Scanning tunneling microscopy of the formation, transformation, and property of oligothiophene self-organizations on graphite and gold surfaces.

PubMed

Yang, Zhi-Yong; Zhang, Hui-Min; Yan, Cun-Ji; Li, Shan-Shan; Yan, Hui-Juan; Song, Wei-Guo; Wan, Li-Jun

2007-03-06

Two alkyl-substituted dual oligothiophenes, quarterthiophene (4T)-trimethylene (tm)-octithiophene (8T) and 4T-tm-4T, were used to fabricate molecular structures on highly oriented pyrolytic graphite and Au(111) surfaces. The resulted structures were investigated by scanning tunneling microscopy. The 4T-tm-8T and 4T-tm-4T molecules self-organize into long-range ordered structures with linear and/or quasi-hexagonal patterns on highly oriented pyrolytic graphite at ambient temperature. Thermal annealing induced a phase transformation from quasi-hexagonal to linear in 4T-tm-8T adlayer. The molecules adsorbed on Au(111) surface in randomly folded and linear conformation. Based on scanning tunneling microscopy results, the structural models for different self-organizations were proposed. Scanning tunneling spectroscopy measurement showed the electronic property of individual molecules in the patterns. These results are significant in understanding the chemistry of molecular structure, including its formation, transformation, and electronic properties. They also help to fabricate oligothiophene assemblies with desired structures for future molecular devices.

Atomistic theory of excitonic fine structure in InAs/InP nanowire quantum dot molecules

NASA Astrophysics Data System (ADS)

Świderski, M.; Zieliński, M.

2017-03-01

Nanowire quantum dots have peculiar electronic and optical properties. In this work we use atomistic tight binding to study excitonic spectra of artificial molecules formed by a double nanowire quantum dot. We demonstrate a key role of atomistic symmetry and nanowire substrate orientation rather than cylindrical shape symmetry of a nanowire and a molecule. In particular for [001 ] nanowire orientation we observe a nonvanishing bright exciton splitting for a quasimolecule formed by two cylindrical quantum dots of different heights. This effect is due to interdot coupling that effectively reduces the overall symmetry, whereas single uncoupled [001 ] quantum dots have zero fine structure splitting. We found that the same double quantum dot system grown on [111 ] nanowire reveals no excitonic fine structure for all considered quantum dot distances and individual quantum dot heights. Further we demonstrate a pronounced, by several orders of magnitude, increase of the dark exciton optical activity in a quantum dot molecule as compared to a single quantum dot. For [111 ] systems we also show spontaneous localization of single particle states in one of nominally identical quantum dots forming a molecule, which is mediated by strain and origins from the lack of the vertical inversion symmetry in [111 ] nanostructures of overall C3 v symmetry. Finally, we study lowering of symmetry due to alloy randomness that triggers nonzero excitonic fine structure and the dark exciton optical activity in realistic nanowire quantum dot molecules of intermixed composition.

Effect of Solvent and Substrate on the Surface Binding Mode of Carboxylate-Functionalized Aromatic Molecules

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

Domenico, Janna; Foster, Michael E.; Spoerke, Erik D.

Here, the efficiency of dye-sensitized solar cells (DSSCs) is strongly influenced by dye molecule orientation and interactions with the substrate. Understanding the factors controlling the surface orientation of sensitizing organic molecules will aid in the improvement of both traditional DSSCs and other devices that integrate molecular linkers at interfaces. Here, we describe a general approach to understand relative dye–substrate orientation and provide analytical expressions predicting orientation. We consider the effects of substrate, solvent, and protonation state on dye molecule orientation. In the absence of solvent, our model predicts that most carboxylic acid-functionalized molecules prefer to lie flat (parallel) on themore » surface, due to van der Waals interactions, as opposed to a tilted orientation with respect to the surface that is favored by covalent bonding of the carboxylic acid group to the substrate. When solvation effects are considered, however, the molecules are predicted to orient perpendicular to the surface. We extend this approach to help understand and guide the orientation of metal–organic framework (MOF) thin-film growth on various metal–oxide substrates. A two-part analytical model is developed on the basis of the results of DFT calculations and ab initio MD simulations that predicts the binding energy of a molecule by chemical and dispersion forces on rutile and anatase TiO 2 surfaces, and quantifies the dye solvation energy for two solvents. The model is in good agreement with the DFT calculations and enables rapid prediction of dye molecule and MOF linker binding preference on the basis of the size of the adsorbing molecule, identity of the surface, and the solvent environment. We establish the threshold molecular size, governing dye molecule orientation, for each condition.« less

Effect of Solvent and Substrate on the Surface Binding Mode of Carboxylate-Functionalized Aromatic Molecules

DOE PAGES

Domenico, Janna; Foster, Michael E.; Spoerke, Erik D.; ...

2018-04-25

Here, the efficiency of dye-sensitized solar cells (DSSCs) is strongly influenced by dye molecule orientation and interactions with the substrate. Understanding the factors controlling the surface orientation of sensitizing organic molecules will aid in the improvement of both traditional DSSCs and other devices that integrate molecular linkers at interfaces. Here, we describe a general approach to understand relative dye–substrate orientation and provide analytical expressions predicting orientation. We consider the effects of substrate, solvent, and protonation state on dye molecule orientation. In the absence of solvent, our model predicts that most carboxylic acid-functionalized molecules prefer to lie flat (parallel) on themore » surface, due to van der Waals interactions, as opposed to a tilted orientation with respect to the surface that is favored by covalent bonding of the carboxylic acid group to the substrate. When solvation effects are considered, however, the molecules are predicted to orient perpendicular to the surface. We extend this approach to help understand and guide the orientation of metal–organic framework (MOF) thin-film growth on various metal–oxide substrates. A two-part analytical model is developed on the basis of the results of DFT calculations and ab initio MD simulations that predicts the binding energy of a molecule by chemical and dispersion forces on rutile and anatase TiO 2 surfaces, and quantifies the dye solvation energy for two solvents. The model is in good agreement with the DFT calculations and enables rapid prediction of dye molecule and MOF linker binding preference on the basis of the size of the adsorbing molecule, identity of the surface, and the solvent environment. We establish the threshold molecular size, governing dye molecule orientation, for each condition.« less

Organic Photovoltaic Devices Based on Oriented n-Type Molecular Films Deposited on Oriented Polythiophene Films.

PubMed

Mizokuro, Toshiko; Tanigaki, Nobutaka; Miyadera, Tetsuhiko; Shibata, Yousei; Koganezawa, Tomoyuki

2018-04-01

The molecular orientation of π-conjugated molecules has been reported to significantly affect the performance of organic photovoltaic devices (OPVs) based on molecular films. Hence, the control of molecular orientation is a key issue toward the improvement of OPV performance. In this research, oriented thin films of an n-type molecule, 3,4,9,10-Perylenetetracarboxylic Bisbenzimida-zole (PTCBI), were formed by deposition on in-plane oriented polythiophene (PT) films. Orientation of the PTCBI films was evaluated by polarized UV-vis spectroscopy and 2D-Grazing incidence X-ray diffraction. Results indicated that PTCBI molecules on PT film exhibit nearly edge-on and in-plane orientation (with molecular long axis along the substrate), whereas PTCBI molecules without PT film exhibit neither. OPVs composed of PTCBI molecular film with and without PT were fabricated and evaluated for correlation of orientation with performance. The OPVs composed of PTCBI film with PT showed higher power conversion efficiency (PCE) than that of film without PT. The experiment indicated that in-plane orientation of PTCBI molecules absorbs incident light more efficiently, leading to increase in PCE.

Ionization Study of Isomeric Molecules in Strong-field Laser Pulses

DOE PAGES

Zigo, Stefan; Le, Anh-Thu; Timilsina, Pratap; ...

2017-02-10

Through the use of the technique of time-of-flight mass spectroscopy, we obtain strong-field ionization yields for randomly oriented 1,2-dichloroethylene (1,2-DCE) (C 2H 2Cl 2) and 2-butene (C 4H 8). Here, we are interested in studying the effect of conformal structure in strong-field ionization and, in particular, the role of molecular polarity. That is, we can perform strong-field ionization studies in polar vs non-polar molecules that have the same chemical composition. Here, we report our findings through the ionization yields and the ratio (trans/cis) of each stereoisomer pair as a function of intensity.

Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells

PubMed Central

McQuilken, Molly; La Riviere, Patrick J.; Occhipinti, Patricia; Verma, Amitabh; Oldenbourg, Rudolf; Gladfelter, Amy S.; Tani, Tomomi

2016-01-01

Regulation of order, such as orientation and conformation, drives the function of most molecular assemblies in living cells but remains difficult to measure accurately through space and time. We built an instantaneous fluorescence polarization microscope, which simultaneously images position and orientation of fluorophores in living cells with single-molecule sensitivity and a time resolution of 100 ms. We developed image acquisition and analysis methods to track single particles that interact with higher-order assemblies of molecules. We tracked the fluctuations in position and orientation of molecules from the level of an ensemble of fluorophores down to single fluorophores. We tested our system in vitro using fluorescently labeled DNA and F-actin, in which the ensemble orientation of polarized fluorescence is known. We then tracked the orientation of sparsely labeled F-actin network at the leading edge of migrating human keratinocytes, revealing the anisotropic distribution of actin filaments relative to the local retrograde flow of the F-actin network. Additionally, we analyzed the position and orientation of septin-GFP molecules incorporated in septin bundles in growing hyphae of a filamentous fungus. Our data indicate that septin-GFP molecules undergo positional fluctuations within ∼350 nm of the binding site and angular fluctuations within ∼30° of the central orientation of the bundle. By reporting position and orientation of molecules while they form dynamic higher-order structures, our approach can provide insights into how micrometer-scale ordered assemblies emerge from nanoscale molecules in living cells. PMID:27679846

Measurement of the orientation of buffer-gas-cooled, electrostatically-guided ammonia molecules

NASA Astrophysics Data System (ADS)

Steer, Edward W.; Petralia, Lorenzo S.; Western, Colin M.; Heazlewood, Brianna R.; Softley, Timothy P.

2017-02-01

The extent to which the spatial orientation of internally and translationally cold ammonia molecules can be controlled as molecules pass out of a quadrupole guide and through different electric field regions is examined. Ammonia molecules are collisionally cooled in a buffer gas cell, and are subsequently guided by a three-bend electrostatic quadrupole into a detection chamber. The orientation of ammonia molecules is probed using (2 + 1) resonance-enhanced multiphoton ionisation (REMPI), with the laser polarisation axis aligned both parallel and perpendicular to the time-of-flight axis. Even with the presence of a near-zero field region, the ammonia REMPI spectra indicate some retention of orientation. Monte Carlo simulations propagating the time-dependent Schrödinger equation in a full basis set including the hyperfine interaction enable the orientation of ammonia molecules to be calculated - with respect to both the local field direction and a space-fixed axis - as the molecules pass through different electric field regions. The simulations indicate that the orientation of ∼95% of ammonia molecules in JK =11 could be achieved with the application of a small bias voltage (17 V) to the mesh separating the quadrupole and detection regions. Following the recent combination of the buffer gas cell and quadrupole guide apparatus with a linear Paul ion trap, this result could enable one to examine the influence of molecular orientation on ion-molecule reaction dynamics and kinetics.

Effect of molecular shape on rotation under severe confinement

DOE PAGES

Dhiman, Indu; Bhowmik, Debsindhu; Shrestha, Utsab R.; ...

2018-01-31

Orientational structure and dynamics of molecules is known to be affected by confinement in space comparable in size to the molecule itself. ZSM-5 with porous channels of ≈0.55 nm is such a porous medium, which offers a strict spatial confinement on low molecular weight hydrocarbons. An important factor that determines these properties is the shape of the confined molecules. In this work, we employed molecular dynamics simulation to study the orientational structure and dynamics of four molecules that differ in shape but have similar kinetic diameters and moments of inertia, confined in ZSM-5. The effect of molecular shape on themore » orientational structure and dynamics of propane, acetonitrile, acetaldehyde and acetone in ZSM-5 is studied by means of probing the differences in the orientational distribution of molecules in the ZSM-5 channels, and extracting time scales of the decay of correlation functions related to rotational motion. Orientational correlation functions of all the four molecules exhibit two regimes of rotational motion. While the short time regime represents free rotation of the molecules before they collide with the pore walls, the long time orientational jumps driven by inter-channel migrations give rise to a very slow varying second regime. Of the molecules studied, orientational structure and dynamics of propane is found to be least affected by confinement under ZSM-5, whereas charge and shape asymmetry of other molecules makes their interchannel migration-driven rotation slow. The time scales involved in the rotational motion for the molecules studied are compared with similar studies reported in literature. Lastly, this study reveals the important role that molecular shape plays in the behavior of confined molecules.« less

Effect of molecular shape on rotation under severe confinement

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

Dhiman, Indu; Bhowmik, Debsindhu; Shrestha, Utsab R.

Orientational structure and dynamics of molecules is known to be affected by confinement in space comparable in size to the molecule itself. ZSM-5 with porous channels of ≈0.55 nm is such a porous medium, which offers a strict spatial confinement on low molecular weight hydrocarbons. An important factor that determines these properties is the shape of the confined molecules. In this work, we employed molecular dynamics simulation to study the orientational structure and dynamics of four molecules that differ in shape but have similar kinetic diameters and moments of inertia, confined in ZSM-5. The effect of molecular shape on themore » orientational structure and dynamics of propane, acetonitrile, acetaldehyde and acetone in ZSM-5 is studied by means of probing the differences in the orientational distribution of molecules in the ZSM-5 channels, and extracting time scales of the decay of correlation functions related to rotational motion. Orientational correlation functions of all the four molecules exhibit two regimes of rotational motion. While the short time regime represents free rotation of the molecules before they collide with the pore walls, the long time orientational jumps driven by inter-channel migrations give rise to a very slow varying second regime. Of the molecules studied, orientational structure and dynamics of propane is found to be least affected by confinement under ZSM-5, whereas charge and shape asymmetry of other molecules makes their interchannel migration-driven rotation slow. The time scales involved in the rotational motion for the molecules studied are compared with similar studies reported in literature. Lastly, this study reveals the important role that molecular shape plays in the behavior of confined molecules.« less

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

Kardash, Maria E.; Dzuba, Sergei A., E-mail: dzuba@kinetics.nsc.ru

Lipid-cholesterol interactions are responsible for different properties of biological membranes including those determining formation in the membrane of spatial inhomogeneities (lipid rafts). To get new information on these interactions, electron spin echo (ESE) spectroscopy, which is a pulsed version of electron paramagnetic resonance (EPR), was applied to study 3β-doxyl-5α-cholestane (DCh), a spin-labeled analog of cholesterol, in phospholipid bilayer consisted of equimolecular mixture of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine and 1,2-dioleoyl-sn-glycero-3-phosphocholine. DCh concentration in the bilayer was between 0.1 mol.% and 4 mol.%. For comparison, a reference system containing a spin-labeled 5-doxyl-stearic acid (5-DSA) instead of DCh was studied as well. The effects of “instantaneousmore » diffusion” in ESE decay and in echo-detected (ED) EPR spectra were explored for both systems. The reference system showed good agreement with the theoretical prediction for the model of spin labels of randomly distributed orientations, but the DCh system demonstrated remarkably smaller effects. The results were explained by assuming that neighboring DCh molecules are oriented in a correlative way. However, this correlation does not imply the formation of clusters of cholesterol molecules, because conventional continuous wave EPR spectra did not show the typical broadening due to aggregation of spin labels and the observed ESE decay was not faster than in the reference system. So the obtained data evidence that cholesterol molecules at low concentrations in biological membranes can interact via large distances of several nanometers which results in their orientational self-ordering.« less

Supramolecular order and structural dynamics: A STM study of 2H-tetraphenylporphycene on Cu(111)

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

Stark, Michael; Träg, Johannes; Ditze, Stefanie

2015-03-14

The adsorption of 2H-tetraphenylporphycene (2HTPPc) on Cu(111) was investigated by scanning tunneling microscopy (STM). At medium coverages, supramolecular ordered islands are observed. The individual 2HTPPc molecules appear as two pairs of intense protrusions which are separated by an elongated depression. In the islands, the molecules are organized in rows oriented along one of the close packed Cu(111) substrate rows; the structure is stabilized by T-type interactions of the phenyl substituents of neighboring molecules. Two types of rows are observed, namely, highly ordered rows in which all molecules exhibit the same orientation, and less ordered rows in which the molecules exhibitmore » two perpendicular orientations. Altogether, three different azimuthal orientations of 2HTPPc are observed within one domain, all of them rotated by 15° ± 1° relative to one closed packed Cu direction. The highly ordered rows are always separated by either one or two less ordered rows, with the latter structure being the thermodynamically more stable one. The situation in the islands is highly dynamic, such that molecules in the less ordered rows occasionally change orientation, also complete highly ordered rows can move. The supramolecular order and structural dynamics are discussed on the basis of the specific molecule-substrate and molecule-molecule interactions.« less

Anisotropic behavior of organic molecules on prepatterned surfaces

NASA Astrophysics Data System (ADS)

Hopp, Stefan Frieder; Heuer, Andreas

2012-04-01

The nucleation of organic molecules on surfaces, prepatterned with stripes, is investigated with emphasis on anisotropy effects. Representing the molecules as ellipsoids, the related particle-particle interaction is modeled by means of a generalized Gay-Berne potential for similar biaxial particles. The orientation behavior of these ellipsoidal molecules induced by the stripe pattern is studied for the first monolayer by performing kinetic Monte Carlo simulations. It is shown how the properties of the particle alignment depend on energy scales, temperature, and flux. Based on the fact the particles strictly arrange in rows, it is furthermore instructive to analyze the orientation behavior within the different rows. Finally, the transfer of orientation from a preset row of molecules with fixed orientation to other nucleating particles is examined.

Photoexcitation circular dichroism in chiral molecules

NASA Astrophysics Data System (ADS)

Beaulieu, S.; Comby, A.; Descamps, D.; Fabre, B.; Garcia, G. A.; Géneaux, R.; Harvey, A. G.; Légaré, F.; Mašín, Z.; Nahon, L.; Ordonez, A. F.; Petit, S.; Pons, B.; Mairesse, Y.; Smirnova, O.; Blanchet, V.

2018-05-01

Chiral effects appear in a wide variety of natural phenomena and are of fundamental importance in science, from particle physics to metamaterials. The standard technique of chiral discrimination—photoabsorption circular dichroism—relies on the magnetic properties of a chiral medium and yields an extremely weak chiral response. Here, we propose and demonstrate an orders of magnitude more sensitive type of circular dichroism in neutral molecules: photoexcitation circular dichroism. This technique does not rely on weak magnetic effects, but takes advantage of the coherent helical motion of bound electrons excited by ultrashort circularly polarized light. It results in an ultrafast chiral response and the efficient excitation of a macroscopic chiral density in an initially isotropic ensemble of randomly oriented chiral molecules. We probe this excitation using linearly polarized laser pulses, without the aid of further chiral interactions. Our time-resolved study of vibronic chiral dynamics opens a way to the efficient initiation, control and monitoring of chiral chemical change in neutral molecules at the level of electrons.

Formation mechanism of human serum albumin monolayers on positively charged polymer microparticles.

PubMed

Nattich-Rak, Małgorzata; Sadowska, Marta; Adamczyk, Zbigniew; Cieśla, Michał; Kąkol, Małgorzata

2017-11-01

Human serum albumin (HSA) adsorption on positively and negatively charged polystyrene microparticles was studied at various pHs and NaCl concentrations. Thorough electrophoretic mobility measurements were carried out that enabled to monitor in situ the progress of protein adsorption. The maximum coverage of irreversibly adsorbed HSA on microparticles was determined by different concentration depletion methods, one of them involving AFM imaging of residual molecules. An anomalous adsorption of HSA on the positive microparticles was observed at pH 3.5 where the maximum coverage attained 1.0mgm -2 for NaCl concentrations of 0.05M despite that the molecules were on average positively charged. For comparison, the maximum coverage of HSA on negatively charged microparticles was equal to 1.3mgm -2 at this pH and NaCl concentration. At pH 7.4 the maximum coverage on positive microparticles was equal to 2.1mgm -2 for 0.05M NaCl concentration. On the other hand, for negative microparticles, negligible adsorption of HSA was observed at pH 7.4 and 9.7. These experimental data were adequately interpreted in terms of the random sequential adsorption approach exploiting the bead model of the HSA molecule. Different orientations of adsorbed molecules, inert alia, the edge-on orientation prevailing for positively charged microparticles at pH 7.4, were confirmed. This was explained in terms of a heterogeneous charge distribution over the HSA molecule prevailing for a wide range of pHs. Copyright © 2017 Elsevier B.V. All rights reserved.

Solution-grown small-molecule organic semiconductor with enhanced crystal alignment and areal coverage for organic thin film transistors

DOE PAGES

Bi, Sheng; He, Zhengran; Chen, Jihua; ...

2015-07-24

Drop casting of small-molecule organic semiconductors typically forms crystals with random orientation and poor areal coverage, which leads to significant performance variations of organic thin-film transistors (OTFTs). In this study, we utilize the controlled evaporative self-assembly (CESA) method combined with binary solvent system to control the crystal growth. A small-molecule organic semiconductor,2,5-Di-(2-ethylhexyl)-3,6-bis(5"-n-hexyl-2,2',5',2"]terthiophen-5-yl)-pyrrolo[3,4-c]pyrrole-1,4-dione (SMDPPEH), is used as an example to demonstrate the effectiveness of our approach. By optimizing the double solvent ratios, well-aligned SMDPPEH crystals with significantly improved areal coverage were achieved. As a result, the SMDPPEH based OTFTs exhibit a mobility of 1.6 × 10 -2 cm 2/V s, whichmore » is the highest mobility from SMDPPEH ever reported.« less

Hierarchical and non-hierarchical mineralisation of collagen

PubMed Central

Liu, Yan; Kim, Young-Kyung; Dai, Lin; Li, Nan; Khan, Sara; Pashley, David H.; Tay, Franklin R.

2010-01-01

Biomineralisation of collagen involves functional motifs incorporated in extracellular matrix protein molecules to accomplish the objectives of stabilising amorphous calcium phosphate into nanoprecursors and directing the nucleation and growth of apatite within collagen fibrils. Here we report the use of small inorganic polyphosphate molecules to template hierarchical intrafibrillar apatite assembly in reconstituted collagen in the presence of polyacrylic acid to sequester calcium and phosphate into transient amorphous nanophases. The use of polyphosphate without a sequestration analogue resulted only in randomly-oriented extrafibrillar precipitations along the fibrillar surface. Conversely, the use of polyacrylic acid without a templating analogue resulted only in non-hierarchical intrafibrillar mineralisation with continuous apatite strands instead of discrete crystallites. The ability of using simple non-protein molecules to recapitulate different levels of structural hierarchy in mineralised collagen signifies the ultimate simplicity in Nature’s biomineralisation design principles and challenges the need for using more complex recombinant matrix proteins in bioengineering applications. PMID:21040969

Orientation of surfactant self-assembled aggregates on graphite

NASA Astrophysics Data System (ADS)

Sammalkorpi, Maria; Hynninen, Antti-Pekka; Panagiotopoulos, Athanassios Z.; Haataja, Mikko

2007-03-01

Micellar aggregates on surfaces can provide a self-healing corrosion protection or lubrication layer. It has been observed experimentally that on a single crystal surface this layer often consists of oriented hemi-cylindrical micelles which are aligned with the underlying crystal lattice (``orientation effect''). A key feature of this self-assembly process is the interplay between detergent--detergent and detergent--surface interactions. Since the dimensions of the detergent molecules and the unit cell of the surface are typically quite different, the origins of this orientation effect remain unclear. Here we address the question and present the results of Molecular Dynamics simulations of sodium dodecyl sulfate (SDS) self-aggregation on graphite. We employ both single-molecule and multi-molecule simulations of SDS to unravel the origins of the orientation effect. We report that the underlying graphite surface is sufficient to impose orientational bias on individual SDS molecules diffusing on the surface. This produces collective effects that give rise to the oriented hemi-micelles.

Jammed systems of oriented needles always percolate on square lattices

NASA Astrophysics Data System (ADS)

Kondrat, Grzegorz; Koza, Zbigniew; Brzeski, Piotr

2017-08-01

Random sequential adsorption (RSA) is a standard method of modeling adsorption of large molecules at the liquid-solid interface. Several studies have recently conjectured that in the RSA of rectangular needles, or k -mers, on a square lattice, percolation is impossible if the needles are sufficiently long (k of order of several thousand). We refute these claims and present rigorous proof that in any jammed configuration of nonoverlapping, fixed-length, horizontal, or vertical needles on a square lattice, all clusters are percolating clusters.

Production of large-scale, freestanding vanadium pentoxide nanobelt porous structures

NASA Astrophysics Data System (ADS)

Yun, Yong Ju; Kim, Byung Hoon; Hong, Won G.; Kim, Chang Hee; Kim, Yark Yeon; Jeong, Eun-Ju; Jang, Won Ick; Yu, Han Young

2012-02-01

Large-scale, freestanding, porous structures of vanadium pentoxide nanobelts (VPNs) were successfully prepared using the template-free freeze-drying method. The porous and multi-layered VPN macrostructures are composed of randomly oriented long nanobelts (over 100 μm) and their side length can be controlled up to a few tens of centimetres. Also, the bulk density and surface area of these macrostructures are 3-5 mg cm-3 and 40-80 m2 g-1, respectively, which are similar to those of the excellent adsorbents. In addition, the removal efficiency measurements of ammonia molecules revealed that the VPN porous structures can adsorb the ammonia molecules with the combinations of van der Waals forces and strong chemical bonding by functional groups on the VPN surface.

Production of large-scale, freestanding vanadium pentoxide nanobelt porous structures.

PubMed

Yun, Yong Ju; Kim, Byung Hoon; Hong, Won G; Kim, Chang Hee; Kim, Yark Yeon; Jeong, Eun-ju; Jang, Won Ick; Yu, Han Young

2012-03-07

Large-scale, freestanding, porous structures of vanadium pentoxide nanobelts (VPNs) were successfully prepared using the template-free freeze-drying method. The porous and multi-layered VPN macrostructures are composed of randomly oriented long nanobelts (over 100 μm) and their side length can be controlled up to a few tens of centimetres. Also, the bulk density and surface area of these macrostructures are 3-5 mg cm(-3) and 40-80 m(2) g(-1), respectively, which are similar to those of the excellent adsorbents. In addition, the removal efficiency measurements of ammonia molecules revealed that the VPN porous structures can adsorb the ammonia molecules with the combinations of van der Waals forces and strong chemical bonding by functional groups on the VPN surface.

Accelerating molecular Monte Carlo simulations using distance and orientation dependent energy tables: tuning from atomistic accuracy to smoothed “coarse-grained” models

PubMed Central

Lettieri, S.; Zuckerman, D.M.

2011-01-01

Typically, the most time consuming part of any atomistic molecular simulation is due to the repeated calculation of distances, energies and forces between pairs of atoms. However, many molecules contain nearly rigid multi-atom groups such as rings and other conjugated moieties, whose rigidity can be exploited to significantly speed up computations. The availability of GB-scale random-access memory (RAM) offers the possibility of tabulation (pre-calculation) of distance and orientation-dependent interactions among such rigid molecular bodies. Here, we perform an investigation of this energy tabulation approach for a fluid of atomistic – but rigid – benzene molecules at standard temperature and density. In particular, using O(1) GB of RAM, we construct an energy look-up table which encompasses the full range of allowed relative positions and orientations between a pair of whole molecules. We obtain a hardware-dependent speed-up of a factor of 24-50 as compared to an ordinary (“exact”) Monte Carlo simulation and find excellent agreement between energetic and structural properties. Second, we examine the somewhat reduced fidelity of results obtained using energy tables based on much less memory use. Third, the energy table serves as a convenient platform to explore potential energy smoothing techniques, akin to coarse-graining. Simulations with smoothed tables exhibit near atomistic accuracy while increasing diffusivity. The combined speed-up in sampling from tabulation and smoothing exceeds a factor of 100. For future applications greater speed-ups can be expected for larger rigid groups, such as those found in biomolecules. PMID:22120971

Orientation and Rotational Motions of Single Molecules by Polarized Total Internal Reflection Fluorescence Microscopy (polTIRFM)

PubMed Central

Beausang, John F.; Sun, Yujie; Quinlan, Margot E.; Forkey, Joseph N.; Goldman, Yale E.

2013-01-01

In this article, we describe methods to detect the spatial orientation and rotational dynamics of single molecules using polarized total internal reflection fluorescence microscopy (polTIRFM). polTIRFM determines the three-dimensional angular orientation and the extent of wobble of a fluorescent probe bound to the macromolecule of interest. We discuss single-molecule versus ensemble measurements, as well as single-molecule techniques for orientation and rotation, and fluorescent probes for orientation studies. Using calmodulin (CaM) as an example of a target protein, we describe a method for labeling CaM with bifunctional rhodamine (BR). We also describe the physical principles and experimental setup of polTIRFM. We conclude with a brief introduction to assays using polTIRFM to assess the interaction of actin and myosin. PMID:22550303

Oriented xenon hydride molecules in the gas phase

NASA Astrophysics Data System (ADS)

Buck, Udo; Fárník, Michal

The production of the xenon hydride molecules HXeX with X = I and Cl in the gas phase is reviewed. These molecules are generated by the photolysis of the hydrogen halide HI and HCl molecules on the surface of large xenon Xen clusters. Molecular dynamics simulations show that the flexible H atoms react with the heavy XeX moiety and form the desired molecules with nearly no rotational motion. They are observed by photodissociation with subsequent detection of the kinetic energy of the H atom fragment. During the generating process, the cluster starts to evaporate and the hydride molecule is left essentially free. For further discrimination against the H atom fragments from HX, the HXeX molecules are oriented in a combined pulsed laser field and a weak electrostatic field. The three topics which represent the background of our experiments are briefly reviewed: the nature and generation of rare gas hydrides, the alignment and orientation of molecules in electric fields, and the photodissociation of selected molecules in rare gas clusters. The conditions for detecting them in the gas phase are discussed. This is the trade off between the stability, which requires high electron affinity, and the conditions for orientation, which necessitate large polarizability anisotropies and dipole moments. Finally the prospects of detecting other classes of molecules are discussed.

Time-dependent analysis of the mixed-field orientation of molecules without rotational symmetry

NASA Astrophysics Data System (ADS)

Thesing, Linda V.; Küpper, Jochen; González-Férez, Rosario

2017-06-01

We present a theoretical study of the mixed-field orientation of molecules without rotational symmetry. The time-dependent one-dimensional and three-dimensional orientation of a thermal ensemble of 6-chloropyridazine-3-carbonitrile molecules in combined linearly or elliptically polarized laser fields and tilted dc electric fields is computed. The results are in good agreement with recent experimental results of one-dimensional orientation for weak dc electric fields [J. L. Hansen, J. Chem. Phys. 139, 234313 (2013)]. Moreover, they predict that using elliptically polarized laser fields or strong dc fields, three-dimensional orientation is obtained. The field-dressed dynamics of excited rotational states is characterized by highly non-adiabatic effects. We analyze the sources of these non-adiabatic effects and investigate their impact on the mixed-field orientation for different field configurations in mixed-field-orientation experiments.

Compass magnetoreception in birds arising from photo-induced radical pairs in rotationally disordered cryptochromes

PubMed Central

Lau, Jason C. S.; Rodgers, Christopher T.; Hore, P. J.

2012-01-01

According to the radical pair model, the magnetic compass sense of migratory birds relies on photochemical transformations in the eye to detect the direction of the geomagnetic field. Magnetically sensitive radical pairs are thought to be generated in cryptochrome proteins contained in magnetoreceptor cells in the retina. A prerequisite of the current model is for some degree of rotational ordering of both the cryptochromes within the cells and of the cells within the retina so that the directional responses of individual molecules do not average to zero. Here, it is argued that anisotropic distributions of radical pairs can be generated by the photoselection effects that arise from the directionality of the light entering the eye. Light-induced rotational order among the transient radical pairs rather than intrinsic ordering of their molecular precursors is seen as the fundamental condition for a magnetoreceptor cell to exhibit an anisotropic response. A theoretical analysis shows that a viable compass magnetoreceptor could result from randomly oriented cryptochromes contained in randomly oriented cells distributed around the retina. PMID:22977104

Exciton-phonon coupling in diindenoperylene thin films

NASA Astrophysics Data System (ADS)

Heinemeyer, U.; Scholz, R.; Gisslén, L.; Alonso, M. I.; Ossó, J. O.; Garriga, M.; Hinderhofer, A.; Kytka, M.; Kowarik, S.; Gerlach, A.; Schreiber, F.

2008-08-01

We investigate exciton-phonon coupling and exciton transfer in diindenoperylene (DIP) thin films on oxidized Si substrates by analyzing the dielectric function determined by variable-angle spectroscopic ellipsometry. Since the molecules in the thin-film phase form crystallites that are randomly oriented azimuthally and highly oriented along the surface normal, DIP films exhibit strongly anisotropic optical properties with uniaxial symmetry. This anisotropy can be determined by multiple sample analysis. The thin-film spectrum is compared with a monomer spectrum in solution, which reveals similar vibronic subbands and a Huang-Rhys parameter of S≈0.87 for an effective internal vibration at ℏωeff=0.17eV . However, employing these parameters the observed dielectric function of the DIP films cannot be described by a pure Frenkel exciton model, and the inclusion of charge-transfer (CT) states becomes mandatory. A model Hamiltonian is parametrized with density-functional theory calculations of single DIP molecules and molecule pairs in the stacking geometry of the thin-film phase, revealing the vibronic coupling constants of DIP in its excited and charged states together with electron and hole transfer integrals along the stack. From a fit of the model calculation to the observed dielectric tensor, we find the lowest CT transition E00CT at 0.26±0.05eV above the neutral molecular excitation energy E00F , which is an important parameter for device applications.

Extended orientational correlation study for molecular liquids containing distorted tetrahedral molecules: Application to methylene halides

NASA Astrophysics Data System (ADS)

Pothoczki, Szilvia; Temleitner, László; Pusztai, László

2010-04-01

The method of Rey [Rey, J. Chem. Phys. 126, 164506 (2007)] for describing how molecules orient toward each other in systems with perfect tetrahedral molecules is extended to the case of distorted tetrahedral molecules of c2v symmetry by means of introducing 28 subgroups. Additionally, the original analysis developed for perfect tetrahedral molecules, based on six groups, is adapted for molecules with imperfect tetrahedral shape. Deriving orientational correlation functions have been complemented with detailed analyses of dipole-dipole correlations. This way, (up to now) the most complete structure determination can be carried out for such molecular systems. In the present work, these calculations have been applied for particle configurations resulting from reverse Monte Carlo computer modeling. These particle arrangements are fully consistent with structure factors from neutron and x-ray diffraction measurements. Here we present a complex structural study for methylene halide (chloride, bromide, and iodide) molecular liquids, as possibly the best representative examples. It has been found that the most frequent orientations of molecules are of the 2:2 type over the entire distance range in these liquids. Focusing on the short range orientation, neighboring molecules turn toward each other with there "H,Y"-"H,Y" (Y: Cl, Br, I) edges, apart from CH2Cl2 where the H,H-H,Cl arrangement is the most frequent. In general, the structure of methylene chloride appears to be different from the structure of the other two liquids.

Single molecule optical measurements of orientation and rotations of biological macromolecules.

PubMed

Shroder, Deborah Y; Lippert, Lisa G; Goldman, Yale E

2016-11-22

Subdomains of macromolecules often undergo large orientation changes during their catalytic cycles that are essential for their activity. Tracking these rearrangements in real time opens a powerful window into the link between protein structure and functional output. Site-specific labeling of individual molecules with polarized optical probes and measurement of their spatial orientation can give insight into the crucial conformational changes, dynamics, and fluctuations of macromolecules. Here we describe the range of single molecule optical technologies that can extract orientation information from these probes, review the relevant types of probes and labeling techniques, and highlight the advantages and disadvantages of these technologies for addressing specific inquiries.

Molecular Orientation in Two Component Vapor-Deposited Glasses: Effect of Substrate Temperature and Molecular Shape

NASA Astrophysics Data System (ADS)

Powell, Charles; Jiang, Jing; Walters, Diane; Ediger, Mark

Vapor-deposited glasses are widely investigated for use in organic electronics including the emitting layers of OLED devices. These materials, while macroscopically homogenous, have anisotropic packing and molecular orientation. By controlling this orientation, outcoupling efficiency can be increased by aligning the transition dipole moment of the light-emitting molecules parallel to the substrate. Light-emitting molecules are typically dispersed in a host matrix, as such, it is imperative to understand molecular orientation in two-component systems. In this study we examine two-component vapor-deposited films and the orientations of the constituent molecules using spectroscopic ellipsometry, UV-vis and IR spectroscopy. The role of temperature, composition and molecular shape as it effects molecular orientation is examined for mixtures of DSA-Ph in Alq3 and in TPD. Deposition temperature relative to the glass transition temperature of the two-component mixture is the primary controlling factor for molecular orientation. In mixtures of DSA-Ph in Alq3, the linear DSA-Ph has a horizontal orientation at low temperatures and slight vertical orientation maximized at 0.96Tg,mixture, analogous to one-component films.

Effect of enzymatic orientation through the use of syringaldazine molecules on multiple multi-copper oxidase enzymes.

PubMed

Ulyanova, Yevgenia; Babanova, Sofia; Pinchon, Erica; Matanovic, Ivana; Singhal, Sameer; Atanassov, Plamen

2014-07-14

The effect of proper enzyme orientation at the electrode surface was explored for two multi-copper oxygen reducing enzymes: Bilirubin Oxidase (BOx) and Laccase (Lac). Simultaneous utilization of "tethering" agent (1-pyrenebutanoic acid, succinimidyl ester; PBSE), for stable enzyme immobilization, and syringaldazine (Syr), for enzyme orientation, of both Lac and BOx led to a notable enhancement of the electrode performance. For Lac cathodes tested in solution it was established that PBSE-Lac and PBSE-Syr-Lac modified cathodes demonstrated approximately 6 and 9 times increase in current density, respectively, compared to physically adsorbed and randomly oriented Lac cathodes. Further testing in solution utilizing BOx showed an even higher increase in achievable current densities, thus BOx was chosen for additional testing in air-breathing mode. In subsequent air-breathing experiments the incorporation of PBSE and Syr with BOx resulted in current densities of 0.65 ± 0.1 mA cm(-2); 2.5 times higher when compared to an unmodified BOx cathode. A fully tethered/oriented BOx cathode was combined with a NAD-dependent Glucose Dehydrogenase anode for the fabrication of a complete enzymatic membraneless fuel cell. A maximum power of 1.03 ± 0.06 mW cm(-2) was recorded for the complete fuel cell. The observed significant enhancement in the performance of "oriented" cathodes was a result of proper enzyme orientation, leading to facilitated enzyme/electrode interface interactions.

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

PubMed

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.

Relative orientation of collagen molecules within a fibril: a homology model for homo sapiens type I collagen.

PubMed

Collier, Thomas A; Nash, Anthony; Birch, Helen L; de Leeuw, Nora H

2018-02-15

Type I collagen is an essential extracellular protein that plays an important structural role in tissues that require high tensile strength. However, owing to the molecule's size, to date no experimental structural data are available for the Homo sapiens species. Therefore, there is a real need to develop a reliable homology model and a method to study the packing of the collagen molecules within the fibril. Through the use of the homology model and implementation of a novel simulation technique, we have ascertained the orientations of the collagen molecules within a fibril, which is currently below the resolution limit of experimental techniques. The longitudinal orientation of collagen molecules within a fibril has a significant effect on the mechanical and biological properties of the fibril, owing to the different amino acid side chains available at the interface between the molecules.

Single molecule optical measurements of orientation and rotations of biological macromolecules

PubMed Central

Shroder, Deborah Y; Lippert, Lisa G; Goldman, Yale E

2016-01-01

The subdomains of macromolecules often undergo large orientation changes during their catalytic cycles that are essential for their activity. Tracking these rearrangements in real time opens a powerful window into the link between protein structure and functional output. Site-specific labeling of individual molecules with polarized optical probes and measuring their spatial orientation can give insight into the crucial conformational changes, dynamics, and fluctuations of macromolecules. Here we describe the range of single molecule optical technologies that can extract orientation information from these probes, we review the relevant types of probes and labeling techniques, and we highlight the advantages and disadvantages of these technologies for addressing specific inquiries. PMID:28192292

Photoinduced random molecular reorientation by nonradiative energy relaxation: An experimental test

NASA Astrophysics Data System (ADS)

Manzo, C.; Paparo, D.; Marrucci, L.

2004-11-01

By measuring the time-resolved fluorescence depolarization as a function of light excitation wavelength we address the question of a possible photoinduced orientational randomization of amino-anthraquinone dyes in liquid solutions. We find no significant dependence within the experimental uncertainties of both the initial molecule anisotropy and of the subsequent rotational diffusion dynamics on the photon energy. This indicates that this effect, if present, must be very small. A simple model of photoinduced local heating and corresponding enhanced rotational diffusion is in accordance with this result. This null result rules out some recent proposals that photoinduced local heating may contribute significantly to molecular reorientation effects in different materials. A small but statistically significant effect of photon energy is instead found in the excited-state lifetime of the dye.

Nanospectroscopy of thiacyanine dye molecules adsorbed on silver nanoparticle clusters

NASA Astrophysics Data System (ADS)

Ralević, Uroš; Isić, Goran; Anicijević, Dragana Vasić; Laban, Bojana; Bogdanović, Una; Lazović, Vladimir M.; Vodnik, Vesna; Gajić, Radoš

2018-03-01

The adsorption of thiacyanine dye molecules on citrate-stabilized silver nanoparticle clusters drop-cast onto freshly cleaved mica or highly oriented pyrolytic graphite surfaces is examined using colocalized surface-enhanced Raman spectroscopy and atomic force microscopy. The incidence of dye Raman signatures in photoluminescence hotspots identified around nanoparticle clusters is considered for both citrate- and borate-capped silver nanoparticles and found to be substantially lower in the former case, suggesting that the citrate anions impede the efficient dye adsorption. Rigorous numerical simulations of light scattering on random nanoparticle clusters are used for estimating the electromagnetic enhancement and elucidating the hotspot formation mechanism. The majority of the enhanced Raman signal, estimated to be more than 90%, is found to originate from the nanogaps between adjacent nanoparticles in the cluster, regardless of the cluster size and geometry.

Fabrication of a highly oriented line structure on an aluminum surface and the nanoscale patterning on the nanoscale structure using highly functional molecules

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

Watanabe, Y.; Kato, H.; Takemura, S.

2009-07-15

The surface of an Al plate was treated with a combination of chemical and electrochemical processes for fabrication of surface nanoscale structures on Al plates. Chemical treatments by using acetone and pure water under supersonic waves were conducted on an Al surface. Additional electrochemical process in H{sub 2}SO{sub 4} solution created a finer and oriented nanoscale structure on the Al surface. Dynamic force microscopy (DFM) measurement clarified that the nanoscale highly oriented line structure was successfully created on the Al surface. The line distance was estimated approximately 30-40 nm. At the next stage, molecular patterning on the highly oriented linemore » structure by functional molecules such as copper phthalocyanine (CuPc) and fullerene C{sub 60} was also conducted. CuPc or C{sub 60} molecules were deposited on the highly oriented line structure on Al. A toluene droplet containing CuPc molecules was cast on the nanostructured Al plate and was extended on the surface. CuPc or C{sub 60} deposition on the nanostructured Al surface proceeded by evaporation of toluene. DFM and x-ray photoemission spectroscopy measurements demonstrated that a unique molecular pattern was fabricated so that the highly oriented groove channels were filled with the functional molecules.« less

Watching How Molecules Orient in a Surface Forces Apparatus, Using Confocal Raman Spectroscopy

NASA Astrophysics Data System (ADS)

Jiang, Shan; Kim, Minsu; Bae, Sung Chul; Granick, Steve

2006-03-01

Much is known about surface forces, less about where they come from. This laboratory is engaged in direct vibrational spectroscopic measurements of how molecules orient in confined geometries. Regarding force measurements, PDMS (polydimethylsiloxane) was a model system for many years. In this study, we describe direct experiments using a novel version of confocal Raman spectroscopy. This experiment allows direct measurement of how the PDMS molecules orient under confinment as well as under subsequent shear. When the thickness of the fluid film is less than the unperturbed radius of gyration of the polymer, we obtain two novel findings: (a) linewidth analysis of peaks reveals that vibrational relaxation times are perturbed in this confined geometry; (b) orientation of the chain backbone is not everywhere the same within the molecularly-thin film; domains of various orientation are observed instead.

X-ray lasers for structural and dynamic biology

NASA Astrophysics Data System (ADS)

Spence, J. C. H.; Weierstall, U.; Chapman, H. N.

2012-10-01

Research opportunities and techniques are reviewed for the application of hard x-ray pulsed free-electron lasers (XFEL) to structural biology. These include the imaging of protein nanocrystals, single particles such as viruses, pump-probe experiments for time-resolved nanocrystallography, and snapshot wide-angle x-ray scattering (WAXS) from molecules in solution. The use of femtosecond exposure times, rather than freezing of samples, as a means of minimizing radiation damage is shown to open up new opportunities for the molecular imaging of biochemical reactions at room temperature in solution. This is possible using a ‘diffract-and-destroy’ mode in which the incident pulse terminates before radiation damage begins. Methods for delivering hundreds of hydrated bioparticles per second (in random orientations) to a pulsed x-ray beam are described. New data analysis approaches are outlined for the correlated fluctuations in fast WAXS, for protein nanocrystals just a few molecules on a side, and for the continuous x-ray scattering from a single virus. Methods for determining the orientation of a molecule from its diffraction pattern are reviewed. Methods for the preparation of protein nanocrystals are also reviewed. New opportunities for solving the phase problem for XFEL data are outlined. A summary of the latest results is given, which now extend to atomic resolution for nanocrystals. Possibilities for time-resolved chemistry using fast WAXS (solution scattering) from mixtures is reviewed, toward the general goal of making molecular movies of biochemical processes.

Specific Effects of Oxygen Molecule and Plasma on Thin-Film Growth of Y-Ba-Cu-O and Bi-Sr-(Ca)-Cu-O Systems

NASA Astrophysics Data System (ADS)

Endo, Tamio; Horie, Munehiro; Hirate, Naoki; Itoh, Katsutoshi; Yamada, Satoshi; Tada, Masaki; Itoh, Ken-ichi; Sugiyama, Morihiro; Sano, Shinji; Watabe, Kinji

1998-07-01

Thin films of a-oriented YBa2Cu3Ox (YBCO), Ca-doped c-oriented Bi2(Sr,Ca)2CuOx and nondoped c-oriented Bi2Sr2CuOx (Bi2201) were prepared at low temperatures by ion beam sputtering with supply of oxygen molecules or plasma. The plasma enhances crystal growth of the a-YBCO and Ca-doped Bi2201 phases. This can be interpreted in terms of their higher surface energies. The growth and quality of nondoped Bi2201 are improved with the supply of oxygen molecules. This particular result could be interpreted by the collision process between the oxygen molecules and the sputtered particles.

How to measure separations and angles between intra-molecular fluorescent markers

NASA Astrophysics Data System (ADS)

Flyvbjerg, Henrik; Mortensen, Kim I.; Sung, Jongmin; Spudich, James A.

We demonstrate a novel, yet simple tool for the study of structure and function of biomolecules by extending two-colour co-localization microscopy to fluorescent molecules with fixed orientations and in intra-molecular proximity. From each color-separated microscope image in a time-lapse movie and using only simple means, we simultaneously determine both the relative (x,y)-separation of the fluorophores and their individual orientations in space with accuracy and precision. The positions and orientations of two domains of the same molecule are thus time-resolved. Using short double-stranded DNA molecules internally labelled with two fixed fluorophores, we demonstrate the accuracy and precision of our method using the known structure of double-stranded DNA as a benchmark, resolve 10-base-pair differences in fluorophore separations, and determine the unique 3D orientation of each DNA molecule, thereby establishing short, double-labelled DNA molecules as probes of 3D orientation of anything to which one can attach them firmly. This work was supported by a Lundbeck fellowship to K.I.M; a Stanford Bio-X fellowship to J.S. and Grants from the NIH (GM33289) to J.A.S. and the Human Frontier Science Program (GP0054/2009-C) to J.A.S. and H.F.

Determination of collagen fibril structure and orientation in connective tissues by X-ray diffraction

NASA Astrophysics Data System (ADS)

Wilkinson, S. J.; Hukins, D. W. L.

1999-08-01

Elastic scattering of X-rays can provide the following information on the fibrous protein collagen: its molecular structure, the axial arrangement of rod-like collagen molecules in a fibril, the lateral arrangement of molecules within a fibril, and the orientation of fibrils within a biological tissue. The first part of the paper reviews the principles involved in deducing this information. The second part describes a new computer program for measuring the equatorial intensity distribution, that provides information on the lateral arrangement of molecules within a fibril, and the angular distribution of the equatorial peaks that provides information on the orientation of fibrils. Orientation of fibrils within a tissue is quantified by the orientation distribution function, g( φ), which represents the probability of finding a fibril oriented between φ and φ+ δφ. The application of the program is illustrated by measurement of g( φ) for the collagen fibrils in demineralised cortical bone from cow tibia.

Adsorption of aromatic hydrocarbons and ozone at environmental aqueous surfaces.

PubMed

Vácha, Robert; Cwiklik, Lukasz; Rezác, Jan; Hobza, Pavel; Jungwirth, Pavel; Valsaraj, Kalliat; Bahr, Stephan; Kempter, Volker

2008-06-05

Adsorption of environmentally important aromatic molecules on a water surface is studied by means of classical and ab initio molecular dynamics simulations and by reflection-absorption infrared spectroscopy. Both techniques show strong activity and orientational preference of these molecules at the surface. Benzene and naphthalene, which bind weakly to water surface with a significant contribution of dispersion interactions, prefer to lie flat on water but retain a large degree of orientational flexibility. Pyridine is more rigid at the surface. It is tilted with the nitrogen end having strong hydrogen bonding interactions with water molecules. The degree of adsorption and orientation of aromatic molecules on aqueous droplets has atmospheric implications for heterogeneous ozonolysis, for which the Langmuir-Hinshelwood kinetics mechanism is discussed. At higher coverages of aromatic molecules the incoming ozone almost does not come into contact with the underlying aqueous phase. This may rationalize the experimental insensitivity of the ozonolysis on the chemical nature of the substrate on which the aromatic molecules adsorb.

Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function.

PubMed

Prill, Dragica; Juhás, Pavol; Billinge, Simon J L; Schmidt, Martin U

2016-01-01

A method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.

Electroluminescence from completely horizontally oriented dye molecules

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

Komino, Takeshi; Center for Organic Photonics and Electronics Research, Kyushu University, 744 Motooka, Nishi, Fukuoka 819-0395; Japan Science and Technology Agency, ERATO, Adachi Molecular Exciton Engineering Project, 744 Motooka, Nishi, Fukuoka 819-0395

2016-06-13

A complete horizontal molecular orientation of a linear-shaped thermally activated delayed fluorescent guest emitter 2,6-bis(4-(10Hphenoxazin-10-yl)phenyl)benzo[1,2-d:5,4-d′] bis(oxazole) (cis-BOX2) was obtained in a glassy host matrix by vapor deposition. The orientational order of cis-BOX2 depended on the combination of deposition temperature and the type of host matrix. Complete horizontal orientation was obtained when a thin film with cis-BOX2 doped in a 4,4′-bis(N-carbazolyl)-1,1′-biphenyl (CBP) host matrix was fabricated at 200 K. The ultimate orientation of guest molecules originates from not only the kinetic relaxation but also the kinetic stability of the deposited guest molecules on the film surface during film growth. Utilizing the ultimatemore » orientation, a highly efficient organic light-emitting diode with the external quantum efficiency of 33.4 ± 2.0% was realized. The thermal stability of the horizontal orientation of cis-BOX2 was governed by the glass transition temperature (T{sub g}) of the CBP host matrix; the horizontal orientation was stable unless the film was annealed above T{sub g}.« less

Theory of fluorescence polarization in magnetically oriented photosynthetic systems.

PubMed Central

Knox, R S; Davidovich, M A

1978-01-01

Many cells and cell fragments are known to assume specific alignments with respect to an applied magnetic field. One indicator of this alignment is a difference between the intensities of fluorescence observed in polarizations parallel and perpendicular to the magnetic filed. We calculate these two intensities using a model that assumes axially symmetric membranes and that covers a wide variety of shapes from flat disk to right cylinder. The fluorescence is assumed to originate at chromophores randomly exicted but nonrandomly oriented in the membranes. The membrane alignment is assumed to be due to the net torque on a nonrandom distribution of diamagnetically anisotropic molecules. The predicted results are consistent with most magnetoorientation data from green cells, but we are able to show that Chlorella data are not consistent with the hypothesis that the membranes have, and maintain, a cuplike configuration. Images FIGURE 4 FIGURE 5 PMID:737283

Cavity-mode selection in spontaneous emission from oriented molecules in a microparticle.

PubMed

Arnold, S; Holler, S; Goddard, N L; Griffel, G

1997-10-01

We observe preferential cavity-mode selection in spontaneous emission by oriented molecules at the surface of a microparticle. Polarization-analyzed images of a levitated microdroplet containing surface active molecules reveal a well-defined system in terms of molecular position and orientation. The measured fluorescence spectrum is compared with that of a semiclassical emission-rate-enhancement model that treats the coupling between an excited state and Mie resonances as an oscillating dipole interacting with its self-scattered field. By comparing results obtained with this theory with the relative strengths of TE to TM modes measured in the emission spectrum, we show that one can elucidate the heterogeneity of a particle from this resonant structure and determine the orientation of the emission moments relative to the phase boundary.

Hydrogen bonded structure, polarity, molecular motion and frequency fluctuations at liquid-vapor interface of a water-methanol mixture: an ab initio molecular dynamics study.

PubMed

Choudhuri, Jyoti Roy; Chandra, Amalendu

2014-10-07

We have performed ab initio molecular dynamics simulations of a liquid-vapor interfacial system consisting of a mixture of water and methanol molecules. Detailed results are obtained for the structural and dynamical properties of the bulk and interfacial regions of the mixture. Among structural properties, we have looked at the inhomogeneous density profiles of water and methanol molecules, hydrogen bond distributions and also the orientational profiles of bulk and interfacial molecules. The methanol molecules are found to have a higher propensity to be at the interface than water molecules. It is found that the interfacial molecules show preference for specific orientations so as to form water-methanol hydrogen bonds at the interface with the hydrophobic methyl group pointing towards the vapor side. It is also found that for both types of molecules, the dipole moment decreases at the interface. It is also found that the local electric field of water influences the dipole moment of methanol molecules. Among the dynamical properties, we have calculated the diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational frequency fluctuations in bulk and interfacial regions. It is found that the diffusion and orientation relaxation of the interfacial molecules are faster than those of the bulk. However, the hydrogen bond lifetimes are longer at the interface which can be correlated with the time scales found from the decay of frequency time correlations. The slower hydrogen bond dynamics for the interfacial molecules with respect to bulk can be attributed to diminished cooperative effects at the interface due to reduced density and number of hydrogen bonds.

Inhomogeneous hard homonuclear molecules

NASA Astrophysics Data System (ADS)

Quintana, Jacqueline

A review is given of some features of theories for inhomogeneous fluids of nonspherical molecules that take as input the direct correlation function of the corresponding homogeneous system. Two different methods are described for defining the structure of hard homonuclear molecules close to a hard planar wall. A spherical harmonics expanison (SHE) within the integral equation (IE) method is presented and, for comparison, a version of density functional theory for orientable hard bodies. In both cases the Pynn-Lado model is employed and a comparison is made with Monte Carlo data. The results indicate that for hard molecules the IE approach does not always capture the effects of orientation due to the characteristics of the SHE for the step function. This disadvantage is particularly true in the case of the orientationally averaged density profile.

A theoretical investigation on optimal structures of ethane clusters (C2H6)n with n ≤ 25 and their building-up principle.

PubMed

Takeuchi, Hiroshi

2011-05-01

Geometry optimization of ethane clusters (C(2)H(6))(n) in the range of n ≤ 25 is carried out with a Morse potential. A heuristic method based on perturbations of geometries is used to locate global minima of the clusters. The following perturbations are carried out: (1) the molecule or group with the highest energy is moved to the interior of a cluster, (2) it is moved to stable positions on the surface of a cluster, and (3) orientations of one and two molecules are randomly modified. The geometry obtained after each perturbation is optimized by a quasi-Newton method. The global minimum of the dimer is consistent with that previously reported. The putative global minima of the clusters with 3 ≤ n ≤ 25 are first proposed and their building-up principle is discussed. Copyright © 2010 Wiley Periodicals, Inc.

Single-protein detection in crowded molecular environments in cryo-EM images

PubMed Central

Rickgauer, J Peter; Grigorieff, Nikolaus; Denk, Winfried

2017-01-01

We present an approach to study macromolecular assemblies by detecting component proteins’ characteristic high-resolution projection patterns, calculated from their known 3D structures, in single electron cryo-micrographs. Our method detects single apoferritin molecules in vitreous ice with high specificity and determines their orientation and location precisely. Simulations show that high spatial-frequency information and—in the presence of protein background—a whitening filter are essential for optimal detection, in particular for images taken far from focus. Experimentally, we could detect small viral RNA polymerase molecules, distributed randomly among binding locations, inside rotavirus particles. Based on the currently attainable image quality, we estimate a threshold for detection that is 150 kDa in ice and 300 kDa in 100 nm thick samples of dense biological material. DOI: http://dx.doi.org/10.7554/eLife.25648.001 PMID:28467302

Preparation and characterization of chemically defined oligomers of rabbit immunoglobulin G molecules for the complement binding studies.

PubMed Central

Wright, J K; Tschopp, J; Jaton, J C

1980-01-01

Pure dimers, trimers, tetramers and pentamers of rabbit non-immune IgG (immunoglobulin G) or antibody IgG were prepared by polymerization in the presence of the bifunctional cross-linking reagent dithiobis (succinimidylpropionate). Oligomerization was performed either in the presence of polysaccharide antigen and specific monomeric antibody (method A) or by random cross-linking of non-immune rabbit IgG in the absence of antigen (method B). By repeated gel-filtration chromatography, samples prepared by both methods exhibited a single band in analytical sodium dodecyl sulphate/polyacrylamide-gel electrophoresis. The electrophoretic mobilities of samples prepared by method A were slightly greater than those for the corresponding samples prepared by method B. This might suggest a role played by antigen in the orientation of IgG molecules within the clusters, which may be more compact than those formed by random cross-linking. The average numbers of cross-linker molecules per oligomer varied between 3 and 6 for clusters made by method A and between 1 and 3 for clusters made by method B. Ultracentrifugal analyses of the oligomers yielded sedimentation coefficients (S20,w) of 9.6S for the dimer, 11.2S for the trimer, 13.6S for the tetramer and 16.1S for the pentamer. Comparison of the observed sedimentation coefficients with those predicted by various hydrodynamic models suggested these oligomers possessed open and linear structures. Reduction of the cross-linking molecules converted oligomers into monomeric species of IgG. C.d. spectra of some oligomers studied in the range 200-250 nm were essentially the same as that of monomeric IgG molecules, thus strongly suggesting no major conformation changes in IgG molecules within clusters. These oligomers were found to be stable for up to 2 months when stored at -70 degrees C. Images Fig. 1. Fig. 4. PMID:7188424

Modeling fluid diffusion in cerebral white matter with random walks in complex environments

NASA Astrophysics Data System (ADS)

Levy, Amichai; Cwilich, Gabriel; Buldyrev, Sergey V.; Weeden, Van J.

2012-02-01

Recent studies with diffusion MRI have shown new aspects of geometric order in the brain, including complex path coherence within the cerebral cortex, and organization of cerebral white matter and connectivity across multiple scales. The main assumption of these studies is that water molecules diffuse along myelin sheaths of neuron axons in the white matter and thus the anisotropy of their diffusion tensor observed by MRI can provide information about the direction of the axons connecting different parts of the brain. We model the diffusion of particles confined in the space of between the bundles of cylindrical obstacles representing fibrous structures of various orientations. We have investigated the directional properties of the diffusion, by studying the angular distribution of the end point of the random walks as a function of their length, to understand the scale over which the distribution randomizes. We will show evidence of qualitative change in the behavior of the diffusion for different volume fractions of obstacles. Comparisons with three-dimensional MRI images will be illustrated.

Influence of Molecular Shape on Molecular Orientation and Stability of Vapor-Deposited Organic Semiconductors

NASA Astrophysics Data System (ADS)

Walters, Diane M.; Johnson, Noah D.; Ediger, M. D.

Physical vapor deposition is commonly used to prepare active layers in organic electronics. Recently, it has been shown that molecular orientation and packing can be tuned by changing the substrate temperature during deposition, while still producing macroscopically homogeneous films. These amorphous materials can be highly anisotropic when prepared with low substrate temperatures, and they can exhibit exceptional kinetic stability; films retain their favorable packing when heated to high temperatures. Here, we study the influence of molecular shape on molecular orientation and stability. We investigate disc-shaped molecules, such as TCTA and m-MTDATA, nearly spherical molecules, such as Alq3, and linear molecules covering a broad range of aspect ratios, such as p-TTP and BSB-Cz. Disc-shaped molecules have preferential horizontal orientation when deposited at low substrate temperatures, and their orientation can be tuned by changing the substrate temperature. Alq3 forms stable, amorphous films that are optically isotropic when vapor deposited over a broad range of substrate temperatures. This work may guide the choice of material and deposition conditions for vapor-deposited films used in organic electronics and allow for more efficient devices to be fabricated.

Light-induced noncentrosymmetry in acceptor-donor-substituted azobenzene solutions

NASA Astrophysics Data System (ADS)

Zhao, Jiang; Si, Jinhai; Wang, Yougui; Ye, Peixian; Fu, Xingfa; Qiu, Ling; Shen, Yuquan

1995-10-01

Light-induced noncentrosymmetry was achieved experimentally in acceptor-donor-substituted azobenzene solutions and observed by phase-matched nondegenerate six-wave mixing. The microscopic origin of the induced noncentrosymmetry was found to be orientational hole burning, which was distinguished directly with net orientation of molecules by experimental observations. The decay time of the induced noncentrosymmetry depended on the rotational orientation time of the sample's molecule, which varied linearly with the viscosity of the solvent.

Concerted orientation induced unidirectional water transport through nanochannels.

PubMed

Wan, Rongzheng; Lu, Hangjun; Li, Jinyuan; Bao, Jingdong; Hu, Jun; Fang, Haiping

2009-11-14

The dynamics of water inside nanochannels is of great importance for biological activities as well as for the design of molecular sensors, devices, and machines, particularly for sea water desalination. When confined in specially sized nanochannels, water molecules form a single-file structure with concerted dipole orientations, which collectively flip between the directions along and against the nanotube axis. In this paper, by using molecular dynamics simulations, we observed a net flux along the dipole-orientation without any application of an external electric field or external pressure difference during the time period of the particular concerted dipole orientations of the molecules along or against the nanotube axis. We found that this unique special-directional water transportation resulted from the asymmetric potential of water-water interaction along the nanochannel, which originated from the concerted dipole orientation of the water molecules that breaks the symmetry of water orientation distribution along the channel within a finite time period. This finding suggests a new mechanism for achieving high-flux water transportation, which may be useful for nanotechnology and biological applications.

On the Concept of Random Orientation in Far-Field Electromagnetic Scattering by Nonspherical Particles

NASA Technical Reports Server (NTRS)

Mishchenko, Michael I.; Yurkin, Maxim A.

2017-01-01

Although the model of randomly oriented nonspherical particles has been used in a great variety of applications of far-field electromagnetic scattering, it has never been defined in strict mathematical terms. In this Letter we use the formalism of Euler rigid-body rotations to clarify the concept of statistically random particle orientations and derive its immediate corollaries in the form of most general mathematical properties of the orientation-averaged extinction and scattering matrices. Our results serve to provide a rigorous mathematical foundation for numerous publications in which the notion of randomly oriented particles and its light-scattering implications have been considered intuitively obvious.

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

PubMed

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

2018-07-05

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

Conductivity of Nanowire Arrays under Random and Ordered Orientation Configurations

PubMed Central

Jagota, Milind; Tansu, Nelson

2015-01-01

A computational model was developed to analyze electrical conductivity of random metal nanowire networks. It was demonstrated for the first time through use of this model that a performance gain in random metal nanowire networks can be achieved by slightly restricting nanowire orientation. It was furthermore shown that heavily ordered configurations do not outperform configurations with some degree of randomness; randomness in the case of metal nanowire orientations acts to increase conductivity. PMID:25976936

Adsorption of methyl green on montmorillonite

NASA Astrophysics Data System (ADS)

Margulies, Leon; Rozen, Harel

1986-03-01

Adsorption of the dye methyl green (MG) on Na -montmorillonite (Clay) takes place through a cation exchange mechanism. At low and high MG loads, each MG molecule replaces approximately two and one Na + ions, respectively. Interactions between MG and Clay were studied using visible absorption and FTIR spectroscopies, and the orientation of the adsorbed molecules were determined by infrared linear dichroism and X-ray powder diffraction. The dye molecules are preferentially oriented with their plane parallel to the clay surface. The influence of MG load on the adsorption of two additional organic molecules, benzyl benzoate and benzophenone, was also studied.

Physical vapor deposition as a route to glasses with liquid crystalline order

NASA Astrophysics Data System (ADS)

Gomez, Jaritza

Physical vapor deposition (PVD) is an effective route to prepare glasses with a unique combination of properties. Substrate temperatures near the glass transition (Tg) and slow deposition rates can access enhanced mobility at the surface of the glass allowing molecules at the surface additional time to sample different molecular configurations. The temperature of the substrate can be used to control molecular mobility during deposition and properties in the resulting glasses such as higher density, kinetic stability and preferential molecular orientation. PVD was used to prepare glasses of itraconazole, a smectic A liquid crystal. We characterized molecular orientation using infrared and ellipsometry. Molecular orientation can be controlled by choice of Tsubstrate in a range of temperatures near Tg. Glasses deposited at Tsubstrate = Tg show nearly vertical molecular orientation relative to the substrate; at lower Tsubstrate, molecules are nearly parallel to the substrate. The molecular orientation depends on the temperature of the substrate during preparation and not on the molecular orientation of the underlying layer. This allows preparing samples of layers with differing orientations. We find these glasses are homogeneous solids without evidence of domain boundaries and are molecularly flat. We interpret the combination of properties obtained for vapor-deposited glasses of itraconazole to result from a process where molecular orientation is determined by the structure and dynamics at the free surface of the glass during deposition. We report the thermal and structural properties of glasses prepared using PVD of a rod-like molecule, posaconazole, which does not show equilibrium liquid crystal phases. These glasses show substantial molecular orientation that can be controlled by choice of Tsubstrate during deposition. Ellipsometry and IR indicate that glasses prepared at Tg - 3 K are highly ordered. At these Tsubstrate, molecules show preferential vertical orientation and orientation is similar to that measured in aligned nematic liquid crystal. Our results are consistent with a recently proposed mechanism where molecular orientation in equilibrium liquids can be trapped in PVD glasses and suggest that the orientation at the free surface of posaconazole is nematic-like. In addition, we show posaconazole glasses show high kinetic stability controlled by Tsubstrate.

Anisotropic kinetic energy release and gyroscopic behavior of CO2 super rotors from an optical centrifuge.

PubMed

Murray, Matthew J; Ogden, Hannah M; Mullin, Amy S

2017-10-21

An optical centrifuge is used to generate an ensemble of CO 2 super rotors with oriented angular momentum. The collision dynamics and energy transfer behavior of the super rotor molecules are investigated using high-resolution transient IR absorption spectroscopy. New multipass IR detection provides improved sensitivity to perform polarization-dependent transient studies for rotational states with 76 ≤ J ≤ 100. Polarization-dependent measurements show that the collision-induced kinetic energy release is spatially anisotropic and results from both near-resonant energy transfer between super rotor molecules and non-resonant energy transfer between super rotors and thermal molecules. J-dependent studies show that the extent and duration of the orientational anisotropy increase with rotational angular momentum. The super rotors exhibit behavior akin to molecular gyroscopes, wherein molecules with larger amounts of angular momentum are less likely to change their angular momentum orientation through collisions.

