Investigation of the spatially anisotropic component of the laterally averaged molecular hydrogen/Ag(111) physisorption potential

NASA Astrophysics Data System (ADS)

Whaley, K. Birgitta; Yu, Chien-fan; Hogg, C. S.; Light, John C.; Sibener, S. J.

1985-10-01

A detailed investigation of the spatially anisotropic component of the laterally averaged molecular hydrogen/Ag(111) physisorption potential is presented. Experimentally derived rotationally inelastic transition probabilities for H2, D2, and HD, taken as a function of collision energy, are compared with those resulting from close-coupled quantum scattering calculations. These calculations utilize exponential-3 and variable exponent parametrizations of the laterally averaged isotropic potential which reproduce the experimental bound state resonance spectra for p-H2 and o-D2 on Ag(111). Complementary information is obtained by analyzing the magnetic sublevel splittings for physisorbed J=1 n-H2, using diffractive selective adsorption resonance energies calculated with first order perturbation theory. Theoretical predictions for HD/Ag(111) rotationally mediated selective adsorption resonances are also compared with previously reported experimental results, which show well resolved J-dependent energy shifts resulting in part from the orientational anisotropy of the potential. The results obtained in this study indicate that both the attractive and repulsive parts of the anisotropic potential exhibit only a weak orientation dependence, in agreement with recent theoretical predictions for this system.

The analysis of the market success of FDA approvals by probing top 100 bestselling drugs.

PubMed

Polanski, Jaroslaw; Bogocz, Jacek; Tkocz, Aleksandra

2016-05-01

Target-oriented drug discovery is the main research paradigm of contemporary drug discovery. In target-oriented approaches, we attempt to maximize in vitro drug potency by finding the optimal fit to the target. This can result in a higher molecular complexity, in particular, the higher molecular weight (MW) of the drugs. However, a comparison of the successful developments of pharmaceuticals with the general trends that can be observed in medicinal chemistry resulted in the conclusion that the so-called molecular obesity is an important reason for the attrition rate of drugs. When analyzing the list of top 100 drug bestsellers versus all of the FDA approvals, we discovered that on average lower-complexity (MW, ADMET score) drugs are winners of the top 100 list in terms of numbers but that, especially, up to some optimal MW value, a higher molecular complexity can pay off with higher incomes. This indicates that slim drugs are doing better but that fat drugs are bigger fishes to catch.

The analysis of the market success of FDA approvals by probing top 100 bestselling drugs

NASA Astrophysics Data System (ADS)

Polanski, Jaroslaw; Bogocz, Jacek; Tkocz, Aleksandra

2016-05-01

Target-oriented drug discovery is the main research paradigm of contemporary drug discovery. In target-oriented approaches, we attempt to maximize in vitro drug potency by finding the optimal fit to the target. This can result in a higher molecular complexity, in particular, the higher molecular weight (MW) of the drugs. However, a comparison of the successful developments of pharmaceuticals with the general trends that can be observed in medicinal chemistry resulted in the conclusion that the so-called molecular obesity is an important reason for the attrition rate of drugs. When analyzing the list of top 100 drug bestsellers versus all of the FDA approvals, we discovered that on average lower-complexity (MW, ADMET score) drugs are winners of the top 100 list in terms of numbers but that, especially, up to some optimal MW value, a higher molecular complexity can pay off with higher incomes. This indicates that slim drugs are doing better but that fat drugs are bigger fishes to catch.

Peculiar orientational disorder in 4-bromo-4'-nitrobiphenyl (BNBP) and 4-bromo-4'-cyanobiphenyl (BCNBP) leading to bipolar crystals.

PubMed

Burgener, Matthias; Aboulfadl, Hanane; Labat, Gaël Charles; Bonin, Michel; Sommer, Martin; Sankolli, Ravish; Wübbenhorst, Michael; Hulliger, Jürg

2016-05-01

180° orientational disorder of molecular building blocks can lead to a peculiar spatial distribution of polar properties in molecular crystals. Here we present two examples [4-bromo-4'-nitrobiphenyl (BNBP) and 4-bromo-4'-cyanobiphenyl (BCNBP)] which develop into a bipolar final growth state. This means orientational disorder taking place at the crystal/nutrient interface produces domains of opposite average polarity for as-grown crystals. The spatial inhomogeneous distribution of polarity was investigated by scanning pyroelectric microscopy (SPEM), phase-sensitive second harmonic microscopy (PS-SHM) and selected volume X-ray diffraction (SVXD). As a result, the acceptor groups (NO2 or CN) are predominantly present at crystal surfaces. However, the stochastic process of polarity formation can be influenced by adding a symmetrical biphenyl to a growing system. For this case, Monte Carlo simulations predict an inverted net polarity compared with the growth of pure BNBP and BCNBP. SPEM results clearly demonstrate that 4,4'-dibromobiphenyl (DBBP) can invert the polarity for both crystals. Phenomena reported in this paper belong to the most striking processes seen for molecular crystals, demonstrated by a stochastic process giving rise to symmetry breaking. We encounter here further examples supporting the general thesis that monodomain polar molecular crystals for fundamental reasons cannot exist.

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

Sabin, Charles; Plevka, Pavel, E-mail: pavel.plevka@ceitec.muni.cz

Molecular replacement and noncrystallographic symmetry averaging were used to detwin a data set affected by perfect hemihedral twinning. The noncrystallographic symmetry averaging of the electron-density map corrected errors in the detwinning introduced by the differences between the molecular-replacement model and the crystallized structure. Hemihedral twinning is a crystal-growth anomaly in which a specimen is composed of two crystal domains that coincide with each other in three dimensions. However, the orientations of the crystal lattices in the two domains differ in a specific way. In diffraction data collected from hemihedrally twinned crystals, each observed intensity contains contributions from both of themore » domains. With perfect hemihedral twinning, the two domains have the same volumes and the observed intensities do not contain sufficient information to detwin the data. Here, the use of molecular replacement and of noncrystallographic symmetry (NCS) averaging to detwin a 2.1 Å resolution data set for Aichi virus 1 affected by perfect hemihedral twinning is described. The NCS averaging enabled the correction of errors in the detwinning introduced by the differences between the molecular-replacement model and the crystallized structure. The procedure permitted the structure to be determined from a molecular-replacement model that had 16% sequence identity and a 1.6 Å r.m.s.d. for C{sup α} atoms in comparison to the crystallized structure. The same approach could be used to solve other data sets affected by perfect hemihedral twinning from crystals with NCS.« less

Anisotropic 2H-nuclear magnetic resonance spin-lattice relaxation in cerebroside- and phospholipid-cholesterol bilayer membranes.

PubMed

Siminovitch, D J; Ruocco, M J; Olejniczak, E T; Das Gupta, S K; Griffin, R G

1988-09-01

The axially symmetric powder pattern 2H-nuclear magnetic resonance (NMR) lineshapes observed in the liquid crystalline phase of pure lipid or lipid/cholesterol bilayers are essentially invariant to temperature, or, equivalently, to variations in the correlation times characterizing C-2H bond reorientations. In either of these melted phases, where correlation times for C-2H bond motions are shorter than 10(-7) s, information on the molecular dynamics of the saturated hydrocarbon chain would be difficult to obtain using lineshape analyses alone, and one must resort to other methods, such as the measurement of 2H spin-lattice relaxation rates, in order to obtain dynamic information. In pure lipid bilayers, the full power of the spin-lattice relaxation technique has yet to be realized, since an important piece of information, namely the orientation dependence of the 2H spin-lattice relaxation rates is usually lost due to orientational averaging of T1 by rapid lateral diffusion. Under more favorable circumstances, such as those encountered in the lipid/cholesterol mixtures of this study, the effects of orientational averaging by lateral diffusion are nullified, due to either a marked reduction (by at least an order of magnitude) in the diffusion rate, or a marked increase in the radii of curvature of the liposomes. In either case, the angular dependence of 2H spin-lattice relaxation is accessible to experimental study, and can be used to test models of molecular dynamics in these systems. Simulations of the partially recovered lineshapes indicate that the observed T1 anisotropies are consistent with large amplitude molecular reorientation of the C-2H bond among a finite number of sites. Furthermore, from the observed orientation dependence of the 2H spin-lattice relaxation rates, we conclude that order director fluctuations cannot provide the dominant relaxation pathway for acyl chain deuterons.

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

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.

Study of Nanoscale Friction Behaviors of Graphene on Gold Substrates Using Molecular Dynamics

NASA Astrophysics Data System (ADS)

Zhu, Pengzhe; Li, Rui

2018-02-01

In this paper, we investigate the friction behaviors of graphene flakes sliding on a gold substrate using molecular dynamics simulations. The effects of flake size, flake shape, relative rotation angle between flake and substrate, and crystal orientation of substrate on the friction process are thoroughly studied. It is found that under the same load, the average friction forces per atom are smaller for a bigger graphene flake, which exhibits an obvious size effect. It is also shown that flake shape is critical in determining the friction in the sliding process. The average friction forces per atom for the square flake are much bigger than those for the triangular and round flakes. Moreover, the average friction forces per atom for the triangular flake are the smallest. We also find that the orientation of graphene flake relative to gold substrate plays a vital role in the friction process. The friction forces for the graphene flake sliding along the armchair direction are much bigger than those for the flakes with rotation. In addition, it is also found that single crystalline gold substrate exhibits a significant anisotropic effect of friction, which is attributed to the anisotropic effect of potential energy corrugation. These understandings not only shed light on the underlying mechanisms of graphene flake sliding on the gold substrates but also may guide the design and fabrication of nanoscale graphene-based devices.

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.

A focus on polarity: Investigating the role of orientation cues in mediating student performance on mRNA synthesis tasks in an introductory cell and molecular biology course.

PubMed

Olimpo, Jeffrey T; Quijas, Daniel A; Quintana, Anita M

2017-11-01

The central dogma has served as a foundational model for information flow, exchange, and storage in the biological sciences for several decades. Despite its continued importance, however, recent research suggests that novices in the domain possess several misconceptions regarding the aforementioned processes, including those pertaining specifically to the formation of messenger ribonucleic acid (mRNA) transcripts. In the present study, we sought to expand upon these observations through exploration of the influence of orientation cues on students' aptitude at synthesizing mRNAs from provided deoxyribonucleic acid (DNA) template strands. Data indicated that participants (n = 45) were proficient at solving tasks of this nature when the DNA template strand and the mRNA molecule were represented in an antiparallel orientation. In contrast, participants' performance decreased significantly on items in which the mRNA was depicted in a parallel orientation relative to the DNA template strand. Furthermore, participants' Grade Point Average, self-reported confidence in understanding the transcriptional process, and spatial ability were found to mediate their performance on the mRNA synthesis tasks. Collectively, these data reaffirm the need for future research and pedagogical interventions designed to enhance students' comprehension of the central dogma in a manner that makes transparent its relevance to real-world scientific phenomena. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(6):501-508, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

Coulomb interactions in charged fluids.

PubMed

Vernizzi, Graziano; Guerrero-García, Guillermo Iván; de la Cruz, Monica Olvera

2011-07-01

The use of Ewald summation schemes for calculating long-range Coulomb interactions, originally applied to ionic crystalline solids, is a very common practice in molecular simulations of charged fluids at present. Such a choice imposes an artificial periodicity which is generally absent in the liquid state. In this paper we propose a simple analytical O(N(2)) method which is based on Gauss's law for computing exactly the Coulomb interaction between charged particles in a simulation box, when it is averaged over all possible orientations of a surrounding infinite lattice. This method mitigates the periodicity typical of crystalline systems and it is suitable for numerical studies of ionic liquids, charged molecular fluids, and colloidal systems with Monte Carlo and molecular dynamics simulations.

Mapping the local organization of cell membranes using excitation-polarization-resolved confocal fluorescence microscopy.

PubMed

Kress, Alla; Wang, Xiao; Ranchon, Hubert; Savatier, Julien; Rigneault, Hervé; Ferrand, Patrick; Brasselet, Sophie

2013-07-02

Fluorescence anisotropy and linear dichroism imaging have been widely used for imaging biomolecular orientational distributions in protein aggregates, fibrillar structures of cells, and cell membranes. However, these techniques do not give access to complete orientational order information in a whole image, because their use is limited to parts of the sample where the average orientation of molecules is known a priori. Fluorescence anisotropy is also highly sensitive to depolarization mechanisms such as those induced by fluorescence energy transfer. A fully excitation-polarization-resolved fluorescence microscopy imaging that relies on the use of a tunable incident polarization and a nonpolarized detection is able to circumvent these limitations. We have developed such a technique in confocal epifluorescence microscopy, giving access to new regions of study in the complex and heterogeneous molecular organization of cell membranes. Using this technique, we demonstrate morphological changes at the subdiffraction scale in labeled COS-7 cell membranes whose cytoskeleton is perturbed. Molecular orientational order is also seen to be affected by cholesterol depletion, reflecting the strong interplay between lipid-packing regions and their nearby cytoskeleton. This noninvasive optical technique can reveal local organization in cell membranes when used as a complement to existing methods such as generalized polarization. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Molecular dynamics of the water liquid-vapor interface

NASA Technical Reports Server (NTRS)

Wilson, M. A.; Pohorille, A.; Pratt, L. R.; MacElroy, R. D. (Principal Investigator)

1987-01-01

The results of molecular dynamics calculations on the equilibrium interface between liquid water and its vapor at 325 K are presented. For the TIP4P model of water intermolecular pair potentials, the average surface dipole density points from the vapor to the liquid. The most common orientations of water molecules have the C2 nu molecular axis roughly parallel to the interface. The distributions are quite broad and therefore compatible with the intermolecular correlations characteristic of bulk liquid water. All near-neighbor pairs in the outermost interfacial layers are hydrogen bonded according to the common definition adopted here. The orientational preferences of water molecules near a free surface differ from those near rigidly planar walls which can be interpreted in terms of patterns found in hexagonal ice 1. The mean electric field in the interfacial region is parallel to the mean polarization which indicates that attention cannot be limited to dipolar charge distributions in macroscopic descriptions of the electrical properties of this interface. The value of the surface tension obtained is 132 +/- 46 dyn/cm, significantly different from the value for experimental water of 68 dyn/cm at 325 K.

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.

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

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.

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.

Rotating fiber array molecular driver and molecular momentum transfer device constructed therewith

DOEpatents

Milleron, Norman

1983-01-01

A rotating fiber array molecular driver is disclosed which includes a magnetically suspended and rotated central hub to which is attached a plurality of elongated fibers extending radially therefrom. The hub is rotated so as to straighten and axially extend the fibers and to provide the fibers with a tip speed which exceeds the average molecular velocity of fluid molecules entering between the fibers. Molecules colliding with the sides of the rotating fibers are accelerated to the tip speed of the fiber and given a momentum having a directional orientation within a relatively narrow distribution angle at a point radially outward of the hub, which is centered and peaks at the normal to the fiber sides in the direction of fiber rotation. The rotating fiber array may be used with other like fiber arrays or with other stationary structures to form molecular momentum transfer devices such as vacuum pumps, molecular separators, molecular coaters, or molecular reactors.

Molecular order and T1-relaxation, cross-relaxation in nitroxide spin labels

NASA Astrophysics Data System (ADS)

Marsh, Derek

2018-05-01

Interpretation of saturation-recovery EPR experiments on nitroxide spin labels whose angular rotation is restricted by the orienting potential of the environment (e.g., membranes) currently concentrates on the influence of rotational rates and not of molecular order. Here, I consider the dependence on molecular ordering of contributions to the rates of electron spin-lattice relaxation and cross relaxation from modulation of N-hyperfine and Zeeman anisotropies. These are determined by the averages and , where θ is the angle between the nitroxide z-axis and the static magnetic field, which in turn depends on the angles that these two directions make with the director of uniaxial ordering. For saturation-recovery EPR at 9 GHz, the recovery rate constant is predicted to decrease with increasing order for the magnetic field oriented parallel to the director, and to increase slightly for the perpendicular field orientation. The latter situation corresponds to the usual experimental protocol and is consistent with the dependence on chain-labelling position in lipid bilayer membranes. An altered dependence on order parameter is predicted for saturation-recovery EPR at high field (94 GHz) that is not entirely consistent with observation. Comparisons with experiment are complicated by contributions from slow-motional components, and an unexplained background recovery rate that most probably is independent of order parameter. In general, this analysis supports the interpretation that recovery rates are determined principally by rotational diffusion rates, but experiments at other spectral positions/field orientations could increase the sensitivity to order parameter.

Molecular three-body Brauner-Briggs-Klar theory for ion-impact ionization of molecules

NASA Astrophysics Data System (ADS)

Ghanbari-Adivi, E.

2016-12-01

Molecular three-body Brauner-Briggs-Klar (M3BBK) theory is developed to study the single ionization of diatomic molecules by ion impact. The orientation-averaged molecular orbital (OAMO) approximation is used to reduce the required computer time without sacrificing the performance of the method. The post-collision interaction (PCI) between the scattered projectile and the ejected electron is included. The theory is applied to collision of protons with hydrogen molecules. Results are obtained for two different kinematical regimes: i) fast collisions and low emission energies, and ii) not so fast collisions and higher emission energies. For both considered regimes, experimental fully differential cross-sections as well as different theoretical calculations are available for comparison. These comparisons are carried out and discussed.

Comparison of prestellar core elongations and large-scale molecular cloud structures in the Lupus I region

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

Poidevin, Frédérick; Ade, Peter A. R.; Hargrave, Peter C.

2014-08-10

Turbulence and magnetic fields are expected to be important for regulating molecular cloud formation and evolution. However, their effects on sub-parsec to 100 parsec scales, leading to the formation of starless cores, are not well understood. We investigate the prestellar core structure morphologies obtained from analysis of the Herschel-SPIRE 350 μm maps of the Lupus I cloud. This distribution is first compared on a statistical basis to the large-scale shape of the main filament. We find the distribution of the elongation position angle of the cores to be consistent with a random distribution, which means no specific orientation of themore » morphology of the cores is observed with respect to the mean orientation of the large-scale filament in Lupus I, nor relative to a large-scale bent filament model. This distribution is also compared to the mean orientation of the large-scale magnetic fields probed at 350 μm with the Balloon-borne Large Aperture Telescope for Polarimetry during its 2010 campaign. Here again we do not find any correlation between the core morphology distribution and the average orientation of the magnetic fields on parsec scales. Our main conclusion is that the local filament dynamics—including secondary filaments that often run orthogonally to the primary filament—and possibly small-scale variations in the local magnetic field direction, could be the dominant factors for explaining the final orientation of each core.« less

Influence of vapor deposition on structural and charge transport properties of ethylbenzene films

DOE PAGES

Antony, Lucas W.; Jackson, Nicholas E.; Lyubimov, Ivan; ...

2017-04-14

Organic glass films formed by physical vapor deposition exhibit enhanced stability relative to those formed by conventional liquid cooling and aging techniques. Recently, experimental and computational evidence has emerged indicating that the average molecular orientation can be tuned by controlling the substrate temperature at which these “stable glasses” are grown. In this work, we present a comprehensive all-atom simulation study of ethylbenzene, a canonical stable-glass former, using a computational film formation procedure that closely mimics the vapor deposition process. Atomistic studies of experimentally formed vapor-deposited glasses have not been performed before, and this study therefore begins by verifying that themore » model and method utilized here reproduces key structural features observed experimentally. Having established agreement between several simulated and experimental macroscopic observables, simulations are used to examine the substrate temperature dependence of molecular orientation. The results indicate that ethylbenzene glasses are anisotropic, depending upon substrate temperature, and that this dependence can be understood from the orientation present at the surface of the equilibrium liquid. By treating ethylbenzene as a simple model for molecular semiconducting materials, a quantum-chemical analysis is then used to show that the vapor-deposited glasses exhibit decreased energetic disorder and increased magnitude of the mean-squared transfer integral relative to isotropic, liquid-cooled films, an effect that is attributed to the anisotropic ordering of the molecular film. Finally, these results suggest a novel structure–function simulation strategy capable of tuning the electronic properties of organic semiconducting glasses prior to experimental deposition, which could have considerable potential for organic electronic materials design.« less

Influence of vapor deposition on structural and charge transport properties of ethylbenzene films

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

Antony, Lucas W.; Jackson, Nicholas E.; Lyubimov, Ivan

Organic glass films formed by physical vapor deposition exhibit enhanced stability relative to those formed by conventional liquid cooling and aging techniques. Recently, experimental and computational evidence has emerged indicating that the average molecular orientation can be tuned by controlling the substrate temperature at which these “stable glasses” are grown. In this work, we present a comprehensive all-atom simulation study of ethylbenzene, a canonical stable-glass former, using a computational film formation procedure that closely mimics the vapor deposition process. Atomistic studies of experimentally formed vapor-deposited glasses have not been performed before, and this study therefore begins by verifying that themore » model and method utilized here reproduces key structural features observed experimentally. Having established agreement between several simulated and experimental macroscopic observables, simulations are used to examine the substrate temperature dependence of molecular orientation. The results indicate that ethylbenzene glasses are anisotropic, depending upon substrate temperature, and that this dependence can be understood from the orientation present at the surface of the equilibrium liquid. By treating ethylbenzene as a simple model for molecular semiconducting materials, a quantum-chemical analysis is then used to show that the vapor-deposited glasses exhibit decreased energetic disorder and increased magnitude of the mean-squared transfer integral relative to isotropic, liquid-cooled films, an effect that is attributed to the anisotropic ordering of the molecular film. Finally, these results suggest a novel structure–function simulation strategy capable of tuning the electronic properties of organic semiconducting glasses prior to experimental deposition, which could have considerable potential for organic electronic materials design.« less

Influence of Vapor Deposition on Structural and Charge Transport Properties of Ethylbenzene Films

PubMed Central

2017-01-01

Organic glass films formed by physical vapor deposition exhibit enhanced stability relative to those formed by conventional liquid cooling and aging techniques. Recently, experimental and computational evidence has emerged indicating that the average molecular orientation can be tuned by controlling the substrate temperature at which these “stable glasses” are grown. In this work, we present a comprehensive all-atom simulation study of ethylbenzene, a canonical stable-glass former, using a computational film formation procedure that closely mimics the vapor deposition process. Atomistic studies of experimentally formed vapor-deposited glasses have not been performed before, and this study therefore begins by verifying that the model and method utilized here reproduces key structural features observed experimentally. Having established agreement between several simulated and experimental macroscopic observables, simulations are used to examine the substrate temperature dependence of molecular orientation. The results indicate that ethylbenzene glasses are anisotropic, depending upon substrate temperature, and that this dependence can be understood from the orientation present at the surface of the equilibrium liquid. By treating ethylbenzene as a simple model for molecular semiconducting materials, a quantum-chemical analysis is then used to show that the vapor-deposited glasses exhibit decreased energetic disorder and increased magnitude of the mean-squared transfer integral relative to isotropic, liquid-cooled films, an effect that is attributed to the anisotropic ordering of the molecular film. These results suggest a novel structure–function simulation strategy capable of tuning the electronic properties of organic semiconducting glasses prior to experimental deposition, which could have considerable potential for organic electronic materials design. PMID:28573203

Application of the phase extension method in virus crystallography.

PubMed

Reddy, Vijay S

2016-01-01

The procedure for phase extension (PX) involves gradually extending the initial phases from low resolution (e.g., ~8Å) to the high-resolution limit of a diffraction data set. Structural redundancy present in the viral capsids that display icosahedral symmetry results in a high degree of non-crystallographic symmetry (NCS), which in turn translates into higher phasing power and is critical for improving and extending phases to higher resolution. Greater completeness of the diffraction data and determination of a molecular replacement solution, which entails accurately identifying the virus particle orientation(s) and position(s), are important for the smooth progression of the PX procedure. In addition, proper definition of a molecular mask (envelope) around the NCS-asymmetric unit has been found to be important for the success of density modification procedures, such as density averaging and solvent flattening. Regardless of the degree of NCS, the PX method appears to work well in all space groups, provided an accurate molecular mask is used along with reasonable initial phases. However, in the cases with space group P1, in addition to requiring a molecular mask, starting the phase extension at a higher resolution (e.g., 6Å) overcame the previously reported problems due to Babinet phases and phase flipping errors.

The microscopic structure of an exactly solvable model binary solution that exhibits two closed loops in the phase diagram.

PubMed

Lungu, Radu P; Huckaby, Dale A

2008-07-21

An exactly solvable lattice model describing a binary solution is considered where rodlike molecules of types AA and BB cover the links of a honeycomb lattice, the neighboring molecular ends having three-body and orientation-dependent bonding interactions. At phase coexistence of AA-rich and BB-rich phases, the average fraction of each type of triangle of neighboring molecular ends is calculated exactly. The fractions of the different types of triangles are then used to deduce the local microscopic structure of the coexisting phases for a case of the model that contains two closed loops in the phase diagram.

Tuning polymorphism and orientation in organic semiconductor thin films via post-deposition processing.

PubMed

Hiszpanski, Anna M; Baur, Robin M; Kim, Bumjung; Tremblay, Noah J; Nuckolls, Colin; Woll, Arthur R; Loo, Yueh-Lin

2014-11-05

Though both the crystal structure and molecular orientation of organic semiconductors are known to impact charge transport in thin-film devices, separately accessing different polymorphs and varying the out-of-plane molecular orientation is challenging, typically requiring stringent control over film deposition conditions, film thickness, and substrate chemistry. Here we demonstrate independent tuning of the crystalline polymorph and molecular orientation in thin films of contorted hexabenzocoronene, c-HBC, during post-deposition processing without the need to adjust deposition conditions. Three polymorphs are observed, two of which have not been previously reported. Using our ability to independently tune the crystal structure and out-of-plane molecular orientation in thin films of c-HBC, we have decoupled and evaluated the effects that molecular packing and orientation have on device performance in thin-film transistors (TFTs). In the case of TFTs comprising c-HBC, polymorphism and molecular orientation are equally important; independently changing either one affects the field-effect mobility by an order of magnitude.

Molecular deformation and stress-strain behavior of poly(bisphenol-A-diphenyl sulfone)

NASA Technical Reports Server (NTRS)

Hong, S.-D.; Chung, S. Y.; Fedors, R. F.

1983-01-01

The strain-birefringence response of poly(bisphenol-A-diphenyl sulfone) is found to be independent of temperature at temperatures below -100 C; at higher temperatures, the response becomes slightly dependent on temperature, with lower birefringence seen at higher temperatures. The stress-strain behavior and the stress-birefringence response both depend on temperature over the entire testing temperature range (-179 C to 150 C) studied; this dependence, however, is not pronounced. The evidence is seen as suggesting that the polymer molecules respond to deformation by undergoing conformational rearrangements; the mode of the molecular deformation remains unchanged for temperatures of -100 C or lower. At higher temperatures, the average length of the chain segments involved in the rearrangement increases. The stress-strain response is attributed mainly to chain orientation. The entropic contribution deriving from chain orientation at temperatures below -100 C is still substantial. The modest temperature dependence of the stress-strain response suggests that the energy barriers for the chain segments involved in the rearrangement are relatively low.

A polarized view on DNA under tension

NASA Astrophysics Data System (ADS)

van Mameren, Joost; Vermeulen, Karen; Wuite, Gijs J. L.; Peterman, Erwin J. G.

2018-03-01

In the past decades, sensitive fluorescence microscopy techniques have contributed significantly to our understanding of the dynamics of DNA. The specific labeling of DNA using intercalating dyes has allowed for quantitative measurement of the thermal fluctuations the polymers undergo. On the other hand, recent advances in single-molecule manipulation techniques have unraveled the mechanical and elastic properties of this intricate polymer. Here, we have combined these two approaches to study the conformational dynamics of DNA under a wide range of tensions. Using polarized fluorescence microscopy in conjunction with optical-tweezers-based manipulation of YOYO-intercalated DNA, we controllably align the YOYO dyes using DNA tension, enabling us to disentangle the rapid dynamics of the dyes from that of the DNA itself. With unprecedented control of the DNA alignment, we resolve an inconsistency in reports about the tilted orientation of intercalated dyes. We find that intercalated dyes are on average oriented perpendicular to the long axis of the DNA, yet undergo fast dynamics on the time scale of absorption and fluorescence emission. In the overstretching transition of double-stranded DNA, we do not observe changes in orientation or orientational dynamics of the dyes. Only beyond the overstretching transition, a considerable depolarization is observed, presumably caused by an average tilting of the DNA base pairs. Our combined approach thus contributes to the elucidation of unique features of the molecular dynamics of DNA.

Melting/freezing behavior of a fluid confined in porous glasses and MCM-41: Dielectric spectroscopy and molecular simulation

NASA Astrophysics Data System (ADS)

Sliwinska-Bartkowiak, Malgorzata; Dudziak, Grazyna; Sikorski, Roman; Gras, Roman; Radhakrishnan, Ravi; Gubbins, Keith E.

2001-01-01

We report both experimental measurements and molecular simulations of the melting and freezing behavior of fluids in nanoporous media. The experimental studies are for nitrobenzene in the silica-based pores of controlled pore glass, Vycor, and MCM-41. Dielectric relaxation spectroscopy is used to determine melting points and the orientational relaxation times of the nitrobenzene molecules in the bulk and the confined phase. Monte Carlo simulations, together with a bond orientational order parameter method, are used to determine the melting point and fluid structure inside cylindrical pores modeled on silica. Qualitative comparison between experiment and simulation are made for the shift in the freezing temperatures and the structure of confined phases. From both the experiments and the simulations, it is found that the confined fluid freezes into a single crystalline structure for average pore diameters greater than 20σ, where σ is the diameter of the fluid molecule. For average pore sizes between 20σ and 15σ, part of the confined fluid freezes into a frustrated crystal structure with the rest forming an amorphous region. For pore sizes smaller than 15σ, even the partial crystallization did not occur. Our measurements and calculations show clear evidence of a novel intermediate "contact layer" phase lying between liquid and crystal; the contact layer is the confined molecular layer adjacent to the pore wall and experiences a deeper fluid-wall potential energy compared to the inner layers. We also find evidence of a liquid to "hexatic" transition in the quasi-two-dimensional contact layer at high temperatures.

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

Preferred Molecular Orientation of Coumarin 343 on TiO 2 Surfaces: Application to Dye-Sensitized Solar Cells

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

McCree-Grey, Jonathan; Cole, Jacqueline M.; Evans, Peter J.

2015-07-21

The dye…TiO2 interfacial structure in working electrodes of dye-sensitized solar cells (DSCs) is known to influence its photovoltaic device performance. Despite this, direct and quantitative reports of such structure remain sparse. This case study presents the application of X-ray reflectometry to determine the preferred structural orientation and molecular packing of the organic dye, coumarin 343, adsorbed onto amorphous TiO2. Results show that the dye molecules are, on average, tilted by 61.1° relative to the TiO2 surface, and are separated from each other by 8.2 Å. These findings emulate the molecular packing arrangement of a monolayer of coumarin 343 within itsmore » crystal structure. This suggests that the dye adsorbs onto TiO2 in one of its lowest energy configurations, i.e. dye…TiO2 self assembly is driven more by thermodynamic rather than kinetic means. Complementary DSC device tests illustrate that this interfacial structure compromises photovoltaic performance, unless a suitably sized co-adsorbant is interdispersed between the coumarin 343 chromophores on the TiO2 surface.« less

Nanohashtag structures based on carbon nanotubes and molecular linkers

NASA Astrophysics Data System (ADS)

Frye, Connor W.; Rybolt, Thomas R.

2018-03-01

Molecular mechanics was used to study the noncovalent interactions between single-walled carbon nanotubes and molecular linkers. Groups of nanotubes have the tendency to form tight, parallel bundles (||||). Molecular linkers were introduced into our models to stabilize nanostructures with carbon nanotubes held in perpendicular orientations. Molecular mechanics makes it possible to estimate the strength of noncovalent interactions holding these structures together and to calculate the overall binding energy of the structures. A set of linkers were designed and built around a 1,3,5,7-cyclooctatetraene tether with two corannulene containing pincers that extend in opposite directions from the central cyclooctatetraene portion. Each pincer consists of a pairs of "arms." These molecular linkers were modified so that the "hand" portions of each pair of "arms" could close together to grab and hold two carbon nanotubes in a perpendicular arrangement. To illustrate the possibility of more complicated and open perpendicular CNTs structures, our primary goal was to create a model of a nanohashtag (#) CNT conformation that is more stable than any parallel CNT arrangements with bound linker molecules forming clumps of CNTs and linkers in non-hashtag arrangements. This goal was achieved using a molecular linker (C280H96) that utilizes van der Waals interactions to two perpendicular oriented CNTs. Hydrogen bonding was then added between linker molecules to augment the stability of the hashtag structure. In the hashtag structure with hydrogen bonding, four (5,5) CNTs of length 4.46 nm (18 rings) and four linkers (C276H92N8O8) stabilized the hashtag so that the average binding energy per pincer was 118 kcal/mol.

Donor/Acceptor Molecular Orientation-Dependent Photovoltaic Performance in All-Polymer Solar Cells.

PubMed

Zhou, Ke; Zhang, Rui; Liu, Jiangang; Li, Mingguang; Yu, Xinhong; Xing, Rubo; Han, Yanchun

2015-11-18

The correlated donor/acceptor (D/A) molecular orientation plays a crucial role in solution-processed all-polymer solar cells in term of photovoltaic performance. For the conjugated polymers PTB7-th and P(NDI2OD-T2), the preferential molecular orientation of neat PTB7-th films kept face-on regardless of the properties of processing solvents. However, an increasing content of face-on molecular orientation in the neat P(NDI2OD-T2) films could be found by changing processing solvents from chloronaphthalene (CN) and o-dichlorobenzene (oDCB) to chlorobenzene (CB). Besides, the neat P(NDI2OD-T2) films also exhibited a transformation of preferential molecular orientation from face-on to edge-on when extending film drying time by casting in the same solution. Consequently, a distribution diagram of molecular orientation for P(NDI2OD-T2) films was depicted and the same trend could be observed for the PTB7-th/P(NDI2OD-T2) blend films. By manufacture of photovoltaic devices with blend films, the relationship between the correlated D/A molecular orientation and device performance was established. The short-circuit current (Jsc) of devices processed by CN, oDCB, and CB enhanced gradually from 1.24 to 8.86 mA/cm(2) with the correlated D/A molecular orientation changing from face-on/edge-on to face-on/face-on, which could be attributed to facile exciton dissociation at D/A interface with the same molecular orientation. Therefore, the power conversion efficiency (PCE) of devices processed by CN, oDCB, and CB improved from 0.53% to 3.52% ultimately.

Angular selectivity asymmetry of holograms recorded in near infrared sensitive liquid crystal photopolymerizable materials

NASA Astrophysics Data System (ADS)

Harbour, Steven; Galstian, Tigran; Akopyan, Rafik; Galstyan, Artur

2004-08-01

We have experimentally observed and theoretically explained the angular selectivity asymmetry in polymer dispersed liquid crystal holograms. Experiments are conducted in compounds with near infrared sensitivity. The coupled-wave theory is used to describe the diffraction properties of obtained anisotropic holographic gratings. Furthermore, the comparison of theory and experiments provides information about the optical axis direction that is defined by the average molecular orientation of the liquid crystal in the polymer matrix.

Oppugning the assumptions of spatial averaging of segment and joint orientations.

PubMed

Pierrynowski, Michael Raymond; Ball, Kevin Arthur

2009-02-09

Movement scientists frequently calculate "arithmetic averages" when examining body segment or joint orientations. Such calculations appear routinely, yet are fundamentally flawed. Three-dimensional orientation data are computed as matrices, yet three-ordered Euler/Cardan/Bryant angle parameters are frequently used for interpretation. These parameters are not geometrically independent; thus, the conventional process of averaging each parameter is incorrect. The process of arithmetic averaging also assumes that the distances between data are linear (Euclidean); however, for the orientation data these distances are geodesically curved (Riemannian). Therefore we question (oppugn) whether use of the conventional averaging approach is an appropriate statistic. Fortunately, exact methods of averaging orientation data have been developed which both circumvent the parameterization issue, and explicitly acknowledge the Euclidean or Riemannian distance measures. The details of these matrix-based averaging methods are presented and their theoretical advantages discussed. The Euclidian and Riemannian approaches offer appealing advantages over the conventional technique. With respect to practical biomechanical relevancy, examinations of simulated data suggest that for sets of orientation data possessing characteristics of low dispersion, an isotropic distribution, and less than 30 degrees second and third angle parameters, discrepancies with the conventional approach are less than 1.1 degrees . However, beyond these limits, arithmetic averaging can have substantive non-linear inaccuracies in all three parameterized angles. The biomechanics community is encouraged to recognize that limitations exist with the use of the conventional method of averaging orientations. Investigations requiring more robust spatial averaging over a broader range of orientations may benefit from the use of matrix-based Euclidean or Riemannian calculations.

Origin of the Low Rigidity of the Earth's Inner Core

NASA Astrophysics Data System (ADS)

Belonoshko, A. B.; Skorodumova, N. V.; Davis, S.; Osiptsov, A. N.; Rosengren, A.; Johansson, B.

2007-12-01

The solid iron Earth's inner core has a low rigidity which manifests itself in the anomalously low velocities of shear waves as compared to those in iron alloys. Normally, when estimating elastic properties of a polycrystal one calculates an average over different orientations of a single crystal. This approach does not take into account the grain boundaries and defects likely to be abundant at high temperatures relevant for the inner core conditions. We show, by molecular dynamics simulations that if defects are considered, the calculated shear modulus and shear wave velocity decrease dramatically compared to the averaged single crystal values. Thus, the low shear wave velocity in the inner core receives its explanation (Science 316, 1603 (2007)).

Theory of attosecond delays in molecular photoionization.

PubMed

Baykusheva, Denitsa; Wörner, Hans Jakob

2017-03-28

We present a theoretical formalism for the calculation of attosecond delays in molecular photoionization. It is shown how delays relevant to one-photon-ionization, also known as Eisenbud-Wigner-Smith delays, can be obtained from the complex dipole matrix elements provided by molecular quantum scattering theory. These results are used to derive formulae for the delays measured by two-photon attosecond interferometry based on an attosecond pulse train and a dressing femtosecond infrared pulse. These effective delays are first expressed in the molecular frame where maximal information about the molecular photoionization dynamics is available. The effects of averaging over the emission direction of the electron and the molecular orientation are introduced analytically. We illustrate this general formalism for the case of two polyatomic molecules. N 2 O serves as an example of a polar linear molecule characterized by complex photoionization dynamics resulting from the presence of molecular shape resonances. H 2 O illustrates the case of a non-linear molecule with comparably simple photoionization dynamics resulting from a flat continuum. Our theory establishes the foundation for interpreting measurements of the photoionization dynamics of all molecules by attosecond metrology.

Problems in obtaining perfect images by single-particle electron cryomicroscopy of biological structures in amorphous ice.

PubMed

Henderson, Richard; McMullan, Greg

2013-02-01

Theoretical considerations together with simulations of single-particle electron cryomicroscopy images of biological assemblies in ice demonstrate that atomic structures should be obtainable from images of a few thousand asymmetric units, provided the molecular weight of the whole assembly being studied is greater than the minimum needed for accurate position and orientation determination. However, with present methods of specimen preparation and current microscope and detector technologies, many more particles are needed, and the alignment of smaller assemblies is difficult or impossible. Only larger structures, with enough signal to allow good orientation determination and with enough images to allow averaging of many hundreds of thousands or even millions of asymmetric units, have successfully produced high-resolution maps. In this review, we compare the contrast of experimental electron cryomicroscopy images of two smaller molecular assemblies, namely apoferritin and beta-galactosidase, with that expected from perfect simulated images calculated from their known X-ray structures. We show that the contrast and signal-to-noise ratio of experimental images still require significant improvement before it will be possible to realize the full potential of single-particle electron cryomicroscopy. In particular, although reasonably good orientations can be obtained for beta-galactosidase, we have been unable to obtain reliable orientation determination from experimental images of apoferritin. Simulations suggest that at least 2-fold improvement of the contrast in experimental images at ~10 Å resolution is needed and should be possible.

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

Effect of Backbone Chemistry on the Structure of Polyurea Films Deposited by Molecular Layer Deposition

DOE PAGES

Bergsman, David S.; Closser, Richard G.; Tassone, Christopher J.; ...

2017-01-01

An experimental investigation into the growth of polyurea films by molecular layer deposition was performed by examining trends in the growth rate, crystallinity, and orientation of chains as a function of backbone flexibility. Growth curves obtained for films containing backbones of aliphatic and phenyl groups indicate that an increase in backbone flexibility leads to a reduction in growth rate from 4 to 1 Å/cycle. Crystallinity measurements collected using grazing incidence X-ray diffraction and Fourier transform infrared spectroscopy suggest that some chains form paracrystalline, out-of-plane stacks of polymer segments with packing distances ranging from 4.4 to 3.7 Å depending on themore » monomer size. Diffraction intensity is largely a function of the homogeneity of the backbone. Near-edge X-ray absorption fine structure measurements for thin and thick samples show an average chain orientation of ~25° relative to the substrate across all samples, suggesting that changes in growth rate are not caused by differences in chain angle but instead may be caused by differences in the frequency of chain terminations. In conclusion, these results suggest a model of molecular layer deposition-based chain growth in which films consist of a mixture of upward growing chains and horizontally aligned layers of paracrystalline polymer segments.« less

Oriented molecular sieve membranes by heteroepitaxial growth.

PubMed

Jeong, Hae-Kwon; Krohn, John; Sujaoti, Khristina; Tsapatsis, Michael

2002-11-06

Heteroepitaxial growth of titanosilicates (ETS-10 and ETS-4) is reported. Using this heteroepitaxial growth, oriented ETS-10/-4 membranes have been fabricated, demonstrating a novel way to achieve preferred orientation of molecular sieve films.

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.

Atomic and Molecular Systems in Intense Ultrashort Laser Pulses

NASA Astrophysics Data System (ADS)

Saenz, A.

2008-07-01

The full quantum mechanical treatment of atomic and molecular systems exposed to intense laser pulses is a so far unsolved challenge, even for systems as small as molecular hydrogen. Therefore, a number of simplified qualitative and quantitative models have been introduced in order to provide at least some interpretational tools for experimental data. The assessment of these models describing the molecular response is complicated, since a comparison to experiment requires often a number of averages to be performed. This includes in many cases averaging of different orientations of the molecule with respect to the laser field, focal volume effects, etc. Furthermore, the pulse shape and even the peak intensity is experimentally not known with very high precision; considering, e.g., the exponential intensity dependence of the ionization signal. Finally, experiments usually provide only relative yields. As a consequence of all these averagings and uncertainties, it is possible that different models may successfully explain some experimental results or features, although these models disagree substantially, if their predictions are compared before averaging. Therefore, fully quantum-mechanical approaches at least for small atomic and molecular systems are highly desirable and have been developed in our group. This includes efficient codes for solving the time-dependent Schrodinger equation of atomic hydrogen, helium or other effective one- or two-electron atoms as well as for the electronic motion in linear (effective) one-and two-electron diatomic molecules like H_2.Very recently, a code for larger molecular systems that adopts the so-called single-active electron approximation was also successfully implemented and applied. In the first part of this talk popular models describing intense laser-field ionization of atoms and their extensions to molecules are described. Then their validity is discussed on the basis of quantum-mechanical calculations. Finally, some peculiar molecular strong-field effects and the possibility of strong-field control mechanisms will be demonstrated. This includes phenomena like enhanced ionization and bond softening as well as the creation of vibrational wavepacket in the non-ionized electronic ground state of H_2 by creating a Schrodinger-cat state between the ionized and the non-ionized molecules. The latter, theoretically predicted phenomenon was very recently experimentally observed and lead to the real-time observation of the so far fastest molecular motion.

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

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.

Effect of orientation on deformation behavior of Fe nanowires: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Sainath, G.; Srinivasan, V. S.; Choudhary, B. K.; Mathew, M. D.; Jayakumar, T.

2014-04-01

Molecular dynamics simulations have been carried out to study the effect of crystal orientation on tensile deformation behaviour of single crystal BCC Fe nanowires at 10 K. Two nanowires with an initial orientation of <100>/{100} and <110>/{111} have been chosen for this study. The simulation results show that the deformation mechanisms varied with crystal orientation. The nanowire with an initial orientation of <100>/{100} deforms predominantly by twinning mechanism, whereas the nanowire oriented in <110>/{111}, deforms by dislocation plasticity. In addition, the single crystal oriented in <110>/{111} shows higher strength and elastic modulus than <100>/{100} oriented nanowire.

Probing molecular orientation of P3HT nanofibers in fiber-based organic solar cells

NASA Astrophysics Data System (ADS)

Yoon, Sangcheol; Han, Yaeeun; Hwang, Inchan

2018-01-01

Molecular orientation of conjugated polymers plays a key role in exciton generation/separation and charge transport, and thus significantly influence photovoltaic devices. Herein, we fabricated fiber-based organic solar cells and investigated the photovoltaic parameters with different diameters of fibers and PCBM diffusion. The open-circuit voltage that varies with molecular orientation whether it is face-on or edge-on was observed to differ. The investigation of the open-circuit voltage dependence reveals that thick fibers have core/shell like structures with different orientations. Thick fibers have face-on in the core and edge-on orientations in the shell. The face-on orientations are not preferentially formed in thin fibers, but the PCBM diffusion can induce face-on orientations that exist within the intermixed phase. Our results may shed a light on better understanding on fiber-based solar cells and suggest a way toward improving photovoltaic efficiency. [Figure not available: see fulltext.

Analysis of the binding loops configuration and surface adaptation of different crystallized single-domain antibodies in response to various antigens.

PubMed

Al Qaraghuli, Mohammed M; Ferro, Valerie A

2017-04-01

Monoclonal antibodies have revolutionized the biomedical field through their ubiquitous utilization in different diagnostics and therapeutic applications. Despite this widespread use, their large size and structural complexity have limited their versatility in specific applications. The antibody variable region that is responsible for binding antigen is embodied within domains that can be rescued individually as single-domain antibody (sdAb) fragments. Because of the unique characteristics of sdAbs, such as low molecular weight, high physicochemical stability, and the ability to bind antigens inaccessible to conventional antibodies, they represent a viable alternative to full-length antibodies. Consequently, 149 crystal structures of sdAbs, originating from human (VH), camelids (VHH), or sharks (VNAR), were retrieved from the Protein Data Bank, and their structures were compared. The 3 types of sdAbs displayed complementarity determining regions (CDRs) with different lengths and configurations. CDR3 of the VHH and VNAR domains were dominated by pleated and extended orientations, respectively. Although VNAR showed the smallest average molecular weight and molecular surface area compared with VHH and VH antibodies. However, the solvent accessible surface area measurements of the 3 tested sdAbs types were very similar. All the antihapten VHH antibodies showed pleated CDR3, which were sufficient to create a binding pocket to accommodate haptens (methotrexate and azo dyes) in terms of shape and electrostatic potential. The sdAbs that recognized lysozyme showed more diversity in their CDR3 orientation to enable them to recognize various topographies of lysozyme. Subsequently, the three sdAb classes were different in size and surface area and have shown distinguishable ability to optimize their CDR length and orientation to recognize different antigen classes. Copyright © 2016 John Wiley & Sons, Ltd.

Symmetry Breaking in Side Chains Leading to Mixed Orientations and Improved Charge Transport in Isoindigo-alt-Bithiophene Based Polymer Thin Films.

PubMed

Xue, Guobiao; Zhao, Xikang; Qu, Ge; Xu, Tianbai; Gumyusenge, Aristide; Zhang, Zhuorui; Zhao, Yan; Diao, Ying; Li, Hanying; Mei, Jianguo

2017-08-02

The selection of side chains is important in design of conjugated polymers. It not only affects their intrinsic physical properties, but also has an impact on thin film morphologies. Recent reports suggested that a face-on/edge-on bimodal orientation observed in polymer thin films may be responsible for a three-dimensional (3D) charge transport and leads to dramatically improved mobility in donor-acceptor based conjugated polymers. To achieve a bimodal orientation in thin films has been seldom explored from the aspect of molecular design. Here, we demonstrate a design strategy involving the use of asymmetric side chains that enables an isoindigo-based polymer to adopt a distinct bimodal orientation, confirmed by the grazing incidence X-ray diffraction. As a result, the polymer presents an average high mobility of 3.8 ± 0.7 cm 2 V -1 s -1 with a maximum value of 5.1 cm 2 V -1 s -1 , in comparison with 0.47 and 0.51 cm 2 V -1 s -1 obtained from the two reference polymers. This study exemplifies a new strategy to develop the next generation polymers through understanding the property-structure relationship.

Average Orientation Is More Accessible through Object Boundaries than Surface Features

ERIC Educational Resources Information Center

Choo, Heeyoung; Levinthal, Brian R.; Franconeri, Steven L.

2012-01-01

In a glance, the visual system can provide a summary of some kinds of information about objects in a scene. We explore how summary information about "orientation" is extracted and find that some representations of orientation are privileged over others. Participants judged the average orientation of either a set of 6 bars or 6 circular…

Ultrafast electron transfer at organic semiconductor interfaces: Importance of molecular orientation

DOE PAGES

Ayzner, Alexander L.; Nordlund, Dennis; Kim, Do -Hwan; ...

2014-12-04

Much is known about the rate of photoexcited charge generation in at organic donor/acceptor (D/A) heterojunctions overaged over all relative arrangements. However, there has been very little experimental work investigating how the photoexcited electron transfer (ET) rate depends on the precise relative molecular orientation between D and A in thin solid films. This is the question that we address in this work. We find that the ET rate depends strongly on the relative molecular arrangement: The interface where the model donor compound copper phthalocyanine is oriented face-on with respect to the fullerene C 60 acceptor yields a rate that ismore » approximately 4 times faster than that of the edge-on oriented interface. Our results suggest that the D/A electronic coupling is significantly enhanced in the face-on case, which agrees well with theoretical predictions, underscoring the importance of controlling the relative interfacial molecular orientation.« less

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

Molecular orientation in a dielectric liquid-vapor interphase

NASA Astrophysics Data System (ADS)

Chacón, E.; Mederos, L.; Navascués, G.; Tarazona, P.

1985-04-01

The density functional theory of Chacón et al. is used to study the molecular orientation in an interphase of a weak dipolar fluid. Explicit expressions are obtained using standard perturbation techniques. Molecular orientation, local susceptibility, and the Gibbsean surface susceptibility are evaluated for a Stockmayer model of dipolar fluid. The effect of the surface structure on the bulk ferroelectric transition is discussed in the light of the present theory and the numerical results.

Orientations of nonlocal vibrational modes from combined experimental and theoretical sum frequency spectroscopy

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

Chase, Hilary M.; Chen, Shunli; Fu, Li

2017-09-01

Inferring molecular orientations from vibrational sum frequency generation (SFG) spectra is challenging in polarization combinations that result in low signal intensities, or when the local point group symmetry approximation fails. While combining experiments with density functional theory (DFT) could overcome this problem, the scope of the combined method has yet to be established. Here, we assess its feasibility of determining the distributions of molecular orientations for one monobasic ester, two epoxides and three alcohols at the vapor/fused silica interface. We find that molecular orientations of nonlocal vibrational modes cannot be determined using polarization-resolved SFG measurements alone.

Molecular dynamics simulations of shock waves in oriented nitromethane single crystals.

PubMed

He, Lan; Sewell, Thomas D; Thompson, Donald L

2011-03-28

The structural relaxation of crystalline nitromethane initially at T = 200 K subjected to moderate (~15 GPa) supported shocks on the (100), (010), and (001) crystal planes has been studied using microcanonical molecular dynamics with the nonreactive Sorescu-Rice-Thompson force field [D. C. Sorescu, B. M. Rice, and D. L. Thompson, J. Phys. Chem. B 104, 8406 (2000)]. The responses to the shocks were determined by monitoring the mass density, the intermolecular, intramolecular, and total temperatures (average kinetic energies), the partitioning of total kinetic energy among Cartesian directions, the radial distribution functions for directions perpendicular to those of shock propagation, the mean-square displacements in directions perpendicular to those of shock propagation, and the time dependence of molecular rotational relaxation as a function of time. The results show that the mechanical response of crystalline nitromethane strongly depends on the orientation of the shock wave. Shocks propagating along [100] and [001] result in translational disordering in some crystal planes but not in others, a phenomenon that we refer to as plane-specific disordering; whereas for [010] the shock-induced stresses are relieved by a complicated structural rearrangement that leads to a paracrystalline structure. The plane-specific translational disordering is more complete by the end of the simulations (~6 ps) for shock propagation along [001] than along [100]. Transient excitation of the intermolecular degrees of freedom occurs in the immediate vicinity of the shock front for all three orientations; the effect is most pronounced for the [010] shock. In all three cases excitation of molecular vibrations occurs more slowly than the intermolecular excitation. The intermolecular and intramolecular temperatures are nearly equal by the end of the simulations, with 400-500 K of net shock heating. Results for two-dimensional mean-square molecular center-of-mass displacements, calculated as a function of time since shock wave passage in planes perpendicular to the direction of shock propagation, show that the molecular translational mobility in the picoseconds following shock wave passage is greatest for [001] and least for the [010] case. In all cases the root-mean-square center-of-mass displacement is small compared to the molecular diameter of nitromethane on the time scale of the simulations. The calculated time scales for the approach to thermal equilibrium are generally consistent with the predictions of a recent theoretical analysis due to Hooper [J. Chem. Phys. 132, 014507 (2010)].

A Graphics Processing Unit Implementation of Coulomb Interaction in Molecular Dynamics.

PubMed

Jha, Prateek K; Sknepnek, Rastko; Guerrero-García, Guillermo Iván; Olvera de la Cruz, Monica

2010-10-12

We report a GPU implementation in HOOMD Blue of long-range electrostatic interactions based on the orientation-averaged Ewald sum scheme, introduced by Yakub and Ronchi (J. Chem. Phys. 2003, 119, 11556). The performance of the method is compared to an optimized CPU version of the traditional Ewald sum available in LAMMPS, in the molecular dynamics of electrolytes. Our GPU implementation is significantly faster than the CPU implementation of the Ewald method for small to a sizable number of particles (∼10(5)). Thermodynamic and structural properties of monovalent and divalent hydrated salts in the bulk are calculated for a wide range of ionic concentrations. An excellent agreement between the two methods was found at the level of electrostatic energy, heat capacity, radial distribution functions, and integrated charge of the electrolytes.

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

Control of liquid crystal molecular orientation using ultrasound vibration

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

Taniguchi, Satoki; Wave Electronics Research Center, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321; Koyama, Daisuke

2016-03-07

We propose a technique to control the orientation of nematic liquid crystals using ultrasound and investigate the optical characteristics of the oriented samples. An ultrasonic liquid crystal cell with a thickness of 5–25 μm and two ultrasonic lead zirconate titanate transducers was fabricated. By exciting the ultrasonic transducers, the flexural vibration modes were generated on the cell. An acoustic radiation force to the liquid crystal layer was generated, changing the molecular orientation and thus the light transmission. By modulating the ultrasonic driving frequency and voltage, the spatial distribution of the molecular orientation of the liquid crystals could be controlled. The distributionmore » of the transmitted light intensity depends on the thickness of the liquid crystal layer because the acoustic field in the liquid crystal layer is changed by the orientational film.« less

Simulation of Young’s moduli for hexagonal ZnO [0 0 0 1]-oriented nanowires: first principles and molecular mechanical calculations

NASA Astrophysics Data System (ADS)

Bandura, Andrei V.; Evarestov, Robert A.; Lukyanov, Sergey I.; Piskunov, Sergei; Zhukovskii, Yuri F.

2017-08-01

Morphologically reproducible wurtzite-structured zinc oxide nanowires (ZnO NWs) can be synthesized by different methods. Since ZnO NWs have been found to possess piezoelectricity, a comprehensive study of their mechanical properties, e.g. deformations caused by external compression or stretching, is one of the actual tasks of this paper. We have calculated wurtzite-structured [0 0 0 1]-oriented ZnO NWs whose diameters have been varied within 1-5 nm and 1-20 nm ranges when using either ab initio (hybrid DFT-LCAO) or force-field (molecular mechanical) methods, respectively (the minimum diameter d NW of experimentally synthesized NWs has been estimated on average to be ~20 nm). When using both chosen calculation approaches, the values of Young’s moduli determined for the mentioned ranges of NW diameters have been found to be qualitatively compatible (168-169 GPa for 5 nm NW thickness), whereas results of molecular mechanical simulations on Y NW for 20 nm-thick NWs (160-162 GPa) have been qualitatively comparable with those experimentally measured along the [0 0 0 1] direction of NW loading. In all the cases, a gradual increase of the NW diameter has resulted in an asymptotic decrease of Young’s modulus consequently approaching that (Y b) of wurtzite-structured ZnO bulk along its [0 0 0 1] axis. The novelty of this study is that we combine the computation methods of quantum chemistry and molecular mechanics, while the majority of previous studies with the same aim have focused on the application of different classical molecular dynamical methods.

