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Sample records for molecules clusters surfaces

  1. Dynamics of molecules and clusters at surfaces

    CERN Document Server

    Goldby, I M

    1996-01-01

    and aggregate into round particles with a 'universal' diameter of approx 14 nm. This preferred diameter is attributed to the strain between the silver and graphite lattices. The deposition rate and the cluster impact angle are also shown to be important parameters, which strongly influence the morphology of the islands. Computer simulation results indicate that, to produce the observed island size distributions, the mobility of the particles must fall off rapidly as their size increases. In chapter five, I present results from angular resolved electron stimulated desorption studies of 0 sup - , 0 sub 2 sup - , and 0 sub 3 sup - , produced from ordered films of 0 sub 2 on HOPG. Resonances in the yields of all products as a function of electron impact energy are attributed to dissociative electron attachment, generating 0 sup - ions, which can react with neighbouring O sub 2 molecules in the film. Characteristic differences in the ion yield profiles from one product to another are explained in terms of a binary...

  2. Three-cluster nuclear molecules

    CERN Document Server

    Poenaru, D N; Greiner, W

    2000-01-01

    A three-center phenomenological model able to explain, at least from a qualitative point of view, the difference in the observed yield of a particle-accompanied fission and that of binary fission was developed. It is derived from the liquid drop model under the assumption that the aligned configuration, with the emitted particle between the light and heavy fragment is obtained by increasing continuously the separation distance, while the radii of the light fragment and of the light particle are kept constant. During the first stage of the deformation one has a two-center evolution until the neck radius becomes equal to the radius of the emitted particle. Then the three center starts developing by decreasing with the same amount the two tip distances. In such a way a second minimum, typical for a cluster molecule, appears in the deformation energy. Examples are presented for $^{240}$Pu parent nucleus emitting $\\alpha$-particles and $^{14}$C in a ternary process.

  3. Cluster ions and van der Waals molecules

    CERN Document Server

    Smirnov, Boris M

    1992-01-01

    This review discusses current ideas in the physics and chemistry of cluster ions and Van der Waals molecules as well as presenting numerical data on their parameters and the processes involving them. It is also a detailed reference on basic data relating to many species.

  4. Multiple Ionic-Covalent Couplings in Molecules and Clusters

    Institute of Scientific and Technical Information of China (English)

    GwangHi Jeung

    2009-01-01

    The electronic states of molecules made of electropositive and electronegative components result from the interfcrence between the covalent configurations and the ionic configurations.This work shows complex aspects of these ionic-covalent couplings in small molecules such as Li2H, Li2F, and Li4F. The extension of this type of analysis to the adsorption of the electrophilic molecules on the metal clusters or on the metal surfaces is supposed to lead to a radically new interpretation of the observed physical and chemical properties.

  5. Surface processing using water cluster ion beams

    Science.gov (United States)

    Takaoka, Gikan H.; Ryuto, Hiromichi; Takeuchi, Mitsuaki; Ichihashi, Gaku

    2013-07-01

    Vaporized water clusters were produced by an adiabatic expansion phenomenon, and various substrates such as Si(1 0 0), SiO2, polymethyl methacrylate (PMMA), polyethylene terephthalate (PET), and polycarbonate (PC) were irradiated by water cluster ion beams. The sputtered depth increased with increasing acceleration voltage, and the sputtering rate was much larger than that obtained using Ar monomer ion irradiation. The sputtering yield for PMMA was approximately 200 molecules per ion, at an acceleration voltage of 9 kV. X-ray photoelectron spectroscopy (XPS) measurements showed that high-rate sputtering for the PMMA surface can be ascribed to the surface erosion by the water cluster ion irradiation. Furthermore, the micropatterning was demonstrated on the PMMA substrate. Thus, the surface irradiation by water cluster ion beams exhibited a chemical reaction based on OH radicals, as well as excited hydrogen atoms, which resulted in a high sputtering rate and low irradiation damage of the substrate surfaces.

  6. Surface processing using water cluster ion beams

    Energy Technology Data Exchange (ETDEWEB)

    Takaoka, Gikan H., E-mail: gtakaoka@kuee.kyoto-u.ac.jp [Photonics and Electronics Science and Engineering Center, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510 (Japan); Ryuto, Hiromichi; Takeuchi, Mitsuaki; Ichihashi, Gaku [Photonics and Electronics Science and Engineering Center, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510 (Japan)

    2013-07-15

    Vaporized water clusters were produced by an adiabatic expansion phenomenon, and various substrates such as Si(1 0 0), SiO{sub 2}, polymethyl methacrylate (PMMA), polyethylene terephthalate (PET), and polycarbonate (PC) were irradiated by water cluster ion beams. The sputtered depth increased with increasing acceleration voltage, and the sputtering rate was much larger than that obtained using Ar monomer ion irradiation. The sputtering yield for PMMA was approximately 200 molecules per ion, at an acceleration voltage of 9 kV. X-ray photoelectron spectroscopy (XPS) measurements showed that high-rate sputtering for the PMMA surface can be ascribed to the surface erosion by the water cluster ion irradiation. Furthermore, the micropatterning was demonstrated on the PMMA substrate. Thus, the surface irradiation by water cluster ion beams exhibited a chemical reaction based on OH radicals, as well as excited hydrogen atoms, which resulted in a high sputtering rate and low irradiation damage of the substrate surfaces.

  7. Scanning the potential energy surface for synthesis of dendrimer-wrapped gold clusters: design rules for true single-molecule nanostructures.

    Science.gov (United States)

    Thompson, Damien; Hermes, Jens P; Quinn, Aidan J; Mayor, Marcel

    2012-04-24

    The formation of true single-molecule complexes between organic ligands and nanoparticles is challenging and requires careful design of molecules with size, shape, and chemical properties tailored for the specific nanoparticle. Here we use computer simulations to describe the atomic-scale structure, dynamics, and energetics of ligand-mediated synthesis and interlinking of 1 nm gold clusters. The models help explain recent experimental results and provide insight into how multidentate thioether dendrimers can be employed for synthesis of true single-ligand-nanoparticle complexes and also nanoparticle-molecule-nanoparticle "dumbbell" nanostructures. Electronic structure calculations reveal the individually weak thioether-gold bonds (325 ± 36 meV), which act collectively through the multivalent (multisite) anchoring to stabilize the ligand-nanoparticle complex (∼7 eV total binding energy) and offset the conformational and solvation penalties involved in this "wrapping" process. Molecular dynamics simulations show that the dendrimer is sufficiently flexible to tolerate the strained conformations and desolvation penalties involved in fully wrapping the particle, quantifying the subtle balance between covalent anchoring and noncovalent wrapping in the assembly of ligand-nanoparticle complexes. The computed preference for binding of a single dendrimer to the cluster reveals the prohibitively high dendrimer desolvation barrier (1.5 ± 0.5 eV) to form the alternative double-dendrimer structure. Finally, the models show formation of an additional electron transfer channel between nitrogen and gold for ligands with a central pyridine unit, which gives a stiff binding orientation and explains the recently measured larger interparticle distances for particles synthesized and interlinked using linear ligands with a central pyridine rather than a benzene moiety. The findings stress the importance of organic-inorganic interactions, the control of which is central to the

  8. Coupled Cluster Theory for Large Molecules

    DEFF Research Database (Denmark)

    Baudin, Pablo

    2017-01-01

    This thesis describes the development of local approximations to coupled cluster (CC) theory for large molecules. Two different methods are presented, the divide–expand–consolidate scheme (DEC), for the calculation of ground state energies, and a local framework denoted LoFEx, for the calculation...... of electronic excitation energies and oscillator strengths. After an introduction to the relevant notions of electronic-structure theory, the principal aspects of DEC and LoFEx are summarized. For comparison, a selected review of the state-of-the-art is presented for each domain. This thesis should serve...... as an introduction to the work developed and presented in the scientific articles collected as appendices. The DEC scheme has been applied successfully to the calculation of MP2, CCSD and CCSD(T) ground state energies. The intrinsic structure of DEC allows for a linear-scaling (with system size) and massively...

  9. Water molecules orientation in surface layer

    Science.gov (United States)

    Klingo, V. V.

    2000-08-01

    The water molecules orientation has been investigated theoretically in the water surface layer. The surface molecule orientation is determined by the direction of a molecule dipole moment in relation to outward normal to the water surface. Entropy expressions of the superficial molecules in statistical meaning and from thermodynamical approach to a liquid surface tension have been found. The molecules share directed opposite to the outward normal that is hydrogen protons inside is equal 51.6%. 48.4% water molecules are directed along to surface outward normal that is by oxygen inside. A potential jump at the water surface layer amounts about 0.2 volts.

  10. "Magic" surface clustering of borazines driven by repulsive intermolecular forces.

    Science.gov (United States)

    Kervyn, Simon; Kalashnyk, Nataliya; Riello, Massimo; Moreton, Ben; Tasseroul, Jonathan; Wouters, Johan; Jones, Tim S; De Vita, Alessandro; Costantini, Giovanni; Bonifazi, Davide

    2013-07-15

    It's a kind of magic: Hydroxy pentaaryl borazine molecules self-assemble into small clusters (see structure) on Cu(111) surfaces, whereas with symmetric hexaaryl borazine molecules large islands are obtained. Simulations indicate that the observed "magic" cluster sizes result from long-range repulsive Coulomb forces arising from the deprotonation of the B-OH groups of the hydroxy pentaaryl borazine.

  11. Organising Atoms, Clusters and Proteins on Surfaces

    Science.gov (United States)

    Palmer, Richard E.

    2008-10-01

    This talk will discuss new developments in the creation of nanoscale surface features and their applications in biomedicine. Electron-surface interactions and plasma methods play a crucial role in both the production and analysis of these ``atomic architectures.'' At the extreme limit, electron injection from the tip of a scanning tunnelling microscope (STM) enables bond-selective manipulation of individual polyatomic molecules [1]. On a more practical level, the controlled deposition of size-selected clusters [2], generated by magnetron sputtering and gas condensation followed by mass selection, represents a surprisingly efficient route to the fabrication of surface features of size 1-10 nm, the size scale of biological molecules such as proteins. STM and AFM measurements show the clusters can act as binding sites for individual protein molecules. For example, the pinning of size-selected AuN clusters (N = 1--2000) to the (hydrophobic) graphite surface presents bindings site for sulphur atoms and thus for the cysteine residues in protein molecules. Systematic studies of different proteins [3] provide ``ground rules'' for residue-specific protein immobilisation by clusters and have led to the development of a novel biochip for protein screening by a spin-off company. The 3D atomic structure of the clusters is highly relevant to such applications. We show that measurement of the scattered electron beam intensity - specifically, the high angle annular dark field (HAADF) signal - in the scanning transmission electron microscope (STEM) allows us (a) to count the number of atoms in a cluster on the surface and (b) to determine a 3D atom-density map of the cluster when an aberration-corrected STEM is used [4]. 1. P.A. Sloan and R.E. Palmer, Nature 434 367 (2005). 2. S. Pratontep, P. Preece, C. Xirouchaki, R.E. Palmer, C.F. Sanz-Navarro, S.D. Kenny and R. Smith, Phys. Rev. Lett. 90 055503 (2003). 3. R.E. Palmer, S. Pratontep and H.-G. Boyen, Nature Materials 2 443 (2003

  12. Quantum simulations of the hydrogen molecule on ammonia clusters

    Science.gov (United States)

    Mella, Massimo; Curotto, E.

    2013-09-01

    Mixed ammonia-hydrogen molecule clusters [H2-(NH3)n] have been studied with the aim of exploring the quantitative importance of the H2 quantum motion in defining their structure and energetics. Minimum energy structures have been obtained employing genetic algorithm-based optimization methods in conjunction with accurate pair potentials for NH3-NH3 and H2-NH3. These include both a full 5D potential and a spherically averaged reduced surface mimicking the presence of a para-H2. All the putative global minima for n ⩾ 7 are characterized by H2 being adsorbed onto a rhomboidal ammonia tetramer motif formed by two double donor and two double acceptor ammonia molecules. In a few cases, the choice of specific rhombus seems to be directed by the vicinity of an ammonia ad-molecule. Diffusion Monte Carlo simulations on a subset of the species obtained highlighted important quantum effects in defining the H2 surface distribution, often resulting in populating rhomboidal sites different from the global minimum one, and showing a compelling correlation between local geometrical features and the relative stability of surface H2. Clathrate-like species have also been studied and suggested to be metastable over a broad range of conditions if formed.

  13. Quantum simulations of the hydrogen molecule on ammonia clusters.

    Science.gov (United States)

    Mella, Massimo; Curotto, E

    2013-09-28

    Mixed ammonia-hydrogen molecule clusters [H2-(NH3)n] have been studied with the aim of exploring the quantitative importance of the H2 quantum motion in defining their structure and energetics. Minimum energy structures have been obtained employing genetic algorithm-based optimization methods in conjunction with accurate pair potentials for NH3-NH3 and H2-NH3. These include both a full 5D potential and a spherically averaged reduced surface mimicking the presence of a para-H2. All the putative global minima for n ≥ 7 are characterized by H2 being adsorbed onto a rhomboidal ammonia tetramer motif formed by two double donor and two double acceptor ammonia molecules. In a few cases, the choice of specific rhombus seems to be directed by the vicinity of an ammonia ad-molecule. Diffusion Monte Carlo simulations on a subset of the species obtained highlighted important quantum effects in defining the H2 surface distribution, often resulting in populating rhomboidal sites different from the global minimum one, and showing a compelling correlation between local geometrical features and the relative stability of surface H2. Clathrate-like species have also been studied and suggested to be metastable over a broad range of conditions if formed.

  14. Far-Infrared Spectroscopy of Weakly Bound Hydrated Cluster Molecules

    DEFF Research Database (Denmark)

    Andersen, Jonas

    -sized molecular clusters with water by means of far-infrared and terahertz neon matrix isolation spectroscopy. The embedding of non-covalent cluster molecules in solid cryogenic neon matrices at 2.8 K ensures a high sensitivity for direct spectroscopic observations of the large-amplitude intermolecular...... vibrational bands of the cluster molecules in the challenging far-infrared and terahertz spectral regions.A key parameter in the validation of the performance of theoretical predictions for weak non-covalent intermolecular interactions is the dissociation energy D0 that depends heavily on the class of large...

  15. Infrared Spectroscopy of New Molecules and Clusters

    Science.gov (United States)

    Zhou, Mingfei

    2017-06-01

    Gas phase infrared photodissociation spectroscopy and matrix isolation infrared absorption spectroscopy have proven to be effective spectroscopic methods to investigate novel molecular and cluster species. Vibrational spectroscopy combined with state-of-the-art quantum chemical calculations provides detailed information on geometric and electronic structures as well as chemical bonding of the observed species. In this presentation, I will highlight our recent studies on the formation and infrared spectroscopic characterization of a number of neutral and charged metal-containing compounds including high oxidation state transition metal and lanthanide oxide species and metal carbonyl clusters featuring unprecedented metal-metal multiple bonds. These findings help to expand chemical understanding of the behavior of elements and their compounds.

  16. Dynamics of clusters and molecules in contact with an environment

    CERN Document Server

    Dinh, P M; Suraud, E

    2009-01-01

    We present recent theoretical investigations on the dynamics of metal clusters in contact with an environment, deposited of embedded. This concerns soft deposition as well as irradiation of the deposited/embedded clusters by intense laser pulses. We discuss examples of applications for two typical test cases, Na clusters deposited on MgO(001) surface and Na clusters in/on Ar substrate. Both environments are insulators with sizeable polarizability. They differ in their geometrical and mechanical properties.

  17. Surface decorated platinum carbonyl clusters

    Science.gov (United States)

    Ciabatti, Iacopo; Femoni, Cristina; Iapalucci, Maria Carmela; Longoni, Giuliano; Zacchini, Stefano; Zarra, Salvatore

    2012-06-01

    Four molecular Pt-carbonyl clusters decorated by Cd-Br fragments, i.e., [Pt13(CO)12{Cd5(μ-Br)5Br2(dmf)3}2]2- (1), [Pt19(CO)17{Cd5(μ-Br)5Br3(Me2CO)2}{Cd5(μ-Br)5Br(Me2CO)4}]2- (2), [H2Pt26(CO)20(CdBr)12]8- (3) and [H4Pt26(CO)20(CdBr)12(PtBr)x]6- (4) (x = 0-2), have been obtained from the reactions between [Pt3n(CO)6n]2- (n = 2-6) and CdBr2.H2O in dmf at 120 °C. The structures of these molecular clusters with diameters of 1.5-2 nm have been determined by X-ray crystallography. Both 1 and 2 are composed of icosahedral or bis-icosahedral Pt-CO cores decorated on the surface by Cd-Br motifs, whereas 3 and 4 display a cubic close packed Pt26Cd12 metal frame decorated by CO and Br ligands. An oversimplified and unifying approach to interpret the electron count of these surface decorated platinum carbonyl clusters is suggested, and extended to other low-valent organometallic clusters and Au-thiolate nanoclusters.Four molecular Pt-carbonyl clusters decorated by Cd-Br fragments, i.e., [Pt13(CO)12{Cd5(μ-Br)5Br2(dmf)3}2]2- (1), [Pt19(CO)17{Cd5(μ-Br)5Br3(Me2CO)2}{Cd5(μ-Br)5Br(Me2CO)4}]2- (2), [H2Pt26(CO)20(CdBr)12]8- (3) and [H4Pt26(CO)20(CdBr)12(PtBr)x]6- (4) (x = 0-2), have been obtained from the reactions between [Pt3n(CO)6n]2- (n = 2-6) and CdBr2.H2O in dmf at 120 °C. The structures of these molecular clusters with diameters of 1.5-2 nm have been determined by X-ray crystallography. Both 1 and 2 are composed of icosahedral or bis-icosahedral Pt-CO cores decorated on the surface by Cd-Br motifs, whereas 3 and 4 display a cubic close packed Pt26Cd12 metal frame decorated by CO and Br ligands. An oversimplified and unifying approach to interpret the electron count of these surface decorated platinum carbonyl clusters is suggested, and extended to other low-valent organometallic clusters and Au-thiolate nanoclusters. CCDC 867747 and 867748. For crystallographic data in CIF or other electronic format see DOI: 10.1039/c2nr30400g

  18. Clusters of atoms and molecules theory, experiment, and clusters of atoms

    CERN Document Server

    1994-01-01

    Clusters of Atoms and Molecules is devoted to theoretical concepts and experimental techniques important in the rapidly expanding field of cluster science. Cluster properties are dicussed for clusteres composed of alkali metals, semiconductors, transition metals, carbon, oxides and halides of alkali metals, rare gases, and neutral molecules. The book is composed of several well-integrated treatments all prepared by experts. Each contribution starts out as simple as possible and ends with the latest results so that the book can serve as a text for a course, an introduction into the field, or as a reference book for the expert.

  19. Spectral simulations of polar diatomic molecules immersed in He clusters: application to the ICl (X) molecule

    Energy Technology Data Exchange (ETDEWEB)

    Villarreal, P [Instituto de Matematicas y Fasica Fundamental (CSIC), Serrano 123, E-28006-Madrid (Spain); Lara-Castells, M P de [Instituto de Matematicas y Fasica Fundamental (CSIC), Serrano 123, E-28006-Madrid (Spain); Prosmiti, R [Instituto de Matematicas y Fasica Fundamental (CSIC), Serrano 123, E-28006-Madrid (Spain); Delgado-Barrio, G [Instituto de Matematicas y Fasica Fundamental (CSIC), Serrano 123, E-28006-Madrid (Spain); Lopez-Duran, D [Instituto de Matematicas y Fasica Fundamental (CSIC), Serrano 123, E-28006-Madrid (Spain); Gianturco, F A [Department of Chemistry and INFM, The University of Rome, Citta Universitaria, 00185, Rome (Italy); Jellinek, J [Chemistry Division, Argonne National Laboratory, Argonne, IL 60439 (United States)

    2007-09-15

    A recently developed quantum-chemistry-like methodology to study molecules solvated in atomic clusters is applied to the ICl (iodine chloride) polar diatomic molecule immersed in clusters of He atoms. The atoms of the solvent clusters are treated as the 'electrons' and the solvated molecule as a structured 'nucleus' of the combined solvent-solute system. The helium-helium and helium-dopant interactions are represented by parametrized two-body and ab initio three-body potentials, respectively. The ground-state wavefunctions are used to compute the infrared (IR) spectra of the solvated molecule. In agreement with the experimental observations, the computed spectra exhibit considerable differences depending on whether the solvent cluster is comprised of bosonic ({sup 4}He) or fermionic ({sup 3}He) atoms. The source of these differences is attributed to the different spin-statistics of the solvent clusters. The bosonic versus fermionic nature of the solvent is reflected in the IR absorption selection rules. Only P and R branches with single state transitions appear in the spectrum when the molecule is solvated in a bosonic cluster. On the other hand, when the solvent represents a fermionic environment, quasi-degenerate multiplets of spin states contribute to each branch and, in addition, the Q-branch becomes also allowed. Combined, these two factors explain the more congested nature of the spectrum in the fermionic case.

  20. Interaction of aromatic molecules with small gold clusters

    Science.gov (United States)

    Molina, Luis M.; López, María. J.; Alonso, Julio A.

    2017-09-01

    Ab initio density functional simulations have been performed to study the adsorption of aromatic molecules (benzene and toluene) on small Aun clusters. The calculations reveal a strong interaction between gold and π electrons of benzene, accompanied by a small electronic charge transfer from benzene to gold. We report a variety of binding conformations, with varying degrees of contact between the carbon atoms in benzene and the cluster. Therefore, the interaction between the aromatic part of molecules involved in the synthesis of fine chemicals catalyzed by gold must not be neglected, and could play an important role during some reaction stages.

  1. Simulation of water cluster assembly on a graphite surface.

    Science.gov (United States)

    Lin, C S; Zhang, R Q; Lee, S T; Elstner, M; Frauenheim, Th; Wan, L J

    2005-07-28

    The assembly of small water clusters (H2O)n, n = 1-6, on a graphite surface is studied using a density functional tight-binding method complemented with an empirical van der Waals force correction, with confirmation using second-order Møller-Plesset perturbation theory. It is shown that the optimized geometry of the water hexamer may change its original structure to an isoenergy one when interacting with a graphite surface in some specific orientation, while the smaller water cluster will maintain its cyclic or linear configurations (for the water dimer). The binding energy of water clusters interacting with graphite is dependent on the number of water molecules that form hydrogen bonds, but is independent of the water cluster size. These physically adsorbed water clusters show little change in their IR peak position and leave an almost perfect graphite surface.

  2. Thermal behavior of a 13-molecule hydrogen cluster under pressure.

    Science.gov (United States)

    Santamaria, Rubén; Soullard, Jacques; Jellinek, Julius

    2010-03-28

    The thermal behavior of a 13-molecule hydrogen cluster is studied as a function of pressure and temperature using a combination of trajectory and density functional theory simulations. The analysis is performed in terms of characteristic descriptors such as caloric curve, root-mean-square bond length fluctuation, pair correlation function, velocity autocorrelation function, volume thermal expansion, and diffusion coefficients. The discussion addresses on the peculiarities of the transition from the ordered-to-disordered state as exhibited by the cluster under different pressures and temperatures.

  3. Knockout driven reactions in complex molecules and their clusters

    Science.gov (United States)

    Gatchell, Michael; Zettergren, Henning

    2016-08-01

    Energetic ions lose some of their kinetic energy when interacting with electrons or nuclei in matter. Here, we discuss combined experimental and theoretical studies on such impulse driven reactions in polycyclic aromatic hydrocarbons (PAHs), fullerenes, and pure or mixed clusters of these molecules. These studies show that the nature of excitation is important for how complex molecular systems respond to ion/atom impact. Rutherford-like nuclear scattering processes may lead to prompt atom knockout and formation of highly reactive fragments, while heating of the molecular electron clouds in general lead to formation of more stable and less reactive fragments. In this topical review, we focus on recent studies of knockout driven reactions, and present new calculations of the angular dependent threshold (displacement) energies for such processes in PAHs. The so-formed fragments may efficiently form covalent bonds with neighboring molecules in clusters. These unique molecular growth processes may be important in astrophysical environments such as low velocity shock waves.

  4. MEASUREMENT OF NANOMETER SCALE CADMIUM SELENIDE NANOCRYSTALS AND CLUSTER MOLECULES

    Institute of Scientific and Technical Information of China (English)

    Jeffrey Yang

    2003-01-01

    High performance Dynamic Light Scattering (DLS) has been used to determine the hydrodynamic diameters of CdSe nanocrystals as well as CdSe cluster molecules in a size range of 1 to 10 nm (Eichh(o)fer et al., 2001).The method enables the determination of their particle size, including their ligand shells, in solution. The results are consistent with the blue shift of the absorption bands, as well as Transmission Electron Microscope (TEM) experiments.The sizes of the cluster molecules were estimated from space filling models constructed from the results of a single crystal X-ray structure determination. DLS gave comparable results for the size of both types of compound, indicating that it is potentially an important additional measurement technique to TEM, which uses harsh measurement conditions,and to powder X-ray diffraction, which is difficult to interpret below 5 nm.

  5. Low-energy ions interacting with anthracene molecules and clusters

    Energy Technology Data Exchange (ETDEWEB)

    Rousseau, P., E-mail: prousseau@ganil.fr [CEA, UMR 6252 CIMAP, Boulevard Henri Becquerel, BP 5133, F-14070 Caen cedex 5 (France); CNRS, UMR 6252 CIMAP, Boulevard Henri Becquerel, BP 5133, F-14070 Caen cedex 5 (France); ENSICAEN, UMR 6252 CIMAP, Boulevard Henri Becquerel, BP 5133, F-14070 Caen cedex 5 (France); Universite de Caen Basse-Normandie, UMR 6252 CIMAP, Boulevard Henri Becquerel, BP 5133, F-14070 Caen cedex 5 (France); Lawicki, A. [CEA, UMR 6252 CIMAP, Boulevard Henri Becquerel, BP 5133, F-14070 Caen cedex 5 (France); CNRS, UMR 6252 CIMAP, Boulevard Henri Becquerel, BP 5133, F-14070 Caen cedex 5 (France); ENSICAEN, UMR 6252 CIMAP, Boulevard Henri Becquerel, BP 5133, F-14070 Caen cedex 5 (France); Universite de Caen Basse-Normandie, UMR 6252 CIMAP, Boulevard Henri Becquerel, BP 5133, F-14070 Caen cedex 5 (France); Holm, A.I.S. [Department of Physics, Stockholm University, AlbaNova University Center, S-10691 Stockholm (Sweden); Capron, M.; Maisonny, R.; Maclot, S.; Lattouf, E. [CEA, UMR 6252 CIMAP, Boulevard Henri Becquerel, BP 5133, F-14070 Caen cedex 5 (France); CNRS, UMR 6252 CIMAP, Boulevard Henri Becquerel, BP 5133, F-14070 Caen cedex 5 (France); ENSICAEN, UMR 6252 CIMAP, Boulevard Henri Becquerel, BP 5133, F-14070 Caen cedex 5 (France); Universite de Caen Basse-Normandie, UMR 6252 CIMAP, Boulevard Henri Becquerel, BP 5133, F-14070 Caen cedex 5 (France); Johansson, H.A.B.; Seitz, F. [Department of Physics, Stockholm University, AlbaNova University Center, S-10691 Stockholm (Sweden); and others

    2012-05-15

    The interaction of slow ions (v{approx}0.4a.u.) with a small polycyclic aromatic hydrocarbon, namely anthracene (C{sub 14}H{sub 10}), is studied in the gas-phase either with the isolated molecule or with a pure cluster target. We discuss the ionization and fragmentation of the molecule with respect to the projectile charge state, i.e. for singly charged He{sup +} ions and for multiply charged Xe{sup 20+} ions. For the isolated C{sub 14}H{sub 10}, single or multiple ionization of the molecule occurs under ion impact. The (multi) cation relative yields are compared with those obtained by other ionization methods (electron and fs-laser). The molecular dissociation occurs by loss of hydrogen and small hydrocarbon molecules, leading to the formation of C{sub n}H{sub x} cations. The interaction of Xe{sup 20+} with C{sub 14}H{sub 10} clusters gives surprising results, i.e. the emission of hotter monomer compared to the interaction with He{sup +}.

  6. Molecule scattering from solid surfaces : Orientation and surface corrugation effects

    NARCIS (Netherlands)

    Vicanek, M; Schlatholter, T; Heiland, W

    1997-01-01

    Various effects connected with orientation and surface corrugation in molecule scattering from solid surfaces are investigated by means of classical trajectories simulations for H-2 impinging on Pd(110). Primary excitation of the projectiles is modeled according to the situation in molecular beam ex

  7. Tunneling magnetoresistance of C{sub 2}H{sub 2} molecules sandwiched between Co clusters

    Energy Technology Data Exchange (ETDEWEB)

    Zare-Kolsaraki, H. E-mail: kolsarak@ph2.uni-koeln.de; Micklitz, H

    2004-09-01

    The tunneling magnetoresistance (TMR) of samples containing well-defined Co clusters ({approx}4.5 nm mean diameter) embedded in C{sub 2}H{sub 2} matrices essentially is independent of Co-cluster volume fraction v{sub Co} and reveals a value of about 26% at T=2 K. This result is in contrast to that obtained for Co clusters embedded in C{sub 2}H{sub 4} matrices (Phys. Rev. B 67 (2003) 094433). In the latter system the TMR strongly decreased with increasing v{sub Co} indicating different possible orientation of the C{sub 2}H{sub 4} molecule sandwiched between the Co clusters. We, therefore, conclude that the C{sub 2}H{sub 2} molecules are sandwiched in a rather well-defined orientation between the Co clusters. They probably form double layers of C{sub 2}H{sub 2} molecules with the C-C bond axis parallel to the Co cluster surface.

  8. Scaling law of Wolff cluster surface energy

    Science.gov (United States)

    Hsiao, Pai-Yi; Monceau, Pascal

    2003-05-01

    We study the scaling properties of the clusters grown by the Wolff algorithm on seven different Sierpinski-type fractals of Hausdorff dimension 1Wolff cluster follows a power law with respect to the lattice size. Moreover, we investigate the probability density distribution of the surface energy of the Wolff cluster and are able to establish a different scaling relation. It enables us to introduce an exponent that is associated to the surface energy of the Wolff cluster. Finally, this exponent is linked to a dynamical exponent via an inequality.

  9. Mechanism of the Ammonia Molecules Protonation on the Naturally Oxidized Silicon Surface

    Directory of Open Access Journals (Sweden)

    F.A. Ptashchenko

    2015-10-01

    Full Text Available The protonation of a single ammonia molecule in the presence of several (1-5 water molecules on the surface of the hydroxylated β-cristobalite surface was studied by means of density functional method with the potential B3LYP using 6-311 ++ g (d, p basis set in the cluster approximation. The important role of surface OH-groups and H2O molecules in this process is shown. The energy required for the ammonia molecule protonation decreases with the number of adsorbed H2O molecules in the vicinity of this molecule, and the protonation becomes energetically favorable when the adsorbed water molecules form more than one layer. The phenomenon of Si natural surface charging in wet ammonia vapors can also be explained by protonation of NH3 molecules.

  10. Simulating the Formation of Carbon-rich Molecules on an idealised Graphitic Surface

    CERN Document Server

    Marshall, David W

    2015-01-01

    There is accumulating evidence for the presence of complex molecules, including carbon-bearing and organic molecules, in the interstellar medium. Much of this evidence comes to us from studies of chemical composition, photo- and mass-spectroscopy in cometary, meteoritic and asteroid samples, indicating a need to better understand the surface chemistry of astrophysical objects. There is also considerable interest in the origins of life-forming and life-sustaining molecules on Earth. Here, we perform reactive molecular dynamics simulations to probe the formation of carbon-rich molecules and clusters on carbonaceous surfaces resembling dust grains and meteoroids. Our results show that large chains form on graphitic surfaces at low temperatures (100K - 500K) and smaller fullerene-like molecules form at higher temperatures (2000K - 3000K). The formation is faster on the surface than in the gas at low temperatures but slower at high temperatures as surface interactions prevent small clusters from coagulation. We fi...

  11. Orientational dependence of electronic stopping of molecule and cluster ions

    Science.gov (United States)

    Jensen, J.; Mikkelsen, H. H.; Sigmund, P.

    1994-04-01

    The electronic energy deposited by a fast molecule or cluster penetrating through matter is estimated on the basis of a multipole expansion of the Coulomb interaction between the projectile and the target electrons. The treatment is directed at distant collisions, and the primary purpose has been to gain an impression of the dependence of the electronic energy loss on the orientation of the projectile relative to the beam direction. With this qualitative goal in mind, and considering that the total charge of a moving cluster can be quite high, we chose Bohr's classical-oscillator model of the target atom as the theoretical basis. The energy loss versus impact parameter consists of the familiar monopole term which applies to a point charge, plus a number of multipole terms, the leading one of which is found to be a monopole-quadrupole term. In the energy loss averaged over all orientations, that term vanishes, and the leading nonvanishing term then becomes the quadrupole-quadrupole term which reflects the properties of expressions in the literature based on Bethe theory. It is concluded that for anisotropic molecules, the directional dependence of electronic energy loss is more pronounced than what could be expected from published proximity factors. Explicit examples refer to a diatomic molecule.

  12. Bases for cluster algebras from surfaces

    CERN Document Server

    Musiker, Gregg; Williams, Lauren

    2011-01-01

    We construct two bases for each cluster algebra coming from a triangulated surface without punctures. We work in the context of a coefficient system coming from a full-rank exchange matrix, for example, principal coefficients.

  13. Electric dipole moments of nanosolvated acid molecules in water clusters

    CERN Document Server

    Guggemos, Nicholas; Kresin, Vitaly V

    2015-01-01

    The electric dipole moments of $(H_{2}O)_{n}DCl$ ($n=3-9$) clusters have been measured by the beam deflection method. Reflecting the (dynamical) charge distribution within the system, the dipole moment contributes information about the microscopic structure of nanoscale solvation. The addition of a DCl molecule to a water cluster results in a strongly enhanced susceptibility. There is evidence for a noticeable rise in the dipole moment occurring at $n\\approx5-6$. This size is consistent with predictions for the onset of ionic dissociation. Additionally, a molecular dynamics model suggests that even with a nominally bound impurity an enhanced dipole moment can arise due to the thermal and zero point motion of the proton and the water molecules. The experimental measurements and the calculations draw attention to the importance of fluctuations in defining the polarity of water-based nanoclusters, and generally to the essential role played by motional effects in determining the response of fluxional nanoscale sy...

  14. Scaling law of Wolff cluster surface energy

    OpenAIRE

    Hsiao, Pai-Yi; Monceau, Pascal

    2003-01-01

    We study the scaling properties of the clusters grown by the Wolff algorithm on seven different Sierpinski-type fractals of Hausdorff dimension $1 < d_f \\le 3$ in the framework of the Ising model. The mean absolute value of the surface energy of Wolff cluster follows a power law with respect to the lattice size. Moreover, we investigate the probability density distribution of the surface energy of Wolff cluster and are able to establish a new scaling relation. It enables us to introduce a new...

  15. DFT Investigations About Pyrazine Molecules on Si(100)-2×1 Surface

    Institute of Scientific and Technical Information of China (English)

    YU Ang-yang; QU Yong-quan; HAN Ke-li; HE Guo-zhong

    2007-01-01

    It is important to understand the interface of aromatic molecules on semiconductor surfaces because of the rich functionality of such molecules on semiconductor surfaces. The chemisorption of pyrazine molecules on the Si( 100)-2×1 surface has been investigated using the B3LYP density functional theory with Si9H12 one-dimer and Si15H16 twodimer cluster models. The calculated results predict that N-dative bonded-state, C2= C5 [ 4 + 2 ] and the tightbridge1, 2, 5,6 products may coexist on the Si(100)-2×1 surface.

  16. Modelling Catalyst Surfaces Using DFT Cluster Calculations

    Directory of Open Access Journals (Sweden)

    Oliver Kröcher

    2009-09-01

    Full Text Available We review our recent theoretical DFT cluster studies of a variety of industrially relevant catalysts such as TiO2, γ-Al2O3, V2O5-WO3-TiO2 and Ni/Al2O3. Aspects of the metal oxide surface structure and the stability and structure of metal clusters on the support are discussed as well as the reactivity of surfaces, including their behaviour upon poisoning. It is exemplarily demonstrated how such theoretical considerations can be combined with DRIFT and XPS results from experimental studies.

  17. Modelling catalyst surfaces using DFT cluster calculations.

    Science.gov (United States)

    Czekaj, Izabela; Wambach, Jörg; Kröcher, Oliver

    2009-11-20

    We review our recent theoretical DFT cluster studies of a variety of industrially relevant catalysts such as TiO(2), gamma-Al(2)O(3), V(2)O(5)-WO(3)-TiO(2) and Ni/Al(2)O(3). Aspects of the metal oxide surface structure and the stability and structure of metal clusters on the support are discussed as well as the reactivity of surfaces, including their behaviour upon poisoning. It is exemplarily demonstrated how such theoretical considerations can be combined with DRIFT and XPS results from experimental studies.

  18. Simulating the formation of carbon-rich molecules on an idealized graphitic surface

    Science.gov (United States)

    Marshall, David W.; Sadeghpour, H. R.

    2016-01-01

    There is accumulating evidence for the presence of complex molecules, including carbon-bearing and organic molecules, in the interstellar medium. Much of this evidence comes to us from studies of chemical composition, photo- and mass spectroscopy in cometary, meteoritic and asteroid samples, indicating a need to better understand the surface chemistry of astrophysical objects. There is also considerable interest in the origins of life-forming and life-sustaining molecules on the Earth. Here, we perform reactive molecular dynamics simulations to probe the formation of carbon-rich molecules and clusters on carbonaceous surfaces resembling dust grains and meteoroids. Our results show that large chains form on graphitic surfaces at low temperatures (100-500 K) and smaller fullerene-like molecules form at higher temperatures (2000-3000 K). The formation is faster on the surface than in the gas at low temperatures but slower at high temperatures as surface interactions prevent small clusters from coagulation. We find that for efficient formation of molecular complexity, mobility about the surface is important and helps to build larger carbon chains on the surface than in the gas phase at low temperatures. Finally, we show that the temperature of the surface strongly determines what kind of structures forms and that low turbulent environments are needed for efficient formation.

  19. Single-molecule atomic force microscopy reveals clustering of the yeast plasma-membrane sensor Wsc1.

    Science.gov (United States)

    Heinisch, Jürgen J; Dupres, Vincent; Wilk, Sabrina; Jendretzki, Arne; Dufrêne, Yves F

    2010-06-14

    Signalling is a key feature of living cells which frequently involves the local clustering of specific proteins in the plasma membrane. How such protein clustering is achieved within membrane microdomains ("rafts") is an important, yet largely unsolved problem in cell biology. The plasma membrane of yeast cells represents a good model to address this issue, since it features protein domains that are sufficiently large and stable to be observed by fluorescence microscopy. Here, we demonstrate the ability of single-molecule atomic force microscopy to resolve lateral clustering of the cell integrity sensor Wsc1 in living Saccharomyces cerevisiae cells. We first localize individual wild-type sensors on the cell surface, revealing that they form clusters of approximately 200 nm size. Analyses of three different mutants indicate that the cysteine-rich domain of Wsc1 has a crucial, not yet anticipated function in sensor clustering and signalling. Clustering of Wsc1 is strongly enhanced in deionized water or at elevated temperature, suggesting its relevance in proper stress response. Using in vivo GFP-localization, we also find that non-clustering mutant sensors accumulate in the vacuole, indicating that clustering may prevent endocytosis and sensor turnover. This study represents the first in vivo single-molecule demonstration for clustering of a transmembrane protein in S. cerevisiae. Our findings indicate that in yeast, like in higher eukaryotes, signalling is coupled to the localized enrichment of sensors and receptors within membrane patches.

  20. Single-molecule atomic force microscopy reveals clustering of the yeast plasma-membrane sensor Wsc1.

    Directory of Open Access Journals (Sweden)

    Jürgen J Heinisch

    Full Text Available Signalling is a key feature of living cells which frequently involves the local clustering of specific proteins in the plasma membrane. How such protein clustering is achieved within membrane microdomains ("rafts" is an important, yet largely unsolved problem in cell biology. The plasma membrane of yeast cells represents a good model to address this issue, since it features protein domains that are sufficiently large and stable to be observed by fluorescence microscopy. Here, we demonstrate the ability of single-molecule atomic force microscopy to resolve lateral clustering of the cell integrity sensor Wsc1 in living Saccharomyces cerevisiae cells. We first localize individual wild-type sensors on the cell surface, revealing that they form clusters of approximately 200 nm size. Analyses of three different mutants indicate that the cysteine-rich domain of Wsc1 has a crucial, not yet anticipated function in sensor clustering and signalling. Clustering of Wsc1 is strongly enhanced in deionized water or at elevated temperature, suggesting its relevance in proper stress response. Using in vivo GFP-localization, we also find that non-clustering mutant sensors accumulate in the vacuole, indicating that clustering may prevent endocytosis and sensor turnover. This study represents the first in vivo single-molecule demonstration for clustering of a transmembrane protein in S. cerevisiae. Our findings indicate that in yeast, like in higher eukaryotes, signalling is coupled to the localized enrichment of sensors and receptors within membrane patches.

  1. Experimental Study of Water Cluster Molecules with Relevance to Mesospheric Clouds

    Science.gov (United States)

    Robertson, Scott; Sternovsky, Zoltan; Horanyi, Mihaly

    2000-10-01

    We have begun an experimental investigation of the properties of the water cluster molecules responsible for clouds occurring in the polar mesopause. These clusters disturb the charge balance in the ionosphere by attaching electrons which then creates localized reductions in the electron density. A supersonic nozzle sprays a mixture of water vapor and argon into vacuum and the expansion leads to condensation of clusters with 4 to 11 water molecules. Initial measurements are of the collision cross section of these molecules with neutral gas. The cross sections have a minimum at six waters consistent with the tighter molecular arrangement predicted for this cluster number. Additional measurements are underway for charging processes.

  2. Advances in single-molecule magnet surface patterning through microcontact printing

    NARCIS (Netherlands)

    Mannini, Matteo; Bonacchi, D.; Bonacchi, Daniele; Zobbi, Laura; Piras, Federica M.; Speets, E.A.; Caneschi, Andrea; Cornia, Andrea; Magnani, Agnese; Ravoo, B.J.; Reinhoudt, David; Sessoli, Roberta; Gatteschi, Dante

    2005-01-01

    We present an implementation of strategies to deposit single-molecule magnets (SMMs) using microcontact printing (uCP). We describe different approaches of CP to print stripes of a sulfur-functionalized dodecamanganese(III,IV) cluster on gold surfaces. Comparison by atomic force microscopy profile

  3. A Density-Dependent Switch Drives Stochastic Clustering and Polarization of Signaling Molecules

    Science.gov (United States)

    Jilkine, Alexandra; Angenent, Sigurd B.; Wu, Lani F.; Altschuler, Steven J.

    2011-01-01

    Positive feedback plays a key role in the ability of signaling molecules to form highly localized clusters in the membrane or cytosol of cells. Such clustering can occur in the absence of localizing mechanisms such as pre-existing spatial cues, diffusional barriers, or molecular cross-linking. What prevents positive feedback from amplifying inevitable biological noise when an un-clustered “off” state is desired? And, what limits the spread of clusters when an “on” state is desired? Here, we show that a minimal positive feedback circuit provides the general principle for both suppressing and amplifying noise: below a critical density of signaling molecules, clustering switches off; above this threshold, highly localized clusters are recurrently generated. Clustering occurs only in the stochastic regime, suggesting that finite sizes of molecular populations cannot be ignored in signal transduction networks. The emergence of a dominant cluster for finite numbers of molecules is partly a phenomenon of random sampling, analogous to the fixation or loss of neutral mutations in finite populations. We refer to our model as the “neutral drift polarity model.” Regulating the density of signaling molecules provides a simple mechanism for a positive feedback circuit to robustly switch between clustered and un-clustered states. The intrinsic ability of positive feedback both to create and suppress clustering is a general mechanism that could operate within diverse biological networks to create dynamic spatial organization. PMID:22102805

  4. A density-dependent switch drives stochastic clustering and polarization of signaling molecules.

    Directory of Open Access Journals (Sweden)

    Alexandra Jilkine

    2011-11-01

    Full Text Available Positive feedback plays a key role in the ability of signaling molecules to form highly localized clusters in the membrane or cytosol of cells. Such clustering can occur in the absence of localizing mechanisms such as pre-existing spatial cues, diffusional barriers, or molecular cross-linking. What prevents positive feedback from amplifying inevitable biological noise when an un-clustered "off" state is desired? And, what limits the spread of clusters when an "on" state is desired? Here, we show that a minimal positive feedback circuit provides the general principle for both suppressing and amplifying noise: below a critical density of signaling molecules, clustering switches off; above this threshold, highly localized clusters are recurrently generated. Clustering occurs only in the stochastic regime, suggesting that finite sizes of molecular populations cannot be ignored in signal transduction networks. The emergence of a dominant cluster for finite numbers of molecules is partly a phenomenon of random sampling, analogous to the fixation or loss of neutral mutations in finite populations. We refer to our model as the "neutral drift polarity model." Regulating the density of signaling molecules provides a simple mechanism for a positive feedback circuit to robustly switch between clustered and un-clustered states. The intrinsic ability of positive feedback both to create and suppress clustering is a general mechanism that could operate within diverse biological networks to create dynamic spatial organization.

  5. Definition of supertypes for HLA molecules using clustering of specificity matrices

    DEFF Research Database (Denmark)

    Lund, Ole; Nielsen, Morten; Kesmir, Can;

    2004-01-01

    a novel method for clustering sequence motifs. We construct hidden Markov models for HLA class I molecules using a Gibbs sampling procedure and use the similarities among these to define clusters of specificities. These clusters are extensions of the previously suggested ones. We suggest splitting some...... report that the previously observed specificities of these class II molecules can be clustered into nine classes, which only partly correspond to the serological classification. We show that classification of HLA molecules may be done in a uniform and automated way. The definition of clusters allows......Major histocompatibility complex (MHC) proteins are encoded by extremely polymorphic genes and play a crucial role in immunity. However, not all genetically different MHC molecules are functionally different. Sette and Sidney (1999) have defined nine HLA class I supertypes and showed that with only...

  6. State selective dynamics of molecules, clusters, and nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Keto, John W. [Univ. of Texas, Austin, TX (United States)

    2005-06-01

    Early objectives of this grant were: (1) Measure two-photon excitation of even parity excitons in liquid an solid xenon, (2) Study state-to-state energy transver between two-photon laser excited states or rare-gas atoms to other rare has atoms, (3) study reactive half-collisions between xenon and chlorine leading to the XeCl* B state, (4) measure the spectra of ro-vibrational states of cluster ions and radicals formed in high-pressure discharges and to study their dynamics, (5) measure the surface and bulk electronic states of nanoparticles produced by a unique method of synthesis--laser ablation of microspheres (LAM). Using near-field and microluminescence techniques, we obtained spectra of single nanocrystals to compare with spectra obtained in a supersonic jet apparatus using resonance excitation followed by photoionization (REMPI) with time-of-flight mass analysis. These materials combine the functional advantages obtained from the size-tunable properties of nanocomposite materials with the fabrication and direct-write advantages of NPs manufactured by LAM. We demostrated that CdSe nanoparticles produced by LAM were efficiient fluorescers, even when deposited dry on sapphire substrates. Si nanoparticles were fluorescent when captured in ethylene glycol. We also obtiained efficient fluorescence from Er doped phosphate glass nanopartiicles which have application to gain wafeguides in integrated optics or to nanoslush lasers. We used a femptosecond laser to study the nonlinear spectra of NC composites. We are currently measuring fluorescence and second and third-order susceptibilities of composites of Ag, Si, and GaN nanoparticles encapsulated within thin films of sapphire or SiO 2.

  7. Fullerene Molecules and Other Clusters of III-V Compounds

    Science.gov (United States)

    Hira, Ajit; Auxier, John, II; Lucero, Melinda

    2010-03-01

    The goal of the our work is to derive geometries of fullerene-like cages and other clusters of atoms from groups III and V of the periodic table. Our previous research focused on Carbon Fullerenes and on GanAsn clusters (n = 1 thru 12). Our research group has made an original discovery about GanAsn clusters. In our work on nanotechnology to date, we used the hybrid ab initio methods of quantum chemistry to derive the different geometries for the clusters of interest. We also calculated binding energies, bond-lengths, ionization potentials, electron affinities and HOMO-LUMO gaps, and IR spectra for these geometries. Of particular significance was the magic number for GaAs cluster stability that we found at n = 8. This is important because materials containing controlled III-V nanostructures provide the capability of preparing new classes of materials with enhanced optical, magnetic, chemical sensor and photo-catalytic properties. The second phase of the investigation will examine the effects of confinement on the optical properties the clusters. It will be interesting to observe novel linear as well as nonlinear optical processes in them. The third phase of the investigation will focus on the improved design of solar cells based on the optical properties of the clusters.

  8. Ultrathin magnesia films as support for molecules and metal clusters: Tuning reactivity by thickness and composition

    Energy Technology Data Exchange (ETDEWEB)

    Vaida, Mihai E.; Bernhardt, Thorsten M. [Institute of Surface Chemistry and Catalysis, University of Ulm (Germany); Barth, Clemens [CINAM-CNRS, Marseille (France); Esch, Friedrich; Heiz, Ueli [Department of Chemistry, Technical University of Munich, Garching (Germany); Landman, Uzi [School of Physics, Georgia Institute of Technology, Atlanta, Georgia (United States)

    2010-05-15

    Ultrathin metal oxide films have attracted considerable interest in recent years as versatile substrate for the design of nanocatalytic model systems. In particular, it has been proposed theoretically and confirmed experimentally that the electronic structure of adsorbates can be influenced by the layer thickness and the stoichiometry, i.e., the type and number of defects, of the oxide film. This has important consequences on the chemical reactivity of the oxide surface itself and of oxide supported metal clusters. It also opens new possibilities to influence and to control chemical reactions occurring at the surface of these systems. The present feature focuses on very recent experiments that illustrate the effects of a proper adjustment of layer thickness and composition of ultrathin MgO(100) films on chemical transformations. On the magnesia surface itself, the photodissociation dynamics of methyl iodide molecules is investigated via femtosecond-laser pump-probe mass spectrometry. Furthermore, the catalytic oxidation of carbon monoxide at mass-selected Au{sub 20} clusters deposited on magnesia is explored through temperature programmed reaction measurements. In the latter case, detailed first principles calculations are able to correlate the experimentally observed reactivity with structural dimensionality changes that are induced by the changing thickness and composition of the magnesia support. (Abstract Copyright [2010], Wiley Periodicals, Inc.)

  9. Derivative fluorimetry analysis of new cluster structures formed by ethanol and Water molecules

    Institute of Scientific and Technical Information of China (English)

    Bin Wu; Ying Liu; Caiqin Han; Xiaosen Luo; Jian Lu; Xiaowu Ni

    2009-01-01

    The ultraviolet (UV) light excited fluorescence spectra of ethanol-water mixture with different concentra-tions are investigated by derivative fluorimetry. It is found that there are 8 types of luminescent cluster molecules, formed by ethanol and water molecules in different ways, existing in the solution. The peak wavelengths of all these clusters' fluorescence spectra are measured and their contents are obtained by measuring the peak values in the second derivative fluorescence spectra. The spectra corresponding to the 8 types of clusters are obtained by Gaussian decomposition. It is found that two kinds of cluster molecules whose peak wavelengths are 330 and 345 nm have an optimal excitation wavelength located at (236±3) nm. This research contributes to the study of ethanol-water cluster structures and their physical and chemical characteristics.

  10. Electrospray deposition of organic molecules on bulk insulator surfaces.

    Science.gov (United States)

    Hinaut, Antoine; Pawlak, Rémy; Meyer, Ernst; Glatzel, Thilo

    2015-01-01

    Large organic molecules are of important interest for organic-based devices such as hybrid photovoltaics or molecular electronics. Knowing their adsorption geometries and electronic structures allows to design and predict macroscopic device properties. Fundamental investigations in ultra-high vacuum (UHV) are thus mandatory to analyze and engineer processes in this prospects. With increasing size, complexity or chemical reactivity, depositing molecules by thermal evaporation becomes challenging. A recent way to deposit molecules in clean conditions is Electrospray Ionization (ESI). ESI keeps the possibility to work with large molecules, to introduce them in vacuum, and to deposit them on a large variety of surfaces. Here, ESI has been successfully applied to deposit triply fused porphyrin molecules on an insulating KBr(001) surface in UHV environment. Different deposition coverages have been obtained and characterization of the surface by in-situ atomic force microscopy working in the non-contact mode shows details of the molecular structures adsorbed on the surface. We show that UHV-ESI, can be performed on insulating surfaces in the sub-monolayer regime and to single molecules which opens the possibility to study a variety of complex molecules.

  11. Single-molecule imaging of protein adsorption mechanisms to surfaces.

    Science.gov (United States)

    Zareh, Shannon Kian; Wang, Yan Mei

    2011-07-01

    Protein-surface interactions cause the desirable effect of controlled protein adsorption onto biodevices as well as the undesirable effect of protein fouling. The key to controlling protein-surface adsorptions is to identify and quantify the main adsorption mechanisms: adsorptions that occur (1) while depositing a protein solution onto dry surfaces and (2) after the deposition onto wet surfaces. Bulk measurements cannot reveal the dynamic protein adsorption pathways and thus cannot differentiate between the two adsorption mechanisms. We imaged the interactions of single streptavidin molecules with hydrophobic fused-silica surfaces in real-time. We observed both adsorbed proteins on surfaces and diffusing proteins near surfaces and analyzed their adsorption kinetics. Our analysis shows that the protein solution deposition process is the primary mechanism of streptavidin adsorption onto surfaces at the subnanomolar to nanomolar protein concentrations. Furthermore, we found that hydrophilic fused-silica surfaces can prevent the adsorption of streptavidin molecules. Copyright © 2010 Wiley-Liss, Inc.

  12. Surface passivation for single-molecule protein studies.

    Science.gov (United States)

    Chandradoss, Stanley D; Haagsma, Anna C; Lee, Young Kwang; Hwang, Jae-Ho; Nam, Jwa-Min; Joo, Chirlmin

    2014-04-24

    Single-molecule fluorescence spectroscopy has proven to be instrumental in understanding a wide range of biological phenomena at the nanoscale. Important examples of what this technique can yield to biological sciences are the mechanistic insights on protein-protein and protein-nucleic acid interactions. When interactions of proteins are probed at the single-molecule level, the proteins or their substrates are often immobilized on a glass surface, which allows for a long-term observation. This immobilization scheme may introduce unwanted surface artifacts. Therefore, it is essential to passivate the glass surface to make it inert. Surface coating using polyethylene glycol (PEG) stands out for its high performance in preventing proteins from non-specifically interacting with a glass surface. However, the polymer coating procedure is difficult, due to the complication arising from a series of surface treatments and the stringent requirement that a surface needs to be free of any fluorescent molecules at the end of the procedure. Here, we provide a robust protocol with step-by-step instructions. It covers surface cleaning including piranha etching, surface functionalization with amine groups, and finally PEG coating. To obtain a high density of a PEG layer, we introduce a new strategy of treating the surface with PEG molecules over two rounds, which remarkably improves the quality of passivation. We provide representative results as well as practical advice for each critical step so that anyone can achieve the high quality surface passivation.

  13. Adherence of Model Molecules to Silica Surfaces: First Principle Calculations

    Science.gov (United States)

    Nuñez, Matías; Prado, Miguel Oscar

    The adherence of "model molecules" methylene blue and eosine Y ("positive" and "negatively" charged respectively) to crystal SiO2 surfaces is studied from first principle calculations at the DFT level. Adsorption energies are calculated which follow the experimental threads obtained elsewhere (Rivera et al., 2013). We study the quantum nature of the electronic charge transfer between the surface and the molecules, showing the localized and delocalized patterns associated to the repulsive and attractive case respectively.

  14. Molecules at Solid Surfaces: A Personal Reminiscence

    Science.gov (United States)

    Ertl, Gerhard

    2017-05-01

    I was fortunate to start my career in physical chemistry at a time when the development of the ultrahigh vacuum technique and of novel physical methods enabled the study of processes on well-defined surfaces at an atomic scale. These investigations included the mechanisms of heterogeneously catalyzed reactions, such as CO oxidation and ammonia synthesis, and phenomena of spatio-temporal self-organization, as described by the concepts of nonlinear dynamics.

  15. Cluster-in-molecule local correlation method for large systems

    Institute of Scientific and Technical Information of China (English)

    LI Wei; LI ShuHua

    2014-01-01

    A linear scaling local correlation method,cluster-in-molecule(CIM)method,was developed in the last decade for large systems.The basic idea of the CIM method is that the electron correlation energy of a large system,within the M ller-Plesset perturbation theory(MP)or coupled cluster(CC)theory,can be approximately obtained from solving the corresponding MP or CC equations of various clusters.Each of such clusters consists of a subset of localized molecular orbitals(LMOs)of the target system,and can be treated independently at various theory levels.In the present article,the main idea of the CIM method is reviewed,followed by brief descriptions of some recent developments,including its multilevel extension and different ways of constructing clusters.Then,some applications for large systems are illustrated.The CIM method is shown to be an efficient and reliable method for electron correlation calculations of large systems,including biomolecules and supramolecular complexes.

  16. Self-assembly patterning of organic molecules on a surface

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Minghu; Fuentes-Cabrera, Miguel; Maksymovych, Petro; Sumpter, Bobby G.; Li, Qing

    2017-04-04

    The embodiments disclosed herein include all-electron control over a chemical attachment and the subsequent self-assembly of an organic molecule into a well-ordered three-dimensional monolayer on a metal surface. The ordering or assembly of the organic molecule may be through electron excitation. Hot-electron and hot-hole excitation enables tethering of the organic molecule to a metal substrate, such as an alkyne group to a gold surface. All-electron reactions may allow a direct control over the size and shape of the self-assembly, defect structures and the reverse process of molecular disassembly from single molecular level to mesoscopic scale.

  17. Self-assembly patterning of organic molecules on a surface

    Science.gov (United States)

    Pan, Minghu; Fuentes-Cabrera, Miguel; Maksymovych, Petro; Sumpter, Bobby G.; Li, Qing

    2017-04-04

    The embodiments disclosed herein include all-electron control over a chemical attachment and the subsequent self-assembly of an organic molecule into a well-ordered three-dimensional monolayer on a metal surface. The ordering or assembly of the organic molecule may be through electron excitation. Hot-electron and hot-hole excitation enables tethering of the organic molecule to a metal substrate, such as an alkyne group to a gold surface. All-electron reactions may allow a direct control over the size and shape of the self-assembly, defect structures and the reverse process of molecular disassembly from single molecular level to mesoscopic scale.

  18. Surface reconstruction precursor to melting in Au309 clusters

    Directory of Open Access Journals (Sweden)

    Fuyi Chen

    2011-09-01

    Full Text Available The melting of gold cluster is one of essential properties of nanoparticles and revisited to clarify the role played by the surface facets in the melting transition by molecular dynamics simulations. The occurrence of elaborate surface reconstruction is observed using many-body Gupta potential as energetic model for 309-atom (2.6 nm decahedral, cuboctahedral and icosahedral gold clusters. Our results reveal for the first time a surface reconstruction as precursor to the melting transitions. The surface reconstruction lead to an enhanced melting temperature for (100 faceted decahedral and cuboctahedral cluster than (111 faceted icosahedral gold cluster, which form a liquid patch due to surface vacancy.

  19. Identification of complex molecules at surfaces

    Science.gov (United States)

    Green, F. M.; Dell, E. J.; Gilmore, I. S.; Seah, M. P.

    2008-04-01

    In this study, we develop a simple method using the SMILES molecular structure format to simulate fragmentation pathways in secondary ion mass spectrometry (SIMS). These pathways are found to have good agreement with fragmentation pathways identified using G-SIMS-FPM (Fragmentation Pathway Mapping) using the two examples of folic acid and Irganox 1010. G-SIMS is an easy-to-use method that considerably simplifies complex static SIMS spectra. G-SIMS-FPM allows the molecular structure to be re-assembled by following fragmentation pathways as the G-SIMS surface plasma temperature is varied. The simulated pathways help reduce the wide choice of possible structures faced by analysts as the molecular structure is reassembled, leading to more reliable molecular identification. A rapid method to establish a foundation database of simulated pathways using the community and a web-based system is proposed.

  20. Adsorption mechanism of water molecule on goethite (010) surface

    Science.gov (United States)

    Xiu, Fangyuan; Zhou, Long; Xia, Shuwei; Yu, Liangmin

    2016-12-01

    Goethite widely exists among ocean sediments; it plays an important role in fixing heavy metals and adsorbing organic contaminants. So the understanding of the adsorbing process of water molecule on its surface will be very helpful to further reveal such environmental friendly processes. The configuration, electronic properties and interaction energy of water molecules adsorbed on pnma goethite (010) surface were investigated in detail by using density functional theory on 6-31G (d,p) basis set and projector- augment wave (PAW) method. The mechanism of the interaction between goethite surface and H2O was proposed. Despite the differences in total energy, there are four possible types of water molecule adsorption configurations on goethite (010) surface (Aa, Ab, Ba, Bb), forming coordination bond with surface Fe atom. Results of theoretical modeling indicate that the dissociation process of adsorbed water is an endothermic reaction with high activation energy. The dissociation of adsorbed water molecule is a proton transportation process between water's O atoms and surface. PDOS results indicate that the bonding between H2O and (010) surface is due to the overlapping of water's 2p orbitals and Fe's 3d orbitals. These results clarify the mechanism on how adsorbed water is dissociated on the surface of goethite and potentially provide useful information of the surface chemistry of goethite.

  1. UV and VUV ionization of organic molecules, clusters and complexes

    CERN Document Server

    Marksteiner, M; Sclafani, M; Ulbricht, H; Arndt, M

    2014-01-01

    The generation of organic particle beams is studied in combination with photoionization using uv radiation at 266 nm and vuv light at 157 nm. Single-photon ionization with pulsed vuv light turns out to be sensitive enough to detect various large neutral biomolecular complexes ranging from metal-amino acid complexes to nucleotide clusters and aggregates of polypeptides. Different biomolecular clusters are shown to exhibit rather specific binding characteristics with regard to the various metals that are co-desorbed in the source. We also find that the ion signal of gramicidin can be increased by a factor of fifteen when the photon energy is increased from 4.66 eV to 7.9 eV.

  2. UV and VUV ionization of organic molecules, clusters, and complexes.

    Science.gov (United States)

    Marksteiner, Markus; Haslinger, Philipp; Sclafani, Michele; Ulbricht, Hendrik; Arndt, Markus

    2009-09-17

    The generation of organic particle beams is studied in combination with photoionization using UV radiation at 266 nm and vacuum ultraviolet (VUV) light at 157 nm. Single-photon ionization with pulsed VUV light turns out to be sensitive enough to detect various large neutral biomolecular complexes ranging from metal-amino acid complexes to nucleotide clusters and aggregates of polypeptides. Different biomolecular clusters are shown to exhibit rather specific binding characteristics with regard to the various metals that are codesorbed in the source. We also find that the ion signal of gramicidin can be increased by a factor of 15 when the photon energy is increased from 4.66 to 7.9 eV.

  3. Surface functionalization of aluminosilicate nanotubes with organic molecules

    Directory of Open Access Journals (Sweden)

    Wei Ma

    2012-02-01

    Full Text Available The surface functionalization of inorganic nanostructures is an effective approach for enriching the potential applications of existing nanomaterials. Inorganic nanotubes attract great research interest due to their one-dimensional structure and reactive surfaces. In this review paper, recent developments in surface functionalization of an aluminosilicate nanotube, “imogolite”, are introduced. The functionalization processes are based on the robust affinity between phosphate groups of organic molecules and the aluminol (AlOH surface of imogolite nanotubes. An aqueous modification process employing a water soluble ammonium salt of alkyl phosphate led to chemisorption of molecules on imogolite at the nanotube level. Polymer-chain-grafted imogolite nanotubes were prepared through surface-initiated polymerization. In addition, the assembly of conjugated molecules, 2-(5’’-hexyl-2,2’:5’,2’’-terthiophen-5-ylethylphosphonic acid (HT3P and 2-(5’’-hexyl-2,2’:5’,2’’-terthiophen-5-ylethylphosphonic acid 1,1-dioxide (HT3OP, on the imogolite nanotube surface was achieved by introducing a phosphonic acid group to the corresponding molecules. The optical and photophysical properties of these conjugated-molecule-decorated imogolite nanotubes were characterized. Moreover, poly(3-hexylthiophene (P3HT chains were further hybridized with HT3P modified imogolite to form a nanofiber hybrid.

  4. Synthesis, Structure and Reactivity of Molecules Attached to Electrode Surfaces.

    Science.gov (United States)

    2014-09-26

    Structure and Reactivity of Molecules Attached to Electrode Surfaces", AFOSR #81-0149 III. REPORTING PERIOD: April 15, 1981 through April 14, 1985 IV...Adsorption .... ............... 17 9. Effect of Surface Roughness on Adsorbate Orientation and Reactivity . 20 10. Ordered/ Disordered Packing in Chemisorbed... reactivity only when present in the edge-pendant orientation. Clearly, molecular orientation (i.e., mode of +. .4 o,, -12- attachment to the surface) is a

  5. Ionization and fragmentation of cold clusters of PAH molecules - collisions with keV ions

    Science.gov (United States)

    Holm, A. I. S.; Zettergren, H.; Gatchell, M.; Johansson, H. A. B.; Seitz, F.; Schmidt, H. T.; Rousseau, P.; Ławicki, A.; Capron, M.; Domaracka, A.; Lattouf, E.; Maclot, S.; Maisonny, R.; Chesnel, J.-Y.; Manil, B.; Adoui, L.; Huber, B. A.; Cederquist, H.

    2012-11-01

    We discuss the ionization and fragmentation of isolated monomers and cold clusters of polycyclic aromatic hydrocarbon (PAH) molecules in collisions with keV ions in low or high charge states. With low charge state projectile ions, PAH cluster or monomer targets are thermally excited through electronic stopping processes directly in close peripheral or penetrating collisions while only single or few electrons are removed. With high charge state projectiles, electrons are very effectively removed from both the cluster and the monomer target already at very large distances with very little direct target heating. Singly charged and internally very hot PAH monomers are dominant fragmentation products following collisions between Xe20+ ions and PAH clusters. We suggest that this due to an unusually strong dominance of multiple-ionization over single ionization for PAH clusters interacting with highly charged ions. Here, charge and excitation energy is very rapidly redistributed within the clusters before they Coulomb explode and we suggest that these Coulomb explosions induce strong internal heating in the individual PAH molecules. We thus conclude that PAH cluster fragmentation always dominates strongly for all ionization processes regardless if these are due to interactions with ions in high or low charge states. These findings are discussed in view of simple models for cluster evaporation or single and multiple ionizations of PAH clusters.

  6. Reactions of metal cluster anions with inorganic and organic molecules in the gas phase.

    Science.gov (United States)

    Zhao, Yan-Xia; Liu, Qing-Yu; Zhang, Mei-Qi; He, Sheng-Gui

    2016-07-28

    The study of gas phase ion-molecule reactions by state-of-the-art mass spectrometric experiments in conjunction with quantum chemistry calculations offers an opportunity to clarify the elementary steps and mechanistic details of bond activation and conversion processes. In the past few decades, a considerable number of publications have been devoted to the ion-molecule reactions of metal clusters, the experimentally and theoretically tractable models for the active phase of condensed phase systems. The focus of this perspective concerns progress on activation and transformation of important inorganic and organic molecules by negatively charged metal clusters. The metal cluster anions cover bare metal clusters as well as ligated systems with oxygen, carbon, and nitrogen, among others. The following important issues have been summarized and discussed: (i) dependence of chemical reactivity and selectivity on cluster structures and sizes, metals and metal oxidation states, odd-even electron numbers, etc. and (ii) effects of doping, ligation, and pre-adsorption on the reactivity of metal clusters toward rather inert molecules.