Anisotropic kinetic energy release and gyroscopic behavior of CO2 super rotors from an optical centrifuge

NASA Astrophysics Data System (ADS)

Murray, Matthew J.; Ogden, Hannah M.; Mullin, Amy S.

2017-10-01

An optical centrifuge is used to generate an ensemble of CO2 super rotors with oriented angular momentum. The collision dynamics and energy transfer behavior of the super rotor molecules are investigated using high-resolution transient IR absorption spectroscopy. New multipass IR detection provides improved sensitivity to perform polarization-dependent transient studies for rotational states with 76 ≤ J ≤ 100. Polarization-dependent measurements show that the collision-induced kinetic energy release is spatially anisotropic and results from both near-resonant energy transfer between super rotor molecules and non-resonant energy transfer between super rotors and thermal molecules. J-dependent studies show that the extent and duration of the orientational anisotropy increase with rotational angular momentum. The super rotors exhibit behavior akin to molecular gyroscopes, wherein molecules with larger amounts of angular momentum are less likely to change their angular momentum orientation through collisions.

Visualizing the orientational dependence of an intermolecular potential

NASA Astrophysics Data System (ADS)

Sweetman, Adam; Rashid, Mohammad A.; Jarvis, Samuel P.; Dunn, Janette L.; Rahe, Philipp; Moriarty, Philip

2016-02-01

Scanning probe microscopy can now be used to map the properties of single molecules with intramolecular precision by functionalization of the apex of the scanning probe tip with a single atom or molecule. Here we report on the mapping of the three-dimensional potential between fullerene (C60) molecules in different relative orientations, with sub-Angstrom resolution, using dynamic force microscopy (DFM). We introduce a visualization method which is capable of directly imaging the variation in equilibrium binding energy of different molecular orientations. We model the interaction using both a simple approach based around analytical Lennard-Jones potentials, and with dispersion-force-corrected density functional theory (DFT), and show that the positional variation in the binding energy between the molecules is dominated by the onset of repulsive interactions. Our modelling suggests that variations in the dispersion interaction are masked by repulsive interactions even at displacements significantly larger than the equilibrium intermolecular separation.

Aligned 1-D nanorods of a π-gelator exhibit molecular orientation and excitation energy transport different from entangled fiber networks.

PubMed

Sakakibara, Keita; Chithra, Parayalil; Das, Bidisa; Mori, Taizo; Akada, Misaho; Labuta, Jan; Tsuruoka, Tohru; Maji, Subrata; Furumi, Seiichi; Shrestha, Lok Kumar; Hill, Jonathan P; Acharya, Somobrata; Ariga, Katsuhiko; Ajayaghosh, Ayyappanpillai

2014-06-18

Linear π-gelators self-assemble into entangled fibers in which the molecules are arranged perpendicular to the fiber long axis. However, orientation of gelator molecules in a direction parallel to the long axes of the one-dimensional (1-D) structures remains challenging. Herein we demonstrate that, at the air-water interface, an oligo(p-phenylenevinylene)-derived π-gelator forms aligned nanorods of 340 ± 120 nm length and 34 ± 5 nm width, in which the gelator molecules are reoriented parallel to the long axis of the rods. The orientation change of the molecules results in distinct excited-state properties upon local photoexcitation, as evidenced by near-field scanning optical microscopy. A detailed understanding of the mechanism by which excitation energy migrates through these 1-D molecular assemblies might help in the design of supramolecular structures with improved charge-transport properties.

Trimethylamine N-oxide (TMAO) and tert-butyl alcohol (TBA) at hydrophobic interfaces: insights from molecular dynamics simulations.

PubMed

Fiore, Andrew; Venkateshwaran, Vasudevan; Garde, Shekhar

2013-06-25

TMAO, a potent osmolyte, and TBA, a denaturant, have similar molecular architecture but somewhat different chemistry. We employ extensive molecular dynamics simulations to quantify their behavior at vapor-water and octane-water interfaces. We show that interfacial structure-density and orientation-and their dependence on solution concentration are markedly different for the two molecules. TMAO molecules are moderately surface active and adopt orientations with their N-O vector approximately parallel to the aqueous interface. That is, not all methyl groups of TMAO at the interface point away from the water phase. In contrast, TBA molecules act as molecular amphiphiles, are highly surface active, and, at low concentrations, adopt orientations with their methyl groups pointing away and the C-O vector pointing directly into water. The behavior of TMAO at aqueous interfaces is only weakly dependent on its solution concentration, whereas that of TBA depends strongly on concentration. We show that this concentration dependence arises from their different hydrogen bonding capabilities-TMAO can only accept hydrogen bonds from water, whereas TBA can accept (donate) hydrogen bonds from (to) water or other TBA molecules. The ability to self-associate, particularly visible in TBA molecules in the interfacial layer, allows them to sample a broad range of orientations at higher concentrations. In light of the role of TMAO and TBA in biomolecular stability, our results provide a reference with which to compare their behavior near biological interfaces. Also, given the ubiquity of aqueous interfaces in biology, chemistry, and technology, our results may be useful in the design of interfacially active small molecules with the aim to control their orientations and interactions.

New approximate orientation averaging of the water molecule interacting with the thermal neutron

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

Markovic, M.I.; Minic, D.M.; Rakic, A.D.

1992-02-01

This paper reports that exactly describing the time of thermal neutron collisions with water molecules, orientation averaging is performed by an exact method (EOA{sub k}) and four approximate methods (two well known and two less known). Expressions for the microscopic scattering kernel are developed. The two well-known approximate orientation averaging methods are Krieger-Nelkin (K-N) and Koppel-Young (K-Y). The results obtained by one of the two proposed approximate orientation averaging methods agree best with the corresponding results obtained by EOA{sub k}. The largest discrepancies between the EOA{sub k} results and the results of the approximate methods are obtained using the well-knowmore » K-N approximate orientation averaging method.« less

Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function

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

Prill, Dragica; Juhas, Pavol; Billinge, Simon J. L.

2016-01-01

In this study, a method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may bemore » used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.« less

Polarized Raman Spectroscopy for Determining the Orientation of di-D-phenylalanine Molecules in a Nanotube.

PubMed

Sereda, Valentin; Ralbovsky, Nicole M; Vasudev, Milana C; Naik, Rajesh R; Lednev, Igor K

2016-09-01

Self-assembly of short peptides into nanostructures has become an important strategy for the bottom-up fabrication of nanomaterials. Significant interest to such peptide-based building blocks is due to the opportunity to control the structure and properties of well-structured nanotubes, nanofibrils, and hydrogels. X-ray crystallography and solution NMR, two major tools of structural biology, have significant limitations when applied to peptide nanotubes because of their non-crystalline structure and large weight. Polarized Raman spectroscopy was utilized for structural characterization of well-aligned D-Diphenylalanine nanotubes. The orientation of selected chemical groups relative to the main axis of the nanotube was determined. Specifically, the C-N bond of CNH 3 + groups is oriented parallel to the nanotube axis, the peptides' carbonyl groups are tilted at approximately 54° from the axis and the COO - groups run perpendicular to the axis. The determined orientation of chemical groups allowed the understanding of the orientation of D-diphenylalanine molecule that is consistent with its equilibrium conformation. The obtained data indicate that there is only one orientation of D-diphenylalanine molecules with respect to the nanotube main axis.

Automatic Nanodesign Using Evolutionary Techniques

NASA Technical Reports Server (NTRS)

Globus, Al; Saini, Subhash (Technical Monitor)

1998-01-01

Many problems associated with the development of nanotechnology require custom designed molecules. We use genetic graph software, a new development, to automatically evolve molecules of interest when only the requirements are known. Genetic graph software designs molecules, and potentially nanoelectronic circuits, given a fitness function that determines which of two molecules is better. A set of molecules, the first generation, is generated at random then tested with the fitness function, Subsequent generations are created by randomly choosing two parent molecules with a bias towards high scoring molecules, tearing each molecules in two at random, and mating parts from the mother and father to create two children. This procedure is repeated until a satisfactory molecule is found. An atom pair similarity test is currently used as the fitness function to evolve molecules similar to existing pharmaceuticals.

Oriented Polar Molecules in a Solid Inert-Gas Matrix: A Proposed Method for Measuring the Electric Dipole Moment of the Electron

NASA Astrophysics Data System (ADS)

Vutha, A.; Horbatsch, M.; Hessels, E.

2018-01-01

We propose a very sensitive method for measuring the electric dipole moment of the electron using polar molecules embedded in a cryogenic solid matrix of inert-gas atoms. The polar molecules can be oriented in the $\\hat{\\rm{z}}$ direction by an applied electric field, as has recently been demonstrated by Park, et al. [Angewandte Chemie {\\bf 129}, 1066 (2017)]. The trapped molecules are prepared into a state which has its electron spin perpendicular to $\\hat{\\rm{z}}$, and a magnetic field along $\\hat{\\rm{z}}$ causes precession of this spin. An electron electric dipole moment $d_e$ would affect this precession due to the up to 100~GV/cm effective electric field produced by the polar molecule. The large number of polar molecules that can be embedded in a matrix, along with the expected long coherence times for the precession, allows for the possibility of measuring $d_e$ to an accuracy that surpasses current measurements by many orders of magnitude. Because the matrix can inhibit molecular rotations and lock the orientation of the polar molecules, it may not be necessary to have an electric field present during the precession. The proposed technique can be applied using a variety of polar molecules and inert gases, which, along with other experimental variables, should allow for careful study of systematic uncertainties in the measurement.

Femtosecond spectroscopic study of the solvation of amphiphilic molecules by water

NASA Astrophysics Data System (ADS)

Rezus, Y. L. A.; Bakker, H. J.

2008-06-01

We use polarization-resolved mid-infrared pump-probe spectroscopy to study the aqueous solvation of proline and N-methylacetamide. These molecules serve as models to study the solvation of proteins. We monitor the orientational dynamics of partly deuterated water molecules (HDO) that are present at a low concentration in the water. We find that the OD vibration of HDO relaxes via an intermediate level, that is characterized by a hydrogen-bond that is stronger than in the ground state. With increasing concentration the lifetime of the excited state increases from 1.8 ps to 2.4 ps and the lifetime of the intermediate level from 0.6 ps to 1.0 ps. Regarding the orientational dynamics we observe biexponential behavior, which finds its origin in the presence of two classes of water molecules. There is a fraction of water molecules that has bulk-like orientational dynamics ( τrot = 2.5 ps) and a fraction of immobilized water molecules ( τrot > 10 ps). The relative abundance of the two fractions is determined by the nature and concentration of the solute. We find that the hydrophobic solute groups are responsible for the immobilization of water molecules. Every methyl group causes the immobilization of approximately 4 water OH groups. The hydrophilic solute groups, on the other hand, do not hinder the reorientation and the water molecules solvating them reorient with the same rate as in the bulk liquid.

Plasmon-induced absorption of blind chlorophylls in photosynthetic proteins assembled on silver nanowires.

PubMed

Szalkowski, Marcin; Janna Olmos, Julian David; Buczyńska, Dorota; Maćkowski, Sebastian; Kowalska, Dorota; Kargul, Joanna

2017-07-27

We demonstrate that controlled assembly of eukaryotic photosystem I with its associated light harvesting antenna complex (PSI-LHCI) on plasmonically active silver nanowires (AgNWs) substantially improves the optical functionality of such a novel biohybrid nanostructure. By comparing fluorescence intensities measured for PSI-LHCI complex randomly oriented on AgNWs and the results obtained for the PSI-LHCI/cytochrome c 553 (cyt c 553 ) bioconjugate with AgNWs we conclude that the specific binding of photosynthetic complexes with defined uniform orientation yields selective excitation of a pool of chlorophyll (Chl) molecules that are otherwise almost non-absorbing. This is remarkable, as this study shows for the first time that plasmonic excitations in metallic nanostructures can not only be used to enhance native absorption of photosynthetic pigments, but also - by employing cyt c 553 as the conjugation cofactor - to activate the specific Chl pools as the absorbing sites only when the uniform and well-defined orientation of PSI-LHCI with respect to plasmonic nanostructures is achieved. As absorption of PSI alone is comparatively low, our approach lends itself as an innovative approach to outperform the reported-to-date biohybrid devices with respect to solar energy conversion.

LIMAO: Cross-platform software for simulating laser-induced alignment and orientation dynamics of linear-, symmetric- and asymmetric tops

NASA Astrophysics Data System (ADS)

Szidarovszky, Tamás; Jono, Maho; Yamanouchi, Kaoru

2018-07-01

A user-friendly and cross-platform software called Laser-Induced Molecular Alignment and Orientation simulator (LIMAO) has been developed. The program can be used to simulate within the rigid rotor approximation the rotational dynamics of gas phase molecules induced by linearly polarized intense laser fields at a given temperature. The software is implemented in the Java and Mathematica programming languages. The primary aim of LIMAO is to aid experimental scientists in predicting and analyzing experimental data representing laser-induced spatial alignment and orientation of molecules.

Polymer poling characterization using second harmonic generation (SHG)

NASA Astrophysics Data System (ADS)

Tellier, Gildas; Averty, Dominique; Blart, Errol; Boisrobert, Christian; Gundel, Hartmut; Le Tacon, Sylvain; Monnereau, Cyrille; Odobel, Fabrice; Seveno, Raynald

2006-04-01

Several polymer molecules have structures which are suitable for the non-linear optic applications. We report on the design and fabrication of a high performance electro-optic modulator made of polymer thin films. The polymer we study contains a chromophore based on Disperse Red One covalently grafted to a host-matrix. The polymer materials are deposited in thin layers on a glass substrate by chemical solution deposition, either by spin-coating or by dip-coating. The thickness of the films is ranging from a hundred nanometers to several micrometers. Initially, the polymer molecules are randomly oriented and the films are isotropic, hence no electro-optic effect can be observed. In order to break the symmetry and align the chromophores, the films are submitted to the so-called corona poling process. As a result, their structure become non-centrosymmetric and the second-order susceptibility is no longer zero. The corona poling method consists of applying a high electric field to the polymer by means of a needle electrode, placed above the polymer film which is posed on a grounded sample support electrode. Thermal regulation of the support electrode allows to control the temperature during the poling of the films. Once the poling process has been established, a chemical cross-linking function is thermally activated in order to fix the orientation of the chromophores in the polymer matrix. The orientation and its stability in time is evaluated with a Second Harmonic Generation measurement set-up using the Makers Fringes configuration. We studied the influence of the poling temperature, the distance between the corona needle electrode and the sample, the high voltage applied, and the duration of the poling process on the efficiency of chromophore orientation in order to optimize the poling procedure. Finally, aging of poled polymer samples has been investigated at elevated temperatures, confirming the stability of the cross-linking process.

Preferred orientation of albumin adsorption on a hydrophilic surface from molecular simulation.

PubMed

Hsu, Hao-Jen; Sheu, Sheh-Yi; Tsay, Ruey-Yug

2008-12-01

In general, non-specific protein adsorption follows a two-step procedure, i.e. first adsorption onto a surface in native form, and a subsequent conformational change on the surface. In order to predict the subsequent conformational change, it is important to determine the preferred orientation of an adsorbed protein in the first step of the adsorption. In this work, a method based on finding the global minimum of the interaction potential energy of an adsorbed protein has been developed to delineate the preferred orientations for the adsorption of human serum albumin (HSA) on a model surface with a hydrophilic self-assembled monolayer (SAM). For computational efficiency, solvation effects were greatly simplified by only including the dampening of electrostatic effects while neglecting contributions due to the competition of water molecules for the functional groups on the surface. A contour map obtained by systematic rotation of a molecule in conjunction with perpendicular motion to the surface gives the minimum interaction energy of the adsorbed molecule at various adsorption orientations. Simulation results show that for an -OH terminated SAM surface, a "back-on" orientation of HSA is the preferred orientation. The projection area of this adsorption orientation corresponds with the "triangular-side-on" adsorption of a heart shaped HSA molecule. The method proposed herein is able to provide results which are consistent with those predicted by Monte Carlo (MC) simulations with a substantially less computing cost. The high computing efficiency of the current method makes it possible to be implemented as a design tool for the control of protein adsorption on surfaces; however, before this can be fully realized, these methods must be further developed to enable interaction free energy to be calculated in place of potential energy, along with a more realistic representation of solvation effects.

Molecular near-field antenna effect in resonance hyper-Raman scattering: Intermolecular vibronic intensity borrowing of solvent from solute through dipole-dipole and dipole-quadrupole interactions

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

Shimada, Rintaro; Hamaguchi, Hiro-o, E-mail: hhama@nctu.edu.tw

2014-05-28

We quantitatively interpret the recently discovered intriguing phenomenon related to resonance Hyper-Raman (HR) scattering. In resonance HR spectra of all-trans-β-carotene (β-carotene) in solution, vibrations of proximate solvent molecules are observed concomitantly with the solute β-carotene HR bands. It has been shown that these solvent bands are subject to marked intensity enhancements by more than 5 orders of magnitude under the presence of β-carotene. We have called this phenomenon the molecular-near field effect. Resonance HR spectra of β-carotene in benzene, deuterated benzene, cyclohexane, and deuterated cyclohexane have been measured precisely for a quantitative analysis of this effect. The assignments of themore » observed peaks are made by referring to the infrared, Raman, and HR spectra of neat solvents. It has been revealed that infrared active and some Raman active vibrations are active in the HR molecular near-field effect. The observed spectra in the form of difference spectra (between benzene/deuterated benzene and cyclohexane/deuterated cyclohexane) are quantitatively analyzed on the basis of the extended vibronic theory of resonance HR scattering. The theory incorporates the coupling of excited electronic states of β-carotene with the vibrations of a proximate solvent molecule through solute–solvent dipole–dipole and dipole–quadrupole interactions. It is shown that the infrared active modes arise from the dipole–dipole interaction, whereas Raman active modes from the dipole–quadrupole interaction. It is also shown that vibrations that give strongly polarized Raman bands are weak in the HR molecular near-field effect. The observed solvent HR spectra are simulated with the help of quantum chemical calculations for various orientations and distances of a solvent molecule with respect to the solute. The observed spectra are best simulated with random orientations of the solvent molecule at an intermolecular distance of 10 Å.« less

Small-amplitude backbone motions of the spin-labeled lipopeptide trichogin GA IV in a lipid membrane as revealed by electron spin echo.

PubMed

Syryamina, Victoria N; Isaev, Nikolay P; Peggion, Cristina; Formaggio, Fernando; Toniolo, Claudio; Raap, Jan; Dzuba, Sergei A

2010-09-30

Trichogin GA IV is a lipopeptide antibiotic of fungal origin, which is known to be able to modify the membrane permeability. TOAC nitroxide spin-labeled analogues of this membrane active peptide were investigated in hydrated bilayers of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) by electron spin echo (ESE) spectroscopy. Because the TOAC nitroxide spin label is rigidly attached to the peptide backbone, it may report on the backbone orientational dynamics. The ESE signal in this system is observed below ∼150 K. Previously, three-pulse stimulated ESE was found to be sensitive to two types of orientational motion of spin-labeled POPC lipid bilayers at these temperatures. The first type is fast stochastic librations, with a correlation time on the nanosecond scale (which also manifests itself in a two-pulse primary ESE experiment). The second type is slow millisecond inertial rotations. In the present work, we find that at low molar peptide to lipid ratio (1:200), where the individual peptide molecules are randomly distributed at the membrane surface, the spin labels show only a fast type of motion. At the high molar peptide to lipid ratio (1:20), a slow motion is also observed. Because at this high concentration trichogin GA IV is known to change its orientation from the in-plane topology to the transmembrane disposition, the observed onset of a slow motion may be safely attributed to the dynamics of peptides, which are elongated along the lipid molecules of the membrane. The possible interrelation between this backbone rotational motion of the peptide antibiotic and the membrane leakage is discussed.

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

Jiang, J.; Walters, D. M.; Zhou, D.

Vapor-deposited glasses can be anisotropic and molecular orientation is important for organic electronics applications. In organic light emitting diodes (OLEDs), for example, the orientation of dye molecules in two-component emitting layers significantly influences emission efficiency. Here we investigate how substrate temperature during vapor deposition influences the orientation of dye molecules in a model two-component system. We determine the average orientation of a linear blue light emitter 1,4-di-[4-( N,N-diphenyl)amino]styrylbenzene (DSA-Ph) in mixtures with aluminum-tris(8-hydroxyquinoline) (Alq 3) by spectroscopic ellipsometry and IR dichroism. We find that molecular orientation is controlled by the ratio of the substrate temperature during deposition and the glassmore » transition temperature of the mixture. Furthermore, these findings extend recent results for single component vapor-deposited glasses and suggest that, during vapor deposition, surface mobility allows partial equilibration towards orientations preferred at the free surface of the equilibrium liquid.« less

Ultralong copper phthalocyanine nanowires with new crystal structure and broad optical absorption.

PubMed

Wang, Hai; Mauthoor, Soumaya; Din, Salahud; Gardener, Jules A; Chang, Rio; Warner, Marc; Aeppli, Gabriel; McComb, David W; Ryan, Mary P; Wu, Wei; Fisher, Andrew J; Stoneham, Marshall; Heutz, Sandrine

2010-07-27

The development of molecular nanostructures plays a major role in emerging organic electronic applications, as it leads to improved performance and is compatible with our increasing need for miniaturization. In particular, nanowires have been obtained from solution or vapor phase and have displayed high conductivity or large interfacial areas in solar cells. In all cases however, the crystal structure remains as in films or bulk, and the exploitation of wires requires extensive postgrowth manipulation as their orientations are random. Here we report copper phthalocyanine (CuPc) nanowires with diameters of 10-100 nm, high directionality, and unprecedented aspect ratios. We demonstrate that they adopt a new crystal phase, designated eta-CuPc, where the molecules stack along the long axis. The resulting high electronic overlap along the centimeter length stacks achieved in our wires mediates antiferromagnetic couplings and broadens the optical absorption spectrum. The ability to fabricate ultralong, flexible metal phthalocyanine nanowires opens new possibilities for applications of these simple molecules.

Vibrationally induced inversion of photoelectron forward-backward asymmetry in chiral molecule photoionization by circularly polarized light

PubMed Central

Garcia, Gustavo A.; Nahon, Laurent; Daly, Steven; Powis, Ivan

2013-01-01

Electron–nuclei coupling accompanying excitation and relaxation processes is a fascinating phenomenon in molecular dynamics. A striking and unexpected example of such coupling is presented here in the context of photoelectron circular dichroism measurements on randomly oriented, chiral methyloxirane molecules, unaffected by any continuum resonance. Here, we report that the forward-backward asymmetry in the electron angular distribution, with respect to the photon axis, which is associated with photoelectron circular dichroism can surprisingly reverse direction according to the ion vibrational mode excited. This vibrational dependence represents a clear breakdown of the usual Franck–Condon assumption, ascribed to the enhanced sensitivity of photoelectron circular dichroism (compared with other observables like cross-sections or the conventional anisotropy parameter-β) to the scattering phase off the chiral molecular potential, inducing a dependence on the nuclear geometry sampled in the photoionization process. Important consequences for the interpretation of such dichroism measurements within analytical contexts are discussed. PMID:23828557

Fabrication of antibody microarrays by light-induced covalent and oriented immobilization.

PubMed

Adak, Avijit K; Li, Ben-Yuan; Huang, Li-De; Lin, Ting-Wei; Chang, Tsung-Che; Hwang, Kuo Chu; Lin, Chun-Cheng

2014-07-09

Antibody microarrays have important applications for the sensitive detection of biologically important target molecules and as biosensors for clinical applications. Microarrays produced by oriented immobilization of antibodies generally have higher antigen-binding capacities than those in which antibodies are immobilized with random orientations. Here, we present a UV photo-cross-linking approach that utilizes boronic acid to achieve oriented immobilization of an antibody on a surface while retaining the antigen-binding activity of the immobilized antibody. A photoactive boronic acid probe was designed and synthesized in which boronic acid provided good affinity and specificity for the recognition of glycan chains on the Fc region of the antibody, enabling covalent tethering to the antibody upon exposure to UV light. Once irradiated with optimal UV exposure (16 mW/cm(2)), significant antibody immobilization on a boronic acid-presenting surface with maximal antigen detection sensitivity in a single step was achieved, thus obviating the necessity of prior antibody modifications. The developed approach is highly modular, as demonstrated by its implementation in sensitive sandwich immunoassays for the protein analytes Ricinus communis agglutinin 120, human prostate-specific antigen, and interleukin-6 with limits of detection of 7.4, 29, and 16 pM, respectively. Furthermore, the present system enabled the detection of multiple analytes in samples without any noticeable cross-reactivities. Antibody coupling via the use of boronic acid and UV light represents a practical, oriented immobilization method with significant implications for the construction of a large array of immunosensors for diagnostic applications.

Molecular orientation of organic thin films on dielectric solid substrates: a phase-sensitive vibrational SFG study.

PubMed

Ge, Aimin; Peng, Qiling; Qiao, Lin; Yepuri, Nageshwar R; Darwish, Tamim A; Matsusaki, Michiya; Akashi, Mitsuru; Ye, Shen

2015-07-21

Broadband phase-sensitive vibrational sum frequency generation (SFG) spectroscopy was utilized to study the molecular orientation of molecules adsorbed on dielectric solid substrates. A gold thin film was employed to generate a SFG signal as a local oscillator (LO). To simplify the phase measurement, a self-assembled monolayer (SAM) of octadecyltrichlorosilane (OTS) was used as a standard sample for phase correction of the phase-sensitive SFG measurements on the solid/air interface. It was demonstrated that the absolute orientation of molecules in the LB films on a fused quartz surface can be clearly distinguished by phase-sensitive SFG measurement. In addition, the observation on the SAM of d35-OTS reveals that the two C-H stretching modes for α-CH2 group are in opposite phase. Furthermore, by using the present phase-sensitive SFG setup, the orientation flipping of water molecules on positively and negatively charged solid/liquid interface can be distinguished.

Measurement of Single Macromolecule Orientation by Total Internal Reflection Fluorescence Polarization Microscopy

PubMed Central

Forkey, Joseph N.; Quinlan, Margot E.; Goldman, Yale E.

2005-01-01

A new approach is presented for measuring the three-dimensional orientation of individual macromolecules using single molecule fluorescence polarization (SMFP) microscopy. The technique uses the unique polarizations of evanescent waves generated by total internal reflection to excite the dipole moment of individual fluorophores. To evaluate the new SMFP technique, single molecule orientation measurements from sparsely labeled F-actin are compared to ensemble-averaged orientation data from similarly prepared densely labeled F-actin. Standard deviations of the SMFP measurements taken at 40 ms time intervals indicate that the uncertainty for individual measurements of axial and azimuthal angles is ∼10° at 40 ms time resolution. Comparison with ensemble data shows there are no substantial systematic errors associated with the single molecule measurements. In addition to evaluating the technique, the data also provide a new measurement of the torsional rigidity of F-actin. These measurements support the smaller of two values of the torsional rigidity of F-actin previously reported. PMID:15894632

Influence of Molecular Shape on the Thermal Stability and Molecular Orientation of Vapor-Deposited Organic Semiconductors

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

Walters, Diane M; Antony, Lucas; de Pablo, Juan

High thermal stability and anisotropic molecular orientation enhance the performance of vapor-deposited organic semiconductors, but controlling these properties is a challenge in amorphous materials. To understand the influence of molecular shape on these properties, vapor-deposited glasses of three disk-shaped molecules were prepared. For all three systems, enhanced thermal stability is observed for glasses prepared over a wide range of substrate temperatures and anisotropic molecular orientation is observed at lower substrate temperatures. For two of the disk-shaped molecules, atomistic simulations of thin films were also performed and anisotropic molecular orientation was observed at the equilibrium liquid surface. We find that themore » structure and thermal stability of these vapor-deposited glasses results from high surface mobility and partial equilibration toward the structure of the equilibrium liquid surface during the deposition process. For the three molecules studied, molecular shape is a dominant factor in determining the anisotropy of vapor-deposited glasses.« less

Machine Learning and Infrared Thermography for Fiber Orientation Assessment on Randomly-Oriented Strands Parts.

PubMed

Fernandes, Henrique; Zhang, Hai; Figueiredo, Alisson; Malheiros, Fernando; Ignacio, Luis Henrique; Sfarra, Stefano; Ibarra-Castanedo, Clemente; Guimaraes, Gilmar; Maldague, Xavier

2018-01-19

The use of fiber reinforced materials such as randomly-oriented strands has grown in recent years, especially for manufacturing of aerospace composite structures. This growth is mainly due to their advantageous properties: they are lighter and more resistant to corrosion when compared to metals and are more easily shaped than continuous fiber composites. The resistance and stiffness of these materials are directly related to their fiber orientation. Thus, efficient approaches to assess their fiber orientation are in demand. In this paper, a non-destructive evaluation method is applied to assess the fiber orientation on laminates reinforced with randomly-oriented strands. More specifically, a method called pulsed thermal ellipsometry combined with an artificial neural network, a machine learning technique, is used in order to estimate the fiber orientation on the surface of inspected parts. Results showed that the method can be potentially used to inspect large areas with good accuracy and speed.

Machine Learning and Infrared Thermography for Fiber Orientation Assessment on Randomly-Oriented Strands Parts

PubMed Central

Maldague, Xavier

2018-01-01

The use of fiber reinforced materials such as randomly-oriented strands has grown in recent years, especially for manufacturing of aerospace composite structures. This growth is mainly due to their advantageous properties: they are lighter and more resistant to corrosion when compared to metals and are more easily shaped than continuous fiber composites. The resistance and stiffness of these materials are directly related to their fiber orientation. Thus, efficient approaches to assess their fiber orientation are in demand. In this paper, a non-destructive evaluation method is applied to assess the fiber orientation on laminates reinforced with randomly-oriented strands. More specifically, a method called pulsed thermal ellipsometry combined with an artificial neural network, a machine learning technique, is used in order to estimate the fiber orientation on the surface of inspected parts. Results showed that the method can be potentially used to inspect large areas with good accuracy and speed. PMID:29351240

High-ionic-strength electroosmotic flows in uncharged hydrophobic nanochannels.

PubMed

Kim, Daejoong; Darve, Eric

2009-02-01

We report molecular dynamics simulation results of high-ionic-strength electroosmotic flows inside uncharged nanochannels. The possibility of this unusual electrokinetic phenomenon has been discussed by Dukhin et al. [A. Dukhin, S. Dukhin, P. Goetz, Langmuir 21 (2005) 9990]. Our computed velocity profiles clearly indicate the presence of a net flow with a maximum velocity around 2 m/s. We found the apparent zeta potential to be -29.7+/-6.8 mV, using the Helmholtz-Smoluchowski relation and the measured mean velocity. This value is comparable to experimentally measured values in Dukhin et al. and references therein. We also investigate the orientations of water molecules in response to an electric field by computing polarization density. Water molecules in the bulk region are oriented along the direction of the external electric field, while their near-wall orientation shows oscillations. The computation of three-dimensional density distributions of sodium and chloride ions around each individual water molecule show that chloride ions tend to concentrate near a water molecule, whereas sodium ions are diffusely distributed.

Asymmetric nanoparticle may go "active" at room temperature

NASA Astrophysics Data System (ADS)

Sheng, Nan; Tu, YuSong; Guo, Pan; Wan, RongZheng; Wang, ZuoWei; Fang, HaiPing

2017-04-01

Using molecular dynamics simulations, we show that an asymmetrically shaped nanoparticle in dilute solution possesses a spontaneously curved trajectory within a finite time interval, instead of the generally expected random walk. This unexpected dynamic behavior has a similarity to that of active matters, such as swimming bacteria, cells, or even fish, but is of a different physical origin. The key to the curved trajectory lies in the non-zero resultant force originated from the imbalance of the collision forces acted by surrounding solvent molecules on the asymmetrically shaped nanoparticle during its orientation regulation. Theoretical formulae based on microscopic observations have been derived to describe this non-zero force and the resulting motion of the asymmetrically shaped nanoparticle.

Ion penetration depth in the plant cell wall

NASA Astrophysics Data System (ADS)

Yu, L. D.; Vilaithong, T.; Phanchaisri, B.; Apavatjrut, P.; Anuntalabhochai, S.; Evans, P.; Brown, I. G.

2003-05-01

This study investigates the depth of ion penetration in plant cell wall material. Based on the biological structure of the plant cell wall, a physical model is proposed which assumes that the wall is composed of randomly orientated layers of cylindrical microfibrils made from cellulose molecules of C 6H 12O 6. With this model, we have determined numerical factors for ion implantation in the plant cell wall to correct values calculated from conventional ion implantation programs. Using these correction factors, it is possible to apply common ion implantation programs to estimate the ion penetration depth in the cell for bioengineering purposes. These estimates are compared with measured data from experiments and good agreement is achieved.

Substrate temperature controls molecular orientation in two-component vapor-deposited glasses

DOE PAGES

Jiang, J.; Walters, D. M.; Zhou, D.; ...

2016-02-22

Vapor-deposited glasses can be anisotropic and molecular orientation is important for organic electronics applications. In organic light emitting diodes (OLEDs), for example, the orientation of dye molecules in two-component emitting layers significantly influences emission efficiency. Here we investigate how substrate temperature during vapor deposition influences the orientation of dye molecules in a model two-component system. We determine the average orientation of a linear blue light emitter 1,4-di-[4-( N,N-diphenyl)amino]styrylbenzene (DSA-Ph) in mixtures with aluminum-tris(8-hydroxyquinoline) (Alq 3) by spectroscopic ellipsometry and IR dichroism. We find that molecular orientation is controlled by the ratio of the substrate temperature during deposition and the glassmore » transition temperature of the mixture. Furthermore, these findings extend recent results for single component vapor-deposited glasses and suggest that, during vapor deposition, surface mobility allows partial equilibration towards orientations preferred at the free surface of the equilibrium liquid.« less

Oriented and covalent immobilization of target molecules to solid supports: synthesis and application of a light-activatable and thiol-reactive cross-linking reagent.

PubMed

Collioud, A; Clémence, J F; Sänger, M; Sigrist, H

1993-01-01

Light-dependent oriented and covalent immobilization of target molecules has been achieved by combining two modification procedures: light-dependent coupling of target molecules to inert surfaces and thiol-selective reactions occurring at macromolecule or substrate surfaces. For immobilization purposes the heterobifunctional reagent N-[m-[3-(trifluoromethyl)diazirin-3-yl]phenyl]-4-maleimidobutyr amide was synthesized and chemically characterized. The photosensitivity of the carbene-generating reagent and its reactivity toward thiols were ascertained. Light-induced cross-linking properties of the reagent were documented (i) by reacting first the maleimide function with a thiolated surface, followed by carbene insertion into applied target molecules, (ii) by photochemical coupling of the reagent to an inert support followed by thermochemical reactions with thiol functions, and (iii) by thermochemical modification of target molecules prior to carbene-mediated insertion into surface materials. Procedures mentioned led to light-dependent covalent immobilization of target molecules including amino acids, a synthetic peptide, and antibody-derived F(ab') fragments. Topically selective, light-dependent immobilization was attained with the bifunctional reagent by irradiation of coated surfaces through patterned masks. Glass and polystyrene served as substrates. Molecular orientation is asserted by inherently available or selectively introduced terminal thiol functions in F(ab') fragments and synthetic polypeptides, respectively.

Tunable molecular orientation and elevated thermal stability of vapor-deposited organic semiconductors

PubMed Central

Walters, Diane M.; Lyubimov, Ivan; de Pablo, Juan J.; Ediger, M. D.

2015-01-01

Physical vapor deposition is commonly used to prepare organic glasses that serve as the active layers in light-emitting diodes, photovoltaics, and other devices. Recent work has shown that orienting the molecules in such organic semiconductors can significantly enhance device performance. We apply a high-throughput characterization scheme to investigate the effect of the substrate temperature (Tsubstrate) on glasses of three organic molecules used as semiconductors. The optical and material properties are evaluated with spectroscopic ellipsometry. We find that molecular orientation in these glasses is continuously tunable and controlled by Tsubstrate/Tg, where Tg is the glass transition temperature. All three molecules can produce highly anisotropic glasses; the dependence of molecular orientation upon substrate temperature is remarkably similar and nearly independent of molecular length. All three compounds form “stable glasses” with high density and thermal stability, and have properties similar to stable glasses prepared from model glass formers. Simulations reproduce the experimental trends and explain molecular orientation in the deposited glasses in terms of the surface properties of the equilibrium liquid. By showing that organic semiconductors form stable glasses, these results provide an avenue for systematic performance optimization of active layers in organic electronics. PMID:25831545

Controlling Growth Orientation of Phthalocyanine Films by Electrical Fields

NASA Technical Reports Server (NTRS)

Zhu, S.; Banks, C. E.; Frazier, D. O.; Ila, D.; Muntele, I.; Penn, B. G.; Sharma, A.; Rose, M. Franklin (Technical Monitor)

2001-01-01

Organic Phthalocyanine films have many applications ranging from data storage to various non-linear optical devices whose quality is affected by the growth orientation of Phthalocyanine films. Due to the structural and electrical properties of Phthalocyanine molecules, the film growth orientation depends strongly on the substrate surface states. In this presentation, an electrical field up to 4000 V/cm is introduced during film growth. The Phthalocyanine films are synthesized on quartz substrates using thermal evaporation. An intermediate layer is deposited on some substrates for introducing the electrical field. Scanning electron microscopy, x-ray diffraction, and Fourier transform infrared spectroscopy are used for measuring surface morphology, film structure, and optical properties, respectively. The comparison of Phthalocyanine films grown with and without the electrical field reveals different morphology, film density, and growth orientation, which eventually change optical properties of these films. These results suggest that the growth method in the electrical field can be used to synthesized Phthalocyanine films with a preferred crystal orientation as well as propose an interaction mechanism between the substrate surface and the depositing molecules. The details of growth conditions and of the growth model of how the Phthalocyanine molecules grow in the electrical field will be discussed.

Enhancing scattering images for orientation recovery with diffusion map

DOE PAGES

Winter, Martin; Saalmann, Ulf; Rost, Jan M.

2016-02-12

We explore the possibility for orientation recovery in single-molecule coherent diffractive imaging with diffusion map. This algorithm approximates the Laplace-Beltrami operator, which we diagonalize with a metric that corresponds to the mapping of Euler angles onto scattering images. While suitable for images of objects with specific properties we show why this approach fails for realistic molecules. Here, we introduce a modification of the form factor in the scattering images which facilitates the orientation recovery and should be suitable for all recovery algorithms based on the distance of individual images. (C) 2016 Optical Society of America

The role played by self-orientational properties in nematics of colloids with molecules axially symmetric.

PubMed

Alarcón-Waess, O

2010-04-14

The self-orientational structure factor as well as the short-time self-orientational diffusion coefficient is computed for colloids composed by nonspherical molecules. To compute the short-time dynamics the hydrodynamic interactions are not taken into account. The hard molecules with at least one symmetry axis considered are: rods, spherocylinders, and tetragonal parallelepipeds. Because both orientational properties in study are written in terms of the second and fourth order parameters, these automatically hold the features of the order parameters. That is, they present a discontinuity for first order transitions, determining in this way the spinodal line. In order to analyze the nematic phase only, we choose the appropriate values for the representative quantities that characterize the molecules. Different formalisms are used to compute the structural properties: de Gennes-Landau approach, Smoluchowski equation and computer simulations. Some of the necessary inputs are taken from literature. Our results show that the self-orientational properties play an important role in the characterization and the localization of axially symmetric phases. While the self-structure decreases throughout the nematics, the short-time self-diffusion does not decrease but rather increases. We study the evolution of the second and fourth order parameters; we find different responses for axial and biaxial nematics, predicting the possibility of a biaxial nematics in tetragonal parallelepiped molecules. By considering the second order in the axial-biaxial phase transition, with the support of the self-orientational structure factor, we are able to propose the density at which this occurs. The short-time dynamics is able to predict a different value in the axial and the biaxial phases. Because the different behavior of the fourth order parameter, the diffusion coefficient is lower for a biaxial phase than for an axial one. Therefore the self-structure factor is able to localize continuous phase transitions involving axially symmetric phases and the short-time self-orientational diffusion is able to distinguish the ordered phase by considering the degree of alignment, that is, axial or biaxial.

Epitaxially Grown Films of Standing and Lying Pentacene Molecules on Cu(110) Surfaces

PubMed Central

2011-01-01

Here, it is shown that pentacene thin films (30 nm) with distinctively different crystallographic structures and molecular orientations can be grown under essentially identical growth conditions in UHV on clean Cu(110) surfaces. By X-ray diffraction, we show that the epitaxially oriented pentacene films crystallize either in the “thin film” phase with standing molecules or in the “single crystal” structure with molecules lying with their long axes parallel to the substrate. The morphology of the samples observed by atomic force microscopy shows an epitaxial alignment of pentacene crystallites, which corroborates the molecular orientation observed by X-ray diffraction pole figures. Low energy electron diffraction measurements reveal that these dissimilar growth behaviors are induced by subtle differences in the monolayer structures formed by slightly different preparation procedures. PMID:21479111

Monitoring structural transformations in crystals. 7. 1-Chloroanthracene and its photodimer.

PubMed

Turowska-Tyrk, Ilona; Grześniak, Karolina

2004-02-01

Crystals of the 1-chloroanthracene photodimer, viz. trans-bi(1-chloro-9,10-dihydro-9,10-anthracenediyl), C(28)H(18)Cl(2), were obtained from the solid-state [4+4]-photodimerization of the monomer, C(14)H(9)Cl, followed by recrystallization. The symmetry of the product molecules is defined by the orientation of the reactant molecules in the crystal. The mutual orientation parameters calculated for adjacent monomers explain the reactivity of the compound. The molecules in the crystal of the monomer and the recrystallized photodimer pack differently and the photodimer has crystallographically imposed inversion symmetry.

Heterogeneous nucleation of polymorphs on polymer surfaces: polymer-molecule interactions using a Coulomb and van der Waals model.

PubMed

Wahlberg, Nanna; Madsen, Anders Ø; Mikkelsen, Kurt V

2018-06-09

The nucleation processes of acetaminophen on poly(methyl methacrylate) and poly(vinyl acetate) have been investigated and the mechanisms of the processes are studied. This is achieved by a combination of theoretical models and computational investigations within the framework of a modified QM/MM method; a Coulomb-van der Waals model. We have combined quantum mechanical computations and electrostatic models at the atomistic level for investigating the stability of different orientations of acetaminophen on the polymer surfaces. Based on the Coulomb-van der Waals model, we have determined the most stable orientation to be a flat orientation, and the strongest interaction is seen between poly(vinyl acetate) and the molecule in a flat orientation in vacuum.

Covariance Matrix Estimation for the Cryo-EM Heterogeneity Problem*

PubMed Central

Katsevich, E.; Katsevich, A.; Singer, A.

2015-01-01

In cryo-electron microscopy (cryo-EM), a microscope generates a top view of a sample of randomly oriented copies of a molecule. The problem of single particle reconstruction (SPR) from cryo-EM is to use the resulting set of noisy two-dimensional projection images taken at unknown directions to reconstruct the three-dimensional (3D) structure of the molecule. In some situations, the molecule under examination exhibits structural variability, which poses a fundamental challenge in SPR. The heterogeneity problem is the task of mapping the space of conformational states of a molecule. It has been previously suggested that the leading eigenvectors of the covariance matrix of the 3D molecules can be used to solve the heterogeneity problem. Estimating the covariance matrix is challenging, since only projections of the molecules are observed, but not the molecules themselves. In this paper, we formulate a general problem of covariance estimation from noisy projections of samples. This problem has intimate connections with matrix completion problems and high-dimensional principal component analysis. We propose an estimator and prove its consistency. When there are finitely many heterogeneity classes, the spectrum of the estimated covariance matrix reveals the number of classes. The estimator can be found as the solution to a certain linear system. In the cryo-EM case, the linear operator to be inverted, which we term the projection covariance transform, is an important object in covariance estimation for tomographic problems involving structural variation. Inverting it involves applying a filter akin to the ramp filter in tomography. We design a basis in which this linear operator is sparse and thus can be tractably inverted despite its large size. We demonstrate via numerical experiments on synthetic datasets the robustness of our algorithm to high levels of noise. PMID:25699132

Nematic-like stable glasses without equilibrium liquid crystal phases

DOE Data Explorer

Gomez, Jaritza [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; Gujral, Ankit [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; Huang, Chengbin [School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA; Bishop, Camille [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; Yu, Lian [School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA; Ediger, Mark [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA

2017-02-01

We report the thermal and structural properties of glasses of posaconazole, a rod-like molecule, prepared using physical vapor deposition (PVD). PVD glasses of posaconazole can show substantial molecular orientation depending upon the choice of substrate temperature, Tsubstrate, during deposition.Ellipsometry and IR measurements indicate that glasses prepared at Tsubstrate very near the glass transition temperature (Tg) are highly ordered. For these posaconazole glasses, the orientation order parameter is similar to that observed in macroscopically aligned nematic liquid crystals, indicating that the molecules are mostly parallel to one another and perpendicular to the interface. To our knowledge, these are the most anisotropic glasses ever prepared by PVD from a molecule that does not form equilibrium liquid crystal phases. These results are consistent with a previously proposed mechanism in which molecular orientation in PVD glasses is inherited from the orientation present at the free surface of the equilibrium liquid. This mechanism suggests that molecular orientation at the surface of the equilibrium liquid of posaconazole is nematic-like. Posaconazole glasses can show very high kinetic stability; the isothermal transformation of a 400 nm glass into the supercooled liquid occurs via a propagating front that originates at the free surface and requires ~105 times the structural relaxation time of the liquid (τα). We also studied the kinetic stability of PVD glasses of itraconazole, which is a structurally similar molecule with equilibrium liquid crystal phases. While itraconazole glasses can be even more anisotropic than posaconazole glasses, they exhibit lower kinetic stability.

One-step formation of straight nanostripes from a mammal lipid-oleamide directly on highly oriented pyrolytic graphite.

PubMed

Zhang, Renjie; Möhwald, Helmuth; Kurth, Dirk G

2009-02-17

Hierarchical nanostructures are obtained directly on highly oriented pyrolytic graphite (HOPG) by spin coating of dilute chloroform solution of 9-Z-octadecenamide (oleamide), a natural lipid with cis-CdC- conformation, existing in the cerebrospinal fluid of mammal animals and being an additive for medical use and food packaging. Straight separated nanostripes with a length of 70-300 nm exist in the topmost layer and compact nanostripes in the bottom layer contacting HOPG. Compact nanostripes have a periodicity spacing of 3.8 nm, indicating H-bonding between two rows of oleamide molecules. The orientation of the hierarchical nanostructures differs by n60 degrees+/-8 degrees (n=1 or 2), reflecting the epitaxial ordering along theHOPGsubstrate. The nanostripes are stable against annealing.Amolecular packing scheme for the nanostructures is proposed, where the -C=C bond angle in oleamide is 120 degrees and the plane of the carbon skeleton lies parallel to the HOPG substrate. Nanostripes in the topmost layer are formed from separated rows of oleamide molecules, due to the short-range surface potential of the substrate. The scheme involves direct influence ofHOPGon the orientation of oleamide molecules to form nanostripes without any purposely added saturated alkanes and H-bonds between amide groups in adjacent two rows of oleamide molecules.

Insights into the effects of solvent properties in graphene based electric double-layer capacitors with organic electrolytes

NASA Astrophysics Data System (ADS)

Zhang, Shuo; Bo, Zheng; Yang, Huachao; Yang, Jinyuan; Duan, Liangping; Yan, Jianhua; Cen, Kefa

2016-12-01

Organic electrolytes are widely used in electric double-layer capacitors (EDLCs). In this work, the microstructure of planar graphene-based EDLCs with different organic solvents are investigated with molecular dynamics simulations. Results show that an increase of solvent polarity could weaken the accumulation of counter-ions nearby the electrode surface, due to the screen of electrode charges and relatively lower ionic desolvation. It thus suggests that solvents with low polarity could be preferable to yield high EDL capacitance. Meanwhile, the significant effects of the size and structure of solvent molecules are reflected by non-electrostatic molecule-electrode interactions, further influencing the adsorption of solvent molecules on electrode surface. Compared with dimethyl carbonate, γ-butyrolactone, and propylene carbonate, acetonitrile with relatively small-size and linear structure owns weak non-electrostatic interactions, which favors the easy re-orientation of solvent molecules. Moreover, the shift of solvent orientation in surface layer, from parallel orientation to perpendicular orientation relative to the electrode surface, deciphers the solvent twin-peak behavior near negative electrode. The as-obtained insights into the roles of solvent properties on the interplays among particles and electrodes elucidate the solvent influences on the microstructure and capacitive behavior of EDLCs using organic electrolytes.

The correlations of the electronic structure and film growth of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on SiO2.

PubMed

Lyu, Lu; Niu, Dongmei; Xie, Haipeng; Zhao, Yuan; Cao, Ningtong; Zhang, Hong; Zhang, Yuhe; Liu, Peng; Gao, Yongli

2017-01-04

Combining ultraviolet photoemission spectroscopy (UPS), X-ray photoemission spectroscopy (XPS), atomic force microscopy (AFM) and small angle X-ray diffraction (SAXD) measurements, we perform a systematic investigation on the correlations of the electronic structure, film growth and molecular orientation of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on silicon oxide (SiO 2 ). AFM analysis reveals a phase transition of disorderedly oriented molecules in clusters in thinner films to highly ordered standing-up molecules in islands in thicker films. SAXD peaks consistently support the standing-up configuration in islands. The increasing ordering of the molecular orientation with film thickness contributes to the changing of the shape and lowering of the leading edge of the highest occupied molecular orbital (HOMO). The end methyl of the highly ordered standing molecules forms an outward pointing dipole layer which makes the work function (WF) decrease with increasing thickness. The downward shift of the HOMO and a decrease of WF result in unconventional downward band bending and decreased ionization potential (IP). The correlations of the orientation ordering of molecules, film growth and interface electronic structures provide a useful design strategy to improve the performance of C8-BTBT thin film based field effect transistors.

Polarizable continuum model associated with the self-consistent-reaction field for molecular adsorbates at the interface.

PubMed

Wang, Jing-Bo; Ma, Jian-Yi; Li, Xiang-Yuan

2010-01-07

In this work, a new procedure has been developed in order to realize the self-consistent-reaction field computation for interfacial molecules. Based on the extension of the dielectric polarizable continuum model, the quantum-continuum calculations for interfacial molecules have been carried out. This work presents an investigation into how the molecular structure influences the adsorbate-solvent interaction and consequently alters the orientation angle at the air/water interface. Taking both electrostatic and non-electrostatic energies into account, we investigate the orientation behavior of three interfacial molecules, 2,6-dimethyl-4-hydroxy-benzonitrile, 3,5-dimethyl-4-hydroxy-benzonitrile and p-cyanophenol, at the air/water interface. The results show that the hydrophilic hydroxyl groups in 2,6-dimethyl-4-hydroxy-benzonitrile and in p-cyanophenol point from the air to the water side, but the hydroxyl group in 3,5-dimethyl-4-hydroxy-benzonitrile takes the opposite direction. Our detailed analysis reveals that the opposite orientation of 3,5-dimethyl-4-hydroxy-benzonitrile results mainly from the cavitation energy. The different orientations of the hydrophilic hydroxyl group indicate the competition of electrostatic and cavitation energies. The theoretical prediction gives a satisfied explanation of the most recent sum frequency generation measurement for these molecules at the interface.

Testing a new analytical approach for determination of vibrational transition moment directions in low symmetry planar molecules: 1-D- and 2-D-naphthalene.

PubMed

Rogojerov, Marin; Keresztury, Gábor; Kamenova-Nacheva, Mariana; Sundius, Tom

2012-12-01

A new analytical approach for improving the precision in determination of vibrational transition moment directions of low symmetry molecules (lacking orthogonal axes) is discussed in this paper. The target molecules are partially uniaxially oriented in nematic liquid crystalline solvent and are studied by IR absorption spectroscopy using polarized light. The fundamental problem addressed is that IR linear dichroism measurements of low symmetry molecules alone cannot provide sufficient information on molecular orientation and transition moment directions. It is shown that computational prediction of these quantities can supply relevant complementary data, helping to reveal the hidden information content and achieve a more meaningful and more precise interpretation of the measured dichroic ratios. The combined experimental and theoretical/computational method proposed by us recently for determination of the average orientation of molecules with C(s) symmetry has now been replaced by a more precise analytical approach. The new method introduced and discussed in full detail here uses a mathematically evaluated angle between two vibrational transition moment vectors as a reference. The discussion also deals with error analysis and estimation of uncertainties of the orientational parameters. The proposed procedure has been tested in an analysis of the infrared linear dichroism (IR-LD) spectra of 1-D- and 2-D-naphthalene complemented with DFT calculations using the scaled quantum mechanical force field (SQM FF) method. Copyright © 2012 Elsevier B.V. All rights reserved.

Maintained expression of the planar cell polarity molecule Vangl2 and reformation of hair cell orientation in the regenerating inner ear.

PubMed

Warchol, Mark E; Montcouquiol, Mireille

2010-09-01

The avian inner ear possesses a remarkable ability to regenerate sensory hair cells after ototoxic injury. Regenerated hair cells possess phenotypes and innervation that are similar to those found in the undamaged ear, but little is known about the signaling pathways that guide hair cell differentiation during the regenerative process. The aim of the present study was to examine the factors that specify the orientation of hair cell stereocilia bundles during regeneration. Using organ cultures of the chick utricle, we show that hair cells are properly oriented after having regenerated entirely in vitro and that orientation is not affected by surgical removal of the striolar reversal zone. These results suggest that the orientation of regenerating stereocilia is not guided by the release of a diffusible morphogen from the striolar reversal zone but is specified locally within the regenerating sensory organ. In order to determine the nature of the reorientation cues, we examined the expression patterns of the core planar cell polarity molecule Vangl2 in the normal and regenerating utricle. We found that Vangl2 is asymmetrically expressed on cells within the sensory epithelium and that this expression pattern is maintained after ototoxic injury and throughout regeneration. Notably, treatment with a small molecule inhibitor of c-Jun-N-terminal kinase disrupted the orientation of regenerated hair cells. Both of these results are consistent with the hypothesis that noncanonical Wnt signaling guides hair cell orientation during regeneration.

Water Dynamics in Nafion Fuel Cell Membranes: the Effects of Confinement and Structural Changes on the Hydrogen Bond Network

PubMed Central

Moilanen, David E.; Piletic, Ivan R.; Fayer, Michael D.

2008-01-01

The complex environments experienced by water molecules in the hydrophilic channels of Nafion membranes are studied by ultrafast infrared pump-probe spectroscopy. A wavelength dependent study of the vibrational lifetime of the O-D stretch of dilute HOD in H2O confined in Nafion membranes provides evidence of two distinct ensembles of water molecules. While only two ensembles are present at each level of membrane hydration studied, the characteristics of the two ensembles change as the water content of the membrane changes. Time dependent anisotropy measurements show that the orientational motions of water molecules in Nafion membranes are significantly slower than in bulk water and that lower hydration levels result in slower orientational relaxation. Initial wavelength dependent results for the anisotropy show no clear variation in the time scale for orientational motion across a broad range of frequencies. The anisotropy decay is analyzed using a model based on restricted orientational diffusion within a hydrogen bond configuration followed by total reorientation through jump diffusion. PMID:18728757

Structural investigation of porcine stomach mucin by X-ray fiber diffraction and homology modeling

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

Veluraja, K., E-mail: veluraja@msuniv.ac.in; Vennila, K.N.; Umamakeshvari, K.

Research highlights: {yields} Techniques to get oriented mucin fibre. {yields} X-ray fibre diffraction pattern for mucin. {yields} Molecular modeling of mucin based on X-ray fibre diffraction pattern. -- Abstract: The basic understanding of the three dimensional structure of mucin is essential to understand its physiological function. Technology has been developed to achieve orientated porcine stomach mucin molecules. X-ray fiber diffraction of partially orientated porcine stomach mucin molecules show d-spacing signals at 2.99, 4.06, 4.22, 4.7, 5.37 and 6.5 A. The high intense d-spacing signal at 4.22 A is attributed to the antiparallel {beta}-sheet structure identified in the fraction of themore » homology modeled mucin molecule (amino acid residues 800-980) using Nidogen-Laminin complex structure as a template. The X-ray fiber diffraction signal at 6.5 A reveals partial organization of oligosaccharides in porcine stomach mucin. This partial structure of mucin will be helpful in establishing a three dimensional structure for the whole mucin molecule.« less

Nuclear magnetic relaxation induced by exchange-mediated orientational randomization: longitudinal relaxation dispersion for spin I = 1.

PubMed

Nilsson, Tomas; Halle, Bertil

2012-08-07

The frequency dependence of the longitudinal relaxation rate, known as the magnetic relaxation dispersion (MRD), can provide a frequency-resolved characterization of molecular motions in complex biological and colloidal systems on time scales ranging from 1 ns to 100 μs. The conformational dynamics of immobilized proteins and other biopolymers can thus be probed in vitro or in vivo by exploiting internal water molecules or labile hydrogens that exchange with a dominant bulk water pool. Numerous water (1)H and (2)H MRD studies of such systems have been reported, but the widely different theoretical models currently used to analyze the MRD data have resulted in divergent views of the underlying molecular motions. We have argued that the essential mechanism responsible for the main dispersion is the exchange-mediated orientational randomization (EMOR) of anisotropic nuclear (electric quadrupole or magnetic dipole) couplings when internal water molecules or labile hydrogens escape from orientationally confining macromolecular sites. In the EMOR model, the exchange process is thus not just a means of mixing spin populations but it is also the direct cause of spin relaxation. Although the EMOR theory has been used in several studies to analyze water (2)H MRD data from immobilized biopolymers, the fully developed theory has not been described. Here, we present a comprehensive account of a generalized version of the EMOR theory for spin I = 1 nuclides like (2)H. As compared to a previously described version of the EMOR theory, the present version incorporates three generalizations that are all essential in applications to experimental data: (i) a biaxial (residual) electric field gradient tensor, (ii) direct and indirect effects of internal motions, and (iii) multiple sites with different exchange rates. In addition, we describe and assess different approximations to the exact EMOR theory that are useful in various regimes. In particular, we consider the experimentally important dilute regime, for which approximate analytical results are derived. As shown by the analytical expressions, and confirmed by exact numerical calculations, the dispersion is governed by the pure nuclear quadrupole resonance frequencies in the ultraslow-motion regime, where the relaxation rate also exhibits a much stronger dependence on the electric field gradient asymmetry than in the motional-narrowing regime.

On the connection between the Koppel-Young and the Nelkin Models for thermal neutron scattering in water molecules

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

Markovic, M.I.

1982-10-01

A critical analysis of the Koppel-Young model is presented and compared with Nelkin's model and their equivalence is asserted. It is shown that the only distinction between the two models is in the orientational averaging of the rotational-vibrational intermedial scattering function. Based on total cross sections, the Krieger-Nelkin orientation averaging has been confirmed to give excellent agreement with the Koppel-Young orientation averaging. However, significant quasi-periodical differences are observed when calculating differential cross sections. As a result of these insights, a new unified model is proposed for microdynamics of water molecules.

Investigation of ferroelectric liquid crystal orientation in the silica microcapillaries

NASA Astrophysics Data System (ADS)

Budaszewski, D.; Domański, A. W.; Woliński, T. R.

2013-05-01

In the paper we present our recent results concerning the orientation of ferroelectric liquid crystal molecules inside silica micro capillaries. We have infiltrated the silica micro capillaries with experimental ferroelectric liquid crystal material W-260K synthesized in the Military University of Technology. The infiltrated micro capillaries were observed under the polarization microscope while both a polarizer and an analyzer were crossed. The studies on the orientation of ferroelectric liquid crystal molecules may contribute to further studies on behavior of this group of liquid crystal materials inside photonic crystal fiber. The obtained results may lead to design of a new type of fast optical fiber sensors.

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

NASA Astrophysics Data System (ADS)

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.”

Discrimination among individual Watson–Crick base pairs at the termini of single DNA hairpin molecules

PubMed Central

Vercoutere, Wenonah A.; Winters-Hilt, Stephen; DeGuzman, Veronica S.; Deamer, David; Ridino, Sam E.; Rodgers, Joseph T.; Olsen, Hugh E.; Marziali, Andre; Akeson, Mark

2003-01-01

Nanoscale α-hemolysin pores can be used to analyze individual DNA or RNA molecules. Serial examination of hundreds to thousands of molecules per minute is possible using ionic current impedance as the measured property. In a recent report, we showed that a nanopore device coupled with machine learning algorithms could automatically discriminate among the four combinations of Watson–Crick base pairs and their orientations at the ends of individual DNA hairpin molecules. Here we use kinetic analysis to demonstrate that ionic current signatures caused by these hairpin molecules depend on the number of hydrogen bonds within the terminal base pair, stacking between the terminal base pair and its nearest neighbor, and 5′ versus 3′ orientation of the terminal bases independent of their nearest neighbors. This report constitutes evidence that single Watson–Crick base pairs can be identified within individual unmodified DNA hairpin molecules based on their dynamic behavior in a nanoscale pore. PMID:12582251

Extensive first-principles molecular dynamics study on Li encapsulation into C60 and its experimental confirmation.

PubMed

Ohno, K; Manjanath, A; Kawazoe, Y; Hatakeyama, R; Misaizu, F; Kwon, E; Fukumura, H; Ogasawara, H; Yamada, Y; Zhang, C; Sumi, N; Kamigaki, T; Kawachi, K; Yokoo, K; Ono, S; Kasama, Y

2018-01-25

The aim of increasing the production ratio of endohedral C 60 by impinging foreign atoms against C 60 is a crucial matter of the science and technology employed towards industrialization of these functional building block materials. Among these endohedral fullerenes, Li + @C 60 exhibits a wide variety of physical and chemical phenomena and has the potential to be applicable in areas spanning the medical field to photovoltaics. However, currently, Li + @C 60 can be experimentally produced with only ∼1% ratio using the plasma shower method with a 30 eV kinetic energy provided to the impinging Li + ion. From extensive first-principles molecular dynamics simulations, it is found that the maximum production ratio of Li + @C 60 per hit is increased to about 5.1% (5.3%) when a Li + ion impinges vertically on a six-membered ring of C 60 with 30 eV (40 eV) kinetic energy, although many C 60 molecules are damaged during this collision. On the contrary, when it impinges vertically on a six-membered ring with 10 eV kinetic energy, the production ratio remains at 1.3%, but the C 60 molecules are not damaged at all. On the other hand, when the C 60 is randomly oriented, the production ratio reduces to about 3.7 ± 0.5%, 3.3 ± 0.5%, and 0.2 ± 0.03% for 30 eV, 40 eV, and 10 eV kinetic energy, respectively. Based on these observations we demonstrate the possibility of increasing the production ratio by fixing six-membered rings atop C 60 using the Cu(111) substrate or UV light irradiation. In order to assess the ideal experimental production ratio, the 7 Li solid NMR spectroscopy measurement is also performed for the multilayer randomly oriented C 60 sample irradiated by Li + using the plasma shower method combined with inductively coupled plasma atomic emission spectroscopy (ICP-AES). Time-of-flight mass spectroscopy measurements are also performed to cross check whether Li + @C 60 molecules are produced in the sample. The resulting experimental estimate, 4% for 30 eV incident kinetic energy, fully agrees with our simulation results mentioned above, suggesting the consistency and accuracy of our simulations and experiments.

Geometric Modeling of Inclusions as Ellipsoids

NASA Technical Reports Server (NTRS)

Bonacuse, Peter J.

2008-01-01

Nonmetallic inclusions in gas turbine disk alloys can have a significant detrimental impact on fatigue life. Because large inclusions that lead to anomalously low lives occur infrequently, probabilistic approaches can be utilized to avoid the excessively conservative assumption of lifing to a large inclusion in a high stress location. A prerequisite to modeling the impact of inclusions on the fatigue life distribution is a characterization of the inclusion occurrence rate and size distribution. To help facilitate this process, a geometric simulation of the inclusions was devised. To make the simulation problem tractable, the irregularly sized and shaped inclusions were modeled as arbitrarily oriented, three independent dimensioned, ellipsoids. Random orientation of the ellipsoid is accomplished through a series of three orthogonal rotations of axes. In this report, a set of mathematical models for the following parameters are described: the intercepted area of a randomly sectioned ellipsoid, the dimensions and orientation of the intercepted ellipse, the area of a randomly oriented sectioned ellipse, the depth and width of a randomly oriented sectioned ellipse, and the projected area of a randomly oriented ellipsoid. These parameters are necessary to determine an inclusion s potential to develop a propagating fatigue crack. Without these mathematical models, computationally expensive search algorithms would be required to compute these parameters.

Current-induced switching of magnetic molecules on topological insulator surfaces

NASA Astrophysics Data System (ADS)

Locane, Elina; Brouwer, Piet W.

2017-03-01

Electrical currents at the surface or edge of a topological insulator are intrinsically spin polarized. We show that such surface or edge currents can be used to switch the orientation of a molecular magnet weakly coupled to the surface or edge of a topological insulator. For the edge of a two-dimensional topological insulator as well as for the surface of a three-dimensional topological insulator the application of a well-chosen surface or edge current can lead to a complete polarization of the molecule if the molecule's magnetic anisotropy axis is appropriately aligned with the current direction. For a generic orientation of the molecule a nonzero but incomplete polarization is obtained. We calculate the probability distribution of the magnetic states and the switching rates as a function of the applied current.

Rolling Circle Amplification For Spatially Directed Synthesis Of A Solid Phase Anchored Single-Stranded DNA Molecule

NASA Astrophysics Data System (ADS)

Reiß, Edda; Hölzel, Ralph; von Nickisch-Rosenegk, Markus; Bier, Frank F.

2006-09-01

In this article the usefulness of the enzyme phi29 DNA polymerase and the principle of rolling circle amplification (RCA) for creating single-stranded DNA (ssDNA) nanostructures is described. Currently we are working on the spatial orientation of a growing ssDNA molecule during its RCA-based synthesis by the application of a hydrodynamic force. Starting at an immobilized primer at single molecule level, the aim is to construct a nanostructure of known location and orientation, providing multiple repeating binding sites that can be addressed via complementary base-pairing. Proof-of-principle experiments demonstrate the potential of the enzymatic reaction. ssDNA molecules of more than 20 μm length were created at an immobilized primer and detected by means of fluorescence microscopy.

Circular-polarization-sensitive metamaterial based on triple-quantum-dot molecules.

PubMed

Kotetes, Panagiotis; Jin, Pei-Qing; Marthaler, Michael; Schön, Gerd

2014-12-05

We propose a new type of chiral metamaterial based on an ensemble of artificial molecules formed by three identical quantum dots in a triangular arrangement. A static magnetic field oriented perpendicular to the plane breaks mirror symmetry, rendering the molecules sensitive to the circular polarization of light. By varying the orientation and magnitude of the magnetic field one can control the polarization and frequency of the emission spectrum. We identify a threshold frequency Ω, above which we find strong birefringence. In addition, Kerr rotation and circular-polarized lasing action can be implemented. We investigate the single-molecule lasing properties for different energy-level arrangements and demonstrate the possibility of circular-polarization conversion. Finally, we analyze the effect of weak stray electric fields or deviations from the equilateral triangular geometry.

Structural Studies of Three-Arm Star Block Copolymers Exposed to Extreme Stretch Suggests a Persistent Polymer Tube

NASA Astrophysics Data System (ADS)

Mortensen, Kell; Borger, Anine L.; Kirkensgaard, Jacob J. K.; Garvey, Christopher J.; Almdal, Kristoffer; Dorokhin, Andriy; Huang, Qian; Hassager, Ole

2018-05-01

We present structural small-angle neutron scattering studies of a three-armed polystyrene star polymer with short deuterated segments at the end of each arm. We show that the form factor of the three-armed star molecules in the relaxed state agrees with that of the random phase approximation of Gaussian chains. Upon exposure to large extensional flow conditions, the star polymers change conformation resulting in a highly stretched structure that mimics a fully extended three-armed tube model. All three arms are parallel to the flow, one arm being either in positive or negative stretching direction, while the two other arms are oriented parallel, right next to each other in the direction opposite to the first arm.

Tunable molecular orientation and elevated thermal stability of vapor-deposited organic semiconductors

DOE PAGES

Dalal, Shakeel S.; Walters, Diane M.; Lyubimov, Ivan; ...