Triple Differential Cross Sections for single ionization of the Ethane molecule

NASA Astrophysics Data System (ADS)

Ali, Esam; Nixon, Kate; Ning, Chuangang; Murray, Andrew; Madison, Don

2015-09-01

We report experimental and theoretical results for electron-impact (e,2e) ionization of the Ethane molecule (C2H6) in the coplanar scattering geometry for four different ejected electron energies Ea = 5,10,15, and 20 eV respectively, and for each ejected electron energy, the projectile scattering angle is fixed at 10°. We will show that the TDCS is very sensitive for the case of two heavy nuclei surrounded by lighter H nuclei. On the theoretical side, we have used the M3DW coupled with the Orientation Averaged Molecular Orbital (OAMO) approximation and proper average (PA) over all orientations. These approximations show good agreement with experimental data for the binary peaks. However, for the recoil peak region, experiment finds a noticeable peak while theory predicts no peak. No recoil peak suggests no (or very weak) nuclear scattering, so we have investigated the importance of nuclear scattering by moving the nuclei closer to the center of mass. This work is supported by the US National Science Foundation under Grant No. PHY-1068237 and XSEDE resources provided by the Texas Advanced Computing Center (Grant No. TG-MCA07S029).

Perceived Average Orientation Reflects Effective Gist of the Surface.

PubMed

Cha, Oakyoon; Chong, Sang Chul

2018-03-01

The human ability to represent ensemble visual information, such as average orientation and size, has been suggested as the foundation of gist perception. To effectively summarize different groups of objects into the gist of a scene, observers should form ensembles separately for different groups, even when objects have similar visual features across groups. We hypothesized that the visual system utilizes perceptual groups characterized by spatial configuration and represents separate ensembles for different groups. Therefore, participants could not integrate ensembles of different perceptual groups on a task basis. We asked participants to determine the average orientation of visual elements comprising a surface with a contour situated inside. Although participants were asked to estimate the average orientation of all the elements, they ignored orientation signals embedded in the contour. This constraint may help the visual system to keep the visual features of occluding objects separate from those of the occluded objects.

Atomic density effects on temperature characteristics and thermal transport at grain boundaries through a proper bin size selection

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

Vo, Truong Quoc; Kim, BoHung, E-mail: muratbarisik@iyte.edu.tr, E-mail: bohungk@ulsan.ac.kr; Barisik, Murat, E-mail: muratbarisik@iyte.edu.tr, E-mail: bohungk@ulsan.ac.kr

2016-05-21

This study focuses on the proper characterization of temperature profiles across grain boundaries (GBs) in order to calculate the correct interfacial thermal resistance (ITR) and reveal the influence of GB geometries onto thermal transport. The solid-solid interfaces resulting from the orientation difference between the (001), (011), and (111) copper surfaces were investigated. Temperature discontinuities were observed at the boundary of grains due to the phonon mismatch, phonon backscattering, and atomic forces between dissimilar structures at the GBs. We observed that the temperature decreases gradually in the GB area rather than a sharp drop at the interface. As a result, threemore » distinct temperature gradients developed at the GB which were different than the one observed in the bulk solid. This behavior extends a couple molecular diameters into both sides of the interface where we defined a thickness at GB based on the measured temperature profiles for characterization. Results showed dependence on the selection of the bin size used to average the temperature data from the molecular dynamics system. The bin size on the order of the crystal layer spacing was found to present an accurate temperature profile through the GB. We further calculated the GB thickness of various cases by using potential energy (PE) distributions which showed agreement with direct measurements from the temperature profile and validated the proper binning. The variation of grain crystal orientation developed different molecular densities which were characterized by the average atomic surface density (ASD) definition. Our results revealed that the ASD is the primary factor affecting the structural disorders and heat transfer at the solid-solid interfaces. Using a system in which the planes are highly close-packed can enhance the probability of interactions and the degree of overlap between vibrational density of states (VDOS) of atoms forming at interfaces, leading to a reduced ITR. Thus, an accurate understanding of thermal characteristics at the GB can be formulated by selecting a proper bin size.« less

Atomic density effects on temperature characteristics and thermal transport at grain boundaries through a proper bin size selection

NASA Astrophysics Data System (ADS)

Vo, Truong Quoc; Barisik, Murat; Kim, BoHung

2016-05-01

This study focuses on the proper characterization of temperature profiles across grain boundaries (GBs) in order to calculate the correct interfacial thermal resistance (ITR) and reveal the influence of GB geometries onto thermal transport. The solid-solid interfaces resulting from the orientation difference between the (001), (011), and (111) copper surfaces were investigated. Temperature discontinuities were observed at the boundary of grains due to the phonon mismatch, phonon backscattering, and atomic forces between dissimilar structures at the GBs. We observed that the temperature decreases gradually in the GB area rather than a sharp drop at the interface. As a result, three distinct temperature gradients developed at the GB which were different than the one observed in the bulk solid. This behavior extends a couple molecular diameters into both sides of the interface where we defined a thickness at GB based on the measured temperature profiles for characterization. Results showed dependence on the selection of the bin size used to average the temperature data from the molecular dynamics system. The bin size on the order of the crystal layer spacing was found to present an accurate temperature profile through the GB. We further calculated the GB thickness of various cases by using potential energy (PE) distributions which showed agreement with direct measurements from the temperature profile and validated the proper binning. The variation of grain crystal orientation developed different molecular densities which were characterized by the average atomic surface density (ASD) definition. Our results revealed that the ASD is the primary factor affecting the structural disorders and heat transfer at the solid-solid interfaces. Using a system in which the planes are highly close-packed can enhance the probability of interactions and the degree of overlap between vibrational density of states (VDOS) of atoms forming at interfaces, leading to a reduced ITR. Thus, an accurate understanding of thermal characteristics at the GB can be formulated by selecting a proper bin size.

Interfacial free energy of the NaCl crystal-melt interface from capillary wave fluctuations.

PubMed

Benet, Jorge; MacDowell, Luis G; Sanz, Eduardo

2015-04-07

In this work we study, by means of molecular dynamics simulations, the solid-liquid interface of NaCl under coexistence conditions. By analysing capillary waves, we obtain the stiffness for different orientations of the solid and calculate the interfacial free energy by expanding the dependency of the interfacial free energy with the solid orientation in terms of cubic harmonics. We obtain an average value for the solid-fluid interfacial free energy of 89 ± 6 mN m(-1) that is consistent with previous results based on the measure of nucleation free energy barriers [Valeriani et al., J. Chem. Phys. 122, 194501 (2005)]. We analyse the influence of the simulation setup on interfacial properties and find that facets prepared as an elongated rectangular stripe give the same results as those prepared as squares for all cases but the 111 face. For some crystal orientations, we observe at small wave-vectors a behaviour not consistent with capillary wave theory and show that this behavior does not depend on the simulation setup.

The effect of the molecular orientation on the release of antimicrobial substances from uniaxially drawn polymer matrixes.

PubMed

Iconomopoulou, S M; Voyiatzis, G A

2005-03-21

A new method of controlled release of low molecular weight biocides incorporated in polymer matrixes is described. The molecular orientation of uniaxially drawn biocide doped polymer films is suggested as a significant parameter for controlled release monitoring. Triclosan, a well-established widespread antibacterial agent, has been incorporated into high density polyethylene (HDPE) films that have been subsequently uniaxially drawn at different draw ratios. The molecular orientation developed was estimated utilizing polarized mu-Raman spectra. Biocide incorporated polymer films, drawn at different draw ratios, have been immersed in ethanol-water solutions (EtOH) and in physiological saline. The release of Triclosan out of the polymer matrix was probed with UV-Vis absorption spectroscopy for a period of time up to 15 months. In all cases, although the film surface of the drawn samples exposed to the liquid solution was higher than the undrawn one, the relevant release rate from the drawn specimens was lower than the non-stretched samples depending on the molecular orientation developed during the drawing process. A note is made of the fact that no significant molecular orientation relaxation of the polyethylene films has been observed even after such a long time of immersion of the drawn films in the liquid solutions.

Molecular insight into the inclusion of the dietary plant flavonol fisetin and its chromophore within a chemically modified γ-cyclodextrin: Multi-spectroscopic, molecular docking and solubility studies.

PubMed

Pahari, Biswapathik; Chakraborty, Sandipan; Sengupta, Pradeep K

2018-09-15

We explored the encapsulation of dietary plant flavonols fisetin and its chromophore 3-hydroxyflavone, within 2-hydroxypropyl-γ-cyclodextrin (HPγ-CDx) nano-cavity in aqueous solution using multi-spectroscopic approaches and molecular docking. Upon addition of HPγ-CDx, dramatic changes occur in the intrinsic 'two color' fluorescence behavior of the fluorophores. This is manifested by significant increase in the steady state fluorescence intensities, anisotropies, average fluorescence lifetimes and rotational correlation times. Furthermore, in the CDx environment, intrinsically achiral flavonols exhibit prominent induced circular dichroism bands. These findings indicate that the flavonol molecules spontaneously enter the relatively hydrophobic, chiral environment of the HPγ-CDx nano-cavities. Molecular docking computations corroborate the spectroscopic findings, and predict selectivity in orientation of the encapsulated flavonols. HPγ-CDx inclusion increases the aqueous solubility of individual flavonols ∼100-1000 times. The present study demonstrates that the hydroxypropyl substituent in γ-CDx controls the inclusion mode of the flavonols, leading to their enhanced solubilization and altered spectral signatures. Copyright © 2018 Elsevier Ltd. All rights reserved.

Biophysical aspects of cyclodextrin interaction with paraoxon.

PubMed

Soni, Sunil-Datta; Bhonsle, Jayendra B; Garcia, Gregory E

2014-03-01

Cyclodextrins are torus-shaped polymers of glucose that can bind organophosphorous compounds such as nerve agents and pesticides. We demonstrate here that cyclodextrin can bind up to two paraoxon molecules with a K(av) of 6775 M(-1). Molecular modeling shows that the paraoxon appears to bind in polar opposite orientation and have an average binding energy of -89 Kcals/mol. Published 2013. This article is a U.S. Government work and is in the public domain in the USA. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.

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

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.

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

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.

A fiber orientation-adapted integration scheme for computing the hyperelastic Tucker average for short fiber reinforced composites

NASA Astrophysics Data System (ADS)

Goldberg, Niels; Ospald, Felix; Schneider, Matti

2017-10-01

In this article we introduce a fiber orientation-adapted integration scheme for Tucker's orientation averaging procedure applied to non-linear material laws, based on angular central Gaussian fiber orientation distributions. This method is stable w.r.t. fiber orientations degenerating into planar states and enables the construction of orthotropic hyperelastic energies for truly orthotropic fiber orientation states. We establish a reference scenario for fitting the Tucker average of a transversely isotropic hyperelastic energy, corresponding to a uni-directional fiber orientation, to microstructural simulations, obtained by FFT-based computational homogenization of neo-Hookean constituents. We carefully discuss ideas for accelerating the identification process, leading to a tremendous speed-up compared to a naive approach. The resulting hyperelastic material map turns out to be surprisingly accurate, simple to integrate in commercial finite element codes and fast in its execution. We demonstrate the capabilities of the extracted model by a finite element analysis of a fiber reinforced chain link.

Symmetry Breaking in Side Chains Leading to Mixed Orientations and Improved Charge Transport in Isoindigo- alt -Bithiophene Based Polymer Thin Films

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

Xue, Guobiao; Zhao, Xikang; Qu, Ge

The selection of side chains is important in design of conjugated polymers. It not only affects their intrinsic physical properties, but also has an impact on thin film morphologies. Recent reports suggested that a face-on/edge-on bimodal orientation observed in polymer thin films may be responsible for a three-dimensional (3D) charge transport and leads to dramatically improved mobility in donor–acceptor based conjugated polymers. To achieve a bimodal orientation in thin films has been seldom explored from the aspect of molecular design. Here, we demonstrate a design strategy involving the use of asymmetric side chains that enables an isoindigo-based polymer to adoptmore » a distinct bimodal orientation, confirmed by the grazing incidence X-ray diffraction. As a result, the polymer presents an average high mobility of 3.8 ± 0.7 cm2 V–1 s–1 with a maximum value of 5.1 cm2 V–1 s–1, in comparison with 0.47 and 0.51 cm2 V–1 s–1 obtained from the two reference polymers. This study exemplifies a new strategy to develop the next generation polymers through understanding the property-structure relationship.« less

Different interface orientations of pentacene and PTCDA induce different degrees of disorder

PubMed Central

2012-01-01

Organic polymers or crystals are commonly used in manufacturing of today‘s electronically functional devices (OLEDs, organic solar cells, etc). Understanding their morphology in general and at the interface in particular is of paramount importance. Proper knowledge of molecular orientation at interfaces is essential for predicting optoelectronic properties such as exciton diffusion length, charge carrier mobility, and molecular quadrupole moments. Two promising candidates are pentacene and 3,4:9,10-perylenetetracarboxylic dianhydride (PTCDA). Different orientations of pentacene on PTCDA have been investigated using an atomistic molecular dynamics approach. Here, we show that the degree of disorder at the interface depends largely on the crystal orientation and that more ordered interfaces generally suffer from large vacancy formation. PMID:22583772

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.

Investigating Factors that Generate and Maintain Variation in Migratory Orientation: A Primer for Recent and Future Work.

PubMed

Delmore, Kira E; Liedvogel, Miriam

2016-01-01

The amazing accuracy of migratory orientation performance across the animal kingdom is facilitated by the use of magnetic and celestial compass systems that provide individuals with both directional and positional information. Quantitative genetics analyses in several animal systems suggests that migratory orientation has a strong genetic component. Nevertheless, the exact identity of genes controlling orientation remains largely unknown, making it difficult to obtain an accurate understanding of this fascinating behavior on the molecular level. Here, we provide an overview of molecular genetic techniques employed thus far, highlight the pros and cons of various approaches, generalize results from species-specific studies whenever possible, and evaluate how far the field has come since early quantitative genetics studies. We emphasize the importance of examining different levels of molecular control, and outline how future studies can take advantage of high-resolution tracking and sequencing techniques to characterize the genomic architecture of migratory orientation.

Theoretical vibrational sum-frequency generation spectroscopy of water near lipid and surfactant monolayer interfaces.

PubMed

Roy, S; Gruenbaum, S M; Skinner, J L

2014-11-14

Understanding the structure of water near cell membranes is crucial for characterizing water-mediated events such as molecular transport. To obtain structural information of water near a membrane, it is useful to have a surface-selective technique that can probe only interfacial water molecules. One such technique is vibrational sum-frequency generation (VSFG) spectroscopy. As model systems for studying membrane headgroup/water interactions, in this paper we consider lipid and surfactant monolayers on water. We adopt a theoretical approach combining molecular dynamics simulations and phase-sensitive VSFG to investigate water structure near these interfaces. Our simulated spectra are in qualitative agreement with experiments and reveal orientational ordering of interfacial water molecules near cationic, anionic, and zwitterionic interfaces. OH bonds of water molecules point toward an anionic interface leading to a positive VSFG peak, whereas the water hydrogen atoms point away from a cationic interface leading to a negative VSFG peak. Coexistence of these two interfacial water species is observed near interfaces between water and mixtures of cationic and anionic lipids, as indicated by the presence of both negative and positive peaks in their VSFG spectra. In the case of a zwitterionic interface, OH orientation is toward the interface on the average, resulting in a positive VSFG peak.

Molecular alignment and orientation with a hybrid Raman scattering technique

NASA Astrophysics Data System (ADS)

Bustard, Philip J.; Lausten, R.; Sussman, Benjamin J.

2012-11-01

We demonstrate a scheme for the preparation of molecular alignment and angular momentum orientation using a hybrid combination of two limits of Raman scattering. First a weak, impulsive pump pulse initializes the system via the nonresonant dynamic Stark effect. Then, having overcome the influence of the vacuum fluctuations, an amplification pulse selectively enhances the initial coherences by transient stimulated Raman scattering, generating alignment and angular momentum orientation of molecular hydrogen. The amplitude and phase of the resulting coherent dynamics are experimentally probed, indicating an amplification factor of 4.5. An analytic theory is developed to model the dynamics.

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

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.

In Situ Electrochemical Synthesis of Oriented and Defect-Free AEL Molecular-Sieve Films Using Ionic Liquids.

PubMed

Yu, Tongwen; Chu, Wenling; Cai, Rui; Liu, Yanchun; Yang, Weishen

2015-10-26

Simply preparing oriented and defect-free molecular-sieve films have been a long-standing challenge both in academia and industry. Most of the early works focus on the careful and multiple controls of the seeds layer or synthesis conditions. Herein, we report a one-step in situ electrochemical ionothermal method that combines a controllable electric field with ionic liquids. We demonstrate that an in-plane oriented and defect-free AEL (one molecular-sieve framework type) molecular-sieve film was obtained using an Al electrode as the Al source. The excellent corrosion-resistant performance of the film makes this technology promising in multiple applications, such as anti-corrosion coatings. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Incorporation of the TIP4P water model into a continuum solvent for computing solvation free energy

NASA Astrophysics Data System (ADS)

Yang, Pei-Kun

2014-10-01

The continuum solvent model is one of the commonly used strategies to compute solvation free energy especially for large-scale conformational transitions such as protein folding or to calculate the binding affinity of protein-protein/ligand interactions. However, the dielectric polarization for computing solvation free energy from the continuum solvent is different than that obtained from molecular dynamic simulations. To mimic the dielectric polarization surrounding a solute in molecular dynamic simulations, the first-shell water molecules was modeled using a charge distribution of TIP4P in a hard sphere; the time-averaged charge distribution from the first-shell water molecules were estimated based on the coordination number of the solute, and the orientation distribution of the first-shell waters and the intermediate water molecules were treated as that of a bulk solvent. Based on this strategy, an equation describing the solvation free energy of ions was derived.

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)

Xiong, L. H.; Wang, X. D.; Yu, Q.

Temperature-dependent atomistic structure evolution of liquid gallium (Ga) has been investigated by using in situ high energy X-ray diffraction experiment and ab initio molecular dynamics simulation. Both experimental and theoretical results reveal the existence of a liquid structural change around 1000 K in liquid Ga. Below and above this temperature the liquid exhibits differences in activation energy for selfdiffusion, temperature-dependent heat capacity, coordination numbers, density, viscosity, electric resistivity and thermoelectric power, which are reflected from structural changes of the bond-orientational order parameter Q6, fraction of covalent dimers, averaged string length and local atomic packing. This finding will trigger more studiesmore » on the liquid-to-liquid crossover in metallic melts.« less

Molecular orientation distributions during injection molding of liquid crystalline polymers: Ex situ investigation of partially filled moldings

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

Fang, Jun; Burghardt, Wesley R.; Bubeck, Robert A.

The development of molecular orientation in thermotropic liquid crystalline polymers (TLCPs) during injection molding has been investigated using two-dimensional wide-angle X-ray scattering coordinated with numerical computations employing the Larson-Doi polydomain model. Orientation distributions were measured in 'short shot' moldings to characterize structural evolution prior to completion of mold filling, in both thin and thick rectangular plaques. Distinct orientation patterns are observed near the filling front. In particular, strong extension at the melt front results in nearly transverse molecular alignment. Far away from the flow front shear competes with extension to produce complex spatial distributions of orientation. The relative influence ofmore » shear is stronger in the thin plaque, producing orientation along the filling direction. Exploiting an analogy between the Larson-Doi model and a fiber orientation model, we test the ability of process simulation tools to predict TLCP orientation distributions during molding. Substantial discrepancies between model predictions and experimental measurements are found near the flow front in partially filled short shots, attributed to the limits of the Hele-Shaw approximation used in the computations. Much of the flow front effect is however 'washed out' by subsequent shear flow as mold filling progresses, leading to improved agreement between experiment and corresponding numerical predictions.« less

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

Javaid, Saqib; National Centre of Physics, Islamabad 45320; Javed Akhtar, M., E-mail: javedakhtar6@gmail.com

Recently, experimental results have shown that photovoltaic properties of Fullerene (C60)/Phthalocyanine based devices improve considerably as molecular orientation is changed from edge-on to face-on. In this work, we have studied the impact of molecular orientation on C60/ZnPc interfacial properties, particularly focusing on experimentally observed face-on and edge-on configuration, using density functional theory based simulations. The results show that the interfacial electronic properties are strongly anisotropic: direction of charge transfer and interface dipole fluctuates as molecular orientation is switched. As a result of orientation dependant interface dipole, difference between acceptor LUMO and donor HOMO increases as the orientation is changed frommore » edge-on to face-on, suggesting a consequent increase in open circuit voltage (V{sub OC}). Moreover, adsorption and electronic properties indicate that the interfacial interactions are much stronger in the face-on configuration which should further facilitate the charge-separation process. These findings elucidate the energy level alignment at C60/ZnPc interface and help to identify interface dipole as the origin of the orientation dependence of V{sub OC}.« less

Single molecular orientation switching of an endohedral metallofullerene.

PubMed

Yasutake, Yuhsuke; Shi, Zujin; Okazaki, Toshiya; Shinohara, Hisanori; Majima, Yutaka

2005-06-01

The single molecular orientation switching of the Tb@C82 endohedral metallofullerene has been studied by using low-temperature ultrahigh vacuum (UHV) scanning tunneling microscopy (STM). An octanethiol self-assembled monolayer (SAM) was introduced between Tb@C82 and the Au111 substrate to control the thermal rotational states of Tb@C82. Scanning tunneling spectroscopy (STS) of Tb@C82 on an octanethiol SAM at 13 K demonstrated hysteresis including negative differential conductance (NDC). This observed hysteresis and NDC is interpreted in terms of a switching of the Tb@C82 molecular orientation caused by the interaction between its electric dipole moment and an external electric field.

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

NASA Astrophysics Data System (ADS)

Sinha, Sumona; Wang, C.-H.; Mukherjee, M.

2017-07-01

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

Infrared vibrational nanocrystallography and nanoimaging

PubMed Central

Muller, Eric A.; Pollard, Benjamin; Bechtel, Hans A.; van Blerkom, Peter; Raschke, Markus B.

2016-01-01

Molecular solids and polymers can form low-symmetry crystal structures that exhibit anisotropic electron and ion mobility in engineered devices or biological systems. The distribution of molecular orientation and disorder then controls the macroscopic material response, yet it is difficult to image with conventional techniques on the nanoscale. We demonstrated a new form of optical nanocrystallography that combines scattering-type scanning near-field optical microscopy with both optical antenna and tip-selective infrared vibrational spectroscopy. From the symmetry-selective probing of molecular bond orientation with nanometer spatial resolution, we determined crystalline phases and orientation in aggregates and films of the organic electronic material perylenetetracarboxylic dianhydride. Mapping disorder within and between individual nanoscale domains, the correlative hybrid imaging of nanoscale heterogeneity provides insight into defect formation and propagation during growth in functional molecular solids. PMID:27730212

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.

Crystallography and Molecular Arrangement of Polymorphic Monolayer J-Aggregates of a Cyanine Dye: Multiangle Polarized Light Fluorescence Optical Microscopy Study.

PubMed

Prokhorov, Valery V; Pozin, Sergey I; Perelygina, Olga M; Mal'tsev, Eugene I

2018-04-24

The molecular orientation in monolayer J-aggregates of 3,3-di(γ-sulfopropyl)-5,5-dichlorotiamonomethinecyanine dye has been precisely estimated using improved linear polarization measurements in the fluorescence microscope in which a multiangle set of polarization data is obtained using sample rotation. The estimated molecular orientation supplemented with the previously established crystallographic constraints based on the analysis of the well-developed two-dimensional J-aggregate shapes unambiguously indicate the staircase type of molecular arrangement for striplike J-aggregates with the staircases oriented along strips. The molecular transition dipoles are inclined at an angle of ∼25° to the strip direction, whereas the characteristic strip vertex angle ∼45° is formed by the [100] and [1-10] directions of the monoclinic unit cell. Measurements of the geometry of partially unwound tubes and their polarization properties support the model of tube formation by close-packed helical winding of flexible monolayer strips. In the tubes, the long molecular axes are oriented at a small angle in the range of 5-15° to the normal to the tube axis providing low bending energy. At a nanoscale, high-resolution atomic force microscopy imaging of J-aggregate monolayers reveals a complex quasi-one-dimensional organization.

Temporal-frequency tuning of cross-orientation suppression in the cat striate cortex.

PubMed

Allison, J D; Smith, K R; Bonds, A B

2001-01-01

A sinusoidal mask grating oriented orthogonally to and superimposed onto an optimally oriented base grating reduces a cortical neuron's response amplitude. The spatial selectivity of cross-orientation suppression (XOR) has been described, so for this paper we investigated the temporal properties of XOR. We recorded from single striate cortical neurons (n = 72) in anesthetized and paralyzed cats. After quantifying the spatial and temporal characteristics of each cell's excitatory response to a base grating, we measured the temporal-frequency tuning of XOR by systematically varying the temporal frequency of a mask grating placed at a null orientation outside of the cell's excitatory orientation domain. The average preferred temporal frequency of the excitatory response of the neurons in our sample was 3.8 (+/- 1.5 S.D.) Hz. The average cutoff frequency for the sample was 16.3 (+/- 1.7) Hz. The average preferred temporal frequency (7.0 +/- 2.6 Hz) and cutoff frequency (20.4 +/- 6.9 Hz) of the XOR were significantly higher. The differences averaged 1.1 (+/- 0.6) octaves for the peaks and 0.3 (+/- 0.4) octaves for the cutoffs. The XOR mechanism's preference for high temporal frequencies suggests a possible extrastriate origin for the effect and could help explain the low-pass temporal-frequency response profile displayed by most striate cortical neurons.

Influence of Molecular Orientation on Charge-Transfer Processes at Phthalocyanine/Metal Oxide Interfaces and Relationship to Organic Photovoltaic Performance

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

Lin, Hsiao-Chu; MacDonald, Gordon A.; Shi, Yanrong

2015-05-04

The effect of the molecular orientation distribution of the first monolayer of donor molecules at the hole-harvesting contact in an organic photovoltaic (OPV) on device efficiency was investigated. Two zinc phthalocyanine (ZnPc) phosphonic acids (PA) deposited on indium tin oxide (ITO) electrodes are compared: ZnPc(PA)4 contains PA linkers in all four quadrants, and ZnPcPA contains a PA linker in one quadrant. ZnPcPA monolayers exhibited a broad distribution of molecular orientations whereas ZnPc(PA)4 adsorption produced a monolayer with a narrower orientation distribution with the molecular plane more parallel to the ITO surface. We used potential-modulated attenuated total reflectance spectroelectrochemistry (PM-ATR) tomore » characterize the charge-transfer kinetics of these films and show that the highest rate constants correspond to ZnPc subpopulations that are oriented more parallel to the ITO surface plane. For ZnPc(PA)4, rate constants exceeded 104 s–1 and are among the highest ever reported for a surface-confined redox couple, which is attributable to both its orientation and the small ZnPc–electrode separation distance. The performance of OPVs with ITO hole-harvesting contacts modified with ZnPc(PA)4 was comparable to that achieved with highly activated bare ITO contacts, whereas for ZnPcPA-modified contacts, the OPV performance was similar to that observed with (hole-blocking) alkyl-PA modifiers. These results demonstrate the synergism between molecular structure, energetics, and dynamics at interfaces in OPVs.« less

Formation of Ordered Arrays of Proteins on Surfaces

NASA Technical Reports Server (NTRS)

Lenhoff, A. M.

1996-01-01

Van der Waals (dispersion) forces contribute to interactions of proteins with other molecules or with surfaces, but because of the structural complexity of protein molecules, the magnitude of these effects is usually estimated based on idealized models of the molecular geometry, e.g., spheres or spheroids. The calculations reported here seek to account for both the geometric irregularity of protein molecules and the material properties of the interacting media. While the latter are found to fall in the generally accepted range, the molecular shape is shown to cause the magnitudes of the interactions to differ significantly from those calculated using idealized models, with important consequences. First, the roughness of the molecular surface leads to much lower average interaction energies for both protein-protein and protein-surface cases relative to calculations in which the protein molecule is approximated as a sphere. These results indicate that a form of steric stabilization may be an important effect in protein solutions. Underlying this behavior is appreciable orientational dependence, one reflection of which is that molecules of complementary shape are found to exhibit very strong attractive dispersion interactions. Although this has been widely discussed previously in the context of molecular recognition processes, the broader implications of these phenomena may also be important at larger molecular separations, e.g., in the dynamics of aggregation, precipitation and crystal growth.

Molecular Packing of Amphiphilic Nanosheets Resolved by X-ray Scattering

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

Harutyunyan, Boris; Dannenhoffer, Adam; Kewalramani, Sumit

2016-12-29

Molecular packing in light harvesting 2D assemblies of photocatalytic materials is a critical factor for solar-to-fuel conversion efficiency. However, structure–function correlations have yet to be fully established. This is partly due to the difficulties in extracting the molecular arrangements from the complex 3D powder averaged diffraction patterns of 2D lattices, obtained via in situ wide-angle X-ray scattering. Here, we develop a scattering theory formalism and couple it with a simple geometrical model for the molecular shape of chromophore 9-methoxy-N-(sodium hexanoate)perylene-3,4-dicarboximide (MeO-PMI) used in our study. This generally applicable method fully reproduces the measured diffraction pattern including the asymmetric line shapesmore » for the Bragg reflections and yields the molecular packing arrangement within a 2D crystal structure with a remarkable degree of detail. We find an approximate edge-centered herringbone structure for the PMI fused aromatic rings and ordering of the carboxypentyl chains above and below the nanosheets. Such a packing arrangement differs from the more symmetric face-to-face orientation of the unsubstituted PMI rings. This structural difference is correlated to our measurement of the reduced catalytic performance of MeO-PMI nanosheets as compared to the mesoscopically similar unsubstituted PMI assemblies.« less

Van der Waals Interactions Involving Proteins

NASA Technical Reports Server (NTRS)

Roth, Charles M.; Neal, Brian L.; Lenhoff, Abraham M.

1996-01-01

Van der Waals (dispersion) forces contribute to interactions of proteins with other molecules or with surfaces, but because of the structural complexity of protein molecules, the magnitude of these effects is usually estimated based on idealized models of the molecular geometry, e.g., spheres or spheroids. The calculations reported here seek to account for both the geometric irregularity of protein molecules and the material properties of the interacting media. Whereas the latter are found to fall in the generally accepted range, the molecular shape is shown to cause the magnitudes of the interactions to differ significantly from those calculated using idealized models. with important consequences. First, the roughness of the molecular surface leads to much lower average interaction energies for both protein-protein and protein-surface cases relative to calculations in which the protein molecule is approximated as a sphere. These results indicate that a form of steric stabilization may be an important effect in protein solutions. Underlying this behavior is appreciable orientational dependence, one reflection of which is that molecules of complementary shape are found to exhibit very strong attractive dispersion interactions. Although this has been widely discussed previously in the context of molecular recognition processes, the broader implications of these phenomena may also be important at larger molecular separations, e.g., in the dynamics of aggregation, precipitation, and crystal growth.

Molecular adsorption and multilayer growth of pentacene on Cu(100):Layer structure and energetics

NASA Astrophysics Data System (ADS)

Satta, M.; Iacobucci, S.; Larciprete, R.

2007-04-01

We used the partial charge tight binding method to perform a full structure optimization to determine equilibrium adsorption geometries, energetics, and local charge redistribution for molecular adsorption and multilayer growth of pentacene on Cu(100). We found that single molecule adsorption induces only a localized perturbation of the metal lattice which is limited to the topmost layers. At saturation coverage four stable topologies (Brick, Wave, Lines and Zigzag) were identified, all based on pentacene molecules lying flat on the metal surface and with the central phenyl ring adsorbed in top position. Only two (Brick and Wave) out of the four structures are able to sustain multilayer growth. In both cases, assembling beyond the second layer corresponds to a transition from the flat to a tilted geometry, in which the pentacenes adopt a face-plane-face arrangement leading to a herringbone structure. The energetics of the different structure are reported as a function of the molecular number density of the pentacene multilayer by calculating cohesive, stress, and electrostatic energies. The dominant tilted molecular orientation in the pentacene multilayer is in agreement with the average tilt angle of 65° between the molecular plane and the Cu surface derived by near edge x-ray absorption spectroscopy of a four monolayer pentacene film deposited on Cu(100).

Effect of Interfacial Molecular Orientation on Power Conversion Efficiency of Perovskite Solar Cells.

PubMed

Xiao, Minyu; Joglekar, Suneel; Zhang, Xiaoxian; Jasensky, Joshua; Ma, Jialiu; Cui, Qingyu; Guo, L Jay; Chen, Zhan

2017-03-08

A wide variety of charge carrier dynamics, such as transport, separation, and extraction, occur at the interfaces of planar heterojunction solar cells. Such factors can affect the overall device performance. Therefore, understanding the buried interfacial molecular structure in various devices and the correlation between interfacial structure and function has become increasingly important. Current characterization techniques for thin films such as X-ray diffraction, cross section scanning electronmicroscopy, and UV-visible absorption spectroscopy are unable to provide the needed molecular structural information at buried interfaces. In this study, by controlling the structure of the hole transport layer (HTL) in a perovskite solar cell and applying a surface/interface-sensitive nonlinear vibrational spectroscopic technique (sum frequency generation vibrational spectroscopy (SFG)), we successfully probed the molecular structure at the buried interface and correlated its structural characteristics to solar cell performance. Here, an edge-on (normal to the interface) polythiophene (PT) interfacial molecular orientation at the buried perovskite (photoactive layer)/PT (HTL) interface showed more than two times the power conversion efficiency (PCE) of a lying down (tangential) PT interfacial orientation. The difference in interfacial molecular structure was achieved by altering the alkyl side chain length of the PT derivatives, where PT with a shorter alkyl side chain showed an edge-on interfacial orientation with a higher PCE than that of PT with a longer alkyl side chain. With similar band gap alignment and bulk structure within the PT layer, it is believed that the interfacial molecular structural variation (i.e., the orientation difference) of the various PT derivatives is the underlying cause of the difference in perovskite solar cell PCE.

Effect of substrates on the molecular orientation of silicon phthalocyanine dichloride thin films

NASA Astrophysics Data System (ADS)

Deng, Juzhi; Baba, Yuji; Sekiguchi, Tetsuhiro; Hirao, Norie; Honda, Mitsunori

2007-05-01

Molecular orientations of silicon phthalocyanine dichloride (SiPcCl2) thin films deposited on three different substrates have been measured by near-edge x-ray absorption fine structure (NEXAFS) spectroscopy using linearly polarized synchrotron radiation. The substrates investigated were highly oriented pyrolitic graphite (HOPG), polycrystalline gold and indium tin oxide (ITO). For thin films of about five monolayers, the polarization dependences of the Si K-edge NEXAFS spectra showed that the molecular planes of SiPcCl2 on three substrates were nearly parallel to the surface. Quantitative analyses of the polarization dependences revealed that the tilted angle on HOPG was only 2°, which is interpreted by the perfect flatness of the HOPG surface. On the other hand, the tilted angle on ITO was 26°. Atomic force microscopy (AFM) observation of the ITO surface showed that the periodicity of the horizontal roughness is of the order of a few nanometres, which is larger than the molecular size of SiPcCl2. It is concluded that the morphology of the top surface layer of the substrate affects the molecular orientation of SiPcCl2 molecules not only for mono-layered adsorbates but also for multi-layered thin films.

Nanoindentation of HMX and Idoxuridine to Determine Mechanical Similarity

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

Burch, Alexandra; Yeager, John; Bahr, David

Assessing the mechanical behavior (elastic properties, plastic properties, and fracture phenomena) of molecular crystals is often complicated by the difficulty in preparing samples. Pharmaceuticals and energetic materials in particular are often used in composite structures or tablets, where the individual grains can strongly impact the solid behavior. Nanoindentation is a convenient method to experimentally assess these properties, and it is used here to demonstrate the similarity in the mechanical properties of two distinct systems: individual crystals of the explosive cyclotetramethylene tetranitramine (HMX) and the pharmaceutical idoxuridine were tested in their as-precipitated state, and the effective average modulus and hardness (whichmore » can be orientation dependent) were determined. Both exhibit a hardness of 1.0 GPa, with an effective reduced modulus of 25 and 23 GPa for the HMX and idoxuridine, respectively. They also exhibit similar yield point behavior. This indicates idoxuridine may be a suitable mechanical surrogate (or “mock”) for HMX. While the methodology to assess elastic and plastic properties was relatively insensitive to specific crystal orientation (i.e., a uniform distribution in properties was observed for all random crystals tested), the indentation-induced fracture properties appear to be much more sensitive to tip-crystal orientation, and an unloading slope analysis is used to demonstrate the need for further refinement in relating toughness to orientation in these materials with relatively complex slip systems and crystal structures. View Full-Text« less

Nanoindentation of HMX and Idoxuridine to Determine Mechanical Similarity

DOE PAGES

Burch, Alexandra; Yeager, John; Bahr, David

2017-11-01

Assessing the mechanical behavior (elastic properties, plastic properties, and fracture phenomena) of molecular crystals is often complicated by the difficulty in preparing samples. Pharmaceuticals and energetic materials in particular are often used in composite structures or tablets, where the individual grains can strongly impact the solid behavior. Nanoindentation is a convenient method to experimentally assess these properties, and it is used here to demonstrate the similarity in the mechanical properties of two distinct systems: individual crystals of the explosive cyclotetramethylene tetranitramine (HMX) and the pharmaceutical idoxuridine were tested in their as-precipitated state, and the effective average modulus and hardness (whichmore » can be orientation dependent) were determined. Both exhibit a hardness of 1.0 GPa, with an effective reduced modulus of 25 and 23 GPa for the HMX and idoxuridine, respectively. They also exhibit similar yield point behavior. This indicates idoxuridine may be a suitable mechanical surrogate (or “mock”) for HMX. While the methodology to assess elastic and plastic properties was relatively insensitive to specific crystal orientation (i.e., a uniform distribution in properties was observed for all random crystals tested), the indentation-induced fracture properties appear to be much more sensitive to tip-crystal orientation, and an unloading slope analysis is used to demonstrate the need for further refinement in relating toughness to orientation in these materials with relatively complex slip systems and crystal structures. View Full-Text« less

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.

Processing-microstructure relationships in thermotropic liquid crystalline polymers: Experimental and numerical modeling studies

NASA Astrophysics Data System (ADS)

Fang, Jun

Thermotropic liquid crystalline polymers (TLCPs) are a class of promising engineering materials for high-demanding structural applications. Their excellent mechanical properties are highly correlated to the underlying molecular orientation states, which may be affected by complex flow fields during melt processing. Thus, understanding and eventually predicting how processing flows impact molecular orientation is a critical step towards rational design work in order to achieve favorable, balanced physical properties in finished products. This thesis aims to develop deeper understanding of orientation development in commercial TLCPs during processing by coordinating extensive experimental measurements with numerical computations. In situ measurements of orientation development of LCPs during processing are a focal point of this thesis. An x-ray capable injection molding apparatus is enhanced and utilized for time-resolved measurements of orientation development in multiple commercial TLCPs during injection molding. Ex situ wide angle x-ray scattering is also employed for more thorough characterization of molecular orientation distributions in molded plaques. Incompletely injection molded plaques ("short shots") are studied to gain further insights into the intermediate orientation states during mold filling. Finally, two surface orientation characterization techniques, near edge x-ray absorption fine structure (NEXAFS) and infrared attenuated total reflectance (FTIR-ATR) are combined to investigate the surface orientation distribution of injection molded plaques. Surface orientation states are found to be vastly different from their bulk counterparts due to different kinematics involved in mold filling. In general, complex distributions of orientation in molded plaques reflect the spatially varying competition between shear and extension during mold filling. To complement these experimental measurements, numerical calculations based on the Larson-Doi polydomain model are performed. The implementation of the Larson-Doi in complex processing flows is performed using a commercial process modeling software suite (MOLDFLOWRTM), exploiting a nearly exact analogy between the Larson-Doi model and a fiber orientation model that has been widely used in composites processing simulations. The modeling scheme is first verified by predicting many qualitative and quantitative features of molecular orientation distributions in isothermal extrusion-fed channel flows. In coordination with experiments, the model predictions are found to capture many qualitative features observed in injection molded plaques (including short shots). The final, stringent test of Larson-Doi model performance is prediction of in situ transient orientation data collected during mold filling. The model yields satisfactory results, though certain numerical approximations limit performance near the mold front.

Molecular dynamics simulations of the orientation properties of cytochrome c on the surface of single-walled carbon nanotubes.

PubMed

Zhang, Bing; Xu, Jia; Mo, Shu-Fan; Yao, Jian-Xi; Dai, Song-Yuan

2016-12-01

Electron transfer between cytochrome c (Cytc) and electrodes can be influenced greatly by the orientation of protein on the surface of the electrodes. In the present study, different initial orientations of Cytc on the surface of five types of single-walled carbon nanotubes (SWNTs), with different diameters and chirality, were constructed. Properties of the orientations of proteins on the surface of these tubes were first investigated through molecular dynamics simulations. It was shown that variations in SWNT diameter do not significantly affect the orientation; however, the chirality of the SWNTs is crucial to the orientation of the heme embedded in Cytc, and the orientation of the protein can consequently be influenced by the heme orientation. A new electron pathway between Cytc and SWNT, which hopefully benefits electron transfer efficiency, has also been proposed. This study promises to provide theoretical guidance for the rational design of bio-sensors or bio-fuel cells by using Cytc-decorated carbon nanotube electrodes.

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.

Storm orientation impacts on atmospheric river induced precipitation efficiency

NASA Astrophysics Data System (ADS)

Mehran, A.; Lettenmaier, D. P.

2016-12-01

Atmospheric Rivers (ARs) along the Pacific North coast are often associated with heavy winter precipitation and flooding. We analyze 35 years (1981 2016) of landfalling ARs over a transect along the U.S. West Coast consisting of four river basins from coastal Washington to Southern California (Chehalis, Russian, Santa Ana, and Santa Margarita Rivers) to assess the impact of storm orientation on precipitation rainout efficiency. We define precipitation rainout efficiency as the correlation coefficient between the net integrated vapor transport and precipitation rate. We use 6-hourly climate data from the Climate Forecast System Reanalysis (CFSR) for each of the landfalling ARs. We compute storm orientation from CFSR wind vectors (daily averaged over atmospheric levels between 1000 hPa and 300 hPa) associated with each AR event. We also compute integrated vapor transport (IVT) by multiplying precipitable water by the wind vector and compare with daily averaged precipitation averaged over the river basins, where daily precipitation is taken from Parameter-Elevation Relationships on Independent Slopes Model (PRISM) to evaluate the impact of storm orientation on rainfall efficiency. We calculate the local topographic orientation of each river basin (slope and aspect) from ArcGIS, which we related to storm orientation. To evaluate the impact of storm orientation on rainout efficiency over the Russian River basin (Northern California), we first calculated approaching IVT (for all of AR induced precipitations from 1981 to 2016) and daily averaged precipitation rate. Next, we calculated the correlation coefficient between IVT and precipitation rate (for all AR induced rainouts over the Russian River basin). Finally, by considering the local topographical changes (slope and aspect from ArcGIS) and integrating them into an effective IVT, we compared the correlation coefficients between actual and effective IVT and basin-average precipitation. We find that over the Russian River basin, the rainout efficiency increases from 55 to 75 % when we account for storm orientation relative to topography.

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.

Molecular Packing of High-Mobility Diketo Pyrrolo-Pyrrole Polymer Semiconductors with Branched Alkyl Side Chains

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

X Zhang; L Richter; D DeLongchamp

We describe a series of highly soluble diketo pyrrolo-pyrrole (DPP)-bithiophene copolymers exhibiting field effect hole mobilities up to 0.74 cm{sup 2} V{sup -1} s{sup -1}, with a common synthetic motif of bulky 2-octyldodecyl side groups on the conjugated backbone. Spectroscopy, diffraction, and microscopy measurements reveal a transition in molecular packing behavior from a preferentially edge-on orientation of the conjugated plane to a preferentially face-on orientation as the attachment density of the side chains increases. Thermal annealing generally reduces both the face-on population and the misoriented edge-on domains. The highest hole mobilities of this series were obtained from edge-on molecular packingmore » and in-plane liquid-crystalline texture, but films with a bimodal orientation distribution and no discernible in-plane texture exhibited surprisingly comparable mobilities. The high hole mobility may therefore arise from the molecular packing feature common to the entire polymer series: backbones that are strictly oriented parallel to the substrate plane and coplanar with other backbones in the same layer.« less

Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.

PubMed

Vorobjev, Y N; Almagro, J C; Hermans, J

1998-09-01

A new method for calculating the total conformational free energy of proteins in water solvent is presented. The method consists of a relatively brief simulation by molecular dynamics with explicit solvent (ES) molecules to produce a set of microstates of the macroscopic conformation. Conformational energy and entropy are obtained from the simulation, the latter in the quasi-harmonic approximation by analysis of the covariance matrix. The implicit solvent (IS) dielectric continuum model is used to calculate the average solvation free energy as the sum of the free energies of creating the solute-size hydrophobic cavity, of the van der Waals solute-solvent interactions, and of the polarization of water solvent by the solute's charges. The reliability of the solvation free energy depends on a number of factors: the details of arrangement of the protein's charges, especially those near the surface; the definition of the molecular surface; and the method chosen for solving the Poisson equation. Molecular dynamics simulation in explicit solvent relaxes the protein's conformation and allows polar surface groups to assume conformations compatible with interaction with solvent, while averaging of internal energy and solvation free energy tend to enhance the precision. Two recently developed methods--SIMS, for calculation of a smooth invariant molecular surface, and FAMBE, for solution of the Poisson equation via a fast adaptive multigrid boundary element--have been employed. The SIMS and FAMBE programs scale linearly with the number of atoms. SIMS is superior to Connolly's MS (molecular surface) program: it is faster, more accurate, and more stable, and it smooths singularities of the molecular surface. Solvation free energies calculated with these two programs do not depend on molecular position or orientation and are stable along a molecular dynamics trajectory. We have applied this method to calculate the conformational free energy of native and intentionally misfolded globular conformations of proteins (the EMBL set of deliberately misfolded proteins) and have obtained good discrimination in favor of the native conformations in all instances.

A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer.

PubMed

Tieleman, D P; Berendsen, H J

1998-06-01

In this paper we study the properties of pores formed by OmpF porin from Escherichia coli, based on a molecular dynamics simulation of the OmpF trimer, 318 palmitoyl-oleoyl-phosphatidylethanolamine lipids, 27 Na+ ions, and 12,992 water molecules. After equilibration and a nanosecond production run, the OmpF trimer exhibits a C-alpha root mean square deviation from the crystal structure of 0.23 nm and a stable secondary structure. No evidence is found for large-scale motions of the L3 loop. We investigate the pore dimensions, conductance, and the properties of water inside the pore. This water forms a complicated pattern, even when averaged over 1 ns of simulation time. Around the pore constriction zone the water dipoles are highly structured in the plane of the membrane, oriented by the strong transversal electric field. In addition, there is a net orientation along the pore axis pointing from the extracellular to the intracellular side of the bilayer. The diffusion coefficients of water inside the pore are greatly reduced compared to bulk. We compare our results to results from model pores (Breed et al., 1996. Biophys. J. 70:1 643-1 661; Sansom et al. 1997. Biophys. J. 73:2404-241 5) and discuss implications for further theoretical work.

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

Theoretical study of the transfer integral and density of states in spiro-linked triphenylamine derivatives.

PubMed

Kirkpatrick, James; Nelson, Jenny

2005-08-22

We present a method for calculating the parameters that control hopping transport in disordered molecular solids, i.e., the transfer integrals and the distribution of transport site energies. Average values of these parameters are obtained by performing quantum-chemical calculations on a large ensemble of bimolecular complexes in random relative orientations. The method is applied to triphenylamine (TPA) and three differently substituted spiro-linked phenylamine compounds, 2,2',7,7'-tetrakis-(N,N-di-4-methoxyphenylamino)-9,9'-spirobifluorene (spiro-MeOTAD), 2,2'7,7'-tetrakis-(N,N-diphenylhenylamino)-9,9'-spirobifluorene (spiro-TAD), and 2,2',7,7'-tetrakis-(N,N-di-m-methylphenylamino)-9,9'-spirobifluorene (spiro-m-TTB). In the case of TPA, the dependence of the root-mean-square hole transfer integral J on intermolecular separation r for the ensemble of relative orientations is compared with that obtained by performing the same calculations for a fixed, approximately cofacial, orientation of the two TPA molecules. The calculation for the disordered geometry predicts a larger localization radius r0, where J approximately exp(-r/r0), than the calculation for the fixed orientation and is in better agreement with experiment. In the case of the spiro-linked compounds, results from our method are compared with parameters extracted from time-of-flight mobility measurements analyzed with the Gaussian disorder model (GDM). We find that the highest occupied molecular-orbital (HOMO) energies of the bimolecular complexes are distributed on an asymmetric peak, whose width varies in qualitative agreement with the value of the energetic disorder sigma obtained from experimental data using the GDM. The mean-square hole transfer integral varies in accordance with the experimentally determined value of the mobility prefactor micro0. The differences between the differently substituted compounds are interpreted in terms of differences in the spatial extent of the wave function. Spiro-MeOTAD was found to have a greater localization radius, which leads to both a larger transfer integral and a broader distribution of HOMO energies than either of the other compounds. For these compounds, differences in energetic disorder could not be explained in terms of differences in the permanent dipole moment. Our method is proposed as an approximate means of predicting the effect of chemical structure on the values of transport parameters in disordered molecular films.

Prenatal Influences on Human Sexual Orientation: Expectations versus Data.

PubMed

Breedlove, S Marc

2017-08-01

In non-human vertebrate species, sexual differentiation of the brain is primarily driven by androgens such as testosterone organizing the brains of males in a masculine fashion early in life, while the lower levels of androgen in developing females organize their brains in a feminine fashion. These principles may be relevant to the development of sexual orientation in humans, because retrospective markers of prenatal androgen exposure, namely digit ratios and otoacoustic emissions, indicate that lesbians, on average, were exposed to greater prenatal androgen than were straight women. Thus, the even greater levels of prenatal androgen exposure experienced by fetal males may explain why the vast majority of them grow up to be attracted to women. However, the same markers indicate no significant differences between gay and straight men in terms of average prenatal androgen exposure, so the variance in orientation in men cannot be accounted for by variance in prenatal androgen exposure, but may be due to variance in response to prenatal androgens. These data contradict several popular notions about human sexual orientation. Sexual orientation in women is said to be fluid, sometimes implying that only social influences in adulthood are at work, yet the data indicate prenatal influences matter as well. Gay men are widely perceived as under-masculinized, yet the data indicate they are exposed to as much prenatal androgen as straight men. There is growing sentiment to reject "binary" conceptions of human sexual orientations, to emphasize instead a spectrum of orientations. Yet the data indicate that human sexual orientation is sufficiently polarized that groups of lesbians, on average, show evidence of greater prenatal androgen exposure than groups of straight women, while groups of gay men have, on average, a greater proportion of brothers among their older siblings than do straight men.

Spherical tensor analysis of polar liquid crystals with biaxial and chiral molecules

NASA Astrophysics Data System (ADS)

Iwamoto, Mitsumasa; Zhong-can, Ou-Yang

2012-11-01

With the help of spherical tensor expression, an irreducible calculus of a Lth-rank macroscopic susceptibility χ for a polar liquid crystal (PLC) of biaxial and chiral molecules written as the average of molecular hyperpolarizability tensor β associated with their spherical orientational order parameters (0⩽l⩽L) is presented. Comprehensive formulas of L=1,2 have been obtained and the latter explains the optical activity and spontaneous splay texture observed in bent-core PLC. The expression of L=3 specifies for the molecules with D2 symmetry which can be applied to analyze the nonlinear optical second harmonic generation (SHG) observed in proteins, peptides, and double-stranded DNA at interfaces.

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.

Material for "Substrate temperature controls molecular orientation in two-component vapor- deposited glasses." Soft Matter, 2016, 12, 3265.

DOE Data Explorer

Jiang, Jing [Nanjing University; Walters, Diane M [University of Wisconsin-Madison; Zhou, Dongshan [Nanjing University; Ediger, Mark D [University of Wisconsin-Madison

2016-08-18

Data set for work presented in Jiang, J.; Walters, D. M.; Zhou, D.; Ediger, M. D. “Substrate Temperature Controls Molecular Orientation in Two -Component Vapor-deposited Glasses.” Soft Matt. 2016, 12, 3265. Includes all data presented in the manuscript as well as example raw data and analysis.

The Effect of Molecular Orientation to Solid-Solid and Melting Transitions

NASA Astrophysics Data System (ADS)

Yazici, Mustafa; Özgan, Şükrü

The thermodynamics of solid-solid and solid-liquid transitions are investigated with an account of the number of molecular orientation. The variations of the positional and orientational orders with the reduced temperature are studied. It is found out that orientational order parameter is very sensitive to the number of allowed orientation. The reduced transition temperatures, volume changes and entropy changes of the phase transitions and theoretical phase diagrams are obtained. The entropy changes of melting transitions for different numbers of allowed orientation of the present model are compared with the theoretical results and some experimental data. The quantitative predictions of the model are compared with experimental results for plastic crystals and agreement between predictions of the model and the experimental results are approximately good. Also, different numbers of allowed orientation D correspond to different experimental results HI, HBr, H2S for D = 2; HBr, CCl4, HI for D = 4; C2H12 for D = 6; CH4, PH3 for D = 20.

A device-oriented optimizer for solving ground state problems on an approximate quantum computer, Part II: Experiments for interacting spin and molecular systems

NASA Astrophysics Data System (ADS)

Kandala, Abhinav; Mezzacapo, Antonio; Temme, Kristan; Bravyi, Sergey; Takita, Maika; Chavez-Garcia, Jose; Córcoles, Antonio; Smolin, John; Chow, Jerry; Gambetta, Jay

Hybrid quantum-classical algorithms can be used to find variational solutions to generic quantum problems. Here, we present an experimental implementation of a device-oriented optimizer that uses superconducting quantum hardware. The experiment relies on feedback between the quantum device and classical optimization software which is robust to measurement noise. Our device-oriented approach uses naturally available interactions for the preparation of trial states. We demonstrate the application of this technique for solving interacting spin and molecular structure problems.

Functional imaging of skeletal muscle fiber in different physiological states by second harmonic generation

NASA Astrophysics Data System (ADS)

Nucciotti, V.; Stringari, C.; Sacconi, L.; Vanzi, F.; Tesi, C.; Piroddi, N.; Poggesi, C.; Castiglioni, C.; Milani, A.; Linari, M.; Piazzesi, G.; Lombardi, V.; Pavone, F. S.

2007-07-01

The intrinsically ordered arrays of proteins in skeletal muscle allows imaging of this tissue by Second Harmonic Generation (SHG). Biochemical and colocalization studies have gathered an increasing wealth of clues for the attribution of the molecular origin of the muscle SHG signal to the motor protein myosin. Thus, SHG represents a potentially very powerful tool in the investigation of structural dynamics occurring in muscle during active production of force. A full characterization of the polarization-dependence of the SHG signal represents a very selective information on the orientation of the emitting proteins and their dynamics during contraction, provided that different physiological states of muscle (relaxed, rigor and active) exhibit distinct patterns of SHG polarization dependence. Here polarization data are obtained from single frog muscle fibers at rest and during isometric contraction and interpreted, by means of a model, in terms of an average orientation of the SHG emitters which are structured with a cylindrical symmetry about the fiber axis. Optimizing the setup for accurate polarization measurements with SHG, we developed a line scan imaging method allowing measurement of SHG polarization curves in different physiological states. We demonstrate that muscle fiber displays a measurable variation of the orientation of SHG emitters with the transition from rest to isometric contraction.

Study of skeletal muscle cross-bridge population dynamics by second harmonic generation

NASA Astrophysics Data System (ADS)

Nucciotti, V.; Stringari, C.; Sacconi, L.; Vanzi, F.; Tesi, C.; Pirrodi, N.; Poggesi, C.; Castiglioni, C.; Milani, A.; Linari, M.; Piazzesi, G.; Lombardi, V.; Pavone, F. S.