  7. Surface-enhanced resonance Raman scattering spectroscopy of single R6G molecules

    Institute of Scientific and Technical Information of China (English)

    Zhou Zeng-Hui; Liu Li; Wang Gui-Ying; Xu Zhi-Zhan

    2006-01-01

    Surface-enhanced resonance Raman scattering (SERRS) of Rhodamine 6G (R6G) adsorbed on colloidal silver clusters has been studied. Based on the great enhancement of the Raman signal and the quench of the fluorescence, the SERRS spectra of R6G were recorded for the samples of dye colloidal solution with different concentrations. Spectral inhomogeneity behaviours from single molecules in the dried sample films were observed with complementary evidences, such as spectral polarization, spectral diffusion, intensity fluctuation of vibrational lines and even "breathing" of the molecules. Sequential spectra observed from a liquid sample with an average of 0.3 dye molecules in the probed volume exhibited the expected Poisson distribution for actually measuring 0, 1 or 2 molecules. Difference between the SERRS spectra of R6G excited by linearly and circularly polarized light were experimentally measured.

  8. Global structure search for molecules on surfaces: Efficient sampling with curvilinear coordinates.

    Science.gov (United States)

    Krautgasser, Konstantin; Panosetti, Chiara; Palagin, Dennis; Reuter, Karsten; Maurer, Reinhard J

    2016-08-28

    Efficient structure search is a major challenge in computational materials science. We present a modification of the basin hopping global geometry optimization approach that uses a curvilinear coordinate system to describe global trial moves. This approach has recently been shown to be efficient in structure determination of clusters [C. Panosetti et al., Nano Lett. 15, 8044-8048 (2015)] and is here extended for its application to covalent, complex molecules and large adsorbates on surfaces. The employed automatically constructed delocalized internal coordinates are similar to molecular vibrations, which enhances the generation of chemically meaningful trial structures. By introducing flexible constraints and local translation and rotation of independent geometrical subunits, we enable the use of this method for molecules adsorbed on surfaces and interfaces. For two test systems, trans-β-ionylideneacetic acid adsorbed on a Au(111) surface and methane adsorbed on a Ag(111) surface, we obtain superior performance of the method compared to standard optimization moves based on Cartesian coordinates.

  9. Global structure search for molecules on surfaces: Efficient sampling with curvilinear coordinates

    Science.gov (United States)

    Krautgasser, Konstantin; Panosetti, Chiara; Palagin, Dennis; Reuter, Karsten; Maurer, Reinhard J.

    2016-08-01

    Efficient structure search is a major challenge in computational materials science. We present a modification of the basin hopping global geometry optimization approach that uses a curvilinear coordinate system to describe global trial moves. This approach has recently been shown to be efficient in structure determination of clusters [C. Panosetti et al., Nano Lett. 15, 8044-8048 (2015)] and is here extended for its application to covalent, complex molecules and large adsorbates on surfaces. The employed automatically constructed delocalized internal coordinates are similar to molecular vibrations, which enhances the generation of chemically meaningful trial structures. By introducing flexible constraints and local translation and rotation of independent geometrical subunits, we enable the use of this method for molecules adsorbed on surfaces and interfaces. For two test systems, trans-β-ionylideneacetic acid adsorbed on a Au(111) surface and methane adsorbed on a Ag(111) surface, we obtain superior performance of the method compared to standard optimization moves based on Cartesian coordinates.

  10. Cluster-surface interaction: from soft landing to implantation

    DEFF Research Database (Denmark)

    Popok, Vladimir; Barke, Ingo; Campbell, Eleanor E.B.

    2011-01-01

    The current paper presents a state-of-the-art review in the field of interaction of atomic and molecular clusters with solids. We do not attempt to overview the entire broad field but rather concentrate on impact phenomena: how the physics of the cluster-surface interaction depends on the kinetic...... energy and what effects are induced under different energetic regimes. The review starts with an introduction to the field and a short history of cluster beam development. Then fundamental physical aspects of cluster formation and the most common methods for the production of cluster beams are overviewed....... For cluster-surface interactions, one of the important scenarios is the low-energy regime where the kinetic energy per atom of the accelerated cluster stays well below the binding (cohesive) energy of the cluster constituents. This case is often called soft landing: the deposition typically does not induce...

  11. MS/MS networking guided analysis of molecule and gene cluster families.

    Science.gov (United States)

    Nguyen, Don Duy; Wu, Cheng-Hsuan; Moree, Wilna J; Lamsa, Anne; Medema, Marnix H; Zhao, Xiling; Gavilan, Ronnie G; Aparicio, Marystella; Atencio, Librada; Jackson, Chanaye; Ballesteros, Javier; Sanchez, Joel; Watrous, Jeramie D; Phelan, Vanessa V; van de Wiel, Corine; Kersten, Roland D; Mehnaz, Samina; De Mot, René; Shank, Elizabeth A; Charusanti, Pep; Nagarajan, Harish; Duggan, Brendan M; Moore, Bradley S; Bandeira, Nuno; Palsson, Bernhard Ø; Pogliano, Kit; Gutiérrez, Marcelino; Dorrestein, Pieter C

    2013-07-09

    The ability to correlate the production of specialized metabolites to the genetic capacity of the organism that produces such molecules has become an invaluable tool in aiding the discovery of biotechnologically applicable molecules. Here, we accomplish this task by matching molecular families with gene cluster families, making these correlations to 60 microbes at one time instead of connecting one molecule to one organism at a time, such as how it is traditionally done. We can correlate these families through the use of nanospray desorption electrospray ionization MS/MS, an ambient pressure MS technique, in conjunction with MS/MS networking and peptidogenomics. We matched the molecular families of peptide natural products produced by 42 bacilli and 18 pseudomonads through the generation of amino acid sequence tags from MS/MS data of specific clusters found in the MS/MS network. These sequence tags were then linked to biosynthetic gene clusters in publicly accessible genomes, providing us with the ability to link particular molecules with the genes that produced them. As an example of its use, this approach was applied to two unsequenced Pseudoalteromonas species, leading to the discovery of the gene cluster for a molecular family, the bromoalterochromides, in the previously sequenced strain P. piscicida JCM 20779(T). The approach itself is not limited to 60 related strains, because spectral networking can be readily adopted to look at molecular family-gene cluster families of hundreds or more diverse organisms in one single MS/MS network.

  12. MS/MS networking guided analysis of molecule and gene cluster families

    Science.gov (United States)

    Nguyen, Don Duy; Wu, Cheng-Hsuan; Moree, Wilna J.; Lamsa, Anne; Medema, Marnix H.; Zhao, Xiling; Gavilan, Ronnie G.; Aparicio, Marystella; Atencio, Librada; Jackson, Chanaye; Ballesteros, Javier; Sanchez, Joel; Watrous, Jeramie D.; Phelan, Vanessa V.; van de Wiel, Corine; Kersten, Roland D.; Mehnaz, Samina; De Mot, René; Shank, Elizabeth A.; Charusanti, Pep; Nagarajan, Harish; Duggan, Brendan M.; Moore, Bradley S.; Bandeira, Nuno; Palsson, Bernhard Ø.; Pogliano, Kit; Gutiérrez, Marcelino; Dorrestein, Pieter C.

    2013-01-01

    The ability to correlate the production of specialized metabolites to the genetic capacity of the organism that produces such molecules has become an invaluable tool in aiding the discovery of biotechnologically applicable molecules. Here, we accomplish this task by matching molecular families with gene cluster families, making these correlations to 60 microbes at one time instead of connecting one molecule to one organism at a time, such as how it is traditionally done. We can correlate these families through the use of nanospray desorption electrospray ionization MS/MS, an ambient pressure MS technique, in conjunction with MS/MS networking and peptidogenomics. We matched the molecular families of peptide natural products produced by 42 bacilli and 18 pseudomonads through the generation of amino acid sequence tags from MS/MS data of specific clusters found in the MS/MS network. These sequence tags were then linked to biosynthetic gene clusters in publicly accessible genomes, providing us with the ability to link particular molecules with the genes that produced them. As an example of its use, this approach was applied to two unsequenced Pseudoalteromonas species, leading to the discovery of the gene cluster for a molecular family, the bromoalterochromides, in the previously sequenced strain P. piscicida JCM 20779T. The approach itself is not limited to 60 related strains, because spectral networking can be readily adopted to look at molecular family–gene cluster families of hundreds or more diverse organisms in one single MS/MS network. PMID:23798442

  13. Eliminating interactions between non-neighboring qubits in the preparation of cluster states in quantum molecules

    CERN Document Server

    Guo, G P; Hao, X J; Tu, T; Zhu, Z C; Guo, Guang-Can; Guo, Guo-Ping; Hao, Xiao-Jie; Tu, Tao; Zhu, Zhi-Cheng

    2007-01-01

    We propose a scheme to eliminate the effect of non-nearest-neighbor qubits in preparing cluster state with double-dot molecules. As the interaction Hamiltonians between qubits are Ising-model and mutually commute, we can get positive and negative effective interactions between qubits to cancel the effect of non-nearest-neighbor qubits by properly changing the electron charge states of each quantum dot molecule. The total time for the present multi-step cluster state preparation scheme is only doubled for one-dimensional qubit chain and tripled for two-dimensional qubit array comparing with the time of previous protocol leaving out the non-nearest-neighbor interactions.

  14. A density functional study on the adsorption of hydrogen molecule onto small copper clusters

    Indian Academy of Sciences (India)

    Xiang-Jun Kuang; Xin-Qiang Wang; Gao-Bin Liu

    2011-09-01

    An all-electron scalar relativistic calculation on the adsorption of hydrogen molecule onto small copper clusters has been performed by using density functional theory with the generalized gradient approximation (GGA) at PW91 level. Our results reveal that after adsorption of H2 molecule, the Cu-Cu interaction is strengthened and the H-H interaction is weakened, the reactivity enhancement of H2 molecule is obvious. The VIPs, HLGs and VEAs of CuH2 clusters show an obvious odd-even oscillation. It is suggested that the H2 molecule is more favourable to be adsorbed by the even-numbered small copper clusters. Meanwhile, the odd-even alteration of magnetic moments is also observed and may be served as the material with tunable code capacity of `0’ and `1' by adsorbing hydrogen molecule onto odd or even-numbered small copper clusters. Some discrepancies of dissociative adsorption between our work and previous works are found and may be understood in terms of the electron pairing effect and the scalar relativistic effect.

  15. Optical properties of molecules chemisorbed on the Ni (111) surface

    Energy Technology Data Exchange (ETDEWEB)

    Robota, H. J. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States); Whitmore, P. M. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States); Harris, C. B. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)

    1982-02-15

    The adsorption of a variety of molecules on Ni(111) is studied by UV/visible spectroscopic ellipsometry. The spectra were analyzed within a simple dielectric model. The absorption spectra of annealed, thin, condensed layers of pyrazine, pyridine, and naphthalene on the Ni(111) surface resemble bulk crystal spectra, indicating minimal perturbations due to the metal substrate. Chemisorption of molecules on the Ni(111) surface produced enhanced absorption between 2800Å and 3100Å. The wide range of adsorbate properties and surface chemistry suggest a modification of the optical response of the metal upon chemisorption. Furthermore, this enhanced optical absorption is attributed to nonvertical interband transitions made possible by loss of translational invariance at the surface.

  16. Ion-molecule clustering in differential mobility spectrometry: lessons learned from tetraalkylammonium cations and their isomers.

    Science.gov (United States)

    Campbell, J Larry; Zhu, Mabel; Hopkins, W Scott

    2014-09-01

    Differential mobility spectrometry (DMS) can distinguish ions based upon the differences in their high- and low-field ion mobilities as they experience the asymmetric waveform applied to the DMS cell. These mobilities are known to be influenced by the ions' structure, m/z, and charge distribution (i.e., resonance structures) within the ions themselves, as well as by the gas-phase environment of the DMS cell. While these associations have been developed over time through empirical observations, the exact role of ion structures or their interactions with clustering molecules remains generally unknown. In this study, that relationship is explored by observing the DMS behaviors of a series of tetraalkylammonium ions as a function of their structures and the gas-phase environment of the DMS cell. To support the DMS experiments, the basin-hopping search strategy was employed to identify candidate cluster structures for density functional theory treatment. More than a million cluster structures distributed across 72 different ion-molecule cluster systems were sampled to determine global minimum structures and cluster binding energies. This joint computational and experimental approach suggests that cluster geometry, in particular ion-molecule intermolecular separation, plays a critical role in DMS.

  17. The Role of Molecule Clustering by Hydrogen Bond in Hydrous Ethanol on Laminar Burning Velocity

    Directory of Open Access Journals (Sweden)

    I Made Suarta

    2016-01-01

    Full Text Available The role of hydrogen bond molecule clustering in laminar burning velocities was observed. The water in hydrous ethanol can change the interaction between water-ethanol molecules. A certain amount of water can become oxygenated which increases the burning velocity. The hydrogen bond interaction pattern of ethanol and water molecules was modeled. Based on the molecular model, azeotropic behavior emerges from ethanol-water hydrogen bond, which is at a 95.1%v composition. The interaction with water molecule causes the ethanol molecule to be clustered with centered oxygenated compound. So, it supplies extra oxygen and provides intermolecular empty spaces that are easily infiltrated by the air. In the azeotropic composition, the molecular bond chain is the shortest, so hypothetically the burning velocity is anticipated to increase. The laminar burning velocity of ethanol fuel was tested in a cylindrical explosion bomb in lean, stoichiometric, and rich mixtures. The experimental result showed that the maximum burning velocity occurred at hydrous ethanol of 95.5%v composition. This discrepancy is the result of the addition of energy from 7.7% free ethanol molecules that are not clustered. At the rich mixture, the burning velocity of this composition is higher than that of anhydrous ethanol.

  18. Current status and future perspectives of electron interactions with molecules, clusters, surfaces, and interfaces [Workshop on Fundamental challenges in electron-driven chemistry; Workshop on Electron-driven processes: Scientific challenges and technological opportunities

    Energy Technology Data Exchange (ETDEWEB)

    Becker, Kurt H.; McCurdy, C. William; Orlando, Thomas M.; Rescigno, Thomas N.

    2000-09-01

    This report is based largely on presentations and discussions at two workshops and contributions from workshop participants. The workshop on Fundamental Challenges in Electron-Driven Chemistry was held in Berkeley, October 9-10, 1998, and addressed questions regarding theory, computation, and simulation. The workshop on Electron-Driven Processes: Scientific Challenges and Technological Opportunities was held at Stevens Institute of Technology, March 16-17, 2000, and focused largely on experiments. Electron-molecule and electron-atom collisions initiate and drive almost all the relevant chemical processes associated with radiation chemistry, environmental chemistry, stability of waste repositories, plasma-enhanced chemical vapor deposition, plasma processing of materials for microelectronic devices and other applications, and novel light sources for research purposes (e.g. excimer lamps in the extreme ultraviolet) and in everyday lighting applications. The life sciences are a rapidly advancing field where the important role of electron-driven processes is only now beginning to be recognized. Many of the applications of electron-initiated chemical processes require results in the near term. A large-scale, multidisciplinary and collaborative effort should be mounted to solve these problems in a timely way so that their solution will have the needed impact on the urgent questions of understanding the physico-chemical processes initiated and driven by electron interactions.

  19. Polishing superhard material surfaces with gas-cluster ion beams

    Science.gov (United States)

    Ieshkin, A. E.; Kushkina, K. D.; Kireev, D. S.; Ermakov, Yu. A.; Chernysh, V. S.

    2017-01-01

    We have studied the influence of bombardment with accelerated gas-cluster ions on the surface topography of silicon carbide and diamond. Atomic-force microscopy shows that exposure to 10-keV gas-cluster ions at a total dose above 1016 cm-2 leads to smoothing of the surface relief. The ion-etching rate and efficiency of the surface relief smoothing as dependent on the thickness of removed layer have been estimated. Raman-spectroscopy data show that surface irradiation with gas-cluster ions does not introduce defects into the crystalline structure of irradiated material.

  20. A Bayesian cluster analysis method for single-molecule localization microscopy data.

    Science.gov (United States)

    Griffié, Juliette; Shannon, Michael; Bromley, Claire L; Boelen, Lies; Burn, Garth L; Williamson, David J; Heard, Nicholas A; Cope, Andrew P; Owen, Dylan M; Rubin-Delanchy, Patrick

    2016-12-01

    Cell function is regulated by the spatiotemporal organization of the signaling machinery, and a key facet of this is molecular clustering. Here, we present a protocol for the analysis of clustering in data generated by 2D single-molecule localization microscopy (SMLM)-for example, photoactivated localization microscopy (PALM) or stochastic optical reconstruction microscopy (STORM). Three features of such data can cause standard cluster analysis approaches to be ineffective: (i) the data take the form of a list of points rather than a pixel array; (ii) there is a non-negligible unclustered background density of points that must be accounted for; and (iii) each localization has an associated uncertainty in regard to its position. These issues are overcome using a Bayesian, model-based approach. Many possible cluster configurations are proposed and scored against a generative model, which assumes Gaussian clusters overlaid on a completely spatially random (CSR) background, before every point is scrambled by its localization precision. We present the process of generating simulated and experimental data that are suitable to our algorithm, the analysis itself, and the extraction and interpretation of key cluster descriptors such as the number of clusters, cluster radii and the number of localizations per cluster. Variations in these descriptors can be interpreted as arising from changes in the organization of the cellular nanoarchitecture. The protocol requires no specific programming ability, and the processing time for one data set, typically containing 30 regions of interest, is ∼18 h; user input takes ∼1 h.

  1. Structured free-water clusters near lubricating surfaces are essential in water-based lubrication.

    Science.gov (United States)

    Hou, Jiapeng; Veeregowda, Deepak H; de Vries, Joop; Van der Mei, Henny C; Busscher, Henk J

    2016-10-01

    Water-based lubrication provides cheap and environmentally friendly lubrication and, although hydrophilic surfaces are preferred in water-based lubrication, often lubricating surfaces do not retain water molecules during shear. We show here that hydrophilic (42° water contact angle) quartz surfaces facilitate water-based lubrication to the same extent as more hydrophobic Si crystal surfaces (61°), while lubrication by hydrophilic Ge crystal surfaces (44°) is best. Thus surface hydrophilicity is not sufficient for water-based lubrication. Surface-thermodynamic analyses demonstrated that all surfaces, regardless of their water-based lubrication, were predominantly electron donating, implying water binding with their hydrogen groups. X-ray photoelectron spectroscopy showed that Ge crystal surfaces providing optimal lubrication consisted of a mixture of -O and =O functionalities, while Si crystal and quartz surfaces solely possessed -O functionalities. Comparison of infrared absorption bands of the crystals in water indicated fewer bound-water layers on hydrophilic Ge than on hydrophobic Si crystal surfaces, while absorption bands for free water on the Ge crystal surface indicated a much more pronounced presence of structured, free-water clusters near the Ge crystal than near Si crystal surfaces. Accordingly, we conclude that the presence of structured, free-water clusters is essential for water-based lubrication. The prevalence of structured water clusters can be regulated by adjusting the ratio between surface electron-donating and electron-accepting groups and between -O and =O functionalities.

  2. Surface reconstruction precursor to melting in Au309 clusters

    OpenAIRE

    Fuyi Chen; Li, Z. Y.; Roy L. Johnston

    2011-01-01

    The melting of gold cluster is one of essential properties of nanoparticles and revisited to clarify the role played by the surface facets in the melting transition by molecular dynamics simulations. The occurrence of elaborate surface reconstruction is observed using many-body Gupta potential as energetic model for 309-atom (2.6 nm) decahedral, cuboctahedral and icosahedral gold clusters. Our results reveal for the first time a surface reconstruction as precursor to the melting transitions. ...

  3. Low-energy electron scattering from molecules, biomolecules and surfaces

    CERN Document Server

    Carsky, Petr

    2011-01-01

    Since the turn of the 21st century, the field of electron molecule collisions has undergone a renaissance. The importance of such collisions in applications from radiation chemistry to astrochemistry has flowered, and their role in industrial processes such as plasma technology and lighting are vital to the advancement of next generation devices. Furthermore, the development of the scanning tunneling microscope highlights the role of such collisions in the condensed phase, in surface processing, and in the development of nanotechnology.Low-Energy Electron Scattering from Molecules, Biomolecule

  4. Self-assembly of molecule-like nanoparticle clusters directed by DNA nanocages.

    Science.gov (United States)

    Li, Yulin; Liu, Zhiyu; Yu, Guimei; Jiang, Wen; Mao, Chengde

    2015-04-01

    Analogous to the atom-molecule relationship, nanoparticle (NP) clusters (or NP-molecules) with defined compositions and directional bonds could potentially integrate the properties of the component individual NPs, leading to emergent properties. Despite extensive efforts in this direction, no general approach is available for assembly of such NP-molecules. Here we report a general method for building this type of structures by encapsulating NPs into self-assembled DNA polyhedral wireframe nanocages, which serve as guiding agents for further assembly. As a demonstration, a series of NP-molecules have been assembled and validated. Such NP-molecules will, we believe, pave a way to explore new nanomaterials with emergent functions/properties that are related to, but do not belong to the individual component nanoparticles.

  5. M3C: A Computational Approach To Describe Statistical Fragmentation of Excited Molecules and Clusters.

    Science.gov (United States)

    Aguirre, Néstor F; Díaz-Tendero, Sergio; Hervieux, Paul-Antoine; Alcamí, Manuel; Martín, Fernando

    2017-02-07

    The Microcanonical Metropolis Monte Carlo method, based on a random sampling of the density of states, is revisited for the study of molecular fragmentation in the gas phase (isolated molecules, atomic and molecular clusters, complex biomolecules, etc.). A random walk or uniform random sampling in the configurational space (atomic positions) and a uniform random sampling of the relative orientation, vibrational energy, and chemical composition of the fragments is used to estimate the density of states of the system, which is continuously updated as the random sampling populates individual states. The validity and usefulness of the method is demonstrated by applying it to evaluate the caloric curve of a weakly bound rare gas cluster (Ar13), to interpret the fragmentation of highly excited small neutral and singly positively charged carbon clusters (Cn, n = 5,7,9 and Cn(+), n = 4,5) and to simulate the mass spectrum of the acetylene molecule (C2H2).

  6. Modeling adsorption and reactions of organic molecules at metal surfaces.

    Science.gov (United States)

    Liu, Wei; Tkatchenko, Alexandre; Scheffler, Matthias

    2014-11-18

    CONSPECTUS: The understanding of adsorption and reactions of (large) organic molecules at metal surfaces plays an increasingly important role in modern surface science and technology. Such hybrid inorganic/organic systems (HIOS) are relevant for many applications in catalysis, light-emitting diodes, single-molecule junctions, molecular sensors and switches, and photovoltaics. Obviously, the predictive modeling and understanding of the structure and stability of such hybrid systems is an essential prerequisite for tuning their electronic properties and functions. At present, density-functional theory (DFT) is the most promising approach to study the structure, stability, and electronic properties of complex systems, because it can be applied to both molecules and solids comprising thousands of atoms. However, state-of-the-art approximations to DFT do not provide a consistent and reliable description for HIOS, which is largely due to two issues: (i) the self-interaction of the electrons with themselves arising from the Hartree term of the total energy that is not fully compensated in approximate exchange-correlation functionals, and (ii) the lack of long-range part of the ubiquitous van der Waals (vdW) interactions. The self-interaction errors sometimes lead to incorrect description of charge transfer and electronic level alignment in HIOS, although for molecules adsorbed on metals these effects will often cancel out in total energy differences. Regarding vdW interactions, several promising vdW-inclusive DFT-based methods have been recently demonstrated to yield remarkable accuracy for intermolecular interactions in the gas phase. However, the majority of these approaches neglect the nonlocal collective electron response in the vdW energy tail, an effect that is particularly strong in condensed phases and at interfaces between different materials. Here we show that the recently developed DFT+vdW(surf) method that accurately accounts for the collective electronic

  7. Challenges in imaging cell surface receptor clusters

    Science.gov (United States)

    Medda, Rebecca; Giske, Arnold; Cavalcanti-Adam, Elisabetta Ada

    2016-01-01

    Super-resolution microscopy offers unique tools for visualizing and resolving cellular structures at the molecular level. STED microscopy is a purely optical method where neither complex sample preparation nor mathematical post-processing is required. Here we present the use of STED microscopy for imaging receptor cluster composition. We use two-color STED to further determine the distribution of two different receptor subunits of the family of receptor serine/threonine kinases in the presence or absence of their ligands. The implications of receptor clustering on the downstream signaling are discussed, and future challenges are also presented.

  8. Surface Chemistry and Growth of Large Molecules in Protoplanetary Disks

    Science.gov (United States)

    Walsh, Catherine; Aikawa, Yuri; Herbst, Eric; Millar, Tom; Widicus Weaver, Susanna; Nomura, Hideko

    Protoplanetary disks are vital objects in star and planet formation, possessing all the material - dust, gas, and ice - which may form a planetary system orbiting the new star. To date, a handful of small and relatively simple molecules have been observed in nearby disks reflecting the limitations of existing telescopes. However, in the era of ALMA, the Atacama Large Millimeter/Submillimeter Array, we expect the molecular inventory of protoplanetary disks to significantly increase. Of particular interest are so-called complex organic molecules (COMs) which are thought to be necessary precursors to molecules important for prebiotic chemistry, such as, amino acids. The formation of COMs remains one of the puzzles of astrochemistry. Under the physical conditions in interstellar and circumstellar environments, COMs do not have efficient gas-phase routes to formation. Instead, they are postulated to form via association reactions on and within ice mantles on the the surfaces of dust grains and released to the gas phase via either thermal desorption (sublimation) or desorpton triggered by the absorption of UV radiation (photodesorption). In this presentation, I will discuss the synthesis of COMs in protoplanetary disks to investigate the potential origin of complex molecules in planetary systems. I will present results from exploratory models of a protoplanetary disk around a low-mass star including a large grain-surface chemical network to model the formation of large complex organic molecules. I will compare the resulting abundances of COMs in the gas phase and in the solid phase with existing observations towards nearby low-mass star-disk systems and comets, respectively. I will also discuss how the formation of COMs is influenced by the birth environment of the young stellar system.

  9. Towards attosecond measurement in molecules and at surfaces

    Science.gov (United States)

    Marangos, Jonathan

    2015-05-01

    1) We will present a number of experimental approaches that are being developed at Imperial College to make attosecond timescale measurements of electronic dynamics in suddenly photoionized molecules and at surfaces. A brief overview will be given of some of the unanswered questions in ultrafast electron and hole dynamics in molecules and solids. These questions include the existence of electronic charge migration in molecules and how this process might couple to nuclear motion even on the few femtosecond timescale. How the timescale of photoemission from a surface may differ from that of an isolated atom, e.g. due to electron transport phenomena associated with the distance from the surface of the emitting atom and the electron dispersion relation, is also an open question. 2) The measurement techniques we are currently developing to answer these questions are HHG spectroscopy, attosecond pump-probe photoelectron/photoion studies, and attosecond pump-probe transient absorption as well as attosecond streaking for measuring surface emission. We will present recent advances in generating two synchronized isolated attosecond pulses at different colours for pump-probe measurements (at 20 eV and 90 eV respectively). Results on generation of isolated attosecond pulses at 300 eV and higher photon energy using a few-cycle 1800 nm OPG source will be presented. The use of these resources for making pump-probe measurements will be discussed. Finally we will present the results of streaking measurement of photoemission wavepackets from two types of surface (WO3 and a evaporated Au film) that show a temporal broadening of ~ 100 as compared to atomic streaks that is consistent with the electron mean free path in these materials. Work supported by ERC and EPSRC.

  10. Dynamic Scaling of Ramified Clusters Formed on Liquid Surfaces

    Institute of Scientific and Technical Information of China (English)

    WU Feng-Min; XU You-Sheng; LI Qiao-Wen

    2006-01-01

    A comprehensive simulation model -deposition,diffusion, rotation, reaction and aggregation model is presented to simulate the formation processes of ramified clusters on liquid surfaces, where clusters can diffuse and rotate easily. The mobility (including diffusion and rotation) of clusters is related to its mass, which is given by Dm = Dos-γD and θm =′θos-γθ, respectively. The influence of the reaction probability on the kinetics and structure formation is included in the simulation model. We concentrate on revealing dynamic scaling during ramified cluster formation. For this purpose, the time evolution of the cluster density and the weight-average cluster size as well as the cluster-size distribution scaling function at different time are determined for various conditions. The dependence of the cluster density on the deposition flux and time-dependence of fractal dimension are also investigated. The obtained results are helpful in understanding the formation of clusters or thin film growth on liquid surfaces.

  11. The Application of High-Level Iterative Coupled-Cluster Methods to the Cytosine Molecule

    Energy Technology Data Exchange (ETDEWEB)

    Kowalski, Karol; Valiev, Marat

    2008-06-19

    The need for inclusion higher-order correlation effects for adequate description of the excitation energies of the DNA bases became clear in the last few years. In particular, we demonstrated that there is a sizable effect of triply excited configurations estimated in a non-iterative manner on the coupled-cluster excitation energies of the cytosine molecule in DNA environment. In this paper we discuss the accuracies of the non-iterative methods for biologically relevant systems in realistic environment in comparison with interative formulations that explicitly include the effect of triply excited clusters.

  12. Measurement of cluster-cluster interaction in liquids by deposition and AFM of silicon clusters onto HOPG surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Galinis, Gediminas; Torricelli, Gauthier; Akraiam, Atea; Haeften, Klaus von, E-mail: kvh6@le.ac.uk [University of Leicester, Department of Physics and Astronomy (United Kingdom)

    2012-08-15

    We have investigated the interaction and aggregation of novel fluorescent silicon nanoclusters in liquids by measuring the size distribution of dried clusters on graphite. The clusters were produced by gas aggregation and co-deposition with a beam of water vapour. Drops of the solutions were placed on freshly cleaved highly oriented pyrolitic graphite, subsequently vacuum dried and investigated by atomic force microscopy (AFM) in ultra high vacuum. The AFM images show single clusters and agglomerates. The height distributions are Gaussian-shaped with average heights of 1 nm and widths of 1 nm. The heights never exceed 3 nm. In some regions a second cluster layer is observed. In all samples the separation between first and second layers is larger than the separation between the first layer and the graphite substrate, which we attribute to a stronger interaction between clusters and surface than the cluster self-interaction. We conclude that the separation between first and second layer represents a much better fingerprint of the original size distribution of the clusters in solution than the height of the first layer. The observation of a second cluster layer is important for using silicon clusters as building blocks for cluster-assembled materials.

  13. Deposition of size-selected atomic clusters on surfaces

    CERN Document Server

    Carroll, S J

    1999-01-01

    implant into the surface. For Ag sub 2 sub 0 -Ag sub 2 sub 0 sub 0 clusters, the implantation depth is found to scale linearly with the impact energy and inversely with the cross-sectional area of the cluster, with an offset due to energy lost to the elastic compression of the surface (Paper VI). For smaller (Ag sub 3) clusters the orientation of the cluster with respect to the surface and the precise impact site play an important role; the impact energy has to be 'focused' in order for cluster implantation to occur (Paper VII). The application of deposited clusters for the creation of Si nanostructures by plasma etching is explored in Paper VIII. This dissertation presents technical developments and experimental and computational investigations concerned with the deposition of atomic clusters onto surfaces. It consists of a collection of papers, in which the main body of results are contained, and four chapters presenting a subject review, computational and experimental techniques and a summary of the result...

  14. Dissociative chemisorption dynamics of small molecules on metal surfaces

    Institute of Scientific and Technical Information of China (English)

    JIANG Bin; XIE DaiQian

    2014-01-01

    Much progress has been achieved for both experimental and theoretical studies on the dissociative chemisorption of molecules on surfaces.Quantum state-resolved experimental data has provided unprecedented details for these fundamental steps in heterogeneous catalysis,while the quantitative dynamics is still not fully understood in theory.An in-depth understanding of experimental observations relies on accurate dynamical calculations,in which the potential energy surface and adequate quantum mechanical implementation are desired.This article summarizes the current methodologies on the construction of potential energy surfaces and the quantum mechanical treatments,some of which are promising for future applications.The challenges in this field are also addressed.

  15. Non-lithographic SERS substrates: tailoring surface chemistry for Au nanoparticle cluster assembly.

    Science.gov (United States)

    Adams, Sarah M; Campione, Salvatore; Caldwell, Joshua D; Bezares, Francisco J; Culbertson, James C; Capolino, Filippo; Ragan, Regina

    2012-07-23

    Near-field plasmonic coupling and local field enhancement in metal nanoarchitectures, such as arrangements of nanoparticle clusters, have application in many technologies from medical diagnostics, solar cells, to sensors. Although nanoparticle-based cluster assemblies have exhibited signal enhancements in surface-enhanced Raman scattering (SERS) sensors, it is challenging to achieve high reproducibility in SERS response using low-cost fabrication methods. Here an innovative method is developed for fabricating self-organized clusters of metal nanoparticles on diblock copolymer thin films as SERS-active structures. Monodisperse, colloidal gold nanoparticles are attached via a crosslinking reaction on self-organized chemically functionalized poly(methyl methacrylate) domains on polystyrene-block-poly(methyl methacrylate) templates. Thereby nanoparticle clusters with sub-10-nanometer interparticle spacing are achieved. Varying the molar concentration of functional chemical groups and crosslinking agent during the assembly process is found to affect the agglomeration of Au nanoparticles into clusters. Samples with a high surface coverage of nanoparticle cluster assemblies yield relative enhancement factors on the order of 10⁹ while simultaneously producing uniform signal enhancements in point-to-point measurements across each sample. High enhancement factors are associated with the narrow gap between nanoparticles assembled in clusters in full-wave electromagnetic simulations. Reusability for small-molecule detection is also demonstrated. Thus it is shown that the combination of high signal enhancement and reproducibility is achievable using a completely non-lithographic fabrication process, thereby producing SERS substrates having high performance at low cost.

  16. Analysis of reaction rates of single molecules on metal surfaces

    Science.gov (United States)

    Ueba, H.

    2017-10-01

    The experimental results of the action spectra i.e., reaction rate R(V) as a function of a bias voltage V are analyzed for rotation of a single CCH (D) molecule on a Cu (100) surface [5] and hopping of a single H(D)2O molecule on Pd(111) surface [6]. In the former system it is identified that rotation occurs if enough energy stored in the C-H (D) in-plane bending (IPB) mode excited by tunneling electron is transferred to the C-H (D) out of plane bending (OPB) mode (reaction coordinate mode) via the anharmonic mode coupling in a single electron process. The calculated R(V) shows an excellent agreement with the experimental results except at the low bias voltages below V ≃ 60 mV where no experimental data is available for the nonlinear current I dependence of R(I). A reproduction of the experimental R(V) at the higher voltage region allows us to determine the vibrational density of states of the C-H IPB mode and its coupling rate to the C-H (D) OPB mode as well as the inelastic tunneling current to excite IPB mode. A change of a conductance upon excitation of the C-H IPB mode enables us to evaluate the electron-vibration coupling strength inducing the rotation motion of CCH molecule. In the latter system investigated at a high temperature of about 40 K, the constant R(V) due to thermal hopping followed by the rapid increase is satisfactory explained by anharmonic inter-mode coupling between the scissor mode excited by tunneling electrons and the frustrated translation mode for H(D)2O molecule on Pd(111).

  17. Dimensional scale effects on surface enhanced Raman scattering efficiency of self-assembled silver nanoparticle clusters

    Energy Technology Data Exchange (ETDEWEB)

    Fasolato, C. [Dip. Fisica, Università Sapienza, P.le Aldo Moro, 5, 00185 Rome (Italy); Center for Life Nanoscience@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena, 291, 00185 Rome (Italy); Domenici, F., E-mail: fabiodomenici@gmail.com, E-mail: paolo.postorino@roma1.infn.it; De Angelis, L.; Luongo, F.; Postorino, P., E-mail: fabiodomenici@gmail.com, E-mail: paolo.postorino@roma1.infn.it [Dip. Fisica, Università Sapienza, P.le Aldo Moro, 5, 00185 Rome (Italy); Sennato, S. [Dip. Fisica, Università Sapienza, P.le Aldo Moro, 5, 00185 Rome (Italy); CNR-IPCS UOS Roma, Dip. Fisica, Università Sapienza, P.le Aldo Moro, 5, 00185 Rome (Italy); Mura, F. [Dip. Scienze di Base Applicate all' Ingegneria, Università Sapienza, Via A. Scarpa, 16, 00185 Rome (Italy); Costantini, F. [Dip. Ingegneria Astronautica Elettrica ed Energetica, Università Sapienza, Via Eudossiana, 18, 00184 Rome (Italy); Bordi, F. [Dip. Fisica, Università Sapienza, P.le Aldo Moro, 5, 00185 Rome (Italy); Center for Life Nanoscience@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena, 291, 00185 Rome (Italy); CNR-IPCS UOS Roma, Dip. Fisica, Università Sapienza, P.le Aldo Moro, 5, 00185 Rome (Italy)

    2014-08-18

    A study of the Surface Enhanced Raman Scattering (SERS) from micrometric metallic nanoparticle aggregates is presented. The sample is obtained from the self-assembly on glass slides of micro-clusters of silver nanoparticles (60 and 100 nm diameter), functionalized with the organic molecule 4-aminothiophenol in water solution. For nanoparticle clusters at the micron scale, a maximum enhancement factor of 10{sup 9} is estimated from the SERS over the Raman intensity ratio normalized to the single molecule contribution. Atomic force microscopy, correlated to spatially resolved Raman measurements, allows highlighting the connection between morphology and efficiency of the plasmonic system. The correlation between geometric features and SERS response of the metallic structures reveals a linear trend of the cluster maximum scattered intensity as a function of the surface area of the aggregate. On given clusters, the intensity turns out to be also influenced by the number of stacking planes of the aggregate, thus suggesting a plasmonic waveguide effect. The linear dependence results weakened for the largest area clusters, suggesting 30 μm{sup 2} as the upper limit for exploiting the coherence over large scale of the plasmonic response.

  18. Improved cluster-in-molecule local correlation approach for electron correlation calculation of large systems.

    Science.gov (United States)

    Guo, Yang; Li, Wei; Li, Shuhua

    2014-10-02

    An improved cluster-in-molecule (CIM) local correlation approach is developed to allow electron correlation calculations of large systems more accurate and faster. We have proposed a refined strategy of constructing virtual LMOs of various clusters, which is suitable for basis sets of various types. To recover medium-range electron correlation, which is important for quantitative descriptions of large systems, we find that a larger distance threshold (ξ) is necessary for highly accurate results. Our illustrative calculations show that the present CIM-MP2 (second-order Møller-Plesser perturbation theory, MP2) or CIM-CCSD (coupled cluster singles and doubles, CCSD) scheme with a suitable ξ value is capable of recovering more than 99.8% correlation energies for a wide range of systems at different basis sets. Furthermore, the present CIM-MP2 scheme can provide reliable relative energy differences as the conventional MP2 method for secondary structures of polypeptides.

  19. Normal Globular Cluster Systems in Massive Low Surface Brightness Galaxies

    CERN Document Server

    Villegas, Daniela; Jordán, Andrés; Goudfrooij, Paul; Zwaan, Martin

    2007-01-01

    We present the results of a study of the globular cluster systems of 6 massive spiral galaxies, originally cataloged as low surface brightness galaxies but here shown to span a wide range of central surface brightness values, including two intermediate to low surface brightness galaxies. We used the Advanced Camera for Surveys on board HST to obtain photometry in the F475W and F775W bands and select sources with photometric and morphological properties consistent with those of globular clusters. A total of 206 candidates were identified in our target galaxies. From a direct comparison with the Galactic globular cluster system we derive specific frequency values for each galaxy that are in the expected range for late-type galaxies. We show that the globular cluster candidates in all galaxies have properties consistent with globular cluster systems of previously studied galaxies in terms of luminosity, sizes and color. We establish the presence of globular clusters in the two intermediate to low surface brightn...

  20. Formation of clusters composed of C60 molecules via self-assembly in critical fluids

    Science.gov (United States)

    Fukuda, Takahiro; Ishii, Koji; Kurosu, Shunji; Whitby, Raymond; Maekawa, Toru

    2007-04-01

    Fullerenes are promising candidates for intelligent, functional nanomaterials because of their unique mechanical, electronic and chemical properties. However, it is necessary to invent some efficient but relatively simple methods of producing structures composed of fullerenes for the development of nanomechatronic, nanoelectronic and biochemical devices and sensors. In this paper, we show that various structures such as straight fibres, networks formed by fibres, wide sheets and helical structures, which are composed of C60 molecules, are created by placing C60-crystals in critical ethane, carbon dioxide and xenon even though C60 molecules do not dissolve or disperse in the above fluids. It is supposed, judging by the intermolecular potentials between C60 and C60, between C60 and ethane, and between ethane and ethane, that C60-clusters grow with the assistance of solvent molecules, which are trapped between C60 molecules under critical conditions. This room-temperature self-assembly cluster growth process in critical fluids may open up a new methodology of forming structures built up with fullerenes without the need for any ultra-fine processing technologies.

  1. Proton Migration in Clusters Consisting of Protonated Pyridine Solvated by Water Molecules.

    Science.gov (United States)

    Berthias, Francis; Feketeová, Linda; Chermette, Henry; Forquet, Valérian; Morell, Christophe; Abdoul-Carime, Hassan; Farizon, Bernadette; Farizon, Michel; Märk, Tilmann D

    2015-10-26

    Proton transfer (PT) from protonated pyridine to water molecules is observed after excitation of microhydrated protonated pyridine (Py) clusters PyH(+) (H2 O)n (n=0-5) is induced by a single collision with an Ar atom at high incident velocity (95×10(3)  m s(-1) ). Besides the fragmentation channel associated with the evaporation of water molecules, the charged-fragment mass spectrum shows competition between the production of the PyH(+) ion (or its corresponding charged fragments) and the production of H(+) (H2 O) or H(+) (H2 O)2 ions. The increase in the production of protonated water fragments as a function of the number of H2 O molecules in the parent cluster ion as well sd the observation of a stable H(+) (H2 O)2 fragment, even in the case of the dissociation of PyH(+) (H2 O)2 , are evidence of the crucial role of PT in the relaxation process, even for a small number of solvating water molecules.

  2. Single molecule magnets on a gold surface: in situ electrospray deposition, x-ray absorption and photoemission

    Energy Technology Data Exchange (ETDEWEB)

    Saywell, Alex; Britton, Andrew J; Beton, Peter H; O' Shea, James N [School of Physics and Astronomy, University of Nottingham, Nottingham, NG7 2RD (United Kingdom); Taleb, Nassiba; Del Carmen Gimenez-Lopez, Maria; Champness, Neil R, E-mail: james.oshea@nottingham.ac.uk [School of Chemistry, University of Nottingham, Nottingham, NG7 2RD (United Kingdom)

    2011-02-18

    Single molecule magnets based on the dodecamanganese (III, IV) cluster with two different types of ligand (acetate and benzoate) have been studied on the Au(111) surface. Due to the non-volatile and fragile nature of the molecules, we have used ultra-high vacuum electrospray deposition to produce a series of surface coverages from a fraction of a monolayer to multilayer films in both cases. Synchrotron radiation based electron spectroscopy has been used to study the adsorption of the molecules on the Au(111) surface and the effect that this has on the oxidation states of the manganese atoms in the core. In both cases, reduction of the core is observed due to the interaction with the surface, to essentially the same extent despite substantial differences in the size and nature of the ligand shell.

  3. Permutation invariant polynomial neural network approach to fitting potential energy surfaces. III. Molecule-surface interactions

    Science.gov (United States)

    Jiang, Bin; Guo, Hua

    2014-07-01

    The permutation invariant polynomial-neural network (PIP-NN) method for constructing highly accurate potential energy surfaces (PESs) for gas phase molecules is extended to molecule-surface interaction PESs. The symmetry adaptation in the NN fitting of a PES is achieved by employing as the input symmetry functions that fulfill both the translational symmetry of the surface and permutation symmetry of the molecule. These symmetry functions are low-order PIPs of the primitive symmetry functions containing the surface periodic symmetry. It is stressed that permutationally invariant cross terms are needed to avoid oversymmetrization. The accuracy and efficiency are demonstrated in fitting both a model PES for the H2 + Cu(111) system and density functional theory points for the H2 + Ag(111) system.

  4. Diffusion Dynamics of Cux Cluster on Cu(111) Surface

    Institute of Scientific and Technical Information of China (English)

    Jian-feng Tang; Mai-chang Xu; Xue-song Li; Wo-yun Long

    2008-01-01

    The diffusion dynamics of small two-dimensional atomic clusters Cux(1≤x≤8) on Cu(111) surface were studied using the molecular dynamics simulations and a modified analytic embedded-atom method in the temperature range from 200 K to 800 K.The cluster size and temperature dependence of the diffusion coefficients and migration energies are presented.Our simulations show that the diffusion migration energy of the Cu7 cluster is the highest and the prefactor for the CuT cluster is almost three orders of magnitude larger than that for single atom diffusion.This conclusion is consistent with the experimental results for similar metals.In addition,the dependence of cluster diffusion on film growth is also discussed.

  5. Atomically precise gold nanocrystal molecules with surface plasmon resonance.

    Science.gov (United States)

    Qian, Huifeng; Zhu, Yan; Jin, Rongchao

    2012-01-17

    Since Faraday's pioneering work on gold colloids, tremendous scientific research on plasmonic gold nanoparticles has been carried out, but no atomically precise Au nanocrystals have been achieved. This work reports the first example of gold nanocrystal molecules. Mass spectrometry analysis has determined its formula to be Au(333)(SR)(79) (R = CH(2)CH(2)Ph). This magic sized nanocrystal molecule exhibits fcc-crystallinity and surface plasmon resonance at approximately 520 nm, hence, a metallic nanomolecule. Simulations have revealed that atomic shell closing largely contributes to the particular robustness of Au(333)(SR)(79), albeit the number of free electrons (i.e., 333 - 79 = 254) is also consistent with electron shell closing based on calculations using a confined free electron model. Guided by the atomic shell closing growth mode, we have also found the next larger size of extraordinarily stability to be Au(~530)(SR)(~100) after a size-focusing selection--which selects the robust size available in the starting polydisperse nanoparticles. This work clearly demonstrates that atomically precise nanocrystal molecules are achievable and that the factor of atomic shell closing contributes to their extraordinary stability compared to other sizes. Overall, this work opens up new opportunities for investigating many fundamental issues of nanocrystals, such as the formation of metallic state, and will have potential impact on condensed matter physics, nanochemistry, and catalysis as well.

  6. Quark-cluster Stars: hints from the surface

    CERN Document Server

    Dai, Shi

    2012-01-01

    The matter inside pulsar-like compact stars could be in a quark-cluster phase since in cold dense matter at a few nuclear densities (2 to 10 times), quarks could be coupled still very strongly and condensate in position space to form quark clusters. Quark-cluster stars are chromatically confined and could initially be bare, therefore the surface properties of quark-cluster stars would be quite different from that of conventional neutron stars. Some facts indicate that a bare and self-confined surface of pulsar-like compact stars might be necessary in order to naturally understand different observational manifestations. On one hand, as for explaining the drifting sub-pulse phenomena, the binding energy of particles on pulsar surface should be high enough to produce vacuum gaps, which indicates that pulsar's surface might be strongly self-confined. On the other hand, a bare surface of quark-cluster star can overcome the baryon contamination problem of Gamma-ray burst as well as promote a successful core-collaps...

  7. Contact angle hysteresis on textured surfaces with nanowire clusters.

    Science.gov (United States)

    Liao, Ying-Chih; Chiang, Cheng-Kun; Lu, Yen-Wen

    2013-04-01

    Nanowire arrays with various agglomeration patterns were synthesized by adjusting the solvent evaporation rates. Nanowires with 200 nm diameter and 2-25 microm in length were fabricated from an anodic aluminum oxide (AAO) porous template. Various drying treatments were applied to develop nanostructured surfaces with topological differences. Due to surface tension forces, copper nanowires after thermal and evaporative drying treatments agglomerated into clusters, while supercritical drying technique provided excellent bundled-free and vertically-standing nanowire arrays. Although all dried surfaces exhibited hydrophobic nature, the contact angle hysteresis, or the difference between advancing and receding angles, was found to be larger on those surfaces with bundled nanowire clusters. To explain the difference, the wetted solid fraction on each surface was calculated using the Cassie-Baxter model to show that the hysteresis was contributed by liquid/solid contact area on the textured surfaces.

  8. Preservation of organic molecules at Mars' near-surface

    Science.gov (United States)

    Freissinet, Caroline

    2016-07-01

    One of the biggest concerns for the in situ detection of organics on extraterrestrial environment is the preservation potential of the molecules at the surface and subsurface given the harsh radiation conditions and oxidants they are exposed to. The Mars Science Laboratory (MSL) search for hydrocarbons is designed to understand taphonomic windows of organic preservation in the Mars' near-surface. The Sample Analysis at Mars (SAM) instrument on the MSL Curiosity rover discovered chlorohydrocarbon indigenous to a mudstone drilled sample, Cumberland (CB). The discovery of chlorohydrocarbons in the martian surface means that reduced material with covalent bonds has survived despite the severe degrading conditions. However, the precursors of the chlorohydrocarbons detected by pyrolysis at CB remain unknown. Organic compounds in this ancient sedimentary rock on Mars could include polycyclic aromatic hydrocarbons and refractory organic material, either formed on Mars from igneous, hydrothermal, atmospheric, or biological processes or, alternatively, delivered directly to Mars via meteorites, comets, or interplanetary dust particles. It has been postulated that organic compounds in near-surface rocks may undergo successive oxidation reactions that eventually form metastable benzenecarboxylates, including phthalic and mellitic acids. These benzenecarboxylates are good candidates as the precursors of the chlorohydrocarbons detected in SAM pyrolysis at CB. Indeed, recently, SAM performed a derivatization experiments on a CB sample, using the residual vapor of N-methyl-N-tertbutylsilyltrifluoroacetamide (MTBSTFA) leaking into the system. The preliminary interpretations are compatible with the presence of benzocarboxylates, coincidently with long chain carboxylic acids and alcohols. The analysis of this interesting data set to identify these derivatization products, as well as future SAM measurements on Mt Sharp, should shed additional light on the chemical nature and the

  9. Reaction dynamics of small molecules at metal surfaces

    CERN Document Server

    Samson, P A

    1999-01-01

    directed angular distributions suggest the influence of a trapping mechanism, recombining molecules scattering through a molecularly adsorbed state, with a transition state of large d sub N sub N responsible for the product vibrational excitation. Although N sub 2 dissociation on Fe(100) forms a simple overlayer structure, on Fe(110), molecular chemisorption does not occur at or above room temperature and the sticking is extremely small (approx 10 sup - sup 6 to 10 sup - sup 7). Activated nitrogen bombardment can be used to prepare a 'surface nitride' with a structure related to the geometry of bulk Fe sub 4 N. Scanning tunnelling microscopy yields atomic scale features that cannot be explained by simple overlayers. It is proposed that the uppermost iron layer reconstructs to generate quasi-octahedral sites between the top two layers, with sub-surface nitrogen in these sites forming a model for the 'surface nitride' structure. The dissociation-desorption dynamics of D sub 2 upon the Sn/Pt(111) surface alloy a...

  10. Does the MgO(100)-support facilitate the reaction of nitrogen and hydrogen molecules catalyzed by Zr2Pd2 clusters? A computational study.

    Science.gov (United States)

    Kuznetsov, Aleksey E; Musaev, Djamaladdin G

    2010-03-01

    Reactions of the "naked" and MgO(100) supported Zr(2)Pd(2) cluster with nitrogen and four hydrogen molecules were studied at the density functional level using the periodic slab approach (VASP). It was shown that adsorption of the Zr(2)Pd(2) cluster on the MgO(100) surface does not change its gas-phase geometry and electronic structure significantly. In spite of this the N(2) coordination to the MgO(100)-supported Zr(2)Pd(2) cluster, I/MgO, is found to be almost 30 kcal/mol less favorable than for the "naked" one. The addition of the first H(2) molecule to the resulting II/MgO, that is, II/MgO + H(2) --> IV/MgO reaction, proceeds with a relatively small, 9.0 kcal/mol, barrier and is exothermic by 8.3 kcal/mol. The same reaction for the "naked" Zr(2)Pd(2) cluster requires a slightly larger barrier (10.1 kcal/mol) and is highly exothermic (by 23.3 kcal/mol). The interaction of the H(2) molecule with the intermediate IV/MgO (i.e., the second H(2) molecule addition to II/MgO) requires larger energy barrier, 23.3 kcal/mol vs 8.8 kcal/mol for the "naked" cluster, and is exothermic by 20.5 kcal/mol (vs 18.2 kcal/mol reported for the "naked" Zr(2)Pd(2) cluster). The addition of the H(2) molecule to VI/MgO and VI (i.e., the third H(2) molecule addition to II/MgO and II, respectively) requires similar barriers, 12.0 versus 16.8 kcal/mol, respectively, but is highly exothermic for the supported cluster compared to the "naked" one, 13.6 versus 0.1 kcal/mol. The addition of the fourth H(2) molecule occurs with almost twice larger barrier for the "naked" cluster compared to the adsorbed species, 30.7 versus 15.9 kcal/mol. Furthermore, this reaction step is endothermic (by 11.4 kcal/mol) for the gas-phase cluster but exothermic by 7.8 kcal/mol for the adsorbed cluster. Dissociation of the formed hydrazine molecule from the on-surface complex X/MgO and the "naked" complex X requires 19.1 and 26.3 kcal/mol, respectively. Thus, the Zr(2)Pd(2) adsorption on the MgO(100) surface

  11. Efficient generation of cluster states with semiconductor double-dot molecules on a chip

    Energy Technology Data Exchange (ETDEWEB)

    Zhou Jian [Anhui Xinhua University, Hefei 230088 (China); Dong Ping, E-mail: dongping9979@163.co [Department of Physics and Electronic Engineering, Hefei Normal University, Hefei 230061 (China); Zou Weiping; Xue Zhengyuan [Laboratory of Quantum Information Technology, ICMP and School of Physics and Telecommunication Engineering, South China Normal University, Guangzhou 510006 (China)

    2011-03-01

    We propose an efficient scheme for the generation of the cluster states directly using the iSWAP gate, with semiconductor double-dot molecules on a chip. The implementation of an iSWAP gate only requires resonant interaction between a molecule and a transmission line resonator, which results in considerable improvement for gate speed comparing to conventional dispersive techniques. Meanwhile, the fast generation speed is also very important in view of decoherence. Therefore, our approach makes one-way quantum computation more feasible via this on chip architecture. -- Research highlights: {yields} An efficient generation scheme of the cluster states is proposed with iSWAP gate in semiconductor double-dot molecules on a chip. {yields} The implementation of an iSWAP gate only requires resonant qubit-resonator interaction, which results in considerable improvement of gate speed comparing to dispersive interaction techniques. {yields} Resonant qubit-resonator interaction results in fast generation, which is very important in view of systematical decoherence. {yields} Our generation approach makes one-way quantum computation more feasible via this on chip architecture.

  12. Linear and nonlinear surface spectroscopy of supported size selected metal clusters and organic adsorbates

    Energy Technology Data Exchange (ETDEWEB)

    Thaemer, Martin Georg

    2012-03-08

    The spectroscopic investigation of supported size selected metal clusters over a wide wavelength range plays an important role for understanding their outstanding catalytic properties. The challenge which must be overcome to perform such measurements is the difficult detection of the weak spectroscopic signals from these samples. As a consequence, highly sensitive spectroscopic methods are applied, such as surface Cavity Ringdown Spectroscopy and surface Second Harmonic Generation Spectroscopy. The spectroscopic apparatus developed is shown to have a sensitivity which is high enough to detect sub-monolayer coverages of adsorbates on surfaces. In the measured spectra of small supported silver clusters of the sizes Ag{sub 4}2, Ag{sub 2}1, Ag{sub 9}, and Ag atoms a stepwise transition from particles with purely metallic character to particles with molecule-like properties can be observed within this size range.

  13. GPI-anchored receptor clusters transiently recruit Lyn and Gα for temporary cluster immobilization and Lyn activation: single-molecule tracking study 1

    OpenAIRE

    2007-01-01

    The signaling mechanisms for glycosylphosphatidylinositol-anchored receptors (GPI-ARs) have been investigated by tracking single molecules in living cells. Upon the engagement or colloidal gold–induced cross-linking of CD59 (and other GPI-ARs) at physiological levels, CD59 clusters containing three to nine CD59 molecules were formed, and single molecules of Gαi2 or Lyn (GFP conjugates) exhibited the frequent but transient (133 and 200 ms, respectively) recruitment to CD59 clusters, via both p...

  14. Thermal dynamics of silver clusters grown on rippled silica surfaces

    Science.gov (United States)

    Bhatnagar, Mukul; Ranjan, Mukesh; Jolley, Kenny; Lloyd, Adam; Smith, Roger; Mukherjee, Subroto

    2017-02-01

    Silver nanoparticles have been deposited on silicon rippled patterned templates at an angle of incidence of 70° to the surface normal. The templates are produced by oblique incidence argon ion bombardment and as the fluence increases, the periods and heights of the structures increase. Structures with periods of 20 nm, 35 nm and 45 nm have been produced. Moderate temperature vacuum annealing shows the phenomenon of cluster coalescence following the contour of the more exposed faces of the ripple for the case of 35 nm and 45 nm but not at 20 nm where the silver aggregates into larger randomly distributed clusters. In order to understand this effect, the morphological changes of silver nanoparticles deposited on an asymmetric rippled silica surface are investigated through the use of molecular dynamics simulations for different deposition angles of incidence between 0° and 70° and annealing temperatures between 500 K and 900 K. Near to normal incidence, clusters are observed to migrate over the entire surface but for deposition at 70°, a similar patterning is observed as in the experiment. The random distribution of clusters for the periodicity ≈ of 20 nm is linked to the geometry of the silica surface which has a lower ripple height than the longer wavelength structures. Calculations carried out on a surface with such a lower ripple height also demonstrate a similar effect.

  15. Electron attachment to molecules and clusters of atmospheric relevance: oxygen and ozone

    Science.gov (United States)

    Matejcik, S.; Kiendler, A.; Cicman, P.; Skalny, J.; Stampfli, P.; Illenberger, E.; Chu, Y.; Stamatovic, A.; Märk, T. D.

    1997-05-01

    Highly monochromatized electrons are used in a crossed beams experiment to investigate electron attachment to oxygen clusters 0963-0252/6/2/007/img1 at electron energies from approximately zero up to 2 eV. At energies close to zero the attachment cross section for the reaction 0963-0252/6/2/007/img2 varies inversely with the electron energy, indicative of s-wave electron capture to 0963-0252/6/2/007/img1. Peaks in the attachment cross section present at higher energies can be ascribed to vibrational levels of the oxygen anion. The vibrational spacings observed can be quantitatively accounted for. In addition, electron attachment to ozone and mixed oxygen/ozone clusters has been studied in the energy range up to 4 eV. Absolute attachment cross sections for both fragment ions, 0963-0252/6/2/007/img4 and 0963-0252/6/2/007/img5, from ozone could be deduced. Moreover, despite the initially large excess of oxygen molecules in the neutral oxygen/ozone clusters the dominant attachment products are undissociated clusters ions 0963-0252/6/2/007/img6 including the 0963-0252/6/2/007/img7 monomer while oxygen ions 0963-0252/6/2/007/img8 appear with comparatively low intensity.

  16. Electrochemically Inducible Surfaces for Patterning Two Distinct Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Inseong; Yeo, Woon-Seok [Konkuk University,Seoul (Korea, Republic of)

    2016-04-15

    Herein, we report on a new multicomponent patterning method based on electrochemically inducible self-assembled monolayers on gold. Two different masked functional groups on monolayers are activated to give amine and acetylene moieties through electrochemical activations at negative potential and positive potential, respectively. The resulting amine and acetylene groups are further used as chemical handles for incorporation of ligand molecules via well-known chemoselective conjugation reactions such as amine-specific conjugation chemistry and click reaction. The chemical conversions of masked functional groups to amine and acetylene groups were characterized by cyclic voltammetry. We demonstrated the orthogonal immobilization of two fluorescent dyes on the patterned surface along the patterned features. Our strategy can provide a useful platform technology for the preparation of multicomponent ligand-patterned substrates with various advantages such as chemical flexibility, mild reaction conditions, and high yields of two orthogonal chemical reactions of amine-specific conjugation and click reaction.

  17. Lanczos-driven coupled-cluster damped linear response theory for molecules in polarizable environments

    DEFF Research Database (Denmark)

    List, Nanna Holmgaard; Coriani, Sonia; Kongsted, Jacob

    2014-01-01

    We present an extension of a previously reported implementation of a Lanczos-driven coupled-cluster (CC) damped linear response approach to molecules in condensed phases, where the effects of a surrounding environment are incorporated by means of the polarizable embedding formalism. We...... are specifically motivated by a twofold aim: (i) computation of core excitations in realistic surroundings and (ii) examination of the effect of the differential response of the environment upon excitation solely related to the CC multipliers (herein denoted the J matrix) in computations of excitation energies...

  18. A cruise in the archipelagos of superheavy elements, heavy-cluster emitters and nuclear molecules

    CERN Document Server

    Greiner, W

    2002-01-01

    I review some of the most important achievements in the theoretical investigations that we carried out in the last three decades at Frankfurt on the extension of the periodic system and heavy-ion emission. After discussing the problem of cold fusion and formation of Superheavy Elements (SHE) I will consider the reverse process, i.e. the spontaneous cold fragmentation of heavy nuclei into different channels like cluster radioactivity and cold fission. I will speculate on the properties of the putative quasi-molecules arising in the recent discovery of the triple fission of sup 2 sup 5 sup 2 Cf. (author)

  19. High-intensity X-rays interaction with matter processes in plasmas, clusters, molecules and solids

    CERN Document Server

    Hau-Riege, Stefan P

    2012-01-01

    Filling the need for a book bridging the effect of matter on X-ray radiation and the interaction of x-rays with plasmas, this monograph provides comprehensive coverage of the topic. As such, it presents and explains such powerful new X-ray sources as X-ray free-electron lasers, as well as short pulse interactions with solids, clusters, molecules, and plasmas, and X-ray matter interactions as a diagnostic tool. Equally useful for researchers and practitioners working in the field.

  20. Cyclic single-molecule magnets: from the odd-numbered heptanuclear to a dimer of heptanuclear dysprosium clusters.

    Science.gov (United States)

    Tian, Haiquan; Bao, Song-Song; Zheng, Li-Min

    2016-02-01

    A heptanuclear and a dimer of heptanuclear dysprosium clusters (Dy7 and Dy14) have been successfully synthesized by ingenious coalescence of the single and double pyrazinyl hydrazone as well as phosphonate ligands. The complexes feature the largest odd-numbered cyclic lanthanide clusters reported thus far. Both exhibit single molecule magnet behaviors at low temperature.

  1. Calculation of vibrational energy of molecule using coupled cluster linear response theory in bosonic representation: convergence studies.

    Science.gov (United States)

    Banik, Subrata; Pal, Sourav; Prasad, M Durga

    2008-10-07

    Vibrational excited state energies have been calculated using vibrational coupled cluster linear response theory (CCLRT). The method has been implemented on formaldehyde and water molecule. Convergence studies have been shown with varying the cluster operator from S(4) to S(6) as well as the excitation operator from four bosons to six bosons. A good agreement with full configuration interaction results has been observed with S(6) truncation at coupled-cluster method level and six bosonic excitations at CCLRT level.

  2. Fundamental properties of molecules on surfaces. Molecular switching and interaction of magnetic molecules with superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Hatter, Nino

    2016-12-14

    In this thesis, we investigate individual molecular switches and metal-organic complexes on surfaces with scanning tunneling microscopy (STM) and spectroscopy (STS) at low temperatures. One focus addresses the switching ability and mechanism of diarylethene on Ag(111). The other focus lies on resolving and tuning magnetic interactions of individual molecules with superconductors. 4,4'-(4,4'-(perfluorocyclopent-1-ene-1,2-diyl)bis (5-methylthiophene-4,2-diyl)dip yridine (PDTE) is a prototypical photochromic switch. We can induce a structural change of individual PDTE molecules on Ag(111) with the STM tip. This change is accompanied by a reduction of the energy gap between the occupied and unoccupied molecular orbitals. Density functional theory (DFT) calculations reveal that the induced switching corresponds to a ring-closing reaction from an open isomer in a flat adsorption configuration to a ring-closed isomer with its methyl groups in a cis configuration. The final product is thermodynamically stabilized by strong dispersion interactions with the surface. A linear dependence of the switching threshold with the tip-sample distance with a minimal threshold of 1.4 V is found, which we assign to a combination of an electric-field induced process and a tunneling-electron contribution. DFT calculations suggest a large activation barrier for a ring-closing reaction from the open flat configuration into the closed cis configuration. The interaction of magnetic molecules with superconductors is studied on manganese phthalocyanine (MnPc) adsorbed on Pb(111). We find triplets of Shiba states inside the superconducting gap. Different adsorption sites of MnPc provide a large variety of exchange coupling strengths, which lead to a collective energy shift of the Shiba triplets. We can assign the splitting of the Shiba states to be an effect of magnetic anisotropy in the system. A quantum phase transition from a ''Kondo screened'' to a &apos

  3. A theoretical study of water clusters: the relation between hydrogen-bond topology and interaction energy from quantum-chemical computations for clusters with up to 22 molecules.

    Science.gov (United States)

    Lenz, Annika; Ojamäe, Lars

    2005-05-07

    Quantum-chemical calculations of a variety of water clusters with eight, ten and twelve molecules were performed, as well as for selected clusters with up to 22 water molecules. Geometry optimizations were carried out at the B3LYP/cc-pVDZ level and single-point energies were calculated at the B3LYP/aug-cc-pVDZ level for selected clusters. The electronic energies were studied with respect to the geometry of the oxygen arrangement and six different characteristics of the hydrogen-bond arrangement in the cluster. Especially the effect of the placement of the non-hydrogen bonding hydrogens on the interaction energy was studied. Models for the interaction energy with respect to different characteristics of the hydrogen-bond arrangement were derived through least-square fits. The results from the study of the clusters with eight, ten and twelve molecules are used to predict possible low-energy structures for various shapes of clusters with up to 22 molecules.

  4. Surface roughness stabilizes the clustering of self-propelled triangles

    Science.gov (United States)

    Ilse, Sven Erik; Holm, Christian; de Graaf, Joost

    2016-10-01

    Self-propelled particles can spontaneously form dense phases from a dilute suspension in a process referred to as motility-induced phase separation. The properties of the out-of-equilibrium structures that are formed are governed by the specifics of the particle interactions and the strength of the activity. Thus far, most studies into the formation of these structures have focused on spherical colloids, dumbbells, and rod-like particles endowed with various interaction potentials. Only a few studies have examined the collective behavior of more complex particle shapes. Here, we increase the geometric complexity and use molecular dynamics simulations to consider the structures formed by triangular self-propelled particles with surface roughness. These triangles either move towards their apex or towards their base, i.e., they possess a polarity. We find that apex-directed triangles cluster more readily, more stably, and have a smoother cluster interface than their base-directed counterparts. A difference between the two polarities is in line with the results of Wensink et al. [Phys. Rev. E 89, 010302 (2014)]; however, we obtain the reversed result when it comes to clustering, namely, that apex-directed triangles cluster more successfully. We further show that reducing the surface roughness negatively impacts the stability of the base-directed structures, suggesting that their formation is in large part due to surface roughness. Our results lay a solid foundation for future experimental and computational studies into the effect of roughness on the collective dynamics of swimmers.

