can considerably alter its properties, for example, turning electrostatic self-repulsion into attraction. Yet, elucidating the precise microscopic structure and mechanism of DNA-DNA interaction in confined environment remains beyond the experimental capability. Here, we report the results of all-atom molecular dynamics simulations that investigated the microscopic structure of dense DNA assemblies and the physics of interactions that makes such assemblies possible. First, we show that a refined parameterization of ion-DNA interaction [1] permits the all-atom MD method to quantitatively reproduce experimentally known properties [2,3] of dense DNA arrays. Next we characterize the microscopic structure of the arrays, elucidating their ionic atmosphere, preferred azimuthal orientation of DNA molecules, the pair-wise additivity of DNA-DNA forces, the longitudinal friction forces between DNA molecules, and the role of solvation force. Our study demonstrates the ability of all-atom molecular dynamics simulations to provide quantitative, accurate information about dense DNA systems, opening exciting opportunities for future work in the area of synthetic DNA nanostructures, DNA packaging in viral capsids and cell nuclei.[1] J Phys Chem Lett 3:45-50.[2] Proc Natl Acad Sci U S A 81:2621-2625.[3] Biophys J 94:4775-82.

Spectroscopy of isolated PTCDA molecules on the KCl(100) surface: Vibrational spectra and azimuthal orientation

Small amounts of the model molecule perylene-3,4,9,10-tetracarboxylic acid dianhydride (PTCDA) were vacuum deposited on epitaxial KCl films on Ag(100). The use of a low substrate temperature (20 K) during deposition hampered molecular diffusion resulting in isolated monomers on the surface. Fluorescence and fluorescence excitation spectroscopy performed on these monomers yielded highly resolved spectra with narrow lines corresponding to individual vibronic modes. This high resolution in our spectra is caused by a very small inhomogeneous broadening due to well-defined adsorption sites of the molecule on the substrate. Indeed, by polarization dependent fluorescence spectroscopy we show that the flat-lying molecules exhibit a preferred azimuthal orientation on the surface, the long molecular axis being oriented along the [011] or the equivalent [011] direction of the substrate. Furthermore, the high resolution in the spectra allowed a detailed analysis of the vibronic modes. The vibrational modes of the adsorbed molecule are very similar to those of the free PTCDA molecule, but due to the presence of the substrate additional low energy modes which are relevant for the full understanding of the spectra couple to the transition.

Complex orientational ordering of C60 molecules on Au(111)

The orientation and adsorption site for C(60) molecules on Au(111) has been studied using low temperature scanning tunneling microscopy. A complex orientational ordering has been observed for molecules inside the "in-phase" (R0°) domain. A 7-molecule cluster consisting a central molecule sitting atop of a gold atom and 6 tilted surrounding molecules is identified as the structural motif. The 2√3 × 2√3-R30° phase consists of molecules bonding to a gold atomic vacancies with a preferred azimuthal orientation. The quasi-periodic R14° phase is composed of groups of similarly oriented molecules with the groups organized into a 4√3 × 4√3-R30° like super-lattice unit cell.

Organization of layer-type supramolecular nanostructures of a combined liquid-crystalline homopolymer toward lattice packing

For a designed LC homopolymer, bearing a polyimide backbone mesogen and two terminally-connected cyanobiphenyl mesogens via aliphatic spacers in a repeat unit, the formation of layer-type supramolecular nanostructures, and involved organization route within sheared film have been studied in this research. The anisotropic layer scheme induced within sheared film identified the feasible phase separation between distinct mesogens under the restriction of connection spacers. Further considering the periodic correlation of 2.3nm preferably along the stacking direction, alternate stacks of mesogen bilayers were accounted for the growth of nanostructures. The shear-aligned assembly of layer-type nanostructures led to the presence of orientational order along the film x- and z-axes, and thus the formation of biaxial supramolecular nematic phase. The further annealing process at 160°C initiated the development of orthorhombic lattice packing, which is conceivably via parallel sliding motion of nanostructures. This growth mechanism explains the existence of large range of bond orientation order, but less extensive positional order. For this orthorhombic lattice, the preferred azimuthal orientation and unusually high aspect ratio between transverse lattice dimensions approved the development of lattice packing from prior stacking of layer-type nanostructures. Upon annealing at 240°C, the continue ordering process favored closer interaction between neighboring backbone mesogens along the b-axis, which nevertheless expanded the a-axis dimension and caused the packing of cyanobiphenyl mesogens much less oriented. These evolved structural features were attributed to the presence of a regular buckled pattern of cyanobiphenyl bilayers within lattices, as a result of mechanical deformation while being unable to linearly extend within insufficient lattice dimension. These structural analyses helps to describe multiple-step organization of layer-type nanostructures toward lattice packing, which is not likely referred to the packing behavior of individual repeat units.