2007-02-01

The high degree of structural order in skeletal muscle allows imaging of this tissue by Second Harmonic Generation (SHG). Biochemical and colocalization studies have gathered an increasing wealth of clues for the attribution of the molecular origin of the muscle SHG signal to the motor protein myosin. Thus, SHG represents a potentially very powerful tool in the investigation of structural dynamics occurring in muscle during active production of force and/or shortening. A full characterization of the polarization-dependence of the SHG signal represents a very selective information on the orientation of the emitting proteins and their dynamics during contraction, provided that different physiological states of muscle (relaxed, rigor and active) exhibit distinct patterns of SHG polarization dependence. Here polarization data are obtained from single frog muscle fibers at rest and during isometric contraction and interpreted, by means of a model, in terms of an average orientation of the SHG emitters which are structured with a cylindrical symmetry about the fiber axis. The setup is optimized for accurate polarization measurements with SHG, combined with a line scan imaging method allowing acquisition of SHG polarization curves in different physiological states. We demonstrate that muscle fiber displays a measurable variation of the orientation of SHG emitters with the transition from rest to isometric contraction.

Mapping molecular orientational distributions for biological sample in 3D (Conference Presentation)

NASA Astrophysics Data System (ADS)

HE, Wei; Ferrand, Patrick; Richter, Benjamin; Bastmeyer, Martin; Brasselet, Sophie

2016-04-01

Measuring molecular orientation properties is very appealing for scientists in molecular and cell biology, as well as biomedical research. Orientational organization at the molecular scale is indeed an important brick to cells and tissues morphology, mechanics, functions and pathologies. Recent work has shown that polarized fluorescence imaging, based on excitation polarization tuning in the sample plane, is able to probe molecular orientational order in biological samples; however this applies only to information in 2D, projected in the sample plane. To surpass this limitation, we extended this approach to excitation polarization tuning in 3D. The principle is based on the decomposition of any arbitrary 3D linear excitation in a polarization along the longitudinal z-axis, and a polarization in the transverse xy-sample plane. We designed an interferometer with one arm generating radial polarization light (thus producing longitudinal polarization under high numerical aperture focusing), the other arm controlling a linear polarization in the transverse plane. The amplitude ratio between the two arms can vary so as to get any linear polarized excitation in 3D at the focus of a high NA objective. This technique has been characterized by polarimetry imaging at the back focal plane of the focusing objective, and modeled theoretically. 3D polarized fluorescence microscopy is demonstrated on actin stress fibers in non-flat cells suspended on synthetic polymer structures forming supporting pillars, for which heterogeneous actin orientational order could be identified. This technique shows a great potential in structural investigations in 3D biological systems, such as cell spheroids and tissues.

Absolute Molecular Orientation of Isopropanol at Ceria (100) Surfaces: Insight into Catalytic Selectivity from the Interfacial Structure

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

Doughty, Benjamin; Goverapet Srinivasan, Sriram; Bryantsev, Vyacheslav S.

The initial mechanistic steps underlying heterogeneous chemical catalysis can be described in a framework where the composition, structure, and orientation of molecules adsorbed to reactive interfaces are known. However, extracting this vital information is the limiting step in most cases due in part to challenges in probing the interfacial monolayer with enough chemical specificity to characterize the surface molecular constituents. These challenges are exacerbated at complex or spatially heterogeneous interfaces where competing processes and a distribution of local environments can uniquely drive chemistry. To address these limitations, this work presents a distinctive combination of materials synthesis, surface specific optical experiments,more » and theory to probe and understand molecular structure at catalytic interfaces. Specifically, isopropanol was adsorbed to surfaces of the model CeO 2 catalyst that were synthesized with only the (100) facet exposed. Vibrational sum-frequency generation was used to probe the molecular monolayer, and with the guidance of density functional theory calculations, was used to extract the structure and absolute molecular orientation of isopropanol at the CeO 2 (100) surface. Our results show that isopropanol is readily deprotonated at the surface, and through the measured absolute molecular orientation of isopropanol, we obtain new insight into the selectivity of the (100) surface to form propylene. Our findings reveal key insight into the chemical and physical phenomena taking place at pristine interfaces thereby pointing to intuitive structural arguments to describe catalytic selectivity in more complex systems.« less

Absolute Molecular Orientation of Isopropanol at Ceria (100) Surfaces: Insight into Catalytic Selectivity from the Interfacial Structure

DOE PAGES

Doughty, Benjamin; Goverapet Srinivasan, Sriram; Bryantsev, Vyacheslav S.; ...

2017-06-12

The initial mechanistic steps underlying heterogeneous chemical catalysis can be described in a framework where the composition, structure, and orientation of molecules adsorbed to reactive interfaces are known. However, extracting this vital information is the limiting step in most cases due in part to challenges in probing the interfacial monolayer with enough chemical specificity to characterize the surface molecular constituents. These challenges are exacerbated at complex or spatially heterogeneous interfaces where competing processes and a distribution of local environments can uniquely drive chemistry. To address these limitations, this work presents a distinctive combination of materials synthesis, surface specific optical experiments,more » and theory to probe and understand molecular structure at catalytic interfaces. Specifically, isopropanol was adsorbed to surfaces of the model CeO 2 catalyst that were synthesized with only the (100) facet exposed. Vibrational sum-frequency generation was used to probe the molecular monolayer, and with the guidance of density functional theory calculations, was used to extract the structure and absolute molecular orientation of isopropanol at the CeO 2 (100) surface. Our results show that isopropanol is readily deprotonated at the surface, and through the measured absolute molecular orientation of isopropanol, we obtain new insight into the selectivity of the (100) surface to form propylene. Our findings reveal key insight into the chemical and physical phenomena taking place at pristine interfaces thereby pointing to intuitive structural arguments to describe catalytic selectivity in more complex systems.« less

Chemical synthesis of oriented ferromagnetic LaSr-2 × 4 manganese oxide molecular sieve nanowires

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

Carretero-Genevrier, Adrián; Gazquez, Jaume; Magen, Cesar

2012-04-25

Here we report a chemical solution based method using nanoporous track-etched polymer templates for producing long and oriented LaSr-2 × 4 manganese oxide molecular sieve nanowires. Scanning transmission electron microscopy and electron energy loss spectroscopy analyses show that the nanowires are ferromagnetic at room temperature, single crystalline, epitaxially grown and self-aligned.

Molecular insight into the electrostatic membrane surface potential by 14n/31p MAS NMR spectroscopy: nociceptin-lipid association.

PubMed

Lindström, Fredrick; Williamson, Philip T F; Gröbner, Gerhard

2005-05-11

Exploiting naturally abundant (14)N and (31)P nuclei by high-resolution MAS NMR (magic angle spinning nuclear magnetic resonance) provides a molecular view of the electrostatic potential present at the surface of biological model membranes, the electrostatic charge distribution across the membrane interface, and changes that occur upon peptide association. The spectral resolution in (31)P and (14)N MAS NMR spectra is sufficient to probe directly the negatively charged phosphate and positively charged choline segment of the electrostatic P(-)-O-CH(2)-CH(2)-N(+)(CH(3))(3) headgroup dipole of zwitterionic DMPC (dimyristoylphosphatidylcholine) in mixed-lipid systems. The isotropic shifts report on the size of the potential existing at the phosphate and ammonium group within the lipid headgroup while the chemical shielding anisotropy ((31)P) and anisotropic quadrupolar interaction ((14)N) characterize changes in headgroup orientation in response to surface potential. The (31)P/(14)N isotropic chemical shifts for DMPC show opposing systematic changes in response to changing membrane potential, reflecting the size of the electrostatic potential at opposing ends of the P(-)-N(+) dipole. The orientational response of the DMPC lipid headgroup to electrostatic surface variations is visible in the anisotropic features of (14)N and (31)P NMR spectra. These features are analyzed in terms of a modified "molecular voltmeter" model, with changes in dynamic averaging reflecting the tilt of the C(beta)-N(+)(CH)(3) choline and PO(4)(-) segment. These properties have been exploited to characterize the changes in surface potential upon the binding of nociceptin to negatively charged membranes, a process assumed to proceed its agonistic binding to its opoid G-protein coupled receptor.

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.

Heliconical smectic phases formed by achiral molecules

DOE PAGES

Abberley, Jordan P.; Killah, Ross; Walker, Rebecca; ...

2018-01-15

Chiral symmetry breaking in soft matter is a hot topic of current research. Recently, such a phenomenon was found in a fluidic phase showing orientational order of molecules - the nematic phase; although built of achiral molecules, the phase can exhibit structural chirality - average molecular direction follows a short-pitch helix. Here in this paper, we report a series of achiral asymmetric dimers with an odd number of atoms in the spacer, which form twisted structures in nematic as well as in lamellar phases. The tight pitch heliconical nematic (N TB) phase and heliconical tilted smectic C (SmC TB) phasemore » are formed. The formation of a variety of helical structures is accompanied by a gradual freezing of molecular rotation. In the lowest temperature smectic phase, HexI, the twist is expressed through the formation of hierarchical structure: nanoscale helices and mesoscopic helical filaments. The short-pitch helical structure in the smectic phases is confirmed by resonant X-ray measurements.« less

Heliconical smectic phases formed by achiral molecules

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

Abberley, Jordan P.; Killah, Ross; Walker, Rebecca

Chiral symmetry breaking in soft matter is a hot topic of current research. Recently, such a phenomenon was found in a fluidic phase showing orientational order of molecules - the nematic phase; although built of achiral molecules, the phase can exhibit structural chirality - average molecular direction follows a short-pitch helix. Here in this paper, we report a series of achiral asymmetric dimers with an odd number of atoms in the spacer, which form twisted structures in nematic as well as in lamellar phases. The tight pitch heliconical nematic (N TB) phase and heliconical tilted smectic C (SmC TB) phasemore » are formed. The formation of a variety of helical structures is accompanied by a gradual freezing of molecular rotation. In the lowest temperature smectic phase, HexI, the twist is expressed through the formation of hierarchical structure: nanoscale helices and mesoscopic helical filaments. The short-pitch helical structure in the smectic phases is confirmed by resonant X-ray measurements.« less

Structure refinement of membrane proteins via molecular dynamics simulations.

PubMed

Dutagaci, Bercem; Heo, Lim; Feig, Michael

2018-07-01

A refinement protocol based on physics-based techniques established for water soluble proteins is tested for membrane protein structures. Initial structures were generated by homology modeling and sampled via molecular dynamics simulations in explicit lipid bilayer and aqueous solvent systems. Snapshots from the simulations were selected based on scoring with either knowledge-based or implicit membrane-based scoring functions and averaged to obtain refined models. The protocol resulted in consistent and significant refinement of the membrane protein structures similar to the performance of refinement methods for soluble proteins. Refinement success was similar between sampling in the presence of lipid bilayers and aqueous solvent but the presence of lipid bilayers may benefit the improvement of lipid-facing residues. Scoring with knowledge-based functions (DFIRE and RWplus) was found to be as good as scoring using implicit membrane-based scoring functions suggesting that differences in internal packing is more important than orientations relative to the membrane during the refinement of membrane protein homology models. © 2018 Wiley Periodicals, Inc.

Effects of substrate orientation on the growth of InSb nanostructures by molecular beam epitaxy

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

Chou, C. Y.; Torfi, A.; Pei, C.

2016-05-09

In this work, the effects of substrate orientation on InSb quantum structure growth by molecular beam epitaxy (MBE) are presented. Motivated by the observation that (411) evolves naturally as a stable facet during MBE crystal growth, comparison studies have been carried out to investigate the effects of the crystal orientation of the underlying GaSb substrate on the growth of InSb by MBE. By depositing InSb on a number of different substrate orientations, namely: (100), (311), (411), and (511), a higher nanostructure density was observed on the (411) surface compared with the other orientations. This result suggests that the (411) orientationmore » presents a superior surface in MBE growth to develop a super-flat GaSb buffer surface, naturally favorable for nanostructure growth.« less

Fabrication of field-effect transistor utilizing oriented thin film of octahexyl-substituted phthalocyanine and its electrical anisotropy based on columnar structure

NASA Astrophysics Data System (ADS)

Ohmori, Masashi; Nakatani, Mitsuhiro; Kajii, Hirotake; Miyamoto, Ayano; Yoneya, Makoto; Fujii, Akihiko; Ozaki, Masanori

2018-03-01

Field-effect transistors with molecularly oriented thin films of metal-free non-peripherally octahexyl-substituted phthalocyanine (C6PcH2), which characteristically form a columnar structure, have been fabricated, and the electrical anisotropy of C6PcH2 has been investigated. The molecularly oriented thin films of C6PcH2 were prepared by the bar-coating technique, and the uniform orientation in a large area and the surface roughness at a molecular level were observed by polarized spectroscopy and atomic force microscopy, respectively. The field effect mobilities parallel and perpendicular to the column axis of C6PcH2 were estimated to be (1.54 ± 0.24) × 10-2 and (2.10 ± 0.23) × 10-3 cm2 V-1 s-1, respectively. The electrical anisotropy based on the columnar structure has been discussed by taking the simulated results obtained by density functional theory calculation into consideration.

Molecular ordering and molecular dynamics in isotactic-polypropylene characterized by solid state NMR.

PubMed

Miyoshi, Toshikazu; Mamun, Al; Hu, Wei

2010-01-14

The order-disorder phenomenon of local packing structures, space heterogeneity, and molecular dynamics and average lamellar thickness, , of the alpha form of isotactic polypropylene (iPP) crystallized at various supercooling temperatures, DeltaT, are investigated by solid-state (SS) NMR and SAXS, respectively. increases with lowering DeltaT, and extrapolations of (-1) versus averaged melting point, , gives an equilibrium melting temperature, T(m)(0) = 457 +/- 4 K. High-power TPPM decoupling with a field strength of 110 kHz extremely improves (13)C high-resolution SS-NMR spectral resolution of the ordered crystalline signals at various DeltaT. A high-resolution (13)C SS-NMR spectrum combined with a conventional spin-lattice relaxation time in the rotating frame (T(1rhoH)) filter easily accesses an order-disorder phenomenon for upward and downward orientations of stems and their packing in the crystalline region. It is found that ordered packing fraction, f(order), increases with lowering DeltaT and reaches a maximum value of 62% at DeltaT = 34 K. The ordering phenomenon of stem packing indicates that chain-folding direction changes from random in the disordered packing to order in the ordered packing along the a sin theta axis under a hypothesis of adjacent re-entry structures. It is also found that f(order) significantly increases prior to enhancement of lamellar thickness. Additionally, annealing experiments indicate that is significantly enhanced after a simultaneous process of partial melting and recrystallization/reorganization into the ordered packing at annealing temperature >/=423 K. Furthermore, the center-bands only detection of exchange (CODEX) NMR method demonstrates that time-kinetic parameters of helical jump motions are highly influenced by DeltaT. These dynamic constraints are interpreted in terms of increment of and packing ordering. Through these new results related to molecular structures and dynamics, roles of polymer chain trajectory and molecular dynamics for the lamellar thickening process are discussed.

A Mixed-Methods Study Investigating the Relationship between Media Multitasking Orientation and Grade Point Average

ERIC Educational Resources Information Center

Lee, Jennifer

2012-01-01

The intent of this study was to examine the relationship between media multitasking orientation and grade point average. The study utilized a mixed-methods approach to investigate the research questions. In the quantitative section of the study, the primary method of statistical analyses was multiple regression. The independent variables for the…

Structure and orientation of interfacial proteins determined by sum frequency generation vibrational spectroscopy: method and application.

PubMed

Ye, Shuji; Wei, Feng; Li, Hongchun; Tian, Kangzhen; Luo, Yi

2013-01-01

In situ and real-time characterization of molecular structures and orientation of proteins at interfaces is essential to understand the nature of interfacial protein interaction. Such work will undoubtedly provide important clues to control biointerface in a desired manner. Sum frequency generation vibrational spectroscopy (SFG-VS) has been demonstrated to be a powerful technique to study the interfacial structures and interactions at the molecular level. This paper first systematically introduced the methods for the calculation of the Raman polarizability tensor, infrared transition dipole moment, and SFG molecular hyperpolarizability tensor elements of proteins/peptides with the secondary structures of α-helix, 310-helix, antiparallel β-sheet, and parallel β-sheet, as well as the methodology to determine the orientation of interfacial protein secondary structures using SFG amide I spectra. After that, recent progresses on the determination of protein structure and orientation at different interfaces by SFG-VS were then reviewed, which provides a molecular-level understanding of the structures and interactions of interfacial proteins, specially understanding the nature of driving force behind such interactions. Although this review has focused on analysis of amide I spectra, it will be expected to offer a basic idea for the spectral analysis of amide III SFG signals and other complicated molecular systems such as RNA and DNA. Copyright © 2013 Elsevier Inc. All rights reserved.

Photovoltaic performance of block copolymer devices is independent of the crystalline texture in the active layer

DOE PAGES

Guo, Changhe; Lee, Youngmin; Lin, Yen -Hao; ...

2016-06-15

The electronic properties of organic semiconductors are strongly influenced by intermolecular packing. When cast as thin films, crystalline π-conjugated molecules are strongly textured, potentially leading to anisotropic charge transport. Consequently, it is hypothesized that the orientation of crystallites in the active layer plays an important role in charge extraction and organic photovoltaic device performance. Here we demonstrate orientation control of molecular packing from mostly face-on to edge-on configurations in the active layer of P3HT- b-PFTBT block copolymer photovoltaics using 1-chloronaphthalene as a solvent additive. The effect of molecular orientations in P3HT crystals on charge transport and solar cell performance ismore » examined. We find that optimized photovoltaic device performance is independent of the crystalline texture of P3HT. Our observations provide further insights into the molecular organization required for efficient charge transport and overall device efficiencies. That is, the dominant crystal orientation, whether face-on or edge-on, is not critical to organic solar cells. Furthermore, a broad distribution of crystallite orientations ensures pathways for charge transport in any direction and enables efficient charge extraction in photovoltaic devices.« less

Infrared study on the molecular orientation in bulk-heterojunction films based on perylene and 3,4,9,10-perylenetetracarboxylic dianhydride

NASA Astrophysics Data System (ADS)

Seto, Keisuke; Pham, John; Furukawa, Yukio

2012-03-01

Solid-state structures of thin blend films of perylene and 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) formed on the Au surface have been studied by a combination of infrared reflection-absorption spectroscopy and the RATIO method of Debe. In the blend films, PTCDA molecules take the face-on orientation in the whole range of PTCDA contents from 7.5 to 88 mol%. On the other hand, the molecular orientation of perylene molecules changes from edge-on toward random as the PTCDA content increases.

Room temperature structures and odd even behaviour of a homologous series of anhydrous lithium n-alkanoates

NASA Astrophysics Data System (ADS)

White, Nicole A. S.; Ellis, Henry A.

2008-10-01

The molecular structures of a homologous series of lithium n-alkanoates have been determined at room temperature using infrared spectroscopy, polarizing light microscopy and X-ray powder diffraction in conjunction with density and melting point measurements. For all the compounds investigated, asymmetric ionic metal-carboxylate coordination is proposed, with the molecules located within a triclinic crystal system with P1¯ space group. The molecules are nearly all of similar structure and are arranged within lamellar layers with four molecules per unit cell. The hydrocarbon chains, in nearly all trans conformation, are arranged tail-to-tail and tilted at an average angle of 55 ο to the planes containing lithium ions. The unit cell parameters such as sides: b and c increase linearly with increasing chain length whilst side a shows a linear decrease. Furthermore, the measured densities and melting points show odd-even behaviour, suggesting differences in molecular packing between odd and even chain length homologues. Geometric models are proposed to explain molecular orientation within a lamella and odd-even behaviour, involving the influence of terminal groups on the packing geometry of hydrocarbon chains within the lattice.

A Structural Model for the Single-Stranded DNA Genome of Filamentous Bacteriophage Pf1†

PubMed Central

Tsuboi, Masamichi; Tsunoda, Masaru; Overman, Stacy A.; Benevides, James M.; Thomas, George J.

2010-01-01

The filamentous bacteriophage Pf1, which infects strain PAK of Pseudomonas aeruginosa, is a flexible filament (~2000 × 6.5 nm) consisting of a covalently closed DNA loop of 7349 nucleotides sheathed by 7350 copies of a 46-residue α-helical subunit. The subunit α-helices, which are inclined at a small average angle (~16°) from the virion axis, are arranged compactly around the DNA core. Orientations of the Pf1 DNA nucleotides with respect to the filament axis are not known. In this work we report and interpret the polarized Raman spectra of oriented Pf1 filaments. We demonstrate that the polarizations of DNA Raman band intensities establish that the nucleotide bases of packaged Pf1 DNA are well ordered within the virion and that the base planes are positioned close to parallel to the filament axis. The present results are combined with a previously proposed projection of the intraviral path of Pf1 DNA (1) to develop a novel molecular model for the Pf1 assembly. PMID:20078135

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

Angular-dependent EDMR linewidth for spin-dependent space charge limited conduction in a polycrystalline pentacene

NASA Astrophysics Data System (ADS)

Fukuda, Kunito; Asakawa, Naoki

2017-08-01

Spin-dependent space charge limited carrier conduction in a Schottky barrier diode using polycrystalline p-type π-conjugated molecular pentacene is explored using multiple-frequency electrically detected magnetic resonance (EDMR) spectroscopy with a variable-angle configuration. The measured EDMR spectra are decomposed into two components derived respectively from mobile and trapped positive polarons. The linewidth of the EDMR signal for the trapped polarons increases with increasing resonance magnetic field for an in-plane configuration where the normal vector of the device substrate is perpendicular to the resonance magnetic field, while it is independent of the field for an out-of-plane configuration. This difference is consistent with the pentacene arrangement on the device substrate, where pentacene molecules exhibit a uniaxial orientation on the out-of-substrate plane. By contrast, the mobile polarons do not show anisotropic behavior with respect to the resonance magnetic field, indicating that the anisotropic effect is averaged out owing to carrier motion. These results suggest that the orientational arrangements of polycrystalline pentacene molecules in a nano thin film play a crucial role in spin-dependent electrical conduction.

Orientation distribution and process modeling of thermotropic liquid crystalline copolyester (TLCP) injection-moldings

NASA Astrophysics Data System (ADS)

Bubeck, Robert; Fang, Jun; Burghardt, Wesley; Burgard, Susan; Fischer, Daniel

2009-03-01

The influence of melt processing conditions upon mechanical properties and degrees of compound molecular orientation have been thoroughly studied for a series of well-defined injection molded samples fabricated from VECTRA (TM) A950 and 4,4'-dihydroxy-a-methylstilbene TLCPs. Fracture and tensile data were correlated with processing conditions, orientation, and molecular weight. Mechanical properties for both TLCPs were found to follow a ``universal'' Anisotropy Factor (AF) associated with the bimodal orientation states in the plaques determined from 2-D WAXS. Surface orientations were globally surveyed using Attenuated Total Reflectance -- Fourier Transform Infrared (ATR-FTIR) spectroscopy and C K edge Near-Edge X-ray Absorption Fine Structure (NEXAFS). The results derived from the two spectroscopy techniques confirmed each other well. These results along with those from 2-D WAXS in transmission were compared with the results of process modeling using a commercial program, MOLDFLOW(TM). The agreement between model predictions and the measured orientation states was gratifyingly good.

Interfacial Structures of Trihexyltetradecylphosphonium-bis(mandelato)borate Ionic Liquid Confined between Gold Electrodes.

PubMed

Wang, Yong-Lei; Golets, Mikhail; Li, Bin; Sarman, Sten; Laaksonen, Aatto

2017-02-08

Atomistic molecular dynamics simulations have been performed to study microscopic the interfacial ionic structures, molecular arrangements, and orientational preferences of trihexyltetradecylphosphonium-bis(mandelato)borate ([P 6,6,6,14 ][BMB]) ionic liquid confined between neutral and charged gold electrodes. It was found that both [P 6,6,6,14 ] cations and [BMB] anions are coabsorbed onto neutral electrodes at different temperatures. The hexyl and tetradecyl chains in [P 6,6,6,14 ] cations lie preferentially flat on neutral electrodes. The oxalato and phenyl rings in [BMB] anions are characterized by alternative parallel-perpendicular orientations in the mixed innermost ionic layer adjacent to neutral electrodes. An increase in temperature has a marginal effect on the interfacial ionic structures and molecular orientations of [P 6,6,6,14 ][BMB] ionic species in a confined environment. Electrifying gold electrodes leads to peculiar changes in the interfacial ionic structures and molecular orientational arrangements of [P 6,6,6,14 ] cations and [BMB] anions in negatively and positively charged gold electrodes, respectively. As surface charge density increases (but lower than 20 μC/cm 2 ), the layer thickness of the mixed innermost interfacial layer gradually increases due to a consecutive accumulation of [P 6,6,6,14 ] cations and [BMB] anions at negatively and positively charged electrodes, respectively, before the formation of distinct cationic and anionic innermost layers. Meanwhile, the molecular orientations of two oxalato rings in the same [BMB] anions change gradually from a parallel-perpendicular feature to being partially characterized by a tilted arrangement at an angle of 45° from the electrodes and finally to a dominant parallel coordination pattern along positively charged electrodes. Distinctive interfacial distribution patterns are also observed accordingly for phenyl rings that are directly connected to neighboring oxalato rings in [BMB] anions.

Simple estimation of Förster Resonance Energy Transfer (FRET) orientation factor distribution in membranes.

PubMed

Loura, Luís M S

2012-11-19

Because of its acute sensitivity to distance in the nanometer scale, Förster resonance energy transfer (FRET) has found a large variety of applications in many fields of chemistry, physics, and biology. One important issue regarding the correct usage of FRET is its dependence on the donor-acceptor relative orientation, expressed as the orientation factor k(2). Different donor/acceptor conformations can lead to k(2) values in the 0 ≤ k(2) ≤ 4 range. Because the characteristic distance for FRET, R(0), is proportional to (k(2))1/6, uncertainties in the orientation factor are reflected in the quality of information that can be retrieved from a FRET experiment. In most cases, the average value of k(2) corresponding to the dynamic isotropic limit ( = 2/3) is used for computation of R(0) and hence donor-acceptor distances and acceptor concentrations. However, this can lead to significant error in unfavorable cases. This issue is more critical in membrane systems, because of their intrinsically anisotropic nature and their reduced fluidity in comparison to most common solvents. Here, a simple numerical simulation method for estimation of the probability density function of k(2) for membrane-embedded donor and acceptor fluorophores in the dynamic regime is presented. In the simplest form, the proposed procedure uses as input the most probable orientations of the donor and acceptor transition dipoles, obtained by experimental (including linear dichroism) or theoretical (such as molecular dynamics simulation) techniques. Optionally, information about the widths of the donor and/or acceptor angular distributions may be incorporated. The methodology is illustrated for special limiting cases and common membrane FRET pairs.

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

760 nm high-performance VCSEL growth and characterization

NASA Astrophysics Data System (ADS)

Rinaldi, Fernando; Ostermann, Johannes M.; Kroner, Andrea; Riedl, Michael C.; Michalzik, Rainer

2006-04-01

High-performance vertical-cavity surface-emitting lasers (VCSELs) with an emission wavelength of approximately 764 nm are demonstrated. This wavelength is very attractive for oxygen sensing. Low threshold currents, high optical output power, single-mode operation, and stable polarization are obtained. Using the surface relief technique and in particular the grating relief technique, we have increased the single-mode output power to more than 2.5mW averaged over a large device quantity. The laser structure was grown by molecular beam epitaxy (MBE) on GaAs (100)-oriented substrates. The devices are entirely based on the AlGaAs mixed compound semiconductor material system. The growth process, the investigations of the epitaxial material together with the device fabrication and characterization are discussed in detail.

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

Molecular orientation of copper phthalocyanine thin films on different monolayers of fullerene on SiO{sub 2} or highly oriented pyrolytic graphite

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

Wang, Chenggong; Wang, Congcong; Liu, Xiaoliang

2015-03-23

The interface electronic structures of copper phthalocyanine (CuPc) have been studied using ultraviolet photoemission spectroscopy as different monolayers of C{sub 60} were inserted between CuPc and a SiO{sub 2} or highly ordered pyrolytic graphite (HOPG) substrate. The results show that CuPc has standing up configuration with one monolayer of C{sub 60} insertion on SiO{sub 2} while lying down on HOPG, indicating that the insertion layer propagates the CuPc-substrate interaction. Meanwhile, CuPc on more than one monolayers of C{sub 60} on different substrates show that the substrate orientation effect quickly vanished. Our study elucidates intriguing molecular interactions that manipulate molecular orientationmore » and donor-acceptor energy level alignment.« less

Members Matter in Team Training: Multilevel and Longitudinal Relationships between Goal Orientation, Self-Regulation, and Team Outcomes

ERIC Educational Resources Information Center

Dierdorff, Erich C.; Ellington, J. Kemp

2012-01-01

Longitudinal data from 338 individuals across 64 teams in a simulation-based team-training context were used to examine the effects of dispositional goal orientation on self-regulated learning (self-efficacy and metacognition). Team goal orientation compositions, as reflected by average goal orientations of team members, were examined for…

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 mechanism of transforming diamond nanowires to carbon nanostructures.

PubMed

Sorkin, Anastassia; Su, Haibin

2014-01-24

The transformation of diamond nanowires (DNWs) with different diameters and geometries upon heating is investigated with density-functional-based tight-binding molecular dynamics. DNWs of {100} and {111} oriented cross-section with projected average line density between 7 and 20 atoms Å(-1) transform into carbon nanotubes (CNTs) under gradual heating up to 3500-4000 K. DNWs with projected average line density larger than 25 atoms Å(-1) transform into double-wall CNTs. The route of transformation into CNTs clearly exhibits three stages, with the intriguing intermediate structural motif of a carbon nanoscroll (CNS). Moreover, the morphology plays an important role in the transformation involving the CNS as one important intermediate motif to form CNTs. When starting with [Formula: see text] oriented DNWs with a square cross-section consisting of two {111} facets facing each other, one interesting structure with 'nano-bookshelf' shape emerges: a number of graphene 'shelves' located inside the CNT, bonding to the CNT walls with sp(3) hybridized atoms. The nano-bookshelf structures exist in a wide range of temperatures up to 3,000 K. The further transformation from nano-bookshelf structures depends on the strength of the joints connecting shelves with CNT walls. Notably, the nano-bookshelf structure can evolve into two end products: one is CNT via the CNS pathway, the other is graphene transformed directly from the nano-bookshelf structure at high temperature. This work sheds light on the microscopic insight of carbon nanostructure formation mechanisms with the featured motifs highlighted in the pathways.

Critical CuI buffer layer surface density for organic molecular crystal orientation change

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

Ahn, Kwangseok; Kim, Jong Beom; Lee, Dong Ryeol, E-mail: drlee@ssu.ac.kr

We have determined the critical surface density of the CuI buffer layer inserted to change the preferred orientation of copper phthalocyanine (CuPc) crystals grown on the buffer layer. X-ray reflectivity measurements were performed to obtain the density profiles of the buffer layers and out-of-plane and 2D grazing-incidence X-ray diffraction measurements were performed to determine the preferred orientations of the molecular crystals. Remarkably, it was found that the preferred orientation of the CuPc film is completely changed from edge-on (1 0 0) to face-on (1 1 −2) by a CuI buffer layer with a very low surface density, so low thatmore » a large proportion of the substrate surface is bare.« less

An excellent navigation system and experience in craniomaxillofacial navigation surgery: a double-center study

PubMed Central

Dai, Jiewen; Wu, Jinyang; Wang, Xudong; Yang, Xudong; Wu, Yunong; Xu, Bing; Shi, Jun; Yu, Hongbo; Cai, Min; Zhang, Wenbin; Zhang, Lei; Sun, Hao; Shen, Guofang; Zhang, Shilei

2016-01-01

Numerous problems regarding craniomaxillofacial navigation surgery are not well understood. In this study, we performed a double-center clinical study to quantitatively evaluate the characteristics of our navigation system and experience in craniomaxillofacial navigation surgery. Fifty-six patients with craniomaxillofacial disease were included and randomly divided into experimental (using our AccuNavi-A system) and control (using Strker system) groups to compare the surgical effects. The results revealed that the average pre-operative planning time was 32.32 mins vs 29.74 mins between the experimental and control group, respectively (p > 0.05). The average operative time was 295.61 mins vs 233.56 mins (p > 0.05). The point registration orientation accuracy was 0.83 mm vs 0.92 mm. The maximal average preoperative navigation orientation accuracy was 1.03 mm vs 1.17 mm. The maximal average persistent navigation orientation accuracy was 1.15 mm vs 0.09 mm. The maximal average navigation orientation accuracy after registration recovery was 1.15 mm vs 1.39 mm between the experimental and control group. All patients healed, and their function and profile improved. These findings demonstrate that although surgeons should consider the patients’ time and monetary costs, our qualified navigation surgery system and experience could offer an accurate guide during a variety of craniomaxillofacial surgeries. PMID:27305855

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.

Well-tempered metadynamics as a tool for characterizing multi-component, crystalline molecular machines.

PubMed

Ilott, Andrew J; Palucha, Sebastian; Hodgkinson, Paul; Wilson, Mark R

2013-10-10

The well-tempered, smoothly converging form of the metadynamics algorithm has been implemented in classical molecular dynamics simulations and used to obtain an estimate of the free energy surface explored by the molecular rotations in the plastic crystal, octafluoronaphthalene. The biased simulations explore the full energy surface extremely efficiently, more than 4 orders of magnitude faster than unbiased molecular dynamics runs. The metadynamics collective variables used have also been expanded to include the simultaneous orientations of three neighboring octafluoronaphthalene molecules. Analysis of the resultant three-dimensional free energy surface, which is sampled to a very high degree despite its significant complexity, demonstrates that there are strong correlations between the molecular orientations. Although this correlated motion is of limited applicability in terms of exploiting dynamical motion in octafluoronaphthalene, the approach used is extremely well suited to the investigation of the function of crystalline molecular machines.

Individual differences in ensemble perception reveal multiple, independent levels of ensemble representation.

PubMed

Haberman, Jason; Brady, Timothy F; Alvarez, George A

2015-04-01

Ensemble perception, including the ability to "see the average" from a group of items, operates in numerous feature domains (size, orientation, speed, facial expression, etc.). Although the ubiquity of ensemble representations is well established, the large-scale cognitive architecture of this process remains poorly defined. We address this using an individual differences approach. In a series of experiments, observers saw groups of objects and reported either a single item from the group or the average of the entire group. High-level ensemble representations (e.g., average facial expression) showed complete independence from low-level ensemble representations (e.g., average orientation). In contrast, low-level ensemble representations (e.g., orientation and color) were correlated with each other, but not with high-level ensemble representations (e.g., facial expression and person identity). These results suggest that there is not a single domain-general ensemble mechanism, and that the relationship among various ensemble representations depends on how proximal they are in representational space. (c) 2015 APA, all rights reserved).

Warts phosphorylates Mud to promote Pins-mediated mitotic spindle orientation in Drosophila independent of Yorkie

PubMed Central

Dewey, Evan B.; Sanchez, Desiree; Johnston, Christopher A.

2015-01-01

SUMMARY Multicellular animals have evolved conserved signaling pathways that translate cell polarity cues into mitotic spindle positioning to control the orientation of cell division within complex tissue structures. These oriented cell divisions are essential for the development of cell diversity and the maintenance of tissue homeostasis. Despite intense efforts, the molecular mechanisms that control spindle orientation remain incompletely defined. Here we describe a role for the Hippo (Hpo) kinase complex in promoting Partner of Inscuteable (Pins)-mediated spindle orientation. Knockdown of Hpo, Salvador (Sav), or Warts (Wts) each result in a partial loss of spindle orientation, a phenotype previously described following loss of the Pins-binding protein Mushroom body defect (Mud). Similar to orthologs spanning yeast to mammals, Wts kinase localizes to mitotic spindle poles, a prominent site of Mud localization. Wts directly phosphorylates Mud in vitro within its C-terminal coiled-coil domain. This Mud coiled-coil domain directly binds the adjacent Pins-binding domain to dampen the Pins/Mud interaction, and Wts-mediated phosphorylation uncouples this intramolecular Mud interaction. Loss of Wts prevents cortical Pins/Mud association without affecting Mud accumulation at spindle poles, suggesting phosphorylation acts as a molecular switch to specifically activate cortical Mud function. Finally, loss of Wts in Drosophila imaginal disc epithelial cells results in diminished cortical Mud and defective planar spindle orientation. Our results provide new insights into the molecular basis for dynamic regulation of the cortical Pins/Mud spindle positioning complex and highlight a novel link with an essential, evolutionarily-conserved cell proliferation pathway. PMID:26592339

Warts phosphorylates mud to promote pins-mediated mitotic spindle orientation in Drosophila, independent of Yorkie.

PubMed

Dewey, Evan B; Sanchez, Desiree; Johnston, Christopher A

2015-11-02

Multicellular animals have evolved conserved signaling pathways that translate cell polarity cues into mitotic spindle positioning to control the orientation of cell division within complex tissue structures. These oriented cell divisions are essential for the development of cell diversity and the maintenance of tissue homeostasis. Despite intense efforts, the molecular mechanisms that control spindle orientation remain incompletely defined. Here, we describe a role for the Hippo (Hpo) kinase complex in promoting Partner of Inscuteable (Pins)-mediated spindle orientation. Knockdown of Hpo, Salvador (Sav), or Warts (Wts) each result in a partial loss of spindle orientation, a phenotype previously described following loss of the Pins-binding protein Mushroom body defect (Mud). Similar to orthologs spanning yeast to mammals, Wts kinase localizes to mitotic spindle poles, a prominent site of Mud localization. Wts directly phosphorylates Mud in vitro within its C-terminal coiled-coil domain. This Mud coiled-coil domain directly binds the adjacent Pins-binding domain to dampen the Pins/Mud interaction, and Wts-mediated phosphorylation uncouples this intramolecular Mud interaction. Loss of Wts prevents cortical Pins/Mud association without affecting Mud accumulation at spindle poles, suggesting phosphorylation acts as a molecular switch to specifically activate cortical Mud function. Finally, loss of Wts in Drosophila imaginal disc epithelial cells results in diminished cortical Mud and defective planar spindle orientation. Our results provide new insights into the molecular basis for dynamic regulation of the cortical Pins/Mud spindle positioning complex and highlight a novel link with an essential, evolutionarily conserved cell proliferation pathway. Copyright © 2015 Elsevier Ltd. All rights reserved.

Phase separation of DMDBS from iPP, and controlled crystalline orientation

NASA Astrophysics Data System (ADS)

Sreenivas, K.; Kumaraswamy, Guruswamy; Basargekar, R. S.

2012-02-01

We report an unexpected dependence of DMDBS phase separation temperature on the molecular weight of the matrix isotactic polypropylene (iPP). DMDBS crystallizes out at lower temperatures for iPP with decreasing molecular weight (and correspondingly lower tacticity). This molecular weight dependence is unique to iPP, and is not observed for either syndiotactic PP or for random ethylene-PP copolymers. We show that thermodynamic Flory-type arguments are unable to rationalize the observed results. We also results on extrusion film casting of iPP containing DMDBS and show that flow-alignment of DMDBS networks template the orientation of PP crystals. The modulus and yield strength increase on addition of DMDBS, relative to the neat iPP. Tensile modulus and yield stress of drawn films increase with the degree of orientation, and we are able to achieve a substantial increase even at relatively low draw ratios.

Evolution of an ancient protein function involved in organized multicellularity in animals.

PubMed

Anderson, Douglas P; Whitney, Dustin S; Hanson-Smith, Victor; Woznica, Arielle; Campodonico-Burnett, William; Volkman, Brian F; King, Nicole; Thornton, Joseph W; Prehoda, Kenneth E

2016-01-07

To form and maintain organized tissues, multicellular organisms orient their mitotic spindles relative to neighboring cells. A molecular complex scaffolded by the GK protein-interaction domain (GKPID) mediates spindle orientation in diverse animal taxa by linking microtubule motor proteins to a marker protein on the cell cortex localized by external cues. Here we illuminate how this complex evolved and commandeered control of spindle orientation from a more ancient mechanism. The complex was assembled through a series of molecular exploitation events, one of which - the evolution of GKPID's capacity to bind the cortical marker protein - can be recapitulated by reintroducing a single historical substitution into the reconstructed ancestral GKPID. This change revealed and repurposed an ancient molecular surface that previously had a radically different function. We show how the physical simplicity of this binding interface enabled the evolution of a new protein function now essential to the biological complexity of many animals.

Modification of response functions of cat visual cortical cells by spatially congruent perturbing stimuli.

PubMed

Kabara, J F; Bonds, A B

2001-12-01

Responses of cat striate cortical cells to a drifting sinusoidal grating were modified by the superimposition of a second, perturbing grating (PG) that did not excite the cell when presented alone. One consequence of the presence of a PG was a shift in the tuning curves. The orientation tuning of all 41 cells exposed to a PG and the spatial frequency tuning of 83% of the 23 cells exposed to a PG showed statistically significant dislocations of both the response function peak and center of mass from their single grating values. As found in earlier reports, the presence of PGs suppressed responsiveness. However, reductions measured at the single grating optimum orientation or spatial frequency were on average 1.3 times greater than the suppression found at the peak of the response function modified by the presence of the PG. Much of the loss in response seen at the single grating optimum is thus a result of a shift in the tuning function rather than outright suppression. On average orientation shifts were repulsive and proportional (approximately 0.10 deg/deg) to the angle between the perturbing stimulus and the optimum single grating orientation. Shifts in the spatial frequency response function were both attractive and repulsive, resulting in an overall average of zero. For both simple and complex cells, PGs generally broadened orientation response function bandwidths. Similarly, complex cell spatial frequency response function bandwidths broadened. Simple cell spatial frequency response functions usually did not change, and those that did broadened only 4% on average. These data support the hypothesis that additional sinusoidal components in compound stimuli retune cells' response functions for orientation and spatial frequency.

Epitaxial Growth of an Organic p-n Heterojunction: C60 on Single-Crystal Pentacene.

PubMed

Nakayama, Yasuo; Mizuno, Yuta; Hosokai, Takuya; Koganezawa, Tomoyuki; Tsuruta, Ryohei; Hinderhofer, Alexander; Gerlach, Alexander; Broch, Katharina; Belova, Valentina; Frank, Heiko; Yamamoto, Masayuki; Niederhausen, Jens; Glowatzki, Hendrik; Rabe, Jürgen P; Koch, Norbert; Ishii, Hisao; Schreiber, Frank; Ueno, Nobuo

2016-06-01

Designing molecular p-n heterojunction structures, i.e., electron donor-acceptor contacts, is one of the central challenges for further development of organic electronic devices. In the present study, a well-defined p-n heterojunction of two representative molecular semiconductors, pentacene and C60, formed on the single-crystal surface of pentacene is precisely investigated in terms of its growth behavior and crystallographic structure. C60 assembles into a (111)-oriented face-centered-cubic crystal structure with a specific epitaxial orientation on the (001) surface of the pentacene single crystal. The present experimental findings provide molecular scale insights into the formation mechanisms of the organic p-n heterojunction through an accurate structural analysis of the single-crystalline molecular contact.

Macroscopically Oriented Porous Materials with Periodic Ordered Structures: From Zeolites and Metal-Organic Frameworks to Liquid-Crystal-Templated Mesoporous Materials.

PubMed

Cho, Joonil; Ishida, Yasuhiro

2017-07-01

Porous materials with molecular-sized periodic structures, as exemplified by zeolites, metal-organic frameworks, or mesoporous silica, have attracted increasing attention due to their range of applications in storage, sensing, separation, and transformation of small molecules. Although the components of such porous materials have a tendency to pack in unidirectionally oriented periodic structures, such ideal types of packing cannot continue indefinitely, generally ceasing when they reach a micrometer scale. Consequently, most porous materials are composed of multiple randomly oriented domains, and overall behave as isotropic materials from a macroscopic viewpoint. However, if their channels could be unidirectionally oriented over a macroscopic scale, the resultant porous materials might serve as powerful tools for manipulating molecules. Guest molecules captured in macroscopically oriented channels would have their positions and directions well-defined, so that molecular events in the channels would proceed in a highly controlled manner. To realize such an ideal situation, numerous efforts have been made to develop various porous materials with macroscopically oriented channels. An overview of recent studies on the synthesis, properties, and applications of macroscopically oriented porous materials is presented. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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).

What is measured by hyper-Rayleigh scattering from a liquid?

NASA Astrophysics Data System (ADS)

Rodriquez, Micheal B.; Shelton, David P.

2018-04-01

Polarization and angle dependence of hyper-Rayleigh scattering (HRS) measured for liquid acetonitrile and dimethyl sulfoxide (DMSO) is analyzed in terms of contributions from randomly oriented molecules and additional contributions produced during intermolecular collisions and induced by the electric field of dissolved ions. All three contributions show the effect of long-range correlation, and the correlation functions are determined using the HRS observations combined with the results of molecular dynamics simulations. HRS from acetonitrile is polarized transverse to the scattering vector. This is due to long-range molecular orientation correlation produced by the dipole-dipole interaction, and correlation at distances r > 100 nm must be included to account for the HRS observations. Analysis of the HRS measurements for acetonitrile determines the length scale a = 0.185 nm for the long-range longitudinal and transverse orientation correlation functions BL=-2 BT=a3/r3. Transverse polarized collision-induced HRS is also observed for acetonitrile, indicating long-range correlation of intermolecular modes. Strong longitudinal HRS is induced by the radial electric field of dissolved ions in acetonitrile. For DMSO, the angle between the molecular dipole and the vector part of the first hyperpolarizability tensor is about 100°. As a result, HRS from the randomly oriented molecules in DMSO is nearly unaffected by dipole correlation, and ion-induced HRS is weak. The strong longitudinal polarized HRS observed for DMSO is due to the collision-induced contribution, indicating long-range correlation of intermolecular modes. The HRS observations require correlation that has r-3 long-range asymptotic form, for molecular orientation and for intermolecular vibration and libration, for both acetonitrile and DMSO.

Self-oriented nanoparticles for site-selective immunoglobulin G recognition via epitope imprinting approach.

PubMed

Çorman, Mehmet Emin; Armutcu, Canan; Uzun, Lokman; Say, Rıdvan; Denizli, Adil

2014-11-01

Molecular imprinting is a polymerization technique that provides synthetic analogs for template molecules. Molecularly imprinted polymers (MIPs) have gained much attention due to their unique properties such as selectivity and specificity for target molecules. In this study, we focused on the development of polymeric materials with molecular recognition ability, so molecular imprinting was combined with miniemulsion polymerization to synthesize self-orienting nanoparticles through the use of an epitope imprinting approach. Thus, L-lysine imprinted nanoparticles (LMIP) were synthesized via miniemulsion polymerization technique. Immunoglobulin G (IgG) was then bound to the cavities that specifically formed for L-lysine molecules that are typically found at the C-terminus of the Fc region of antibody molecules. The resulting nanoparticles makes it possible to minimize the nonspecific interaction between monomer and template molecules. In addition, the orientation of the entire IgG molecule was controlled, and random imprinting of the IgG was prevented. The optimum conditions were determined for IgG recognition using the imprinted nanoparticles. The selectivity of the nanoparticles against IgG molecules was also evaluated using albumin and hemoglobin as competitor molecules. In order to show the self-orientation capability of imprinted nanoparticles, human serum albumin (HSA) adsorption onto both the plain nanoparticles and immobilized nanoparticles by anti-human serum albumin antibody (anti-HSA antibody) was also carried out. Due to anti-HSA antibody immobilization on the imprinted nanoparticles, the adsorption capability of nanoparticles against HSA molecules vigorously enhanced. It is proved that the oriented immobilization of antibodies was appropriately succeeded. Copyright © 2014 Elsevier B.V. All rights reserved.

Cross-Lagged Relationships between Career Aspirations and Goal Orientation in Early Adolescents

ERIC Educational Resources Information Center

Creed, Peter; Tilbury, Clare; Buys, Nick; Crawford, Meegan

2011-01-01

We surveyed 217 students (145 girls; average age = 14.6 years) on two occasions, twelve months apart, on measures of career aspirations (job aspirations, job expectations, educational aspirations) and goal orientation (learning, performance-prove, performance-avoid), and tested the causal relationship between goal orientation and aspirations. We…

Concentration of Swiss Elite Orienteers.

ERIC Educational Resources Information Center

Seiler, Roland; Wetzel, Jorg

1997-01-01

A visual discrimination task was used to measure concentration among 43 members of Swiss national orienteering teams. Subjects were above average in the number of target objects dealt with and in duration of continuous concentration. For females only, ranking in orienteering performance was related to quality of concentration (ratio of correct to…

Molecular Orientation in Dry and Hydrated Cellulose Fibers: A Coherent Anti-Stokes Raman Scattering Microscopy Study

PubMed Central

Zimmerley, Maxwell; Younger, Rebecca; Valenton, Tiffany; Oertel, David C.; Ward, Jimmie L.; Potma, Eric O.

2012-01-01

Coherent anti-Stokes Raman scattering (CARS) microscopy is combined with spontaneous Raman scattering microspectroscopy and second harmonic generation (SHG) microscopy to interrogate the molecular alignment in dry and hydrated cellulose fibers. Two types of cellulose were investigated: natural cellulose I in cotton fibers and regenerated cellulose II in rayon fibers. On the basis of the orientation of the methylene symmetric stretching vibration, the molecular alignment of cellulose microfibrils is found to be conserved on the micrometer scale. Whereas the molecular orientation in cotton shows modest variability along the fiber, the alignment of the cellulose units in rayon is highly consistent throughout the fiber. The ordered alignment is retained upon fiber hydration. Upon hydration of the cellulose fibers, an anisotropic electronic contribution is observed, which indicates an ordered incorporation of water molecules into the fiber structure. The third-order and second-order electronic polarizability of cellulose I are directed along the axis of the polyglucan chain. No second-order optical response is observed in cellulose II, supporting the antiparallel arrangement of the polyglucan chains in regenerated cellulose. PMID:20684644

Structure and Orientation Behavior of Highly Oriented Polymers Under Tensile and Compressive Stresses

NASA Astrophysics Data System (ADS)

Garcia-Ramirez, Rafael

The birefringence of Kevlar 49^ circler fibers has been shown to decrease with compressive strain, suggesting that structure changes under compression involve decreasing crystallite orientation. This mechanism appears to be the inverse of that occurring under tension, for which increasing crystallite orientation has been reported to occur, leading to non-linear elasticity. A contrast between the effects of both stress modes on structure (orientation) response is presented. While birefringence presents itself as a technically convenient and economically attractive technique for this type of study, caution must be exercised when interpreting results from measurements under stress. For highly crystalline fibers, experiments have led to the attribution of the observed changes in birefringence almost entirely to crystallite orientation. This study presents an analysis of the different contributions to birefringence under stress. X-ray diffraction experiments have been performed for Kevlar 49^ circler fibers under tensile stress. Results from crystal orientation cannot account for changes observed in birefringence. Moreover, they appear to account only for a small fraction of the total change. These observations suggest significant contributions from other sources. Theoretical calculations have been carried out under simulated stress conditions to quantify the effect of molecular deformation on the observed birefringence of Kevlar 49^circler fibers. The results have been obtained using semi-empirical molecular orbital calculations with the AM1 Hamiltonian in MOPAC. This analysis has been applied to poly(p^' -phenylene terephthalamide) (PPTA) and polyethylene (PE) chains. For PE, stress-free computations were performed on segments of up to 50 -(CH_2-CH _2)- units. Strains up to 1% were applied on segments of up to 40 units. For PPTA, segments of up to 5 PTA units were analyzed. Strain-free results indicate a linear dependence of molecular polarizability on chain length. The treatment yields also a linear trend for the effect of strain on the polarizability of PE segments. Thus, the calculations predict a plane in 3-D space for the dependence of molecular polarizability on both chain size and strain. The predicted molecular polarizabilities are used to evaluate the effect of stress on birefringence of the idealized polymers, by applying existing internal-field theory. Results indicate significant effects from molecules deforming under the stress field.

Molecular Beam Epitaxial Growth of GaAs on (631) Oriented Substrates

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

Cruz Hernandez, Esteban; Rojas Ramirez, Juan-Salvador; Contreras Hernandez, Rocio

2007-02-09

In this work, we report the study of the homoepitaxial growth of GaAs on (631) oriented substrates by molecular beam epitaxy (MBE). We observed the spontaneous formation of a high density of large scale features on the surface. The hilly like features are elongated towards the [-5, 9, 3] direction. We show the dependence of these structures with the growth conditions and we present the possibility of to create quantum wires structures on this surface.

Molecular phylogeny of Anopheles hyrcanus group (Diptera: Culicidae) based on mtDNA COI.

PubMed

Fang, Yuan; Shi, Wen-Qi; Zhang, Yi

2017-05-08

The Anopheles hyrcanus group, which includes at least 25 species, is widely distributed in the Oriental and Palearctic regions. Some group members have been incriminated as vectors of malaria and other mosquito-borne diseases. It is difficult to identify Hyrcanus Group members by morphological features. Thus, molecular phylogeny has been proposed as an important complementary method to traditional morphological taxonomy. Based on the GenBank database and our original study data, we used 466 mitochondrial DNA COI sequences belonging to 18 species to reconstruct the molecular phylogeny of the Hyrcanus Group across its worldwide geographic range. The results are as follows. 1) The average conspecific K2P divergence was 0.008 (range 0.002-0.017), whereas sequence divergence between congroup species averaged 0.064 (range 0.026-0.108). 2) The topology of COI tree of the Hyrcanus Group was generally consistent with classical morphological taxonomy in terms of species classification, but disagreed in subgroup division. In the COI tree, the group was divided into at least three main clusters. The first cluster contained An. nimpe; the second was composed of the Nigerrimus Subgroup and An. argyropus; and the third cluster was comprised of the Lesteri Subgroup and other unassociated species. 3) Phylogenetic analysis of COI indicated that ancient hybridizations probably occurred among the three closely related species, An. sinensis, An. belenrae, and An. kleini. 4) The results supported An. paraliae as a probable synonym of An. lesteri, and it was possible that An. pseudopictus and An. hyrcanus were the same species, as evident from their extremely low interspecific genetic divergence (0.020 and 0.007, respectively) and their phylogenetic positions. In summary, we reconstructed the molecular phylogeny and analysed genetic divergence of the Hyrcanus Group using mitochondrial COI sequences. Our results suggest that in the future of malaria surveillance, we should not only pay much attention to those known vectors of malaria, but also their closely related species.

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.

Single neural code for blur in subjects with different interocular optical blur orientation

PubMed Central

Radhakrishnan, Aiswaryah; Sawides, Lucie; Dorronsoro, Carlos; Peli, Eli; Marcos, Susana

2015-01-01

The ability of the visual system to compensate for differences in blur orientation between eyes is not well understood. We measured the orientation of the internal blur code in both eyes of the same subject monocularly by presenting pairs of images blurred with real ocular point spread functions (PSFs) of similar blur magnitude but varying in orientations. Subjects assigned a level of confidence to their selection of the best perceived image in each pair. Using a classification-images–inspired paradigm and applying a reverse correlation technique, a classification map was obtained from the weighted averages of the PSFs, representing the internal blur code. Positive and negative neural PSFs were obtained from the classification map, representing the neural blur for best and worse perceived blur, respectively. The neural PSF was found to be highly correlated in both eyes, even for eyes with different ocular PSF orientations (rPos = 0.95; rNeg = 0.99; p < 0.001). We found that in subjects with similar and with different ocular PSF orientations between eyes, the orientation of the positive neural PSF was closer to the orientation of the ocular PSF of the eye with the better optical quality (average difference was ∼10°), while the orientation of the positive and negative neural PSFs tended to be orthogonal. These results suggest a single internal code for blur with orientation driven by the orientation of the optical blur of the eye with better optical quality. PMID:26114678

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.

Combined Near and Far Field High Energy Diffraction Microscopy Dataset for Ti-7Al Tensile Specimen Elastically Loaded In Situ

DOE Data Explorer

Turner, Todd J.; Shade, Paul A; Bernier, Joel V.; Li, Shiu Fai; Schuren, Jay C.; Lind, Jonathan F.; Lienert, Ulrich; Kenesei, Peter; Suter, Robert; Blank, Basil; Almer, Jonathan

2016-01-01

We present both near-field HEDM data that maps out the grain morphology and intragranular crystallographic orientations and far-field HEDM data that provides the grain centroid, grain average crystallographic orientation, and grain average elastic strain tensor for each grain. Finally, we provide a finite element mesh that can be utilized to simulate deformation in the volume of this Ti-7Al specimen.