  5. Surface-enhanced and tip-enhanced Raman spectroscopy of biological molecules on nanostructured metallic surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Hennemann, Laura E.; Mihaljevic, Josip; Braun, Kai; Meixner, Alfred J.; Zhang, Dai [Institute of Physical and Theoretical Chemistry, University of Tuebingen, Tuebingen (Germany); Kolloch, Andreas [Department of Physics, University of Konstanz, Universitaetsstrasse 10, 78457 Konstanz (Germany)

    2011-07-01

    We use a custom built apertureless scanning near-field optical microscope (SNOM) to investigate several kinds of biological molecules. The setup is an extended parabolic mirror based confocal microscope working with higher order laser modes in order to tune the polarization of the light in its focus. We detected the presence of a (sub)monolayer of biological molecules ranging from DNA bases to double stranded DNA by collecting their unique Raman fingerprint spectrum. In order to detect such small amounts of molecules, we performed surface-enhanced Raman scattering (SERS) or tip-enhanced Raman scattering (TERS). For SERS, either the irregular rough edges of evaporated noble metal grids or regular arrays of gold nano triangles served as enhancing substrates. We compared the plasmonic properties of gold triangles of different aspect ratios and on different substrates to optimize the electromagnetic enhancement for the 632.8 nm laser excitation. The obtained optical patterns were compared to those computed in simulations. In the case of TERS, an electrochemically etched sharp gold tip (approx. 20 nm tip apex diameter) was approached to the surface, thus acting simultaneously as a scanning probe microscopy tip for topographic measurements and as a near-field antenna collecting optical information. We collected TERS spectra of single calf thymus DNA molecules immobilized on smooth Au(111) surfaces. Strongly enhanced spectra were obtained both in the SERS and in the TERS measurements.

  6. Laws of thermal diffusion of individual molecules on the gold surface.

    Science.gov (United States)

    Sändig, Nadja; Zerbetto, Francesco

    2011-08-14

    By molecular dynamics simulations, we describe and discuss the mobility of single molecules on a metal surface. The calculated trajectories of 28 different molecules show that diffusion, subdiffusion and superdiffusion regimes exist. The trajectories also share some common features, which are expressed in the form of power laws that link the length of the path walked by the molecule, the molecular mass, and the surface-molecule interaction energy. The values of the exponents of the laws are easily rationalized and provide insight into the molecular behaviour on the surface. The calculations also show that the adsorption is governed by the combination of van der Waals and Coulomb molecule-surface interactions.

  7. Super-Resolution Imaging and Quantitative Analysis of Membrane Protein/Lipid Raft Clustering Mediated by Cell-Surface Self-Assembly of Hybrid Nanoconjugates.

    Science.gov (United States)

    Hartley, Jonathan M; Chu, Te-Wei; Peterson, Eric M; Zhang, Rui; Yang, Jiyuan; Harris, Joel; Kopeček, Jindřich

    2015-08-17

    Super-resolution imaging was used to quantify organizational changes in the plasma membrane after treatment with hybrid nanoconjugates. The nanoconjugates crosslinked CD20 on the surface of malignant B cells, thereby inducing apoptosis. Super-resolution images were analyzed by using pair-correlation analysis to determine cluster size and to count the average number of molecules in the clusters. The role of lipid rafts was investigated by pre-treating cells with a cholesterol chelator and actin destabilizer to prevent lipid raft formation. Lipid raft cluster size correlated with apoptosis induction after treatment with the nanoconjugates. Lipid raft clusters had radii of ∼ 200 nm in cells treated with the hybrid nanoconjugates. Super-resolution images provided precise molecule location coordinates that could be used to determine density of bound conjugates, cluster size, and number of molecules per cluster.

  8. Modulation of genetic clusters for synthesis of bioactive molecules in fungal endophytes: A review.

    Science.gov (United States)

    Deepika, V B; Murali, T S; Satyamoorthy, K

    2016-01-01

    Novel drugs with unique and targeted mode of action are very much need of the hour to treat and manage severe multidrug infections and other life-threatening complications. Though natural molecules have proved to be effective and environmentally safe, the relative paucity of discovery of new drugs has forced us to lean towards synthetic chemistry for developing novel drug molecules. Plants and microbes are the major resources that we rely upon in our pursuit towards discovery of novel compounds of pharmacological importance with less toxicity. Endophytes, an eclectic group of microbes having the potential to chemically bridge the gap between plants and microbes, have attracted the most attention due to their relatively high metabolic versatility. Since continuous large scale supply of major metabolites from microfungi and especially endophytes is severely impeded by the phenomenon of attenuation in axenic cultures, the major challenge is to understand the regulatory mechanisms in operation that drive the expression of metabolic gene clusters of pharmaceutical importance. This review is focused on the major regulatory elements that operate in filamentous fungi and various combinatorial multi-disciplinary approaches involving bioinformatics, molecular biology, and metabolomics that could aid in large scale synthesis of important lead molecules.

  9. Comparison of cluster expansion fitting algorithms for interactions at surfaces

    Science.gov (United States)

    Herder, Laura M.; Bray, Jason M.; Schneider, William F.

    2015-10-01

    Cluster expansions (CEs) are Ising-type interaction models that are increasingly used to model interaction and ordering phenomena at surfaces, such as the adsorbate-adsorbate interactions that control coverage-dependent adsorption or surface-vacancy interactions that control surface reconstructions. CEs are typically fit to a limited set of data derived from density functional theory (DFT) calculations. The CE fitting process involves iterative selection of DFT data points to include in a fit set and selection of interaction clusters to include in the CE. Here we compare the performance of three CE fitting algorithms-the MIT Ab-initio Phase Stability code (MAPS, the default in ATAT software), a genetic algorithm (GA), and a steepest descent (SD) algorithm-against synthetic data. The synthetic data is encoded in model Hamiltonians of varying complexity motivated by the observed behavior of atomic adsorbates on a face-centered-cubic transition metal close-packed (111) surface. We compare the performance of the leave-one-out cross-validation score against the true fitting error available from knowledge of the hidden CEs. For these systems, SD achieves lowest overall fitting and prediction error independent of the underlying system complexity. SD also most accurately predicts cluster interaction energies without ignoring or introducing extra interactions into the CE. MAPS achieves good results in fewer iterations, while the GA performs least well for these particular problems.

  10. Coupling of Surface and Volume Dipole Oscillations in C-60 Molecules

    CERN Document Server

    Brack, M; Murthy, M V N

    2007-01-01

    We first give a short review of the ``local-current approximation'' (LCA), derived from a general variation principle, which serves as a semiclassical description of strongly collective excitations in finite fermion systems starting from their quantum-mechanical mean-field ground state. We illustrate it for the example of coupled translational and compressional dipole excitations in metal clusters. We then discuss collective electronic dipole excitations in C$_{60}$ molecules (Buckminster fullerenes). We show that the coupling of the pure translational mode (``surface plasmon'') with compressional volume modes in the semiclasscial LCA yields semi-quantitative agreement with microscopic time-dependent density functional (TDLDA) calculations, while both theories yield qualitative agreement with the recent experimental observation of a ``volume plasmon''.

  11. Thermal control of sequential on-surface transformation of a hydrocarbon molecule on a copper surface

    Science.gov (United States)

    Kawai, Shigeki; Haapasilta, Ville; Lindner, Benjamin D.; Tahara, Kazukuni; Spijker, Peter; Buitendijk, Jeroen A.; Pawlak, Rémy; Meier, Tobias; Tobe, Yoshito; Foster, Adam S.; Meyer, Ernst

    2016-09-01

    On-surface chemical reactions hold the potential for manufacturing nanoscale structures directly onto surfaces by linking carbon atoms in a single-step reaction. To fabricate more complex and functionalized structures, the control of the on-surface chemical reactions must be developed significantly. Here, we present a thermally controlled sequential three-step chemical transformation of a hydrocarbon molecule on a Cu(111) surface. With a combination of high-resolution atomic force microscopy and first-principles computations, we investigate the transformation process in step-by-step detail from the initial structure to the final product via two intermediate states. The results demonstrate that surfaces can be used as catalysing templates to obtain compounds, which cannot easily be synthesized by solution chemistry.

  12. Suzaku observations of the low surface brightness cluster A76

    CERN Document Server

    Ota, N; Ibaraki, Y; Boehringer, H; Chon, G

    2013-01-01

    Context: We present results of Suzaku observations of a nearby galaxy cluster A76 at z=0.0395. This cluster is characterized by extremely low X-ray surface brightness and is hereafter referred to as the LSB cluster. Aims: To understand the nature and thermodynamic evolution of the LSB cluster by studying the physical properties of the hot intracluster medium in A76. Methods: We conducted two-pointed Suzaku observations of A76 and examined the global gas properties of the cluster by XIS spectral analysis. We also performed deprojection analysis of annular spectra and derived radial profiles of gas temperature, density and entropy out to approximately 850 kpc (~ 0.6 r_200) and 560 kpc (~0.4 r_200) in A76 East and A76 West, respectively. Results: The measured global temperature and metal abundance are approximately 3.3 keV and 0.24 solar, respectively. From the deprojection analysis, the entropy profile is found to be flat with respect to radius. The entropy within the central region (r < 0.2r_200) is excepti...

  13. Dissociation and suppressed ionization of H2O molecules embedded in He clusters: The role of the cluster as a cage

    Science.gov (United States)

    Kanaev, A. V.; Museur, L.; Laarmann, T.; Monticone, S.; Castex, M. C.; von Haeften, K.; Möller, T.

    2001-12-01

    Electronic structure and energy transfer in H2O doped HeN clusters (N≈104 is studied with photoexcitation in the spectral range of 140-40 nm (9-30 eV). The reaction dynamics is investigated by fluorescence of neutral OH* and H* and ionic H2O+* fragments. The rotational temperature of embedded water molecules has been estimated from the 124 nm line shape (3pa1C1B1←1b1 X˜ 1A1 transition). Two different temperatures (T1⩽5 K and T2≈30 K) have been found. We propose that the lower temperature (T1) is due to completely thermalized water molecules trapped inside helium clusters, while the warmer molecules (T2) are formed if they are first captured by helium clusters but then leave the clusters again. Predissociation of H2,/SUBO with excitation below the ionization limit (λexc>100 nm) is found to be unaffected by the cluster environment. On the other hand, the ionization (λexc<100 nm) seems to be suppressed inside helium clusters in favor of the fragmentation into neutral products.

  14. Review Article: Structures of phthalocyanine molecules on surfaces studied by STM

    Directory of Open Access Journals (Sweden)

    Yongfeng Wang

    2012-12-01

    Full Text Available This review mainly focuses on progress recently achieved in the growth of phthalocyanine molecules on single-crystal surfaces of sub-monolayer up to few-monolayer thin films studied by scanning tunneling microscopy in our groups. On metallic surfaces such as Au(111, Ag(111 and Cu(111, molecular superstructures are determined by combining directional intermolecular interactions caused by symmetry reduction, molecule-substrate interactions and indirect long-range interactions due to quantum interference of surface state electrons. On semiconducting TiO2 surface, molecular assembling structures are dictated by the strong molecule-substrate interaction. However, on insulating NaCl film, molecule-molecule interaction dominates over the molecule-NaCl coupling, leading to molecular growth behavior. Knowledge obtained from these studies would help people better understand the physicochemical properties of the phthalocyanine molecules at surfaces so that their new applications could be further explored and uncovered in the future.

  15. Two-Color Surface Photometry of Brightest Cluster Members

    CERN Document Server

    Garilli, B; Andreon, S; MacCagni, D; Carrasco, L; Recillas, E; Garilli, Bianca; Sangalli, Giorgio; Andreon, Stefano; Maccagni, Dario; Carrasco, Luis; Recillas, Elsa

    1997-01-01

    The Gunn g, r and i CCD images of a representative sample of 17 Brightest Cluster Galaxies (BCM) have been analyzed in order to derive surface brightness and color profiles, together with geometrical parameters like eccentricity and position angle. The sample includes both X-ray and optically selected clusters, ranging in redshift from z=0.049 to z=0.191. We find that BCMs are substantially well described by de Vaucouleurs' law out to radii of cases we find a surface brightness excess with respect to the $r^{1/4}$ law, which for A150 is coupled with a change in the $g-r$ color. The rest frame colors of BCMs do not show any intrinsic dispersion. By parametrizing the environment with the local galaxy number density, we find that it is correlated with the BCM extension, i.e. BCMs with larger effective radii are found in denser environments.

  16. Lipid-Mediated Clusters of Guest Molecules in Model Membranes and Their Dissolving in the Presence of Lipid Rafts.

    Science.gov (United States)

    Kardash, Maria E; Dzuba, Sergei A

    2017-05-25

    The clustering of molecules is an important feature of plasma membrane organization. It is challenging to develop methods for quantifying membrane heterogeneities because of their transient nature and small size. Here, we obtained evidence that transient membrane heterogeneities can be frozen at cryogenic temperatures which allows the application of solid-state experimental techniques sensitive to the nanoscale distance range. We employed the pulsed version of electron paramagnetic resonance (EPR) spectroscopy, the electron spin echo (ESE) technique, for spin-labeled molecules in multilamellar lipid bilayers. ESE decays were refined for pure contribution of spin-spin magnetic dipole-dipolar interaction between the labels; these interactions manifest themselves at a nanometer distance range. The bilayers were prepared from different types of saturated and unsaturated lipids and cholesterol (Chol); in all cases, a small amount of guest spin-labeled substances 5-doxyl-stearic-acid (5-DSA) or 3β-doxyl-5α-cholestane (DChl) was added. The local concentration found of 5-DSA and DChl molecules was remarkably higher than the mean concentration in the bilayer, evidencing the formation of lipid-mediated clusters of these molecules. To our knowledge, formation of nanoscale clusters of guest amphiphilic molecules in biological membranes is a new phenomenon suggested only recently. Two-dimensional 5-DSA molecular clusters were found, whereas flat DChl molecules were found to be clustered into stacked one-dimensional structures. These clusters disappear when the Chol content is varied between the boundaries known for lipid raft formation at room temperatures. The room temperature EPR evidenced entrapping of DChl molecules in the rafts.

  17. Supramolecular Photochemistry in Solution and on Surfaces: Encapsulation and Dynamics of Guest Molecules and Communication between Encapsulated and Free Molecules.

    Science.gov (United States)

    Ramamurthy, V; Jockusch, Steffen; Porel, Mintu

    2015-05-26

    Supramolecular assemblies that help to preorganize reactant molecules have played an important role in the development of concepts related to the control of excited-state processes. This has led to a persistent search for newer supramolecular systems (hosts), and this review briefly presents our work with octa acid (OA) to a host to control excited-state processes of organic molecules. Octa acid, a water-soluble host, forms 1:1, 2:1, and 2:2 (host-guest) complexes with various organic molecules. A majority of the guest molecules are enclosed within a capsule made up of two molecules of OA whereas OA by itself remains as a monomer or aggregates. Luminescence and (1)H NMR spectroscopy help to characterize the structure and dynamics of these host-guest complexes. The guest molecule as well as the host-guest complex as a whole undergoes various types of motion, suggesting that the guests possess freedom inside the confined space of the octa acid capsule. In addition, the confined guests are not isolated but are able to communicate (energy, electron, and spin) with molecules present closer to the capsule. The host-guest complexes are stable even on solid surfaces such as silica, clay, α-Zr phosphate, TiO2, and gold nanoparticles. This opens up new opportunities to explore the interaction between confined guests and active surfaces of TiO2 and gold nanoparticles. In addition, this allows the possibility of performing energy and electron transfer between organic molecules that do not adsorb on inert surfaces of silica, clay, or α-Zr phosphate. The results summarized here, in addition to providing a fundamental understanding of the behavior of molecules in a confined space provided by the host OA, are likely to have a long-range effect on the capture and release of solar energy.

  18. The Cloud Paradigm: Geostable molecules as proxies for surface oxygenation

    Science.gov (United States)

    Summons, R. E.; Hallmann, C.

    2011-12-01

    Geoscientists continue to puzzle over when and by which means Earth's surface environment became oxygenated. One of the prevailing scenarios, articulated by Cloud, Holland and Walker, proposes an initially anoxic or very low O2 atmosphere. Although photosystem II is thought to have appeared early, there was an extended period of imbalance between sources & sinks of O2 due to pervasive feedback between biosphere, atmosphere, hydrosphere & lithosphere. Ultimately O2 accumulated in the atmosphere to such levels that it left geochemical and physical evidence for mobilization of redox-sensitive elements in what is currently referred to as the 'Great Oxidation Event' or GOE at c. 2.45 Ga. While some researchers hold that the GOE marks the advent of oxygenic photosynthesis (e.g. Kopp et al., 2005), a wealth of geochemical and paleontological data is consistent with the presence of both cyanobacteria (e.g. Bosak et al., 2009) and traces of environmental oxygen (e.g. Anbar et al., 2007) several hundred million years prior. Further, molecular fossils present in 2.7-2.5 Ga rocks from the Transvaal Supergroup of the Kaapvaal Craton include steroids and other molecules indicative of oxygen-dependent biosynthesis and oxygen-respiring methanotrophic bacteria (Waldbauer et al., 2008). New molecular data for samples from the Mount McRae Formation in the Mt Bruce Supergroup, Pilbara Craton, identifies a diverse array of hydrocarbons including steroids and carotenoid residues diagnostic of phototrophic green sulfur bacteria. Co-variance of biomarker ratios with inorganic proxies-each leading to similar environmental reconstructions- confirm the authenticity of this signal. The carotenoid biomarkers indicate that the surface waters of the Hamersley Basin provided a sustained supply of hydrogen sulfide for anoxygenic photosynthesis and, indirectly, suggest the presence of precursor sulfate derived from the oxidative weathering of metal sulfides. Anbar A.D. et al. A whiff of oxygen

  19. A magnetic nanoparticle-clustering biosensor for blu-ray based optical detection of small-molecules

    DEFF Research Database (Denmark)

    Yang, Jaeyoung; Donolato, Marco; Antunes, Paula Soares Martins

    2014-01-01

    by adopting an inhibition mechanism. Next, frequency-dependent optical measurements enabled us to resolve signals depending on the cluster size. Lastly, a low-cost and miniaturized optical readout setup was established by implementing a Blu-ray pickup head. Consequently, our low-cost optical biosensor using...... dependent behavior of signals in micromolar ranges (Fig. 5). These results support that our MNP-clustering optical biosensor is capable of specific and quantitative detection of small-molecules....

  20. Coalescence control of elastomer clusters by fixed surface charges.

    Science.gov (United States)

    Gauer, Cornelius; Wu, Hua; Morbidelli, Massimo

    2010-02-04

    We studied the coalescence behavior of a fluorinated elastomer colloid, stabilized by fixed surface charges, with a glass transition temperature of about -20 degrees C, as a function of temperature under diffusion-limited cluster-cluster aggregation (DLCA) conditions. We first measured the aggregation kinetics by in situ dynamic light scattering and then simulated it through the Smoluchowski approach (i.e., population balance equations) using the only unknown parameter, the fractal dimension D(f) of the clusters, as the fit parameter. It was found that the estimated D(f) value increased as the temperature increased, starting from 1.7 at 25 degrees C and reaching the upper limit of 3.0 for T > or = 55 degrees C. These results indicate that the coalescence extent increases as the temperature increases. Such temperature-dependent coalescence behavior cannot be explained by thermodynamic considerations, and it must be related to a certain kinetic resistance. We explain this effect by considering the resistance of the fixed charges to relocation on the particle surface, which decreases as the temperature increases.

  1. Ab initio tensorial electronic friction for molecules on metal surfaces: Nonadiabatic vibrational relaxation

    Science.gov (United States)

    Maurer, Reinhard J.; Askerka, Mikhail; Batista, Victor S.; Tully, John C.

    2016-09-01

    Molecular adsorbates on metal surfaces exchange energy with substrate phonons and low-lying electron-hole pair excitations. In the limit of weak coupling, electron-hole pair excitations can be seen as exerting frictional forces on adsorbates that enhance energy transfer and facilitate vibrational relaxation or hot-electron-mediated chemistry. We have recently reported on the relevance of tensorial properties of electronic friction [M. Askerka et al., Phys. Rev. Lett. 116, 217601 (2016), 10.1103/PhysRevLett.116.217601] in dynamics at surfaces. Here we present the underlying implementation of tensorial electronic friction based on Kohn-Sham density functional theory for condensed phase and cluster systems. Using local atomic-orbital basis sets, we calculate nonadiabatic coupling matrix elements and evaluate the full electronic friction tensor in the Markov limit. Our approach is numerically stable and robust, as shown by a detailed convergence analysis. We furthermore benchmark the accuracy of our approach by calculation of vibrational relaxation rates and lifetimes for a number of diatomic molecules at metal surfaces. We find friction-induced mode-coupling between neighboring CO adsorbates on Cu(100) in a c (2 ×2 ) overlayer to be important for understanding experimental findings.

  2. Selection of conformational states in surface self-assembly for a molecule with eight possible pairs of surface enantiomers

    DEFF Research Database (Denmark)

    Nuermaimaiti, Ajiguli; Schultz-Falk, Vickie; Lind Cramer, Jacob

    2016-01-01

    Self-assembly of a molecule with many distinct conformational states, resulting in eight possible pairs of surface enantiomers, is investigated on a Au(111) surface under UHV conditions. The complex molecule is equipped with alkyl and carboxyl moieties to promote controlled self-assembly of lamel...

  3. Delta self-consistent field method to obtain potential energy surfaces of excited molecules on surfaces

    DEFF Research Database (Denmark)

    Gavnholt, Jeppe; Olsen, Thomas; Engelund, Mads;

    2008-01-01

    We present a modification of the Delta self-consistent field (Delta SCF) method of calculating energies of excited states in order to make it applicable to resonance calculations of molecules adsorbed on metal surfaces, where the molecular orbitals are highly hybridized. The Delta SCF approximation...... is a density-functional method closely resembling standard density-functional theory (DFT), the only difference being that in Delta SCF one or more electrons are placed in higher lying Kohn-Sham orbitals instead of placing all electrons in the lowest possible orbitals as one does when calculating the ground......-state energy within standard DFT. We extend the Delta SCF method by allowing excited electrons to occupy orbitals which are linear combinations of Kohn-Sham orbitals. With this extra freedom it is possible to place charge locally on adsorbed molecules in the calculations, such that resonance energies can...

  4. Tuning stamp surface energy for soft lithography of polar molecules to fabricate bioactive small-molecule microarrays.

    Science.gov (United States)

    Vaish, Amit; Shuster, Mitchell J; Cheunkar, Sarawut; Weiss, Paul S; Andrews, Anne M

    2011-05-23

    Soft-lithography-based techniques are widely used to fabricate microarrays. Here, the use of microcontact insertion printing is described, a soft-lithography method specifically developed for patterning at the dilute scales necessary for highly selective biorecognition. By carefully tuning the polar surface energy of polymeric stamps, problems associated with patterning hydrophilic tether molecules inserted into hydrophilic host self-assembled monolayers (SAMs) are surmounted. Both prefunctionalized tethers and on-chip functionalization of SAMs patterned by microcontact insertion printing enable the fabrication of small-molecule microarrays. Substrates patterned with the neurotransmitter precursor 5-hydroxytryptophan selectively capture a number of different types of membrane-associated receptor proteins, which are native binding partners evolved to recognize free serotonin. These advances provide new avenues for chemically patterning small molecules and fabricating small molecule microarrays with highly specific molecular recognition capabilities. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Proteomic and bioinformatic analysis of epithelial tight junction reveals an unexpected cluster of synaptic molecules

    Directory of Open Access Journals (Sweden)

    Tang Vivian W

    2006-12-01

    Full Text Available Abstract Background Zonula occludens, also known as the tight junction, is a specialized cell-cell interaction characterized by membrane "kisses" between epithelial cells. A cytoplasmic plaque of ~100 nm corresponding to a meshwork of densely packed proteins underlies the tight junction membrane domain. Due to its enormous size and difficulties in obtaining a biochemically pure fraction, the molecular composition of the tight junction remains largely unknown. Results A novel biochemical purification protocol has been developed to isolate tight junction protein complexes from cultured human epithelial cells. After identification of proteins by mass spectroscopy and fingerprint analysis, candidate proteins are scored and assessed individually. A simple algorithm has been devised to incorporate transmembrane domains and protein modification sites for scoring membrane proteins. Using this new scoring system, a total of 912 proteins have been identified. These 912 hits are analyzed using a bioinformatics approach to bin the hits in 4 categories: configuration, molecular function, cellular function, and specialized process. Prominent clusters of proteins related to the cytoskeleton, cell adhesion, and vesicular traffic have been identified. Weaker clusters of proteins associated with cell growth, cell migration, translation, and transcription are also found. However, the strongest clusters belong to synaptic proteins and signaling molecules. Localization studies of key components of synaptic transmission have confirmed the presence of both presynaptic and postsynaptic proteins at the tight junction domain. To correlate proteomics data with structure, the tight junction has been examined using electron microscopy. This has revealed many novel structures including end-on cytoskeletal attachments, vesicles fusing/budding at the tight junction membrane domain, secreted substances encased between the tight junction kisses, endocytosis of tight junction

  6. Large molecules on surfaces: deposition and intramolecular STM manipulation by directional forces

    Science.gov (United States)

    Grill, Leonhard

    2010-03-01

    Intramolecular manipulation of single molecules on a surface with a scanning tunnelling microscope enables the controlled modification of their structure and, consequently, their physical and chemical properties. This review presents examples of intramolecular manipulation experiments with rather large molecules, driven by directional, i.e. chemical or electrostatic, forces between tip and molecule. It is shown how various regimes of forces can be explored and characterized with one and the same manipulation of a single molecule by changing the tip-surface distance. Furthermore, different deposition techniques under ultrahigh vacuum conditions are discussed because the increasing functionality of such molecules can lead to fragmentation during the heating step, making their clean deposition difficult.

  7. Hovering and Twirling of Tethered Molecules by Confinement between Surfaces.

    Science.gov (United States)

    Rios, Laura; Lee, Joonhee; Tallarida, Nicholas; Apkarian, V Ara

    2016-07-07

    Through STM images, we show that azobenzene-terminated alkanethiols hover and twirl when confined between the Ag tip and Au(111) substrate of an STM junction. In contrast with mechanisms of activation used to drive molecular rotors, twirling is induced by the effective elimination of lateral corrugation in the energy landscape when molecules hover by their van der Waals attraction to the approaching tip. While in the stationary state the benzenes of the head group lie flat with an inter-ring separation of 7.5 Å, they stand on-edge as the molecule twirls and their separation contracts to 5.2 Å, close to the value of the free molecule. The captured images of motion allow the characterization of physisorption potentials.

  8. Structural Integrity of Single - Molecules on Metal Surfaces with Different Reactivity

    Science.gov (United States)

    Fahrendorf, Sarah; Matthes, Frank; Bürgler, Daniel E.; Schneider, Claus M.; Atodiresei, Nicolae; Caciuc, Vasile; Blügel, Stefan; Besson, Claire; Kögerler, Paul

    2014-07-01

    Magnetic molecules are auspicious candidates to act as functional units in molecular spintronics. Integrating molecules into a device environment providing mechanical support and electrical contacts requires their deposition as intact entities onto substrates. Thermal sublimation is a very clean deposition process that, however, thermally decomposes molecules of insufficient stability leading to the deposition of molecular fragments. Here, we show that the molecule-surface interaction of chemisorbed molecules affects the intramolecular bonding and can lead depending on the surface reactivity to either molecular decomposition or enhanced stability. We study the integrity of single bis(phthalocyaninato)-neodymium(III) molecules (NdPc2) deposited by sublimation on differently reactive surfaces, namely Au(111), Cu(100), and two atomic layers of Fe on W(110), on the single molecular level by scanning tunneling microscopy (STM) and spectroscopy. We find a strongly substrate-dependent tendency of the NdPc2 molecules to decompose into two Pc molecules. Surprisingly, the most reactive Fe/W(110) surface shows the lowest molecular decomposition probability, whereas there are no intact NdPc2 molecules at all on the least reactive Au(111) surface. We attribute these findings to substrate-dependent partial charge transfer from the substrate to the Pc ligands of the molecule, which strengthens the intramolecular bonding mediated predominantly by electrostatic interaction.

  9. One-end immobilization of individual DNA molecules on a functional hydrophobic glass surface.

    Science.gov (United States)

    Matsuura, Shun-ichi; Kurita, Hirofumi; Nakano, Michihiko; Komatsu, Jun; Takashima, Kazunori; Katsura, Shinji; Mizuno, Akira

    2002-12-01

    We demonstrate an effective method for DNA immobilization on a hydrophobic glass surface. The new DNA immobilizing technique is extremely simple compared with conventional techniques that require heterobifunctional crosslinking reagent between DNA and substrate surface that are both modified chemically. In the first process, a coverslip was treated with dichlorodimethylsilane resulting in hydrophobic surface. lambda DNA molecules were ligated with 3'-terminus disulfide-modified 14 mer oligonucleotides at one cohesive end. After reduction of the disulfide to sulfhydryl (thiol) groups the resulting thiol-modified lambda DNA molecules were reacted on silanized coverslip. Fluorescent observation showed that the thiol-modified lambda DNA molecules were anchored specifically to the hydrophobic surface at one terminus, although non-specific binding of the DNA molecules was suppressed. It was observed that the one-end-attached DNA molecule was bound firmly to the surface and stretched reversibly in one direction when a d.c. electric field was applied.

  10. Bonding in Mercury Molecules Described by the Normalized Elimination of the Small Component and Coupled Cluster Theory

    NARCIS (Netherlands)

    Cremer, Dieter; Kraka, Elfi; Filatov, Michael

    2008-01-01

    Bond dissociation energies (BDEs) of neutral HgX and cationic HgX(+) molecules range from less than a kcal mol(-1) to as much as 60 kcal mol(-1). Using NESCICCCSD(T) [normalized elimination of the small component and coupled-cluster theory with all single and double excitations and a perturbative tr

  11. Bonding in Mercury Molecules Described by the Normalized Elimination of the Small Component and Coupled Cluster Theory

    NARCIS (Netherlands)

    Cremer, Dieter; Kraka, Elfi; Filatov, Michael

    2008-01-01

    Bond dissociation energies (BDEs) of neutral HgX and cationic HgX(+) molecules range from less than a kcal mol(-1) to as much as 60 kcal mol(-1). Using NESCICCCSD(T) [normalized elimination of the small component and coupled-cluster theory with all single and double excitations and a perturbative

  12. Measuring Complementary Electronic Structure Properties of both Deposited and Gas Phase Clusters using STM, UPS, and PES: Size-Selected Clusters on Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Bowen, Kit H.

    2014-03-05

    In this project, we studied size-selected cluster interactions with surfaces, with other clusters on surfaces, and with external stimuli. These studies focused on mobility as a function of cluster size, surface morphologies as a function of composition and coverage, ion-induced modification and reactivity of clusters as a function of composition, the structural evolution of cluster cuboids culminating in the characterization of theoretically-predicted “baby crystal” clusters, and unusual fractal pattern formation due to deposition.

  13. Advances on the nanostructuration of magnetic molecules on surfaces: the case of single-molecule magnets (SMM).

    Science.gov (United States)

    Gómez-Segura, Jordi; Veciana, Jaume; Ruiz-Molina, Daniel

    2007-09-28

    SMMs exhibit slow magnetization relaxation rates characteristic of nanodomain particles whose origin is however on individual molecules. For this reason, they have attracted much interest due to their potential applications in high-density information storage devices and quantum computing applications, where for instance, each molecule can be used as a magnetic bit of information. However, for this to become a reality, several basic studies such as their deposition on surfaces are still highly required. Here we will revise all the experimental approximations that have been so far reported for their addressing, nanostructuration and study on surfaces, from the use of stamps as templates to their anchorage to gold surface through the use of thiol-based ligands. It is also important to emphasize that the results and methodologies described along this review are applicable not only to SMMs but to any molecular material.

  14. Substrate-mediated interactions and intermolecular forces between molecules adsorbed on surfaces.

    Science.gov (United States)

    Sykes, E Charles H; Han, Patrick; Kandel, S Alex; Kelly, Kevin F; McCarty, Gregory S; Weiss, Paul S

    2003-12-01

    Adsorbate interactions and reactions on metal surfaces have been investigated using scanning tunneling microscopy. The manners in which adsorbates perturb the surface electronic structure in their vicinity are discussed. The effects these perturbations have on other molecules are shown to be important in overlayer growth. Interactions of molecules with surface steps are addressed, and each molecule's electron affinity is shown to dictate its adsorption sites at step edges. Standing waves emanating from steps are demonstrated to effect transient molecular adsorption up to 40 A away from the step edge. Halobenzene derivatives are used to demonstrate how the surface is important in aligning reactive intermediates.

  15. Matrix formulae and skein relations for cluster algebras from surfaces

    CERN Document Server

    Musiker, Gregg

    2011-01-01

    This paper concerns cluster algebras with principal coefficients A(S,M) associated to bordered surfaces (S,M), and is a companion to a concurrent work of the authors with Schiffler [MSW2]. Given any (generalized) arc or loop in the surface -- with or without self-intersections -- we associate an element of (the fraction field of) A(S,M), using products of elements of PSL_2(R). We give a direct proof that our matrix formulas for arcs and loops agree with the combinatorial formulas for arcs and loops in terms of matchings, which were given in [MSW, MSW2]. Finally, we use our matrix formulas to prove skein relations for the cluster algebra elements associated to arcs and loops. Our matrix formulas and skein relations generalize prior work of Fock and Goncharov [FG1, FG2, FG3], who worked in the coefficient-free case. The results of this paper will be used in [MSW2] in order to show that certain collections of arcs and loops comprise a vector-space basis for A(S,M).

  16. Single-molecule chemistry of metal phthalocyanine on noble metal surfaces.

    Science.gov (United States)

    Li, Zhenyu; Li, Bin; Yang, Jinlong; Hou, Jian Guo

    2010-07-20

    To develop new functional materials and nanoscale electronics, researchers would like to accurately describe and precisely control the quantum state of a single molecule on a surface. Scanning tunneling microscopy (STM), combined with first-principles simulations, provides a powerful technique for acquiring this level of understanding. Traditionally, metal phthalocyanine (MPc) molecules, composed of a metal atom surrounded by a ligand ring, have been used as dyes and pigments. Recently, MPc molecules have shown great promise as components of light-emitting diodes, field-effect transistors, photovoltaic cells, and single-molecule devices. In this Account, we describe recent research on the characterization and control of adsorption and electronic states of a single MPc molecule on noble metal surfaces. In general, the electronic and magnetic properties of a MPc molecule largely depend on the type of metal ion within the phthalocyanine ligand and the type of surface on which the molecule is adsorbed. However, with the STM technique, we can use on-site molecular "surgery" to manipulate the structure and the properties of the molecule. For example, STM can induce a dehydrogenation reaction of the MPc, which allows us to control the Kondo effect, which describes the spin polarization of the molecule and its interaction with the complex environment. A specially designed STM tip can allow researchers to detect certain molecule-surface hybrid states that are not accessible by other techniques. By matching the local orbital symmetry of the STM tip and the molecule, we can generate the negative differential resistance effect in the formed molecular junction. This orbital symmetry based mechanism is extremely robust and does not critically depend on the geometry of the STM tip. In summary, this simple model system, a MPc molecule absorbed on a noble metal surface, demonstrates the power of STM for quantum characterization and manipulation of single molecules, highlighting the

  17. Multilayer adsorption mechanism of coal surface adsorption to three oxygen molecule

    Institute of Scientific and Technical Information of China (English)

    WANG Xue-feng; LI Zhi-gang; WANG Xin-yang; SUN Yan-qiu

    2008-01-01

    Compared chemical bonds change situation of coal surface and oxygen mole-cules before and after coal surface adsorption to three oxygen molecules, after adsorption each oxygen molecule's chemical bond got longer, but had not broken, the coal surface's chemical bonds changed a little. It proves that the coal surface adsorption to five oxygen molecules is the physical adsorption and is the multilayer adsorption according to the op-timized geometry structure. The oxygen molecule's bond length that adsorbed by the side chain of coal surface changes most from 1.258 2×10-10 m to 1.316 8×10-10 m, which indi-cates this oxygen molecular to be the liveliest. The analysis of charge population reveals that how many electrons shift in the atom is directly proportional to the change of chemical bonds. The more electrons shift in the atom, the more molecule chemical bond changes. In the adsorption state, which is composed of coal surface and five oxygen molecules, the vibration frequency of oxygen molecules drops off, and the adsorption energy reached by calculation is 202.11 kJ/mol.

  18. Multilayer adsorption mechanism of coal surface adsorption to three oxygen molecule

    Institute of Scientific and Technical Information of China (English)

    WANG Xue-feng; LI Zhi-gang; WANG Xin-yang; SUN Yan-qiu

    2008-01-01

    Compared chemical bonds change situation of coal surface and oxygen mole-cules before and after coal surface adsorption to three oxygen molecules,after adsorption each oxygen molecule's chemical bond got longer,but had not broken,the coal surface's chemical bonds changed a little.It proves that the coal surface adsorption to five oxygen molecules is the physical adsorption and is the multilayer adsorption according to the optimized geometry structure.The oxygen molecule's bond length that adsorbed by the side chain of coal surface changes most from 1.258 2×10 10 m to 1.316 8×10 10 m,which indicates this oxygen molecular to be the liveliest.The analysis of charge population reveals that how many electrons shift in the atom is directly proportional to the change of chemical bonds.The more electrons shift in the atom,the more molecule chemical bond changes.In the adsorption state,which is composed of coal surface and five oxygen molecules,the vibration frequency of oxygen molecules drops off,and the adsorption energy reached by calculation is 202.11 kJ/mol.

  19. Spontaneous dissociation of a conjugated molecule on the Si(100) surface

    DEFF Research Database (Denmark)

    Lin, Rong; Galili, Michael; Quaade, Ulrich

    2002-01-01

    The adsorption mechanism of alpha-sexithiophene (alpha-6T) on the clean Si(100)-(2x1) surface has been investigated using scanning tunneling microscopy (STM) and first principles electronic structure calculations. We find that at submonolayer coverage, the alpha-6T molecules are not stable...... and dissociate into monomers. We observe two different configurations of the monomers and have discussed the corresponding adsorption geometries based on theoretical calculations. The calculations elucidate how the fragments are absorbed on the surface, giving rise to the observed STM images. With increasing...... coverage, the STM images show the existence of complete alpha-6T molecules. In addition, results of the adsorption behavior of alpha-6T molecules on the H-passivated Si(100)-(2x1) surface are reported. On this surface the molecules are highly mobile at room temperature due to the weak molecule...

  20. Stability of two-dimensional clusters on crystal surfaces: from Ostwald ripening to single-cluster decay

    NARCIS (Netherlands)

    Rosenfeld, G.; Morgenstern, Karina; Beckmann, Ingo; Wulfhekel, Wulf; Wulfhekel, W.C.U.; Laegsgaard, Erik; Besenbacher, Flemming; Comsa, George

    1998-01-01

    An overview is given of recent work on the decay of two-dimensional clusters on a Ag(111) surface. Experimental studies using scanning tunnelling microscopy are presented, and various approaches to extract quantitative information on the relevant atomic processes from cluster decay experiments are

  1. Hidden force stiffening molecular clusters, surface skins, and ultrathin films of water

    CERN Document Server

    Sun, Chang Q

    2013-01-01

    A slight, molecular-undercoordination-induced contraction of the stiffer O-H real-bond and a significant, inter-electron-pair repulsion driven, elongation of the softer H:O non-bond, and the associated stiffness relaxation, of the segmented O-H:O bond, are recognized as the key to stiffening molecular clusters, surface skins, and ultrathin films of water. Agreement between calculations and measurements verified our expectations that the shortened-and-stiffened real-bond stiffens the stiffer phonons (>3000 cm-1), densifies bonding electrons, entraps binding energy, and elevates the melting point and hence the viscosity, surface tension, and elasticity, and that the lengthened-and-softened non-bond softens the softer phonons (<300 cm-1), expands the volume, and polarizes the electron pairs of the undercoordinated molecules in freestanding and encapsuled clusters, water surfaces, and ultrathin films that exhibit ice- or glue-like and hydrophobic nature at the ambient. This effect becomes more significant as N...

  2. A refined cluster-in-molecule local correlation approach for predicting the relative energies of large systems.

    Science.gov (United States)

    Li, Wei; Guo, Yang; Li, Shuhua

    2012-06-07

    A refined cluster-in-molecule (CIM) method for local correlation calculations of large molecules is presented. In the present work, two new strategies are introduced to further improve the CIM approach: (1) Some medium-range electron correlation energies, which are neglected in the previous CIM approach, are taken into account. (2) A much simpler procedure using only a distance threshold is used to construct various clusters. To cover the medium-range correlation effect as much as possible, some two-atom-centered clusters are built, in addition to one-atom-centered clusters. Our test calculations at the second order perturbation theory (MP2) level show that the refined CIM method can recover about 99.9% of the conventional MP2 correlation energy using an appropriate distance threshold. The accuracy of the present CIM method is capable of providing reliable relative energies of medium-sized systems such as polyalanines with 10 residues, and water molecules with 50 water molecules. For polyalanines with up to 30 residues, we have demonstrated that the computational cost of the CIM-MP2 calculation increases linearly with the molecular size, but the required memory and disc-space do not need to increase for large systems. The improved CIM method has been used to compute the relative energy of ice-like (H(2)O)(96) clusters (with 2400 basis functions) and to predict the dimerization energy of a double-helical foldamer (with 2330 basis functions). The present CIM method is expected to be a practical local correlation method for describing the relative energies of large systems.

  3. Potential energy surfaces and reaction dynamics of polyatomic molecules

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Yan-Tyng.

    1991-11-01

    A simple empirical valence bond (EVB) model approach is suggested for constructing global potential energy surfaces for reactions of polyatomic molecular systems. This approach produces smooth and continuous potential surfaces which can be directly utilized in a dynamical study. Two types of reactions are of special interest, the unimolecular dissociation and the unimolecular isomerization. For the first type, the molecular dissociation dynamics of formaldehyde on the ground electronic surface is investigated through classical trajectory calculations on EVB surfaces. The product state distributions and vector correlations obtained from this study suggest very similar behaviors seen in the experiments. The intramolecular hydrogen atom transfer in the formic acid dimer is an example of the isomerization reaction. High level ab initio quantum chemistry calculations are performed to obtain optimized equilibrium and transition state dimer geometries and also the harmonic frequencies.

  4. Surface functionalization of bioactive glasses with natural molecules of biological significance, Part I: Gallic acid as model molecule

    Science.gov (United States)

    Zhang, Xin; Ferraris, Sara; Prenesti, Enrico; Verné, Enrica

    2013-12-01

    Gallic acid (3,4,5-trihydroxybenzoic acid, GA) and its derivatives are a group of biomolecules (polyphenols) obtained from plants. They have effects which are potentially beneficial to heath, for example they are antioxidant, anticarcinogenic and antibacterial, as recently investigated in many fields such as medicine, food and plant sciences. The main drawbacks of these molecules are both low stability and bioavailability. In this research work the opportunity to graft GA to bioactive glasses is investigated, in order to deliver the undamaged biological molecule into the body, using the biomaterial surfaces as a localized carrier. GA was considered for functionalization since it is a good model molecule for polyphenols and presents several interesting biological activities, like antibacterial, antioxidant and anticarcinogenic properties. Two different silica based bioactive glasses (SCNA and CEL2), with different reactivity, were employed as substrates. UV photometry combined with the Folin&Ciocalteu reagent was adopted to test the concentration of GA in uptake solution after functionalization. This test verified how much GA consumption occurred with surface modification and it was also used on solid samples to test the presence of GA on functionalized glasses. XPS and SEM-EDS techniques were employed to characterize the modification of material surface properties and functional group composition before and after functionalization.

  5. Probing characteristics of collagen molecules on various surfaces via atomic force microscopy

    Science.gov (United States)

    Su, Hao-Wei; Ho, Mon-Shu; Cheng, Chao-Min

    2012-06-01

    We examine, herein, specific dynamic responses of collagen molecules (i.e., observations of self-assembly and nanometric adhesion force measurements of type-I collagen molecules) as they interact with either a hydrophobic or a hydrophilic surface at two distinct temperatures, using a liquid-type atomic force microscope. We conclude that, regardless of surface hydrophobicity/hydrophilicity, assembled microfibrils eventually distribute homogeneously in accordance with changes in surface-related mechanical properties of collagen molecules at different self-assembly stages.

  6. H2 Molecular Clusters with Embedded Molecules and Atoms as the Source of the Diffuse Interstellar Bands

    Science.gov (United States)

    Bernstein, L. S.; Clark, F. O.; Lynch, D. K.

    2013-05-01

    We suggest that the diffuse interstellar bands (DIBs) arise from absorption lines of electronic transitions in molecular clusters primarily composed of a single molecule, atom, or ion ("seed"), embedded in a single-layer shell of H2 molecules. Less abundant variants of the cluster, including two seed molecules and/or a two-layer shell of H2 molecules, may also occur. The lines are broadened, blended, and wavelength-shifted by interactions between the seed and surrounding H2 shell. We refer to these clusters as contaminated H2 clusters (CHCs). We show that CHC spectroscopy matches the diversity of observed DIB spectral profiles and provides good fits to several DIB profiles based on a rotational temperature of 10 K. CHCs arise from ~centimeter-sized, dirty H2 ice balls, called contaminated H2 ice macro-particles (CHIMPs), formed in cold, dense, giant molecular clouds (GMCs), and later released into the interstellar medium (ISM) upon GMC disruption. Attractive interactions, arising from Van der Waals and ion-induced dipole potentials, between the seeds and H2 molecules enable CHIMPs to attain centimeter-sized dimensions. When an ultraviolet (UV) photon is absorbed in the outer layer of a CHIMP, it heats the icy matrix and expels CHCs into the ISM. While CHCs are quickly destroyed by absorbing UV photons, they are replenished by the slowly eroding CHIMPs. Since CHCs require UV photons for their release, they are most abundant at, but not limited to, the edges of UV-opaque molecular clouds, consistent with the observed, preferred location of DIBs. An inherent property of CHCs, which can be characterized as nanometer size, spinning, dipolar dust grains, is that they emit in the radio-frequency region. We also show that the CHCs offer a natural explanation for the anomalous microwave emission feature in the ~10-100 GHz spectral region.

  7. Modeling of helix molecules formation on a surface of nanotube and inside it

    Directory of Open Access Journals (Sweden)

    Belolipetskaya Anna

    2017-01-01

    Full Text Available “On-surface” synthesis of large molecules and assemblies is a great challenge in molecular electronics, biomedical devices, sensors, energy harnessing and catalysis. Usually, plane surfaces are used for these purposes. We study a possibility of macro molecules formation on the surface of nanotube and inside it. It can be used for synthesis of helix molecules, particularly, organic and biological. Nanotubes of different structures were considered. Point-like approximation is used for atoms. The Lennard-Jones 6-12 potential is taken as the interaction potential. Possibilities of helix molecules and ring-like molecules formations were shown. A hypothesis of such processes influence on the organic molecules formation during the early Earth history is suggested and discussed.

  8. Surface structure and stability of MoSx model clusters.

    Science.gov (United States)

    Wen, Xiao-Dong; Zeng, Tao; Li, Yong-Wang; Wang, Jianguo; Jiao, Haijun

    2005-10-01

    Density functional theory (DFT) computations have been carried out to study the structure and stability of MoSx clusters with the change of sulfur coverage at both Mo and S edges. DFT shows that adding sulfur to the Mo edge is always exothermic. However, deleting corner sulfur from the S edge is exothermic for 67 and 50% sulfur coverages, while deleting edge sulfur from the S edge is endothermic for 33 and 0% sulfur coverages. On the basis of the computed free energies along a wide range of H2S/H2 ratios, it is found that there are two stable structures with 33 and 50% sulfur coverages on the Mo edge by having 100% sulfur coverage on the S edge and one stable structure with 67% sulfur coverage on the S edge by having 0% sulfur coverage on the Mo edge. Under fully sulfiding atmosphere or at a very high H2S/H2 ratio, triangle MoSx structures with 100% sulfur coverage on the Mo edge are computed to be more stable than those with 100% sulfur coverage on the S edge, in agreement with the observation of scanning tunneling microscopy. In addition, the effects of cluster sizes on the surface structures are discussed.

  9. Computer simulation structure and vibrations of small metal cluster on the Cu (111) surface

    Science.gov (United States)

    Borisova, Svetlana D.; Rusina, Galina G.

    2015-10-01

    Vibrational properties of the small tetrahedral cluster of Co on the Cu (111) surface are studied by using tight-binding second moment approximation interatomic interaction potentials. It was shown that interaction of the clusters with substrate leads to arising of frustrated translation and frustrated rotation in-plane polarized vibrational modes localized on the cluster atoms. The Co4 cluster on the surface the high frequency modes remain strongly localized and mixed with the nearest neighbor atoms vibrations.

  10. Computer simulation structure and vibrations of small metal cluster on the Cu (111) surface

    Energy Technology Data Exchange (ETDEWEB)

    Borisova, Svetlana D., E-mail: svbor@ispms.tsc.ru; Rusina, Galina G., E-mail: rusina@ispms.tsc.ru [Institute of Strength Physics and Materials Science SB RAS, Tomsk, 634055 (Russian Federation); National Research Tomsk State University, Tomsk 634050 (Russian Federation)

    2015-10-27

    Vibrational properties of the small tetrahedral cluster of Co on the Cu (111) surface are studied by using tight-binding second moment approximation interatomic interaction potentials. It was shown that interaction of the clusters with substrate leads to arising of frustrated translation and frustrated rotation in-plane polarized vibrational modes localized on the cluster atoms. The Co{sub 4} cluster on the surface the high frequency modes remain strongly localized and mixed with the nearest neighbor atoms vibrations.

  11. Cluster-induced desorption from metal organic surfaces: Structural effects

    Energy Technology Data Exchange (ETDEWEB)

    Delcorte, A., E-mail: arnaud.delcorte@uclouvain.be [Institute of Condensed Matter and Nanosciences, Université catholique de Louvain, 1 Croix du Sud, B-1348 Louvain-la-Neuve (Belgium); Hoecke, E. van; Restrepo, O.A. [Institute of Condensed Matter and Nanosciences, Université catholique de Louvain, 1 Croix du Sud, B-1348 Louvain-la-Neuve (Belgium)

    2013-05-15

    Molecular dynamics (MD) simulations are used to model the 10 keV bombardment of Au-nanoparticle (NP)-covered polymeric samples by Ga, C{sub 60} and Au{sub 400} projectiles, at normal incidence. While the presence of the Au-NPs tends to enhance the organic material emission upon Ga and Au{sub 400} bombardment, as a result of increased projectile stopping, it strongly reduces the organic emission upon C{sub 60} bombardment because of the projectile reflection. Our results show that these trends are valid for kDa polymers (which can be emitted intact) as well as for virtually infinite length chains (which require fragmentation), but that the polymer sputtered mass is consistently >3 times larger in the case of the kDa molecules for all impact points and projectiles. Using a series of samples, it is also shown that embedding the Au-NPs in the organic material leads to completely different results, with, upon C{sub 60} bombardment, the largest sputtered masses observed for impacts above the NPs. For Au{sub 400} bombardment, the burial of the Au-NPs leads to comparatively lower sputtered masses. These new results demonstrate the complexity of the sputtering of nanostructured hybrid materials by cluster projectiles and suggest various artifacts that should complicate the analysis and depth profiling of such materials.

  12. Optical detection of single non-absorbing molecules using the surface plasmon of a gold nanorod

    CERN Document Server

    Zijlstra, Peter; Orrit, Michel

    2012-01-01

    Current optical detection schemes for single molecules require light absorption, either to produce fluorescence or direct absorption signals. This severely limits the range of molecules that can be detected, because most molecules are purely refractive. Metal nanoparticles or dielectric resonators detect non-absorbing molecules by a resonance shift in response to a local perturbation of the refractive index, but neither has reached single-protein sensitivity. The most sensitive plasmon sensors to date detect single molecules only when the plasmon shift is amplified by a highly polarizable label or by a localized precipitation reaction on the particle's surface. Without amplification, the sensitivity only allows for the statistical detection of single molecules. Here we demonstrate plasmonic detection of single molecules in realtime, without the need for labeling or amplification. We monitor the plasmon resonance of a single gold nanorod with a sensitive photothermal assay and achieve a ~ 700-fold increase in ...

  13. Elasticity Dominated Surface Segregation of Small Molecules in Polymer Mixtures

    Science.gov (United States)

    Krawczyk, Jarosław; Croce, Salvatore; McLeish, T. C. B.; Chakrabarti, Buddhapriya

    2016-05-01

    We study the phenomenon of migration of the small molecular weight component of a binary polymer mixture to the free surface using mean field and self-consistent field theories. By proposing a free energy functional that incorporates polymer-matrix elasticity explicitly, we compute the migrant volume fraction and show that it decreases significantly as the sample rigidity is increased. A wetting transition, observed for high values of the miscibility parameter can be prevented by increasing the matrix rigidity. Estimated values of the bulk modulus suggest that the effect should be observable experimentally for rubberlike materials. This provides a simple way of controlling surface migration in polymer mixtures and can play an important role in industrial formulations, where surface migration often leads to decreased product functionality.

  14. Nanocoating of titanium implant surfaces with organic molecules. Polysaccharides including glycosaminoglycans

    DEFF Research Database (Denmark)

    Gurzawska, Katarzyna; Svava, Rikke; Jørgensen, Niklas Rye

    2012-01-01

    and roughness. This influences cell behaviour on the surface such as adhesion, proliferation and differentiation of cells as well as the mineralization of the extracellular matrix at the implant surfaces. The aim of the present systematic review was to describe organic molecules used for surface nanocoating...

  15. Anchoring of organic molecules to a metal surface: HtBDC on Cu(110)

    DEFF Research Database (Denmark)

    Schunack, M.; Petersen, L.; Kuhnle, A.

    2001-01-01

    The interaction of largish molecules with metal surfaces has been studied by combining the imaging and manipulation capabilities of the scanning tunneling microscope (STM). At the atomic scale, the STM results directly reveal that the adsorption of a largish organic molecule can induce a restruct...

  16. Formation of self-assembled monolayer of curcuminoid molecules on gold surfaces

    Science.gov (United States)

    Berlanga, Isadora; Etcheverry-Berríos, Álvaro; Mella, Andy; Jullian, Domingo; Gómez, Victoria Alejandra; Aliaga-Alcalde, Núria; Fuenzalida, Victor; Flores, Marcos; Soler, Monica

    2017-01-01

    We investigated the formation of self-assembled monolayers of two thiophene curcuminoid molecules, 2-thphCCM (1) and 3-thphCCM (2), on polycrystalline gold substrates prepared by immersion of the surfaces in a solution of the molecules during 24 h. The functionalized surfaces were studied by scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS). Despite the fact that both molecules have the same composition and almost the same structure, these molecules exhibit different behavior on the gold surface, which can be explained by the different positions of the sulfur atoms in the terminal aromatic rings. In the case of molecule 1, the complete formation of a SAM can be observed after 24 h of immersion. In the case of molecule 2, the transition from flat-lying to upright configuration on the surface is still in process after 24 h of immersion. This is attributed to the fact that molecule 2 have the sulfur atoms more exposed than molecule 1.

  17. Renormalization of Optical Excitations in Molecules near a Metal Surface

    DEFF Research Database (Denmark)

    García Lastra, Juan Maria; Thygesen, Kristian Sommer

    2011-01-01

    The lowest electronic excitations of benzene and a set of donor-acceptor molecular complexes are calculated for the gas phase and on the Al(111) surface using the many-body Bethe-Salpeter equation. The energy of the charge-transfer excitations obtained for the gas phase complexes are found to be ...

  18. Photoactive Fluoropolymer Surfaces that Release Sensitizer Drug Molecules

    Science.gov (United States)

    Ghosh, Goutam; Minnis, Mihaela; Ghogare, Ashwini A.; Abramova, Inna; Cengel, Keith; Busch, Theresa M.; Greer, Alexander

    2015-01-01

    We describe a physical-organic study of two fluoropolymers bearing a photoreleasable PEGylated photosensitizer which generates 1O2(1Δg) [chlorin e6 methoxy tri(ethylene glycol) triester]. The surfaces are Teflon/polyvinylalcohol (PVA) nanocomposite and fluorinated silica. The relative efficiency of these surfaces to photorelease the PEGylated sensitizer [shown previously to be phototoxic to ovarian cancer cells (Kimani, S. et al J. Org. Chem 2012, 77, 10638)] was slightly higher for the nanocomposite. In the presence of red light and O2, 1O2 is formed, which cleaves an ethene linkage to liberate the sensitizer in 68–92% yields. The fluoropolymers were designed to deal with multiple problems. Namely, their success relied not only high O2 solubility and drug repellency, but that the C−F bonds physically quench little 1O2 for its productive use away from the surface. The results obtained here indicate that Teflon-like surfaces have potential uses of delivering sensitizer and singlet oxygen for applications in tissue repair and photodynamic therapy (PDT). PMID:25686407

  19. Photoactive fluoropolymer surfaces that release sensitizer drug molecules.

    Science.gov (United States)

    Ghosh, Goutam; Minnis, Mihaela; Ghogare, Ashwini A; Abramova, Inna; Cengel, Keith A; Busch, Theresa M; Greer, Alexander

    2015-03-12

    We describe a physical-organic study of two fluoropolymers bearing a photoreleasable PEGylated photosensitizer that generates (1)O2((1)Δg) [chlorin e6 methoxy tri(ethylene glycol) triester]. The surfaces are Teflon/poly(vinyl alcohol) (PVA) nanocomposite and fluorinated silica. The relative efficiency of these surfaces to photorelease the PEGylated sensitizer [shown previously to be phototoxic to ovarian cancer cells (Kimani, S. et al. J. Org. Chem 2012, 77, 10638)] was slightly higher for the nanocomposite. In the presence of red light and O2, (1)O2 is formed, which cleaves an ethene linkage to liberate the sensitizer in 68-92% yield. The fluoropolymers were designed to deal with multiple problems. Namely, their success relied not only on high O2 solubility and drug repellency but also on the C-F bonds, which physically quench little (1)O2, for singlet oxygen's productive use away from the surface. The results obtained here indicate that Teflon-like surfaces have potential uses in delivering sensitizer and singlet oxygen for applications in tissue repair and photodynamic therapy (PDT).

  20. Is the effect of surface modifying molecules on antibacterial activity universal for a given material?

    Science.gov (United States)

    Hsu, Alexander; Liu, Fangzhou; Leung, Yu Hang; Ma, Angel P. Y.; Djurišić, Aleksandra B.; Leung, Frederick C. C.; Chan, Wai Kin; Lee, Hung Kay

    2014-08-01

    Antibacterial activity of nanomaterials is strongly dependent on their properties, and their stability and toxicity can be varied using surface coatings. We investigated the effect of different surface modifying molecules on the antibacterial properties of two ZnO nanoparticle samples. We found that the starting surface properties of the nanoparticles have significant effects on the attachment of the surface modifying molecules and consequent antibacterial activity. Two out of five investigated surface modifying molecules not only had a significant difference in the magnitude of their effect on different nanoparticles, but also resulted in the opposite effects on two ZnO nanoparticle samples (an enhancement of antibacterial activity for one and a reduction of antibacterial activity for the other ZnO sample). This indicates that no general rule on the effect of a specific molecule on the toxicity of a metal oxide nanoparticle can be derived without knowing the nanoparticle properties, due to the fact that surface modifier attachment onto the surface is affected by the initial surface properties.Antibacterial activity of nanomaterials is strongly dependent on their properties, and their stability and toxicity can be varied using surface coatings. We investigated the effect of different surface modifying molecules on the antibacterial properties of two ZnO nanoparticle samples. We found that the starting surface properties of the nanoparticles have significant effects on the attachment of the surface modifying molecules and consequent antibacterial activity. Two out of five investigated surface modifying molecules not only had a significant difference in the magnitude of their effect on different nanoparticles, but also resulted in the opposite effects on two ZnO nanoparticle samples (an enhancement of antibacterial activity for one and a reduction of antibacterial activity for the other ZnO sample). This indicates that no general rule on the effect of a specific

  1. The Partial Density of States of CO2 Molecules Adsorption on the Fe (111) Surface

    Science.gov (United States)

    Wu, Junfang

    2017-09-01

    The state of CO2 molecules adsorption on Fe (111) surface is studied by simulation with the software, the partial density of states the adsorption is obtained. Through the graphical distribution, the pseudogap and the partial density of states at the Fermi level of the CO2 molecules adsorption on the Fe (111) surface is analyzed and compared. The key mechanism of CO2 molecules adsorption on the Fe (111) surface is revealed. The results showed that the CO2 molecules adsorption on the bridge position of Fe (111) surface is stable. The main reason of O atom and Fe atom combining with the bonding is that the resonance of the density of states happed between the O 2p orbital and Fe 3d orbital.

  2. Mapping lipid and detergent molecules at the surface of membrane proteins.

    Science.gov (United States)

    Cogdell, Richard J; Gardiner, Alastair T; Roszak, Aleksander W; Stončius, Sigitas; Kočovský, Pavel; Isaacs, Neil W

    2011-06-01

    Electron-density maps for the crystal structures of membrane proteins often show features suggesting binding of lipids and/or detergent molecules on the hydrophobic surface, but usually it is difficult to identify the bound molecules. In our studies, heavy-atom-labelled phospholipids and detergents have been used to unequivocally identify these binding sites at the surfaces of test membrane proteins, the reaction centres from Rhodobacter sphaeroides and Blastochloris viridis. The generality of this method is discussed in the present article.

  3. Porous silicon Bloch surface and sub-surface wave structure for simultaneous detection of small and large molecules

    Science.gov (United States)

    Rodriguez, Gilberto A.; Lonai, John D.; Mernaugh, Raymond L.; Weiss, Sharon M.

    2014-08-01

    A porous silicon (PSi) Bloch surface wave (BSW) and Bloch sub-surface wave (BSSW) composite biosensor is designed and used for the size-selective detection of both small and large molecules. The BSW/BSSW structure consists of a periodic stack of high and low refractive index PSi layers and a reduced optical thickness surface layer that gives rise to a BSW with an evanescent tail that extends above the surface to enable the detection of large surface-bound molecules. Small molecules were detected in the sensor by the BSSW, which is a large electric field intensity spatially localized to a desired region of the Bragg mirror and is generated by the implementation of a step or gradient refractive index profile within the Bragg mirror. The step and gradient BSW/BSSW sensors are designed to maximize both resonance reflectance intensity and sensitivity to large molecules. Size-selective detection of large molecules including latex nanospheres and the M13KO7 bacteriophage as well as small chemical linker molecules is reported.

  4. A systematic investigation of cooperativity between two types of hydrogen bonding in the nonlinear clusters of an aromatic molecule: Pyrazole

    Science.gov (United States)

    Amini, Saeed K.

    2014-06-01

    Crystalline pyrazole consists of nonlinear chains of an aromatic molecule. It includes two independent molecules which in turn causes two different types of hydrogen bonds (HBs). These two types of HBs with slight differences in their Nsbnd H⋯N geometries can be considered as interesting ones in the recent studies of cooperativity between different HBs. These HBs are investigated in several pyrazole clusters by electronic structure calculations. Parameters such as structure, binding energy, charge transfer, chemical shielding and electric field gradient (EFG) parameters calculated at the second order Moller-Plesset perturbation (MP2) and density functional (DF) levels of theory. Both the basis set superposition error (BSSE) and zero point vibrational energy (ZPVE) corrections on the cooperativity enhancement were considered. Changes of different properties of clusters against crystal size were investigated by proposed diagrams fitted to a logarithmic function which renders their extrema in the crystal limit. In each cluster, pyrazole molecules for which their parameters are more affected by cooperativity enhancement were explored employing these fitted diagrams. Most calculated energetic and spectroscopic parameters were in good linear correlations with both the structural parameters and charge transfer along HB (q). These correlations in the cases of nuclear magnetic resonance (NMR) and nuclear quadrupolar resonance (NQR) parameters, were explained in the terms of natural charges of bonding (σ(N1sbnd H1)) and antibonding (σ*(N1sbnd H1)) orbitals. Organizing calculated data for mental clusters with similar molecules and HB types produced better regression values in all linear correlations. According to the experimental CQ of N(2) in solid state and zero charge transfer in the gas phase, the value of charge transfer in the crystalline pyrazole and gas phase value of CQ of N(2) were assessed, respectively. Diagrams of the structural parameters against either

  5. In Situ Detection of Organic Molecules on the Martian Surface With the Mars Organic Molecule Analyzer (MOMA) on Exomars 2018

    Science.gov (United States)

    Li, Xiang; Brinckerhoff, William B.; Pinnick, Veronica T; van Amerom, Friso H. W.; Danell, Ryan M.; Arevalo, Ricardo D., Jr.; Getty, Stephanie; Mahaffy, Paul R.

    2015-01-01

    The Mars Organic Molecule Analyzer (MOMA) investigation on the 2018 ExoMars rover will examine the chemical composition of samples acquired from depths of up to two meters below the martian surface, where organics may be protected from radiative and oxidative degradation. The MOMA instrument is centered around a miniaturized linear ion trap (LIT) that facilitates two modes of operation: i) pyrolysisgas chromatography mass spectrometry (pyrGC-MS); and, ii) laser desorptionionization mass spectrometry (LDI-MS) at ambient Mars pressures. The LIT also enables the structural characterization of complex molecules via complementary analytical capabilities, such as multi-frequency waveforms (i.e., SWIFT) and tandem mass spectrometry (MSMS). When combined with the complement of instruments in the rovers Pasteur Payload, MOMA has the potential to reveal the presence of a wide range of organics preserved in a variety of mineralogical environments, and to begin to understand the structural character and potential origin of those compounds.

  6. Local field distribution and configuration of CO molecules adsorbed on the nanostructure platinum surface

    Institute of Scientific and Technical Information of China (English)

    Huang Xiao-Jing; He Su-Zhen; Wu Chen-Xu

    2006-01-01

    This paper shows that the local electric field distribution near the nanostructure metallic surface is obtained by solving the Laplace equation, and furthermore, the configuration of CO molecules adsorbed on a Pt nanoparticle surface is obtained by using Monte Carlo simulation. It is found that the uneven local electric field distribution induced by the nanostructure surface can influence the configuration of carbon monoxide (CO) molecules by a force, which drags the adsorbates to the poles of the nanoparticles. This result, together with our results obtained before, may explain the experimental results that the nanostructure metallic surface can lead to abnormal phenomena such as anti-absorption infrared effects.

  7. Cluster-surface interaction: from soft landing to implantation

    DEFF Research Database (Denmark)

    Popok, Vladimir; Barke, Ingo; Campbell, Eleanor E.B.;

    2011-01-01

    energy and what effects are induced under different energetic regimes. The review starts with an introduction to the field and a short history of cluster beam development. Then fundamental physical aspects of cluster formation and the most common methods for the production of cluster beams are overviewed...

  8. Adsorption configuration effects on the surface diffusion of large organic molecules

    DEFF Research Database (Denmark)

    Sato, F.; Legoas, S.B.; Hummelink, F.