The structure of the Au(111)/methylthiolate interface: New insights from near-edge x-ray absorption spectroscopy and x-ray standing waves

The local structure of the Au(111)(square root(3) x square root(3))R30 degrees-methylthiolate surface phase has been investigated by S K-edge near-edge s-ray absorption fine structure (NEXAFS) both experimentally and theoretically and by experimental normal-incidence x-ray standing waves (NIXSW) at both the C and S atomic sites. NEXAFS shows not only excitation into the intramolecular sigma(*) S-C resonance but also into a sigma(*) S-Au orbital perpendicular to the surface, clearly identifying the local S headgroup site as atop a Au atom. Simulations show that it is not possible, however, to distinguish between the two possible adatom reconstruction models; a single thiolate species atop a hollow-site Au adatom or a dithiolate moiety comprising two thiolate species bonded to a bridge-bonded Au adatom. Within this dithiolate moiety a second sigma(*) S-Au orbital that lies near parallel to the surface has a higher energy that overlaps that of the sigma(*) S-C resonance. The new NIXSW data show the S-C bond to be tilted by 61 degrees relative to the surface normal, with a preferred azimuthal orientation in <211>, corresponding to the intermolecular nearest-neighbor directions. This azimuthal orientation is consistent with the thiolate being atop a hollow-site Au adatom, but not consistent with the originally proposed Au-adatom-dithiolate moiety. However, internal conformational changes within this species could, perhaps, render this model also consistent with the experimental data.

Anisotropic mobility in large grain size solution processed organic semiconductor thin films

The hollow pen method for writing thin films of materials from solution is utilized to deposit films of 6,13-bis(tri-isopropylsilylethynyl) pentacene (TIPS pentacene) onto SiO2 surfaces with pre-patterned source/drain gold contacts. We demonstrate that large domains are obtained for TIPS pentacene films deposited from 0.5–4.0wt% solutions with toluene. Crystalline grains with (001) orientation are observed to grow with sizes that can exceed 1mm along the writing direction. A preferred azimuthal orientation is also selected by the process, resulting in anisotropic field effect transistor mobility in the films.

Anchorage of mature conifers: resistive turning moment, root-soil plate geometry and root growth orientation

Eighty-four mature Norway spruce (Picea abies L. Karst), silver fir (Abies alba Mill) and Scots pine (Pinus sylvestris L.) trees were winched over to determine the maximum resistive turning moment (M(a)) of the root-soil system, the root-soil plate geometry, the azimuthal orientation of root growth, and the occurrence of root rot. The calculation of M(a), based on digital image tracking of stem deflection, accounted not only for the force application and its changing geometry, but also for the weight of the overhanging tree, representing up to 42% of M(a). Root rot reduced M(a) significantly and was detected in 25% of the Norway spruce and 5% of the silver fir trees. Excluding trees with root rot, differences in M(a) between species were small and insignificant. About 75% of the variance in M(a) could be explained by one of the four variables--tree mass, stem mass, stem diameter at breast height squared times tree height, and stem diameter at breast height squared. Among the seven allometric variables assessed above ground, stem diameter at breast height best described the root-soil plate dimensions, but the correlations were weak and the differences between species were insignificant. The shape of the root-soil plate was well described by a depth-dependent taper model with an elliptical cross section. Roots displayed a preferred azimuthal orientation of growth in the axis of prevailing winds, and the direction of frequent weak winds matched the orientation of growth better than that of rare strong winds. The lack of difference in anchorage parameters among species probably reflects the similar belowground growth conditions of the mature trees.

Computational Study of the Adsorption Energetics and Vibrational Wavenumbers of NH3 Adsorbed on the Ni(111) Surface

The structure and stabilities of NH(3) adsorbed on different sites of a Ni(111) surface are compared based on density functional, plane-waves calculations within a periodic framework. The surface has been modeled by 4- and 5-layer slabs with 2 x 2 and 3 x 3 unit cells. Calculated results are in good agreement with available experimental data, confirming the atop adsorption site to be the most favorable, with no preferred azimuthal orientation for the H atoms. For NH(3) adsorbed at the atop site, the one-dimensional potential energy profiles along the N-H and N-Ni bonds and the coupling between adjacent N-H bond oscillators have been calculated and fitted to an analytical expression using an accurate anharmonic potential model. Variational calculations have been performed to obtain frequencies for the N-H and N-Ni stretching vibrations and N-H stretching line widths. The model for calculating line widths has also been tested with CO adsorbed at the hcp hollow of the Ni(111) surface.