The Relations between Filial Piety, Goal Orientations and Academic Achievement in Hong Kong

ERIC Educational Resources Information Center

Chen, Wei-Wen

2016-01-01

This study examined the relationships among filial piety, goal orientations, and academic achievement among Chinese students. A survey of 336 university students in Hong Kong was carried out to collect information on their filial piety beliefs, goal orientations and grade point averages. Structural equation modelling indicated that reciprocal…

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

DOE PAGES

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

2016-02-09

Within ten nearby (d < 450 pc) Gould belt molecular clouds we evaluate in this paper statistically the relative orientation between the magnetic field projected on the plane of sky, inferred from the polarized thermal emission of Galactic dust observed by Planck at 353 GHz, and the gas column density structures, quantified by the gradient of the column density, N H. The selected regions, covering several degrees in size, are analysed at an effective angular resolution of 10' FWHM, thus sampling physical scales from 0.4 to 40 pc in the nearest cloud. The column densities in the selected regions rangemore » from N H≈ 10 21 to10 23 cm -2, and hence they correspond to the bulk of the molecular clouds. The relative orientation is evaluated pixel by pixel and analysed in bins of column density using the novel statistical tool called “histogram of relative orientations”. Throughout this study, we assume that the polarized emission observed by Planck at 353 GHz is representative of the projected morphology of the magnetic field in each region, i.e., we assume a constant dust grain alignment efficiency, independent of the local environment. Within most clouds we find that the relative orientation changes progressively with increasing N H, from mostly parallel or having no preferred orientation to mostly perpendicular. In simulations of magnetohydrodynamic turbulence in molecular clouds this trend in relative orientation is a signature of Alfvénic or sub-Alfvénic turbulence, implying that the magnetic field is significant for the gas dynamics at the scales probed by Planck. Finally, we compare the deduced magnetic field strength with estimates we obtain from other methods and discuss the implications of the Planck observations for the general picture of molecular cloud formation and evolution.« less

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.

Theoretical and experimental examination of SFG polarization analysis at acetonitrile-water solution surfaces.

PubMed

Saito, Kengo; Peng, Qiling; Qiao, Lin; Wang, Lin; Joutsuka, Tatsuya; Ishiyama, Tatsuya; Ye, Shen; Morita, Akihiro

2017-03-29

Sum frequency generation (SFG) spectroscopy is widely used to observe molecular orientation at interfaces through a combination of various types of polarization. The present work thoroughly examines the relation between the polarization dependence of SFG signals and the molecular orientation, by comparing SFG measurements and molecular dynamics (MD) simulations of acetonitrile/water solutions. The present SFG experiment and MD simulations yield quite consistent results on the ratios of χ (2) elements, supporting the reliability of both means. However, the subsequent polarization analysis tends to derive more upright tilt angles of acetonitrile than the direct MD calculations. The reasons for discrepancy are examined in terms of three issues; (i) anisotropy of the Raman tensor, (ii) cross-correlation, and (iii) orientational distribution. The analysis revealed that the issues (i) and (iii) are the main causes of errors in the conventional polarization analysis of SFG spectra. In methyl CH stretching, the anisotropy of Raman tensor cannot be estimated from the simple bond polarizability model. The neglect of the orientational distribution is shown to systematically underestimate the tilt angle of acetonitrile. Further refined use of polarization analysis in collaboration with MD simulations should be proposed.

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

J Cai; B Hsiao; R Gross

Poly({omega}-pentadecalactone) (PPDL), a model polymer in the poly({omega}-hydroxyl fatty acids) family, is a new biopolymer with monomer synthesized by yeast-catalyzed {omega}-hydroxylation of fatty acids. In this study, deformation-induced structural changes in two PPDL samples with different molecular weights were studied by in situ wide-angle X-ray diffraction (WAXD) and small-angle X-ray scattering (SAXS) techniques. The high molecular weight PPDL (PPDL-high) sample exhibited notable strain hardening, while the low molecular weight PPDL (PPDL-low) sample did not. The behavior can be explained by the entanglement density concept. The evolution of crystallinity (from WAXD) as a function of strain could be divided into fourmore » distinct regions, but their respective mechanisms differ slightly in each sample. During stretching, a mesomorphic phase formed in both samples, bridging between the amorphous and strain-induced crystal phases. The SAXS data verified the effect of molecular weight (or the entanglement density) on the deformation-induced structure of PPDL. The parameters of chain orientation factor (f) calculated from the orthorhombic crystal cell as well as the nonorthorhombic crystal cell proposed by Wilchinsky were used to follow the orientation process during stretching of PPDLs. It was found that the different molecular entanglement network (i.e., PPDL-low versus PPDL-high) led to different crystal orientation behavior, especially in the low strain range.« less

Quantum mechanical/molecular mechanical molecular dynamics and free energy simulations of the thiopurine S-methyltransferase reaction with 6-mercaptopurine.

PubMed

Pan, Xiao-Liang; Cui, Feng-Chao; Liu, Jing-Yao

2011-06-23

Quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations were performed to investigate the methylation of 6-mercaptopurine catalyzed by thiopurine S-methyltransferase. Several setups with different tautomeric forms and orientations of the substrate were considered. It is found that, with the orientation in chain A of the X-ray structure, the substrate can form an ideal near-attack configuration for the methylation reaction, which may take place after the deprotonation of the substrate by the conserved residue Asp23 through a water chain. The potential of mean force (PMF) of the methyl-transfer step for the most favorable pathway is 19.6 kcal/mol, which is in good agreement with the available experimental rate constant data.

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.

Cyclotron resonance in ferromagnetic InMnAs and InMnSb

NASA Astrophysics Data System (ADS)

Khodaparast, G. A.; Matsuda, Y. H.; Saha, D.; Sanders, G. D.; Stanton, C. J.; Saito, H.; Takeyama, S.; Merritt, T. R.; Feeser, C.; Wessels, B. W.; Liu, X.; Furdyna, J.

2013-12-01

We present experimental and theoretical studies of the magneto-optical properties of p-type In1-xMnxAs and In1-xMnxSb ferromagnetic semiconductor films in ultrahigh magnetic fields oriented along [001]. Samples were fabricated by molecular beam epitaxy (MBE) and metal-organic vapor phase epitaxy (MOVPE). To model the results, we used an 8-band Pidgeon-Brown model generalized to include the wave vector dependence of the elec-tronic states along kz as well as the s-d and p-d exchange interactions with the localized Mn d electrons. The Curie temperature is taken as an input parameter and the average Mn spin is treated in mean-field theory. We compared Landau level and band structure calculations with observed cyclotron resonance (CR) measurements. While differences between the CR measurements are seen for MBE and MOVPE samples, our calculations indicate that they arise from differences in the carrier densities. In addition, the difference in the carrier densities suggests significantly larger average spin for the MOVPE structures; this fact could be responsible for higher Curie temperatures in this material system.

Dynamic evolution of light-induced orientation of dye-doped liquid crystals in liquid phase studied by time-resolved optically heterodyned optical Kerr effect technique.

PubMed

Yang, Pei; Liu, Liying; Xu, Lei

2008-02-28

Transient evolution of light-induced molecular reorientation both in 1-amino-anthraquinone (1AAQ) dye and azobenzene doped isotropic liquid crystals (LCs) were studied by time-resolved optically heterodyned optical Kerr effect method. The results give clear direct experimental proof that under short pulse (30 ps) excitation, LC molecules orientate toward the excitation light polarization direction in the 1AAQ/LC system. However, LC molecular orientation becomes orthogonal to the light polarization in azobenzene/LC system. Time-resolved excited-state absorption of 1AAQ and wavelength dependent excited-state absorption of azobenzene were also observed and their contributions to the early dynamics of the third order optical responses of the two systems were confirmed. A simplified two-level mean-field theory was derived to reveal the intensity dependence of orientation enhancement factor in azobenzene/LC system considering the photoisomerization process.

Matrix assisted laser desorption ionization time-of-flight mass spectrometry: Velocity measurements using orthogonal and axial injection and applications to characterization of wheat proteins

NASA Astrophysics Data System (ADS)

Dworschak, Ragnar G.

Orthogonal-injection was introduced to allow continuous ion sources to be coupled to time-of-flight mass spectrometers, but also demonstrated promising features for pulsed sources such as MALDI. We tested the feasibility of using a simple implementation orthogonal injection TOF with a MALDI source without collisional cooling. The experiment demonstrated that high resolution is achievable in principle in such an instrument, but only with impractical sacrifices in intensity. Subsequent work in this laboratory has demonstrated that the addition of collisional cooling makes orthogonal MALDI not only feasible, but advantageous in several respects. The instrument used for the above feasibility test was well-suited for measurements of initial velocity distributions in MALDI, avoiding problems of field penetration and questions of timescale of the plume expansion that seemed to produce rather conflicting results in axial TOF measurements. Average initial velocities of peptides and proteins above about 1000 daltons were found to be largely mass independent around 800 m/s, plus or minus about 15% depending on the matrix used. This result is slightly higher, but still quite consistent with earlier measurements using axial TOF with the field-free method (˜750 m/s), but a factor of two higher than the first reports using the delayed-extraction method. The experiments also showed that in contrast to the average velocity, the width of the velocity distribution increases significantly with increasing mass. The matrix velocity measurements confirm earlier experiments that show the benzoic acid derivatives have generally higher velocities than the cinnamic acid derivatives. Measurements of the velocity component in the direction back toward the laser with different sample orientations suggest that the surface orientation is the main determiner of the plume direction. On the other hand, preliminary measurements using the field-free method in the axial TOF geometry show higher velocities of matrix and analyte ions for more normal laser incidence, and for single crystals parallel to the sample surface compared to polycrystalline surfaces, suggesting the orientation of the crystal face with respect to the incident laser direction plays a role in the desorption process. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI/MS) was used to analyse the protein composition in several common and durum wheat varieties. Mass spectra were obtained directly from crude and partially purified wheat gliadin and reduced glutenin subunit fractions. Mass spectra of the gliadins and the low molecular weight glutenin subunits show a complex pattern of proteins in the 30--40 kDa range. The observed gliadin patterns showed some promise for variety identification. The mass spectra of the high molecular weight glutenin subunits are much simpler and the complete high molecular weight subunit profile can be determined directly from a single mass spectrum. This may prove particularly useful in wheat breeding programs for rapid identification of lines containing subunits associated with superior quality.

The role of phosphorylation in dentin phosphoprotein peptide absorption to hydroxyapatite surfaces: a molecular dynamics study

PubMed Central

Villarreal-Ramirez, Eduardo; Garduño-Juarez, Ramon; Gericke, Arne; Boskey, Adele

2015-01-01

Dentin phosphoprotein (DPP) is a protein expressed mainly in dentin and to a lesser extent in bone. DPP has a disordered structure, rich in glutamic acid, aspartic acid and phosphorylated serine/threonine residues. It has a high capacity for binding to calcium ions and to hydroxyapatite (HA) crystal surfaces. We used molecular dynamics (MD) simulations as a method for virtually screening interactions between DPP motifs and HA. The goal was to determine which motifs are absorbed to HA surfaces. For these simulations, we considered five peptides from the human DPP sequence. All-atom MD simulations were performed using GROMACS, the peptides were oriented parallel to the {100} HA crystal surface, the distance between the HA and the peptide was 3 nm. The system was simulated for 20 ns. Preliminary results show that for the unphosphorylated peptides, the acidic amino acids present an electrostatic attraction where their side chains are oriented towards HA. This attraction, however, is slow to facilitate bulk transport to the crystal surface. On the other hand, the phosphorylated (PP) peptides are rapidly absorbed on the surface of the HA with their centers of mass closer to the HA surface. More importantly, the root mean square fluctuation (RMSF) indicates that the average structures of the phosphorylated peptides are very inflexible and elongate, while that of the unphosphorylated peptides are flexible. Radius of gyration (Rg) analysis showed the compactness of un-phosphorylated peptides is lower than phosphorylated peptides. Phosphorylation of the DPP peptides is necessary for binding to HA surfaces. PMID:25158198

Pessimistic orientation in relation to telomere length in older men: the VA Normative Aging Study

PubMed Central

Ikeda, Ai; Schwartz, Joel; Peters, Junenette L.; Baccarelli, Andrea A.; Hoxha, Mirjam; Dioni, Laura; Spiro, Avron; Sparrow, David; Vokonas, Pantel; Kubzansky, Laura D.

2014-01-01

Background Recent research suggests pessimistic orientation is associated with shorter leukocyte telomere length (LTL). However, this is the first study to look not only at effects of pessimistic orientation on average LTL at multiple time points, but also at effects on the rate of change in LTL over time. Methods Participants were older men from the VA Normative Aging Study (n=490). The Life Orientation Test (LOT) was used to measure optimistic and pessimistic orientations at study baseline, and relative LTL by telomere to single copy gene ratio (T:S ratio) was obtained repeatedly over the course of the study (1999-2008). A total of 1,010 observations were included in the analysis. Linear mixed effect models with a random subject intercept were used to estimate associations. Results Higher pessimistic orientation scores were associated with shorter average LTL (percent difference by 1-SD increase in pessimistic orientation (95% CI): -3.08 (-5.62, -0.46)), and the finding was maintained after adjusting for the higher likelihood that healthier individuals return for follow-up visits (-3.44 (-5.95,-0.86)). However, pessimistic orientation scores were not associated with rate of change in LTL over time. No associations were found between overall optimism and optimistic orientation subscale scores and LTL. Conclusion Higher pessimistic orientation scores were associated with shorter LTL in older men. While there was no evidence that pessimistic orientation was associated with rate of change in LTL over time, higher levels of pessimistic orientation were associated with shorter LTL at baseline and this association persisted over time. PMID:24636503

The Determination of Molecular Structure from Rotational Spectra

DOE R&D Accomplishments Database

Laurie, V. W.; Herschbach, D. R.

1962-07-01

An analysis is presented concerning the average molecular configuration variations and their effects on molecular structure determinations. It is noted that the isotopic dependence of the zero-point is often primarily governed by the isotopic variation of the average molecular configuration. (J.R.D.)

Tilt-Pair Analysis of Images from a Range of Different Specimens in Single-Particle Electron Cryomicroscopy

PubMed Central

Henderson, Richard; Chen, Shaoxia; Chen, James Z.; Grigorieff, Nikolaus; Passmore, Lori A.; Ciccarelli, Luciano; Rubinstein, John L.; Crowther, R. Anthony; Stewart, Phoebe L.; Rosenthal, Peter B.

2011-01-01

The comparison of a pair of electron microscope images recorded at different specimen tilt angles provides a powerful approach for evaluating the quality of images, image-processing procedures, or three-dimensional structures. Here, we analyze tilt-pair images recorded from a range of specimens with different symmetries and molecular masses and show how the analysis can produce valuable information not easily obtained otherwise. We show that the accuracy of orientation determination of individual single particles depends on molecular mass, as expected theoretically since the information in each particle image increases with molecular mass. The angular uncertainty is less than 1° for particles of high molecular mass (∼ 50 MDa), several degrees for particles in the range 1–5 MDa, and tens of degrees for particles below 1 MDa. Orientational uncertainty may be the major contributor to the effective temperature factor (B-factor) describing contrast loss and therefore the maximum resolution of a structure determination. We also made two unexpected observations. Single particles that are known to be flexible showed a wider spread in orientation accuracy, and the orientations of the largest particles examined changed by several degrees during typical low-dose exposures. Smaller particles presumably also reorient during the exposure; hence, specimen movement is a second major factor that limits resolution. Tilt pairs thus enable assessment of orientation accuracy, map quality, specimen motion, and conformational heterogeneity. A convincing tilt-pair parameter plot, where 60% of the particles show a single cluster around the expected tilt axis and tilt angle, provides confidence in a structure determined using electron cryomicroscopy. PMID:21939668

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.

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.

The Light Intermediate Chain 2 Subpopulation of Dynein Regulates Mitotic Spindle Orientation.

PubMed

Mahale, Sagar; Kumar, Megha; Sharma, Amit; Babu, Aswini; Ranjan, Shashi; Sachidanandan, Chetana; Mylavarapu, Sivaram V S

2016-12-23

Cytoplasmic dynein 1 is a multi-protein intracellular motor essential for mediating several mitotic functions, including the establishment of proper spindle orientation. The functional relevance and mechanistic distinctions between two discrete dynein subpopulations distinguished only by Light Intermediate Chain (LIC) homologues, LIC1 and LIC2 is unknown during mitosis. Here, we identify LIC2-dynein as the major mediator of proper spindle orientation and uncover its underlying molecular mechanism. Cortically localized dynein, essential for maintaining correct spindle orientation, consists majorly of LIC2-dynein, which interacts with cortical 14-3-3 ε- ζ and Par3, conserved proteins required for orienting the spindle. LIC2-dynein is also responsible for the majority of dynein-mediated asymmetric poleward transport of NuMA, helping focus microtubule minus ends. In addition, LIC2-dynein dominates in equatorially aligning chromosomes at metaphase and in regulating mitotic spindle length. Key mitotic functions of LIC2 were remarkably conserved in and essential for early embryonic divisions and development in zebrafish. Thus LIC2-dynein exclusively engages with two major cortical pathways to govern spindle orientation. Overall, we identify a novel selectivity of molecular interactions between the two LICs in mitosis as the underlying basis for their uneven distribution of labour in ensuring proper spindle orientation.

The mechanism of transforming diamond nanowires to carbon nanostructures

NASA Astrophysics Data System (ADS)

Sorkin, Anastassia; Su, Haibin

2014-01-01

The transformation of diamond nanowires (DNWs) with different diameters and geometries upon heating is investigated with density-functional-based tight-binding molecular dynamics. DNWs of <100> and <111> oriented cross-section with projected average line density between 7 and 20 atoms Å-1 transform into carbon nanotubes (CNTs) under gradual heating up to 3500-4000 K. DNWs with projected average line density larger than 25 atoms Å-1 transform into double-wall CNTs. The route of transformation into CNTs clearly exhibits three stages, with the intriguing intermediate structural motif of a carbon nanoscroll (CNS). Moreover, the morphology plays an important role in the transformation involving the CNS as one important intermediate motif to form CNTs. When starting with \\langle \\bar {2}1 1\\rangle oriented DNWs with a square cross-section consisting of two {111} facets facing each other, one interesting structure with ‘nano-bookshelf’ shape emerges: a number of graphene ‘shelves’ located inside the CNT, bonding to the CNT walls with sp3 hybridized atoms. The nano-bookshelf structures exist in a wide range of temperatures up to 3000 K. The further transformation from nano-bookshelf structures depends on the strength of the joints connecting shelves with CNT walls. Notably, the nano-bookshelf structure can evolve into two end products: one is CNT via the CNS pathway, the other is graphene transformed directly from the nano-bookshelf structure at high temperature. This work sheds light on the microscopic insight of carbon nanostructure formation mechanisms with the featured motifs highlighted in the pathways.

Radiation Force Caused by Scattering, Absorption, and Emission of Light by Nonspherical Particles

NASA Technical Reports Server (NTRS)

Mishchenko, Michael I.; Hansen, James E. (Technical Monitor)

2001-01-01

General formulas for computing the radiation force exerted on arbitrarily oriented and arbitrarily shaped nonspherical particles due to scattering, absorption, and emission of electromagnetic radiation are derived. For randomly oriented particles with a plane of symmetry, the formula for the average radiation force caused by the particle response to external illumination reduces to the standard Debye formula derived from the Lorenz-Mie theory, whereas the average radiation force caused by emission vanishes.

Accuracy of theory for calculating electron impact ionization of molecules

NASA Astrophysics Data System (ADS)

Chaluvadi, Hari Hara Kumar

The study of electron impact single ionization of atoms and molecules has provided valuable information about fundamental collisions. The most detailed information is obtained from triple differential cross sections (TDCS) in which the energy and momentum of all three final state particles are determined. These cross sections are much more difficult for theory since the detailed kinematics of the experiment become important. There are many theoretical approximations for ionization of molecules. One of the successful methods is the molecular 3-body distorted wave (M3DW) approximation. One of the strengths of the DW approximation is that it can be applied for any energy and any size molecule. One of the approximations that has been made to significantly reduce the required computer time is the OAMO (orientation averaged molecular orbital) approximation. In this dissertation, the accuracy of the M3DW-OAMO is tested for different molecules. Surprisingly, the M3DW-OAMO approximation yields reasonably good agreement with experiment for ionization of H2 and N2. On the other hand, the M3DW-OAMO results for ionization of CH4, NH3 and DNA derivative molecules did not agree very well with experiment. Consequently, we proposed the M3DW with a proper average (PA) calculation. In this dissertation, it is shown that the M3DW-PA calculations for CH4 and SF6 are in much better agreement with experimental data than the M3DW-OAMO results.

An Experiment-Oriented Approach to Teaching the Kinetic Molecular Theory.

ERIC Educational Resources Information Center

Wiseman, Frank L., Jr.

1979-01-01

This paper reports an experiment in the teaching of the kinetic molecular theory to nonscience majors by the inquiry method. It allows the student to develop an essentially correct view of gases, liquids, and solids on the atomic or molecular level, and illustrates how one can draw conclusions about the molecular level by simple visual…

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

Resonant spin tunneling in randomly oriented nanospheres of Mn 12 acetate

DOE PAGES

Lendínez, S.; Zarzuela, R.; Tejada, J.; ...

2015-01-06

We report measurements and theoretical analysis of resonant spin tunneling in randomly oriented nanospheres of a molecular magnet. Amorphous nanospheres of Mn₁₂ acetate have been fabricated and characterized by chemical, infrared, TEM, X-ray, and magnetic methods. Magnetic measurements have revealed sharp tunneling peaks in the field derivative of the magnetization that occur at the typical resonant field values for the Mn₁₂ acetate crystal in the field parallel to the easy axis.Theoretical analysis is provided that explains these observations. We argue that resonant spin tunneling in a molecular magnet can be established in a powder sample, without the need for amore » single crystal and without aligning the easy magnetization axes of the molecules. This is confirmed by re-analyzing the old data on a powdered sample of non-oriented micron-size crystals of Mn₁₂ acetate. In conclusion, our findings can greatly simplify the selection of candidates for quantum spin tunneling among newly synthesized molecular magnets.« less

Resonant spin tunneling in randomly oriented nanospheres of Mn 12 acetate

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

Lendínez, S.; Zarzuela, R.; Tejada, J.

We report measurements and theoretical analysis of resonant spin tunneling in randomly oriented nanospheres of a molecular magnet. Amorphous nanospheres of Mn₁₂ acetate have been fabricated and characterized by chemical, infrared, TEM, X-ray, and magnetic methods. Magnetic measurements have revealed sharp tunneling peaks in the field derivative of the magnetization that occur at the typical resonant field values for the Mn₁₂ acetate crystal in the field parallel to the easy axis.Theoretical analysis is provided that explains these observations. We argue that resonant spin tunneling in a molecular magnet can be established in a powder sample, without the need for amore » single crystal and without aligning the easy magnetization axes of the molecules. This is confirmed by re-analyzing the old data on a powdered sample of non-oriented micron-size crystals of Mn₁₂ acetate. In conclusion, our findings can greatly simplify the selection of candidates for quantum spin tunneling among newly synthesized molecular magnets.« less

Evolution of an ancient protein function involved in organized multicellularity in animals

PubMed Central

Anderson, Douglas P; Whitney, Dustin S; Hanson-Smith, Victor; Woznica, Arielle; Campodonico-Burnett, William; Volkman, Brian F; King, Nicole; Thornton, Joseph W; Prehoda, Kenneth E

2016-01-01

To form and maintain organized tissues, multicellular organisms orient their mitotic spindles relative to neighboring cells. A molecular complex scaffolded by the GK protein-interaction domain (GKPID) mediates spindle orientation in diverse animal taxa by linking microtubule motor proteins to a marker protein on the cell cortex localized by external cues. Here we illuminate how this complex evolved and commandeered control of spindle orientation from a more ancient mechanism. The complex was assembled through a series of molecular exploitation events, one of which – the evolution of GKPID’s capacity to bind the cortical marker protein – can be recapitulated by reintroducing a single historical substitution into the reconstructed ancestral GKPID. This change revealed and repurposed an ancient molecular surface that previously had a radically different function. We show how the physical simplicity of this binding interface enabled the evolution of a new protein function now essential to the biological complexity of many animals. DOI: http://dx.doi.org/10.7554/eLife.10147.001 PMID:26740169

Cluster analysis of molecular simulation trajectories for systems where both conformation and orientation of the sampled states are important.

PubMed

Abramyan, Tigran M; Snyder, James A; Thyparambil, Aby A; Stuart, Steven J; Latour, Robert A

2016-08-05

Clustering methods have been widely used to group together similar conformational states from molecular simulations of biomolecules in solution. For applications such as the interaction of a protein with a surface, the orientation of the protein relative to the surface is also an important clustering parameter because of its potential effect on adsorbed-state bioactivity. This study presents cluster analysis methods that are specifically designed for systems where both molecular orientation and conformation are important, and the methods are demonstrated using test cases of adsorbed proteins for validation. Additionally, because cluster analysis can be a very subjective process, an objective procedure for identifying both the optimal number of clusters and the best clustering algorithm to be applied to analyze a given dataset is presented. The method is demonstrated for several agglomerative hierarchical clustering algorithms used in conjunction with three cluster validation techniques. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

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

Academic Identity Status, Goal Orientation, and Academic Achievement among High School Students

ERIC Educational Resources Information Center

Hejazi, Elaheh; Lavasani, Masoud Gholamali; Amani, Habib; Was, Christopher A.

2012-01-01

The aim of the present study was to determine the relationship between academic identity status, goal orientations and academic achievement. 301 first year high school students completed the Academic Identity Measure and Goal Orientation Questionnaire. The average of 10 exam scores in the final semester was used as an index of academic…

Magnetically induced orientation of mesochannels in mesoporous silica films at 30 tesla.

PubMed

Yamauchi, Yusuke; Sawada, Makoto; Komatsu, Masaki; Sugiyama, Atsushi; Osaka, Tetsuya; Hirota, Noriyuki; Sakka, Yoshio; Kuroda, Kazuyuki

2007-12-03

We demonstrate the magnetically induced orientation of mesochannels in mesoporous silica films prepared with low-molecular-weight surfactants under an extremely high magnetic field of 30 T. This process is principally applicable to any type of surfactant that has magnetic anisotropy because such a high magnetic field provides sufficient magnetic energy for smooth magnetic orientation. Hexadecyltrimethylammonium bromide (CTAB) and polyoxyethylene-10-cetyl ether (Brij 56) were used as cationic and nonionic surfactants, respectively. According to XRD and cross-sectional TEM, mesochannels aligned perpendicular to the substrates were observed in films prepared with low-molecular-weight surfactants, although the effect was incomplete. The evolution of these types of films should lead to future applications such as highly sensitive chemical sensors and selective separation.

Robust generation of Fourier-synthesized laser fields and their estimation of the optical phase by using quantum control of molecular tunneling ionization

NASA Astrophysics Data System (ADS)

Yoshida, Tsuyoshi; Saito, Naoaki; Ohmura, Hideki

2018-03-01

Intense (5.0 × 1012 W cm-2) nanosecond Fourier-synthesized laser fields consisting of fundamental, second-, third-, and fourth-harmonic light generated by an interferometer-free Fourier-synthesized laser field generator induce orientation-selective ionization based on directionally asymmetric molecular tunneling ionization (TI). The laser field generator ensures adjustment-free operation, high stability, and high reproducibility. Phase-sensitive, orientation-selective molecular TI provides a simple way to estimate the relative phase differences between the fundamental light and each harmonic by data-fitting analysis. This application of Fourier-synthesized laser fields will facilitate not only lightwave engineering but also the control of matter.

“Combination-oriented molecular-targeting prevention” of cancer: a model involving the combination of TRAIL and a DR5 inducer

PubMed Central

Yoshida, Tatsushi; Horinaka, Mano

2010-01-01

Malignant tumors carry a high risk of death, and the prevention of malignant tumors is a crucial issue in preventive medicine. To this end, many chemopreventive agents have been tested, but the effects of single agents have been found to be insufficient to justify clinical trials. We have therefore hypothesized that combinations of different chemopreventive agents may synergistically enhance the preventive effect of chemopreventive agents used singly. To provide the treating physician with some guideline by which to choose the most effective agents to be combined, we propose a strategy which we have termed the “combination-oriented molecular-targeting prevention” of cancer. As the molecular target of our model, we focused on tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), which specifically causes apoptosis in malignant tumor cells. Many of these agents were found to up-regulate the expression of death receptor 5, a TRAIL receptor. They were also found to synergistically induce apoptosis in malignant tumor cells when combined with TRAIL. Here, we strongly advocate that the strategy of “combination-oriented molecular-targeting prevention” of cancer will be a practical approach for chemoprevention against human malignant tumors. PMID:21432546

Avoiding polar catastrophe in the growth of polarly orientated nickel perovskite thin films by reactive oxide molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Yang, H. F.; Liu, Z. T.; Fan, C. C.; Yao, Q.; Xiang, P.; Zhang, K. L.; Li, M. Y.; Liu, J. S.; Shen, D. W.

2016-08-01

By means of the state-of-the-art reactive oxide molecular beam epitaxy, we synthesized (001)- and (111)-orientated polar LaNiO3 thin films. In order to avoid the interfacial reconstructions induced by polar catastrophe, screening metallic Nb-doped SrTiO3 and iso-polarity LaAlO3 substrates were chosen to achieve high-quality (001)-orientated films in a layer-by-layer growth mode. For largely polar (111)-orientated films, we showed that iso-polarity LaAlO3 (111) substrate was more suitable than Nb-doped SrTiO3. In situ reflection high-energy electron diffraction, ex situ high-resolution X-ray diffraction, and atomic force microscopy were used to characterize these films. Our results show that special attentions need to be paid to grow high-quality oxide films with polar orientations, which can prompt the explorations of all-oxide electronics and artificial interfacial engineering to pursue intriguing emergent physics like proposed interfacial superconductivity and topological phases in LaNiO3 based superlattices.

Genetic interactions underlying tree branch orientation

USDA-ARS?s Scientific Manuscript database

Expanding our understanding of the molecular and genetic mechanisms behind branch orientation in trees both addresses a fundamental developmental phenomenon and can lead to significant impacts on tree crop agriculture and forestry. Using the p-nome (pooled genome) sequencing-based mapping approac...

Robust averaging protects decisions from noise in neural computations

PubMed Central

Herce Castañón, Santiago; Solomon, Joshua A.; Vandormael, Hildward

2017-01-01

An ideal observer will give equivalent weight to sources of information that are equally reliable. However, when averaging visual information, human observers tend to downweight or discount features that are relatively outlying or deviant (‘robust averaging’). Why humans adopt an integration policy that discards important decision information remains unknown. Here, observers were asked to judge the average tilt in a circular array of high-contrast gratings, relative to an orientation boundary defined by a central reference grating. Observers showed robust averaging of orientation, but the extent to which they did so was a positive predictor of their overall performance. Using computational simulations, we show that although robust averaging is suboptimal for a perfect integrator, it paradoxically enhances performance in the presence of “late” noise, i.e. which corrupts decisions during integration. In other words, robust decision strategies increase the brain’s resilience to noise arising in neural computations during decision-making. PMID:28841644

The relation between the column density structures and the magnetic field orientation in the Vela C molecular complex

NASA Astrophysics Data System (ADS)

Soler, J. D.; Ade, P. A. R.; Angilè, F. E.; Ashton, P.; Benton, S. J.; Devlin, M. J.; Dober, B.; Fissel, L. M.; Fukui, Y.; Galitzki, N.; Gandilo, N. N.; Hennebelle, P.; Klein, J.; Li, Z.-Y.; Korotkov, A. L.; Martin, P. G.; Matthews, T. G.; Moncelsi, L.; Netterfield, C. B.; Novak, G.; Pascale, E.; Poidevin, F.; Santos, F. P.; Savini, G.; Scott, D.; Shariff, J. A.; Thomas, N. E.; Tucker, C. E.; Tucker, G. S.; Ward-Thompson, D.

2017-07-01

We statistically evaluated the relative orientation between gas column density structures, inferred from Herschel submillimetre observations, and the magnetic field projected on the plane of sky, inferred from polarized thermal emission of Galactic dust observed by the Balloon-borne Large-Aperture Submillimetre Telescope for Polarimetry (BLASTPol) at 250, 350, and 500 μm, towards the Vela C molecular complex. First, we find very good agreement between the polarization orientations in the three wavelength-bands, suggesting that, at the considered common angular resolution of 3.´0 that corresponds to a physical scale of approximately 0.61 pc, the inferred magnetic field orientation is not significantly affected by temperature or dust grain alignment effects. Second, we find that the relative orientation between gas column density structures and the magnetic field changes progressively with increasing gas column density, from mostly parallel or having no preferred orientation at low column densities to mostly perpendicular at the highest column densities. This observation is in agreement with previous studies by the Planck collaboration towards more nearby molecular clouds. Finally, we find a correspondencebetween (a) the trends in relative orientation between the column density structures and the projected magnetic field; and (b) the shape of the column density probability distribution functions (PDFs). In the sub-regions of Vela C dominated by one clear filamentary structure, or "ridges", where the high-column density tails of the PDFs are flatter, we find a sharp transition from preferentially parallel or having no preferred relative orientation at low column densities to preferentially perpendicular at highest column densities. In the sub-regions of Vela C dominated by several filamentary structures with multiple orientations, or "nests", where the maximum values of the column density are smaller than in the ridge-like sub-regions and the high-column density tails of the PDFs are steeper, such a transition is also present, but it is clearly less sharp than in the ridge-like sub-regions. Both of these results suggest that the magnetic field is dynamically important for the formation of density structures in this region.

An infrared and Raman study of the reorientational motions and phase transition in and structure of CsPF6

NASA Astrophysics Data System (ADS)

Heyns, Anton M.; de Waal, Danita

1992-12-01

CsPF6I is face-centered cubic and the PF6- ions are randomly distributed among the six equivalent orientations in the crystal. The ions librate in equilibrium positions for an average time τ, and also jump from one orientation to another in a time which is much shorter than τ. The six different orientations in CsPF6I are of much lower symmetry than the full molecular one. The full vibrational spectra of CsPF6 are reported over the temperature range of 300-4 K and can be analyzed in Phase I in terms of (Oh,C¯4v) where C¯4v denotes the symmetry of the ion and Oh that of the site symmetry S. The polarized Raman spectra of single crystals of CsPF6I are interpreted in terms of all the different orientations of the PF6- ions and excellent agreement is obtained between predicted and experimental results. At 90 K CsPF6 undergoes a phase transition and a crystal structure of P4/nmm-D4h7 is assigned to Phase II. This transition is of the second order and shows behavior which corresponds to those of critical phenomena. An order parameter ξ is defined and a critical constant β is calculated to be equal to 0.3. In CsPF6II two orientations of the PF6- ions exist, both conforming to 4mm-C4v symmetry and the disorder persisting in this phase causes the splitting of the vibrational bands to be fully resolved below 60 K only. An activation energy of ˜3.0 kJ/mol is calculated for the motions of the PF6- ions between 90 and 60 K from the variation of the linewidths and intensities of vibrational bands.

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.

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.

Alienation, learning or grade orientation, and achievement as correlates of attitudes toward cheating.

PubMed

Roig, M; Neaman, M A

1994-06-01

154 undergraduate students were given Gardner and Melvin's Attitudes Toward Cheating Scale, Ray's General Alienation Scale, and Eison's Learning Orientation/Grade Orientation Scale. Scores indicating condemnatory (unfavorable) attitudes toward cheating were positively correlated with grade point average and negatively correlated with alienation. Our results are consistent with a previous study which showed an association between cheating and alienation.

Shock wave-induced phase transition in RDX single crystals.

PubMed

Patterson, James E; Dreger, Zbigniew A; Gupta, Yogendra M

2007-09-20

The real-time, molecular-level response of oriented single crystals of hexahydro-1,3,5-trinitro-s-triazine (RDX) to shock compression was examined using Raman spectroscopy. Single crystals of [111], [210], or [100] orientation were shocked under stepwise loading to peak stresses from 3.0 to 5.5 GPa. Two types of measurements were performed: (i) high-resolution Raman spectroscopy to probe the material at peak stress and (ii) time-resolved Raman spectroscopy to monitor the evolution of molecular changes as the shock wave reverberated through the material. The frequency shift of the CH stretching modes under shock loading appeared to be similar for all three crystal orientations below 3.5 GPa. Significant spectral changes were observed in crystals shocked above 4.5 GPa. These changes were similar to those observed in static pressure measurements, indicating the occurrence of the alpha-gamma phase transition in shocked RDX crystals. No apparent orientation dependence in the molecular response of RDX to shock compression up to 5.5 GPa was observed. The phase transition had an incubation time of approximately 100 ns when RDX was shocked to 5.5 GPa peak stress. The observation of the alpha-gamma phase transition under shock wave loading is briefly discussed in connection with the onset of chemical decomposition in shocked RDX.

Characterization of the Adult Head Transcriptome and Identification of Migration and Olfaction Genes in the Oriental Armyworm Mythimna separate.

PubMed

Bian, Hai-Xu; Ma, Hong-Fang; Zheng, Xi-Xi; Peng, Ming-Hui; Li, Yu-Ping; Su, Jun-Fang; Wang, Huan; Li, Qun; Xia, Run-Xi; Liu, Yan-Qun; Jiang, Xing-Fu

2017-05-24

The oriental armyworm Mythimna separate is an economically important insect with a wide distribution and strong migratory activity. However, knowledge about the molecular mechanisms regulating the physiological and behavioural responses of the oriental armyworm is scarce. In the present study, we took a transcriptomic approach to characterize the gene network in the adult head of M. separate. The sequencing and de novo assembly yielded 63,499 transcripts, which were further assembled into 46,459 unigenes with an N50 of 1,153 bp. In the head transcriptome data, unigenes involved in the 'signal transduction mechanism' are the most abundant. In total, 937 signal transduction unigenes were assigned to 22 signalling pathways. The circadian clock, melanin synthesis, and non-receptor protein of olfactory gene families were then identified, and phylogenetic analyses were performed with these M. separate genes, the model insect Bombyx mori and other insects. Furthermore, 1,372 simple sequence repeats of 2-6 bp in unit length were identified. The transcriptome data represent a comprehensive molecular resource for the adult head of M. separate, and these identified genes can be valid targets for further gene function research to address the molecular mechanisms regulating the migratory and olfaction genes of the oriental armyworm.

Examining the Self-Assembly of Rod-Coil Block Copolymers via Physics Based Polymer Models and Polarized X-Ray Scattering

NASA Astrophysics Data System (ADS)

Hannon, Adam; Sunday, Daniel; Windover, Donald; Liman, Christopher; Bowen, Alec; Khaira, Gurdaman; de Pablo, Juan; Delongchamp, Dean; Kline, R. Joseph

Photovoltaics, flexible electronics, and stimuli-responsive materials all require enhanced methodology to examine their nanoscale molecular orientation. The mechanical, electronic, optical, and transport properties of devices made from these materials are all a function of this orientation. The polymer chains in these materials are best modeled as semi-flexible to rigid rods. Characterizing the rigidity and molecular orientation of these polymers non-invasively is currently being pursued by using polarized resonant soft X-ray scattering (P-RSoXS). In this presentation, we show recent work on implementing such a characterization process using a rod-coil block copolymer system in the rigid-rod limit. We first demonstrate how we have used physics based models such as self-consistent field theory (SCFT) in non-polarized RSoXS work to fit scattering profiles for thin film coil-coil PS- b-PMMA block copolymer systems. We then show by using a wormlike chain partition function in the SCFT formulism to model the rigid-rod block, the methodology can be used there as well to extract the molecular orientation of the rod block from a simulated P-RSoXS experiment. The results from the work show the potential of the technique to extract thermodynamic and morphological sample information.

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.

Mean-field density functional theory of a nanoconfined classical, three-dimensional Heisenberg fluid. I. The role of molecular anchoring

NASA Astrophysics Data System (ADS)

Cattes, Stefanie M.; Gubbins, Keith E.; Schoen, Martin

2016-05-01

In this work, we employ classical density functional theory (DFT) to investigate for the first time equilibrium properties of a Heisenberg fluid confined to nanoscopic slit pores of variable width. Within DFT pair correlations are treated at modified mean-field level. We consider three types of walls: hard ones, where the fluid-wall potential becomes infinite upon molecular contact but vanishes otherwise, and hard walls with superimposed short-range attraction with and without explicit orientation dependence. To model the distance dependence of the attractions, we employ a Yukawa potential. The orientation dependence is realized through anchoring of molecules at the substrates, i.e., an energetic discrimination of specific molecular orientations. If the walls are hard or attractive without specific anchoring, the results are "quasi-bulk"-like in that they can be linked to a confinement-induced reduction of the bulk mean field. In these cases, the precise nature of the walls is completely irrelevant at coexistence. Only for specific anchoring nontrivial features arise, because then the fluid-wall interaction potential affects the orientation distribution function in a nontrivial way and thus appears explicitly in the Euler-Lagrange equations to be solved for minima of the grand potential of coexisting phases.

Electron paramagnetic resonance study of alinement induced by magnetic fields in two smectic-A liquid crystals not exhibiting nematic phases

NASA Technical Reports Server (NTRS)

Fryburg, G. C.; Gelerinter, E.

1972-01-01

Using vanadyl acetylacetonate (VAAC) as a paramagnetic probe, the molecular ordering in two smectic-A liquid crystals that do not display nematic phases were studied. Reproducible alinement was attained by slow cooling throughout the isotropic smectic-A transition in dc magnetic fields of 1.1 and 2.15 teslas. The degree of order attained is small for a smectic-A liquid crystal. Measurements were made of the variation of the average hyperfine splitting of the alined samples as a function of orientation relative to the dc magnetic field of the spectrometer. This functional dependence is in agreement with the theoretical prediction except where the viscosity of the liquid crystal becomes large enough to slow the tumbling of the VAAC, as indicated by asymmetry in the end lines of the spectrum.

Birefringence control of solution-cast film of cellulose triacetate

NASA Astrophysics Data System (ADS)

Kiyama, Ayumi; Nobukawa, Shogo; Yamaguchi, Masayuki

2017-10-01

We controlled the optical anisotropy of a solution-cast film composed of cellulose triacetate (CTA) by adding ferrocene. Owing to the molecular orientation in the film plane of solution-cast films, which results from the normal stress applied during the solvent evaporation process, the average refractive index is usually higher in the plane of the film than in the thickness direction. We found that the addition of ferrocene, which is miscible with CTA, reduced the optical anisotropy by nematic interaction; i.e., ferrocene molecules are forcibly embedded into the film plane accompanying the CTA chains. Because the direction of anisotropic polarizability of ferrocene is perpendicular to the long axis of the molecule, the refractive index in the thickness direction is reduced. Furthermore, the stress-optical coefficient in the glassy state is reduced by the addition of ferrocene.

Vertical transport in isotype InAlN/GaN dipole induced diodes grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Fireman, M. N.; Li, Haoran; Keller, Stacia; Mishra, Umesh K.; Speck, James S.

2017-05-01

InAlN dipole diodes were developed and fabricated on both (0001) Ga-Face and (" separators="| 000 1 ¯) N-face oriented GaN on sapphire templates by molecular beam epitaxy. The orientation and direction of the InAlN polarization dipole are functions of the substrate orientation and composition, respectively. Special consideration was taken to minimize growth differences and impurity uptake during growth on these orientations of opposite polarity. Comparison of devices on similarly grown structures with In compositions in excess of 50% reveals that dipole diodes shows poorer forward bias performance and exhibited an increase in reverse bias leakage, regardless of orientation. Similarly, (0001) Ga-face oriented InAlN at a lowered 40% In composition had poor device characteristics, namely, the absence of expected exponential turn on in forward bias. By contrast, at In compositions close to 40%, (" separators="| 000 1 ¯) N-face oriented InAlN devices had excellent performance, with over five orders of magnitude of rectification and extracted barrier heights of 0.53- 0.62 eV; these values are in close agreement with simulation. Extracted ideality factors ranging from 1.08 to 1.38 on these devices are further evidence of their optimal performance. Further discussion focuses on the growth and orientation conditions that may lead to this discrepancy yet emphasizes that with proper design and growth strategy, the rectifying dipole diodes can be achieved with InAlN nitride dipole layers.

The good pharmacy practice on Einstein Program at Paraisópolis Community

PubMed Central

de Oliveira, Lara Tânia de Assumpção Domingues Gonçalves; da Silva, Camila Pontes; Guedes, Maria das Vitorias; Sousa, Ana Célia de Oliveira; Sarno, Flávio

2016-01-01

ABSTRACT Objectives: To describe indicators and processes developed and implemented for pharmaceutical assistance at the Einstein Program at Paraisópolis Community pharmacy. Methods: This was a descriptive study of retrospective data from January 2012 to December 2015. Data were obtained from spreadsheets developed for monitoring the productivity and care quality provided at the pharmacy. The evaluated variables were pharmaceutical assistance to prescription, pharmaceutical intervention, orientation (standard and pharmaceutical) and pharmaceutical orientation rate. Results: The pharmacy assisted, on average, 2,308 prescriptions monthly, dispensing 4,871 items, including medications, materials and food supplements. Since March 2015, virtually, the pharmacist analyzed all prescriptions, prior to dispensing. In the analyzed period, there was an increase in monthly pharmaceutical interventions from 7 to 32 on average, and, although there was a decrease in the number of standard orientation, the pharmaceutical orientation had an increase, causing a rise of pharmaceutical orientation rate from 4 to 11%. Conclusion: The processes developed and implemented at the program pharmacy sought to follow the good pharmacy practice, and help patients to make the best use of their medications. PMID:27759833

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.

Birefringent Stable Glass with Predominantly Isotropic Molecular Orientation

NASA Astrophysics Data System (ADS)

Liu, Tianyi; Exarhos, Annemarie L.; Alguire, Ethan C.; Gao, Feng; Salami-Ranjbaran, Elmira; Cheng, Kevin; Jia, Tiezheng; Subotnik, Joseph E.; Walsh, Patrick J.; Kikkawa, James M.; Fakhraai, Zahra

2017-09-01

Birefringence in stable glasses produced by physical vapor deposition often implies molecular alignment similar to liquid crystals. As such, it remains unclear whether these glasses share the same energy landscape as liquid-quenched glasses that have been aged for millions of years. Here, we produce stable glasses of 9-(3,5-di(naphthalen-1-yl)phenyl)anthracene molecules that retain three-dimensional shapes and do not preferentially align in a specific direction. Using a combination of angle- and polarization-dependent photoluminescence and ellipsometry experiments, we show that these stable glasses possess a predominantly isotropic molecular orientation while being optically birefringent. The intrinsic birefringence strongly correlates with increased density, showing that molecular ordering is not required to produce stable glasses or optical birefringence, and provides important insights into the process of stable glass formation via surface-mediated equilibration. To our knowledge, such novel amorphous packing has never been reported in the past.

Faunus: An object oriented framework for molecular simulation

PubMed Central

Lund, Mikael; Trulsson, Martin; Persson, Björn

2008-01-01

Background We present a C++ class library for Monte Carlo simulation of molecular systems, including proteins in solution. The design is generic and highly modular, enabling multiple developers to easily implement additional features. The statistical mechanical methods are documented by extensive use of code comments that – subsequently – are collected to automatically build a web-based manual. Results We show how an object oriented design can be used to create an intuitively appealing coding framework for molecular simulation. This is exemplified in a minimalistic C++ program that can calculate protein protonation states. We further discuss performance issues related to high level coding abstraction. Conclusion C++ and the Standard Template Library (STL) provide a high-performance platform for generic molecular modeling. Automatic generation of code documentation from inline comments has proven particularly useful in that no separate manual needs to be maintained. PMID:18241331

Dipole-Oriented Molecular Solids Can Undergo a Phase Change and Still Maintain Electrical Polarization

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

Cassidy, Andrew; Jørgensen, Mads R. V.; Rosu-Finsen, Alexander

2016-10-02

It has recently been demonstrated that nanoscale molecular films can spontaneously assemble to self-generate intrinsic electric fields that can exceed 10 8 V/m. These electric fields originate from polarization charges in the material that arise because the films self-assemble to orient molecular dipole moments. This has been called the spontelectric effect. Such growth of spontaneously polarized layers of molecular solids has implications for our understanding of how intermolecular interactions dictate the structure of molecular materials used in a range of applications, for example, molecular semiconductors, sensors, and catalysts. In this paper, we present the first in situ structural characterization ofmore » a representative spontelectric solid, nitrous oxide. Infrared spectroscopy, temperature-programmed desorption, and neutron reflectivity measurements demonstrate that polarized films of nitrous oxide undergo a structural phase transformation upon heating above 48 K. A mean-field model can be used to describe quantitatively the magnitude of the spontaneously generated field as a function of film-growth temperature, and this model also recreates the phase change. Finally, this reinforces the spontelectric model as a means of describing long-range dipole–dipole interactions and points to a new type of ordering in molecular thin films.« less

Energetic basis for the molecular-scale organization of bone

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

Tao, Jinhui; Battle, Keith C.; Pan, Haihua

2014-12-24

The remarkable properties of bone derive from a highly organized arrangement of co-aligned nm-scale apatite platelets within a fibrillar collagen matrix. The origin of this arrangement is poorly understood and the crystal structures of hydroxyapatite (HAP) and the non-mineralized collagen fibrils alone do not provide an explanation. Moreover, little is known about collagen-apatite interaction energies, which should strongly influence both the molecular-scale organization and the resulting mechanical properties of the composite. We investigated collagen-mineral interactions by combining dynamic force spectroscopy (DFS) measurements of binding energies with molecular dynamics (MD) simulations of binding and AFM observations of collagen adsorption on singlemore » crystals of calcium phosphate for four mineral phases of potential importance in bone formation. In all cases, we observe a strong preferential orientation of collagen binding, but comparison between the observed orientations and TEM analyses native tissues shows only calcium-deficient apatite (CDAP) provides an interface with collagen that is consistent with both. MD simulations predict preferred collagen orientations that agree with observations and results from both MD and DFS reveal large values for the binding energy due to multiple binding sites. These findings reconcile apparent contradictions inherent in a hydroxyapatite or carbonated apatite (CAP) model of bone mineral and provide an energetic rationale for the molecular scale organization of bone.« less

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.

Energetic basis for the molecular-scale organization of bone

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

Tao, Jinhui; Battle, Keith C.; Pan, Haihua

The remarkable properties of bone derive from a highly organized arrangement of co-aligned nm-scale apatite platelets within a fibrillar collagen matrix. The origin of this arrangement is poorly understood and the crystal structures of hydroxyapatite (HAP) and the non-mineralized collagen fibrils alone do not provide an explanation. Moreover, little is known about collagen-apatite interaction energies, which should strongly influence both the molecular-scale organization and the resulting mechanical properties of the composite. We investigated collagen-mineral interactions by combining dynamic force spectroscopy (DFS) measurements of binding energies with molecular dynamics (MD) simulations of binding and AFM observations of collagen adsorption on singlemore » crystals of calcium phosphate for four mineral phases of potential importance in bone formation. In all cases, we observe a strong preferential orientation of collagen binding, but comparison between the observed orientations and TEM analyses native tissues shows only calcium-deficient apatite (CDAP) provides an interface with collagen that is consistent with both. MD simulations predict preferred collagen orientations that agree with observations and results from both MD and DFS reveal large values for the binding energy due to multiple binding sites. These findings reconcile apparent contradictions inherent in a hydroxyapatite or carbonated apatite (CAP) model of bone mineral and provide an energetic rationale for the molecular scale organization of bone.« less

Pubertal Stress and Nutrition and their Association with Sexual Orientation and Height in the Add Health Data

PubMed Central

Bogaert, Anthony F.

2018-01-01

A number of studies have indicated that gay men tend to be shorter, on average, than heterosexual men. Less evidence exists that lesbian women are taller, on average, than heterosexual women. The most popular explanation of the association between sexual orientation and height involves prenatal factors, such that, for example, gay men may have been exposed to lower than typical androgens during fetal development, which impacts their height and sexual orientation as adults. An alternative explanation involves stress, given that stress has been associated with sexual minority identification and with lower height. Another alternative explanation involves nutrition, although its relationship is less clear with sexual minority identification. Using the Add Health data, which is a large, nationally representative and longitudinal sample of American adolescents (n = 14,786), we tested a mediation model, such that sexual orientation → pubertal stress/nutrition → height. Within men, we found that gay men (n = 126) were shorter, on average, than heterosexual men (n = 6412). None of the 24 pubertal stress-related and 15 pubertal nutrition-related variables assessed in the Add Health data mediated the relationship between sexual orientation and height in men. Within women, lesbians (n = 75) did not differ significantly in stature compared to heterosexual women (n = 6267). Thus, prenatal mechanisms (e.g., hormones, maternal immune response) are likely better candidates for explaining the height difference between gay men and heterosexual men. PMID:27511207

Pubertal Stress and Nutrition and their Association with Sexual Orientation and Height in the Add Health Data.

PubMed

Skorska, Malvina N; Bogaert, Anthony F

2017-01-01

A number of studies have indicated that gay men tend to be shorter, on average, than heterosexual men. Less evidence exists that lesbian women are taller, on average, than heterosexual women. The most popular explanation of the association between sexual orientation and height involves prenatal factors, such that, for example, gay men may have been exposed to lower than typical androgens during fetal development, which impacts their height and sexual orientation as adults. An alternative explanation involves stress, given that stress has been associated with sexual minority identification and with lower height. Another alternative explanation involves nutrition, although its relationship is less clear with sexual minority identification. Using the Add Health data, which is a large, nationally representative and longitudinal sample of American adolescents (n = 14,786), we tested a mediation model, such that sexual orientation → pubertal stress/nutrition → height. Within men, we found that gay men (n = 126) were shorter, on average, than heterosexual men (n = 6412). None of the 24 pubertal stress-related and 15 pubertal nutrition-related variables assessed in the Add Health data mediated the relationship between sexual orientation and height in men. Within women, lesbians (n = 75) did not differ significantly in stature compared to heterosexual women (n = 6267). Thus, prenatal mechanisms (e.g., hormones, maternal immune response) are likely better candidates for explaining the height difference between gay men and heterosexual men.

Quinuclidinium salt ferroelectric thin-film with duodecuple-rotational polarization-directions

NASA Astrophysics Data System (ADS)

You, Yu-Meng; Tang, Yuan-Yuan; Li, Peng-Fei; Zhang, Han-Yue; Zhang, Wan-Ying; Zhang, Yi; Ye, Heng-Yun; Nakamura, Takayoshi; Xiong, Ren-Gen

2017-04-01

Ferroelectric thin-films are highly desirable for their applications on energy conversion, data storage and so on. Molecular ferroelectrics had been expected to be a better candidate compared to conventional ferroelectric ceramics, due to its simple and low-cost film-processability. However, most molecular ferroelectrics are mono-polar-axial, and the polar axes of the entire thin-film must be well oriented to a specific direction to realize the macroscopic ferroelectricity. To align the polar axes, an orientation-controlled single-crystalline thin-film growth method must be employed, which is complicated, high-cost and is extremely substrate-dependent. In this work, we discover a new molecular ferroelectric of quinuclidinium periodate, which possesses six-fold rotational polar axes. The multi-axes nature allows the thin-film of quinuclidinium periodate to be simply prepared on various substrates including flexible polymer, transparent glasses and amorphous metal plates, without considering the crystallinity and crystal orientation. With those benefits and excellent ferroelectric properties, quinuclidinium periodate shows great potential in applications like wearable devices, flexible materials, bio-machines and so on.

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.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D).

PubMed

van de Streek, Jacco; Neumann, Marcus A

2014-12-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

PubMed Central

van de Streek, Jacco; Neumann, Marcus A.

2014-01-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom. PMID:25449625

Factors determining electrostatic fields in molecular dynamics simulations of the Ras/effector interface.

PubMed

Ensign, Daniel L; Webb, Lauren J

2011-12-01

Using molecular dynamics simulations, we explore geometric and physical factors contributing to calculated electrostatic fields at the binding surface of the GTPase Ras with a spectroscopically labeled variant of a downstream effector, the Ras-binding domain of Ral guanine nucleotide dissociation stimulator (RalGDS). A related system (differing by mutation of one amino acid) has been studied in our group using vibrational Stark effect spectroscopy, a technique sensitive to electrostatic fields. Electrostatic fields were computed using the AMBER 2003 force field and averaged over snapshots from molecular dynamics simulation. We investigate geometric factors by exploring how the orientation of the spectroscopic probe changes on Ras-effector binding. In addition, we explore the physical origin of electrostatic fields at our spectroscopic probe by comparing contributions to the field from discrete components of the system, such as explicit solvent, residues on the Ras surface, and residues on the RalGDS surface. These models support our experimental hypothesis that vibrational Stark shifts are caused by Ras binding to its effector and not the structural rearrangements of the effector surface or probe reorientation on Ras-effector binding, for at least some of our experimental probes. These calculations provide physical insight into the origin, magnitude, and importance of electrostatic fields in protein-protein interactions and suggest new experiments to probe the field's role in protein docking. Copyright © 2011 Wiley-Liss, Inc.