    2010-01-01

    Violet Lander (C108H104) is a large organic molecule that when deposited on Cu(110) surface exhibits lock-and-key like behavior [Otero et al., Nature Mater. 3, 779 (2004)]. In this work, we report a detailed fully atomistic molecular mechanics and molecular dynamics study of this phenomenon. Our...... results show that it has its physical basis on the interplay of the molecular hydrogens and the Cu(110) atomic spacing, which is a direct consequence of the matching between molecule and surface dimensions. This information could be used to find new molecules capable of displaying lock-and-key behavior...

  9. Formation of clusters composed of C{sub 60} molecules via self-assembly in critical fluids

    Energy Technology Data Exchange (ETDEWEB)

    Fukuda, Takahiro [Bio-Nano Electronics Research Centre, Toyo University, 2100, Kujirai, Kawagoe, Saitama 350-8585 (Japan); Ishii, Koji [Bio-Nano Electronics Research Centre, Toyo University, 2100, Kujirai, Kawagoe, Saitama 350-8585 (Japan); Kurosu, Shunji [Bio-Nano Electronics Research Centre, Toyo University, 2100, Kujirai, Kawagoe, Saitama 350-8585 (Japan); Whitby, Raymond [School of Pharmacy and Biomolecular Sciences, University of Brighton, Cockroft Building, Lewes Road, Brighton BN2 4GJ (United Kingdom); Maekawa, Toru [Bio-Nano Electronics Research Centre, Toyo University, 2100, Kujirai, Kawagoe, Saitama 350-8585 (Japan)

    2007-04-11

    Fullerenes are promising candidates for intelligent, functional nanomaterials because of their unique mechanical, electronic and chemical properties. However, it is necessary to invent some efficient but relatively simple methods of producing structures composed of fullerenes for the development of nanomechatronic, nanoelectronic and biochemical devices and sensors. In this paper, we show that various structures such as straight fibres, networks formed by fibres, wide sheets and helical structures, which are composed of C{sub 60} molecules, are created by placing C{sub 60}-crystals in critical ethane, carbon dioxide and xenon even though C{sub 60} molecules do not dissolve or disperse in the above fluids. It is supposed, judging by the intermolecular potentials between C{sub 60} and C{sub 60}, between C{sub 60} and ethane, and between ethane and ethane, that C{sub 60}-clusters grow with the assistance of solvent molecules, which are trapped between C{sub 60} molecules under critical conditions. This room-temperature self-assembly cluster growth process in critical fluids may open up a new methodology of forming structures built up with fullerenes without the need for any ultra-fine processing technologies.

  10. Dipole-driven self-organization of zwitterionic molecules on alkali halide surfaces

    Directory of Open Access Journals (Sweden)

    Laurent Nony

    2012-03-01

    Full Text Available We investigated the adsorption of 4-methoxy-4′-(3-sulfonatopropylstilbazolium (MSPS on different ionic (001 crystal surfaces by means of noncontact atomic force microscopy. MSPS is a zwitterionic molecule with a strong electric dipole moment. When deposited onto the substrates at room temperature, MSPS diffuses to step edges and defect sites and forms disordered assemblies of molecules. Subsequent annealing induces two different processes: First, at high coverage, the molecules assemble into a well-organized quadratic lattice, which is perfectly aligned with the directions of the substrate surface (i.e., rows of equal charges and which produces a Moiré pattern due to coincidences with the substrate lattice constant. Second, at low coverage, we observe step edges decorated with MSPS molecules that run along the direction. These polar steps most probably minimize the surface energy as they counterbalance the molecular dipole by presenting oppositely charged ions on the rearranged step edge.

  11. Local lateral environment of the molecules at the surface of DMSO-water mixtures

    Science.gov (United States)

    Fábián, Balázs; Idrissi, Abdenacer; Marekha, Bogdan; Jedlovszky, Pál

    2016-10-01

    Molecular dynamics simulations of the liquid-vapour interface of dimethyl sulphoxide (DMSO)-water mixtures of 11 different compositions, including two neat systems are performed on the canonical (N, V, T) ensemble at 298 K. The molecules constituting the surface layer of these systems are selected by means of the identification of the truly interfacial molecules (ITIM) method, and their local lateral environment at the liquid surface is investigated by performing Voronoi analysis. The obtained results reveal that both molecules prefer to be in a mixed local environment, consisting of both kinds of molecules, at the liquid surface, and this preference is even stronger here than in the bulk liquid phase. Neat-like patches, in which a molecule is surrounded by like neighbours, are not found. However, vacancies that are surrounded solely by water molecules are observed at the liquid surface. Our results show that strongly hydrogen bonded DMSO·H2O complexes, known to exist in the bulk phase of these mixtures, are absent from the liquid surface.

  12. Adsorption of CO molecules on Rh low index and (331) stepped surfaces

    Institute of Scientific and Technical Information of China (English)

    WANG Zexin; PANG Xuehui; WANG Rui

    2004-01-01

    The 5-parameter Morse potential (for short 5-MP) of the interaction between C, O atom and Rh surface and the extended LEPS potential have been constructed, and the adsorption and diffusion of CO molecules on Rh low index surfaces and open rough Rh(331) stepped surface are investigated. This work puts forward the concept of vibration dactylogram property for molecular adsorption states. The calculation results and the analysis of vibration dactylogram show that there exists the commonness in the adsorption on Rh low index surfaces and Rh(331) stepped surface : with the increasing coverage, the top, bridge sites are adsorbed in perpendicularly in sequence, and the top sites are the steady adsorption sites and the bridge sites are the next. On (100) surface, CO molecules obtain the eigenvibration of 2009, 1946 cm-1 on the top and bridge sites respectively and the difference between the binding energy of above two sites is 0.09 eV; on (110) surface, CO molecules obtain the eigenvibration of 2019, 1961 cm-1 respectively; on (111) surface, CO molecules on the top、bridge and hollow sites produce the eigenvibration of 2000, 1912, 1894 cm-1 respectively, the binding energies of the three sites decrease in turn and the discrepancy between the top and bridge sites is 0.03 eV; on (331) surface, top and bridge sites between two equivalent top sites are adsorbed in, and then obtain the eigenvibration of 2018, 1987 cm-1; 1969, 1927 cm-1 respectively.

  13. Adherence of Molecules to Silica Glass Surface: Experimental Results and Theoretical Calculations

    Science.gov (United States)

    Rivera, Edison; Prado, Miguel Oscar; Nuñez, Matias

    The adherence of molecules to surfaces is used in a wide scope of technological applications. In this work we study the attachment of molecules onto porous silica glass surface obtained from a Vycor glass, after glass- glass phase separation and leaching of the soluble phase with water. Nitrogen adsorption at 77 K was used for the determination of the specific surface area (BET area) and pore size distribution on the leached glass. The adherence onto the glass surface, of model molecules methylene blue (MB) and eosine yellow (EY), with positive and negative electrical charges respectively, was studied. The adsorption kinetics was determined from aqueous solutions using UV-VIS spectroscopy. It was found that the silica glass surface as prepared in this work is selective for positively charged molecules at pH≈5.20, an adsorption of 1 mg MB per gram of glass was found for methylene blue, and almost null adsorption for eosine yellow. First principles calculations were performed using the Density Functional Theory in order to model the interaction between both molecules and the glass surface.

  14. DNA origami as biocompatible surface to match single-molecule and ensemble experiments.

    Science.gov (United States)

    Gietl, Andreas; Holzmeister, Phil; Grohmann, Dina; Tinnefeld, Philip

    2012-08-01

    Single-molecule experiments on immobilized molecules allow unique insights into the dynamics of molecular machines and enzymes as well as their interactions. The immobilization, however, can invoke perturbation to the activity of biomolecules causing incongruities between single molecule and ensemble measurements. Here we introduce the recently developed DNA origami as a platform to transfer ensemble assays to the immobilized single molecule level without changing the nano-environment of the biomolecules. The idea is a stepwise transfer of common functional assays first to the surface of a DNA origami, which can be checked at the ensemble level, and then to the microscope glass slide for single-molecule inquiry using the DNA origami as a transfer platform. We studied the structural flexibility of a DNA Holliday junction and the TATA-binding protein (TBP)-induced bending of DNA both on freely diffusing molecules and attached to the origami structure by fluorescence resonance energy transfer. This resulted in highly congruent data sets demonstrating that the DNA origami does not influence the functionality of the biomolecule. Single-molecule data collected from surface-immobilized biomolecule-loaded DNA origami are in very good agreement with data from solution measurements supporting the fact that the DNA origami can be used as biocompatible surface in many fluorescence-based measurements.

  15. DNA origami as biocompatible surface to match single-molecule and ensemble experiments

    Science.gov (United States)

    Gietl, Andreas; Holzmeister, Phil; Grohmann, Dina; Tinnefeld, Philip

    2012-01-01

    Single-molecule experiments on immobilized molecules allow unique insights into the dynamics of molecular machines and enzymes as well as their interactions. The immobilization, however, can invoke perturbation to the activity of biomolecules causing incongruities between single molecule and ensemble measurements. Here we introduce the recently developed DNA origami as a platform to transfer ensemble assays to the immobilized single molecule level without changing the nano-environment of the biomolecules. The idea is a stepwise transfer of common functional assays first to the surface of a DNA origami, which can be checked at the ensemble level, and then to the microscope glass slide for single-molecule inquiry using the DNA origami as a transfer platform. We studied the structural flexibility of a DNA Holliday junction and the TATA-binding protein (TBP)-induced bending of DNA both on freely diffusing molecules and attached to the origami structure by fluorescence resonance energy transfer. This resulted in highly congruent data sets demonstrating that the DNA origami does not influence the functionality of the biomolecule. Single-molecule data collected from surface-immobilized biomolecule-loaded DNA origami are in very good agreement with data from solution measurements supporting the fact that the DNA origami can be used as biocompatible surface in many fluorescence-based measurements. PMID:22523083

  16. MS/MS networking guided analysis of molecule and gene cluster families

    NARCIS (Netherlands)

    Don Duy Nguyen, [No Value; Wu, Cheng-Hsuan; Moree, Wilna J.; Lamsa, Anne; Medema, Marnix H.; Zhao, Xiling; Gavilan, Ronnie G.; Aparicio, Marystella; Atencio, Librada; Jackson, Chanaye; Ballesteros, Javier; Sanchez, Joel; Watrous, Jeramie D.; Phelan, Vanessa V.; van de Wiel, Corine; Kersten, Roland D.; Mehnaz, Samina; De Mot, Rene; Shank, Elizabeth A.; Charusanti, Pep; Nagarajan, Harish; Duggan, Brendan M.; Moore, Bradley S.; Bandeira, Nuno; Palsson, Bernhard O.; Pogliano, Kit; Gutierrez, Marcelino; Dorrestein, Pieter C.

    2013-01-01

    The ability to correlate the production of specialized metabolites to the genetic capacity of the organism that produces such molecules has become an invaluable tool in aiding the discovery of biotechnologically applicable molecules. Here, we accomplish this task by matching molecular families with

  17. Molecules at surfaces: 100 years of physical chemistry in Berlin-Dahlem.

    Science.gov (United States)

    Ertl, Gerhard

    2013-01-02

    Scratching the surface: for over 100 years the interactions of molecules at surfaces have been studied at the Fritz Haber Institute of the Max Planck Society, Berlin. Nobel Laureate Gerhard Ertl looks back at some of the key developments in this time, and the people who made them. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Preparation and single molecule structure of electroactive polysilane end-grafted on a crystalline silicon surface

    Science.gov (United States)

    Furukawa, Kazuaki; Ebata, Keisuke

    2000-12-01

    Electrically active polysilanes of poly(methylphenylsilane) (PMPS) and poly[bis(p-n-butylphenyl)silane] (PBPS), which are, respectively, known as a good hole transporting material and a near-ultraviolet electroluminescent material, are end-grafted directly on a crystalline silicon surface. The single polysilane molecules are clearly distinguished one from the other on the surface by means of atomic force microscopy observations. End-grafted single molecules of PMPS are observed as dots while end-grafted PBPS appear as worms extending for more than 100 nm on the crystalline silicon surface.

  19. A novel method of aligning molecules by local surface shape similarity

    Science.gov (United States)

    Cosgrove, D. A.; Bayada, D. M.; Johnson, A. P.

    2000-08-01

    A novel shape-based method has been developed for overlaying a series of molecule surfaces into a common reference frame. The surfaces are represented by a set of circular patches of approximately constant curvature. Two molecules are overlaid using a clique-detection algorithm to find a set of patches in the two surfaces that correspond, and overlaying the molecules so that the similar patches on the two surfaces are coincident. The method is thus able to detect areas of local, rather than global, similarity. A consensus overlay for a group of molecules is performed by examining the scores of all pairwise overlays and performing a set of overlays with the highest scores. The utility of the method has been examined by comparing the overlaid and experimental configurations of 4 sets of molecules for which there are X-ray crystal structures of the molecules bound to a protein active site. Results for the overlays are generally encouraging. Of particular note is the correct prediction of the `reverse orientation' for ligands binding to human rhinovirus coat protein HRV14.

  20. Mobility of large clusters on a semiconductor surface: Kinetic Monte Carlo simulation results

    Science.gov (United States)

    M, Esen; A, T. Tüzemen; M, Ozdemir

    2016-01-01

    The mobility of clusters on a semiconductor surface for various values of cluster size is studied as a function of temperature by kinetic Monte Carlo method. The cluster resides on the surface of a square grid. Kinetic processes such as the diffusion of single particles on the surface, their attachment and detachment to/from clusters, diffusion of particles along cluster edges are considered. The clusters considered in this study consist of 150-6000 atoms per cluster on average. A statistical probability of motion to each direction is assigned to each particle where a particle with four nearest neighbors is assumed to be immobile. The mobility of a cluster is found from the root mean square displacement of the center of mass of the cluster as a function of time. It is found that the diffusion coefficient of clusters goes as D = A(T)Nα where N is the average number of particles in the cluster, A(T) is a temperature-dependent constant and α is a parameter with a value of about -0.64 a value of -0.5. The diffusion coefficient is found to change by one order of magnitude as a function of cluster size.

  1. Generation of Quantum Cluster States using Surface Acoustic Waves

    CERN Document Server

    Majumdar, Mrittunjoy Guha

    2016-01-01

    One-way quantum computation, also known as Cluster State Quantum Computation, provides a robust and efficient tool to perform universal quantum computation using only single-qubit projective measurements, given a highly entangled cluster state. The cluster-state approach to quantum computation also leads to certain practical advantages such as robustness against errors. In this paper, we propose a SAW-driven One-Way Quantum Computation approach that is realizable using a mentioned architecture and elements.

  2. Comprehensive photoelectron spectroscopic study of anionic clusters of anthracene and its alkyl derivatives: Electronic structures bridging molecules to bulk

    Science.gov (United States)

    Ando, Naoto; Mitsui, Masaaki; Nakajima, Atsushi

    2007-12-01

    The evolution of the electronic structure of molecular aggregates is investigated using anion photoelectron (PE) spectroscopy for anionic clusters of anthracene (Ac) and its alkyl derivatives: 1-methylanthracene (1MA), 2-methylanthracene (2MA), 9-methylanthracene (9MA), 9,10-dimethylanthracene (DMA), and 2-tert-butylanthracene (2TBA). For their monomer anions (n=1), electron affinities are confined to the range from 0.47to0.59eV and are well reproduced by density functional theory calculations, showing the isoelectronic character of these molecules. For cluster anions (n=2-100) of Ac and 2MA, two types of isomers I and II coexist over a wide size range: isomers I and II-1 (4⩽nVDEs) of isomer I in all the anionic clusters depend almost linearly on n-1/3. In contrast, the VDEs of isomers II-1 (n⩾14) and II-2 (n=40-100), appeared only in Ac and 2MA cluster anions, remain constant with n and are ˜0.5eV lower than those of isomer I. The PE spectra revealed the characteristics of each isomer: isomer I possesses a monomeric anion core that is gradually embedded into the interior of the cluster with increasing n. On the other hand, isomers II-1 and II-2 possess a multimeric (perhaps tetrameric) anion core, but they differ in the number of layers from which they are made up; monolayer (isomer II-1) and multilayers (isomer II-2) of a two-dimensionally ordered, finite herringbone-type structure, in which electron attachment produces only little geometrical rearrangement. Moreover, the agreement of the constant VDEs of isomer II-2 with the bulk data demonstrates the largely localized nature of the electronic polarization around the excess charge in a crystal-like environment, where about 50molecules provide a charge stabilization energy comparable to the bulk.

  3. Optical Absorption of CdI2 Single Molecule and Clusters Incorporated into Zeolite Na-FAU

    Science.gov (United States)

    Nishida, Koji; Ohnishi, Akimasa; Kitaura, Mamoru; Sasaki, Minoru; Kuriyama, Yasunao

    2009-10-01

    The absorption spectra of CdI2 molecules adsorbed through a vapor phase into zeolite Na-FAU are investigated at liquid nitrogen temperature by changing the loading density Ld of CdI2 per supercage from a dilute condition of 0.1 to a saturated condition of 5.5. The theoretical absorption spectrum of a CdI2 molecule is also derived using the wave functions obtained from a relativistic self-consistent-field discrete-variational Xα calculation. A predominant band is observed at 5.8 eV together with sub-bands at 5.0 and 5.5 eV at Ld = 0.1. The comparison between the experimental and theoretical spectra clarifies that these bands originate from the electronic transitions of an isolated CdI2 molecule. Moreover, it suggests that the CdI2 molecule interacts with zeolite. Another three bands appear at 4.8, 5.3, and 6.0 eV at Ld = 2.0 when Ld increases, which are attributed to a CdI2 two-molecule cluster. The lowest absorption band continuously shifts toward the lower-energy side with an increase in Ld between 2.0 and 5.5. This shift is explained by the quantum size effect on photoexcitation energy.

  4. Nanocoating of titanium implant surfaces with organic molecules. Polysaccharides including glycosaminoglycans

    DEFF Research Database (Denmark)

    Gurzawska, Katarzyna Aleksandra; Svava, Rikke; Jørgensen, Niklas Rye;

    2012-01-01

    Long-term stability of titanium implants are dependent on a variety of factors. Nanocoating with organic molecules is one of the method used to improve osseointegration. Nanoscale modification of titanium implants affects surface properties, such as hydrophilicity, biochemical bonding capacity...... and roughness. This influences cell behaviour on the surface such as adhesion, proliferation and differentiation of cells as well as the mineralization of the extracellular matrix at the implant surfaces. The aim of the present systematic review was to describe organic molecules used for surface nanocoating...... nanocoatings. The included in vivo studies, showed improvement of bone interface reactions measured as increased Bone-to-Implant Contact length and Bone Mineral Density adjacent to the polysaccharide coated surfaces. Based on existing literature, surface modification with polysaccharide and glycosaminoglycans...

  5. Mononuclear Clusterfullerene Single‐Molecule Magnet Containing Strained Fused‐Pentagons Stabilized by a Nearly Linear Metal Cyanide Cluster

    Science.gov (United States)

    Liu, Fupin; Wang, Song; Gao, Cong‐Li; Deng, Qingming; Zhu, Xianjun; Kostanyan, Aram; Westerström, Rasmus; Jin, Fei

    2017-01-01

    Abstract Fused‐pentagons results in an increase of local steric strain according to the isolated pentagon rule (IPR), and for all reported non‐IPR clusterfullerenes multiple (two or three) metals are required to stabilize the strained fused‐pentagons, making it difficult to access the single‐atom properties. Herein, we report the syntheses and isolations of novel non‐IPR mononuclear clusterfullerenes MNC@C76 (M=Tb, Y), in which one pair of strained fused‐pentagon is stabilized by a mononuclear cluster. The molecular structures of MNC@C76 (M=Tb, Y) were determined unambiguously by single‐crystal X‐ray diffraction, featuring a non‐IPR C 2v(19138)‐C76 cage entrapping a nearly linear MNC cluster, which is remarkably different from the triangular MNC cluster within the reported analogous clusterfullerenes based on IPR‐obeying C82 cages. The TbNC@C76 molecule is found to be a field‐induced single‐molecule magnet (SMM). PMID:28079303

  6. Local electric field and configuration of CO molecules adsorbed on a nanostructured surface with nanocones

    Institute of Scientific and Technical Information of China (English)

    You Rong-Yi; Huang Xiao-Jing

    2009-01-01

    Based on the nanostructured surface model that the (platinum,Pt) nanocones grow out symmetrically from a plane substrate,the local electric field near the conical nanoparticle surface is computed and discussed. On the basis of these results,the adsorbed CO molecules are modelled as dipoles,and three kinds of interactions,I.e. Interactions between dipoles and local electric field,between dipoles and dipoles,as well as between dipoles and nanostructured substrate,are taken into account. The spatial configuration of CO molecules adsorbed on the nanocone surface is then given by Monte-Carlo simulation. Our results show that the CO molecules adsorbed on the nanocone surface cause local agglomeration under the action of an external electric field,and this agglomeration becomes more compact with decreasing conical angle,which results in a stronger interaction among molecules. These results serve as a basis for explaining abnormal phenomena such as the abnormal infrared effect (AIRE),which was found when CO molecules were adsorbed on the nancetructured transition-metal surface.

  7. Single-molecule studies on individual peptides and peptide assemblies on surfaces.

    Science.gov (United States)

    Yang, Yanlian; Wang, Chen

    2013-10-13

    This review is intended to reflect the recent progress in single-molecule studies of individual peptides and peptide assemblies on surfaces. The structures and the mechanism of peptide assembly are discussed in detail. The contents include the following topics: structural analysis of single peptide molecules, adsorption and assembly of peptides on surfaces, folding structures of the amyloid peptides, interaction between amyloid peptides and dye or drug molecules, and modulation of peptide assemblies by small molecules. The explorations of peptide adsorption and assembly will benefit the understanding of the mechanisms for protein-protein interactions, protein-drug interactions and the pathogenesis of amyloidoses. The investigations on peptide assembly and its modulations could also provide a potential approach towards the treatment of the amyloidoses.

  8. Electrostatic surface guiding of cold polar molecules with double charged wires

    Institute of Scientific and Technical Information of China (English)

    Yong Xia; Lianzhong Deng; Jinming Liu; Jianping Yin

    2005-01-01

    We propose a novel scheme to guide cold polar molecules on the surface of an insulating substrate (i.e., a chip) using a static electric field generated by the combination of a pair of parallel charged wires and a grounded metal plate. We calculate the spatial distributions of the electric fields from the above chargedwire layout and their Stark potentials for cold CO molecules, and analyze the relationships between the electric field and the parameters of the charged-wire layout. The result shows that this charged-wire scheme can be used to guide cold polar molecules in the weak-field-seeking state and to form various molecule-optical elements, even to realize a single-mode molecular waveguide on a molecule chip under certain conditions.

  9. Surface single-molecule dynamics controlled by entropy at low temperatures

    Science.gov (United States)

    Gehrig, J. C.; Penedo, M.; Parschau, M.; Schwenk, J.; Marioni, M. A.; Hudson, E. W.; Hug, H. J.

    2017-02-01

    Configuration transitions of individual molecules and atoms on surfaces are traditionally described using an Arrhenius equation with energy barrier and pre-exponential factor (attempt rate) parameters. Characteristic parameters can vary even for identical systems, and pre-exponential factors sometimes differ by orders of magnitude. Using low-temperature scanning tunnelling microscopy (STM) to measure an individual dibutyl sulfide molecule on Au(111), we show that the differences arise when the relative position of tip apex and molecule changes by a fraction of the molecule size. Altering the tip position on that scale modifies the transition's barrier and attempt rate in a highly correlated fashion, which results in a single-molecular enthalpy-entropy compensation. Conversely, appropriately positioning the STM tip allows selecting the operating point on the compensation line and modifying the transition rates. The results highlight the need to consider entropy in transition rates of single molecules, even at low temperatures.

  10. A scale-bridging modeling approach for anisotropic organic molecules at patterned semiconductor surfaces

    OpenAIRE

    Kleppmann, Nicola; Klapp, Sabine H. L.

    2014-01-01

    Hybrid systems consisting of organic molecules at inorganic semiconductor surfaces are gaining increasing importance as thin film devices for optoelectronics. The efficiency of such devices strongly depends on the collective behavior of the adsorbed molecules. In the present paper we propose a novel, coarse-grained model addressing the condensed phases of a representative hybrid system, that is, para-sexiphenyl (6P) at zinc-oxide (ZnO). Within our model, intermolecular interactions are repre-...

  11. Detection of Fluorescence from Single Chlorophyll a Molecules Absorbed on Glass Surface

    Institute of Scientific and Technical Information of China (English)

    JI Dong-Mei; HUANG Zheng-Xi; XIA An-Dong

    2005-01-01

    @@ We investigate the single molecule spectroscopy of chlorophyll a molecules on glass surface in N2-saturated environment. The basic photodynamic parameters of chlorophyll a molecules, such as fluorescence lifetime,survival time before photobleaching, on-time, and off-time, are reported. A four-level model is employed to describe the possible dynamics and photobleaching of chlorophyll a upon excitation. Broad distributions in fluorescence lifetimes and survival times are mainly due to the heterogeneities of both molecular conformation and local environment.

  12. Diffraction of fast atoms and molecules during grazing scattering from surfaces

    Science.gov (United States)

    Schüller, A.; Busch, M.; Seifert, J.; Wethekam, S.; Winter, H.

    2009-11-01

    Grazing scattering of light atoms and small molecules with energies up to several keV from atomically clean and flat surfaces along low-indexed directions gives rise to diffraction phenomena. The potential of this new method of Fast Atom Diffraction (FAD) as surface analytical tool is discussed. We show that, despite substantial decoherence due to thermal vibrations, nuclear energy loss, and, especially, excitations of the electronic system, FAD is not limited to insulator or semiconductor surfaces. Detailed studies of the geometric structure of insulator surfaces and superstructures on metal surfaces performed using FAD as an efficient virtually non-destructive method are presented.

  13. Ir Spectroscopy of First-Row Transition Metal Clusters and Their Complexes with Simple Molecules

    Science.gov (United States)

    Kiawi, D. M.; Bakker, J.; Oomens, J.; Buma, W. J.; Waters, L. B. F. M.

    2014-06-01

    Iron is an important element in the formation of solids in space. Spectroscopic observations of interstellar iron shows that its atomic gas-phase abundance is strongly depleted with respect to that of hydrogen. In contrast, sulfur is mostly found in the gas phase in low-density regions of interstellar space, but is highly depleted in regions of star- and planet formation. Furthermore, the dominant source of sulfur in our solar system is solid FeS, as found in primitive meteorites, implying an efficient chemical pathway to convert sulphur or sulphur containing compounds into solid FeS during the (early phases of) the star formation process. We address the evolution of iron and sulfur in space on a molecular level by studying metal nanoclusters and their interaction with ligands using IR action spectroscopy. Clusters are formed through laser ablation of solid precursor materials and brought into a molecular beam environment. Complexes with ligands are obtained by directing the beam through a reaction channel containing low-pressure reactant gas. Mass-selected IR action spectra are recorded by irradiating the clusters using the Free Electron Laser for Infrared eXperiments (FELIX). Experimental spectra are then compared with DFT predictions which enables us to determine the structure of the selected cluster and its binding interactions with ligands. As part of this project, we here present IR action spectra of size-selected Fe clusters and the chemically closely related Co clusters, and their complexes with relevant ligands.

  14. DFT-investigations of coalescence behaviour of small magic Si clusters on surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Quester, Wolfram; Nielaba, Peter [Fachbereich Physik, Universitaet Konstanz, 78457 Konstanz (Germany)

    2007-07-01

    Experimental results indicate that small magic Si clusters do not form islands of bulk Si on weakly interacting surfaces (HOPG). For Si{sub 4} this was confirmed in earlier calculations. This leads to the question if these clusters are suited as building blocks for new cluster materials. These investigations were extended to Si{sub 7}. Potential energy curves of two approaching Si{sub 7} clusters were calculated for different reaction channels using Density Functional Theory implemented in the CPMD code available. It could be shown that the cluster-cluster interaction is either repulsive or there are fusion barriers higher than room temperature. Since the influence of the surface is important, the next step was to include the graphite surface in the simulations. Also the influence of defects was to be studied.

  15. Cluster observations of surface waves on the dawn flank magnetopause

    Directory of Open Access Journals (Sweden)

    C. J. Owen

    2004-03-01

    Full Text Available On 14 June 2001 the four Cluster spacecraft recorded multiple encounters of the dawn-side flank magnetopause. The characteristics of the observed electron populations varied between a cold, dense magnetosheath population and warmer, more rarified boundary layer population on a quasi-periodic basis. The demarcation between these two populations can be readily identified by gradients in the scalar temperature of the electrons. An analysis of the differences in the observed timings of the boundary at each spacecraft indicates that these magnetopause crossings are consistent with a surface wave moving across the flank magnetopause. When compared to the orientation of the magnetopause expected from models, we find that the leading edges of these waves are approximately 45° steeper than the trailing edges, consistent with the Kelvin-Helmholtz (KH driving mechanism. A stability analysis of this interval suggests that the magnetopause is marginally stable to this mechanism during this event. Periods in which the analysis predicts that the magnetopause is unstable correspond to observations of greater wave steepening. Analysis of the pulses suggests that the waves have an average wavelength of approximately 3.4 RE and move at an average speed of ~65km s-1 in an anti-sunward and northward direction, despite the spacecraft location somewhat south of the GSE Z=0 plane. This wave propagation direction lies close to perpendicular to the average magnetic field direction in the external magnetosheath, suggesting that these waves may preferentially propagate in the direction that requires no bending of these external field lines

    Key words. Magnetospheric physics (magnetospheric configuration and dynamics; MHD waves and unstabilities; solar wind-magnetosphere interactions

  16. The mean cluster size near the surface of a percolating system

    Science.gov (United States)

    Korneta, W.; Pytel, Z.

    1989-04-01

    The bond percolation on a three-dimensional semi-infinite simple cubic lattice is considered. It is assumed that the probability of a bond being present in the surface layer may be different from the probability of a bond inside the lattice. The mean size of finite clusters is studied. Using the relation between the Potts model and the bond percolation process, and applying the mean-field approximation, analytical formulae for the mean cluster size near the ordinary, surface-bulk, extraordinary and surface second-order phase transitions are obtained. The effect of the surface on the mean cluster size is discussed.

  17. Density functional study of adsorptions of CO2, NO2 and SO2 molecules on Zn(0002) surfaces

    Science.gov (United States)

    Nugraha; Saputro, A. G.; Agusta, M. K.; Yuliarto, B.; Dipojono, H. K.; Maezono, R.

    2016-08-01

    We report on a theoretical study of adsorptions of CO2, NO2 and SO2 molecules on ZnO(0002) surfaces using density functional theory-based (DFT-based) calculations. These adsorptions are done on perfect and defective ZnO(0002) surfaces. We find that all of these molecules are chemically adsorbed on the perfect ZnO(0002) surface. In the presence of Zn vacancy, we find that the surface is only active toward SO2 molecule. On the hydroxylated ZnO(0002) surfaces, CO2 and SO2 molecules can react with the preadsorbed OH molecule to form various adsorbates such as: carboxyl (COOH), bicarbonate (CO3H), sulfonyl hydroxide (SO3H), SO3 and water. However, NO2 molecule cannot react with the pre-adsorbed OH molecule and only physically adsorbed on the surface.

  18. Low energy molecule-surface interaction processes of relevance to next-generation fusion devices

    Energy Technology Data Exchange (ETDEWEB)

    Snowdon, K.J.; Tawara, H.

    1996-03-01

    The mechanisms which may lead to molecular release or scattering from surfaces exposed to low energy (0.1-100 eV) particle irradiation or photon and electron irradiation are summarized. The charge and electronic state, angular, translational and internal energies of the departing molecules are, where possible, described and the physical origin of the characteristics of each distribution explained. On the basis of our current understanding of these surface processes, we argue for the use of medium- to high-Z metal surfaces in plasma facing components of the gas-blanket type divertor recently proposed for ITER. By operating such surfaces at sufficiently elevated temperatures, the release of highly vibrationally excited hydrogen molecules via Eley-Rideal-like surface recombination reactions could be suppressed. (author). 73 refs.

  19. Endocytic pathway rapidly delivers internalized molecules to lysosomes: an analysis of vesicle trafficking, clustering and mass transfer.

    Science.gov (United States)

    Pangarkar, Chinmay; Dinh, Anh-Tuan; Mitragotri, Samir

    2012-08-20

    Lysosomes play a critical role in intracellular drug delivery. For enzyme-based therapies, they represent a potential target site whereas for nucleic acid or many protein drugs, they represent the potential degradation site. Either way, understanding the mechanisms and processes involved in routing of materials to lysosomes after cellular entry is of high interest to the field of drug delivery. Most therapeutic cargoes other than small hydrophobic molecules enter the cells through endocytosis. Endocytosed cargoes are routed to lysosomes via microtubule-based transport and are ultimately shared by various lysosomes via tethering and clustering of endocytic vesicles followed by exchange of their contents. Using a combined experimental and numerical approach, here we studied the rates of mass transfer into and among the endocytic vesicles in a model cell line, 3T3 fibroblasts. In order to understand the relationship of mass transfer with microtubular transport and vesicle clustering, we varied both properties through various pharmacological agents. At the same time, microtubular transport and vesicle clustering were modeled through diffusion-advection equations and the Smoluchowski equations, respectively. Our analysis revealed that the rate of mass transfer is optimally related to microtubular transport and clustering properties of vesicles. Further, the rate of mass transfer is highest in the innate state of the cell. Any perturbation to either microtubular transport or vesicle aggregation led to reduced mass transfer to lysosome. These results suggest that in the absence of an external intervention the endocytic pathway appears to maximize molecular delivery to lysosomes. Strategies are discussed to reduce mass transfer to lysosomes so as to extend the residence time of molecules in endosomes or late endosomes, thus potentially increasing the likelihood of their escape before disposition in the lysosomes.

  20. Near infrared emission from molecule-like silver clusters confined in zeolite A assisted by thermal activation

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Hui, E-mail: linh8112@163.com; Imakita, Kenji; Rong Gui, Sa Chu; Fujii, Minoru, E-mail: fujii@eedept.kobe-u.ac.jp [Department of Electrical and Electronic Engineering, Graduate School of Engineering, Kobe University, Rokkodai, Nada, Kobe 657-8501 (Japan)

    2014-07-07

    Strong and broad near infrared (NIR) emission peaked at ~855 nm upon optimal excitation at 342 nm has been observed from molecule-like silver clusters (MLSCs) confined in zeolite A assisted by thermal activation. To the best of our knowledge, this is the first observation of NIR emission peaked at longer than 800 nm from MLSCs confined in solid matrices. The decay time of the NIR emission is over 10 μs, which indicates that it is a spin-forbidden transition. The ~855 nm NIR emission shows strong dependence on the silver loading concentration and the thermal activation temperature.

  1. Magnetism of Fe clusters and islands on Pt surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Repetto, D.; Honolka, J.; Enders, A.; Kern, K. [MPI fuer Festkoerperforschung, Stuttgart (Germany); Rusponi, S.; Brune, H. [Institut de Physique des Nanostructures, EPFL, Lausanne (Switzerland)

    2006-01-01

    Clusters and islands of Fe atoms have been prepared by noble gas buffer layer assisted growth as well as by standard molecular beam epitaxy on Pt substrates. Xe buffer layers have been utilized to promote the formation of compact, relaxed Fe clusters with narrow size distribution. Without the Xe buffer, strained Fe islands with a characteristic misfit dislocation network are formed. Magnetization loops obtained by magneto-optical Kerr effect measurements reveal that in-plane easy magnetization axis is only found for the relaxed clusters, pointing out the important role of epitaxial lattice deformations for the magnetic anisotropy. (orig.)

  2. Raman scattering enhanced by plasmonic clusters and its application to single-molecule imaging

    Energy Technology Data Exchange (ETDEWEB)

    Yasuike, Tomokazu [The Open University of Japan, Wakaba 2-11, Mihama-ku, Chiba 261-8586 (Japan); ESICB, Kyoto University, Kyoto daigaku-Katsura, Nishikyo-ku, Kyoto 615-8530 (Japan); Nobusada, Katsuyuki [Institute for Molecular Science and SOKENDAI, Nishigonaka 38, Okazaki, 444-8585 (Japan); ESICB, Kyoto University, Kyoto daigaku-Katsura, Nishikyo-ku, Kyoto 615-8530 (Japan)

    2015-12-31

    The optical response of the linear Au{sub 8} cluster is investigated by the linear response theory based on the density functional theory. It is revealed that the observed many peaks in the visible region originate from the interaction of the ideal plasmonic excitation along the molecular axis with the background d-electron excitations, i.e., the Landau damping. In spite of the existence of the damping, the Raman scattering is shown to be enhanced remarkably by the incident light resonant to the visible excitations. The novel imaging experiment with the atomic resolution is proposed by utilizing a plasmonic cluster as the probing tip.

  3. Small Al clusters on the Cu(111) surface: Atomic relaxation and vibrational properties

    Science.gov (United States)

    Rusina, G. G.; Borisova, S. D.; Chulkov, E. V.

    2010-11-01

    The relaxation and vibrational properties of both Al clusters and the (111) surface of a copper sub-strate were studied using the interatomic interaction potentials obtained in a tight-binding approximation. The presence of small aluminum clusters led to modification of the vibrational states of the substrate, a shift of the Rayleigh mode, and excitation of new Z-polarized modes. Hybridized modes localized on the cluster adatoms and the neighboring atoms of the substrate were found in the phonon spectrum. The localized dipole-active modes of the cluster and their strong hybridization with vibrations of the substrate points to desorption stability of the tri- and heptaatomic clusters.

  4. Interface properties of organic molecules on metal surfaces; Grenzflaecheneigenschaften organischer Molekuele auf Metalloberflaechen

    Energy Technology Data Exchange (ETDEWEB)

    Karacuban, Hatice

    2010-01-28

    In this work, the growth of the archetype molecules CuPc and PTCDA was investigated on Cu(111). PTCDA was also studied on NaCl/Cu(111). The main experiments were carried out with a scanning tunneling microscope. Structural analysis of CuPc on Cu (111) is only possible at low temperatures, since at room temperature the molecules exhibit a high surface mobility. For the investigation of these structures and especially to enable scanning tunneling spectroscopy, a low-temperature scanning tunneling microscope was developed. Using this home built STM the experiments could be carried out at about 10 K. After the adsorption of CuPc on Cu (111) a substrate-induced symmetry reduction of the molecules can be observed in scanning tunneling microscopy. When the occupied states of the molecules are imaged, a switching between two distinct levels is found. These modifications are determined by the adsorption geometry of the molecules. Based on high resolution STM data, an on-top adsorption geometry of the CuPc-molecules on Cu (111)-substrate can be deducted. At low temperatures, two new superstructures of PTCDA on Cu(111) are observed. The molecules within these superstructures are tilted with respect to the substrate. Intermolecular interactions may be the crucial factor for the realignment of the molecules. If PTCDA molecules are adsorbed on a NaCl/Cu (111) substrate, at room temperature, also two new superstructures on the copper substrate were found. They indicate the formation of a metall-organic-complex. On top of the NaCl layer the molecules exclusively grow at polar NaCl step edges. This is an indication for electrostatic interaction between the PTCDA molecules and the NaCl layer. When the molecule density is further increased, a Vollmer-Weber growth sets in. If both molecules PTCDA and CuPc are present on the sample at the same time, local spectroscopy provides information on the metal-organic interface in direct comparison. The STS-results of CuPc/PTCDA on Cu (111

  5. A comparative study between all-electron scalar relativistic calculation and all-electron calculation on the adsorption of hydrogen molecule onto small gold clusters

    Indian Academy of Sciences (India)

    Xiang-Jun Kuang; Xin-Qiang Wang; Gao-Bin Liu

    2013-03-01

    A comparative study between all-electron relativistic (AER) calculation and all-electron (AE) calculation on the H2 molecule adsorption onto small gold clusters has been performed. Compared with the corresponding AuH2 cluster obtained by AE method, the AuH2 cluster obtained by AER method has much shorter Au-H bond-length, much longer H-H distance, larger binding energy and adsorption energy, higher vertical ionization potentials (VIP), greater charge transfer, higher vibrational frequency of Au-H mode and lower vibrational frequency of H-H mode. The delocalization of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) for AuH2 cluster obtained by AER method is obvious. All these characteristics suggest that the scalar relativistic effect might strengthen the Au-H bond and weaken the H-H bond. It is believed that the scalar relativistic effect is favourable to the H2 molecule adsorption onto small gold cluster and the reactivity enhancement of H2 molecule. It may be one of the reasons why the dissociative adsorptions take place in some AuH2 clusters. With increasing size of AuH2 clusters, the influence of scalar relativistic effect becomes more significant. Some further studies focused on the influence of scalar relativistic effect on the adsorption behaviour of other small molecules onto gold clusters are necessary in the future.

  6. Nano-clustered Pd catalysts formed on GaN surface for green chemistry

    Science.gov (United States)

    Hirayama, Motoi; Ueta, Yukiko; Konishi, Tomoya; Tsukamoto, Shiro

    2011-05-01

    We have succeeded in observing Pd nano-clusters, catalytic prime elements, on a GaN(0 0 0 1) surface by a scanning tunneling microscope for the first time. After the sample was reused, we found that nano-clusters (width: 11 nm, height: 2.2 nm) existed on the surface which still kept the catalytic activity, resulting that the neutral Pd atoms formed the nano-cluster. Moreover, the S-termination contributed to the formation of the dense and flat structure consisting of the Pd nano-clusters.

  7. Vibrational properties of small cobalt clusters on the Cu(111) surface

    Science.gov (United States)

    Borisova, S. D.; Rusina, G. G.; Eremeev, S. V.; Chulkov, E. V.

    2009-06-01

    Vibrational properties of small cobalt clusters (dimer and trimer) adsorbed on the Cu(111) surface are studied using interatomic interaction potentials obtained in a tight-binding approximation. The complete (lateral and vertical) relaxation of the surface, the local phonon density of states, and the polarization of vibration modes of clusters and atoms of the substrate are discussed. It is shown that the adsorption of small cobalt clusters leads to a local modification of the vibrational properties of the substrate surface and to excitation of new vibration modes localized on both the cluster adatoms and substrate surface atoms. An increase in the cluster size causes a decrease in the intensity of peaks of the local density of states and their broadening and also a shift in the frequencies of the peaks.

  8. Deposition of metal Islands, metal clusters and metal containing single molecules on self-assembled monolayers

    NARCIS (Netherlands)

    Speets, Emiel Adrianus

    2005-01-01

    The central topic of this thesis is the deposition of metals on Self-Assembled Monolayers (SAMs). Metals are deposited in the form of submicron scale islands, nanometer scale clusters, and as supramolecular, organometallic coordination cages. Several SAMs on various substrates were prepared and anal

  9. Model HULIS compounds in nanoaerosol clusters – investigations of surface tension and aggregate formation using molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    T. Hede

    2011-07-01

    Full Text Available Cloud condensation nuclei act as cores for water vapour condensation, and their composition and chemical properties may enhance or depress the ability for droplet growth. In this study we use molecular dynamics simulations to show that model humic-like substances (HULIS in systems containing 10 000 water molecules mimic experimental data well referring to reduction of surface tension. The model HULIS compounds investigated in this study are cis-pinonic acid (CPA, pinic acid (PAD and pinonaldehyde (PAL. The structural properties examined show the ability for the model HULIS compounds to aggregate inside the nanoaerosol clusters.

  10. Molecular dynamics simulation of nanoscale surface diffusion of heterogeneous adatoms clusters

    Institute of Scientific and Technical Information of China (English)

    Muhammad Imran; Fayyaz Hussain; Muhammad Rashid; Muhammad Ismail; Hafeez Ullah; Yongqing Cai; M Arshad Javid; Ejaz Ahmad; S A Ahmad

    2016-01-01

    Molecular dynamics simulation employing the embedded atom method potential is utilized to investigate nanoscale surface diffusion mechanisms of binary heterogeneous adatoms clusters at 300 K, 500 K, and 700 K. Surface diffusion of heterogeneous adatoms clusters can be vital for the binary island growth on the surface and can be useful for the formation of alloy-based thin film surface through atomic exchange process. The results of the diffusion process show that at 300 K, the diffusion of small adatoms clusters shows hopping, sliding, and shear motion;whereas for large adatoms clusters (hexamer and above), the diffusion is negligible. At 500 K, small adatoms clusters, i.e., dimer, show almost all possible diffusion mechanisms including the atomic exchange process;however no such exchange is observed for adatoms clusters greater than dimer. At 700 K, the exchange mechanism dominates for all types of clusters, where Zr adatoms show maximum tendency and Ag adatoms show minimum or no tendency toward the exchange process. Separation and recombination of one or more adatoms are also observed at 500 K and 700 K. The Ag adatoms also occupy pop-up positions over the adatoms clusters for short intervals. At 700 K, the vacancies are also generated in the vicinity of the adatoms cluster, vacancy formation, filling, and shifting can be observed from the results.

  11. Molecular dynamics simulation of nanoscale surface diffusion of heterogeneous adatoms clusters

    Science.gov (United States)

    Muhammad, Imran; Fayyaz, Hussain; Muhammad, Rashid; Muhammad, Ismail; Hafeez, Ullah; Yongqing, Cai; M Arshad, Javid; Ejaz, Ahmad; S, A. Ahmad

    2016-07-01

    Molecular dynamics simulation employing the embedded atom method potential is utilized to investigate nanoscale surface diffusion mechanisms of binary heterogeneous adatoms clusters at 300 K, 500 K, and 700 K. Surface diffusion of heterogeneous adatoms clusters can be vital for the binary island growth on the surface and can be useful for the formation of alloy-based thin film surface through atomic exchange process. The results of the diffusion process show that at 300 K, the diffusion of small adatoms clusters shows hopping, sliding, and shear motion; whereas for large adatoms clusters (hexamer and above), the diffusion is negligible. At 500 K, small adatoms clusters, i.e., dimer, show almost all possible diffusion mechanisms including the atomic exchange process; however no such exchange is observed for adatoms clusters greater than dimer. At 700 K, the exchange mechanism dominates for all types of clusters, where Zr adatoms show maximum tendency and Ag adatoms show minimum or no tendency toward the exchange process. Separation and recombination of one or more adatoms are also observed at 500 K and 700 K. The Ag adatoms also occupy pop-up positions over the adatoms clusters for short intervals. At 700 K, the vacancies are also generated in the vicinity of the adatoms cluster, vacancy formation, filling, and shifting can be observed from the results.

  12. Adsorption of CO molecules on the Si(111)-(7×7) surface

    Science.gov (United States)

    Seo, Eonmi; Eom, Daejin; Hyun, Jung-Min; Kim, Hanchul; Koo, Ja-Yong

    2017-02-01

    Adsorption of CO molecules on Si(111)-(7×7) is investigated by using scanning tunneling microscopy (STM) and density-functional theory calculations. The most reactive site on the Si(111)-(7×7) surface is the corner adatom in the faulted half unit (FHU), followed by the center adatom in the FHU. The initial sticking probability of CO molecules on Si(111)-(7×7) at room temperature (RT) is estimated to be ∼ 4 ×1010 molecules/(cm2·Langmuir), which is comparable with that on Si(001)-(2×1). From the experiments and theoretical calculations, the adsorption of CO molecules are found to occur on Si adatoms either in the upright on-top configuration or in the back-bond inserted configuration, while the adsorption on the rest and the corner hole atoms (which are theoretically probable) are not observable using STM due to their low-lying geometries. Though the sticking probability is very low, every surface dangling bond on the surface can bind strongly with the C atom of a CO molecule even at temperatures higher than RT.

  13. Electrostatic Surface Trap for Cold Polar Molecules with a Charged Circular Wire

    Institute of Scientific and Technical Information of China (English)

    MA Hui; ZHOU Bei; LIAO Bin; YIN Jian-Ping

    2007-01-01

    We propose a novel scheme to trap cold polar molecules on the surface of an insulating substrate (i.e. a chip) by using an inhomogeneous electrostatic field, which is generated by the combination of a circular charged wire (a ring electrode) and a grounded metal plate. The spatial distributions of the electrostatic field from the above charged wire layout and its Stark potentials for CO molecules are calculated. Our study shows that when the voltage applied to the wire is U = 15 kV, a ring radius is R = 5 mm, the thickness of the insulating substrate is b = 5 mm, and a wire radius is r = 1 mm, the maximum efficient trapping potential (i.e., as equivalent temperature) for CO molecules is greater than 141.7mK, which is high enough to trap cold polar molecules with a temperature of 50 mK in the low-field-seeking states.

  14. Electronic friction near metal surfaces: a case where molecule-metal couplings depend on nuclear coordinates

    CERN Document Server

    Dou, Wenjie

    2016-01-01

    We derive an explicit form for the electronic friction as felt by a molecule near a metal surface for the general case that molecule-metal couplings depend on nuclear coordinates. Our work generalizes a previous study by von Oppen et al [Beilstein Journal of Nanotechnology, 3, 144, 2012], where we now go beyond the Condon approximation (i.e. molecule-metal couplings are not held constant). Using a non-equilibrium Green's function formalism in the adiabatic limit, we show that fluctuating metal-molecule couplings lead to new frictional damping terms and random forces, plus a correction to the potential of mean force. Numerical tests are performed and compared with a modified classical master equation; our results indicate that violating the Condon approximation can have a large effect on dynamics.

  15. Electronic friction near metal surfaces: A case where molecule-metal couplings depend on nuclear coordinates

    Science.gov (United States)

    Dou, Wenjie; Subotnik, Joseph E.

    2017-03-01

    We derive an explicit form for the electronic friction as felt by a molecule near a metal surface for the general case that molecule-metal couplings depend on nuclear coordinates. Our work generalizes a previous study by von Oppen et al. [Beilstein J. Nanotechnol. 3, 144 (2012)], where we now go beyond the Condon approximation (i.e., molecule-metal couplings are not held constant). Using a non-equilibrium Green's function formalism in the adiabatic limit, we show that fluctuating metal-molecule couplings lead to new frictional damping terms and random forces, plus a correction to the potential of mean force. Numerical tests are performed and compared with a modified classical master equation; our results indicate that violating the Condon approximation can have a large effect on dynamics.

  16. Novel aspects of fluorescence lifetime for molecules positioned close to metal surfaces

    Science.gov (United States)

    Aussenegg, F. R.; Leitner, A.; Lippitsch, M. E.; Reinisch, H.; Riegler, M.

    1987-10-01

    On metal surfaces with submicroscopic corrugations, surface-enhanced optical processes can be observed. Results obtained by picosecond time-resolved fluorescence spectroscopy for dye molecules in the proximity (0-50 nm) of silver islands films are reported. It is demonstrated how the rather complex dependence of the integral fluorescence intensity on the distance dye-islands, can be resolved in the contributions of different mechanisms by analysing the fluorescence decay curves at various distances. It turns out, that the enhancement of absorption influences only the peak fluorescence intensity without changing the decay time, while the enhancement of emission and dissipative losses reduces the decay time. Thus time-resolved spectroscopy opens the possibility to test theoretical concepts on surface enhancement and provides basic data for tailoring molecule-metal structures with well-defined surface-enhancement properties.

  17. Surface structures from low energy electron diffraction: Atoms, small molecules and an ordered ice film on metal surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Materer, N.F.

    1995-09-01

    We investigated the surface bonding of various adsorbates (0, S, C{sub 2}H{sub 3} and NO) along with the resulting relaxation of the Pt(111) surface using low energy electron diffiraction (LEED). LEED experiments have been performed on these ordered overlayers along with theoretical structural analysis using automated tensor LEED (ATLEED). The resulting surface structures of these ordered overlayers exhibit similar adsorbate-induced relaxations. In all cases the adsorbate occupies the fcc hollow site and induces an approximately 0.1 A buckling of the metal surface. The three metal atoms directly bonded to the adsorbate are ``pulled`` out of the surface and the metal atom that is not bound to the adsorbate is `pushed`` inward. In order to understand the reliability of such details, we have carried out a comprehensive study of various non-structural parameters used in a LEED computation. We also studied the adsorption of water on the Pt(lll) surface. We ordered an ultra thin ice film on this surface. The film`s surface is found to be the (0001) face of hexagonal ice. This surface is apparently terminated by a full-bilayer, in which the uppermost water molecules have large vibrational amplitudes even at temperatures as low as 90 K. We examined two other metal surfaces besides Pt(111): Ni(111) and Fe(lll). On Ni(111), we have studied the surface under a high coverage of NO. On both Ni(111) and Pt(111) NO molecules occupy the hollow sites and the N-0 bond distances are practically identical. The challenging sample preparation of an Fe(111) surface has been investigated and a successful procedure has been obtained. The small interlayer spacing found on Fe(111) required special treatment in the LEED calculations. A new ATLEED program has been developed to handle this surface.

  18. Evidence for photo-induced charge separation between dye molecules adsorbed to aluminium oxide surfaces.

    Science.gov (United States)

    Cappel, Ute B; Moia, Davide; Bruno, Annalisa; Vaissier, Valerie; Haque, Saif A; Barnes, Piers R F

    2016-02-19

    Excited state dynamics and photo-induced charge transfer of dye molecules have been widely studied due to their relevance for organic and dye-sensitised solar cells. Herein, we present a femtosecond transient absorption spectroscopy study of the indolene dye D131 when adsorbed to inert Al2O3 substrates for different surface concentration of the dye. Surprisingly, we find that at high surface concentrations, the first singlet excited state of the dye is converted into a new state with an efficiency of about 80%. We assign the absorption features of this state to the oxidised dye and discuss the possibility of photo-induced charge separation between neighboring dye molecules. Our study is the first to show that this process can be highly efficient without the use of donor and acceptor molecules of different chemical structures.

  19. Particle, Energy and Rovibrational Spectra of Molecules Chemically Sputtered of Carbon Surfaces

    Science.gov (United States)

    Krstic, Predrag; Reinhold, Carlos; Stuart, Steven

    2007-06-01

    We perform classical molecular dynamics simulations of the chemical sputtering of deuterated amorphous carbon surfaces by deuterium atoms and molecules at impact energies from threshold to 50 eV/D. Particular attention is paid to the preparation of the target surfaces for varying impact projectile fluence, energy and species [1]. The spectra of hydrocarbon molecules CxDy, with x in range 1 to 5 are observed, and spectral distributions of their translational, rotational and vibrational energies are analyzed. Angular spectra of the sputtered molecules are also analyzed. Our results show good agreement with existing experimental data. [1] P. S. Krstic, C. O. Reinhold, and S. J. Stuart, Europhysics Letters 77, 33002(2007).

  20. Cluster beam steering onto silicon surfaces studied by molecular dynamics

    CERN Document Server

    Mazzone, A M

    2002-01-01

    The purpose of this study is to investigate the effects of the impact conditions on cluster deposition in silicon and is motivated by recent results obtained using a variable incidence angle during deposition of metallic clusters and atoms. Therefore deposition of silicon clusters with a kinetic energy in the range from 0.5 to 10 eV/atom directed at normal and grazing incidence onto crystalline silicon has been studied using a molecular dynamics simulation method. The influence of other relevant parameters, such as the interatomic forces and the cluster size and shape, has also been investigated. This study shows that the physics of deposition is almost entirely dictated by the nature of the interatomic forces. When using potentials with the four-fold coordination typical of bulk a clear dependence on the size N is observed and the spreading index eta decreases with the increase of N for all incidence conditions. The cluster binding strength is perceptibly increased when using a potential accounting for the c...

  1. Reversible capture of small molecules on bimetallaborane clusters: synthesis, structural characterization, and photophysical aspects.

    Science.gov (United States)

    Bould, Jonathan; Baše, Tomáš; Londesborough, Michael G S; Oro, Luis A; Macías, Ramón; Kennedy, John D; Kubát, Pavel; Fuciman, Marcel; Polívka, Tomáš; Lang, Kamil

    2011-08-15

    Metallaborane compounds containing two adjacent metal atoms, [(PMe(2)Ph)(4)MM'B(10)H(10)] (where MM' = Pt(2), 1; PtPd, 7; Pd(2), 8), have been synthesized, and their propensity to sequester O(2), CO, and SO(2) and to then release them under pulsed and continuous irradiation are described. Only [(PMe(2)Ph)(4)Pt(2)B(10)H(10)], 1, undergoes reversible binding of O(2) to form [(PMe(2)Ph)(4)(O(2))Pt(2)B(10)H(10)] 3, but solutions of 1, 7, and 8 all quantitatively take up CO across their metal-metal vectors to form [(PMe(2)Ph)(4)(CO)Pt(2)B(10)H(10)] 4, [(PMe(2)Ph)(4)(CO)PtPdB(10)H(10)] 10, and [(PMe(2)Ph)(4)(CO)Pd(2)B(10)H(10)] 11, respectively. Crystallographically determined interatomic M-M distances and infrared CO stretching frequencies show that the CO molecule is bound progressively more weakly in the sequence {PtPt} > {PtPd} > {PdPd}. Similarly, SO(2) forms [(PMe(2)Ph)(4)(SO(2))Pt(2)B(10)H(10)] 5, [(PMe(2)Ph)(4)(SO(2))PtPdB(10)H(10)] 12, and [(PMe(2)Ph)(4)(SO(2))Pd(2)B(10)H(10)] 13 with progressively weaker binding of the SO(2) molecule. The uptake and release of gas molecules are accompanied by changes in their absorption spectra. Nanosecond transient absorption spectroscopy clearly shows that the O(2) and CO molecules are liberated from the bimetallic binding site with high quantum yields of about 0.6. For 3, in addition to dioxygen release in the triplet ground state, singlet oxygen O(2)((1)Δ(g)) was also detected with a quantum yield 1 ns). All these compounds may have potential to serve as light-triggered local and instantaneous sources of the studied gases.

  2. Theory of the reaction dynamics of small molecules on metal surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, Bret [Univ. of Massachusetts, Amherst, MA (United States)

    2016-09-09

    The objective of this project has been to develop realistic theoretical models for gas-surface interactions, with a focus on processes important in heterogeneous catalysis. The dissociative chemisorption of a molecule on a metal is a key step in many catalyzed reactions, and is often the rate-limiting step. We have explored the dissociative chemisorption of H2, H2O and CH4 on a variety of metal surfaces. Most recently, our extensive studies of methane dissociation on Ni and Pt surfaces have fully elucidated its dependence on translational energy, vibrational state and surface temperature, providing the first accurate comparisons with experimental data. We have explored Eley-Rideal and hot atom reactions of H atoms with H- and C-covered metal surfaces. H atom interactions with graphite have also been explored, including both sticking and Eley-Rideal recombination processes. Again, our methods made it possible to explain several experiments studying these reactions. The sticking of atoms on metal surfaces has also been studied. To help elucidate the experiments that study these processes, we examine how the reaction dynamics depend upon the nature of the molecule-metal interaction, as well as experimental variables such as substrate temperature, beam energy, angle of impact, and the internal states of the molecules. Electronic structure methods based on Density Functional Theory are used to compute each molecule-metal potential energy surface. Both time-dependent quantum scattering techniques and quasi-classical methods are used to examine the reaction or scattering dynamics. Much of our effort has been directed towards developing improved quantum methods that can accurately describe reactions, as well as include the effects of substrate temperature (lattice vibration).

  3. Density functional theory study of nitrogen atoms and molecules interacting with Fe(1 1 1) surfaces

    Science.gov (United States)

    Nosir, M. A.; Martin-Gondre, L.; Bocan, G. A.; Díez Muiño, R.

    2016-09-01

    We present Density functional theory (DFT) calculations for the investigation of the structural relaxation of Fe(1 1 1), as well as for the study of the interaction of nitrogen atoms and molecules with this surface. We perform spin polarized DFT calculations using VASP (Vienna Ab-initio Simulation Package) code. We use the supercell approach and up to 19 slab layers for the relaxation of the Fe(1 1 1) surface. We find a contraction of the first two interlayer distances with a relative value of Δ12 = - 7.8 % and Δ23 = - 21.7 % with respect to the bulk reference. The third interlayer distance is however expanded with a relative change of Δ34 = 9.7 % . Early experimental studies of the surface relaxation using Low Energy Electron Diffraction (LEED) and Medium Energy Ion Scattering (MEIS) showed contradictory results, even on the relaxation general trend. Our current theoretical results support the LEED conclusions and are consistent qualitatively with other recent theoretical calculations. In addition, we study the interaction energy of nitrogen atoms and molecules on the Fe(1 1 1) surface. The nitrogen atoms are adsorbed in the hollow site of the unit cell, with an adsorption energy consistent with the one found in previous studies. In addition, we find the three molecularly adsorbed states that are observed experimentally. Two of them correspond to the adsorbed molecule oriented normal to the surface and a third one corresponds to the molecule adsorbed parallel to the surface. We conclude that our results are accurate enough to be used to build a full six-dimensional potential energy surface for the N2 system.

  4. Combining Theory and Experiment to Characterize the Atomic Structures of Surface-Deposited Au309 Clusters

    NARCIS (Netherlands)

    Curley, B.C.; Johnston, R.L.; Young, N.P.; Li, Z.; Di Vece, M.; Palmer, R.E.; Bleloch, A.l.

    2007-01-01

    Gold clusters with icosahedral, decahedral, and cuboctahedral shell structures, have been studied using the Gupta many-body potential, to aid in the structural characterization of surface-deposited Au309 clusters using high-angle annular dark field-scanning transmission electron microscopy (HAADF-ST

  5. Donor-Acceptor Properties of a Single-Molecule Altered by On-Surface Complex Formation.

    Science.gov (United States)

    Meier, Tobias; Pawlak, Rémy; Kawai, Shigeki; Geng, Yan; Liu, Xunshan; Decurtins, Silvio; Hapala, Prokop; Baratoff, Alexis; Liu, Shi-Xia; Jelínek, Pavel; Meyer, Ernst; Glatzel, Thilo

    2017-08-22

    Electron donor-acceptor molecules are of outstanding interest in molecular electronics and organic solar cells for their intramolecular charge transfer controlled via electrical or optical excitation. The preservation of their electronic character in the ground state upon adsorption on a surface is cardinal for their implementation in such single-molecule devices. Here, we investigate by atomic force microscopy and scanning tunneling microscopy a prototypical system consisting of a π-conjugated tetrathiafulvalene-fused dipyridophenazine molecule adsorbed on thin NaCl films on Cu(111). Depending on the adsorption site, the molecule is found either in a nearly undisturbed free state or in a bound state. In the latter case, the molecule adopts a specific adsorption site, leading to the formation of a chelate complex with a single Na(+) alkali cation pulled out from the insulating film. Although expected to be electronically decoupled, the charge distribution of the complex is drastically modified, leading to the loss of the intrinsic donor-acceptor character. The chelate complex formation is reversible with respect to lateral manipulations, enabling tunable donor-acceptor molecular switches activated by on-surface coordination.

  6. Non-additivity of molecule-surface van der Waals potentials from force measurements.

    Science.gov (United States)

    Wagner, Christian; Fournier, Norman; Ruiz, Victor G; Li, Chen; Müllen, Klaus; Rohlfing, Michael; Tkatchenko, Alexandre; Temirov, Ruslan; Tautz, F Stefan

    2014-11-26

    Van der Waals (vdW) forces act ubiquitously in condensed matter. Despite being weak on an atomic level, they substantially influence molecular and biological systems due to their long range and system-size scaling. The difficulty to isolate and measure vdW forces on a single-molecule level causes our present understanding to be strongly theory based. Here we show measurements of the attractive potential between differently sized organic molecules and a metal surface using an atomic force microscope. Our choice of molecules and the large molecule-surface separation cause this attraction to be purely of vdW type. The experiment allows testing the asymptotic vdW force law and its validity range. We find a superlinear growth of the vdW attraction with molecular size, originating from the increased deconfinement of electrons in the molecules. Because such non-additive vdW contributions are not accounted for in most first-principles or empirical calculations, we suggest further development in that direction.

  7. Nonlinear reconstruction of single-molecule free-energy surfaces from univariate time series.

    Science.gov (United States)

    Wang, Jiang; Ferguson, Andrew L

    2016-03-01

    The stable conformations and dynamical fluctuations of polymers and macromolecules are governed by the underlying single-molecule free energy surface. By integrating ideas from dynamical systems theory with nonlinear manifold learning, we have recovered single-molecule free energy surfaces from univariate time series in a single coarse-grained system observable. Using Takens' Delay Embedding Theorem, we expand the univariate time series into a high dimensional space in which the dynamics are equivalent to those of the molecular motions in real space. We then apply the diffusion map nonlinear manifold learning algorithm to extract a low-dimensional representation of the free energy surface that is diffeomorphic to that computed from a complete knowledge of all system degrees of freedom. We validate our approach in molecular dynamics simulations of a C(24)H(50) n-alkane chain to demonstrate that the two-dimensional free energy surface extracted from the atomistic simulation trajectory is - subject to spatial and temporal symmetries - geometrically and topologically equivalent to that recovered from a knowledge of only the head-to-tail distance of the chain. Our approach lays the foundations to extract empirical single-molecule free energy surfaces directly from experimental measurements.

  8. Interplay of radiative and nonradiative transitions in surface hopping with radiation-molecule interactions

    Energy Technology Data Exchange (ETDEWEB)

    Bajo, Juan José [Departamento de Química-Física I, Universidad Complutense de Madrid, 28040 Madrid (Spain); Granucci, Giovanni, E-mail: giovanni.granucci@unipi.it; Persico, Maurizio [Università di Pisa, Dipartimento di Chimica e Chimica Industriale, via Risorgimento 35, 56126 Pisa (Italy)

    2014-01-28

    We implemented a method for the treatment of field induced transitions in trajectory surface hopping simulations, in the framework of the local diabatization scheme, especially suited for on-the-fly dynamics. The method is applied to a simple one-dimensional model with an avoided crossing and compared with quantum wavepacket dynamics. The results show the importance of introducing a proper decoherence correction to surface hopping, in order to obtain meaningful results. Also the energy conservation policy of standard surface hopping must be revised: in fact, the quantum wavepacket energetics is well reproduced if energy absorption/emission is allowed for in the hops determined by radiation-molecule coupling. To our knowledge, this is the first time the issues of decoherence and energy conservation have been analyzed in depth to devise a mixed quantum-classical method for dynamics with molecule-field interactions.

  9. Multiple atomic scale solid surface interconnects for atom circuits and molecule logic gates.

    Science.gov (United States)

    Joachim, C; Martrou, D; Rezeq, M; Troadec, C; Jie, Deng; Chandrasekhar, N; Gauthier, S

    2010-03-05

    The scientific and technical challenges involved in building the planar electrical connection of an atomic scale circuit to N electrodes (N > 2) are discussed. The practical, laboratory scale approach explored today to assemble a multi-access atomic scale precision interconnection machine is presented. Depending on the surface electronic properties of the targeted substrates, two types of machines are considered: on moderate surface band gap materials, scanning tunneling microscopy can be combined with scanning electron microscopy to provide an efficient navigation system, while on wide surface band gap materials, atomic force microscopy can be used in conjunction with optical microscopy. The size of the planar part of the circuit should be minimized on moderate band gap surfaces to avoid current leakage, while this requirement does not apply to wide band gap surfaces. These constraints impose different methods of connection, which are thoroughly discussed, in particular regarding the recent progress in single atom and molecule manipulations on a surface.