2015-03-23

Physical vapor deposition is commonly used to prepare organic glasses that serve as the active layers in light-emitting diodes, photovoltaics, and other devices. Recent work has shown that orienting the molecules in such organic semiconductors can significantly enhance device performance. In this paper, we apply a high-throughput characterization scheme to investigate the effect of the substrate temperature (T substrate) on glasses of three organic molecules used as semiconductors. The optical and material properties are evaluated with spectroscopic ellipsometry. We find that molecular orientation in these glasses is continuously tunable and controlled by T substrate/T g, where T g is themore » glass transition temperature. All three molecules can produce highly anisotropic glasses; the dependence of molecular orientation upon substrate temperature is remarkably similar and nearly independent of molecular length. All three compounds form “stable glasses” with high density and thermal stability, and have properties similar to stable glasses prepared from model glass formers. Simulations reproduce the experimental trends and explain molecular orientation in the deposited glasses in terms of the surface properties of the equilibrium liquid. Finally, by showing that organic semiconductors form stable glasses, these results provide an avenue for systematic performance optimization of active layers in organic electronics.« less

Linear dichroism of DNA: Characterization of the orientation distribution function caused by hydrodynamic shear

DOE PAGES

Sutherland, John C.

2017-04-15

Linear dichroism provides information on the orientation of chromophores part of, or bound to, an orientable molecule such as DNA. For molecular alignment induced by hydrodynamic shear, the principal axes orthogonal to the direction of alignment are not equivalent. Thus, the magnitude of the flow-induced change in absorption for light polarized parallel to the direction of flow can be more than a factor of two greater than the corresponding change for light polarized perpendicular to both that direction and the shear axis. The ratio of the two flow-induced changes in absorption, the dichroic increment ratio, is characterized using the orthogonalmore » orientation model, which assumes that each absorbing unit is aligned parallel to one of the principal axes of the apparatus. The absorption of the alienable molecules is characterized by components parallel and perpendicular to the orientable axis of the molecule. The dichroic increment ratio indicates that for the alignment of DNA in rectangular flow cells, average alignment is not uniaxial, but for higher shear, as produced in a Couette cell, it can be. The results from the simple model are identical to tensor models for typical experimental configuration. Approaches for measuring the dichroic increment ratio with modern dichrometers are further discussed.« less

Linear dichroism of DNA: Characterization of the orientation distribution function caused by hydrodynamic shear

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

Sutherland, John C.

Linear dichroism provides information on the orientation of chromophores part of, or bound to, an orientable molecule such as DNA. For molecular alignment induced by hydrodynamic shear, the principal axes orthogonal to the direction of alignment are not equivalent. Thus, the magnitude of the flow-induced change in absorption for light polarized parallel to the direction of flow can be more than a factor of two greater than the corresponding change for light polarized perpendicular to both that direction and the shear axis. The ratio of the two flow-induced changes in absorption, the dichroic increment ratio, is characterized using the orthogonalmore » orientation model, which assumes that each absorbing unit is aligned parallel to one of the principal axes of the apparatus. The absorption of the alienable molecules is characterized by components parallel and perpendicular to the orientable axis of the molecule. The dichroic increment ratio indicates that for the alignment of DNA in rectangular flow cells, average alignment is not uniaxial, but for higher shear, as produced in a Couette cell, it can be. The results from the simple model are identical to tensor models for typical experimental configuration. Approaches for measuring the dichroic increment ratio with modern dichrometers are further discussed.« less

Linear dichroism of DNA: Characterization of the orientation distribution function caused by hydrodynamic shear.

PubMed

Sutherland, John C

2017-04-15

Linear dichroism provides information on the orientation of chromophores part of, or bound to, an orientable molecule such as DNA. For molecular alignment induced by hydrodynamic shear, the principal axes orthogonal to the direction of alignment are not equivalent. Thus, the magnitude of the flow-induced change in absorption for light polarized parallel to the direction of flow can be more than a factor of two greater than the corresponding change for light polarized perpendicular to both that direction and the shear axis. The ratio of the two flow-induced changes in absorption, the dichroic increment ratio, is characterized using the orthogonal orientation model, which assumes that each absorbing unit is aligned parallel to one of the principal axes of the apparatus. The absorption of the alienable molecules is characterized by components parallel and perpendicular to the orientable axis of the molecule. The dichroic increment ratio indicates that for the alignment of DNA in rectangular flow cells, average alignment is not uniaxial, but for higher shear, as produced in a Couette cell, it can be. The results from the simple model are identical to tensor models for typical experimental configurations. Approaches for measuring the dichroic increment ratio with modern dichrometers are discussed. Copyright © 2017. Published by Elsevier Inc.

Attachment of second harmonic-active moiety to molecules for detection of molecules at interfaces

DOEpatents

Salafsky, Joshua S.; Eisenthal, Kenneth B.

2005-10-11

This invention provides methods of detecting molecules at an interface, which comprise labeling the molecules with a second harmonic-active moiety and detecting the labeled molecules at the interface using a surface selective technique. The invention also provides methods for detecting a molecule in a medium and for determining the orientation of a molecular species within a planar surface using a second harmonic-active moiety and a surface selective technique.

An alternative NMR method to determine nuclear shielding anisotropies for molecules in liquid-crystalline solutions with (13)C shielding anisotropy of methyl iodide as an example.

PubMed

Tallavaara, Pekka; Jokisaari, Jukka

2008-03-28

An alternative NMR method for determining nuclear shielding anisotropies in molecules is proposed. The method is quite simple, linear and particularly applicable for heteronuclear spin systems. In the technique, molecules of interest are dissolved in a thermotropic liquid crystal (LC) which is confined in a mesoporous material, such as controlled pore glass (CPG) used in this study. CPG materials consist of roughly spherical particles with a randomly oriented and connected pore network inside. LC Merck Phase 4 was confined in the pores of average diameter from 81 to 375 A and LC Merck ZLI 1115 in the pores of average diameter 81 A. In order to demonstrate the functionality of the method, the (13)C shielding anisotropy of (13)C-enriched methyl iodide, (13)CH(3)I, was determined as a function of temperature using one dimensional (13)C NMR spectroscopy. Methane gas, (13)CH(4), was used as an internal chemical shift reference. It appeared that methyl iodide molecules experience on average an isotropic environment in LCs inside the smallest pores within the whole temperature range studied, ranging from bulk solid to isotropic phase. In contrast, in the spaces in between the particles, whose diameter is approximately 150 microm, LCs behave as in the bulk. Consequently, isotropic values of the shielding tensor can be determined from spectra arising from molecules inside the pores at exactly the same temperature as the anisotropic ones from molecules outside the pores. Thus, for the first time in the solution state, shielding anisotropies can easily be determined as a function of temperature. The effects of pore size as well as of different LC media on the shielding anisotropy are examined and discussed.

Grafting odorant binding proteins on diamond bio-MEMS.

PubMed

Manai, R; Scorsone, E; Rousseau, L; Ghassemi, F; Possas Abreu, M; Lissorgues, G; Tremillon, N; Ginisty, H; Arnault, J-C; Tuccori, E; Bernabei, M; Cali, K; Persaud, K C; Bergonzo, P

2014-10-15

Odorant binding proteins (OBPs) are small soluble proteins found in olfactory systems that are capable of binding several types of odorant molecules. Cantilevers based on polycrystalline diamond surfaces are very promising as chemical transducers. Here two methods were investigated for chemically grafting porcine OBPs on polycrystalline diamond surfaces for biosensor development. The first approach resulted in random orientation of the immobilized proteins over the surface. The second approach based on complexing a histidine-tag located on the protein with nickel allowed control of the proteins' orientation. Evidence confirming protein grafting was obtained using electrochemical impedance spectroscopy, fluorescence imaging and X-ray photoelectron spectroscopy. The chemical sensing performances of these OBP modified transducers were assessed. The second grafting method led to typically 20% more sensitive sensors, as a result of better access of ligands to the proteins active sites and also perhaps a better yield of protein immobilization. This new grafting method appears to be highly promising for further investigation of the ligand binding properties of OBPs in general and for the development of arrays of non-specific biosensors for artificial olfaction applications. Copyright © 2014 Elsevier B.V. All rights reserved.

Mesoscale martensitic transformation in single crystals of topological defects

PubMed Central

Martínez-González, José A.; Ramírez-Hernández, Abelardo; Zhou, Ye; Sadati, Monirosadat; Zhang, Rui; Nealey, Paul F.; de Pablo, Juan J.

2017-01-01

Liquid-crystal blue phases (BPs) are highly ordered at two levels. Molecules exhibit orientational order at nanometer length scales, while chirality leads to ordered arrays of double-twisted cylinders over micrometer scales. Past studies of polycrystalline BPs were challenged by the existence of grain boundaries between randomly oriented crystalline nanodomains. Here, the nucleation of BPs is controlled with precision by relying on chemically nanopatterned surfaces, leading to macroscopic single-crystal BP specimens where the dynamics of mesocrystal formation can be directly observed. Theory and experiments show that transitions between two BPs having a different network structure proceed through local reorganization of the crystalline array, without diffusion of the double-twisted cylinders. In solid crystals, martensitic transformations between crystal structures involve the concerted motion of a few atoms, without diffusion. The transformation between BPs, where crystal features arise in the submicron regime, is found to be martensitic in nature when one considers the collective behavior of the double-twist cylinders. Single-crystal BPs are shown to offer fertile grounds for the study of directed crystal nucleation and the controlled growth of soft matter. PMID:28874557

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

Li, Xiao; Martínez-González, José A.; Hernández-Ortiz, Juan P.

Liquid crystal blue phases (BPs) are highly ordered at two levels. Molecules exhibit orientational order at nanometer length scales, while chirality leads to ordered arrays of doubletwisted cylinders over micrometer scales. Past studies of polycrystalline BPs were challenged by grain boundaries between randomly oriented crystalline nanodomains. Here, the nucleation of BPs is controlled with considerable precision by relying on chemically nano-patterned surfaces, leading to macroscopic single-crystal BP specimens where the dynamics of meso-crystal formation can be directly observed. Theory and experiments show that transitions between two BPs having a different network structure proceed through local re-organization of the crystalline array,more » without diffusion of the double twisted cylinders. In solid crystals, martensitic transformations between crystal structures involve the concerted motion of a few atoms, without diffusion. The transformation between BPs, where crystal features arise in the sub-micron regime, is found to be martensitic in nature, with the diffusion-less feature associated to the collective behavior of the double twist cylinders. Single-crystal BPs are shown to offer fertile grounds for the study of directed crystal-nucleation and the controlled growth of soft matter.« less

Determination of the two methyl group orientations at vapor/acetone interface with polarization null angle method in SFG vibrational spectroscopy

NASA Astrophysics Data System (ADS)

Chen, Hua; Gan, Wei; Wu, Bao-hua; Wu, Dan; Zhang, Zhen; Wang, Hong-fei

2005-06-01

We report a direct measurement of the orientation of the two CH 3 groups of acetone molecule at the vapor/acetone interface. The interfacial acetone molecule is found well-ordered, with one methyl group points away around 14.4° ± 1.9° and another into the bulk liquid around 102.8° ± 1.9° from the interface normal, and thus the C dbnd O group points into the bulk around 135.8° ± 1.9°. These results directly confirmed the highly ordered and even crystal like interfacial structure of the vapor/acetone interface from previous MD simulation. The general formulation and accurate determination of the orientational parameter D can be used to treat interfaces with complex molecular orientations.

Conserved linear dynamics of single-molecule Brownian motion.

PubMed

Serag, Maged F; Habuchi, Satoshi

2017-06-06

Macromolecular diffusion in homogeneous fluid at length scales greater than the size of the molecule is regarded as a random process. The mean-squared displacement (MSD) of molecules in this regime increases linearly with time. Here we show that non-random motion of DNA molecules in this regime that is undetectable by the MSD analysis can be quantified by characterizing the molecular motion relative to a latticed frame of reference. Our lattice occupancy analysis reveals unexpected sub-modes of motion of DNA that deviate from expected random motion in the linear, diffusive regime. We demonstrate that a subtle interplay between these sub-modes causes the overall diffusive motion of DNA to appear to conform to the linear regime. Our results show that apparently random motion of macromolecules could be governed by non-random dynamics that are detectable only by their relative motion. Our analytical approach should advance broad understanding of diffusion processes of fundamental relevance.

Conserved linear dynamics of single-molecule Brownian motion

PubMed Central

Serag, Maged F.; Habuchi, Satoshi

2017-01-01

Macromolecular diffusion in homogeneous fluid at length scales greater than the size of the molecule is regarded as a random process. The mean-squared displacement (MSD) of molecules in this regime increases linearly with time. Here we show that non-random motion of DNA molecules in this regime that is undetectable by the MSD analysis can be quantified by characterizing the molecular motion relative to a latticed frame of reference. Our lattice occupancy analysis reveals unexpected sub-modes of motion of DNA that deviate from expected random motion in the linear, diffusive regime. We demonstrate that a subtle interplay between these sub-modes causes the overall diffusive motion of DNA to appear to conform to the linear regime. Our results show that apparently random motion of macromolecules could be governed by non-random dynamics that are detectable only by their relative motion. Our analytical approach should advance broad understanding of diffusion processes of fundamental relevance. PMID:28585925

Conserved linear dynamics of single-molecule Brownian motion

NASA Astrophysics Data System (ADS)

Serag, Maged F.; Habuchi, Satoshi

2017-06-01

Macromolecular diffusion in homogeneous fluid at length scales greater than the size of the molecule is regarded as a random process. The mean-squared displacement (MSD) of molecules in this regime increases linearly with time. Here we show that non-random motion of DNA molecules in this regime that is undetectable by the MSD analysis can be quantified by characterizing the molecular motion relative to a latticed frame of reference. Our lattice occupancy analysis reveals unexpected sub-modes of motion of DNA that deviate from expected random motion in the linear, diffusive regime. We demonstrate that a subtle interplay between these sub-modes causes the overall diffusive motion of DNA to appear to conform to the linear regime. Our results show that apparently random motion of macromolecules could be governed by non-random dynamics that are detectable only by their relative motion. Our analytical approach should advance broad understanding of diffusion processes of fundamental relevance.

Effect of molecular properties on the performance of polymer light-emitting diodes

NASA Astrophysics Data System (ADS)

Ramos, Marta M. D.; Almeida, A. M.; Correia, Helena M. G.; Ribeiro, R. Mendes; Stoneham, A. M.

2004-11-01

The performance of a single layer polymer light-emitting diode depends on several interdependent factors, although recombination between electrons and holes within the polymer layer is believed to play an important role. Our aim is to carry out computer experiments in which bipolar charge carriers are injected in polymer networks made of poly(p-phenylene vinylene) chains randomly oriented. In these simulations, we follow the charge evolution in time from some initial state to the steady state. The intra-molecular properties of the polymer molecules obtained from self-consistent quantum molecular dynamics calculations are used in the mesoscopic model. The purpose of the present work is to clarify the effects of intra-molecular charge mobility and energy disorder on recombination efficiency. In particular, we find that charge mobility along the polymer chains has a serious influence on recombination within the polymer layer. Our results also show that energy disorder due to differences in ionization potential and electron affinity of neighbouring molecules affects mainly recombinations that occur near the electrodes at polymer chains parallel to them.

Highly mesoporous single-crystalline zeolite beta synthesized using a nonsurfactant cationic polymer as a dual-function template.

PubMed

Zhu, Jie; Zhu, Yihan; Zhu, Liangkui; Rigutto, Marcello; van der Made, Alexander; Yang, Chengguang; Pan, Shuxiang; Wang, Liang; Zhu, Longfeng; Jin, Yinying; Sun, Qi; Wu, Qinming; Meng, Xiangju; Zhang, Daliang; Han, Yu; Li, Jixue; Chu, Yueying; Zheng, Anmin; Qiu, Shilun; Zheng, Xiaoming; Xiao, Feng-Shou

2014-02-12

Mesoporous zeolites are useful solid catalysts for conversion of bulky molecules because they offer fast mass transfer along with size and shape selectivity. We report here the successful synthesis of mesoporous aluminosilicate zeolite Beta from a commercial cationic polymer that acts as a dual-function template to generate zeolitic micropores and mesopores simultaneously. This is the first demonstration of a single nonsurfactant polymer acting as such a template. Using high-resolution electron microscopy and tomography, we discovered that the resulting material (Beta-MS) has abundant and highly interconnected mesopores. More importantly, we demonstrated using a three-dimensional electron diffraction technique that each Beta-MS particle is a single crystal, whereas most previously reported mesoporous zeolites are comprised of nanosized zeolitic grains with random orientations. The use of nonsurfactant templates is essential to gaining single-crystalline mesoporous zeolites. The single-crystalline nature endows Beta-MS with better hydrothermal stability compared with surfactant-derived mesoporous zeolite Beta. Beta-MS also exhibited remarkably higher catalytic activity than did conventional zeolite Beta in acid-catalyzed reactions involving large molecules.

Theory of liquid crystal orientation under action of light wave field and aligning surfaces

NASA Astrophysics Data System (ADS)

Dadivanyan, A. K.; Chausov, D. N.; Belyaev, V. V.; Barabanova, N. N.; Chausova, O. V.; Kuleshova, Yu D.

2018-03-01

Theoretical models developed in the MRSU group under leadership of Professor Artem Dadivanyan in area of the LC orientation and photo-induced effects are presented. Angular distribution functions of the dye and liquid crystal molecules under action of intensive light beam have been derived. The number of molecules in cluster is estimated. A model of dimers formation in the photoalignment dye is suggested that explains influence of the dye molecular structure on both polar and azimuthal anchoring energy.

Aligned Immobilization of Proteins Using AC Electric Fields.

PubMed

Laux, Eva-Maria; Knigge, Xenia; Bier, Frank F; Wenger, Christian; Hölzel, Ralph

2016-03-01

Protein molecules are aligned and immobilized from solution by AC electric fields. In a single-step experiment, the enhanced green fluorescent proteins are immobilized on the surface as well as at the edges of planar nanoelectrodes. Alignment is found to follow the molecules' geometrical shape with their longitudinal axes parallel to the electric field. Simultaneous dielectrophoretic attraction and AC electroosmotic flow are identified as the dominant forces causing protein movement and alignment. Molecular orientation is determined by fluorescence microscopy based on polarized excitation of the proteins' chromophores. The chromophores' orientation with respect to the whole molecule supports X-ray crystal data. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Photoelectron Diffraction from Valence States of Oriented Molecules

NASA Astrophysics Data System (ADS)

Krüger, Peter

2018-06-01

The angular distribution of photoelectrons emitted from valence states of oriented molecules is investigated. The principles underlying the angular pattern formation are explained in terms of photoelectron wave interference, caused by initial state delocalization and final state photoelectron scattering. Computational approaches to photoelectron spectroscopy from molecules are briefly reviewed. Here a combination of molecular orbital calculations for the initial state and multiple scattering theory for the photoelectron final state is used and applied to the 3σ and 4σ orbitals of nitrogen and the highest occupied molecular orbital of pentacene. Appreciable perpendicular emission and circular dichroism in angular distributions is found, two effects that cannot be described by the popular plane wave approximation to the photoelectron final state.

Cholesterol orientation and tilt modulus in DMPC bilayers

PubMed Central

Khelashvili, George; Pabst, Georg; Harries, Daniel

2010-01-01

We performed molecular dynamics (MD) simulations of hydrated bilayers containing mixtures of dimyristoylphosphatidylcholine (DMPC) and Cholesterol at various ratios, to study the effect of cholesterol concentration on its orientation, and to characterize the link between cholesterol tilt and overall phospholipid membrane organization. The simulations show a substantial probability for cholesterol molecules to transiently orient perpendicular to the bilayer normal, and suggest that cholesterol tilt may be an important factor for inducing membrane ordering. In particular, we find that as cholesterol concentration increases (1%–40% cholesterol) the average cholesterol orientation changes in a manner strongly (anti)correlated with the variation in membrane thickness. Furthermore, cholesterol orientation is found to be determined by the aligning force exerted by other cholesterol molecules. To quantify this aligning field, we analyzed cholesterol orientation using, to our knowledge, the first estimates of the cholesterol tilt modulus χ from MD simulations. Our calculations suggest that the aligning field that determines χ is indeed strongly linked to sterol composition. This empirical parameter (χ) should therefore become a useful quantitative measure to describe cholesterol interaction with other lipids in bilayers, particularly in various coarse-grained force fields. PMID:20518573

Field-free orientation of diatomic molecule via the linearly polarized resonant pulses

NASA Astrophysics Data System (ADS)

Li, Su-Yu; Guo, Fu-Ming; Wang, Jun; Yang, Yu-Jun; Jin, Ming-Xing

2015-10-01

We propose a scheme to coherently control the field-free orientation of NO molecule whose rotational temperature is above 0 K. It is found that the maximum molecular orientation is affected by two factors: one is the sum of the population of M = 0 rotational states and the other is their distribution, however, their distribution plays a much more significant role in molecular orientation than the sum of their population. By adopting a series of linearly polarized pulses resonant with the rotational states, the distribution of M = 0 rotational states is well rearranged. Though the number of pulses used is small, a relatively high orientation degree can be obtained. This scheme provides a promising approach to the achievement of a good orientation effect. Project supported by the National Basic Research Program of China (Grant No. 2013CB922200), the National Natural Science Foundation of China (Grant Nos. 11034003, 11474129, 11274141, and 11304116), the Research Fund for the Doctoral Program of Higher Education of China (Grant No. 20130061110021), and the Graduate Innovation Fund of Jilin University (Grant No. 2015091).

Protein denaturants at aqueous-hydrophobic interfaces: self-consistent correlation between induced interfacial fluctuations and denaturant stability at the interface.

PubMed

Cui, Di; Ou, Shu-Ching; Patel, Sandeep

2015-01-08

The notion of direct interaction between denaturing cosolvent and protein residues has been proposed in dialogue relevant to molecular mechanisms of protein denaturation. Here we consider the correlation between free energetic stability and induced fluctuations of an aqueous-hydrophobic interface between a model hydrophobically associating protein, HFBII, and two common protein denaturants, guanidinium cation (Gdm(+)) and urea. We compute potentials of mean force along an order parameter that brings the solute molecule close to the known hydrophobic region of the protein. We assess potentials of mean force for different relative orientations between the protein and denaturant molecule. We find that in both cases of guanidinium cation and urea relative orientations of the denaturant molecule that are parallel to the local protein-water interface exhibit greater stability compared to edge-on or perpendicular orientations. This behavior has been observed for guanidinium/methylguanidinium cations at the liquid-vapor interface of water, and thus the present results further corroborate earlier findings. Further analysis of the induced fluctuations of the aqueous-hydrophobic interface upon approach of the denaturant molecule indicates that the parallel orientation, displaying a greater stability at the interface, also induces larger fluctuations of the interface compared to the perpendicular orientations. The correlation of interfacial stability and induced interface fluctuation is a recurring theme for interface-stable solutes at hydrophobic interfaces. Moreover, observed correlations between interface stability and induced fluctuations recapitulate connections to local hydration structure and patterns around solutes as evidenced by experiment (Cooper et al., J. Phys. Chem. A 2014, 118, 5657.) and high-level ab initio/DFT calculations (Baer et al., Faraday Discuss 2013, 160, 89).

Protein Denaturants at Aqueous–Hydrophobic Interfaces: Self-Consistent Correlation between Induced Interfacial Fluctuations and Denaturant Stability at the Interface

PubMed Central

2015-01-01

The notion of direct interaction between denaturing cosolvent and protein residues has been proposed in dialogue relevant to molecular mechanisms of protein denaturation. Here we consider the correlation between free energetic stability and induced fluctuations of an aqueous–hydrophobic interface between a model hydrophobically associating protein, HFBII, and two common protein denaturants, guanidinium cation (Gdm+) and urea. We compute potentials of mean force along an order parameter that brings the solute molecule close to the known hydrophobic region of the protein. We assess potentials of mean force for different relative orientations between the protein and denaturant molecule. We find that in both cases of guanidinium cation and urea relative orientations of the denaturant molecule that are parallel to the local protein–water interface exhibit greater stability compared to edge-on or perpendicular orientations. This behavior has been observed for guanidinium/methylguanidinium cations at the liquid–vapor interface of water, and thus the present results further corroborate earlier findings. Further analysis of the induced fluctuations of the aqueous–hydrophobic interface upon approach of the denaturant molecule indicates that the parallel orientation, displaying a greater stability at the interface, also induces larger fluctuations of the interface compared to the perpendicular orientations. The correlation of interfacial stability and induced interface fluctuation is a recurring theme for interface-stable solutes at hydrophobic interfaces. Moreover, observed correlations between interface stability and induced fluctuations recapitulate connections to local hydration structure and patterns around solutes as evidenced by experiment (Cooper et al., J. Phys. Chem. A2014, 118, 5657.) and high-level ab initio/DFT calculations (Baer et al., Faraday Discuss2013, 160, 89). PMID:25536388

Simultaneous, accurate measurement of the 3D position and orientation of single molecules

PubMed Central

Backlund, Mikael P.; Lew, Matthew D.; Backer, Adam S.; Sahl, Steffen J.; Grover, Ginni; Agrawal, Anurag; Piestun, Rafael; Moerner, W. E.

2012-01-01

Recently, single molecule-based superresolution fluorescence microscopy has surpassed the diffraction limit to improve resolution to the order of 20 nm or better. These methods typically use image fitting that assumes an isotropic emission pattern from the single emitters as well as control of the emitter concentration. However, anisotropic single-molecule emission patterns arise from the transition dipole when it is rotationally immobile, depending highly on the molecule’s 3D orientation and z position. Failure to account for this fact can lead to significant lateral (x, y) mislocalizations (up to ∼50–200 nm). This systematic error can cause distortions in the reconstructed images, which can translate into degraded resolution. Using parameters uniquely inherent in the double-lobed nature of the Double-Helix Point Spread Function, we account for such mislocalizations and simultaneously measure 3D molecular orientation and 3D position. Mislocalizations during an axial scan of a single molecule manifest themselves as an apparent lateral shift in its position, which causes the standard deviation (SD) of its lateral position to appear larger than the SD expected from photon shot noise. By correcting each localization based on an estimated orientation, we are able to improve SDs in lateral localization from ∼2× worse than photon-limited precision (48 vs. 25 nm) to within 5 nm of photon-limited precision. Furthermore, by averaging many estimations of orientation over different depths, we are able to improve from a lateral SD of 116 (∼4× worse than the photon-limited precision; 28 nm) to 34 nm (within 6 nm of the photon limit). PMID:23129640

Precise Orientation of a Single C60 Molecule on the Tip of a Scanning Probe Microscope

NASA Astrophysics Data System (ADS)

Chiutu, C.; Sweetman, A. M.; Lakin, A. J.; Stannard, A.; Jarvis, S.; Kantorovich, L.; Dunn, J. L.; Moriarty, P.

2012-06-01

We show that the precise orientation of a C60 molecule which terminates the tip of a scanning probe microscope can be determined with atomic precision from submolecular contrast images of the fullerene cage. A comparison of experimental scanning tunneling microscopy data with images simulated using computationally inexpensive Hückel theory provides a robust method of identifying molecular rotation and tilt at the end of the probe microscope tip. Noncontact atomic force microscopy resolves the atoms of the C60 cage closest to the surface for a range of molecular orientations at tip-sample separations where the molecule-substrate interaction potential is weakly attractive. Measurements of the C60C60 pair potential acquired using a fullerene-terminated tip are in excellent agreement with theoretical predictions based on a pairwise summation of the van der Waals interactions between C atoms in each cage, i.e., the Girifalco potential [L. Girifalco, J. Phys. Chem. 95, 5370 (1991)JPCHAX0022-365410.1021/j100167a002].

Neutron Nucleic Acid Crystallography.

PubMed

Chatake, Toshiyuki

2016-01-01

The hydration shells surrounding nucleic acids and hydrogen-bonding networks involving water molecules and nucleic acids are essential interactions for the structural stability and function of nucleic acids. Water molecules in the hydration shells influence various conformations of DNA and RNA by specific hydrogen-bonding networks, which often contribute to the chemical reactivity and molecular recognition of nucleic acids. However, X-ray crystallography could not provide a complete description of structural information with respect to hydrogen bonds. Indeed, X-ray crystallography is a powerful tool for determining the locations of water molecules, i.e., the location of the oxygen atom of H2O; however, it is very difficult to determine the orientation of the water molecules, i.e., the orientation of the two hydrogen atoms of H2O, because X-ray scattering from the hydrogen atom is very small.Neutron crystallography is a specialized tool for determining the positions of hydrogen atoms. Neutrons are not diffracted by electrons, but are diffracted by atomic nuclei; accordingly, neutron scattering lengths of hydrogen and its isotopes are comparable to those of non-hydrogen atoms. Therefore, neutron crystallography can determine both of the locations and orientations of water molecules. This chapter describes the current status of neutron nucleic acid crystallographic research as well as the basic principles of neutron diffraction experiments performed on nucleic acid crystals: materials, crystallization, diffraction experiments, and structure determination.

Continuous diffraction of molecules and disordered molecular crystals

PubMed Central

Yefanov, Oleksandr M.; Ayyer, Kartik; White, Thomas A.; Barty, Anton; Morgan, Andrew; Mariani, Valerio; Oberthuer, Dominik; Pande, Kanupriya

2017-01-01

The intensities of far-field diffraction patterns of orientationally aligned molecules obey Wilson statistics, whether those molecules are in isolation (giving rise to a continuous diffraction pattern) or arranged in a crystal (giving rise to Bragg peaks). Ensembles of molecules in several orientations, but uncorrelated in position, give rise to the incoherent sum of the diffraction from those objects, modifying the statistics in a similar way as crystal twinning modifies the distribution of Bragg intensities. This situation arises in the continuous diffraction of laser-aligned molecules or translationally disordered molecular crystals. This paper develops the analysis of the intensity statistics of such continuous diffraction to obtain parameters such as scaling, beam coherence and the number of contributing independent object orientations. When measured, continuous molecular diffraction is generally weak and accompanied by a background that far exceeds the strength of the signal. Instead of just relying upon the smallest measured intensities or their mean value to guide the subtraction of the background, it is shown how all measured values can be utilized to estimate the background, noise and signal, by employing a modified ‘noisy Wilson’ distribution that explicitly includes the background. Parameters relating to the background and signal quantities can be estimated from the moments of the measured intensities. The analysis method is demonstrated on previously published continuous diffraction data measured from crystals of photosystem II [Ayyer et al. (2016 ▸), Nature, 530, 202–206]. PMID:28808434

Snow Crystal Orientation Effects on the Scattering of Passive Microwave Radiation

NASA Technical Reports Server (NTRS)

Foster, J. L.; Barton, J. S.; Chang, A. T. C.; Hall, D. K.

1999-01-01

For this study, consideration is given to the role crystal orientation plays in scattering and absorbing microwave radiation. A discrete dipole scattering model is used to measure the passive microwave radiation, at two polarizations (horizontal and vertical), scattered by snow crystals oriented in random and non random positions, having various sizes (ranging between 1 micrometers to 10,000 micrometers in radius), and shapes (including spheroids, cylinders, hexagons). The model results demonstrate that for the crystal sizes typically found in a snowpack, crystal orientation is insignificant compared to crystal size in terms of scattering microwave energy in the 8,100 gm (37 GHz) region of the spectrum. Therefore, the assumption used in radiative transfer approaches, where snow crystals are modeled as randomly oriented spheres, is adequate to account for the transfer of microwave energy emanating from the ground and passing through a snowpack.

Time scale of random sequential adsorption.

PubMed

Erban, Radek; Chapman, S Jonathan

2007-04-01

A simple multiscale approach to the diffusion-driven adsorption from a solution to a solid surface is presented. The model combines two important features of the adsorption process: (i) The kinetics of the chemical reaction between adsorbing molecules and the surface and (ii) geometrical constraints on the surface made by molecules which are already adsorbed. The process (i) is modeled in a diffusion-driven context, i.e., the conditional probability of adsorbing a molecule provided that the molecule hits the surface is related to the macroscopic surface reaction rate. The geometrical constraint (ii) is modeled using random sequential adsorption (RSA), which is the sequential addition of molecules at random positions on a surface; one attempt to attach a molecule is made per one RSA simulation time step. By coupling RSA with the diffusion of molecules in the solution above the surface the RSA simulation time step is related to the real physical time. The method is illustrated on a model of chemisorption of reactive polymers to a virus surface.

Dermal Aged and Fetal Fibroblasts Realign in Response to Mechanical Strain

NASA Technical Reports Server (NTRS)

Sawyer, Christine; Grymes, Rose; Alvarez, Teresa (Technical Monitor)

1994-01-01

Integrins specifically recognize and bind extracellular matrix components, providing physical anchor points and functional setpoints. Focal adhesion complexes, containing integrin and cytoskeletal proteins, are potential mechanoreceptors, poised to distribute applied forces through the cytoskeleton. Pursuing the hypothesis that cells both perceive and respond to external force, we applied a stretch/relaxation regimen to normal human fetal and aged dermal fibroblast monolayers cultured on flexible membranes. The frequency and magnitude of the applied force is precisely controlled by the Flexercell Unit(Trademark). A protocol of stretch (20% elongation of the monolayer) at a frequency of 6 cycles/min caused a progressive change from a randomly distributed pattern of cells to a symmetric, radial distribution with cells aligned parallel to the applied force. We have coined the term 'orienteering' as the process of active alignment of cells in response to applied force. Cytochalasin D was added in graded doses to investigate the role of the actin cytoskeleton in force perception and transmission. A clear dose response was found; at high concentrations orienteering was abolished; and the drug's impact was reversible. The two cell strains used were similar in their alignment behavior and in their responses to cytochalasin D. Orienteering was influenced by cell density, and the cell strains studied differed in this respect. Fetal cells, unlike their aged counterparts, failed to orient at high cell density. In both cell strains, mid-density cultures aligned rapidly and sparse cultures lagged. These results indicate that both cell-cell adhesion and cytoskeleton integrity are critical in mediating the orienteering response. Differences between these two cell strains may relate to their expression of extracellular matrix molecules (fibronectin, collagen type 1) integrins and their relative binding affinities.

Equatorial and Apical Solvent Shells of the UO₂²⁺ Ion.

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

Nichols, Pat; Bylaska, Eric J.; Schenter, Gregory K.

2008-03-08

First principles molecular dynamics simulations of the hydration shells surrounding UO₂²⁺ ions are reported for temperatures near 300 K. Most of the simulations were done with 64 solvating water molecules (22 ps). Simulations with 122 water molecules (9 ps) were also carried out. The hydration structure predicted from the simulations was found to agree very well known results from X-ray data. The average U=O bond length was found to be 1.77Å . The first hydration shell contained five trigonally coordinated water molecules that were equatorially oriented about the O-U-O axis with the hydrogen atoms oriented away from the uranium atom.more » The five waters in the first shell were located at an average distance of 2.44Å (2.46Å - 122 water simulation). The second hydration shell was composed of distinct equatorial and apical regions resulting in a peak in the U-O radial distribution function at 4.59Å. The equatorial second shell contained 10 water molecules hydrogen-bonded to the five first shell molecules. Above and below the UO₂²⁺ ion, the water molecules were found to be significantly less structured. In these apical regions, water molecules were found to sporadically hydrogen bond to the oxygen atoms of the UO₂²⁺; oriented in such way as to have their protons pointed towards the cation. While the number of apical waters varied greatly, an average of 5-6 waters was found in this region. Many water transfers into and out of the equatorial and apical second solvation shells were observed to occur on a picosecond (ps) time scale via dissociative mechanisms. Beyond these shells, the bonding pattern substantially returned to the tetrahedral structure of bulk water.« less

Diffusion of flexible random-coil dextran polymers measured in anisotropic brain extracellular space by integrative optical imaging.

PubMed

Xiao, Fanrong; Nicholson, Charles; Hrabe, Jan; Hrabetová, Sabina

2008-08-01

There are a limited number of methods available to quantify the extracellular diffusion of macromolecules in an anisotropic brain region, e.g., an area containing numerous aligned fibers where diffusion is faster along the fibers than across. We applied the integrative optical imaging method to measure diffusion of the fluorophore Alexa Fluor 488 (molecular weight (MW) 547) and fluorophore-labeled flexible random-coil dextran polymers (dex3, MW 3000; dex75, MW 75,000; dex282, MW 282,000; dex525, MW 525,000) in the extracellular space (ECS) of the anisotropic molecular layer of the isolated turtle cerebellum. For all molecules, two-dimensional images acquired an elliptical shape with major and minor axes oriented along and across, respectively, the unmyelinated parallel fibers. The effective diffusion coefficients, D*(major) and D*(minor), decreased with molecular size. The diffusion anisotropy ratio (DAR = D*(major)/D*(minor)) increased for Alexa Fluor 488 through dex75 but then unexpectedly reached a plateau. We argue that dex282 and dex525 approach the ECS width and deform to diffuse. In support of this concept, scaling theory shows the diffusion behavior of dex282 and dex525 to be consistent with transition to a reptation regime, and estimates the average ECS width at approximately 31 nm. These findings have implications for the interstitial transport of molecules and drugs, and for modeling neurotransmitter diffusion during ectopic release and spillover.

The behaviour of water and sodium chloride solution confined into asbestos nanotube

NASA Astrophysics Data System (ADS)

Fomin, Yu. D.; Ryzhov, V. N.; Tsiok, E. N.

2016-08-01

We present the molecular simulation study of the behaviour of water and sodium chloride solution confined in lizardite asbestos nanotube which is a typical example of hydrophilic confinement. The local structure and orientational and dynamic properties are studied. It is shown that at low enough temperatures there is a well-defined orientational ordering of the water molecules. At high local densities corresponding to the maxima of the density distribution function, the water molecules are oriented parallel to the axis of the tube. It is also shown that the diffusion coefficient drops about two orders of magnitude comparing to the bulk case. The behaviour of sodium chloride solutions is also considered and the formation of double layer is observed.

Thermophoretic force on nonspherical particles in the free-molecule regime

NASA Astrophysics Data System (ADS)

Yu, Song; Wang, Jun; Xia, Guodong; Zong, Luxiang

2018-05-01

The present paper is devoted to studying the thermophoresis of a nonspherical convex particle suspended in a gas with nonuniform temperature distribution in the free-molecule regime. Based on the gas kinetic theory and the assumption of a rigid-body collision for the gas-particle interaction, analytical expressions for the thermophoretic forces are obtained for several typical nonspherical bodies, including cylinders, spheroids, needles, disks, and cuboids. The orientation dependences of the thermophoretic forces and thermophoretic velocities are evaluated based on these expressions. It is found that the influence of the pitching effect of the nonspheres can be significant. The expressions for the orientation-averaged thermophoretic forces are also obtained under the assumption of a uniform particle orientation distribution.

Crystal structure of solid molecular hydrogen under high pressures

NASA Astrophysics Data System (ADS)

Cui, T.; Ma, Y.; Zou, G.

2002-11-01

In an effort to achieve a comprehensive understanding of the structure of dense H2, we have performed path-integral Monte Carlo simulations for three combinations of pressures and temperatures corresponding to three phases of solid hydrogen. Our results suggest three kinds of distribution of molecules: orientationally disordered hexagonal close packed (hcp), orientationally ordered hcp with Pa3-type local orientation order and orientationally ordered orthorhombic structure of Cmca symmetry, for the three phases.

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

NASA Astrophysics Data System (ADS)

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.

Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid-vapor interface

NASA Astrophysics Data System (ADS)

Nagayama, Gyoko; Takematsu, Masaki; Mizuguchi, Hirotaka; Tsuruta, Takaharu

2015-07-01

The structure and thermodynamic properties of the liquid-vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid-vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid-vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid-vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid-vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.

Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid–vapor interface

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

Nagayama, Gyoko, E-mail: nagayama@mech.kyutech.ac.jp; Takematsu, Masaki; Mizuguchi, Hirotaka

2015-07-07

The structure and thermodynamic properties of the liquid–vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid–vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain lengthmore » of the molecules affects the condensation/evaporation behavior at the liquid–vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid–vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid–vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.« less

Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid-vapor interface.

PubMed

Nagayama, Gyoko; Takematsu, Masaki; Mizuguchi, Hirotaka; Tsuruta, Takaharu

2015-07-07

The structure and thermodynamic properties of the liquid-vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid-vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid-vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid-vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid-vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.

The effect of pressure on the hydration structure around hydrophobic solute: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Sarma, Rahul; Paul, Sandip

2012-03-01

Molecular dynamics simulations are performed to study the effects of pressure on the hydrophobic interactions between neopentane molecules immersed in water. Simulations are carried out for five different pressure values ranging from 1 atm to 8000 atm. From potential of mean force calculations, we find that with enhancement of pressure, there is decrease in the well depth of contact minimum (CM) and the relative stability of solvent separated minimum over CM increases. Lower clustering of neopentane at high pressure is also observed in association constant and cluster-structure analysis. Selected site-site radial distribution functions suggest efficient packing of water molecules around neopentane molecules at elevated pressure. The orientational profile calculations of water molecules show that the orientation of water molecules in the vicinity of solute molecule is anisotropic and this distribution becomes flatter as we move away from the solute. Increasing pressure slightly changes the water distribution. Our hydrogen bond properties and dynamics calculations reveal pressure-induced formation of more and more number of water molecules with five and four hydrogen bond at the expense of breaking of two and three hydrogen bonded water molecules. We also find lowering of water-water continuous hydrogen bond lifetime on application of pressure. Implication of these results for relative dispersion of hydrophobic molecules at high pressure are discussed.

Rotationally inelastic collisions of excited NaK and NaCs molecules with noble gas and alkali atom perturbers.

PubMed

Jones, J; Richter, K; Price, T J; Ross, A J; Crozet, P; Faust, C; Malenda, R F; Carlus, S; Hickman, A P; Huennekens, J

2017-10-14

We report measurements of rate coefficients at T ≈ 600 K for rotationally inelastic collisions of NaK molecules in the 2(A) 1 Σ + electronic state with helium, argon, and potassium atom perturbers. Several initial rotational levels J between 14 and 44 were investigated. Collisions involving molecules in low-lying vibrational levels (v = 0, 1, and 2) of the 2(A) 1 Σ + state were studied using Fourier-transform spectroscopy. Collisions involving molecules in a higher vibrational level, v = 16, were studied using pump/probe, optical-optical double resonance spectroscopy. In addition, polarization spectroscopy measurements were carried out to study the transfer of orientation in these collisions. Many, but not all, of the measurements were carried out in the "single-collision regime" where more than one collision is unlikely to occur within the lifetime of the excited molecule. The analysis of the experimental data, which is described in detail, includes an estimate of effects of multiple collisions on the reported rate coefficients. The most significant result of these experiments is the observation of a strong propensity for ΔJ = even transitions in collisions involving either helium or argon atoms; the propensity is much stronger for helium than for argon. For the initial rotational levels studied experimentally, almost all initial orientation is preserved in collisions of NaK 2(A) 1 Σ + molecules with helium. Roughly between 1/3 and 2/3 of the orientation is preserved in collisions with argon, and almost all orientation is destroyed in collisions with potassium atoms. Complementary measurements on rotationally inelastic collisions of NaCs 2(A) 1 Σ + with argon do not show a ΔJ = even propensity. The experimental results are compared with new theoretical calculations of collisions of NaK 2(A) 1 Σ + with helium and argon. The calculations are in good agreement with the absolute magnitudes of the experimentally determined rate coefficients and accurately reproduce the very strong propensity for ΔJ = even transitions in helium collisions and the less strong propensity for ΔJ = even transitions in argon collisions. The calculations also show that collisions with helium are less likely to destroy orientation than collisions with argon, in agreement with the experimental results.

Rotationally inelastic collisions of excited NaK and NaCs molecules with noble gas and alkali atom perturbers

NASA Astrophysics Data System (ADS)

Jones, J.; Richter, K.; Price, T. J.; Ross, A. J.; Crozet, P.; Faust, C.; Malenda, R. F.; Carlus, S.; Hickman, A. P.; Huennekens, J.

2017-10-01

We report measurements of rate coefficients at T ≈ 600 K for rotationally inelastic collisions of NaK molecules in the 2(A)1Σ+ electronic state with helium, argon, and potassium atom perturbers. Several initial rotational levels J between 14 and 44 were investigated. Collisions involving molecules in low-lying vibrational levels (v = 0, 1, and 2) of the 2(A)1Σ+ state were studied using Fourier-transform spectroscopy. Collisions involving molecules in a higher vibrational level, v = 16, were studied using pump/probe, optical-optical double resonance spectroscopy. In addition, polarization spectroscopy measurements were carried out to study the transfer of orientation in these collisions. Many, but not all, of the measurements were carried out in the "single-collision regime" where more than one collision is unlikely to occur within the lifetime of the excited molecule. The analysis of the experimental data, which is described in detail, includes an estimate of effects of multiple collisions on the reported rate coefficients. The most significant result of these experiments is the observation of a strong propensity for ΔJ = even transitions in collisions involving either helium or argon atoms; the propensity is much stronger for helium than for argon. For the initial rotational levels studied experimentally, almost all initial orientation is preserved in collisions of NaK 2(A)1Σ+ molecules with helium. Roughly between 1/3 and 2/3 of the orientation is preserved in collisions with argon, and almost all orientation is destroyed in collisions with potassium atoms. Complementary measurements on rotationally inelastic collisions of NaCs 2(A)1Σ+ with argon do not show a ΔJ = even propensity. The experimental results are compared with new theoretical calculations of collisions of NaK 2(A)1Σ+ with helium and argon. The calculations are in good agreement with the absolute magnitudes of the experimentally determined rate coefficients and accurately reproduce the very strong propensity for ΔJ = even transitions in helium collisions and the less strong propensity for ΔJ = even transitions in argon collisions. The calculations also show that collisions with helium are less likely to destroy orientation than collisions with argon, in agreement with the experimental results.

Pharmacophore modeling, molecular docking, and molecular dynamics simulation approaches for identifying new lead compounds for inhibiting aldose reductase 2.

PubMed

Sakkiah, Sugunadevi; Thangapandian, Sundarapandian; Lee, Keun Woo

2012-07-01

Aldose reductase 2 (ALR2), which catalyzes the reduction of glucose to sorbitol using NADP as a cofactor, has been implicated in the etiology of secondary complications of diabetes. A pharmacophore model, Hypo1, was built based on 26 compounds with known ALR2-inhibiting activity values. Hypo1 contains important chemical features required for an ALR2 inhibitor, and demonstrates good predictive ability by having a high correlation coefficient (0.95) as well as the highest cost difference (128.44) and the lowest RMS deviation (1.02) among the ten pharmacophore models examined. Hypo1 was further validated by Fisher's randomization method (95%), test set (r = 0.91), and the decoy set shows the goodness of fit (0.70). Furthermore, during virtual screening, Hypo1 was used as a 3D query to screen the NCI database, and the hit leads were sorted by applying Lipinski's rule of five and ADME properties. The best-fitting leads were subjected to docking to identify a suitable orientation at the ALR2 active site. The molecule that showed the strongest interactions with the critical amino acids was used in molecular dynamics simulations to calculate its binding affinity to the candidate molecules. Thus, Hypo1 describes the key structure-activity relationship along with the estimated activities of ALR2 inhibitors. The hit molecules were searched against PubChem to find similar molecules with new scaffolds. Finally, four molecules were found to satisfy all of the chemical features and the geometric constraints of Hypo1, as well as to show good dock scores, PLPs and PMFs. Thus, we believe that Hypo1 facilitates the selection of novel scaffolds for ALR2, allowing new classes of ALR2 inhibitors to be designed.

Orientational order and rotational relaxation in the plastic crystal phase of tetrahedral molecules.

PubMed

Rey, Rossend

2008-01-17

A methodology recently introduced to describe orientational order in liquid carbon tetrachloride is extended to the plastic crystal phase of XY4 molecules. The notion that liquid and plastic crystal phases are germane regarding orientational order is confirmed for short intermolecular distances but is seen to fail beyond, as long range orientational correlations are found for the simulated solid phase. It is argued that, if real, such a phenomenon may not to be accessible with direct (diffraction) methods due to the high molecular symmetry. This behavior is linked to the existence of preferential orientation with respect to the fcc crystalline network defined by the centers of mass. It is found that the dominant class accounts, at most, for one-third of all configurations, with a feeble dependence on temperature. Finally, the issue of rotational relaxation is also addressed, with an excellent agreement with experimental measures. It is shown that relaxation is nonhomogeneous in the picosecond range, with a slight dispersion of decay times depending on the initial orientational class. The results reported mainly correspond to neopentane over a wide temperature range, although results for carbon tetrachloride are included, as well.

Photostop of iodine atoms from electrically oriented ICl molecules

NASA Astrophysics Data System (ADS)

Bao, Da-Xiao; Deng, Lian-Zhong; Xu, Liang; Yin, Jian-Ping

2015-11-01

The dynamics of photostopping iodine atoms from electrically oriented ICl molecules was numerically studied based on their orientational probability distribution functions. Velocity distributions of the iodine atoms and their production rates were investigated for orienting electrical fields of various intensities. For the ICl precursor beams with an initial rotational temperature of ∼ 1 K, the production of the iodine atoms near zero speed will be improved by about ∼ 5 times when an orienting electrical field of ∼ 200 kV/cm is present. A production rate of ∼ 0.5‰ is obtained for photostopped iodine atoms with speeds less than 10 m/s, which are suitable for magnetic trapping. The electrical orientation of ICl precursors and magnetic trapping of photostopped iodine atoms in situ can be conveniently realized with a pair of charged ring magnets. With the maximal value of the trapping field being ∼ 0.28 T, the largest trapping speed is ∼ 7.0 m/s for the iodine atom. Project supported by the National Natural Science Foundation of China (Grant Nos. 11034002, 61205198, and 11274114) and the National Key Basic Research and Development Program of China (Grant No. 2011CB921602).

Optimal control of the orientation and alignment of an asymmetric-top molecule with terahertz and laser pulses

NASA Astrophysics Data System (ADS)

Coudert, L. H.

2018-03-01

Quantum optimal control theory is applied to determine numerically the terahertz and nonresonant laser pulses leading, respectively, to the highest degree of orientation and alignment of the asymmetric-top H2S molecule. The optimized terahertz pulses retrieved for temperatures of zero and 50 K lead after 50 ps to an orientation with ⟨ΦZx⟩ = 0.959 73 and ⟨⟨ΦZx⟩⟩ = 0.742 30, respectively. For the zero temperature, the orientation is close to its maximum theoretical value; for the higher temperature, it is below the maximum theoretical value. The mechanism by which the terahertz pulse populates high lying rotational levels is elucidated. The 5 ps long optimized laser pulse calculated for a zero temperature leads to an alignment with ⟨ΦZy 2 ⟩ =0.944 16 and consists of several kick pulses with a duration of ≈0.1 ps. It is found that the timing of these kick pulses is such that it leads to an increase of the rotational energy of the molecule. The optimized laser pulse retrieved for a temperature of 20 K is 6 ps long and yields a lower alignment with ⟨⟨ΦZy 2 ⟩ ⟩ =0.717 20 .

Layers: A molecular surface peeling algorithm and its applications to analyze protein structures

PubMed Central

Karampudi, Naga Bhushana Rao; Bahadur, Ranjit Prasad

2015-01-01

We present an algorithm ‘Layers’ to peel the atoms of proteins as layers. Using Layers we show an efficient way to transform protein structures into 2D pattern, named residue transition pattern (RTP), which is independent of molecular orientations. RTP explains the folding patterns of proteins and hence identification of similarity between proteins is simple and reliable using RTP than with the standard sequence or structure based methods. Moreover, Layers generates a fine-tunable coarse model for the molecular surface by using non-random sampling. The coarse model can be used for shape comparison, protein recognition and ligand design. Additionally, Layers can be used to develop biased initial configuration of molecules for protein folding simulations. We have developed a random forest classifier to predict the RTP of a given polypeptide sequence. Layers is a standalone application; however, it can be merged with other applications to reduce the computational load when working with large datasets of protein structures. Layers is available freely at http://www.csb.iitkgp.ernet.in/applications/mol_layers/main. PMID:26553411

Analysis of the substrate influence on the ordering of epitaxial molecular layers: The special case of point-on-line coincidence

NASA Astrophysics Data System (ADS)

Mannsfeld, S. C.; Fritz, T.

2004-02-01

The physical structure of organic-inorganic heteroepitaxial thin films is usually governed by a fine balance between weak molecule-molecule interactions and a weakly laterally varying molecule-substrate interaction potential. Therefore, in order to investigate the energetics of such a layer system one has to consider large molecular domains. So far, layer potential calculations for large domains of organic thin films on crystalline substrates were difficult to perform concerning the computational effort which stems from the vast number of atoms which have to be included. Here, we present a technique which enables the calculation of the molecule-substrate interaction potential for large molecular domains by utilizing potential energy grid files. This technique allows the investigation of the substrate influence in systems prepared by organic molecular beam epitaxy (OMBE), like 3,4,9,10-perylenetetracarboxylicdianhydride on highly oriented pyrolytic graphite. For this system the so-called point-on-line coincidence was proposed, a growth mode which has been controversially discussed in literature. Furthermore, we are able to provide evidence for a general energetic advantage of such point-on-line coincident domain orientations over arbitrarily oriented domains which substantiates that energetically favorable lattice structures in OMBE systems are not restricted to commensurate unit cells or coincident super cells.

Role of quinones in electron transfer of PQQ–glucose dehydrogenase anodes—mediation or orientation effect

DOE PAGES

Babanova, Sofia; Matanovic, Ivana; Chavez, Madelaine Seow; ...

2015-06-16

In this study, the influence of two quinones (1,2- and 1,4-benzoquinone) on the operation and mechanism of electron transfer in PQQ-sGDH anodes has been determined. Benzoquinones were experimentally explored as mediators present in the electrolyte. The electrochemical performance of the PQQ–sGDH anodes with and without the mediators was examined and for the first time molecular docking simulations were used to gain a fundamental understanding to explain the role of the mediator molecules in the design and operation of the enzymatic electrodes. It was proposed that the higher performance of the PQQ–sGDH anodes in the presence of 1,2- and 1,4-benzoquinones introducedmore » in the solution is due to the shorter distance between these molecules and PQQ in the enzymatic molecule. It was also hypothesized that when 1,4-benzoquinone is adsorbed on a carbon support, it would play the dual role of a mediator and an orienting agent. At the same time, when 1,2-benzoquinone and ubiquinone are adsorbed on the electrode surface, the enzyme would transfer the electrons directly to the support, and these molecules would primarily play the role of an orienting agent.« less

Supersonic molecular beam experiments on surface chemical reactions.

PubMed

Okada, Michio

2014-10-01

The interaction of a molecule and a surface is important in various fields, and in particular in complex systems like biomaterials and their related chemistry. However, the detailed understanding of the elementary steps in the surface chemistry, for example, stereodynamics, is still insufficient even for simple model systems. In this Personal Account, I review our recent studies of chemical reactions on single-crystalline Cu and Si surfaces induced by hyperthermal oxygen molecular beams and by oriented molecular beams, respectively. Studies of oxide formation on Cu induced by hyperthermal molecular beams demonstrate a significant role of the translational energy of the incident molecules. The use of hyperthermal molecular beams enables us to open up new chemical reaction paths specific for the hyperthermal energy region, and to develop new methods for the fabrication of thin films. On the other hand, oriented molecular beams also demonstrate the possibility of understanding surface chemical reactions in detail by varying the orientation of the incident molecules. The steric effects found on Si surfaces hint at new ways of material fabrication on Si surfaces. Controlling the initial conditions of incoming molecules is a powerful tool for finely monitoring the elementary step of the surface chemical reactions and creating new materials on surfaces. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Role of Quinones in Electron Transfer of PQQ–Glucose Dehydrogenase Anodes—Mediation or Orientation Effect

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

Babanova, Sofia; Matanovic, Ivana; Chavez, Madelaine Seow

2015-06-24

In this study, the influence of two quinones (1,2- and 1,4-benzoquinone) on the operation and mechanism of electron transfer in PQQ-dependent glucose dehydrogenase (PQQ–sGDH) anodes has been determined. Benzoquinones were experimentally explored as mediators present in the electrolyte. The electrochemical performance of the PQQ–sGDH anodes with and without the mediators was examined and for the first time molecular docking simulations were used to gain a fundamental understanding to explain the role of the mediator molecules in the design and operation of the enzymatic electrodes. It was proposed that the higher performance of the PQQ–sGDH anodes in the presence of 1,2-more » and 1,4-benzoquinones introduced in the solution is due to the shorter distance between these molecules and PQQ in the enzymatic molecule. It was also hypothesized that when 1,4-benzoquinone is adsorbed on a carbon support, it would play the dual role of a mediator and an orienting agent. At the same time, when 1,2-benzoquinone and ubiquinone are adsorbed on the electrode surface, the enzyme would transfer the electrons directly to the support, and these molecules would primarily play the role of an orienting agent.« less

Wave propagation modeling in composites reinforced by randomly oriented fibers

NASA Astrophysics Data System (ADS)

Kudela, Pawel; Radzienski, Maciej; Ostachowicz, Wieslaw

2018-02-01

A new method for prediction of elastic constants in randomly oriented fiber composites is proposed. It is based on mechanics of composites, the rule of mixtures and total mass balance tailored to the spectral element mesh composed of 3D brick elements. Selected elastic properties predicted by the proposed method are compared with values obtained by another theoretical method. The proposed method is applied for simulation of Lamb waves in glass-epoxy composite plate reinforced by randomly oriented fibers. Full wavefield measurements conducted by the scanning laser Doppler vibrometer are in good agreement with simulations performed by using the time domain spectral element method.

Highly Polarized Fluorescent Illumination Using Liquid Crystal Phase.

PubMed

Gim, Min-Jun; Turlapati, Srikanth; Debnath, Somen; Rao, Nandiraju V S; Yoon, Dong Ki

2016-02-10

Liquid crystal (LC) materials are currently the dominant electronic materials in display technology because of the ease of control of molecular orientation using an electric field. However, this technology requires the fabrication of two polarizers to create operational displays, reducing light transmission efficiency below 10%. It is therefore desirable to develop new technologies to enhance the light efficiency while maintaining or improving other properties such as the modulation speed of the molecular orientation. Here we report a uniaxial-oriented B7 smectic liquid crystalline film, using fluorescent bent-core LC molecules, a chemically modified substrate, and an in-plane electric field. A LC droplet under homeotropic boundary conditions of air/LC as well as LC/substrate exhibits large focal conic like optical textures. The in-plane electric field induced uniaxial orientation of the LC molecules, in which molecular polar directors are aligned in the direction of the electric field. This highly oriented LC film exhibits linearly polarized luminescence and microsecond time-scale modulation characteristics. The resultant device is both cheap and easy to fabricate and thus has great potential for electro-optic applications, including LC displays, bioimaging systems, and optical communications.

Distinct crystallinity and orientations of hydroxyapatite thin films deposited on C- and A-plane sapphire substrates

NASA Astrophysics Data System (ADS)

Akazawa, Housei; Ueno, Yuko

2014-10-01

We report how the crystallinity and orientation of hydroxyapatite (HAp) films deposited on sapphire substrates depend on the crystallographic planes. Both solid-phase crystallization of amorphous HAp films and crystallization during sputter deposition at elevated temperatures were examined. The low-temperature epitaxial phase on C-plane sapphire substrates has c-axis orientated HAp crystals regardless of the crystallization route, whereas the preferred orientation switches to the (310) direction at higher temperatures. Only the symmetric stretching mode (ν1) of PO43- units appears in the Raman scattering spectra, confirming well-ordered crystalline domains. In contrast, HAp crystals grown on A-plane sapphire substrates are always oriented toward random orientations. Exhibiting all vibrational modes (ν1, ν3, and ν4) of PO43- units in the Raman scattering spectra reflects random orientation, violating the Raman selection rule. If we assume that Raman intensities of PO43- units represent the crystallinity of HAp films, crystallization terminating the surface with the C-plane is hindered by the presence of excess H2O and OH species in the film, whereas crystallization at random orientations on the A-plane sapphire is rather promoted by these species. Such contrasting behaviors between C-plane and A-plane substrates will reflect surface-plane dependent creation of crystalline seeds and eventually determine the orientation of resulting HAp films.

Free Vibration of Uncertain Unsymmetrically Laminated Beams

NASA Technical Reports Server (NTRS)

Kapania, Rakesh K.; Goyal, Vijay K.

2001-01-01

Monte Carlo Simulation and Stochastic FEA are used to predict randomness in the free vibration response of thin unsymmetrically laminated beams. For the present study, it is assumed that randomness in the response is only caused by uncertainties in the ply orientations. The ply orientations may become random or uncertain during the manufacturing process. A new 16-dof beam element, based on the first-order shear deformation beam theory, is used to study the stochastic nature of the natural frequencies. Using variational principles, the element stiffness matrix and mass matrix are obtained through analytical integration. Using a random sequence a large data set is generated, containing possible random ply-orientations. This data is assumed to be symmetric. The stochastic-based finite element model for free vibrations predicts the relation between the randomness in fundamental natural frequencies and the randomness in ply-orientation. The sensitivity derivatives are calculated numerically through an exact formulation. The squared fundamental natural frequencies are expressed in terms of deterministic and probabilistic quantities, allowing to determine how sensitive they are to variations in ply angles. The predicted mean-valued fundamental natural frequency squared and the variance of the present model are in good agreement with Monte Carlo Simulation. Results, also, show that variations between plus or minus 5 degrees in ply-angles can affect free vibration response of unsymmetrically and symmetrically laminated beams.

Strong-field approximation for ionization of a diatomic molecule by a strong laser field. II. The role of electron rescattering off the molecular centers

NASA Astrophysics Data System (ADS)

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

2008-09-01

The strong-field approximation for ionization of diatomic molecules by a strong laser field [D. B. Milošević, Phys. Rev. A 74, 063404 (2006)] is generalized to include rescattering of the ionized electron wave packet off the molecular centers (the electron’s parent ion or the second atom). There are four rescattering contributions to the ionization rate, which are responsible for the high-energy plateau in the electron spectra and which interfere in a complicated manner. The spectra are even more complicated due to the different symmetry properties of the atomic orbitals of which a particular molecular orbital consists. Nevertheless, a comparatively simple condition emerges for the destructive interference of all these contributions, which yields a curve in the (Epf,θ) plane. Here θ is the electron emission angle and Epf is the electron kinetic energy. The resulting suppression of the rescattering plateau can be strong and affect a large area of the (Epf,θ) plane, depending on the orientation of the molecule. We illustrate this using the examples of the 3σg molecular orbital of N2 and the 1πg molecular orbital of O2 for various orientations of these molecules with respect to the laser polarization axis. For N2 , for perpendicular orientation and the equilibrium internuclear distance R0 , we find that the minima of the ionization rate form the curve Epfcos2θ=π2/(2R02) in the (Epf,θ) plane. For O2 the rescattering plateau is absent for perpendicular orientation.

Probing molecular orientations in thin films by x-ray photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Li, Y.; Li, P.; Lu, Z.-H.

2018-03-01

A great number of functional organic molecules in active thin-film layers of optoelectronic devices have highly asymmetric structures, such as plate-like, rod-like, etc. This makes molecular orientation an important aspect in thin-films as it can significantly affect both the optical and electrical performance of optoelectronic devices. With a combination of in-situ ultra violet photoelectron spectroscopy (UPS) and x-ray photoelectron spectroscopy (XPS) investigations for organic molecules having a broad range of structural properties, we discovered a rigid connection of core levels and frontier highest occupied molecular orbital levels at organic interfaces. This finding opens up opportunities of using X-ray photoemission spectroscopy as an alternative tool to UPS for providing an easy and unambiguous data interpretation in probing molecular orientations.

A scanning tunneling microscope study on an ordered mixed monolayer of bis(4,5-dihydronaphtho[1,2-d])-tetrathiafulvalene and n-tetradecane on highly oriented pyrolytic graphite.

PubMed

Zhao, Miao; Jiang, Peng; Deng, Ke; Jiang, Chao

2010-11-01

Tetrathiafulvalene (TTF) and its derivatives (TTFs) have been successfully used as building blocks to form charge transfer salts and organic semiconductors because of their special structures and rich electron nature. We report the formation of ordered mixed binary-component monolayer consisting of Bis(4,5-dihydronaphtho[1,2-d])tetrathiafulvalene (DH-TTF) and n-tetradecane (n-C14H30) molecules on highly oriented pyrolytic graphite (HOPG) surface. Scanning tunneling microscope (STM) imaging reveals that the two different kinds of molecules can spontaneously form ordered periodic phase separation structures on the substrate, in which ordered DH-TTF double- (or single-) lamella structures are periodically tuned by ordered n-C14H30 double- (or single-) lamella structures. Furthermore, scanning tunneling spectrum (STS) measurements by addressing the individual DH-TTF and n-C14H30 molecules in the ordered monolayer show that the two different kinds of molecules exhibit completely different I(V) characters on the HOPG substrate. The modulated arrangement of the TTF derivative by insulating molecules opens a possible route to construct organic conducting molecule ribbons for potential application in nanodevices.

Structural features of the adsorption layer of pentacene on the graphite surface and the PMMA/graphite hybrid surface

NASA Astrophysics Data System (ADS)

Fadeeva, A. I.; Gorbunov, V. A.; Litunenko, T. A.

2017-08-01

Using the molecular dynamics and the Monte Carlo methods, we have studied the structural features and growth mechanism of the pentacene film on graphite and polymethylmethacrylate /graphite surfaces. Monolayer capacity and molecular area, optimal angles between the pentacene molecules and graphite and PMMA/graphite surfaces as well as the characteristic angles between the neighboring pentacene molecules in the adsorption layer were estimated. It is shown that the orientation of the pentacene molecules in the film is determined by a number of factors, including the surface concentration of the molecules, relief of the surface, presence or absence of the polymer layer and its thickness. The pentacene molecules adsorbed on the graphite surface keep a horizontal position relative to the long axis at any surface coverage/thickness of the film. In the presence of the PMMA layer on the graphite, the increase of the number of pentacene molecules as well as the thickness of the PMMA layer induce the change of molecular orientation from predominantly horizontal to vertical one. The reason for such behavior is supposed to be the roughness of the PMMA surface.

Hydrophobic fluorine mediated switching of the hydrogen bonding site as well as orientation of water molecules in the aqueous mixture of monofluoroethanol: IR, molecular dynamics and quantum chemical studies.

PubMed

Mondal, Saptarsi; Biswas, Biswajit; Nandy, Tonima; Singh, Prashant Chandra

2017-09-20

The local structures between water-water, alcohol-water and alcohol-alcohol have been investigated for aqueous mixtures of ethanol (ETH) and monofluoroethanol (MFE) by the deconvolution of IR bands in the OH stretching region, molecular dynamics simulation and quantum chemical calculations. It has been found that the addition of a small amount of ETH into the aqueous medium increases the strength of the hydrogen bonds between water molecules. In an aqueous mixture of MFE, the substitution of a single fluorine induces a change in the orientation as well as the hydrogen bonding site of water molecules from the oxygen to the fluorine terminal of MFE. The switching of the hydrogen bonding site of water in the aqueous mixture of MFE results in comparatively strong hydrogen bonds between MFE and water molecules as well as less clustering of water molecules, unlike the case of the aqueous mixture of ETH. These findings about the modification of a hydrogen bond network by the hydrophobic fluorine group probably make fluorinated molecules useful for pharmaceutical as well as biological applications.