Understanding the Association Between School Climate and Future Orientation.

PubMed

Lindstrom Johnson, Sarah; Pas, Elise; Bradshaw, Catherine P

2016-08-01

Promoting students' future orientation is inherently a goal of the educational system. Recently, it has received more explicit attention given the increased focus on career readiness. This study aimed to examine the association between school climate and adolescents' report of future orientation using data from youth (N = 27,698; 49.4 % female) across 58 high schools. Three-level hierarchical linear models indicated that perceptions of available emotional and service supports, rules and consequences, and parent engagement were positively related to adolescents' future orientation. Additionally, the school-level average future orientation was significantly related to individuals' future orientation, indicating a potential influence of contextual effects on this construct. Taken together, these findings suggest that interventions targeting school climate may hold promise for promoting future orientation.

Seismic properties and mineral crystallographic preferred orientations from EBSD data: Results from a crustal-scale detachment system, Aegean region

NASA Astrophysics Data System (ADS)

Cossette, Élise; Schneider, David; Audet, Pascal; Grasemann, Bernhard; Habler, Gerlinde

2015-05-01

The crystallographic preferred orientations (CPOs) were measured on a suite of samples representative of different structural depths along the West Cycladic Detachment System, Greece. Electron backscatter diffraction (EBSD) analyses were conducted on calcitic and mica schists, impure quartzites, and a blueschist, and the average seismic properties of the rocks were calculated with the Voigt-Reuss-Hill average of the single minerals' elastic stiffness tensor. The calcitic and quartzitic rocks have P- and S-wave velocity anisotropies (AVp, AVs) averaging 8.1% and 7.1%, respectively. The anisotropy increases with depth represented by the blueschist, with AVp averaging 20.3% and AVs averaging 14.5%, due to the content of aligned glaucophane and mica, which strongly control the seismic properties of the rocks. Localised anisotropies of very high magnitudes are caused by the presence of mica schists as they possess the strongest anisotropies, with values of ~ 25% for AVp and AVs. The direction of the fast and slow P-wave velocities occurs parallel and perpendicular to the foliation, respectively, for most samples. The fast propagation has the same NE-SW orientation as the lithospheric stretching direction experienced in the Cyclades since the Late Oligocene. The maximum shear wave anisotropy is subhorizontal, similarly concordant with mineral alignment that developed during extension in the Aegean. Radial anisotropy in the Aegean mid-crust is strongly favoured to azimuthal anisotropy by our results.

Effects of field orientation during 700-MHz radiofrequency irradiation of rats

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

Frei, M.R.; Jauchem, J.R.; Padilla, J.M.

1989-01-01

Ketamine-anesthetized Sprague-Dawley rats were exposed to far-field 700-MHz continuous-wave radiofrequency radiation (RFR) in both E and H orientations. Irradiation was conducted at whole-body average specific absorption rates (SARs) of 9.2 and 13.0 W/kg (E and H, respectively) that resulted in approximately equivalent colonic specific heating rates (SHRs). Exposures were performed to repeatedly increase colonic temperature by 1 deg C (38.5 to 39.5 deg C). Tympanic, tail, left and right subcutaneous (toward and away from RFR source), and colonic temperatures, arterial blood pressure, and respiratory rate were continuously recorded. In spite of equivalent colonic SHRs and the reduced E-orientation average SAR,more » the right subcutaneous, tympanic, and tail SARs, SHRs and absolute temperature increases were significantly greater in E than in H orientation. The cooling rate at all monitoring sites was also significantly greater in E than in H orientation. Heart rate and mean arterial blood pressure significantly increased during irradiation; however, changer between orientations were not different. Respiratory rate significantly increased during irradiation in H, but not in E orientation. These results indicate that during resonant frequency irradiation, differences occur in the pattern of heat deposition between E- and H-orientation exposure. When compared with previous investigations performed at supraresonant frequencies, the lower level of cardiovascular change in this study was probably related to the lower periphery-to-core thermal gradient.« less

Effects of field orientation during 700-MHz radiofrequency irradiation of rats

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

Frei, M.R.; Jauchem, J.R.; Padilla, J.M.

1989-01-01

Ketamine-anesthetized Sprague-Dawley rats were exposed to far-field 700-MHz continuous-wave radiofrequency radiation (RFR) in both E and H orientations. Irradiation was conducted at whole-body average specific absorption rates (SARs) of 9.2 and 13.0 W/kg (E and H, respectively) that resulted in approximately equivalent colonic specific heating rates (SHRs). Exposures were performed to repeatedly increase colonic temperature by 1 degree C (38.5 to 39.5 degrees C). Tympanic, tail, left and right subcutaneous (toward and away from RFR source), and colonic temperatures, arterial blood pressure, and respiratory rate were continuously recorded. In spite of equivalent colonic SHRs and the reduced E-orientation average SAR,more » the right subcutaneous, tympanic, and tail SARs, SHRs and absolute temperature increases were significantly greater in E than in H orientation. The cooling rate at all monitoring sites was also significantly greater in E than in H orientation. Heart rate and mean arterial blood pressure significantly increased during irradiation; however, changes between orientations were not different. Respiratory rate significantly increased during irradiation in H, but not in E orientation. These results indicate that during resonant frequency irradiation, differences occur in the pattern of heat deposition between E- and H-orientation exposure. When compared with previous investigations performed at supraresonant frequencies, the lower level of cardiovascular change in this study was probably related to the lower periphery-to-core thermal gradient.« less

Avoiding polar catastrophe in the growth of polarly orientated nickel perovskite thin films by reactive oxide molecular beam epitaxy

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

Yang, H. F.; Liu, Z. T.; Fan, C. C.

2016-08-15

By means of the state-of-the-art reactive oxide molecular beam epitaxy, we synthesized (001)- and (111)-orientated polar LaNiO{sub 3} thin films. In order to avoid the interfacial reconstructions induced by polar catastrophe, screening metallic Nb-doped SrTiO{sub 3} and iso-polarity LaAlO{sub 3} substrates were chosen to achieve high-quality (001)-orientated films in a layer-by-layer growth mode. For largely polar (111)-orientated films, we showed that iso-polarity LaAlO{sub 3} (111) substrate was more suitable than Nb-doped SrTiO{sub 3}. In situ reflection high-energy electron diffraction, ex situ high-resolution X-ray diffraction, and atomic force microscopy were used to characterize these films. Our results show that special attentionsmore » need to be paid to grow high-quality oxide films with polar orientations, which can prompt the explorations of all-oxide electronics and artificial interfacial engineering to pursue intriguing emergent physics like proposed interfacial superconductivity and topological phases in LaNiO{sub 3} based superlattices.« less

Flipped Phenyl Ring Orientations of Dopamine Binding with Human and Drosophila Dopamine Transporters: Remarkable Role of Three Nonconserved Residues.

PubMed

Yuan, Yaxia; Zhu, Jun; Zhan, Chang-Guo

2018-03-09

Molecular modeling and molecular dynamics simulations were performed in the present study to examine the modes of dopamine binding with human and Drosophila dopamine transporters (hDAT and dDAT). The computational data revealed flipped binding orientations of dopamine in hDAT and dDAT due to the major differences in three key residues (S149, G153, and A423 of hDAT vs A117, D121, and S422 of dDAT) in the binding pocket. These three residues dictate the binding orientation of dopamine in the binding pocket, as the aromatic ring of dopamine tends to take an orientation with both the para- and meta-hydroxyl groups being close to polar residues and away from nonpolar residues of the protein. The flipped binding orientations of dopamine in hDAT and dDAT clearly demonstrate a generally valuable insight concerning how the species difference could drastically affect the protein-ligand binding modes, demonstrating that the species difference, which is a factor rarely considered in early drug design stage, must be accounted for throughout the ligand/drug design and discovery processes in general.

A new formulation of the dispersion tensor in homogeneous porous media

NASA Astrophysics Data System (ADS)

Valdés-Parada, Francisco J.; Lasseux, Didier; Bellet, Fabien

2016-04-01

Dispersion is the result of two mass transport processes, namely molecular diffusion, which is a pure mixing effect and hydrodynamic dispersion, which combines mixing and spreading. The identification of each contribution is crucial and is often misinterpreted. Traditionally, under a volume averaging framework, a single closure problem is solved and the resulting fields are substituted into diffusive and dispersive filters. However the diffusive filter (that leads to the effective diffusivity) allows passing information from convection, which leads to an incorrect definition of the effective medium coefficients composing the total dispersion tensor. In this work, we revisit the definitions of the effective diffusivity and hydrodynamic dispersion tensors using the method of volume averaging. Our analysis shows that, in the context of laminar flow with or without inertial effects, two closure problems need to be computed in order to correctly define the corresponding effective medium coefficients. The first closure problem is associated to momentum transport and needs to be solved for a prescribed Reynolds number and flow orientation. The second closure problem is related to mass transport and it is solved first with a zero Péclet number and second with the required Péclet number and flow orientation. All the closure problems are written using closure variables only as required by the upscaling method. The total dispersion tensor is shown to depend on the microstructure, macroscopic flow angles, the cell (or pore) Péclet number and the cell (or pore) Reynolds number. It is non-symmetric in the general case. The condition for quasi-symmetry is highlighted. The functionality of the longitudinal and transverse components of this tensor with the flow angle is investigated for a 2D model porous structure obtaining consistent results with previous studies.

Relationship between open-circuit voltage in Cu(In,Ga)Se2 solar cell and peak position of (220/204) preferred orientation near its absorber surface

NASA Astrophysics Data System (ADS)

Chantana, J.; Watanabe, T.; Teraji, S.; Kawamura, K.; Minemoto, T.

2013-11-01

Cu(In,Ga)Se2 (CIGS) absorbers with various Ga/III, Ga/(In+Ga), profiles are prepared by the so-called "multi-layer precursor method" using multi-layer co-evaporation of material sources. It is revealed that open-circuit voltage (VOC) of CIGS solar cell is primarily dependent on averaged Ga/III near the surface of its absorber. This averaged Ga/III is well predicted by peak position of (220/204) preferred orientation of CIGS film near its surface investigated by glancing-incidence X-ray diffraction with 0.1° incident angle. Finally, the peak position of (220/204) preferred orientation is proposed as a measure of VOC before solar cell fabrication.

Vibrational sum-frequency generation spectroscopy of lipid bilayers at repetition rates up to 100 kHz

NASA Astrophysics Data System (ADS)

Yesudas, Freeda; Mero, Mark; Kneipp, Janina; Heiner, Zsuzsanna

2018-03-01

Broadband vibrational sum-frequency generation (BB-VSFG) spectroscopy has become a well-established surface analytical tool capable of identifying the orientation and structure of molecular layers. A straightforward way to boost the sensitivity of the technique could be to increase the laser repetition rate beyond that of standard BB-VSFG spectrometers, which rely on Ti:sapphire lasers operating at repetition rates of 1-5 kHz. Nevertheless, possible thermally induced artifacts in the vibrational spectra due to higher laser average powers are unexplored. Here, we discuss laser power induced temperature accumulation effects that distort the BB-VSFG spectra of 1,2-diacyl-sn-glycero-3-phosphocholine at an interface between two transparent phases at repetition rates of 5, 10, 50, and 100 kHz at constant pulse energy. No heat-induced distortions were found in the spectra, suggesting that the increase in the laser repetition rate provides a feasible route to an improved signal-to-noise ratio or shorter data acquisition times in BB-VSFG spectroscopy for thin films on transparent substrates. The results have implications for future BB-VSFG spectrometers pushing the detection limit for molecular layers with low surface coverage.

Transcriptome analysis of molecular mechanisms responsible for light-stress response in Mythimna separata (Walker)

PubMed Central

Duan, Yun; Gong, ZhongJun; Wu, RenHai; Miao, Jin; Jiang, YueLi; Li, Tong; Wu, XiaoBo; Wu, YuQing

2017-01-01

Light is an important environmental signal for most insects. The Oriental Armyworm, Mythimna separata, is a serious pest of cereal crops worldwide, and is highly sensitive to light signals during its developmental and reproductive stages. However, molecular biological studies of its response to light stress are scarce, and related genomic information is not available. In this study, we sequenced and de novo assembled the transcriptomes of M. separata exposed to four different light conditions: dark, white light (WL), UV light (UVL) and yellow light (YL). A total of 46,327 unigenes with an average size of 571 base pairs (bp) were obtained, among which 24,344 (52.55%) matched to public databases. The numbers of genes differentially expressed between dark vs WL, dark vs UVL, dark vs YL, and UVL vs YL were 12,012, 12,950, 14,855, and 13,504, respectively. These results suggest that light exposure altered gene expression patterns in M. separata. Putative genes involved in phototransduction-fly, phototransduction, circadian rhythm-fly, olfactory transduction, and taste transduction were identified. This study thus identified a series of candidate genes and pathways potentially related to light stress in M. separata. PMID:28345615

2D-HB-Network at the air-water interface: A structural and dynamical characterization by means of ab initio and classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Pezzotti, Simone; Serva, Alessandra; Gaigeot, Marie-Pierre

2018-05-01

Following our previous work where the existence of a special 2-Dimensional H-Bond (2D-HB)-Network was revealed at the air-water interface [S. Pezzotti et al., J. Phys. Chem. Lett. 8, 3133 (2017)], we provide here a full structural and dynamical characterization of this specific arrangement by means of both Density Functional Theory based and Force Field based molecular dynamics simulations. We show in particular that water at the interface with air reconstructs to maximize H-Bonds formed between interfacial molecules, which leads to the formation of an extended and non-interrupted 2-Dimensional H-Bond structure involving on average ˜90% of water molecules at the interface. We also show that the existence of such an extended structure, composed of H-Bonds all oriented parallel to the surface, constrains the reorientional dynamics of water that is hence slower at the interface than in the bulk. The structure and dynamics of the 2D-HB-Network provide new elements to possibly rationalize several specific properties of the air-water interface, such as water surface tension, anisotropic reorientation of interfacial water under an external field, and proton hopping.

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.

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

Chemical mixing at “Al on Fe” and “Fe on Al” interfaces

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

Süle, P.; Horváth, Z. E.; Kaptás, D.

2015-10-07

The chemical mixing at the “Al on Fe” and “Fe on Al” interfaces was studied by molecular dynamics simulations of the layer growth and by {sup 57}Fe Mössbauer spectroscopy. The concentration distribution along the layer growth direction was calculated for different crystallographic orientations, and atomically sharp “Al on Fe” interfaces were found when Al grows over (001) and (110) oriented Fe layers. The Al/Fe(111) interface is also narrow as compared to the intermixing found at the “Fe on Al” interfaces for any orientation. Conversion electron Mössbauer measurements of trilayers—Al/{sup 57}Fe/Al and Al/{sup 57}Fe/Ag grown simultaneously over Si(111) substrate by vacuummore » evaporation—support the results of the molecular dynamics calculations.« less

Moxie matters: associations of future orientation with active life expectancy.

PubMed

Laditka, Sarah B; Laditka, James N

2017-10-01

Being oriented toward the future has been associated with better future health. We studied associations of future orientation with life expectancy and the percentage of life with disability. We used the Panel Study of Income Dynamics (n = 5249). Participants' average age in 1968 was 33.0. Six questions repeatedly measured future orientation, 1968-1976. Seven waves (1999-2011, 33,331 person-years) measured disability in activities of daily living for the same individuals, whose average age in 1999 was 64.0. We estimated monthly probabilities of disability and death with multinomial logistic Markov models adjusted for age, sex, race/ethnicity, childhood health, and education. Using the probabilities, we created large populations with microsimulation, measuring disability in each month for each individual, age 55 through death. Life expectancy from age 55 for white men with high future orientation was age 77.6 (95% confidence interval 75.5-79.0), 6.9% (4.9-7.2) of those years with disability; results with low future orientation were 73.6 (72.2-75.4) and 9.6% (7.7-10.7). Comparable results for African American men were 74.8 (72.9-75.3), 8.1 (5.6-9.3), 71.0 (69.6-72.8), and 11.3 (9.1-11.7). For women, there were no significant differences associated with levels of future orientation for life expectancy. For white women with high future orientation 9.1% of remaining life from age 55 was disabled (6.3-9.9), compared to 12.4% (10.2-13.2) with low future orientation. Disability results for African American women were similar but statistically significant only at age 80 and over. High future orientation during early to middle adult ages may be associated with better health in older age.

The molecular orientation of CO on Pd(1 1 1): a polarization-dependent SFG study

NASA Astrophysics Data System (ADS)

Galletto, Paolo; Unterhalt, Holger; Rupprechter, Günther

2003-01-01

The molecular orientation of carbon monoxide adsorbed on Pd(1 1 1) was examined by sum frequency generation (SFG) vibrational spectroscopy utilizing different polarization combinations of the visible and SFG light. This allows to determine the CO tilt angle with respect to the substrate, provided that a proper optical model for the interface can be defined. It is demonstrated that it is essential to invoke the βaac hyperpolarizability into the analysis and that polarization-dependent SFG of CO/Pd(1 1 1) yields information on βaac/ βccc rather than the tilt angle.

Molecular Packing of Amiphiphiles with Crown Polar Heads at the Air-Water Interface

NASA Astrophysics Data System (ADS)

Larson, K.; Vaknin, D.; Villavicencio, O.; McGrath, D.; Tsukruk, V. V.

2002-03-01

An amphiphilic compound containing a benzyl-15-crown-5 focal point, azobenzene spacer, and a dodecyl tail as a peripheral group has been investigated at the air-water interface. X-ray grazing incident diffraction and reflectivity were preformed on the Langmuir monolayers to elucidate molecular packing and orientation. At high surface pressure, we observed intralayer packing of the alkyl tails with doubling parameters of the conventional orthorhombic unit cell (supercell) and long-range positional ordering. High tilt of the alkyl tails of about 58º from the surface normal was a signature of molecular packing caused by a large mismatch between the cross-sectional areas of the polar heads and the alkyl tail. Higher generation molecules of the same series display straight tail orientation and hexagonal lateral packing.

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

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

Thermal properties of halogen-ethane glassy crystals: Effects of orientational disorder and the role of internal molecular degrees of freedom.

PubMed

Vdovichenko, G A; Krivchikov, A I; Korolyuk, O A; Tamarit, J Ll; Pardo, L C; Rovira-Esteva, M; Bermejo, F J; Hassaine, M; Ramos, M A

2015-08-28

The thermal conductivity, specific heat, and specific volume of the orientational glass former 1,1,2-trichloro-1,2,2-trifluoroethane (CCl2F-CClF2, F-113) have been measured under equilibrium pressure within the low-temperature range, showing thermodynamic anomalies at ca. 120, 72, and 20 K. The results are discussed together with those pertaining to the structurally related 1,1,2,2-tetrachloro-1,2-difluoroethane (CCl2F-CCl2F, F-112), which also shows anomalies at 130, 90, and 60 K. The rich phase behavior of these compounds can be accounted for by the interplay between several of their degrees of freedom. The arrest of the degrees of freedom corresponding to the internal molecular rotation, responsible for the existence of two energetically distinct isomers, and the overall molecular orientation, source of the characteristic orientational disorder of plastic phases, can explain the anomalies at higher and intermediate temperatures, respectively. The soft-potential model has been used as the framework to describe the thermal properties at low temperatures. We show that the low-temperature anomaly of the compounds corresponds to a secondary relaxation, which can be associated with the appearance of Umklapp processes, i.e., anharmonic phonon-phonon scattering, that dominate thermal transport in that temperature range.

Thermal properties of halogen-ethane glassy crystals: Effects of orientational disorder and the role of internal molecular degrees of freedom

NASA Astrophysics Data System (ADS)

Vdovichenko, G. A.; Krivchikov, A. I.; Korolyuk, O. A.; Tamarit, J. Ll.; Pardo, L. C.; Rovira-Esteva, M.; Bermejo, F. J.; Hassaine, M.; Ramos, M. A.

2015-08-01

The thermal conductivity, specific heat, and specific volume of the orientational glass former 1,1,2-trichloro-1,2,2-trifluoroethane (CCl2F-CClF2, F-113) have been measured under equilibrium pressure within the low-temperature range, showing thermodynamic anomalies at ca. 120, 72, and 20 K. The results are discussed together with those pertaining to the structurally related 1,1,2,2-tetrachloro-1,2-difluoroethane (CCl2F-CCl2F, F-112), which also shows anomalies at 130, 90, and 60 K. The rich phase behavior of these compounds can be accounted for by the interplay between several of their degrees of freedom. The arrest of the degrees of freedom corresponding to the internal molecular rotation, responsible for the existence of two energetically distinct isomers, and the overall molecular orientation, source of the characteristic orientational disorder of plastic phases, can explain the anomalies at higher and intermediate temperatures, respectively. The soft-potential model has been used as the framework to describe the thermal properties at low temperatures. We show that the low-temperature anomaly of the compounds corresponds to a secondary relaxation, which can be associated with the appearance of Umklapp processes, i.e., anharmonic phonon-phonon scattering, that dominate thermal transport in that temperature range.

Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory

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

Wang, Hao; Yang, Weitao, E-mail: weitao.yang@duke.edu; Department of Physics, Duke University, Durham, North Carolina 27708

We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniformmore » external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics’ force fields and nontransferable molecule-specific atomic polarizabilities.« less

Thermal properties of halogen-ethane glassy crystals: Effects of orientational disorder and the role of internal molecular degrees of freedom

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

Vdovichenko, G. A.; Krivchikov, A. I.; Korolyuk, O. A.

2015-08-28

The thermal conductivity, specific heat, and specific volume of the orientational glass former 1,1,2-trichloro-1,2,2-trifluoroethane (CCl{sub 2}F–CClF{sub 2}, F-113) have been measured under equilibrium pressure within the low-temperature range, showing thermodynamic anomalies at ca. 120, 72, and 20 K. The results are discussed together with those pertaining to the structurally related 1,1,2,2-tetrachloro-1,2-difluoroethane (CCl{sub 2}F–CCl{sub 2}F, F-112), which also shows anomalies at 130, 90, and 60 K. The rich phase behavior of these compounds can be accounted for by the interplay between several of their degrees of freedom. The arrest of the degrees of freedom corresponding to the internal molecular rotation, responsiblemore » for the existence of two energetically distinct isomers, and the overall molecular orientation, source of the characteristic orientational disorder of plastic phases, can explain the anomalies at higher and intermediate temperatures, respectively. The soft-potential model has been used as the framework to describe the thermal properties at low temperatures. We show that the low-temperature anomaly of the compounds corresponds to a secondary relaxation, which can be associated with the appearance of Umklapp processes, i.e., anharmonic phonon-phonon scattering, that dominate thermal transport in that temperature range.« less

Flat-on ambipolar triphenylamine/C60 nano-stacks formed from the self-organization of a pyramid-sphere-shaped amphiphile.

PubMed

Liang, Wei-Wei; Huang, Chi-Feng; Wu, Kuan-Yi; Wu, San-Lien; Chang, Shu-Ting; Cheng, Yen-Ju; Wang, Chien-Lung

2016-04-21

A giant amphiphile, which is constructed with an amorphous nano-pyramid (triphenylamine, TPA) and a crystalline nano-sphere (C 60 ), was synthesized. Structural characterization indicates that this pyramid-sphere-shaped amphiphile ( TPA-C 60 ) forms a solvent-induced ordered phase, in which the two constituent units self-assemble into alternating stacks of two-dimensional (2D) TPA and C 60 nano-sheets. Due to the complexity of the molecular structure and the amorphous nature of the nano-pyramid, phase formation was driven by intermolecular C 60 -C 60 interactions and the ordered phase could not be reformed from the TPA-C 60 melt. Oriented crystal arrays of TPA-C 60 , which contain flat-on TPA/C 60 nano-stacks, can be obtained via a PDMS-assisted crystallization (PAC) technique. The flat-on dual-channel supramolecular structure of TPA-C 60 delivered ambipolar and balanced charge-transport characteristics with an average μ e of 2.11 × 10 -4 cm 2 V -1 s -1 and μ h of 3.37 × 10 -4 cm 2 V -1 s -1 . The anisotropic charge-transport ability of the pyramid-sphere-shaped amphiphile was further understood based on the lattice structure and the lattice orientation of TPA-C 60 revealed from electron diffraction analyses.

Displacement Threshold Energy and Recovery in an Al-Ti Nanolayered System with Intrinsic Point Defect Partitioning

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

Gerboth, Matthew D.; Setyawan, Wahyu; Henager, Charles H.

2014-01-07

A method is established and validated using molecular dynamics (MD) to determine the displacement threshold energies as Ed in nanolayered, multilayered systems of dissimilar metals. The method is applied to specifically oriented nanolayered films of Al-Ti where the crystal structure and interface orientations are varied in atomic models and Ed is calculated. Methods for defect detection are developed and discussed based on prior research in the literature and based on specific crystallographic directions available in the nanolayered systems. These are compared and contrasted to similar calculations in corresponding bulk materials, including fcc Al, fcc Ti, hcp Al, and hcp Ti.more » In all cases, the calculated Ed in the multilayers are intermediate to the corresponding bulk values but exhibit some important directionality. In the nanolayer, defect detection demonstrated systematic differences in the behavior of Ed in each layer. Importantly, collision cascade damage exhibits significant defect partitioning within the Al and Ti layers that is hypothesized to be an intrinsic property of dissimilar nanolayered systems. This type of partitioning could be partly responsible for observed asymmetric radiation damage responses in many multilayered systems. In addition, a pseudo-random direction was introduced to approximate the average Ed without performing numerous simulations with random directions.« less

In Situ Nondestructive Analysis of Kalanchoe pinnata Leaf Surface Structure by Polarization-Modulation Infrared Reflection-Absorption Spectroscopy.

PubMed

Hama, Tetsuya; Kouchi, Akira; Watanabe, Naoki; Enami, Shinichi; Shimoaka, Takafumi; Hasegawa, Takeshi

2017-12-14

The outermost surface of the leaves of land plants is covered with a lipid membrane called the cuticle that protects against various stress factors. Probing the molecular-level structure of the intact cuticle is highly desirable for understanding its multifunctional properties. We report the in situ characterization of the surface structure of Kalanchoe pinnata leaves using polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS). Without sample pretreatment, PM-IRRAS measures the IR spectra of the leaf cuticle of a potted K. pinnata plant. The peak position of the CH 2 -related modes shows that the cuticular waxes on the leaf surface are mainly crystalline, and the alkyl chains are highly packed in an all-trans zigzag conformation. The surface selection rule of PM-IRRAS revealed the average orientation of the cuticular molecules, as indicated by the positive and negative signals of the IR peaks. This unique property of PM-IRRAS revealed that the alkyl chains of the waxes and the main chains of polysaccharides are oriented almost perpendicular to the leaf surface. The nondestructive, background-free, and environmental gas-free nature of PM-IRRAS allows the structure and chemistry of the leaf cuticle to be studied directly in its native environment.

Probing the core of Cepheus A - Millimeter and submillimeter observations

NASA Astrophysics Data System (ADS)

Moriarty-Schieven, G. H.; Snell, R. L.; Hughes, V. A.

1991-06-01

Moderate and high angular resolution (40-7 arcsec) maps are presented of the core of the Cepheus A star-forming region using CS J = 3-2 and J = 7-6 emission, which traces the dense gas component of the cloud core, and using far-infrared (450 and 800 microns) continuum emission tracing the warm dust component. Three regimes in the core are traced by these observations: (1) a small (about 0.14 pc), nearly circular central core of high density (1-10 x 10 to the 6th/cu cm) and temperature (30-100 K) containing at least 25 percent of the mass and which contains the active early-type star formation; (2) an extended (0.5 x 0.25 pc), NE-SW oriented core of mass 200-300 solar masses, temperature 30-40 K, and average density nH2 of about 10 to the 5th/cu cm and which, together with the central core, contains 60-80 percent of the total core mass; and (3) an extended core envelope of dimensions 0.5 x 0.85 pc oriented primarily north-south, and a lower density. The velocity structure of the core suggests that it is being disrupted by the high-velocity winds driving the molecular outflow and is not due to a rotating circumstellar disk.

Quantification of gastric emptying and duodenogastric reflux stroke volumes using three-dimensional guided digital color Doppler imaging.

PubMed

Hausken, T; Li, X N; Goldman, B; Leotta, D; Ødegaard, S; Martin, R W

2001-07-01

To develop a non-invasive method for evaluating gastric emptying and duodenogastric reflux stroke volumes using three-dimensional (3D) guided digital color Doppler imaging. The technique involved color Doppler digital images of transpyloric flow in which the 3D position and orientation of the images were known by using a magnetic location system. In vitro, the system was found to slightly underestimate the reference flow (by average 8.8%). In vivo (five volunteers), stroke volume of gastric emptying episodes lasted on average only 0.69 s with a volume on average of 4.3 ml (range 1.1-7.4 ml), and duodenogastric reflux episodes on average 1.4 s with a volume of 8.3 ml (range 1.3-14.1 ml). With the appropriate instrument settings, orientation determined color Doppler can be used for stroke volume quantification of gastric emptying and duodenogastric reflux episodes.

Metallographic Characterization of Wrought Depleted Uranium

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

Forsyth, Robert Thomas; Hill, Mary Ann

Metallographic characterization was performed on wrought depleted uranium (DU) samples taken from the longitudinal and transverse orientations from specific locations on two specimens. Characterization of the samples included general microstructure, inclusion analysis, grain size analysis, and microhardness testing. Comparisons of the characterization results were made to determine any differences based on specimen, sample orientation, or sample location. In addition, the characterization results for the wrought DU samples were also compared with data obtained from the metallographic characterization of cast DU samples previously characterized. No differences were observed in microstructure, inclusion size, morphology, and distribution, or grain size in regard tomore » specimen, location, or orientation for the wrought depleted uranium samples. However, a small difference was observed in average hardness with regard to orientation at the same locations within the same specimen. The longitudinal samples were slightly harder than the transverse samples from the same location of the same specimen. This was true for both wrought DU specimens. Comparing the wrought DU sample data with the previously characterized cast DU sample data, distinct differences in microstructure, inclusion size, morphology and distribution, grain size, and microhardness were observed. As expected, the microstructure of the wrought DU samples consisted of small recrystallized grains which were uniform, randomly oriented, and equiaxed with minimal twinning observed in only a few grains. In contrast, the cast DU microstructure consisted of large irregularly shaped grains with extensive twinning observed in most grains. Inclusions in the wrought DU samples were elongated, broken and cracked and light and dark phases were observed in some inclusions. The mean inclusion area percentage for the wrought DU samples ranged from 0.08% to 0.34% and the average density from all wrought DU samples was 1.62E+04/cm 2. Inclusions in the cast DU samples were equiaxed and intact with light and dark phases observed in some inclusions. The mean inclusion area percentage for the cast DU samples ranged from 0.93% to 1.00% and the average density from all wrought DU samples was 2.83E+04/cm 2. The average mean grain area from all wrought DU samples was 141 μm 2 while the average mean grain area from all cast DU samples was 1.7 mm2. The average Knoop microhardness from all wrought DU samples was 215 HK and the average Knoop microhardness from all cast DU samples was 264 HK.« less

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

NASA Astrophysics Data System (ADS)

Stolow, Albert

We discuss the probing and control of molecular wavepacket dynamics in the context of three main `pillars' of light-matter interaction: time, phase, intensity. Time: Using short, coherent laser pulses and perturbative matter-field interactions, we study molecular wavepackets with a focus on the ultrafast non-Born-Oppenheimer dynamics, that is, the coupling of electronic and nuclear motions. Time-Resolved Photoelectron Spectroscopy (TRPES) is a powerful ultrafast probe of these processes in polyatomic molecules because it is sensitive both electronic and vibrational dynamics. Ideally, one would like to observe these ultrafast processes from the molecule's point of view - the Molecular Frame - thereby avoiding loss of information due to orientational averaging. This can be achieved by Time-Resolved Coincidence Imaging Spectroscopy (TRCIS) which images 3D recoil vectors of both photofragments and photoelectrons, in coincidence and as a function of time, permitting direct Molecular Frame imaging of valence electronic dynamics during a molecular dynamics. Phase: Using intermediate strength non-perturbative interactions, we apply the second order (polarizability) Non-Resonant Dynamic Stark Effect (NRDSE) to control molecular dynamics without any net absorption of light. NRDSE is also the interaction underlying molecular alignment and applies to field-free 1D of linear molecules and field-free 3D alignment of general (asymmetric) molecules. Using laser alignment, we can transiently fix a molecule in space, yielding a more general approach to direct Molecular Frame imaging of valence electronic dynamics during a chemical reaction. Intensity: In strong (ionizing) laser fields, a new laser-matter physics emerges for polyatomic systems wherein both the single active electron picture and the adiabatic electron response, both implicit in the standard 3-step models, can fail dramatically. This has important consequences for all attosecond strong field spectroscopies of polyatomic molecules, including high harmonic generation (HHG). We discuss an experimental method, Channel-Resolved Above Threshold Ionization (CRATI), which directly unveils the electronic channels participating in the attosecond molecular strong field ionization response [10]. This work was supported by the National Research Council of Canada and the Natural Sciences & Engineering Research Council.

For the Love of Science: Learning Orientation and Physical Science Success

NASA Astrophysics Data System (ADS)

Hazari, Zahra; Potvin, Geoff; Tai, Robert; Almarode, John

2010-02-01

An individual's motivational orientation serves as a drive to action and can influence their productivity. This study examines how the goal orientation of students towards the pursuit of their graduate degree in physics and chemistry influences their future success outcomes as practicing scientists. Two main orientations are focused on: performance (or ego/ability) orientation and learning (or task/mastery) orientation. The data was obtained as part of Project Crossover, which applied a mixed methodological approach to studying the transition from graduate student to scientist in the physical sciences. Using regression analysis on survey data from 2353 PhD holders in physics and chemistry, we found that individuals exhibiting a learning orientation were more productive than those exhibiting a performance orientation in terms of first-author publications and grant funding. Furthermore, given equal salary, learning-oriented physical scientists produced more first-author publications than average. )

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 dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor.

PubMed Central

Guenot, J.; Kollman, P. A.

1992-01-01

Although aqueous simulations with periodic boundary conditions more accurately describe protein dynamics than in vacuo simulations, these are computationally intensive for most proteins. Trp repressor dynamic simulations with a small water shell surrounding the starting model yield protein trajectories that are markedly improved over gas phase, yet computationally efficient. Explicit water in molecular dynamics simulations maintains surface exposure of protein hydrophilic atoms and burial of hydrophobic atoms by opposing the otherwise asymmetric protein-protein forces. This properly orients protein surface side chains, reduces protein fluctuations, and lowers the overall root mean square deviation from the crystal structure. For simulations with crystallographic waters only, a linear or sigmoidal distance-dependent dielectric yields a much better trajectory than does a constant dielectric model. As more water is added to the starting model, the differences between using distance-dependent and constant dielectric models becomes smaller, although the linear distance-dependent dielectric yields an average structure closer to the crystal structure than does a constant dielectric model. Multiplicative constants greater than one, for the linear distance-dependent dielectric simulations, produced trajectories that are progressively worse in describing trp repressor dynamics. Simulations of bovine pancreatic trypsin were used to ensure that the trp repressor results were not protein dependent and to explore the effect of the nonbonded cutoff on the distance-dependent and constant dielectric simulation models. The nonbonded cutoff markedly affected the constant but not distance-dependent dielectric bovine pancreatic trypsin inhibitor simulations. As with trp repressor, the distance-dependent dielectric model with a shell of water surrounding the protein produced a trajectory in better agreement with the crystal structure than a constant dielectric model, and the physical properties of the trajectory average structure, both with and without a nonbonded cutoff, were comparable. PMID:1304396

Etomica: an object-oriented framework for molecular simulation.

PubMed

Schultz, Andrew J; Kofke, David A

2015-03-30

We describe the design of an object-oriented library of software components that are suitable for constructing simulations of systems of interacting particles. The emphasis of the discussion is on the general design of the components and how they interact, and less on details of the programming interface or its implementation. Example code is provided as an aid to understanding object-oriented programming structures and to demonstrate how the framework is applied. © 2015 Wiley Periodicals, Inc.

An Adaptive 6-DOF Tracking Method by Hybrid Sensing for Ultrasonic Endoscopes

PubMed Central

Du, Chengyang; Chen, Xiaodong; Wang, Yi; Li, Junwei; Yu, Daoyin

2014-01-01

In this paper, a novel hybrid sensing method for tracking an ultrasonic endoscope within the gastrointestinal (GI) track is presented, and the prototype of the tracking system is also developed. We implement 6-DOF localization by sensing integration and information fusion. On the hardware level, a tri-axis gyroscope and accelerometer, and a magnetic angular rate and gravity (MARG) sensor array are attached at the end of endoscopes, and three symmetric cylindrical coils are placed around patients' abdomens. On the algorithm level, an adaptive fast quaternion convergence (AFQC) algorithm is introduced to determine the orientation by fusing inertial/magnetic measurements, in which the effects of magnetic disturbance and acceleration are estimated to gain an adaptive convergence output. A simplified electro-magnetic tracking (SEMT) algorithm for dimensional position is also implemented, which can easily integrate the AFQC's results and magnetic measurements. Subsequently, the average position error is under 0.3 cm by reasonable setting, and the average orientation error is 1° without noise. If magnetic disturbance or acceleration exists, the average orientation error can be controlled to less than 3.5°. PMID:24915179

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

Defining behavioral and molecular differences between summer and migratory monarch butterflies

PubMed Central

Zhu, Haisun; Gegear, Robert J; Casselman, Amy; Kanginakudru, Sriramana; Reppert, Steven M

2009-01-01

Background In the fall, Eastern North American monarch butterflies (Danaus plexippus) undergo a magnificent long-range migration. In contrast to spring and summer butterflies, fall migrants are juvenile hormone deficient, which leads to reproductive arrest and increased longevity. Migrants also use a time-compensated sun compass to help them navigate in the south/southwesterly direction en route for Mexico. Central issues in this area are defining the relationship between juvenile hormone status and oriented flight, critical features that differentiate summer monarchs from fall migrants, and identifying molecular correlates of behavioral state. Results Here we show that increasing juvenile hormone activity to induce summer-like reproductive development in fall migrants does not alter directional flight behavior or its time-compensated orientation, as monitored in a flight simulator. Reproductive summer butterflies, in contrast, uniformly fail to exhibit directional, oriented flight. To define molecular correlates of behavioral state, we used microarray analysis of 9417 unique cDNA sequences. Gene expression profiles reveal a suite of 40 genes whose differential expression in brain correlates with oriented flight behavior in individual migrants, independent of juvenile hormone activity, thereby molecularly separating fall migrants from summer butterflies. Intriguing genes that are differentially regulated include the clock gene vrille and the locomotion-relevant tyramine beta hydroxylase gene. In addition, several differentially regulated genes (37.5% of total) are not annotated. We also identified 23 juvenile hormone-dependent genes in brain, which separate reproductive from non-reproductive monarchs; genes involved in longevity, fatty acid metabolism, and innate immunity are upregulated in non-reproductive (juvenile-hormone deficient) migrants. Conclusion The results link key behavioral traits with gene expression profiles in brain that differentiate migratory from summer butterflies and thus show that seasonal changes in genomic function help define the migratory state. PMID:19335876

Impact of anisotropy on the structure and dynamics of ionic liquids: A computational study of 1-butyl-3-methyl-imidazolium trifluoroacetate

NASA Astrophysics Data System (ADS)

Schröder, C.; Rudas, T.; Neumayr, G.; Gansterer, W.; Steinhauser, O.

2007-07-01

The complex ionic network of 1-butyl-3-methyl-imidazolium trifluoroacetate was simulated by means of the molecular dynamics methods over a time period of 100ns. The influence of the anisotropy of the shape and charge distribution of both the cations and the anions on the local (molecular) and global (collective) structure and dynamics is analyzed. The distance-dependent g coefficients of the orientational probability function g(r,Ω) were found to be an excellent way to interpret local structure. Thereby, the combination and interrelation of individual g coefficients elucidate the mutual orientation. Dynamics at the molecular level is characterized by the time correlation function of the center-of-mass corrected molecular dipole moment μcm. Upon uniting the set of molecular dipoles to a single collective rotational dipole moment, MD, dynamics on a global level is studied. Decomposing into subsets of cations and anions respective self terms as well as the prominent cross term can be extracted. This decomposition also enables a detailed peak assignment in dielectric spectra.

Impact of anisotropy on the structure and dynamics of ionic liquids: a computational study of 1-butyl-3-methyl-imidazolium trifluoroacetate.

PubMed

Schröder, C; Rudas, T; Neumayr, G; Gansterer, W; Steinhauser, O

2007-07-28

The complex ionic network of 1-butyl-3-methyl-imidazolium trifluoroacetate was simulated by means of the molecular dynamics methods over a time period of 100 ns. The influence of the anisotropy of the shape and charge distribution of both the cations and the anions on the local (molecular) and global (collective) structure and dynamics is analyzed. The distance-dependent g coefficients of the orientational probability function g(r,Omega) were found to be an excellent way to interpret local structure. Thereby, the combination and interrelation of individual g coefficients elucidate the mutual orientation. Dynamics at the molecular level is characterized by the time correlation function of the center-of-mass corrected molecular dipole moment mucm. Upon uniting the set of molecular dipoles to a single collective rotational dipole moment, MD, dynamics on a global level is studied. Decomposing into subsets of cations and anions respective self terms as well as the prominent cross term can be extracted. This decomposition also enables a detailed peak assignment in dielectric spectra.

Efficient molecular density functional theory using generalized spherical harmonics expansions.

PubMed

Ding, Lu; Levesque, Maximilien; Borgis, Daniel; Belloni, Luc

2017-09-07

We show that generalized spherical harmonics are well suited for representing the space and orientation molecular density in the resolution of the molecular density functional theory. We consider the common system made of a rigid solute of arbitrary complexity immersed in a molecular solvent, both represented by molecules with interacting atomic sites and classical force fields. The molecular solvent density ρ(r,Ω) around the solute is a function of the position r≡(x,y,z) and of the three Euler angles Ω≡(θ,ϕ,ψ) describing the solvent orientation. The standard density functional, equivalent to the hypernetted-chain closure for the solute-solvent correlations in the liquid theory, is minimized with respect to ρ(r,Ω). The up-to-now very expensive angular convolution products are advantageously replaced by simple products between projections onto generalized spherical harmonics. The dramatic gain in speed of resolution enables to explore in a systematic way molecular solutes of up to nanometric sizes in arbitrary solvents and to calculate their solvation free energy and associated microscopic solvent structure in at most a few minutes. We finally illustrate the formalism by tackling the solvation of molecules of various complexities in water.

Snapshots of crystal growth: Nanoclusters of organic conductors on Au(111) surfaces

NASA Astrophysics Data System (ADS)

Schott, J. H.; Ward, M. D.

1994-06-01

Mono- and multilayer crystalline nanoclusters of tetra-hiafulvalene-tetracyanoquinodimethane ((TTF) (TCNO)), a low-dimensional organic conductor in the bulk form, can be formed readily on Au(111) surfaces by vapor phase sublimation under ambient conditions. Scanning tunneling microscopy of monolayer (TTF)(TCNQ) films reveals a two-dimensional density of states (DOS) that is consistent with the arrangement of TTF and TCNO molecules in the ac face of bulk (TTF)(TCNO), in which the molecular planes are nearly parallel to the Au(111) substrate. In contrast, clusters with thicknesses corresponding to two or three molecular layers exhibit a transformation to a highly anisotropic DOS that can be attributed to interlayer molecular overlap in segregated TTF and TCNQ molecular chains along the c-axis, which can be described as 'molecular wires'. The orientation of the crystalline (TTF)(TCNO) clusters is preserved throughout the crystal growth sequence, leading to meso- and macroscopic (TTF)(TCNO) needles that are oriented perpendicular to the Au(111) substrate. These studies provide visualization of crystal growth from the initial stages of nucleation to macroscopic crystals, and a revealing example of the changes in electronic structure that occur during the evolution of molecular (TTF)(TCNQ) nuclei into a bulk crystalline phase.

Epitaxially grown strained pentacene thin film on graphene membrane.

PubMed

Kim, Kwanpyo; Santos, Elton J G; Lee, Tae Hoon; Nishi, Yoshio; Bao, Zhenan

2015-05-06

Organic-graphene system has emerged as a new platform for various applications such as flexible organic photovoltaics and organic light emitting diodes. Due to its important implication in charge transport, the study and reliable control of molecular packing structures at the graphene-molecule interface are of great importance for successful incorporation of graphene in related organic devices. Here, an ideal membrane of suspended graphene as a molecular assembly template is utilized to investigate thin-film epitaxial behaviors. Using transmission electron microscopy, two distinct molecular packing structures of pentacene on graphene are found. One observed packing structure is similar to the well-known bulk-phase, which adapts a face-on molecular orientation on graphene substrate. On the other hand, a rare polymorph of pentacene crystal, which shows significant strain along the c-axis, is identified. In particular, the strained film exhibits a specific molecular orientation and a strong azimuthal correlation with underlying graphene. Through ab initio electronic structure calculations, including van der Waals interactions, the unusual polymorph is attributed to the strong graphene-pentacene interaction. The observed strained organic film growth on graphene demonstrates the possibility to tune molecular packing via graphene-molecule interactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thermomagnetic processing of liquid-crystalline epoxy resins and their mechanical characterization using nanoindentation.

PubMed

Li, Yuzhan; Rios, Orlando; Kessler, Michael R

2014-11-12

A thermomagnetic processing method was used to produce a biphenyl-based liquid-crystalline epoxy resin (LCER) with oriented liquid-crystalline (LC) domains. The orientation of the LCER was confirmed and quantified using two-dimensional X-ray diffraction. The effect of molecular alignment on the mechanical and thermomechanical properties of the LCER was investigated using nanoindentation and thermomechanical analysis, respectively. The effect of the orientation on the fracture behavior was also examined. The results showed that macroscopic orientation of the LC domains was achieved, resulting in an epoxy network with an anisotropic modulus, hardness, creep behavior, and thermal expansion.

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.

Effet de l'anisotropie élastique cristalline sur la distribution des facteurs de Schmid à la surface des polycristaux

NASA Astrophysics Data System (ADS)

Sauzay, Maxime

2006-06-01

Experimental studies of the plasticity mechanisms of polycrystals are usually based on the Schmid factor distribution supposing crystalline elasticity isotropy. A numerical evaluation of the effect of crystalline elasticity anisotropy on the apparent Schmid factor distribution at the free surface of polycrystals is presented. Cubic elasticity is considered. Order II stresses (averaged on all grains with the same crystallographic orientation) as well as variations between averages computed on grains with the same crystallographic orientation but with different neighbour grains are computed. The Finite Element Method is used. Commonly studied metals presenting an increasing anisotropy degree are considered (aluminium, nickel, austenite, copper). Concerning order II stresses in strongly anisotropic metals, the apparent Schmid factor distribution is drifted towards small Schmid factor values (the maximum Schmid factor is equal to 0.43 instead of 0.5) and the slip activation order between characteristic orientations of the crystallographic standard triangle is modified. The computed square deviations of the stresses averaged on grains with the same crystallographic orientation but with different neighbour grains are a bit higher than the second order ones (inter-orientation scatter). Our numerical evaluations agree quantitatively with several observations and measures of the literature concerning stress and strain distribution in copper and austenite polycrystals submitted to low amplitude loadings. Hopefully, the given apparent Schmid factor distributions could help to better understand the observations of the plasticity mechanisms taking place at the free surface of polycrystals. To cite this article: M. Sauzay, C. R. Mecanique 334 (2006).

Thermal Expansion of Self-Organized and Shear-Oriented Cellulose Nanocrystal Films

Treesearch

Jairo A. Diaz; Xiawa Wu; Ashlie Martini; Jeffrey P. Youngblood; Robert J. Moon

2013-01-01

The coefficient of thermal expansion (CTE) of cellulose nanocrystal (CNC) films was characterized using novel experimental techniques complemented by molecular simulations. The characteristic birefringence exhibited by CNC films was utilized to calculate the in-plane CTE of selforganized and shear-oriented self-standing CNC films from room temperature to 100 °...

Clustering and negative feedback by endocytosis in planar cell polarity signaling is modulated by ubiquitinylation of prickle.

PubMed

Cho, Bomsoo; Pierre-Louis, Gandhy; Sagner, Andreas; Eaton, Suzanne; Axelrod, Jeffrey D

2015-05-01

The core components of the planar cell polarity (PCP) signaling system, including both transmembrane and peripheral membrane associated proteins, form asymmetric complexes that bridge apical intercellular junctions. While these can assemble in either orientation, coordinated cell polarization requires the enrichment of complexes of a given orientation at specific junctions. This might occur by both positive and negative feedback between oppositely oriented complexes, and requires the peripheral membrane associated PCP components. However, the molecular mechanisms underlying feedback are not understood. We find that the E3 ubiquitin ligase complex Cullin1(Cul1)/SkpA/Supernumerary limbs(Slimb) regulates the stability of one of the peripheral membrane components, Prickle (Pk). Excess Pk disrupts PCP feedback and prevents asymmetry. We show that Pk participates in negative feedback by mediating internalization of PCP complexes containing the transmembrane components Van Gogh (Vang) and Flamingo (Fmi), and that internalization is activated by oppositely oriented complexes within clusters. Pk also participates in positive feedback through an unknown mechanism promoting clustering. Our results therefore identify a molecular mechanism underlying generation of asymmetry in PCP signaling.

Growth and optical property characterization of textured barium titanate thin films for photonic applications

NASA Astrophysics Data System (ADS)

Dicken, Matthew J.; Diest, Kenneth; Park, Young-Bae; Atwater, Harry A.

2007-03-01

We have investigated the growth of barium titanate thin films on bulk crystalline and amorphous substrates utilizing biaxially oriented template layers. Ion beam-assisted deposition was used to grow thin, biaxially textured, magnesium oxide template layers on amorphous and silicon substrates. Growth of highly oriented barium titanate films on these template layers was achieved by molecular beam epitaxy using a layer-by-layer growth process. Barium titanate thin films were grown in molecular oxygen and in the presence of oxygen radicals produced by a 300 W radio frequency plasma. We used X-ray and in situ reflection high-energy electron diffraction (RHEED) to analyze the structural properties and show the predominantly c-oriented grains in the films. Variable angle spectroscopic ellipsometry was used to analyze and compare the optical properties of the thin films grown with and without oxygen plasma. We have shown that optical quality barium titanate thin films, which show bulk crystal-like properties, can be grown on any substrate through the use of biaxially oriented magnesium oxide template layers.

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

Bowers, Geoffrey M.; Schaef, H. Todd; Loring, John S.

This paper explores the molecular-scale interactions between CO 2 and the representative smectite mineral hectorite under supercritical conditions (90 bar, 50°C) using novel in situ X-ray diffraction (XRD), infrared (IR) spectroscopy, and magic angle spinning (MAS) nuclear magnetic resonance (NMR) techniques. Particular emphasis is placed on understanding the roles of the smectite charge balancing cation (CBC) and H O in these interactions. The data show that supercritical CO 2 (scCO 2) can be adsorbed on external surfaces and in the confined interlayer spaces of hectorite at 50°C and 90 bar, with the uptake of CO 2 into the interlayer favoredmore » at low H 2O content and when the basal spacing is similar to a monolayer hydrate of hectorite (1WL, ~12.5 Å). These results are in agreement with published spectroscopic and molecular modeling data for the related smectite Na-montmorillonite.Charge balancing cations with small radii, large hydration energies, and low polarizabilities tend to scavenge H 2O from humid scCO 2 or retain the H 2O they held before scCO 2 exposure, swelling spontaneously to a bilayer hydrate (2WL) dominated state that largely prevents CO 2-ion interactions and influences the extent of CO 2 intercalation into the interlayer. In contrast, ions with large radii, low hydration energies, and large polarizabilities more readily form close associations with CO 2 with the energetics enabling coexistence of CO 2 and H2O in the interlayer over a wide range of scCO 2 humidities. Integrating our results with those from molecular dynamics simulations of wet CO 2-bearing montmorillonites suggest that adsorbed CO 2 in 1WL-type interlayers is oriented with its long axis parallel to the clay sheets and experiences dynamics dominated by anisotropic rotation about the axis perpendicular to the CO 2 long axis at rates of at least ~105 Hz. If appreciable CO 2 is adsorbed in 2WL-type interlayers, it must experience a mean orientation and dynamic averaging affects that mimic the 1WL-type adsorption environment. External surface adsorbed CO 2 is dynamically similar to the 1WL case, but the CO 2 long axis samples a larger range of orientations with respect to the smectite surface and adopts a different mean angle between the long axis and the smectite surface. Our data also suggest that equilibrating hectorite with a largevolume of scCO 2 at 50°C and 90 bar leads to interlayer dehydration, with the extent of dehydration correlating with the hydrophilicity of the CBC.« less

Probe for high resolution NMR with sample reorientation

DOEpatents

Pines, Alexander; Samoson, Ago

1990-01-01

An improved NMR probe and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise orientationally disordered samples. The apparatus mechanically varies the orientation of the sample such that the time average of two or more sets of spherical harmonic functions are zero.

Traveler oriented traffic performance metrics using real time traffic data from the Midtown-in-Motion (MIM) project in Manhattan, NY.

DOT National Transportation Integrated Search

2013-10-01

In a congested urban street network the average traffic speed is an inadequate metric for measuring : speed changes that drivers can perceive from changes in traffic control strategies. : A driver oriented metric is needed. Stop frequency distrib...

Self-Efficacy, Goal Orientations and Learning Strategies as Mediators between Preceding and Subsequent Academic Achievement

ERIC Educational Resources Information Center

Diseth, Age

2011-01-01

High school grade point average (HSGPA), self-efficacy, goal orientations, learning strategies, and examination grade were measured in a sample of Norwegian undergraduate psychology students in order to investigate motives and strategies as mediators between preceding and subsequent academic achievement. Correlation analysis showed strong…

Six-dimensional quantum dynamics study for the dissociative adsorption of HCl on Au(111) surface

NASA Astrophysics Data System (ADS)

Liu, Tianhui; Fu, Bina; Zhang, Dong H.

2013-11-01

The six-dimensional quantum dynamics calculations for the dissociative chemisorption of HCl on Au(111) are carried out using the time-dependent wave-packet approach, based on an accurate PES which was recently developed by neural network fitting to density functional theory energy points. The influence of vibrational excitation and rotational orientation of HCl on the reactivity is investigated by calculating the exact six-dimensional dissociation probabilities, as well as the four-dimensional fixed-site dissociation probabilities. The vibrational excitation of HCl enhances the reactivity and the helicopter orientation yields higher dissociation probability than the cartwheel orientation. A new interesting site-averaged effect is found for the title molecule-surface system that one can essentially reproduce the six-dimensional dissociation probability by averaging the four-dimensional dissociation probabilities over 25 fixed sites.

Relationship between open-circuit voltage in Cu(In,Ga)Se{sub 2} solar cell and peak position of (220/204) preferred orientation near its absorber surface

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

Chantana, J., E-mail: jakapan@fc.ritsumei.ac.jp; Minemoto, T.; Watanabe, T.

2013-11-25

Cu(In,Ga)Se{sub 2} (CIGS) absorbers with various Ga/III, Ga/(In+Ga), profiles are prepared by the so-called “multi-layer precursor method” using multi-layer co-evaporation of material sources. It is revealed that open-circuit voltage (V{sub OC}) of CIGS solar cell is primarily dependent on averaged Ga/III near the surface of its absorber. This averaged Ga/III is well predicted by peak position of (220/204) preferred orientation of CIGS film near its surface investigated by glancing-incidence X-ray diffraction with 0.1° incident angle. Finally, the peak position of (220/204) preferred orientation is proposed as a measure of V{sub OC} before solar cell fabrication.

Molecular theory of smectic ordering in liquid crystals with nanoscale segregation of different molecular fragments

NASA Astrophysics Data System (ADS)

Gorkunov, M. V.; Osipov, M. A.; Kapernaum, N.; Nonnenmacher, D.; Giesselmann, F.