  10. The Surface Morphology and Optical Properties of Refined Glasses with Inorganic Nano-molecules

    Science.gov (United States)

    Drajewicz, Marcin; Pytel, Maciej; Rokicki, Paweł; Góral, Marek

    2015-05-01

    New refining technology of soda-calcium-silicon glass surfaces with inorganic compounds nano-molecules has been presented in the study. In order to determine modification of the glass surface SEM observation and EDX analysis have been carried out. The UV-VIS, photo-elasticity and ellipsometry examinations were carried out on glass samples. The results of investigations that have been conducted show that refining process of the glass surface by use of nanopowder inorganic compounds deposited electrostatically on glass surface provides forming of very thin (about 50 nm) surface layers [1]. This method of surface modification improves physical and chemical glass properties. In this paper results of microhardness test of refined glass were also presented.

  11. Time persistency of floating particle clusters in free-surface turbulence

    CERN Document Server

    Lovecchio, Salvatore; Soldati, Alfredo

    2013-01-01

    We study the dispersion of light particles floating on a flat shear-free surface of an open channel in which the flow is turbulent. This configuration mimics the motion of buoyant matter (e.g. phytoplankton, pollutants or nutrients) in water bodies when surface waves and ripples are smooth or absent. We perform direct numerical simulation of turbulence coupled with Lagrangian particle tracking, considering different values of the shear Reynolds number (Re{\\tau} = 171 and 509) and of the Stokes number (0.06 < St < 1 in viscous units). Results show that particle buoyancy induces clusters that evolve towards a long-term fractal distribution in a time much longer than the Lagrangian integral fluid time scale, indicating that such clusters over-live the surface turbulent structures which produced them. We quantify cluster dynamics, crucial when modeling dispersion in free-surface flow turbulence, via the time evolution of the cluster correlation dimension.

  12. Molecule-surface interaction processes of relevance to gas blanket type fusion device divertor design

    Energy Technology Data Exchange (ETDEWEB)

    Snowdon, K.J. [Newcastle Univ. (United Kingdom). Dept. of Physics; Tawara, H.

    1997-01-01

    The mechanisms which may lead to the departure of molecular species from surfaces exposed to low energy (0.1-100 eV) particle or photon and electron irradiation are reviewed. Where possible, the charge and electronic state, angular, translational and internal energy distributions of the departing molecules are described and the physical origin of the nature of those distributions identified. The consequences, for the departing molecules, of certain material choices become apparent from such an analysis. Such information may help guide the choice of appropriate materials for plasma facing components of gas-blanket type divertors such as that recently proposed for the International Thermonuclear Experimental Reactor (ITER). (author). 71 refs.

  13. Selective on site separation and detection of molecules in diluted solutions with super-hydrophobic clusters of plasmonic nanoparticles

    KAUST Repository

    Gentile, Francesco T.

    2014-01-01

    Super-hydrophobic surfaces are bio-inspired interfaces with a superficial texture that, in its most common evolution, is formed by a periodic lattice of silicon micro-pillars. Similar surfaces reveal superior properties compared to conventional flat surfaces, including very low friction coefficients. In this work, we modified meso-porous silicon micro-pillars to incorporate networks of metal nano-particles into the porous matrix. In doing so, we obtained a multifunctional-hierarchical system in which (i) at a larger micrometric scale, the super-hydrophobic pillars bring the molecules dissolved in an ultralow-concentration droplet to the active sites of the device, (ii) at an intermediate meso-scale, the meso-porous silicon film adsorbs the low molecular weight content of the solution and, (iii) at a smaller nanometric scale, the aggregates of silver nano-particles would measure the target molecules with unprecedented sensitivity. In the results, we demonstrated how this scheme can be utilized to isolate and detect small molecules in a diluted solution in very low abundance ranges. The presented platform, coupled to Raman or other spectroscopy techniques, is a realistic candidate for the protein expression profiling of biological fluids. © 2014 the Partner Organisations.

  14. Chemistry of the interaction between azole type corrosion inhibitor molecules and metal surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Kovacevic, Natasa [Department of Physical and Organic Chemistry, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia); Kokalj, Anton, E-mail: tone.kokalj@ijs.si [Department of Physical and Organic Chemistry, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia)

    2012-11-15

    By means of density functional theory calculations, it has been shown how typical organic corrosion inhibitors-molecules that have the ability to remarkably slow down the corrosion of metals and alloys-interact with bare surfaces of various types of metals. As representative model systems, benzimidazole and benzotriazole inhibitors on iron, copper, and aluminum surfaces are considered. It is found that bonding depends sensitively on the type of metal. On transition metals with open d-band the inhibitor molecules can chemisorb strongly either parallel to the surface with a pronounced {pi}-d hybridization or perpendicularly with unsaturated N atom(s) through {sigma}-molecular orbitals, whereas on transition metals with fully occupied d-band and on sp-metals the molecules weakly chemisorb only with the latter mode. In addition to neutral inhibitor molecules also inhibitors in deprotonated (anionic) and protonated (cationic) forms are considered, because many corrosion inhibitors possess acidic hydrogens as well as basic heteroatoms. It is shown that the chemisorptive bonding is far the strongest for deprotonated inhibitors and, moreover, that even protonated inhibitors may chemisorb, although such bonding is characteristic of more reactive metals. However adsorbed protonated inhibitors are likely to deprotonate on all considered metals, whereas further deprotonation from neutral to deprotonated form is more likely on more reactive metals. Highlights: Black-Right-Pointing-Pointer Bonding of azole corrosion inhibitors onto metal surfaces characterized by DFT calculations. Black-Right-Pointing-Pointer Adsorption bonding depends sensitively on the type of metal. Black-Right-Pointing-Pointer Azoles bond with either {pi}-system or {sigma}-orbitals to transition metals with open d-band. Black-Right-Pointing-Pointer Azoles bond with {sigma}-orbitals to transition metals with fully occupied d-band and to sp-metals. Black-Right-Pointing-Pointer Among various molecular forms

  15. Binding of Solvent Molecules to a Protein Surface in Binary Mixtures Follows a Competitive Langmuir Model.

    Science.gov (United States)

    Kulschewski, Tobias; Pleiss, Jürgen

    2016-09-06

    The binding of solvent molecules to a protein surface was modeled by molecular dynamics simulations of of Candida antarctica (C. antarctica) lipase B in binary mixtures of water, methanol, and toluene. Two models were analyzed: a competitive Langmuir model which assumes identical solvent binding sites with a different affinity toward water (KWat), methanol (KMet), and toluene (KTol) and a competitive Langmuir model with an additional interaction between free water and already bound water (KWatWat). The numbers of protein-bound molecules of both components of a binary mixture were determined for different compositions as a function of their thermodynamic activities in the bulk phase, and the binding constants were simultaneously fitted to the six binding curves (two components of three different mixtures). For both Langmuir models, the values of KWat, KMet, and KTol were highly correlated. The highest binding affinity was found for methanol, which was almost 4-fold higher than the binding affinities of water and toluene (KMet ≫ KWat ≈ KTol). Binding of water was dominated by the water-water interaction (KWatWat). Even for the three protein surface patches of highest water affinity, the binding affinity of methanol was 2-fold higher than water and 8-fold higher than toluene (KMet > KWat > KTol). The Langmuir model provides insights into the protein destabilizing mechanism of methanol which has a high binding affinity toward the protein surface. Thus, destabilizing solvents compete with intraprotein interactions and disrupt the tertiary structure. In contrast, benign solvents such as water or toluene have a low affinity toward the protein surface. Water is a special solvent: only few water molecules bind directly to the protein; most water molecules bind to already bound water molecules thus forming water patches. A quantitative mechanistic model of protein-solvent interactions that includes competition and miscibility of the components contributes a robust basis

  16. First-principles investigation of helium dissolution and clustering at a tungsten (1 1 0) surface

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jinlong; Zhang, Ying, E-mail: zhyi@buaa.edu.cn; Zhou, Hong-Bo; Jin, Shuo; Lu, Guang-Hong, E-mail: lgh@buaa.edu.cn

    2015-06-15

    Using a first-principles method, we have investigated dissolution, self-trapping and clustering of He at a W(1 1 0) surface. We found that the He atom is not energetically favorable at both the surface and the subsurface, but it becomes stable under the second atomic layer from the surface. The He is easier to be self-trapped to form an He cluster at the near surface in comparison with the bulk due to the larger self-trapping range and the stronger binding energy. With the formation of such He cluster, the vacancy and thus the He-vacancy complex are able to form at the near surface. The results will provide a useful reference for understanding formation of the He bubble at the W surface.

  17. Atomic scale modelling of Al and Ni(1 1 1) surface erosion under cluster impact

    CERN Document Server

    Zhurkin, E E

    2003-01-01

    We have studied sputtering of Al and Ni(1 1 1) surfaces under impact of Al sub N and Ni sub N clusters (1=13. The pronounced microcraters are formed in the impact region above a threshold cluster size of around N=13. As a sensitivity study, we show that interaction with electronic subsystem of the target has a strong influence on secondary emission, but almost does not affect the features of surface microstructure of irradiated target.

  18. Structural Stabilities of Ordered Nb4 Clusters on the Cu(111) and Cu(100) Surfaces

    Institute of Scientific and Technical Information of China (English)

    WANG Xiao-Chun; ZHU Zi-Zhong

    2007-01-01

    @@ Based on first-principles calculations, we show that very high-density periodic arrays of Nb4 clusters with both the tetrahedron and quadrangle configurations can be stably absorbed on the Cu(111) and Cu(100) surfaces,with the quadrangle configurations more stable than the tetrahedron ones. The strong covalent bonding between atoms within the Nb4 clusters contributes to the stability of Nb4 adsorptions on the Cu surfaces.

  19. Design and preparation of matrine surface-imprinted material and studies on its molecule recognition selectivity.

    Science.gov (United States)

    Lei, Qingjuan; Gao, Baojiao; Zhang, Dandan

    2016-01-01

    A matrine molecule surface-imprinted material was designed and prepared using an effective surface-imprinting technique developed by our group, and its molecular recognition performance and mechanism were investigated in depth. Monomer glycidyl methacrylate (GMA) was first graft-polymerized on the surfaces of micron-sized silica gel particles in surface-initiated graft polymerization manner, obtaining the grafted particles PGMA/SiO(2) with high grafting degree. Subsequently, the ring-opening reaction of the epoxy groups of the grafted macromolecules PGMA with 5-aminosalicylic acid (5-ASA) was carried out, resulting in the functional grafted particle SA-PGMA/SiO(2), on whose surfaces salicylic acid as functional group was chemically bonded. By right of the mutual strong secondary bond forces, electrostatic interaction and hydrogen bonding, SA-PGMA/SiO(2) particles produced strong adsorption for matrine. Finally, with this strong adsorption, matrine molecule surface imprinting was carried out on the surfaces of SA-PGMA/SiO(2) particles with ethylene glycol diglycidyl ether as cross-linking agent, resulting in the matrine molecule surface-imprinted material MIP-SAP/SiO(2). The binding characteristic of MIP-SAP/SiO(2) toward matrine was investigated in depth with both batch and column methods and using oxymatrine and cytisine as two contrast alkaloids. The experimental results show that MIP-SAP/SiO(2) has special recognition selectivity and excellent binding affinity for matrine. Relative to oxymatrine and cytisine, the selectivity coefficients of MIP-SAP/SiO(2) for matrine are 5.66 and 11.17, respectively.

  20. Detecting edges in the X-ray surface brightness of galaxy clusters

    CERN Document Server

    Sanders, J S; Russell, H R; Walker, S A; Blundell, K M

    2016-01-01

    The effects of many physical processes in the intracluster medium of galaxy clusters imprint themselves in X-ray surface brightness images. It is therefore important to choose optimal methods for extracting information from and enhancing the interpretability of such images. We describe in detail a gradient filtering edge detection method that we previously applied to images of the Centaurus cluster of galaxies. The Gaussian gradient filter measures the gradient in the surface brightness distribution on particular spatial scales. We apply this filter on different scales to Chandra X-ray observatory images of two clusters with AGN feedback, the Perseus cluster and M87, and a merging system, A3667. By combining filtered images on different scales using radial filters spectacular images of the edges in a cluster are produced. We describe how to assess the significance of features in filtered images. We find the gradient filtering technique to have significant advantages for detecting many kinds of features compar...

  1. Structures of Adatom Clusters on Ag(111) Surface by Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    SUN Zhi-Hua; LIU Qing-Wei; LI Yu-Fen; ZHUANG Jun

    2004-01-01

    @@ We study the structures of Ag adatom clusters supported on the metal Ag(111) surface using the genetic algorithm (GA). The atomic interactions are modelled by the surface-embedded-atom method. The lowest-energy structures of adatom clusters with sizes n = 3-20 are obtained, in which n = 7, 10, 12, 14, 16, 19 are the magic numbers.Furthermore, we give a series of structures with energies close to the lowest energy (the lower-energy isomers), and the structure features are studied in detail. Except for some magic clusters and small clusters, every configuration of adatom clusters generally has two distinct adsorption ways, so the isomers always appear in pairs.

  2. Post-deposition dynamics of multiple cluster aggregation on liquid surfaces

    Institute of Scientific and Technical Information of China (English)

    Wu Feng-Min; Xu You-Sheng; Ye Gao-Xiang; Wu Zi-Qin

    2005-01-01

    A comprehensive simulation model-deposition, diffusion, rotation and aggregation-is presented to demonstrate the post-deposition phenomena of multiple cluster growth on liquid surfaces, such as post-deposition nucleation, postdeposition growth and post-deposition coalescence. Emphasis is placed on the relaxations of monomer density, dimer density and cluster density as well as combined cluster-plus-monomer density with time after deposition ending. It isshown that post-deposition coalescence largely takes place after deposition due to the large mobility of clusters on liquid surfaces, while the post-deposition nucleation is only possible before the saturation cluster density is reached at the end of the deposition. The deposition flux and the moment of deposition ending play important roles in the post-deposition dynamics.

  3. Coronene molecules in helium clusters: Quantum and classical studies of energies and configurations

    Energy Technology Data Exchange (ETDEWEB)

    Rodríguez-Cantano, Rocío; Pérez de Tudela, Ricardo; Bartolomei, Massimiliano; Hernández, Marta I.; Campos-Martínez, José; González-Lezana, Tomás, E-mail: t.gonzalez.lezana@csic.es; Villarreal, Pablo [Instituto de Física Fundamental, IFF-CSIC, Serrano 123, 28006 Madrid (Spain); Hernández-Rojas, Javier; Bretón, José [Departamento de Física and IUdEA, Universidad de La Laguna, 38205 Tenerife (Spain)

    2015-12-14

    Coronene-doped helium clusters have been studied by means of classical and quantum mechanical (QM) methods using a recently developed He–C{sub 24}H{sub 12} global potential based on the use of optimized atom-bond improved Lennard-Jones functions. Equilibrium energies and geometries at global and local minima for systems with up to 69 He atoms were calculated by means of an evolutive algorithm and a basin-hopping approach and compared with results from path integral Monte Carlo (PIMC) calculations at 2 K. A detailed analysis performed for the smallest sizes shows that the precise localization of the He atoms forming the first solvation layer over the molecular substrate is affected by differences between relative potential minima. The comparison of the PIMC results with the predictions from the classical approaches and with diffusion Monte Carlo results allows to examine the importance of both the QM and thermal effects.

  4. Stability of Ta-encapsulating Si clusters on Si(111)-(7x7) surfaces

    CERN Document Server

    Uchida, N; Miyazaki, T; Kanayama, T

    2003-01-01

    Tantalum containing Si cluster ions TaSi sub 1 sub 0 sub - sub 1 sub 3 H sub x sup + were synthesized in an ion trap and deposited onto Si(111)-(7x7) surfaces with a kinetic energy of 18 eV. Scanning tunnelling microscope observations revealed that the clusters adsorbed on the surface without decomposition, consistent with ab initio calculation results, that predicted the clusters would have stable Si-cage structures with a Ta atom at the centre. (rapid communication)

  5. Single molecule detection of 4-dimethylaminoazobenzene by surface-enhanced Raman spectroscopy

    Science.gov (United States)

    Zhang, Z. L.; Yin, Y. F.; Jiang, J. W.; Mo, Y. J.

    2009-02-01

    4-Dimethylaminoazobenzene (DAB) is anticipated to be a human carcinogen based on sufficient evidence of carcinogenicity in experimental animals. The trace detection of DAB is of great significance in environmental protection and safe life of the people. To test the availability of DAB trace detection using surface-enhanced Raman scattering (SERS), the SERS spectra of DAB single molecules adsorbed on the silver particle aggregates in colloid were investigated. The phenomena of blinking, spectral diffusion, and intensity fluctuations of the vibrational lines in the SERS spectra were observed. Statistical analysis of spectral intensity fluctuations indicates a multimodal distribution of some specific Raman bands, which are consistent with the identification of single molecule detection. Our results demonstrated that SERS can be applied to the trace detection of DAB molecules and other azo dyes.

  6. Formation and local electronic structure of Ge clusters on Si(111)-7×7 surfaces

    Institute of Scientific and Technical Information of China (English)

    Ma Hai-Feng; Xu Ming-Chun; Yang Bing; Shi Dong-Xia; Guo Hai-Ming; Pang Shi-Jin; Gao Hong-Jun

    2007-01-01

    We report the formation and local electronic structure of Ge clusters on the Si(111)-7×7 surface studied by using variable temperature scanning tunnelling microscopy (VT-STM) and low-temperature scanning tunnelling spectroscopy (STS). Atom-resolved STM images reveal that the Ge atoms are prone to forming clusters with 1.0 nm in diameter for coverage up to 0.12 ML. Such Ge clusters preferentially nucleate at the centre of the faulted-half unit cells, leading to the 'dark sites' of Si centre adatoms from the surrounding three unfaulted-half unit cells in filled-state images. Biasdependent STM images show the charge transfer from the neighbouring Si adatoms to Ge clusters. Low-temperature STS of the Ge clusters reveals that there is a band gap on the Ge cluster and the large voltage threshold is about 0.9 V.

  7. Structures and stabilities of small Co clusters on a Cu(111) surface: A theoretical study

    Science.gov (United States)

    Huang, R. Z.; Chen, C.; Li, C. M.; Jiang, C. H.; Zhang, R. J.; Gao, Y.

    2017-10-01

    Structures and relative stabilities of small Con clusters (n = 1-12) on a Cu(111) surface are studied using molecular dynamics simulations. It is shown that the supported clusters are all in two-dimensional island structures of the edges forming square microfacets (A step) and/or triangular microfacets (B step) with the substrate. For non-magic-number clusters, the lowest energy structures are the ones of the edges with more A steps and the most unstable structures are the ones of the edges with only A steps or B steps due to the lattice mismatch of the Con/Cu(111) system. Magic number clusters are truncated triangular or elongated shapes with a closed atomic shell and maximum nearest-neighbor bonds. In addition, the anomalous mobility is found for Co3 and Co6 clusters in the diffusion processes of these clusters. The concerted translation and rotation movements are responsible for their special diffusion behaviors.

  8. Modelling molecule-surface interactions--an automated quantum-classical approach using a genetic algorithm.

    Science.gov (United States)

    Herbers, Claudia R; Johnston, Karen; van der Vegt, Nico F A

    2011-06-14

    We present an automated and efficient method to develop force fields for molecule-surface interactions. A genetic algorithm (GA) is used to parameterise a classical force field so that the classical adsorption energy landscape of a molecule on a surface matches the corresponding landscape from density functional theory (DFT) calculations. The procedure performs a sophisticated search in the parameter phase space and converges very quickly. The method is capable of fitting a significant number of structures and corresponding adsorption energies. Water on a ZnO(0001) surface was chosen as a benchmark system but the method is implemented in a flexible way and can be applied to any system of interest. In the present case, pairwise Lennard Jones (LJ) and Coulomb potentials are used to describe the molecule-surface interactions. In the course of the fitting procedure, the LJ parameters are refined in order to reproduce the adsorption energy landscape. The classical model is capable of describing a wide range of energies, which is essential for a realistic description of a fluid-solid interface.

  9. Surface plasmon engineering in graphene functionalized with organic molecules: a multiscale theoretical investigation.

    Science.gov (United States)

    Cheng, Jierong; Wang, Wei Li; Mosallaei, Hossein; Kaxiras, Efthimios

    2014-01-08

    Graphene was recently shown to support deep subwavelength surface plasmons at terahertz frequencies characterized by low energy loss and strong field localization, both highly desirable. The properties of graphene can be locally tuned by applying an external gate voltage or by the adsorption of organic molecules that lead to doping through charge transfer. Local tuning of the electronic features of graphene opens the possibility to realize any desired gradient index profile and thus brings large flexibility to control and manipulate the propagation of surface plasmons. Here, we explore this possibility created by functionalizing graphene with organic molecules. We employ a multiscale theoretical approach that combines first-principles electronic structure calculations and finite-difference time-domain simulations coupled by surface conductivity. We show that by patterning two types of organic molecules on graphene, a plasmonic metasurface can be realized with any gradient effective refractive index profile to manipulate surface plasmon beams as desired. The special properties of such devices based on functionalized graphene are compared to the similar metamaterials based on metallic films on top of a gradient index dielectric substrate. Using this idea, we design and analyze an ultrathin broadband THz plasmonic lens as proof-of-concept, while more sophisticated index profiles can also be realized and various plasmonic applications are readily accessible.

  10. Single-Molecule Tribology: Force Microscopy Manipulation of a Porphyrin Derivative on a Copper Surface.

    Science.gov (United States)

    Pawlak, Rémy; Ouyang, Wengen; Filippov, Alexander E; Kalikhman-Razvozov, Lena; Kawai, Shigeki; Glatzel, Thilo; Gnecco, Enrico; Baratoff, Alexis; Zheng, Quanshui; Hod, Oded; Urbakh, Michael; Meyer, Ernst

    2016-01-26

    The low-temperature mechanical response of a single porphyrin molecule attached to the apex of an atomic force microscope (AFM) tip during vertical and lateral manipulations is studied. We find that approach-retraction cycles as well as surface scanning with the terminated tip result in atomic-scale friction patterns induced by the internal reorientations of the molecule. With a joint experimental and computational effort, we identify the dicyanophenyl side groups of the molecule interacting with the surface as the dominant factor determining the observed frictional behavior. To this end, we developed a generalized Prandtl-Tomlinson model parametrized using density functional theory calculations that includes the internal degrees of freedom of the side group with respect to the core and its interactions with the underlying surface. We demonstrate that the friction pattern results from the variations of the bond length and bond angles between the dicyanophenyl side group and the porphyrin backbone as well as those of the CN group facing the surface during the lateral and vertical motion of the AFM tip.

  11. Measuring binding kinetics of aromatic thiolated molecules with nanoparticles via surface-enhanced Raman spectroscopy

    Science.gov (United States)

    Devetter, Brent M.; Mukherjee, Prabuddha; Murphy, Catherine J.; Bhargava, Rohit

    2015-05-01

    Colloidal plasmonic nanomaterials, consisting of metals such as gold and silver, are excellent candidates for advanced optical probes and devices, but precise control over surface chemistry is essential for realizing their full potential. Coupling thiolated (R-SH) molecules to nanoprobe surfaces is a convenient and established route to tailor surface properties. The ability to dynamically probe and monitor the surface chemistry of nanoparticles in solution is essential for rapidly manufacturing spectroscopically tunable nanoparticles. In this study, we report the development of surface-enhanced Raman spectroscopy (SERS) as a method to monitor the kinetics of gold-thiolate bond formation on colloidal gold nanoparticles. A theoretical model combining SERS enhancement with the Beer-Lambert law is proposed to explain ensemble scattering and absorption effects in colloids during chemisorption. In order to maximize biological relevance and signal reproducibility, experiments used to validate the model focused on maintaining nanoparticle stability after the addition of water-soluble aromatic thiolated molecules. Our results indicate that ligand exchange on gold nanoparticles follow a first-order Langmuir adsorption model with rate constants on the order of 0.01 min-1. This study demonstrates an experimental spectroscopic method and theoretical model for monitoring binding kinetics that may prove useful for designing novel probes.Colloidal plasmonic nanomaterials, consisting of metals such as gold and silver, are excellent candidates for advanced optical probes and devices, but precise control over surface chemistry is essential for realizing their full potential. Coupling thiolated (R-SH) molecules to nanoprobe surfaces is a convenient and established route to tailor surface properties. The ability to dynamically probe and monitor the surface chemistry of nanoparticles in solution is essential for rapidly manufacturing spectroscopically tunable nanoparticles. In this

  12. Effective medium potentials for molecule-surface interactions: H2 on Cu and Ni surfaces

    DEFF Research Database (Denmark)

    Nørskov, Jens Kehlet

    1989-01-01

    that the functional form of the total energy expression is derived from density functional theory, that each of the terms entering can be given a precise physical interpretation, and that most of the parameters entering can be calculated, within the local density approximation. The method is explicitly derived for H2...... outside metal surfaces and the applicability is illustrated for H2 adsorbing on various Cu and Ni surfaces. Although very approximate, the calculated potentials seem to include a number of features observed experimentally: Ni is more active in dissociating H2 than Cu, and open surfaces are more active...

  13. Interface formation between hydrocarbon ring molecules and III-V semiconductor surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Passmann, Regina

    2008-08-15

    In this work a systematical study to investigate the adsorption structures of small hydrocarbon ring shaped molecules on III-V semiconductor surfaces with Photo-Emission Spectroscopy (PES), Reflectance Anisotropy Spectroscopy (RAS), Scanning Tunneling Microscopy (STM) as well as Low Electron Energy Diffraction (LEED) was performed. To investigate the influence of the surface structure in detail the surface dimer configuration to the adsorption process of organic molecules GaAs(001) surfaces, the c(4 x 4), the (2 x 4) and the (4 x 2) have been investigated as well as the adsorption of cyclopentene on the InP(001)(2 x 4) reconstructed surface. In the direct comparison it is shown that cyclopentene bonds to the InP(001)(2 x 4) surface via a cycloaddition like reaction. During this adsorption the double bond splits which is in contrast to the adsorption of cyclopentene on the GaAs(001) surfaces. Therefrom it is concluded that the surface geometry has an influence on the resulting adsorption structure. In order to investigate the influence of the intra-molecular double bonds, cyclopentene (one double bond), 1,4-cyclohexadiene (two double bonds) and benzene (three double bonds) were used for the characterization of the interface formation. With the investigations on the GaAs(001) reconstructed surfaces it was shown that a dependency of the bonding configuration on the intra-molecular double bonds exists. During the adsorption of cyclopentene no evidence was found that the double bond has to be involved in the interface formation while during the adsorption of 1,4-cyclohexadiene and benzene the double bonds are involved. Furthermore it was found that a bonding to As atoms of the surface is more likely than a bonding to Ga atoms. (orig.)

  14. Bio-active molecules modified surfaces enhanced mesenchymal stem cell adhesion and proliferation.

    Science.gov (United States)

    Mobasseri, Rezvan; Tian, Lingling; Soleimani, Masoud; Ramakrishna, Seeram; Naderi-Manesh, Hossein

    2017-01-29

    Surface modification of the substrate as a component of in vitro cell culture and tissue engineering, using bio-active molecules including extracellular matrix (ECM) proteins or peptides derived ECM proteins can modulate the surface properties and thereby induce the desired signaling pathways in cells. The aim of this study was to evaluate the behavior of human bone marrow mesenchymal stem cells (hBM-MSCs) on glass substrates modified with fibronectin (Fn), collagen (Coll), RGD peptides (RGD) and designed peptide (R-pept) as bio-active molecules. The glass coverslips were coated with fibronectin, collagen, RGD peptide and R-peptide. Bone marrow mesenchymal stem cells were cultured on different substrates and the adhesion behavior in early incubation times was investigated using scanning electron microscopy (SEM) and confocal microscopy. The MTT assay was performed to evaluate the effect of different bio-active molecules on MSCs proliferation rate during 24 and 72 h. Formation of filopodia and focal adhesion (FA) complexes, two steps of cell adhesion process, were observed in MSCs cultured on bio-active molecules modified coverslips, specifically in Fn coated and R-pept coated groups. SEM image showed well adhesion pattern for MSCs cultured on Fn and R-pept after 2 h incubation, while the shape of cells cultured on Coll and RGD substrates indicated that they might experience stress condition in early hours of culture. Investigation of adhesion behavior, as well as proliferation pattern, suggests R-peptide as a promising bio-active molecule to be used for surface modification of substrate in supporting and inducing cell adhesion and proliferation.

  15. Revisiting the Challenges in Fabricating Uniform Coatings with Polyfunctional Molecules on High Surface Energy Materials

    Directory of Open Access Journals (Sweden)

    Stephanie Oyola-Reynoso

    2015-12-01

    Full Text Available Modifying the chemistry of a surface has been widely used to influence interfacial properties of a material or nature of interaction between two materials. This article provides an overview on the role of polyfunctional molecules, specifically silanes, in surface modification of polar surfaces (bearing soft nucleophiles. An emphasis on the mechanism of the reaction in the presence of adsorbed water, where the modifying reagents are hydrolysable, is discussed. To highlight the complexity of the reaction, modification of paper with trichlorosilanes is highlighted. Preparation of hydrophobic cellulosic paper, and structure–property relations under different treatment conditions is used to highlight that a monolayer is not always formed during the surface modification. Gel-formation via step-growth polymerization suggests that at the right monomer:adsorbed water ratio, a monolayer will not form but rather self-assembly driven particle formation will occur leading to a textured surface. The review highlights recent work indicating that the focus on monolayer formation, is at the very least, not always the case but gel formation, with concomitant self-assembly, might be the culprit in understanding challenges associated with the use of polyfunctional molecules in surface modification.

  16. Aromatic molecules on low-index coinage metal surfaces: Many-body dispersion effects

    Science.gov (United States)

    Jiang, Yingda; Yang, Sha; Li, Shuang; Liu, Wei

    2016-12-01

    Understanding the binding mechanism for aromatic molecules on transition-metal surfaces in atomic scale is a major challenge in designing functional interfaces for to (opto)electronic devices. Here, we employ the state-of-the-art many-body dispersion (MBD) approach, coupled with density functional theory methods, to study the interactions of benzene with low-index coinage metal surfaces. The many-body effects contribute mostly to the (111) surface, and leastly to the (110) surface. This corresponds to the same sequence of planar atomic density of face-centered-cubic lattices, i.e., (111) > (100) > (110). The binding energy for benzene/Au(110) is even stronger than that for benzene/Ag(110), due to a larger broadening of molecular orbitals in the former case. On the other hand, our calculations show almost identical binding energies for benzene on Ag(111) and Au(111), which contradicts the classic d-band center theory that could well predict the trend in chemisorption energies for various small molecules on a number of metal surfaces. Our results provide important insight into the benchmark adsorption systems with opener surfaces, which could help in designing more complex functional interfaces.

  17. Adhesion of single polyelectrolyte molecules on silica, mica, and bitumen surfaces.

    Science.gov (United States)

    Long, Jun; Xu, Zhenghe; Masliyah, Jacob H

    2006-02-14

    In a recent study (Energy Fuels 2005, 19, 936), a partially hydrolyzed polyacrylamide (HPAM) was used as a process aid to recover bitumen from oil sand ores. It was found that HPAM addition at the bitumen extraction step not only improved bitumen recovery but also enhanced fine solids settling in the tailings stream. To understand the role of HPAM, single-molecule force spectroscopy was employed for the first time to measure the desorption/adhesion forces of single HPAM molecules on silica, mica, and bitumen surfaces using an atomic force microscope (AFM). Silicon wafers with an oxidized surface layer and newly cleaved mica were used, respectively, to represent sand grains and clays in oil sands. The force measurements were carried out in deionized water and in commercial plant process water under equilibrium conditions. The desorption/adhesion forces of HPAM obtained on mica, silica, and bitumen surfaces were approximately 200, 40, and 80 pN in deionized water and approximately 100, 50, and 40 pN in the plant process water, respectively. The measured adhesion forces together with the zeta potential values of these surfaces indicate that the polymer would preferentially adsorb onto clay surfaces rather than onto bitumen surfaces. It is the selective adsorption of HPAM that benefits both bitumen recovery and tailings settling when the polymer was added directly to the bitumen extraction process at an appropriate dosage.

  18. Collisions of ideal gas molecules with a rough/fractal surface. A computational study.

    Science.gov (United States)

    Panczyk, Tomasz

    2007-02-01

    The frequency of collisions of ideal gas molecules (argon) with a rough surface has been studied. The rough/fractal surface was created using random deposition technique. By applying various depositions, the roughness of the surface was controlled and, as a measure of the irregularity, the fractal dimensions of the surfaces were determined. The surfaces were next immersed in argon (under pressures 2 x 10(3) to 2 x 10(5) Pa) and the numbers of collisions with these surfaces were counted. The calculations were carried out using a simplified molecular dynamics simulation technique (only hard core repulsions were assumed). As a result, it was stated that the frequency of collisions is a linear function of pressure for all fractal dimensions studied (D = 2, ..., 2.5). The frequency per unit pressure is quite complex function of the fractal dimension; however, the changes of that frequency with the fractal dimension are not strong. It was found that the frequency of collisions is controlled by the number of weakly folded sites on the surfaces and there is some mapping between the shape of adsorption energy distribution functions and this number of weakly folded sites. The results for the rough/fractal surfaces were compared with the prediction given by the Langmuir-Hertz equation (valid for smooth surface), generally the departure from the Langmuir-Hertz equation is not higher than 48% for the studied systems (i.e. for the surfaces created using the random deposition technique).

  19. Highly Ordered Surface Self-Assembly of Fe₄ Single Molecule Magnets.

    Science.gov (United States)

    Erler, Philipp; Schmitt, Peter; Barth, Nicole; Irmler, Andreas; Bouvron, Samuel; Huhn, Thomas; Groth, Ulrich; Pauly, Fabian; Gragnaniello, Luca; Fonin, Mikhail

    2015-07-08

    Single molecule magnets (SMMs) have attracted considerable attention due to low-temperature magnetic hysteresis and fascinating quantum effects. The investigation of these properties requires the possibility to deposit well-defined monolayers or spatially isolated molecules within a well-controlled adsorption geometry. Here we present a successful fabrication of self-organized arrays of Fe4 SMMs on hexagonal boron nitride (h-BN) on Rh(111) as template. Using a rational design of the ligand shell optimized for surface assembly and electrospray as a gentle deposition method, we demonstrate how to obtain ordered arrays of molecules forming perfect hexagonal superlattices of tunable size, from small islands to an almost perfect monolayer. High-resolution low temperature scanning tunneling microscopy (STM) reveals that the Fe4 molecule adsorbs on the substrate in a flat geometry, meaning that its magnetic easy axis is perpendicular to the surface. By scanning tunneling spectroscopy (STS) and density functional theory (DFT) calculations, we infer that the majority- and minority-spin components of the spin-split lowest unoccupied molecular orbital (LUMO) can be addressed separately on a submolecular level.

  20. A scale-bridging modeling approach for anisotropic organic molecules at patterned semiconductor surfaces.

    Science.gov (United States)

    Kleppmann, Nicola; Klapp, Sabine H L

    2015-02-14

    Hybrid systems consisting of organic molecules at inorganic semiconductor surfaces are gaining increasing importance as thin film devices for optoelectronics. The efficiency of such devices strongly depends on the collective behavior of the adsorbed molecules. In the present paper, we propose a novel, coarse-grained model addressing the condensed phases of a representative hybrid system, that is, para-sexiphenyl (6P) at zinc-oxide (ZnO). Within our model, intermolecular interactions are represented via a Gay-Berne potential (describing steric and van-der-Waals interactions) combined with the electrostatic potential between two linear quadrupoles. Similarly, the molecule-substrate interactions include a coupling between a linear molecular quadrupole to the electric field generated by the line charges characterizing ZnO(10-10). To validate our approach, we perform equilibrium Monte Carlo simulations, where the lateral positions are fixed to a 2D lattice, while the rotational degrees of freedom are continuous. We use these simulations to investigate orientational ordering in the condensed state. We reproduce various experimentally observed features such as the alignment of individual molecules with the line charges on the surface, the formation of a standing uniaxial phase with a herringbone structure, as well as the formation of a lying nematic phase.

  1. Adhesion molecule expression stimulated by Bacteroides thetaiotaomicron cell-surface antigens.

    Science.gov (United States)

    Rokosz, A; Meisel-Mikołajczyk, F; Malchar, C; Nowaczyk, M; Górski, A

    1999-01-01

    Bacteroides thetaiotaomicron, a Gram-negative anaerobic rod belonging to the Bacteroides fragilis group (BFG), is involved in many systemic and local, most frequently suppurative infections in man. The cell envelope of these rods is composed of two carbohydrate-containing antigens: lipopolysaccharide (LPS) and capsular polysaccharide (CPS). Adhesion molecules ICAM-1, VCAM-1 and E-selectin (ELAM-1) are induced on the endothelial cells by mediators of inflammation. The aim of this study was to assay the ability of B. thetaiotaomicron surface antigens to induce adhesion molecule expression on the endothelial cells. The influence of LPS and CPS on the expression of adhesion molecules on HMEC-1 cell line was examined in an ELISA test. ELISA was performed with monoclonal mouse anti-human: ICAM-1, VCAM-1 and E-selectin antibodies of the IgG class. B. thetaiotaomicron lipopolysaccharides revealed the ability to induce ICAM-1, VCAM-1 and E-selectin expression on the endothelial cells. Their activities were similar, but lower than the activity of Eschericha coli LPS. ICAM-1 was the most stimulated adhesion molecule. The strongest activation by LPS was achieved at the concentrations of 10.0 and 1.0 micrograms/ml. The ability of capsular polysaccharide to induce the expression of adhesion molecules was considerably weaker.

  2. Time Dependent Coupled Cluster Approach to Resonance Raman Excitation Profiles from General Anharmonic Surfaces

    Directory of Open Access Journals (Sweden)

    M. Durga Prasad

    2002-05-01

    Full Text Available Abstract: A time dependent coupled cluster approach to the calculation of Resonance Raman excitation profiles on general anharmonic surfaces is presented. The vibrational wave functions on the ground electronic surface are obtained by the coupled cluster method (CCM. It is shown that the propagation of the vibrational ground state on the upper surface is equivalent to propagation of the vacuum state by an effective hamiltonian generated by the similarity transformation of the vibrational hamiltonian of that surface by the CCM wave operator of the lower surface up to a normalization constant. This time propagation is carried out by the time-dependent coupled cluster method in a time dependent frame. Numerical studies are presented to asses the validity of the approach.

  3. Surface enhanced Raman scattering detection of single R6G molecules on nanoporous gold films

    Science.gov (United States)

    Liu, Hongwen; Zhang, L.; Yamaguchi, Y.; Iwasaki, H.; Inouye, Y.; Xue, Q. K.; Chen, M. W.

    2011-03-01

    Detecting single molecules with high sensitivity and molecular specificity is of great practical interest in many fields such as chemistry, biology, medicine, and pharmacology. For this purpose, cheap and highly active substrates are of crucial importance. Recently, nanoporous metals (NPMs), with a three-dimensional continuous network structure and pore channels usually much smaller than the wavelength of visible light, revealed outstanding optical properties in surface enhanced Raman scattering (SERS). In this work, we further modify the nanoporous gold films by growing a high density of gold nano-tips on the surface. Extremely focused electromagnetic fields can be produced at the apex of the nano-tips, resulting in so-called hot spots. With this NPM-based and affordable substrate, single molecule-detection is achievable with ultrahigh enhancement in SERS.

  4. Feasibility of Single Molecule DNA Sequencing using Surface-Enhanced Raman Scattering

    Energy Technology Data Exchange (ETDEWEB)

    Talley, C E; Reboredo, F; Chan, J; Lane, S M

    2006-02-03

    We have used a combined theoretical and experimental approach in order to assess the feasibility of using surface-enhanced Raman scattering (SERS) for DNA sequencing at the single molecule level. We have developed a numerical tool capable of calculating the E-field and resulting SERS enhancement factors for metallic structures of arbitrary size and shape. Measurements of the additional SERS enhancement by combining SERS with coherent antistokes Raman scattering (CARS) show that only modest increases in the signal are achievable due to thermal damage at higher laser powers. Finally, measurements of the SERS enhancement from nanoparticles coated with an insulating layer show that the SERS enhancement is decreased by as much as two orders of magnitude when the molecule is not in contact with the metal surface.

  5. Molecular resonant dissociation of surface-adsorbed molecules by plasmonic nanoscissors

    Science.gov (United States)

    Zhang, Zhenglong; Sheng, Shaoxiang; Zheng, Hairong; Xu, Hongxing; Sun, Mengtao

    2014-04-01

    The ability to break individual bonds or specific modes in chemical reactions is an ardently sought goal by chemists and physicists. While photochemistry based methodologies are very successful in controlling e.g. photocatalysis, photosynthesis and the degradation of plastic, it is hard to break individual molecular bonds for those molecules adsorbed on the surface because of the weak light-absorption in molecules and the redistribution of the resulting vibrational energy both inside the molecule and to its surrounding environment. Here we show how to overcome these obstacles with a plasmonic hot-electron mediated process and demonstrate a new method that allows the sensitive control of resonant dissociation of surface-adsorbed molecules by `plasmonic' scissors. To that end, we used a high-vacuum tip-enhanced Raman spectroscopy (HV-TERS) setup to dissociate resonantly excited NC2H6 fragments from Malachite green. The surface plasmons (SPs) excited at the sharp metal tip not only enhance the local electric field to harvest the light incident from the laser, but crucially supply `hot electrons' whose energy can be transferred to individual bonds. These processes are resonant Raman, which result in some active chemical bonds and then weaken these bonds, followed by dumping in lots of indiscriminant energy and breaking the weakest bond. The method allows for sensitive control of both the rate and probability of dissociation through their dependence on the density of hot electrons, which can be manipulated by tuning the laser intensity or tunneling current/bias voltage in the HV-TERS setup, respectively. The concepts of plasmonic scissors open up new versatile avenues for the deep understanding of in situ surface-catalyzed chemistry.The ability to break individual bonds or specific modes in chemical reactions is an ardently sought goal by chemists and physicists. While photochemistry based methodologies are very successful in controlling e.g. photocatalysis

  6. Composition dependent adsorption of multiple CO molecules on binary silver-gold clusters Ag(n)Au(m)+ (n + m = 5): theory and experiment.

    Science.gov (United States)

    Popolan, Denisia M; Nössler, Melanie; Mitrić, Roland; Bernhardt, Thorsten M; Bonacić-Koutecký, Vlasta

    2010-07-28

    The binding energies of multiple CO molecules to five-atom silver-gold cluster cations have been obtained employing temperature dependent gas phase ion trap measurements and ab initio calculations. The CO binding energies to Ag(n)Au(m)(+) (n + m = 5) decrease with increasing number of silver atoms. Most strikingly, after the adsorption of the fourth CO to Au(5)(+) and of the third CO to Ag(5)(+), respectively, a pronounced decrease in the binding energies of further CO molecules was observed. This is related to a CO-induced structural transformation yielding more compact metal cluster geometries. First principles calculations revealed that the exact structure of the carbonyl complexes with multiple CO and the nature of the CO-induced structural transformation strongly depend on the composition of the metal cluster as well as on the number of adsorbed CO molecules.

  7. Photoionization and Velocity Map Imaging spectroscopy of atoms, molecules and clusters with Synchrotron and Free Electron Laser radiation at Elettra

    Energy Technology Data Exchange (ETDEWEB)

    Di Fraia, M., E-mail: michele.di.fraia@desy.de [University of Trieste, Department of Physics, via Valerio 2, 34127 Trieste (Italy); Sergo, R.; Stebel, L.; Giuressi, D.; Cautero, G.; Tudor, M.; Callegari, C. [Elettra-Sincrotrone Trieste S.C.p.A., S.S. 14 – Km 163.5, 34149 Basovizza, Trieste (Italy); O’Keeffe, P. [CNR-ISM, Area della Ricerca di Roma 1, Monterotondo Scalo, 00015 Roma (Italy); Ovcharenko, Y. [Institut für Optik und Atomare Physik, Technische Universität Berlin, Berlin (Germany); Lyamayev, V. [European XFEL GmbH, Hamburg (Germany); Feyer, V.; Moise, A. [Elettra-Sincrotrone Trieste S.C.p.A., S.S. 14 – Km 163.5, 34149 Basovizza, Trieste (Italy); Devetta, M.; Piseri, P. [Dipartimento di Fisica, Universitá degli Studi di Milano, Milan (Italy); Grazioli, C. [Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste (Italy); Coreno, M. [CNR-ISM, Area della Ricerca di Roma 1, Monterotondo Scalo, 00015 Roma (Italy)

    2015-12-01

    Advances in laser and Synchrotron Radiation instrumentation are continuously boosting fundamental research on the electronic structure of matter. At Elettra the collaboration between several groups active in the field of atomic, molecular and cluster physics and the Instrumentation and Detector Laboratory has resulted in an experimental set-up that successfully tackles the challenges posed by the investigation of the electronic structure of isolated species in the gas phase. The use of Synchrotron Radiation (SR) and Free Electron Laser (FEL) light, allows to cover a wide spectrum of targets from energetic to dynamics. We developed a Velocity Map Imaging (VMI) spectrometer that allows to perform as well SR as FEL experiments, just by changing part of the detection system. In SR experiments, at the Gasphase beamline of Elettra, a cross delay line detector is used, coupled to a 4-channel time-to-digital converter that reconstructs the position of the electrons. Simultaneously, a Time-of-Flight (TOF) mass spectrometer is used to acquire photoion spectra. Such a system allows PhotoElectron-PhotoIon-Coincidence (PEPICO) spectroscopy of atoms, molecules and clusters. In FEL experiments (notably differing from SR experiments in the much higher rate of events produced and detected, which forces one to forfeit coincidence detection), at the Low Density Matter (LDM) beamline of FERMI, a Micro Channel Plate (MCP) a phosphor screen and a CCD camera are used instead, capable of shot-by-shot collection of practically all events, albeit without time resolution.

  8. Single NdPc{sub 2} molecules on surfaces. Adsorption, interaction, and molecular magnetism

    Energy Technology Data Exchange (ETDEWEB)

    Fahrendorf, Sarah

    2013-01-24

    They have huge potential for application in molecular-spin-transistors, molecular-spinvalves, and molecular quantum computing. SMMs are characterized by high spin ground states with zero-field splitting leading to high relaxation barriers and long relaxation times. A relevant class of molecules are the lanthanide double-decker phthalocyanines (LaPc{sub 2}) with only one metal atom sandwiched between two organic phthalocyanine (Pc) ligands. For envisaged spintronic applications it is important to understand the interaction between the molecules and the substrate and its influence on the electronic and magnetic properties. The subject of this thesis is the investigation of the adsorbed neodymium double-decker phthalocyanine (NdPc{sub 2}) by means of low temperature scanning tunneling microscopy and spectroscopy (STM and STS). The molecules are deposited by sublimation onto different substrates. It is observed that a large fraction of the double-decker molecules decomposes during deposition. The decomposition probability strongly depends on the chosen substrate. Therefore it is concluded that the substrate modifies the electronic structure of the molecule leading to a stabilization or destabilization of the molecular entity. Charge transfer from the surface to the molecule is identified as a potential stabilizing mechanism. The electronic and magnetic properties are investigated in detail for adsorbed NdPc{sub 2} molecules on Cu(100). The results of the experimental study are compared to state-of-the-art density functional theory calculations performed by our colleagues from the Peter Gruenberg Institute (PGI-1) at the Forschungszentrum Juelich. Interestingly, the lower Pc ring of the molecule hybridizes intensely with the substrate leading to strong chemisorption of the molecule, while the upper Pc ring keeps its molecular type electronic states, which can be energetically shifted by an external electric field. Importantly, it is possible to get direct access to the

  9. Control of structure and growth of polymorphic crystalline thin films of amphiphilic molecules on liquid surfaces

    DEFF Research Database (Denmark)

    Weinbach, S.P.; Kjær, K.; Bouwman, W.G.;

    1994-01-01

    The spontaneous formation and coexistence of crystalline polymorphic trilayer domains in amphiphilic films at air-liquid interfaces is demonstrated by grazing incidence synchrotron x-ray diffraction. These polymorphic crystallites may serve as models for the early stages of crystal nucleation...... and growth, helping to elucidate the manner in which additives influence the progress of crystal nucleation, growth, and polymorphism and suggesting ways of selectively generating and controlling multilayers on liquid surfaces. Auxiliary molecules have been designed to selectively inhibit development...

  10. SEM visualization of glycosylated surface molecules using lectin-coated microspheres

    Science.gov (United States)

    Duke, J.; Janer, L.; Campbell, M.

    1985-01-01

    There are several techniques currently used to localize glycosylated surface molecules by scanning electron microscopy (Grinnell, 1980; Molday, 1976; Linthicum and Sell, 1975; Nicolson, 1974; Lo Buglio, et al, 1972). A simple and rapid method, using a modification of Grinnell's technique is reported here. Essentially, microspheres coated with Concavalin A are used to bind to glycosylated regions of the palatal shelf epithelium and are visualized in the scanning electron microscope (SEM).

  11. Surface-enhanced Raman spectroscopy at single-molecule scale and its implications in biology

    OpenAIRE

    Wang, Yuling; Irudayaraj, Joseph

    2013-01-01

    Single-molecule (SM) spectroscopy has been an exciting area of research offering significant promise and hope in the field of sensor development to detect targets at ultra-low levels down to SM resolution. To the experts and developers in the field of surface-enhanced Raman spectroscopy (SERS), this has often been a challenge and a significant opportunity for exploration. Needless to say, the opportunities and excitement of this multidisciplinary area impacts span the fields of physics, chemi...

  12. Investigation of Molecule-Surface Interactions With Overtone Absorption Spectroscopy and Computational Methods

    Science.gov (United States)

    2010-11-01

    resulting system for the pure local mode model can be expressed as" , H\\u)-H\\0) , , , . —LJ- >-*• = vco \\v) - (Oexe(u + v)\\o) he (2) where |u...ABSTRACT The objective of this study is to determine the optimal methodology for the computational modeling of a molecule surface interaction. As a...standard FTIR measurements, as well as laser photoacoustic spcctroscopy and compared with spectra that are predicted from computational models . Using

  13. Detecting groups of coevolving positions in a molecule: a clustering approach

    Directory of Open Access Journals (Sweden)

    Galtier Nicolas

    2007-11-01

    Full Text Available Abstract Background Although the patterns of co-substitutions in RNA is now well characterized, detection of coevolving positions in proteins remains a difficult task. It has been recognized that the signal is typically weak, due to the fact that (i amino-acid are characterized by various biochemical properties, so that distinct amino acids changes are not functionally equivalent, and (ii a given mutation can be compensated by more than one mutation, at more than one position. Results We present a new method based on phylogenetic substitution mapping. The two above-mentioned problems are addressed by (i the introduction of a weighted mapping, which accounts for the biochemical effects (volume, polarity, charge of amino-acid changes, (ii the use of a clustering approach to detect groups of coevolving sites of virtually any size, and (iii the distinction between biochemical compensation and other coevolutionary mechanisms. We apply this methodology to a previously studied data set of bacterial ribosomal RNA, and to three protein data sets (myoglobin of vertebrates, S-locus Receptor Kinase and Methionine Amino-Peptidase. Conclusion We succeed in detecting groups of sites which significantly depart the null hypothesis of independence. Group sizes range from pairs to groups of size ≃ 10, depending on the substitution weights used. The structural and functional relevance of these groups of sites are assessed, and the various evolutionary processes potentially generating correlated substitution patterns are discussed.

  14. Interaction of Epithelial Cells with Surfaces and Surfaces Decorated by Molecules

    CERN Document Server

    Martini, Daniele; Beil, Michael; Paust, T; Huang, C; Moosmann, M; Jin, J; Heiler, T; Gröger, R; Schimmel, Thomas; Walheim, Stefan

    2013-01-01

    A detailed understanding of the interface between living cells and substrate materials is of rising importance in many fields of medicine, biology and biotechnology. Cells at interfaces often form epithelia. The physical barrier that they form is one of their main functions. It is governed by the properties of the networks forming the cytoskeleton systems and by cell-to-cell contacts. Different substrates with varying surface properties modify the migration velocity of the cells. On the one hand one can change the materials composition. Organic and inorganic materials induce differing migration velocities in the same cell system. Within the same class of materials, a change of the surface stiffness or of the surface energy modifies the migration velocity, too. For our cell adhesion studies a variety of different, homogeneous substrates were used (polymers, bio-polymers, metals, oxides). In addition, an effective lithographic method, Polymer Blend Lithography (PBL), is reported, to produce patterned Self-Assem...

  15. Conformational adaptation and selective adatom capturing of tetrapyridyl-porphyrin molecules on a copper (111) surface.

    Science.gov (United States)

    Auwärter, Willi; Klappenberger, Florian; Weber-Bargioni, Alexander; Schiffrin, Agustin; Strunskus, Thomas; Wöll, Christof; Pennec, Yan; Riemann, Andreas; Barth, Johannes V

    2007-09-12

    We present a combined low-temperature scanning tunneling microscopy and near-edge X-ray adsorption fine structure study on the interaction of tetrapyridyl-porphyrin (TPyP) molecules with a Cu(111) surface. A novel approach using data from complementary experimental techniques and charge density calculations allows us to determine the adsorption geometry of TPyP on Cu(111). The molecules are centered on "bridge" sites of the substrate lattice and exhibit a strong deformation involving a saddle-shaped macrocycle distortion as well as considerable rotation and tilting of the meso-substituents. We propose a bonding mechanism based on the pyridyl-surface interaction, which mediates the molecular deformation upon adsorption. Accordingly, a functionalization by pyridyl groups opens up pathways to control the anchoring of large organic molecules on metal surfaces and tune their conformational state. Furthermore, we demonstrate that the affinity of the terminal groups for metal centers permits the selective capture of individual iron atoms at low temperature.

  16. Strategies for creating antifouling surfaces using selfassembled poly(ethylene glycol) thiol molecules

    DEFF Research Database (Denmark)

    Lokanathan, Arcot R.

    2011-01-01

    conditions for the reversible, initial attachment of microbial cells. This effect can be obtained by grafting hydrophilic polymeric chains onto surfaces and thereby provide a steric barrier between the substrate surface and the microbial cell. Poly (ethylene glycol) (PEG) is one of the most widely used....... The work focuses on novel strategies to self assemble PEG thiol monolayers with high graft density. One of the strategies investigated involved backfilling a self assembled layer of 2000 Da PEG thiol with shorter oligo (ethylene glycol) (OEG) thiol molecules to form a mixed monolayer. Detailed quantitative...

  17. Quantum Monte-Carlo programming for atoms, molecules, clusters, and solids

    Energy Technology Data Exchange (ETDEWEB)

    Schattke, Wolfgang [Kiel Univ. (Germany). Inst. of Theoretical Physics and Astrophysics; Ikerbasque Foundation/Donostia International Physics Center, San Sebastian (Spain); Diez Muino, Ricardo [Centro de Fisica de Materiales CSIC-UPV/EHU (Spain); Donostia International Physics Center, San Sebastian (Spain)

    2013-11-01

    This is a book that initiates the reader into the basic concepts and practical applications of Quantum Monte Carlo. Because of the simplicity of its theoretical concept, the authors focus on the variational Quantum Monte Carlo scheme. The reader is enabled to proceed from simple examples as the hydrogen atom to advanced ones as the Lithium solid. In between, several intermediate steps are introduced, including the Hydrogen molecule (2 electrons), the Lithium atom (3 electrons) and expanding to an arbitrary number of electrons to finally treat the three-dimensional periodic array of Lithium atoms in a crystal. The book is unique, because it provides both theory and numerical programs. It pedagogically explains how to transfer into computational tools what is usually described in a theoretical textbook. It also includes the detailed physical understanding of methodology that cannot be found in a code manual. The combination of both aspects allows the reader to assimilate the fundamentals of Quantum Monte Carlo not only by reading but also by practice.

  18. The Time Evolution of the Surface Segregation of Hyperbranched Molecules from a Linear Matrix

    Science.gov (United States)

    Swader, Onome; Dadmun, Mark; Hutchings, Lian; Thompson, Richard

    2010-03-01

    Modification of a surface by the selective surface segregation of an additive in a mixture is a process with many commercial applications including biocompatibility, wettability, and anti-fouling in coatings. In a blend of branched and linear polymers, there exists an entropic driving force for the selective surface segregation of the branched polymer. Unfortunately, a systematic study of the impact of the branched copolymer structure on the dynamics and thermodynamics of this surface segregation is not currently available. Neutron reflectivity experiments that seek to fill this void have been completed and will be discussed. High molecular weight poly(styrene) (PS) hyperbranched molecules, hypermacs (HM) and dendrimacs (DM), with 10 % HM or DM and 90 % deuterated PS are the model systems studied. Reflectivity profiles for all blends were obtained as a function of annealing time from 30 minutes up to 48 hours.

  19. Adsorption of ethyl xanthate on ZnS(110) surface in the presence of water molecules: A DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Long, Xianhao [School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004 (China); Chen, Jianhua, E-mail: jhchen@gxu.edu.cn [School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004 (China); Guangxi Colleges and University Key Laboratory of Minerals Engineering, 530004 (China); Chen, Ye, E-mail: fby18@126.com [College of Resources and Metallurgy, Guangxi University, Nanning 530004 (China)

    2016-05-01

    Graphical abstract: - Highlights: • Adsorption of water molecules decreases the reactivity of surface Zn atom. • Copper impurities decrease the band gap of ZnS surface. • Copper impurities enhance the adsorption of xanthate on the ZnS surface. • Water molecules have little influence on the properties of Cu-substituted ZnS surface. • The xanthate S atom can interact with the surface S atom of Cu-substituted ZnS surface. - Abstracts: The interaction of collector with the mineral surface plays a very important role in the froth flotation of sphalerite. The adsorptions occurred at the interface between the mineral surface and waters; however most of DFT simulations are performed in vacuum, without consideration of water effect. Semiconductor surface has an obvious proximity effect, which will greatly influence the surface reactivity. To understand the mechanism of xanthate interacting with sphalerite surface in the presence of water molecules, the ethyl xanthate molecule adsorption on un-activated and Cu-activated ZnS(110) surface in the absence and presence of water molecules were performed using the density functional theory (DFT) method. The calculated results show that the adsorption of water molecules dramatically changes the properties of ZnS surface, resulting in decreasing the reactivity of surface Zn atoms with xanthate. Copper activation of ZnS surface changes the surface properties, leading to the totally different adsorption behaviors of xanthate. The presence of waters has little influence on the properties of Cu-activated ZnS surface. The xanthate S atom can interact with the surface S atom of Cu-substituted ZnS surface, which would result in the formation of dixanthogen.

  20. Adhesion of Model Molecules to Metallic Surfaces, the Implications for Corrosion Protection

    Energy Technology Data Exchange (ETDEWEB)

    De Wit, J. H. W.; Van den Brand, J.; De Wit, F. M.; Mol, J. M. C. [Delf University of Technology and Netherlaands Institute for Metals Research, Delf (Netherlands)

    2008-02-15

    The majority of the described experimental results deal with relatively pure aluminium. Variations were made in the pretreatment of the aluminum substrates and an investigation was performed on the resulting changes in oxide layer composition and chemistry. Subsequently, the bonding behavior of the surfaces was investigated by using model adhesion molecules. These molecules were chosen to represent the bonding functionality of an organic polymer. They were applied onto the pretreated surfaces as a monolayer and the bonding behavior was studied using infrared reflection absorption spectroscopy. A direct and clear relation was found between the hydroxyl fraction on the oxide surfaces and the amount of molecules that subsequently bonded to the surface. Moreover, it was found that most bonds between the oxide surface and organic functional groups are not stable in the presence of water. The best performance was obtained using molecules, which are capable of chemisorption with the oxide surface. Finally, it was found that freshly prepared relatively pure aluminum substrates, which are left in air, rapidly lose their bonding capacity towards organic functional groups. This can be attributed to the adsorption of contamination and water to the oxide surface. in addition the adhesion of a typical epoxy-coated aluminum system was investigated during exposure to water at different temperatures. The coating was found to quite rapidly lose its adhesion upon exposure to water. This rapid loss of adhesion corresponds well with the data where it was demonstrated that the studied epoxy coating only bonds through physisorptive hydrogen bonding, these bonds not being stable in the presence of water. After the initial loss the adhesion of the coating was however found to recover again and even exceeded the adhesion prior to exposure. The improvement could be ascribed to the growth of a thin oxyhydroxide layer on the aluminum substrate, which forms a new, water-stable and stronger bond

  1. EFFECT OF SMALL CLUSTER DIFFUSION DURING TWO-DIMENSIONAL THIN FILM GROWTH ON METAL SURFACE

    Institute of Scientific and Technical Information of China (English)

    WU FENG-MIN; LI QIAO-WEN; WU ZI-QIN

    2000-01-01

    The diffusion of small clusters such as dimers and trimers on metal surface and the growth of two-dimensional thin films are studied by Monte Carlo simulation, using realistic growth model and physical parameters. It is found that small cluster diffusion plays an important role in the process of thin film growth at not very low temperature. It affects not only the island density and the size of islands but also the critical value of saturation occurring during growth of thin films. The effect of small cluster diffusion depends on both the size of critical nucleus and the growth temperature.The simulation results also show that the larger the cluster allowed to diffuse, the easier the saturation that takes place,giving rise to the lower critical coverage of saturation occurring. It is suggested that the effect of small cluster diffusion should be included in establishing the growth models of thin films.

  2. Single-molecule conductivity of non-redox and redox molecules at pure and gold-mined Au(111)-electrode surfaces

    DEFF Research Database (Denmark)

    Zhang, Jingdong; Chi, Qijin; Ulstrup, Jens

    metalloproteins such as blue copper, heme, and iron-sulfur proteins as well as redox metalloenzymes are other new targets for single-molecule electrochemical and bioelectrochemical surface science. Electrochemistry combined with scanning tunnelling and atomic force microscopy in aqueous chemical or biological...... to surface-mined Au-atoms. In addition the SAMs ensure protein/enzyme immobilization gentle enough that the proteins retain electron transfer or enzyme activity in a variety of local environments. The second area is the mapping and control of the immobilized redox molecules and metalloproteins themselves...

  3. Cytokine-Induced Cell Surface Expression of Adhesion Molecules in Vascular Endothelial Cells In vitro

    Institute of Scientific and Technical Information of China (English)

    陈红辉; 刘昌勤; 孙圣刚; 梅元武; 童萼塘

    2001-01-01

    Regulation of the adhesion molecules expression by cytokine in vascular endothelial cells was investigated. Human umbilical vein endothelial cells (HUVEC) were stimulated with cytokines, TNF-α (1-250 U/ml) or IL-1β (0.1-50 U/ml) for 24 h. HUVEC were also cultured with cytokines, TNF-α (100 U/ml) or IL-1β (10 U/ml), for 4-72 h, cell surface expression of adhesion molecules (ICAM-1 and VCAM-1) were detected and quantitated by immunocytochemical methods and computerized imaging analysis technique. Adhesion molecules expression were up-regulated by TNF-α, IL-1β in a concentration- and time-dependent manner. Some significant differences were observed between the effects of cytokines on the ICAM-1 and on VCAM-1 expression. Cytokines might directly induce the expression of ICAM-1 and VCAM-1 in vascular endothelial cells. Our observations indicate differential functions of the two adhesion molecules during the evolution of inflammatory responses in stroke.

  4. Chemical effects on vibrational properties of adsorbed molecules on metal surfaces: Coverage dependence

    Science.gov (United States)

    Ueba, H.

    1987-10-01

    Vibrational properties of chemisorbed molecules on metal surfaces are studied with a focus on the coverage dependent chemical shift of the frequencies. Available experimental data of a CO adsorption on transition metal and noble metal surfaces are analyzed in the light of the coverage dependent back-donation into the 2 π* orbitals of chemisorbed CO molecules. The vibrational frequency ωCO of the intramolecular stretching mode exhibits a downward shift of varying magnitude, depending on the amount of back-donation into the 2 π* orbitals of the chemisorbed CO. On increasing the coverage θ, ωCO usually increases due to the dipole-dipole interaction. On Cu surfaces, however, the shifts are relatively small, or in some cases, negative. So far, this anomalous frequency shift with θ is understood as a result of competitive effect between the upward dipole Ωdip and the downward chemical shift Ωchem associated with back-donation. The purpose of this paper is to establish the possible origin of the downward frequency shift through the electronic properties of an incomplete monolayer of adsorbates. The adsorbate density of states ρa is calculated by means of the coherent potential approximation, in which the electron hopping between the adsorbates (band formation effect) and the depolarization effect due to the proximity of ionized adsorbed molecules are taken into account. The change of the occupied portion of ρa and ρa ( ɛF) at the Fermi level ɛF with increasing θ then manifests itself in the coverage dependent Ωchem not only due to the static back-donation, but also due to the dynamical charge fluctuation during vibrational excitation. It is found that in a weakly chemisorbed system, such as CO/Cu, the negative Ωchem amounts to Ωdip at low θ. Consequently the apparent total frequency shift remains almost constant. As the coverage increases, Ωchem becomes larger than Ωdip due to the band effect. It is also shown that the variation of the back

  5. Surface Modification of Gold Nanoparticles with Small Molecules for Biochemical Analysis.

    Science.gov (United States)

    Chen, Yiping; Xianyu, Yunlei; Jiang, Xingyu

    2017-02-21

    As one of the major tools for and by chemical science, biochemical analysis is becoming increasingly important in fields like clinical diagnosis, food safety, environmental monitoring, and the development of chemistry and biochemistry. The advancement of nanotechnology boosts the development of analytical chemistry, particularly the nanoparticle (NP)-based approaches for biochemical assays. Functional NPs can greatly improve the performance of biochemical analysis because they can accelerate signal transduction, enhance the signal intensity, and enable convenient signal readout due to their unique physical and chemical properties. Surface chemistry is a widely used tool to functionalize NPs, and the strategy for surface modification is of great significance to the application of NP-mediated biochemical assays. Surface chemistry not only affects the quality of NPs (stability, monodispersity, and biocompatibility) but also provides functional groups (-COO(-), -NH3(+), -CHO, and so on) or charges that can be exploited for bioconjugation or ligand exchange. Surface chemistry also dictates the sensitivity and specificity of the NP-mediated biochemical assays, since it is vital to the orientation, accessibility, and bioactivity of the functionalized ligands on the NPs. In this Account, we will focus on surface chemistry for functionalization of gold nanoparticles (AuNPs) with small organic molecules for biochemical analysis. Compared to other NPs, AuNPs have many merits including controllable synthesis, easy surface modification and high molar absorption coefficient, making them ideal probes for biochemical assays. Small-molecule functionalized AuNPs are widely employed to develop sensors for biochemical analysis, considering that small molecules, such as amino acids and sulfhydryl compounds, are more easily and controllably bioconjugated to the surface of AuNPs than biomacromolecules due to their less complex structure and steric hindrance. The orientation and

  6. Observations of Photo-Dissociation Reaction of TEOS Molecules on Silicon Clean Surfaces

    Science.gov (United States)

    Yanagita, Hideaki; Uemura, Kazuhide; Yokotani, Atsushi; Kurosawa, Kou

    Tetraethoxysilane (TEOS : SiO4(C2H5)4) is widely used to fabricate silicon-dioxide insulator thin films in LSI device technologies. We have already reported that TEOS is photo-dissociated to result in oxide layer deposition at room temperature by a vacuum ultraviolet excimer lamp (λ=172 nm). In this paper, we have observed the initial stages of oxide layer deposition on silicon clean surfaces with the scanning tunneling microscope (STM) and time-of-flight (TOF) mass spectrometer. An argon excimer lamp (λ=126 nm) is used for the photo-chemical vapor deposition (CVD). TEOS molecules have been dissociated to be SiO4(C2H5)n(n=1, 2, 3) groups on the clean surfaces. The 126 nm photons dissociate the molecules or radicals to Si-Om(m=1, 3, 4) after 2 min. Finally, the Si-Om adsorbed molecules and Si atoms in the substrate are re-arranged to be a disorder structure by the photons.