A highly oriented hybrid microarray modified electrode fabricated by a template-free method for ultrasensitive electrochemical DNA recognition

NASA Astrophysics Data System (ADS)

Shi, Lei; Chu, Zhenyu; Dong, Xueliang; Jin, Wanqin; Dempsey, Eithne

2013-10-01

Highly oriented growth of a hybrid microarray was realized by a facile template-free method on gold substrates for the first time. The proposed formation mechanism involves an interfacial structure-directing force arising from self-assembled monolayers (SAMs) between gold substrates and hybrid crystals. Different SAMs and variable surface coverage of the assembled molecules play a critical role in the interfacial directing forces and influence the morphologies of hybrid films. A highly oriented hybrid microarray was formed on the highly aligned and vertical SAMs of 1,4-benzenedithiol molecules with rigid backbones, which afforded an intense structure-directing power for the oriented growth of hybrid crystals. Additionally, the density of the microarray could be adjusted by controlling the surface coverage of assembled molecules. Based on the hybrid microarray modified electrode with a large specific area (ca. 10 times its geometrical area), a label-free electrochemical DNA biosensor was constructed for the detection of an oligonucleotide fragment of the avian flu virus H5N1. The DNA biosensor displayed a significantly low detection limit of 5 pM (S/N = 3), a wide linear response from 10 pM to 10 nM, as well as excellent selectivity, good regeneration and high stability. We expect that the proposed template-free method can provide a new reference for the fabrication of a highly oriented hybrid array and the as-prepared microarray modified electrode will be a promising paradigm in constructing highly sensitive and selective biosensors.Highly oriented growth of a hybrid microarray was realized by a facile template-free method on gold substrates for the first time. The proposed formation mechanism involves an interfacial structure-directing force arising from self-assembled monolayers (SAMs) between gold substrates and hybrid crystals. Different SAMs and variable surface coverage of the assembled molecules play a critical role in the interfacial directing forces and influence the morphologies of hybrid films. A highly oriented hybrid microarray was formed on the highly aligned and vertical SAMs of 1,4-benzenedithiol molecules with rigid backbones, which afforded an intense structure-directing power for the oriented growth of hybrid crystals. Additionally, the density of the microarray could be adjusted by controlling the surface coverage of assembled molecules. Based on the hybrid microarray modified electrode with a large specific area (ca. 10 times its geometrical area), a label-free electrochemical DNA biosensor was constructed for the detection of an oligonucleotide fragment of the avian flu virus H5N1. The DNA biosensor displayed a significantly low detection limit of 5 pM (S/N = 3), a wide linear response from 10 pM to 10 nM, as well as excellent selectivity, good regeneration and high stability. We expect that the proposed template-free method can provide a new reference for the fabrication of a highly oriented hybrid array and the as-prepared microarray modified electrode will be a promising paradigm in constructing highly sensitive and selective biosensors. Electronic supplementary information (ESI) available: Four-probe method for determining the conductivity of the hybrid crystal (Fig. S1); stability comparisons of the hybrid films (Fig. S2); FESEM images of the hybrid microarray (Fig. S3); electrochemical characterizations of the hybrid films (Fig. S4); DFT simulations (Fig. S5); cross-sectional FESEM image of the hybrid microarray (Fig. S6); regeneration and stability tests of the DNA biosensor (Fig. S7). See DOI: 10.1039/c3nr03097k

New Ro-Vibrational Kinetic Energy Operators using Polyspherical Coordinates for Polyatomic Molecules

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Kwak, Dochan (Technical Monitor)

2002-01-01

We illustrate how one can easily derive kinetic energy operators for polyatomic molecules using polyspherical coordinates with very general choices for z-axis embeddings arid angles used to specify relative orientations of internal vectors. Computer algebra is not required.

Pressure-induced orientational glass phase in molecular para-hydrogen.

PubMed

Schelkacheva, T I; Tareyeva, E E; Chtchelkatchev, N M

2009-02-01

We propose a theoretical description of a possible orientational glass transition in solid molecular para-hydrogen and ortho-deuterium under pressure supposing that they are mixtures of J=0 and J=2 states of molecules. The theory uses the basic concepts and methods of standard spin-glass theory. We expect our orientational glass to correspond to the II' phase of the high-pressure hydrogen phase diagram.

[From Brownian motion to mind imaging: diffusion MRI].

PubMed

Le Bihan, Denis

2006-11-01

The success of diffusion MRI, which was introduced in the mid 1980s is deeply rooted in the powerful concept that during their random, diffusion-driven movements water molecules probe tissue structure at a microscopic scale well beyond the usual image resolution. The observation of these movements thus provides valuable information on the structure and the geometric organization of tissues. The most successful application of diffusion MRI has been in brain ischemia, following the discovery that water diffusion drops at a very early stage of the ischemic event. Diffusion MRI provides some patients with the opportunity to receive suitable treatment at a very acute stage when brain tissue might still be salvageable. On the other hand, diffusion is modulated by the spatial orientation of large bundles of myelinated axons running in parallel through in brain white matter. This feature can be exploited to map out the orientation in space of the white matter tracks and to visualize the connections between different parts of the brain on an individual basis. Furthermore, recent data suggest that diffusion MRI may also be used to visualize rapid dynamic tissue changes, such as neuronal swelling, associated with cortical activation, offering a new and direct approach to brain functional imaging.

Studies of Inelastic Collisions of NaK and NaCs Molecules with Atomic Perturbers

NASA Astrophysics Data System (ADS)

Jones, Joshua A.

We have investigated collisions of NaK molecules in the first excited state [2(A)1Sigma+], with Ar and He collision partners using laser-induced fluorescence spectroscopy (LIF) and polarization-labeling (PL) spectroscopy in a two-step excitation scheme. Additionally, we have investigated collisions of NaCs molecules in the first excited state [2(A)1Sigma +] with Ar and He perturbers using the LIF technique. We use a pump-probe, two-step excitation process. The pump laser prepares the molecule in a particular ro-vibrational (v, J) level in the A state. The probe laser frequency is scanned over transitions to the 31Π in NaK or to the 53Π in NaCs. In addition to observing strong direct lines, we also see weak collisional satellite lines that arise from collisions in the intermediate state that take the molecule from the prepared level (v, J) to level (v, J + Delta J). The ratio of the intensity of the collisional line to the intensity of the direct line in LIF and PL yield information about population and orientation transfer. Our results show a propensity for DeltaJ=even collisions of NaK with Ar and an even stronger propensity for collisions with He. Collisions of NaCs with Ar do not show any such J=even propensity. Preliminary investigations of collisions of NaCs with He seem to indicate a slight J=even propensity. In addition, we observe that rotationally inelastic collisions of excited NaK molecules with potassium atoms destroy almost all of the orientation, while collisions with argon destroy about one third to two thirds and collisions with helium destroy only about zero to one third of the initial orientation.

Is there a common orientational order for the liquid phase of tetrahedral molecules?

PubMed

Rey, Rossend

2009-08-14

The title question is addressed with molecular dynamics simulations for a broad set of molecules: methane (CH4), neopentane (C(CH3)4), carbon tetrafluoride (CF4), carbon tetrachloride (CCl4), silicon tetrachloride (SiCl4), vanadium tetrachloride (VCl4), tin tetrachloride (SnCl4), carbon tetrabromide (CBr4), and tin tetraiodide (SnI4). In all cases the sequence of most populated relative orientations, for increasing distances, is found to be identical: The closest distances correspond to face-to-face followed by a dominant role of edge-to-face, while for larger distances the main configuration is edge-to-edge. The corner-to-face configuration plays an almost negligible role. The range of orientational order is also similar, with remnants of orientational correlation discernible up to the fourth solvation shell. The equivalence does not only hold in the qualitative terms just stated but is also quantitative to a large extent once the center-center distance is properly scaled.

Is there a common orientational order for the liquid phase of tetrahedral molecules?

NASA Astrophysics Data System (ADS)

Rey, Rossend

2009-08-01

The title question is addressed with molecular dynamics simulations for a broad set of molecules: methane (CH4), neopentane (C(CH3)4), carbon tetrafluoride (CF4), carbon tetrachloride (CCl4), silicon tetrachloride (SiCl4), vanadium tetrachloride (VCl4), tin tetrachloride (SnCl4), carbon tetrabromide (CBr4), and tin tetraiodide (SnI4). In all cases the sequence of most populated relative orientations, for increasing distances, is found to be identical: The closest distances correspond to face-to-face followed by a dominant role of edge-to-face, while for larger distances the main configuration is edge-to-edge. The corner-to-face configuration plays an almost negligible role. The range of orientational order is also similar, with remnants of orientational correlation discernible up to the fourth solvation shell. The equivalence does not only hold in the qualitative terms just stated but is also quantitative to a large extent once the center-center distance is properly scaled.

Observation of pendular butterfly Rydberg molecules

PubMed Central

Niederprüm, Thomas; Thomas, Oliver; Eichert, Tanita; Lippe, Carsten; Pérez-Ríos, Jesús; Greene, Chris H.; Ott, Herwig

2016-01-01

Engineering molecules with a tunable bond length and defined quantum states lies at the heart of quantum chemistry. The unconventional binding mechanism of Rydberg molecules makes them a promising candidate to implement such tunable molecules. A very peculiar type of Rydberg molecules are the so-called butterfly molecules, which are bound by a shape resonance in the electron–perturber scattering. Here we report the observation of these exotic molecules and employ their exceptional properties to engineer their bond length, vibrational state, angular momentum and orientation in a small electric field. Combining the variable bond length with their giant dipole moment of several hundred Debye, we observe counter-intuitive molecules which locate the average electron position beyond the internuclear distance. PMID:27703143

3D Representative Volume Element Reconstruction of Fiber Composites via Orientation Tensor and Substructure Features

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

Li, Yi; Chen, Wei; Xu, Hongyi

To provide a seamless integration of manufacturing processing simulation and fiber microstructure modeling, two new stochastic 3D microstructure reconstruction methods are proposed for two types of random fiber composites: random short fiber composites, and Sheet Molding Compounds (SMC) chopped fiber composites. A Random Sequential Adsorption (RSA) algorithm is first developed to embed statistical orientation information into 3D RVE reconstruction of random short fiber composites. For the SMC composites, an optimized Voronoi diagram based approach is developed for capturing the substructure features of SMC chopped fiber composites. The proposed methods are distinguished from other reconstruction works by providing a way ofmore » integrating statistical information (fiber orientation tensor) obtained from material processing simulation, as well as capturing the multiscale substructures of the SMC composites.« less

Critical evaluation of methods to incorporate entropy loss upon binding in high-throughput docking.

PubMed

Salaniwal, Sumeet; Manas, Eric S; Alvarez, Juan C; Unwalla, Rayomand J

2007-02-01

Proper accounting of the positional/orientational/conformational entropy loss associated with protein-ligand binding is important to obtain reliable predictions of binding affinity. Herein, we critically examine two simplified statistical mechanics-based approaches, namely a constant penalty per rotor method, and a more rigorous method, referred to here as the partition function-based scoring (PFS) method, to account for such entropy losses in high-throughput docking calculations. Our results on the estrogen receptor beta and dihydrofolate reductase proteins demonstrate that, while the constant penalty method over-penalizes molecules for their conformational flexibility, the PFS method behaves in a more "DeltaG-like" manner by penalizing different rotors differently depending on their residual entropy in the bound state. Furthermore, in contrast to no entropic penalty or the constant penalty approximation, the PFS method does not exhibit any bias towards either rigid or flexible molecules in the hit list. Preliminary enrichment studies using a lead-like random molecular database suggest that an accurate representation of the "true" energy landscape of the protein-ligand complex is critical for reliable predictions of relative binding affinities by the PFS method. Copyright 2006 Wiley-Liss, Inc.

Differences in single and aggregated nanoparticle plasmon spectroscopy.

PubMed

Singh, Pushkar; Deckert-Gaudig, Tanja; Schneidewind, Henrik; Kirsch, Konstantin; van Schrojenstein Lantman, Evelien M; Weckhuysen, Bert M; Deckert, Volker

2015-02-07

Vibrational spectroscopy usually provides structural information averaged over many molecules. We report a larger peak position variation and reproducibly smaller FWHM of TERS spectra compared to SERS spectra indicating that the number of molecules excited in a TERS experiment is extremely low. Thus, orientational averaging effects are suppressed and micro ensembles are investigated. This is shown for a thiophenol molecule adsorbed on Au nanoplates and nanoparticles.

Coverage induced structural transformations of tetracene on Ag(110)

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

Takasugi, Kazushiro; Yokoyama, Takashi, E-mail: tyoko@yokohama-cu.ac.jp

2016-03-14

Self-assembly of tetracene on an anisotropic surface of Ag(110) has been investigated using scanning tunneling microscopy and low-energy electron diffraction. We observe multistage structural transformations of the self-assembled tetracene on Ag(110) as a function of molecular coverages, which are accompanied by the changes in molecular orientations. They are analyzed by a balance between multiple molecule-molecule and anisotropic substrate-molecule interactions.

Single electron impact ionization of the methane molecule

NASA Astrophysics Data System (ADS)

Bouamoud, Mammar; Sahlaoui, Mohammed; Benmansour, Nour El Houda; Atomic and Molecular Collisions Team

2014-10-01

Triply differential cross sections (TDCS) results of electron-impact ionization of the inner 2a1 molecular orbital of CH4 are presented in the framework of the Second Born Approximation and compared with the experimental data performed in coplanar asymmetric geometry. The cross sections are averaged on the random orientations of the molecular target for accurate comparison with experiments and are compared also with the theoretical calculations of the Three Coulomb wave (3CW) model. Our results are in good agreement with experiments and 3CW results in the binary peak. In contrast the Second Born Approximation yields a significant higher values compared to the 3CW results for the recoil peak and seems to describe suitably the recoil region where higher order effects can occur with the participation of the recoiling ion in the collision process.

Structural arrest in an ideal gas.

PubMed

van Ketel, Willem; Das, Chinmay; Frenkel, Daan

2005-04-08

We report a molecular dynamics study of a simple model system that has the static properties of an ideal gas, yet exhibits nontrivial "glassy" dynamics behavior at high densities. The constituent molecules of this system are constructs of three infinitely thin hard rods of length L, rigidly joined at their midpoints. The crosses have random but fixed orientation. The static properties of this system are those of an ideal gas, and its collision frequency can be computed analytically. For number densities NL(3)/V>1, the single-particle diffusivity goes to zero. As the system is completely structureless, standard mode-coupling theory cannot describe the observed structural arrest. Nevertheless, the system exhibits many dynamical features that appear to be mode-coupling-like. All high-density incoherent intermediate scattering functions collapse onto master curves that depend only on the wave vector.

Evidence of thermal transport anisotropy in stable glasses of vapor deposited organic molecules

NASA Astrophysics Data System (ADS)

Ràfols-Ribé, Joan; Dettori, Riccardo; Ferrando-Villalba, Pablo; Gonzalez-Silveira, Marta; Abad, Llibertat; Lopeandía, Aitor F.; Colombo, Luciano; Rodríguez-Viejo, Javier

2018-03-01

Vapor deposited organic glasses are currently in use in many optoelectronic devices. Their operation temperature is limited by the glass transition temperature of the organic layers and thermal management strategies become increasingly important to improve the lifetime of the device. Here we report the unusual finding that molecular orientation heavily influences heat flow propagation in glassy films of small molecule organic semiconductors. The thermal conductivity of vapor deposited thin-film semiconductor glasses is anisotropic and controlled by the deposition temperature. We compare our data with extensive molecular dynamics simulations to disentangle the role of density and molecular orientation on heat propagation. Simulations do support the view that thermal transport along the backbone of the organic molecule is strongly preferred with respect to the perpendicular direction. This is due to the anisotropy of the molecular interaction strength that limits the transport of atomic vibrations. This approach could be used in future developments to implement small molecule glassy films in thermoelectric or other organic electronic devices.

Rotor-stator molecular crystals of fullerenes with cubane.

PubMed

Pekker, Sándor; Kováts, Eva; Oszlányi, Gábor; Bényei, Gyula; Klupp, Gyöngyi; Bortel, Gábor; Jalsovszky, István; Jakab, Emma; Borondics, Ferenc; Kamarás, Katalin; Bokor, Mónika; Kriza, György; Tompa, Kálmán; Faigel, Gyula

2005-10-01

Cubane (C8H8) and fullerene (C60) are famous cage molecules with shapes of platonic or archimedean solids. Their remarkable chemical and solid-state properties have induced great scientific interest. Both materials form polymorphic crystals of molecules with variable orientational ordering. The idea of intercalating fullerene with cubane was raised several years ago but no attempts at preparation have been reported. Here we show that C60 and similarly C70 form high-symmetry molecular crystals with cubane owing to topological molecular recognition between the convex surface of fullerenes and the concave cubane. Static cubane occupies the octahedral voids of the face-centred-cubic structures and acts as a bearing between the rotating fullerene molecules. The smooth contact of the rotor and stator molecules decreases significantly the temperature of orientational ordering. These materials have great topochemical importance: at elevated temperatures they transform to high-stability covalent derivatives although preserving their crystalline appearance. The size-dependent molecular recognition promises selective formation of related structures with higher fullerenes and/or substituted cubanes.

A diversity oriented synthesis of natural product inspired molecular libraries.

PubMed

Chauhan, Jyoti; Luthra, Tania; Gundla, Rambabu; Ferraro, Antonio; Holzgrabe, Ulrike; Sen, Subhabrata

2017-11-07

Natural products are the source of innumerable pharmaceutical drug candidates and also form an important aspect of herbal remedies. They are also a source of various bioactive compounds. Herein we have leveraged the structural attributes of several natural products in building a library of architecturally diverse chiral molecules by harnessing R-tryptophan as the chiral auxiliary. It is converted to its corresponding methyl ester 1 which in turn provided a bevy of 1-aryl-tetrahydro-β-carbolines 2a-d, which were then converted to chiral compounds via a diversity oriented synthetic strategy (DOS). In general, intermolecular and intramolecular ring rearrangements facilitated the formation of the final compounds. Four different classes of molecules with distinct architectures were generated, adding up to nearly twenty-two individual molecules. Phenotypic screening of a representative section of the library revealed two molecules that selectively inhibit MCF7 breast cancer cells with IC 50 of ∼5 μg mL -1 potency.

Bioinspired Design of Polycaprolactone Composite Nanofibers as Artificial Bone Extracellular Matrix for Bone Regeneration Application.

PubMed

Gao, Xiang; Song, Jinlin; Zhang, Yancong; Xu, Xiao; Zhang, Siqi; Ji, Ping; Wei, Shicheng

2016-10-07

The design and development of functional biomimetic systems for programmed stem cell response is a field of topical interest. To mimic bone extracellular matrix, we present an innovative strategy for constructing drug-loaded composite nanofibrous scaffolds in this study, which could integrate multiple cues from calcium phosphate mineral, bioactive molecule, and highly ordered fiber topography for the control of stem cell fate. Briefly, inspired by mussel adhesion mechanism, a polydopamine (pDA)-templated nanohydroxyapatite (tHA) was synthesized and then surface-functionalized with bone morphogenetic protein-7-derived peptides via catechol chemistry. Afterward, the resulting peptide-loaded tHA (tHA/pep) particles were blended with polycaprolactone (PCL) solution to fabricate electrospun hybrid nanofibers with random and aligned orientation. Our research demonstrated that the bioactivity of grafted peptides was retained in composite nanofibers. Compared to controls, PCL-tHA/pep composite nanofibers showed improved cytocompatibility. Moreover, the incorporated tHA/pep particles in nanofibers could further facilitate osteogenic differentiation potential of human mesenchymal stem cells (hMSCs). More importantly, the aligned PCL-tHA/pep composite nanofibers showed more osteogenic activity than did randomly oriented counterparts, even under nonosteoinductive conditions, indicating excellent performance of biomimetic design in cell fate decision. After in vivo implantation, the PCL-tHA/pep composite nanofibers with highly ordered structure could significantly promote the regeneration of lamellar-like bones in a rat calvarial critical-sized defect. Accordingly, the presented strategy in our work could be applied for a wide range of potential applications in not only bone regeneration application but also pharmaceutical science.

Transport of water molecules through noncylindrical pores in multilayer nanoporous graphene.

PubMed

Shahbabaei, Majid; Kim, Daejoong

2017-08-09

In this study, molecular dynamics (MD) simulations are used to examine the water transport properties through asymmetric hourglass-shaped pores in multilayer nanoporous graphene with a constant interlayer separation of 6 Å. The properties of the tested asymmetric hourglass-shaped pores [with the models having long cone (l 1 , -P) and short cone (l 2 , +P) entrances] are compared to a symmetric pore model. The study findings indicate that the water occupancy increases across the asymmetric pore (l 1 , -P) compared to (l 2 , +P), because of the length effect. The asymmetric pore, (l 1 , -P), yields higher flux compared to (l 2 , +P) and even the symmetric model, which can be attributed to the increase in the hydrogen bonds. In addition, the single-file water molecules across the narrowest pore diameter inside the (l 2 , +P) pore exhibit higher viscosity compared to those in the (l 1 , -P) pore because of the increase in the water layering effect. Moreover, it is found that the permeability inside the multilayer hourglass-shaped pore depends on the length of the flow path of the water molecules before approaching the layer with the smallest pore diameter. The probability of dipole orientation exhibits wider distribution inside the (l 1 , -P) system compared to (l 2 , +P), implying an enhanced formation of hydrogen bonding of water molecules. This results in the fast flow of water molecules. The MD trajectory shows that the dipole orientation across the single-layer graphene has frequently flipped compared to the dipole orientation across the pores in multilayer graphene, which is maintained during the whole simulation time (although the dipole orientation has flipped for a few picoseconds at the beginning of the simulation). This can be attributed to the energy barrier induced by the individual layer. The diffusion coefficient of water molecules inside the (l 2 , +P) system increases with pressure difference, however, it decreases inside the (l 1 , -P) system because of the increase in the number of collisions. It was found that the velocity in the axial direction (z-direction) has a significant impact on the permeation ability of water molecules across the asymmetric nanopores examined in this study. Finally, the study results suggest that the appropriate design of an asymmetric hourglass-shaped nanopore in multilayer graphene can significantly improve the water permeation rate even compared to a symmetric structure.

Oriented antibody immobilization on self-assembled monolayers applied as impedance biosensors

NASA Astrophysics Data System (ADS)

Tsugimura, Kaiki; Ohnuki, Hitoshi; Wu, Haiyun; Endo, Hideaki; Tsuya, Daiju; Izumi, Mitsuru

2017-11-01

Oriented immobilization of antibodies on a sensor chip is crucial for enhancing both the sensitivity and antigen-binding capacity of immunosensors. Here, we report a comparative study of the effect of oriented and random antibody immobilization on the binding efficiency by electrochemical impedance spectroscopy (EIS). Oriented immobilization of anti-myoglobin immunoglobulin G (anti-Myo IgG) was achieved by bonding to an Fc receptor of protein G (PrG) on a self-assembled monolayer (SAM), which results in the myoglobin (Myo) binding sites being exposed outside the sensing surface. Random immobilization of anti-Myo IgG was achieved by direct covalent attachment to the SAM surface. Both immobilizations were applied to interdigitated electrodes to enhance the electrochemical signal, and the Myo biosensor performance was then evaluated by a series of EIS measurements. We found that (i) the rate of the normalized charge transfer resistance for the oriented sample was 3 times higher than that for the random sample and (ii) the detection limit was 0.001 ng/mL, which is the lowest recorded detection limit among Myo immunosensors based on EIS. These findings indicate that oriented antibody immobilization is crucial for preparing highly sensitive EIS-based biosensors.

Quantitation of protein orientation in flow-oriented unilamellar liposomes by linear dichroism

NASA Astrophysics Data System (ADS)

Rajendra, Jascindra; Damianoglou, Angeliki; Hicks, Matthew; Booth, Paula; Rodger, P. Mark; Rodger, Alison

2006-07-01

The linear dichroism of the visible wavelength transitions of retinal have been used to analyse linear dichroism spectra to determine the orientation of aromatic and peptide structural motifs of Bacteriorhodopsin incorporated into unilamellar soy bean liposomes. The results are consistent with the available X-ray data. This proves that visible light absorbing chromophores can be used to analyse linear dichroism data to give the orientation of membrane proteins in membrane mimicking environments. The work has been extended by screening a wide range of hydrophobic molecules with high extinction coefficients in transitions above 300 nm to find molecules that could be used as independent probes of liposome orientation for experiments involving proteins incorporated into liposomes. Three probes were found to have potential for future work: bis-(1,3-dibutylbarbituric acid)pentamethine oxonol (DiBAC 4), retinol and rhodamine B. All three can be used to determine the orientation of the porphyrin of cytochrome c, the aromatic residues of gramicidin and the helices of both proteins. The orientation parameter, S, for the liposomes varied from batch to batch of unilamellar liposomes prepared by extruding through a 100 nm membrane. The value and variation in S was 0.030 ± 0.010. Repeat experiments with the same batch of liposomes showed less variation. Film LD data were measured for DiBAC 4 and rhodamine B to determine the polarisations of their long wavelength transitions.

Orientation-dependent energy level alignment and film growth of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on HOPG

NASA Astrophysics Data System (ADS)

Lyu, Lu; Niu, Dongmei; Xie, Haipeng; Cao, Ningtong; Zhang, Hong; Zhang, Yuhe; Liu, Peng; Gao, Yongli

2016-01-01

Combining ultraviolet photoemission spectroscopy, X-ray photoemission spectroscopy, atomic force microscopy, and X-ray diffraction measurements, we performed a systematic investigation on the correlation of energy level alignment, film growth, and molecular orientation of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on highly oriented pyrolytic graphite. The molecules lie down in the first layer and then stand up from the second layer. The ionization potential shows a sharp decrease from the lying down region to the standing up region. When C8-BTBT molecules start standing up, unconventional energy level band-bending-like shifts are observed as the film thickness increases. These shifts are ascribed to gradual decreasing of the molecular tilt angle about the substrate normal with the increasing film thickness.

Orientation-dependent energy level alignment and film growth of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on HOPG.

PubMed

Lyu, Lu; Niu, Dongmei; Xie, Haipeng; Cao, Ningtong; Zhang, Hong; Zhang, Yuhe; Liu, Peng; Gao, Yongli

2016-01-21

Combining ultraviolet photoemission spectroscopy, X-ray photoemission spectroscopy, atomic force microscopy, and X-ray diffraction measurements, we performed a systematic investigation on the correlation of energy level alignment, film growth, and molecular orientation of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on highly oriented pyrolytic graphite. The molecules lie down in the first layer and then stand up from the second layer. The ionization potential shows a sharp decrease from the lying down region to the standing up region. When C8-BTBT molecules start standing up, unconventional energy level band-bending-like shifts are observed as the film thickness increases. These shifts are ascribed to gradual decreasing of the molecular tilt angle about the substrate normal with the increasing film thickness.

Supramolecular order following binding of the dichroic birefringent sulfonic dye Ponceau SS to collagen fibers.

PubMed

Vidal, B C; Mello, M L S

2005-06-15

The optical anisotropies (linear dichroism or LD and birefringence) of crystalline aggregates of the sulfonic azo-dye Ponceau SS and of dye complexed with chicken tendon collagen fibers were investigated in order to assess their polarizing properties and similarity to liquid crystals. In some experiments, the staining was preceded by treatment with picric acid. Crystalline fibrous aggregates of the dye had a negative LD, and their electronic transitions were oriented perpendicular to the filamentary structures. The binding of Ponceau SS molecules to the collagen fibers altered the LD signal, with variations in the fiber orientation affecting the resulting dichroic ratios. The long axis of the rod-like dye molecule was assumed to be bound in register, parallel to the collagen fiber. Picric acid did not affect the oriented binding of the azo dye to collagen fibers. There were differences in the optical anisotropy of Ponceau SS-stained tendons from 21-day-old and 41-day-old chickens, indicating that Ponceau SS was able to distinguish between different ordered states of macromolecular aggregation in chicken tendon collagen fibers. In the presence of dichroic rod-like azo-dye molecules such as Ponceau SS, collagen also formed structures with a much higher degree of orientation. The presence of LD in the Ponceau SS-collagen complex even in unpolarized light indicated that this complex can act as a polarizer. Copyright 2005 Wiley Periodicals, Inc.

Dielectric relaxation of guest molecules in a clathrate structure of syndiotactic polystyrene.

PubMed

Urakawa, Osamu; Kaneko, Fumitoshi; Kobayashi, Hideo

2012-12-13

Structure and dynamics of semicrystalline polymer films composed of syndiotactic polystyrene (sPS) and 2-butanone were examined through X-ray diffraction, polarized FTIR, and dielectric relaxation measurements. The X-ray and FTIR measurements revealed its crystal structure to be δ-clathrate containing 2-butanone molecules inside. The carbonyl group of 2-butanone in the crystal was found to orient preferentially parallel to the ac plane of the crystal through the polarized ATR FTIR measurements. Dielectric measurements were also conducted on these film samples to see only the relaxation dynamics of 2-butanone thanks to the high dielectric intensity of 2-butanone compared to sPS. Two relaxation modes denoted by slow and fast modes appeared. The former was assigned to the motion of 2-butanone molecules entrapped in the cavities of the crystalline (δ-form) and the latter to those in the amorphous region. We focused on the slow mode in order to elucidate the specific dynamics of the guest molecule confined in the crystalline region. The relaxation time of the slow mode was about 4 orders of magnitude longer than that of liquid 2-butanone. This suggests that the dynamics of guest molecules is highly restricted due to the high barrier to conformational and/or orientational change of the guest molecule in the cavity of δ-crystal. Furthermore, the dielectric intensity Δε of the slow mode was much smaller than the one calculated from that of bulk liquid 2-butanone and the guest concentration in the crystalline region (the intensity was only 10% of the estimated value from the bulk liquid data). This result also indicates that the free rotational motion of 2-butanone molecules is restricted inside the crystal. This will be consistently related to the weak uniplanar orientation of the carbonyl group of 2-butanone parallel to the ac plane revealed by the X-ray and polarized ATR FTIR measurements.

Symmetry in circularly polarized molecular high-order harmonic generation with intense bicircular laser pulses

NASA Astrophysics Data System (ADS)

Yuan, Kai-Jun; Bandrauk, André D.

2018-02-01

We present symmetry effects of laser fields and molecular geometries in circularly polarized high-order harmonic generation by bichromatic counter-rotating circularly polarized laser pulses. Simulations are performed on oriented molecules by numerically solving time-dependent Schrödinger equations. We discuss how electron recollision trajectories by the orthogonal laser field polarizations influence the harmonic polarization by using a time-frequency analysis of harmonics. It is found that orientation-dependent asymmetric ionization in linear molecules due to Coulomb potentials gives rise to a dependence of the polarization on the harmonic frequency. Effects of Coriolis forces are also presented on harmonic generation. Electron recollision trajectories illustrate the effects of the relative symmetry of the field and the molecule, thus paving a method for circularly polarized attosecond pulse generation and molecular orbital imaging in more complex systems.

[See the thinking brain: a story about water].

PubMed

Le Bihan, D

2008-01-01

Among the astonishing Einstein's papers from 1905, there is one which unexpectedly gave birth to a powerful method to explore the brain. Molecular diffusion was explained by Einstein on the basis of the random translational motion of molecules which results from their thermal energy. In the mid 1980s it was shown that water diffusion in the brain could be imaged using MRI. During their random displacements water molecules probe tissue structure at a microscopic scale, interacting with cell membranes and, thus, providing unique information on the functional architecture of tissues. A dramatic application of diffusion MRI has been brain ischemia, following the discovery that water diffusion drops immediately after the onset of an ischemic event, when brain cells undergo swelling through cytotoxic edema. On the other hand, water diffusion is anisotropic in white matter, because axon membranes limit molecular movement perpendicularly to the fibers. This feature can be exploited to map out the orientation in space of the white matter tracks and image brain connections. More recently, it has been shown that diffusion MRI could accurately detect cortical activation. As the diffusion response precedes by several seconds the hemodynamic response captured by BOLD fMRI, it has been suggested that water diffusion could reflect early neuronal events, such as the transient swelling of activated cortical cells. If confirmed, this discovery will represent a significant breakthrough, allowing non invasive access to a direct physiological marker of brain activation. This approach will bridge the gap between invasive optical imaging techniques in neuronal cell cultures, and current functional neuroimaging approaches in humans, which are based on indirect and remote blood flow changes.

Impact of straight, unconnected, radially-oriented, and tapered mesopores on column efficiency: A theoretical investigation.

PubMed

Gritti, Fabrice

2017-02-17

Superficially porous particles (SPPs) can be prepared from a pseudomorphic transformation (PMT) which produces straight, unconnected, and radially-oriented mesopores (ROMs). ROMs can be either both ends open in fully porous particles (FPPs) or one-end-closed in SPPs. The impact of ROMs on the longitudinal diffusion (B/u), solid-liquid mass transfer resistance (C s u), and on the eddy dispersion (A(u)) height equivalent to a theoretical plate (HETP) of 3D randomly packed columns was investigated based on theoretical viewpoints. Torquato's theory of effective diffusion in packed beds (B term), Giddings' coupling theory of eddy dispersion (A term), and Giddings' generalized nonequilibrium theory (C s term) are applied to make predictions. First, it is found that the A term is nearly independent on the internal structure of the particle. Secondly, in the absence of flow, infinitely narrow and both ends open (no constriction effect) ROMs induce an internal hindrance factor of 23 regarding diffusion along the axial direction. Experimental data reveal that one-end-closed and 80Å wide ROMs in SPPs lead to a measurable internal hindrance factor of 27 regarding diffusion in the porous shell. Thirdly, above the optimum speed, the C s coefficient is dependent on the geometry (cylinders, cones, etc.) of the ROMs: when ROMs are conical in SPPs, C s is expected to decrease by 80% with respect to cylindrical ROMs. From an application perspective, PMT-SPPs prepared with narrow ROMs are well suited for the analysis of small molecules at or below optimum speed (lowest B term) while PMT-SPPs made of wide and conical ROMs are ideal for the analysis of large molecules above optimum speed (smallest C s term). Copyright © 2017. Published by Elsevier B.V.

[Three-dimensional parallel collagen scaffold promotes tendon extracellular matrix formation].

PubMed

Zheng, Zefeng; Shen, Weiliang; Le, Huihui; Dai, Xuesong; Ouyang, Hongwei; Chen, Weishan

2016-03-01

To investigate the effects of three-dimensional parallel collagen scaffold on the cell shape, arrangement and extracellular matrix formation of tendon stem cells. Parallel collagen scaffold was fabricated by unidirectional freezing technique, while random collagen scaffold was fabricated by freeze-drying technique. The effects of two scaffolds on cell shape and extracellular matrix formation were investigated in vitro by seeding tendon stem/progenitor cells and in vivo by ectopic implantation. Parallel and random collagen scaffolds were produced successfully. Parallel collagen scaffold was more akin to tendon than random collagen scaffold. Tendon stem/progenitor cells were spindle-shaped and unified orientated in parallel collagen scaffold, while cells on random collagen scaffold had disorder orientation. Two weeks after ectopic implantation, cells had nearly the same orientation with the collagen substance. In parallel collagen scaffold, cells had parallel arrangement, and more spindly cells were observed. By contrast, cells in random collagen scaffold were disorder. Parallel collagen scaffold can induce cells to be in spindly and parallel arrangement, and promote parallel extracellular matrix formation; while random collagen scaffold can induce cells in random arrangement. The results indicate that parallel collagen scaffold is an ideal structure to promote tendon repairing.

Population gratings in saturable optical fibers with randomly oriented rare-earth ions

NASA Astrophysics Data System (ADS)

Stepanov, S.; Martinez, L. M.; Hernandez, E. H.; Agruzov, P.; Shamray, A.

2015-07-01

Formation of the dynamic population gratings in optical fibers with randomly oriented rare-earth ions is analyzed with a special interest to the grating component for readout with the orthogonal light polarization. It is shown that as compared with a simple model case of the collinearly oriented dipole-like centers their random orientation leads to approximately 2-times growth of the effective saturation power P sat when it is estimated from the incident power dependence of the fiber absorption or from that of the fluorescence intensity. An optimal incident power, for which the maximum of the dynamic population grating amplitude for collinear light polarization is observed, also follows this change in P sat, while formation of the grating for orthogonal polarization needs essentially higher light power. The reduced anisotropy of the active centers, which is in charge of the experimentally observed weakening of the polarization hole burning (PHB) and of the fluorescence polarization, compensates in some way the effect of random ion orientation. The ratio between the maximum conventional (i.e. for the interacting waves collinear polarizations) two-wave mixing (TWM) amplitude and the initial not saturable fiber optical density proves to be, however, nearly the same as in the model case of collinearly oriented dipoles. The ratio between the PHB effect and the amplitude of the anisotropic grating, which is responsible for TWM of the orthogonally polarized waves, is also not influenced significantly by the reduced anisotropy of ions.

Order from Force; A natural history of the vacuum

NASA Astrophysics Data System (ADS)

Williams, Jeffrey H.

2015-11-01

The laws of physics govern our lives, and the fundamental constants of Nature (for example, the mass and charge of the electron) define our very morphology. If a human body were totally dehydrated there would only remain about thirty kilograms of crystals and powder, after having removed about fifty litres of water. Yet the amazing machine that is our body functions because of the forces of interaction (attraction and repulsion) that exist between the molecules in that powder when fully hydrated. These forces of interaction are mediated and directed by the vast amount of water that is present. It is the precise orientation of one hydrated molecule with respect to another hydrated molecule, at a well-defined separation, in our central nervous systems that allows a nerve impulse to tunnel quantum-mechanically through the intermediate space between two nerve cells at a synapse. Thereby allowing us to observe our environment, and contemplate our existence. It is the arrangement of the water molecules along molecules of muscle proteins that allows one protein molecule to slide over neighbouring protein molecules, thereby allowing us to do exercise and work, or to hunt and to gather. The precise distances and orientations between the molecules of which our bodies are composed are determined by subtle intermolecular electrostatic forces, whose magnitude is determined by the various constants of Nature, and whose operation is dictated by the laws of physics. We are merely living representations of these immutable physical laws.

Single-Molecule Electrical Random Resequencing of DNA and RNA

NASA Astrophysics Data System (ADS)

Ohshiro, Takahito; Matsubara, Kazuki; Tsutsui, Makusu; Furuhashi, Masayuki; Taniguchi, Masateru; Kawai, Tomoji

2012-07-01

Two paradigm shifts in DNA sequencing technologies--from bulk to single molecules and from optical to electrical detection--are expected to realize label-free, low-cost DNA sequencing that does not require PCR amplification. It will lead to development of high-throughput third-generation sequencing technologies for personalized medicine. Although nanopore devices have been proposed as third-generation DNA-sequencing devices, a significant milestone in these technologies has been attained by demonstrating a novel technique for resequencing DNA using electrical signals. Here we report single-molecule electrical resequencing of DNA and RNA using a hybrid method of identifying single-base molecules via tunneling currents and random sequencing. Our method reads sequences of nine types of DNA oligomers. The complete sequence of 5'-UGAGGUA-3' from the let-7 microRNA family was also identified by creating a composite of overlapping fragment sequences, which was randomly determined using tunneling current conducted by single-base molecules as they passed between a pair of nanoelectrodes.

Predicting bending stiffness of randomly oriented hybrid panels

Treesearch

Laura Moya; William T.Y. Tze; Jerrold E. Winandy

2010-01-01

This study was conducted to develop a simple model to predict the bending modulus of elasticity (MOE) of randomly oriented hybrid panels. The modeling process involved three modules: the behavior of a single layer was computed by applying micromechanics equations, layer properties were adjusted for densification effects, and the entire panel was modeled as a three-...

Methylbenzenes on graphene

NASA Astrophysics Data System (ADS)

Borck, Øyvind; Schröder, Elsebeth

2017-10-01

We present a theory study of the physisorption of the series of methylbenzenes (toluene, xylene and mesitylene), as well as benzene, on graphene. The aim is two fold: we provide data that will be used as input to larger-scale methods like molecular-dynamics simulations, and at the same time we enhance the basic understanding of graphene used as a material for sensors and as an idealized model for the carbon in active carbon filters. The molecules are studied in a number of positions and orientations relative to graphene, using density functional theory with the van der Waals functional vdW-DF. The molecules are adsorbed fractional coverage. We focus on the vdW-DF1 and vdW-DF-cx functionals, and find that the binding energy of the molecules on graphene grows linearly with the number of methyl groups, at the rate of 0.09 eV (vdW-DF1) to 0.11 eV (vdW-DF-cx) per added methyl group. We further find that the orientation of the methyl groups of the molecules relative to graphene is at least as important as the lateral position of the whole molecule on graphene.

Dual-modality single particle orientation and rotational tracking of intracellular transport of nanocargos.

PubMed

Sun, Wei; Gu, Yan; Wang, Gufeng; Fang, Ning

2012-01-17

The single particle orientation and rotational tracking (SPORT) technique was introduced recently to follow the rotational motion of plasmonic gold nanorod under a differential interference contrast (DIC) microscope. In biological studies, however, cellular activities usually involve a multiplicity of molecules; thus, tracking the motion of a single molecule/object is insufficient. Fluorescence-based techniques have long been used to follow the spatial and temporal distributions of biomolecules of interest thanks to the availability of multiplexing fluorescent probes. To know the type and number of molecules and the timing of their involvement in a biological process under investigation by SPORT, we constructed a dual-modality DIC/fluorescence microscope to simultaneously image fluorescently tagged biomolecules and plasmonic nanoprobes in living cells. With the dual-modality SPORT technique, the microtubule-based intracellular transport can be unambiguously identified while the dynamic orientation of nanometer-sized cargos can be monitored at video rate. Furthermore, the active transport on the microtubule can be easily separated from the diffusion before the nanocargo docks on the microtubule or after it undocks from the microtubule. The potential of dual-modality SPORT is demonstrated for shedding new light on unresolved questions in intracellular transport.

Conformational distribution of n-hexane in a nematic liquid crystal obtained from nuclear spin dipolar couplings by Monte Carlo sampling

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

Luzar, M.; Rosen, M.E.; Caldarelli, S.

Motionally averaged proton-proton dipolar couplings measured by nuclear magnetic resonance (NMR) spectroscopy can provide information about the conformations and orientations sampled by partially oriented molecules. In this study, the measured dipolar couplings between pairs of protons on n-hexane dissolved in a nematic liquid crystal solvent are used as constraints in a Monte Carlo sampling of the conformations and orientations of n-hexane. Rotation about each carbon-carbon bond in the molecule is modeled by the complete sinusoidal torsional potential of Ryckaert and Bellemans rather than by the three-state rotational isomeric states (RIS) model that has been used in previous studies. Comparison ofmore » the results of the simulations using the Ryckaert-Bellemans potential and the RIS model indicates little difference in the values of the adjustable parameters and the quality of the fits to the experimental data. The primary difference between the models appears in the calculated conformer probability distributions for n-hexane, highlighting the importance of the exact shape of the torsional potential used to model carbon-carbon bond rotation in organic molecules. 23 refs., 3 figs., 4 tabs.« less

Growth and magnetoelectric properties of (00l)-oriented La{sub 0.67}Sr{sub 0.33}MnO{sub 3}/PbZr{sub 0.52}Ti{sub 0.48}O{sub 3} heterostructure films

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

Yan, Fuxue, E-mail: yanfuxue@126.com; Han, Kai, E-

2017-02-15

C-axis oriented La{sub 0.67}Sr{sub 0.33}MnO{sub 3}(LSMO)/PbZr{sub 0.52}Ti{sub 0.48}O{sub 3}(PZT) films are fabricated successfully by sol-gel method on LaAlO{sub 3} (00l) substrates. The structure, composition and morphology of the films are investigated by X-ray diffractometer (XRD, θ-2θ scan, ω-scan and ϕ-scan), X-ray photoelectron spectroscope (XPS), field emission scanning electron microscope (FESEM) and high resolution transmission electron microscope (HRTEM). The electric and magnetic properties of randomly and c-axis oriented LSMO/PZT films are studied comparably using ferroelectric testing apparatus and physical property measurement system (PPMS). It is found that the epitaxial LSMO/PZT composite films show well controlled growth along c-axis, and much bettermore » magnetoelectric properties than the randomly oriented ones. The ME voltage coefficient increases from 23 mV cm{sup −1} Oe{sup −1} for the randomly oriented LSMO/PZT composite films to 52 mV cm{sup −1} Oe{sup −1} for c-axis oriented ones prepared using the low cost sol-gel method presented in this study, which shows high potential in promising applications. - Highlights: •Epitaxial LSMO/PZT films were fabricated successfully by sol-gel method on LAO (00l) substrate. •The prepared films exhibit well-defined multiferroic properties for the epitaxial LSMO/PZT films. •Epitaxial LSMO/PZT films show superior magnetoelectric properties to the randomly oriented ones.« less

Cell Motility by Labile Association of Molecules

PubMed Central

Inoué, Shinya; Sato, Hidemi

1967-01-01

This article summarizes our current views on the dynamic structure of the mitotic spindle and its relation to mitotic chromosome movements. The following statements are based on measurements of birefringence of spindle fibers in living cells, normally developing or experimentally modified by various physical and chemical agents, including high and low temperatures, antimitotic drugs, heavy water, and ultraviolet microbeam irradiation. Data were also obtained concomitantly with electron microscopy employing a new fixative and through measurements of isolated spindle protein. Spindle fibers in living cells are labile dynamic structures whose constituent filaments (microtubules) undergo cyclic breakdown and reformation. The dynamic state is maintained by an equilibrium between a pool of protein molecules and their linearly aggregated polymers, which constitute the microtubules or filaments. In living cells under physiological conditions, the association of the molecules into polymers is very weak (absolute value of ΔF 25°C < 1 kcal), and the equilibrium is readily shifted to dissociation by low temperature or by high hydrostatic pressure. The equilibrium is shifted toward formation of polymer by increase in temperature (with a large increase in entropy: ΔS 25°C ≃ 100 eu) or by the addition of heavy water. The spindle proteins tend to polymerize with orienting centers as their geometrical foci. The centrioles, kinetochores, and cell plate act as orienting centers successively during mitosis. Filaments are more concentrated adjacent to an orienting center and yield higher birefringence. Astral rays, continuous fibers, chromosomal fibers, and phragmoplast fibers are thus formed by successive reorganization of the same protein molecules. During late prophase and metaphase, polymerization takes place predominantly at the kinetochores; in metaphase and anaphase, depolymerization is prevalent near the spindle poles. When the concentration of spindle protein is high, fusiform bundles of polymer are precipitated out even in the absence of obvious orienting centers. The shift of equilibrium from free protein molecules to polymer increases the length and number of the spindle microtubules or filaments. Slow depolymerization of the polymers, which can be brought about by low concentrations of colchicine or by gradual cooling, allows the filaments to shorten and perform work. The dynamic equilibrium controlled by orienting centers and other factors provides a plasusible mechanism by which chromosomes and other organelles, as well as the cell surface, are deformed or moved by temporarily organized arrays of microtubules or filaments. PMID:6058222

Scattering by randomly oriented ellipsoids: Application to aerosol and cloud problems

NASA Technical Reports Server (NTRS)

Asano, S.; Sato, M.; Hansen, J. E.

1979-01-01

A program was developed for computing the scattering and absorption by arbitrarily oriented and randomly oriented prolate and oblate spheroids. This permits examination of the effect of particle shape for cases ranging from needles through spheres to platelets. Applications of this capability to aerosol and cloud problems are discussed. Initial results suggest that the effect of nonspherical particle shape on transfer of radiation through aerosol layers and cirrus clouds, as required for many climate studies, can be readily accounted for by defining an appropriate effective spherical particle radius.

Enantiospecific electrodeposition of chiral CuO films on single-crystal Cu(111).

PubMed

Bohannan, Eric W; Kothari, Hiten M; Nicic, Igor M; Switzer, Jay A

2004-01-21

Epitaxial films of monoclinic CuO have been electrodeposited on single-crystal Cu(111) from solutions containing either (S,S)- or (R,R)-tartrate. X-ray pole figure analysis reveals that the CuO film grown from (S,S)-tartrate exhibits a (1) out-of-plane orientation while the film grown from (R,R)-tartrate has a (11) orientation. Even though CuO does not crystallize within a chiral space group, the orientations obtained exhibit a surface chirality similar to that obtained from high index fcc metal surfaces. The films were shown to be enantioselective toward the catalytic oxidation of tartrate molecules by cyclic voltammetry. The technique should prove to be applicable to the electrodeposition of chiral surfaces of other low-symmetry materials on achiral substrates and should prove to be of use to those interested in the synthesis, separation, and detection of chiral molecules.

Macroscopic ordering of helical pores for arraying guest molecules noncentrosymmetrically

PubMed Central

Li, Chunji; Cho, Joonil; Yamada, Kuniyo; Hashizume, Daisuke; Araoka, Fumito; Takezoe, Hideo; Aida, Takuzo; Ishida, Yasuhiro

2015-01-01

Helical nanostructures have attracted continuous attention, not only as media for chiral recognition and synthesis, but also as motifs for studying intriguing physical phenomena that never occur in centrosymmetric systems. To improve the quality of signals from these phenomena, which is a key issue for their further exploration, the most straightforward is the macroscopic orientation of helices. Here as a versatile scaffold to rationally construct this hardly accessible structure, we report a polymer framework with helical pores that unidirectionally orient over a large area (∼10 cm2). The framework, prepared by crosslinking a supramolecular liquid crystal preorganized in a magnetic field, is chemically robust, functionalized with carboxyl groups and capable of incorporating various basic or cationic guest molecules. When a nonlinear optical chromophore is incorporated in the framework, the resultant complex displays a markedly efficient nonlinear optical output, owing to the coherence of signals ensured by the macroscopically oriented helical structure. PMID:26416086

Orientation-dependent energy level alignment and film growth of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on HOPG

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

Lyu, Lu; Niu, Dongmei, E-mail: mayee@csu.edu.cnmailto; Xie, Haipeng

Combining ultraviolet photoemission spectroscopy, X-ray photoemission spectroscopy, atomic force microscopy, and X-ray diffraction measurements, we performed a systematic investigation on the correlation of energy level alignment, film growth, and molecular orientation of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on highly oriented pyrolytic graphite. The molecules lie down in the first layer and then stand up from the second layer. The ionization potential shows a sharp decrease from the lying down region to the standing up region. When C8-BTBT molecules start standing up, unconventional energy level band-bending-like shifts are observed as the film thickness increases. These shifts are ascribed to gradual decreasing of the molecularmore » tilt angle about the substrate normal with the increasing film thickness.« less

Theoretical description of the mixed-field orientation of asymmetric-top molecules: A time-dependent study

NASA Astrophysics Data System (ADS)

Omiste, Juan J.; González-Férez, Rosario

2016-12-01

We present a theoretical study of the mixed-field-orientation of asymmetric-top molecules in tilted static electric field and nonresonant linearly polarized laser pulse by solving the time-dependent Schrödinger equation. Within this framework, we compute the mixed-field orientation of a state-selected molecular beam of benzonitrile (C7H5N ) and compare with the experimental observations [J. L. Hansen et al., Phys. Rev. A 83, 023406 (2011), 10.1103/PhysRevA.83.023406] and with our previous time-independent descriptions [J. J. Omiste et al., Phys. Chem. Chem. Phys. 13, 18815 (2011), 10.1039/c1cp21195a]. For an excited rotational state, we investigate the field-dressed dynamics for several field configurations as those used in the mixed-field experiments. The nonadiabatic phenomena and their consequences on the rotational dynamics are analyzed in detail.

Modeling and simulation of Li-ion conduction in poly(ethylene oxide)

NASA Astrophysics Data System (ADS)

Gitelman, L.; Israeli, M.; Averbuch, A.; Nathan, M.; Schuss, Z.; Golodnitsky, D.

2007-12-01

Polyethylene oxide (PEO) containing a lithium salt (e.g., LiI) serves as a solid polymer electrolyte (SPE) in thin-film batteries and its ionic conductivity is a key parameter of their performance. We model and simulate Li + ion conduction in a single PEO molecule. Our simplified stochastic model of ionic motion is based on an analogy between protein channels of biological membranes that conduct Na +, K +, and other ions, and the PEO helical chain that conducts Li + ions. In contrast with protein channels and salt solutions, the PEO is both the channel and the solvent for the lithium salt (e.g., LiI). The mobile ions are treated as charged spherical Brownian particles. We simulate Smoluchowski dynamics in channels with a radius of ca. 0.1 nm and study the effect of stretching and temperature on ion conductivity. We assume that each helix (molecule) forms a random angle with the axis between these electrodes and the polymeric film is composed of many uniformly distributed oriented boxes that include molecules with the same direction. We further assume that mechanical stretching aligns the molecular structures in each box along the axis of stretching (intra-box alignment). Our model thus predicts the PEO conductivity as a function of the stretching, the salt concentration and the temperature. The computed enhancement of the ionic conductivity in the stretch direction is in good agreement with experimental results. The simulation results are also in qualitative agreement with recent theoretical and experimental results.

Children's Engagement and Competence in Personal Recollection: Effects of Parents' Reminiscing Goals

ERIC Educational Resources Information Center

Cleveland, Emily Sutcliffe; Reese, Elaine; Grolnick, Wendy S.

2007-01-01

Parents' goal orientations in parent-child reminiscing were examined in this study, where 28 preschoolers (mean age = 46 months) experienced a standardized event. Dyads discussed the event that evening, with parents randomly assigned to either an "outcome-oriented" or a "process-oriented" condition. Outcome-oriented parents, who were told that…

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

NASA Astrophysics Data System (ADS)

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

1994-07-01

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

IV INTERNATIONAL CONFERENCE ON ATOM AND MOLECULAR PULSED LASERS (AMPL'99): Spectral properties of optical anisotropy induced by laser radiation in dye solutions

NASA Astrophysics Data System (ADS)

Pikulik, L. G.; Chernyavskii, V. A.; Grib, A. F.

2000-06-01

Spectral studies of induced quasi-crystal properties (which can be quantitatively characterised by the difference in the refractive indices of ordinary and extraordinary waves, Δn=no—ne) in Rhodamine 6G and Rhodamine 4C solutions in glycerine excited in the visible and UV ranges of the absorption spectrum are presented. It is demonstrated that the observed spectral dependences of Δn of these dye solutions excited in the visible (long-wavelength) and UV (short-wavelength) ranges of the absorption spectrum can be interpreted in terms of an oscillator model of a molecule. The proposed method for the analysis of induced optical anisotropy in solutions of organic compounds allows the relative orientation of oscillators in a molecule and, thus, the relative orientation of electronic transitions in a molecule to be determined in a reliable way.

Chiral Asymmetric Structures in Aspartic Acid and Valine Crystals Assessed by Atomic Force Microscopy.

PubMed

Teschke, Omar; Soares, David Mendez

2016-03-29

Structures of crystallized deposits formed by the molecular self-assembly of aspartic acid and valine on silicon substrates were imaged by atomic force microscopy. Images of d- and l-aspartic acid crystal surfaces showing extended molecularly flat sheets or regions separated by single molecule thick steps are presented. Distinct orientation surfaces were imaged, which, combined with the single molecule step size, defines the geometry of the crystal. However, single molecule step growth also reveals the crystal chirality, i.e., growth orientations. The imaged ordered lattice of aspartic acid (asp) and valine (val) mostly revealed periodicities corresponding to bulk terminations, but a previously unreported molecular hexagonal lattice configuration was observed for both l-asp and l-val but not for d-asp or d-val. Atomic force microscopy can then be used to identify the different chiral forms of aspartic acid and valine crystals.

An all-electric single-molecule motor.

PubMed

Seldenthuis, Johannes S; Prins, Ferry; Thijssen, Joseph M; van der Zant, Herre S J

2010-11-23

Many types of molecular motors have been proposed and synthesized in recent years, displaying different kinds of motion, and fueled by different driving forces such as light, heat, or chemical reactions. We propose a new type of molecular motor based on electric field actuation and electric current detection of the rotational motion of a molecular dipole embedded in a three-terminal single-molecule device. The key aspect of this all-electronic design is the conjugated backbone of the molecule, which simultaneously provides the potential landscape of the rotor orientation and a real-time measure of that orientation through the modulation of the conductivity. Using quantum chemistry calculations, we show that this approach provides full control over the speed and continuity of motion, thereby combining electrical and mechanical control at the molecular level over a wide range of temperatures. Moreover, chemistry can be used to change all key parameters of the device, enabling a variety of new experiments on molecular motors.

Perfluoropentacene adsorption on Cu(110)

NASA Astrophysics Data System (ADS)

Gall, J.; Zhang, L.; Fu, X.; Zeppenfeld, P.; Sun, L. D.

2017-09-01

The adsorption of perfluoropentacene (PFP) on the Cu(110) surface has been investigated using reflectance difference spectroscopy (RDS), low-energy electron diffraction, and low-temperature scanning tunneling microscopy. The PFP molecules within the first monolayer align their long molecular axis exclusively oriented along the [001] azimuthal direction of the Cu substrate. In comparison with the adsorption behavior of pentacene on the same surface, a strong effect of the fluorination regarding the molecular orientation and the intermolecular and molecule-substrate interactions was identified. Furthermore, a two-dimensional gas-solid phase transition accompanied by a reversible azimuthal rotation of the PFP molecules was observed at the beginning of the second monolayer growth. The change of the optical anisotropy associated with this reorientation was used to explore the two-dimensional (2D) condensation as a function of coverage and temperature by RDS, and the 2D heat of condensation in the PFP bilayer on Cu(110) was determined to be 105 meV.

Diversity-oriented synthetic strategy for developing a chemical modulator of protein-protein interaction

NASA Astrophysics Data System (ADS)

Kim, Jonghoon; Jung, Jinjoo; Koo, Jaeyoung; Cho, Wansang; Lee, Won Seok; Kim, Chanwoo; Park, Wonwoo; Park, Seung Bum

2016-10-01

Diversity-oriented synthesis (DOS) can provide a collection of diverse and complex drug-like small molecules, which is critical in the development of new chemical probes for biological research of undruggable targets. However, the design and synthesis of small-molecule libraries with improved biological relevance as well as maximized molecular diversity represent a key challenge. Herein, we employ functional group-pairing strategy for the DOS of a chemical library containing privileged substructures, pyrimidodiazepine or pyrimidine moieties, as chemical navigators towards unexplored bioactive chemical space. To validate the utility of this DOS library, we identify a new small-molecule inhibitor of leucyl-tRNA synthetase-RagD protein-protein interaction, which regulates the amino acid-dependent activation of mechanistic target of rapamycin complex 1 signalling pathway. This work highlights that privileged substructure-based DOS strategy can be a powerful research tool for the construction of drug-like compounds to address challenging biological targets.

Molecular reorientation of a nematic liquid crystal by thermal expansion

PubMed Central

Kim, Young-Ki; Senyuk, Bohdan; Lavrentovich, Oleg D.

2012-01-01

A unique feature of nematic liquid crystals is orientational order of molecules that can be controlled by electromagnetic fields, surface modifications and pressure gradients. Here we demonstrate a new effect in which the orientation of nematic liquid crystal molecules is altered by thermal expansion. Thermal expansion (or contraction) causes the nematic liquid crystal to flow; the flow imposes a realigning torque on the nematic liquid crystal molecules and the optic axis. The optical and mechanical responses activated by a simple temperature change can be used in sensing, photonics, microfluidic, optofluidic and lab-on-a-chip applications as they do not require externally imposed gradients of temperature, pressure, surface realignment, nor electromagnetic fields. The effect has important ramifications for the current search of the biaxial nematic phase as the optical features of thermally induced structural changes in the uniaxial nematic liquid crystal mimic the features expected of the biaxial nematic liquid crystal. PMID:23072803

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

PubMed

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

2015-07-13

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

Modeling and Predicting the Stress Relaxation of Composites with Short and Randomly Oriented Fibers

PubMed Central

Obaid, Numaira; Sain, Mohini

2017-01-01

The addition of short fibers has been experimentally observed to slow the stress relaxation of viscoelastic polymers, producing a change in the relaxation time constant. Our recent study attributed this effect of fibers on stress relaxation behavior to the interfacial shear stress transfer at the fiber-matrix interface. This model explained the effect of fiber addition on stress relaxation without the need to postulate structural changes at the interface. In our previous study, we developed an analytical model for the effect of fully aligned short fibers, and the model predictions were successfully compared to finite element simulations. However, in most industrial applications of short-fiber composites, fibers are not aligned, and hence it is necessary to examine the time dependence of viscoelastic polymers containing randomly oriented short fibers. In this study, we propose an analytical model to predict the stress relaxation behavior of short-fiber composites where the fibers are randomly oriented. The model predictions were compared to results obtained from Monte Carlo finite element simulations, and good agreement between the two was observed. The analytical model provides an excellent tool to accurately predict the stress relaxation behavior of randomly oriented short-fiber composites. PMID:29053601

Face perception is tuned to horizontal orientation in the N170 time window.

PubMed

Jacques, Corentin; Schiltz, Christine; Goffaux, Valerie

2014-02-07

The specificity of face perception is thought to reside both in its dramatic vulnerability to picture-plane inversion and its strong reliance on horizontally oriented image content. Here we asked when in the visual processing stream face-specific perception is tuned to horizontal information. We measured the behavioral performance and scalp event-related potentials (ERP) when participants viewed upright and inverted images of faces and cars (and natural scenes) that were phase-randomized in a narrow orientation band centered either on vertical or horizontal orientation. For faces, the magnitude of the inversion effect (IE) on behavioral discrimination performance was significantly reduced for horizontally randomized compared to vertically or nonrandomized images, confirming the importance of horizontal information for the recruitment of face-specific processing. Inversion affected the processing of nonrandomized and vertically randomized faces early, in the N170 time window. In contrast, the magnitude of the N170 IE was much smaller for horizontally randomized faces. The present research indicates that the early face-specific neural representations are preferentially tuned to horizontal information and offers new perspectives for a description of the visual information feeding face-specific perception.

Molecular dynamics simulations on PGLa using NMR orientational constraints.

PubMed

Sternberg, Ulrich; Witter, Raiker

2015-11-01

NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.

Replica amplification of nucleic acid arrays

DOEpatents

Church, George M.

2002-01-01

A method of producing a plurality of a nucleic acid array, comprising, in order, the steps of amplifying in situ nucleic acid molecules of a first randomly-patterned, immobilized nucleic acid array comprising a heterogeneous pool of nucleic acid molecules affixed to a support, transferring at least a subset of the nucleic acid molecules produced by such amplifying to a second support, and affixing the subset so transferred to the second support to form a second randomly-patterned, immobilized nucleic acid array, wherein the nucleic acid molecules of the second array occupy positions that correspond to those of the nucleic acid molecules from which they were amplified on the first array, so that the first array serves as a template to produce a plurality, is disclosed.

V-Shaped Molecular Configuration of Wax Esters of Jojoba Oil in a Langmuir Film Model.

PubMed

Caruso, Benjamín; Martini, M Florencia; Pickholz, Mónica; Perillo, María A

2018-06-19

The aim of the present work was to understand the interfacial properties of a complex mixture of wax esters (WEs) obtained from Jojoba oil (JO). Previously, on the basis of molecular area measurements, a hairpin structure was proposed as the hypothetical configuration of WEs, allowing their organization as compressible monolayers at the air-water interface. In the present work, we contributed with further experimental evidence by combining surface pressure (π), surface potential (Δ V), and PM-IRRAS measurements of JO monolayers and molecular dynamic simulations (MD) on a modified JO model. WEs were self-assembled in Langmuir films. Compression isotherms exhibited π lift-off at 100 Å 2 /molecule mean molecular area ( A lift-off ) and a collapse point at π c ≈ 2.2 mN/m and A c ≈ 77 Å 2 /molecule. The Δ V profile reflected two dipolar reorganizations, with one of them at A > A lift-off due to the release of loosely bound water molecules and another one at A c < A < A lift-off possibly due to reorientations of a more tightly bound water population. This was consistent with the maximal SP value that was calculated according to a model that considered two populations of oriented water and was very close to the experimental value. The orientation of the ester group that was assumed in that calculation was coherent with the PM-IRRAS behavior of the carbonyl group with the C═O oriented toward the water and the C-O oriented parallel to the surface and was in accordance with their orientational angles (∼45 and ∼90°, respectively) determined by MD simulations. Taken together, the present results confirm a V shape rather than a hairpin configuration of WEs at the air-water interface.

Molecule signatures in photoluminescence spectra of transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Feierabend, Maja; Berghäuser, Gunnar; Selig, Malte; Brem, Samuel; Shegai, Timur; Eigler, Siegfried; Malic, Ermin

2018-01-01

Monolayer transition metal dichalcogenides (TMDs) show an optimal surface-to-volume ratio and are thus promising candidates for novel molecule sensor devices. It was recently predicted that a certain class of molecules exhibiting a large dipole moment can be detected through the activation of optically inaccessible (dark) excitonic states in absorption spectra of tungsten-based TMDs. In this paper, we investigate the molecule signatures in photoluminescence spectra in dependence of a number of different experimentally accessible quantities, such as excitation density, temperature, as well as molecular characteristics including the dipole moment and its orientation, molecule-TMD distance, molecular coverage, and distribution. We show that under certain optimal conditions even room-temperature detection of molecules can be achieved.

Diffusion of water in the endosperm tissue of wheat grains as studied by pulsed field gradient nuclear magnetic resonance.

PubMed

Callaghan, P T; Jolley, K W; Lelievre, J

1979-10-01

Pulsed field gradient nuclear magnetic resonance has been used to measure water self-diffusion coefficients in the endosperm tissue of wheat grains as a function of the tissue water content. A model that confines the water molecules to a randomly oriented array of capillaries with both transverse dimension less than 100 nm has been used to fit the data and give a unique diffusion coefficient at each water content. The diffusion rates vary from 1.8 x 10(-10) m2s-1 at the lowest to 1.2 x 10(-9) m2s-1 at the highest moisture content. This variation can be explained in terms of an increase in water film thickness from approximately 0.5 to approximately 2.5 nm over the moisture range investigated (200-360 mg g-1).

Liquid-Vapor Interfacial Properties of Aqueous Solutions of Guanidinium and Methyl Guanidinium Chloride: Influence of Molecular Orientation on Interface Fluctuations

PubMed Central

Ou, Shuching; Cui, Di; Patel, Sandeep

2014-01-01

The guanidinium cation (C(NH2)3+) is a highly stable cation in aqueous solution due to its efficient solvation by water molecules and resonance stabilization of the charge. Its salts increase the solubility of nonpolar molecules (”salting-in”) and decrease the ordering of water. It is one of the strongest denaturants used in biophysical studies of protein folding. We investigate the behavior of guanidinium and its derivative, methyl guanidinium (an amino acid analogue) at the air-water surface, using atomistic molecular dynamics (MD) simulations and calculation of potentials of mean force. Methyl guanidinium cation is less excluded from the air-water surface than guanidinium cation, but both cations show orientational dependence of surface affinity. Parallel orientations of the guanidinium ring (relative to the Gibbs dividing surface) show pronounced free energy minima in the interfacial region, while ring orientations perpendicular to the GDS exhibit no discernible surface stability. Calculations of surface fluctuations demonstrate that near the air-water surface, the parallel-oriented cations generate significantly greater interfacial fluctuations compared to other orientations, which induces more long-ranged perturbations and solvent density redistribution. Our results suggest a strong correlation with induced interfacial fluctuations and ion surface stability. These results have implications for interpreting molecular-level, mechanistic action of this osmolyte’s interaction with hydrophobic interfaces as they impact protein denaturation (solubilization). PMID:23937431

Fluorescence Imaging of Two-Photon Linear Dichroism: Cholesterol Depletion Disrupts Molecular Orientation in Cell Membranes

PubMed Central

Benninger, Richard K. P.; Önfelt, Björn; Neil, Mark A. A.; Davis, Daniel M.; French, Paul M. W.

2005-01-01

The plasma membrane of cells is an ordered environment, giving rise to anisotropic orientation and restricted motion of molecules and proteins residing in the membrane. At the same time as being an organized matrix of defined structure, the cell membrane is heterogeneous and dynamic. Here we present a method where we use fluorescence imaging of linear dichroism to measure the orientation of molecules relative to the cell membrane. By detecting linear dichroism as well as fluorescence anisotropy, the orientation parameters are separated from dynamic properties such as rotational diffusion and homo energy transfer (energy migration). The sensitivity of the technique is enhanced by using two-photon excitation for higher photo-selection compared to single photon excitation. We show here that we can accurately image lipid organization in whole cell membranes and in delicate structures such as membrane nanotubes connecting two cells. The speed of our wide-field imaging system makes it possible to image changes in orientation and anisotropy occurring on a subsecond timescale. This is demonstrated by time-lapse studies showing that cholesterol depletion rapidly disrupts the orientation of a fluorophore located within the hydrophobic region of the cell membrane but not of a surface bound probe. This is consistent with cholesterol having an important role in stabilizing and ordering the lipid tails within the plasma membrane. PMID:15520272

Nanostructured double-layer FeO as nanotemplate for tuning adsorption of titanyl phthalocyanine molecules

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

Lu, Shuangzan; University of Chinese Academy of Sciences, Beijing 100049; Qin, Zhihui, E-mail: zhqin@wipm.ac.cn

2014-06-23

The growth, structure of Pt(111) supported double-layer FeO and the adsorption of titanyl phthalocyanine (TiOPc) molecules with tunable site and orientation were presented. According to the atomic-resolution STM image, the structure was rationalized as (8√3 × 8√3) R30°/Pt(111) nanostructure constructed by Fe species coordinated with different number of oxygen on top of non-rotated (8 × 8) FeO /Pt(111) structure. Due to the modulation of the stacking of Fe atoms in the second layer relative to the O atoms in the second layer and the underlying layer, the interface and total dipole moment periodically vary within (8√3 × 8√3) R30°/Pt(111) structure. The resulted periodically distributed dipole-dipole interactionmore » benefits the growth of TiOPc molecules with area-selective sites and molecular orientations. Thus, this study provides a reliable method to govern the adsorption process of the polar molecules for potential applications in future functional molecular devices.« less

Visualization of the membrane engineering concept: evidence for the specific orientation of electroinserted antibodies and selective binding of target analytes.