2011-11-01

A molecular statistical theory of the smectic A phase is developed taking into account specific interactions between different molecular fragments which enables one to describe different microscopic scenario of the transition into the smectic phase. The effects of nanoscale segregation are described using molecular models with different combinations of attractive and repulsive sites. These models have been used to calculate numerically coefficients in the mean filed potential as functions of molecular model parameters and the period of the smectic structure. The same coefficients are calculated also for a conventional smectic with standard Gay-Berne interaction potential which does not promote the segregation. The free energy is minimized numerically to calculate the order parameters of the smectic A phases and to study the nature of the smectic transition in both systems. It has been found that in conventional materials the smectic order can be stabilized only when the orientational order is sufficiently high, In contrast, in materials with nanosegregation the smectic order develops mainly in the form of the orientational-translational wave while the nematic order parameter remains relatively small. Microscopic mechanisms of smectic ordering in both systems are discussed in detail, and the results for smectic order parameters are compared with experimental data for materials of various molecular structure.

Investigation of binding features: effects on the interaction between CYP2A6 and inhibitors.

PubMed

Ai, Chunzhi; Li, Yan; Wang, Yonghua; Li, Wei; Dong, Peipei; Ge, Guangbo; Yang, Ling

2010-07-15

A computational investigation has been carried out on CYP2A6 and its naphthalene inhibitors to explore the crucial molecular features contributing to binding specificity. The molecular bioactive orientations were obtained by docking (FlexX) these compounds into the active site of the enzyme. And the density functional theory method was further used to optimize the molecular structures with the subsequent analysis of molecular lipophilic potential (MLP) and molecular electrostatic potential (MEP). The minimal MLPs, minimal MEPs, and the band gap energies (the energy difference between the highest occupied molecular orbital and lowest unoccupied molecular orbital) showed high correlations with the inhibition activities (pIC(50)s), illustrating their significant roles in driving the inhibitor to adopt an appropriate bioactive conformation oriented in the active site of CYP2A6 enzyme. The differences in MLPs, MEPs, and the orbital energies have been identified as key features in determining the binding specificity of this series of compounds to CYP2A6 and the consequent inhibitory effects. In addition, the combinational use of the docking, MLP and MEP analysis is also demonstrated as a good attempt to gain an insight into the interaction between CYP2A6 and its inhibitors. Copyright 2010 Wiley Periodicals, Inc.

Fast determination of three-dimensional fibril orientation of type-I collagen via macroscopic chirality

NASA Astrophysics Data System (ADS)

Zhuo, Guan-Yu; Chen, Mei-Yu; Yeh, Chao-Yuan; Guo, Chin-Lin; Kao, Fu-Jen

2017-01-01

Polarization-resolved second harmonic generation (SHG) microscopy is appealing for studying structural proteins and well-organized biophotonic nanostructures, due to its highly sensitized structural specificity. In recent years, it has been used to investigate the chiroptical effect, particularly SHG circular dichroism (SHG-CD) in biological tissues. Although SHG-CD attributed to macromolecular structures has been demonstrated, the corresponding quantitative analysis and interpretation on how SHG correlates with second-order susceptibility χ(2) under circularly polarized excitations remains unclear. In this study, we demonstrate a method based on macroscopic chirality to elucidate the correlation between SHG-CD and the orientation angle of the molecular structure. By exploiting this approach, three-dimensional (3D) molecular orientation of type-I collagen is revealed with only two cross polarized SHG images (i.e., interactions of left and right circular polarizations) without acquiring an image stack of varying polarization.

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.

Orientation and temperature dependent adsorption of H 2S on GaAs: Valence band photoemission

NASA Astrophysics Data System (ADS)

Ranke, W.; Kuhr, H. J.; Finster, J.

A cylindrically shaped GaAs single crystal was used to study the adsorption of H 2S on the six inequivalent orientations (001), (113), (111), (110), (111) and (113) by angle resolved valence band photoelectron spectroscopy and surface dipole measurements. Adsorption at 150 K on the surface prepared by molecular beam epitaxy (MBE) yields similar adsorbate induced emission on all orientations which were ascribed to SH radicals. On (110), where preferential adsorption occurs additional features from molecular H 2S are observed. The adsorbate spectra at 720 K are ascribed to atomic sulphur. On the surface prepared by ion bombardment and annealing, defect enhanced adsorption occurs in the range (111)-(113). The adsorbate spectra are very similar to those on the MBE surface at 720 K. Thus, no new species are adsorbed on defects but only sticking probability and penetration capability are increased.

Ultrasound liquid crystal lens

NASA Astrophysics Data System (ADS)

Shimizu, Yuki; Koyama, Daisuke; Fukui, Marina; Emoto, Akira; Nakamura, Kentaro; Matsukawa, Mami

2018-04-01

A variable-focus lens using a combination of liquid crystals and ultrasound is discussed. The lens uses a technique based on ultrasound vibration to control the molecular orientation of the liquid crystal. The lens structure is simple, with no mechanical moving parts and no transparent electrodes, which is helpful for device downsizing; the structure consists of a liquid crystal layer sandwiched between two glass substrates with a piezoelectric ring. The tens-of-kHz ultrasonic resonance flexural vibration used to excite the lens generates an acoustic radiation force on the liquid crystal layer to induce changes in the molecular orientation of the liquid crystal. The orientations of the liquid crystal molecules and the optical characteristics of the lens were investigated under ultrasound excitation. Clear optical images were observed through the lens, and the focal point could be controlled using the input voltage to the piezoelectric ring to give the lens its variable-focus action.

Zebrafish respond to the geomagnetic field by bimodal and group-dependent orientation.

PubMed

Takebe, Akira; Furutani, Toshiki; Wada, Tatsunori; Koinuma, Masami; Kubo, Yoko; Okano, Keiko; Okano, Toshiyuki

2012-01-01

A variety of animals use Earth's magnetic field as a reference for their orientation behaviour. Although distinctive magnetoreception mechanisms have been postulated for many migrating or homing animals, the molecular mechanisms are still undefined. In this study, we found that zebrafish, a model organism suitable for genetic manipulation, responded to a magnetic field as weak as the geomagnetic field. Without any training, zebrafish were individually released into a circular arena that was placed in an artificial geomagnetic field, and their preferred magnetic directions were recorded. Individuals from five out of the seven zebrafish groups studied, groups mostly comprised of the offspring of predetermined pairs, showed bidirectional orientation with group-specific preferences regardless of close kinships. The preferred directions did not seem to depend on gender, age or surrounding environmental factors, implying that directional preference was genetically defined. The present findings may facilitate future study on the molecular mechanisms underlying magnetoreception.

Magnetic field effect on the structural properties of a peptide model: Molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Housaindokht, Mohammad Reza; Moosavi, Fatemeh

2018-06-01

The effect of magnetization on the properties of a system containing a peptide model is studied by molecular dynamics simulation at a range of 298-318 K. Two mole fractions of 0.001 and 0.002 of peptide were simulated and the variation of hydrogen bond number, orientational ordering parameter, gyration radius, mean square displacement, as well as radial distribution function, were under consideration. The results show that applying magnetic field will increase the number of hydrogen bonds between water molecules by clustering them and decreases the interaction of water and peptide. This reduction may cause more available free space and enhance the movement of the peptide. As a result, the diffusion coefficient of the peptide becomes greater and its conformation changes. Orientational ordering parameter besides radius of gyration demonstrates that peptide is expanded by static magnetic field and its orientational ordering parameter is affected.

Energetic basis for the molecular-scale organization of bone

DOE PAGES

Tao, Jinhui; Battle, Keith C.; Pan, Haihua; ...

2014-12-24

Here, the remarkable properties of bone derive from a highly organized arrangement of co-aligned nm-scale apatite platelets within a fibrillar collagen matrix. The origin of this arrangement is poorly understood and the crystal structures of hydroxyapatite (HAP) and the non-mineralized collagen fibrils alone do not provide an explanation. Moreover, little is known about collagen-apatite interaction energies, which should strongly influence both the molecular-scale organization and the resulting mechanical properties of the composite. We investigated collagen-mineral interactions by combining dynamic force spectroscopy (DFS) measurements of binding energies with molecular dynamics (MD) simulations of binding and AFM observations of collagen adsorption onmore » single crystals of calcium phosphate for four mineral phases of potential importance in bone formation. In all cases, we observe a strong preferential orientation of collagen binding, but comparison between the observed orientations and TEM analyses native tissues shows only calcium-deficient apatite (CDAP) provides an interface with collagen that is consistent with both. MD simulations predict preferred collagen orientations that agree with observations and results from both MD and DFS reveal large values for the binding energy due to multiple binding sites. These findings reconcile apparent contradictions inherent in a hydroxyapatite or carbonated apatite (CAP) model of bone mineral and provide an energetic rationale for the molecular scale organization of bone.« less

Energetic basis for the molecular-scale organization of bone.

PubMed

Tao, Jinhui; Battle, Keith C; Pan, Haihua; Salter, E Alan; Chien, Yung-Ching; Wierzbicki, Andrzej; De Yoreo, James J

2015-01-13

The remarkable properties of bone derive from a highly organized arrangement of coaligned nanometer-scale apatite platelets within a fibrillar collagen matrix. The origin of this arrangement is poorly understood and the crystal structures of hydroxyapatite (HAP) and the nonmineralized collagen fibrils alone do not provide an explanation. Moreover, little is known about collagen-apatite interaction energies, which should strongly influence both the molecular-scale organization and the resulting mechanical properties of the composite. We investigated collagen-mineral interactions by combining dynamic force spectroscopy (DFS) measurements of binding energies with molecular dynamics (MD) simulations of binding and atomic force microscopy (AFM) observations of collagen adsorption on single crystals of calcium phosphate for four mineral phases of potential importance in bone formation. In all cases, we observe a strong preferential orientation of collagen binding, but comparison between the observed orientations and transmission electron microscopy (TEM) analyses of native tissues shows that only calcium-deficient apatite (CDAP) provides an interface with collagen that is consistent with both. MD simulations predict preferred collagen orientations that agree with observations, and results from both MD and DFS reveal large values for the binding energy due to multiple binding sites. These findings reconcile apparent contradictions inherent in a hydroxyapatite or carbonated apatite (CAP) model of bone mineral and provide an energetic rationale for the molecular-scale organization of bone.

Quantitative spectral and orientational analysis in surface sum frequency generation vibrational spectroscopy (SFG-VS)

NASA Astrophysics Data System (ADS)

Wang, Hong-Fei; Gan, Wei; Lu, Rong; Rao, Yi; Wu, Bao-Hua

Sum frequency generation vibrational spectroscopy (SFG-VS) has been proven to be a uniquely effective spectroscopic technique in the investigation of molecular structure and conformations, as well as the dynamics of molecular interfaces. However, the ability to apply SFG-VS to complex molecular interfaces has been limited by the ability to abstract quantitative information from SFG-VS experiments. In this review, we try to make assessments of the limitations, issues and techniques as well as methodologies in quantitative orientational and spectral analysis with SFG-VS. Based on these assessments, we also try to summarize recent developments in methodologies on quantitative orientational and spectral analysis in SFG-VS, and their applications to detailed analysis of SFG-VS data of various vapour/neat liquid interfaces. A rigorous formulation of the polarization null angle (PNA) method is given for accurate determination of the orientational parameter D = /, and comparison between the PNA method with the commonly used polarization intensity ratio (PIR) method is discussed. The polarization and incident angle dependencies of the SFG-VS intensity are also reviewed, in the light of how experimental arrangements can be optimized to effectively abstract crucial information from the SFG-VS experiments. The values and models of the local field factors in the molecular layers are discussed. In order to examine the validity and limitations of the bond polarizability derivative model, the general expressions for molecular hyperpolarizability tensors and their expression with the bond polarizability derivative model for C3v, C2v and C∞v molecular groups are given in the two appendixes. We show that the bond polarizability derivative model can quantitatively describe many aspects of the intensities observed in the SFG-VS spectrum of the vapour/neat liquid interfaces in different polarizations. Using the polarization analysis in SFG-VS, polarization selection rules or guidelines are developed for assignment of the SFG-VS spectrum. Using the selection rules, SFG-VS spectra of vapour/diol, and vapour/n-normal alcohol (n˜ 1-8) interfaces are assigned, and some of the ambiguity and confusion, as well as their implications in previous IR and Raman assignment, are duly discussed. The ability to assign a SFG-VS spectrum using the polarization selection rules makes SFG-VS not only an effective and useful vibrational spectroscopy technique for interface studies, but also a complementary vibrational spectroscopy method in general condensed phase studies. These developments will put quantitative orientational and spectral analysis in SFG-VS on a more solid foundation. The formulations, concepts and issues discussed in this review are expected to find broad applications for investigations on molecular interfaces in the future.

Chiral symmetry breaking by spatial confinement in tactoidal droplets of lyotropic chromonic liquid crystals

PubMed Central

Tortora, Luana; Lavrentovich, Oleg D.

2011-01-01

In many colloidal systems, an orientationally ordered nematic (N) phase emerges from the isotropic (I) melt in the form of spindle-like birefringent tactoids. In cases studied so far, the tactoids always reveal a mirror-symmetric nonchiral structure, sometimes even when the building units are chiral. We report on chiral symmetry breaking in the nematic tactoids formed in molecularly nonchiral polymer-crowded aqueous solutions of low-molecular weight disodium cromoglycate. The parity is broken by twisted packing of self-assembled molecular aggregates within the tactoids as manifested by the observed optical activity. Fluorescent confocal microscopy reveals that the chiral N tactoids are located at the boundaries of cells. We explain the chirality induction as a replacement of energetically costly splay packing of the aggregates within the curved bipolar tactoidal shape with twisted packing. The effect represents a simple pathway of macroscopic chirality induction in an organic system with no molecular chirality, as the only requirements are orientational order and curved shape of confinement. PMID:21402929

Influence of orbital symmetry on diffraction imaging with rescattering electron wave packets

DOE PAGES

Pullen, M. G.; Wolter, B.; Le, A. -T.; ...

2016-06-22

The ability to directly follow and time-resolve the rearrangement of the nuclei within molecules is a frontier of science that requires atomic spatial and few-femtosecond temporal resolutions. While laser-induced electron diffraction can meet these requirements, it was recently concluded that molecules with particular orbital symmetries (such as pg) cannot be imaged using purely backscattering electron wave packets without molecular alignment. Here, we demonstrate, in direct contradiction to these findings, that the orientation and shape of molecular orbitals presents no impediment for retrieving molecular structure with adequate sampling of the momentum transfer space. We overcome previous issues by showcasing retrieval ofmore » the structure of randomly oriented O 2 and C 2H 2 molecules, with π g and π u symmetries, respectively, and where their ionization probabilities do not maximize along their molecular axes. As a result, while this removes a serious bottleneck for laser-induced diffraction imaging, we find unexpectedly strong backscattering contributions from low-Z atoms.« less

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.

Molecular resolution friction microscopy of Cu phthalocyanine thin films on dolomite (104) in water

NASA Astrophysics Data System (ADS)

Nita, Paweł; Pimentel, Carlos; Luo, Feng; Milián-Medina, Begoña; Gierschner, Johannes; Pina, Carlos M.; Gnecco, Enrico

2014-06-01

The reliability of ultrathin organic layers as active components for molecular electronic devices depends ultimately on an accurate characterization of the layer morphology and ability to withstand mechanical stresses on the nanoscale. To this end, since the molecular layers need to be electrically decoupled using thick insulating substrates, the use of AFM becomes mandatory. Here, we show how friction force microscopy (FFM) in water allows us to identify the orientation of copper(ii)phthalocyanine (CuPc) molecules previously self-assembled on a dolomite (104) mineral surface in ultra-high vacuum. The molecular features observed in the friction images show that the CuPc molecules are stacked in parallel rows with no preferential orientation with respect to the dolomite lattice, while the stacking features resemble well the single CuPc crystal structure. This proves that the substrate induction is low and makes friction force microscopy in water a suitable alternative to more demanding dynamic AFM techniques in ultra-high vacuum.

Molecular resolution friction microscopy of Cu phthalocyanine thin films on dolomite (104) in water.

PubMed

Nita, Paweł; Pimentel, Carlos; Luo, Feng; Milián-Medina, Begoña; Gierschner, Johannes; Pina, Carlos M; Gnecco, Enrico

2014-07-21

The reliability of ultrathin organic layers as active components for molecular electronic devices depends ultimately on an accurate characterization of the layer morphology and ability to withstand mechanical stresses on the nanoscale. To this end, since the molecular layers need to be electrically decoupled using thick insulating substrates, the use of AFM becomes mandatory. Here, we show how friction force microscopy (FFM) in water allows us to identify the orientation of copper(ii)phthalocyanine (CuPc) molecules previously self-assembled on a dolomite (104) mineral surface in ultra-high vacuum. The molecular features observed in the friction images show that the CuPc molecules are stacked in parallel rows with no preferential orientation with respect to the dolomite lattice, while the stacking features resemble well the single CuPc crystal structure. This proves that the substrate induction is low and makes friction force microscopy in water a suitable alternative to more demanding dynamic AFM techniques in ultra-high vacuum.

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.

Molecular organization, localization and orientation of antifungal antibiotic amphotericin B in a single lipid bilayer

PubMed Central

Grudzinski, Wojciech; Sagan, Joanna; Welc, Renata; Luchowski, Rafal; Gruszecki, Wieslaw I.

2016-01-01

Amphotericin B is a popular antifungal antibiotic, a gold standard in treatment of systemic mycotic infections, due to its high effectiveness. On the other hand, applicability of the drug is limited by its considerable toxicity to patients. Biomembranes are a primary target of physiological activity of amphotericin B and both the pharmacologically desired and toxic side effects of the drug relay on its molecular organization in the lipid phase. In the present work, molecular organization, localization and orientation of amphotericin B, in a single lipid bilayer system, was analysed simultaneously, thanks to application of a confocal fluorescence lifetime imaging microscopy of giant unilamellar vesicles. The results show that the presence of sterols, in the lipid phase, promotes formation of supramolecular structures of amphotericin B and their penetration into the membrane hydrophobic core. The fact that such an effect is substantially less pronounced in the case of cholesterol than ergosterol, the sterol of fungal membranes, provides molecular insight into the selectivity of the drug. PMID:27620838

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.

The mechanical properties of as-grown noncubic organic molecular crystals assessed by nanoindentation

DOE PAGES

Taw, Matthew R.; Yeager, John D.; Hooks, Daniel E.; ...

2017-06-19

Organic molecular crystals are often noncubic and contain significant steric hindrance within their structure to resist dislocation motion. Plastic deformation in these systems can be imparted during processing (tableting and comminution of powders), and the defect density impacts subsequent properties and performance. This paper measured the elastic and plastic properties of representative monoclinic, orthorhombic, and triclinic molecular crystalline structures using nanoindentation of as-grown sub-mm single crystals. The variation in modulus due to in-plane rotational orientation, relative to a Berkovich tip, was approximately equal to the variation of a given crystal at a fixed orientation. The onset of plasticity occurs consistentlymore » at shear stresses between 1 and 5% of the elastic modulus in all three crystal systems, and the hardness to modulus ratio suggests conventional Berkovich tips do not generate fully self-similar plastic zones in these materials. Finally, this provides guidance for mechanical models of tableting, machining, and property assessment of molecular crystals.« less

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.

Charged patchy particle models in explicit salt: Ion distributions, electrostatic potentials, and effective interactions.

PubMed

Yigit, Cemil; Heyda, Jan; Dzubiella, Joachim

2015-08-14

We introduce a set of charged patchy particle models (CPPMs) in order to systematically study the influence of electrostatic charge patchiness and multipolarity on macromolecular interactions by means of implicit-solvent, explicit-ion Langevin dynamics simulations employing the Gromacs software. We consider well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size which are composed of discrete atoms. The studied mono- and multipole moments of the CPPMs are comparable to those of globular proteins with similar size. We first characterize ion distributions and electrostatic potentials around a single CPPM. Although angle-resolved radial distribution functions reveal the expected local accumulation and depletion of counter- and co-ions around the patches, respectively, the orientation-averaged electrostatic potential shows only a small variation among the various CPPMs due to space charge cancellations. Furthermore, we study the orientation-averaged potential of mean force (PMF), the number of accumulated ions on the patches, as well as the CPPM orientations along the center-to-center distance of a pair of CPPMs. We compare the PMFs to the classical Derjaguin-Verwey-Landau-Overbeek theory and previously introduced orientation-averaged Debye-Hückel pair potentials including dipolar interactions. Our simulations confirm the adequacy of the theories in their respective regimes of validity, while low salt concentrations and large multipolar interactions remain a challenge for tractable theoretical descriptions.

Ordering of anisotropic nanoparticles in diblock copolymer lamellae: Simulations with dissipative particle dynamics and a molecular theory.

PubMed

Berezkin, Anatoly V; Kudryavtsev, Yaroslav V; Gorkunov, Maxim V; Osipov, Mikhail A

2017-04-14

Local distribution and orientation of anisotropic nanoparticles in microphase-separated symmetric diblock copolymers has been simulated using dissipative particle dynamics and analyzed with a molecular theory. It has been demonstrated that nanoparticles are characterized by a non-trivial orientational ordering in the lamellar phase due to their anisotropic interactions with isotropic monomer units. In the simulations, the maximum concentration and degree of ordering are attained for non-selective nanorods near the domain boundary. In this case, the nanorods have a certain tendency to align parallel to the interface in the boundary region and perpendicular to it inside the domains. Similar orientation ordering of nanoparticles located at the lamellar interface is predicted by the molecular theory which takes into account that the nanoparticles interact with monomer units via both isotropic and anisotropic potentials. Computer simulations enable one to study the effects of the nanorod concentration, length, stiffness, and selectivity of their interactions with the copolymer components on the phase stability and orientational order of nanoparticles. If the volume fraction of the nanorods is lower than 0.1, they have no effect on the copolymer transition from the disordered state into a lamellar microstructure. Increasing nanorod concentration or nanorod length results in clustering of the nanorods and eventually leads to a macrophase separation, whereas the copolymer preserves its lamellar morphology. Segregated nanorods of length close to the width of the diblock copolymer domains are stacked side by side into smectic layers that fill the domain space. Thus, spontaneous organization and orientation of nanorods leads to a spatial modulation of anisotropic composite properties which may be important for various applications.

Ordering of anisotropic nanoparticles in diblock copolymer lamellae: Simulations with dissipative particle dynamics and a molecular theory

NASA Astrophysics Data System (ADS)

Berezkin, Anatoly V.; Kudryavtsev, Yaroslav V.; Gorkunov, Maxim V.; Osipov, Mikhail A.

2017-04-01

Local distribution and orientation of anisotropic nanoparticles in microphase-separated symmetric diblock copolymers has been simulated using dissipative particle dynamics and analyzed with a molecular theory. It has been demonstrated that nanoparticles are characterized by a non-trivial orientational ordering in the lamellar phase due to their anisotropic interactions with isotropic monomer units. In the simulations, the maximum concentration and degree of ordering are attained for non-selective nanorods near the domain boundary. In this case, the nanorods have a certain tendency to align parallel to the interface in the boundary region and perpendicular to it inside the domains. Similar orientation ordering of nanoparticles located at the lamellar interface is predicted by the molecular theory which takes into account that the nanoparticles interact with monomer units via both isotropic and anisotropic potentials. Computer simulations enable one to study the effects of the nanorod concentration, length, stiffness, and selectivity of their interactions with the copolymer components on the phase stability and orientational order of nanoparticles. If the volume fraction of the nanorods is lower than 0.1, they have no effect on the copolymer transition from the disordered state into a lamellar microstructure. Increasing nanorod concentration or nanorod length results in clustering of the nanorods and eventually leads to a macrophase separation, whereas the copolymer preserves its lamellar morphology. Segregated nanorods of length close to the width of the diblock copolymer domains are stacked side by side into smectic layers that fill the domain space. Thus, spontaneous organization and orientation of nanorods leads to a spatial modulation of anisotropic composite properties which may be important for various applications.

Unidirectional self-assembly of soft templated mesoporous carbons by zone annealing

NASA Astrophysics Data System (ADS)

Xue, Jiachen; Singh, Gurpreet; Qiang, Zhe; Karim, Alamgir; Vogt, Bryan D.

2013-08-01

Surfactant or block copolymer-templated mesoporous films have been extensively explored, but achieving mesostructure coherence and unidirectional orientation over macroscopic dimensions has remained quite challenging for these self-assembled systems. Here, we extend the concepts associated with zone refinement of crystalline materials to soft templated mesoporous carbon films based on the cooperative assembly of commercial non-ionic surfactants (block copolymers) and phenolic resin oligomers (resol) to provide macroscopic alignment of both cubic (FDU-16) and hexagonal (FDU-15) mesostructures. The average orientation of these mesophases is determined from rotation grazing incidence small angle X-ray scattering (GISAXS) measurements. For FDU-15 templated by Pluronic P123, the orientation factor for the zone-annealed film is 0.98 based on the average of the second Legendre polynomial, but this orientation deteriorates significantly during carbonization. Notably, a thermal stabilization step following zone annealing preserves the orientation of the mesostructure during carbonization. The orientation factor for an isotropic cubic structure (FDU-16 templated by Pluronic F127) is only 0.48 (based on the 111 reflection with incident angle 0.15°) for the same zone annealing protocol, but this illustrates the versatility of zone annealing to different mesostructures. Unexpectedly, zone annealing of FDU-15 templated by Pluronic F127 leads to stabilization of the mesostructure through carbonization, whereas this structure collapses fully during carbonization even after extended oven annealing; despite no clear macroscopic orientation of the cylindrical mesostructure from zone annealing. Thermal zone annealing provides a simple methodology to produce highly ordered and macroscopically oriented stable mesoporous carbon films, but the efficacy is strongly tied to the mobility of the template during the zone annealing.Surfactant or block copolymer-templated mesoporous films have been extensively explored, but achieving mesostructure coherence and unidirectional orientation over macroscopic dimensions has remained quite challenging for these self-assembled systems. Here, we extend the concepts associated with zone refinement of crystalline materials to soft templated mesoporous carbon films based on the cooperative assembly of commercial non-ionic surfactants (block copolymers) and phenolic resin oligomers (resol) to provide macroscopic alignment of both cubic (FDU-16) and hexagonal (FDU-15) mesostructures. The average orientation of these mesophases is determined from rotation grazing incidence small angle X-ray scattering (GISAXS) measurements. For FDU-15 templated by Pluronic P123, the orientation factor for the zone-annealed film is 0.98 based on the average of the second Legendre polynomial, but this orientation deteriorates significantly during carbonization. Notably, a thermal stabilization step following zone annealing preserves the orientation of the mesostructure during carbonization. The orientation factor for an isotropic cubic structure (FDU-16 templated by Pluronic F127) is only 0.48 (based on the 111 reflection with incident angle 0.15°) for the same zone annealing protocol, but this illustrates the versatility of zone annealing to different mesostructures. Unexpectedly, zone annealing of FDU-15 templated by Pluronic F127 leads to stabilization of the mesostructure through carbonization, whereas this structure collapses fully during carbonization even after extended oven annealing; despite no clear macroscopic orientation of the cylindrical mesostructure from zone annealing. Thermal zone annealing provides a simple methodology to produce highly ordered and macroscopically oriented stable mesoporous carbon films, but the efficacy is strongly tied to the mobility of the template during the zone annealing. Electronic supplementary information (ESI) available: GISAXS profiles for the FDU-15-F127 at φ = 0° and φ = 90° is included along with 2D GISAXS data for all azimuthal data associated with FDU-15-P123 to illustrate the azimuthal dependence on the diffraction patterns. See DOI: 10.1039/c3nr02821f

The Study on the Mechanical Properties of Multi-walled Carbon Nanotube/Polypropylene Fibers

NASA Astrophysics Data System (ADS)

Youssefi, Mostafa; Safaie, Banafsheh

2018-06-01

Polypropylene (PP) is an important semicrystalline polymer with various applications. Polypropylene fibers containing 1 wt% of multi-walled carbon nanotube was spun using a conventional melt spinning apparatus. The produced fibers were drawn with varying levels of draw ratio. The mechanical properties of the composites were studied. Tensile strength and modulus of the composite fibers were increased with the increase in draw ratio. Molecular orientation and helical content of the composite fibers were increased after drawing. To conclude, tensile properties and molecular orientation of the composite fibers were higher than those of neat polypropylene fibers with the same draw ratio.

Comparison of short-range-order in liquid- and rotator-phase states of a simple molecular liquid: A reverse Monte Carlo and molecular dynamics analysis of neutron diffraction data

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

Pardo, Luis Carlos; Tamarit, Josep Lluis; Veglio, Nestor

2007-10-01

The short-range order (SRO) correlations in liquid- and rotator-phase states of carbon tetrachloride are revisited here. The correlation of some angular magnitudes is used to evaluate the positional and orientational correlations in the liquid as well as in the rotator phase. The results show significant similitudes in the relative position of the molecules surrounding a central one but striking differences in their relative orientations, which could explain the changes in SRO between the two phases and the puzzling behavior of the local density in the liquid and rotator phases.

The Study on the Mechanical Properties of Multi-walled Carbon Nanotube/Polypropylene Fibers

NASA Astrophysics Data System (ADS)

Youssefi, Mostafa; Safaie, Banafsheh

2018-01-01

Polypropylene (PP) is an important semicrystalline polymer with various applications. Polypropylene fibers containing 1 wt% of multi-walled carbon nanotube was spun using a conventional melt spinning apparatus. The produced fibers were drawn with varying levels of draw ratio. The mechanical properties of the composites were studied. Tensile strength and modulus of the composite fibers were increased with the increase in draw ratio. Molecular orientation and helical content of the composite fibers were increased after drawing. To conclude, tensile properties and molecular orientation of the composite fibers were higher than those of neat polypropylene fibers with the same draw ratio.

Characterizing hydrophobicity at the nanoscale: a molecular dynamics simulation study.

PubMed

Bandyopadhyay, Dibyendu; Choudhury, Niharendu

2012-06-14

We use molecular dynamics (MD) simulations of water near nanoscopic surfaces to characterize hydrophobic solute-water interfaces. By using nanoscopic paraffin like plates as model solutes, MD simulations in isothermal-isobaric ensemble have been employed to identify characteristic features of such an interface. Enhanced water correlation, density fluctuations, and position dependent compressibility apart from surface specific hydrogen bond distribution and molecular orientations have been identified as characteristic features of such interfaces. Tetrahedral order parameter that quantifies the degree of tetrahedrality in the water structure and an orientational order parameter, which quantifies the orientational preferences of the second solvation shell water around a central water molecule, have also been calculated as a function of distance from the plate surface. In the vicinity of the surface these two order parameters too show considerable sensitivity to the surface hydrophobicity. The potential of mean force (PMF) between water and the surface as a function of the distance from the surface has also been analyzed in terms of direct interaction and induced contribution, which shows unusual effect of plate hydrophobicity on the solvent induced PMF. In order to investigate hydrophobic nature of these plates, we have also investigated interplate dewetting when two such plates are immersed in water.

Organic heterojunctions: Contact-induced molecular reorientation, interface states, and charge re-distribution

PubMed Central

Opitz, Andreas; Wilke, Andreas; Amsalem, Patrick; Oehzelt, Martin; Blum, Ralf-Peter; Rabe, Jürgen P.; Mizokuro, Toshiko; Hörmann, Ulrich; Hansson, Rickard; Moons, Ellen; Koch, Norbert

2016-01-01

We reveal the rather complex interplay of contact-induced re-orientation and interfacial electronic structure – in the presence of Fermi-level pinning – at prototypical molecular heterojunctions comprising copper phthalocyanine (H16CuPc) and its perfluorinated analogue (F16CuPc), by employing ultraviolet photoelectron and X-ray absorption spectroscopy. For both layer sequences, we find that Fermi-level (EF) pinning of the first layer on the conductive polymer substrate modifies the work function encountered by the second layer such that it also becomes EF-pinned, however, at the interface towards the first molecular layer. This results in a charge transfer accompanied by a sheet charge density at the organic/organic interface. While molecules in the bulk of the films exhibit upright orientation, contact formation at the heterojunction results in an interfacial bilayer with lying and co-facial orientation. This interfacial layer is not EF-pinned, but provides for an additional density of states at the interface that is not present in the bulk. With reliable knowledge of the organic heterojunction’s electronic structure we can explain the poor performance of these in photovoltaic cells as well as their valuable function as charge generation layer in electronic devices. PMID:26887445

Understanding misfit strain releasing mechanisms via molecular dynamics simulations of CdTe growth on {112}zinc-blende CdS

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

Zhou, Xiaowang; Chavez, Jose J.; Almeida, Sergio F.

Molecular dynamics simulations have been used to analyse microstructures of CdTe films grown on {112} surfaces of zinc-blende CdS. Interestingly, CdTe films grow in <331> orientations as opposed to <112> epitaxial orientations. At the CdTe-{331}/CdS-{112} interface, however, there exists an axis that is parallel to the <110> orientation of both CdS and CdTe. It is the direction orthogonal to this <110> that becomes different, being <116> for CdTe and <111> for CdS, respectively. Missing CdTe-{110} planes are found along the <110> axis, suggesting that the misfit strain is released by the conventional misfit dislocation mechanism along this axis. In themore » orthogonal axis, the misfit strain is found to be more effectively released by the new grain orientation mechanism. Our finding is supported by literature experimental observations of the change of growth direction when Cd 0.96Zn 0.04Te films are deposited on GaAs. Lastly the analyses of energetics clearly demonstrate the cause for the formation of the new orientation, and the insights gained from our studies can help understand the grain structures experimentally observed in lattice mismatched systems.« less

Antifreeze Proteins at the Ice/Water Interface: Three Calculated Discriminating Properties for Orientation of Type I Proteins

PubMed Central

Wierzbicki, Andrzej; Dalal, Pranav; Cheatham, Thomas E.; Knickelbein, Jared E.; Haymet, A. D. J.; Madura, Jeffry D.

2007-01-01

Antifreeze proteins (AFPs) protect many plants and organisms from freezing in low temperatures. Of the different AFPs, the most studied AFP Type I from winter flounder is used in the current computational studies to gain molecular insight into its adsorption at the ice/water interface. Employing molecular dynamics simulations, we calculate the free energy difference between the hydrophilic and hydrophobic faces of the protein interacting with ice. Furthermore, we identify three properties of Type I “antifreeze” proteins that discriminate among these two orientations of the protein at the ice/water interface. The three properties are: the “surface area” of the protein; a measure of the interaction of the protein with neighboring water molecules as determined by the number of hydrogen bond count, for example; and the side-chain orientation angles of the threonine residues. All three discriminants are consistent with our free energy results, which clearly show that the hydrophilic protein face orientations toward the ice/water interface, as hypothesized from experimental and ice/vacuum simulations, are incorrect and support the hypothesis that the hydrophobic face is oriented toward the ice/water interface. The adsorption free energy is calculated to be 2–3 kJ/mol. PMID:17526572

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.

Understanding misfit strain releasing mechanisms via molecular dynamics simulations of CdTe growth on {112}zinc-blende CdS

DOE PAGES

Zhou, Xiaowang; Chavez, Jose J.; Almeida, Sergio F.; ...

2016-07-25

Molecular dynamics simulations have been used to analyse microstructures of CdTe films grown on {112} surfaces of zinc-blende CdS. Interestingly, CdTe films grow in <331> orientations as opposed to <112> epitaxial orientations. At the CdTe-{331}/CdS-{112} interface, however, there exists an axis that is parallel to the <110> orientation of both CdS and CdTe. It is the direction orthogonal to this <110> that becomes different, being <116> for CdTe and <111> for CdS, respectively. Missing CdTe-{110} planes are found along the <110> axis, suggesting that the misfit strain is released by the conventional misfit dislocation mechanism along this axis. In themore » orthogonal axis, the misfit strain is found to be more effectively released by the new grain orientation mechanism. Our finding is supported by literature experimental observations of the change of growth direction when Cd 0.96Zn 0.04Te films are deposited on GaAs. Lastly the analyses of energetics clearly demonstrate the cause for the formation of the new orientation, and the insights gained from our studies can help understand the grain structures experimentally observed in lattice mismatched systems.« less

Measuring Filament Orientation: A New Quantitative, Local Approach

NASA Astrophysics Data System (ADS)

Green, C.-E.; Dawson, J. R.; Cunningham, M. R.; Jones, P. A.; Novak, G.; Fissel, L. M.

2017-09-01

The relative orientation between filamentary structures in molecular clouds and the ambient magnetic field provides insight into filament formation and stability. To calculate the relative orientation, a measurement of filament orientation is first required. We propose a new method to calculate the orientation of the one-pixel-wide filament skeleton that is output by filament identification algorithms such as filfinder. We derive the local filament orientation from the direction of the intensity gradient in the skeleton image using the Sobel filter and a few simple post-processing steps. We call this the “Sobel-gradient method.” The resulting filament orientation map can be compared quantitatively on a local scale with the magnetic field orientation map to then find the relative orientation of the filament with respect to the magnetic field at each point along the filament. It can also be used for constructing radial profiles for filament width fitting. The proposed method facilitates automation in analyses of filament skeletons, which is imperative in this era of “big data.”

Molecular alignment dependent electron interference in attosecond ultraviolet photoionization

PubMed Central

Yuan, Kai-Jun; Bandrauk, André D.

2015-01-01

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

Electron backscatter diffraction studies of focused ion beam induced phase transformation in cobalt

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

Jones, H.G., E-mail: helen.jones@npl.co.uk

A focused ion beam microscope was used to induce cubic to hexagonal phase transformation in a cobalt alloy, of similar composition to that of the binder phase in a hardmetal, in a controlled manner at 0°, 45° and 80° ion incident angles. The cobalt had an average grain size of ~ 20 μm, allowing multiple orientations to be studied, exposed to a range of doses between 6 × 10{sup 7} and 2 × 10{sup 10} ions/μm{sup 2}. Electron backscatter diffraction (EBSD) was used to determine the original and induced phase orientations, and area fractions, before and after the ion beammore » exposure. On average, less phase transformation was observed at higher incident angles and after lower ion doses. However there was an orientation effect where grains with an orientation close to (111) planes were most susceptible to phase transformation, and (101) the least, where grains partially and fully transformed at varying ion doses. - Highlights: •Ion-induced phase change in FCC cobalt was observed at multiple incidence angles. •EBSD was used to study the relationship between grain orientation and transformation. •Custom software analysed ion dose and phase change with respect to grain orientation. •A predictive capability of ion-induced phase change in cobalt was enabled.« less

Molecular modeling study of binding to the catalytic site of PDE4 enzymes by a novel class of inhibitors

NASA Astrophysics Data System (ADS)

Lawrenz, Morgan E.; Salter, E. A.; Wierzbicki, Andrzej; Thompson, W. J.

Cyclic nucleotide phosphodiesterases (PDEs) comprise a superfamily of enzymes that hydrolyze the second messengers adenosine and guanosine 3',5'-cyclic monophosphate (cAMP and cGMP) to their noncyclic nucleotides (5'-AMP and 5'-GMP). Selective inhibitors of all 11 gene families of PDEs are being sought based on the different biochemical properties of the different isoforms, including their substrate specificities. The PDE4 gene family consists of cAMP-specific isoforms; selective PDE4 inhibitors such as rolipram have been developed, and related agents are used clinically as anti-inflammatory agents for asthma and COPD. The known crystal structures of PDE4 bound with rolipram and IBMX have allowed us to define plausible binding orientations for a novel class of benzylpyridazinone-based PDE4 inhibitors represented by EMD 94360 and EMD 95832 that are structurally distinct from rolipram. Molecular mechanics modeling with autodocking is used to explore energetically favorable binding orientations within the PDE4 catalytic site. We present two putative orientations for EMD 94360/95832 inhibitor binding. Our estimated interaction energies for rolipram, IBMX, EMD 94360, and EMD 95832 are consistent with the experimental data for their IC50 values. Key binding residues and interactions in these orientations are identified and compared with known binding motifs proposed for rolipram. The experimentally observed improved strength of inhibition exhibited by this novel class of PDE4 inhibitors is explained by the molecular modeling reported here.

Mean-field calculations of chain packing and conformational statistics in lipid bilayers: comparison with experiments and molecular dynamics studies.

PubMed Central

Fattal, D R; Ben-Shaul, A

1994-01-01

A molecular, mean-field theory of chain packing statistics in aggregates of amphiphilic molecules is applied to calculate the conformational properties of the lipid chains comprising the hydrophobic cores of dipalmitoyl-phosphatidylcholine (DPPC), dioleoyl-phosphatidylcholine (DOPC), and palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayers in their fluid state. The central quantity in this theory, the probability distribution of chain conformations, is evaluated by minimizing the free energy of the bilayer assuming only that the segment density within the hydrophobic region is uniform (liquidlike). Using this distribution we calculate chain conformational properties such as bond orientational order parameters and spatial distributions of the various chain segments. The lipid chains, both the saturated palmitoyl (-(CH2)14-CH3) and the unsaturated oleoyl (-(CH2)7-CH = CH-(CH2)7-CH3) chains are modeled using rotational isomeric state schemes. All possible chain conformations are enumerated and their statistical weights are determined by the self-consistency equations expressing the condition of uniform density. The hydrophobic core of the DPPC bilayer is treated as composed of single (palmitoyl) chain amphiphiles, i.e., the interactions between chains originating from the same lipid headgroup are assumed to be the same as those between chains belonging to different molecules. Similarly, the DOPC system is treated as a bilayer of oleoyl chains. The POPC bilayer is modeled as an equimolar mixture of palmitoyl and oleoyl chains. Bond orientational order parameter profiles, and segment spatial distributions are calculated for the three systems above, for several values of the bilayer thickness (or, equivalently, average area/headgroup) chosen, where possible, so as to allow for comparisons with available experimental data and/or molecular dynamics simulations. In most cases the agreement between the mean-field calculations, which are relatively easy to perform, and the experimental and simulation data is very good, supporting their use as an efficient tool for analyzing a variety of systems subject to varying conditions (e.g., bilayers of different compositions or thicknesses at different temperatures). PMID:7811955

Molecular Level Understanding of Interfaces and Excited State Electronic Structure in Organic Solar Cells Using Soft X-ray Techniques

NASA Astrophysics Data System (ADS)

Gliboff, Matthew

Transparent conductive oxides like indium tin oxide (ITO) are common substrates for optoelectronic devices, including organic light emitting diodes and organic solar cells. Tailoring the interface between the oxide and the active layer by adjusting the work function or wettability of the oxide can improve the performance of these devices in both emissive and photovoltaic applications. Molecular design of self-assembled monolayers (SAMs) allows for a range of surface properties using the same oxide material. The molecular ordering and conformation adopted by the SAMs determine properties such as work function and wettability at these critical interfaces. I use angle-dependent near edge x-ray absorption fine structure (NEXAFS) spectroscopy, to determine the molecular orientations of a variety of dipolar phosphonic acid surface modifiers. For a model system, phenylphosphonic acid on indium zinc oxide, the SAMs prove to be surprisingly well-oriented, with the phenyl ring adopting a well-defined tilt angle of 12-16° from the surface normal. The NEXAFS results agree with polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) results and orientations calculated from density functional theory (DFT). These results not only provide a detailed picture of the molecular structure of a technologically important class of SAMs, but they also resolve a long-standing ambiguity regarding the vibrational-mode assignments for phosphonic acids on oxide surfaces, thus improving the utility of PM-IRRAS for future studies. The effect of fluorination on the orientation of these phosponic-acid SAMs is non-trivial, due to the combined effects of the fluorination on binding mode and steric packing. The latter effects are found to be more dominant in aliphatic SAMs, leading to a more upright orientation in the fluorinated SAM. In the aromatic case, the fluorinated SAM adopted a less upright orientation which I attribute to changes in binding mode. The relationship between structure and performance in active layer polymers for organic electronics is not yet well understood. To gain insight into the effect of the excited state electronic structure on device performance, we examine two similar donor-acceptor polymers: PCPDTBT and PCDTBT, which produce devices with internal quantum efficiency (IQE) of 70% and 100% respectively. We use time-dependent density functional theory (TD-DFT) in combination with near edge x-ray absorption fine structure (NEXAFS) and resonant Auger spectroscopy to predict the electronic structure of the lowest unoccupied molecular orbital (LUMO). The resonant Auger results are found to be independent of film morphology and likely dominated by monomer structure. We show that the degree of LUMO localization onto the benzothiadiazole acceptor group in each polymer is similar, indicating that that the differences in IQE between these two polymers are driven by larger-scale morphology and not explained by the electronic structure of the excited state.

Probe for high resolution NMR with sample reorientation

DOEpatents

Pines, A.; Samoson, A.

1990-02-06

An improved NMR probe and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise orientationally disordered samples. The apparatus mechanically varies the orientation of the sample such that the time average of two or more sets of spherical harmonic functions are zero. 8 figs.

The Role of Behavioral and Cognitive Cultural Orientation on Mexican American College Students' Life Satisfaction

ERIC Educational Resources Information Center

Ojeda, Lizette; Edwards, Lisa M.; Hardin, Erin E.; Piña-Watson, Brandy

2014-01-01

We examined the role of behavioral (acculturation and enculturation) and cognitive cultural orientation (independent and interdependent self-construal) on Mexican American college students' life satisfaction. Analyses explained 28% of the variance in life satisfaction, with social class, grade point average, and independent self-construal being…

Oriented cell division: new roles in guiding skin wound repair and regeneration

PubMed Central

Yang, Shaowei; Ma, Kui; Geng, Zhijun; Sun, Xiaoyan; Fu, Xiaobing

2015-01-01

Tissue morphogenesis depends on precise regulation and timely co-ordination of cell division and also on the control of the direction of cell division. Establishment of polarity division axis, correct alignment of the mitotic spindle, segregation of fate determinants equally or unequally between daughter cells, are essential for the realization of oriented cell division. Furthermore, oriented cell division is regulated by intrinsic cues, extrinsic cues and other cues, such as cell geometry and polarity. However, dysregulation of cell division orientation could lead to abnormal tissue development and function. In the present study, we review recent studies on the molecular mechanism of cell division orientation and explain their new roles in skin repair and regeneration. PMID:26582817

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.

Drug Distribution. Part 1. Models to Predict Membrane Partitioning.

PubMed

Nagar, Swati; Korzekwa, Ken

2017-03-01

Tissue partitioning is an important component of drug distribution and half-life. Protein binding and lipid partitioning together determine drug distribution. Two structure-based models to predict partitioning into microsomal membranes are presented. An orientation-based model was developed using a membrane template and atom-based relative free energy functions to select drug conformations and orientations for neutral and basic drugs. The resulting model predicts the correct membrane positions for nine compounds tested, and predicts the membrane partitioning for n = 67 drugs with an average fold-error of 2.4. Next, a more facile descriptor-based model was developed for acids, neutrals and bases. This model considers the partitioning of neutral and ionized species at equilibrium, and can predict membrane partitioning with an average fold-error of 2.0 (n = 92 drugs). Together these models suggest that drug orientation is important for membrane partitioning and that membrane partitioning can be well predicted from physicochemical properties.

Six-dimensional quantum dynamics study for the dissociative adsorption of HCl on Au(111) surface

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

Liu, Tianhui; Fu, Bina; Zhang, Dong H., E-mail: zhangdh@dicp.ac.cn

The six-dimensional quantum dynamics calculations for the dissociative chemisorption of HCl on Au(111) are carried out using the time-dependent wave-packet approach, based on an accurate PES which was recently developed by neural network fitting to density functional theory energy points. The influence of vibrational excitation and rotational orientation of HCl on the reactivity is investigated by calculating the exact six-dimensional dissociation probabilities, as well as the four-dimensional fixed-site dissociation probabilities. The vibrational excitation of HCl enhances the reactivity and the helicopter orientation yields higher dissociation probability than the cartwheel orientation. A new interesting site-averaged effect is found for the titlemore » molecule-surface system that one can essentially reproduce the six-dimensional dissociation probability by averaging the four-dimensional dissociation probabilities over 25 fixed sites.« less

On the use of a sunward libration-point-orbiting spacecraft as an interplanetary magnetic field monitor for magnetospheric studies

NASA Technical Reports Server (NTRS)

Kelly, T. J.; Crooker, N. U.; Siscoe, G. L.; Russell, C. T.; Smith, E. J.

1986-01-01

In order to test the accuracy of using magnetometer data from a spacecraft orbiting the sunward libration point to determine the orientation of the interplanetary magnetic field (IMF), the angle between the IMF at ISEE 3, when it was positioned around the libration point, and at ISEE 1, orbiting the earth, has been calculated for a data set of 1-hour periods covering four months. For each period, a 10-minute average of ISEE 1 data is compared with 10-minute averages of ISEE 3 data at successively lagged intervals. It is concluded that the IMF orientation at a libration-point-orbiting spacecraft, lagged by the time required for the solar wind to convect to the earth, is a convenient predictor of IMF orientation near the earth, to within about 20-degree accuracy.

Regulation of migration in Mythimna separata (Walker) in China: A review integrating environmental, physiological, hormonal, genetic, and molecular factors

USDA-ARS?s Scientific Manuscript database

Each year the oriental armyworm, Mythimna separata, undertakes a seasonal, long-distance, multigeneration roundtrip migration between Southern and Northern China. The developmental decision to migrate is facultative and controlled by environmental, physiological, hormonal, genetic, and molecular fac...

Object-oriented design tools for supramolecular devices and biomedical nanotechnology.

PubMed

Lee, Stephen C; Bhalerao, Khaustaub; Ferrari, Mauro

2004-05-01

Nanotechnology provides multifunctional agents for in vivo use that increasingly blur the distinction between pharmaceuticals and medical devices. Realization of such therapeutic nanodevices requires multidisciplinary effort that is difficult for individual device developers to sustain, and identification of appropriate collaborations outside ones own field can itself be challenging. Further, as in vivo nanodevices become increasingly complex, their design will increasingly demand systems level thinking. System engineering tools such as object-oriented analysis, object-oriented design (OOA/D) and unified modeling language (UML) are applicable to nanodevices built from biological components, help logically manage the knowledge needed to design them, and help identify useful collaborative relationships for device designers. We demonstrate the utility of these systems engineering tools by reverse engineering an existing molecular device (the bacmid molecular cloning system) using them, and illustrate how object-oriented approaches identify fungible components (objects) in nanodevices in a way that facilitates design of families of related devices, rather than single inventions. We also explore the utility of object-oriented approaches for design of another class of therapeutic nanodevices, vaccines. While they are useful for design of current nanodevices, the power of systems design tools for biomedical nanotechnology will become increasingly apparent as the complexity and sophistication of in vivo nanosystems increases. The nested, hierarchical nature of object-oriented approaches allows treatment of devices as objects in higher-order structures, and so will facilitate concatenation of multiple devices into higher-order, higher-function nanosystems.

Comparative measurement of collagen bundle orientation by Fourier analysis and semiquantitative evaluation: reliability and agreement in Masson's trichrome, Picrosirius red and confocal microscopy techniques.

PubMed

Marcos-Garcés, V; Harvat, M; Molina Aguilar, P; Ferrández Izquierdo, A; Ruiz-Saurí, A

2017-08-01

Measurement of collagen bundle orientation in histopathological samples is a widely used and useful technique in many research and clinical scenarios. Fourier analysis is the preferred method for performing this measurement, but the most appropriate staining and microscopy technique remains unclear. Some authors advocate the use of Haematoxylin-Eosin (H&E) and confocal microscopy, but there are no studies comparing this technique with other classical collagen stainings. In our study, 46 human skin samples were collected, processed for histological analysis and stained with Masson's trichrome, Picrosirius red and H&E. Five microphotographs of the reticular dermis were taken with a 200× magnification with light microscopy, polarized microscopy and confocal microscopy, respectively. Two independent observers measured collagen bundle orientation with semiautomated Fourier analysis with the Image-Pro Plus 7.0 software and three independent observers performed a semiquantitative evaluation of the same parameter. The average orientation for each case was calculated with the values of the five pictures. We analyzed the interrater reliability, the consistency between Fourier analysis and average semiquantitative evaluation and the consistency between measurements in Masson's trichrome, Picrosirius red and H&E-confocal. Statistical analysis for reliability and agreement was performed with the SPSS 22.0 software and consisted of intraclass correlation coefficient (ICC), Bland-Altman plots and limits of agreement and coefficient of variation. Interrater reliability was almost perfect (ICC > 0.8) with all three histological and microscopy techniques and always superior in Fourier analysis than in average semiquantitative evaluation. Measurements were consistent between Fourier analysis by one observer and average semiquantitative evaluation by three observers, with an almost perfect agreement with Masson's trichrome and Picrosirius red techniques (ICC > 0.8) and a strong agreement with H&E-confocal (0.7 < ICC < 0.8). Comparison of measurements between the three techniques for the same observer showed an almost perfect agreement (ICC > 0.8), better with Fourier analysis than with semiquantitative evaluation (single and average). These results in nonpathological skin samples were also confirmed in a preliminary analysis in eight scleroderma skin samples. Our results show that Masson's trichrome and Picrosirius red are consistent with H&E-confocal for measuring collagen bundle orientation in histological samples and could thus be used indistinctly for this purpose. Fourier analysis is superior to average semiquantitative evaluation and should keep being used as the preferred method. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

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.

Scratching experiments on quartz crystals: Orientation effects in chipping

NASA Astrophysics Data System (ADS)

Tellier, C. R.; Benmessaouda, D.

1994-06-01

The deformation and microfracture properties of quartz crystals were studied by scratching experiments. The critical load at which microfractures are initiated was found to be orientation dependent, whereas the average width of ductile grooves and chips remained relatively insensitive to crystal orientation. In contrast, a marked anisotropy in the shape of chips was observed. This anisotropy has been interpreted in terms of microfractures propagating preferentially along slip planes. Simple geometrical conditions for the SEM (scanning electron microscopy) observation of active slip planes are proposed.

Evolution of molecular crystal optical phonons near structural phase transitions

NASA Astrophysics Data System (ADS)

Michki, Nigel; Niessen, Katherine; Xu, Mengyang; Markelz, Andrea

Molecular crystals are increasingly important photonic and electronic materials. For example organic semiconductors are lightweight compared to inorganic semiconductors and have inexpensive scale up processing with roll to roll printing. However their implementation is limited by their environmental sensitivity, in part arising from the weak intermolecular interactions of the crystal. These weak interactions result in optical phonons in the terahertz frequency range. We examine the evolution of intermolecular interactions near structural phase transitions by measuring the optical phonons as a function of temperature and crystal orientation using terahertz time-domain spectroscopy. The measured orientation dependence of the resonances provides an additional constraint for comparison of the observed spectra with the density functional calculations, enabling us to follow specific phonon modes. We observe crystal reorganization near 350 K for oxalic acid as it transforms from dihydrate to anhydrous form. We also report the first THz spectra for the molecular crystal fructose through its melting point.

Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample

NASA Technical Reports Server (NTRS)

Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)

2001-01-01

Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.

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 ).

Communication: Photoionization of degenerate orbitals for randomly oriented molecules: The effect of time-reversal symmetry on recoil-ion momentum angular distributions

NASA Astrophysics Data System (ADS)

Suzuki, Yoshi-Ichi

2018-04-01

The photoelectron asymmetry parameter β, which characterizes the direction of electrons ejected from a randomly oriented molecular ensemble by linearly polarized light, is investigated for degenerate orbitals. We show that β is totally symmetric under the symmetry operation of the point group of a molecule, and it has mixed properties under time reversal. Therefore, all degenerate molecular orbitals, except for the case of degeneracy due to time reversal, have the same β (Wigner-Eckart theorem). The exceptions are e-type complex orbitals of the Cn, Sn, Cnh, T, and Th point groups, and calculations on boric acid (C3h symmetry) are performed as an example. However, including those point groups, all degenerate orbitals have the same β if those orbitals are real. We discuss the implications of this operator formalism for molecular alignment and photoelectron circular dichroism.

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.

The alignment of molecular cloud magnetic fields with the spiral arms in M33.

PubMed

Li, Hua-bai; Henning, Thomas

2011-11-16

The formation of molecular clouds, which serve as stellar nurseries in galaxies, is poorly understood. A class of cloud formation models suggests that a large-scale galactic magnetic field is irrelevant at the scale of individual clouds, because the turbulence and rotation of a cloud may randomize the orientation of its magnetic field. Alternatively, galactic fields could be strong enough to impose their direction upon individual clouds, thereby regulating cloud accumulation and fragmentation, and affecting the rate and efficiency of star formation. Our location in the disk of the Galaxy makes an assessment of the situation difficult. Here we report observations of the magnetic field orientation of six giant molecular cloud complexes in the nearby, almost face-on, galaxy M33. The fields are aligned with the spiral arms, suggesting that the large-scale field in M33 anchors the clouds. ©2011 Macmillan Publishers Limited. All rights reserved

Fully invariant wavelet enhanced minimum average correlation energy filter for object recognition in cluttered and occluded environments

NASA Astrophysics Data System (ADS)

Tehsin, Sara; Rehman, Saad; Riaz, Farhan; Saeed, Omer; Hassan, Ali; Khan, Muazzam; Alam, Muhammad S.