  7. The specificity of targeted vaccines for APC surface molecules influences the immune response phenotype.

    Directory of Open Access Journals (Sweden)

    Gunnveig Grødeland

    Full Text Available Different diseases require different immune responses for efficient protection. Thus, prophylactic vaccines should prime the immune system for the particular type of response needed for protection against a given infectious agent. We have here tested fusion DNA vaccines which encode proteins that bivalently target influenza hemagglutinins (HA to different surface molecules on antigen presenting cells (APC. We demonstrate that targeting to MHC class II molecules predominantly induced an antibody/Th2 response, whereas targeting to CCR1/3/5 predominantly induced a CD8(+/Th1 T cell response. With respect to antibodies, the polarizing effect was even more pronounced upon intramuscular (i.m delivery as compared to intradermal (i.d. vaccination. Despite these differences in induced immune responses, both vaccines protected against a viral challenge with influenza H1N1. Substitution of HA with ovalbumin (OVA demonstrated that polarization of immune responses, as a consequence of APC targeting specificity, could be extended to other antigens. Taken together, the results demonstrate that vaccination can be tailor-made to induce a particular phenotype of adaptive immune responses by specifically targeting different surface molecules on APCs.

  8. Characterizing the fluorescence intermittency and photobleaching kinetics of dye molecules immobilized on a glass surface.

    Science.gov (United States)

    Yeow, Edwin K L; Melnikov, Sergey M; Bell, Toby D M; De Schryver, Frans C; Hofkens, Johan

    2006-02-09

    The blinking behavior of single Atto565 molecules on a glass surface is studied under air or nitrogen atmospheres using confocal microscopy. The broad distributions for both on- and off-time durations obey power law kinetics that are rationalized using a charge tunneling model. In this case, a charge is transferred from the Atto565 molecule to localized states found on the glass surface. Subsequent charge recombination by back charge tunneling from trap to Atto565 cation (i.e., dark state) restores the fluorescence. The off-time distribution is independent of excitation intensity (I), whereas the on-time distribution exhibits a power law exponent that varies with I. Two pathways have been identified to lead to the formation of the radical dark state. The first involves direct charge tunneling from the excited singlet S1 state to charge traps in the surrounding matrix, and the second requires charge ejection from the triplet T1 state after intersystem crossing from S1. Monte Carlo simulation studies complement the two-pathway model. Photobleaching curves of both single and ensemble molecules do not exhibit monoexponential decays suggesting complex bleaching dynamics arising from triplet and radical states.

  9. Mass Spectrometry as a Preparative Tool for the Surface Science of Large Molecules

    Science.gov (United States)

    Rauschenbach, Stephan; Ternes, Markus; Harnau, Ludger; Kern, Klaus

    2016-06-01

    Measuring and understanding the complexity that arises when nanostructures interact with their environment are one of the major current challenges of nanoscale science and technology. High-resolution microscopy methods such as scanning probe microscopy have the capacity to investigate nanoscale systems with ultimate precision, for which, however, atomic scale precise preparation methods of surface science are a necessity. Preparative mass spectrometry (pMS), defined as the controlled deposition of m/z filtered ion beams, with soft ionization sources links the world of large, biological molecules and surface science, enabling atomic scale chemical control of molecular deposition in ultrahigh vacuum (UHV). Here we explore the application of high-resolution scanning probe microscopy and spectroscopy to the characterization of structure and properties of large molecules. We introduce the fundamental principles of the combined experiments electrospray ion beam deposition and scanning tunneling microscopy. Examples for the deposition and investigation of single particles, for layer and film growth, and for the investigation of electronic properties of individual nonvolatile molecules show that state-of-the-art pMS technology provides a platform analog to thermal evaporation in conventional molecular beam epitaxy. Additionally, it offers additional, unique features due to the use of charged polyatomic particles. This new field is an enormous sandbox for novel molecular materials research and demands the development of advanced molecular ion beam technology.

  10. Surface Molecules Released by Trypanosoma cruzi Metacyclic Forms Downregulate Host Cell Invasion

    Science.gov (United States)

    Clemente, Tatiana Mordente; Cortez, Cristian; Novaes, Antônio da Silva; Yoshida, Nobuko

    2016-01-01

    Background The question whether metacylic trypomastigote (MT) forms of different T. cruzi strains differentially release surface molecules, and how they affect host cell invasion, remains to be fully clarified. We addressed that question using T. cruzi strains that differ widely in the ability to invade cells. Methodology/Principal Findings Metacyclic forms were incubated at 37°C for 1 h in complete D10 medium or in nutrient-deprived PBS containing Ca2+ and Mg2+ (PBS++). The conditioned medium (CM), collected after parasite centrifugation, was used for cell invasion assays and Western blot analysis, using monoclonal antibodies directed to gp82 and gp90, the MT surface molecules that promote and negatively regulate invasion, respectively. CM of poorly invasive G strain (G-CM) contained high amounts of gp90 and gp82, either in vesicles or as soluble molecules. CM of highly invasive CL strain (CL-CM) contained gp90 and gp82 at very low levels. HeLa cells were incubated for 1 h with CL strain MT in D10, in absence or in the presence of G-CM or CL-CM. Parasite invasion was significantly inhibited by G-CM, but not by CL-CM. As G strain MT invasion rate in D10 is very low, assays with this strain were performed in PBS++, which induces invasion-promoting lysosome-spreading. G-CM, but not CL-CM, significantly inhibited G strain internalization, effect that was counteracted by preincubating G-CM with an anti-gp90 monoclonal antibody or anti-gp82 polyclonal antibody that do not recognize live MT. G strain CM generated in PBS++ contained much lower amounts of gp90 and gp82 as compared to CM produced in D10, and exhibited lower inhibitory effect on host cell invasion. Conclusion/Significance Our data suggest that the surface molecules spontaneously released by MT impair parasite-host cell interaction, gp82 presumably competing with the molecule expressed on MT surface for the host cell receptor, and gp90 further contributing to down modulate invasion. PMID:27483135

  11. Both host and parasite MIF molecules bind to chicken macrophages via CD74 surface receptor.

    Science.gov (United States)

    Kim, Sungwon; Cox, Chasity M; Jenkins, Mark C; Fetterer, Ray H; Miska, Katarzyna B; Dalloul, Rami A

    2014-12-01

    Macrophage migration inhibitory factor (MIF) is recognized as a soluble protein that inhibits the random migration of macrophages and plays a pivotal immunoregulatory function in innate and adaptive immunity. Our group has identified both chicken and Eimeria MIFs, and characterized their function in enhancing innate immune responses during inflammation. In this study, we report that chicken CD74 (ChCD74), a type II transmembrane protein, functions as a macrophage surface receptor that binds to MIF molecules. First, to examine the binding of MIF to chicken monocytes/macrophages, fresh isolated chicken peripheral blood mononuclear cells (PBMCs) were stimulated with rChIFN-γ and then incubated with recombinant chicken MIF (rChMIF). Immunofluorescence staining with anti-ChMIF followed by flow cytometry revealed the binding of MIF to stimulated PBMCs. To verify that ChCD74 acts as a surface receptor for MIF molecules, full-length ChCD74p41 was cloned, expressed and its recombinant protein (rChCD74p41) transiently over-expressed with green fluorescent protein in chicken fibroblast DF-1 cells. Fluorescence analysis revealed a higher population of cells double positive for CD74p41 and rChMIF, indicating the binding of rChMIF to DF-1 cells via rChCD74p41. Using a similar approach, it was found that Eimeria MIF (EMIF), which is secreted by Eimeria sp. during infection, bound to chicken macrophages via ChCD74p41 as a surface receptor. Together, this study provides conclusive evidence that both host and parasite MIF molecules bind to chicken macrophages via the surface receptor ChCD74.

  12. Vibrations of tetrahedral Co and Cu clusters on a Cu(111) surface

    Energy Technology Data Exchange (ETDEWEB)

    Borisova, Svetlana D.; Rusina, Galina G. [Institute of Strength Physics and Materials Science SB RAS, pr. Akademichesky 2/4, 634021 Tomsk (Russian Federation); Eremeev, Sergey V. [Institute of Strength Physics and Materials Science SB RAS, pr. Akademichesky 2/4, 634021 Tomsk (Russian Federation); Tomsk State University, pr. Lenina 36, 634050 Tomsk (Russian Federation); Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal, 4, 20018 San Sebastian/Donostia (Spain); Chulkov, Evgueni V. [Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal, 4, 20018 San Sebastian/Donostia (Spain); Depto. de Fisica de Materiales and Centro de Fisica de Materiales - CFM (CSIS-UPV/EHU), Facultad de Ciencias Quimicas, Universidad del Pais Vasco/Euskal Herriko Unibertsitatea, Apdo. 1072, 20018 San Sebastian/Donostia (Spain)

    2010-11-15

    Vibrational properties of tetrahedral clusters of Cu and Co on the Cu(111) surface are studied by using interatomic interaction potentials constructed within tight-binding second moment approximation. It was shown that interaction of the Co{sub 4} and Cu{sub 4} clusters with the substrate leads to arising of frustrated translation and frustrated rotation in-plane polarized vibrational modes localized on the cluster atoms. The vibrational modes of the free Cu{sub 4} cluster upon its adsorption on the Cu(111) surface mix with Cu bulk phonons and become almost delocalized. Contrary to that, in the Co{sub 4} cluster on the surface the high frequency modes remain strongly localized and mixed with the nearest neighbor atoms vibrations. The highest frequency vibration of the Co{sub 4} cluster splits due to different interaction with certain groups of nearest neighbor atoms (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  13. Strategies For Immobilization Of Bioactive Organic Molecules On Titanium Implant Surfaces – A Review

    Directory of Open Access Journals (Sweden)

    Panayotov Ivan V.

    2015-03-01

    Full Text Available Numerous approaches have been used to improve the tissue-implant interface of titanium (Ti and titanium alloy (Ti6Al4V. They all aim at increasing cell migration and attachment to the metal, preventing unspecific protein adsorption and improving post-implantation healing process. Promising methods for titanium and titanium alloy surface modification are based on the immobilization of biologically active organic molecules. New and interesting biochemical approaches to such surface modification include layer-by-layer deposition of polyelectrolyte films, phage display-selected surface binding peptides and self-assembled DNA monolayer systems. The present review summarizes the scientific information about these methods, which are at in vitro or in vivo development stages, and hopes to promote their future application in dental implantology and in oral and maxillofacial surgery.

  14. Line printing solution-processable small molecules with uniform surface profile via ink-jet printer.

    Science.gov (United States)

    Liu, Huimin; Xu, Wei; Tan, Wanyi; Zhu, Xuhui; Wang, Jian; Peng, Junbiao; Cao, Yong

    2016-03-01

    Line printing offers a feasible approach to remove the pixel well structure which is widely used to confine the ink-jet printed solution. In the study, a uniform line is printed by an ink-jet printer. To achieve a uniform surface profile of the printed line, 10vol% low-volatile solvent DMA (3,4-Dimethylanisole) is mixed with high-volatile solvent Pxy (p-xylene) as the solvent. After a solution-processable small molecule is dissolved, the surface tension of DMA solution becomes lower than that of Pxy solution, which creates an inward Marangoni flow during the solvent evaporation. The inward Marangoni flow balances out the outward capillary flow, thereby forming a flat film surface. The line width of the printed line depends on the contact angle of the solution on the hole injection layer.

  15. Electronic properties and assambly of DNA-based molecules on gold surfaces

    DEFF Research Database (Denmark)

    Salvatore, Princia

    , highly base specific voltammetric peak in the presence of spermidine ions. A capacitive origin was attributed to this peak, and a novel route to detection of hybridization and base pair mismatches proposed on the basis of the high sensitivity to base pair mismatches showed by such ON-based monolayers...... voltammetry and in situSTM) and SERS, respectively. Such studies proved adsorption of DNA bases (adenine, cytosine, guanine, and thymine) on the gold substrate, disclosing distinct adsorption patterns for each of them, with new insight into nucleobase assembly on a freshly cleaned Au(110) surface (not nearly...... as widely employed as Au(111) surfaces). In particular, SERS offered a valuable and rapid way ofcharacterising interactions between the DNA-based molecules and the NP surface, with no need for complex sample preparation....

  16. Photophysical properties of luminescent silicon nanoparticles surface-modified with organic molecules via hydrosilylation.

    Science.gov (United States)

    Miyano, Mari; Kitagawa, Yuichi; Wada, Satoshi; Kawashima, Akira; Nakajima, Ayako; Nakanishi, Takayuki; Ishioka, Junya; Shibayama, Tamaki; Watanabe, Seiichi; Hasegawa, Yasuchika

    2016-01-01

    Luminescent silicon nanoparticles have attracted considerable attention for their potential uses in various applications. Many approaches have been reported to protect the surface of silicon nanoparticles and prevent their easy oxidation. Various air-stable luminescent silicon nanoparticles have been successfully prepared. However, the effect of interactions of the π-electron system with the silicon surface on the excited state properties of silicon nanoparticles is unclear. In this study, we have successfully prepared silicon nanoparticles protected with three organic compounds (styrene, 1-decene, and 1-vinyl naphthalene) and have examined their photophysical properties. The ligand π-electron systems on the silicon surface promoted the light harvesting ability for the luminescence through a charge transfer transition between the protective molecules and silicon nanoparticles and also enhanced the radiative rate of the silicon nanoparticles.

  17. An SCF-CI method for determining the potential energy surface of a triatomic molecule

    Institute of Scientific and Technical Information of China (English)

    谢代前; 鄢国森

    1996-01-01

    A self-consistent-field (SCF)-configuration interaction (CI) (SCF-CI) method for determining the potential energy surface of a triatomic molecule from the observed vibrational band origins has been suggested. By this method, the SCF-CI procedure in the internal coordinates is used to calculate the vibrational bond origins and their first derivatives with respect to parameters in the potential energy function using the exact vibrational Hamiltonian, and the optimizer LMF in the nonlinear-squares problem is employed to optimize parameters in the potential energy function. This approach is used to optimize the potential energy function of the water molecule. The standard deviation of this fitting to the 70 observed band origins is 1.154cm-1.

  18. Desorption Dynamics of Rb_2 Molecules off the Surface of Helium Nanodroplets

    CERN Document Server

    Sieg, A; Stienkemeier, F; Dulieu, O; Mudrich, M

    2016-01-01

    The desorption dynamics of rubidium dimers (Rb_2) off the surface of helium nanodroplets induced by laser excitation is studied employing both nanosecond and femtosecond ion imaging spectroscopy. Similarly to alkali metal atoms, we find that the Rb_2 desorption process resembles the dissociation of a diatomic molecule. However, both angular and energy distributions of detected Rb_2^+ ions appear to be most crucially determined by the Rb_2 intramolecular degrees of freedom rather than by those of the Rb_2He_N complex. The pump-probe dynamics of Rb_2^+ is found to be slower than that of Rb^+ pointing at a weaker effective guest-host repulsion for excited molecules than for single atoms.

  19. Flow cytometric investigation of immune-response-related surface molecules on human colorectal cancers

    DEFF Research Database (Denmark)

    Diederichsen, Axel Cosmus Pyndt; Stenholm, A C; Kronborg, O;

    1998-01-01

    Our purpose was to clarify whether human colorectal cancer cells are equipped to present tumour-associated-antigens to the immune system, and whether this ability correlates with lymphoid infiltration, the Dukes' stage and Jass classification. Enzymatically dissociated tumour cells from 70...... molecules, but not the class II, was correlated with lymphoid infiltration and the Jass classification. Expression of these surface molecules was not correlated with the Dukes' stage. The tumour cells were generally equipped to present antigens to the effector arm of the immune system since HLA class I...... is expressed, but the tumour cells were not optimal in stimulating an immune response, since HLA class II and CD58 were only marginally expressed and CD80 and CD54 were absent....

  20. Weak competing interactions control assembly of strongly bonded TCNQ ionic acceptor molecules on silver surfaces

    Science.gov (United States)

    Park, Changwon; Rojas, Geoffrey A.; Jeon, Seokmin; Kelly, Simon J.; Smith, Sean C.; Sumpter, Bobby G.; Yoon, Mina; Maksymovych, Petro

    2014-09-01

    The energy scales of interactions that control molecular adsorption and assembly on surfaces can vary by several orders of magnitude, yet the importance of each contributing interaction is not apparent a priori. Tetracyanoquinodimethane (TCNQ) is an archetypal electron acceptor molecule and it is a key component of organic metals. On metal surfaces, this molecule also acts as an electron acceptor, producing negatively charged adsorbates. It is therefore rather intriguing to observe attractive molecular interactions in this system that were reported previously for copper and silver surfaces. Our experiments compared TCNQ adsorption on noble metal surfaces of Ag(100) and Ag(111). In both cases we found net attractive interactions down to the lowest coverage. However, the morphology of the assemblies was strikingly different, with two-dimensional islands on Ag(100) and one-dimensional chains on Ag(111) surfaces. This observation suggests that the registry effect governed by the molecular interaction with the underlying lattice potential is critical in determining the dimensionality of the molecular assembly. Using first-principles density functional calculations with a van der Waals correction scheme, we revealed that the strengths of major interactions (i.e., lattice potential corrugation, intermolecular attraction, and charge-transfer-induced repulsion) are all similar in energy. The van der Waals interactions, in particular, almost double the strength of attractive interactions, making the intermolecular potential comparable in strength to the diffusion potential and promoting self-assembly. However, it is the anisotropy of local intermolecular interactions that is primarily responsible for the difference in the topology of the molecular islands on Ag(100) and Ag(111) surfaces. We anticipate that the intermolecular potential will become more attractive and dominant over the diffusion potential with increasing molecular size, providing new design strategies for the

  1. Application of a convergent, composite coupled cluster approach to bound state, adiabatic electron affinities in atoms and small molecules

    Science.gov (United States)

    Feller, David

    2016-01-01

    Benchmark quality adiabatic electron affinities for a collection of atoms and small molecules were obtained with the Feller-Peterson-Dixon composite coupled cluster theory method. Prior applications of this method demonstrated its ability to accurately predict atomization energies/heats of formation for more than 170 molecules. In the current work, the 1-particle expansion involved very large correlation consistent basis sets, ranging up to aug-cc-pV9Z (aug-cc-pV10Z for H and H2), with the goal of minimizing the residual basis set truncation error that must otherwise be approximated with extrapolation formulas. The n-particle expansion begins with coupled cluster calculations through iterative single and double excitations plus a quasiperturbative treatment of "connected" triple excitations (CCSD(T)) pushed to the complete basis set limit followed by CCSDT, CCSDTQ, or CCSDTQ5 corrections. Due to the small size of the systems examined here, it was possible in many cases to extend the n-particle expansion to the full configuration interaction wave function limit. Additional, smaller corrections associated with core/valence correlation, scalar relativity, anharmonic zero point vibrational energies, and non-adiabatic effects were also included. The overall root mean square (RMS) deviation was 0.005 eV (0.12 kcal/mol). This level of agreement was comparable to what was found with molecular heats of formation. A 95% confidence level corresponds to roughly twice the RMS value or 0.01 eV. While the atomic electron affinities are known experimentally to high accuracy, the molecular values are less certain. This contributes to the difficulty of gauging the accuracy of the theoretical results. A limited number of electron affinities were determined with the explicitly correlated CCSD(T)-F12b method. After extending the VnZ-F12 orbital basis sets with additional diffuse functions, the F12b method was found to accurately reproduce the best F/F- value obtained with standard

  2. Coupled cluster calculations of mean excitation energies of the noble gas atoms He, Ne and Ar and of the H2 molecule

    DEFF Research Database (Denmark)

    Sauer, Stephan P. A.; Haq, Inam U.; Sabin, John R.

    2013-01-01

    Using an asymmetric-Lanczos-chain algorithm for the calculation of the coupled cluster linear response functions at the CCSD and CC2 levels of approximation, we have calculated the mean excitation energies of the noble gases He, Ne and Ar, and of the hydrogen molecule H2. Convergence with respect...

  3. Effect of heating of the electronic subsystem on the thermal stability of the C-60 and C-20 fullerenes and (C-20)(2) cluster molecule

    NARCIS (Netherlands)

    Davydov, I. V.

    2007-01-01

    The effect of heating of the electronic subsystem on the thermal stability of C-60 and C-20 fullerenes and a (C-20)(2) cluster molecule is investigated theoretically. It is demonstrated that the excitation of electrons to upper energy levels in accordance with the Fermi-Dirac distribution function d

  4. Electrons as probes of dynamics in molecules and clusters: A contribution from Time Dependent Density Functional Theory

    Energy Technology Data Exchange (ETDEWEB)

    Wopperer, P. [CNRS, LPT (IRSAMC), 118 route de Narbonne, F-31062 Toulouse Cédex (France); Université de Toulouse, UPS, Laboratoire de Physique Théorique (IRSAMC), 118 route de Narbonne, F-31062 Toulouse Cédex (France); Dinh, P.M., E-mail: dinh@irsamc.ups-tlse.fr [CNRS, LPT (IRSAMC), 118 route de Narbonne, F-31062 Toulouse Cédex (France); Université de Toulouse, UPS, Laboratoire de Physique Théorique (IRSAMC), 118 route de Narbonne, F-31062 Toulouse Cédex (France); Reinhard, P.-G. [Institut für Theoretische Physik, Universität Erlangen, Staudtstrasse 7, D-91058 Erlangen (Germany); Suraud, E. [CNRS, LPT (IRSAMC), 118 route de Narbonne, F-31062 Toulouse Cédex (France); Université de Toulouse, UPS, Laboratoire de Physique Théorique (IRSAMC), 118 route de Narbonne, F-31062 Toulouse Cédex (France); Physics Department, University at Buffalo, The State University New York, Buffalo, NY 14260 (United States)

    2015-02-28

    There are various ways to analyze the dynamical response of clusters and molecules to electromagnetic perturbations. Particularly rich information can be obtained from measuring the properties of electrons emitted in the course of the excitation dynamics. Such an analysis of electron signals covers observables such as total ionization, Photo-Electron Spectra (PES), Photoelectron Angular Distributions (PAD), and ideally combined PES/PAD. It has a long history in molecular physics and was increasingly used in cluster physics as well. Recent progress in the design of new light sources (high intensity, high frequency, ultra short pulses) opens new possibilities for measurements and thus has renewed the interest on these observables, especially for the analysis of various dynamical scenarios, well beyond a simple access to electronic density of states. This, in turn, has motivated many theoretical investigations of the dynamics of electronic emission for molecules and clusters up to such a complex and interesting system as C{sub 60}. A theoretical tool of choice is here Time-Dependent Density Functional Theory (TDDFT) propagated in real time and on a spatial grid, and augmented by a Self-Interaction Correction (SIC). This provides a pertinent, robust, and efficient description of electronic emission including the detailed pattern of PES and PAD. A direct comparison between experiments and well founded elaborate microscopic theories is thus readily possible, at variance with more demanding observables such as for example fragmentation or dissociation cross sections. The purpose of this paper is to describe the theoretical tools developed on the basis of real-time and real-space TDDFT and to address in a realistic manner the analysis of electronic emission following irradiation of clusters and molecules by various laser pulses. After a general introduction, we shall present in a second part the available experimental results motivating such studies, starting from the

  5. Electrons as probes of dynamics in molecules and clusters: A contribution from Time Dependent Density Functional Theory

    Science.gov (United States)

    Wopperer, P.; Dinh, P. M.; Reinhard, P.-G.; Suraud, E.

    2015-02-01

    There are various ways to analyze the dynamical response of clusters and molecules to electromagnetic perturbations. Particularly rich information can be obtained from measuring the properties of electrons emitted in the course of the excitation dynamics. Such an analysis of electron signals covers observables such as total ionization, Photo-Electron Spectra (PES), Photoelectron Angular Distributions (PAD), and ideally combined PES/PAD. It has a long history in molecular physics and was increasingly used in cluster physics as well. Recent progress in the design of new light sources (high intensity, high frequency, ultra short pulses) opens new possibilities for measurements and thus has renewed the interest on these observables, especially for the analysis of various dynamical scenarios, well beyond a simple access to electronic density of states. This, in turn, has motivated many theoretical investigations of the dynamics of electronic emission for molecules and clusters up to such a complex and interesting system as C60. A theoretical tool of choice is here Time-Dependent Density Functional Theory (TDDFT) propagated in real time and on a spatial grid, and augmented by a Self-Interaction Correction (SIC). This provides a pertinent, robust, and efficient description of electronic emission including the detailed pattern of PES and PAD. A direct comparison between experiments and well founded elaborate microscopic theories is thus readily possible, at variance with more demanding observables such as for example fragmentation or dissociation cross sections. The purpose of this paper is to describe the theoretical tools developed on the basis of real-time and real-space TDDFT and to address in a realistic manner the analysis of electronic emission following irradiation of clusters and molecules by various laser pulses. After a general introduction, we shall present in a second part the available experimental results motivating such studies, starting from the simplest

  6. Cross-Linking Poly(lactic acid) Film Surface by Neutral Hyperthermal Hydrogen Molecule Bombardment.

    Science.gov (United States)

    Du, Wangli; Shao, Hong; He, Zhoukun; Tang, Changyu; Liu, Yu; Shen, Tao; Zhu, Yan; Lau, Woon-ming; Hui, David

    2015-12-16

    Constructing a dense cross-linking layer on a polymer film surface is a good way to improve the water resistance of poly(lactic acid) (PLA). However, conventional plasma treatments have failed to achieve the aim as a result of the unavoidable surface damage arising from the charged species caused by the uncontrolled high energy coming from colliding ions and electrons. In this work, we report a modified plasma method called hyperthermal hydrogen-induced cross-linking (HHIC) technology to construct a dense cross-linking layer on PLA film surfaces. This method produces energy-controlled neutral hyperthermal hydrogen, which selectively cleaves C-H bonds by molecule collision from the PLA film without breaking other bonds (e.g., C-C bonds in the polymer backbone), and results in subsequent cross-linking of the carbon radicals generated from the organic molecules. The formation of a dense cross-linking layer can serve as a barrier layer to significantly improve both the hydrophobicity and water vapor barrier property of the PLA film. Because of the advantage of selective cleavage of C-H bonds by HHIC treatment, the original physical properties (e.g., mechanical strength and light transmittance) of the PLA films are well-preserved.

  7. Surface composition gradients of immobilized cell signaling molecules. Epidermal growth factor on gold

    Energy Technology Data Exchange (ETDEWEB)

    Wang Qian [Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 (United States); Bohn, Paul W. [Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 (United States)]. E-mail: bohn@scs.uiuc.edu

    2006-08-14

    Surface composition gradients of the signaling molecule, epidermal growth factor (EGF), have been prepared by an adaptation of the electrochemical gradient technique. EGF is covalently bound to the reactive component, 11-amino-l-undecanethiol (AUT), in a counterpropagating two-component gradient composed of AUT and poly(ethylene glycol) thiol (PEG) using carbodiimide coupling chemistry. Areas of the surface presenting -NH{sub 2} termination react with succinimidyl esters of solvent-accessible acidic amino acids in EGF, while non-specific protein adsorption is resisted in the PEG regions. The maximum surface coverage of EGF prepared in this manner was determined by surface plasmon resonance reflectometry (SPR) on spatially uniform films to be 20% < {gamma} {sub EGF} < 70% depending on the concentration of the EGF derivatization solution. EGF retains its biological activity with this immobilization process, as verified by culturing human umbilical vein endothelial cell (HUVEC) on an EGF-terminated surface for 24 h. PEG shows good resistance to EGF physical adsorption as demonstrated by both SPR and X-ray photoelectron spectroscopy (XPS). The N / C ratio of EGF gradients, which is characteristic of EGF adsorption, because only the protein contains N, while both protein and PEG contain C, was spatially mapped with XPS. The gradient composition distributions are sigmoidal with lateral distance, with the position of the gradient transition region being readily controlled by adjusting the applied potential window. EGF gradients with variable quantitative surface coverage profiles were generated by varying EGF and AUT concentrations.

  8. Simple coupling chemistry linking carboxyl-containing organic molecules to silicon oxide surfaces under acidic conditions.

    Science.gov (United States)

    Schmidt, Sebastian W; Christ, Timo; Glockner, Christian; Beyer, Martin K; Clausen-Schaumann, Hauke

    2010-10-05

    The coupling chemistry of carboxymethylated amylose with organo-silanized silicon oxide surfaces at pH 7.4 and 2.0 was investigated using atomic force microscopy (AFM) based single-molecule force spectroscopy. At close to neutral pH, carbodiimide activation of a carboxylic acid affords formation of an amide bond with an amino surface linker. At pH 2.0, no activation with carbodiimide was required to anchor carboxymethylated amylose between an AFM tip and a glass substrate. At the same time, the mean bond rupture force f(r) dropped from 1.65 ± 0.37 nN at pH 7.4 to 1.39 ± 0.30 nN at pH 2.0 without carbodiimide, indicating that a different link to the surface can be formed at low pH. The coupling mechanism at pH 2.0 was elucidated by a series of experiments, in which the surface was functionalized with four different organosilanes, each containing characteristic functional groups. The results are rationalized with an acid-catalyzed ester condensation between a carboxyl group and a free, unreacted silanol group in the surface anchor or on the surface.

  9. Bacteroidales Secreted Antimicrobial Proteins Target Surface Molecules Necessary for Gut Colonization and Mediate Competition In Vivo

    Directory of Open Access Journals (Sweden)

    Kevin G. Roelofs

    2016-08-01

    Full Text Available We recently showed that human gut Bacteroidales species secrete antimicrobial proteins (BSAPs, and we characterized in vitro the first such BSAP produced by Bacteroides fragilis. In this study, we identified a second potent BSAP produced by the ubiquitous and abundant human gut species Bacteroides uniformis. The two BSAPs contain a membrane attack complex/perforin (MACPF domain but share very little sequence similarity. We identified the target molecules of BSAP-sensitive cells and showed that each BSAP targets a different class of surface molecule: BSAP-1 targets an outer membrane protein of sensitive B. fragilis strains, and BSAP-2 targets the O-antigen glycan of lipopolysaccharide (LPS of sensitive B. uniformis strains. Species-wide genomic and phenotypic analyses of B. fragilis and B. uniformis showed that BSAP-producing strains circumvent killing by synthesizing an orthologous nontargeted surface molecule. The BSAP genes are adjacent to the gene(s encoding their target replacements, suggesting coacquisition. Using a gnotobiotic mouse competitive-colonization model, we found that the BSAP surface targets are important for colonization of the mammalian gut, thereby explaining why they are maintained in sensitive strains and why they were replaced rather than deleted in BSAP-producing strains. Using isogenic BSAP-producing, -sensitive, and -resistant strains, we show that a BSAP-producing strain outcompetes a sensitive strain but not a resistant strain in the mammalian gut. Human gut metagenomic datasets reveal that BSAP-1-sensitive strains do not cooccur with BSAP-1-producing strains in human gut microbiotas, further supporting the idea that BSAPs are important competitive factors with relevance to the strain-level composition of the human gut microbiota.

  10. Single-molecule force spectroscopy reveals the individual mechanical unfolding pathways of a surface layer protein.

    Science.gov (United States)

    Horejs, Christine; Ristl, Robin; Tscheliessnig, Rupert; Sleytr, Uwe B; Pum, Dietmar

    2011-08-05

    Surface layers (S-layers) represent an almost universal feature of archaeal cell envelopes and are probably the most abundant bacterial cell proteins. S-layers are monomolecular crystalline structures of single protein or glycoprotein monomers that completely cover the cell surface during all stages of the cell growth cycle, thereby performing their intrinsic function under a constant intra- and intermolecular mechanical stress. In gram-positive bacteria, the individual S-layer proteins are anchored by a specific binding mechanism to polysaccharides (secondary cell wall polymers) that are linked to the underlying peptidoglycan layer. In this work, atomic force microscopy-based single-molecule force spectroscopy and a polyprotein approach are used to study the individual mechanical unfolding pathways of an S-layer protein. We uncover complex unfolding pathways involving the consecutive unfolding of structural intermediates, where a mechanical stability of 87 pN is revealed. Different initial extensibilities allow the hypothesis that S-layer proteins adapt highly stable, mechanically resilient conformations that are not extensible under the presence of a pulling force. Interestingly, a change of the unfolding pathway is observed when individual S-layer proteins interact with secondary cell wall polymers, which is a direct signature of a conformational change induced by the ligand. Moreover, the mechanical stability increases up to 110 pN. This work demonstrates that single-molecule force spectroscopy offers a powerful tool to detect subtle changes in the structure of an individual protein upon binding of a ligand and constitutes the first conformational study of surface layer proteins at the single-molecule level.

  11. The interaction of gold clusters with methanol molecules: Infrared photodissociation of mass-selected Aun+(CH3OH)m

    Science.gov (United States)

    Dietrich, G.; Krückeberg, S.; Lützenkirchen, K.; Schweikhard, L.; Walther, C.

    2000-01-01

    Structural and energetic properties of the adducts formed by adsorbing methanol onto size-selected gold clusters are investigated by infrared photodissociation of trapped Aun+(CH3OH)m, n=1-10,15 and m=1-3. The excitation of vibrational modes of methanol leads to the desorption of neutral molecules which is monitored by time-of-flight mass spectrometry. Spectra are obtained by measuring the fragment ion intensity as a function of photon energy. The C-O stretching vibration of adsorbed methanol changes discontinuously with cluster size. By comparison with Car-Parrinello calculations this change is traced back to the dimensionality of the gold clusters. The number of photons necessary for the desorption of methanol molecules provides an estimate of the respective separation energies.

  12. Ab-initio tensorial electronic friction for molecules on metal surfaces: nonadiabatic vibrational relaxation

    CERN Document Server

    Maurer, Reinhard J; Batista, Victor S; Tully, John C

    2016-01-01

    Molecular adsorbates on metal surfaces exchange energy with substrate phonons and low-lying electron-hole pair excitations. In the limit of weak coupling, electron-hole pair excitations can be seen as exerting frictional forces on adsorbates that enhance energy transfer and facilitate vibrational relaxation or hot-electron mediated chemistry. We have recently reported on the relevance of tensorial properties of electronic friction [Phys. Rev. Lett. 116, 217601 (2016)] in dynamics at surfaces. Here we present the underlying implementation of tensorial electronic friction based on Kohn-Sham Density Functional Theory for condensed phase and cluster systems. Using local atomic-orbital basis sets, we calculate nonadiabatic coupling matrix elements and evaluate the full electronic friction tensor in the classical limit. Our approach is numerically stable and robust as shown by a detailed convergence analysis. We furthermore benchmark the accuracy of our approach by calculation of vibrational relaxation rates and li...

  13. Electron collisions with atoms, ions, molecules, and surfaces: Fundamental science empowering advances in technology

    Science.gov (United States)

    Bartschat, Klaus; Kushner, Mark J.

    2016-06-01

    Electron collisions with atoms, ions, molecules, and surfaces are critically important to the understanding and modeling of low-temperature plasmas (LTPs), and so in the development of technologies based on LTPs. Recent progress in obtaining experimental benchmark data and the development of highly sophisticated computational methods is highlighted. With the cesium-based diode-pumped alkali laser and remote plasma etching of Si3N4 as examples, we demonstrate how accurate and comprehensive datasets for electron collisions enable complex modeling of plasma-using technologies that empower our high-technology-based society.

  14. Scaling properties of adsorption energies for hydrogen-containing molecules on transition-metal surfaces

    DEFF Research Database (Denmark)

    Abild-Pedersen, Frank; Greeley, Jeffrey Philip; Studt, Felix

    2007-01-01

    with the adsorption energy of the central, C, N, O, or S atom, the scaling constant depending only on x. A model is proposed to understand this behavior. The scaling model is developed into a general framework for estimating the reaction energies for hydrogenation and dehydrogenation reactions.......Density functional theory calculations are presented for CHx, x=0,1,2,3, NHx, x=0,1,2, OHx, x=0,1, and SHx, x=0,1 adsorption on a range of close-packed and stepped transition-metal surfaces. We find that the adsorption energy of any of the molecules considered scales approximately...

  15. Combined fragment molecular orbital cluster in molecule approach to massively parallel electron correlation calculations for large systems.

    Science.gov (United States)

    Findlater, Alexander D; Zahariev, Federico; Gordon, Mark S

    2015-04-16

    The local correlation "cluster-in-molecule" (CIM) method is combined with the fragment molecular orbital (FMO) method, providing a flexible, massively parallel, and near-linear scaling approach to the calculation of electron correlation energies for large molecular systems. Although the computational scaling of the CIM algorithm is already formally linear, previous knowledge of the Hartree-Fock (HF) reference wave function and subsequent localized orbitals is required; therefore, extending the CIM method to arbitrarily large systems requires the aid of low-scaling/linear-scaling approaches to HF and orbital localization. Through fragmentation, the combined FMO-CIM method linearizes the scaling, with respect to system size, of the HF reference and orbital localization calculations, achieving near-linear scaling at both the reference and electron correlation levels. For the 20-residue alanine α helix, the preliminary implementation of the FMO-CIM method captures 99.6% of the MP2 correlation energy, requiring 21% of the MP2 wall time. The new method is also applied to solvated adamantine to illustrate the multilevel capability of the FMO-CIM method.

  16. Multifractal analysis of slacken surface in hydrocarbon molecules through fuel additives

    Directory of Open Access Journals (Sweden)

    G. Arockia Prabakar

    2014-09-01

    Full Text Available This paper investigates the effect of organic fuel additives (Bio-Glycerol on fuel savings, emission reduction and extend engine life. Using this enzyme, a motor cycle is tested five times. The test report shows the reduction in the release of carbon monoxide (CO and hydrocarbon upto 60%. The use of organic fuel additives in diesel vehicles for different periods of time reveals the reduction in air pollution by 55%. Finally, we have experimented scanning electron microscope (SEM test for organic fuel additives with biodiesel. The SEM image shows the existence of molecules of hydrocarbons. The analysis elucidated the complex morphology of molecules of hydrocarbons in fuel additives with biodiesel. The hydrocarbon molecules are slackened and irregular as it refers to the fractal form. SEM Photograph images are analyzed by multifractal analysis. MFA (multifractal analysis is carried out according to the method of moments, i.e., the probability distribution is estimated for moments which differ from -150surface.

  17. Self-diffusion dynamic behavior of atomic clusters on Re(0 0 0 1) surface

    Energy Technology Data Exchange (ETDEWEB)

    Liu Fusheng [Department of Applied Physics, Hunan University, Changsha 410082 (China); Hu Wangyu, E-mail: wangyuhu2001cn@yahoo.com.cn [Department of Applied Physics, Hunan University, Changsha 410082 (China); Deng Huiqiu; Luo Wenhua; Xiao Shifang [Department of Applied Physics, Hunan University, Changsha 410082 (China); Yang Jianyu [Department of Maths and Physics, Hunan Institute of Engineering, Xiangtan 411104 (China)

    2009-08-15

    Using molecular dynamics simulations and a modified analytic embedded atom potential, the self-diffusion dynamics of rhenium atomic clusters up to seven atoms on Re(0 0 0 1) surface have been studied in the temperature ranges from 600 K to 1900 K. The simulation time varies from 20 ns to 200 ns according to the cluster sizes and the temperature. The heptamer and trimer are more stable comparing to other neighboring non-compact clusters. The diffusion coefficients of clusters are derived from the mean square displacement of cluster's mass-center, and diffusion prefactors D{sub 0} and activation energies E{sub a} are derived from the Arrhenius relation. It is found that the Arrhenius relation of the adatom can be divided into two parts at different temperature range. The activation energy of clusters increases with the increasing of the atom number in clusters. The prefactor of the heptamer is 2-3 orders of magnitude higher than a usual prefactor because of a large number of nonequivalent diffusion processes. The trimer and heptamer are the nuclei at different temperature range according to the nucleation theory.

  18. Method and apparatus for enhanced sequencing of complex molecules using surface-induced dissociation in conjunction with mass spectrometric analysis

    Science.gov (United States)

    Laskin, Julia [Richland, WA; Futrell, Jean H [Richland, WA

    2008-04-29

    The invention relates to a method and apparatus for enhanced sequencing of complex molecules using surface-induced dissociation (SID) in conjunction with mass spectrometric analysis. Results demonstrate formation of a wide distribution of structure-specific fragments having wide sequence coverage useful for sequencing and identifying the complex molecules.

  19. Mode conversion of Mie plasmons at the surface of metallic atomic clusters

    Science.gov (United States)

    El-Khawaldeh, A.; Kull, H.-J.

    2017-04-01

    The dynamics of the Mie plasmon is described in the framework of the self-consistent quantum Vlasov theory by a reduced single-state model. The single-state model is validated by many-electron calculations for Na clusters. In this framework, collisionless damping of the Mie plasmon can be investigated for a wide range of cluster parameters by linear perturbation theory. The characteristic scaling of the damping rate with the inverse cluster radius is demonstrated. The basic damping mechanism of the Mie plasmon can be explained by a conversion of surface modes into volume modes due to the scattering by the self-consistent potential of the electron-electron interaction at the cluster boundary.

  20. The mechanics of bacterial cluster formation on plant leaf surfaces as revealed by bioreporter technology.

    Science.gov (United States)

    Tecon, Robin; Leveau, Johan H J

    2012-05-01

    Bacteria that colonize the leaves of terrestrial plants often occur in clusters whose size varies from a few to thousands of cells. For the formation of such bacterial clusters, two non-mutually exclusive but very different mechanisms may be proposed: aggregation of multiple cells or clonal reproduction of a single cell. Here we assessed the contribution of both mechanisms on the leaves of bean plants that were colonized by the bacterium Pantoea agglomerans. In one approach, we used a mixture of green and red fluorescent P. agglomerans cells to populate bean leaves. We observed that this resulted in clusters made up of only one colour as well as two-colour clusters, thus providing evidence for both mechanisms. Another P. agglomerans bioreporter, designed to quantify the reproductive success of bacterial colonizers by proxy to the rate at which green fluorescent protein is diluted from dividing cells, revealed that during the first hours on the leaf surface, many bacteria were dividing, but not staying together and forming clusters, which is suggestive of bacterial relocation. Together, these findings support a dynamic model of leaf surface colonization, where both aggregative and reproductive mechanisms take place. The bioreporter-based approach we employed here should be broadly applicable towards a more quantitative and mechanistic understanding of bacterial colonization of surfaces in general. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  1. Growth mechanism of palladium clusters on rutile TiO2(110) surface

    Institute of Scientific and Technical Information of China (English)

    Weina Zhao; Huaxiang Lin; Yi Li; Yongfan Zhang; Xin Huang; Wenkai Chen

    2012-01-01

    Oxide-supported transition metal systems have been the subject of enormous interest due to the improvement of catalytic properties relative to the separate metal.Thus in this paper,we embark on a systematic study for Pdn (n =1-5) clusters adsorbed on TiO2(110) surface based on DFT-GGA calculations utilizing periodic supercell models.A single Pd adatom on the defect-free surface prefers to adsorb at a hollow site bridging a protruded oxygen and a five-fold titanium atom along the [110] direction,while Pd dimer is located on the channels with the Pd-Pd bond parallel to the surface.According to the transition states (TSs) search,the adsorbed Pd trimer tends to triangular growth mode,rather than linear mode,while the Pd4 and Pd5 clusters prefer three-dimensional (3D) models.However,the oxygen vacancy has almost no influence on the promotion of Pdn cluster nucleation.Additionally,of particular significance is that the Pd-TiO2 interaction is the main driving force at the beginning of Pd nucleation,whereas the Pd-Pd interaction gets down to control the growth process of Pd cluster as the cluster gets larger.It is hoped that our theoretical study would shed light on further designing high-performance TiO2 supported Pd-based catalysts.

  2. Probing the Low Surface Brightness Dwarf Galaxy Population of the Virgo Cluster

    CERN Document Server

    Davies, J I; Keenan, O C

    2015-01-01

    We have used public data from the Next Generation Virgo Survey (NGVS) to investigate the dwarf galaxy population of the Virgo cluster beyond what has previously been discovered. We initially mask and smooth the data, and then use the object detection algorithm Sextractor to make our initial dwarf galaxy selection. All candidates are then visually inspected to remove artefacts and duplicates. We derive Sextractor parameters to best select low surface brightness galaxies using g band central surface brightness values of 22.5 to 26.0 mag sq arc sec and exponential scale lengths of 3.0 - 10.0 arc sec to identify 443 cluster dwarf galaxies - 303 of which are new detections. These new detections have a surface density that decreases with radius from the cluster centre. We also apply our selection algorithm to 'background', non-cluster, fields and find zero detections. In combination, this leads us to believe that we have isolated a cluster dwarf galaxy population. The range of objects we are able to detect is limit...

  3. Surface chemical reactions induced by molecules electronically-excited in the gas

    DEFF Research Database (Denmark)

    Petrunin, Victor V.

    2011-01-01

    be readily produced. Products of chemical adsorption and/or chemical reactions induced within adsorbates are aggregated on the surface and observed by light scattering. We will demonstrate how pressure and spectral dependencies of the chemical outcomes, polarization of the light and interference of two laser...... and alignment are taking place, guiding all the molecules towards the intersections with the ground state PES, where transitions to the ground state PES will occur with minimum energy dissipation. The accumulated kinetic energy may be used to overcome the chemical reaction barrier. While recombination chemical...... reactions in a gas phase require participation of a third body, this strong limitation on the reaction rates is removed upon interaction with a surface. To observe the predicted phenomenon, we suggested a new experimental approach, Evanescent Wave Photocatalysis1, based on application of total internal...

  4. Strategies for creating antifouling surfaces using selfassembled poly(ethylene glycol) thiol molecules

    DEFF Research Database (Denmark)

    Lokanathan, Arcot R.

    2011-01-01

    conditions for the reversible, initial attachment of microbial cells. This effect can be obtained by grafting hydrophilic polymeric chains onto surfaces and thereby provide a steric barrier between the substrate surface and the microbial cell. Poly (ethylene glycol) (PEG) is one of the most widely used....... The work focuses on novel strategies to self assemble PEG thiol monolayers with high graft density. One of the strategies investigated involved backfilling a self assembled layer of 2000 Da PEG thiol with shorter oligo (ethylene glycol) (OEG) thiol molecules to form a mixed monolayer. Detailed quantitative......Microorganisms are one of the most important parts of our ecosystem influencing the sustenance of human society. The beneficial microbes are of high relevance to food industry, development of antibiotics and processing of many raw materials. Mankind has indeed benefitted a lot from large number...

  5. Interaction of mineral surfaces with simple organic molecules by diffuse reflectance IR spectroscopy (DRIFT)

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, Joan E.; Kelley, Michael J.

    2008-06-01

    Diffuse reflectance Fourier-transform infrared spectroscopy (DRIFTS) was used to characterize multi-layers of lysine, glutamic acid and salicylic acid on -alumina and kaolinite surfaces. The results agreed well with those previously obtained by ATR-IR in aqueous media where available, indicating that DRIFT may be regarded as effectively an in-situ spectroscopy for these materials. In the case of salicylic acid adsorption onto γ-alumina, DRIFTS was used to identify monolayer coverage and to detect molecules down to coverage of 3% of a monolayer. The spectroscopic results as to coverage were confirmed by analysis of the solutions used for treatment. The spectra obtained allowed identification of changes in the bonding environment with increasing surface coverage. DRIFTS, offers several advantages in terms of materials, experimental technique and data treatment, motivating further investigations.

  6. Formation of prebiotic molecules in liquid water environments on the surface of Titan

    Science.gov (United States)

    Neish, Catherine Dorothy

    Saturn's moon Titan represents a unique locale for studying prebiotic chemistry. Reactions occurring in its thick nitrogen-methane atmosphere produce a wide variety of carbon, hydrogen, and nitrogen containing organic molecules. If these molecules are exposed to liquid water, they may react further to produce oxygen-containing species, a key step in the formation of terrestrial biomolecules. On average, Titan's surface is too cold for liquid water. However, models indicate that melting caused by impacts and/or cryovolcanism may lead to its episodic availability. One possible cryovolcanic dome, Ganesa Macula, was identified in early observations by the Cassini spacecraft. In this work, I estimate the height and morphology of this feature using a synthetic aperture radar (SAR) image. I then use a thermal conduction code to calculate the freezing timescale for an initially liquid dome, yielding freezing timescales of ~10^2 - 10^5 years. To determine how far aqueous organic chemistry can proceed in liquid water environments on Titan, I measure the rate coefficients of Titan analogue organic molecules ("tholins") with low temperature aqueous solutions to produce oxygenated species. These reactions display first-order kinetics with half- lives between 0.4 and 7 days at 273 K (in water) and between 0.3 and 14 days at 253 K (in 13 wt. % ammonia-water). Tholin hydrolysis in aqueous solutions is thus very fast compared to the freezing timescales of impact melts and volcanic sites on Titan, which take hundreds to thousands of years to freeze. The fast incorporation of oxygen, along with new chemistry made available by the introduction of ammonia, may lead to the formation of molecules of prebiotic interest in these transient liquid water environments. This chemistry makes impact craters and cryovolcanoes important targets for future missions to Titan.

  7. Neutrophil surface adhesion molecule and toll like receptor dynamics in crossbred cows suffering from Staphylococcus aureus subclinical and clinical mastitis

    Directory of Open Access Journals (Sweden)

    Dilip Kumar Swain

    2016-06-01

    Conclusion: Host elicits stage specific expression of surface adhesion molecules and TLR2 and TLR4 as dynamic host innate immune response against Staphylococcal mastitis. [J Adv Vet Anim Res 2016; 3(2.000: 99-105

  8. Bacteroidales Secreted Antimicrobial Proteins Target Surface Molecules Necessary for Gut Colonization and Mediate Competition In Vivo.

    Science.gov (United States)

    Roelofs, Kevin G; Coyne, Michael J; Gentyala, Rahul R; Chatzidaki-Livanis, Maria; Comstock, Laurie E

    2016-08-23

    We recently showed that human gut Bacteroidales species secrete antimicrobial proteins (BSAPs), and we characterized in vitro the first such BSAP produced by Bacteroides fragilis In this study, we identified a second potent BSAP produced by the ubiquitous and abundant human gut species Bacteroides uniformis The two BSAPs contain a membrane attack complex/perforin (MACPF) domain but share very little sequence similarity. We identified the target molecules of BSAP-sensitive cells and showed that each BSAP targets a different class of surface molecule: BSAP-1 targets an outer membrane protein of sensitive B. fragilis strains, and BSAP-2 targets the O-antigen glycan of lipopolysaccharide (LPS) of sensitive B. uniformis strains. Species-wide genomic and phenotypic analyses of B. fragilis and B. uniformis showed that BSAP-producing strains circumvent killing by synthesizing an orthologous nontargeted surface molecule. The BSAP genes are adjacent to the gene(s) encoding their target replacements, suggesting coacquisition. Using a gnotobiotic mouse competitive-colonization model, we found that the BSAP surface targets are important for colonization of the mammalian gut, thereby explaining why they are maintained in sensitive strains and why they were replaced rather than deleted in BSAP-producing strains. Using isogenic BSAP-producing, -sensitive, and -resistant strains, we show that a BSAP-producing strain outcompetes a sensitive strain but not a resistant strain in the mammalian gut. Human gut metagenomic datasets reveal that BSAP-1-sensitive strains do not cooccur with BSAP-1-producing strains in human gut microbiotas, further supporting the idea that BSAPs are important competitive factors with relevance to the strain-level composition of the human gut microbiota. We know relatively little about the ecology of the human intestinal microbiota and the combination of factors that dictate which strains and species occupy an individual's gut microbial community

  9. Theoretical Simulations of Reactive and Nonreactive Scattering of Light Diatomic Molecules from Metal Surfaces: Past, Present, and Future

    Directory of Open Access Journals (Sweden)

    C. Díaz

    2014-01-01

    Full Text Available In everyday life we are surrounded by surfaces and, therefore, by phenomena involving molecule-surface interactions. Furthermore, the processes of heterogeneous catalysis, which are governed by molecule-surface interactions, are of huge practical importance, because the production of most synthetic compounds involves catalytic processes, which explains the tremendous effort that surface science scientists have invested to understand the basic principles underlying elementary interactions between light molecules and surfaces. This effort was recognized in 2007 with the Nobel prize in chemistry awarded to Gerhard Ertl. Here we revise some of the most relevant studies performed so far in this field. We also point out the major challenges that the surface science community may face in this field in the years to come.

  10. Computational studies of atmospherically-relevant chemical reactions in water clusters and on liquid water and ice surfaces.

    Science.gov (United States)

    Gerber, R Benny; Varner, Mychel E; Hammerich, Audrey D; Riikonen, Sampsa; Murdachaew, Garold; Shemesh, Dorit; Finlayson-Pitts, Barbara J

    2015-02-17

    CONSPECTUS: Reactions on water and ice surfaces and in other aqueous media are ubiquitous in the atmosphere, but the microscopic mechanisms of most of these processes are as yet unknown. This Account examines recent progress in atomistic simulations of such reactions and the insights provided into mechanisms and interpretation of experiments. Illustrative examples are discussed. The main computational approaches employed are classical trajectory simulations using interaction potentials derived from quantum chemical methods. This comprises both ab initio molecular dynamics (AIMD) and semiempirical molecular dynamics (SEMD), the latter referring to semiempirical quantum chemical methods. Presented examples are as follows: (i) Reaction of the (NO(+))(NO3(-)) ion pair with a water cluster to produce the atmospherically important HONO and HNO3. The simulations show that a cluster with four water molecules describes the reaction. This provides a hydrogen-bonding network supporting the transition state. The reaction is triggered by thermal structural fluctuations, and ultrafast changes in atomic partial charges play a key role. This is an example where a reaction in a small cluster can provide a model for a corresponding bulk process. The results support the proposed mechanism for production of HONO by hydrolysis of NO2 (N2O4). (ii) The reactions of gaseous HCl with N2O4 and N2O5 on liquid water surfaces. Ionization of HCl at the water/air interface is followed by nucleophilic attack of Cl(-) on N2O4 or N2O5. Both reactions proceed by an SN2 mechanism. The products are ClNO and ClNO2, precursors of atmospheric atomic chlorine. Because this mechanism cannot result from a cluster too small for HCl ionization, an extended water film model was simulated. The results explain ClNO formation experiments. Predicted ClNO2 formation is less efficient. (iii) Ionization of acids at ice surfaces. No ionization is found on ideal crystalline surfaces, but the process is efficient on

  11. Atomistic interactions of clusters on surfaces using molecular dynamics and hyper molecular dynamics

    CERN Document Server

    Sanz-Navarro, C F

    2002-01-01

    The work presented in this thesis describes the results of Molecular Dynamics (MD) simulations applied to the interaction of silver clusters with graphite surfaces and some numerical and theoretical methods concerning the extension of MD simulations to longer time scales (hyper-MD). The first part of this thesis studies the implantation of clusters at normal incidence onto a graphite surface in order to determine the scaling of the penetration depth (PD) against the impact energy. A comparison with experimental results is made with good agreement. The main physical observations of the impact process are described and analysed. It is shown that there is a threshold impact velocity above which the linear dependence on PD on impact energy changes to a linear dependence on velocity. Implantation of silver clusters at oblique incidence is also considered. The second part of this work analyses the validity and feasibility of the three minimisation methods for the hyper-MD simulation method whereby time scales of an...

  12. Road Surface Modeling and Representation from Point Cloud Based on Fuzzy Clustering

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yi; YAN Li

    2007-01-01

    A scheme for an automatic road surface modeling from a noisy point cloud is presented. The normal vectors of the point cloud are estimated by distance-weighted fitting of local plane. Then, an automatic recognition of the road surface from noise is performed based on the fuzzy clustering of normal vectors, with which the mean value is calculated and the projecting plane of point cloud is created to obtain the geometric model accordingly. Based on fuzzy clustering of the intensity attributed to each point, different objects on the road surface are assigned different colors for representing abundant appearances.This unsupervised method is demonstrated in the experiment and shows great effectiveness in reconstructing and rendering better road surface.

  13. Tailoring activated carbon by surface chemical modification with O, S, and N containing molecules

    Directory of Open Access Journals (Sweden)

    Rachel RibeiroVieira Azzi Rios

    2003-06-01

    Full Text Available In this work the surface of activated carbon was chemically modified in order to introduce O, S and N containing groups. The activated carbon surface was selectively oxidized with concentrated HNO3 under controlled conditions. Characterization by thermogravimetric analyses, infrared spectroscopy and NaOH titration suggested the formation of mainly -COOH and small amounts of -OH groups, with concentration of approximately 4.10(21 groups/g of carbon. These -COOH functionalized carbons showed high adsorption capacity for metal cations in aqueous solution in the following order: Pb+2>Cu+2>Ni+2 >Cd+2~Co+2>Ca+2 , suggesting a cation exchange mechanism via a surface complex [COO-M+2]. These -COOHsurf groups can be reacted with SOCl2 to produce a surface acylchloride group, -COCl. This surface -COCl group proved to be a very reactive and versatile intermediate for the grafting of different S and N containing molecules onto the carbon surface, such as 1,2-ethaneditiol (EDT-, HSCH2CH2SH 1,7-dimercapto-4-thioheptane (DMTH-HSCH2CH2CH2SCH2CH 2CH2SH or 1,2-ethylenediamine (EDA- NH2CH2CH2NH2 and triethyltetraamine, TEA (H2NCH2CH2NHCH2CH 2NHCH2CH2 NH2. The characterization of these materials was carried out by TG, IR and TPDMS (Temperature Programmed Decomposition Mass Spectrometry experiments suggesting the formation of thioesther and amide surface groups, i.e. -COSR and -CONHR, with yields of approximately 50 and 75% for the reaction with DME and EDA, respectively. Preliminary adsorption experiments showed that these materials can efficiently remove metals such as Pb+2, Cu+2 and Ni+2 from aqueous medium.

  14. A theoretical study of the XP and NEXAFS spectra of alanine: gas phase molecule, crystal, and adsorbate at the ZnO(10 ̅10) surface.

    Science.gov (United States)

    Gao, You Kun; Traeger, Franziska; Kotsis, Konstantinos; Staemmler, Volker

    2011-06-14

    The adsorption of alanine on the mixed-terminated ZnO(10 ̅10) surface is studied by means of quantum-chemical ab initio calculations. Using a finite cluster model and the adsorption geometry as obtained both by periodic CPMD and embedded cluster calculations, the C1s, N1s and O1s X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectra are calculated for single alanine molecules on ZnO(10 ̅10). These spectra are compared with the spectra calculated for alanine in the gas phase and in its crystalline form and with experimental XPS and NEXAFS data for the isolated alanine molecule and for alanine adsorbed on ZnO(10 ̅10) at multilayer and monolayer coverage. The excellent agreement between the experimental and calculated XP and NEXAFS spectra confirms the calculated adsorption geometry: A single alanine molecule is bound to ZnO(10 ̅10) in a dissociated bidentate form with the two O atoms of the acid group bound to two Zn atoms of the surface and the proton transferred to one O atom of the surface. Other possible structures, such as adsorption of alanine in one of its neutral or zwitterionic forms in which the proton of the -COOH group remains at this group or is transferred to the amino group, can be excluded since they would give rise to quite different XP spectra. In the multilayer coverage regime, on the other hand, alanine is in its crystalline form as is also shown by the analysis of the XP spectra.

  15. The outer regions of galaxy clusters: Chandra constraints on the X-ray surface brightness

    CERN Document Server

    Ettori, S

    2008-01-01

    (Abridged version) We study the properties of the X-ray surface brightness profiles in a sample of galaxy clusters that are observed with Chandra and have emission detectable with a signal-to-noise ratio larger than 2 at a radius beyond R500 ~ 0.7 R200. Our study aims at measuring the slopes of the X-ray surface brightness and of the gas density profiles in the outskirts of massive clusters. These constraints are then compared to similar results obtained from observations and numerical simulations of the temperature and dark matter density profiles with the intention to present a consistent picture of the outer regions of galaxy clusters. We extract the surface brightness profiles S_b(r) from X-ray exposures obtained with Chandra of 52 X-ray luminous galaxy clusters at z>0.3. We estimate R200 both using a beta-model to reproduce the surface brightness profile and scaling relations from the literature, showing that the two methods converge to comparable values. We evaluate then the radius, R_S2N, at which the ...

  16. Dependence of surface smoothing, sputtering and etching phenomena on cluster ion dosage

    CERN Document Server

    Song, J H; Choi, W K

    2002-01-01

    The dependence of surface smoothing and sputtering phenomena of Si (1 0 0) solid surfaces irradiated by CO sub 2 cluster ions on cluster-ion dosage was investigated using an atomic force microscope. The flux and total ion dosage of impinging cluster ions at the acceleration voltage of 50 kV were fixed at 10 sup 9 ions/cm sup 2 s and were scanned from 5x10 sup 1 sup 0 to 5x10 sup 1 sup 3 ions/cm sup 2 , respectively. The density of hillocks induced by cluster ion impact was gradually increased with the dosage up to 5x10 sup 1 sup 1 ions/cm sup 2 , which caused that the irradiated surface became rough from 0.4 to 1.24 nm in root-mean-square roughness (sigma sub r sub m sub s). At the boundary of the ion dosage of 10 sup 1 sup 2 ions/cm sup 2 , the density of the induced hillocks was decreased and sigma sub r sub m sub s was about 1.21 nm, not being deteriorated further. At the dosage of 5x10 sup 1 sup 3 ions/cm sup 2 , the induced hillocks completely disappeared and the surface became very flat as much as sigma...

  17. Differential Expression of Osteo-Modulatory Molecules in Periodontal Ligament Stem Cells in Response to Modified Titanium Surfaces

    Directory of Open Access Journals (Sweden)

    So Yeon Kim

    2014-01-01

    Full Text Available This study assessed differential gene expression of signaling molecules involved in osteogenic differentiation of periodontal ligament stem cells (PDLSCs subjected to different titanium (Ti surface types. PDLSCs were cultured on tissue culture polystyrene (TCPS, and four types of Ti discs (PT, SLA, hydrophilic PT (pmodPT, and hydrophilic SLA (modSLA with no osteoinductive factor and then osteogenic activity, including alkaline phosphatase (ALP activity, mRNA expression of runt-related gene 2, osterix, FOSB, FRA1, and protein levels of osteopontin and collagen type IA, were examined. The highest osteogenic activity appeared in PDLSCs cultured on SLA, compared with the TCPS and other Ti surfaces. The role of surface properties in affecting signaling molecules to modulate PDLSC behavior was determined by examining the regulation of Wnt pathways. mRNA expression of the canonical Wnt signaling molecules, Wnt3a and β-catenin, was higher on SLA and modSLA than on smooth surfaces, but gene expression of the calcium-dependent Wnt signaling molecules Wnt5a, calmodulin, and NFATc1 was increased significantly on PT and pmodPT. Moreover, integrin α2/β1, sonic hedgehog, and Notch signaling molecules were affected differently by each surface modification. In conclusion, surface roughness and hydrophilicity can affect differential Wnt pathways and signaling molecules, targeting the osteogenic differentiation of PDLSCs.

  18. Electronic structure and binding geometry of tetraphenylporphyrin-derived molecules adsorbed on metal and metal oxide surfaces

    Science.gov (United States)

    Coh, Senia

    Tetraphenylporphyrin (TPP)-derived molecules have been studied extensively as efficient photosensitizers when chemisorbed on the metal oxide substrates in dye-sensitized solar cells. Still, many fundamental electronic properties of the dye/oxide interface are not understood and need careful consideration. In this thesis we present a comprehensive study of the electronic structure, energy level alignment and the adsorption geometry of the TPP-derived dye molecules adsorbed on TiO2(110), ZnO(1120) and Ag(100) single crystal surfaces using ultra-high vacuum (UHV) based surface sensitive techniques. The alignment of the molecular energy levels with respect to the TiO 2 and ZnO band edges for all TPP-derived molecules we studied was found to be insensitive to either the nature of the functional groups located on the phenyl rings, presence of zinc as a central metal ion and different binding geometry of the molecules. Binding geometry, molecule-molecule interaction and the aggregation effects in the adsorbed layer, that were observed in the UV-visible spectra of the molecules adsorbed on ZnO substrate were not observed in the ultraviolet photoemission (UPS) and inverse photoemission (IPS) spectra of the occupied and unoccupied molecular states. Using near edge X-ray absorption fine structure (NEXAFS) and scanning tunneling microscopy (STM), binding geometry of the two representative TPP-derivatives was directly determined to be upright, with the porphyrin ring under large angle with respect to the surface for the p-ZnTCPP molecules and with the porphyrin ring parallel to the surface for the m-ZnTCPP molecules. We observe that the energies and the energy level alignment of the ZnTPP molecular levels measured in UPS and IPS depend on the substrate on which the molecules are adsorbed (Ag(100) or TiO2(110) single crystal surfaces). The differences are attributed to different charge screening properties of these two materials. Image charges created in the substrates during

  19. Probing Heterogeneity and Bonding at Silica Surfaces through Single-Molecule Investigation of Base-Mediated Linkage Failure.

    Science.gov (United States)

    Lupo, Katherine M; Hinton, Daniel A; Ng, James D; Padilla, Nicolas A; Goldsmith, Randall H

    2016-09-13

    The nature of silica surfaces is relevant to many chemical systems, including heterogeneous catalysis and chromatographies utilizing functionalized-silica stationary phases. Surface linkages must be robust to achieve wide and reliable applicability. However, silyl ether-silica support linkages are known to be susceptible to detachment when exposed to basic conditions. We use single-molecule spectroscopy to examine the rate of surface linkage failure upon exposure to base at a variety of deposition conditions. Kinetic analysis elucidates the role of thermal annealing and addition of blocking layers in increasing stability. Critically, it was found that successful surface modification strategies alter the rate at which base molecules approach the silica surface as opposed to reducing surface linkage reactivity. Our results also demonstrate that the innate structural diversity of the silica surface is likely the cause of observed heterogeneity in surface-linkage disruption kinetics.

  20. Collisions of slow multicharged ions with atoms, molecules, clusters and surfaces

    NARCIS (Netherlands)

    Morgenstern, R; Schlatholter, T; Hoekstra, R; Itikawa, Y; Okuno, K; TanakaA, H; Yagishita, A; Matsuzawa, M

    2000-01-01

    Dynamic processes induced by the high potential energy of multiply charged ions have been investigated in a large number of collision systems during the last years. We give a review of these activities with special emphasis on the developments since the last ICPEAC in Vienna 1997.

  1. Adsorption of organic molecules on rutile TiO2 and anatase TiO2 single crystal surfaces.

    Science.gov (United States)

    Thomas, Andrew G; Syres, Karen L

    2012-06-07

    The interaction of organic molecules with titanium dioxide surfaces has been the subject of many studies over the last few decades. Numerous surface science techniques have been utilised to understand the often complex nature of these systems. The reasons for studying these systems are hugely diverse given that titanium dioxide has many technological and medical applications. Although surface science experiments investigating the adsorption of organic molecules on titanium dioxide surfaces is not a new area of research, the field continues to change and evolve as new potential applications are discovered and new techniques to study the systems are developed. This tutorial review aims to update previous reviews on the subject. It describes experimental and theoretical work on the adsorption of carboxylic acids, dye molecules, amino acids, alcohols, catechols and nitrogen containing compounds on single crystal TiO(2) surfaces.