Molecular Dynamics Simulation of Transmembrane Polypeptide Orientational Fluctuations

The orientation and motion of a model lysine-terminated transmembrane polypeptide were investigated by molecular dynamics simulation. Recent 2H NMR studies of synthetic polypeptides with deuterated alanine side chains suggest that such transmembrane polypeptides undergo fast, axially symmetric reorientation about the bilayer normal but have a preferred average azimuthal orientation about the helix axis. In this work, interactions that might contribute to this behavior were investigated in a simulated system consisting of 64 molecules of 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine (POPC) and one α-helical polypeptide with the sequence acetyl-KK-(LA) 11-KK-amide. In one simulation, initiated with the peptide oriented along the bilayer normal, the system was allowed to evolve for 8.5 ns at 1 atm of pressure and a temperature of 55°C. A second simulation was initiated with the peptide orientation chosen to match a set of experimentally observed alanine methyl deuteron quadrupole splittings and allowed to proceed for 10 ns. Simulated alanine methyl group orientations were found to be inequivalent, a result that is consistent with 2H NMR observations of specifically labeled polypeptides in POPC bilayers. Helix tilt varied substantially over the durations of both simulations. In the first simulation, the peptide tended toward an orientation about the helix axis similar to that suggested by experiment. In the second simulation, orientation about the helix axis tended to return to this value after an excursion. These results provide some insight into how interactions at the bilayer surface can constrain reorientation about the helix axis while accommodating large changes in helix tilt.

Geometrical and electronic structure of Pd clusters on graphite

Pd clusters formed by physical vapor deposition at room temperature (RT) on highly oriented pyrolytic graphite were investigated by a combination of X-ray photoelectron spectroscopy and diffraction, angle-resolved ultraviolet photoelectron spectroscopy, scanning tunneling microscopy and calculations based on the local density functional theory. Different coverages with nominally 3, 5 and 10 Å were studied after deposition at RT and after heat treatment at 600°C. Local ordering exhibiting growth with an fcc(1 1 1) orientation is already observed at the lowest coverage, but with no preferred azimuthal orientation in accordance with the substrate itself. However electronic structure features characteristic for a Pd(1 1 1) single crystal appear only after heat treatment.

Aligned fractures in carbonate rocks: laboratory and in situ measurements of seismic anisotropy

By vertical seismic profiling and shear wave analysis we show that a packet of carbonate reservoir rocks, found at nearly 3000 m depth in the North German Basin, is seismically anisotropic. For vertical paths of wave propagation the estimated velocity difference of the split shear waves is 10%. No shear wave birefrigence is observed within the hangingwall which, therefore, has to be regarded as isotropic or transversely isotropic. Additional laboratory investigations of the petrography of drilled carbonate samples and of their seismic velocities show that the anisotropy is most probably caused by subvertical fractures with preferred azimuthal orientation. The strike direction of the aligned fractures determined by analysis of split shear waves is approximately N55°E. This value agrees with recently published directions of maximum horizontal tectonic stress in pre-Zechstein sediments in the eastern part of the North German Basin, but it is in contrast to the world stress map.

A Strategy for Electron Tomographic Data Collection and Crystallographic Reconstruction of Biological Bundles

Structures of highly ordered biological bundles have unique features which call for special experimental and computational methods in electron cryomicroscopy. They can be considered as three-dimensional quasi-crystals and reconstructed using a crystallographic approach. However, they are neither “infinitely” large with respect to the borders of the bundle, nor are they a single unit cell in thickness along the viewing direction. Also, because of their shape, bundles do not generally have a preferred azimuthal orientation, which poses challenges for orientation estimation and refinement. We developed a strategy for recording and processing electron cryomicroscopic images that differs from classical two-dimensional crystalline reconstruction techniques. These developments allowed us to merge data from tomographic tilt series of ice-embedded acrosomal bundles. The goal is to determine accurately amplitudes and phases at the diffraction maxima in terms ofhklindices, and compute a three-dimensional map from the diffraction data.

A simulation of the phase transition in monolayer CO/NaCl(001)

We report a Monte Carlo simulation of the p(2×1)→p(1×1) phase transition in a monolayer of CO molecules adsorbed on a NaCl(001) surface. In the p(2×1) phase the CO molecules are tilted by 24° from the surface normal and have preferred azimuthal orientations whereas in the p(1×1) phase the molecules are oriented perpendicular to the surface with no preferred azimuthal orientation. The transition temperature is estimated to lie in the range 30–35 K. Multiple domains and phase coexistence are also observed.