2017-05-01

A fully invariant system helps in resolving difficulties in object detection when camera or object orientation and position are unknown. In this paper, the proposed correlation filter based mechanism provides the capability to suppress noise, clutter and occlusion. Minimum Average Correlation Energy (MACE) filter yields sharp correlation peaks while considering the controlled correlation peak value. Difference of Gaussian (DOG) Wavelet has been added at the preprocessing stage in proposed filter design that facilitates target detection in orientation variant cluttered environment. Logarithmic transformation is combined with a DOG composite minimum average correlation energy filter (WMACE), capable of producing sharp correlation peaks despite any kind of geometric distortion of target object. The proposed filter has shown improved performance over some of the other variant correlation filters which are discussed in the result section.

Colour differences in Caucasian and Oriental women's faces illuminated by white LED sources.

PubMed

Melgosa, M; Richard, N; Fernández-Maloigne, C; Xiao, K; de Clermont-Gallerande, H; Jost-Boissard, S; Okajima, K

2018-04-10

To provide an approach to facial contrast, analysing CIELAB colour differences (ΔE* ab,10 ) and its components in women's faces from two different ethnic groups, illuminated by modern white light-emitting diodes (LEDs) or traditional illuminants recommended by the International Commission on Illumination (CIE). We performed spectrophotometric measurements of spectral reflectance factors on forehead and cheek of 87 young healthy women (50 Caucasians and 37 Orientals), plus 5 commercial red lipsticks. We considered a set of 10 white LED illuminants, representative of technologies currently available on the market, plus 8 main illuminants currently recommended by the CIE, representative of conventional incandescent, daylight, and fluorescent light sources. Under each of these 18 illuminants we analysed the magnitude and components of ΔE* ab,10 between Caucasian and Oriental women (considering cheek and forehead), as well as for cheek-forehead and cheek-lipsticks in Caucasian and Oriental women. Colour-inconstancy indices for cheek, forehead, and lipsticks were computed, assuming D65 and A as reference illuminants. ΔE* ab,10 between forehead and cheek were quantitatively and qualitatively different in Orientals and Caucasians, but discrepancies with respect to average values for 18 illuminants were small (1.5% and 5.0% for Orientals and Caucasians, respectively). ΔE* ab,10 between Caucasians and Orientals were also quantitatively and qualitatively different both for forehead and cheek, and discrepancies with respect to average values were again small (1.0% and 3.9% for forehead and cheek, respectively). ΔE* ab,10 between lipsticks and cheek were at least 2 times higher than those between forehead and cheek. Regarding ΔE* ab,10 between lipsticks and cheeks, discrepancies with respect to average values were in the range 1.5% - 12.3%, although higher values of up to 54.2% were found for a white RGB LED. This white RGB LED provided the highest average colour-inconstancy indices: 17.1 and 11.5 CIELAB units, under reference illuminants D65 and A, respectively. Colour contrasts in women's faces under CIE standard illuminants for outdoor and indoor conditions may be strongly altered by using specific white LEDs. More research needs to be done on the impact of spectral power distribution of light sources with high colour rendering indices on visual colour appearance of cosmetic products. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

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.

Defining Protein Electrostatic Recognition Processes

DTIC Science & Technology

1989-11-30

of the electrostatic potentiai on the molecular surface of negatively charged Asp-101 in the fifth residue of JH1. the hapten and the V regions of...making and aligning expanded molecular dot surfaces for each molecule and checking these surfaces for interpenetration. The program TURNIP used these...the molecular surfaces are separated by 6 and 12A. All orientations have the exposed heme edge of cytochrome c facing the acidic patch of plastocyanin

Statistical errors in molecular dynamics averages

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

Schiferl, S.K.; Wallace, D.C.

1985-11-15

A molecular dynamics calculation produces a time-dependent fluctuating signal whose average is a thermodynamic quantity of interest. The average of the kinetic energy, for example, is proportional to the temperature. A procedure is described for determining when the molecular dynamics system is in equilibrium with respect to a given variable, according to the condition that the mean and the bandwidth of the signal should be sensibly constant in time. Confidence limits for the mean are obtained from an analysis of a finite length of the equilibrium signal. The role of serial correlation in this analysis is discussed. The occurence ofmore » unstable behavior in molecular dynamics data is noted, and a statistical test for a level shift is described.« less

Brownian systems with spatially inhomogeneous activity

NASA Astrophysics Data System (ADS)

Sharma, A.; Brader, J. M.

2017-09-01

We generalize the Green-Kubo approach, previously applied to bulk systems of spherically symmetric active particles [J. Chem. Phys. 145, 161101 (2016), 10.1063/1.4966153], to include spatially inhomogeneous activity. The method is applied to predict the spatial dependence of the average orientation per particle and the density. The average orientation is given by an integral over the self part of the Van Hove function and a simple Gaussian approximation to this quantity yields an accurate analytical expression. Taking this analytical result as input to a dynamic density functional theory approximates the spatial dependence of the density in good agreement with simulation data. All theoretical predictions are validated using Brownian dynamics simulations.

Care and Justice orientations to moral decision making in veterinary students.

PubMed

Quinn, C; Kinnison, T; May, S A

2012-11-03

An adapted version of the Moral Justification Scale was used to assess moral decision-making orientation in veterinary students, comparing sex and year of study. The Scale consists of vignettes and related statements, each of which was classified as Justice, Care for People or Care for Animals. The importance of each statement in the decision-making process was rated by 204 students on a 10-point Likert Scale. An average score of importance for Justice, Care for People and Care for Animals related statements were calculated for each individual. General inclination scores were calculated by subtracting an individual's average Care score from their average Justice score. Inclination scores suggested that two-thirds of students have a balanced approach, using Justice and Care almost equally in approaching ethical dilemmas. The majority of students, however, show an overall Justice orientation. The attitude towards the importance of Justice did not vary between students of different years or sexes. Students' attitudes towards the importance of Care for People in their decision making were, however, significantly lower for final-year students. Reasons hypothesised include the start of placements. Care for Animals scores were affected by sex, whereby females give more importance to such statements than males.

Revisiting elastic anisotropy of biotite gneiss from the Outokumpu scientific drill hole based on new texture measurements and texture-based velocity calculations

NASA Astrophysics Data System (ADS)

Wenk, H.-R.; Vasin, R. N.; Kern, H.; Matthies, S.; Vogel, S. C.; Ivankina, T. I.

2012-10-01

A sample of biotite gneiss from the Outokumpu deep drilling project in Finland was investigated by Kern et al. (2008) for crystal preferred orientation and elastic anisotropy. Considerable differences between measured acoustic velocities and velocities calculated on the basis of texture patterns were observed. Measured P-wave anisotropy was 15.1% versus a Voigt average yielding 7.9%. Here we investigate the same sample with different methods and using different averaging techniques. Analyzing time-of-flight neutron diffraction data from Dubna-SKAT and LANSCE-HIPPO diffractometers with the Rietveld technique, much stronger preferred orientation for biotite is determined, compared to conventional pole-figure analysis reported previously. The comparison reveals important differences: HIPPO has much better counting statistics but pole figure coverage is poor. SKAT has better angular resolution. Using the new preferred orientation data and applying a self-consistent averaging method that takes grain shapes into account, close agreement of calculated and measured P-wave velocities is observed (12.6%). This is further improved by adding 0.1 vol.% flat micropores parallel to the biotite platelets in the simulation (14.9%).

SOLINS- SOLAR INSOLATION MODEL FOR COMPUTING AVAILABLE SOLAR ENERGY TO A SURFACE OF ARBITRARY ORIENTATION

NASA Technical Reports Server (NTRS)

Smith, J. H.

1994-01-01

This computer program, SOLINS, was developed to aid engineers and solar system designers in the accurate modeling of the average hourly solar insolation on a surface of arbitrary orientation. The program can be used to study insolation problems specific to residential and commercial applications where the amount of space available for solar collectors is limited by shadowing problems, energy output requirements, and costs. For tandem rack arrays, SOLINS will accommodate the use of augmentation reflectors built into the support structure to increase insolation values at the collector surface. As the use of flat plate solar collectors becomes more prevalent in the building industry, the engineer and designer must have the capability to conduct extensive sensitivity analyses on the orientation and location of solar collectors. SOLINS should prove to be a valuable aid in this area of engineering. SOLINS uses a modified version of the National Bureau of Standards model to calculate the direct, diffuse, and reflected components of total insolation on a tilted surface with a given azimuthal orientation. The model is based on the work of Liu and Jordan with corrections by Kusuda and Ishii to account for early morning and late afternoon errors. The model uses a parametric description of the average day solar climate to generate monthly average day profiles by hour of the insolation level on the collector surface. The model includes accommodation of user specified ground and landscape reflectivities at the collector site. For roof or ground mounted, tilted arrays, SOLINS will calculate insolation including the effects of shadowing and augmentation reflectors. The user provides SOLINS with data describing the array design, array orientation, the month, the solar climate parameter, the ground reflectance, and printout control specifications. For the specified array and environmental conditions, SOLINS outputs the hourly insolation the array will receive during an average day during the month specified, along with the total insolation the collector surface will receive over an average 24-hour period. This program is written in FORTRAN IV for batch execution and has been implemented on an IBM 370 computer with a central memory requirement of approximately 46K of 8 bit bytes. The SOLINS routines were developed in 1979.

Real-time detection with AdaBoost-svm combination in various face orientation

NASA Astrophysics Data System (ADS)

Fhonna, R. P.; Nasution, M. K. M.; Tulus

2018-03-01

Most of the research has used algorithm AdaBoost-SVM for face detection. However, to our knowledge so far there is no research has been facing detection on real-time data with various orientations using the combination of AdaBoost and Support Vector Machine (SVM). Characteristics of complex and diverse face variations and real-time data in various orientations, and with a very complex application will slow down the performance of the face detection system this becomes a challenge in this research. Face orientation performed on the detection system, that is 900, 450, 00, -450, and -900. This combination method is expected to be an effective and efficient solution in various face orientations. The results showed that the highest average detection rate is on the face detection oriented 00 and the lowest detection rate is in the face orientation 900.

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.

Novel Determination of the Orientation of Calcite on Mineral Substrates

NASA Astrophysics Data System (ADS)

Zhao, L.; Ji, X.; Teng, H.

2016-12-01

In the threat of global warming, the transformation from CO2 to stable carbonate minerals is significant to geological CO2 sequestration in the long term.Previous efforts have found that when carbonate minerals nucleate on some mineral substrates ,the time of carbon capture can be shorted .Many efforts have been focused on the dynamics when carbonate minerals nucleate on mineral substrates, but few have studied the orientation of carbonate minerals on mineral substrates. In our experiment, we mainly focused on the orientation of calcite on mineral substrates.We mixed NaHCO3 and CaCl2 to nucleate when mineral substrates were added and a multi-parameter analyzer was used to monitor in real time to determine the induction time for nucleation. On the basis of classical nucleation theory, we got a brand new formula to decide the orientation of calcite on mineral substrates. lntind=(2-cosθ+cos3θ)*16πγ3vm2(12*(kBT)3*(lnS)2)+ln(1/N0v)+ ΔEa/(kBT)where θ is the angle between the substrate and the nuclei, tind is the induction time for nucleation, γ is he average surface free energy, N0 is the total number of particles per unit volume of solution, ΔEa is the activation energy for molecular motion across the embryo-matrix interface, S is the supersaturation index ,kB is the Boltzmann constant. Using the new formula above , when biotite was used as substrate mineral ,we found that the angle between the biotite and the nuclei was 119°. Angle measured on SEM images also supported our conclusion above. Combined with SEM and Debye ring analysed by Rigaku 2D data processing software, we only found one point of (006) in Debye ring, unlike (104)(many points in one ring and it meant that the orientation of (104) is random ). That meant (001) of calcite was first formed on biotite (001). In that case we inferred that 119° was formed by (001) of botite and (012) of calcite for the intersection angle of (001) and (012) was 120°. Future research will focus on the orientation of calcite on muscovite and feldspar to find out the main influence factor of the contact relationship.

The structure of PX3 (X = Cl, Br, I) molecular liquids from X-ray diffraction, molecular dynamics simulations, and reverse Monte Carlo modeling.

PubMed

Pothoczki, Szilvia; Temleitner, László; Pusztai, László

2014-02-07

Synchrotron X-ray diffraction measurements have been conducted on liquid phosphorus trichloride, tribromide, and triiodide. Molecular Dynamics simulations for these molecular liquids were performed with a dual purpose: (1) to establish whether existing intermolecular potential functions can provide a picture that is consistent with diffraction data and (2) to generate reliable starting configurations for subsequent Reverse Monte Carlo modelling. Structural models (i.e., sets of coordinates of thousands of atoms) that were fully consistent with experimental diffraction information, within errors, have been prepared by means of the Reverse Monte Carlo method. Comparison with reference systems, generated by hard sphere-like Monte Carlo simulations, was also carried out to demonstrate the extent to which simple space filling effects determine the structure of the liquids (and thus, also estimating the information content of measured data). Total scattering structure factors, partial radial distribution functions and orientational correlations as a function of distances between the molecular centres have been calculated from the models. In general, more or less antiparallel arrangements of the primary molecular axes that are found to be the most favourable orientation of two neighbouring molecules. In liquid PBr3 electrostatic interactions seem to play a more important role in determining intermolecular correlations than in the other two liquids; molecular arrangements in both PCl3 and PI3 are largely driven by steric effects.

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

PubMed

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

2017-07-12

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

Linking preferred orientations to elastic anisotropy in Muderong Shale, Australia

DOE PAGES

Kanitpanyacharoen, Waruntorn; Vasin, Roman; Wenk, Hans -Rudolf; ...

2015-01-01

The significance of shales as unconventional hydrocarbon reservoirs, nuclear waste repositories, and geological carbon storage has opened new research frontiers in geophysics. Among many of its unique physical properties, elastic anisotropy has long been investigated by both experimental and computational approaches. Here we calculate elastic properties of Cretaceous Muderong Shale from Australia with a self-consistent averaging method based on microstructural information. The volume fraction and crystallographic preferred orientation distributions of constituent minerals are based on synchrotron X-ray diffraction experiments. Aspect ratios of minerals and pores, determined from scanning electron microscopy (SEM), are introduced in the self-consistent averaging. Our analysis suggestsmore » that phyllosilicates (i.e., illite-mica, illite-smectite, kaolinite, and chlorite) are dominant with ~70 vol.%. The shape of clay platelets displays an average aspect ratio of 0.05. These platelets are aligned parallel to the bedding plane with a rather high degree of preferred orientation. The estimated porosity at ambient pressure is ~17 vol.% and is divided into equiaxial pores and flat pores with an average aspect ratio of 0.01. Our model shows results (e.g. at pressure of ~50 MPa with C 11 = 26.3; C 13 =12.5; C 33 = 18.2; C 44 = 2.8; C 66 = 6.8 [GPa]) that compare satisfactorily with values derived from ultrasonic velocity measurements (C 11 = 26.6; C 13 = 16.2; C 33 = 18.3; C 44 = 4.5; C 66 = 8.8 [GPa]), confirming the validity and reliability of our approximations and averaging approach.« less

Theory of "laser distillation" of enantiomers: purification of a racemic mixture of randomly oriented dimethylallene in a collisional environment.

PubMed

Gerbasi, David; Shapiro, Moshe; Brumer, Paul

2006-02-21

Enantiomeric control of 1,3 dimethylallene in a collisional environment is examined. Specifically, our previous "laser distillation" scenario wherein three perpendicular linearly polarized light fields are applied to excite a set of vib-rotational eigenstates of a randomly oriented sample is considered. The addition of internal conversion, dissociation, decoherence, and collisional relaxation mimics experimental conditions and molecular decay processes. Of greatest relevance is internal conversion which, in the case of dimethylallene, is followed by molecular dissociation. For various rates of internal conversion, enantiomeric control is maintained in this scenario by a delicate balance between collisional relaxation of excited dimethylallene that enhances control and collisional dephasing, which diminishes control.

Determination of three-dimensional molecular orientation of type-I collagen by circularly-polarized second harmonic generation imaging

NASA Astrophysics Data System (ADS)

Zhuo, Guan-Yu; Hung, Wei-Han; Kao, Fu-Jen

2017-04-01

The content of collagen is up to 30% existing in mammals. It supports the main component of connective tissues such as skin, ligament, and cartilage. Among various types of collagen, type-I collagen is of the most abundance and has been broadly studied due to the importance in bioscience. Second harmonic generation (SHG) microscopy is an effective tool used to study the collagen organization without labeling. In this study, we used circular polarization instead of linear polarization to retrieve three-dimensional (3D) molecular orientation of type-I collagen with only two cross polarized SHG images without acquiring an image stack of varying polarization.

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.

Graphene-Based Polymer Nanocomposites

DTIC Science & Technology

2015-03-31

Raman band I(δ) X - ray scattering intensity in the azimuthal scan I(r) Raman band intensity within laser spot I(ω...Krenchel orientation factor Θ Angle between the incident and the scattering X - ray θ Angle between the surface normal of graphene and sample λ...Wavelength of laser or X - ray λ2/λ4 Parameter in orientation distribution function µ Molecular dipole moment

Method and apparatus for measuring the NMR spectrum of an orientationally disordered sample

DOEpatents

Pines, Alexander; Samoson, Ago

1990-01-01

An improved NMR probe and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise oreintationally disordered samples. The apparatus mechanically varies the orientation of the sample such that the time average of two or more sets of spherical harmonic functions is zero.

A Ballistic Material Model for Cross-Plied Unidirectional Ultra-High Molecular-Weight Polyethylene Fiber-Reinforced Armor-Grade Composites

DTIC Science & Technology

2008-01-01

strength polymeric fibers such as aramid (e.g. Kevlar ®, Twaron®, etc.) or oriented polyethy- lene fibers (e.g. Spectra®, Dyneema®, etc.) with an... phenolic -poly-vinyl-butyral resin and on 0◦/90◦ cross- plied oriented polyethylene fiber-reinforced vinyl-ester resin are widely used in hard personnel...are: (a) poly-aramids (e.g. Kevlar ®, Twaron®, Technora®); (b) highly oriented ultra-highmolecular-weight polyethylene, UHMWPE (e.g. Spectra®, Dyneema

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.

Pattern formation of microtubules and motors: inelastic interaction of polar rods.

PubMed

Aranson, Igor S; Tsimring, Lev S

2005-05-01

We derive a model describing spatiotemporal organization of an array of microtubules interacting via molecular motors. Starting from a stochastic model of inelastic polar rods with a generic anisotropic interaction kernel we obtain a set of equations for the local rods concentration and orientation. At large enough mean density of rods and concentration of motors, the model describes orientational instability. We demonstrate that the orientational instability leads to the formation of vortices and (for large density and/or kernel anisotropy) asters seen in recent experiments.

Structure and dynamics in self-organized C60 fullerenes.

PubMed

Patnaik, Archita

2007-01-01

This manuscript on 'structure and dynamics in self-organized C60 fullerenes' has three sections dealing with: (A) pristine C60 aggregate structure and geometry in solvents of varying dielectric constant. Here, using positronium (Ps) as a fundamental probe which maps changes in the local electron density of the microenvironment, the onset concentration for stable C60 aggregate formation and its phase behavior is deduced from the specific interactions of the Ps atom with the surrounding. (B) A novel methanofullerene dyad, based on a hydrophobic (acceptor C60 moiety)-hydrophilic (bridge with benzene and ester functionalities)-hydrophobic (donor didodecyloxybenzene) network is chosen for investigation of characteristic self-assembly it undergoes leading to supramolecular aggregates. The pi-electronic amphiphile, necessitating a critical dielectric constant epsilon > or = 30 in binary THF-water mixtures, dictated the formation of bilayer vesicles as precursors for spherical fractal aggregates upon complete dyad extraction into a more polar water phase. (C) While the molecular orientation is dependent on the packing density, the ordering of the molecular arrangement, indispensable for self-assembly depends on the balance between the structures demanded by inter-molecular and molecule-substrate interactions. The molecular orientation in a monolayer affects the orientation in a multilayer, formed on the monolayer, suggesting the possibility of the latter to act as a template for controlling the structure of the three dimensionally grown self-assembled molecular aggregation. A systematic study on the electronic structure and orientation associated with C60 functionalized aminothiol self-assembled monolayers on Au(111) surface is presented using surface sensitive Ultra-Violet Photoelectron Spectroscopy (UPS) and C-K edge Near-Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy. The results revealed drastic modifications to d-band structure of Au(111) and the electronic structure was found sensitive towards the S-Au interface and the C60 end functional moiety with formation of localized sigma-(S-Au) and sigma(N-C) bonds, respectively. Upon binding C60 to the amine-terminated alkanethiol SAM, a drastically reduced HOMO-LUMO gap of 2.7 eV as compared to a large electronic gap of approximately 8 eV in alkanethiols enables the SAM to be a potential electron transport medium.

Electrostatic differences: A possible source for the functional differences between MCF7 and brain microtubules.

PubMed

Feizabadi, Mitra Shojania; Rosario, Brandon; Hernandez, Marcos A V

2017-11-04

Recent studies suggested a link between diversity of beta tubulin isotypes in microtubule structures and the regulatory roles that they play not only on microtubules' intrinsic dynamic, but also on the translocation characteristics of some of the molecular motors along microtubules. Remarkably, unlike porcine brain microtubules, MCF7 microtubules are structured from a different beta tubulin distribution. These types of cancer microtubules show a relatively stable and slow dynamic. In addition, the translocation parameters of some molecular motors are distinctly different along MCF7 as compared to those parameters on brain microtubules. It is known that the diversity of beta tubulin isotypes differ predominantly in the specifications and the electric charge of their carboxy-terminal tails. A key question is to identify whether the negative electrostatic charge of tubulin isotypes and, consequently, microtubules, can potentially be considered as one of the sources of functional differences in MCF7 vs. brain microtubules. We tested this possibility experimentally by monitoring the electro-orientation of these two types of microtubules inside a uniform electric field. Through this evaluation, we quantified and compared the average normalized polarization coefficient of MCF7 vs. Porcine brain microtubules. The higher value obtained for the polarization of MCF7 microtubules, which is associated to the higher negative charge of these types of microtubules, is significant as it can further explain the slow intrinsic dynamic that has been recently reported for single MCF7 microtubules in vitro. Furthermore, it can be potentially considered as a factor that can directly impact the translocation parameters of some molecular motors along MCF7 microtubules, by altering the mutual electrostatic interactions between microtubules and molecular motors. Copyright © 2017 Elsevier Inc. All rights reserved.

Orientation and Order of the Amide Group of Sphingomyelin in Bilayers Determined by Solid-State NMR

PubMed Central

Matsumori, Nobuaki; Yamaguchi, Toshiyuki; Maeta, Yoshiko; Murata, Michio

2015-01-01

Sphingomyelin (SM) and cholesterol (Chol) are considered essential for the formation of lipid rafts; however, the types of molecular interactions involved in this process, such as intermolecular hydrogen bonding, are not well understood. Since, unlike other phospholipids, SM is characterized by the presence of an amide group, it is essential to determine the orientation of the amide and its order in the lipid bilayers to understand the nature of the hydrogen bonds in lipid rafts. For this study, 1′-13C-2-15N-labeled and 2′-13C-2-15N-labeled SMs were prepared, and the rotational-axis direction and order parameters of the SM amide in bilayers were determined based on 13C and 15N chemical-shift anisotropies and intramolecular 13C-15N dipole coupling constants. Results revealed that the amide orientation was minimally affected by Chol, whereas the order was enhanced significantly in its presence. Thus, Chol likely promotes the formation of an intermolecular hydrogen-bond network involving the SM amide without significantly changing its orientation, providing a higher order to the SM amide. To our knowledge, this study offers new insight into the significance of the SM amide orientation with regard to molecular recognition in lipid rafts, and therefore provides a deeper understanding of the mechanism of their formation. PMID:26083921

Phase behavior and orientational ordering in block copolymers doped with anisotropic nanoparticles

NASA Astrophysics Data System (ADS)

Osipov, M. A.; Gorkunov, M. V.; Berezkin, A. V.; Kudryavtsev, Y. V.

2018-04-01

A molecular field theory and coarse-grained computer simulations with dissipative particle dynamics have been used to study the spontaneous orientational ordering of anisotropic nanoparticles in the lamellar and hexagonal phases of diblock copolymers and the effect of nanoparticles on the phase behavior of these systems. Both the molecular theory and computer simulations indicate that strongly anisotropic nanoparticles are ordered orientationally mainly in the boundary region between the domains and the nematic order parameter possesses opposite signs in adjacent domains. The orientational order is induced by the boundary and by the interaction between nanoparticles and the monomer units in different domains. In simulations, sufficiently long and strongly selective nanoparticles are ordered also inside the domains. The nematic order parameter and local concentration profiles of nanoparticles have been calculated numerically using the model of a nanoparticle with two interaction centers and also determined using the results of computer simulations. A number of phase diagrams have been obtained which illustrate the effect of nanoparticle selectivity and molar fraction of the stability ranges of various phases. Different morphologies have been identified by analyzing the static structure factor and a phase diagram has been constructed in coordinates' nanoparticle concentration-copolymer composition. Orientational ordering of even a small fraction of nanoparticles may result in a significant increase of the dielectric anisotropy of a polymer nanocomposite, which is important for various applications.

Activity-dependent gene expression in honey bee mushroom bodies in response to orientation flight.

PubMed

Lutz, Claudia C; Robinson, Gene E

2013-06-01

The natural history of adult worker honey bees (Apis mellifera) provides an opportunity to study the molecular basis of learning in an ecological context. Foragers must learn to navigate between the hive and floral locations that may be up to miles away. Young pre-foragers prepare for this task by performing orientation flights near the hive, during which they begin to learn navigational cues such as the appearance of the hive, the position of landmarks, and the movement of the sun. Despite well-described spatial learning and navigation behavior, there is currently limited information on the neural basis of insect spatial learning. We found that Egr, an insect homolog of Egr-1, is rapidly and transiently upregulated in the mushroom bodies in response to orientation. This result is the first example of an Egr-1 homolog acting as a learning-related immediate-early gene in an insect and also demonstrates that honey bee orientation uses a molecular mechanism that is known to be involved in many other forms of learning. This transcriptional response occurred both in naïve bees and in foragers induced to re-orient. Further experiments suggest that visual environmental novelty, rather than exercise or memorization of specific visual cues, acts as the stimulus for Egr upregulation. Our results implicate the mushroom bodies in spatial learning and emphasize the deep conservation of Egr-related pathways in experience-dependent plasticity.

Surface Structure Spread Single Crystals (S4C): Preparation and characterization

NASA Astrophysics Data System (ADS)

de Alwis, A.; Holsclaw, B.; Pushkarev, V. V.; Reinicker, A.; Lawton, T. J.; Blecher, M. E.; Sykes, E. C. H.; Gellman, A. J.

2013-02-01

A set of six spherically curved Cu single crystals referred to as Surface Structure Spread Single Crystals (S4Cs) has been prepared in such a way that their exposed surfaces collectively span all possible crystallographic surface orientations that can be cleaved from the face centered cubic Cu lattice. The method for preparing these S4Cs and for finding the high symmetry pole point is described. Optical profilometry has been used to determine the true shapes of the S4Cs and show that over the majority of the surface, the shape is extremely close to that of a perfect sphere. The local orientations of the surfaces lie within ± 1° of the orientation expected on the basis of the spherical shape; their orientation is as good as that of many commercially prepared single crystals. STM imaging has been used to characterize the atomic level structure of the Cu(111) ± 11°-S4C. This has shown that the average step densities and the average step orientations match those expected based on the spherical shape. In other words, although there is some distribution of step-step spacing and step orientations, there is no evidence of large scale reconstruction or faceting. The Cu S4Cs have local structures based on the ideal termination of the face centered cubic Cu lattice in the direction of termination. The set of Cu S4Cs will serve as the basis for high throughput investigations of structure sensitive surface chemistry on Cu.

Measuring Filament Orientation: A New Quantitative, Local Approach

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

Green, C.-E.; Cunningham, M. R.; Jones, P. A.

The relative orientation between filamentary structures in molecular clouds and the ambient magnetic field provides insight into filament formation and stability. To calculate the relative orientation, a measurement of filament orientation is first required. We propose a new method to calculate the orientation of the one-pixel-wide filament skeleton that is output by filament identification algorithms such as filfinder. We derive the local filament orientation from the direction of the intensity gradient in the skeleton image using the Sobel filter and a few simple post-processing steps. We call this the “Sobel-gradient method.” The resulting filament orientation map can be compared quantitativelymore » on a local scale with the magnetic field orientation map to then find the relative orientation of the filament with respect to the magnetic field at each point along the filament. It can also be used for constructing radial profiles for filament width fitting. The proposed method facilitates automation in analyses of filament skeletons, which is imperative in this era of “big data.”.« less

Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome.

PubMed

Hacker, William C; Li, Shuxiang; Elcock, Adrian H

2017-07-27

We describe structural models of the Escherichia coli chromosome in which the positions of all 4.6 million nucleotides of each DNA strand are resolved. Models consistent with two basic chromosomal orientations, differing in their positioning of the origin of replication, have been constructed. In both types of model, the chromosome is partitioned into plectoneme-abundant and plectoneme-free regions, with plectoneme lengths and branching patterns matching experimental distributions, and with spatial distributions of highly-transcribed chromosomal regions matching recent experimental measurements of the distribution of RNA polymerases. Physical analysis of the models indicates that the effective persistence length of the DNA and relative contributions of twist and writhe to the chromosome's negative supercoiling are in good correspondence with experimental estimates. The models exhibit characteristics similar to those of 'fractal globules,' and even the most genomically-distant parts of the chromosome can be physically connected, through paths combining linear diffusion and inter-segmental transfer, by an average of only ∼10 000 bp. Finally, macrodomain structures and the spatial distributions of co-expressed genes are analyzed: the latter are shown to depend strongly on the overall orientation of the chromosome. We anticipate that the models will prove useful in exploring other static and dynamic features of the bacterial chromosome. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Using Osteoclast Differentiation as a Model for Gene Discovery in an Undergraduate Cell Biology Laboratory

ERIC Educational Resources Information Center

Birnbaum, Mark J.; Picco, Jenna; Clements, Meghan; Witwicka, Hanna; Yang, Meiheng; Hoey, Margaret T.; Odgren, Paul R.

2010-01-01

A key goal of molecular/cell biology/biotechnology is to identify essential genes in virtually every physiological process to uncover basic mechanisms of cell function and to establish potential targets of drug therapy combating human disease. This article describes a semester-long, project-oriented molecular/cellular/biotechnology laboratory…

Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus.

PubMed

Yoshimura, Masato; Chen, Nai Chi; Guan, Hong Hsiang; Chuankhayan, Phimonphan; Lin, Chien Chih; Nakagawa, Atsushi; Chen, Chun Jung

2016-07-01

Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures.

jMetalCpp: optimizing molecular docking problems with a C++ metaheuristic framework.

PubMed

López-Camacho, Esteban; García Godoy, María Jesús; Nebro, Antonio J; Aldana-Montes, José F

2014-02-01

Molecular docking is a method for structure-based drug design and structural molecular biology, which attempts to predict the position and orientation of a small molecule (ligand) in relation to a protein (receptor) to produce a stable complex with a minimum binding energy. One of the most widely used software packages for this purpose is AutoDock, which incorporates three metaheuristic techniques. We propose the integration of AutoDock with jMetalCpp, an optimization framework, thereby providing both single- and multi-objective algorithms that can be used to effectively solve docking problems. The resulting combination of AutoDock + jMetalCpp allows users of the former to easily use the metaheuristics provided by the latter. In this way, biologists have at their disposal a richer set of optimization techniques than those already provided in AutoDock. Moreover, designers of metaheuristic techniques can use molecular docking for case studies, which can lead to more efficient algorithms oriented to solving the target problems.  jMetalCpp software adapted to AutoDock is freely available as a C++ source code at http://khaos.uma.es/AutodockjMetal/.

Molecular Dynamics Simulations of Shock Wave Propagation across the Nitromethane Crystal-Melt Interface

NASA Astrophysics Data System (ADS)

Jiang, Shan; Sewell, Thomas D.; Thompson, Donald L.

2015-06-01

We are interested in understanding the fundamental processes that occur during propagation of shock waves across the crystal-melt interface in molecular substances. We have carried out molecular dynamics simulations of shock passage from the nitromethane (100)-oriented crystal into the melt and vice versa using the fully flexible, non-reactive Sorescu, Rice, and Thompson force field. A stable interface was established for a temperature near the melting point by using a combination of isobaric-isothermal (NPT) and isochoric-isothermal (NVT) simulations. The equilibrium bulk and interfacial regions were characterized using spatial-temporal distributions of molecular number density, kinetic and potential energy, and C-N bond orientations. Those same properties were calculated as functions of time during shock propagation. As expected, the local temperatures (intermolecular, intramolecular, and total) and stress states differed significantly between the liquid and crystal regions and depending on the direction of shock propagation. Substantial differences in the spatial distribution of shock-induced defect structures in the crystalline region were observed depending on the direction of shock propagation. Research supported by the U.S. Army Research Office.

Experimental and modelling study of the effect of airflow orientation with respect to strip electrode on ozone production of surface dielectric barrier discharge

NASA Astrophysics Data System (ADS)

Mikeš, J.; Pekárek, S.; Soukup, I.

2016-11-01

This study examines the effect of airflow orientation with respect to the strip active electrode on concentration of ozone and nitrogen dioxide produced in a planar generator based on the surface dielectric barrier discharge. The orientation of the airflow was tested in parallel and perpendicular with respect to the strips. It was found that in the investigated range of average discharge power, the ozone concentration increases approximately by 25% when airflow was oriented in parallel with respect to the strips in comparison with perpendicular orientation of the airflow. Similarly the increase of nitrogen dioxide concentration was observed for parallel orientation of the airflow with respect to the strips in comparison with the perpendicular orientation of the airflow. Within the range of wavelengths from 250 to 1100 nm, the changes of intensities of spectral lines associated with airflow orientation have been observed. A 3D numerical model describing ion trajectories and airflow patterns have also been developed.

Molecular weight of Escherichia coli β-galactosidase in concentrated solutions of guanidine hydrochloride

PubMed Central

Erickson, Robert P.

1970-01-01

The molecular weight of Escherichia coli β-galactosidase was determined in 6m- and 8m-guanidine hydrochloride by meniscus-depletion sedimentation equilibrium, sedimentation velocity and viscosity. Sedimentation equilibrium revealed heterogeneity with the smallest component having a molecular weight of about 50000. At lower speeds, the apparent weight-average molecular weight is about 80000. By use of a calculation based on an empirical correlation for proteins that are random coils in 6m-guanidine hydrochloride, sedimentation velocity gave a molecular weight of 91000, and the intrinsic viscosity indicated a viscosity-average molecular weight of 84000. Heating in 6m-guanidine hydrochloride lowered the viscosity of β-galactosidase in a variable manner. PMID:4924171

Conformation of glycomimetics in the free and protein-bound state: structural and binding features of the C-glycosyl analogue of the core trisaccharide alpha-D-Man-(1 --> 3)-[alpha-D-Man-(1 --> 6)]-D-Man.

PubMed

Mikkelsen, Lise Munch; Hernáiz, María José; Martín-Pastor, M; Skrydstrup, Troels; Jiménez-Barbero, Jesús

2002-12-18

The conformational properties of the C-glycosyl analogue of the core trisaccharide alpha-D-Man-(1 --> 3)-[alpha-D-Man-(1 --> 6)]-D-Man in solution have been carefully analyzed by a combination of NMR spectroscopy and time-averaged restrained molecular dynamics. It has been found that both the alpha-1,3- and the alpha-1,6-glycosidic linkages show a major conformational averaging. Unusual Phi ca. 60 degrees orientations for both Phi torsion angles are found. Moreover, a major conformational distinction between the natural compound and the glycomimetic affects to the behavior of the omega(16) torsion angle around the alpha-1 --> 6-linkage. Despite this increased flexibility, the C-glycosyl analogue is recognized by three mannose binding lectins, as shown by NMR (line broadening, TR-NOE, and STD) and surface plasmon resonance (SPR) methods. Moreover, a process of conformational selection takes place, so that these lectins probably bind the glycomimetic similarly to the way they recognize the natural analogue. Depending upon the architecture and extension of the binding site of the lectin, loss or gain of binding affinity with respect to the natural analogue is found.

SCATTERING OF SLOW NEUTRONS FROM PROPANE GAS

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

Strong, K.A.; Marshall, G.D.; Brugger, R.M.

1962-02-01

Measurements of the partial differential neutron scattering cross sections for room-temperature propane gas are reported. These measurements were made at incident energies of 0.0l01, 0.0254, 0.0736, and 0.102 ev at seven scattering angles between 16.3 and 84.7 deg using the Materials Testing Reactor phased chopper velocity selector. The data are convented to the scattering-law presentation and compared with three theoretical calculations: The ideal gas, using an effective mass obtained from an average of the mass tensors for the three types of H atoms in propane, gives poor agreement. The Krieger-Nelkin approximation, which includes the effect of zero-point vibrations, gives limitedmore » agreement for energy transfer less than 0.5 k/sub b/T at intermediate momentum transfers. At large momentum transfers where vibrational effects become important it underestimates the cross section. A modification of the Krieger- Nelkin theory that includes the effects of single-quantum transitions from the three lowest vibratlonal states gives better agreement. The discrepancies still present at large momentum and energy transfers are attributed to an uncertainty in the methylgroup barrier height for the three lowest energy modes, to the harmonlc oscillator approximation for these modes, and to the approximate molecular orientation averaging used in the calculation. (auth)« less

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].

[Research-oriented experimental course of plant cell and gene engineering for undergraduates].

PubMed

Xiaofei, Lin; Rong, Zheng; Morigen, Morigen

2015-04-01

Research-oriented comprehensive experimental course for undergraduates is an important part for their training of innovation. We established an optional course of plant cell and gene engineering for undergraduates using our research platform. The course is designed to study the cellular and molecular basis and experimental techniques for plant tissue culture, isolation and culture of protoplast, genetic transformation, and screening and identification of transgenic plants. To develop undergraduates' ability in experimental design and operation, and inspire their interest in scientific research and innovation consciousness, we integrated experimental teaching and practice in plant genetic engineering on the tissue, cellular, and molecular levels. Students in the course practiced an experimental teaching model featured by two-week teaching of principles, independent experimental design and bench work, and ready-to-access laboratory. In this paper, we describe the contents, methods, evaluation system and a few issues to be solved in this course, as well as the general application and significance of the research-oriented experimental course in reforming undergraduates' teaching and training innovative talents.

Hexatic smectic phase with algebraically decaying bond-orientational order

NASA Astrophysics Data System (ADS)

Agosta, Lorenzo; Metere, Alfredo; Dzugutov, Mikhail

2018-05-01

The hexatic phase predicted by the theories of two-dimensional melting is characterized by the power-law decay of the orientational correlations, whereas the in-layer bond orientational order in all the hexatic smectic phases observed so far was found to be long range. We report a hexatic smectic phase where the in-layer bond orientational correlations decay algebraically, in quantitative agreement with the hexatic ordering predicted by the theory for two dimensions. The phase was formed in a molecular dynamics simulation of a one-component system of particles interacting via a spherically symmetric potential. The present results thus demonstrate that the theoretically predicted two-dimensional hexatic order can exist in a three-dimensional system.

An orientation sensitive approach in biomolecule interaction quantitative structure-activity relationship modeling and its application in ion-exchange chromatography.

PubMed

Kittelmann, Jörg; Lang, Katharina M H; Ottens, Marcel; Hubbuch, Jürgen

2017-01-27

Quantitative structure-activity relationship (QSAR) modeling for prediction of biomolecule parameters has become an established technique in chromatographic purification process design. Unfortunately available descriptor sets fail to describe the orientation of biomolecules and the effects of ionic strength in the mobile phase on the interaction with the stationary phase. The literature describes several special descriptors used for chromatographic retention modeling, all of these do not describe the screening of electrostatic potential by the mobile phase in use. In this work we introduce two new approaches of descriptor calculations, namely surface patches and plane projection, which capture an oriented binding to charged surfaces and steric hindrance of the interaction with chromatographic ligands with regard to electrostatic potential screening by mobile phase ions. We present the use of the developed descriptor sets for predictive modeling of Langmuir isotherms for proteins at different pH values between pH 5 and 10 and varying ionic strength in the range of 10-100mM. The resulting model has a high correlation of calculated descriptors and experimental results, with a coefficient of determination of 0.82 and a predictive coefficient of determination of 0.92 for unknown molecular structures and conditions. The agreement of calculated molecular interaction orientations with both, experimental results as well as molecular dynamic simulations from literature is shown. The developed descriptors provide the means for improved QSAR models of chromatographic processes, as they reflect the complex interactions of biomolecules with chromatographic phases. Copyright © 2016 Elsevier B.V. All rights reserved.

On the use of hydroxyl radical kinetics to assess the number-average molecular weight of dissolved organic matter.

PubMed

Appiani, Elena; Page, Sarah E; McNeill, Kristopher

2014-10-21

Dissolved organic matter (DOM) is involved in numerous environmental processes, and its molecular size is important in many of these processes, such as DOM bioavailability, DOM sorptive capacity, and the formation of disinfection byproducts during water treatment. The size and size distribution of the molecules composing DOM remains an open question. In this contribution, an indirect method to assess the average size of DOM is described, which is based on the reaction of hydroxyl radical (HO(•)) quenching by DOM. HO(•) is often assumed to be relatively unselective, reacting with nearly all organic molecules with similar rate constants. Literature values for HO(•) reaction with organic molecules were surveyed to assess the unselectivity of DOM and to determine a representative quenching rate constant (k(rep) = 5.6 × 10(9) M(-1) s(-1)). This value was used to assess the average molecular weight of various humic and fulvic acid isolates as model DOM, using literature HO(•) quenching constants, kC,DOM. The results obtained by this method were compared with previous estimates of average molecular weight. The average molecular weight (Mn) values obtained with this approach are lower than the Mn measured by other techniques such as size exclusion chromatography (SEC), vapor pressure osmometry (VPO), and flow field fractionation (FFF). This suggests that DOM is an especially good quencher for HO(•), reacting at rates close to the diffusion-control limit. It was further observed that humic acids generally react faster than fulvic acids. The high reactivity of humic acids toward HO(•) is in line with the antioxidant properties of DOM. The benefit of this method is that it provides a firm upper bound on the average molecular weight of DOM, based on the kinetic limits of the HO(•) reaction. The results indicate low average molecular weight values, which is most consistent with the recent understanding of DOM. A possible DOM size distribution is discussed to reconcile the small nature of DOM with the large-molecule behavior observed in other studies.

Fairness emergence from zero-intelligence agents

NASA Astrophysics Data System (ADS)

Duan, Wen-Qi; Stanley, H. Eugene

2010-02-01

Fairness plays a key role in explaining the emergence and maintenance of cooperation. Opponent-oriented social utility models were often proposed to explain the origins of fairness preferences in which agents take into account not only their own outcomes but are also concerned with the outcomes of their opponents. Here, we propose a payoff-oriented mechanism in which agents update their beliefs only based on the payoff signals of the previous ultimatum game, regardless of the behaviors and outcomes of the opponents themselves. Employing adaptive ultimatum game, we show that (1) fairness behaviors can emerge out even under such minimalist assumptions, provided that agents are capable of responding to their payoff signals, (2) the average game payoff per agent per round decreases with the increasing discrepancy rate between the average giving rate and the average asking rate, and (3) the belief update process will lead to 50%-50% fair split provided that there is no mutation in the evolutionary dynamics.

The Orientation of Eta Carinae and the Powering Mechanism of Intermediate-luminosity Optical Transients (ILOTS)

NASA Astrophysics Data System (ADS)

Kashi, Amit; Soker, Noam

2018-05-01

Contrary to recent claims, we argue that the orientation of the massive binary system Eta Carinae is such that the secondary star is closer to us at periastron passage, and it is on the far side during most of the time of the eccentric orbit. The binary orientation we dispute is based on problematic interpretations of recent observations. Among these are the radial velocity of the absorption component of He I P-Cyg lines, of the He II λ4686 emission line, and of the Br γ line emitted by clumps close to the binary system. We also base our orientation on observations of asymmetric molecular clumps that were recently observed by ALMA around the binary system, and were claimed to compose a torus with a missing segment. The orientation has implications for the modeling of the binary interaction during the nineteenth century Great Eruption (GE) of Eta Carinae that occurred close to periastron passage. The orientation where the secondary is closer to us at periastron leads us to suggest that the mass-missing side of the molecular clumps is a result of accretion onto the secondary star during periastron passage when the clumps were ejected, probably during the GE. The secondary star accreted a few solar masses during the GE and the energy from the accretion process consists of the majority of the GE energy. This in turn strengthens the more general model according to which many intermediate-luminosity optical transients (ILOTS) are powered by accretion onto a secondary star.

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.

Determination of the absolute molecular weight averages and molecular weight distributions of alginates used as ice cream stabilizers by using multiangle laser light scattering measurements.

PubMed

Turquois, T; Gloria, H

2000-11-01

High-performance size exclusion chromatography with multiangle laser light scattering detection (HPSEC-MALLS) was used for characterizing complete molecular weight distributions for a range of commercial alginates used as ice cream stabilizers. For the samples investigated, molecular weight averages were found to vary between 115 000 and 321 700 g/mol and polydispersity indexes varied from 1. 53 to 3.25. These samples displayed a high content of low molecular weights. Thus, the weight percentage of material below 100 000 g/mol ranged between 6.9 and 54.4%.

Fast electron transfer through a single molecule natively structured redox protein

NASA Astrophysics Data System (ADS)

Della Pia, Eduardo Antonio; Chi, Qijin; MacDonald, J. Emyr; Ulstrup, Jens; Jones, D. Dafydd; Elliott, Martin

2012-10-01

The electron transfer properties of proteins are normally measured as molecularly averaged ensembles. Through these and related measurements, proteins are widely regarded as macroscopically insulating materials. Using scanning tunnelling microscopy (STM), we present new measurements of the conductance through single-molecules of the electron transfer protein cytochrome b562 in its native conformation, under pseudo-physiological conditions. This is achieved by thiol (SH) linker pairs at opposite ends of the molecule through protein engineering, resulting in defined covalent contact between a gold surface and a platinum-iridium STM tip. Two different orientations of the linkers were examined: a long-axis configuration (SH-LA) and a short-axis configuration (SH-SA). In each case, the molecular conductance could be `gated' through electrochemical control of the heme redox state. Reproducible and remarkably high conductance was observed in this relatively complex electron transfer system, with single-molecule conductance values peaking around 18 nS and 12 nS for the SH-SA and SH-LA cytochrome b562 molecules near zero electrochemical overpotential. This strongly points to the important role of the heme co-factor bound to the natively structured protein. We suggest that the two-step model of protein electron transfer in the STM geometry requires a multi-electron transfer to explain such a high conductance. The model also yields a low value for the reorganisation energy, implying that solvent reorganisation is largely absent.The electron transfer properties of proteins are normally measured as molecularly averaged ensembles. Through these and related measurements, proteins are widely regarded as macroscopically insulating materials. Using scanning tunnelling microscopy (STM), we present new measurements of the conductance through single-molecules of the electron transfer protein cytochrome b562 in its native conformation, under pseudo-physiological conditions. This is achieved by thiol (SH) linker pairs at opposite ends of the molecule through protein engineering, resulting in defined covalent contact between a gold surface and a platinum-iridium STM tip. Two different orientations of the linkers were examined: a long-axis configuration (SH-LA) and a short-axis configuration (SH-SA). In each case, the molecular conductance could be `gated' through electrochemical control of the heme redox state. Reproducible and remarkably high conductance was observed in this relatively complex electron transfer system, with single-molecule conductance values peaking around 18 nS and 12 nS for the SH-SA and SH-LA cytochrome b562 molecules near zero electrochemical overpotential. This strongly points to the important role of the heme co-factor bound to the natively structured protein. We suggest that the two-step model of protein electron transfer in the STM geometry requires a multi-electron transfer to explain such a high conductance. The model also yields a low value for the reorganisation energy, implying that solvent reorganisation is largely absent. Electronic supplementary information (ESI) available: Experimental methods, DNA and protein sequences, additional STM statistical analysis and images, electrochemical data and It-z data analysis. See DOI: 10.1039/c2nr32131a

High average power pockels cell

DOEpatents

Daly, Thomas P.

1991-01-01

A high average power pockels cell is disclosed which reduces the effect of thermally induced strains in high average power laser technology. The pockels cell includes an elongated, substantially rectangular crystalline structure formed from a KDP-type material to eliminate shear strains. The X- and Y-axes are oriented substantially perpendicular to the edges of the crystal cross-section and to the C-axis direction of propagation to eliminate shear strains.

Method and sample spinning apparatus for measuring the NMR spectrum of an orientationally disordered sample

DOEpatents

Pines, Alexander; Samoson, Ago

1990-01-01

An improved NMR apparatus and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise orientationally disordered samples. The apparatus spins the sample about an axis. The angle of the axis is mechanically varied such that the time average of two or more Legendre polynomials are zero.

16 CFR 1500.47 - Method for determining the sound pressure level produced by toy caps.

Code of Federal Regulations, 2012 CFR

2012-01-01

...'s instructions. (2) The oscilloscope shall be the storage type or one equipped with a camera. It...) Fire 10 shots at each of the six orientations, obtaining readings on the oscilloscope of the maximum peak voltage for each shot. Average the results of the 10 firings for each of the six orientations. (4...

16 CFR 1500.47 - Method for determining the sound pressure level produced by toy caps.

Code of Federal Regulations, 2010 CFR

2010-01-01

...'s instructions. (2) The oscilloscope shall be the storage type or one equipped with a camera. It...) Fire 10 shots at each of the six orientations, obtaining readings on the oscilloscope of the maximum peak voltage for each shot. Average the results of the 10 firings for each of the six orientations. (4...

16 CFR § 1500.47 - Method for determining the sound pressure level produced by toy caps.

Code of Federal Regulations, 2013 CFR

2013-01-01

...'s instructions. (2) The oscilloscope shall be the storage type or one equipped with a camera. It...) Fire 10 shots at each of the six orientations, obtaining readings on the oscilloscope of the maximum peak voltage for each shot. Average the results of the 10 firings for each of the six orientations. (4...

16 CFR 1500.47 - Method for determining the sound pressure level produced by toy caps.

Code of Federal Regulations, 2011 CFR

2011-01-01

...'s instructions. (2) The oscilloscope shall be the storage type or one equipped with a camera. It...) Fire 10 shots at each of the six orientations, obtaining readings on the oscilloscope of the maximum peak voltage for each shot. Average the results of the 10 firings for each of the six orientations. (4...

Time Orientation and Human Performance

DTIC Science & Technology

2004-06-01

Work with Computing Systems 2004. H.M. Khalid, M.G. Helander, A.W. Yeo (Editors) . Kuala Lumpur: Damai Sciences. 1 Time Orientation and Human...Multi-tasking. 1 . Introduction With increased globalization, understanding the various cultures and people’s attitudes and behaviours is crucial...reporting burden for the collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching

Free swimming organisms: Microgravity as an investigative tool

NASA Technical Reports Server (NTRS)

Kessler, John O.

1989-01-01

On earth, micro-organisms are in the grip of gravitational and viscous forces. These forces, in combination with sensory stimuli, determine the average orientation of the organisms' swimming trajectories relative to the fluid environment. Microgravity provides the opportunity to study the rules which govern the summation or orienting influences and to develop quantitative physical measurements of sensory responses, e.g. the measurement of phototactic orientation tendency in torque units. Also, by reducing or eliminating density anisotropy-driven buoyant convection, it will be possible to study illumination, temperature gradient and concentration gradient-mediated collective dynamics.

A finite-strain homogenization model for viscoplastic porous single crystals: I - Theory

NASA Astrophysics Data System (ADS)

Song, Dawei; Ponte Castañeda, P.

2017-10-01

This paper presents a homogenization-based constitutive model for the finite-strain, macroscopic response of porous viscoplastic single crystals. The model accounts explicitly for the evolution of the average lattice orientation, as well as the porosity, average shape and orientation of the voids (and their distribution), by means of appropriate microstructural variables playing the role of internal variables and serving to characterize the evolution of both the "crystallographic" and "morphological" anisotropy of the porous single crystals. The model makes use of the fully optimized second-order variational method of Ponte Castañeda (2015), together with the iterated homogenization approach of Agoras and Ponte Castañeda (2013), to characterize the instantaneous effective response of the porous single crystals with fixed values of the microstructural variables. Consistent homogenization estimates for the average strain rate and vorticity fields in the phases are then used to derive evolution equations for the associated microstructural variables. The model is 100% predictive, requiring no fitting parameters, and applies for porous viscoplastic single crystals with general crystal anisotropy and average void shape and orientation, which are subjected to general loading conditions. In Part II of this work (Song and Ponte Castañeda, 2017a), results for both the instantaneous response and the evolution of the microstructure will be presented for porous FCC and HCP single crystals under a wide range of loading conditions, and good agreement with available FEM results will be shown.

Ensemble Sampling vs. Time Sampling in Molecular Dynamics Simulations of Thermal Conductivity

DOE PAGES

Gordiz, Kiarash; Singh, David J.; Henry, Asegun

2015-01-29

In this report we compare time sampling and ensemble averaging as two different methods available for phase space sampling. For the comparison, we calculate thermal conductivities of solid argon and silicon structures, using equilibrium molecular dynamics. We introduce two different schemes for the ensemble averaging approach, and show that both can reduce the total simulation time as compared to time averaging. It is also found that velocity rescaling is an efficient mechanism for phase space exploration. Although our methodology is tested using classical molecular dynamics, the ensemble generation approaches may find their greatest utility in computationally expensive simulations such asmore » first principles molecular dynamics. For such simulations, where each time step is costly, time sampling can require long simulation times because each time step must be evaluated sequentially and therefore phase space averaging is achieved through sequential operations. On the other hand, with ensemble averaging, phase space sampling can be achieved through parallel operations, since each ensemble is independent. For this reason, particularly when using massively parallel architectures, ensemble sampling can result in much shorter simulation times and exhibits similar overall computational effort.« less

Validation of an improved method to calculate the orientation and magnitude of pedicle screw bending moments.

PubMed

Freeman, Andrew L; Fahim, Mina S; Bechtold, Joan E

2012-10-01

Previous methods of pedicle screw strain measurement have utilized complex, time consuming methods of strain gauge application, experience high failure rates, do not effectively measure resultant bending moments, and cannot predict moment orientation. The purpose of this biomechanical study was to validate an improved method of quantifying pedicle screw bending moment orientation and magnitude. Pedicle screws were instrumented to measure biplanar screw bending moments by positioning four strain gauges on flat, machined surfaces below the screw head. Screws were calibrated to measure bending moments by hanging certified weights a known distance from the strain gauges. Loads were applied in 30 deg increments at 12 different angles while recording data from two independent strain channels. The data were then analyzed to calculate the predicted orientation and magnitude of the resultant bending moment. Finally, flexibility tests were performed on a cadaveric motion segment implanted with the instrumented screws to demonstrate the implementation of this technique. The difference between the applied and calculated orientation of the bending moments averaged (±standard error of the mean (SEM)) 0.3 ± 0.1 deg across the four screws for all rotations and loading conditions. The calculated resultant bending moments deviated from the actual magnitudes by an average of 0.00 ± 0.00 Nm for all loading conditions. During cadaveric testing, the bending moment orientations were medial/lateral in flexion-extension, variable in lateral bending, and diagonal in axial torsion. The technique developed in this study provides an accurate method of calculating the orientation and magnitude of screw bending moments and can be utilized with any pedicle screw fixation system.

Men's sexual orientation and suicide: evidence for U.S. adolescent-specific risk.