PubMed

Kokla, Anna; Blouchos, Petros; Livaniou, Evangelia; Zikos, Christos; Kakabakos, Sotiris E; Petrou, Panagiota S; Kintzios, Spyridon

2013-12-01

Membrane engineering is a generic methodology for increasing the selectivity of a cell biosensor against a target molecule, by electroinserting target-specific receptor-like molecules on the cell surface. Previous studies have elucidated the biochemical aspects of the interaction between various analytes (including viruses) and their homologous membrane-engineered cells. In the present study, purified anti-biotin antibodies from a rabbit antiserum along with in-house prepared biotinylated bovine serum albumin (BSA) were used as a model antibody-antigen pair of molecules for facilitating membrane engineering experiments. It was proven, with the aid of fluorescence microscopy, that (i) membrane-engineered cells incorporated the specific antibodies in the correct orientation and that (ii) the inserted antibodies are selectively interacting with the homologous target molecules. This is the first time the actual working concept of membrane engineering has been visualized, thus providing a final proof of the concept behind this innovative process. In addition, the fluorescence microscopy measurements were highly correlated with bioelectric measurements done with the aid of a bioelectric recognition assay. Copyright © 2013 John Wiley & Sons, Ltd.

Molecular layers of ZnPc and FePc on Au(111) surface: Charge transfer and chemical interaction

NASA Astrophysics Data System (ADS)

Ahmadi, Sareh; Shariati, M. Nina; Yu, Shun; Göthelid, Mats

2012-08-01

We have studied zinc phthalocyanine (ZnPc) and iron phthalocyanine (FePc) thick films and monolayers on Au(111) using photoelectron spectroscopy and x-ray absorption spectroscopy. Both molecules are adsorbed flat on the surface at monolayer. ZnPc keeps this orientation in all investigated coverages, whereas FePc molecules stand up in the thick film. The stronger inter-molecular interaction of FePc molecules leads to change of orientation, as well as higher conductivity in FePc layer in comparison with ZnPc, which is reflected in thickness-dependent differences in core-level shifts. Work function changes indicate that both molecules donate charge to Au; through the π-system. However, the Fe3d derived lowest unoccupied molecular orbital receives charge from the substrate when forming an interface state at the Fermi level. Thus, the central atom plays an important role in mediating the charge, but the charge transfer as a whole is a balance between the two different charge transfer channels; π-system and the central atom.

Low-temperature matrix effects on orientational motion of Methyl radical trapped in gas solids: Angular tunneling vs. libration

NASA Astrophysics Data System (ADS)

Dmitriev, Yurij A.; Zelenetckii, Ilia A.; Benetis, Nikolas P.

2018-05-01

EPR investigation of the lineshape of matrix -isolated methyl radical, CH3, spectra recorded in solid N2O and CO2 was carried out. Reversible temperature-dependent line width anisotropy was observed in both matrices. This effect is a fingerprint of the extra-slow radical rotation about the in-plane C2 axes. The rotation was found to be anisotropic and closely correlated to the orientational dynamics of the matrix molecules. It was suggested that a recently discovered "hoping precession" effect of matrix molecules in solid CO2 is a common feature of matrices of the linear molecules CO, N2O, and CO2. A new low-temperature matrix effect, referred to as "libration trap", was proposed which accounts for the changing CH3 reorientational motion about the radical C3-axis from rotation to libration. Temperature dependence of the intensity of the EPR satellites produced by these nonrotating-but librating methyls was presented. This allowed for a rough estimation of the rotation hindering potential due to correlation mismatch between the radical and the nearest matrix molecules' librations.

Amphiphile-Induced Reorganization of Nematic Liquid Crystals at Aqueous Interfaces

NASA Astrophysics Data System (ADS)

Rahimi, Amin; Ramezani-Dakhel, Hadi; Pendery, Joel; Abbott, Nicholas; de Pablo, Juan; Juan de Pablo Team, Prof; Nicholas Abbott Collaboration, Prof

Recent studies have shown that ordering transitions in 4-cyano-4'-pentylbiphenyl (5CB) molecules can be triggered by the self-assembly of specific amphiphiles near a flat aqueous-LC interface. In the absence of adsorbed amphiphiles, LC molecules adopt a parallel orientation at the aqueous interface. Self-assembly of amphiphile molecules at the LC-aqueous interface triggers a spontaneous reorientation of the LC at the aqueous interface. A number of observations indicate that the hydrophilic headgroup of the surfactant has marginal effect on the orientation of 5CB whereas the aliphatic tail structure, length, and conformation greatly affect the ordering of the LC. The structural reorganization of liquid crystals at aqueous interfaces has been primarily ascribed to a weakening of the surface anchoring strength induced by amphiphile molecules. Such explanations, however, have only been supported by a posteriorimicroscopic observations. The underlying mechanism of such an ordering transition and the effect of amphiphile structure remain poorly understood. Here, we study the nature of molecular interactions between amphiphiles, 5CB, and water to understand the mechanism of ordering transitions using atomistic molecular dynamics simulations.

A molecular dynamics study of the effect of thermal boundary conductance on thermal transport of ideal crystal of n-alkanes with different number of carbon atoms

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

Rastgarkafshgarkolaei, Rouzbeh; Zeng, Yi; Khodadadi, J. M., E-mail: khodajm@auburn.edu

2016-05-28

Phase change materials such as n-alkanes that exhibit desirable characteristics such as high latent heat, chemical stability, and negligible supercooling are widely used in thermal energy storage applications. However, n-alkanes have the drawback of low thermal conductivity values. The low thermal conductivity of n-alkanes is linked to formation of randomly oriented nano-domains of molecules in their solid structure that is responsible for excessive phonon scattering at the grain boundaries. Thus, understanding the thermal boundary conductance at the grain boundaries can be crucial for improving the effectiveness of thermal storage systems. The concept of the ideal crystal is proposed in thismore » paper, which describes a simplified model such that all the nano-domains of long-chain n-alkanes are artificially aligned perfectly in one direction. In order to study thermal transport of the ideal crystal of long-chain n-alkanes, four (4) systems (C{sub 20}H{sub 42}, C{sub 24}H{sub 50}, C{sub 26}H{sub 54}, and C{sub 30}H{sub 62}) are investigated by the molecular dynamics simulations. Thermal boundary conductance between the layers of ideal crystals is determined using both non-equilibrium molecular dynamics (NEMD) and equilibrium molecular dynamics (EMD) simulations. Both NEMD and EMD simulations exhibit no significant change in thermal conductance with the molecular length. However, the values obtained from the EMD simulations are less than the values from NEMD simulations with the ratio being nearly three (3) in most cases. This difference is due to the nature of EMD simulations where all the phonons are assumed to be in equilibrium at the interface. Thermal conductivity of the n-alkanes in three structures including liquid, solid, and ideal crystal is investigated utilizing NEMD simulations. Our results exhibit a very slight rise in thermal conductivity values as the number of carbon atoms of the chain increases. The key understanding is that thermal transport can be significantly altered by how the molecules and the nano-domains are oriented in the structure rather than by the length of the n-alkane molecules.« less

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

PubMed

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.

Flake Orientation Effects On Physical and Mechanical Properties of Sweetgum Flakeboard

Treesearch

T.F. Shupe; Chung-Yun Hse; E.W. Price

2001-01-01

Research was initiated to determine the effect of flake orientation on the physical and mechanical properties offlakeboard. The panel fabrication techniques investigated were single-layer panels with random and oriented flake distribution, three-layer, five-layer, and seven-layer panels. Single-layer oriented panels had panel directional property ratios of 11.8 and 12....

Scattering from randomly oriented circular discs with application to vegetation

NASA Technical Reports Server (NTRS)

Karam, M. A.; Fung, A. K.

1984-01-01

A vegetation layer is modeled by a collection of randomly oriented circular discs over a half space. The backscattering coefficient from such a half space is computed using the radiative transfer theory. It is shown that significantly different results are obtained from this theory as compared with some earlier investigations using the same modeling approach but with restricted disc orientations. In particular, the backscattered cross polarized returns cannot have a fast increasing angular trend which is inconsistent with measurements. By setting the appropriate angle of orientation to zero the theory reduces to previously published results. Comparisons are shown with measurements taken from milo, corn and wheat and good agreements are obtained for both polarized and cross polarized returns.

Scattering from randomly oriented circular discs with application to vegetation

NASA Technical Reports Server (NTRS)

Karam, M. A.; Fung, A. K.

1983-01-01

A vegetation layer is modeled by a collection of randomly oriented circular discs over a half space. The backscattering coefficient from such a half space is computed using the radiative transfer theory. It is shown that significantly different results are obtained from this theory as compared with some earlier investigations using the same modeling approach but with restricted disc orientations. In particular, the backscattered cross-polarized returns cannot have a fast increasing angular trend which is inconsistent with measurements. By setting the appropriate angle of orientation to zero the theory reduces to previously published results. Comparisons are shown with measurements taken from milo, corn and wheat and good agreements are obtained for both polarized and cross-polarized returns.

Collisional Transfer of Population and Orientation in NaK

NASA Astrophysics Data System (ADS)

Wolfe, C. M.; Ashman, S.; Huennekens, J.; Beser, B.; Bai, J.; Lyyra, A. M.

2010-03-01

We report current work to study transfer of population and orientation in collisions of NaK molecules with argon and potassium atoms using polarization labeling (PL) and laser- induced fluorescence (LIF) spectroscopy. In the PL experiment, a circularly polarized pump laser excites a specific NaK A^1&+circ;(v'=16, J') <- X^1&+circ;(v''=0, J'±1) transition, creating an orientation (non-uniform MJ' level distribution) in both levels. The linearly polarized probe laser is scanned over various 3^1π(v, J'±1) <- A^1&+circ;(v'=16, J') transitions. The probe laser passes through a crossed linear polarizer before detection, and signal is recorded if the probe laser polarization has been modified by the vapor (which occurs when it comes into resonance with an oriented level). Using both spectroscopic methods, analysis of weak collisional satellite lines adjacent to these directly populated lines, as a function of argon buffer gas pressure and cell temperature, allows us to discern separately the effects collisions with argon atoms and potassium atoms have on the population and orientation of the molecule. In addition, code has been written which provides a theoretical analysis of the process, through a solution of the density matrix equations of motion for the system.

Estimating the distance separating fluorescent protein FRET pairs

PubMed Central

van der Meer, B. Wieb; Blank, Paul S.

2014-01-01

Förster resonance energy transfer (FRET) describes a physical phenomenon widely applied in biomedical research to estimate separations between biological molecules. Routinely, genetic engineering is used to incorporate spectral variants of the green fluorescent protein (GFPs), into cellular expressed proteins. The transfer efficiency or rate of energy transfer between donor and acceptor FPs is then assayed. As appreciable FRET occurs only when donors and acceptors are in close proximity (1–10 nm), the presence of FRET may indicate that the engineered proteins associate as interacting species. For a homogeneous population of FRET pairs the separations between FRET donors and acceptors can be estimated from a measured FRET efficiency if it is assumed that donors and acceptors are randomly oriented and rotate extensively during their excited state (dynamic regime). Unlike typical organic fluorophores, the rotational correlation-times of FPs are typically much longer than their fluorescence lifetime; accordingly FPs are virtually static during their excited state. Thus, estimating separations between FP FRET pairs is problematic. To overcome this obstacle, we present here a simple method for estimating separations between FPs using the experimentally measured average FRET efficiency. This approach assumes that donor and acceptor fluorophores are randomly oriented, but do not rotate during their excited state (static regime). This approach utilizes a Monte-Carlo simulation generated look-up table that allows one to estimate the separation, normalized to the Förster distance, from the average FRET efficiency. Assuming a dynamic regime overestimates the separation significantly (by 10% near 0.5 and 30% near 0.75 efficiencies) compared to assuming a static regime, which is more appropriate for estimates of separations between FPs. PMID:23811334

Have You Been Oriented? An Analysis of New Student Orientation and E-Orientation Programs at U.S. Community Colleges

ERIC Educational Resources Information Center

Chan, Matthew

2017-01-01

This study provides an overview and a snapshot of new student orientation (NSO) and new student e-orientation (NSEO) programs, with a focus on the content and feature analysis of the NSEOs. It offers an overview of currently available NSO programs of 100 randomly selected community colleges from a master list of nearly 900 community colleges in…

Self-organization of gold nanoparticles on silanated surfaces.

PubMed

Kyaw, Htet H; Al-Harthi, Salim H; Sellai, Azzouz; Dutta, Joydeep

2015-01-01

The self-organization of monolayer gold nanoparticles (AuNPs) on 3-aminopropyltriethoxysilane (APTES)-functionalized glass substrate is reported. The orientation of APTES molecules on glass substrates plays an important role in the interaction between AuNPs and APTES molecules on the glass substrates. Different orientations of APTES affect the self-organization of AuNps on APTES-functionalized glass substrates. The as grown monolayers and films annealed in ultrahigh vacuum and air (600 °C) were studied by water contact angle measurements, atomic force microscopy, X-ray photoelectron spectroscopy, UV-visible spectroscopy and ultraviolet photoelectron spectroscopy. Results of this study are fundamentally important and also can be applied for designing and modelling of surface plasmon resonance based sensor applications.

Random Walks on a Simple Cubic Lattice, the Multinomial Theorem, and Configurational Properties of Polymers

ERIC Educational Resources Information Center

Hladky, Paul W.

2007-01-01

Random-climb models enable undergraduate chemistry students to visualize polymer molecules, quantify their configurational properties, and relate molecular structure to a variety of physical properties. The model could serve as an introduction to more elaborate models of polymer molecules and could help in learning topics such as lattice models of…

Constitutive Modeling of Nanotube-Reinforced Polymer Composites

NASA Technical Reports Server (NTRS)

Odegard, G. M.; Gates, T. S.; Wise, K. E.

2002-01-01

In this study, a technique is presented for developing constitutive models for polymer composite systems reinforced with single-walled carbon nanotubes (SWNT). Because the polymer molecules are on the same size scale as the nanotubes, the interaction at the polymer/nanotube interface is highly dependent on the local molecular structure and bonding. At these small length scales, the lattice structures of the nanotube and polymer chains cannot be considered continuous, and the bulk mechanical properties can no longer be determined through traditional micromechanical approaches that are formulated by using continuum mechanics. It is proposed herein that the nanotube, the local polymer near the nanotube, and the nanotube/polymer interface can be modeled as an effective continuum fiber using an equivalent-continuum modeling method. The effective fiber serves as a means for incorporating micromechanical analyses for the prediction of bulk mechanical properties of SWNT/polymer composites with various nanotube shapes, sizes, concentrations, and orientations. As an example, the proposed approach is used for the constitutive modeling of two SWNT/LaRC-SI (with a PmPV interface) composite systems, one with aligned SWNTs and the other with three-dimensionally randomly oriented SWNTs. The Young's modulus and shear modulus have been calculated for the two systems for various nanotube lengths and volume fractions.

Electromagnetic wave extinction within a forested canopy

NASA Technical Reports Server (NTRS)

Karam, M. A.; Fung, A. K.

1989-01-01

A forested canopy is modeled by a collection of randomly oriented finite-length cylinders shaded by randomly oriented and distributed disk- or needle-shaped leaves. For a plane wave exciting the forested canopy, the extinction coefficient is formulated in terms of the extinction cross sections (ECSs) in the local frame of each forest component and the Eulerian angles of orientation (used to describe the orientation of each component). The ECSs in the local frame for the finite-length cylinders used to model the branches are obtained by using the forward-scattering theorem. ECSs in the local frame for the disk- and needle-shaped leaves are obtained by the summation of the absorption and scattering cross-sections. The behavior of the extinction coefficients with the incidence angle is investigated numerically for both deciduous and coniferous forest. The dependencies of the extinction coefficients on the orientation of the leaves are illustrated numerically.

Random waves in the brain: Symmetries and defect generation in the visual cortex

NASA Astrophysics Data System (ADS)

Schnabel, M.; Kaschube, M.; Löwel, S.; Wolf, F.

2007-06-01

How orientation maps in the visual cortex of the brain develop is a matter of long standing debate. Experimental and theoretical evidence suggests that their development represents an activity-dependent self-organization process. Theoretical analysis [1] exploring this hypothesis predicted that maps at an early developmental stage are realizations of Gaussian random fields exhibiting a rigorous lower bound for their densities of topological defects, called pinwheels. As a consequence, lower pinwheel densities, if observed in adult animals, are predicted to develop through the motion and annihilation of pinwheel pairs. Despite of being valid for a large class of developmental models this result depends on the symmetries of the models and thus of the predicted random field ensembles. In [1] invariance of the orientation map's statistical properties under independent space rotations and orientation shifts was assumed. However, full rotation symmetry appears to be broken by interactions of cortical neurons, e.g. selective couplings between groups of neurons with collinear orientation preferences [2]. A recently proposed new symmetry, called shift-twist symmetry [3], stating that spatial rotations have to occur together with orientation shifts in order to be an appropriate symmetry transformation, is more consistent with this organization. Here we generalize our random field approach to this important symmetry class. We propose a new class of shift-twist symmetric Gaussian random fields and derive the general correlation functions of this ensemble. It turns out that despite strong effects of the shift-twist symmetry on the structure of the correlation functions and on the map layout the lower bound on the pinwheel densities remains unaffected, predicting pinwheel annihilation in systems with low pinwheel densities.

Heterogeneous nucleation of polymorphs on polymer surfaces: polymer-molecule interactions using a heterogeneous dielectric solvation model.

PubMed

Wahlberg, Nanna; Madsen, Anders Ø; Mikkelsen, Kurt V

2018-06-09

We have investigated the mechanism of the nucleation of acetaminophen on poly(methyl-methacrylate) and poly(vinyl-acetate) utilizing a combination of quantum mechanical computations and electrostatic models. We have used a heterogeneous dielectric solvation model to determine the stability of different orientations of acetaminophen on polymer surfaces. We find that for the nucleation of acetaminophen on the polymer surfaces in vacuum, the most stable orientation is a flat orientation. For the nucleation process in solution where acetaminophen and the polymer surface are surrounded by a solvent, we find that the heterogeneous dielectric solvation model predicts that a sideways orientation is the most stable orientation.

Chromosome Gene Orientation Inversion Networks (GOINs) of Plasmodium Proteome.

PubMed

Quevedo-Tumailli, Viviana F; Ortega-Tenezaca, Bernabé; González-Díaz, Humbert

2018-03-02

The spatial distribution of genes in chromosomes seems not to be random. For instance, only 10% of genes are transcribed from bidirectional promoters in humans, and many more are organized into larger clusters. This raises intriguing questions previously asked by different authors. We would like to add a few more questions in this context, related to gene orientation inversions. Does gene orientation (inversion) follow a random pattern? Is it relevant to biological activity somehow? We define a new kind of network coined as the gene orientation inversion network (GOIN). GOIN's complex network encodes short- and long-range patterns of inversion of the orientation of pairs of gene in the chromosome. We selected Plasmodium falciparum as a case of study due to the high relevance of this parasite to public health (causal agent of malaria). We constructed here for the first time all of the GOINs for the genome of this parasite. These networks have an average of 383 nodes (genes in one chromosome) and 1314 links (pairs of gene with inverse orientation). We calculated node centralities and other parameters of these networks. These numerical parameters were used to study different properties of gene inversion patterns, for example, distribution, local communities, similarity to Erdös-Rényi random networks, randomness, and so on. We find clues that seem to indicate that gene orientation inversion does not follow a random pattern. We noted that some gene communities in the GOINs tend to group genes encoding for RIFIN-related proteins in the proteome of the parasite. RIFIN-like proteins are a second family of clonally variant proteins expressed on the surface of red cells infected with Plasmodium falciparum. Consequently, we used these centralities as input of machine learning (ML) models to predict the RIFIN-like activity of 5365 proteins in the proteome of Plasmodium sp. The best linear ML model found discriminates RIFIN-like from other proteins with sensitivity and specificity 70-80% in training and external validation series. All of these results may point to a possible biological relevance of gene orientation inversion not directly dependent on genetic sequence information. This work opens the gate to the use of GOINs as a tool for the study of the structure of chromosomes and the study of protein function in proteome research.

Micropatterning stretched and aligned DNA using microfluidics and surface patterning for applications in hybridization-mediated templated assembly of nanostructures

NASA Astrophysics Data System (ADS)

Carbeck, Jeffrey; Petit, Cecilia

2004-03-01

Current efforts in nanotechnology use one of two basic approaches: top-down fabrication and bottom-up assembly. Top-down strategies use lithography and contact printing to create patterned surfaces and microfluidic channels that, in turn, can corral and organize nanoscale structures. Bottom-up approaches use templates to direct the assembly of atoms, molecules, and nanoparticles through molecular recognition. The goal of this work is to integrate these strategies by first patterning and orienting DNA molecules through top-down tools so that single DNA chains can then serve as templates for the bottom-up construction of hetero-structures composed of proteins and nanoparticles, both metallic and semi-conducting. The first part of this talk focuses on the top-down strategies used to create microscopic patterns of stretched and aligned molecules of DNA. Specifically, it presents a new method in which molecular combing -- a process by which molecules are deposited and stretched onto a surface by the passage of an air-water interface -- is performed in microchannels. This approach demonstrates that the shape and motion of this interface serve as an effective local field directing the chains dynamically as they are stretched onto the surface. The geometry of the microchannel directs the placement of the DNA molecules, while the geometry of the air-water interface directs the local orientation and curvature of the molecules. This ability to control both the placement and orientation of chains has implication for the use of this technique in genetic analysis and in the bottom up approach to nanofabrication.The second half of this talk presents our bottom-up strategy, which allows placement of nanoparticles along individual DNA chains with a theoretical resolution of less than 1 nm. Specifically, we demonstrate the sequence-specific patterning of nanoparticles via the hybridization of functionalized complementary probes to surface-bound chains of double-stranded DNA. Using this technique, we demonstrate the ability to assemble metals, semiconductors, and a composite of both on a single molecule.

Electroactive BaTiO3 nanoparticle-functionalized fibrous scaffolds enhance osteogenic differentiation of mesenchymal stem cells

PubMed Central

Li, Yiping; Dai, Xiaohan; Bai, Yunyang; Liu, Yun; Wang, Yuehong; Liu, Ousheng; Yan, Fei; Tang, Zhangui; Zhang, Xuehui; Deng, Xuliang

2017-01-01

It has been proven that the surface topographic cues of fiber arrangement can induce osteogenic differentiation of mesenchymal stem cells. However, this effect alone is weak and insufficient to meet the needs of regenerative medicine. In this work, electroactivity concept was introduced to enhance the osteoinductivity of fibrous scaffolds. The randomly oriented and aligned electroactive fibrous scaffolds of poly-(l-lactic acid) (PLLA) with incorporation of ferroelectric ceramic BaTiO3 (BTO) nanoparticles (NPs) were fabricated by electrospinning. Physicochemical properties, including fiber morphology, microstructure, composition, thermal stability, surface roughness, and surface wettability, of these fibrous scaffolds were studied. The dielectric properties of the scaffolds were evaluated. The results showed that the randomly oriented BTO/PLLA composite fibrous scaffolds had the highest dielectric permittivity of 1.19, which is of the same order of magnitude as the natural bone. The combined effects of fiber orientation and electrical activity on the osteogenic responses of bone marrow mesenchymal stem cells (BM-MSCs) were specifically investigated. Randomly oriented composite fibrous scaffolds significantly promoted polygonal spreading and encouraged early osteogenic differentiation in BM-MSCs, whereas aligned composite fibrous scaffolds promoted cell elongation and discouraged osteogenic differentiation. These results evidenced that randomly fiber orientation and biomimetic electric activity have combining effects on osteogenic differentiation of BM-MSCs. Our findings indicate that coupling effects of multi-physical properties should be paid more attention to mimic the microenvironment for enhancing osteogenic differentiation of BM-MSCs. PMID:28603415

Computational Modeling | Bioenergy | NREL

Science.gov Websites

molecules dissociates and an H-H pair is formed. The atomic structure of state 3 is shown in the lower inset -dissociation of the first H2 molecule. The structure and partial charge density (at the highest occupied band depicted by the illustration to the left determined the structure and binding orientation of several

Spectral assignment and orientational analysis in a vibrational sum frequency generation study of DPPC monolayers at the air/water interface

NASA Astrophysics Data System (ADS)

Feng, Rong-Juan; Li, Xia; Zhang, Zhen; Lu, Zhou; Guo, Yuan

2016-12-01

The interfacial behavior of the benchmark zwitterionic phospholipid molecule dipalmitoylphosphatidylcholine (DPPC) has been extensively investigated by surface-selective vibrational sum frequency generation spectroscopy (VSFG). However, there is still a lack of agreement between various orientational measurements of phospholipid monolayers at the air/water interface, mainly because of the difficulty in assigning congested VSFG features. In this study, polarization-dependent VSFG measurements reveal a frequency shift between the in-plane and out-of-plane antisymmetric stretching modes of the terminal methyl groups in the DPPC alkyl tails, favoring the model of Cs local symmetry rather than the previously assumed C3v symmetry. Further VSFG experiments of isotopically labeled DPPC successfully capture the vibrational signatures of the glycerol backbone. With the newly derived VSFG polarization selection rules for Cs symmetry and the refreshed spectral assignments, the average tilt angles of the alkyl tail groups, choline headgroup, and glycerol backbone of DPPC molecules can all be determined, showing the powerful capability of VSFG spectroscopy in revealing the structural details at interfaces. The VSFG polarization dependence rules and the orientational analysis procedures developed for Cs symmetry in this work are applicable to other bulky molecules in which the methyl group cannot freely rotate, and they therefore have general applications in future VSFG studies.

A special method for analyzing anisotropic nuclear magnetic resonance parameters: Acetonitrile in liquid crystals

NASA Astrophysics Data System (ADS)

Lounila, Juhani; Ala-Korpela, Mika; Jokisaari, Jukka

1990-12-01

A reliable analysis of the nuclear magnetic resonance (NMR) spectral parameters of partially oriented molecules requires the calculation of the effects of the correlation between the molecular vibration and rotation. However, in many cases the information content of the spectral data is not sufficient for an unambiguous determination of all the adjustable parameters involved in such an analysis. The present paper describes a special method to simplify the analysis significantly, so as to make seemingly underdetermined problems solvable. The method is applicable to the molecules which contain segments composed of one or more light bonds attached to a heavier bond. It is applied to the anisotropic couplings Dij of acetonitrile (CH3CN) oriented in various liquid crystals. The analysis leads to the following rα geometry: ∠HCH=109.22°±0.06°, rCH/rCC =0.751±0.002 and rCN/rCC =0.788±0.005. In addition, detailed information on (1) the indirect coupling anisotropies ΔJCC and 2ΔJCN, (2) the 1H and 13C chemical shift anisotropies, (3) the external torques acting on the CH bonds, and (4) the orientational order parameters of the CH3C segment of the acetonitrile molecule is obtained.

Field-free molecular orientation of nonadiabatically aligned OCS

NASA Astrophysics Data System (ADS)

Sonoda, Kotaro; Iwasaki, Atsushi; Yamanouchi, Kaoru; Hasegawa, Hirokazu

2018-02-01

We investigate an enhancement of the orientation of OCS molecules by irradiating them with a near IR (ω) ultrashort laser pulse for alignment followed by another ultrashort laser pulse for orientation, which is synthesized by a phase-locked coherent superposition of the near IR laser pulse and its second harmonic (2ω). On the basis of the asymmetry in the ejection direction of S3+ fragment ions generated by the Coulomb explosion of multiply charged OCS, we show that the extent of the orientation of OCS is significantly enhanced when the delay between the alignment pulse and the orientation pulse is a quarter or three quarters of the rotational period. The recorded enhanced orientation was interpreted well by a numerical simulation of the temporal evolution of a rotational wave packet prepared by the alignment and orientation pulses.

Method for in vitro recombination

DOEpatents

Gibson, Daniel Glenn; Smith, Hamilton O

2013-05-07

The present invention relates to an in vitro method, using isolated protein reagents, for joining two double-stranded (ds) DNA molecules of interest, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule share a region of sequence identity. The method allows the joining of a number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes. It can be used, e.g., to join synthetically produced sub-fragments of a gene or genome of interest.

Viewpoint 9--molecular structure of aqueous interfaces

NASA Technical Reports Server (NTRS)

Pohorille, A.; Wilson, M. A.

1993-01-01

In this review we summarize recent progress in our understanding of the structure of aqueous interfaces emerging from molecular level computer simulations. It is emphasized that the presence of the interface induces specific structural effects which, in turn, influence a wide variety of phenomena occurring near the phase boundaries. At the liquid-vapor interface, the most probable orientations of a water molecule is such that its dipole moment lies parallel to the interface, one O-H bond points toward the vapor and the other O-H bond is directed toward the liquid. The orientational distributions are broad and slightly asymmetric, resulting in an excess dipole moment pointing toward the liquid. These structural preferences persist at interfaces between water and nonpolar liquids, indicating that the interactions between the two liquids in contact are weak. It was found that liquid-liquid interfaces are locally sharp but broadened by capillary waves. One consequence of anisotropic orientations of interfacial water molecules is asymmetric interactions, with respect to the sign of the charge, of ions with the water surface. It was found that even very close to the surface ions retain their hydration shells. New features of aqueous interfaces have been revealed in studies of water-membrane and water-monolayer systems. In particular, water molecules are strongly oriented by the polar head groups of the amphiphilic phase, and they penetrate the hydrophilic head-group region, but not the hydrophobic core. At infinite dilution near interfaces, amphiphilic molecules exhibit behavior different from that in the gas phase or in bulk water. This result sheds new light on the nature of hydrophobic effect in the interfacial regions. The presence of interfaces was also shown to affect both equilibrium and dynamic components of rates of chemical reactions. Applications of continuum models to interfacial problems have been, so far, unsuccessful. This, again, underscores the importance of molecular-level information about interfaces.

Expert Design Advisor

DTIC Science & Technology

1990-10-01

to economic, technological, spatial or logistic concerns, or involve training, man-machine interfaces, or integration into existing systems. Once the...probabilistic reasoning, mixed analysis- and simulation-oriented, mixed computation- and communication-oriented, nonpreemptive static priority...scheduling base, nonrandomized, preemptive static priority scheduling base, randomized, simulation-oriented, and static scheduling base. The selection of both

Orienting apples for imaging using their inertial properties and random apple loading

USDA-ARS?s Scientific Manuscript database

The inability to control apple orientation during imaging has hindered development of automated systems for sorting apples for defects such as bruises and for safety issues such as fecal contamination. Recently, a potential method for orienting apples based on their inertial properties was discovere...

Topographic Independent Component Analysis reveals random scrambling of orientation in visual space

PubMed Central

Martinez-Garcia, Marina; Martinez, Luis M.

2017-01-01

Neurons at primary visual cortex (V1) in humans and other species are edge filters organized in orientation maps. In these maps, neurons with similar orientation preference are clustered together in iso-orientation domains. These maps have two fundamental properties: (1) retinotopy, i.e. correspondence between displacements at the image space and displacements at the cortical surface, and (2) a trade-off between good coverage of the visual field with all orientations and continuity of iso-orientation domains in the cortical space. There is an active debate on the origin of these locally continuous maps. While most of the existing descriptions take purely geometric/mechanistic approaches which disregard the network function, a clear exception to this trend in the literature is the original approach of Hyvärinen and Hoyer based on infomax and Topographic Independent Component Analysis (TICA). Although TICA successfully addresses a number of other properties of V1 simple and complex cells, in this work we question the validity of the orientation maps obtained from TICA. We argue that the maps predicted by TICA can be analyzed in the retinal space, and when doing so, it is apparent that they lack the required continuity and retinotopy. Here we show that in the orientation maps reported in the TICA literature it is easy to find examples of violation of the continuity between similarly tuned mechanisms in the retinal space, which suggest a random scrambling incompatible with the maps in primates. The new experiments in the retinal space presented here confirm this guess: TICA basis vectors actually follow a random salt-and-pepper organization back in the image space. Therefore, the interesting clusters found in the TICA topology cannot be interpreted as the actual cortical orientation maps found in cats, primates or humans. In conclusion, Topographic ICA does not reproduce cortical orientation maps. PMID:28640816

Topographic Independent Component Analysis reveals random scrambling of orientation in visual space.

PubMed

Martinez-Garcia, Marina; Martinez, Luis M; Malo, Jesús

2017-01-01

Neurons at primary visual cortex (V1) in humans and other species are edge filters organized in orientation maps. In these maps, neurons with similar orientation preference are clustered together in iso-orientation domains. These maps have two fundamental properties: (1) retinotopy, i.e. correspondence between displacements at the image space and displacements at the cortical surface, and (2) a trade-off between good coverage of the visual field with all orientations and continuity of iso-orientation domains in the cortical space. There is an active debate on the origin of these locally continuous maps. While most of the existing descriptions take purely geometric/mechanistic approaches which disregard the network function, a clear exception to this trend in the literature is the original approach of Hyvärinen and Hoyer based on infomax and Topographic Independent Component Analysis (TICA). Although TICA successfully addresses a number of other properties of V1 simple and complex cells, in this work we question the validity of the orientation maps obtained from TICA. We argue that the maps predicted by TICA can be analyzed in the retinal space, and when doing so, it is apparent that they lack the required continuity and retinotopy. Here we show that in the orientation maps reported in the TICA literature it is easy to find examples of violation of the continuity between similarly tuned mechanisms in the retinal space, which suggest a random scrambling incompatible with the maps in primates. The new experiments in the retinal space presented here confirm this guess: TICA basis vectors actually follow a random salt-and-pepper organization back in the image space. Therefore, the interesting clusters found in the TICA topology cannot be interpreted as the actual cortical orientation maps found in cats, primates or humans. In conclusion, Topographic ICA does not reproduce cortical orientation maps.

Liquid crystalline ordering and charge transport in semiconducting materials.

PubMed

Pisula, Wojciech; Zorn, Matthias; Chang, Ji Young; Müllen, Klaus; Zentel, Rudolf

2009-07-16

Organic semiconducting materials offer the advantage of solution processability into flexible films. In most cases, their drawback is based on their low charge carrier mobility, which is directly related to the packing of the molecules both on local (amorphous versus crystalline) and on macroscopic (grain boundaries) length scales. Liquid crystalline ordering offers the possibility of circumventing this problem. An advanced concept comprises: i) the application of materials with different liquid crystalline phases, ii) the orientation of a low viscosity high temperature phase, and, iii) the transfer of the macroscopic orientation during cooling to a highly ordered (at best, crystalline-like) phase at room temperature. At the same time, the desired orientation for the application (OLED or field-effect transistor) can be obtained. This review presents the use of molecules with discotic, calamitic and sanidic phases and discusses the sensitivity of the phases with regard to defects depending on the dimensionality of the ordered structure (columns: 1D, smectic layers and sanidic phases: 2D). It presents ways to systematically improve charge carrier mobility by proper variation of the electronic and steric (packing) structure of the constituting molecules and to reach charge carrier mobilities that are close to and comparable to amorphous silicon, with values of 0.1 to 0.7 cm(2)  · V(-1)  · s(-1) . In this context, the significance of cross-linking to stabilize the orientation and liquid crystalline behavior of inorganic/organic hybrids is also discussed. Copyright © 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Orientation of chain molecules in ionotropic gels: a Brownian dynamics model

NASA Astrophysics Data System (ADS)

Woelki, Stefan; Kohler, Hans-Helmut

2003-09-01

As is known from birefringence measurements, polysaccharide molecules of ionotropic gels are preferentially orientated normal to the direction of gel growth. In this paper the orientation effect is investigated by means of an off-lattice Brownian dynamics model simulating the gel formation process. The model describes the integration of a single coarse grained phantom chain into the growing gel. The equations of motion of the chain are derived. The computer simulations show that, during the process of integration, the chain is contracting normal to the direction of gel growth. A scaling relation is obtained for the degree of contraction as a function of the length parameters of the chain, the velocity of the gel formation front and the rate constant of the crosslinking reaction. It is shown that the scaling relation, if applied to the example of ionotropic copper alginate gel, leads to reasonable predictions of the time course of the degree of contraction of the alginate chains.

Impact of interfacial molecular orientation on radiative recombination and charge generation efficiency

DOE PAGES

Ran, Niva A.; Roland, Steffen; Love, John A.; ...

2017-07-19

Here, a long standing question in organic electronics concerns the effects of molecular orientation at donor/acceptor heterojunctions. Given a well-controlled donor/acceptor bilayer system, we uncover the genuine effects of molecular orientation on charge generation and recombination. These effects are studied through the point of view of photovoltaics—however, the results have important implications on the operation of all optoelectronic devices with donor/acceptor interfaces, such as light emitting diodes and photodetectors. Our findings can be summarized by two points. First, devices with donor molecules face-on to the acceptor interface have a higher charge transfer state energy and less non-radiative recombination, resulting inmore » larger open-circuit voltages and higher radiative efficiencies. Second, devices with donor molecules edge-on to the acceptor interface are more efficient at charge generation, attributed to smaller electronic coupling between the charge transfer states and the ground state, and lower activation energy for charge generation.« less

Determination of helix orientations in a flexible DNA by multi-frequency EPR spectroscopy.

PubMed

Grytz, C M; Kazemi, S; Marko, A; Cekan, P; Güntert, P; Sigurdsson, S Th; Prisner, T F

2017-11-15

Distance measurements are performed between a pair of spin labels attached to nucleic acids using Pulsed Electron-Electron Double Resonance (PELDOR, also called DEER) spectroscopy which is a complementary tool to other structure determination methods in structural biology. The rigid spin label Ç, when incorporated pairwise into two helical parts of a nucleic acid molecule, allows the determination of both the mutual orientation and the distance between those labels, since Ç moves rigidly with the helix to which it is attached. We have developed a two-step protocol to investigate the conformational flexibility of flexible nucleic acid molecules by multi-frequency PELDOR. In the first step, a library with a broad collection of conformers, which are in agreement with topological constraints, NMR restraints and distances derived from PELDOR, was created. In the second step, a weighted structural ensemble of these conformers was chosen, such that it fits the multi-frequency PELDOR time traces of all doubly Ç-labelled samples simultaneously. This ensemble reflects the global structure and the conformational flexibility of the two-way DNA junction. We demonstrate this approach on a flexible bent DNA molecule, consisting of two short helical parts with a five adenine bulge at the center. The kink and twist motions between both helical parts were quantitatively determined and showed high flexibility, in agreement with a Förster Resonance Energy Transfer (FRET) study on a similar bent DNA motif. The approach presented here should be useful to describe the relative orientation of helical motifs and the conformational flexibility of nucleic acid structures, both alone and in complexes with proteins and other molecules.

Effect of horizontal molecular orientation on triplet-exciton diffusion in amorphous organic films

NASA Astrophysics Data System (ADS)

Sawabe, T.; Takasu, I.; Yonehara, T.; Ono, T.; Yoshida, J.; Enomoto, S.; Amemiya, I.; Adachi, C.

2012-09-01

Triplet harvesting is a candidate technology for highly efficient and long-life white OLEDs, where green or red phosphorescent emitters are activated by the triplet-excitons diffused from blue fluorescent emitters. We examined two oxadiazole-based electron transport materials with different horizontal molecular orientation as a triplet-exciton diffusion layer (TDL) in triplet-harvesting OLEDs. The device characteristics and the transient electroluminescent analyses of the red phosphorescent emitter showed that the triplet-exciton diffusion was more effective in the highly oriented TDL. The results are ascribed to the strong orbital overlap between the oriented molecules, which provides rapid electron exchange (Dexter energy transfer) in the TDL.

Quadratic stark effect in the fullerene C60 at low symmetry orientation in the field

NASA Astrophysics Data System (ADS)

Tuchin, A. V.; Bityutskaya, L. A.; Bormontov, E. N.

2014-08-01

Results of numeric simulation of the influence of the electric field E = 0 - 1 V/Å on the electronic structure of the neutral fullerene C60 taking into account orientational deformation of its carbon cage at arbitrary orientations in the electric field including low symmetry orientations are presented. Splitting of the frontier t 1 u - and h u -levels of the molecule due to the quadratic Stark effect has been investigated. Dependencies of the effective electron work function and the energy gap between the lowest unoccupied and highest occupied molecular orbitals on the strengths of the electric field have been determined.

A scattering model for forested area

NASA Technical Reports Server (NTRS)

Karam, M. A.; Fung, A. K.

1988-01-01

A forested area is modeled as a volume of randomly oriented and distributed disc-shaped, or needle-shaped leaves shading a distribution of branches modeled as randomly oriented finite-length, dielectric cylinders above an irregular soil surface. Since the radii of branches have a wide range of sizes, the model only requires the length of a branch to be large compared with its radius which may be any size relative to the incident wavelength. In addition, the model also assumes the thickness of a disc-shaped leaf or the radius of a needle-shaped leaf is much smaller than the electromagnetic wavelength. The scattering phase matrices for disc, needle, and cylinder are developed in terms of the scattering amplitudes of the corresponding fields which are computed by the forward scattering theorem. These quantities along with the Kirchoff scattering model for a randomly rough surface are used in the standard radiative transfer formulation to compute the backscattering coefficient. Numerical illustrations for the backscattering coefficient are given as a function of the shading factor, incidence angle, leaf orientation distribution, branch orientation distribution, and the number density of leaves. Also illustrated are the properties of the extinction coefficient as a function of leaf and branch orientation distributions. Comparisons are made with measured backscattering coefficients from forested areas reported in the literature.

Asymmetric orientation of toluene molecules at oil-silica interfaces

NASA Astrophysics Data System (ADS)

Ledyastuti, Mia; Liang, Yunfeng; Kunieda, Makoto; Matsuoka, Toshifumi

2012-08-01

The interfacial structure of heptane and toluene at oil-silica interfaces has previously been studied by sum frequency generation [Z. Yang et al., J. Phys. Chem. C. 113, 20355 (2009)], 10.1021/jp9043122. It was found that the toluene molecule is almost perpendicular to the silica surface with a tilt angle of about 25°. Here, we have investigated the structural properties of toluene and heptane at oil-silica interfaces using molecular dynamics simulations for two different surfaces: the oxygen-bridging (hydrophobic) and hydroxyl-terminated (hydrophilic) surfaces of quartz (silica). Based on the density profile, it was found that both heptane and toluene oscillate on silica surfaces, with heptane showing more oscillation peaks. Furthermore, the toluene molecules of the first layer were found to have an asymmetric distribution of orientations, with more CH3 groups pointed away from the silica surface than towards the silica surface. These findings are generally consistent with previous experiments, and reveal enhanced molecular structures of liquids at oil-silica interfaces.

Asymmetric orientation of toluene molecules at oil-silica interfaces.

PubMed

Ledyastuti, Mia; Liang, Yunfeng; Kunieda, Makoto; Matsuoka, Toshifumi

2012-08-14

The interfacial structure of heptane and toluene at oil-silica interfaces has previously been studied by sum frequency generation [Z. Yang et al., J. Phys. Chem. C. 113, 20355 (2009)]. It was found that the toluene molecule is almost perpendicular to the silica surface with a tilt angle of about 25°. Here, we have investigated the structural properties of toluene and heptane at oil-silica interfaces using molecular dynamics simulations for two different surfaces: the oxygen-bridging (hydrophobic) and hydroxyl-terminated (hydrophilic) surfaces of quartz (silica). Based on the density profile, it was found that both heptane and toluene oscillate on silica surfaces, with heptane showing more oscillation peaks. Furthermore, the toluene molecules of the first layer were found to have an asymmetric distribution of orientations, with more CH(3) groups pointed away from the silica surface than towards the silica surface. These findings are generally consistent with previous experiments, and reveal enhanced molecular structures of liquids at oil-silica interfaces.

Manipulating the dipole layer of polar organic molecules on metal surfaces via different charge-transfer channels

NASA Astrophysics Data System (ADS)

Lin, Meng-Kai; Nakayama, Yasuo; Zhuang, Ying-Jie; Wang, Chin-Yung; Pi, Tun-Wen; Ishii, Hisao; Tang, S.-J.

The key properties of organic films such as energy level alignment (ELA), work functions, and injection barriers are closely linked to this dipole layer. Using angle resolved photoemission spectroscopy (ARPES), we systemically investigate the coverage-dependent work functions and spectra line shapes of occupied molecular orbital states of a polar molecule, chloroaluminium phthalocyanine (ClAlPc), grown on Ag(111) to show that the orientations of the first ClAlPc layer can be manipulated via the molecule deposition rate and post annealing, causing ELA at organic-metal interface to differ for about 0.3 eV between Cl-up and Cl-down configuration. Moreover, by comparing the experimental results with the calculations based on both gas-phase model and realistic model of ClAlPc on Ag(111) , we evidence that the different orientations of ClAlPc dipole layers lead to different charge-transfer channels between ClAlPc and Ag, a key factor that controls the ELA at organic-metal interface.

Experimental Studies of the Brownian Diffusion of Boomerang Colloidal Particle in a Confined Geometry

NASA Astrophysics Data System (ADS)

Chakrabarty, Ayan; Wang, Feng; Joshi, Bhuwan; Wei, Qi-Huo

2011-03-01

Recent studies shows that the boomerang shaped molecules can form various kinds of liquid crystalline phases. One debated topic related to boomerang molecules is the existence of biaxial nematic liquid crystalline phase. Developing and optical microscopic studies of colloidal systems of boomerang particles would allow us to gain better understanding of orientation ordering and dynamics at ``single molecule'' level. Here we report the fabrication and experimental studies of the Brownian motion of individual boomerang colloidal particles confined between two glass plates. We used dark-field optical microscopy to directly visualize the Brownian motion of the single colloidal particles in a quasi two dimensional geometry. An EMCCD was used to capture the motion in real time. An indigenously developed imaging processing algorithm based on MatLab program was used to precisely track the position and orientation of the particles with sub-pixel accuracy. The experimental finding of the Brownian diffusion of a single boomerang colloidal particle will be discussed.

Inserting Thienyl Linkers into Conjugated Molecules for Efficient Multilevel Electronic Memory: A New Understanding of Charge-Trapping in Organic Materials.

PubMed

Li, Yang; Li, Hua; He, Jinghui; Xu, Qingfeng; Li, Najun; Chen, Dongyun; Lu, Jianmei

2016-03-18

The practical application of organic memory devices requires low power consumption and reliable device quality. Herein, we report that inserting thienyl units into D-π-A molecules can improve these parameters by tuning the texture of the film. Theoretical calculations revealed that introducing thienyl π bridges increased the planarity of the molecular backbone and extended the D-A conjugation. Thus, molecules with more thienyl spacers showed improved stacking and orientation in the film state relative to the substrates. The corresponding sandwiched memory devices showed enhanced ternary memory behavior, with lower threshold voltages and better repeatability. The conductive switching and variation in the performance of the memory devices were interpreted by using an extended-charge-trapping mechanism. Our study suggests that judicious molecular engineering can facilitate control of the orientation of the crystallite in the solid state to achieve superior multilevel memory performance. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Differentiating Amino Acid Residues and Side Chain Orientations in Peptides Using Scanning Tunneling Microscopy

PubMed Central

Claridge, Shelley A.; Thomas, John C.; Silverman, Miles A.; Schwartz, Jeffrey J.; Yang, Yanlian; Wang, Chen; Weiss, Paul S.

2014-01-01

Single-molecule measurements of complex biological structures such as proteins are an attractive route for determining structures of the large number of important biomolecules that have proved refractory to analysis through standard techniques such as X-ray crystallography and nuclear magnetic resonance. We use a custom-built low-current scanning tunneling microscope to image peptide structure at the single-molecule scale in a model peptide that forms β sheets, a structural motif common in protein misfolding diseases. We successfully differentiate between histidine and alanine amino acid residues, and further differentiate side chain orientations in individual histidine residues, by correlating features in scanning tunneling microscope images with those in energy-optimized models. Beta sheets containing histidine residues are used as a model system due to the role histidine plays in transition metal binding associated with amyloid oligomerization in Alzheimer’s and other diseases. Such measurements are a first step toward analyzing peptide and protein structures at the single-molecule level. PMID:24219245

Quasi-2D Liquid State at Metal-Organic Interface and Adsorption State Manipulation

NASA Astrophysics Data System (ADS)

Mehdizadeh, Masih

The metal/organic interface between noble metal close-packed (111) surfaces and organic semiconducting molecules is studied using Scanning tunneling microscopy and Photoelectron Spectroscopy, supplemented by first principles density functional theory calculations and Markov Chain Monte Carlo simulations. Copper Phthalocyanine molecules were shown to have dual adsorption states: a liquid state where intermolecular interactions were shown to be repulsive in nature and largely due to entropic effects, and a disordered immobilized state triggered by annealing or applying a tip-sample bias larger than a certain temperature or voltage respectively where intermolecular forces were demonstrated to be attractive. A methodology for altering molecular orientation on the aforementioned surfaces is also proposed through introduction of a Fullerene C60 buffer layer. Density functional theory calculations demonstrate orientation-switching of Copper Phthalocyanine molecules based on the amount of charges transferred to/from the substrate to the C60-CuPc layers; suggesting existence of critical substrate work functions that cause reorientation.

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

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

Conformational adaptation and manipulation of manganese tetra(4-pyridyl)porphyrin molecules on Cu(111)

NASA Astrophysics Data System (ADS)

Chen, Xianwen; Lei, Shulai; Lotze, Christian; Czekelius, Constantin; Paulus, Beate; Franke, Katharina J.

2017-03-01

Porphyrins are highly flexible molecules and well known to adapt to their local environment via conformational changes. We studied the self-assembly of manganese meso-tetra(4-pyridyl)porphyrin (Mn-TPyP) molecules on a Cu(111) surface by low temperature scanning tunneling microscopy (STM) and atomic force microscopy (ATM). We observe molecular chains along the ⟨1 1 ¯ 0 ⟩ direction of the substrate. Within these chains, we identify two molecular conformations, which differ by the orientation of the upward bending of the macrocycle. Using density functional theory, we show that this saddle shape is a consequence of the rotation and inclination of the pyridyl groups towards Cu adatoms, which stabilize the metal-organic chains. The molecular conformations obey a strict alternation, reflecting the mutual enforcement of conformational adaptation in densely packed structures. Tunneling electrons from the STM tip can induce changes in the orientation of the pyridyl endgroups. The switching behaviour varies with the different adsorption configurations.

Nanofiber Orientation and Surface Functionalization Modulate Human Mesenchymal Stem Cell Behavior In Vitro

PubMed Central

Kolambkar, Yash M.; Bajin, Mehmet; Wojtowicz, Abigail; Hutmacher, Dietmar W.; García, Andrés J.

2014-01-01

Electrospun nanofiber meshes have emerged as a new generation of scaffold membranes possessing a number of features suitable for tissue regeneration. One of these features is the flexibility to modify their structure and composition to orchestrate specific cellular responses. In this study, we investigated the effects of nanofiber orientation and surface functionalization on human mesenchymal stem cell (hMSC) migration and osteogenic differentiation. We used an in vitro model to examine hMSC migration into a cell-free zone on nanofiber meshes and mitomycin C treatment to assess the contribution of proliferation to the observed migration. Poly (ɛ-caprolactone) meshes with oriented topography were created by electrospinning aligned nanofibers on a rotating mandrel, while randomly oriented controls were collected on a stationary collector. Both aligned and random meshes were coated with a triple-helical, type I collagen-mimetic peptide, containing the glycine-phenylalanine-hydroxyproline-glycine-glutamate-arginine (GFOGER) motif. Our results indicate that nanofiber GFOGER peptide functionalization and orientation modulate cellular behavior, individually, and in combination. GFOGER significantly enhanced the migration, proliferation, and osteogenic differentiation of hMSCs on nanofiber meshes. Aligned nanofiber meshes displayed increased cell migration along the direction of fiber orientation compared to random meshes; however, fiber alignment did not influence osteogenic differentiation. Compared to each other, GFOGER coating resulted in a higher proliferation-driven cell migration, whereas fiber orientation appeared to generate a larger direct migratory effect. This study demonstrates that peptide surface modification and topographical cues associated with fiber alignment can be used to direct cellular behavior on nanofiber mesh scaffolds, which may be exploited for tissue regeneration. PMID:24020454

Automatic Molecular Design using Evolutionary Techniques

NASA Technical Reports Server (NTRS)

Globus, Al; Lawton, John; Wipke, Todd; Saini, Subhash (Technical Monitor)

1998-01-01

Molecular nanotechnology is the precise, three-dimensional control of materials and devices at the atomic scale. An important part of nanotechnology is the design of molecules for specific purposes. This paper describes early results using genetic software techniques to automatically design molecules under the control of a fitness function. The fitness function must be capable of determining which of two arbitrary molecules is better for a specific task. The software begins by generating a population of random molecules. The population is then evolved towards greater fitness by randomly combining parts of the better individuals to create new molecules. These new molecules then replace some of the worst molecules in the population. The unique aspect of our approach is that we apply genetic crossover to molecules represented by graphs, i.e., sets of atoms and the bonds that connect them. We present evidence suggesting that crossover alone, operating on graphs, can evolve any possible molecule given an appropriate fitness function and a population containing both rings and chains. Prior work evolved strings or trees that were subsequently processed to generate molecular graphs. In principle, genetic graph software should be able to evolve other graph representable systems such as circuits, transportation networks, metabolic pathways, computer networks, etc.

Crystal water dynamics of guanosine dihydrate: analysis of atomic displacement parameters, time profile of hydrogen-bonding probability, and translocation of water by MD simulation.

PubMed

Yoneda, Shigetaka; Sugawara, Yoko; Urabe, Hisako

2005-01-27

The dynamics of crystal water molecules of guanosine dihydrate are investigated in detail by molecular dynamics (MD) simulation. A 2 ns simulation is performed using a periodic boundary box composed of 4 x 5 x 8 crystallographic unit cells and using the particle-mesh Ewald method for calculation of electrostatic energy. The simulated average atomic positions and atomic displacement parameters are remarkably coincident with the experimental values determined by X-ray analysis, confirming the high accuracy of this simulation. The dynamics of crystal water are analyzed in terms of atomic displacement parameters, orientation vectors, order parameters, self-correlation functions of the orientation vectors, time profiles of hydrogen-bonding probability, and translocations. The simulation clarifies that the average structure is composed of various stable and transient structures of the molecules. The simulated guanosine crystal forms a layered structure, with four water sites per asymmetric unit, classified as either interlayer water or intralayer water. From a detailed analysis of the translocations of water molecules in the simulation, columns of intralayer water molecules along the c axis appear to represent a pathway for hydration and dehydration by a kind of molecular valve mechanism.

Self-organization of gold nanoparticles on silanated surfaces

PubMed Central

Kyaw, Htet H; Sellai, Azzouz; Dutta, Joydeep

2015-01-01

Summary The self-organization of monolayer gold nanoparticles (AuNPs) on 3-aminopropyltriethoxysilane (APTES)-functionalized glass substrate is reported. The orientation of APTES molecules on glass substrates plays an important role in the interaction between AuNPs and APTES molecules on the glass substrates. Different orientations of APTES affect the self-organization of AuNps on APTES-functionalized glass substrates. The as grown monolayers and films annealed in ultrahigh vacuum and air (600 °C) were studied by water contact angle measurements, atomic force microscopy, X-ray photoelectron spectroscopy, UV–visible spectroscopy and ultraviolet photoelectron spectroscopy. Results of this study are fundamentally important and also can be applied for designing and modelling of surface plasmon resonance based sensor applications. PMID:26734526

Cryptotomography: reconstructing 3D Fourier intensities from randomly oriented single-shot diffraction patterns (CXIDB ID 9)

DOE Data Explorer

Loh, Ne-Te Duane

2011-08-01

These 2000 single-shot diffraction patterns include were either background-scattering only or hits (background-scattering plus diffraction signal from sub-micron ellipsoidal particles at random, undetermined orientations). Candidate hits were identified by eye, and the remainder were presumed as background. 54 usable, background-subtracted hits in this set (procedure in referenced article) were used to reconstruct the 3D diffraction intensities of the average ellipsoidal particle.

Strategy to discover diverse optimal molecules in the small molecule universe.

PubMed

Rupakheti, Chetan; Virshup, Aaron; Yang, Weitao; Beratan, David N

2015-03-23

The small molecule universe (SMU) is defined as a set of over 10(60) synthetically feasible organic molecules with molecular weight less than ∼500 Da. Exhaustive enumerations and evaluation of all SMU molecules for the purpose of discovering favorable structures is impossible. We take a stochastic approach and extend the ACSESS framework ( Virshup et al. J. Am. Chem. Soc. 2013 , 135 , 7296 - 7303 ) to develop diversity oriented molecular libraries that can generate a set of compounds that is representative of the small molecule universe and that also biases the library toward favorable physical property values. We show that the approach is efficient compared to exhaustive enumeration and to existing evolutionary algorithms for generating such libraries by testing in the NKp fitness landscape model and in the fully enumerated GDB-9 chemical universe containing 3 × 10(5) molecules.

Strategy To Discover Diverse Optimal Molecules in the Small Molecule Universe

PubMed Central

2015-01-01

The small molecule universe (SMU) is defined as a set of over 1060 synthetically feasible organic molecules with molecular weight less than ∼500 Da. Exhaustive enumerations and evaluation of all SMU molecules for the purpose of discovering favorable structures is impossible. We take a stochastic approach and extend the ACSESS framework (Virshup et al. J. Am. Chem. Soc.2013, 135, 7296–730323548177) to develop diversity oriented molecular libraries that can generate a set of compounds that is representative of the small molecule universe and that also biases the library toward favorable physical property values. We show that the approach is efficient compared to exhaustive enumeration and to existing evolutionary algorithms for generating such libraries by testing in the NKp fitness landscape model and in the fully enumerated GDB-9 chemical universe containing 3 × 105 molecules. PMID:25594586

Origin of the blueshift of water molecules at interfaces of hydrophilic cyclic compounds

PubMed Central

Tomobe, Katsufumi; Yamamoto, Eiji; Kojić, Dušan; Sato, Yohei; Yasui, Masato; Yasuoka, Kenji

2017-01-01

Water molecules at interfaces of materials exhibit enigmatic properties. A variety of spectroscopic studies have observed a high-frequency motion in these water molecules, represented by a blueshift, at both hydrophobic and hydrophilic interfaces. However, the molecular mechanism behind this blueshift has remained unclear. Using Raman spectroscopy and ab initio molecular dynamics simulations, we reveal the molecular mechanism of the blueshift of water molecules around six monosaccharide isomers. In the first hydration shell, we found weak hydrogen-bonded water molecules that cannot have a stable tetrahedral water network. In the water molecules, the vibrational state of the OH bond oriented toward the bulk solvent strongly contributes to the observed blueshift. Our work suggests that the blueshift in various solutions originates from the vibrational motions of these observed water molecules. PMID:29282448

Magnetic moment enhancement and spin polarization switch of the manganese phthalocyanine molecule on an IrMn(100) surface

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

Sun, X.; National Institute for Materials Science, 1-2-1 Sengen, Tsukuba 305-0047; Wang, B.

2014-07-21

The geometric, electronic, and magnetic structures of a manganese phthalocyanine (MnPc) molecule on an antiferromagnetic IrMn(100) surface are studied by density functional theory calculations. Two kinds of orientation of the adsorbed MnPc molecule are predicted to coexist due to molecular self-assembly on the surface—a top-site geometry with the Mn–N bonds aligned along the 〈100〉 direction, and a hollow-site orientation in which the Mn–N bonds are parallel to the 〈110〉 direction. The MnPc molecule is antiferromagnetically coupled to the substrate at the top site with a slight reduction in the magnetic moment of the Mn atom of the MnPc molecule (Mn{submore » mol}). In contrast, the magnetic moment of the Mn{sub mol} is enhanced to 4.28 μB at the hollow site, a value larger than that in the free MnPc molecule (3.51 μB). Molecular distortion induced by adsorption is revealed to be responsible for the enhancement of the magnetic moment. Furthermore, the spin polarization of the Mn{sub mol} atom at around the Fermi level is found to change from negative to positive through an elongation of the Mn–N bonds of the MnPc. We propose that a reversible switch of the low/high magnetic moment and negative/positive spin polarization might be realized through some mechanical engineering methods.« less

Vectorial nanoscale mapping of optical antenna fields by single molecule dipoles.

PubMed

Singh, Anshuman; Calbris, Gaëtan; van Hulst, Niek F

2014-08-13

Optical nanoantennas confine light on the nanoscale, enabling strong light-matter interactions and ultracompact optical devices. Such confined nanovolumes of light have nonzero field components in all directions (x, y, and z). Unfortunately mapping of the actual nanoscale field vectors has so far remained elusive, though antenna hotspots have been explored by several techniques. In this paper, we present a novel method to probe all three components of the local antenna field. To this end a resonant nanoantenna is fabricated at the vertex of a scanning tip. Next, the nanoantenna is deterministically scanned in close proximity to single fluorescent molecules, whose fixed excitation dipole moment reads out the local field vector. With nanometer molecular resolution, we distinctly map x-, y-, and z-field components of the dipole antenna, i.e. a full vectorial mode map, and show good agreement with full 3D FDTD simulations. Moreover, the fluorescence polarization maps the localized coupling, with emission through the longitudinal antenna mode. Finally, the resonant antenna probe is used for single molecule imaging with 40 nm fwhm response function. The total fluorescence enhancement is 7.6 times, while out-of-plane molecules, almost undetectable in far-field, are made visible by the strong antenna z-field with a fluorescence enhancement up to 100 times. Interestingly, the apparent position of molecules shifts up to 20 nm depending on their orientation. The capability to resolve orientational information on the single molecule level makes the scanning resonant antenna an ideal tool for extreme resolution bioimaging.

Single-molecule designs for electric switches and rectifiers.

PubMed

Kornilovitch, Pavel; Bratkovsky, Alexander; Williams, Stanley

2003-12-01

A design for molecular rectifiers is proposed. Current rectification is based on the spatial asymmetry of a molecule and requires only one resonant conducting molecular orbital. Rectification is caused by asymmetric coupling of the orbital to the electrodes, which results in asymmetric movement of the two Fermi levels with respect to the orbital under external bias. Results from numerical studies of the family of suggested molecular rectifiers, HS-(CH(2))(n)-C(6)H(4)(CH(2))(m)SH, are presented. Current rectification ratios in excess of 100 are achievable for n = 2 and m > 6. A class of bistable stator-rotor molecules is proposed. The stationary part connects the two electrodes and facilitates electron transport between them. The rotary part, which has a large dipole moment, is attached to an atom of the stator via a single sigma bond. Electrostatic bonds formed between the oxygen atom of the rotor and hydrogen atoms of the stator make the symmetric orientation of the dipole unstable. The rotor has two potential minima with equal energy for rotation about the sigma bond. The dipole can be flipped between the two states by an external electric field. Both rotor-orientation states have asymmetric current-voltage characteristics that are the reverse of each other, so they are distinguishable electrically. Theoretical results on conformation, energy barriers, retention times, switching voltages, and current-voltage characteristics are presented for a particular stator-rotor molecule. Such molecules could be the base for single-molecule switches, reversible diodes, and other molecular electronic devices.

Conformation-based signal transfer and processing at the single-molecule level

NASA Astrophysics Data System (ADS)

Li, Chao; Wang, Zhongping; Lu, Yan; Liu, Xiaoqing; Wang, Li

2017-11-01

Building electronic components made of individual molecules is a promising strategy for the miniaturization and integration of electronic devices. However, the practical realization of molecular devices and circuits for signal transmission and processing at room temperature has proven challenging. Here, we present room-temperature intermolecular signal transfer and processing using SnCl2Pc molecules on a Cu(100) surface. The in-plane orientations of the molecules are effectively coupled via intermolecular interaction and serve as the information carrier. In the coupled molecular arrays, the signal can be transferred from one molecule to another in the in-plane direction along predesigned routes and processed to realize logical operations. These phenomena enable the use of molecules displaying intrinsic bistable states as complex molecular devices and circuits with novel functions.

Determining the orientation of a chiral substrate using full-hemisphere angle-resolved photoelectron spectroscopy.

PubMed

Tadich, A; Riley, J; Thomsen, L; Cowie, B C C; Gladys, M J

2011-10-21

Chiral interfaces and substrates are of increasing importance in the field of enantioselective chemistry. To fully understand the enantiospecific interactions between chiral adsorbate molecules and the chiral substrate, it is vital that the chiral orientation of the substrate is known. In this Letter we demonstrate that full-hemisphere angle-resolved photoemission permits straightforward identification of the orientation of a chiral surface. The technique can be applied to any solid state system for which photoemission measurements are possible. © 2011 American Physical Society

Impact of Oriented Clay Particles on X-Ray Spectroscopy Analysis

NASA Astrophysics Data System (ADS)

Lim, A. J. M. S.; Syazwani, R. N.; Wijeyesekera, D. C.

2016-07-01

Understanding the engineering properties of the mineralogy and microfabic of clayey soils is very complex and thus very difficult for soil characterization. Micromechanics of soils recognize that the micro structure and mineralogy of clay have a significant influence on its engineering behaviour. To achieve a more reliable quantitative evaluation of clay mineralogy, a proper sample preparation technique for quantitative clay mineral analysis is necessary. This paper presents the quantitative evaluation of elemental analysis and chemical characterization of oriented and random oriented clay particles using X-ray spectroscopy. Three different types of clays namely marine clay, bentonite and kaolin clay were studied. The oriented samples were prepared by placing the dispersed clay in water and left to settle on porous ceramic tiles by applying a relatively weak suction through a vacuum pump. Images form a Scanning Electron Microscope (SEM) was also used to show the comparison between the orientation patterns of both the sample preparation techniques. From the quantitative analysis of the X-ray spectroscopy, oriented sampling method showed more accuracy in identifying mineral deposits, because it produced better peak intensity on the spectrum and more mineral content can be identified compared to randomly oriented samples.

Elastic properties of woven bone: effect of mineral content and collagen fibrils orientation.

PubMed

García-Rodríguez, J; Martínez-Reina, J

2017-02-01

Woven bone is a type of tissue that forms mainly during fracture healing or fetal bone development. Its microstructure can be modeled as a composite with a matrix of mineral (hydroxyapatite) and inclusions of collagen fibrils with a more or less random orientation. In the present study, its elastic properties were estimated as a function of composition (degree of mineralization) and fibril orientation. A self-consistent homogenization scheme considering randomness of inclusions' orientation was used for this purpose. Lacuno-canalicular porosity in the form of periodically distributed void inclusions was also considered. Assuming collagen fibrils to be uniformly oriented in all directions led to an isotropic tissue with a Young's modulus [Formula: see text] GPa, which is of the same order of magnitude as that of woven bone in fracture calluses. By contrast, assuming fibrils to have a preferential orientation resulted in a Young's modulus in the preferential direction of 9-16 GPa depending on the mineral content of the tissue. These results are consistent with experimental evidence for woven bone in foetuses, where collagen fibrils are aligned to a certain extent.

Bilateral robotic priming before task-oriented approach in subacute stroke rehabilitation: a pilot randomized controlled trial.

PubMed

Hsieh, Yu-Wei; Wu, Ching-Yi; Wang, Wei-En; Lin, Keh-Chung; Chang, Ku-Chou; Chen, Chih-Chi; Liu, Chien-Ting

2017-02-01

To investigate the treatment effects of bilateral robotic priming combined with the task-oriented approach on motor impairment, disability, daily function, and quality of life in patients with subacute stroke. A randomized controlled trial. Occupational therapy clinics in medical centers. Thirty-one subacute stroke patients were recruited. Participants were randomly assigned to receive bilateral priming combined with the task-oriented approach (i.e., primed group) or to the task-oriented approach alone (i.e., unprimed group) for 90 minutes/day, 5 days/week for 4 weeks. The primed group began with the bilateral priming technique by using a bimanual robot-aided device. Motor impairments were assessed by the Fugal-Meyer Assessment, grip strength, and the Box and Block Test. Disability and daily function were measured by the modified Rankin Scale, the Functional Independence Measure, and actigraphy. Quality of life was examined by the Stroke Impact Scale. The primed and unprimed groups improved significantly on most outcomes over time. The primed group demonstrated significantly better improvement on the Stroke Impact Scale strength subscale ( p = 0.012) and a trend for greater improvement on the modified Rankin Scale ( p = 0.065) than the unprimed group. Bilateral priming combined with the task-oriented approach elicited more improvements in self-reported strength and disability degrees than the task-oriented approach by itself. Further large-scale research with at least 31 participants in each intervention group is suggested to confirm the study findings.