  2. Self-organization of clusters by a standing surface acoustic wave

    Science.gov (United States)

    Taillan, Christophe; Combe, Nicolas; Morillo, Joseph

    2017-07-01

    The diffusion of clusters on a crystalline substrate submitted to a standing surface acoustic wave (StSAW) is studied using molecular dynamics simulations. The distributions of positions of clusters with two, three, and four atoms are calculated and evidence that the wave encourages the presence of the clusters in the vicinity of the maximum transverse displacement field of the substrate. The physical mechanism leading to this self-organization is expected to be equivalent to the one operating for a single adatom, i.e., the displacement of the clusters induced by the longitudinal displacement field of the wave. The detailed shapes of the distributions of positions of clusters are related to the different clusters' orientation and configurations. Finally, the possibility to use a StSAW to self-organize nanostructures during growth is addressed by simulating a deposition process on the substrate. We evidence that the use of a StSAW allows to especially control the spatial repartition of grown nanostructures.

  3. Asymmetrical A-Frame Triplatinum Clusters Bridged by Small Organic Molecules and Bis((diphenylphosphino)methyl)phenylphosphine.

    Science.gov (United States)

    Tanase, Tomoaki; Ukaji, Hirokazu; Igoshi, Toshiaki; Yamamoto, Yasuhiro

    1996-07-03

    Reactions of the linear triplatinum complex [Pt(3)(&mgr;-dpmp)(2)(XylNC)(2)](2+) (3) with small organic molecules led to formation of asymmetrical A-frame triplatinum complexes with an additional bridge across one of the metal-metal bonds, where dpmp is bis((diphenylphosphino)methyl)phenylphosphine. Reaction of complex 3 with electron deficient alkynes (R(1)C&tbd1;CR(2): R(1) = R(2) = CO(2)Me; R(1) = H, R(2) = CO(2)Me; R(1) = R(2) = CO(2)Et) afforded a new series of triplatinum clusters formulated as [Pt(3)(&mgr;-dpmp)(2)(&mgr;-R(1)CCR(2))(XylNC)(2)](PF(6))(2) (5a, R(1) = R(2) = CO(2)Me; 5b, R(1) = H, R(2) = CO(2)Me; 5c, R(1) = R(2) = CO(2)Et) in good yields. The complex cation of 5b was characterized by X-ray crystallography to have an asymmetrical A-frame structure comprising three Pt atoms bridged by two dpmp ligands, in which an acetylene molecule was inserted into one of the Pt-Pt bonds (triclinic, P&onemacr;, a = 19.507(3) Å, b = 20.327(4) Å, c = 14.499(4) Å, alpha = 107.69(2) degrees, beta = 102.08(2) degrees, gamma = 71.30(1) degrees, V = 5148 Å(3), Z = 2, R = 0.070, and R(w) = 0.084). The Pt-Pt bond length is 2.718(1) Å and the Pt.Pt nonbonded distance is 3.582(1) Å. Treatment of 3 with an excess of HBF(4).Et(2)O gave the asymmetrical cluster [Pt(3)(&mgr;-dpmp)(2)(&mgr;-H)(XylNC)(2)](BF(4))(3).CH(2)Cl(2) (6.CH(2)Cl(2)), in 61% yield, and a similar reaction with p-NO(2)C(6)H(4)NC led to the formation of [Pt(3)(&mgr;-dpmp)(2)(&mgr;-R(3)NC)(XylNC)(2)](PF(6))(2).CH(2)Cl(2) (7.CH(2)Cl(2)) in 94% yield (R(3) = p-NO(2)C(6)H(4)). Complexes 6 and 7 are assumed to have a single atom-bridged, asymmetrical A-frame structures. Reaction of the complex syn-[Pt(2)(&mgr;-dpmp)(2)(XylNC)(2)](2+) (1) with [MCl(2)(cod)] (M = Pt, Pd) gave the dimer-monomer combined trinuclear cluster [Pt(2)MCl(2)(&mgr;-dpmp)(2)(XylNC)(2)](PF(6))(2) (8a, M = Pt, 89%; 8b, M = Pd, 55%). The structure of 8a was determined by X-ray crystallography to be comprised of a metal

  4. A surface acoustic wave bio-electronic nose for detection of volatile odorant molecules.

    Science.gov (United States)

    Di Pietrantonio, F; Benetti, M; Cannatà, D; Verona, E; Palla-Papavlu, A; Fernández-Pradas, J M; Serra, P; Staiano, M; Varriale, A; D'Auria, S

    2015-05-15

    In this work, a "bio-electronic nose" for vapour phase detection of odorant molecules based on surface acoustic wave (SAW) resonators is presented. The biosensor system is composed of an array of five SAW resonators coated with three types of odorant-binding proteins (OBPs): the wild-type OBP from bovine (wtbOBP), a double-mutant of the OBP from bovine (dmbOBP), and the wild-type OBP from pig (wtpOBP). High resolution deposition of OBPs onto the active area of SAW resonators was implemented through laser-induced forward transfer (LIFT). The resonant frequency shifts of the SAW resonators after the deposition of the biomolecules confirmed the immobilisation of the proteins onto the Al/Au inter-digital transducers (IDTs). In addition, a low increase of insertion losses with a limited degradation of Q-factors is reported. The "bio-electronic nose" fabricated by LIFT is tested in nitrogen upon exposure to separated concentrations of R-(-)-1-octen-3-ol (octenol) and R-(-)-carvone (carvone) vapours. The "bio-electronic nose" showed low detection limits for the tested compounds (i.e. 0.48 ppm for the detection of octenol, and 0.74 ppm for the detection of carvone). In addition, the bio-sensing system was able to discriminate the octenol molecules from the carvone molecules, making it pertinent for the assessment of food contamination by moulds, or for the evaluation of indoor air quality in buildings. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Structural Stabilities of Ordered Arrays of Nb4 Clusters on NaCl(100) Surface

    Institute of Scientific and Technical Information of China (English)

    WANG Xiao-Chun; ZHANG Jian-Hua; WEN Yu-Hua; ZHU Zi-Zhong

    2009-01-01

    Adsorption of ordered (2 × 2) arrays of Nb4 clusters on the insulating surface of NaCl(100) is studied by the first-principles calculations within the density functional theory. The calculations on the relaxed geometries and cohesive energies show that both the tetrahedron and quadrangle-Nb4 can be stably adsorbed on this substrate, which may have important applications. The adsorption of quadrangle-Nb4 on the NaCl(100) surface is more stable than that of tetrahedron-Nb4. Both the Nb4 clusters studied and a single Nb atom prefer the top site of the Cl atom in the NaCl(100) surface. Electronic structure analysis suggests that the interactions between the Nb4 dusters and the substrate are weak.

  6. Vibrations of small cobalt clusters on low-index surfaces of copper: Tight-binding simulations

    Science.gov (United States)

    Borisova, S. D.; Eremeev, S. V.; Rusina, G. G.; Stepanyuk, V. S.; Bruno, P.; Chulkov, E. V.

    2008-08-01

    Vibrational properties (frequencies, polarizations, and lifetimes) of a single adatom, dimer, and trimer of Co on low-index Cu surfaces, Cu(111), Cu(001), and Cu(110) are studied by using tight-binding second moment approximation interatomic interaction potentials. We show that structural and vibrational properties of the Co clusters strongly depend on the substrate orientation. The longest lifetimes of 1-2.5 ps have been found for high-frequency z -polarized vibrations in all the Co clusters considered. The shortest lifetimes of 0.1-0.8 ps have been obtained for low-frequency horizontal (frustrated translation) vibrational modes.

  7. Coupling between diffusion and orientation of pentacene molecules on an organic surface

    Science.gov (United States)

    Rotter, Paul; Lechner, Barbara A. J.; Morherr, Antonia; Chisnall, David M.; Ward, David J.; Jardine, Andrew P.; Ellis, John; Allison, William; Eckhardt, Bruno; Witte, Gregor

    2016-04-01

    The realization of efficient organic electronic devices requires the controlled preparation of molecular thin films and heterostructures. As top-down structuring methods such as lithography cannot be applied to van der Waals bound materials, surface diffusion becomes a structure-determining factor that requires microscopic understanding. Scanning probe techniques provide atomic resolution, but are limited to observations of slow movements, and therefore constrained to low temperatures. In contrast, the helium-3 spin-echo (HeSE) technique achieves spatial and time resolution on the nm and ps scale, respectively, thus enabling measurements at elevated temperatures. Here we use HeSE to unveil the intricate motion of pentacene admolecules diffusing on a chemisorbed monolayer of pentacene on Cu(110) that serves as a stable, well-ordered organic model surface. We find that pentacene moves along rails parallel and perpendicular to the surface molecules. The experimental data are explained by admolecule rotation that enables a switching between diffusion directions, which extends our molecular level understanding of diffusion in complex organic systems.

  8. TMAA surface-molecule photon interactions on Au-supported TiO2 nanocrystals

    Science.gov (United States)

    Osgood, Richard; Potapenko, Denis; Li, Zhisheng

    2015-03-01

    Nanostructured titanium dioxide is a versatile photocatalytic material. While its photocatalytic properties have been extensively studied in liquid/gas-phase environments, studies of the physics of photoinduced dynamics and reactions on bare well characterized titania nanoparticles using surface science tools have been lacking. Here we explore these photoinduced properties of TMAA-dosed TiO2 nanocrystals prepared in situ on Au(111) substrate with Scanning Tunneling Microscopy (STM) and Temperature Programmed Desorption (TPD). Photodesorption of trimethyl acetic acid was chosen as a model for light-driven reaction dynamics since it is easily imaged with STM and since this system has been the subject of many earlier studies. For comparison, we explored dynamics of TMAA on TiO2 rutile(110) by exposing it to monochromatized UV light and by injecting charges from the STM tip. We then demonstrated that 1-3 nm high and 10-25 nm wide nanocrystals of TiO2 grown on Au(111) surface also exhibit photoreaction activity for TMAA when illumined with UV light. TPD results, which provided surface-averaged information, agree well with STM data and demonstrate TMAA desorption on a single-molecule basis.

  9. Switching orientation of adsorbed molecules: Reverse domino on a metal surface

    Science.gov (United States)

    Braatz, C. R.; Esat, T.; Wagner, C.; Temirov, R.; Tautz, F. S.; Jakob, P.

    2016-01-01

    A thus far unknown phase of 1,4,5,8-naphthalene-tetracarboxylic dianhydride (NTCDA) on Ag(111), characterized by an all perpendicular orientation of the planar molecules and bound to the Ag substrate through the carboxyl oxygen atoms has been identified using infrared absorption spectroscopy and scanning tunneling microscopy. Its formation process requires second layer NTCDA to squeeze into empty spaces between relaxed monolayer NTCDA molecules. Remarkably, this process causes initially parallel oriented NTCDA to likewise adopt the new, highly inclined adsorption geometry. According to our SPA-LEED and STM findings, the new phase displays a distinct long range order and shows a pronounced tendency to form 1D rows or narrow islands. We suggest that extra NTCDA preferentially transforms into the upright configuration close to existing islands and attaches to them, i.e. the transformation process proceeds in a directed and recurrent manner (reverse domino scenario). Identical processing starting with a compressed NTCDA/Ag(111) monolayer leads to a purely parallel oriented bilayer, that is, the NTCDA monolayer phase is retained and merely acts as a passive template for bilayer NTCDA. The new vertical NTCDA phase represents an unusual molecular system with π-orbitals oriented parallel to a metal surface. A substantially reduced coupling of these orbitals to Ag(111) electronic levels is conjectured, which will have a major impact on intermolecular couplings and electronically excited state lifetimes.

  10. Solution-based single molecule imaging of surface-immobilized conjugated polymers.

    Science.gov (United States)

    Dalgarno, Paul A; Traina, Christopher A; Penedo, J Carlos; Bazan, Guillermo C; Samuel, Ifor D W

    2013-05-15

    The photophysical behavior of conjugated polymers used in modern optoelectronic devices is strongly influenced by their structural dynamics and conformational heterogeneity, both of which are dependent on solvent properties. Single molecule studies of these polymer systems embedded in a host matrix have proven to be very powerful to investigate the fundamental fluorescent properties. However, such studies lack the possibility of examining the relationship between conformational dynamics and photophysical response in solution, which is the phase from which films for devices are deposited. By developing a synthetic strategy to incorporate a biotin moiety as a surface attachment point at one end of a polyalkylthiophene, we immobilize it, enabling us to make the first single molecule fluorescence measurements of conjugated polymers for long periods of time in solution. We identify fluctuation patterns in the fluorescence signal that can be rationalized in terms of photobleaching and stochastic transitions to reversible dark states. Moreover, by using the advantages of solution-based imaging, we demonstrate that the addition of oxygen scavengers improves optical stability by significantly decreasing the photobleaching rates.

  11. Adsorption and decomposition of monopropellant molecule HAN on Pd(100) and Ir(100) surfaces: A DFT study

    Science.gov (United States)

    Banerjee, Sourav; Shetty, Sharath A.; Gowrav, M. N.; Oommen, Charlie; Bhattacharya, Atanu

    2016-11-01

    We have performed density functional theory calculations with the generalized gradient approximation to investigate the catalytic decomposition reactions of one of the most promising monopropellants, hydroxylammonium nitrate (HAN), on two catalytically active single crystal Pd(100) and Ir(100) surfaces, aiming at exploring different reaction pathways and reactivities of these two surfaces towards the catalytic decomposition of HAN. We find that the HAN molecule binds both the Pd(100) and Ir(100) surfaces molecularly in different orientations with respect to the surface. The HONO elimination is found to possess the lowest activation energy on the Pd(100) surface; whereas, NO2 elimination is predicted to show the lowest activation energy on the Ir(100) surface. Exothermicities associated with different reaction steps are also discussed. This is the first theoretical report on the catalytic decomposition reactions of the HAN molecule on the single crystal Pd(100) and the Ir(100) surfaces using the periodic DFT calculations.

  12. Structure investigation of organic molecules on Au(111) surfaces; Strukturuntersuchung organischer Molekuele auf Au(111)-Oberflaechen

    Energy Technology Data Exchange (ETDEWEB)

    Kazempoor, Michel

    2009-02-02

    The present work covers two topics namely the coadsorption of formic acid and water on Au(111) and the structure of biphenylalkanthiole SAMs on Au(111) surfaces. The coadsorption of formic acid and water on Au(111) surfaces has been investigated by means of vibrational and photoelectron spectroscopy (HREELS, XPS). Formic acid adsorbs at 90 K molecularly with vibrational modes characteristic for flat lying zig-zag chains in the mono- and multilayer regime, like in solid formic acid. The structure of the flat lying formic acid chains was determined by low energy electron diffraction (LEED) as a (2r3 x r19) unit cell. Annealing results in a complete desorption at 190 K. Sequential adsorption of formic acid and water at 90 K shows no significant chemical interaction. Upon annealing the coadsorbed layer to 140 K a hydrogenbonded cyclic complex of formic acid with one water molecule could be identified using isotopically labelled adsorbates. Upon further annealing this complex decomposes leaving molecularly adsorbed formic acid on the surface at 160 K, accompanied by a proton exchange between formic acid and water. The influence of the alkane spacer chain length on the structure of biphenylalkanethiols on Au(111) surfaces was investigated as well. A systematic study was done on BPn-SAMs deposited from the gas phase. For every chain length a structure was found by LEED. Furthermore the influence of temperature on the structure was investigated in the range from room temperature up to about 400 K. To obviate influences from different preparation methods BP3 and BP4 was deposited from gas phase and from solution. No LEED spots were observed on BP4 SAMs deposited from solution. For BP3 an influence of the preparation could be excluded. For all BPn-SAMs a good agreement between LEED and STM data's was found. Nevertheless different unit cells were determined by LEED and STM consistent structures could be suggested considering the unit cell size given by LEED and the

  13. Surface-enhanced Raman spectroscopy at single-molecule scale and its implications in biology.

    Science.gov (United States)

    Wang, Yuling; Irudayaraj, Joseph

    2013-02-05

    Single-molecule (SM) spectroscopy has been an exciting area of research offering significant promise and hope in the field of sensor development to detect targets at ultra-low levels down to SM resolution. To the experts and developers in the field of surface-enhanced Raman spectroscopy (SERS), this has often been a challenge and a significant opportunity for exploration. Needless to say, the opportunities and excitement of this multidisciplinary area impacts span the fields of physics, chemistry and engineering, along with a significant thrust in applications constituting areas in medicine, biology, environment and agriculture among others. In this review, we will attempt to provide a quick snapshot of the basics of SM-SERS, nanostructures and devices that can enable SM Raman measurement. We will conclude with a discussion on SERS implications in biomedical sciences.

  14. Electronic properties and assambly of DNA-based molecules on gold surfaces

    DEFF Research Database (Denmark)

    Salvatore, Princia

    This thesis presents a multifaceted study of deoxyribonucleic acid (DNA) in the form of strands and individual components, attached/adsorbed on single-crystal Au(111) and Au(110) gold surfaces, and on citrate-reduced gold nanoparticles. Strategically designed DNA moieties were addressed directly......-assembled monolayers(SAMs), grafted to the substrate through the strong gold-sulphur bond. The voltammetric behaviour of such DNA-based systems was analysed in the presence of “smart” redox molecules, the intercalating aromatic anthraquinone monosulfonate (AQMS) and a covalently attached terpyridine (terpy) redox unit...... and addressing metal coordination of ONs with the terpyridine ligand in the highly flexible structure ofthe new synthetic unlocked nucleic acid (UNA). Composite voltammetric behaviour for each of the metal-functionalized ONbased monolayers was observed and supported by in situscanning tunnelling microscopy...

  15. Probing the orientations of coordination complex molecules onto the surface of ZnO nanoparticles by means of surface enhanced Raman scattering, UV–vis and DFT methods

    Energy Technology Data Exchange (ETDEWEB)

    Prakash, Om; Gautam, Priyanka; Singh, Ranjan K., E-mail: ranjanksingh65@rediffmail.com

    2015-09-15

    Graphical abstract: - Highlights: • The adsorption geometry of three complex molecules onto the surface of ZnO nanoparticles is investigated by Raman, SERS and UV–vis techniques. • All the three complex molecules are adsorbed in flat-on geometry. • On the adsorption onto the ZnO NPs, the fluorescence background of Raman spectra of Zn complex is quenched. - Abstract: The surface enhanced Raman scattering (SERS) is a highly surface sensitive technique to study inter-surface properties of biological, organic, and inorganic materials. It is a precise technique to determine the adsorption geometry/orientation of the molecules as the intensity enhancement of the SERS bands depends on the adsorption geometry/orientation of molecules on SERS substrate. In the present work, Ni, Cu and Zn complexes of (Z)-N′(1,3,4-thiadiazol-2-yl) acetimidate were synthesized and adsorbed on ZnO nanoparticles. The surface enhanced Raman scattering (SERS), UV–vis and DFT techniques were applied to investigate the possible adsorption geometries of the complexes on ZnO. Consequently, it was found that the orientation of all three complex molecules is flat-on onto the surface of ZnO nanoparticles. The fluorescence background of Raman spectra of Zn complex is quenched and its geometry is isomerized after the adsorption onto the surface of ZnO nanoparticles. The adsorbed Cu complex on ZnO NPs absorbed UV radiations efficiently.

  16. The influence of galvanic currents and voltage on the proliferation activity of lymphocytes and expression of cell surface molecules.

    Science.gov (United States)

    Podzimek, S; Hána, K; Miksovský, M; Pousek, L; Matucha, P; Meloun, M; Procházková, J

    2008-01-01

    Release of metal ions from dental metal fillings supported by galvanism can cause local or general pathological problems in sensitive and genetically susceptible individuals. We aimed to investigate in vitro lymphocyte responses and expression of surface molecules influenced by galvanic currents and voltage. Human peripheral blood lymphocytes were influenced by galvanic currents and voltages and lymphocyte proliferation was measured. Control samples were not exposed to the influence of galvanism. We also studied the expression of surface molecules by the FACS analysis. A 15-h and shorter influence of almost all tested currents and voltages caused a significant decrease in lymphocyte proliferation and the 15-h influence of 20 microA currents significantly increased expression of surface molecules CD 19, 11a/18, 19/69 and 19/95. An influence of 10 and 3 microA currents led to a significant decrease in the expression of surface molecules CD 3, 11a/18, 3/69 and 3/95 and to a significant increase in CD 19 expression. An 80 mV voltage influence led to a significant decrease in the expression of surface molecules CD 3, 11a/18, 3/69, 3/95, 19/69 and 19/95, and 200 and 300 mV voltages significantly decreased the expression of surface molecules CD 3, 19, 11a/18, 3/95 and 19/95 and significantly increased CD 19/69 expression. A long-lasting influence of galvanism can, in sensitive and genetically susceptible individuals, influence lymphocyte proliferation and surface molecule expression. The threshold for pathological values of 5 microA for galvanic currents and 100 mV for galvanic voltage was confirmed.

  17. Direct Estimation of the Surface Location of Immobilized Functional Groups for Concerted Catalysis Using a Probe Molecule.

    Science.gov (United States)

    Noda, Hiroto; Motokura, Ken; Wakabayashi, Yusuke; Sasaki, Kaori; Tajiri, Hiroo; Miyaji, Akimitsu; Yamaguchi, Sho; Baba, Toshihide

    2016-04-04

    The location of active sites during concerted catalysis by a metal complex and tertiary amine on a SiO2 surface is discussed based on the interaction between the functionalized SiO2 surface and a probe molecule, p-formyl phenylboronic acid. The interactions of the probe molecule with the surface functionalities, diamine ligand, and tertiary amine, were analyzed by FT-IR and solid-state (13)C and (11)B MAS NMR. For the catalyst exhibiting high 1,4-addition activity, the diamine ligand and tertiary amine base exist in closer proximity than in the catalyst with low activity.

  18. One_dimensional chains of gold clusters on the surface of highly oriented pyrolytic graphite

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    We have investigated the growth of gold nanoclusters on thesurface of highly oriented pyrolytic graphite in ultrahigh vacuum. Studies of ultrahigh vacuum scanning tunneling microscopy revealed that the size distribution of gold clusters was very narrow and quasi-one-dimensional chains of gold nanoclusters of approximately 2 nm diameter were produced after being annealed at 74℃. Unlike the results obtained by previous workers, these chains of gold clusters were not formed along steps on the substrate surface, and some of them could even go across monoatomic steps. The orientation of chains of gold clusters was also dependent on the size of gold nanoclusters. These results suggest the viability of a new route to the creation of ordered nanoscale structures.

  19. Evanescent high pressure during hypersonic cluster-surface impact characterized by the virial theorem.

    Science.gov (United States)

    Gross, A; Levine, R D

    2005-11-15

    Matter under extreme conditions can be generated by a collision of a hypersonic cluster with a surface. The ultra-high-pressure interlude lasts only briefly from the impact until the cluster shatters. We discuss the theoretical characterization of the pressure using the virial theorem and develop a constrained molecular-dynamics procedure to compute it. The simulations show that for rare-gas clusters the pressures reach the megabar range. The contribution to the pressure from momentum transfer is comparable in magnitude and is of the same sign as that ("the internal pressure") due to repulsive interatomic forces. The scaling of the pressure with the reduced mechanical variables is derived and validated with reference to the simulations.

  20. Surfactant molecules to promote removal of cadmium ions from solid surfaces: A complementary experimental-simulational study

    Science.gov (United States)

    Pacheco-Blas, María del Alba; Dominguez, Hector; Rivera, Margarita

    2017-03-01

    Sodium dodecyl sulfate (SDS) was used to interact with metallic ions to demonstrate the efficiency of surfactant molecules to promote desorption of metals from solid surfaces. Scanning electron and atomic force microscopy were employed to study desorption of cadmium ions from highly oriented pyrolytic graphite (HOPG), as a model to understand the removal of metallic ions from carbon substrates. Contact angle measurements were carried out to investigate the wettability behavior of the surfactant on the contaminated surface. The desorption mechanism from a microscopic level was studied by using molecular dynamic simulations. Density profiles and pair correlation functions were analyzed to determine the cadmium-surface interaction in the presence of surfactant molecules to improve ion detachment. Simulations showed that surfactant molecules moved in between the adsorbed cadmium ions and the graphite surface pushing up the metallic groups to improve metal desorption. The experimental and theoretical results agree with atomic absorption spectroscopy results.

  1. Plasmonic atoms and plasmonic molecules

    CERN Document Server

    Klimov, V V

    2007-01-01

    The proposed paradigm of plasmonic atoms and plasmonic molecules allows one to describe and predict the strongly localized plasmonic oscillations in the clusters of nanoparticles and some other nanostructures in uniform way. Strongly localized plasmonic molecules near the contacting surfaces might become the fundamental elements (by analogy with Lego bricks) for a construction of fully integrated opto-electronic nanodevices of any complexity and scale of integration.

  2. Plasmonic atoms and plasmonic molecules

    Science.gov (United States)

    Klimov, V. V.; Guzatov, D. V.

    2007-11-01

    The proposed paradigm of plasmonic atoms and plasmonic molecules allows one to describe and predict the strongly localized plasmonic oscillations in the clusters of nanoparticles and some other nanostructures in uniform way. Strongly localized plasmonic molecules near the contacting surfaces might become the fundamental elements (by analogy with Lego bricks) for the construction of fully integrated opto-electronic nanodevices of any complexity and scale of integration.

  3. Computer modeling and electron microscopy of silicon surfaces irradiated by cluster ion impacts

    CERN Document Server

    Insepov, Z; Santeufemio, C; Jones, K S; Yamada, I

    2003-01-01

    A hybrid molecular dynamics model has been applied for modeling impacts of Ar and decaborane clusters, with energies ranging from 25 to 1500 eV/atom, impacting Si surfaces. Crater formation, sputtering, and the shapes of craters and rims were studied. Our simulation predicts that on a Si(1 0 0), craters are nearly triangular in cross-section, with the facets directed along the close-packed (1 1 1) planes. The Si(1 0 0) craters exhibit four fold symmetry. The craters on Si(1 1 1) surface are well rounded in cross-section and the top-view shows a complicated six fold or triangular image. The simulation results for individual gas cluster impacts were compared with experiments at low dose (10 sup 1 sup 0 ions/cm sup 2 charge fluence) for Ar impacts into Si(1 0 0) and Si(1 1 1) substrate surfaces. Atomic force microscopy and cross-sectional high-resolution transmission electron microscope imaging of individual gas cluster ion impacts into Si(1 0 0) and Si(1 1 1) substrate surfaces revealed faceting properties of t...

  4. Electrochemistry of single metalloprotein and DNA-based molecules at Au(111) electrode surfaces.

    Science.gov (United States)

    Salvatore, Princia; Zeng, Dongdong; Karlsen, Kasper K; Chi, Qijin; Wengel, Jesper; Ulstrup, Jens

    2013-07-22

    We have briefly overviewed recent efforts in the electrochemistry of single transition metal complex, redox metalloprotein, and redox-marked oligonucleotide (ON) molecules. We have particularly studied self-assembled molecular monolayers (SAMs) of several 5'-C6-SH single- (ss) and double-strand (ds) ONs immobilized on Au(111) electrode surfaces via Au-S bond formation, using a combination of nucleic acid chemistry, electrochemistry and electrochemically controlled scanning tunnelling microscopy (in situ STM). Ds ONs stabilized by multiply charged cations and locked nucleic acid (LNA) monomers have been primary targets, with a view on stabilizing the ds-ONs and improving voltammetric signals of intercalating electrochemical redox probes. Voltammetric signals of the intercalator anthraquinone monosulfonate (AQMS) at ds-DNA/Au(111) surfaces diluted by mercaptohexanol are significantly sharpened and more robust in the presence than in the absence of [Co(NH3)6](3+). AQMS also displays robust Faradaic voltammetric signals specific to the ds form on binding to similar LNA/Au(111) surfaces, but this signal only evolves after successive voltammetric scanning into negative potential ranges. Triply charged spermidine (Spd) invokes itself a strong voltammetric signal, which is specific to the ds form and fully matched sequences. This signal is of non-Faradaic, capacitive origin but appears in the same potential range as the Faradaic AQMS signal. In situ STM shows that molecular scale structures of the size of Spd-stabilized ds-ONs are densely packed over the Au(111) surface in potential ranges around the capacitive peak potential.

  5. The Neural Cell Adhesion Molecule (NCAM) Promotes Clustering and Activation of EphA3 Receptors in GABAergic Interneurons to Induce Ras Homolog Gene Family, Member A (RhoA)/Rho-associated protein kinase (ROCK)-mediated Growth Cone Collapse.

    Science.gov (United States)

    Sullivan, Chelsea S; Kümper, Maike; Temple, Brenda S; Maness, Patricia F

    2016-12-16

    Establishment of a proper balance of excitatory and inhibitory connectivity is achieved during development of cortical networks and adjusted through synaptic plasticity. The neural cell adhesion molecule (NCAM) and the receptor tyrosine kinase EphA3 regulate the perisomatic synapse density of inhibitory GABAergic interneurons in the mouse frontal cortex through ephrin-A5-induced growth cone collapse. In this study, it was demonstrated that binding of NCAM and EphA3 occurred between the NCAM Ig2 domain and EphA3 cysteine-rich domain (CRD). The binding interface was further refined through molecular modeling and mutagenesis and shown to be comprised of complementary charged residues in the NCAM Ig2 domain (Arg-156 and Lys-162) and the EphA3 CRD (Glu-248 and Glu-264). Ephrin-A5 induced co-clustering of surface-bound NCAM and EphA3 in GABAergic cortical interneurons in culture. Receptor clustering was impaired by a charge reversal mutation that disrupted NCAM/EphA3 association, emphasizing the importance of the NCAM/EphA3 binding interface for cluster formation. NCAM enhanced ephrin-A5-induced EphA3 autophosphorylation and activation of RhoA GTPase, indicating a role for NCAM in activating EphA3 signaling through clustering. NCAM-mediated clustering of EphA3 was essential for ephrin-A5-induced growth cone collapse in cortical GABAergic interneurons, and RhoA and a principal effector, Rho-associated protein kinase, mediated the collapse response. This study delineates a mechanism in which NCAM promotes ephrin-A5-dependent clustering of EphA3 through interaction of the NCAM Ig2 domain and the EphA3 CRD, stimulating EphA3 autophosphorylation and RhoA signaling necessary for growth cone repulsion in GABAergic interneurons in vitro, which may extend to remodeling of axonal terminals of interneurons in vivo.

  6. Surface Water Quality Assessment of the Jirania Brick Cluster – A Case Study

    Directory of Open Access Journals (Sweden)

    Amarendra Jamatia

    2014-06-01

    Full Text Available Along with the infrastructural development works, the demand for construction materials is increasing rapidly, which in turns lead to the rapid growth of brick manufacturing industries. Large demand of bricks in development and construction sectors has resulted in mushrooming of brick industries clusters at the outskirt of Agartala City. Jirania brick industries cluster is one of largest cluster of the Tripura State (India. Approximately 45% of total bricks of the State are being produced from the Jirania brick industries clusters. The use of conventional technology for brick making has resulted significant contribution of pollution load to the environment. The main components of environment which are being affected by the brick industries include but not limited to air, water, soil etc. The present study is carried out to identify the potential contribution of pollution load on surface water sources of the region from the mentioned brick industries. The surface water samples collected from nine sampling station located at different places in the area are analyzed and the experimental results of various quality parameters are presented in the paper. Such a study will help to estimate the total pollution load of the brick industry in the mentioned area.

  7. Surface Brightness Profiles for a sample of LMC, SMC and Fornax galaxy Globular Clusters

    CERN Document Server

    Noyola, Eva

    2007-01-01

    We use Hubble Space Telescope archival images to measure central surface brightness profiles of globular clusters around satellite galaxies of the Milky Way. We report results for 21 clusters around the LMC, 5 around the SMC, and 4 around the Fornax dwarf galaxy. The profiles are obtained using a recently developed technique based on measuring integrated light, which is tested on an extensive simulated dataset. Our results show that for 70% of the sample, the central photometric points of our profiles are brighter than previous measurements using star counts with deviations as large as 2 mag/arcsec^2. About 40% of the objects have central profiles deviating from a flat central core, with central logarithmic slopes continuously distributed between -0.2 and -1.2. These results are compared with those found for a sample of Galactic clusters using the same method. We confirm the known correlation in which younger clusters tend to have smaller core radii, and we find that they also have brighter central surface br...

  8. A population of faint low surface brightness galaxies in the Perseus cluster core

    Science.gov (United States)

    Wittmann, Carolin; Lisker, Thorsten; Ambachew Tilahun, Liyualem; Grebel, Eva K.; Conselice, Christopher J.; Penny, Samantha; Janz, Joachim; Gallagher, John S.; Kotulla, Ralf; McCormac, James

    2017-09-01

    We present the detection of 89 low surface brightness (LSB), and thus low stellar density galaxy candidates in the Perseus cluster core, of the kind named 'ultra-diffuse galaxies', with mean effective V-band surface brightnesses 24.8-27.1 mag arcsec-2, total V-band magnitudes -11.8 to -15.5 mag, and half-light radii 0.7-4.1 kpc. The candidates have been identified in a deep mosaic covering 0.3 deg2, based on wide-field imaging data obtained with the William Herschel Telescope. We find that the LSB galaxy population is depleted in the cluster centre and only very few LSB candidates have half-light radii larger than 3 kpc. This appears consistent with an estimate of their tidal radius, which does not reach beyond the stellar extent even if we assume a high dark matter content (M/L = 100). In fact, three of our candidates seem to be associated with tidal streams, which points to their current disruption. Given that published data on faint LSB candidates in the Coma cluster - with its comparable central density to Perseus - show the same dearth of large objects in the core region, we conclude that these cannot survive the strong tides in the centres of massive clusters.

  9. Cargo binding promotes KDEL receptor clustering at the mammalian cell surface.

    Science.gov (United States)

    Becker, Björn; Shaebani, M Reza; Rammo, Domenik; Bubel, Tobias; Santen, Ludger; Schmitt, Manfred J

    2016-06-29

    Transmembrane receptor clustering is a ubiquitous phenomenon in pro- and eukaryotic cells to physically sense receptor/ligand interactions and subsequently translate an exogenous signal into a cellular response. Despite that receptor cluster formation has been described for a wide variety of receptors, ranging from chemotactic receptors in bacteria to growth factor and neurotransmitter receptors in mammalian cells, a mechanistic understanding of the underlying molecular processes is still puzzling. In an attempt to fill this gap we followed a combined experimental and theoretical approach by dissecting and modulating cargo binding, internalization and cellular response mediated by KDEL receptors (KDELRs) at the mammalian cell surface after interaction with a model cargo/ligand. Using a fluorescent variant of ricin toxin A chain as KDELR-ligand (eGFP-RTA(H/KDEL)), we demonstrate that cargo binding induces dose-dependent receptor cluster formation at and subsequent internalization from the membrane which is associated and counteracted by anterograde and microtubule-assisted receptor transport to preferred docking sites at the plasma membrane. By means of analytical arguments and extensive numerical simulations we show that cargo-synchronized receptor transport from and to the membrane is causative for KDELR/cargo cluster formation at the mammalian cell surface.

  10. Control of the interparticle spacing in superparamagnetic iron oxide nanoparticle clusters by surface ligand engineering

    Science.gov (United States)

    Dan, Wang; Bingbing, Lin; Taipeng, Shen; Jun, Wu; Fuhua, Hao; Chunchao, Xia; Qiyong, Gong; Huiru, Tang; Bin, Song; Hua, Ai

    2016-07-01

    Polymer-mediated self-assembly of superparamagnetic iron oxide (SPIO) nanoparticles allows modulation of the structure of SPIO nanocrystal cluster and their magnetic properties. In this study, dopamine-functionalized polyesters (DA-polyester) were used to directly control the magnetic nanoparticle spacing and its effect on magnetic resonance relaxation properties of these clusters was investigated. Monodisperse SPIO nanocrystals with different surface coating materials (poly(ɛ-caprolactone), poly(lactic acid)) of different molecular weights containing dopamine (DA) structure (DA-PCL2k, DA-PCL1k, DA-PLA1k)) were prepared via ligand exchange reaction, and these nanocrystals were encapsulated inside amphiphilic polymer micelles to modulate the SPIO nanocrystal interparticle spacing. Small-angle x-ray scattering (SAXS) was applied to quantify the interparticle spacing of SPIO clusters. The results demonstrated that the tailored magnetic nanoparticle clusters featured controllable interparticle spacing providing directly by the different surface coating of SPIO nanocrystals. Systematic modulation of SPIO nanocrystal interparticle spacing can regulate the saturation magnetization (M s) and T 2 relaxation of the aggregation, and lead to increased magnetic resonance (MR) relaxation properties with decreased interparticle spacing. Project supported by the National Key Basic Research Program of China (Grant No. 2013CB933903), the National Key Technology R&D Program of China (Grant No. 2012BAI23B08), and the National Natural Science Foundation of China (Grant Nos. 20974065, 51173117, and 50830107).

  11. Control of the interparticle spacing in superparamagnetic iron oxide nanoparticle clusters by surface ligand engineering

    Institute of Scientific and Technical Information of China (English)

    王丹; 艾华; 林兵兵; 申太鹏; 吴君; 豪富华; 夏春潮; 龚启勇; 唐惠儒; 宋彬

    2016-01-01

    Polymer-mediated self-assembly of superparamagnetic iron oxide (SPIO) nanoparticles allows modulation of the structure of SPIO nanocrystal cluster and their magnetic properties. In this study, dopamine-functionalized polyesters (DA-polyester) were used to directly control the magnetic nanoparticle spacing and its effect on magnetic resonance relaxation properties of these clusters was investigated. Monodisperse SPIO nanocrystals with different surface coating materials (poly(ε-caprolactone), poly(lactic acid)) of different molecular weights containing dopamine (DA) structure (DA-PCL2k, DA-PCL1k, DA-PLA1k)) were prepared via ligand exchange reaction, and these nanocrystals were encapsulated inside am-phiphilic polymer micelles to modulate the SPIO nanocrystal interparticle spacing. Small-angle x-ray scattering (SAXS) was applied to quantify the interparticle spacing of SPIO clusters. The results demonstrated that the tailored magnetic nanoparticle clusters featured controllable interparticle spacing providing directly by the different surface coating of SPIO nanocrystals. Systematic modulation of SPIO nanocrystal interparticle spacing can regulate the saturation magnetization (Ms) and T2 relaxation of the aggregation, and lead to increased magnetic resonance (MR) relaxation properties with de-creased interparticle spacing.

  12. Experimental study on the clustering of floaters on the free surface of a turbulent flow

    CERN Document Server

    Gutiérrez, Pablo

    2014-01-01

    We present an experimental study of the statistical properties of millimetric spheres floating on the surface of a turbulent flow. The flow is generated in a layer of liquid metal by an electromagnetic forcing. \\textcolor{red}{By using two magnet arrays,} we are able to create one highly fluctuating flow and one almost stationary flow. In both cases, we follow the motion of hundreds of millimeter-size particles floating at the deformed interface of the liquid metal. We evidence the clustering of floaters by a statistical study of the local density of particles. Some dynamical properties of clusters are exposed. With the almost stationary flow obtained with the random array of magnets, we are able to relate the cluster formation to compression effects. Hence, although floaters are not passive scalar and move on a disturbed interface, we propose that the main clustering effect is the same as the one reported for passive scalar on an almost flat surface of a turbulent flow.

  13. Electronic structure and dynamics of ordered clusters with ME or RE ions on oxide surface

    Energy Technology Data Exchange (ETDEWEB)

    Kulagin, N.A., E-mail: nkulagin@bestnet.kharkov.u [Kharkiv National University for Radio Electronics, Avenue Shakespeare 6-48, 61045 Kharkiv (Ukraine)

    2011-03-15

    Selected data of ab initio simulation of the electronic structure and spectral properties of either cluster with ions of iron, rare earth or actinium group elements have been presented here. Appearance of doped Cr{sup +4} ions in oxides, Cu{sup +2} in HTSC, Nd{sup +2} in solids has been discussed. Analysis of experimental data for plasma created ordered structures of crystallites with size of about 10{sup -9} m on surface of separate oxides are given, too. Change in the spectroscopic properties of clusters and nano-structures on surface of strontium titanate crystals discussed shortly using the X-ray line spectroscopy experimental results. - Research highlights: External influence and variation of technology induce changes in valence of nl ions in compounds. Wave function of cluster presented as anti-symmetrical set of ions wave functions. The main equation describes the self-consistent field depending on state of all electrons of cluster. Level scheme of Cr{sup 4+} ions in octo- and tetra-site corresponds to doped oxides spectra after treatment. Plasma treatment effects in appearance of systems of unit crystallites with size of about 10{sup -6}-10{sup -9} m.

  14. Surface EMG decomposition based on K-means clustering and convolution kernel compensation.

    Science.gov (United States)

    Ning, Yong; Zhu, Xiangjun; Zhu, Shanan; Zhang, Yingchun

    2015-03-01

    A new approach has been developed by combining the K-mean clustering (KMC) method and a modified convolution kernel compensation (CKC) method for multichannel surface electromyogram (EMG) decomposition. The KMC method was first utilized to cluster vectors of observations at different time instants and then estimate the initial innervation pulse train (IPT). The CKC method, modified with a novel multistep iterative process, was conducted to update the estimated IPT. The performance of the proposed K-means clustering-Modified CKC (KmCKC) approach was evaluated by reconstructing IPTs from both simulated and experimental surface EMG signals. The KmCKC approach successfully reconstructed all 10 IPTs from the simulated surface EMG signals with true positive rates (TPR) of over 90% with a low signal-to-noise ratio (SNR) of -10 dB. More than 10 motor units were also successfully extracted from the 64-channel experimental surface EMG signals of the first dorsal interosseous (FDI) muscles when a contraction force was held at 8 N by using the KmCKC approach. A "two-source" test was further conducted with 64-channel surface EMG signals. The high percentage of common MUs and common pulses (over 92% at all force levels) between the IPTs reconstructed from the two independent groups of surface EMG signals demonstrates the reliability and capability of the proposed KmCKC approach in multichannel surface EMG decomposition. Results from both simulated and experimental data are consistent and confirm that the proposed KmCKC approach can successfully reconstruct IPTs with high accuracy at different levels of contraction.

  15. A real-time cardiac surface tracking system using Subspace Clustering.

    Science.gov (United States)

    Singh, Vimal; Tewfik, Ahmed H; Gowreesunker, B

    2010-01-01

    Catheter based radio frequency ablation of atrial fibrillation requires real-time 3D tracking of cardiac surfaces with sub-millimeter accuracy. To best of our knowledge, there are no commercial or non-commercial systems capable to do so. In this paper, a system for high-accuracy 3D tracking of cardiac surfaces in real-time is proposed and results applied to a real patient dataset are presented. Proposed system uses Subspace Clustering algorithm to identify the potential deformation subspaces for cardiac surfaces during the training phase from pre-operative MRI scan based training set. In Tracking phase, using low-density outer cardiac surface samples, active deformation subspace is identified and complete inner & outer cardiac surfaces are reconstructed in real-time under a least squares formulation.

  16. Organic molecules as sorbing tracers for the assessment of surface areas in consolidated aquifer systems

    Science.gov (United States)

    Schaffer, Mario; Warner, Wiebke; Kutzner, Susann; Börnick, Hilmar; Worch, Eckhard; Licha, Tobias

    2017-03-01

    Based on the assumption that the specific surface area to volume ratio Asurf/V of consolidated rock materials is proportional to the surface area available for sorption, several inorganic cations were recently proposed as sorbing (cation exchanging) tracers for estimating these ratios in aquifers (e.g., for deriving the efficient heat exchange area of geothermal reservoirs). The main disadvantages of inorganic ions, however, are the limited number of suitable ions, their potential geogenic background, and their challenging online detection at trace concentrations. In this work, the spectrum of chemical substances used as sorbing tracers expands by considering fluorescent organic compounds that are cationic. They have the advantage of being highly water soluble and easy to measure online at very low concentrations. Results from systematic lab column experiments with seven selected organic cations under various conditions (different salinities and temperatures) are presented, emphasizing the potential of organic molecules as alternative sorbing tracers especially in consolidated aquifer systems. This work is a first stepping stone in identifying suitable molecular structures that can be selected or even individually adapted to the requirements of the tracer tests and prevailing aquifer conditions.

  17. Quantum dynamics of STM and laser induced desorption of atoms and molecules from surfaces

    CERN Document Server

    Boendgen, G

    2001-01-01

    The manipulation of atoms and molecules at solid surfaces by electronic excitations with electrons (or holes) emitted from the tip of a scanning tunneling microscope (STM) or with laser radiation is both of applied and fundamental interest, e.g. for micro- and nanostructuring of materials, the clarification of elementary (catalytic) reaction mechanisms and for the question of how to treat the quantum dynamics of a laser or STM driven 'system' (the adsorbate) in contact with a dissipative (energy-withdrawing) 'bath' (the substrate). Desorption induced by electronic transitions (DIET) and its variant DIMET (M = multiple) are among the simplest possible 'reactions' of adsorbate-surface systems; usually involving extremely short-lived electronically excited intermediates. In this thesis, the ultra-short dynamics of directly (localised to the adsorbate-substrate complex) and indirectly (i.e., through the substrate) stimulated DIET and DIMET processes was studied for Si(100)-(2x1):H(D) and Pt(111):NO. Isotope effec...

  18. Single Molecule Raman Detection of Enkephalin on Silver Colloidal Particles

    DEFF Research Database (Denmark)

    Kneipp, Katrin; Kneipp, Holger; Abdali, Salim;

    2004-01-01

    the Raman signal the enkephalin molecules have been attached to silver colloidal cluster structures. The experiments demonstrate that the SERS signal of the strongly enhanced ring breathing vibration of phenylalanine at 1000 cm-1 can be used as “intrinsic marker” for detecting a single enkephalin molecule...... and for monitoring its diffusion on the surface of the silver colloidal cluster without using a specific label molecule....

  19. A "First Principles" Potential Energy Surface for Liquid Water from VRT Spectroscopy of Water Clusters

    Energy Technology Data Exchange (ETDEWEB)

    Goldman, N; Leforestier, C; Saykally, R J

    2004-05-25

    We present results of gas phase cluster and liquid water simulations from the recently determined VRT(ASP-W)III water dimer potential energy surface. VRT(ASP-W)III is shown to not only be a model of high ''spectroscopic'' accuracy for the water dimer, but also makes accurate predictions of vibrational ground-state properties for clusters up through the hexamer. Results of ambient liquid water simulations from VRT(ASP-W)III are compared to those from ab initio Molecular Dynamics, other potentials of ''spectroscopic'' accuracy, and to experiment. The results herein represent the first time that a ''spectroscopic'' potential surface is able to correctly model condensed phase properties of water.

  20. DNA origami as biocompatible surface to match single-molecule and ensemble experiments

    OpenAIRE

    Gietl, Andreas; Holzmeister, Phil; Grohmann, Dina; Tinnefeld, Philip

    2012-01-01

    Single-molecule experiments on immobilized molecules allow unique insights into the dynamics of molecular machines and enzymes as well as their interactions. The immobilization, however, can invoke perturbation to the activity of biomolecules causing incongruities between single molecule and ensemble measurements. Here we introduce the recently developed DNA origami as a platform to transfer ensemble assays to the immobilized single molecule level without changing the nano-environment of the ...

  1. Imbalanced expression of functional surface molecules in regulatory and effector T cells in systemic lupus erythematosus

    Directory of Open Access Journals (Sweden)

    D. Mesquita Júnior

    2014-08-01

    Full Text Available Regulatory T (TREG cells play an important role in maintaining immune tolerance and avoiding autoimmunity. We analyzed the expression of membrane molecules in TREG and effector T cells in systemic lupus erythematosus (SLE. TREG and effector T cells were analyzed for the expression of CTLA-4, PD1, CD28, CD95, GITR, HLA-DR, OX40, CD40L, and CD45RO in 26 patients with active disease, 31 with inactive disease, and 26 healthy controls. TREG cells were defined as CD25+/highCD127Ø/lowFoxP3+, and effector T cells were defined as CD25+CD127+FoxP3Ø. The ratio of TREG to effector T cells expressing GITR, PD1, HLA-DR, OX40, CD40L, and CD45RO was determined in the three groups. The frequency of TREG cells was similar in patients with SLE and controls. However, SLE patients had a decreased frequency of CTLA-4+TREG and CD28+TREG cells and an increased frequency of CD40L+TREG cells. There was a decrease in the TREG/effector-T ratio for GITR+, HLA-DR+, OX40+, and CD45RO+ cells, and an increased ratio of TREG/effector-T CD40L+ cells in patients with SLE. In addition, CD40L+TREG cell frequency correlated with the SLE disease activity index (P=0.0163. In conclusion, our findings showed several abnormalities in the expression of functionally critical surface molecules in TREG and effector T cells in SLE that may be relevant to the pathogenesis of this disease.

  2. Imbalanced expression of functional surface molecules in regulatory and effector T cells in systemic lupus erythematosus

    Energy Technology Data Exchange (ETDEWEB)

    Mesquita Júnior, D. [Disciplina de Reumatologia, Departamento de Medicina, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP (Brazil); Cruvinel, W.M. [Disciplina de Reumatologia, Departamento de Medicina, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP (Brazil); Departamento de Biomedicina, Universidade Católica de Goiás, Goiânia, GO (Brazil); Araujo, J.A.P. [Disciplina de Reumatologia, Departamento de Medicina, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP (Brazil); Salmazi, K.C.; Kallas, E.G. [Disciplina de Imunologia Clínica e Alergia, Departamento de Clínica Médica, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP (Brazil); Andrade, L.E.C. [Disciplina de Reumatologia, Departamento de Medicina, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP (Brazil)

    2014-08-22

    Regulatory T (TREG) cells play an important role in maintaining immune tolerance and avoiding autoimmunity. We analyzed the expression of membrane molecules in TREG and effector T cells in systemic lupus erythematosus (SLE). TREG and effector T cells were analyzed for the expression of CTLA-4, PD1, CD28, CD95, GITR, HLA-DR, OX40, CD40L, and CD45RO in 26 patients with active disease, 31 with inactive disease, and 26 healthy controls. TREG cells were defined as CD25{sup +/high}CD127{sup Ø/low}FoxP3{sup +}, and effector T cells were defined as CD25{sup +}CD127{sup +}FoxP3{sup Ø}. The ratio of TREG to effector T cells expressing GITR, PD1, HLA-DR, OX40, CD40L, and CD45RO was determined in the three groups. The frequency of TREG cells was similar in patients with SLE and controls. However, SLE patients had a decreased frequency of CTLA-4{sup +}TREG and CD28{sup +}TREG cells and an increased frequency of CD40L{sup +}TREG cells. There was a decrease in the TREG/effector-T ratio for GITR{sup +}, HLA-DR{sup +}, OX40{sup +}, and CD45RO{sup +} cells, and an increased ratio of TREG/effector-T CD40L{sup +} cells in patients with SLE. In addition, CD40L{sup +}TREG cell frequency correlated with the SLE disease activity index (P=0.0163). In conclusion, our findings showed several abnormalities in the expression of functionally critical surface molecules in TREG and effector T cells in SLE that may be relevant to the pathogenesis of this disease.

  3. HST Observations of Globular Clusters in M31.I Surface Photometry of 13 Objects

    CERN Document Server

    Pecci, F F; Bendinelli, O; B`onoli, F; Cacciari, C; Djorgovski, S G; Federici, L; Ferraro, F R; Parmeggiani, G; Weir, N; Zavatti, F

    1994-01-01

    We present the initial results of a study of globular clusters in M31, using the Faint Object Camera (FOC) on the Hubble Space Telescope (HST). The sample of objects consists of 13 clusters spanning a range of properties. Three inde- pendent image deconvolution techniques were used in order to compensate for the optical problems of the HST, leading to mutually fully consistent results. We present detailed tests and comparisons to determine the reliability and limits of these deconvolution methods, and conclude that high-quality surface photome- try of M31 globulars is possible with the HST data. Surface brightness profiles have been extracted, and core radii, half-light radii, and central surface brightness values have been measured for all of the clusters in the sample. Their comparison with the values derived from ground-based observations indi- cates the later to be systematically and strongly biased by the seeing effects, as it may be expected. A comparison of the structural parameters with those of the G...

  4. Surface Abundance and Binary Properties of Alternative-Evolution Stars in Open Clusters

    Science.gov (United States)

    Milliman, Katelyn Elise

    There is a large population of stars not described by single-star stellar evolution narratives. These non-standard stars are broadly known as blue stragglers (BS), yellow giants, and subsubgiants (SSG). In this thesis I present my work on the non-standard stellar populations in open clusters focussing on the role of binaries and the information learned from surface abundance measurements, particularly for BS formation. Formation theories for BSs include mergers in hierarchical triple systems, collisions during dynamical encounters, and mass transfer from an evolved companion. Such mass transfer events can pollute the surface abundance of the BS with the nucleosynthesis products from the evolved donor. Specifically, asymptotic giant branch (AGB) mass transfer should enhance the surface abundances of s-process elements, like barium, created during the thermally-pulsing phase of AGB evolution. The products of mergers and collisions would have no such enhancements. This makes barium an excellent marker for a mass-transfer formation history with an AGB-donor. In this thesis I start with the radial velocity (RV) surveys of the open clusters NGC 6819 and NGC 7789. I then introduce my discovery of five barium enriched BSs in NGC 6819, four of which have no RV evidence of a companion. Next, I triple the number of confirmed open cluster SSGs through my discovery of four such systems in NGC 6791 and present robust orbital solutions for three of them. And finally I discuss the implications of my work in context with the extensively studied open clusters M67 and NGC 188.

  5. Interaction of plasma-generated water cluster ions with chemically-modified Si surfaces investigated by infrared absorption spectroscopy

    Directory of Open Access Journals (Sweden)

    Ayumi Hirano-Iwata

    2016-03-01

    Full Text Available We have investigated the interaction of water cluster ions generated by discharge plasma, with chemically modified Si surfaces using infrared absorption spectroscopy in the multiple internal reflection geometry. We observe that water cluster ions readily adsorb on SiO2-covered Si surfaces to form water droplets. We demonstrate that positively- and negatively-charged cluster ions adsorb on the SiO2-covered Si surface in different manners, indicating ionic interaction of the water droplets with the negatively-charged SiO2 surface. Water droplets formed on the protein-coated surface rupture the amide bond of the proteins, suggesting the function of protein decomposition of water cluster ions.

  6. Interaction of plasma-generated water cluster ions with chemically-modified Si surfaces investigated by infrared absorption spectroscopy

    Science.gov (United States)

    Hirano-Iwata, Ayumi; Matsumura, Ryosuke; Ma, Teng; Kimura, Yasuo; Niwano, Michio; Nishikawa, Kazuo

    2016-03-01

    We have investigated the interaction of water cluster ions generated by discharge plasma, with chemically modified Si surfaces using infrared absorption spectroscopy in the multiple internal reflection geometry. We observe that water cluster ions readily adsorb on SiO2-covered Si surfaces to form water droplets. We demonstrate that positively- and negatively-charged cluster ions adsorb on the SiO2-covered Si surface in different manners, indicating ionic interaction of the water droplets with the negatively-charged SiO2 surface. Water droplets formed on the protein-coated surface rupture the amide bond of the proteins, suggesting the function of protein decomposition of water cluster ions.

  7. A climatology of surface ozone in the extra tropics: cluster analysis of observations and model results

    Directory of Open Access Journals (Sweden)

    O. A. Tarasova

    2007-08-01

    Full Text Available Important aspects of the seasonal variations of surface ozone are discussed. The underlying analysis is based on the long-term (1990–2004 ozone records of Co-operative Programme for Monitoring and Evaluation of the Long-range Transmission of Air Pollutants in Europe (EMEP and the World Data Center of Greenhouse Gases which do have a strong Northern Hemisphere bias. Seasonal variations are pronounced at most of the 114 locations for any time of the day. Seasonal-diurnal variability classification using hierarchical agglomeration clustering reveals 5 distinct clusters: clean/rural, semi-polluted non-elevated, semi-polluted semi-elevated, elevated and polar/remote marine types. For the cluster "clean/rural" the seasonal maximum is observed in April, both for night and day. For those sites with a double maximum or a wide spring-summer maximum, the one in spring appears both for day and night, while the one in summer is more pronounced for daytime and hence can be attributed to photochemical processes. For the spring maximum photochemistry is a less plausible explanation as no dependence of the maximum timing is observed. More probably the spring maximum is caused by dynamical/transport processes. Using data from the 3-D atmospheric chemistry general circulation model ECHAM5/MESSy1 covering the period of 1998–2005 a comparison has been performed for the identified clusters. For the model data four distinct classes of variability are detected. The majority of cases are covered by the regimes with a spring seasonal maximum or with a broad spring-summer maximum (with prevailing summer. The regime with winter–early spring maximum is reproduced by the model for southern hemispheric locations. Background and semi-polluted sites appear in the model in the same cluster. The seasonality in this model cluster is characterized by a pronounced spring (May maximum. For the model cluster that covers partly semi-elevated semi-polluted sites the role of the

  8. A climatology of surface ozone in the extra tropics: cluster analysis of observations and model results

    Directory of Open Access Journals (Sweden)

    O. A. Tarasova

    2007-12-01

    Full Text Available Important aspects of the seasonal variations of surface ozone are discussed. The underlying analysis is based on the long-term (1990–2004 ozone records of the Co-operative Programme for Monitoring and Evaluation of the Long-range Transmission of Air Pollutants in Europe (EMEP and the World Data Centre of Greenhouse Gases, which provide data mostly for the Northern Hemisphere. Seasonal variations are pronounced at most of the 114 locations at all times of the day. A seasonal-diurnal variations classification using hierarchical agglomeration clustering reveals 6 distinct clusters: clean background, rural, semi-polluted non-elevated, semi-polluted semi-elevated, elevated and polar/remote marine. For the "clean background" cluster the seasonal maximum is observed in March-April, both for night and day. For those sites with a double maximum or a wide spring-summer maximum, the spring maximum appears both for day and night, while the summer maximum is more pronounced for daytime and hence can be attributed to photochemical processes. The spring maximum is more likely caused by dynamical/transport processes than by photochemistry as it is observed in spring for all times of the day. We compare the identified clusters with corresponding data from the 3-D atmospheric chemistry general circulation model ECHAM5/MESSy1 covering the period of 1998–2005. For the model output as for the measurements 6 clusters are considered. The simulation shows at most of the sites a spring seasonal maximum or a broad spring-summer maximum (with higher summer mixing ratios. For southern hemispheric and polar remote locations the seasonal maximum in the simulation is shifted to spring, while the absolute mixing ratios are in good agreement with the measurements. The seasonality in the model cluster covering background locations is characterized by a pronounced spring (April–May maximum. For the model clusters which cover rural and semi-polluted sites the role of the

  9. On the nature of faint Low Surface Brightness galaxies in the Coma cluster

    CERN Document Server

    Adami, C; Ulmer, M P; Cuillandre, J C; Durret, F; Mazure, A; Picat, J P; Scheidegger, R

    2008-01-01

    This project is the continuation of our study of faint Low Surface Brightness Galaxies (fLSBs) in one of the densest nearby galaxy regions known, the Coma cluster. Our goal is to improve our understanding of the nature of these objects by comparing the broad band spectral energy distribution with population synthesis models. The data were obtained with the MEGACAM and CFH12K cameras at the CFHT. We used the resulting photometry in 5 broad band filters (u*, B, V, R, and I), that included new u*-band data, to fit spectral models. With these spectral fits we inferred a cluster membership criterium, as well as the ages, dust extinctions, and photometric types of these fLSBs. We show that about half of the Coma cluster fLSBs have a spectral energy distribution well represented in our template library while the other half present a flux deficit at ultraviolet wavelengths. Among the well represented, ~80% are probably part of the Coma cluster based on their spectral energy distribution. They are relatively young (yo...

  10. Electronic coupling effects and charge transfer between organic molecules and metal surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Forker, Roman

    2010-07-01

    We employ a variant of optical absorption spectroscopy, namely in situ differential reflectance spectroscopy (DRS), for an analysis of the structure-properties relations of thin epitaxial organic films. Clear correlations between the spectra and the differently intense coupling to the respective substrates are found. While rather broad and almost structureless spectra are obtained for a quaterrylene (QT) monolayer on Au(111), the spectral shape resembles that of isolated molecules when QT is grown on graphite. We even achieve an efficient electronic decoupling from the subjacent Au(111) by inserting an atomically thin organic spacer layer consisting of hexa-peri-hexabenzocoronene (HBC) with a noticeably dissimilar electronic behavior. These observations are further consolidated by a systematic variation of the metal substrate (Au, Ag, and Al), ranging from inert to rather reactive. For this purpose, 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) is chosen to ensure comparability of the molecular film structures on the different metals, and also because its electronic alignment on various metal surfaces has previously been studied with great intensity. We present evidence for ionized PTCDA at several interfaces and propose the charge transfer to be related to the electronic level alignment governed by interface dipole formation on the respective metals. (orig.)

  11. Single molecule force measurements delineate salt, pH and surface effects on biopolymer adhesion

    Science.gov (United States)

    Pirzer, T.; Geisler, M.; Scheibel, T.; Hugel, T.

    2009-06-01

    In this paper we probe the influence of surface properties, pH and salt on the adhesion of recombinant spider silk proteins onto solid substrates with single molecule force spectroscopy. A single engineered spider silk protein (monomeric C16 or dimeric (QAQ)8NR3) is covalently bound with one end to an AFM tip, which assures long-time measurements for hours with one and the same protein. The tip with the protein is brought into contact with various substrates at various buffer conditions and then retracted to desorb the protein. We observe a linear dependence of the adhesion force on the concentration of three selected salts (NaCl, NaH2PO4 and NaI) and a Hofmeister series both for anions and cations. As expected, the more hydrophobic C16 shows a higher adhesion force than (QAQ)8NR3, and the adhesion force rises with the hydrophobicity of the substrate. Unexpected is the magnitude of the dependences—we never observe a change of more than 30%, suggesting a surprisingly well-regulated balance between dispersive forces, water-structure-induced forces as well as co-solute-induced forces in biopolymer adhesion.

  12. Ozone kinetics in low-pressure discharges: vibrationally excited ozone and molecule formation on surfaces

    Science.gov (United States)

    Marinov, Daniil; Guerra, Vasco; Guaitella, Olivier; Booth, Jean-Paul; Rousseau, Antoine

    2013-10-01

    A combined experimental and modeling investigation of the ozone kinetics in the afterglow of pulsed direct current discharges in oxygen is carried out. The discharge is generated in a cylindrical silica tube of radius 1 cm, with short pulse durations between 0.5 and 2 ms, pressures in the range 1-5 Torr and discharge currents ˜40-120 mA. Time-resolved absolute concentrations of ground-state atoms and ozone molecules were measured simultaneously in situ, by two-photon absorption laser-induced fluorescence and ultraviolet absorption, respectively. The experiments were complemented by a self-consistent model developed to interpret the results and, in particular, to evaluate the roles of vibrationally excited ozone and of ozone formation on surfaces. It is found that vibrationally excited ozone, O_3^{*} , plays an important role in the ozone kinetics, leading to a decrease in the ozone concentration and an increase in its formation time. In turn, the kinetics of O_3^{*} is strongly coupled with those of atomic oxygen and O2(a 1Δg) metastables. Ozone formation at the wall does not contribute significantly to the total ozone production under the present conditions. Upper limits for the effective heterogeneous recombination probability of O atoms into ozone are established.

  13. Study of the Adsorption of Atoms and Molecules on Silicon Surfaces Crystallographics and Electronic Structure

    CERN Document Server

    Bengio, S

    2003-01-01

    This thesis work has been concerned with adsorption properties of silicon surfaces.The atomic and electronic structure of molecules and atoms adsorbed on Si has been investigated by means of photoemission experiments combined with synchrotron radiation.The quantitative atomic structure determination was held applying the photoelectron diffraction technique.This technique is sensible to the local structure of a reference atomic specie and has elemental and chemical-state specificity.This approach has been applied to three quite different systems with different degrees of complexity, Sb/Si(111) sq root 3x sq root 3R30 sup 0 , H sub 2 O/Si(100)2x1 and NH sub 3 /Si(111)7x7.Our results show that Sb which forms a ( sq root 3 sq root 3)R30 sup 0 phase produces a bulklike-terminated Si(111)1x1 substrate free of stacking faults.Regarding the atomic structure of its interface, this study strongly favours the T4-site milkstool model over the H3 one.An important aspect regarding the H sub 2 O/Si(100)(2x1) system was esta...

  14. Monocyte and lymphocyte surface molecules in severe sepsis and non-septic critically ill Patients.

    Science.gov (United States)

    Jämsä, Joel; Syrjälä, Hannu; Huotari, Virva; Savolainen, Eeva-Riitta; Ala-Kokko, Tero

    2017-06-01

    The aim of the present study was to investigate whether expression of monocyte and lymphocyte surface molecules differs between patients with severe sepsis and non-septic patients treated in the intensive care unit (ICU). The expression of monocyte CD14, CD40, CD80 and HLA-DR, and lymphocyte CD69 were analyzed using quantitative flow cytometry on three consecutive days in 27 patients with severe sepsis and in 15 non-septic patients. Receiver operating characteristic analyses were performed and each corresponding area under the curve (AUC) was determined. The results showed that the expression levels of CD40 on monocytes and CD69 on CD4+ T cells and on natural killer (NK) cells were highest in patients with severe sepsis (p sepsis and positive blood culture compared with those with negative blood culture (p sepsis detection were 0.836 for CD40, 0.872 for CD69 on NK cells, and 0.795 for CD69 on CD4+ T cells. These findings suggest that monocyte CD40 and CD69 on NK cells and CD4+ T cells could prove useful for new approaches in the identification of severe sepsis in the ICU. © 2017 APMIS. Published by John Wiley & Sons Ltd.

  15. Joint Analysis of near-infrared properties and surface brightness fluctuations of LMC star clusters

    CERN Document Server

    Raimondo, G

    2009-01-01

    Surface brightness fluctuations have been proved to be a very powerful technique to determine the distance and characterize the stellar content in extragalactic systems. Nevertheless, before facing the problem of stellar content in distant galaxies, we need to calibrate the method onto nearby well-known systems. In this paper we analyze the properties at $J$ and $K_s$ bands of a sample of 19 star clusters in the Large Magellanic Cloud (LMC), for which accurate near-infrared (NIR) resolved star photometry, and integrated photometry are available. For the same sample, we derive the SBF measurements in $J$ and $K_s$-bands. We use the multi-purpose stellar population code \\emph{SPoT (Stellar POpulations Tools)} to simulate the color-magnitude diagram, stellar counts, integrated magnitudes, colors, and surface brightness fluctuations of each cluster. The present procedure allows us to estimate the age and metallicity of the clusters in a consistent way, and provides a new calibration of the empirical $s$-parameter...

  16. Barium Surface Abundances of Blue Stragglers in the Open Cluster NGC 6819

    CERN Document Server

    Milliman, Katelyn E; Schuler, Simon C

    2015-01-01

    We present the barium surface abundance of 12 blue stragglers (BSs) and 18 main-sequence (MS) stars in the intermediate-age open cluster NGC 6819 (2.5 Gyr) based on spectra obtained from the Hydra Multi-object Spectrograph on the WIYN 3.5 m telescope. For the MS stars we find [Fe/H] = $+$0.05 $\\pm$ 0.04 and [Ba/Fe] = $-$0.01 $\\pm$ 0.10. The majority of the BS stars are consistent with these values. We identify five BSs with significant barium enhancement. These stars most likely formed through mass transfer from an asymptotic giant branch star that polluted the surface of the BS with the nucleosynthesis products generated during thermal pulsations. This conclusion aligns with the results from the substantial work done on the BSs in old open cluster NGC 188 that identifies mass transfer as the dominant mechanism for BS formation in that open cluster. However, four of the BSs with enhanced barium show no radial-velocity evidence for a companion. The one star that is in a binary is a double-lined system, meaning...