PubMed

Russell, Stephen T; Toomey, Russell B

2012-02-01

There is strong consensus in the research literature that adolescent and adult men who report same-sex sexual orientations, identities, and behaviors are at higher risk for suicide. Recent studies of general adolescent suicide risk have identified developmental trajectories that peak during the teenage years. Because the adolescent years are characterized by the development and heightened awareness of gender roles and sexual scripts closely tied to dominant cultural ideals of masculinity and heterosexuality, an adolescent-focused developmental trajectory for suicide risk might be particularly relevant for males with adolescent same-sex sexual orientations. We provide the first prospective examination of adolescent-specific risk for suicidality based on adolescent same-sex sexual orientation using data from the United States, the National Longitudinal Study of Adolescent Health. Tracing suicide ideation and attempts across four assessments from adolescence (Wave 1 average age 15.3 years) to young adulthood (Wave 4 average age 28.2), we documented that the risk for suicidal thoughts and attempts for adolescent same-sex attracted males is developmental in nature. Specifically, the risk for suicidal thoughts and attempts for males with same-sex attractions is largely limited to the adolescent years. These results offer new insights for suicide prevention and intervention for male adolescents and adults with same-sex sexual orientations. Copyright © 2010 Elsevier Ltd. All rights reserved.

Replica-exchange molecular dynamics simulation of basic fibroblast growth factor adsorption on hydroxyapatite.

PubMed

Liao, Chenyi; Zhou, Jian

2014-06-05

The adsorption of basic fibroblast growth factor (bFGF) on the hydroxyapatite (001) surface was investigated by a combination of replica-exchange molecular dynamics (REMD) and conventional molecular dynamics (CMD) methods. In CMD, the protein cannot readily cross the surface water layer, whereas in REMD, the protein can cross the adsorption barrier from the surface water layer and go through weak, medium, then strong adsorption states with three energetically preferred configurations: heparin-binding-up (HP-up), heparin-binding-middle (HP-middle), and heparin-binding-down (HP-down). The HP-middle orientation, with the strongest adsorption energy (-1149 ± 40 kJ·mol(-1)), has the largest adsorption population (52.1-52.6%) and exhibits the largest conformational charge (RMSD of 0.26 ± 0.01 nm) among the three orientations. The HP-down and HP-up orientations, with smaller adsorption energies of -1022 ± 55 and -894 ± 70 kJ·mol(-1), respectively, have smaller adsorption populations of 27.4-27.7% and 19.7-20.5% and present smaller RMSD values of 0.21 ± 0.01 and 0.19 ± 0.01 nm, respectively. The convergent distribution indicates that nearly half of the population (in the HP-middle orientation) will support both FGF/FGFR and DGR-integrin signaling and another half (in the HP-up and HP-down orientations) will support DGR-integrin signaling. The major population (~80%) has the protein dipole directed outward. In the strong adsorption state, there are usually 2 to 3 basic residues that form the anchoring interactions of 210-332 kJ·mol(-1) per residue or that are accompanied by an acidic residue with an adsorption energy of ~207 kJ·mol(-1). Together, the major bound residues form a triangle or a quadrilateral on the surface and stabilize the adsorption geometrically, which indicates topologic matching between the protein and HAP surfaces.

Are the religious suspicious of science? Investigating religiosity, religious context, and orientations towards science.

PubMed

Chan, Esther

2018-06-01

Are the religious suspicious of science? Drawing on data from 52 nations in the World Values Survey (wave 6) ( N = 58,474), I utilize multilevel models to examine the relationship between religiosity, religious context, and five different orientations towards science: confidence in science, trust in scientific authority under conditions of conflict with religion, faith in science, views on the moral effects of science, and interest in scientific knowledge. Results show that while religiosity is on average negatively associated with the five outcomes, the relationship between religiosity and orientations towards science varies by country such that religiosity is sometimes positively associated with the different outcomes. Religiosity is only consistently negatively associated with trust in scientific authority in all countries and with all orientations towards science in western countries. Finally, differences in orientations towards science also exist across country religious contexts, with countries dominated by the unaffiliated having more positive orientations towards science.

Simulation of Orientation in Injection Molding of High Aspect Ratio Particle Thermoplastic Composites

NASA Astrophysics Data System (ADS)

Vélez-García, Gregorio M.; Ortman, Kevin C.; Eberle, Aaron P. R.; Wapperom, Peter; Baird, Donald G.

2008-07-01

A 2D coupled Hele-Shaw flow approximation for predicting the flow-induced orientation of high aspect ratio particles in injection molded composite parts is presented. For a highly concentrated short glass fiber PBT suspension, the impact of inter-particle interactions and the orientation at the gate is investigated for a center-gated disk using material parameters determined from rheometry. Experimental orientation is determined from confocal laser micrographs using the methods of ellipses. The constitutive equations are discretized using discontinuous Galerkin Finite Elements. Model predictions are significantly improved by using a localized orientation measured experimentally at the gate region instead of random or averaged gapwise measured orientation assumed in previous studies. The predicted profile in different radial positions can be related to the layered structure along the gapwise direction. Model modifications including interactions have lower impact than the initial conditions.

Strong exciton-photon coupling in organic single crystal microcavity with high molecular orientation

NASA Astrophysics Data System (ADS)

Goto, Kaname; Yamashita, Kenichi; Yanagi, Hisao; Yamao, Takeshi; Hotta, Shu

2016-08-01

Strong exciton-photon coupling has been observed in a highly oriented organic single crystal microcavity. This microcavity consists of a thiophene/phenylene co-oligomer (TPCO) single crystal laminated on a high-reflection distributed Bragg reflector. In the TPCO crystal, molecular transition dipole was strongly polarized along a certain horizontal directions with respect to the main crystal plane. This dipole polarization causes significantly large anisotropies in the exciton transition and optical constants. Especially the anisotropic exciton transition was found to provide the strong enhancement in the coupling with the cavity mode, which was demonstrated by a Rabi splitting energy as large as ˜100 meV even in the "half-vertical cavity surface emitting lasing" microcavity structure.

The sign of the polarizability anisotropy of polar molecules is obtained from the terahertz Kerr effect

NASA Astrophysics Data System (ADS)

Kampfrath, Tobias; Wolf, Martin; Sajadi, Mohsen

2018-01-01

The terahertz Kerr effect (TKE) of polar molecular vapors is reported. The birefringence signal of fluoroform appears with opposite polarity compared to acetonitrile and water. This behavior is a hallmark of the opposite sign of a new molecular polarizability anisotropy ΔαTKE =αzz - (αxx +αyy) / 2 , with αzz being the polarizability along the permanent dipole moment. As the excitation of the rotational states orients the permanent dipoles along the terahertz electric field, the orientation is translated into an optical birefringence proportional to ΔαTKE . Thus, the sign of ΔαTKE is imprinted onto the TKE signal, providing novel insights into the polarizability tensor of water.

Possible limitations of the classical model of orientational optical nonlinearity in nematics

NASA Astrophysics Data System (ADS)

Sierakowski, Marek; Teterycz, Małgorzata

2008-09-01

Orientational nonlinearity is the major mechanism of nonlinear optical phenomena observed in liquidcrystalline phase while it does not appear to such extent in any other materials. It is caused by distortion of initial molecular arrangement of an anisotropic medium induced by optical field. Deformation of the anisotropic structure means spatial changes of refractive index of the medium. This effect has been studied in earnest since the 1980s as its application became more apparent. In this paper, some results of experimental examination of molecular reorientation in nematics by optical field are presented, which are not explained in frame of existing Oseen-Frank model and Erickson-Leslie continuous theory. Possible reasons of this discordance are considered and a way of explanation is suggested.

Water tribology on graphene.

PubMed

N'guessan, Hartmann E; Leh, Aisha; Cox, Paris; Bahadur, Prashant; Tadmor, Rafael; Patra, Prabir; Vajtai, Robert; Ajayan, Pulickel M; Wasnik, Priyanka

2012-01-01

Classical experiments show that the force required to slide liquid drops on surfaces increases with the resting time of the drop, t(rest), and reaches a plateau typically after several minutes. Here we use the centrifugal adhesion balance to show that the lateral force required to slide a water drop on a graphene surface is practically invariant with t(rest). In addition, the drop's three-phase contact line adopts a peculiar micrometric serrated form. These observations agree well with current theories that relate the time effect to deformation and molecular re-orientation of the substrate surface. Such molecular re-orientation is non-existent on graphene, which is chemically homogenous. Hence, graphene appears to provide a unique tribological surface test bed for a variety of liquid drop-surface interactions.

Molecular beam epitaxy growth of SrO buffer layers on graphite and graphene for the integration of complex oxides

DOE PAGES

Ahmed, Adam S.; Wen, Hua; Ohta, Taisuke; ...

2016-04-27

Here, we report the successful growth of high-quality SrO films on highly-ordered pyrolytic graphite (HOPG) and single-layer graphene by molecular beam epitaxy. The SrO layers have (001) orientation as confirmed by X-ray diffraction (XRD) while atomic force microscopy measurements show continuous pinhole-free films having rms surface roughness of <1.5 Å. Moreover, transport measurements of exfoliated graphene, after SrO deposition, show a strong dependence between the Dirac point and Sr oxidation. As a result, the SrO is leveraged as a buffer layer for more complex oxide integration via the demonstration of (001) oriented SrTiO3 grown atop a SrO/HOPG stack.

Artificial photosynthetic systems: assemblies of slipped cofacial porphyrins and phthalocyanines showing strong electronic coupling.

PubMed

Satake, Akiharu; Kobuke, Yoshiaki

2007-06-07

This paper reviews selected types of structurally well defined assemblies of porphyrins and phthalocyanines with strong electronic coupling. Face-to-face, head-to-tail, slipped cofacial, and non-parallel dimeric motifs constructed by covalent and non-covalent bonds are compared in the earlier sections. Their molecular orientation, electronic overlap, and absorption and fluorescence properties are discussed with a view towards the development of artificial photosynthetic systems and molecular electronics. Complementary coordination dimers are fully satisfactory in terms of structural stability, orientation factor, pi-electronic overlap, and zero fluorescence quenching. In later sections, several polymeric and macrocyclic porphyrin assemblies constructed by a combination of covalent bonds and complementary coordination bonds are discussed from the viewpoint of light-harvesting antenna functions.

Molecular beam epitaxy growth of SrO buffer layers on graphite and graphene for the integration of complex oxides

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

Ahmed, Adam S.; Wen, Hua; Ohta, Taisuke

Here, we report the successful growth of high-quality SrO films on highly-ordered pyrolytic graphite (HOPG) and single-layer graphene by molecular beam epitaxy. The SrO layers have (001) orientation as confirmed by X-ray diffraction (XRD) while atomic force microscopy measurements show continuous pinhole-free films having rms surface roughness of <1.5 Å. Moreover, transport measurements of exfoliated graphene, after SrO deposition, show a strong dependence between the Dirac point and Sr oxidation. As a result, the SrO is leveraged as a buffer layer for more complex oxide integration via the demonstration of (001) oriented SrTiO3 grown atop a SrO/HOPG stack.

Förster resonance energy transfer: Role of diffusion of fluorophore orientation and separation in observed shifts of FRET efficiency

DOE PAGES

Wallace, Bram; Atzberger, Paul J.; D’Auria, Sabato

2017-05-19

Forster resonance energy transfer (FRET) is a widely used single-molecule technique for measuring nanoscale distances from changes in the non-radiative transfer of energy between donor and acceptor fluorophores. For macromolecules and complexes this observed transfer efficiency is used to infer changes in molecular conformation under differing experimental conditions. But, sometimes shifts are observed in the FRET efficiency even when there is strong experimental evidence that the molecular conformational state is unchanged. Here, we investigate ways in which such discrepancies can arise from kinetic effects. We show that significant shifts can arise from the interplay between excitation kinetics, orientation diffusion ofmore » fluorophores, separation diffusion of fluorophores, and non-emitting quenching.« less

Effect of head group orientation on phospholipid assembly

NASA Astrophysics Data System (ADS)

Paul, Tanay; Saha, Jayashree

2017-06-01

The relationship between bilayer stability and lipid head group orientation is reported. In this work, molecular-dynamics simulations are performed to analyze the structure-property relationship of lipid biomembranes, taking into account coarse-grained model lipid interactions. The work explains the molecular scale mechanism of the phase behavior of lipid systems due to ion-lipid or anesthetic-lipid interactions, where reorientations of dipoles play a key role in modifying lipid phases and thereby alter biomembrane function. Our study demonstrates that simple dipolar reorientation is indeed sufficient in tuning a bilayer to a randomly flipped nonbilayer lamellar phase. This study may be used to assess the impact of changes in lipid phase characteristics on biomembrane structure due to the presence of anesthetics and ions.

Förster resonance energy transfer: Role of diffusion of fluorophore orientation and separation in observed shifts of FRET efficiency

PubMed Central

Wallace, Bram

2017-01-01

Förster resonance energy transfer (FRET) is a widely used single-molecule technique for measuring nanoscale distances from changes in the non-radiative transfer of energy between donor and acceptor fluorophores. For macromolecules and complexes this observed transfer efficiency is used to infer changes in molecular conformation under differing experimental conditions. However, sometimes shifts are observed in the FRET efficiency even when there is strong experimental evidence that the molecular conformational state is unchanged. We investigate ways in which such discrepancies can arise from kinetic effects. We show that significant shifts can arise from the interplay between excitation kinetics, orientation diffusion of fluorophores, separation diffusion of fluorophores, and non-emitting quenching. PMID:28542211

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.

From Gene to Structure: "Lactobacillus Bulgaricus" D-Lactate Dehydrogenase from Yogurt as an Integrated Curriculum Model for Undergraduate Molecular Biology and Biochemistry Laboratory Courses

ERIC Educational Resources Information Center

Lawton, Jeffrey A.; Prescott, Noelle A.; Lawton, Ping X.

2018-01-01

We have developed an integrated, project-oriented curriculum for undergraduate molecular biology and biochemistry laboratory courses spanning two semesters that is organized around the "ldhA" gene from the yogurt-fermenting bacterium "Lactobacillus bulgaricus," which encodes the enzyme d-lactate dehydrogenase. The molecular…

Molecular Modeling of Heme Proteins Using MOE: Bio-Inorganic and Structure-Function Activity for Undergraduates

ERIC Educational Resources Information Center

Ray, Gigi B.; Cook, J. Whitney

2005-01-01

A biochemical molecular modeling project on heme proteins suitable for an introductory Biochemistry I class has been designed with a 2-fold objective: i) to reinforce the correlation between protein three-dimensional structure and function through a discovery oriented project, and ii) to introduce students to the fields of bioinorganic and…

The psychological niche of older Japanese and Americans through auto-photography: aging and the search for peace.

PubMed

Okura, Y; Ziller, R C; Osawa, H

In an effort to understand aging cross-culturally, photography as a universal language was used to perceive the perceiver. Persons averaging seventy-three years of age from Japan and the United States were asked to describe "Who are you?" by taking (or having someone else take) six photographs. A content analysis of the photographs showed that older Japanese appear to be inward oriented (inside own territory, gardens, residence) and aesthetically oriented, while older Americans were more oriented toward other people. The results were interpreted in terms of differences in the search for peace. Peace is sought through self-harmony in the orient, but through social harmony in the occident.

Development and empirical validation of symmetric component measures of multidimensional constructs: customer and competitor orientation.

PubMed

Sørensen, Hans Eibe; Slater, Stanley F

2008-08-01

Atheoretical measure purification may lead to construct deficient measures. The purpose of this paper is to provide a theoretically driven procedure for the development and empirical validation of symmetric component measures of multidimensional constructs. Particular emphasis is placed on establishing a formalized three-step procedure for achieving a posteriori content validity. Then the procedure is applied to development and empirical validation of two symmetrical component measures of market orientation, customer orientation and competitor orientation. Analysis suggests that average variance extracted is particularly critical to reliability in the respecification of multi-indicator measures. In relation to this, the results also identify possible deficiencies in using Cronbach alpha for establishing reliable and valid measures.

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.

Electrostatic Properties of Aqueous Salt Solution Interfaces: A Comparison of Polarizable and Non-Polarizable Ion Models

PubMed Central

Warren, G. Lee; Patel, Sandeep

2014-01-01

The effects of ion force field polarizability on the interfacial electrostatic properties of ~1 M aqueous solutions of NaCl, CsCl and NaI are investigated using molecular dynamics simulations employing both non-polarizable and Drude-polarizable ion sets. Differences in computed depth-dependent orientational distributions, “permanent” and induced dipole and quadrupole moment profiles, and interfacial potentials are obtained for both ion sets to further elucidate how ion polarizability affects interfacial electrostatic properties among the various salts relative to pure water. We observe that the orientations and induced dipoles of water molecules are more strongly perturbed in the presence of polarizable ions via a stronger ionic double layer effect arising from greater charge separation. Both anions and cations exhibit enhanced induced dipole moments and strong z alignment in the vicinity of the Gibbs dividing surface (GDS) with the magnitude of the anion induced dipoles being nearly an order of magnitude larger than those of the cations and directed into the vapor phase. Depth-dependent profiles for the trace and zz components of the water molecular quadrupole moment tensors reveal 40% larger quadrupole moments in the bulk phase relative to the vapor mimicking a similar observed 40% increase in the average water dipole moment. Across the GDS, the water molecular quadrupole moments increase non-monotonically (in contrast to the water dipoles) and exhibit a locally reduced contribution just below the surface due to both orientational and polarization effects. Computed interfacial potentials for the non-polarizable salts yield values 20 to 60 mV more positive than pure water and increase by an additional 30 to 100 mV when ion polarizability is included. A rigorous decomposition of the total interfacial potential into ion monopole, water and ion dipole, and water quadrupole components reveals that a very strong, positive ion monopole contribution is offset by negative contributions from all other potential sources. Water quadrupole components modulated by the water density contribute significantly to the observed interfacial potential increments and almost entirely explain observed differences in the interfacial potentials for the two chloride salts. By lumping all remaining non-quadrupole interfacial potential contributions into a single “effective” dipole potential, we observe that the ratio of quadrupole to “effective” dipole contributions range from 2:1 in CsCl to 1:1.5 in NaI suggesting that both contributions are comparably important in determining the interfacial potential increments. We also find that oscillations in the quadrupole potential in the double layer region are opposite in sign and partially cancel those of the “effective” dipole potential. PMID:18712908

Increasing molecular weight parameters of a helical polymer through polymerization in a chiral solvent.

PubMed

Holder, Simon J; Achilleos, Mariliz; Jones, Richard G

2006-09-27

In this communication, we will demonstrate that polymerization in a chiral solvent can affect the molecular weight distribution of the product by perturbing the balance of the P and M helical screw senses of the growing chains. Specifically, for the Wurtz-type synthesis of polymethylphenylsilane (PMPS) in either (R) or (S)-limonene, the weight-average molecular weight of the products (average Mw = 80 000) was twice that of PMPS synthesized in (R/S)-limonene (average Mw = 39 200). Peturbation of the helical segmentation along the polymer chains leads to a reduction in the rate of occurrence of a key termination step. This the first time that a chiral solvent has been demonstrated to have such an effect on a polymerization process in affecting molecular weight parameters in contrast to affecting tacticity.

EBSD as a tool to identify and quantify bainite and ferrite in low-alloyed Al-TRIP steels.

PubMed

Zaefferer, S; Romano, P; Friedel, F

2008-06-01

Bainite is thought to play an important role for the chemical and mechanical stabilization of metastable austenite in low-alloyed TRIP steels. Therefore, in order to understand and improve the material properties, it is important to locate and quantify the bainitic phase. To this aim, electron backscatter diffraction-based orientation microscopy has been employed. The main difficulty herewith is to distinguish bainitic ferrite from ferrite because both have bcc crystal structure. The most important difference between them is the occurrence of transformation induced geometrically necessary dislocations in the bainitic phase. To determine the areas with larger geometrically necessary dislocation density, the following orientation microscopy maps were explored: pattern quality maps, grain reference orientation deviation maps and kernel average misorientation maps. We show that only the latter allow a reliable separation of the bainitic and ferritic phase. The kernel average misorientation threshold value that separates both constituents is determined by an algorithm that searches for the smoothness of the boundaries between them.

Theoretical studies of the mechanism of the action of the neurohypophyseal hormones. I. Molecular electrostatic potential (MEP) and molecular electrostatic field (MEF) maps of some vasopressin analogues

NASA Astrophysics Data System (ADS)

Liwo, Adam; Tempczyk, Anna; Grzonka, Zbigniew

1989-09-01

Continuing our theoretical studies of the oxytocin and vasopressin analogues, we have analysed the molecular electrostatic potential (MEP) and the norm of the molecular electrostatic field (MEF) of [1- β-mercaptopropionic acid]-arginine-vasopressin ([Mpa1]-AVP), [1-( β-mercapto- β,β-cyclopentamethylene)propionic acid]-arginine-vasopressin ([Cpp']-AVP), and [1-thiosalicylic acid]-arginine-vasopressin ([Ths']-AVP) whose low-energy conformations were calculated in our previous work. These compounds are known from experiment to exhibit different biological activity. The scalar fields mentioned determine the energy of interaction with either charged (MEP) or polar (MEF) species, the energy being in the second case either optimal or Boltzmann-averaged over all the possible orientations of the dipole moment versus the electrostatic field. The electrostatic interactions slowly vanish with distance and can therefore be considered to be the factor determining the molecular shape at greater distances, which can help in both predicting the interactions with the receptor at the stage of remote recognition and in finding the preferred directions of solvation by a polar solvent. In the analysis of the fields three techniques have been used: (i) the construction of maps in certain planes; (ii) the construction of maps on spheres centered in the charge center of the molecule under study and of poles chosen according to the main axes of the quadrupole moment; and (iii) the construction of surfaces corresponding to a given value of potential. The results obtained show that the shapes of both MEP and MEF are similar in the case of [Mpa1]-AVP and [Cpp1-AVP (biologically active), while some differences emerge when comparing these compounds with [Ths1]-AVP (inactive). It has also been found that both MEP and MEF depend even more strongly on conformation.

Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus

PubMed Central

Yoshimura, Masato; Chen, Nai-Chi; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Lin, Chien-Chih; Nakagawa, Atsushi; Chen, Chun-Jung

2016-01-01

Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures. PMID:27377380

Efficacy of spatial averaging of infrasonic pressure in varying wind speeds.

PubMed

DeWolf, Scott; Walker, Kristoffer T; Zumberge, Mark A; Denis, Stephane

2013-06-01

Wind noise reduction (WNR) is important in the measurement of infrasound. Spatial averaging theory led to the development of rosette pipe arrays. The efficacy of rosettes decreases with increasing wind speed and only provides a maximum of ~20 dB WNR due to a maximum size limitation. An Optical Fiber Infrasound Sensor (OFIS) reduces wind noise by instantaneously averaging infrasound along the sensor's length. In this study two experiments quantify the WNR achieved by rosettes and OFISs of various sizes and configurations. Specifically, it is shown that the WNR for a circular OFIS 18 m in diameter is the same as a collocated 32-inlet pipe array of the same diameter. However, linear OFISs ranging in length from 30 to 270 m provide a WNR of up to ~30 dB in winds up to 5 m/s. The measured WNR is a logarithmic function of the OFIS length and depends on the orientation of the OFIS with respect to wind direction. OFISs oriented parallel to the wind direction achieve ~4 dB greater WNR than those oriented perpendicular to the wind. Analytical models for the rosette and OFIS are developed that predict the general observed relationships between wind noise reduction, frequency, and wind speed.

Mesoscopic self-organization of a self-assembled supramolecular rectangle on highly oriented pyrolytic graphite and Au(111) surfaces.

PubMed

Gong, Jian-Ru; Wan, Li-Jun; Yuan, Qun-Hui; Bai, Chun-Li; Jude, Hershel; Stang, Peter J

2005-01-25

A self-assembled supramolecular metallacyclic rectangle was investigated with scanning tunneling microscopy on highly oriented pyrolytic graphite and Au(111) surfaces. The rectangles spontaneously adsorb on both surfaces and self-organize into well ordered adlayers. On highly oriented pyrolytic graphite, the long edge of the rectangle stands on the surface, forming a 2D molecular network. In contrast, the face of the rectangle lays flat on the Au(111) surface, forming linear chains. The structures and intramolecular features obtained through high-resolution scanning tunneling microscopy imaging are discussed.

Photoinduced orientation in natural rubber

NASA Astrophysics Data System (ADS)

de Souza, Nara C.; Cavalheri, Adriana S.; Brito, Jackeline B.; Job, Aldo E.; Oliveira, Osvaldo N.; Giacometti, José A.; Silva, Josmary R.

2012-04-01

Azobenzene molecules and their derivatives have been widely investigated for their potential applications in optical and electrooptical devices. We have prepared a new guest-host system from natural rubber (NR) impregnated with azobenzene derivative Sudan Red B (SRB). The effects of stretching and immersion time on photoinduced orientation were investigated by birefringence signal measurements. We have found that the molecular orientation increase when the samples are stretched and decrease with the increase of immersion time. The first behavior was explained by using the random coil model and the latter was attributed to increase of the aggregation of SRB into NR matrix.

Conversion of calibration curves for accurate estimation of molecular weight averages and distributions of polyether polyols by conventional size exclusion chromatography.

PubMed

Xu, Xiuqing; Yang, Xiuhan; Martin, Steven J; Mes, Edwin; Chen, Junlan; Meunier, David M

2018-08-17

Accurate measurement of molecular weight averages (M¯ n, M¯ w, M¯ z ) and molecular weight distributions (MWD) of polyether polyols by conventional SEC (size exclusion chromatography) is not as straightforward as it would appear. Conventional calibration with polystyrene (PS) standards can only provide PS apparent molecular weights which do not provide accurate estimates of polyol molecular weights. Using polyethylene oxide/polyethylene glycol (PEO/PEG) for molecular weight calibration could improve the accuracy, but the retention behavior of PEO/PEG is not stable in THF-based (tetrahydrofuran) SEC systems. In this work, two approaches for calibration curve conversion with narrow PS and polyol molecular weight standards were developed. Equations to convert PS-apparent molecular weight to polyol-apparent molecular weight were developed using both a rigorous mathematical analysis and graphical plot regression method. The conversion equations obtained by the two approaches were in good agreement. Factors influencing the conversion equation were investigated. It was concluded that the separation conditions such as column batch and operating temperature did not have significant impact on the conversion coefficients and a universal conversion equation could be obtained. With this conversion equation, more accurate estimates of molecular weight averages and MWDs for polyether polyols can be achieved from conventional PS-THF SEC calibration. Moreover, no additional experimentation is required to convert historical PS equivalent data to reasonably accurate molecular weight results. Copyright © 2018. Published by Elsevier B.V.

Influence of container shape on scaling of turbulent fluctuations in convection

NASA Astrophysics Data System (ADS)

Foroozani, Najmeh; Niemela, Joseph J.; Armenio, Vincenzo; Sreenivasan, Katepalli R.

2014-11-01

We perform large-eddy simulations of turbulent convection in a cubic enclosure for Rayleigh numbers 1 ×106 <= Ra <= 1 ×1010 and molecular Prandtl number, Pr = 0 . 7 . The simulations were carried out using a second-order-accurate finite-difference method in which subgrid-scale fluxes of momentum and heat were parametrized using a Lagrangian dynamic Smagorinsky model. The scalings of root-mean-square fluctuations of density and velocity in the cell center with Ra differ significantly from those in cylindrical containers, and are in agreement with laboratory observations by, also using a cell with square cross-section. We find that the time-averaged spatial distributions of the local heat flux and temperature fluctuations are inhomogeneous in the horizontal plane, associated with the forced orientation of the mean wind along either one or the other diagonal. Larger values of the steady-state density (temperature) gradients occur at the mid-plane corners of the diagonal opposite to that of the mean wind, due to the presence of strong counter-rotating circulations.

A Recombinant Secondary Antibody Mimic as a Target-specific Signal Amplifier and an Antibody Immobilizer in Immunoassays.

PubMed

Min, Junseon; Song, Eun Kyung; Kim, Hansol; Kim, Kyoung Taek; Park, Tae Joo; Kang, Sebyung

2016-04-11

We construct a novel recombinant secondary antibody mimic, GST-ABD, which can bind to the Fc regions of target-bound primary antibodies and acquire multiple HRPs simultaneously. We produce it in tenth of mg quantities with a bacterial overexpression system and simple purification procedures, significantly reducing the manufacturing cost and time without the use of animals. GST-ABD is effectively conjugated with 3 HRPs per molecule on an average and selectively bind to the Fc region of primary antibodies derived from three different species (mouse, rabbit, and rat). HRP-conjugated GST-ABD (HRP-GST-ABD) is successfully used as an alternative to secondary antibodies to amplify target-specific signals in both ELISA and immunohistochemistry regardless of the target molecules and origin of primary antibodies used. GST-ABD also successfully serves as an anchoring adaptor on the surface of GSH-coated plates for immobilizing antigen-capturing antibodies in an orientation-controlled manner for sandwich-type indirect ELISA through simple molecular recognition without any complicated chemical modification.

Communication: molecular dynamics and (1)H NMR of n-hexane in liquid crystals.

PubMed

Weber, Adrian C J; Burnell, E Elliott; Meerts, W Leo; de Lange, Cornelis A; Dong, Ronald Y; Muccioli, Luca; Pizzirusso, Antonio; Zannoni, Claudio

2015-07-07

The NMR spectrum of n-hexane orientationally ordered in the nematic liquid crystal ZLI-1132 is analysed using covariance matrix adaptation evolution strategy (CMA-ES). The spectrum contains over 150 000 transitions, with many sharp features appearing above a broad, underlying background signal that results from the plethora of overlapping transitions from the n-hexane as well as from the liquid crystal. The CMA-ES requires initial search ranges for NMR spectral parameters, notably the direct dipolar couplings. Several sets of such ranges were utilized, including three from MD simulations and others from the modified chord model that is specifically designed to predict hydrocarbon-chain dipolar couplings. In the end, only inaccurate dipolar couplings from an earlier study utilizing proton-proton double quantum 2D-NMR techniques on partially deuterated n-hexane provided the necessary estimates. The precise set of dipolar couplings obtained can now be used to investigate conformational averaging of n-hexane in a nematic environment.

Communication: Molecular dynamics and {sup 1}H NMR of n-hexane in liquid crystals

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

Weber, Adrian C. J., E-mail: WeberA@BrandonU.CA; Burnell, E. Elliott, E-mail: elliott.burnell@ubc.ca; Meerts, W. Leo, E-mail: leo.meerts@science.ru.nl

The NMR spectrum of n-hexane orientationally ordered in the nematic liquid crystal ZLI-1132 is analysed using covariance matrix adaptation evolution strategy (CMA-ES). The spectrum contains over 150 000 transitions, with many sharp features appearing above a broad, underlying background signal that results from the plethora of overlapping transitions from the n-hexane as well as from the liquid crystal. The CMA-ES requires initial search ranges for NMR spectral parameters, notably the direct dipolar couplings. Several sets of such ranges were utilized, including three from MD simulations and others from the modified chord model that is specifically designed to predict hydrocarbon-chain dipolar couplings.more » In the end, only inaccurate dipolar couplings from an earlier study utilizing proton-proton double quantum 2D-NMR techniques on partially deuterated n-hexane provided the necessary estimates. The precise set of dipolar couplings obtained can now be used to investigate conformational averaging of n-hexane in a nematic environment.« less

Mechanisms of plastic deformation in highly cross-linked UHMWPE for total hip components--the molecular physics viewpoint.

PubMed

Takahashi, Yasuhito; Shishido, Takaaki; Yamamoto, Kengo; Masaoka, Toshinori; Kubo, Kosuke; Tateiwa, Toshiyuki; Pezzotti, Giuseppe

2015-02-01

Plastic deformation is an unavoidable event in biomedical polymeric implants for load-bearing application during long-term in-vivo service life, which involves a mass transfer process, irreversible chain motion, and molecular reorganization. Deformation-induced microstructural alterations greatly affect mechanical properties and durability of implant devices. The present research focused on evaluating, from a molecular physics viewpoint, the impact of externally applied strain (or stress) in ultra-high molecular weight polyethylene (UHMWPE) prostheses, subjected to radiation cross-linking and subsequent remelting for application in total hip arthroplasty (THA). Two different types of commercial acetabular liners, which belong to the first-generation highly cross-linked UHMWPE (HXLPE), were investigated by means of confocal/polarized Raman microprobe spectroscopy. The amount of crystalline region and the spatial distribution of molecular chain orientation were quantitatively analyzed according to a combined theory including Raman selection rules for the polyethylene orthorhombic structure and the orientation distribution function (ODF) statistical approach. The structurally important finding was that pronounced recrystallization and molecular reorientation increasingly appeared in the near-surface regions of HXLPE liners with increasing the amount of plastic (compressive) deformation stored in the microstructure. Such molecular rearrangements, occurred in response to external strains, locally increase surface cross-shear (CS) stresses, which in turn trigger microscopic wear processes in HXLPE acetabular liners. Thus, on the basis of the results obtained at the molecular scale, we emphasize here the importance of minimizing the development of irrecoverable deformation strain in order to retain the pristine and intrinsically high wear performance of HXLPE components. Copyright © 2014 Elsevier Ltd. All rights reserved.

Factors that affect molecular weight distribution of Suwannee river fulvic acid as determined by electrospray ionization/mass spectrometry

USGS Publications Warehouse

Rostad, Colleen E.; Leenheer, Jerry A.

2004-01-01

Effects of methylation, molar response, multiple charging, solvents, and positive and negative ionization on molecular weight distributions of aquatic fulvic acid were investigated by electrospray ionization/mass spectrometry. After preliminary analysis by positive and negative modes, samples and mixtures of standards were derivatized by methylation to minimize ionization sites and reanalyzed.Positive ionization was less effective and produced more complex spectra than negative ionization. Ionization in methanol/water produced greater response than in acetonitrile/water. Molar response varied widely for the selected free acid standards when analyzed individually and in a mixture, but after methylation this range decreased. After methylation, the number average molecular weight of the Suwannee River fulvic acid remained the same while the weight average molecular weight decreased. These differences are probably indicative of disaggregation of large aggregated ions during methylation. Since the weight average molecular weight decreased, it is likely that aggregate formation in the fulvic acid was present prior to derivatization, rather than multiple charging in the mass spectra.

Source-oriented risk assessment of inhalation exposure to ambient polycyclic aromatic hydrocarbons and contributions of non-priority isomers in urban Nanjing, a megacity located in Yangtze River Delta, China.

PubMed

Zhuo, Shaojie; Shen, Guofeng; Zhu, Ying; Du, Wei; Pan, Xuelian; Li, Tongchao; Han, Yang; Li, Bengang; Liu, Junfeng; Cheng, Hefa; Xing, Baoshan; Tao, Shu

2017-05-01

Sixteen U.S. EPA priority polycyclic aromatic hydrocarbons (PAHs) and eleven non-priority isomers including some dibenzopyrenes were analyzed to evaluate health risk attributable to inhalation exposure to ambient PAHs and contributions of the non-priority PAHs in a megacity Nanjing, east China. The annual average mass concentration of the total 16 EPA priority PAHs in air was 51.1 ± 29.8 ng/m 3 , comprising up to 93% of the mass concentration of all 27 PAHs, however, the estimated Incremental Lifetime Cancer Risk (ILCR) due to inhalation exposure would be underestimated by 63% on average if only accounting the 16 EPA priority PAHs. The risk would be underestimated by 13% if only particulate PAHs were considered, though gaseous PAHs made up to about 70% of the total mass concentration. During the last fifteen years, ambient Benzo[a]pyrene decreased significantly in the city which was consistent with the declining trend of PAHs emissions. Source contributions to the estimated ILCR were much different from the contributions for the total mass concentration, calling for the introduce of important source-oriented risk assessments. Emissions from gasoline vehicles contributed to 12% of the total mass concentration of 27 PAHs analyzed, but regarding relative contributions to the overall health risk, gasoline vehicle emissions contributed 45% of the calculated ILCR. Dibenzopyrenes were a group of non-priority isomers largely contributing to the calculated ILCR, and vehicle emissions were probably important sources of these high molecular weight isomers. Ambient dibenzo[a,l]pyrene positively correlated with the priority PAH Benzo[g,h,i]perylene. The study indicates that inclusion of non-priority PAHs could be valuable for both PAH source apportionment and health risk assessment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Spatial reorientation experiments for NMR of solids and partially oriented liquids.

PubMed

Martin, Rachel W; Kelly, John E; Collier, Kelsey A

2015-11-01

Motional reorientation experiments are extensions of Magic Angle Spinning (MAS) where the rotor axis is changed in order to average out, reintroduce, or scale anisotropic interactions (e.g. dipolar couplings, quadrupolar interactions or chemical shift anisotropies). This review focuses on Variable Angle Spinning (VAS), Switched Angle Spinning (SAS), and Dynamic Angle Spinning (DAS), all of which involve spinning at two or more different angles sequentially, either in successive experiments or during a multidimensional experiment. In all of these experiments, anisotropic terms in the Hamiltonian are scaled by changing the orientation of the spinning sample relative to the static magnetic field. These experiments vary in experimental complexity and instrumentation requirements. In VAS, many one-dimensional spectra are collected as a function of spinning angle. In SAS, dipolar couplings and/or chemical shift anisotropies are reintroduced by switching the sample between two different angles, often 0° or 90° and the magic angle, yielding a two-dimensional isotropic-anisotropic correlation spectrum. Dynamic Angle Spinning (DAS) is a related experiment that is used to simultaneously average out the first- and second-order quadrupolar interactions, which cannot be accomplished by spinning at any unique rotor angle in physical space. Although motional reorientation experiments generally require specialized instrumentation and data analysis schemes, some are accessible with only minor modification of standard MAS probes. In this review, the mechanics of each type of experiment are described, with representative examples. Current and historical probe and coil designs are discussed from the standpoint of how each one accomplishes the particular objectives of the experiment(s) it was designed to perform. Finally, applications to inorganic materials and liquid crystals, which present very different experimental challenges, are discussed. The review concludes with perspectives on how motional reorientation experiments can be applied to current problems in chemistry, molecular biology, and materials science, given the many advances in high-field NMR magnets, fast spinning, and sample preparation realized in recent years. Copyright © 2015 Elsevier B.V. All rights reserved.

Simulated Keratometry Repeatability in Subjects with & without Down Syndrome

PubMed Central

Ravikumar, Ayeswarya; Marsack, Jason D.; Benoit, Julia S.; Anderson, Heather A.

2016-01-01

Purpose To assess the repeatability of simulated keratometry measures obtained with Zeiss Atlas topography for subjects with and without Down syndrome (DS). Methods Corneal topography was attempted on 140 subjects with DS and 138 controls (aged 7 to 59 years). Subjects who had at least 3 measures in each eye were included in analysis (DS: n=140 eyes (70 subjects) and controls: n=264 eyes (132 subjects)). For each measurement the steep corneal power (K), corneal astigmatism, flat K orientation, power vector representation of astigmatism (J0, J45), and astigmatic dioptric difference were determined for each measurement (collectively termed keratometry values here). For flat K orientation comparisons, only eyes with >0.50 DC of astigmatism were included (DS: n=131 eyes (68 subjects) and control: n=217 eyes (119 subjects)). Repeatability was assessed using 1) group mean variability (average standard deviation (SD) across subjects), 2) coefficient of repeatability (COR) 3) coefficient of variation (COV), and 4) intraclass correlation coefficient (ICC). Results The keratometry values showed good repeatability as evidenced by low group mean variability for DS vs control eyes (≤0.26D vs ≤0.09D for all dioptric values; 4.51° vs 3.16° for flat K orientation); however, the group mean variability was significantly higher in DS eyes than control eyes for all parameters (p≤0.03). On average, group mean variability was 2.5× greater in the DS eyes compared to control eyes across the keratometry values. Other metrics of repeatability also indicated good repeatability for both populations for each keratometry value, although repeatability was always better in the control eyes. Conclusions DS eyes showed more variability (on average: 2.5×) compared to controls for all keratometry values. Although differences were statistically significant, on average 91% of DS eyes had variability ≤0.50D for steep K and astigmatism, and 75% of DS eyes had variability ≤5 degrees for flat K orientation. PMID:27741083

Clinical research in small genomically stratified patient populations.

PubMed

Martin-Liberal, J; Rodon, J

2017-07-01

The paradigm of early drug development in cancer is shifting from 'histology-oriented' to 'molecularly oriented' clinical trials. This change can be attributed to the vast amount of tumour biology knowledge generated by large international research initiatives such as The Cancer Genome Atlas (TCGA) and the use of next generation sequencing (NGS) techniques developed in recent years. However, targeting infrequent molecular alterations entails a series of special challenges. The optimal molecular profiling method, the lack of standardised biological thresholds, inter- and intra-tumor heterogeneity, availability of enough tumour material, correct clinical trials design, attrition rate, logistics or costs are only some of the issues that need to be taken into consideration in clinical research in small genomically stratified patient populations. This article examines the most relevant challenges inherent to clinical research in these populations. Moreover, perspectives from the Academia point of view are reviewed as well as initiatives to be taken in forthcoming years. Copyright © 2017 Elsevier Ltd. All rights reserved.

Perfect Composition Depth Profiling of Ionic Liquid Surfaces Using High-resolution RBS/ERDA.

PubMed

Nakajima, Kaoru; Zolboo, Enkhbayar; Ohashi, Tomohiro; Lísal, Martin; Kimura, Kenji

2016-01-01

In order to reveal the surface structures of large molecular ionic liquids (ILs), the near-surface elemental depth distributions of 1-alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([C n C 1 Im][Tf 2 N], n = 2, 6, 10) were studied using high-resolution Rutherford backscattering spectroscopy (HRBS) in combination with high-resolution elastic recoil detection analysis (HR-ERDA). The elemental depth profiles of all constituent elements, including hydrogen, were derived from HR-ERDA/HRBS measurements, so that the profiles would reproduce both HR-ERDA and HRBS spectra simultaneously. The derived elemental depth profiles agree with state-of-the-art molecular dynamics simulations, indicating the feasibility of this method. A controversy concerning the preferential orientation of [C 2 C 1 Im] at the surface has been resolved by this new combination analysis; namely, the [C 2 C 1 Im] cation has a preferential orientation with the ethyl chain pointing towards the vacuum in the topmost molecular layer.

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.

Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement

PubMed Central

Dahms, Sven O.; Kuester, Miriam; Streb, Carsten; Roth, Christian; Sträter, Norbert; Than, Manuel E.

2013-01-01

Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradeca­bromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome. PMID:23385464

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.

Integral Equation Study of Molecular Fluids and Liquid Crystals in Two Dimensions

NASA Astrophysics Data System (ADS)

Ward, David Atlee

The Ornstein-Zernike (OZ) equation is solved with a Percus-Yevick (PY) closure for the hard ellipse and hard planar dumbell fluids in two dimensions. The correlation functions, including the orientation correlation function, are expanded in a set of orthogonal functions and the coefficients are solved for using an iterative algorithm developed by Lado. The pressure, compressibility, and orientation coefficients are computed for a variety of densities and molecular elongations. The hard planar dumbell fluid shows no orientational ordering. The PY values for the pressure differ from the corresponding Monte Carlo (MC) values by as much as 8% for the cases studied. The hard ellipse fluid exhibits some orientational ordering. Ordering is much more pronounced for ellipses with an axis ratio larger than 2.0. Pressure values computed for the hard ellipse fluid from the PY theory differ from the corresponding MC values by as much as 11% for the cases studied. As the PY solutions do exhibit a nematic character in the hard ellipse fluid, we find it to be a viable reference system for further studies of the nematic liquid crystal phase, though the isotropic-nematic (I-N) phase transition found by Vieillard-Baron was not observed in the PY solutions. The Maier-Saupe theory was reformulated based on the density functional formalism of Sluckin and Shukla. Using PY data of the hard ellipse as input for the direct correlation function in the isotropic phase, the orientational distribution was calculated. The values obtained showed only extremely weak nematic behavior.

George Washington High School Bilingual Academic and Career Orientation Program, 1982-1983. O.E.E. Evaluation Report.

ERIC Educational Resources Information Center

Cotayo, Armando; Collins, Carla

This program, in its final year of a two-year funding cycle, offered bilingual instruction and supportive services with a career orientation focus to 250 Hispanic students in grades 9-12. The major program goal was to expedite the acquisition of the English language skills necessary for full mainstreaming within an average period of three years.…

78 FR 54828 - Promulgation of State Implementation Plan Revisions; Infrastructure Requirements for the 1997 and...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-06

...- oriented monitors, and 65 [mu]g/m\\3\\, based on the three-year average of the 98th percentile of 24-hour PM 2.5 concentrations at each population-oriented monitor within an area (62 FR 38652). On October 17...)(2)(G): Emergency powers. 110(a)(2)(H): Future SIP revisions. 110(a)(2)(J): Consultation with...

Probing Selection Mechanism of the Most Favorable Conformation of a Dipeptide in Chaotropic and Kosmotropic Solution.

PubMed

Jas, Gouri S; Middaugh, C Russell; Kuczera, Krzysztof

2016-07-21

Chaotropes like urea and guanidinium chloride (GdmCl) tend to destabilize, and kosmotropes like proline tend to stabilize folded structures of peptides and proteins. Here, we combine fluorescence anisotropy decay measurements and molecular dynamics simulations to gain a microscopic understanding of the molecular mechanism for shifting conformational preferences in aqueous, GdmCl, urea, and proline solutions of a simple model dipeptide, N-acetyl-tryptophan-amide (NATA). Measured anisotropy decay of NATA as a function of temperature, pH, and cosolvent concentrations showed reorientations moderately slower in GdmCl and urea and substantially slower in proline compared to those of aqueous environment. A small change in pH significantly slows orientation time in water and GdmCl and less markedly in urea. Computationally, we use molecular dynamics with dihedral restraints to separately analyze the motions and interactions of the representative NATA conformers in the four different solvent environments. This novel analysis provides a dissection of the observed overall diffusion rates into contributions from individual dipeptide conformations. The variation of rotational diffusion rates with conformation are quite large. Population-weighted averaging or using properties of the major cluster reproduces the dynamical features of the full unrestrained dynamics. Additionally, we correlate the observable diffusion rates with microscopic features of conformer size, shape, and solvation. This analysis uncovered underlying differences in detailed atomistic behavior of the three cosolvents-urea, GdmCl, and proline. For both urea and the pure water system we find good agreement with hydrodynamic theory, with diffusion rates primarily correlated with conformer size and shape. In contrast, for GdmCl and proline solutions, the variation in conformer diffusion rates was mostly determined by specific interactions with the cosolvents. We also find preferences for different molecular shapes by the three cosolvents, with increased preferential solvation of smaller and more spherical conformers by urea and larger and more elongated conformers by GdmCl and proline. Additionally, our results provide a basis for a simple approximate model of the effects of pH lowering on dipeptide conformational equilibria. The translational diffusion rates of NATA are less sensitive to conformations, but variation with solvation strength is similar to rotational diffusion. Our results, combining experiment and simulation, show that we can identify the individual peptide conformers with definite microscopic properties of shape, size, and solvation, that are responsible for producing physical observables, such as translational and orientational diffusion in the complex solvent environments of denaturants and osmolytes.

Some Surprising Implications of NMR-directed Simulations of Substrate Recognition and Binding by Cytochrome P450cam (CYP101A1).

PubMed

Asciutto, Eliana K; Pochapsky, Thomas C

2018-04-27

Cytochrome P450 cam (CYP101A1) catalyzes the stereospecific 5-exo hydroxylation of d-camphor by molecular oxygen. Previously, residual dipolar couplings measured for backbone amide 1 H- 15 N correlations in both substrate-free and bound forms of CYP101A1 were used as restraints in soft annealing molecular dynamic simulations in order to identify average conformations of the enzyme with and without substrate bound. Multiple substrate-dependent conformational changes remote from the enzyme active site were identified, and site-directed mutagenesis and activity assays confirmed the importance of these changes in substrate recognition. The current work makes use of perturbation response scanning (PRS) and umbrella sampling molecular dynamic of the residual dipolar coupling-derived CYP101A1 structures to probe the roles of remote structural features in enforcing the regio- and stereospecific nature of the hydroxylation reaction catalyzed by CYP101A1. An improper dihedral angle Ψ was defined and used to maintain substrate orientation in the CYP101A1 active site, and it was observed that different values of Ψ result in different PRS response maps. Umbrella sampling methods show that the free energy of the system is sensitive to Ψ, and bound substrate forms an important mechanical link in the transmission of mechanical coupling through the enzyme structure. Finally, a qualitative approach to interpreting PRS maps in terms of the roles of secondary structural features is proposed. Copyright © 2018 Elsevier Ltd. All rights reserved.

Flexible bent rod model with a saturating induced dipole moment to study the electric linear dichroism of DNA fragments

NASA Astrophysics Data System (ADS)

Bertolotto, Jorge A.; Umazano, Juan P.

2016-06-01

In the present work we make a theoretical study of the steady state electric linear dichroism of DNA fragments in aqueous solution. The here developed theoretical approach considers a flexible bent rod model with a saturating induced dipole moment. The electric polarizability tensor of bent DNA fragments is calculated considering a phenomenological model which theoretical and experimental backgroung is presented here. The model has into account the electric polarizability longitudinal and transversal to the macroion. Molecular flexibility is described using an elastic potential. We consider DNA fragments originally bent with bending fluctuations around an average bending angle. The induced dipole moment is supposed constant once the electric field strength grows up at critical value. To calculate the reduced electric linear dichroism we determine the optical factor considering the basis of the bent DNA perpendicular to the molecular axis. The orientational distribution function has into account the anisotropic electric properties and the molecule flexibility. We applied the present theoretical background to fit electric dichroism experimental data of DNA fragments reported in the bibliography in a wide range of molecular weight and electric field. From these fits, values of DNA physical properties are estimated. We compare and discuss the results here obtained with the theoretical and experimental data presented by other authors. The original contributions of this work are: the inclusion of the transversal electric polarizability saturating with the electric field, the description of the electric properties with an electric polarizability tensor dependant on the bending angle and the use of an arc model originally bent.

3D variations in human crown dentin tubule orientation: a phase-contrast microtomography study.

PubMed

Zaslansky, Paul; Zabler, Simon; Fratzl, Peter

2010-01-01

Tubules dominate the microstructure of dentin, and in crowns of human teeth they are surrounded by thick mineralized peritubular cuffs of high stiffness. Here we examine the three-dimensional (3D) arrangement of tubules in relation to enamel on the buccal and lingual aspects of intact premolars and molars. Specifically we investigate the angular orientation of tubules relative to the plane of the junction of dentin with enamel (DEJ) by means of wet, non-destructive and high-resolution phase-contrast (coherent) tomography. Enamel capped dentin samples (n=16), cut from the buccal and lingual surfaces of upper and lower premolar and molar teeth, were imaged in water by high-resolution synchrotron-based phase-contrast X-ray radiography. Reconstructed 3D virtual images were co-aligned with respect to the DEJ plane. The average tubule orientation was determined at increasing distances from the DEJ, based on integrated projections onto orthogonal virtual planes. The angle and curl of the tubules were determined every 100 microm to a depth of 1.4mm beneath the DEJ. Most tubules do not extend at right angles from the DEJ. Even when they do, tubules always change their orientations substantially within the first half-millimeter zone beneath the DEJ, both on the buccal and lingual aspects of premolar and molar teeth. Tubules also tend to curl and twist within this zone. Student t-tests indicate that lower teeth seem to have greater tilts in the tubule orientations relative to the DEJ normal with an average angle of 42 degrees (+/-2.0 degrees), whereas upper teeth exhibit a smaller change of orientation, with an average of 32 degrees (+/-2.1 degrees). Tubules are a central characteristic of dentin, with important implications on how it is arranged and what the properties are. Knowing about the path that tubules follow is important for various reasons, ranging form improving control over restorative procedures to understanding or simulating the mechanical properties of teeth. At increasing depths of dentin beneath enamel, tubules are significantly tilted relative to the DEJ norm, which may be important to understand clinical challenges such as sensitivity, effectiveness of bonding techniques or prediction of possible paths for bacterial invasion. Our data show dissimilar average tubule angles of upper versus lower teeth with respect to the DEJ which presumably contributes to different shear responses of the tissue under function. The degree to which this may warrant improved restoratives or new adhesive techniques to enhance adhesive restorations merits further investigation.

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.

Test anxiety, perfectionism, goal orientation, and academic performance.

PubMed

Eum, KoUn; Rice, Kenneth G

2011-03-01

Dimensions of perfectionism and goal orientation have been reported to have differential relationships with test anxiety. However, the degree of inter-relationship between different dimensions of perfectionism, the 2 × 2 model of goal orientations proposed by Elliot and McGregor, cognitive test anxiety, and academic performance indicators is not known. Based on data from 134 university students, we conducted correlation and regression analyses to test associations between adaptive and maladaptive perfectionism, four types of goal orientations, cognitive test anxiety, and two indicators of academic performance: proximal cognitive performance on a word list recall test and distal academic performance in terms of grade point average. Cognitive test anxiety was inversely associated with both performance indicators, and positively associated with maladaptive perfectionism and avoidance goal orientations. Adaptive and maladaptive perfectionism accounted for significant variance in cognitive test anxiety after controlling for approach and avoidance goal orientations. Overall, nearly 50% of the variance in cognitive test anxiety could be attributed to gender, goal orientations, and perfectionism. Results suggested that students who are highly test anxious are likely to be women who endorse avoidance goal orientations and are maladaptively perfectionistic.

Dynamic differentiation of GABAA-sensitive influences on orientation selectivity of complex cells in the cat striate cortex.

PubMed

Pfleger, B; Bonds, A B

1995-01-01

The influence of GABAA receptors on orientation selectivity of cat complex cells was tested by iontophoresis of the GABAA receptor blockers bicuculline and N-methyl-bicuculline while stimulating with drifting sinusoidal gratings. Reduction of orientation tuning was markedly less than reported in previous studies that used drifting bars as visual stimuli. Only 3/31 cells lost orientation selectivity, with an average increase in bandwidth of 33%, as opposed to half the cells losing selectivity and a bandwidth increase for the remainder of 47% as reported previously. Infusion of GABAA blockers revealed a prominent stimulus onset transient response, lasting about 120 ms, that showed a broadening of orientation selectivity comparable to that found using drifting bars under similar circumstances. We believe that drifting gratings emphasize a steady-state response component that retains, in the presence of GABAA blockers, significant orientation selectivity. Because the onset transient is initially unselective for orientation, we suggest that the steady-state, orientation-selective response component develops from an alternate inhibitory mechanism, possibly mediated by GABAB receptors.

Dielectric Properties of Piezoelectric Polyimides

NASA Technical Reports Server (NTRS)

Ounaies, Z.; Young, J. A.; Simpson, J. O.; Farmer, B. L.

1997-01-01

Molecular modeling and dielectric measurements are being used to identify mechanisms governing piezoelectric behavior in polyimides such as dipole orientation during poling, as well as degree of piezoelectricity achievable. Molecular modeling on polyimides containing pendant, polar nitrile (CN) groups has been completed to determine their remanent polarization. Experimental investigation of their dielectric properties evaluated as a function of temperature and frequency has substantiated numerical predictions. With this information in hand, we are then able to suggest changes in the molecular structures, which will then improve upon the piezoelectric response.

Chip-Scale Controlled Storage All-Optical Memory

DTIC Science & Technology

2007-02-01

half width at half maximum KHZ kilo Hertz KK Kramers-Kronig LH light hole MBE molecular beam epitaxy MHz mega Hertz MZI Mach-Zehnder...waveguide geometry. The sample used in experiments 1 and 2 consists of 15 GaAs (135Å)/Al0.3Ga0.7As(150 Å) QWs grown by molecular beam epitaxy (MBE...We developed the capability to grow GaAs QWs on (110)-oriented substrates using molecular beam epitaxy in a very short amount of time. The very

Impact of the Crystallite Orientation Distribution on Exciton Transport in Donor-Acceptor Conjugated Polymers.

PubMed

Ayzner, Alexander L; Mei, Jianguo; Appleton, Anthony; DeLongchamp, Dean; Nardes, Alexandre; Benight, Stephanie; Kopidakis, Nikos; Toney, Michael F; Bao, Zhenan

2015-12-30

Conjugated polymers are widely used materials in organic photovoltaic devices. Owing to their extended electronic wave functions, they often form semicrystalline thin films. In this work, we aim to understand whether distribution of crystallographic orientations affects exciton diffusion using a low-band-gap polymer backbone motif that is representative of the donor/acceptor copolymer class. Using the fact that the polymer side chain can tune the dominant crystallographic orientation in the thin film, we have measured the quenching of polymer photoluminescence, and thus the extent of exciton dissociation, as a function of crystal orientation with respect to a quenching substrate. We find that the crystallite orientation distribution has little effect on the average exciton diffusion length. We suggest several possibilities for the lack of correlation between crystallographic texture and exciton transport in semicrystalline conjugated polymer films.

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