Measuring market orientation: further evidence on Narver and Slater's three-component scale.

PubMed

Chakrabarty, Subhra; Rogé, Joseph N

2003-12-01

A mail survey of a national random sample of 2,000 marketing managers was conducted. The data provided by 222 respondents were analyzed to assess the dimensionality of Narver and Slater's 15-item measure of market orientation. A confirmatory factor analysis, using LISREL 8.53, provided support for each of the separate dimensions of customer orientation, competitor orientation, and interfunctional coordination. However, a combined 3-factor model of market orientation was not supported. Directions for research are suggested.

Probing protein orientation near charged nanosurfaces for simulation-assisted biosensor design.

PubMed

Cooper, Christopher D; Clementi, Natalia C; Barba, Lorena A

2015-09-28

Protein-surface interactions are ubiquitous in biological processes and bioengineering, yet are not fully understood. In biosensors, a key factor determining the sensitivity and thus the performance of the device is the orientation of the ligand molecules on the bioactive device surface. Adsorption studies thus seek to determine how orientation can be influenced by surface preparation, varying surface charge, and ambient salt concentration. In this work, protein orientation near charged nanosurfaces is obtained under electrostatic effects using the Poisson-Boltzmann equation, in an implicit-solvent model. Sampling the free energy for protein G B1 D4' at a range of tilt and rotation angles with respect to the charged surface, we calculated the probability of the protein orientations and observed a dipolar behavior. This result is consistent with published experimental studies and combined Monte Carlo and molecular dynamics simulations using this small protein, validating our method. More relevant to biosensor technology, antibodies such as immunoglobulin G are still a formidable challenge to molecular simulation, due to their large size. With the Poisson-Boltzmann model, we obtained the probability distribution of orientations for the iso-type IgG2a at varying surface charge and salt concentration. This iso-type was not found to have a preferred orientation in previous studies, unlike the iso-type IgG1 whose larger dipole moment was assumed to make it easier to control. Our results show that the preferred orientation of IgG2a can be favorable for biosensing with positive charge on the surface of 0.05 C/m(2) or higher and 37 mM salt concentration. The results also show that local interactions dominate over dipole moment for this protein. Improving immunoassay sensitivity may thus be assisted by numerical studies using our method (and open-source code), guiding changes to fabrication protocols or protein engineering of ligand molecules to obtain more favorable orientations.

Probing protein orientation near charged nanosurfaces for simulation-assisted biosensor design

NASA Astrophysics Data System (ADS)

Cooper, Christopher D.; Clementi, Natalia C.; Barba, Lorena A.

2015-09-01

Protein-surface interactions are ubiquitous in biological processes and bioengineering, yet are not fully understood. In biosensors, a key factor determining the sensitivity and thus the performance of the device is the orientation of the ligand molecules on the bioactive device surface. Adsorption studies thus seek to determine how orientation can be influenced by surface preparation, varying surface charge, and ambient salt concentration. In this work, protein orientation near charged nanosurfaces is obtained under electrostatic effects using the Poisson-Boltzmann equation, in an implicit-solvent model. Sampling the free energy for protein G B1 D4' at a range of tilt and rotation angles with respect to the charged surface, we calculated the probability of the protein orientations and observed a dipolar behavior. This result is consistent with published experimental studies and combined Monte Carlo and molecular dynamics simulations using this small protein, validating our method. More relevant to biosensor technology, antibodies such as immunoglobulin G are still a formidable challenge to molecular simulation, due to their large size. With the Poisson-Boltzmann model, we obtained the probability distribution of orientations for the iso-type IgG2a at varying surface charge and salt concentration. This iso-type was not found to have a preferred orientation in previous studies, unlike the iso-type IgG1 whose larger dipole moment was assumed to make it easier to control. Our results show that the preferred orientation of IgG2a can be favorable for biosensing with positive charge on the surface of 0.05 C/m2 or higher and 37 mM salt concentration. The results also show that local interactions dominate over dipole moment for this protein. Improving immunoassay sensitivity may thus be assisted by numerical studies using our method (and open-source code), guiding changes to fabrication protocols or protein engineering of ligand molecules to obtain more favorable orientations.

Molecular hydrogen solvated in water – A computational study

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

Śmiechowski, Maciej, E-mail: Maciej.Smiechowski@pg.gda.pl

2015-12-28

The aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H{sub 2} molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the H{sub 2} molecule without major structural distortions and two-dimensional, radial-angular distribution functions indicate that as opposed to strictly tangential, the orientation of these water molecules is such that the solute is solvated with one of the free electronmore » pairs of H{sub 2}O. The calculated self-diffusion coefficient of H{sub 2}(aq) agrees very well with experimental results and the time dependence of mean square displacement suggests the presence of caging on a time scale corresponding to hydrogen bond network vibrations in liquid water. Orientational correlation function of H{sub 2} experiences an extremely short-scale decay, making the H{sub 2}–H{sub 2}O interaction potential essentially isotropic by virtue of rotational averaging. The inclusion of explicit polarizability in the model allows for the calculation of Raman spectra that agree very well with available experimental data on H{sub 2}(aq) under differing pressure conditions, including accurate reproduction of the experimentally noted trends with solute pressure or concentration.« less

Diffuse Scattering Investigations of Orientational Pair Potentials in C_60

NASA Astrophysics Data System (ADS)

Wochner, Peter

1996-03-01

Premonitory orientational fluctuations above the first order phase transition of C_60 at 260K have been studied by diffuse X-ray scattering experiments. These experiments probe the orientational pair correlations between C_60 molecules as a function of their separation and therefore the orientational pair potential. In addition to the diffuse scattering due to the orientational disorder of single molecules, we have observed zone boundary diffuse scattering at the X-points related to the Pabar 3 low temperature structure up to 300K. An additional set of diffuse peaks, which are even at room temperature comparable in intensity to the former ones, have been found at (0.5,0.5,0.5) positions (L-point). Similar results have recently been reported by P. Launois et al. (P. Launois, S. Ravy, R. Moret, PRB 52), 5414 (1995) and L. Pintschovius et al. (L. Pintschovius, S.L. Chaplot, G. Roth, G. Heger, PRL 75), 2843 (1995) The temperature dependence of the integrated intensity of both sets of diffuse peaks shows only a weak increase in approaching T_c, indicative of a strongly first order transition. Additional intensity with a very weak temperature dependence but similar correlation length has also been found at (0.5,0.5,0) and (0.5,0,0) positions. The diffuse intensity at the L, Σ and Δ points has probably its origin in competing phases which are not stabilized at low temperatures. Recent DSC measurements show close lying transitions at 260K with a separation of ~= 0.2-0.3K which might be related to these competing phases footnote J. Fischer, private communication. The data will be compared with model calculations using orientational pair potentials which have been used in literature to describe the orientational phase transition in C_60.

Medium scale carbon nanotube thin film integrated circuits on flexible plastic substrates

DOEpatents

Rogers, John A; Cao, Qing; Alam, Muhammad; Pimparkar, Ninad

2015-02-03

The present invention provides device components geometries and fabrication strategies for enhancing the electronic performance of electronic devices based on thin films of randomly oriented or partially aligned semiconducting nanotubes. In certain aspects, devices and methods of the present invention incorporate a patterned layer of randomly oriented or partially aligned carbon nanotubes, such as one or more interconnected SWNT networks, providing a semiconductor channel exhibiting improved electronic properties relative to conventional nanotubes-based electronic systems.

Extending Single-Molecule Microscopy Using Optical Fourier Processing

PubMed Central

2015-01-01

This article surveys the recent application of optical Fourier processing to the long-established but still expanding field of single-molecule imaging and microscopy. A variety of single-molecule studies can benefit from the additional image information that can be obtained by modulating the Fourier, or pupil, plane of a widefield microscope. After briefly reviewing several current applications, we present a comprehensive and computationally efficient theoretical model for simulating single-molecule fluorescence as it propagates through an imaging system. Furthermore, we describe how phase/amplitude-modulating optics inserted in the imaging pathway may be modeled, especially at the Fourier plane. Finally, we discuss selected recent applications of Fourier processing methods to measure the orientation, depth, and rotational mobility of single fluorescent molecules. PMID:24745862

Extending single-molecule microscopy using optical Fourier processing.

PubMed

Backer, Adam S; Moerner, W E

2014-07-17

This article surveys the recent application of optical Fourier processing to the long-established but still expanding field of single-molecule imaging and microscopy. A variety of single-molecule studies can benefit from the additional image information that can be obtained by modulating the Fourier, or pupil, plane of a widefield microscope. After briefly reviewing several current applications, we present a comprehensive and computationally efficient theoretical model for simulating single-molecule fluorescence as it propagates through an imaging system. Furthermore, we describe how phase/amplitude-modulating optics inserted in the imaging pathway may be modeled, especially at the Fourier plane. Finally, we discuss selected recent applications of Fourier processing methods to measure the orientation, depth, and rotational mobility of single fluorescent molecules.

Early Visual Cortex Dynamics during Top-Down Modulated Shifts of Feature-Selective Attention.

PubMed

Müller, Matthias M; Trautmann, Mireille; Keitel, Christian

2016-04-01

Shifting attention from one color to another color or from color to another feature dimension such as shape or orientation is imperative when searching for a certain object in a cluttered scene. Most attention models that emphasize feature-based selection implicitly assume that all shifts in feature-selective attention underlie identical temporal dynamics. Here, we recorded time courses of behavioral data and steady-state visual evoked potentials (SSVEPs), an objective electrophysiological measure of neural dynamics in early visual cortex to investigate temporal dynamics when participants shifted attention from color or orientation toward color or orientation, respectively. SSVEPs were elicited by four random dot kinematograms that flickered at different frequencies. Each random dot kinematogram was composed of dashes that uniquely combined two features from the dimensions color (red or blue) and orientation (slash or backslash). Participants were cued to attend to one feature (such as color or orientation) and respond to coherent motion targets of the to-be-attended feature. We found that shifts toward color occurred earlier after the shifting cue compared with shifts toward orientation, regardless of the original feature (i.e., color or orientation). This was paralleled in SSVEP amplitude modulations as well as in the time course of behavioral data. Overall, our results suggest different neural dynamics during shifts of attention from color and orientation and the respective shifting destinations, namely, either toward color or toward orientation.

Growth of metal phthalocyanine on deactivated semiconducting surfaces steered by selective orbital coupling

DOE PAGES

Wagner, Sean R.; Feng, Jiagui; Yoon, Mina; ...

2015-08-25

Using scanning tunneling microscopy and density functional theory, we show that the molecular ordering and orientation of metal phthalocyanine molecules on the deactivated Si surface display a strong dependency on the central transition-metal ion, driven by the degree of orbital hybridization at the heterointerface via selective p – d orbital coupling. As a result, this Letter identifies a selective mechanism for modifying the molecule-substrate interaction which impacts the growth behavior of transition-metal-incorporated organic molecules on a technologically relevant substrate for silicon-based devices.

Orientational ordering of a banana-shaped solute molecule in a nematic calamitic solvent by {sup 2}H-NMR spectroscopy: An indication of glasslike behavior

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

Cinacchi, Giorgio; Domenici, Valentina

The Saupe ordering matrix of a banana-shaped mesogenic molecule as a solute in a common nematic calamitic solvent has been determined by {sup 2}H-NMR spectroscopy as a function of temperature. The temperature dependence of the Saupe ordering matrix element associated with the principal molecular axis is consistent with a glassy behavior in the reorientational motion of this particular solute molecule. The Haller expression, appropriately modified, provides a good fit to the experimental data.

Improving catalytic selectivity through control of adsorption orientation

NASA Astrophysics Data System (ADS)

Pang, Simon H.

In this thesis, we present an investigation, starting from surface science experiments, leading to design of supported catalysts, of how adsorption orientation can be used to affect reaction selectivity of highly functional molecules. The surface chemistry of furfuryl alcohol and benzyl alcohol and their respective aldehydes was studied on a Pd(111) single-crystal surface under ultra-high vacuum conditions. Temperature-programmed desorption experiments showed that synergistic chemistry existed between the aromatic ring and the oxygen-containing functional group, each allowing the other to participate in reaction pathways that a monofunctional molecule could not. Most important of these was a deoxygenation reaction that occurred more readily when the surface was crowded by the highest exposures. High-resolution electron energy loss spectroscopy revealed that at these high exposures, molecules were oriented upright on the surface, with the aromatic function extending into vacuum. In contrast, at low exposures, molecules were oriented flat on the surface. The upright adsorption geometry was correlated with deoxygenation, whereas the flat-lying geometry was correlated with decarbonylation. The insight gained from surface science experiments was utilized in catalyst design. Self-assembled monolayers of alkanethiolates were used to systematically reduce the average surface ensemble size, and the reaction selectivity was tracked. When a sparsely-packed monolayer was used, such as one formed by 1-adamantanethiol, the reactant furfural was still able to lie flat on the surface and the reaction selectivity was similar to that of the uncoated catalyst. However, when a densely-packed monolayer, formed by 1-octadecanethiol, was used, furfural was not able to adsorb flat on the surface and instead adopted an upright conformation, leading to a drastic increase in aldehyde hydrogenation and hydrodeoxygenation reaction selectivity. Using an even higher sulfur coverage from a monolayer formed by 1,2-benzenedithiol, we determined that hydrodeoxygenation selectively occurred on catalyst particle steps and edges from an upright structure, whereas decarbonylation occurred on particle terraces from a flat-lying structure. Control of furfural adsorption orientation was also achieved through the use of NiCu bimetallic catalysts. The aromatic furan ring was repelled from surface Cu, leading to an upright structure. However, under hydrogenation conditions, Ni tended to be near the surface of thin films and catalysts, leading to less dramatic selectivity enhancement. The presence of a 1-octadecanethiol monolayer kinetically stabilized the surface termination, allowing Cu to remain at the surface.

Adsorption of 6-mercaptopurine and 6-mercaptopurine riboside on silver colloid: a pH dependent surface enhanced Raman spectroscopy and density functional theory study. Part I. 6-Mercaptopurine

NASA Astrophysics Data System (ADS)

Szeghalmi, A. V.; Leopold, L.; Pînzaru, S.; Chis, V.; Silaghi-Dumitrescu, I.; Schmitt, M.; Popp, J.; Kiefer, W.

2005-02-01

Surface enhanced Raman spectroscopy (SERS) on silver colloid has been applied to characterize the interaction of 6-mercaptopurine (6MP), an active drug used in chemotherapy of acute lymphoblastic leukemia, with a model biological substrate at therapeutical concentrations and as function of the pH value. The adsorption active sites and molecular orientation on the metal surface have been determined on the basis of SERS 'surface selection rules' subsequent to a detailed vibrational analysis of the 6MP tautomeric forms. Therefore, DFT calculations (vibrational wavenumbers, Raman scattering activities, partial atomic charges) of the optimized tautomers and potential energy distribution calculations have been performed. Around neutral pH value reorientation of the molecule has been observed. Under basic conditions the 6MP molecule is probably adsorbed on the silver colloid through the N1 atom of the purine ring and possibly the S atom, and adopts a tilted orientation to the surface. A reduction in the number of adsorbed molecules under basic conditions is proposed, since the SERS spectrum recorded at 10-6 M concentration at neutral pH value resembles the SERS spectra obtained under basic conditions at 10-5 M concentration. At acidic pH values a stronger interaction through the N9 and N3 atoms is suggested with an end-on orientation.

DNA Molecules Adsorbed on Rippled Supported Cationic Lipid Membranes -- A new way to stretch DNAs

NASA Astrophysics Data System (ADS)

Golubovic, Leonardo

2005-03-01

We discuss a novel approach to control to shapes of DNA molecules. We elucidate the recent experimental work of M. Hochrein, L. Golubovic and J. Raedler, on the conformational behavior of DNA molecules adsorbed on lipid membranes that are supported on grooved micro-structured surfaces. We explain the striking ability of the edges formed on these supported membranes to adsorb and completely orient (stretch) very long DNA molecules. Here we explain the experimentally observed DNA stretching effect in terms of the surface curvature dependent electrostatic potential seen by the adsorbed DNA molecules. On the curved, rippled membrane, we show that the DNA molecules undergo localization transitions causing them to stretch by binding to the ripple edges of the supported membrane. In the future, this stretching will allow to directly image, by the common fluorescence microscopy, fundamental biological processes of the interactions between DNA and single protein molecules.

Atomistic simulation of orientation dependence in shock-induced initiation of pentaerythritol tetranitrate.

PubMed

Shan, Tzu-Ray; Wixom, Ryan R; Mattsson, Ann E; Thompson, Aidan P

2013-01-24

The dependence of the reaction initiation mechanism of pentaerythritol tetranitrate (PETN) on shock orientation and shock strength is investigated with molecular dynamics simulations using a reactive force field and the multiscale shock technique. In the simulations, a single crystal of PETN is shocked along the [110], [001], and [100] orientations with shock velocities in the range 3-10 km/s. Reactions occur with shock velocities of 6 km/s or stronger, and reactions initiate through the dissociation of nitro and nitrate groups from the PETN molecules. The most sensitive orientation is [110], while [100] is the most insensitive. For the [001] orientation, PETN decomposition via nitro group dissociation is the dominant reaction initiation mechanism, while for the [110] and [100] orientations the decomposition is via mixed nitro and nitrate group dissociation. For shock along the [001] orientation, we find that CO-NO(2) bonds initially acquire more kinetic energy, facilitating nitro dissociation. For the other two orientations, C-ONO(2) bonds acquire more kinetic energy, facilitating nitrate group dissociation.

Robotic virtual reality simulation plus standard robotic orientation versus standard robotic orientation alone: a randomized controlled trial.

PubMed

Vaccaro, Christine M; Crisp, Catrina C; Fellner, Angela N; Jackson, Christopher; Kleeman, Steven D; Pavelka, James

2013-01-01

The objective of this study was to compare the effect of virtual reality simulation training plus robotic orientation versus robotic orientation alone on performance of surgical tasks using an inanimate model. Surgical resident physicians were enrolled in this assessor-blinded randomized controlled trial. Residents were randomized to receive either (1) robotic virtual reality simulation training plus standard robotic orientation or (2) standard robotic orientation alone. Performance of surgical tasks was assessed at baseline and after the intervention. Nine of 33 modules from the da Vinci Skills Simulator were chosen. Experts in robotic surgery evaluated each resident's videotaped performance of the inanimate model using the Global Rating Scale (GRS) and Objective Structured Assessment of Technical Skills-modified for robotic-assisted surgery (rOSATS). Nine resident physicians were enrolled in the simulation group and 9 in the control group. As a whole, participants improved their total time, time to incision, and suture time from baseline to repeat testing on the inanimate model (P = 0.001, 0.003, <0.001, respectively). Both groups improved their GRS and rOSATS scores significantly (both P < 0.001); however, the GRS overall pass rate was higher in the simulation group compared with the control group (89% vs 44%, P = 0.066). Standard robotic orientation and/or robotic virtual reality simulation improve surgical skills on an inanimate model, although this may be a function of the initial "practice" on the inanimate model and repeat testing of a known task. However, robotic virtual reality simulation training increases GRS pass rates consistent with improved robotic technical skills learned in a virtual reality environment.

Motivation and Cognition: The Impact of Ego and Task-Involvement on Levels of Processing.

ERIC Educational Resources Information Center

Golan, Shari; Graham, Sandra

To study the effects of motivation on cognition, 55 fifth- and sixth-grade students were randomly assigned to 3 motivational treatment groups: (1) ego-involved (ability oriented); (2) task-involved (mastery oriented); and (3) control (no orientation). The ego-involvement treatment attempted to make subjects feel that their abilities on the tasks…

Surface Plasmon Resonance kinetic analysis of the interaction between G-quadruplex nucleic acids and an anti-G-quadruplex monoclonal antibody.

PubMed

Lago, Sara; Nadai, Matteo; Rossetto, Monica; Richter, Sara N

2018-06-01

G-quadruplexes (G4s) are nucleic acids secondary structures formed in guanine-rich sequences. Anti-G4 antibodies represent a tool for the direct investigation of G4s in cells. Surface Plasmon Resonance (SPR) is a highly sensitive technology, suitable for assessing the affinity between biomolecules. We here aimed at improving the orientation of an anti-G4 antibody on the SPR sensor chip to optimize detection of binding antigens. SPR was employed to characterize the anti-G4 antibody interaction with G4 and non-G4 oligonucleotides. Dextran-functionalized sensor chips were used both in covalent coupling and capturing procedures. The use of two leading molecule for orienting the antibody of interest allowed to improve its activity from completely non-functional to 65% active. The specificity of the anti-G4 antobody for G4 structures could thus be assessed with high sensitivity and reliability. Optimization of the immobilization protocol for SPR biosensing, allowed us to determine the anti-G4 antibody affinity and specificity for G4 antigens with higher sensitivity with respect to other in vitro assays such as ELISA. Anti-G4 antibody specificity is a fundamental assumption for the future utilization of this kind of antibodies for monitoring G4s directly in cells. The heterogeneous orientation of amine-coupling immobilized ligands is a general problem that often leads to partial or complete inactivation of the molecules. Here we describe a new strategy for improving ligand orientation: driving it from two sides. This principle can be virtually applied to every molecule that loses its activity or is poorly immobilized after standard coupling to the SPR chip surface. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Orientation of Myosin Binding Protein C in the Cardiac Muscle Sarcomere Determined by Domain-Specific Immuno-EM

PubMed Central

Lee, Kyounghwan; Harris, Samantha P.; Sadayappan, Sakthivel; Craig, Roger

2014-01-01

Myosin binding protein-C is a thick filament protein of vertebrate striated muscle. The cardiac isoform (cMyBP-C) is essential for normal cardiac function, and mutations in cMyBP-C cause cardiac muscle disease. The rod-shaped molecule is composed primarily of 11 immunoglobulin- or fibronectin-like domains, and is located at 9 sites, 43 nm apart, in each half of the A-band. To understand how cMyBP-C functions, it is important to know its structural organization in the sarcomere, as this will affect its ability to interact with other sarcomeric proteins. Several models have been proposed, in which cMyBP-C wraps around, extends radially from, or runs axially along the thick filament. Our goal was to define cMyBP-C orientation by determining the relative axial positions of different cMyBP-C domains. Immuno-electron microscopy was performed using mouse cardiac myofibrils labeled with antibodies specific to the N- and C-terminal domains and to the middle of cMyBP-C. Antibodies to all regions of the molecule, except the C-terminus, labeled at the same nine axial positions in each half A-band, consistent with a circumferential and/or radial rather than an axial orientation of the bulk of the molecule. The C-terminal antibody stripes were slightly displaced axially, demonstrating an axial orientation of the C-terminal 3 domains, with the C-terminus closer to the M-line. These results, combined with previous studies, suggest that the C-terminal domains of cMyBP-C run along the thick filament surface, while the N-terminus extends towards neighboring thin filaments. This organization provides a structural framework for understanding cMyBP-C’s modulation of cardiac muscle contraction. PMID:25451032

Insight into the molecular mechanism of water evaporation via the finite temperature string method.

PubMed

Musolino, Nicholas; Trout, Bernhardt L

2013-04-07

The process of water's evaporation at its liquid/air interface has proven challenging to study experimentally and, because it constitutes a rare event on molecular time scales, presents a challenge for computer simulations as well. In this work, we simulated water's evaporation using the classical extended simple point charge model water model, and identified a minimum free energy path for this process in terms of 10 descriptive order parameters. The measured free energy change was 7.4 kcal/mol at 298 K, in reasonable agreement with the experimental value of 6.3 kcal/mol, and the mean first-passage time was 1375 ns for a single molecule, corresponding to an evaporation coefficient of 0.25. In the observed minimum free energy process, the water molecule diffuses to the surface, and tends to rotate so that its dipole and one O-H bond are oriented outward as it crosses the Gibbs dividing surface. As the water molecule moves further outward through the interfacial region, its local density is higher than the time-averaged density, indicating a local solvation shell that protrudes from the interface. The water molecule loses donor and acceptor hydrogen bonds, and then, with its dipole nearly normal to the interface, stops donating its remaining hydrogen bond. At that point, when the final, accepted hydrogen bond is broken, the water molecule is free. We also analyzed which order parameters are most important in the process and in reactive trajectories, and found that the relative orientation of water molecules near the evaporating molecule, and the number of accepted hydrogen bonds, were important variables in reactive trajectories and in kinetic descriptions of the process.

Comparison of cell behavior on pva/pva-gelatin electrospun nanofibers with random and aligned configuration

NASA Astrophysics Data System (ADS)

Huang, Chen-Yu; Hu, Keng-Hsiang; Wei, Zung-Hang

2016-12-01

Electrospinning technique is able to create nanofibers with specific orientation. Poly(vinyl alcohol) (PVA) have good mechanical stability but poor cell adhesion property due to the low affinity of protein. In this paper, extracellular matrix, gelatin is incorporated into PVA solution to form electrospun PVA-gelatin nanofibers membrane. Both randomly oriented and aligned nanofibers are used to investigate the topography-induced behavior of fibroblasts. Surface morphology of the fibers is studied by optical microscopy and scanning electron microscopy (SEM) coupled with image analysis. Functional group composition in PVA or PVA-gelatin is investigated by Fourier Transform Infrared (FTIR). The morphological changes, surface coverage, viability and proliferation of fibroblasts influenced by PVA and PVA-gelatin nanofibers with randomly orientated or aligned configuration are systematically compared. Fibroblasts growing on PVA-gelatin fibers show significantly larger projected areas as compared with those cultivated on PVA fibers which p-value is smaller than 0.005. Cells on PVA-gelatin aligned fibers stretch out extensively and their intracellular stress fiber pull nucleus to deform. Results suggest that instead of the anisotropic topology within the scaffold trigger the preferential orientation of cells, the adhesion of cell membrane to gelatin have substantial influence on cellular behavior.

Limited capacity of working memory in unihemispheric random walks implies conceivable slow dispersal.

PubMed

Wei, Kun; Zhong, Suchuan

2017-08-01

Phenomenologically inspired by dolphins' unihemispheric sleep, we introduce a minimal model for random walks with physiological memory. The physiological memory consists of long-term memory which includes unconscious implicit memory and conscious explicit memory, and working memory which serves as a multi-component system for integrating, manipulating and managing short-term storage. The model assumes that the sleeping state allows retrievals of episodic objects merely from the episodic buffer where these memory objects are invoked corresponding to the ambient objects and are thus object-oriented, together with intermittent but increasing use of implicit memory in which decisions are unconsciously picked up from historical time series. The process of memory decay and forgetting is constructed in the episodic buffer. The walker's risk attitude, as a product of physiological heuristics according to the performance of objected-oriented decisions, is imposed on implicit memory. The analytical results of unihemispheric random walks with the mixture of object-oriented and time-oriented memory, as well as the long-time behavior which tends to the use of implicit memory, are provided, indicating the common sense that a conservative risk attitude is inclinable to slow movement.

Energy level alignment at planar organic heterojunctions: influence of contact doping and molecular orientation.

PubMed

Opitz, Andreas

2017-04-05

Planar organic heterojunctions are widely used in photovoltaic cells, light-emitting diodes, and bilayer field-effect transistors. The energy level alignment in the devices plays an important role in obtaining the aspired gap arrangement. Additionally, the π-orbital overlap between the involved molecules defines e.g. the charge-separation efficiency in solar cells due to charge-transfer effects. To account for both aspects, direct/inverse photoemission spectroscopy and near edge x-ray absorption fine structure spectroscopy were used to determine the energy level landscape and the molecular orientation at prototypical planar organic heterojunctions. The combined experimental approach results in a comprehensive model for the electronic and morphological characteristics of the interface between the two investigated molecular semiconductors. Following an introduction on heterojunctions used in devices and on energy levels of organic materials, the energy level alignment of planar organic heterojunctions will be discussed. The observed energy landscape is always determined by the individual arrangement between the energy levels of the molecules and the work function of the electrode. This might result in contact doping due to Fermi level pinning at the electrode for donor/acceptor heterojunctions, which also improves the solar cell efficiency. This pinning behaviour can be observed across an unpinned interlayer and results in charge accumulation at the donor/acceptor interface, depending on the transport levels of the respective organic semiconductors. Moreover, molecular orientation will affect the energy levels because of the anisotropy in ionisation energy and electron affinity and is influenced by the structural compatibility of the involved molecules at the heterojunction. High structural compatibility leads to π-orbital stacking between different molecules at a heterojunction, which is of additional interest for photovoltaic active interfaces and for ground-state charge-transfer.

Feasibility study on the use of liquid crystal/dye cells for digital signage

NASA Astrophysics Data System (ADS)

Itaya, Shunsuke; Azumi, Nada Dianah B. M.; Ohta, Masamichi; Ozawa, Shintaro; Fujieda, Ichiro

2016-03-01

Elongated dye molecules orient themselves with surrounding liquid crystal molecules. We propose to incorporate such a guest-host cell in a screen of a projection display. This configuration might be applied for digital signage to be installed on building walls. Dual-mode operation is realized by the bias applied to the cell. In display-mode, the dye molecules are oriented in parallel to the substrate of the cell. When excited by ultra-violet light, photoluminescence (PL) is generated. Because it is mostly perpendicular to the long axis of the molecule, it exits the cell efficiently. In powerharvesting mode, they are oriented vertically. The PL generated by ambient light is directed to edge surfaces where solar cells are mounted. In experiment, we fabricated a cell with commonly-available materials (coumarin 6 and a nematic liquid crystal). Anti-parallel alignment condition was adopted. We recorded PL spectra from the cell for the two excitation conditions. First, the center of the cell was irradiated by a 1.69mW blue laser beam. Second, the whole cell was uniformly exposed to the light from a fluorescent lamp at illuminance of 800lx. From the measured spectra for these cases, the contrast of luminance is calculated to be 3.2 ×105 . This factor is improved to 5 7.5×105 by attaching a polarizer sheet on the cell surface. The optical power reaching its edge surfaces is measured and it roughly agrees with the prediction by a simple model neglecting self-absorption. Development of phosphor materials with a large Stokes shift is desired to boost performance of the proposed system.

Molecular relaxations, molecular orientation, and the friction characteristics of polyimide films. [wear characteristics of polymeric lubricant

NASA Technical Reports Server (NTRS)

Fusaro, R. L.

1975-01-01

The friction characteristics of polyimide films bonded to metallic substrates were studied from 25 to 500 C. These results were interpreted in terms of molecular orientation and thermomechanical data obtained by torsional braid analysis (TBA). A large friction transition was found to occur at 40 + or - 10 C in a dry argon atmosphere (10 ppm H2O). It was postulated that the mechanical stresses of sliding transform or reorder the molecules on the surface into a configuration conducive to easy shear, such as an extended chain. The molecular relaxation which occurs in this temperature region appears to give the molecules the necessary freedom for this reordering process to occur. The effects of velocity, reversibility, and thermal prehistory on the friction properties of polyimide were also studied.

Molecular relaxations, molecular orientation and the friction characteristics of polyimide films

NASA Technical Reports Server (NTRS)

Fusaro, R. L.

1975-01-01

The friction characteristics of polyimide films bonded to metallic substrates were studied from 25 to 500 C. These results were interpreted in terms of molecular orientation and thermomechanical data obtained by torsional braid analysis (TBA). A large friction transition was found to occur at 40 plus or minus 10 C in a dry argon atmosphere (10 ppm H2O). It was postulated that the mechanical stresses of sliding transform or reorder the molecules on the surface into a configuration conducive to easy shear, such as an extended chain. The molecular relaxation which occurs in this temperature region appears to give the molecules the necessary freedom for this reordering process to occur. The effects of velocity, reversibility, and thermal prehistory on the friction properties of polyimide were also studied.

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data

DOE PAGES

Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S.; ...

2017-02-23

Here, a newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides,more » important for metal extraction chemistry, are parametrized using ParFit.« less

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data

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

Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S.

Here, a newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides,more » important for metal extraction chemistry, are parametrized using ParFit.« less

Realignment of Nanocrystal Aggregates into Single Crystals as a Result of Inherent Surface Stress

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

Liu, Zhaoming; Pan, Haihua; Zhu, Genxing

2016-07-19

Assembly of nanoparticles building blocks during single crystal growth is widely observed in both natural and synthetic environments. Although this form of non-classical crystallization is generally described by oriented attachment, random aggregation of building blocks leading to single crystal products is also observed, but the mechanism of crystallographic realignment is unknown. We herein reveal that random attachment during aggregation-based growth initially produces a non-oriented growth front. Subsequent evolution of the orientation is driven by the inherent surface stress applied by the disordered surface layer and results in single crystal formation via grain boundary migration. This mechanism is corroborated by measurementsmore » of orientation rate vs external stress, demonstrating a predictive relationship between the two. These findings advance our understanding of aggregation-based growth of natural minerals by nanocrystals, and suggest an approach to material synthesis that takes advantage of stress induced co-alignment.« less

Accelerometry Measuring the Outcome of Robot-Supported Upper Limb Training in Chronic Stroke: A Randomized Controlled Trial

PubMed Central

Lemmens, Ryanne J. M.; Timmermans, Annick A. A.; Janssen-Potten, Yvonne J. M.; Pulles, Sanne A. N. T. D.; Geers, Richard P. J.; Bakx, Wilbert G. M.; Smeets, Rob J. E. M.; Seelen, Henk A. M.

2014-01-01

Purpose This study aims to assess the extent to which accelerometers can be used to determine the effect of robot-supported task-oriented arm-hand training, relative to task-oriented arm-hand training alone, on the actual amount of arm-hand use of chronic stroke patients in their home situation. Methods This single-blind randomized controlled trial included 16 chronic stroke patients, randomly allocated using blocked randomization (n = 2) to receive task-oriented robot-supported arm-hand training or task-oriented (unsupported) arm-hand training. Training lasted 8 weeks, 4 times/week, 2×30 min/day using the (T-)TOAT ((Technology-supported)-Task-Oriented-Arm-Training) method. The actual amount of arm-hand use, was assessed at baseline, after 8 weeks training and 6 months after training cessation. Duration of use and intensity of use of the affected arm-hand during unimanual and bimanual activities were calculated. Results Duration and intensity of use of the affected arm-hand did not change significantly during and after training, with or without robot-support (i.e. duration of use of unimanual use of the affected arm-hand: median difference of −0.17% in the robot-group and −0.08% in the control group between baseline and after training cessation; intensity of the affected arm-hand: median difference of 3.95% in the robot-group and 3.32% in the control group between baseline and after training cessation). No significant between-group differences were found. Conclusions Accelerometer data did not show significant changes in actual amount of arm-hand use after task-oriented training, with or without robot-support. Next to the amount of use, discrimination between activities performed and information about quality of use of the affected arm-hand are essential to determine actual arm-hand performance. Trial Registration Controlled-trials.com ISRCTN82787126 PMID:24823925

Algebraic Approximations to Extinction from Randomly Oriented Circular and Elliptical Cylinders

DTIC Science & Technology

1995-06-01

amplitude (Ref. 3). The strict limit of validity of the formula is therefore the region where ( n - 1) < < 1. The cylinder is in effect treated as a slit... cylinders , l¢1x = 2Im -1lx << 1. This occurs since what we have been calling an edge effect is in fact the field distortion around the boundaries of the...ALGERBRAIC APPROXIMATIONS TO EXTINCTION FROM RANDOMLY ORIENTED CIRCULAR AND ELLIPTICAL CYLINDERS system Number: Patron Number: Requester: Notes

Adsorption of Pyridine at the Au(100)-Solution Interface.

DTIC Science & Technology

1987-09-25

quatiatively characterize the energetics of pyridine adsorption onto a gold ( 100) single crystal electrode surface. Over the potential region investigated...0.8 to +0.6 A., three orientationis of the pyridine molecules on the gold surface have been observed. The pyridine orientation Is strongly 1nflue ied by...the electrode potential. At a positively charged surface, the pyridine assumes a verticle orientation with .fie nitrogen atom facing the gold surface

Random walk of passive tracers among randomly moving obstacles.

PubMed

Gori, Matteo; Donato, Irene; Floriani, Elena; Nardecchia, Ilaria; Pettini, Marco

2016-04-14

This study is mainly motivated by the need of understanding how the diffusion behavior of a biomolecule (or even of a larger object) is affected by other moving macromolecules, organelles, and so on, inside a living cell, whence the possibility of understanding whether or not a randomly walking biomolecule is also subject to a long-range force field driving it to its target. By means of the Continuous Time Random Walk (CTRW) technique the topic of random walk in random environment is here considered in the case of a passively diffusing particle among randomly moving and interacting obstacles. The relevant physical quantity which is worked out is the diffusion coefficient of the passive tracer which is computed as a function of the average inter-obstacles distance. The results reported here suggest that if a biomolecule, let us call it a test molecule, moves towards its target in the presence of other independently interacting molecules, its motion can be considerably slowed down.

Separating the Laparoscopic Camera Cord From the Monopolar "Bovie" Cord Reduces Unintended Thermal Injury From Antenna Coupling: A Randomized Controlled Trial.

PubMed

Robinson, Thomas N; Jones, Edward L; Dunn, Christina L; Dunne, Bruce; Johnson, Elizabeth; Townsend, Nicole T; Paniccia, Alessandro; Stiegmann, Greg V

2015-06-01

The monopolar "Bovie" is used in virtually every laparoscopic operation. The active electrode and its cord emit radiofrequency energy that couples (or transfers) to nearby conductive material without direct contact. This phenomenon is increased when the active electrode cord is oriented parallel to another wire/cord. The parallel orientation of the "Bovie" and laparoscopic camera cords cause transfer of energy to the camera cord resulting in cutaneous burns at the camera trocar incision. We hypothesized that separating the active electrode/camera cords would reduce thermal injury occurring at the camera trocar incision in comparison to parallel oriented active electrode/camera cords. In this prospective, blinded, randomized controlled trial, patients undergoing standardized laparoscopic cholecystectomy were randomized to separated active electrode/camera cords or parallel oriented active electrode/camera cords. The primary outcome variable was thermal injury determined by histology from skin biopsied at the camera trocar incision. Eighty-four patients participated. Baseline demographics were similar in the groups for age, sex, preoperative diagnosis, operative time, and blood loss. Thermal injury at the camera trocar incision was lower in the separated versus parallel group (31% vs 57%; P = 0.027). Separation of the laparoscopic camera cord from the active electrode cord decreases thermal injury from antenna coupling at the camera trocar incision in comparison to the parallel orientation of these cords. Therefore, parallel orientation of these cords (an arrangement promoted by integrated operating rooms) should be abandoned. The findings of this study should influence the operating room setup for all laparoscopic cases.

Texture and anisotropy in ferroelectric lead metaniobate

NASA Astrophysics Data System (ADS)

Iverson, Benjamin John

Ferroelectric lead metaniobate, PbNb2O6, is a piezoelectric ceramic typically used because of its elevated Curie temperature and anisotropic properties. However, the piezoelectric constant, d33, is relatively low in randomly oriented ceramics when compared to other ferroelectrics. Crystallographic texturing is often employed to increase the piezoelectric constant because the spontaneous polarization axes of grains are better aligned. In this research, crystallographic textures induced through tape casting are distinguished from textures induced through electrical poling. Texture is described using multiple quantitative approaches utilizing X-ray and neutron time-of-flight diffraction. Tape casting lead metaniobate with an inclusion of acicular template particles induces an orthotropic texture distribution. Templated grain growth from seed particles oriented during casting results in anisotropic grain structures. The degree of preferred orientation is directly linked to the shear behavior of the tape cast slurry. Increases in template concentration, slurry viscosity, and casting velocity lead to larger textures by inducing more particle orientation in the tape casting plane. The maximum 010 texture distributions were two and a half multiples of a random distribution. Ferroelectric texture was induced by electrical poling. Electric poling increases the volume of material oriented with the spontaneous polarization direction in the material. Samples with an initial paraelectric texture exhibit a greater change in the domain volume fraction during electrical poling than randomly oriented ceramics. In tape cast samples, the resulting piezoelectric response is proportional to the 010 texture present prior to poling. This results in property anisotropy dependent on initial texture. Piezoelectric properties measured on the most textured ceramics were similar to those obtained with a commercial standard.

Engineering giant magnetic anisotropy in single-molecule magnets by dimerizing heavy transition-metal atoms

NASA Astrophysics Data System (ADS)

Qu, Jiaxing; Hu, Jun

2018-05-01

The search for single-molecule magnets with large magnetic anisotropy energy (MAE) is essential for the development of molecular spintronics devices for use at room temperature. Through systematic first-principles calculations, we found that an Os–Os or Ir–Ir dimer embedded in the (5,5‧-Br2-salophen) molecule gives rise to a large MAE of 41.6 or 51.4 meV, respectively, which is large enough to hold the spin orientation at room temperature. Analysis of the electronic structures reveals that the top Os and Ir atoms play the most important part in the total spin moments and large MAEs of the molecules.

Exciton Transport Simulations in Phenyl Cored Thiophene Dendrimers

NASA Astrophysics Data System (ADS)

Kim, Kwiseon; Erkan Kose, Muhammet; Graf, Peter; Kopidakis, Nikos; Rumbles, Garry; Shaheen, Sean E.

2009-03-01

Phenyl cored 3-arm and 4-arm thiophene dendrimers are promising materials for use in photovoltaic devices. It is important to understand the energy transfer mechanisms in these molecules to guide the synthesis of novel dendrimers with improved efficiency. A method is developed to estimate the exciton diffusion lengths for the dendrimers and similar chromophores in amorphous films. The approach exploits Fermi's Golden Rule to estimate the energy transfer rates for an ensemble of bimolecular complexes in random orientations. Using Poisson's equation to evaluate Coulomb integrals led to efficient calculation of excitonic couplings between the transition densities. Monte-Carlo simulations revealed the dynamics of energy transport in the dendrimers. Experimental exciton diffusion lengths of the dendrimers range 10 ˜ 20 nm, increasing with the size of the dendrimer. Simulated diffusion lengths correlate well with experiments. The chemical structure of the chromophore, the shape of the transition densities and the exciton lifetime are found to be the most important factors that determine the exciton diffusion length in amorphous films.

On remote sensing of small aerosol particles with polarized light

NASA Astrophysics Data System (ADS)

Sun, W.

2012-12-01

The CALIPSO satellite mission consistently measures volume (including molecule and particulate) light depolarization ratio of ~2% for smoke, compared to ~1% for marine aerosols and ~15% for dust. The observed ~2% smoke depolarization ratio comes primarily from the nonspherical habits of particles in the smoke at certain particle sizes. The depolarization of linearly polarized light by small sphere aggregates and irregular Gaussian-shaped particles is studied, to reveal the physics between the depolarization of linearly polarized light and aerosol shape and size. It is found that randomly oriented nonspherical particles have some common depolarization properties as functions of scattering angle and size parameter. This may be very useful information for active remote sensing of small nonspherical aerosols using polarized light. We also show that the depolarization ratio from the CALIPSO measurements could be used to derive smoke aerosol particle size. The mean particle size of South-African smoke is estimated to be about half of the 532 nm wavelength of the CALIPSO lidar.

Rapid prototyping of nanofluidic systems using size-reduced electrospun nanofibers for biomolecular analysis.

PubMed

Park, Seung-Min; Huh, Yun Suk; Szeto, Kylan; Joe, Daniel J; Kameoka, Jun; Coates, Geoffrey W; Edel, Joshua B; Erickson, David; Craighead, Harold G

2010-11-05

Biomolecular transport in nanofluidic confinement offers various means to investigate the behavior of biomolecules in their native aqueous environments, and to develop tools for diverse single-molecule manipulations. Recently, a number of simple nanofluidic fabrication techniques has been demonstrated that utilize electrospun nanofibers as a backbone structure. These techniques are limited by the arbitrary dimension of the resulting nanochannels due to the random nature of electrospinning. Here, a new method for fabricating nanofluidic systems from size-reduced electrospun nanofibers is reported and demonstrated. As it is demonstrated, this method uses the scanned electrospinning technique for generation of oriented sacrificial nanofibers and exposes these nanofibers to harsh, but isotropic etching/heating environments to reduce their cross-sectional dimension. The creation of various nanofluidic systems as small as 20 nm is demonstrated, and practical examples of single biomolecular handling, such as DNA elongation in nanochannels and fluorescence correlation spectroscopic analysis of biomolecules passing through nanochannels, are provided.

Terahertz spectroscopic analysis of crystal orientation in polymers

NASA Astrophysics Data System (ADS)

Azeyanagi, Chisato; Kaneko, Takuya; Ohki, Yoshimichi

2018-05-01

Terahertz time-domain spectroscopy (THz-TDS) is attracting keen attention as a new spectroscopic tool for characterizing various materials. In this research, the possibility of analyzing the crystal orientation in a crystalline polymer by THz-TDS is investigated by measuring angle-resolved THz absorption spectra for sheets of poly(ethylene terephthalate), poly(ethylene naphthalate), and poly(phenylene sulfide). The resultant angle dependence of the absorption intensity of each polymer is similar to that of the crystal orientation examined using pole figures of X-ray diffraction. More specifically, THz-TDS can indicate the alignment of molecules in polymers.

Interaction of dyes CD–1 and SD–1 with the surface of oligodimethysiloxane

NASA Astrophysics Data System (ADS)

Chausov, D. N.

2018-03-01

We carried out the modeling orientation of the dyes CD–1 and SD–1 relative to the surface of oligodimethysiloxane using the atom–atom potentials method. We have discovered the dependence of the interaction energy in dyes molecules on the angles which characterizes their orientation relative to the surface of the oligodimethysiloxane crystal. It was found out that the obtained energy value of interaction with the surface can explain weak adhesive qualities of the dyes and the orientation type relative to the surface. We identified the break– loose force for the dyes on the oligodimethysiloxane crystal surface.

Role of step edges on the structure formation of α-6T on Ag(441)

NASA Astrophysics Data System (ADS)

Wagner, Thorsten; Fritz, Daniel Roman; Rudolfová, Zdena; Zeppenfeld, Peter

2018-01-01

Controlling the orientation of organic molecules on surfaces is important in order to tune the physical properties of the organic thin films and, thereby, increase the performance of organic thin film devices. Here, we present a scanning tunneling microscopy (STM) and photoelectron emission microscopy (PEEM) study of the deposition of the organic dye pigment α-sexithiophene (α-6T) on the vicinal Ag(441) surface. In the presence of the steps on the Ag(441) surface, the α-6T molecules exclusively align parallel to the step edges oriented along the [1 1 bar0]-direction of the substrate. The STM results further reveal that the adsorption of the α-6T molecules is accompanied by various restructuring of the substrate surface: Initially, the molecules prefer the Ag(551) building blocks of the Ag(441) surface. The Ag(551) termination of the terraces is then changed to a predominately Ag(331) one upon completion of the first α-6T monolayer. When closing the two layer thick wetting layer, the original ratio of Ag(331) and Ag(551) building blocks ( ≈ 1:1) is recovered, but a phase separation into microfacets, which are composed either of Ag(331) or of Ag(551) building blocks, is found.

Oil Contact Angles in a Water-Decane-Silicon Dioxide System: Effects of Surface Charge

NASA Astrophysics Data System (ADS)

Xu, Shijing; Wang, Jingyao; Wu, Jiazhong; Liu, Qingjie; Sun, Chengzhen; Bai, Bofeng

2018-04-01

Oil wettability in the water-oil-rock systems is very sensitive to the evolution of surface charges on the rock surfaces induced by the adsorption of ions and other chemical agents in water flooding. Through a set of large-scale molecular dynamics simulations, we reveal the effects of surface charge on the oil contact angles in an ideal water-decane-silicon dioxide system. The results show that the contact angles of oil nano-droplets have a great dependence on the surface charges. As the surface charge density exceeds a critical value of 0.992 e/nm2, the contact angle reaches up to 78.8° and the water-wet state is very apparent. The variation of contact angles can be confirmed from the number density distributions of oil molecules. With increasing the surface charge density, the adsorption of oil molecules weakens and the contact areas between nano-droplets and silicon dioxide surface are reduced. In addition, the number density distributions, RDF distributions, and molecular orientations indicate that the oil molecules are adsorbed on the silicon dioxide surface layer-by-layer with an orientation parallel to the surface. However, the layered structure of oil molecules near the silicon dioxide surface becomes more and more obscure at higher surface charge densities.

Using a water-confined carbon nanotube to probe the electricity of sequential charged segments of macromolecules

NASA Astrophysics Data System (ADS)

Wang, Yu; Zhao, Yan-Jiao; Huang, Ji-Ping

2012-07-01

The detection of macromolecular conformation is particularly important in many physical and biological applications. Here we theoretically explore a method for achieving this detection by probing the electricity of sequential charged segments of macromolecules. Our analysis is based on molecular dynamics simulations, and we investigate a single file of water molecules confined in a half-capped single-walled carbon nanotube (SWCNT) with an external electric charge of +e or -e (e is the elementary charge). The charge is located in the vicinity of the cap of the SWCNT and along the centerline of the SWCNT. We reveal the picosecond timescale for the re-orientation (namely, from one unidirectional direction to the other) of the water molecules in response to a switch in the charge signal, -e → +e or +e → -e. Our results are well understood by taking into account the electrical interactions between the water molecules and between the water molecules and the external charge. Because such signals of re-orientation can be magnified and transported according to Tu et al. [2009 Proc. Natl. Acad. Sci. USA 106 18120], it becomes possible to record fingerprints of electric signals arising from sequential charged segments of a macromolecule, which are expected to be useful for recognizing the conformations of some particular macromolecules.

Oil Contact Angles in a Water-Decane-Silicon Dioxide System: Effects of Surface Charge.

PubMed

Xu, Shijing; Wang, Jingyao; Wu, Jiazhong; Liu, Qingjie; Sun, Chengzhen; Bai, Bofeng

2018-04-19

Oil wettability in the water-oil-rock systems is very sensitive to the evolution of surface charges on the rock surfaces induced by the adsorption of ions and other chemical agents in water flooding. Through a set of large-scale molecular dynamics simulations, we reveal the effects of surface charge on the oil contact angles in an ideal water-decane-silicon dioxide system. The results show that the contact angles of oil nano-droplets have a great dependence on the surface charges. As the surface charge density exceeds a critical value of 0.992 e/nm 2 , the contact angle reaches up to 78.8° and the water-wet state is very apparent. The variation of contact angles can be confirmed from the number density distributions of oil molecules. With increasing the surface charge density, the adsorption of oil molecules weakens and the contact areas between nano-droplets and silicon dioxide surface are reduced. In addition, the number density distributions, RDF distributions, and molecular orientations indicate that the oil molecules are adsorbed on the silicon dioxide surface layer-by-layer with an orientation parallel to the surface. However, the layered structure of oil molecules near the silicon dioxide surface becomes more and more obscure at higher surface charge densities.

Controlling the orientation of spin-correlated radical pairs by covalent linkage to nanoporous anodic aluminum oxide membranes.

PubMed

Chen, Hsiao-Fan; Gardner, Daniel M; Carmieli, Raanan; Wasielewski, Michael R

2013-10-07

Ordered multi-spin assemblies are required for developing solid-state molecule-based spintronics. A linear donor-chromophore-acceptor (D-C-A) molecule was covalently attached inside the 150 nm diam. nanopores of an anodic aluminum oxide (AAO) membrane. Photoexcitation of D-C-A in a 343 mT magnetic field results in sub-nanosecond, two-step electron transfer to yield the spin-correlated radical ion pair (SCRP) (1)(D(+)˙-C-A(-)˙), which then undergoes radical pair intersystem crossing (RP-ISC) to yield (3)(D(+)˙-C-A(-)˙). RP-ISC results in S-T0 mixing to selectively populate the coherent superposition states |S'> and |T'>. Microwave-induced transitions between these states and the unpopulated |T(+1)> and |T(-1)> states result in spin-polarized time-resolved EPR (TREPR) spectra. The dependence of the electron spin polarization (ESP) phase of the TREPR spectra on the orientation of the AAO membrane pores relative to the externally applied magnetic field is used to determine the overall orientation of the SCRPs within the pores at room temperature.

Vibrational sum-frequency generation spectroscopy of ionic liquid 1-butyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate at the air-water interface

NASA Astrophysics Data System (ADS)

Saha, Ankur; SenGupta, Sumana; Kumar, Awadhesh; Choudhury, Sipra; Naik, Prakash D.

2016-08-01

The structure and orientation of room temperature ionic liquid (RTIL) 1-butyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate [PF3(C2F5)3], commonly known as [bmim][fap], have been investigated at the air-[bmim][fap] and air-water interfaces, employing vibrational sum-frequency generation (VSFG) spectroscopy. The VSFG spectra in the CH stretch region suggest presence of the [bmim] cation at the interfaces. Studies reveal that the butyl chain protrudes out into air, and the imidazolium ring lies almost planar to the interface. The CH stretch intensities get enhanced at the air-water interface, mainly because of polar orientation of imidazolium cation induced by interfacial water molecules. The OH stretch intensities are also enhanced at the air-water interface due to polar orientation of interfacial water molecules induced by [bmim][fap]. The Brewster angle microscopy suggests self aggregation of [bmim][fap] in the presence of water, and the aggregation becomes extensive showing dense surface domains with time. However, the surface pressure is almost unaffected due to aggregation.

Direct Visualization of Barrier Crossing Dynamics in a Driven Optical Matter System.

PubMed

Figliozzi, Patrick; Peterson, Curtis W; Rice, Stuart A; Scherer, Norbert F

2018-04-25

A major impediment to a more complete understanding of barrier crossing and other single-molecule processes is the inability to directly visualize the trajectories and dynamics of atoms and molecules in reactions. Rather, the kinetics are inferred from ensemble measurements or the position of a transducer ( e. g., an AFM cantilever) as a surrogate variable. Direct visualization is highly desirable. Here, we achieve the direct measurement of barrier crossing trajectories by using optical microscopy to observe position and orientation changes of pairs of Ag nanoparticles, i. e. passing events, in an optical ring trap. A two-step mechanism similar to a bimolecular exchange reaction or the Michaelis-Menten scheme is revealed by analysis that combines detailed knowledge of each trajectory, a statistically significant number of repetitions of the passing events, and the driving force dependence of the process. We find that while the total event rate increases with driving force, this increase is due to an increase in the rate of encounters. There is no drive force dependence on the rate of barrier crossing because the key motion for the process involves a random (thermal) radial fluctuation of one particle allowing the other to pass. This simple experiment can readily be extended to study more complex barrier crossing processes by replacing the spherical metal nanoparticles with anisotropic ones or by creating more intricate optical trapping potentials.

On the orientation of the backbone dipoles in native folds

PubMed Central

Ripoll, Daniel R.; Vila, Jorge A.; Scheraga, Harold A.

2005-01-01

The role of electrostatic interactions in determining the native fold of proteins has been investigated by analyzing the alignment of peptide bond dipole moments with the local electrostatic field generated by the rest of the molecule with and without solvent effects. This alignment was calculated for a set of 112 native proteins by using charges from a gas phase potential. Most of the peptide dipoles in this set of proteins are on average aligned with the electrostatic field. The dipole moments associated with α-helical conformations show the best alignment with the electrostatic field, followed by residues in β-strand conformations. The dipole moments associated with other secondary structure elements are on average better aligned than in randomly generated conformations. The alignment of a dipole with the local electrostatic field depends on both the topology of the native fold and the charge distribution assumed for all of the residues. The influences of (i) solvent effects, (ii) different sets of charges, and (iii) the charge distribution assumed for the whole molecule were examined with a subset of 22 proteins each of which contains <30 ionizable groups. The results show that alternative charge distribution models lead to significant differences among the associated electrostatic fields, whereas the electrostatic field is less sensitive to the particular set of the adopted charges themselves (empirical conformational energy program for peptides or parameters for solvation energy). PMID:15894608

Surface modification of GC and HOPG with diazonium, amine, azide, and olefin derivatives.

PubMed

Tanaka, Mutsuo; Sawaguchi, Takahiro; Sato, Yukari; Yoshioka, Kyoko; Niwa, Osamu

2011-01-04

Surface modification of glassy carbon (GC) and highly oriented pyrolytic graphite (HOPG) was carried out with diazonium, amine, azide, and olefin derivatives bearing ferrocene as an electroactive moiety. Features of the modified surfaces were evaluated by surface concentrations of immobilized molecule, blocking effect of the modified surface against redox reaction, and surface observation using cyclic voltammetry and electrochemical scanning tunneling microscope (EC-STM). The measurement of surface concentrations of immobilized molecule revealed the following three aspects: (i) Diazonium and olefin derivatives could modify substrates with the dense-monolayer concentration. (ii) The surface concentration of immobilized amine derivative did not reach to the dense-monolayer concentration reflecting their low reactivity. (iii) The surface modification with the dense-monolayer concentration was also possible with azide derivative, but the modified surface contained some oligomers produced by the photoreaction of azides. Besides, the blocking effect against redox reaction was observed for GC modified with diazonium derivative and for HOPG modified with diazonium and azide derivatives, suggesting fabrication of a densely modified surface. Finally, the surface observation for HOPG modified with diazonium derivative by EC-STM showed a typical monolayer structure, in which the ferrocene moieties were packed densely at random. On the basis of those results, it was demonstrated that surface modification of carbon substrates with diazonium could afford a dense monolayer similar to the self-assembled monolayer (SAM) formation.

Orientation sensors by defocused imaging of single gold nano-bipyramids

NASA Astrophysics Data System (ADS)

Zhang, Fanwei; Li, Qiang; Rao, Wenye; Hu, Hongjin; Gao, Ye; Wu, Lijun

2018-01-01

Optical probes for nanoscale orientation sensing have attracted much attention in the field of single-molecule detections. Noble metal especially Au nanoparticles (NPs) exhibit extraordinary plasmonic properties, great photostability, excellent biocompatibility and nontoxicity, and thereby could be alternative labels to conventional applied organic dyes or quantum dots. One type of the most interesting metallic NPs is Au nanorods (AuNRs). Its anisotropic emission accompanied with anisotropic shape is potentially applicable in orientation sensing. Recently, we resolved the 3D orientation of single AuNRs within one frame by deliberately introducing an aberration (slight shift of the dipole away from the focal plane) to the imaging system1 . This defocused imaging technique is based on the electron transition dipole approximation and the fact that the dipole radiation exhibits an angular anisotropy. Since the photoluminescence quantum yield (PLQY) can be enhanced by the "lightning rod effect" (at a sharp angled surface) and localized SPR modes, that of the single Au nano-bipyramid (AuNB) with more sharp tips or edges was found to be doubled comparing to AuNRs with a same effective size2. Here, with a 532 nm excitation, we find that the PL properties of individual AuNBs can be described by three perpendicularly-arranged dipoles (with different ratios). Their PL defocused images are bright, clear and exhibit obvious anisotropy. These properties suggest that AuNBs are excellent candidates for orientation sensing labels in single molecule detections.

Three-Dimensional Structural Characterization of HIV-1 Tethered to Human Cells

PubMed Central

Strauss, Joshua D.; Hammonds, Jason E.; Yi, Hong; Ding, Lingmei

2015-01-01

ABSTRACT Tetherin (BST2, CD317, or HM1.24) is a host cellular restriction factor that prevents the release of enveloped viruses by mechanically linking virions to the plasma membrane. The precise arrangement of tetherin molecules at the plasma membrane site of HIV-1 assembly, budding, and restriction is not well understood. To gain insight into the biophysical mechanism underlying tetherin-mediated restriction of HIV-1, we utilized cryo-electron tomography (cryo-ET) to directly visualize HIV-1 virus-like particles (VLPs) and virions tethered to human cells in three dimensions (3D). Rod-like densities that we refer to as tethers were seen connecting HIV-1 virions to each other and to the plasma membrane. Native immunogold labeling showed tetherin molecules located on HIV-1 VLPs and virions in positions similar to those of the densities observed by cryo-ET. The location of the tethers with respect to the ordered immature Gag lattice or mature conical core was random. However, tethers were not uniformly distributed on the viral membrane but rather formed clusters at sites of contact with the cell or other virions. Chains of tethered HIV-1 virions often were arranged in a linear fashion, primarily as single chains and, to a lesser degree, as branched chains. Distance measurements support the extended tetherin model, in which the coiled-coil ectodomains are oriented perpendicular with respect to the viral and plasma membranes. IMPORTANCE Tetherin is a cellular factor that restricts HIV-1 release by directly cross-linking the virus to the host cell plasma membrane. We used cryo-electron tomography to visualize HIV-1 tethered to human cells in 3D. We determined that tetherin-restricted HIV-1 virions were physically connected to each other or to the plasma membrane by filamentous tethers that resembled rods ∼15 nm in length, which is consistent with the extended tetherin model. In addition, we found the position of the tethers to be arbitrary relative to the ordered immature Gag lattice or the mature conical cores. However, when present as multiple copies, the tethers clustered at the interface between virions. Tethered HIV-1 virions were arranged in a linear fashion, with the majority as single chains. This study advances our understanding of tetherin-mediated HIV-1 restriction by defining the spatial arrangement and orientation of tetherin molecules at sites of HIV-1 restriction. PMID:26582000

Listening to the Noise: Random Fluctuations Reveal Gene Network Parameters

NASA Astrophysics Data System (ADS)

Munsky, Brian; Trinh, Brooke; Khammash, Mustafa

2010-03-01

The cellular environment is abuzz with noise originating from the inherent random motion of reacting molecules in the living cell. In this noisy environment, clonal cell populations exhibit cell-to-cell variability that can manifest significant prototypical differences. Noise induced stochastic fluctuations in cellular constituents can be measured and their statistics quantified using flow cytometry, single molecule fluorescence in situ hybridization, time lapse fluorescence microscopy and other single cell and single molecule measurement techniques. We show that these random fluctuations carry within them valuable information about the underlying genetic network. Far from being a nuisance, the ever-present cellular noise acts as a rich source of excitation that, when processed through a gene network, carries its distinctive fingerprint that encodes a wealth of information about that network. We demonstrate that in some cases the analysis of these random fluctuations enables the full identification of network parameters, including those that may otherwise be difficult to measure. We use theoretical investigations to establish experimental guidelines for the identification of gene regulatory networks, and we apply these guideline to experimentally identify predictive models for different regulatory mechanisms in bacteria and yeast.

Atomic force microscope characterization of self-assembly behaviors of cyclo[8] pyrrole on solid substrates

NASA Astrophysics Data System (ADS)

Xu, Hai; Zhao, Siqi; Xiong, Xiang; Jiang, Jinzhi; Xu, Wei; Zhu, Daoben; Zhang, Yi; Liang, Wenjie; Cai, Jianfeng

2017-04-01

Cyclo [8] pyrrole (CP) is a porphyrin analogue containing eight α-conjugated pyrrole units which are arranged in a nearly coplanar conformation. The π-π interactions between CP molecules lead to regular aggregations through a solution casting process. Using tapping mode atomic force microscope (AFM), we investigated the morphology of self-assembled aggregates formed by deposition of different CP solutions on different substrates. We found that in the n-butanol solution, nanofibrous structures could be formed on the silicon or mica surface. Interestingly, on the highly oriented pyrolytic graphite (HOPG) surface, or silicon and mica surface with a toluene solution, only irregular spherical structures were identified. The difference in the nanomorphology may be attributed to distinct interactions between molecule-molecule, molecule-solvent and molecule-substrate.

From dipolar to multipolar interactions between ultracold Feshbach molecules

NASA Astrophysics Data System (ADS)

Quéméner, Goulven; Lepers, Maxence; Luc-Koenig, Eliane; Dulieu, Olivier

2016-05-01

Using the multipolar expansion of electrostatic and magnetostatic potential energies, we characterize the long-range interactions between two weakly-bound diatomic molecules, taking as an example the paramagnetic Er2 Feshbach molecules which were produced recently. The interaction between atomic magnetic dipoles gives rise to the usual R-3 leading term of the multipolar expansion, where R is the intermolecular distance. We show that additional terms scaling as R-5, R-7 and so on also appear, which are strongly anisotropic with respect to the orientation of the molecules. These terms can be seen as effective molecular multipole moments reflecting the spatial extension of the molecules which is non-negligible compared to R. We acknowledge the financial support of the COPOMOL project (ANR-13-IS04-0004) from Agence Nationale de la Recherche.

Depth profiling of high energy nitrogen ions implanted in the <1 0 0>, <1 1 0> and randomly oriented silicon crystals

NASA Astrophysics Data System (ADS)

Erić, M.; Petrović, S.; Kokkoris, M.; Lagoyannis, A.; Paneta, V.; Harissopulos, S.; Telečki, I.

2012-03-01

This work reports on the experimentally obtained depth profiles of 4 MeV 14N2+ ions implanted in the <1 0 0>, <1 1 0> and randomly oriented silicon crystals. The ion fluence was 1017 particles/cm2. The nitrogen depth profiling has been performed using the Nuclear Reaction Analysis (NRA) method, via the study of 14N(d,α0)12C and 14N(d,α1)12C nuclear reactions, and with the implementation of SRIM 2010 and SIMNRA computer simulation codes. For the randomly oriented silicon crystal, change of the density of silicon matrix and the nitrogen "bubble" formation have been proposed as the explanation for the difference between the experimental and simulated nitrogen depth profiles. During the implantation, the RBS/C spectra were measured on the nitrogen implanted and on the virgin crystal spots. These spectra provide information on the amorphization of the silicon crystals induced by the ion implantation.

Collisional transfer of population and orientation in NaK

NASA Astrophysics Data System (ADS)

Wolfe, C. M.; Ashman, S.; Bai, J.; Beser, B.; Ahmed, E. H.; Lyyra, A. M.; Huennekens, J.

2011-05-01

Collisional satellite lines with |ΔJ| ≤ 58 have been identified in recent polarization spectroscopy V-type optical-optical double resonance (OODR) excitation spectra of the Rb2 molecule [H. Salami et al., Phys. Rev. A 80, 022515 (2009)]. Observation of these satellite lines clearly requires a transfer of population from the rotational level directly excited by the pump laser to a neighboring level in a collision of the molecule with an atomic perturber. However to be observed in polarization spectroscopy, the collision must also partially preserve the angular momentum orientation, which is at least somewhat surprising given the extremely large values of ΔJ that were observed. In the present work, we used the two-step OODR fluorescence and polarization spectroscopy techniques to obtain quantitative information on the transfer of population and orientation in rotationally inelastic collisions of the NaK molecules prepared in the 2(A)1Σ+(v' = 16, J' = 30) rovibrational level with argon and potassium perturbers. A rate equation model was used to study the intensities of these satellite lines as a function of argon pressure and heat pipe oven temperature, in order to separate the collisional effects of argon and potassium atoms. Using a fit of this rate equation model to the data, we found that collisions of NaK molecules with potassium atoms are more likely to transfer population and destroy orientation than collisions with argon atoms. Collisions with argon atoms show a strong propensity for population transfer with ΔJ = even. Conversely, collisions with potassium atoms do not show this ΔJ = even propensity, but do show a propensity for ΔJ = positive compared to ΔJ = negative, for this particular initial state. The density matrix equations of motion have also been solved numerically in order to test the approximations used in the rate equation model and to calculate fluorescence and polarization spectroscopy line shapes. In addition, we have measured rate coefficients for broadening of NaK 31Π ← 2(A)1Σ+spectral lines due to collisions with argon and potassium atoms. Additional broadening, due to velocity changes occurring in rotationally inelastic collisions, has also been observed.

Collisional transfer of population and orientation in NaK.