Characterization of silver films deposited by radio frequency magnetron sputtering

Silver thin films have been deposited on various substrates at floating potentials by radio frequency magnetron sputtering of a silver target in pure argon plasma using load-locked sputtering equipment. Under the experimental conditions investigated, the deposition rate of silver films was about 70 nm/min so that metal films as thin as 200 nm could be deposited within easily controllable deposition durations. Film surfaces and cross sections were examined by scanning electron microscopy. The morphology was fully dense. The crystallographic structure was investigated by x-ray diffraction. The grains were preferentially oriented with the (111) lattice planes parallel to the film surface and without preferred azimuthal orientation. The films analyzed by Rutherford backscattering spectroscopy were free of detectable impurities. The residual stresses were determined to be tensile from the measurements of the curvature radius of silicon substrates. The calculated value of the thermal stress showed that the intrinsic stress in the films was compressive. The effective Knoop hardness of 2-μm-thick silver films deposited on glass substrates was in the range 1600–1800 MPa, i.e., three times higher than the hardness of the bulk metal. Pure silver films exhibited an electrical resistivity of 1.5–2 μΩ cm, nearly equal to the bulk resistivity.

Characterization of thinNb3Sn diffusion layers on Nb(110): Low-energy electron-diffraction and photoemission studies

We have carried out low-energy electron-diffraction and ultraviolet photoemission spectroscopy studies of the surface structures formed by annealing Sn overlayers deposited on Nb(110) substrates at room temperature. In addition to the usual ring patterns observed by electron diffraction, we observe a preferred azimuthal orientation with ${\mathrm{Nb}}_{3}$Sn [100] parallel to Nb [111] in the surface plane. The photoemission results show three regimes of Sn coverage extending from submonolayer Sn structures to the limit of thick islands of Sn, the latter being a prerequisite to forming the $A15$, ${\mathrm{Nb}}_{3}$Sn structure. The contribution of the $\mathrm{Sn}4p$ states to the electronic structure is followed as a function of Sn coverage. The evolution of the photoemission spectra as a function of sample annealing shows the trend through the $A15$ structure to the relatively inert $p(1\ifmmode\times\else\texttimes\fi{}1)$ phase of Sn on Nb.

LiInSe 2 thin epitaxial films on {111} a-oriented GaAs

LiInSe 2 thin epitaxial layers were prepared by flash evaporation on {111}a-oriented GaAs substrates and investigated by reflection high energy electron diffraction. The overgrowth is characterized by one-dimensional epitaxy with preferred azimuthal orientation. In general, the LiInSe 2 thin films crystallize in the β-NaFeO 2 structure. In the substrate temperature range from 620 to 670 K a second phase with chalcopyrite structure was observed besides the β-NaFeO 2 structure.

The adsorption of H 2O on Ni(111); influence of preadsorbed oxygen on azimuthal ordering

ESDIAD (electron stimulated desorption ion angular distribution), LEED and TPD (temperature programmed thermal desorption) have been used to study the adsorption of H 2O on Ni(111), both clean and with preadsorbed oxygen. On the clean surface, a fractional H 2O monolayer adsorbed at 80 K exhibits no preferred azimuthal orientation for the H atoms; the local bonding configurations of H 2O have a nearly random distribution. Only one state is seen in TPD for a fractional H 2O monolayer ( T p ∼ 170K) and a weak ( 3 × 3 ) LEED pattern appears after saturation of the first H 2O layer. When a fractional monolayer of H 2O is coadsorbed with a low-coverage annealed oxygen layer ( θ O ≲0.05), a sharp, intense three-fold ESDIAD pattern of H + ions appears, suggesting that there are three configurations of H 2O having H atoms oriented azimuthally in [ 11 2] directions. We postulate that H 2O is bonded to the surface via the oxygen lone-pair orbitals, and that H 2O interacts with a neighboring O atom via a hydrogen bond. This leads to local azimuthal ordering in the absence of long-range order. Upon heating to 120 K, an H-abstraction reaction leads to the formation of OH(ads). Further heating leads to the formation of H 2O (which desorbs) and O(ads).

Radar anisotropy of sea ice due to preferred azimuthal orientation of the horizontal c axes of ice crystals

Results of impulse radar, ice crystal c axis, and subice current measurements on the fast ice near Narwhal Island, Alaska, are presented. The crystal structure of the ice was found to have a horizontal crystal c axis with a preferred azimuthal orientation. This orientation was found to align with the direction of the current at the ice‐water interface. Impulse radar reflection measurements revealed that the preferred orientation of the sea ice crystal structure behaved as a microwave polarizer. It was observed that when the antenna E field was oriented parallel with the c axis of the crystal platelets, a strong reflection of the radar signal from the bottom of the ice was obtained. However, when the antenna E field was oriented perpendicular to the c axis, no bottom reflection was detected. The results of this study fully support earlier reports of sea ice inhomogeneity and anisotropy in reference to both structure and electromagnetic energy transmission.