PubMed

Wolfe, C M; Ashman, S; Bai, J; Beser, B; Ahmed, E H; Lyyra, A M; Huennekens, J

2011-05-07

Collisional satellite lines with |ΔJ| ≤ 58 have been identified in recent polarization spectroscopy V-type optical-optical double resonance (OODR) excitation spectra of the Rb(2) molecule [H. Salami et al., Phys. Rev. A 80, 022515 (2009)]. Observation of these satellite lines clearly requires a transfer of population from the rotational level directly excited by the pump laser to a neighboring level in a collision of the molecule with an atomic perturber. However to be observed in polarization spectroscopy, the collision must also partially preserve the angular momentum orientation, which is at least somewhat surprising given the extremely large values of ΔJ that were observed. In the present work, we used the two-step OODR fluorescence and polarization spectroscopy techniques to obtain quantitative information on the transfer of population and orientation in rotationally inelastic collisions of the NaK molecules prepared in the 2(A)(1)Σ(+)(v' = 16, J' = 30) rovibrational level with argon and potassium perturbers. A rate equation model was used to study the intensities of these satellite lines as a function of argon pressure and heat pipe oven temperature, in order to separate the collisional effects of argon and potassium atoms. Using a fit of this rate equation model to the data, we found that collisions of NaK molecules with potassium atoms are more likely to transfer population and destroy orientation than collisions with argon atoms. Collisions with argon atoms show a strong propensity for population transfer with ΔJ = even. Conversely, collisions with potassium atoms do not show this ΔJ = even propensity, but do show a propensity for ΔJ = positive compared to ΔJ = negative, for this particular initial state. The density matrix equations of motion have also been solved numerically in order to test the approximations used in the rate equation model and to calculate fluorescence and polarization spectroscopy line shapes. In addition, we have measured rate coefficients for broadening of NaK 3(1)Π ← 2(A)(1)Σ(+)spectral lines due to collisions with argon and potassium atoms. Additional broadening, due to velocity changes occurring in rotationally inelastic collisions, has also been observed.

Internal Stress and Microstructure of Zinc Oxide Films Sputter-Deposited with Carbon Dioxide Gas

NASA Astrophysics Data System (ADS)

Toru Ashida,; Kazuhiro Kato,; Hideo Omoto,; Atsushi Takamatsu,

2010-06-01

The internal stress and microstructure of ZnO films were investigated as a function of carbon dioxide (CO2) gas flow ratio [CO2/(O2+CO2)] during sputter deposition. The internal stress of the ZnO films decreased with increasing CO2 gas flow ratio. The carbon concentration in the films deposited using CO2 gas increased by up to 4.0 at. %. Furthermore, the ZnO films deposited without CO2 gas exhibited a preferred orientation of (002); however, the C-doped ZnO films exhibited random orientations. These findings suggest that the C atoms incorporated in the ZnO crystal lattice induce this random orientation, thereby relaxing the internal stress of C-doped ZnO films.

Watching single molecules dance

NASA Astrophysics Data System (ADS)

Mehta, Amit Dinesh

Molecular motors convert chemical energy, from ATP hydrolysis or ion flow, into mechanical motion. A variety of increasingly precise mechanical probes have been developed to monitor and perturb these motors at the single molecule level. Several outstanding questions can be best approached at the single molecule level. These include: how far does a motor progress per energy quanta consumed? how does its reaction cycle respond to load? how many productive catalytic cycles can it undergo per diffusional encounter with its track? and what is the mechanical stiffness of a single molecule connection? A dual beam optical trap, in conjunction with in vitro ensemble motility assays, has been used to characterize two members of the myosin superfamily: muscle myosin II and chick brain myosin V. Both move the helical polymer actin, but myosin II acts in large ensembles to drive muscle contraction or cytokinesis, while myosin V acts in small numbers to transport vesicles. An optical trapping apparatus was rendered sufficiently precise to identify a myosin working stroke with 1nm or so, barring systematic errors such as those perhaps due to random protein orientations. This and other light microscopic motility assays were used to characterize myosin V: unlike myosin II this vesicle transport protein moves through many increments of travel while remaining strongly bound to a single actin filament. The step size, stall force, and travel distance of myosin V reveal a remarkably efficient motor capable of moving along a helical track for over a micrometer without significantly spiraling around it. Such properties are fully consistent with the putative role of an organelle transport motor, present in small numbers to maintain movement over long ranges relative to cellular size scales. The contrast between myosin II and myosin V resembles that between a human running on the moon and one walking on earth, where the former allows for faster motion when in larger ensembles but for less travel distance when in smaller ones.

Crystal structure of NTPDase2 in complex with the sulfoanthraquinone inhibitor PSB-071.

PubMed

Zebisch, Matthias; Baqi, Younis; Schäfer, Petra; Müller, Christa E; Sträter, Norbert

2014-03-01

In many vertebrate tissues CD39-like ecto-nucleoside triphosphate diphosphohydrolases (NTPDases) act in concert with ecto-5'-nucleotidase (e5NT, CD73) to convert extracellular ATP to adenosine. Extracellular ATP is a cytotoxic, pro-inflammatory signalling molecule whereas its product adenosine constitutes a universal and potent immune suppressor. Interference with these ectonucleotidases by use of small molecule inhibitors or inhibitory antibodies appears to be an effective strategy to enhance anti-tumour immunity and suppress neoangiogenesis. Here we present the first crystal structures of an NTPDase catalytic ectodomain in complex with the Reactive Blue 2 (RB2)-derived inhibitor PSB-071. In both of the two crystal forms presented the inhibitor binds as a sandwich of two molecules at the nucleoside binding site. One of the molecules is well defined in its orientation. Specific hydrogen bonds are formed between the sulfonyl group and the nucleoside binding loop. The methylphenyl side chain functionality that improved NTPDase2-specificity is sandwiched between R245 and R394, the latter of which is exclusively found in NTPDase2. The second molecule exhibits great in-plane rotational freedom and could not be modelled in a specific orientation. In addition to this structural insight into NTPDase inhibition, the observation of the putative membrane interaction loop (MIL) in two different conformations related by a 10° rotation identifies the MIL as a dynamic section of NTPDases that is potentially involved in regulation of catalysis. Copyright © 2014 Elsevier Inc. All rights reserved.

Chemistry at molecular junctions: Rotation and dissociation of O2 on the Ag(110) surface induced by a scanning tunneling microscope.

PubMed

Roy, Sharani; Mujica, Vladimiro; Ratner, Mark A

2013-08-21

The scanning tunneling microscope (STM) is a fascinating tool used to perform chemical processes at the single-molecule level, including bond formation, bond breaking, and even chemical reactions. Hahn and Ho [J. Chem. Phys. 123, 214702 (2005)] performed controlled rotations and dissociations of single O2 molecules chemisorbed on the Ag(110) surface at precise bias voltages using STM. These threshold voltages were dependent on the direction of the bias voltage and the initial orientation of the chemisorbed molecule. They also observed an interesting voltage-direction-dependent and orientation-dependent pathway selectivity suggestive of mode-selective chemistry at molecular junctions, such that in one case the molecule underwent direct dissociation, whereas in the other case it underwent rotation-mediated dissociation. We present a detailed, first-principles-based theoretical study to investigate the mechanism of the tunneling-induced O2 dynamics, including the origin of the observed threshold voltages, the pathway dependence, and the rate of O2 dissociation. Results show a direct correspondence between the observed threshold voltage for a process and the activation energy for that process. The pathway selectivity arises from a competition between the voltage-modified barrier heights for rotation and dissociation, and the coupling strength of the tunneling electrons to the rotational and vibrational modes of the adsorbed molecule. Finally, we explore the "dipole" and "resonance" mechanisms of inelastic electron tunneling to elucidate the energy transfer between the tunneling electrons and chemisorbed O2.

Diffusion of biomass pyrolysis products in H-ZSM-5 by molecular dynamics simulations

DOE PAGES

Bu, Lintao; Nimlos, Mark R.; Robichaud, David J.; ...

2016-12-13

Diffusion of biomass pyrolysis vapors and their upgraded products is an essential catalytic property of zeolites during catalytic fast pyrolysis and likely plays a critical role in the selectivity of these catalysts. Characterizing the diffusivities of representative biofuel molecules is critical to understand shape selectivity and interpret product distribution. Yet, experimental measurements on the diffusivities of oxygenated biofuel molecules at pyrolysis temperatures are very limited in the literature. As an alternative approach, we conducted MD simulations to measure the diffusion coefficients of several selected molecules that are representative of biomass pyrolysis vapors, namely water, methanol, glycolaldehyde, and toluene in H-ZSM-5more » zeolite. The results show the diffusion coefficients calculated via MD simulations are consistent with available NMR measurements at room temperature. The effect of molecular weight and molecular critical diameter on the diffusivity among the chosen model compounds is also examined. Furthermore, we have characterized the diffusivities of representative biofuel molecules, namely xylene isomers, in H-ZSM-5. Our calculations determined that the ratio of the diffusion coefficients for xylene isomers is p-xylene: o-xylene: m-xylene ≈ 83:3:1 at 700 K. Furthermore, our results also demonstrate the different diffusivity between p-xylene and toluene is due to the molecular orientations when the molecules diffuse along the channels in H-ZSM-5 and provide deep insight into the effect of molecular orientation on its diffusivity.« less

First-Principles Study of the Self-Assembled Pentacene Molecules on Metal Surfaces

NASA Astrophysics Data System (ADS)

Lee, Kyuho; Han, Myung-Joon; Yu, Jaejun

2003-03-01

Oriented thin films of organic semiconducting small molecules have received considerable attention as active semiconductors for device applications such as Schottky diodes and thin-film transistors (TFTs). Among these organic materials, pentacene has been found to have the highest mobilities for hole transport. Understanding the formation of self-organized ad-layers of pentacene would contribute to the fabrication of nanostructures and possibly highly oriented pentacene layers by epitaxy for use in electronic devices. To understand the ordering patterns of pentacene ad-layers on metal surfaces, we investigated the energetics between pentacene molecules with and without metal substrates and analyzed its electronic structure. We used a self-consistent first-principles calculation method based on the density functional theory (DFT) within local density approximation (LDA). The localized pseudo-atomic orbitals (PAO) are employed for a real-space numerical basis set, which was suggested by Sankey and Niklewski, and the Troullier-Martins-type pseudo-potential is used. As results, we found that the ordering patterns can be explained by the energetics between pentacene molecules, and the metal substrates appears not to influence too much on the interaction between pentacenes. To investigate the nature of the self-assembled structure, we calculated the total energies of various configurations for the molecule pattern, e.g., side-by-side and head-to-head ordering or on-top stacking. Depending on its direction, extremely different interaction character between two pentacenes is found and explained by its electronic structure analysis.

Distribution of Orientation Selectivity in Recurrent Networks of Spiking Neurons with Different Random Topologies

PubMed Central

Sadeh, Sadra; Rotter, Stefan

2014-01-01

Neurons in the primary visual cortex are more or less selective for the orientation of a light bar used for stimulation. A broad distribution of individual grades of orientation selectivity has in fact been reported in all species. A possible reason for emergence of broad distributions is the recurrent network within which the stimulus is being processed. Here we compute the distribution of orientation selectivity in randomly connected model networks that are equipped with different spatial patterns of connectivity. We show that, for a wide variety of connectivity patterns, a linear theory based on firing rates accurately approximates the outcome of direct numerical simulations of networks of spiking neurons. Distance dependent connectivity in networks with a more biologically realistic structure does not compromise our linear analysis, as long as the linearized dynamics, and hence the uniform asynchronous irregular activity state, remain stable. We conclude that linear mechanisms of stimulus processing are indeed responsible for the emergence of orientation selectivity and its distribution in recurrent networks with functionally heterogeneous synaptic connectivity. PMID:25469704

Study the Formation of H2, HD and D2 under Various Interstellar Conditions

NASA Astrophysics Data System (ADS)

Sahu, Dipen; Chakrabarti, Sandip Kumar; Das, Ankan

2016-07-01

Hydrogen is the most abundant molecule in the Interstellar medium (ISM). Formation of gas phase hydrogen molecule is inefficient; perhaps grain surface acts as a necessary ingredients for the formation of H_2 molecule. H atoms accrete on the grain surface, recombine there and desorb in the gas phase. Similarly, deuterium accretion on grain surfaces can produce simple dueterated molecules (HD and D_2) on the ISM. Unlike gas phase reactions, rate equations can not yield accurate result for grain surface reactions due to inherent randomness of surface species. We use Monte-Carlo method to follow this surface chemistry which effectively take care of this randomness. We use square grids and impose periodic boundary condition on them to mimic the spherical nature of grains. Various types of rough surfaces are considered to study the impact on effective production rates. We found that these simple but most important molecules are produced in low temperature (physisorption sites) as well as in high temperature (chemisorption sites) regions.

Modeling molecule-plasmon interactions using quantized radiation fields within time-dependent electronic structure theory

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

Nascimento, Daniel R.; DePrince, A. Eugene, E-mail: deprince@chem.fsu.edu

2015-12-07

We present a combined cavity quantum electrodynamics/ab initio electronic structure approach for simulating plasmon-molecule interactions in the time domain. The simple Jaynes-Cummings-type model Hamiltonian typically utilized in such simulations is replaced with one in which the molecular component of the coupled system is treated in a fully ab initio way, resulting in a computationally efficient description of general plasmon-molecule interactions. Mutual polarization effects are easily incorporated within a standard ground-state Hartree-Fock computation, and time-dependent simulations carry the same formal computational scaling as real-time time-dependent Hartree-Fock theory. As a proof of principle, we apply this generalized method to the emergence ofmore » a Fano-like resonance in coupled molecule-plasmon systems; this feature is quite sensitive to the nanoparticle-molecule separation and the orientation of the molecule relative to the polarization of the external electric field.« less

Influence of Adsorption Orientation on the Statistical Mechanics Model of Type I Antifreeze Protein: The Thermal Hysteresis Temperature.

PubMed

Li, Li-Fen; Liang, Xi-Xia

2017-10-19

The antifreeze activity of type I antifreeze proteins (AFPIs) is studied on the basis of the statistical mechanics theory, by taking the AFP's adsorption orientation into account. The thermal hysteresis temperatures are calculated by determining the system Gibbs function as well as the AFP molecule coverage rate on the ice-crystal surface. The numerical results for the thermal hysteresis temperatures of AFP9, HPLC-6, and AAAA2kE are obtained for both of the cases with and without inclusion of the adsorption orientation. The results show that the influence of the adsorption orientation on the thermal hysteresis temperature cannot be neglected. The theoretical results are coincidental preferably with the experimental data.

Huygens-Fresnel picture for electron-molecule elastic scattering★

NASA Astrophysics Data System (ADS)

Baltenkov, Arkadiy S.; Msezane, Alfred Z.

2017-11-01

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

Orientation of Hittite Monuments

NASA Astrophysics Data System (ADS)

González-García, A. César; Belmonte, Juan Antonio

The possible astronomical or topographical orientations of the Hittite monuments of the Bronze Age has remained unexplored until recently. This would provide an important insight into how temporality was imprinted by this culture in sacred spaces and in the landscape. The authors' analysis of a statistically significant sample of Hittite temples - and a few monumental gates - has demonstrated that ancient Hittite monuments were not randomly orientated as previously thought. On the contrary, there were well-defined patterns of orientation that can be interpreted within the context of Hittite culture and religion.

Theory of third-order spectroscopic methods to extract detailed molecular orientational dynamics for planar surfaces and other uniaxial systems

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

Nishida, Jun; Fayer, Michael D., E-mail: fayer@stanford.edu

Functionalized organic monolayers deposited on planar two-dimensional surfaces are important systems for studying ultrafast orientational motions and structures of interfacial molecules. Several studies have successfully observed the orientational relaxation of functionalized monolayers by fluorescence depolarization experiments and recently by polarization-resolved heterodyne detected vibrational transient grating (HDTG) experiments. In this article we provide a model-independent theory to extract orientational correlation functions unique to interfacial molecules and other uniaxial systems based on polarization-resolved resonant third-order spectroscopies, such as pump-probe spectroscopy, HDTG spectroscopy, and fluorescence depolarization experiment. It will be shown (in the small beam-crossing angle limit) that five measurements are necessary tomore » completely characterize the monolayer's motions: I{sub ∥}(t) and I{sub ⊥}(t) with the incident beams normal to the surface, I{sub ∥}(t) and I{sub ⊥}(t) with a non-zero incident angle, and a time averaged linear dichroism measurement. Once these measurements are performed, two orientational correlation functions corresponding to in-plane and out-of-plane motions are obtained. The procedure is applicable not only for monolayers on flat surfaces, but any samples with uniaxial symmetry such as uniaxial liquid crystals and aligned planar bilayers. The theory is valid regardless of the nature of the actual molecular motions on interface. We then apply the general results to wobbling-in-a-cone model, in which molecular motions are restricted to a limited range of angles. Within the context of the model, the cone angle, the tilt of the cone relative to the surface normal, and the orientational diffusion constant can be determined. The results are extended to describe analysis of experiments where the beams are not crossing in the small angle limit.« less

Method for high-volume sequencing of nucleic acids: random and directed priming with libraries of oligonucleotides

DOEpatents

Studier, F. William

1995-04-18

Random and directed priming methods for determining nucleotide sequences by enzymatic sequencing techniques, using libraries of primers of lengths 8, 9 or 10 bases, are disclosed. These methods permit direct sequencing of nucleic acids as large as 45,000 base pairs or larger without the necessity for subcloning. Individual primers are used repeatedly to prime sequence reactions in many different nucleic acid molecules. Libraries containing as few as 10,000 octamers, 14,200 nonamers, or 44,000 decamers would have the capacity to determine the sequence of almost any cosmid DNA. Random priming with a fixed set of primers from a smaller library can also be used to initiate the sequencing of individual nucleic acid molecules, with the sequence being completed by directed priming with primers from the library. In contrast to random cloning techniques, a combined random and directed priming strategy is far more efficient.

Method for high-volume sequencing of nucleic acids: random and directed priming with libraries of oligonucleotides

DOEpatents

Studier, F.W.

1995-04-18

Random and directed priming methods for determining nucleotide sequences by enzymatic sequencing techniques, using libraries of primers of lengths 8, 9 or 10 bases, are disclosed. These methods permit direct sequencing of nucleic acids as large as 45,000 base pairs or larger without the necessity for subcloning. Individual primers are used repeatedly to prime sequence reactions in many different nucleic acid molecules. Libraries containing as few as 10,000 octamers, 14,200 nonamers, or 44,000 decamers would have the capacity to determine the sequence of almost any cosmid DNA. Random priming with a fixed set of primers from a smaller library can also be used to initiate the sequencing of individual nucleic acid molecules, with the sequence being completed by directed priming with primers from the library. In contrast to random cloning techniques, a combined random and directed priming strategy is far more efficient. 2 figs.

Control of Rotational Energy and Angular Momentum Orientation with an Optical Centrifuge

NASA Astrophysics Data System (ADS)

Ogden, Hannah M.; Murray, Matthew J.; Mullin, Amy S.

2017-04-01

We use an optical centrifuge to trap and spin molecules to an angular frequency of 30 THz with oriented angular momenta and extremely high rotational energy and then investigate their subsequent collision dynamics with transient high resolution IR spectroscopy. The optical centrifuge is formed by combining oppositely-chirped pulses of 800 nm light, and overlapping them spatially and temporally. Polarization-sensitive Doppler-broadened line profiles characterize the anisotropic kinetic energy release of the super rotor molecules, showing that they behave like molecular gyroscopes. Studies are reported for collisions of CO2 super rotors with CO2, He and Ar. These studies reveal how mass, velocity and rotational adiabaticity impact the angular momentum relaxation and reorientation. Quantum scattering calculations provide insight into the J-specific collision cross sections that control the relaxation. NSF-CHE 105 8721.

Conformation of flexibly linked triterpene dimers by using RDC-enhanced NMR spectroscopy

NASA Astrophysics Data System (ADS)

Lakshmi, Jerripothula K.; Pattnaik, Banita; Kavitha, Rachineni; Mallavadhani, Uppuluri V.; Jagadeesh, Bharatam

2018-06-01

Dimers of flexibly linked pentacyclic triterpene ursolic acid (UA) and its related frameworks such as asiatic acid (AA) and oleanolic acid (OA) have recently attracted significant attention due to their enhanced anti-cancer and anti-HCV activity compared to their respective monomers. Determination of conformation/inter-monomer orientation of these molecules is very important to understand their structure-activity relationship and to develop new scaffolds, which, however, is difficult through conventional NOE based solution-state NMR spectroscopy, due to lack of long-range NOEs. In the present work, we report a precise determination of conformation of two 1,2,3-triazole-linked triterpene dimer molecules, UA-AA and UA-OA, by employing one-bond Csbnd H residual dipolar couplings (RDCs) as additional long-range orientational restraints, measured in anisotropic PDMS/CDCl3 solvent medium.

NMR Spectra of Oriented Samples of Intercalated Fluorographite and 19F Chemical Shielding Anisotropy of the CIF 3 Molecule

NASA Astrophysics Data System (ADS)

Panich, A. M.

The analysis of 19F NMR spectra of polycrystalline and partially oriented samples of fluorinated graphite (C 2F) n intercalated with chlorine trifluoride has been carried out. Molecular mobility results in almost complete averaging of the dipole-dipole interactions of nuclei, while the essential chemical shielding anisotropy (CSA) is manifested. There is suggested molecular rotation about its C2 axes, which in turn rotates about the normal to the graphite plane. The CSA (σ || - σ ⊥) is determined to be 510 and -640 ppm, respectively, for the two inequivalent fluorine atoms of the molecule. The effect of the "antiparamagnetic" shielding leading to inversion of the chemical shielding tenser [(σ || - σ ⊥) < 0] for the equatorial F atom and anomalous line disposition in the NMR spectrum is discussed.

The Micromechanics of the Moving Contact Line

NASA Technical Reports Server (NTRS)

Han, Minsub; Lichter, Seth; Lin, Chih-Yu; Perng, Yeong-Yan

1996-01-01

The proposed research is divided into three components concerned with molecular structure, molecular orientation, and continuum averages of discrete systems. In the experimental program, we propose exploring how changes in interfacial molecular structure generate contact line motion. Rather than rely on the electrostatic and electrokinetic fields arising from the molecules themselves, we augment their interactions by an imposed field at the solid/liquid interface. By controling the field, we can manipulate the molecular structure at the solid/liquid interface. In response to controlled changes in molecular structure, we observe the resultant contact line motion. In the analytical portion of the proposed research we seek to formulate a system of equations governing fluid motion which accounts for the orientation of fluid molecules. In preliminary work, we have focused on describing how molecular orientation affects the forces generated at the moving contact line. Ideally, as assumed above, the discrete behavior of molecules can be averaged into a continuum theory. In the numerical portion of the proposed research, we inquire whether the contact line region is, in fact, large enough to possess a well-defined average. Additionally, we ask what types of behavior distinguish discrete systems from continuum systems. Might the smallness of the contact line region, in itself, lead to behavior different from that in the bulk? Taken together, our proposed research seeks to identify and accurately account for some of the molecular dynamics of the moving contact line, and attempts to formulate a description from which one can compute the forces at the moving contact line.

Development of a Model Competency-Based Orientation Program

DTIC Science & Technology

1988-05-01

S. (1938). Basic writings of Sigmund Freud . New York: Random House. Hagerty, B.K. (1986). A competency-based orientation program for psychiatric...education, and nursing will be presented. • ..... Beginning with the field of psychology, Freud (1938) described motivation using the concept of psychic...Gosnell, D.J. (1987). Comparing two methods of hospital orientation for cost effective- ness. Journal of Nursing Staff Development, 3 , 3-8. Freud

Omitted data in randomized controlled trials for anxiety and depression: A systematic review of the inclusion of sexual orientation and gender identity.

PubMed

Heck, Nicholas C; Mirabito, Lucas A; LeMaire, Kelly; Livingston, Nicholas A; Flentje, Annesa

2017-01-01

The current study examined the frequency with which randomized controlled trials (RCTs) of behavioral and psychological interventions for anxiety and depression include data pertaining to participant sexual orientation and nonbinary gender identities. Using systematic review methodology, the databases PubMed and PsycINFO were searched to identify RCTs published in 2004, 2009, and 2014. Random selections of 400 articles per database per year (2,400 articles in total) were considered for inclusion in the review. Articles meeting inclusion criteria were read and coded by the research team to identify whether the trial reported data pertaining to participant sexual orientation and nonbinary gender identities. Additional trial characteristics were also identified and indexed in our database (e.g., sample size, funding source). Of the 232 articles meeting inclusion criteria, only 1 reported participants' sexual orientation, and zero articles included nonbinary gender identities. A total of 52,769 participants were represented in the trials, 93 of which were conducted in the United States, and 43 acknowledged the National Institutes of Health as a source of funding. Despite known mental health disparities on the basis of sexual orientation and nonbinary gender identification, researchers evaluating interventions for anxiety and depression are not reporting on these important demographic characteristics. Reporting practices must change to ensure that our interventions generalize to lesbian, gay, bisexual, and transgender persons. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Interaction of a single acetophenone molecule with group III-IV elements mediated by Si(001)

NASA Astrophysics Data System (ADS)

Racis, A.; Jurczyszyn, L.; Radny, M. W.

2018-03-01

A theoretical study of an influence of the acetophenone molecule adsorbed on the Si(001) on the local chemical reactivity of silicon surface is presented. The obtained results indicate that the interaction of the molecule with silicon substrate breaks the intra-dimer π bonds in four surface silicon dimers interacting directly with adsorbed molecule. This leads to the formation of two pairs of unpaired dangling bonds at two opposite sides of the molecule. It is demonstrated that these dangling bonds increase considerably the local chemical reactivity of the silicon substrate in the vicinity of the adsorbed molecule. Consequently, it is shown that such molecule bonded with Si(001) can stabilize the position of In and Pb adatoms diffusing on silicon substrate at two sides and initiate the one-dimensional aggregation of the metallic adatoms on the Si(001) substrate anchored at both sides of the adsorbed molecule. This type of aggregation leads to the growth of chain-like atomic structures in opposite directions, pinned to adsorbed molecule and oriented perpendicular to the rows of surface silicon dimers.

The Central Limit Theorem for Supercritical Oriented Percolation in Two Dimensions

NASA Astrophysics Data System (ADS)

Tzioufas, Achillefs

2018-04-01

We consider the cardinality of supercritical oriented bond percolation in two dimensions. We show that, whenever the the origin is conditioned to percolate, the process appropriately normalized converges asymptotically in distribution to the standard normal law. This resolves a longstanding open problem pointed out to in several instances in the literature. The result applies also to the continuous-time analog of the process, viz. the basic one-dimensional contact process. We also derive general random-indices central limit theorems for associated random variables as byproducts of our proof.

The Central Limit Theorem for Supercritical Oriented Percolation in Two Dimensions

NASA Astrophysics Data System (ADS)

Tzioufas, Achillefs

2018-06-01

We consider the cardinality of supercritical oriented bond percolation in two dimensions. We show that, whenever the the origin is conditioned to percolate, the process appropriately normalized converges asymptotically in distribution to the standard normal law. This resolves a longstanding open problem pointed out to in several instances in the literature. The result applies also to the continuous-time analog of the process, viz. the basic one-dimensional contact process. We also derive general random-indices central limit theorems for associated random variables as byproducts of our proof.

Source polarization effects in an optical fiber fluorosensor

NASA Technical Reports Server (NTRS)

Egalon, Claudio O.; Rogowski, Robert S.

1992-01-01

The exact field solution of a step-index profile fiber was used to determine the injection efficiency of a thin-film distribution of polarized sources located in the cladding of an optical fiber. Previous results for random source orientation were confirmed. The behavior of the power efficiency, P(eff), of a polarized distribution of sources was found to be similar to the behavior of a fiber with sources with random orientation. However, for sources polarized in either the x or y direction, P(eff) was found to be more efficient.

In Vivo Orientation of Single Myosin Lever Arms in Zebrafish Skeletal Muscle

PubMed Central

Sun, Xiaojing; Ekker, Stephen C.; Shelden, Eric A.; Takubo, Naoko; Wang, Yihua; Burghardt, Thomas P.

2014-01-01

Cardiac and skeletal myosin assembled in the muscle lattice power contraction by transducing ATP free energy into the mechanical work of moving actin. Myosin catalytic/lever-arm domains comprise the transduction/mechanical coupling machinery that move actin by lever-arm rotation. In vivo, myosin is crowded and constrained by the fiber lattice as side chains are mutated and otherwise modified under normal, diseased, or aging conditions that collectively define the native myosin environment. Single-myosin detection uniquely defines bottom-up characterization of myosin functionality. The marriage of in vivo and single-myosin detection to study zebrafish embryo models of human muscle disease is a multiscaled technology that allows one-to-one registration of a selected myosin molecular alteration with muscle filament-sarcomere-cell-fiber-tissue-organ- and organism level phenotypes. In vivo single-myosin lever-arm orientation was observed at superresolution using a photoactivatable-green-fluorescent-protein (PAGFP)-tagged myosin light chain expressed in zebrafish skeletal muscle. By simultaneous observation of multiphoton excitation fluorescence emission and second harmonic generation from myosin, we demonstrated tag specificity for the lever arm. Single-molecule detection used highly inclined parallel beam illumination and was verified by quantized photoactivation and photobleaching. Single-molecule emission patterns from relaxed muscle in vivo provided extensive superresolved dipole orientation constraints that were modeled using docking scenarios generated for the myosin (S1) and GFP crystal structures. The dipole orientation data provided sufficient constraints to estimate S1/GFP coordination. The S1/GFP coordination in vivo is rigid and the lever-arm orientation distribution is well-ordered in relaxed muscle. For comparison, single myosins in relaxed permeabilized porcine papillary muscle fibers indicated slightly differently oriented lever arms and rigid S1/GFP coordination. Lever arms in both muscles indicated one preferred spherical polar orientation and widely distributed azimuthal orientations relative to the fiber symmetry axis. Cardiac myosin is more radially displaced from the fiber axis. Probe rigidity implies the PAGFP tag reliably indicates cross-bridge orientation in situ and in vivo. PMID:25229148

Addressing individual metal ion centers in supramolecules by STS

NASA Astrophysics Data System (ADS)

Alam, M. S.; Ako, A. M.; Ruben, M.; Thompson, L. K.; Lehn, J.-M.

2005-03-01

As the information of STM measurements arises from electronic structure, separating information on the topography is not straightforward for complex molecules. Scanning tunneling spectroscopy (STS) measurements give information about the molecular energy levels, which are next to the molecules Fermi level. Using a home built STM working under ambient conditions, we succeeded to combine high resolution topography mapping with simultaneous current-voltage characteristics (STS) measurements on single molecules deposited on highly oriented pyrolytic graphite surfaces. We present our recent results on grid-type molecules [Co4L4] (L=4,6-bis(2',2''-bipyridyl-6-yl)pyrimidine) and [Mn9L6] (L=2POAP-2H) as well as on ring-shaped Fe ion chains [Fe6Cl6L6] (L=1-Ecosyliminodiethanol). Small, regular molecule clusters as well as separated single molecules were observed. We found a rather large contrast at the expected location of the metal centers in our molecules, i.e. the location of the individual metal ions in their organic matrix is directly addressable by STS.

N-[2-(2,2-Di-methyl-propanamido)-pyrimidin-4-yl]-2,2-di-methyl-propanamide n-hexane 0.25-solvate hemihydrate.

PubMed

Ośmiałowski, Borys; Valkonen, Arto; Chęcińska, Lilianna

2013-10-05

The asymmetric unit of the title compound, C14H22N4O2·0.25C6H14·0.5H2O, contains two independent mol-ecules of 2,4-bis-(pivaloyl-amino)-pyrimidine (M) with similar conformations, one water mol-ecule and one-half n-hexane solvent mol-ecule situated on an inversion center. In one independent M mol-ecule, one of the two tert-butyl groups is rotationally disordered between two orientations in a 3:2 ratio. The n-hexane solvent mol-ecule is disordered between two conformations in the same ratio. The water mol-ecule bridges two independent M mol-ecules via O-H⋯O, N-H⋯O and O-H⋯N hydrogen bonds into a 2M·H2O unit, and these units are further linked by N-H⋯N hydrogen bonds into chains running in the [010] direction. Weak C-H⋯O inter-actions are observed between the adjacent chains.

Observation of anisotropic interactions between metastable atoms and target molecules by two-dimensional collisional ionization electron spectroscopy

NASA Astrophysics Data System (ADS)

Kishimoto, Naoki; Ohno, Koichi

Excited metastable atoms colliding with target molecules can sensitively probe outer properties of molecules by chemi-ionization (Penning ionization) from molecular orbitals in the outer region, since metastable atoms cannot penetrate into the repulsive interaction wall around the molecules. By means of two-dimensional measurements using kinetic energy analysis of electrons combined with a velocity-resolved metastable beam, one can obtain information on the anisotropic interaction between the colliding particles without any control of orientation or alignment of target molecules. We have developed a classical trajectory method to calculate the collision energy dependence of partial ionization cross-sections (CEDPICS) on the anisotropic interaction potential energy surface, which has enabled us to study stereodynamics between metastable atoms and target molecules as well as the spatial distribution of molecular orbitals and electron ejection functions which have a relation with entrance and exit channels of the reaction. Based on the individual CEDPICS, the electronic structure of molecules can also be elucidated.

A novel spiroindoline targets cell cycle and migration via modulation of microtubule cytoskeleton.

PubMed

Kumar, Naveen; Hati, Santanu; Munshi, Parthapratim; Sen, Subhabrata; Sehrawat, Seema; Singh, Shailja

2017-05-01

Natural product-inspired libraries of molecules with diverse architectures have evolved as one of the most useful tools for discovering lead molecules for drug discovery. In comparison to conventional combinatorial libraries, these molecules have been inferred to perform better in phenotypic screening against complicated targets. Diversity-oriented synthesis (DOS) is a forward directional strategy to access such multifaceted library of molecules. From a successful DOS campaign of a natural product-inspired library, recently a small molecule with spiroindoline motif was identified as a potent anti-breast cancer compound. Herein we report the subcellular studies performed for this molecule on breast cancer cells. Our investigation revealed that it repositions microtubule cytoskeleton and displaces AKAP9 located at the microtubule organization centre. DNA ladder assay and cell cycle experiments further established the molecule as an apoptotic agent. This work further substantiated the amalgamation of DOS-phenotypic screening-sub-cellular studies as a consolidated blueprint for the discovery of potential pharmaceutical drug candidates.

A general method for controlling and resolving rotational orientation of molecules in molecule-surface collisions

PubMed Central

Godsi, Oded; Corem, Gefen; Alkoby, Yosef; Cantin, Joshua T.; Krems, Roman V.; Somers, Mark F.; Meyer, Jörg; Kroes, Geert-Jan; Maniv, Tsofar; Alexandrowicz, Gil

2017-01-01

The outcome of molecule–surface collisions can be modified by pre-aligning the molecule; however, experiments accomplishing this are rare because of the difficulty of preparing molecules in aligned quantum states. Here we present a general solution to this problem based on magnetic manipulation of the rotational magnetic moment of the incident molecule. We apply the technique to the scattering of H2 from flat and stepped copper surfaces. We demonstrate control of the molecule's initial quantum state, allowing a direct comparison of differences in the stereodynamic scattering from the two surfaces. Our results show that a stepped surface exhibits a much larger dependence of the corrugation of the interaction on the alignment of the molecule than the low-index surface. We also demonstrate an extension of the technique that transforms the set-up into an interferometer, which is sensitive to molecular quantum states both before and after the scattering event. PMID:28480890

Activity- vs. structural-oriented treatment approach for frozen shoulder: a randomized controlled trial.

PubMed

Horst, Renata; Maicki, Tomasz; Trąbka, Rafał; Albrecht, Sindy; Schmidt, Katharina; Mętel, Sylwia; von Piekartz, Harry

2017-05-01

To compare the short- and long-term effects of a structural-oriented (convential) with an activity-oriented physiotherapeutic treatment in patients with frozen shoulder. Double-blinded, randomized, experimental study. Outpatient clinic. We included patients diagnosed with a limited range of motion and pain in the shoulder region, who had received a prescription for physiotherapy treatment, without additional symptoms of dizziness, a case history of headaches, pain and/or limited range of motion in the cervical spine and/or temporomandibular joint. The study group received treatment during the performance of activities. The comparison group was treated with manual therapy and proprioceptive neuromuscular facilitation (conventional therapy). Both groups received 10 days of therapy, 30 minutes each day. Range of motion, muscle function tests, McGill pain questionnaire and modified Upper Extremity Motor Activity Log were measured at baseline, after two weeks of intervention and after a three-month follow-up period without therapy. A total of 66 patients were randomized into two groups: The activity-oriented group ( n = 33, mean = 44 years, SD = 16 years) including 20 male (61%) and the structural-oriented group ( n = 33, mean = 47 years, SD = 17 years) including 21 male (64%). The activity-oriented group revealed significantly greater improvements in the performance of daily life activities and functional and structural tests compared with the group treated with conventional therapy after 10 days of therapy and at the three-month follow-up ( p < 0.05). Therapy based on performing activities seems to be more effective for pain reduction and the ability to perform daily life activities than conventional treatment methods.

bFGF-containing electrospun gelatin scaffolds with controlled nano-architectural features for directed angiogenesis

PubMed Central

Montero, Ramon B.; Vial, Ximena; Nguyen, Dat Tat; Farhand, Sepehr; Reardon, Mark; Pham, Si M.; Tsechpenakis, Gavriil; Andreopoulos, Fotios M.

2011-01-01

Current therapeutic angiogenesis strategies are focused on the development of biologically responsive scaffolds that can deliver multiple angiogenic cytokines and/or cells in ischemic regions. Herein, we report on a novel electrospinning approach to fabricate cytokine-containing nanofibrous scaffolds with tunable architecture to promote angiogenesis. Fiber diameter and uniformity were controlled by varying the concentration of the polymeric (i.e. gelatin) solution, the feed rate, needle to collector distance, and electric field potential between the collector plate and injection needle. Scaffold fiber orientation (random vs. aligned) was achieved by alternating the polarity of two parallel electrodes placed on the collector plate thus dictating fiber deposition patterns. Basic fibroblast growth factor (bFGF) was physically immobilized within the gelatin scaffolds at variable concentrations and human umbilical vein endothelial cells (HUVEC) were seeded on the top of the scaffolds. Cell proliferation and migration was assessed as a function of growth factor loading and scaffold architecture. HUVECs successfully adhered onto gelatin B scaffolds and cell proliferation was directly proportional to the loading concentrations of the growth factor (0–100 bFGF ng/mL). Fiber orientation had a pronounced effect on cell morphology and orientation. Cells were spread along the fibers of the electrospun scaffolds with the aligned orientation and developed a spindle-like morphology parallel to the scaffold's fibers. In contrast, cells seeded onto the scaffolds with random fiber orientation, did not demonstrate any directionality and appeared to have a rounder shape. Capillary formation (i.e. sprouts length and number of sprouts per bead), assessed in a 3-D in vitro angiogenesis assay, was a function of bFGF loading concentration (0 ng, 50 ng and 100 ng per scaffold) for both types of electrospun scaffolds (i.e. with aligned or random fiber orientation). PMID:22200610

Effects of peripheral sensory nerve stimulation plus task-oriented training on upper extremity function in patients with subacute stroke: a pilot randomized crossover trial.

PubMed

Ikuno, Koki; Kawaguchi, Saori; Kitabeppu, Shinsuke; Kitaura, Masaki; Tokuhisa, Kentaro; Morimoto, Shigeru; Matsuo, Atsushi; Shomoto, Koji

2012-11-01

To investigate the feasibility of peripheral sensory nerve stimulation combined with task-oriented training in patients with stroke during inpatient rehabilitation. A pilot randomized crossover trial. Two rehabilitation hospitals. Twenty-two patients with subacute stroke. Participants were randomly assigned to two groups and underwent two weeks of training in addition to conventional inpatient rehabilitation. The immediate group underwent peripheral sensory nerve stimulation combined with task-oriented training in the first week, followed by another week with task-oriented training alone. The delayed group underwent the same training in reverse order. Outcome measures were the level of fatigue and Wolf Motor Function Test. Patients were assessed at baseline, one and two weeks. All participants completed the study with no adverse events. There was no significant difference in level of fatigue between each treatment. From baseline to one week, the immediate group showed larger improvements than the delayed groups in the Wolf Motor Function Test (decrease in mean time (± SD) from 41.9 ± 16.2 seconds to 30.6 ± 11.4 seconds versus from 46.8 ± 19.4 seconds to 42.9 ± 14.7 seconds, respectively) but the difference did not reach significance after Bonferroni correction (P = 0.041). Within-group comparison showed significant improvements in the Wolf Motor Function Test mean time after the peripheral sensory nerve stimulation combined with task-oriented training periods in each group (P < 0.01). Peripheral sensory nerve stimulation is feasible in clinical settings and may enhance the effects of task-oriented training in patients with subacute stroke.

Precision analysis for standard deviation measurements of immobile single fluorescent molecule images.

PubMed

DeSantis, Michael C; DeCenzo, Shawn H; Li, Je-Luen; Wang, Y M

2010-03-29

Standard deviation measurements of intensity profiles of stationary single fluorescent molecules are useful for studying axial localization, molecular orientation, and a fluorescence imaging system's spatial resolution. Here we report on the analysis of the precision of standard deviation measurements of intensity profiles of single fluorescent molecules imaged using an EMCCD camera.We have developed an analytical expression for the standard deviation measurement error of a single image which is a function of the total number of detected photons, the background photon noise, and the camera pixel size. The theoretical results agree well with the experimental, simulation, and numerical integration results. Using this expression, we show that single-molecule standard deviation measurements offer nanometer precision for a large range of experimental parameters.

Luminescent systems based on the isolation of conjugated PI systems and edge charge compensation with polar molecules on a charged nanostructured surface

DOEpatents

Ivanov, Ilia N.; Puretzky, Alexander A.; Zhao, Bin; Geohegan, David B.; Styers-Barnett, David J.; Hu, Hui

2014-07-15

A photoluminescent or electroluminescent system and method of making a non-luminescent nanostructured material into such a luminescent system is presented. The method of preparing the luminescent system, generally, comprises the steps of modifying the surface of a nanostructured material to create isolated regions to act as luminescent centers and to create a charge imbalance on the surface; applying more than one polar molecule to the charged surface of the nanostructured material; and orienting the polar molecules to compensate for the charge imbalance on the surface of the nanostructured material. The compensation of the surface charge imbalance by the polar molecules allows the isolated regions to exhibit luminescence.

Chiral domain formation from the mixture of achiral rod-like liquid crystal and tri boomerang-shaped molecule

NASA Astrophysics Data System (ADS)

Lee, Ji-Hoon; Yoon, Tae-Hoon

2013-08-01

Spontaneous formation of chiral domains such as a helical filament and a bent-broom texture was observed from the mixture of a rod-like liquid crystal octylcyano-biphenyl (8CB) and a tri boomerang-shaped 2,4,6-triphenoxy-1,3,5-triazine (triphenoxy) molecule. Although the constituent molecules were achiral, their mixture showed the chiral domains with the equal fraction of the opposite handedness. No tilt of 8CB molecules in the smectic layer was observed, implying the chirality is not due to the polar packing and tilt of the molecules. In addition, the splay and bend elastic constant of 8CB was decreased after doping triphenoxy. A structural conformation of triphenoxy and an orientational coupling between 8CB and triphenoxy are considered to be related to the chiral domain formation.

Emergence of chirality in hexagonally packed monolayers of hexapentyloxytriphenylene on Au(111): a joint experimental and theoretical study.

PubMed

Sleczkowski, Piotr; Katsonis, Nathalie; Kapitanchuk, Oleksiy; Marchenko, Alexandr; Mathevet, Fabrice; Croset, Bernard; Lacaze, Emmanuelle

2014-11-11

We investigate the expression of chirality in a monolayer formed spontaneously by 2,3,6,7,10,11-pentyloxytriphenylene (H5T) on Au(111). We resolve its interface morphology by combining scanning tunneling microscopy (STM) with theoretical calculations of intermolecular and interfacial interaction potentials. We observe two commensurate structures. While both of them belong to a hexagonal space group, analogical to the triangular symmetry of the molecule and the hexagonal symmetry of the substrate surface, they surprisingly reveal a 2D chiral character. The corresponding breaking of symmetry arises for two reasons. First it is due to the establishment of a large molecular density on the substrate, which leads to a rotation of the molecules with respect to the molecular network crystallographic axes to avoid steric repulsion between neighboring alkoxy chains. Second it is due to the molecule-substrate interactions, leading to commensurable large crystallographic cells associated with the large size of the molecule. As a consequence, molecular networks disoriented with respect to the high symmetry directions of the substrate are induced. The high simplicity of the intermolecular and molecule-substrate van der Waals interactions leading to these observations suggests a generic character for this kind of symmetry breaking. We demonstrate that, for similar molecular densities, only two kinds of molecular networks are stabilized by the molecule-substrate interactions. The most stable network favors the interfacial interactions between terminal alkoxy tails and Au(111). The metastable one favors a specific orientation of the triphenylene core with its symmetry axes collinear to the Au⟨110⟩. This specific orientation of the triphenylene cores with respect to Au(111) appears associated with an energy advantage larger by at least 0.26 eV with respect to the disoriented core.

Feed mechanism and method for feeding minute items

DOEpatents

Stringer, Timothy Kent; Yerganian, Simon Scott

2012-11-06

A feeding mechanism and method for feeding minute items, such as capacitors, resistors, or solder preforms. The mechanism is adapted to receive a plurality of the randomly-positioned and randomly-oriented extremely small or minute items, and to isolate, orient, and position the items in a specific repeatable pickup location wherefrom they may be removed for use by, for example, a computer-controlled automated assembly machine. The mechanism comprises a sliding shelf adapted to receive and support the items; a wiper arm adapted to achieve a single even layer of the items; and a pushing arm adapted to push the items into the pickup location. The mechanism can be adapted for providing the items with a more exact orientation, and can also be adapted for use in a liquid environment.

Feed mechanism and method for feeding minute items

DOEpatents

Stringer, Timothy Kent [Bucyrus, KS; Yerganian, Simon Scott [Lee's Summit, MO

2009-10-20

A feeding mechanism and method for feeding minute items, such as capacitors, resistors, or solder preforms. The mechanism is adapted to receive a plurality of the randomly-positioned and randomly-oriented extremely small or minute items, and to isolate, orient, and position one or more of the items in a specific repeatable pickup location wherefrom they may be removed for use by, for example, a computer-controlled automated assembly machine. The mechanism comprises a sliding shelf adapted to receive and support the items; a wiper arm adapted to achieve a single even layer of the items; and a pushing arm adapted to push the items into the pickup location. The mechanism can be adapted for providing the items with a more exact orientation, and can also be adapted for use in a liquid environment.

Center of mass perception and inertial frames of reference.

PubMed

Bingham, G P; Muchisky, M M

1993-11-01

Center of mass perception was investigated by varying the shape, size, and orientation of planar objects. Shape was manipulated to investigate symmetries as information. The number of reflective symmetry axes, the amount of rotational symmetry, and the presence of radial symmetry were varied. Orientation affected systematic errors. Judgments tended to undershoot the center of mass. Random errors increased with size and decreased with symmetry. Size had no effect on random errors for maximally symmetric objects, although orientation did. The spatial distributions of judgments were elliptical. Distribution axes were found to align with the principle moments of inertia. Major axes tended to align with gravity in maximally symmetric objects. A functional and physical account was given in terms of the repercussions of error. Overall, judgments were very accurate.

Ordered array of CoPc-vacancies filled with single-molecule rotors

NASA Astrophysics Data System (ADS)

Xie, Zheng-Bo; Wang, Ya-Li; Tao, Min-Long; Sun, Kai; Tu, Yu-Bing; Yuan, Hong-Kuan; Wang, Jun-Zhong

2018-05-01

We report the highly ordered array of CoPc-vacancies and the single-molecule rotors inside the vacancies. When CoPc molecules are deposited on Cd(0001) at low-temperature, three types of molecular vacancies appeared randomly in the CoPc monolayer. Annealing the sample to higher temperature leads to the spontaneous phase separation and self-organized arrangement of the vacancies. Highly ordered arrays of two-molecule vacancies and single-molecule vacancies have been obtained. In particular, there is a rotating CoPc molecule inside each single-molecule vacancy, which constitutes the array of single-molecule rotors. These results provide a new routine to fabricate the nano-machines on a large scale.

Contour symmetry detection: the influence of axis orientation and number of objects.

PubMed

Friedenberg, J; Bertamini, M

2000-09-01

Participants discriminated symmetrical from random contours connected by straight lines to form part of one- or two-objects. In experiment one, symmetrical contours were translated or reflected and presented at vertical, horizontal, and oblique axis orientations with orientation constant within blocks. Translated two-object contours were detected more easily than one, replicating a "lock-and-key" effect obtained previously for vertical orientations only [M. Bertamini, J.D. Friedenberg, M. Kubovy, Acta Psychologica, 95 (1997) 119-140]. A second experiment extended these results to a wider variety of axis orientations under mixed block conditions. The pattern of performance for translation and reflection at different orientations corresponded in both experiments, suggesting that orientation is processed similarly in the detection of these symmetries.

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

Luo, Sijun, E-mail: sluo1@tulane.edu; Riggs, Brian C.; Shipman, Joshua T.

Direct integration of proton conductor films on Pt-coated substrates opens the way to film-based proton transport devices. Columnar SrZr{sub 0.95}Y{sub 0.05}O{sub 3−δ} (SZY) films with dense microstructure were deposited on Pt-coated MgO(100) substrates at 830 °C by pulsed laser deposition. The optimal window of ambient O{sub 2} pressure for good crystallinity of SZY films is from 400 to 600 mTorr. The ambient O{sub 2} compresses the plasma plume of SZY and increases the deposition rate. The 10 nm thick Ti adhesion layer on MgO(100) greatly affects the orientation of the sputtered Pt layers. Pt deposited directly on MgO shows a highly (111)-preferredmore » orientation and leads to preferentially oriented SZY films while the addition of a Ti adhesion layer makes Pt show a less preferential orientation that leads to randomly oriented SZY films. The RMS surface roughness of preferentially oriented SZY films is larger than that of randomly oriented SZY films deposited under the same ambient O{sub 2} pressure. As the O{sub 2} pressure increased, the RMS surface roughness of preferentially oriented SZY films increased, reaching 45.7 nm (2.61% of film thickness) at 600 mTorr. This study revealed the ambient O{sub 2} pressure and orientation dependent surface roughness of SZY films grown on Pt-coated MgO substrates, which provides the potential to control the surface microstructure of SZY films for electrochemical applications in film-based hydrogen devices.« less

Studying the orientation of bio-objects by nematic liquid crystals

NASA Astrophysics Data System (ADS)

Zubtsova, Yu. A.; Kamanin, A. A.; Kamanina, N. V.

2017-05-01

We have studied the ability of a liquid-crystal (LC) matrix to visualize and orient DNA molecules. It is established that the relief of the interface between the LC mesophase and conducting contact can be improved without using an additional high-ohmic polymer layer. Spectroscopic and ellipsometric techniques revealed changes in the refractive properties and structure of composites. The obtained results can be used in creating devices for rapid DNA testing with retained form of biostructures.

Examining the Impact of Public Service Announcements on Help Seeking and Stigma: Results of a Randomized Controlled Trial.

PubMed

Corrigan, Patrick W; Powell, Karina J; Al-Khouja, Maya A

2015-11-01

Health communication campaigns often seek to diminish stigma and promote care seeking, with public service announcements (PSAs) frequently prominent in these campaigns. One example is the Australian-based beyondblue campaign. As an alternative approach, campaigns may seek to reduce stigma by promoting stories of recovery. Participants completed measures of stigmatizing and empowering attitudes at pre-, post-, and 72-hour follow-up after being randomized to a PSA recovery-oriented video, treatable disease-oriented video (beyondblue), or control. When exposed to the recovery-oriented PSA, participants showed significant reduction in stigmatizing attitudes from pre- to posttest than beyondblue or the control group with the emergence of nonsignificant trends identified at follow-up. Findings suggest a recovery-oriented video leads to better change on measures of stigma and affirming attitudes than beyondblue. Despite the aforementioned findings, results failed to show either the recovery or beyondblue videos had a significant impact on intent to seek treatment.

Rapid and Efficient Redox Processes within 2D Covalent Organic Framework Thin Films

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

DeBlase, Catherine R.; Hernández-Burgos, Kenneth; Silberstein, Katharine E.

2015-03-24

Two-dimensional covalent organic frameworks (2D COFs) are ideally suited for organizing redox-active subunits into periodic, permanently porous polymer networks of interest for pseudocapacitive energy storage. Here we describe a method for synthesizing crystalline, oriented thin films of a redox-active 2D COF on Au working electrodes. The thickness of the COF film was controlled by varying the initial monomer concentration. A large percentage (80–99%) of the anthraquinone groups are electrochemically accessible in films thinner than 200 nm, an order of magnitude improvement over the same COF prepared as a randomly oriented microcrystalline powder. As a result, electrodes functionalized with oriented COFmore » films exhibit a 400% increase in capacitance scaled to electrode area as compared to those functionalized with the randomly oriented COF powder. These results demonstrate the promise of redox-active COFs for electrical energy storage and highlight the importance of controlling morphology for optimal performance.« less

Rapid and Efficient Redox Processes within 2D Covalent Organic Framework Thin Films

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

DeBlase, Catherine R.; Hernández-Burgos, Kenneth; Silberstein, Katharine E.

2015-02-17

Two-dimensional covalent organic frameworks (2D COFs) are ideally suited for organizing redox-active subunits into periodic, permanently porous polymer networks of interest for pseudocapacitive energy storage. Here we describe a method for synthesizing crystalline, oriented thin films of a redox-active 2D COF on Au working electrodes. The thickness of the COF film was controlled by varying the initial monomer concentration. A large percentage (80–99%) of the anthraquinone groups are electrochemically accessible in films thinner than 200 nm, an order of magnitude improvement over the same COF prepared as a randomly oriented microcrystalline powder. As a result, electrodes functionalized with oriented COFmore » films exhibit a 400% increase in capacitance scaled to electrode area as compared to those functionalized with the randomly oriented COF powder. These results demonstrate the promise of redox-active COFs for electrical energy storage and highlight the importance of controlling morphology for optimal performance.« less

The organization of repeating units in mitochondrial DNA from yeast petite mutants.

PubMed

Bos, J L; Heyting, C; Van der Horst, G; Borst, P

1980-04-01

We have reinvestigated the linkage orientation of repeating units in mtDNAs of yeast ρ(-) petite mutants containing an inverted duplication. All five petite mtDNAs studied contain a continuous segment of wild-type mtDNA, part of which is duplicated and present in inverted form in the repeat. We show by restriction enzyme analysis that the non-duplicated segments between the inverted duplications are present in random orientation in all five petite mtDNAs. There is no segregation of sub-types with unique orientation. We attribute this to the high rate of intramolecular recombination between the inverted duplications. The results provide additional evidence for the high rate of recombination of yeast mtDNA even in haploid ρ(-) petite cells.We conclude that only two types of stable sequence organization exist in petite mtDNA: petites without an inverted duplication have repeats linked in straight head-to-tail arrangement (abcabc); petites with an inverted duplication have repeats in which the non-duplicated segments are present in random orientation.

Surface engineering with functional random copolymers for nanolithographic applications

NASA Astrophysics Data System (ADS)

Sparnacci, Katia; Antonioli, Diego; Gianotti, Valentina; Lupi, Federico Ferrarese; Giammaria, Tommaso Jacopo; Seguini, Gabriele; Perego, Michele; Laus, Michele

2016-05-01

Hydroxyl-terminated P(S-r-MMA) random copolymers with molecular weight ranging from 1.7 to 69 kg/mol and a styrene unit fraction of 61% were grafted onto a silicon oxide surface and subsequently used to study the orientation of domains with respect to the substrate, in cylinder-forming PS-b-PMMA block copolymer thin films. When the thickness (H) of the grafted layer is greater than 5-6 nm, a perpendicular orientation is always observed because of the efficient decoupling of the BCP film from the polar SiO2 surface. Conversely, if H is less than 5 nm, the critical thickness of the grafted layer, which allows the neutralization of the substrate and promotion of the perpendicular orientation of the nanodomains in the BCP film, is found to depend on the Mn of the RCP. In particular, when Mn = 1700, a 2.0 nm thick grafted layer is sufficient to promote the perpendicular orientation of the PMMA cylinders in the PS-b-PMMA BCP film.

ORIENTATION AND LOCUS OF TROPIC PHOTORECEPTOR MOLECULES IN SPORES OF BOTRYTIS AND OSMUNDA

PubMed Central

Jaffe, Lionel; Etzold, Helmut

1962-01-01

Study of the tropic responses of Botrytis cinerea and Osmunda cinnamomea spores to blue light shows the photoreceptor molecules to be highly dichroic and oriented: in Botrytis their axes of maximum absorption lie perpendicular to the nearby cell surface; in Osmunda, parallel. The chief evidence lies in a comparison of their responses to plane polarized light—both germinate parallel to the vibration planes (defined by the axis of vibration of the electric vector and the axis of light propagation)—with those to partial illumination with unpolarized light: Botrytis grows from its brighter part; Osmunda, from its darker. The degree of orientation produced by polarized light corresponds, at high intensities, to that produced by the imposition of such large (about 100 per cent) intensity differences across a cell as to preclude all alternatives to oriented dichroic receptors. The photoreceptors of the Botrytis spore lie within the cell wall's inner half. The chief evidence lies in the component of its tropic responses to polarized light within the vibration plane: germination peaks about 10° off the vibration axis. This deviation arises from focusing which is effective only in the wall's inner half. At high intensities, anomalies appear in Botrytis which are interpreted as "centering," i.e., a tendency toward growth from the center of two or more equally illuminated points of a cell rather than from one of them. PMID:14450869

Cellular automata with object-oriented features for parallel molecular network modeling.

PubMed

Zhu, Hao; Wu, Yinghui; Huang, Sui; Sun, Yan; Dhar, Pawan

2005-06-01

Cellular automata are an important modeling paradigm for studying the dynamics of large, parallel systems composed of multiple, interacting components. However, to model biological systems, cellular automata need to be extended beyond the large-scale parallelism and intensive communication in order to capture two fundamental properties characteristic of complex biological systems: hierarchy and heterogeneity. This paper proposes extensions to a cellular automata language, Cellang, to meet this purpose. The extended language, with object-oriented features, can be used to describe the structure and activity of parallel molecular networks within cells. Capabilities of this new programming language include object structure to define molecular programs within a cell, floating-point data type and mathematical functions to perform quantitative computation, message passing capability to describe molecular interactions, as well as new operators, statements, and built-in functions. We discuss relevant programming issues of these features, including the object-oriented description of molecular interactions with molecule encapsulation, message passing, and the description of heterogeneity and anisotropy at the cell and molecule levels. By enabling the integration of modeling at the molecular level with system behavior at cell, tissue, organ, or even organism levels, the program will help improve our understanding of how complex and dynamic biological activities are generated and controlled by parallel functioning of molecular networks. Index Terms-Cellular automata, modeling, molecular network, object-oriented.

Orientation determination of interfacial beta-sheet structures in situ.

PubMed

Nguyen, Khoi Tan; King, John Thomas; Chen, Zhan

2010-07-01

Structural information such as orientations of interfacial proteins and peptides is important for understanding properties and functions of such biological molecules, which play crucial roles in biological applications and processes such as antimicrobial selectivity, membrane protein activity, biocompatibility, and biosensing performance. The alpha-helical and beta-sheet structures are the most widely encountered secondary structures in peptides and proteins. In this paper, for the first time, a method to quantify the orientation of the interfacial beta-sheet structure using a combined attenuated total reflectance Fourier transformation infrared spectroscopic (ATR-FTIR) and sum frequency generation (SFG) vibrational spectroscopic study was developed. As an illustration of the methodology, the orientation of tachyplesin I, a 17 amino acid peptide with an antiparallel beta-sheet, adsorbed to polymer surfaces as well as associated with a lipid bilayer was determined using the regular and chiral SFG spectra, together with polarized ATR-FTIR amide I signals. Both the tilt angle (theta) and the twist angle (psi) of the beta-sheet at interfaces are determined. The developed method in this paper can be used to obtain in situ structural information of beta-sheet components in complex molecules. The combination of this method and the existing methodology that is currently used to investigate alpha-helical structures will greatly broaden the application of optical spectroscopy in physical chemistry, biochemistry, biophysics, and structural biology.

Enantiodiscrimination of flexible cyclic solutes using NMR spectroscopy in polypeptide chiral mesophases: investigation of cis-decalin and THF.

PubMed

Aroulanda, Christie; Lafon, Olivier; Lesot, Philippe

2009-08-06

The conformational dynamics and orientational behavior of two model cyclic molecules, cis-decalin (cis-dec) and tetrahydrofurane (THF), dissolved in weakly ordering, polypeptidic chiral liquid crystals (CLCs) are theoretically discussed and experimentally investigated using deuterium and carbon-13 NMR spectroscopies. The analysis of enantiomeric and enantiotopic discriminations in these compounds is shown to depend on the rate of conformational exchange regime, slow or fast. The slow exchange regime is illustrated through the case of cis-dec at low temperature (243 K). We show that the deuterium NMR spectra in this regime can be qualitatively and quantitatively interpreted by restricting the conformational pathway of cis-dec to two enantiomeric conformers of C(2)-symmetry. The orientational order parameters of these interconverting enantiomers are calculated by matching the (2)H quadrupolar splittings with calculated conformer structures. The fast exchange regime is investigated through the examples of cis-dec at high temperature (356 K) and THF at room temperature (300 K). The (2)H NMR spectra above the coalescence temperature are analyzed by introducing the concept of "average molecular structure". This fictitious structure allows easily identifying NMR equivalences of solutes dissolved in CLC. However, it cannot be applied to determine consistent orientational order parameters. This study emphasizes that enantiotopic discriminations observed for flexible molecules in the fast exchange regime can be quantitatively interpreted only by considering the orientational order of each conformer.

Effects of 3 dimensional crystal geometry and orientation on 1D and 2D time-scale determinations of magmatic processes using olivine and orthopyroxene

NASA Astrophysics Data System (ADS)

Shea, Thomas; Krimer, Daniel; Costa, Fidel; Hammer, Julia

2014-05-01

One of the achievements in recent years in volcanology is the determination of time-scales of magmatic processes via diffusion in minerals and its addition to the petrologists' and volcanologists' toolbox. The method typically requires one-dimensional modeling of randomly cut crystals from two-dimensional thin sections. Here we address the question whether using 1D (traverse) or 2D (surface) datasets exploited from randomly cut 3D crystals introduces a bias or dispersion in the time-scales estimated, and how this error can be improved or eliminated. Computational simulations were performed using a concentration-dependent, finite-difference solution to the diffusion equation in 3D. The starting numerical models involved simple geometries (spheres, parallelepipeds), Mg/Fe zoning patterns (either normal or reverse), and isotropic diffusion coefficients. Subsequent models progressively incorporated more complexity, 3D olivines possessing representative polyhedral morphologies, diffusion anisotropy along the different crystallographic axes, and more intricate core-rim zoning patterns. Sections and profiles used to compare 1, 2 and 3D diffusion models were selected to be (1) parallel to the crystal axes, (2) randomly oriented but passing through the olivine center, or (3) randomly oriented and sectioned. Results show that time-scales estimated on randomly cut traverses (1D) or surfaces (2D) can be widely distributed around the actual durations of 3D diffusion (~0.2 to 10 times the true diffusion time). The magnitude over- or underestimations of duration are a complex combination of the geometry of the crystal, the zoning pattern, the orientation of the cuts with respect to the crystallographic axes, and the degree of diffusion anisotropy. Errors on estimated time-scales retrieved from such models may thus be significant. Drastic reductions in the uncertainty of calculated diffusion times can be obtained by following some simple guidelines during the course of data collection (i.e. selection of crystals and concentration profiles, acquisition of crystallographic orientation data), thus allowing derivation of robust time-scales.

Quantitative analysis of biological tissues using Fourier transform-second-harmonic generation imaging

NASA Astrophysics Data System (ADS)

Ambekar Ramachandra Rao, Raghu; Mehta, Monal R.; Toussaint, Kimani C., Jr.

2010-02-01

We demonstrate the use of Fourier transform-second-harmonic generation (FT-SHG) imaging of collagen fibers as a means of performing quantitative analysis of obtained images of selected spatial regions in porcine trachea, ear, and cornea. Two quantitative markers, preferred orientation and maximum spatial frequency are proposed for differentiating structural information between various spatial regions of interest in the specimens. The ear shows consistent maximum spatial frequency and orientation as also observed in its real-space image. However, there are observable changes in the orientation and minimum feature size of fibers in the trachea indicating a more random organization. Finally, the analysis is applied to a 3D image stack of the cornea. It is shown that the standard deviation of the orientation is sensitive to the randomness in fiber orientation. Regions with variations in the maximum spatial frequency, but with relatively constant orientation, suggest that maximum spatial frequency is useful as an independent quantitative marker. We emphasize that FT-SHG is a simple, yet powerful, tool for extracting information from images that is not obvious in real space. This technique can be used as a quantitative biomarker to assess the structure of collagen fibers that may change due to damage from disease or physical injury.

Task oriented training improves the balance outcome & reducing fall risk in diabetic population.

PubMed

Ghazal, Javeria; Malik, Arshad Nawaz; Amjad, Imran

2016-01-01

The objective was to determine the balance impairments and to compare task oriented versus traditional balance training in fall reduction among diabetic patients. The randomized control trial with descriptive survey and 196 diabetic patients were recruited to assess balance impairments through purposive sampling technique. Eighteen patients were randomly allocated into two groups; task oriented balance training group TOB (n=8) and traditional balance training group TBT (n=10). The inclusion criteria were 30-50 years age bracket and diagnosed cases of Diabetes Mellitus with neuropathy. The demographics were taken through standardized & valid assessment tools include Berg Balance Scale and Functional Reach Test. The measurements were obtained at baseline, after 04 and 08 weeks of training. The mean age of the participants was 49 ±6.79. The result shows that 165(84%) were at moderate risk of fall and 31(15%) were at mild risk of fall among total 196 diabetic patients. There was significant improvement (p <0.05) in task oriented balance training group for dynamic balance, anticipatory balance and reactive balance after 8 weeks of training as compare to traditional balance training. Task oriented balance training is effective in improving the dynamic, anticipator and reactive balance. The task oriented training reduces the risk of falling through enhancing balance outcome.

Task oriented training improves the balance outcome & reducing fall risk in diabetic population

PubMed Central

Ghazal, Javeria; Malik, Arshad Nawaz; Amjad, Imran

2016-01-01

Objectives: The objective was to determine the balance impairments and to compare task oriented versus traditional balance training in fall reduction among diabetic patients. Methods: The randomized control trial with descriptive survey and 196 diabetic patients were recruited to assess balance impairments through purposive sampling technique. Eighteen patients were randomly allocated into two groups; task oriented balance training group TOB (n=8) and traditional balance training group TBT (n=10). The inclusion criteria were 30-50 years age bracket and diagnosed cases of Diabetes Mellitus with neuropathy. The demographics were taken through standardized & valid assessment tools include Berg Balance Scale and Functional Reach Test. The measurements were obtained at baseline, after 04 and 08 weeks of training. Results: The mean age of the participants was 49 ±6.79. The result shows that 165(84%) were at moderate risk of fall and 31(15%) were at mild risk of fall among total 196 diabetic patients. There was significant improvement (p <0.05) in task oriented balance training group for dynamic balance, anticipatory balance and reactive balance after 8 weeks of training as compare to traditional balance training. Conclusion: Task oriented balance training is effective in improving the dynamic, anticipator and reactive balance. The task oriented training reduces the risk of falling through enhancing balance outcome. PMID:27648053

Carrier-envelope phase-dependent field-free molecular orientation

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

Shu Chuancun; Yuan Kaijun; Hu Wenhui

2009-07-15

We present a strategy to achieve carrier-envelope phase-dependent field-free molecular orientation with the use of carrier-envelope phase (CEP) stabilization and asymmetric few-cycle terahertz (THz) laser pulses. The calculations are performed on the LiH molecule by an exact solution of the full time-dependent Schroedinger equation including both the vibrational and the rotational degrees of freedom. Our calculations show that an efficient field-free molecular orientation can be obtained even at considerable temperatures. Moreover, we find a simple dependence of the field-free orientation on the CEP, which implies that the CEP becomes an important parameter for control of molecular orientation. More importantly, themore » realization of this scenario is appealing based on the fact that the intense few-cycle THz pulse with duration as short as a few optical cycles is available as a research tool.« less

Core stability exercise is as effective as task-oriented motor training in improving motor proficiency in children with developmental coordination disorder: a randomized controlled pilot study.

PubMed

Au, Mei K; Chan, Wai M; Lee, Lin; Chen, Tracy Mk; Chau, Rosanna Mw; Pang, Marco Yc

2014-10-01

To compare the effectiveness of a core stability program with a task-oriented motor training program in improving motor proficiency in children with developmental coordination disorder (DCD). Randomized controlled pilot trial. Outpatient unit in a hospital. Twenty-two children diagnosed with DCD aged 6-9 years were randomly allocated to the core stability program or the task-oriented motor program. Both groups underwent their respective face-to-face training session once per week for eight consecutive weeks. They were also instructed to carry out home exercises on a daily basis during the intervention period. Short Form of the Bruininks-Oseretsky Test of Motor Proficiency (Second Edition) and Sensory Organization Test at pre- and post-intervention. Intention-to-treat analysis revealed no significant between-group difference in the change of motor proficiency standard score (P=0.717), and composite equilibrium score derived from the Sensory Organization Test (P=0.100). Further analysis showed significant improvement in motor proficiency in both the core stability (mean change (SD)=6.3(5.4); p=0.008) and task-oriented training groups (mean change(SD)=5.1(4.0); P=0.007). The composite equilibrium score was significantly increased in the task-oriented training group (mean change (SD)=6.0(5.5); P=0.009), but not in the core stability group (mean change(SD) =0.0(9.6); P=0.812). In the task-oriented training group, compliance with the home program was positively correlated with change in motor proficiency (ρ=0.680, P=0.030) and composite equilibrium score (ρ=0.638, P=0.047). The core stability exercise program is as effective as task-oriented training in improving motor proficiency among children with DCD. © The Author(s) 2014.

Polarized light modulates light-dependent magnetic compass orientation in birds

PubMed Central

Muheim, Rachel; Sjöberg, Sissel; Pinzon-Rodriguez, Atticus

2016-01-01

Magnetoreception of the light-dependent magnetic compass in birds is suggested to be mediated by a radical-pair mechanism taking place in the avian retina. Biophysical models on magnetic field effects on radical pairs generally assume that the light activating the magnetoreceptor molecules is nondirectional and unpolarized, and that light absorption is isotropic. However, natural skylight enters the avian retina unidirectionally, through the cornea and the lens, and is often partially polarized. In addition, cryptochromes, the putative magnetoreceptor molecules, absorb light anisotropically, i.e., they preferentially absorb light of a specific direction and polarization, implying that the light-dependent magnetic compass is intrinsically polarization sensitive. To test putative interactions between the avian magnetic compass and polarized light, we developed a spatial orientation assay and trained zebra finches to magnetic and/or overhead polarized light cues in a four-arm “plus” maze. The birds did not use overhead polarized light near the zenith for sky compass orientation. Instead, overhead polarized light modulated light-dependent magnetic compass orientation, i.e., how the birds perceive the magnetic field. Birds were well oriented when tested with the polarized light axis aligned parallel to the magnetic field. When the polarized light axis was aligned perpendicular to the magnetic field, the birds became disoriented. These findings are the first behavioral evidence to our knowledge for a direct interaction between polarized light and the light-dependent magnetic compass in an animal. They reveal a fundamentally new property of the radical pair-based magnetoreceptor with key implications for how birds and other animals perceive the Earth’s magnetic field. PMID:26811473

Polarized light modulates light-dependent magnetic compass orientation in birds.

PubMed

Muheim, Rachel; Sjöberg, Sissel; Pinzon-Rodriguez, Atticus

2016-02-09

Magnetoreception of the light-dependent magnetic compass in birds is suggested to be mediated by a radical-pair mechanism taking place in the avian retina. Biophysical models on magnetic field effects on radical pairs generally assume that the light activating the magnetoreceptor molecules is nondirectional and unpolarized, and that light absorption is isotropic. However, natural skylight enters the avian retina unidirectionally, through the cornea and the lens, and is often partially polarized. In addition, cryptochromes, the putative magnetoreceptor molecules, absorb light anisotropically, i.e., they preferentially absorb light of a specific direction and polarization, implying that the light-dependent magnetic compass is intrinsically polarization sensitive. To test putative interactions between the avian magnetic compass and polarized light, we developed a spatial orientation assay and trained zebra finches to magnetic and/or overhead polarized light cues in a four-arm "plus" maze. The birds did not use overhead polarized light near the zenith for sky compass orientation. Instead, overhead polarized light modulated light-dependent magnetic compass orientation, i.e., how the birds perceive the magnetic field. Birds were well oriented when tested with the polarized light axis aligned parallel to the magnetic field. When the polarized light axis was aligned perpendicular to the magnetic field, the birds became disoriented. These findings are the first behavioral evidence to our knowledge for a direct interaction between polarized light and the light-dependent magnetic compass in an animal. They reveal a fundamentally new property of the radical pair-based magnetoreceptor with key implications for how birds and other animals perceive the Earth's magnetic field.

Random forest models to predict aqueous solubility.

PubMed

Palmer, David S; O'Boyle, Noel M; Glen, Robert C; Mitchell, John B O

2007-01-01

Random Forest regression (RF), Partial-Least-Squares (PLS) regression, Support Vector Machines (SVM), and Artificial Neural Networks (ANN) were used to develop QSPR models for the prediction of aqueous solubility, based on experimental data for 988 organic molecules. The Random Forest regression model predicted aqueous solubility more accurately than those created by PLS, SVM, and ANN and offered methods for automatic descriptor selection, an assessment of descriptor importance, and an in-parallel measure of predictive ability, all of which serve to recommend its use. The prediction of log molar solubility for an external test set of 330 molecules that are solid at 25 degrees C gave an r2 = 0.89 and RMSE = 0.69 log S units. For a standard data set selected from the literature, the model performed well with respect to other documented methods. Finally, the diversity of the training and test sets are compared to the chemical space occupied by molecules in the MDL drug data report, on the basis of molecular descriptors selected by the regression analysis.

Effects of task-oriented robot training on arm function, activity, and quality of life in chronic stroke patients: a randomized controlled trial.

PubMed

Timmermans, Annick A A; Lemmens, Ryanne J M; Monfrance, Maurice; Geers, Richard P J; Bakx, Wilbert; Smeets, Rob J E M; Seelen, Henk A M

2014-03-31

Over fifty percent of stroke patients experience chronic arm hand performance problems, compromising independence in daily life activities and quality of life. Task-oriented training may improve arm hand performance after stroke, whereby augmented therapy may lead to a better treatment outcome. Technology-supported training holds opportunities for increasing training intensity. However, the effects of robot-supported task-oriented training with real life objects in stroke patients are not known to date. The aim of the present study was to investigate the effectiveness and added value of the Haptic Master robot combined with task-oriented arm hand training in chronic stroke patients. In a single-blind randomized controlled trial, 22 chronic stroke patients were randomly allocated to receive either task-oriented robot-assisted arm-hand training (experimental group) or task-oriented non-robotic arm-hand training (control group). For training, the T-TOAT (Technology-supported Task-Oriented Arm Training) method was applied. Training was provided during 8 weeks, 4 times/week, 2 × 30 min/day. A significant improvement after training on the Action Research Arm Test (ARAT) was demonstrated in the experimental group (p = 0.008). Results were maintained until 6 months after cessation of the training. On the perceived performance measure (Motor Activity Log (MAL)), both, the experimental and control group improved significantly after training (control group p = 0.008; experimental group p = 0.013). The improvements on MAL in both groups were maintained until 6 months after cessation of the training. With regard to quality of life, only in the control group a significant improvement after training was found (EuroQol-5D p = 0.015, SF-36 physical p = 0.01). However, the improvement on SF-36 in the control group was not maintained (p = 0.012). No between-group differences could be demonstrated on any of the outcome measures. Arm hand performance improved in chronic stroke patients, after eight weeks of task oriented training. The use of a Haptic Master robot in support of task-oriented arm training did not show additional value over the video-instructed task-oriented exercises in highly functional stroke patients. Current Controlled Trials ISRCTN82787126.

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

Weiss, Paul

Spectroscopic imaging tools and methods, based on scanning tunneling microscopes (STMs), are being developed and applied to examine buried layers and interfaces with ultrahigh resolution. These new methods measure buried contacts, molecule-substrate bonds, buried dipoles in molecular layers, and key structural aspects of adsorbed molecules, such as tilt angles. We are developing the ability to locate lateral projections of molecular parts as a means of determining the structures of molecular layers. We are developing the ability to measure the orientation of buried functionality.

X-ray Birefringence: A New Strategy for Determining Molecular Orientation in Materials.

PubMed

Palmer, Benjamin A; Edwards-Gau, Gregory R; Morte-Ródenas, Anabel; Kariuki, Benson M; Lim, Gin Keat; Harris, Kenneth D M; Dolbnya, Igor P; Collins, Stephen P

2012-11-01

While the phenomenon of birefringence is well-established in the case of visible radiation and is exploited in many fields (e.g., through the use of the polarizing optical microscope), the analogous phenomenon for X-rays has been a virtually neglected topic. Here, we demonstrate the scope and potential for exploiting X-ray birefringence to determine the orientational properties of specific types of bonds in solids. Specifically, orientational characteristics of C-Br bonds in the bromocyclohexane/thiourea inclusion compound are elucidated from X-ray birefringence measurements at energies close to the bromine K-edge, revealing inter alia the changes in the orientational distribution of the C-Br bonds associated with a low-temperature order-disorder phase transition. From fitting a theoretical model to the experimental data, reliable quantitative information on the orientational properties of the C-Br bonds is determined. The experimental strategy reported here represents the basis of a new approach for gaining insights into the orientational properties of molecules in anisotropic materials.

Anisotropy in Third-Order Nonlinear Optical Susceptibility of a Squarylium Dye in a Nematic Liquid Crystal

NASA Astrophysics Data System (ADS)

Jin, Zhao-Hui; Li, Zhong-Yu; Kasatani, Kazuo; Okamoto, Hiroaki

2006-03-01

A squarylium dye is dissolved in 4-cyano-4'-pentylbiphenyl (5CB) and oriented by sandwiching mixtures between two pieces of rubbed glass plates. The optical absorption spectra of the oriented squarylium dye-5CB layers exhibit high anisotropy. The third-order nonlinear optical responses and susceptibilities χ(3)e of squarylium dye in 5CB are measured with light polarizations parallel and perpendicular to the orientational direction by the resonant femtosecond degenerate four-wave mixing (DFWM) technique. Temporal profiles of the DFWM signal of the oriented squarylium dye-5CB layers with light polarizations parallel and perpendicular to the orientational direction are measured with a time resolution of 0.3 ps (FWHM), and are found to consist of two components, i.e., the coherent instantaneous nonlinear response and slow response due to the formation of excited molecules. A high anisotropic ratio of χ(3)e, 10.8±1.2, is observed for the oriented layers.

Useful oriented immobilization of antibodies on chimeric magnetic particles: direct correlation of biomacromolecule orientation with biological activity by AFM studies.

PubMed

Marciello, Marzia; Filice, Marco; Olea, David; Velez, Marisela; Guisan, José M; Mateo, Cesar

2014-12-16

The preparation and performance of a suitable chimeric biosensor based on antibodies (Abs) immobilized on lipase-coated magnetic particles by means of a standing orienting strategy are presented. This novel system is based on hydrophobic magnetic particles coated with modified lipase molecules able to orient and further immobilize different Abs in a covalent way without any previous site-selective chemical modification of biomacromolecules. Different key parameters attending the process were studied and optimized. The optimal preparation was performed using a controlled loading (1 nmol Ab g(-1) chimeric support) at pH 9 and a short reaction time to recover a biological activity of about 80%. AFM microscopy was used to study and confirm the Abs-oriented immobilization on lipase-coated magnetic particles and the final achievement of a highly active and recyclable chimeric immune sensor. This direct technique was demonstrated to be a powerful alternative to the indirect immunoactivity assay methods for the study of biomacromolecule-oriented immobilizations.

Effect of amino on spin-dependent transport through a junction of fused oligothiophenes between graphene electrodes

NASA Astrophysics Data System (ADS)

Cao, Liemao; Li, Xiaobo; Liu, Guang; Liu, Ziran; Zhou, Guanghui

2017-05-01

The influence of chemical side groups is significant in physical or chemical understanding the transport through the single molecular junction. Motivated by the recent successful fabrication and measurement of a single organic molecule sandwiched between graphene electrodes (Prins et al., 2011), here we study the spin-dependent transport properties through a junction of a fused oligothiophenes molecule embedded between two zigzag-edged graphene nanoribbon (ZGNR) electrodes. The molecule with and without an attached amino NH2 side group is considered, respectively, and external magnetic fields or FM stripes are applied onto the ZGNRs to initially orient the magnetic alignment of the electrodes for the spin-dependent consideration. By the ab initio calculations based on the density functional theory combined with nonequilibrium Green's function formalism, we have demonstrated the remarkable difference in the spin-charge transport property between the junctions of the molecule with and without NH2 side group. In particular, the junction with side group shows more obvious NDR. In addition, it exhibits an interesting dual spin-filtering effect when the magnetic alignment in electrodes is initially antiparallel-oriented. The mechanisms of the results are revealed and discussed in terms of the spin-resolved transmission spectrum associated with the frontier molecular orbitals evolution, the molecular projected self-consistent Hamiltonian eigenvalues, and the local density of states.

Prototypical Organic–Oxide Interface: Intramolecular Resolution of Sexiphenyl on In 2O 3 (111)

DOE PAGES

Wagner, Margareta; Hofinger, Jakob; Setvin, Martin; ...

2018-03-28

The performance of an organic semiconductor device is critically determined by the geometric alignment, orientation, and ordering of the organic molecules. Although an organic multilayer eventually adopts the crystal structure of the organic material, the alignment and configuration at the interface with the substrate/electrode material are essential for charge injection into the organic layer. This work focuses on the prototypical organic semiconductor para-sexiphenyl (6P) adsorbed on In 2O 3(111), the thermodynamically most stable surface of the material that the most common transparent conducting oxide, indium tin oxide, is based on. The onset of nucleation and formation of the first monolayermore » are followed with atomically resolved scanning tunneling microscopy and noncontact atomic force microscopy (nc-AFM). Annealing to 200 °C provides sufficient thermal energy for the molecules to orient themselves along the high-symmetry directions of the surface, leading to a single adsorption site. The AFM data suggests an essentially planar adsorption geometry. With increasing coverage, the 6P molecules first form a loose network with a poor long-range order. Eventually, the molecules reorient into an ordered monolayer. In conclusion, this first monolayer has a densely packed, well-ordered (2 × 1) structure with one 6P per In 2O 3(111) substrate unit cell, that is, a molecular density of 5.64 × 10 13 cm –2.« less

Prototypical Organic–Oxide Interface: Intramolecular Resolution of Sexiphenyl on In 2O 3 (111)

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

Wagner, Margareta; Hofinger, Jakob; Setvin, Martin

The performance of an organic semiconductor device is critically determined by the geometric alignment, orientation, and ordering of the organic molecules. Although an organic multilayer eventually adopts the crystal structure of the organic material, the alignment and configuration at the interface with the substrate/electrode material are essential for charge injection into the organic layer. This work focuses on the prototypical organic semiconductor para-sexiphenyl (6P) adsorbed on In 2O 3(111), the thermodynamically most stable surface of the material that the most common transparent conducting oxide, indium tin oxide, is based on. The onset of nucleation and formation of the first monolayermore » are followed with atomically resolved scanning tunneling microscopy and noncontact atomic force microscopy (nc-AFM). Annealing to 200 °C provides sufficient thermal energy for the molecules to orient themselves along the high-symmetry directions of the surface, leading to a single adsorption site. The AFM data suggests an essentially planar adsorption geometry. With increasing coverage, the 6P molecules first form a loose network with a poor long-range order. Eventually, the molecules reorient into an ordered monolayer. In conclusion, this first monolayer has a densely packed, well-ordered (2 × 1) structure with one 6P per In 2O 3(111) substrate unit cell, that is, a molecular density of 5.64 × 10 13 cm –2.« less

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

PubMed

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.

Identification and Characterization of Molecular Bonding Structures by ab initio Quasi-Atomic Orbital Analyses.

PubMed

West, Aaron C; Duchimaza-Heredia, Juan J; Gordon, Mark S; Ruedenberg, Klaus

2017-11-22

The quasi-atomic analysis of ab initio electronic wave functions in full valence spaces, which was developed in preceding papers, yields oriented quasi-atomic orbitals in terms of which the ab initio molecular wave function and energy can be expressed. These oriented quasi-atomic orbitals are the rigorous ab initio counterparts to the conceptual bond forming atomic hybrid orbitals of qualitative chemical reasoning. In the present work, the quasi-atomic orbitals are identified as bonding orbitals, lone pair orbitals, radical orbitals, vacant orbitals and orbitals with intermediate character. A program determines the bonding characteristics of all quasi-atomic orbitals in a molecule on the basis of their occupations, bond orders, kinetic bond orders, hybridizations and local symmetries. These data are collected in a record and provide the information for a comprehensive understanding of the synergism that generates the bonding structure that holds the molecule together. Applications to a series of molecules exhibit the complete bonding structures that are embedded in their ab initio wave functions. For the strong bonds in a molecule, the quasi-atomic orbitals provide quantitative ab initio amplifications of the Lewis dot symbols. Beyond characterizing strong bonds, the quasi-atomic analysis also yields an understanding of the weak interactions, such as vicinal, hyperconjugative and radical stabilizations, which can make substantial contributions to the molecular bonding structure.

Stacking Orientation Mediation of Pentacene and Derivatives for High Open-Circuit Voltage Organic Solar Cells.

PubMed

Chou, Chi-Ta; Lin, Chien-Hung; Tai, Yian; Liu, Chin-Hsin J; Chen, Li-Chyong; Chen, Kuei-Hsien

2012-05-03

In this Letter, we investigated the effect of the molecular stacking orientation on the open circuit voltage (VOC) of pentacene-based organic solar cells. Two functionalized pentacenes, namely, 6,13-diphenyl-pentacene (DP-penta) and 6,13-dibiphenyl-4-yl-pentacene (DB-penta), were utilized. Different molecular stacking orientations of the pentacene derivatives from the pristine pentacene were identified by angle-dependent near-edge X-ray absorption fine structure measurements. It is concluded that pentacene molecules stand up on the substrate surface, while both functionalized pentacenes lie down. A significant increase of the VOC from 0.28 to 0.83 V can be achieved upon the utilization of functionalized pentacene, owing to the modulation of molecular stacking orientation, which induced a vacuum-level shift.

Orientation-Dependent Exciton-Plasmon Coupling in Embedded Organic/Metal Nanowire Heterostructures.

PubMed

Li, Yong Jun; Hong, Yan; Peng, Qian; Yao, Jiannian; Zhao, Yong Sheng

2017-10-24

The excitation of surface plasmons by optical emitters based on exciton-plasmon coupling is important for plasmonic devices with active optical properties. It has been theoretically demonstrated that the orientation of exciton dipole can significantly influence the coupling strength, yet systematic study of the coupling process in nanostructures is still hindered by the lack of proper material systems. In this work, we have experimentally investigated the orientation-dependent exciton-plasmon coupling in a rationally designed organic/metal nanowire heterostructure system. The heterostructures were prepared by inserting silver nanowires into crystalline organic waveguides during the self-assembly of dye molecules. Structures with different exciton orientations exhibited varying coupling efficiencies. The near-field exciton-plasmon coupling facilitates the design of nanophotonic devices based on the directional surface plasmon polariton propagations.

Fluorescence imaging of single-molecule retention trajectories in reversed-phase chromatographic particles.

PubMed

Cooper, Justin T; Peterson, Eric M; Harris, Joel M

2013-10-01

Due to its high specific surface area and chemical stability, porous silica is used as a support structure in numerous applications, including heterogeneous catalysis, biomolecule immobilization, sensors, and liquid chromatography. Reversed-phase liquid chromatography (RPLC), which uses porous silica support particles, has become an indispensable separations tool in quality control, pharmaceutics, and environmental analysis requiring identification of compounds in mixtures. For complex samples, the need for higher resolution separations requires an understanding of the time scale of processes responsible for analyte retention in the stationary phase. In the present work, single-molecule fluorescence imaging is used to observe transport of individual molecules within RPLC porous silica particles. This technique allows direct measurement of intraparticle molecular residence times, intraparticle diffusion rates, and the spatial distribution of molecules within the particle. On the basis of the localization uncertainty and characteristic measured diffusion rates, statistical criteria were developed to resolve the frame-to-frame behavior of molecules into moving and stuck events. The measured diffusion coefficient of moving molecules was used in a Monte Carlo simulation of a random-walk model within the cylindrical geometry of the particle diameter and microscope depth-of-field. The simulated molecular transport is in good agreement with the experimental data, indicating transport of moving molecules in the porous particle is described by a random-walk. Histograms of stuck-molecule event times, locations, and their contributions to intraparticle residence times were also characterized.

Phytochrome-mediated agravitropism in Arabidopsis hypocotyls requires GIL1 and confers a fitness advantage.

PubMed

Allen, Trudie; Ingles, Patricia J; Praekelt, Uta; Smith, Harry; Whitelam, Garry C

2006-05-01

Plants use specialized photoreceptors to detect the amount, quality, periodicity and direction of light and to modulate their growth and development accordingly. These regulatory light signals often interact with other environmental cues. Exposure of etiolated Arabidopsis seedlings to red (R) or far-red (FR) light causes hypocotyls to grow in random orientations with respect to the gravitational vector, thus overcoming the signal from gravity to grow upwards. This light response, mediated by either phytochrome A or phytochrome B, represents a prime example of cross-talk between environmental signalling systems. Here, we report the isolation the mutant gil1 (for gravitropic in the light) in which hypocotyls continue to grow upwards after exposure of seedlings to R or FR light. The gil1 mutant displays no other phenotypic alterations in response to gravity or light. Cloning of GIL1 has identified a novel gene that is necessary for light-dependent randomization of hypocotyl growth orientation. Using gil1, we have demonstrated that phytochrome-mediated randomization of Arabidopsis hypocotyl orientation provides a fitness advantage to seedlings developing in patchy, low-light environments.

Randomized Controlled Trial of a Brief Problem-Orientation Intervention for Suicidal Ideation

ERIC Educational Resources Information Center

Fitzpatrick, Kathleen Kara; Witte, Tracy K.; Schmidt, Norman B.

2005-01-01

Empirical evaluations suggest that problem orientation, the initial reaction to problems, differentiates suicidal youth from nonclinical controls and nonideating psychiatric controls. One promising area for intervention with suicidal youth relates to enhancing this specific coping skill. Nonclinical participants (N = 110) with active suicidal…

Tunable Holstein model with cold polar molecules

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

Herrera, Felipe; Krems, Roman V.

2011-11-15

We show that an ensemble of polar molecules trapped in an optical lattice can be considered as a controllable open quantum system. The coupling between collective rotational excitations and the motion of the molecules in the lattice potential can be controlled by varying the strength and orientation of an external dc electric field as well as the intensity of the trapping laser. The system can be described by a generalized Holstein Hamiltonian with tunable parameters and can be used as a quantum simulator of excitation energy transfer and polaron phenomena. We show that the character of excitation energy transfer canmore » be modified by tuning experimental parameters.« less

Ab initio calculations of the photoionization of diatomic molecules

NASA Astrophysics Data System (ADS)

Lefebvre-Brion, Helene; Raşeev, Georges

2003-01-01

A review is presented of the calculation of photoionization spectra, particularly in the spectral range where electron autoionization of diatomic molecules takes place. In addition to some interesting results obtained over years that compare favourably with experiment, the emphasis here is put on the relation between the methods developed for the calculation of observables associated with the continuum energy spectrum of the electrons and the Alchemy system of programs. This system of programs serves as a basis for initial and intermediate calculations. The examples presented show that diatomic molecules not only in gas phase but also oriented in space or physisorbed at surfaces may be studied readily.

Definition of the persistence length in the coarse-grained models of DNA elasticity.

PubMed

Fathizadeh, A; Eslami-Mossallam, B; Ejtehadi, M R

2012-11-01

By considering the detailed structure of DNA in the base pair level, two possible definitions of the persistence length are compared. One definition is related to the orientation of the terminal base pairs, and the other is based on the vectors which connect two adjacent base pairs at each end of the molecule. It is shown that although these definitions approach each other for long DNA molecules, they are dramatically different on short length scales. We show analytically that the difference mostly comes from the shear flexibility of the molecule and can be used to measure the shear modulus of DNA.

Sustainable reduction of bioreactor contamination in an industrial fermentation pilot plant.

PubMed

Junker, Beth; Lester, Michael; Leporati, James; Schmitt, John; Kovatch, Michael; Borysewicz, Stan; Maciejak, Waldemar; Seeley, Anna; Hesse, Michelle; Connors, Neal; Brix, Thomas; Creveling, Eric; Salmon, Peter

2006-10-01

Facility experience primarily in drug-oriented fermentation equipment (producing small molecules such as secondary metabolites, bioconversions, and enzymes) and, to a lesser extent, in biologics-oriented fermentation equipment (producing large molecules such as recombinant proteins and microbial vaccines) in an industrial fermentation pilot plant over the past 15 years is described. Potential approaches for equipment design and maintenance, operational procedures, validation/verification testing, medium selection, culture purity/sterility analysis, and contamination investigation are presented, and those approaches implemented are identified. Failure data collected for pilot plant operation for nearly 15 years are presented and best practices for documentation and tracking are outlined. This analysis does not exhaustively discuss available design, operational and procedural options; rather it selectively presents what has been determined to be beneficial in an industrial pilot plant setting. Literature references have been incorporated to provide background and context where appropriate.

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data.

PubMed

Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S; Windus, Theresa L; Dick-Perez, Marilu

2017-03-27

A newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides, important for metal extraction chemistry, are parametrized using ParFit. ParFit is in an open source program available for free on GitHub ( https://github.com/fzahari/ParFit ).

Catalytic activity of Cu4-cluster to adsorb H2S gas: h-BN nanosheet

NASA Astrophysics Data System (ADS)

Kansara, Shivam; Gupta, Sanjeev K.; Sonvane, Yogesh

2018-05-01

We have investigated the electronic properties, adsorptions strength and charge transfer using first principles calculations using density functional theory (DFT). The hexagonal boron nitride (h-BN) substrate shows metallic behavior, which helps to enhance the absorption process. The adsorption of three different orientations (S, D and T) of the H2S gas molecules to analyze the maximum adsorption strength from them onto a copper cluster (Cu4) based on h-BN nanosheet. The maximum adsorption energy of the H2S gas molecule is -1.50 eV for the S orientation and for D and U, it is -0.71 eV and -0.78 eV, respectively. The results show that Cu4 cluster helps to capture H2S gas from the environment and results are useful for the cleaning environment from the toxic gases.

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

Ran, Niva A.; Roland, Steffen; Love, John A.

Here, a long standing question in organic electronics concerns the effects of molecular orientation at donor/acceptor heterojunctions. Given a well-controlled donor/acceptor bilayer system, we uncover the genuine effects of molecular orientation on charge generation and recombination. These effects are studied through the point of view of photovoltaics—however, the results have important implications on the operation of all optoelectronic devices with donor/acceptor interfaces, such as light emitting diodes and photodetectors. Our findings can be summarized by two points. First, devices with donor molecules face-on to the acceptor interface have a higher charge transfer state energy and less non-radiative recombination, resulting inmore » larger open-circuit voltages and higher radiative efficiencies. Second, devices with donor molecules edge-on to the acceptor interface are more efficient at charge generation, attributed to smaller electronic coupling between the charge transfer states and the ground state, and lower activation energy for charge generation.« less

Separation of enantiomers by their enantiospecific interaction with achiral magnetic substrates.

PubMed

Banerjee-Ghosh, Koyel; Ben Dor, Oren; Tassinari, Francesco; Capua, Eyal; Yochelis, Shira; Capua, Amir; Yang, See-Hun; Parkin, Stuart S P; Sarkar, Soumyajit; Kronik, Leeor; Baczewski, Lech Tomasz; Naaman, Ron; Paltiel, Yossi

2018-06-22

It is commonly assumed that recognition and discrimination of chirality, both in nature and in artificial systems, depend solely on spatial effects. However, recent studies have suggested that charge redistribution in chiral molecules manifests an enantiospecific preference in electron spin orientation. We therefore reasoned that the induced spin polarization may affect enantiorecognition through exchange interactions. Here we show experimentally that the interaction of chiral molecules with a perpendicularly magnetized substrate is enantiospecific. Thus, one enantiomer adsorbs preferentially when the magnetic dipole is pointing up, whereas the other adsorbs faster for the opposite alignment of the magnetization. The interaction is not controlled by the magnetic field per se, but rather by the electron spin orientations, and opens prospects for a distinct approach to enantiomeric separations. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Random walk on a leash: a simple single-molecule diffusion model for surface-tethered redox molecules with flexible linkers.

PubMed

Huang, Kuan-Chun; White, Ryan J

2013-08-28

We develop a random walk model to simulate the Brownian motion and the electrochemical response of a single molecule confined to an electrode surface via a flexible molecular tether. We use our simple model, which requires no prior knowledge of the physics of the molecular tether, to predict and better understand the voltammetric response of surface-confined redox molecules when motion of the redox molecule becomes important. The single molecule is confined to a hemispherical volume with a maximum radius determined by the flexible molecular tether (5-20 nm) and is allowed to undergo true three-dimensional diffusion. Distance- and potential-dependent electron transfer probabilities are evaluated throughout the simulations to generate cyclic voltammograms of the model system. We find that at sufficiently slow cyclic voltammetric scan rates the electrochemical reaction behaves like an adsorbed redox molecule with no mass transfer limitation; thus, the peak current is proportional to the scan rate. Conversely, at faster scan rates the diffusional motion of the molecule limits the simulated peak current, which exhibits a linear dependence on the square root of the scan rate. The switch between these two limiting regimes occurs when the diffusion layer thickness, (2Dt)(1/2), is ~10 times the tether length. Finally, we find that our model predicts the voltammetric behavior of a redox-active methylene blue tethered to an electrode surface via short flexible single-stranded, polythymine DNAs, allowing the estimation of diffusion coefficients for the end-tethered molecule.

Atomistic Simulation Studies of Cholesteryl Oleates: Model for the Core of Lipoprotein Particles

PubMed Central

Heikelä, Mikko; Vattulainen, Ilpo; Hyvönen, Marja T.

2006-01-01

We have conducted molecular dynamics simulations to gain insight into the atomic-scale properties of an isotropic system of cholesteryl oleate (CO) molecules. Cholesteryl esters are major constituents of low density lipoprotein particles, the key players in the formation of atherosclerosis, as well as the storage form of cholesterol. Here the aim is to clarify structural and dynamical properties of CO molecules under conditions, which are suggestive of those in the core of low density lipoprotein particles. The simulations in the fluid phase indicate that the system of CO molecules is characterized by an absence of translational order, as expected, while the orientational order between distinct CO molecules is significant at short distances, persisting over a molecular size. As for intramolecular properties, the bonds along the oleate chain are observed to be weakly ordered with respect to the sterol structure, unlike the bonds along the short hydrocarbon chain of cholesterol where the ordering is significant. The orientational distribution of the oleate chain as a whole with respect to the sterol moiety is of broad nature, having a major amount of extended and a less considerable proportion of bended structures. Distinct transient peaks at specific angles also appear. The diffusion of CO molecules is found to be a slow process and characterized by a diffusion coefficient of the order of 2 × 10−9 cm2/s. This is considerably slower than diffusion, e.g., in ordered domains of lipid membranes rich in sphingomyelin and cholesterol. Analysis of the rotational diffusion rates and trans-to-gauche transition rates yield results consistent with experiments. PMID:16399839

Solute rotational dynamics at the water liquid/vapor interface.

PubMed

Benjamin, Ilan

2007-11-28

The rotational dynamics of a number of diatomic molecules adsorbed at different locations at the interface between water and its own vapors are studied using classical molecular dynamics computer simulations. Both equilibrium orientational and energy correlations and nonequilibrium orientational and energy relaxation correlations are calculated. By varying the dipole moment of the molecule and its location, and by comparing the results with those in bulk water, the effects of dielectric and mechanical frictions on reorientation dynamics and on rotational energy relaxation can be studied. It is shown that for nonpolar and weekly polar solutes, the equilibrium orientational relaxation is much slower in the bulk than at the interface. As the solute becomes more polar, the rotation slows down and the surface and bulk dynamics become similar. The energy relaxation (both equilibrium and nonequilibrium) has the opposite trend with the solute dipole (larger dipoles relax faster), but here again the bulk and surface results converge as the solute dipole is increased. It is shown that these behaviors correlate with the peak value of the solvent-solute radial distribution function, which demonstrates the importance of the first hydration shell structure in determining the rotational dynamics and dependence of these dynamics on the solute dipole and location.

Nanoscale Control over the Mixing Behavior of Surface-Confined Bicomponent Supramolecular Networks Using an Oriented External Electric Field

PubMed Central

2017-01-01

Strong electric fields are known to influence the properties of molecules as well as materials. Here we show that by changing the orientation of an externally applied electric field, one can locally control the mixing behavior of two molecules physisorbed on a solid surface. Whether the starting two-component network evolves into an ordered two-dimensional (2D) cocrystal, yields an amorphous network where the two components phase separate, or shows preferential adsorption of only one component depends on the solution stoichiometry. The experiments are carried out by changing the orientation of the strong electric field that exists between the tip of a scanning tunneling microscope and a solid substrate. The structure of the two-component network typically changes from open porous at negative substrate bias to relatively compact when the polarity of the applied bias is reversed. The electric-field-induced mixing behavior is reversible, and the supramolecular system exhibits excellent stability and good response efficiency. When molecular guests are adsorbed in the porous networks, the field-induced switching behavior was found to be completely different. Plausible reasons behind the field-induced mixing behavior are discussed. PMID:29112378

Manipulating the motion of large molecules: Information from the molecular frame

NASA Astrophysics Data System (ADS)

Küpper, Jochen

2011-05-01

Large molecules have complex potential-energy surfaces with many local minima. They exhibit multiple stereoisomers, even at the low temperatures (~1 K) in a molecular beam, with rich intra- and intermolecular dynamics. Over the last years, we have developed methods to manipulate the motion of large, complex molecules and to select their quantum states. We have exploited this state-selectivity, for example, to spatially separate individual structural isomers of complex molecules and to demonstrate unprecedented degrees of laser alignment and mixed-field orientation of these molecules. Such clean, well-defined samples strongly benefit, or simply allow, novel experiments on the dynamics of complex molecules, for instance, femtosecond pump-probe measurements, X-ray or electron diffraction of molecular ensembles (including diffraction-from-within experiments), or tomographic reconstructions of molecular orbitals. These samples could also be very advantageous for metrology applications, such as, for example, matter-wave interferometry or the search for electroweak interactions in chiral molecules. Moreover, they provide an extreme level of control for stereo-dynamically controlled reaction dynamics. We have recently exploited these state-selected and oriented samples to measure photoelectron angular distributions in the molecular frame (MFPADs) from non-resonant femtosecond-laser photoionization and using the X-ray Free-Electron-Laser LCLS. We have also investigated X-ray diffraction imaging and, using ion momentum imaging, the induced radiation damage of these samples using the LCLS. This work was carried out within a collaboration for which J. Küpper, H. Chapman, and D. Rolles are spokespersons. The collaboration consists of CFEL (DESY, MPG, University Hamburg), Fritz-Haber-Institute Berlin, MPI Nuclear Physics Heidelberg, MPG Semi-conductor Lab, Aarhus University, FOM AMOLF Amsterdam, Lund University, MPI Medical Research Heidelberg, TU Berlin, Max Born Institute Berlin, and SLAC Menlo Park, CA, USA. The experiments were carried out using CAMP (designed and built by the MPG-ASG at CFEL) at the LCLS (operated by Stanford University on behalf of the US DOE).

Structure and functions of water-membrane interfaces and their role in proto-biological evolution

NASA Technical Reports Server (NTRS)

Pohorille, A.; Wilson, M.; Macelroy, R. D.

1991-01-01

Among the most important developments in proto-biological evolution was the emergence of membrane-like structures. These are formed by spontaneous association of relatively simple amphiphilic molecules that would have been readily available in the primordial environment. The resulting interfacial regions between water and nonpolar interior of the membrane have several properties which made them uniquely suitable for promoting subsequent evolution. They can (1) selectively attract organic material and mediate its transport, (2) serve as simple catalysts for chemical reactions, and (3) promote the formation of trans-membrane electrical and chemical gradients which could provide energy sources for proto-cells. Understanding the structure of interfaces, their interactions with organic molecules and molecular mechanisms of their functions is an essential step to understanding proto-biological evolution. In our computer simulation studies, we showed that the structure of water at interfaces with nonpolar media is significantly different from that in the bulk. In particular, the average surface dipole density points from the vapor to the liquid. As a result, negative ions can approach the interface more easily than positive ions. Amphiphilic molecules composed of hydrocarbon conjugated rings and polar substituents (e.g., phenol) assume at the interface rigid orientations in which polar groups are buried in water while hydrocarbon parts are located in the nonpolar environment. These orientational differences are of special interest in connection with the ability of some of these molecules to efficiently absorb photons. Flexible molecules with polar substituents often adopt at interfaces conformations different from those in the bulk aquaeous solution and in the gas phase. As a result, in many instances both specificity and kinetics of chemical reactions in which these molecules can participate is modified by the presence of surfaces. Of special interest is the mechanism by which polar molecules are transferred across interface between water and a nonpolar medium. Our recent study showed that simple ionophores bind ions by the same mechanisms as ion channels and carriers from modern cells.

Task-Oriented Training with Computer Games for People with Rheumatoid Arthritis or Hand Osteoarthritis: A Feasibility Randomized Controlled Trial.

PubMed

Srikesavan, Cynthia Swarnalatha; Shay, Barbara; Szturm, Tony

2016-09-13

To examine the feasibility of a clinical trial on a novel, home-based task-oriented training with conventional hand exercises in people with rheumatoid arthritis or hand osteoarthritis. To explore the experiences of participants who completed their respective home exercise programmes. Thirty volunteer participants aged between 30 and 60 years and diagnosed with rheumatoid arthritis or hand osteoarthritis were proposed for a single-center, assessor-blinded, randomized controlled trial ( ClinicalTrials.gov : NCT01635582). Participants received task-oriented training with interactive computer games and objects of daily life or finger mobility and strengthening exercises. Both programmes were home based and were done four sessions per week with 20 minutes each session for 6 weeks. Major feasibility outcomes were number of volunteers screened, randomized, and retained; completion of blinded assessments, exercise training, and home exercise sessions; equipment and data management; and clinical outcomes of hand function. Reaching the recruitment target in 18 months and achieving exercise compliance >80% were set as success criteria. Concurrent with the trial, focus group interviews explored experiences of those participants who completed their respective programmes. After trial initiation, revisions in inclusion criteria were required to promote recruitment. A total of 17 participants were randomized and 15 were retained. Completion of assessments, exercise training, and home exercise sessions; equipment and data collection and management demonstrated excellent feasibility. Both groups improved in hand function outcomes and exercise compliance was above 85%. Participants perceived both programmes as appropriate and acceptable. Participants who completed task-oriented training also agreed that playing different computer games was enjoyable, engaging, and motivating. Findings demonstrate initial evidence on recruitment, feasibility of trial procedures, and acceptability of task-oriented training in people with rheumatoid arthritis or hand osteoarthritis. Since the pilot trial was unsuccessful in participant recruitment, a large trial will not follow.

Electrospun meshes possessing region-wise differences in fiber orientation, diameter, chemistry and mechanical properties for engineering bone-ligament-bone tissues.

PubMed

Samavedi, Satyavrata; Vaidya, Prasad; Gaddam, Prudhvidhar; Whittington, Abby R; Goldstein, Aaron S

2014-12-01

Although bone-patellar tendon-bone (B-PT-B) autografts are the gold standard for repair of anterior cruciate ligament ruptures, they suffer from drawbacks such as donor site morbidity and limited supply. Engineered tissues modeled after B-PT-B autografts are promising alternatives because they have the potential to regenerate connective tissue and facilitate osseointegration. Towards the long-term goal of regenerating ligaments and their bony insertions, the objective of this study was to construct 2D meshes and 3D cylindrical composite scaffolds - possessing simultaneous region-wise differences in fiber orientation, diameter, chemistry and mechanical properties - by electrospinning two different polymers from off-set spinnerets. Using a dual drum collector, 2D meshes consisting of an aligned polycaprolactone (PCL) fiber region, randomly oriented poly(lactide-co-glycolide) (PLGA) fiber region and a transition region (comprised of both PCL and PLGA fibers) were prepared, and region-wise differences were confirmed by microscopy and tensile testing. Bone marrow stromal cells (BMSCs) cultured on these meshes exhibited random orientations and low aspect ratios on the random PLGA regions, and high aspect ratios and alignment on the aligned PCL regions. Next, meshes containing an aligned PCL region flanked by two transition regions and two randomly oriented PLGA regions were prepared and processed into 3D cylindrical composite scaffolds using an interpenetrating photo-crosslinkable polyethylene glycol diacrylate hydrogel to recapitulate the shape of B-PT-B autografts. Tensile testing indicated that cylindrical composites were mechanically robust, and eventually failed due to stress concentration in the aligned PCL region. In summary, this study demonstrates a process to fabricate electrospun meshes possessing region-wise differences in properties that can elicit region-dependent cell responses, and be readily processed into scaffolds with the shape of B-PT-B autografts. © 2014 Wiley Periodicals, Inc.

Etiology of homosexuality and attitudes toward same-sex parenting: a randomized study.

PubMed

Frias-Navarro, Dolores; Monterde-I-Bort, Hector; Pascual-Soler, Marcos; Badenes-Ribera, Laura

2015-01-01

Attribution theory suggests the hypothesis that heterosexuals' attitudes toward homosexual sexual orientation will be more negative when homosexuality is attributed to controllable causes. Our randomized study analyzed (a) whether beliefs about the genetic or environmental etiology of the homosexual sexual orientation can be immediately modified by reading a text and (b) the causal effect of attributions about the controllability (environmental etiology) or noncontrollability (genetic etiology) of homosexual sexual orientation on the rejection of same-sex parenting and their social rights. The sample was composed of 190 Spanish university students with a mean age of 22.07 years (SD = 8.46). The results show that beliefs about the etiology of the sexual orientation could be modified by means of a written text. Furthermore, participants who believed that sexual orientation had a genetic etiology showed greater support for social rights and less rejection of same-sex parenting. However, the effects were detected only when there was a traditional opposition to the family with same-sex parenting. When the opposition was normative, the effect was not statistically significant. Our results can be useful in planning variables for intervention programs designed to foster tolerance toward and normality of sexual diversity.

Measurements of orientation, sedimentation, and dispersal of ramified particles in isotropic turbulence

NASA Astrophysics Data System (ADS)

Voth, Greg A.; Kramel, Stefan; Menon, Udayshankar K.; Koch, Donald L.

2017-11-01

We experimentally measure the sedimentation of non-spherical particles in isotropic turbulence. We obtain time-resolved 3D orientations of the particles along with the fluid velocity field around them in a vertical water tunnel. An active jet array with 40 individually controllable jets enables us to adjust the turbulence intensity and observe the transition from strongly aligned to randomized particle orientations. We focus on the orientation statistics of ramified particles formed from several slender arms, including fibers and particles with three arms in planar symmetry (triads), which allows us to study alignment of both fibers and disk-like particles. We can predict the turbulent intensity at which the transition from aligned to randomized particle orientations occurs using a non-dimensional settling factor given by the ratio of rotation timescale of the turbulence at the scale of the particle to the rotation timescale of a particles in quiescent flow due to inertial torques. A model of ramified particle motion based on slender body theory provides accurate predictions of the vertical and horizontal particle velocities relative to the turbulent fluid. Supported by Army Research Office Grant W911NF1510205.

Investigating histological aspects of scars in children.

PubMed

Westra, I; Verhaegen, P D H M; Ibrahim Korkmaz, H; Braam, K I; Kaspers, G J L; Niessen, H W M; Niessen, F B

2017-05-02

Very little is known about histological aspects of paediatric scars and the possible role of the immune system during their formation. In this study, the histology thoracic scars caused by the placement of an implantable central venous access device in children who underwent treatment for cancer was assessed. The amount and type of collagen, the collagen orientation, the type of elastic fibres, the vascularsation, and the count of neutrophils, macrophages, and lymphocytes were analysed. The severity of scarring was assessed using the Vancouver scar scale (VSS). To evaluate the role of the immune system on scar severity and histology, the scars of children suffering from acute lymphoblastic leukaemia (ALL) were compared with the scars of children suffering from other types of childhood cancer. Our results showed an extremely random orientation of the collagen fibres of the paediatric scars with a mean collagen orientation index of 0.22 (standard deviation (SD) 0.10, zero indicating a perfectly random orientation and a perfectly parallel orientation). A lower collagen orientation index was seen in scars with a lower VSS score (VSS score <3: 0.19 versus VSS score ≥3 0.29, p=0.037). A higher total VSS score, resembling a worse scar, was assessed to the scars in the non-ALL group compared with the children with ALL (mean ALL: 0.91 (0-3) versus mean non-ALL: 2.50 (0-6), p=0.037). To our knowledge, this is the first study investigating a wide array of histological aspects in paediatric scars. Compared with adult scars, an extremely random collagen orientation was found (0.22 in children versus 0.41 and 0.46 adult normotrophic and hypertrophic scars, respectively). A lower collagen orientation index was found in scars with a lower VSS score. In addition, less severe scarring was measured in children suffering from ALL compared with children suffering from other types of childhood cancer. This suggests that the immune system could play a role in the development of aberrant scarring and should be a target for future research.

Determinants of antigenic molecules responsible for genetically controlled regulation of immune responses.

PubMed Central

Schwartz, M; Waltenbaugh, C; Dorf, M; Cesla, R; Sela, M; Benacerraf, B

1976-01-01

The ability of mice bearing the H-2S haplotype to develop helper responses to the random copolymer of Glu,Ala while they developed suppressor responses to the terpolymer of Glu,Ala,Tyr suggested the crucial role of tyrosine in these peptides. On the basis of various considerations, it was postulated that many of the tyrosine residues in Glu,Ala,Tyr would be localized at the NH2-terminal end of the molecule. To verify this hypothesis, a block terpolymer composed of a short sequence of homopolymer tyrosine covalently bound to the random copolymer of Glu,Ala was synthesized. The present studies, using this block terpolymer, demonstrated that the chemical determinants stimulating helper and suppressor responses are distinct and can be present simultaneously in the same molecule. Thus, addition of COOH-terminal tyrosine residues to the Glu,Ala polypeptide converted this immunogenic molecule to an immunosuppressive molecule in mice bearing the H-2S haplotype. The mechanism by which these short sequences of tyrosine influence H-2-linked immune responses remains to be determined. PMID:60762

Structural Heterogeneity and Quantitative FRET Efficiency Distributions of Polyprolines through a Hybrid Atomistic Simulation and Monte Carlo Approach

PubMed Central

Hoefling, Martin; Lima, Nicola; Haenni, Dominik; Seidel, Claus A. M.; Schuler, Benjamin; Grubmüller, Helmut

2011-01-01

Förster Resonance Energy Transfer (FRET) experiments probe molecular distances via distance dependent energy transfer from an excited donor dye to an acceptor dye. Single molecule experiments not only probe average distances, but also distance distributions or even fluctuations, and thus provide a powerful tool to study biomolecular structure and dynamics. However, the measured energy transfer efficiency depends not only on the distance between the dyes, but also on their mutual orientation, which is typically inaccessible to experiments. Thus, assumptions on the orientation distributions and averages are usually made, limiting the accuracy of the distance distributions extracted from FRET experiments. Here, we demonstrate that by combining single molecule FRET experiments with the mutual dye orientation statistics obtained from Molecular Dynamics (MD) simulations, improved estimates of distances and distributions are obtained. From the simulated time-dependent mutual orientations, FRET efficiencies are calculated and the full statistics of individual photon absorption, energy transfer, and photon emission events is obtained from subsequent Monte Carlo (MC) simulations of the FRET kinetics. All recorded emission events are collected to bursts from which efficiency distributions are calculated in close resemblance to the actual FRET experiment, taking shot noise fully into account. Using polyproline chains with attached Alexa 488 and Alexa 594 dyes as a test system, we demonstrate the feasibility of this approach by direct comparison to experimental data. We identified cis-isomers and different static local environments as sources of the experimentally observed heterogeneity. Reconstructions of distance distributions from experimental data at different levels of theory demonstrate how the respective underlying assumptions and approximations affect the obtained accuracy. Our results show that dye fluctuations obtained from MD simulations, combined with MC single photon kinetics, provide a versatile tool to improve the accuracy of distance distributions that can be extracted from measured single molecule FRET efficiencies. PMID:21629703

Route to three-dimensional fragments using diversity-oriented synthesis

PubMed Central

Hung, Alvin W.; Ramek, Alex; Wang, Yikai; Kaya, Taner; Wilson, J. Anthony; Clemons, Paul A.; Young, Damian W.

2011-01-01

Fragment-based drug discovery (FBDD) has proven to be an effective means of producing high-quality chemical ligands as starting points for drug-discovery pursuits. The increasing number of clinical candidate drugs developed using FBDD approaches is a testament of the efficacy of this approach. The success of fragment-based methods is highly dependent on the identity of the fragment library used for screening. The vast majority of FBDD has centered on the use of sp2-rich aromatic compounds. An expanded set of fragments that possess more 3D character would provide access to a larger chemical space of fragments than those currently used. Diversity-oriented synthesis (DOS) aims to efficiently generate a set of molecules diverse in skeletal and stereochemical properties. Molecules derived from DOS have also displayed significant success in the modulation of function of various “difficult” targets. Herein, we describe the application of DOS toward the construction of a unique set of fragments containing highly sp3-rich skeletons for fragment-based screening. Using cheminformatic analysis, we quantified the shapes and physical properties of the new 3D fragments and compared them with a database containing known fragment-like molecules. PMID:21482811

Route to three-dimensional fragments using diversity-oriented synthesis.

PubMed

Hung, Alvin W; Ramek, Alex; Wang, Yikai; Kaya, Taner; Wilson, J Anthony; Clemons, Paul A; Young, Damian W

2011-04-26

Fragment-based drug discovery (FBDD) has proven to be an effective means of producing high-quality chemical ligands as starting points for drug-discovery pursuits. The increasing number of clinical candidate drugs developed using FBDD approaches is a testament of the efficacy of this approach. The success of fragment-based methods is highly dependent on the identity of the fragment library used for screening. The vast majority of FBDD has centered on the use of sp(2)-rich aromatic compounds. An expanded set of fragments that possess more 3D character would provide access to a larger chemical space of fragments than those currently used. Diversity-oriented synthesis (DOS) aims to efficiently generate a set of molecules diverse in skeletal and stereochemical properties. Molecules derived from DOS have also displayed significant success in the modulation of function of various "difficult" targets. Herein, we describe the application of DOS toward the construction of a unique set of fragments containing highly sp(3)-rich skeletons for fragment-based screening. Using cheminformatic analysis, we quantified the shapes and physical properties of the new 3D fragments and compared them with a database containing known fragment-like molecules.

Hydrophilization and hydrophobic recovery in polymers obtained by casting of polymer solutions on water surface.

PubMed

Bormashenko, Edward; Chaniel, Gilad; Gendelman, Oleg

2014-12-01

We demonstrate the possibility of hydrophilization of polymer films in situ under the process of their preparation. The polymer surface is hydrophilized when the polymer solution is spread on the water surface and the solvent is evaporated. Essential hydrophilization of the polymer surface is achieved under this process. We relate the observed hydrophilization of polymer films to the dipole-dipole interaction of the polar moieties of polymer chains with highly polar water molecules. The dipole-dipole interaction between water molecules and polar groups of polymer chains, orienting the polar groups of a polymer, may prevail over the London dispersion forces. The process, reported in the paper, allows to manufacture the films in which the hydrophilic moieties of the polymer molecule are oriented toward the polymer/air interface. It is demonstrated that even such traditionally extremely hydrophobic polymers as polydimethylsiloxane can be markedly hydrophilized. This hydrophilization, however, does not persist forever. After removal from the water surface, hydrophobic recovery was observed, i.e. polymer films restored their hydrophobicity with time. The characteristic time of the hydrophobic recovery is on the order of magnitude of hours. Copyright © 2014 Elsevier Inc. All rights reserved.

Multiple groups of orientation-selective visual mechanisms underlying rapid orientated-line detection.

PubMed Central

Foster, D H; Westland, S

1998-01-01

Visual search for an edge or line element differing in orientation from a background of other edge or line elements can be performed rapidly and effortlessly. In this study, based on psychophysical measurements with ten human observers, threshold values of the angle between a target and background line elements were obtained as functions of background-element orientation, in brief masked displays. A repeated-loess analysis of the threshold functions suggested the existence of several groups of orientation-selective mechanisms contributing to rapid orientated-line detection; specifically, coarse, intermediate and fine mechanisms with preferred orientations spaced at angles of approximately 90 degrees, 35 degrees, and 10 degrees-25 degrees, respectively. The preferred orientations of coarse and some intermediate mechanisms coincided with the vertical or horizontal of the frontoparallel plane, but the preferred orientations of fine mechanisms varied randomly from observer to observer, possibly reflecting individual variations in neuronal sampling characteristics. PMID:9753784

Study design and "evidence" in patient-oriented research.

PubMed

Concato, John

2013-06-01

Individual studies in patient-oriented research, whether described as "comparative effectiveness" or using other terms, are based on underlying methodological designs. A simple taxonomy of study designs includes randomized controlled trials on the one hand, and observational studies (such as case series, cohort studies, and case-control studies) on the other. A rigid hierarchy of these design types is a fairly recent phenomenon, promoted as a tenet of "evidence-based medicine," with randomized controlled trials receiving gold-standard status in terms of producing valid results. Although randomized trials have many strengths, and contribute substantially to the evidence base in clinical care, making presumptions about the quality of a study based solely on category of research design is unscientific. Both the limitations of randomized trials as well as the strengths of observational studies tend to be overlooked when a priori assumptions are made. This essay presents an argument in support of a more balanced approach to evaluating evidence, and discusses representative examples from the general medical as well as pulmonary and critical care literature. The simultaneous consideration of validity (whether results are correct "internally") and generalizability (how well results apply to "external" populations) is warranted in assessing whether a study's results are accurate for patients likely to receive the intervention-examining the intersection of clinical and methodological issues in what can be called a medicine-based evidence approach. Examination of cause-effect associations in patient-oriented research should recognize both the strengths and limitations of randomized trials as well as observational studies.

Study of p-diaminobenzene Adsorption on Au(111) by Scanning Tunneling Microscopy

NASA Astrophysics Data System (ADS)

Zhou, Hui; Hu, Zonghai; Eom, Daejin; Rim, Kwang; Liu, Li; Flynn, George; Venkataraman, Latha; Morgante, Alberto; Heinz, Tony

2008-03-01

From the well-defined conductivity obtained for various individual diamino-substituted molecules spanning two gold contacts, as well as from theoretical analysis [1], researchers have suggested that amines adsorb preferentially to coordinatively unsaturated surface Au atoms through the N lone pair. To understand the nature of the amine binding, we have applied ultrahigh vacuum scanning tunneling microscope (STM) to investigate the adsorption of p-diaminobenzene molecules on the reconstructed Au(111) surface. The STM topography images (taken at 4 K) show that the molecules adsorb preferentially to step edges, corresponding to sites of reduced Au atom coordination. The adsorbed molecules are found to display a distinctive orientation along the step edges. The two-lobe topographic structure of each molecule seen by STM is compatible with the previously calculated charge density of the HOMO level. [1] L. Venkataraman at el., Nano Lett. 7, 502 (2007).

"Cleaning" the Surface of Hydroxyapatite Nanorods by a Reaction-Dissolution Approach.

PubMed

Cao, Binrui; Yang, Mingying; Wang, Lin; Xu, Hong; Zhu, Ye; Mao, Chuanbin

2015-10-21

Synthetic nanoparticles are always terminated with coating molecules, which are often cytotoxic and not desired in biomedicine. Here we propose a novel reaction-dissolution approach to remove the cytotoxic coating molecules. A two-component solution is added to the nanoparticle solution; one component reacts with the coating molecules to form a salt whereas another is a solvent for dissolving and thus removing the salt. As a proof of concept, this work uses a NaOH-ethanol solution to remove the cytotoxic linoleic acid molecules coated on the hydroxyapatite nanorods (HAP-NRs). The removal of the coating molecules not only significantly improves the biocompatibility of HAP-NRs but also enables their oriented attachment into tightly-bound superstructures, which mimic the organized HAP crystals in bone and enamel and can promote the osteogenic differentiation of mesenchymal stem cells. Our reaction-dissolution approach can be extended to the surface "cleaning" of other nanomaterials.

Gravity and the orientation of cell division

NASA Technical Reports Server (NTRS)

Helmstetter, C. E.

1997-01-01

A novel culture system for mammalian cells was used to investigate division orientations in populations of Chinese hamster ovary cells and the influence of gravity on the positioning of division axes. The cells were tethered to adhesive sites, smaller in diameter than a newborn cell, distributed over a nonadhesive substrate positioned vertically. The cells grew and divided while attached to the sites, and the angles and directions of elongation during anaphase, projected in the vertical plane, were found to be random with respect to gravity. However, consecutive divisions of individual cells were generally along the same axis or at 90 degrees to the previous division, with equal probability. Thus, successive divisions were restricted to orthogonal planes, but the choice of plane appeared to be random, unlike the ordered sequence of cleavage orientations seen during early embryo development.

Architecture of crossed-lamellar bivalve shells: the southern giant clam (Tridacna derasa, Röding, 1798).

PubMed

Agbaje, O B A; Wirth, R; Morales, L F G; Shirai, K; Kosnik, M; Watanabe, T; Jacob, D E

2017-09-01

Tridacna derasa shells show a crossed lamellar microstructure consisting of three hierarchical lamellar structural orders. The mineral part is intimately intergrown with 0.9 wt% organics, namely polysaccharides, glycosylated and unglycosylated proteins and lipids, identified by Fourier transform infrared spectrometry. Transmission electron microscopy shows nanometre-sized grains with irregular grain boundaries and abundant voids. Twinning is observed across all spatial scales and results in a spread of the crystal orientation angles. Electron backscatter diffraction analysis shows a strong fibre texture with the [001] axes of aragonite aligned radially to the shell surface. The aragonitic [100] and [010] axes are oriented randomly around [001]. The random orientation of anisotropic crystallographic directions in this plane reduces anisotropy of the Young's modulus and adds to the optimization of mechanical properties of bivalve shells.

A Microstructural Analysis of Orientation Variation in Epitaxial AlN on Si, Its Probable Origin, and Effect on Subsequent GaN Growth

NASA Technical Reports Server (NTRS)

Beye, R.; George, T.; Yang, J. W.; Khan, M. A.

1996-01-01

A structural examination of aluminum nitride growth on [111] silicon was carried out using transmission electron microscopy. Electron diffraction indicates that the basal planes of the wurtzitic overlayer mimic the orientation of the close-packed planes of the substrate. However, considerable, random rotation in the basal plane and random out-of-plane tilts were evident. This article examines these issues with a structural examination of AlN and GaN/AlN on silicon and compares the findings to those reported in the literature.

Long-range ordering effect in electrodeposition of zinc and zinc oxide.

PubMed

Liu, Tao; Wang, Sheng; Shi, Zi-Liang; Ma, Guo-Bin; Wang, Mu; Peng, Ru-Wen; Hao, Xi-Ping; Ming, Nai-Ben

2007-05-01

In this paper, we report the long-range ordering effect observed in the electro-crystallization of Zn and ZnO from an ultrathin aqueous electrolyte layer of ZnSO4 . The deposition branches are regularly angled, covered with random-looking, scalelike crystalline platelets of ZnO. Although the orientation of each crystalline platelet of ZnO appears random, transmission electron microscopy shows that they essentially possess the same crystallographic orientation as the single-crystalline zinc electrodeposit underneath. Based on the experimental observations, we suggest that this unique long-range ordering effect results from an epitaxial nucleation effect in electrocrystallization.

Electromagnetic scattering from a layer of finite length, randomly oriented, dielectric, circular cylinders over a rough interface with application to vegetation

NASA Technical Reports Server (NTRS)

Karam, M. A.; Fung, A. K.

1988-01-01

A scattering model for defoliated vegetation is developed by treating a layer of defoliated vegetation as a collection of randomly oriented dielectric cylinders of finite length over an irregular ground surface. Both polarized and depolarized backscattering are computed and their behavior versus the volume fraction, the incidence angle, the frequency, the angular distribution and the cylinder size are illustrated. It is found that both the angular distribution and the cylinder size have significant effects on the backscattered signal. The present theory is compared with measurements from defoliated vegetations.

Complex Fluids at Interfaces and Interfaces of Complex Fluids

NASA Astrophysics Data System (ADS)

Nouri, Mariam

The present thesis deals with two independent projects and is consequently divided into two parts. The first part details a computational study of the fluid structure of ring-shaped molecules and their positional and orientational molecular organizations in different degrees of confinement, while the second part concerns an experimental study of phase behavior and interfacial phenomena in confined colloid-polymer systems. In the first part, ring-shaped molecules are studied using Monte Carlo simulation techniques in one, two and three dimensions. The model used to describe ring-shaped molecules is composed of hard-spheres linked together to form planar rigid rings. For rings of various sizes and for a wide range of densities, positional and orientational orderings are reported in forms of pair distribution functions of the ring centers and correlation functions of the ring normal orientations. Special emphasis is given to understand structural formation at interfaces, i.e., the structure and orderings of these molecules when they are confined to two dimensions. In a plane but the rings themselves are free to rotate around all axes, nematic ordering is observed at sufficiently high densities. In the second part, phase equilibria of confined aqueous colloid-polymer systems are studied experimentally using fluorescence microscopy. Aqueous mixtures of fluorescent polystyrene spheres and polyacrylamide are confined between a glass slide and a coverslip. The phase diagram is determined as a function of the colloidal and polymer concentrations. Liquid-liquid phase coexistence between a colloid-rich phase and a polymer-rich phase occurs at intermediate polymer concentrations, while liquid-solid phase coexistence between a polymer-rich liquid and a colloid-rich solid is observed at high polymer concentrations. Interfacial thickness and tension of the interface between these coexisting phases are measured using image analysis techniques. It is also observed that the colloid-rich solid and liquid domains coarsen mainly by Ostwald ripening.

Nonholonomic diffusion of a stochastic sled

NASA Astrophysics Data System (ADS)

Jung, Peter; Marchegiani, Giampiero; Marchesoni, Fabio

2016-01-01

A sled is a stylized mechanical model of a system which is constrained to move in space in a specific orientation, i.e., in the direction of the runners of the sled or a blade. The negation of motion transverse to the runners renders the sled a nonholonomic mechanical system. In this paper we report on the unexpected and fascinating richness of the dynamics of such a sled if it is subject to random forces. Specifically we show that the ensuing random dynamics is characterized by relatively smooth sections of motion interspersed by episodes of persistent tumbling (change of orientation) and sharp reversals resembling the random walks of bacterial cells. In the presence of self-propulsion, the diffusivity of the sled can be enhanced and suppressed depending on the directionality and strength of the propulsive force.

Change of the isoelectric point of hemoglobin at the air/water interface probed by the orientational flip-flop of water molecules.

PubMed

Devineau, Stéphanie; Inoue, Ken-Ichi; Kusaka, Ryoji; Urashima, Shu-Hei; Nihonyanagi, Satoshi; Baigl, Damien; Tsuneshige, Antonio; Tahara, Tahei

2017-04-19

Elucidation of the molecular mechanisms of protein adsorption is of essential importance for further development of biotechnology. Here, we use interface-selective nonlinear vibrational spectroscopy to investigate protein charge at the air/water interface by probing the orientation of interfacial water molecules. We measured the Im χ (2) spectra of hemoglobin, myoglobin, serum albumin and lysozyme at the air/water interface in the CH and OH stretching regions using heterodyne-detected vibrational sum frequency generation (HD-VSFG) spectroscopy, and we deduced the isoelectric point of the protein by monitoring the orientational flip-flop of water molecules at the interface. Strikingly, our measurements indicate that the isoelectric point of hemoglobin is significantly lowered (by about one pH unit) at the air/water interface compared to that in the bulk. This can be predominantly attributed to the modifications of the protein structure at the air/water interface. Our results also suggest that a similar mechanism accounts for the modification of myoglobin charge at the air/water interface. This effect has not been reported for other model proteins at interfaces probed by conventional VSFG techniques, and it emphasizes the importance of the structural modifications of proteins at the interface, which can drastically affect their charge profiles in a protein-specific manner. The direct experimental approach using HD-VSFG can unveil the changes of the isoelectric point of adsorbed proteins at various interfaces, which is of major relevance to many biological applications and sheds new light on the effect of interfaces on protein charge.

Identifying Mechanisms of Interfacial Dynamics Using Single-Molecule Tracking

PubMed Central

Kastantin, Mark; Walder, Robert; Schwartz, Daniel K.

2012-01-01

The “soft” (i.e. non-covalent) interactions between molecules and surfaces are complex and highly-varied (e.g. hydrophobic, hydrogen bonding, ionic) often leading to heterogeneous interfacial behavior. Heterogeneity can arise either from spatial variation of the surface/interface itself or from molecular configurations (i.e. conformation, orientation, aggregation state, etc.). By observing adsorption, diffusion, and desorption of individual fluorescent molecules, single-molecule tracking can characterize these types of heterogeneous interfacial behavior in ways that are inaccessible to traditional ensemble-averaged methods. Moreover, the fluorescence intensity or emission wavelength (in resonance energy transfer experiments) can be used to simultaneously track molecular configuration and directly relate this to the resulting interfacial mobility or affinity. In this feature article, we review recent advances involving the use of single-molecule tracking to characterize heterogeneous molecule-surface interactions including: multiple modes of diffusion and desorption associated with both internal and external molecular configuration, Arrhenius activated interfacial transport, spatially dependent interactions, and many more. PMID:22716995

Fast Rotational Diffusion of Water Molecules in a 2D Hydrogen Bond Network at Cryogenic Temperatures

NASA Astrophysics Data System (ADS)

Prisk, T. R.; Hoffmann, C.; Kolesnikov, A. I.; Mamontov, E.; Podlesnyak, A. A.; Wang, X.; Kent, P. R. C.; Anovitz, L. M.

2018-05-01

Individual water molecules or small clusters of water molecules contained within microporous minerals present an extreme case of confinement where the local structure of hydrogen bond networks are dramatically altered from bulk water. In the zinc silicate hemimorphite, the water molecules form a two-dimensional hydrogen bond network with hydroxyl groups in the crystal framework. Here, we present a combined experimental and theoretical study of the structure and dynamics of water molecules within this network. The water molecules undergo a continuous phase transition in their orientational configuration analogous to a two-dimensional Ising model. The incoherent dynamic structure factor reveals two thermally activated relaxation processes, one on a subpicosecond timescale and another on a 10-100 ps timescale, between 70 and 130 K. The slow process is an in-plane reorientation of the water molecule involving the breaking of hydrogen bonds with a framework that, despite the low temperatures involved, is analogous to rotational diffusion of water molecules in the bulk liquid. The fast process is a localized motion of the water molecule with no apparent analogs among known bulk or confined phases of water.

Fast Rotational Diffusion of Water Molecules in a 2D Hydrogen Bond Network at Cryogenic Temperatures

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

Prisk, Timothy; Hoffmann, Christina; Kolesnikov, Alexander I.

Individual water molecules or small clusters of water molecules contained within microporous minerals present an extreme case of confinement where the local structure of hydrogen bond networks are dramatically altered from bulk water. In the zinc silicate hemimorphite, the water molecules form a two-dimensional hydrogen bond network with hydroxyl groups in the crystal framework. Here in this paper, we present a combined experimental and theoretical study of the structure and dynamics of water molecules within this network. The water molecules undergo a continuous phase transition in their orientational configuration analogous to a two-dimensional Ising model. The incoherent dynamic structure factormore » reveals two thermally activated relaxation processes, one on a subpicosecond timescale and another on a 10–100 ps timescale, between 70 and 130 K. The slow process is an in-plane reorientation of the water molecule involving the breaking of hydrogen bonds with a framework that, despite the low temperatures involved, is analogous to rotational diffusion of water molecules in the bulk liquid. The fast process is a localized motion of the water molecule with no apparent analogs among known bulk or confined phases of water.« less