  17. Tetrahedral shape and surface density wave of $^{16}$O caused by $\\alpha$-cluster correlations

    CERN Document Server

    Kanada-En'yo, Yoshiko

    2016-01-01

    $\\alpha$-cluster correlations in the $0^+_1$ and $3^-_1$ states of $^{12}$C and $^{16}$O are studied using the method of antisymmetrized molecular dynamics, with which nuclear structures are described from nucleon degrees of freedom without assuming existence of clusters. The intrinsic states of $^{12}$C and $^{16}$O have triangle and tetrahedral shapes, respectively, because of the $\\alpha$-cluster correlations. These shapes can be understood as spontaneous symmetry breaking of rotational invariance, and the resultant surface density oscillation is associated with density wave (DW) caused by the instability of Fermi surface with respect to particle-hole correlations with the wave number $\\lambda=3$. $^{16}$O($0^+_1$) and $^{16}$O($3^-_1$) are regarded as a set of parity partners constructed from the rigid tetrahedral intrinsic state, whereas $^{12}$C($0^+_1$) and $^{12}$C($3^-_1$) are not good parity partners as they have triangle intrinsic states of different sizes with significant shape fluctuation because...

  18. Surface supramolecular organization of a terbium(III) double-decker complex on graphite and its single molecule magnet behavior.

    Science.gov (United States)

    Gonidec, Mathieu; Biagi, Roberto; Corradini, Valdis; Moro, Fabrizio; De Renzi, Valentina; del Pennino, Umberto; Summa, Domenico; Muccioli, Luca; Zannoni, Claudio; Amabilino, David B; Veciana, Jaume

    2011-05-01

    The two-dimensional self-assembly of a terbium(III) double-decker phthalocyanine on highly oriented pyrolitic graphite (HOPG) was studied by atomic force microscopy (AFM), and it was shown that it forms highly regular rectangular two-dimensional nanocrystals on the surface, that are aligned with the graphite symmetry axes, in which the molecules are organized in a rectangular lattice as shown by scanning tunneling microscopy. Molecular dynamics simulations were run in order to model the behavior of a collection of the double-decker complexes on HOPG. The results were in excellent agreement with the experiment, showing that-after diffusion on the graphite surface-the molecules self-assemble into nanoscopic islands which align preferentially along the three main graphite axes. These low dimension assemblies of independent magnetic centers are only one molecule thick (as shown by AFM) and are therefore very interesting nanoscopic magnetic objects, in which all of the molecules are in interaction with the graphite substrate and might therefore be affected by it. The magnetic properties of these self-assembled bar-shaped islands on HOPG were studied by X-ray magnetic circular dichroism, confirming that the compounds maintain their properties as single-molecule magnets when they are in close interaction with the graphite surface.

  19. Nucleation and mobility model of Agn clusters adsorbed on perfect and oxygen vacancy MgO surfaces.

    Science.gov (United States)

    Liu, Yongfei; Wang, Yan; Chen, Guangju

    2011-05-01

    The structures and energy properties for Ag(n) (n = 1-8) metal clusters adsorbed on the perfect and oxygen vacancy MgO surfaces have been studied by using the DFT/UB3LYP method with an embedded cluster model. The nucleation and mobility model for the Ag(n) (n = 1-8) clusters on the perfect and oxygen vacancy MgO(100) surfaces was investigated. The results show that the Ag atoms locate initially at the surface oxygen vacancy sites; then, with the growth of Ag cluster sizes, the large Ag clusters move possibly out of the vacancy sites by a rolling model, and diffuse on the MgO surface under a certain temperature condition. The relative energies needed for moving out of the oxygen vacancy region for the adsorbed Ag(n) clusters with the rolling model have been predicted. The even-odd oscillation behaviors for the cohesive energies, nucleation energies, first ionization potentials and HOMO-LUMO gaps of the adsorbed Ag(n) clusters with the variation of cluster sizes have also been discussed.

  20. Reactivity of niobium-carbon cluster ions with hydrogen molecules in relation to formation mechanism of Met-Car cluster ions.

    Science.gov (United States)

    Miyajima, Ken; Fukushima, Naoya; Mafuné, Fumitaka

    2008-07-03

    It is known that a niobium-carbon Met-Car cluster ion (Nb 8C 12 (+)) and its intermediates (Nb 4C 4 (+), Nb 6C 7 (+), etc.) are selectively formed by the aggregation of the Nb atoms in the presence of hydrocarbons. To elucidate the formation mechanism, we prepared Nb n C m (+) with every combination of n and m in the gas phase by the laser vaporization technique. The reactivity of Nb n C m (+) with H 2 was examined under the multiple collision condition, finding that Nb n C m (+) between Nb 2C 3 (+) and Nb 8C 12 (+) are not reactive with H 2. On the basis of the H 2 affinity of Nb n C m (+) experimentally obtained, we propose a dehydrogenation-controlled formation mechanism of niobium-carbon Met-Car cluster ions.

  1. Preparation of cluster states with trapped electrons on a liquid helium surface

    Institute of Scientific and Technical Information of China (English)

    Ai Ling-Yan; Shi Yan-Li; Zhang Zhi-Ming

    2011-01-01

    We present a scheme for the preparation of one-dimensional (1D) and two-dimensional (2D) cluster states with electrons trapped on a liquid helium surface and driven by a classical laser beam.The two lowest levels of the vertical motion of the electron act as a two-level system,and the quantized vibration of the electron along one of the parallel directions (the x direction) serves as the bosonic mode.The degrees of freedom of the vertical and parallel motions of the trapped electron can be coupled together by a classical laser field.With the proper frequency of the laser field,the cluster states can be realized.

  2. Structure-Function Relationships of Antimicrobial Peptides and Proteins with Respect to Contact Molecules on Pathogen Surfaces

    NARCIS (Netherlands)

    Zhang, Ruiyan; Eckert, Thomas; Lutteke, Thomas; Hanstein, Stefan; Scheidig, Axel; Bonvin, Alexandre M J J; Nifantiev, Nikolay E; Kozar, Tibor; Schauer, Roland; Enani, Mushira Abdulaziz; Siebert, Hans-Christian

    2016-01-01

    The Antimicrobial peptides (e.g. defensins, hevein-like molecules and food-protecting peptides like nisin) are able to interact specifically with contact structures on pathogen surfaces. Besides protein receptors, important recognition points for such contacts are provided by pathogen glycan chains

  3. Series of dinuclear and tetranuclear lanthanide clusters encapsulated by salen-type and β-diketionate ligands: single-molecule magnet and fluorescence properties.

    Science.gov (United States)

    Sun, Wen-Bin; Han, Bing-Lu; Lin, Po-Heng; Li, Hong-Feng; Chen, Peng; Tian, Yong-Mei; Murugesu, Muralee; Yan, Peng-Fei

    2013-10-07

    Three dinuclear [Ln2H2OL(1)2(acac)2]·solvent (1, Ln = Gd, solvent = 2CH2Cl2; 2, Ln = Tb, no solvent; 3, Ln = Er, solvent = (C2H5)2O), and two tetranuclear lanthanide clusters [Ln4(μ3-OH)2L(2)2(acac)6]·2(solvent) (4, Ln = Tb, solvent = CH3OH; 5, Ln = Dy, solvent = CH3CN) were characterized in terms of structure, fluorescence and magnetism. The dinuclear lanthanide complexes were constructed by a rigid salen-type ligand H2L(1) = N,N'-bis(salicylidene)-o-phenylenediamine and β-diketonate (acac = acetylacetonate) ligands, while the tetranuclear clusters were formed from the flexible ligand H2L(2) = N,N'-bis(salicylidene)-1,2-ethanediamine. Crystal structure analysis indicates that the rigid ligand favors the double-decker sandwich structure (Ln2L(1)2), in which the two lanthanide ions have different coordination numbers and geometry, while the more flexible ligand (H2L(2)) leads to planar tetranuclear clusters. The relationship between their respective magnetic anisotropy and ligand-field geometries and their fluorescence properties was investigated. The Dy and Tb-containing clusters exhibit typical visible fluorescence properties, and single-molecule magnet behavior is seen in complex 5.

  4. Calculation of hyperfine structure constants of small molecules using Z-vector method in the relativistic coupled-cluster framework

    Indian Academy of Sciences (India)

    SUDIP SASMAL; KAUSHIK TALUKDAR; MALAYA K NAYAK; NAYANA VAVAL; SOURAV PAL

    2016-10-01

    The Z-vector method in the relativistic coupled-cluster framework is employed to calculate the parallel and perpendicular components of the magnetic hyperfine structure constant of a few small alkaline earth hydrides (BeH, MgH, and CaH) and fluorides (MgF and CaF). We have compared our Z-vector results with the values calculated by the extended coupled-cluster (ECC) method reported in Phys. Rev. A 91 022512 (2015). All these results are compared with the available experimental values. The Z-vector results are found to be in better agreement with the experimental values than those of the ECC values.

  5. Single-molecule surface-enhanced Raman scattering of R6G in aqueous environment under non-resonance conditions

    Institute of Scientific and Technical Information of China (English)

    Enzhong Tan; Penggang Yin; Lidong Li; Lin Guo

    2011-01-01

    The single-molecule surface-enhanced Raman scattering (SERS) spectra of Rhodamine 6G (R6G) in an aqueous environment under non-resonance conditions are studied. Series of spectra are recorded in time-mapping mode, and intensity fluctuations of SERS signals and spectral diffusion are observed. The correlations between the presence frequency of SERS spectra and number of hot spots as well as the quantity of molecules in scattering volume are examined thoroughly. The results indicate that only molecules located at hot spots produce good signal-to-noise ratio Raman spectra and the origin of fluctuating SERS signals are mainly ascribed to the movement of hot spots.%@@ The single-molecule surface-enhanced Raman scattering(SERS) spectra of Rhodamine 6G(R6G) in anaqueous environment under non-resonance conditions are studied.Series of spectra are recorded in timemapping mode,and intensity fluctuations of SERS signals and spectral diffusion are observed.The correlations between the presence frequency of SERS spectra and number of hot spots as well as the quantity of molecules in scattering volume are examined thoroughly.

  6. Systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions

    Energy Technology Data Exchange (ETDEWEB)

    Cooks, Robert Graham; Li, Anyin; Luo, Qingjie

    2017-08-01

    The invention generally relates to systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions. In certain aspects, the invention provides methods that involve providing a metal and a solvent. The methods additionally involve applying voltage to the solvated metal to thereby produce solvent droplets including ions of the metal containing compound, and directing the solvent droplets including the metal ions to a target. In certain embodiments, once at the target, the metal ions can react directly or catalyze reactions.

  7. In situ investigation of the mobility of small gold clusters on cleaved MgO surfaces

    Science.gov (United States)

    Metois, J. J.; Heinemann, K.; Poppa, H.

    1976-01-01

    The mobility of small clusters of gold (about 10 A in diameter) on electron-beam-cleaved MgO surfaces was studied by in situ transmission electron microscopy under controlled vacuum and temperature conditions. During the first 10 min following a deposition at room temperature, over 10 per cent of the crystallites moved over short distances (about 20 A) discontinuously, with a velocity greater than 150 A/sec. Eighty per cent of the mobility events were characterized by the avoidance of proximity of other crystallites, and this was tentatively explained as the result of repulsive elastic forces between the interacting crystallites.

  8. Systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions

    Energy Technology Data Exchange (ETDEWEB)

    Cooks, Robert Graham; Li, Anyin; Luo, Qingjie

    2017-01-24

    The invention generally relates to systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions. In certain aspects, the invention provides methods that involve providing a metal and a solvent. The methods additionally involve applying voltage to the solvated metal to thereby produce solvent droplets including ions of the metal containing compound, and directing the solvent droplets including the metal ions to a target. In certain embodiments, once at the target, the metal ions can react directly or catalyze reactions.

  9. Manipulating the charge state and conductance of a single molecule on a semiconductor surface by electrostatic gating

    Science.gov (United States)

    Martinez-Blanco, Jesus; Nacci, Christophe; Erwin, Steven C.; Kanisawa, Kiyoshi; Locane, Elina; Thomas, Mark; von Oppen, Felix; Brouwer, Piet; Foelsch, Stefan

    2015-03-01

    We studied the charge state and tunneling conductance of single phthalocyanine molecules adsorbed on InAs(111)A using scanning tunneling microscopy (STM) at 5 K. On the InAs(111)A surface, native +1 charged indium adatoms can be repositioned by the STM tip using atom manipulation. This allows us to electrostatically gate an individual adsorbed molecule by placing charged adatoms nearby or, alternatively, by repositioning the molecule within the electrostatic potential landscape created by an STM-engineered adatom corral. By stepwise increasing the gating potential, the molecular charge state can be tuned from neutral to -1, as well as to bistable intermediate states. We find that the molecule changes its orientational conformation when the charge state is switched. Scanning tunneling spectroscopy measurements reveal that the conductance gap of the single-molecule tunneling junction can be precisely controlled by the electrostatic gating. We discuss the observed gating-dependent single-molecule tunneling conductance in terms of charge transport through a gated quantum dot. Granted by the German Research Foundation (FO 362/4-1; SFB 658).

  10. Pyrolysis of Phenethyl Phenyl Ether Tethered in Mesoporous Silica. Effects of Confinement and Surface Spacer Molecules on Product Selectivity

    Energy Technology Data Exchange (ETDEWEB)

    Kidder, Michelle [ORNL; Chaffe, Alan [Monash University, Australia; Nguyen, M [Monash University, Australia; Buchanan III, A C [ORNL

    2011-01-01

    There has been expanding interest in exploring porous metal oxides as a confining environment for organic molecules resulting in altered chemical and physical properties including chemical transformations. In this paper, we examine the pyrolysis behavior of phenethyl phenyl ether (PPE) confined in mesoporous silica by covalent tethers to the pore walls as a function of tether density and the presence of co-tethered surface spacer molecules of varying structure (biphenyl, naphthyl, octyl, and hexadecyl). The PPE pyrolysis product selectivity, which is determined by two competitive free-radical pathways cycling through the two aliphatic radical intermediates (PhCH CH2OPh and PhCH2CH OPh), is shown to be dramatically different from that measured in the liquid phase as well as for PPE tethered to the exterior surface of nonporous silica nanoparticles. Tailoring the pore surface with spacer molecules further alters the selectivity such that the PPE reaction channel involving a molecular rearrangement (O-C phenyl shift in PhCH2CH OPh), which accounts for 25 % of the products in the liquid phase, can be virtually eliminated under pore confinement conditions. The origin of this change in selectivity is discussed in the context of steric constraints on the rearrangement path, confinement effects, pore surface curvature, and hydrogen bonding of PPE with residual surface silanols supplemented by nitrogen physisorption data and molecular dynamics simulations.

  11. Electrostatic surface guiding of cold polar molecules with a single charged wire

    Institute of Scientific and Technical Information of China (English)

    Deng Lian-Zhong; Xia Yong; Yin Jian-Ping

    2007-01-01

    This paper proposes a scheme to guide cold polar molecules by using a single charged wire half embanked in an insulating substrate and a homogeneous bias electric field,which is generated by a plate capacitor composed of two infinite parallel metal plates.The spatial distributions of the electrostatic field produced by the combination of the charged wire and the plate capacitor and the corresponding Stark potentials(including dipole forces) for metastable CO molecules are calculated,the relationships between the electric field and the parameters of our charged-wire layout are analysed.It also studies the influences of the insulator on the electric field distribution and the discharge effect.This study shows that the proposed scheme can be used to guide cold polar molecules in the weak-field-seeking states,and to form various molecule-optical elements,such as molecular funnel,molecular beam-splitters and molecule interferometer,even to construct a variety of integrated molecule-optical elements and their molecule chips.

  12. Manipulating the Lateral Diffusion of Surface-Anchored EGF Demonstrates that Receptor Clustering Modulates its Phosphorylation Levels

    Energy Technology Data Exchange (ETDEWEB)

    Stabley, Daniel [Emory University; Retterer, Scott T [ORNL; Marshal, Stephen [Emory University; Salaita, Khalid [Emory University

    2013-01-01

    Upon activation, the epidermal growth factor (EGF) receptor becomes phosphorylated and triggers a vast signaling network that has profound effects on cell growth. The EGF receptor is observed to assemble into clusters after ligand binding and tyrosine kinase autophosphorylation, but the role of these assemblies in the receptor signaling pathway remains unclear. To address this question, we measured the phosphorylation of EGFR when the EGF ligand was anchored onto laterally mobile and immobile surfaces. We found that cells generated clusters of ligand-receptor complex on mobile EGF surfaces, and generated a lower ratio of phosphorylated EGFR to EGF than when compared to immobilized EGF that is unable to cluster. This result was verified by tuning the lateral assembly of ligand-receptor complexes on the surface of living cells using patterned supported lipid bilayers. Nanoscale metal lines fabricated into the supported membrane constrained lipid diffusion and EGF receptor assembly into micron and sub-micron scale corrals. Single cell analysis indicated that clustering impacts EGF receptor activation, and larger clusters (> 1 m2) of ligand-receptor complex generated lower EGF receptor phosphorylation per ligand than smaller assemblies (< 1 m2) in HCC1143 cells that were engaged to ligand-functionalized surfaces. We investigated EGFR clustering by treating cells with compounds that disrupt the cytoskeleton (Latrunculin-B), clathrin-mediated endocytosis (Pitstop2), and inhibit EGFR activation (Gefitinib). These results help elucidate the nature of large-scale EGFR clustering, thus underscoring the general significance of receptor spatial organization in tuning function.

  13. Impact on surface ozone by fugitive emissons of ethylene and propylene from a petrochemical plant cluster

    Science.gov (United States)

    Hsieh, H.; Chang, J.; Chen, S.; Wang, J.

    2010-12-01

    Ethylene and propylene are two most produced organic compounds in the world which are mainly produced from the cracking process in the oil refinery industry. In a large petrochemical plant cluster a large variety of petrochemical products are derived from these two compounds used as starting reagents. Fugitive emissions of these two compounds from storage tanks and pipelines are often inevitable, which could pose a great burden on the formation of surface ozone and thus deteriorate air quality if leakage is significant. In this study, a photochemical assessment monitoring station (PAMS) was deployed 7 kilometers south of a large petrochemical plant cluster. Concentration spikes of ethylene and propylene were frequently observed by the on-line gas chromatographic system whenever northerly prevailed. The impact of ethylene and propylene’s leakage on ozone formation was simulated by an air quality model (i.e., PAMS-AQM), of which emission inventory of non-methane hydrocarbons (NMHCs) were speciated and calibrated by the PAMS measurements. Contribution to ozone formation by these two compounds in the downwind areas was able to be assessed by turning off the emissions of ethylene and propylene from this plant cluster while maintaining those of other precursors in the model. Scenarios of precursor (NMHC and NOx) reduction or increase were also simulated from the perspectives of ozone control strategies.

  14. Selective chemisorption of graphene-like molecules on the Si(111) 7 x 7 surface: A theoretical study

    Energy Technology Data Exchange (ETDEWEB)

    Kiss, Janos; Gruhn, Thomas; Felser, Claudia [Institut fuer Anorganische Chemie und Analytische Chemie, Johannes Gutenberg-Universitaet, D-55099 Mainz (Germany)

    2011-07-01

    Graphene and porous graphene are very promising materials, which have been widely studied for electronic applications. Because of their improved properties, in the future it is expected, that graphene, porous graphene and graphene-like molecules will replace silicon. Despite its superior material properties, however, the field-effect transistors based on graphene or graphene nanoribbons build so far via top-down approaches have low on/off ratios. On the other hand, molecular nanotransistors build with precisely know atomic structures resembling graphene were synthesized only very recently. In order to pave the way towards the industrial fabrication of molecular nanotransistors, we have investigated the chemisorption of graphene-like molecules on the 7 x 7 reconstructed Si(111) surface via density functional theory (DFT) calculations. We found, that Si(111) is a very promising candidate to serve as substrate for the large-scale fabrication of coronene-based molecular transistors. Moreover, our calculations show, that various adsorbate molecules prefer specific binding sites on the Si(111) surface. By following the template of the Si(111) substrate, the molecules selectively adsorb and form a well defined two-dimensional grid with a 1 x 1 surface pattern.

  15. Adsorption of acetyl halide molecules on the surface of pristine and Al-doped graphene: Ab initio study

    Science.gov (United States)

    Rad, Ali Shokuhi; Kashani, Omid Razaghi

    2015-11-01

    We have scrutinized the adsorption energy, electronic structure, natural bond analysis (NBO), density of state (DOS) and global indices for adsorption of acetyl chloride (AC) and acetyl fluoride (AF) on the surface of pristine graphene as well as Al-doped graphene. The adsorption energies have been calculated for the most stable configurations of the molecules on the surface of pristine and Al-doped graphene. According to the calculated parameters, there is very weak physical adsorption of AC and AF on pristine graphene while strong adsorption takes place in the case of Al-doped graphene. The charge transfer from adsorbed molecules to Al-doped graphene surface was confirmed by the natural bond orbital as well as the Mulliken population analysis while there is no charge transfer with pristine graphene. Additionally, the density of states results reveal that orbital hybridization takes place between above-mentioned molecules and Al-doped graphene sheet, whereas there is no hybridization between the molecules and the pristine graphene. Our calculated adsorption energies for the most stable position configurations of AC and AF on Al-doped graphene were -68.8 kJ mol-1 (-52.6 kJ mol-1 BSSE corrected energy) and -78.4 kJ mol-1 (-64.3 kJ mol-1 BSSE corrected energy) which are correspond to chemisorptions process respectively. These results point to the appropriateness of Al-doped graphene as a powerful adsorbent for practical applications.

  16. Self-consistent meta-generalized gradient approximation study of adsorption of aromatic molecules on noble metal surfaces

    DEFF Research Database (Denmark)

    Ferrighi, Lara; Madsen, Georg Kent Hellerup; Hammer, Bjørk

    2011-01-01

    are shortened and the adsorption bond strengths of the molecules are greatly improved over the virtually non-interacting results obtained when using a plain GGA exchange-correlation functional. The nucleobases containing oxygen atoms show higher corrugation with adsorption site and orientation than the other...... aromatic molecules considered. The adsorption of pentacene is studied on Au, Ag, and Cu surfaces. In agreement with experiment, the adsorption energies are found to increase with decreasing nobleness, but the dependency is underestimated. We point out how the kinetic energy density can discriminate between...

  17. Effect of nontronite smectite clay on the chemical evolution of several organic molecules under simulated Mars surface UV radiation conditions

    Science.gov (United States)

    Poch, Olivier; Dequaire, Tristan; Stalport, Fabien; Jaber, Maguy; Lambert, Jean-François; Szopa, Cyril; Coll, Patrice

    2015-04-01

    The search for organic carbon-containing molecules at the surface of Mars, as clues of past habitability or remnants of life, is a major scientific goal for Mars exploration. Several lines of evidence, including the detection of phyllosilicates, suggest that early Mars offered favorable conditions for long-term sustaining of water. As a consequence, we can assume that in those days, endogenous chemical processes, or even primitive life, may have produced organic matter on Mars. Moreover, exogenous delivery from small bodies or dust particles is likely to have brought fresh organic molecules to the surface of Mars up today. Organic matter is therefore expected to be present at the surface/subsurface of the planet. But the current environmental conditions at the surface - UV radiation, oxidants and energetic particles - generate physico-chemical processes that may affect organic molecules. On the other hand, on Earth, phyllosilicates are known to accumulate and preserve organic matter. But are phyllosilicates efficient at preserving organic molecules under the current environmental conditions at the surface of Mars? We have monitored the qualitative and quantitative evolutions of glycine, urea and adenine interacting with the Fe3+-smectite clay nontronite, one of the most abundant phyllosilicates present at the surface of Mars, under simulated Martian surface ultraviolet light (190-400 nm), mean temperature (218 ± 2 K) and pressure (6 ± 1 mbar) in a laboratory simulation setup. We have tested organic-rich samples which may be representative of the evaporation of a warm little pond of liquid water having concentrated organics on Mars. For each molecule, we have observed how the nontronite influences the quantum efficiency of its photodecomposition and the nature of its solid evolution products. The results reveal a pronounced photoprotective effect of nontronite on the evolution of glycine and adenine: their efficiencies of photodecomposition are reduced by a factor

  18. Model HULIS compounds in nanoaerosol clusters - investigations of surface tension and aggregate formation using molecular dynamics simulations

    National Research Council Canada - National Science Library

    T. Hede; X. Li; C. Leck; Y. Tu; H. Ågren

    2011-01-01

    .... In this study we use molecular dynamics simulations to show that model humic-like substances (HULIS) in systems containing 10 000 water molecules mimic experimental data well referring to reduction of surface tension...

  19. Organomimetic clusters: Precision in 3D

    Science.gov (United States)

    Majewski, Marek B.; Howarth, Ashlee J.; Farha, Omar K.

    2017-03-01

    Biomimetic molecules that can be easily tailored offer numerous opportunities. Now, boron-based clusters have been shown to be excellent biomimetics. The ease with which the cluster surfaces can be modified stands to change how chemists might go about preparing materials for imaging, drug delivery and other applications.

  20. Identification of cell surface molecules involved in dystroglycan-independent Lassa virus cell entry.

    Science.gov (United States)

    Shimojima, Masayuki; Ströher, Ute; Ebihara, Hideki; Feldmann, Heinz; Kawaoka, Yoshihiro

    2012-02-01

    Although O-mannosylated dystroglycan is a receptor for Lassa virus, a causative agent of Lassa fever, recent findings suggest the existence of an alternative receptor(s). Here we identified four molecules as receptors for Lassa virus: Axl and Tyro3, from the TAM family, and dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin (DC-SIGN) and liver and lymph node sinusoidal endothelial calcium-dependent lectin (LSECtin), from the C-type lectin family. These molecules enhanced the binding of Lassa virus to cells and mediated infection independently of dystroglycan. Axl- or Tyro3-mediated infection required intracellular signaling via the tyrosine kinase activity of Axl or Tyro3, whereas DC-SIGN- or LSECtin-mediated infection and binding were dependent on a specific carbohydrate and on ions. The identification of these four molecules as Lassa virus receptors advances our understanding of Lassa virus cell entry.

  1. The neural cell adhesion molecule L1 is distinct from the N-CAM related group of surface antigens BSP-2 and D2

    DEFF Research Database (Denmark)

    Faissner, A; Kruse, J; Goridis, C

    1984-01-01

    The neural cell adhesion molecule L1 and the group of N-CAM related molecules, BSP-2 and D2 antigen, are immunochemically distinct molecular species. The two groups of surface molecules are also functionally distinct entities, since inhibition of Ca2+-independent adhesion among early post...

  2. Near surface soil vapor clusters for monitoring emissions of volatile organic compounds from soils.

    Science.gov (United States)

    Ergas, S J; Hinlein, E S; Reyes, P O; Ostendorf, D W; Tehrany, J P

    2000-01-01

    The overall objective of this research was to develop and test a method of determining emission rates of volatile organic compounds (VOCs) and other gases from soil surfaces. Soil vapor clusters (SVCs) were designed as a low dead volume, robust sampling system to obtain vertically resolved profiles of soil gas contaminant concentrations in the near surface zone. The concentration profiles, when combined with a mathematical model of porous media mass transport, were used to calculate the contaminant flux from the soil surface. Initial experiments were conducted using a mesoscale soil remediation system under a range of experimental conditions. Helium was used as a tracer and trichloroethene was used as a model VOC. Flux estimations using the SVCs were within 25% of independent surface flux estimates and were comparable to measurements made using a surface isolation flux chamber (SIFC). In addition, method detection limits for the SVC were an order of magnitude lower than detection limits with the SIFC. Field trials, conducted with the SVCs at a bioventing site, indicated that the SVC method could be easily used in the field to estimate fugitive VOC emission rates. Major advantages of the SVC method were its low detection limits, lack of required auxiliary equipment, and ability to obtain real-time estimates of fugitive VOC emission rates.

  3. Shell plus pairing effect arguments for cluster preformation at the nuclear surface in cold fission

    CERN Document Server

    Poenaru, D N

    2016-01-01

    In 1928 G. Gamow as well as Condon and Gurney gave the first explanation of alpha decay as a quantum tunnelling of a preformed particle at the nuclear surface. Soon after experimental discovery in 1984 by Rose and Jones of cluster radioactivity, confirming earlier (1980) predictions by Sandulescu, Poenaru and W. Greiner, a microscopic theory also explained the phenomenon in a similar way. Here we show for the first time that in a spontaneous cold fission process the shell plus pairing corrections calculated with Strutinsky's procedure may give a strong argument for preformation of a light fission fragment near the nuclear surface. It is obtained when the radius of the light fragment, $R_2$, is increased linearly with the separation distance, $R$, of the two fragments, while for $R_2=$~constant one gets the well known two hump potential barrier.

  4. Clustered ribbed-nanoneedle structured copper surfaces with high-efficiency dropwise condensation heat transfer performance.

    Science.gov (United States)

    Zhu, Jie; Luo, Yuting; Tian, Jian; Li, Juan; Gao, Xuefeng

    2015-05-27

    We report that the dropwise condensation heat transfer (DCHT) effectiveness of copper surfaces can be dramatically enhanced by in situ grown clustered ribbed-nanoneedles. Combined experiments and theoretical analyses reveal that, due to the microscopically rugged and low-adhesive nature of building blocks, the nanosamples can not only realize high-density nucleation but constrain growing condensates into suspended microdrops via the self-transport and/or self-expansion mode for subsequently self-propelled jumping, powered by coalescence-released excess surface energy. Consequently, our nanosample exhibits over 125% enhancement in DCHT coefficient. This work helps develop advanced heat-transfer materials and devices for efficient thermal management and energy utilization.

  5. School playground surfacing and arm fractures in children: a cluster randomized trial comparing sand to wood chip surfaces.

    Directory of Open Access Journals (Sweden)

    Andrew W Howard

    2009-12-01

    Full Text Available BACKGROUND: The risk of playground injuries, especially fractures, is prevalent in children, and can result in emergency room treatment and hospital admissions. Fall height and surface area are major determinants of playground fall injury risk. The primary objective was to determine if there was a difference in playground upper extremity fracture rates in school playgrounds with wood fibre surfacing versus granite sand surfacing. Secondary objectives were to determine if there were differences in overall playground injury rates or in head injury rates in school playgrounds with wood fibre surfacing compared to school playgrounds with granite sand surfacing. METHODS AND FINDINGS: The cluster randomized trial comprised 37 elementary schools in the Toronto District School Board in Toronto, Canada with a total of 15,074 students. Each school received qualified funding for installation of new playground equipment and surfacing. The risk of arm fracture from playground falls onto granitic sand versus onto engineered wood fibre surfaces was compared, with an outcome measure of estimated arm fracture rate per 100,000 student-months. Schools were randomly assigned by computer generated list to receive either a granitic sand or an engineered wood fibre playground surface (Fibar, and were not blinded. Schools were visited to ascertain details of the playground and surface actually installed and to observe the exposure to play and to periodically monitor the depth of the surfacing material. Injury data, including details of circumstance and diagnosis, were collected at each school by a prospective surveillance system with confirmation of injury details through a validated telephone interview with parents and also through collection (with consent of medical reports regarding treated injuries. All schools were recruited together at the beginning of the trial, which is now closed after 2.5 years of injury data collection. Compliant schools included 12 schools

  6. a Chirped Pulse Fourier Transform Microwave Cp-Ftmw Spectrometer with Laser Ablation Source to Search for Actinide-Containing Molecules and Noble Metal Clusters

    Science.gov (United States)

    Marshall, Frank E.; Gillcrist, David Joseph; Persinger, Thomas D.; Moon, Nicole; Grubbs, G. S., II

    2016-06-01

    Microwave spectroscopic techniques have traditionally been part of the foundation of molecular structure and this conference. Instrumental developments by Brooks Pate and sourcing developments by Steve Cooke on these instruments have allowed for the dawning of a new era in modern microwave spectroscopic techniques. With these advances and the growth of powerful computational approaches, microwave spectroscopists can now search for molecules and/or cluster systems of actinide and noble metal-containing species with increasing certainty in molecular assignment even with the difficulties presented with spin-orbit coupling and relativistic effects. Spectrometer and ablation design will be presented along with any preliminary results on actinide-containing molecules or noble metal clusters or interactions. G. G. Brown, B. C. Dian, K. O. Douglass, S. M. Geyer, S. T. Shipman, B. H. Pate, Rev. Sci. Instrum. 79 (2008) 053103-1 - 053103-13 G. S. Grubbs II, C. T. Dewberry, K. C. Etchison, K. E. Kerr, S. A. Cooke, Rev. Sci. Instrum. 78 (2007) 096106-1 - 096106-3

  7. Surface-enhanced Raman scattering of Ethyl carbamate adsorbed on Ag20 cluster: Enhancement mechanism

    Science.gov (United States)

    Du, Junmei; Wang, Hongyan; Wang, Hui; Chen, Yuanzheng; Guo, Chunsheng; Gan, Liyong; Du, Muying

    2017-03-01

    The normal and surface-enhanced Raman scattering of EC are studied by using the M06-2X functional. Different contributions to Raman enhancements of EC adsorbed on Ag20 cluster are analyzed in detail to explore the enhancement mechanism. The adsorption of EC on Ag20 cluster involves the static chemical enhancement with enhancements factor (EF) of 10 by forming a new EC-Ag20 complex. The charge-transfer enhancement with EF of 104 is found when a 352 nm wavelength, corresponding to the absorption maximum of EC-Ag20 complex, is taken as an incident light. The electromagnetic enhancement EF of 3.6 × 106 due to the localized surface plasmon resonance (LSPR) of Ag nanosphere at the same excitation wavelength are acquired by the discrete dipole approximation (DDA) method. The combined effect of the chemical and electromagnetic enhancement results in the total relative enhancements factor up to 3.6 × 1010. The enhancement mechanisms are successfully explained by the combination of ab initio calculation and discrete dipole appropriation method.

  8. Turbulent clustering of initially well-mixed buoyant particles on a free-surface by Lagrangian coherent structures

    Science.gov (United States)

    Pratt, Kenneth R.; True, Aaron; Crimaldi, John P.

    2017-07-01

    Particles that float on the surface of a 3D incompressible turbulent flow are exposed to non-divergence-free properties that result in clustering and unmixing, a reversal of how turbulence normally acts to mix and dilute scalars. Particle clustering is dominated by Lagrangian processes that depend on the time history of the flow; this suggests that Lagrangian coherent structures (LCS) might serve as templates for cluster formation. In this study, non-divergence-free clustering is examined both experimentally and numerically to elucidate the role of LCS in the formation of particle clusters and voids. Experiments are performed on the free-surface of a water-filled tank with turbulence driven by the random pulsing of centrifugal pumps on the tank bottom. Clustering is quantified by imaging fluorescent, buoyant particles that are placed in an initially random distribution on the free-surface. Within clusters, concentrations are observed to increase by an order of magnitude, with the likelihood of observing enhanced concentrations increasing by two orders of magnitude. LCS, obtained from velocity fields utilizing particle image velocimetry, are shown to act as templates for cluster formation. In addition, LCS are shown to possess a dilatation component in non-divergence-free flows that is responsible for unmixing. Numerically, a non-divergence-free chaotic model consisting of interacting Taylor vortices is utilized to investigate processes responsible for cluster formation seen in the experiments. The model results support the experimental finding that LCS act as templates for particle clusters, with scalar unmixing driven by the dilatation component.

  9. Luminescent systems based on the isolation of conjugated PI systems and edge charge compensation with polar molecules on a charged nanostructured surface

    Science.gov (United States)

    Ivanov, Ilia N.; Puretzky, Alexander A.; Zhao, Bin; Geohegan, David B.; Styers-Barnett, David J.; Hu, Hui

    2014-07-15

    A photoluminescent or electroluminescent system and method of making a non-luminescent nanostructured material into such a luminescent system is presented. The method of preparing the luminescent system, generally, comprises the steps of modifying the surface of a nanostructured material to create isolated regions to act as luminescent centers and to create a charge imbalance on the surface; applying more than one polar molecule to the charged surface of the nanostructured material; and orienting the polar molecules to compensate for the charge imbalance on the surface of the nanostructured material. The compensation of the surface charge imbalance by the polar molecules allows the isolated regions to exhibit luminescence.

  10. Structural study of CH4, CO2 and H2O clusters containing from several tens to several thousands of molecules

    Science.gov (United States)

    Torchet, G.; Farges, J.; de Feraudy, M. F.; Raoult, B.

    Clusters are produced during the free jet expansion of gaseous CH4, CO2 or H2O. For a given stagnation temperature To, the mean cluster size is easily increased by increasing the stagnation pressure p0. On the other hand, the cluster temperature does not depend on stagnation conditions but mainly on properties of the condensed gas. An electron diffraction analysis provides information about the cluster structure. Depending on whether the diffraction patterns exhibit crystalline lines or not, the structure is worked out either by using crystallographic methods or by constructing cluster models. When they contain more than a few thousand molecules, clusters show a crystalline structure identical to that of one phase, namely, the cubic phase, known in bulk solid: plastic phase (CH4), unique solid phase (CO2) or metastable cubic phase (H2O). When decreasing the cluster size, the studied compounds behave quite differently: CO2 clusters keep the same crystalline structure, CH4 clusters show the multilayer icosahedral structure wich has been found in rare gas clusters, and H2O clusters adopt a disordered structure different from the amorphous structures of bulk ice. Des agrégats sont produits au cours de la détente en jet libre des gaz CH4, CO2 ou H2O. Pour une température initiale donnée To, on accroît facilement la taille moyenne des agrégats en augmentant la pression initiale po . Par contre, la température des agrégats dépend principalement des propriétés du gaz condensé. Une analyse par diffraction électronique permet l'étude de la structure des agrégats. Selon que les diagrammes de diffraction contiennent ou non des raies cristallines, on a recours soit à des méthodes cristallographiques soit à la construction de modèles d'agrégats. Lorsqu'ils renferment plus de quelques milliers de molécules, les agrégats adoptent la structure cristalline de l'une des phases connues du solide massif et plus précisément la phase cubique : phase plastique pour

  11. Electrochemical immobilization of Fluorescent labelled probe molecules on a FTO surface for affinity detection based on photo-excited current

    Energy Technology Data Exchange (ETDEWEB)

    Haruyama, Tetsuya; Wakabayashi, Ryo; Cho, Takeshi; Matsuyama, Sho-taro, E-mail: haruyama@life.kyutech.as.jp [Kyushu Institute of Technology, Department of Biological Functions and Engineering, Kitakyushu Science and Research Park, Hibikino, Kitakyushu, Fukuoka 808-0196 (Japan)

    2011-10-29

    Photo-excited current can be generated at a molecular interface between a photo-excited molecules and a semi-conductive material in appropriate condition. The system has been recognized for promoting photo-energy devices such as an organic dye sensitized solar-cell. The photo-current generated reactions are totally dependent on the interfacial energy reactions, which are in a highly fluctuated interfacial environment. The authors investigated the photo-excited current reaction to develop a smart affinity detection method. However, in order to perform both an affinity reaction and a photo-excited current reaction at a molecular interface, ordered fabrications of the functional (affinity, photo-excitation, etc.) molecules layer on a semi-conductive surface is required. In the present research, we would like to present the fabrication and functional performance of photo-excited current-based affinity assay device and its application for detection of endocrine disrupting chemicals. On the FTO surface, fluorescent pigment labelled affinity peptide was immobilized through the EC tag (electrochemical-tag) method. The modified FTO produced a current when it was irradiated with diode laser light. However, the photo current decreased drastically when estrogen (ES) coexisted in the reaction solution. In this case, immobilized affinity probe molecules formed a complex with ES and estrogen receptor (ER). The result strongly suggests that the photo-excited current transduction between probe molecule-labelled cyanine pigment and the FTO surface was partly inhibited by a complex that formed at the affinity oligo-peptide region in a probe molecule on the FTO electrode. The bound bulky complex may act as an impediment to perform smooth transduction of photo-excited current in the molecular interface. The present system is new type of photo-reaction-based analysis. This system can be used to perform simple high-sensitive homogeneous assays.

  12. A Combined Experimental and Theoretical Study of the Neutral, Cationic and Anionic Si3N Cluster Molecule

    Science.gov (United States)

    1994-04-22

    molecules4e by neutralization- reionization mass spectrometry (NRMS). 6 This mass spectrometric technique 3 has been applied successfully for the generation...neutralization- reionization mass spectrometry. 8 High-level ab initio methods have been employed for the structural and energetic description of the various...helium was introduced as a collision gas into the second part of a differentially pumped tandem collision cell. For the neutralization- reionization

  13. Surface diffusion of long chainlike molecules: The role of memory effects and stiffness on effective diffusion barriers

    DEFF Research Database (Denmark)

    Hjelt, T.; Vattulainen, Ilpo Tapio

    2000-01-01

    We study the coverage dependence of surface diffusion for chainlike molecules by the fluctuating-bond model with a Monte Carlo dynamics. The model includes short-ranged excluded volume interactions between different chains as well as an intrachain bond angle potential to describe the chain...... of recent experimental work as regards surface diffusion of long DNA molecules on a biological interface. (C) 2000 American Institute of Physics....... become more pronounced at an increasing coverage as a result of packing requirements. Increasing the chain flexibility furthermore has the same overall effect as increasing the chain length, namely, they both increase E-A(T). We then analyze the influence of memory effects on E-A(T) and find that...

  14. Three-dimensional ab initio dipole moment surfaces and stretching vibrational band intensities of the XH3 molecules

    Institute of Scientific and Technical Information of China (English)

    Liu An-Wen; Hu Shui-Ming; Ding Yun; Zhu Qing-Shi

    2005-01-01

    Stretching vibrational band intensities of XH3 (X=N, Sb) molecules are investigated employing three-dimensional dipole moment surfaces combined with the local mode Hamiltonian model. The dipole moment surfaces of NH3 and SbH3 are calculated with the density functional theory and at the correlated MP2 level, respectively. The calculated band intensities are in good agreement with the available experimental data. The contribution to the band intensities from the different terms in the polynomial expansion of the dipole moments of four group V hydrides (NH3, PH3, AsH3 and SbH3) are discussed. It is concluded that the breakdown of the bond dipole approximation must be considered.The intensity "borrowing" effect due to the wave function mixing among the stretching vibrational states is found to be less significant for the molecules that reach the local mode limit.

  15. Expression of Surface Molecules in Human Mesenchymal Stromal Cells Co-Cultured with Nucleated Umbilical Cord Blood Cells.

    Science.gov (United States)

    Romanov, Yu A; Balashova, E E; Volgina, N E; Kabaeva, N V; Dugina, T N; Sukhikh, G T

    2017-02-01

    We studied the expression of different classes of surface molecules (CD13, CD29, CD40, CD44, CD54, CD71, CD73, CD80, CD86, CD90, CD105, CD106, CD146, HLA-I, and HLA-DR) in mesenchymal stromal cells from human umbilical cord and bone marrow during co-culturing with nucleated umbilical cord blood cells. Expression of the majority of surface markers in both types of mesenchymal stromal cells was stable and did not depend on the presence of the blood cells. Significant differences were found only for cell adhesion molecules CD54 (ICAM-1) and CD106 (VCAM-1) responsible for direct cell-cell contacts with leukocytes and only for bone marrow derived cells.

  16. Low-damage surface smoothing of laser crystallized polycrystalline silicon using gas cluster ion beam

    Science.gov (United States)

    Tokioka, H.; Yamarin, H.; Fujino, T.; Inoue, M.; Seki, T.; Matsuo, J.

    2007-04-01

    Surface smoothing of laser crystallized polycrystalline silicon (poly-Si) films using gas cluster ion beam (GCIB) technology has been studied. It is found that both SF6-GCIB and O2-GCIB decrease the height of hillocks and reduce the surface roughness of the irradiated films. The mean surface roughness value of poly-Si films was reduced from 10.8 nm to 2.8 nm by SF6-GCIB irradiation at 80°. Ultraviolet reflectance measurement reveals that GCIB irradiation causes damage near-surface of the poly-Si films. Formation of the damage, however, can be suppressed by using GCIB irradiation at high incident angle. Effect of GCIB irradiation in a metal-insulator-semiconductor (MIS) capacitor has also been investigated. The capacitance-voltage curves of MIS capacitor with SF6-GCIB irradiation are distorted. On the contrary, the distortion is reduced by O2-GCIB irradiation at 80, which suggests that electrical-activated damage of the films can be decreased by using O2-GCIB irradiation.

  17. Neutrophil surface adhesion molecule and toll like receptor dynamics in crossbred cows suffering from Staphylococcus aureus subclinical and clinical mastitis

    OpenAIRE

    Dilip Kumar Swain; Mohar Singh Kushwah; Ajay Kumar Dang

    2016-01-01

    Objective: The present study was an attempt to delineate the roles played by the neutrophil surface adhesion molecules and toll like receptors (TLRs) in crossbred cows suffering from Staphylococcus aureus subclinical and clinical mastitis. Materials and methods: Thirty six Karan Fries (KF) cows were categorized into three groups namely healthy (n=12), subclinical mastitis (SCM; n=12) and clinical mastitis (CM; n=12) after screening 146 cows. The grouping was done based on evaluation of co...

  18. Catalytically Triggered Energy Release from Strained Organic Molecules: The Surface Chemistry of Quadricyclane and Norbornadiene on Pt(111).

    Science.gov (United States)

    Bauer, Udo; Mohr, Susanne; Döpper, Tibor; Bachmann, Philipp; Späth, Florian; Düll, Fabian; Schwarz, Matthias; Brummel, Olaf; Fromm, Lukas; Pinkert, Ute; Görling, Andreas; Hirsch, Andreas; Bachmann, Julien; Steinrück, Hans-Peter; Libuda, Jörg; Papp, Christian

    2017-01-31

    We have investigated the surface chemistry of the polycyclic valence-isomer pair norbornadiene (NBD) and quadricyclane (QC) on Pt(111). The NBD/QC system is considered to be a prototype for energy storage in strained organic compounds. By using a multimethod approach, including UV photoelectron, high-resolution X-ray photoelectron, and IR reflection-absorption spectroscopic analysis and DFT calculations, we could unambiguously identify and differentiate between the two molecules in the multilayer phase, which implies that the energy-loaded QC molecule is stable in this state. Upon adsorption in the (sub)monolayer regime, the different spectroscopies yielded identical spectra for NBD and QC at 125 and 160 K, when multilayer desorption takes place. This behavior is explained by a rapid cycloreversion of QC to NBD upon contact with the Pt surface. The NBD adsorbs in a η(2) :η(1) geometry with an agostic Pt-H interaction of the bridgehead CH2 subunit and the surface. Strong spectral changes are observed between 190 and 220 K because the hydrogen atom that forms the agostic bond is broke. This reaction yields a norbornadienyl intermediate species that is stable up to approximately 380 K. At higher temperatures, the molecule dehydrogenates and decomposes into smaller carbonaceous fragments.

  19. The active translation of MHCII mRNA during dendritic cells maturation supplies new molecules to the cell surface pool.

    Science.gov (United States)

    Malanga, Donatella; Barba, Pasquale; Harris, Paul E; Maffei, Antonella; Del Pozzo, Giovanna

    2007-04-01

    The transition of human dendritic cells (DCs) from the immature to the mature phenotype is characterized by an increased density of MHC class II (MHCII) molecules on the plasma membrane, a key requirement of their competence as professional antigen presenting cells (APCs). MHCII molecules on the cell surface derive from newly synthesized as well as from preexisting proteins. So far, all the studies done on DCs during maturation, to establish the relative contribution of newly synthesized MHCII molecules to the cell surface pool did not produced a clear, unified scenario. We report that, in human DCs stimulated ex vivo with LPS, the changes in the RNA accumulation specific for at least two MHCII genes (HLA-DRA and HLA-DQA1) due to transcriptional upregulation, is associated with the active translation at high rate of these transcripts. Our finding reveals that, across the 24h of the maturation process in human DCs, newly synthesized MHCII proteins are supplied to the APCs cell surface pool.

  20. Expansion Hamiltonian model for a diatomic molecule adsorbed on a surface: Vibrational states of the CO/Cu(100) system including surface vibrations.

    Science.gov (United States)

    Meng, Qingyong; Meyer, Hans-Dieter

    2015-10-28

    Molecular-surface studies are often done by assuming a corrugated, static (i.e., rigid) surface. To be able to investigate the effects that vibrations of surface atoms may have on spectra and cross sections, an expansion Hamiltonian model is proposed on the basis of the recently reported [R. Marquardt et al., J. Chem. Phys. 132, 074108 (2010)] SAP potential energy surface (PES), which was built for the CO/Cu(100) system with a rigid surface. In contrast to other molecule-surface coupling models, such as the modified surface oscillator model, the coupling between the adsorbed molecule and the surface atoms is already included in the present expansion SAP-PES model, in which a Taylor expansion around the equilibrium positions of the surface atoms is performed. To test the quality of the Taylor expansion, a direct model, that is avoiding the expansion, is also studied. The latter, however, requests that there is only one movable surface atom included. On the basis of the present expansion and direct models, the effects of a moving top copper atom (the one to which CO is bound) on the energy levels of a bound CO/Cu(100) system are studied. For this purpose, the multiconfiguration time-dependent Hartree calculations are carried out to obtain the vibrational fundamentals and overtones of the CO/Cu(100) system including a movable top copper atom. In order to interpret the results, a simple model consisting of two coupled harmonic oscillators is introduced. From these calculations, the vibrational levels of the CO/Cu(100) system as function of the frequency of the top copper atom are discussed.

  1. Expansion Hamiltonian model for a diatomic molecule adsorbed on a surface: Vibrational states of the CO/Cu(100) system including surface vibrations

    Energy Technology Data Exchange (ETDEWEB)

    Meng, Qingyong, E-mail: mengqingyong@dicp.ac.cn [State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, 116023 Dalian (China); Meyer, Hans-Dieter, E-mail: hans-dieter.meyer@pci.uni-heidelberg.de [Theoretische Chemie, Physikalisch-Chemisches Institut, Ruprecht-Karls Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg (Germany)

    2015-10-28

    Molecular-surface studies are often done by assuming a corrugated, static (i.e., rigid) surface. To be able to investigate the effects that vibrations of surface atoms may have on spectra and cross sections, an expansion Hamiltonian model is proposed on the basis of the recently reported [R. Marquardt et al., J. Chem. Phys. 132, 074108 (2010)] SAP potential energy surface (PES), which was built for the CO/Cu(100) system with a rigid surface. In contrast to other molecule-surface coupling models, such as the modified surface oscillator model, the coupling between the adsorbed molecule and the surface atoms is already included in the present expansion SAP-PES model, in which a Taylor expansion around the equilibrium positions of the surface atoms is performed. To test the quality of the Taylor expansion, a direct model, that is avoiding the expansion, is also studied. The latter, however, requests that there is only one movable surface atom included. On the basis of the present expansion and direct models, the effects of a moving top copper atom (the one to which CO is bound) on the energy levels of a bound CO/Cu(100) system are studied. For this purpose, the multiconfiguration time-dependent Hartree calculations are carried out to obtain the vibrational fundamentals and overtones of the CO/Cu(100) system including a movable top copper atom. In order to interpret the results, a simple model consisting of two coupled harmonic oscillators is introduced. From these calculations, the vibrational levels of the CO/Cu(100) system as function of the frequency of the top copper atom are discussed.

  2. First-principles study of the adsorption properties of atoms and molecules on UN2 (001) surface

    Science.gov (United States)

    Xu, Mengjuan; Liu, Guangdong; Ao, Bingyun; Chen, Piheng; Hu, Wangyu; Deng, Huiqiu

    2017-09-01

    Uranium nitrides are one kind of accident-tolerant fuels and have been paid more attention recently. With the first-principles Density-Functional Theory (DFT) calculations, the adsorptions properties of some typical atoms, molecules and radical (including O, H, H2, O2, H2O and OH) adsorbed on the UN2 (001) surface have been studied in the present work. The preferred sites and stable configurations for those adsorbates on the UN2 (001) surface have been obtained. It's found that O or H atom prefers to be adsorbed at the bridge site; O2 adsorption will dissociate into two O atoms and occupy the nearest neighbor bridge sites; the interaction between H2 molecule and the UN2 (001) surface is very weak; OH prefers to occupy the bridge site with its O-H bond vertical to the surface; the surface adsorption of H2O is non-dissociated and adsorption energies are dependent on the initial structures and adsorption modes.

  3. Electrochemistry of Single Metalloprotein and DNA‐Based Molecules at Au(111) Electrode Surfaces

    DEFF Research Database (Denmark)

    Salvatore, Princia; Zeng, Dongdong; Karlsen, Kasper Kannegård;

    2013-01-01

    We have briefly overviewed recent efforts in the electrochemistry of single transition metal complex, redox metalloprotein, and redox‐marked oligonucleotide (ON) molecules. We have particularly studied self‐assembled molecular monolayers (SAMs) of several 5′‐C6‐SH single‐ (ss) and double‐strand (ds...

  4. Dioxygen molecule adsorption and oxygen atom diffusion on clean and defective aluminum(111) surface using first principles calculations

    Science.gov (United States)

    Guiltat, Mathilde; Brut, Marie; Vizzini, Sébastien; Hémeryck, Anne

    2017-03-01

    First principles calculations are conducted to investigate kinetic behavior of oxygen species at the surface of clean and defective Al(111) substrate. Oxygen island, aluminum vacancy, aluminum sub-vacancy, aluminum ad-atom and aluminum terraces defects are addressed. Adsorption of oxygen molecule is first performed on all these systems resulting in dissociated oxygen atoms in main cases. The obtained adsorbed configurations are then picked to study the behavior of atomic oxygen specie and get a detailed understanding on the effect of the local environment on the ability of the oxygen atom to diffuse on the surface. We pointed out that local environment impacts energetics of oxygen atom diffusion. Close packed oxygen island, sub-vacancy and ad-atoms favor oxygen atom stability and decrease mobility of oxygen atom on the surface, to be seen as surface area for further nucleation of oxygen island.

  5. From Boron Cluster to Two-Dimensional Boron Sheet on Cu(111) Surface: Growth Mechanism and Hole Formation

    OpenAIRE

    Hongsheng Liu; Junfeng Gao; Jijun Zhao

    2013-01-01

    As attractive analogue of graphene, boron monolayers have been theoretically predicted. However, due to electron deficiency of boron atom, synthesizing boron monolayer is very challenging in experiments. Using first-principles calculations, we explore stability and growth mechanism of various boron sheets on Cu(111) substrate. The monotonic decrease of formation energy of boron cluster BN with increasing cluster size and low diffusion barrier for a single B atom on Cu(111) surface ensure cont...

  6. Formation of transition metal cluster adducts on the surface of single-walled carbon nanotubes: HRTEM studies

    KAUST Repository

    Kalinina, Irina V.

    2014-01-01

    We report the formation of chromium clusters on the outer walls of single-walled carbon nanotubes (SWNTs). The clusters were obtained by reacting purified SWNTs with chromium hexacarbonyl in dibutyl ether at 100°C. The functionalized SWNTs were characterized by thermogravimetic analysis, XPS, and high-resolution TEM. The curvature of the SWNTs and the high mobility of the chromium moieties on graphitic surfaces allow the growth of the metal clusters and we propose a mechanism for their formation. © 2014 Taylor and Francis Group, LLC.

  7. Osmium Atoms and Os2 Molecules Move Faster on Selenium-Doped Compared to Sulfur-Doped Boronic Graphenic Surfaces.

    Science.gov (United States)

    Barry, Nicolas P E; Pitto-Barry, Anaïs; Tran, Johanna; Spencer, Simon E F; Johansen, Adam M; Sanchez, Ana M; Dove, Andrew P; O'Reilly, Rachel K; Deeth, Robert J; Beanland, Richard; Sadler, Peter J

    2015-07-28

    We deposited Os atoms on S- and Se-doped boronic graphenic surfaces by electron bombardment of micelles containing 16e complexes [Os(p-cymene)(1,2-dicarba-closo-dodecarborane-1,2-diselenate/dithiolate)] encapsulated in a triblock copolymer. The surfaces were characterized by energy-dispersive X-ray (EDX) analysis and electron energy loss spectroscopy of energy filtered TEM (EFTEM). Os atoms moved ca. 26× faster on the B/Se surface compared to the B/S surface (233 ± 34 pm·s(-1) versus 8.9 ± 1.9 pm·s(-1)). Os atoms formed dimers with an average Os-Os distance of 0.284 ± 0.077 nm on the B/Se surface and 0.243 ± 0.059 nm on B/S, close to that in metallic Os. The Os2 molecules moved 0.83× and 0.65× more slowly than single Os atoms on B/S and B/Se surfaces, respectively, and again markedly faster (ca. 20×) on the B/Se surface (151 ± 45 pm·s(-1) versus 7.4 ± 2.8 pm·s(-1)). Os atom motion did not follow Brownian motion and appears to involve anchoring sites, probably S and Se atoms. The ability to control the atomic motion of metal atoms and molecules on surfaces has potential for exploitation in nanodevices of the future.

  8. Gas surface density, star formation rate surface density, and the maximum mass of young star clusters in a disk galaxy. II. The grand-design galaxy M51

    CERN Document Server

    Gonzalez-Lopezlira, Rosa A; Kroupa, Pavel

    2013-01-01

    We analyze the relationship between maximum cluster mass, and surface densities of total gas (Sigma_gas), molecular gas (Sigma_H_2), neutral gas (Sigma_HI) and star formation rate (Sigma_SFR) in the grand design galaxy M51, using published gas data and a catalog of masses, ages, and reddenings of more than 1800 star clusters in its disk, of which 223 are above the cluster mass distribution function completeness limit. We find for clusters older than 25 Myr that M_3rd, the median of the 5 most massive clusters, is proportional to Sigma_HI^0.4. There is no correlation with Sigma_gas, Sigma_H2, or Sigma_SFR. For clusters younger than 10 Myr, M_3rd is proportional to Sigma_HI^0.6, M_3rd is proportional to Sigma_gas^0.5; there is no correlation with either Sigma_H_2 or Sigma_SFR. The results could hardly be more different than those found for clusters younger than 25 Myr in M33. For the flocculent galaxy M33, there is no correlation between maximum cluster mass and neutral gas, but M_3rd is proportional to Sigma_g...

  9. X-Ray surface brightness and gas density fluctuations in the Coma cluster

    CERN Document Server

    Churazov, E; Zhuravleva, I; Schekochihin, A; Parrish, I; Sunyaev, R; Forman, W; Boehringer, H; Randall, S

    2011-01-01

    X-ray surface brightness fluctuations in the core ($650 \\times 650$ kpc) region of the Coma cluster observed with XMM-Newton and Chandra are analyzed using a 2D power spectrum approach. The resulting 2D spectra are converted to 3D power spectra of gas density fluctuations. The characteristic amplitude of the volume filling density fluctuations relative to the smooth underlying density distribution varies from 7-10% on scales of $\\sim$500 kpc down to $\\sim$5% at scales $\\sim$ 30 kpc. On smaller spatial scales, projection effects smear the density fluctuations by a large factor, precluding strong limits on the fluctuations in 3D. On the largest scales probed (hundreds of kpc), the dominant contributions to the observed fluctuations most likely arise from perturbations of the gravitational potential by the two most massive galaxies in Coma, NGC4874 and NGC4889, and the low entropy gas brought to the cluster by an infalling group. Other plausible sources of density fluctuations are discussed, including turbulence...

  10. Surface self-diffusion of adatom on Pt cluster with truncated octahedron structure

    Energy Technology Data Exchange (ETDEWEB)

    Yang Jianyu, E-mail: wuliyangjianyu@yahoo.com.c [Department of Maths and Physics, Hunan Institute of Engineering, Xiangtan 411104 (China); Hu Wangyu, E-mail: wangyuhu2001@yahoo.com.c [Department of Applied Physics, Hunan University, Changsha 410082 (China); Chen Shuguang [Department of Applied Physics, Hunan University, Changsha 410082 (China)

    2010-05-03

    Surface diffusion of single Pt adatom on Pt cluster with truncated octahedron structure is investigated through a combination of molecular dynamics and nudged elastic band method. Using an embedded atom method to describe the atomic interactions, the minimum energy paths are determined and the energy barriers for adatom diffusion across and along step are evaluated. The diffusion of adatom crossing step edge between {l_brace}111{r_brace} and {l_brace}100{r_brace} facets has a surprisingly low barrier of 0.03 eV, which is 0.12 eV lower than the barrier for adatom diffusion from {l_brace}111{r_brace} to neighboring {l_brace}111{r_brace} facet. Owing to the small barrier of adatom diffusion across the step edge between {l_brace}111{r_brace} and {l_brace}100{r_brace} facets, the diffusion of adatom along the step edge cannot occur. The molecular dynamics simulations at low temperatures also support these results. Our results show that mass transport will prefer step with {l_brace}100{r_brace} microfacet and the Pt clusters can have only {l_brace}111{r_brace} facets in epitaxial growth.

  11. Three-Dimensional Clustered Nanostructures for Microfluidic Surface-Enhanced Raman Detection.

    Science.gov (United States)

    Wang, Gang; Li, Kerui; Purcell, Francis J; Zhao, De; Zhang, Wei; He, Zhongyuan; Tan, Shuai; Tang, Zhenguan; Wang, Hongzhi; Reichmanis, Elsa

    2016-09-21

    A materials fabrication concept based on a fluid-construction strategy to create three-dimensional (3D) ZnO@ZnS-Ag active nanostructures at arbitrary position within confined microchannels to form an integrated microfluidic surface-enhanced Raman spectroscopy (SERS) system is presented. The fluid-construction process allowed facile construction of the nanostructured substrates, which were shown to possess a substantial number of integrated hot spots that support SERS activity. Finite-difference time-domain (FDTD) analysis suggested that the 3D clustered geometry facilitated hot spot formation. High sensitivity and good recycle performance were demonstrated using 4-mercaptobenzoic acid (4-MBA) and a mixture of Rhodamine 6G (R6G) and 4-MBA as target organic pollutants to evaluate the SERS microfluidic device performance. The 3D clustered nanostructures were also effective in the detection of a representative nerve agent and biomolecule. The results of this investigation provide a materials and process approach to the fabrication of requisite nanostructures for the online detection of organic pollutants, devices for real-time observation of environmental hazards, and personal-health monitoring.

  12. Surface density of dark matter haloes on galactic and cluster scales

    Science.gov (United States)

    Del Popolo, A.; Cardone, V. F.; Belvedere, G.

    2013-02-01

    In this paper, we analysed the correlation between the central surface density and the halo core radius of galaxies, and cluster of galaxies dark matter (DM) haloes, in the framework of the secondary infall model. We used Del Popolo secondary infall model taking into account ordered and random angular momentum, dynamical friction and DM adiabatic contraction to calculate the density profile of haloes, and then these profiles are used to determine the surface density of DM haloes. The main result is that r* (the halo characteristic radius) is not a universal quantity as claimed by Donato et al. and Gentile et al. On the contrary, we find a correlation with the halo mass M200 in agreement with Cardone & Tortora, Boyarsky et al. and Napolitano, Romanowsky & Tortora, but with a significantly smaller scatter, namely 0.16 ± 0.05. We also consider the baryon column density finding this latter being indeed a constant for low-mass systems, such as dwarfs, but correlating with mass with a slope of α = 0.18 ± 0.05. In the case of the surface density of DM for a system composed only of DM, as in dissipationless simulations, we get α = 0.20 ± 0.05. These results leave little room for the recently claimed universality of (dark and stellar) column density.

  13. Adsorption of acetyl halide molecules on the surface of pristine and Al-doped graphene: Ab initio study

    Energy Technology Data Exchange (ETDEWEB)

    Rad, Ali Shokuhi, E-mail: a.shokuhi@gmail.com [Department of Chemical Engineering, Qaemshahr Branch, Islamic Azad University, Qaemshahr (Iran, Islamic Republic of); Kashani, Omid Razaghi [Department of Polymer Engineering, Qaemshahr Branch, Islamic Azad University, Qaemshahr (Iran, Islamic Republic of)

    2015-11-15

    Graphical abstract: - Highlights: • The adsorption of acetyl chloride and acetyl fluoride on Al-doped graphene were investigated. • The doped Al induces some changes in the electronic structure of graphene. • Notable orbital hybridizations are achieved upon adsorption. • Al-doped graphene can be used as a superior sensor for Acetyl halides. - Abstract: We have scrutinized the adsorption energy, electronic structure, natural bond analysis (NBO), density of state (DOS) and global indices for adsorption of acetyl chloride (AC) and acetyl fluoride (AF) on the surface of pristine graphene as well as Al-doped graphene. The adsorption energies have been calculated for the most stable configurations of the molecules on the surface of pristine and Al-doped graphene. According to the calculated parameters, there is very weak physical adsorption of AC and AF on pristine graphene while strong adsorption takes place in the case of Al-doped graphene. The charge transfer from adsorbed molecules to Al-doped graphene surface was confirmed by the natural bond orbital as well as the Mulliken population analysis while there is no charge transfer with pristine graphene. Additionally, the density of states results reveal that orbital hybridization takes place between above-mentioned molecules and Al-doped graphene sheet, whereas there is no hybridization between the molecules and the pristine graphene. Our calculated adsorption energies for the most stable position configurations of AC and AF on Al-doped graphene were −68.8 kJ mol{sup −1} (−52.6 kJ mol{sup −1} BSSE corrected energy) and −78.4 kJ mol{sup −1} (−64.3 kJ mol{sup −1} BSSE corrected energy) which are correspond to chemisorptions process respectively. These results point to the appropriateness of Al-doped graphene as a powerful adsorbent for practical applications.

  14. Bacterial Surface-Displayed GII.4 Human Norovirus Capsid Proteins Bound to HBGA-Like Molecules in Romaine Lettuce.

    Science.gov (United States)

    Wang, Ming; Rong, Shaofeng; Tian, Peng; Zhou, Yue; Guan, Shimin; Li, Qianqian; Wang, Dapeng

    2017-01-01

    Human Noroviruses (HuNoVs) are the main cause of non-bacterial gastroenteritis. Contaminated produce is a main vehicle for dissemination of HuNoVs. In this study, we used an ice nucleation protein mediated surface display system to present the protruding domain of GII.4 HuNoV capsid protein on bacterial surface and used it as a new strategy to explore interaction between HuNoV protein and receptor candidates from romaine lettuce. The surface-displayed HuNoV proteins were confirmed on the surface of the transformed bacteria by an immunofluorescence assay. The distribution patterns of the surface-displayed HuNoV proteins in romaine lettuce were identified through a confocal immunofluorescence assay. The surface-displayed HuNoV proteins could be found in the stomata, and the surfaces of vein and leaf of romaine lettuce. The surface-displayed HuNoV proteins could be captured by an ELISA assay utilizing extract from leaf (LE) or vein (VE). The binding of the surface-displayed HuNoV proteins to LE or VE could be competitively blocked by histo-blood group antigens from human saliva. In addition, the binding of the surface-displayed HuNoV proteins to LE or VE could also be attenuated by heat denaturation of lettuce proteins, and abolished by oxidation of lettuce carbohydrates. The results indicated that histo-blood group antigen-like molecules in LE or VE were involved in the binding of the surface-displayed HuNoV proteins to romaine lettuce. All data demonstrated that the surface-displayed HuNoV proteins could be utilized in a new and simple system for investigation of the interaction between the HuNoVs and their candidate ligands.

  15. Metallic nanocone array photonic substrate for high-uniformity surface deposition and optical detection of small molecules

    Science.gov (United States)

    Coppé, Jean-Philippe; Xu, Zhida; Chen, Yi; Logan Liu, G.

    2011-06-01

    Molecular probe arrays printed on solid surfaces such as DNA, peptide, and protein microarrays are widely used in chemical and biomedical applications especially genomic and proteomic studies (Pollack et al 1999 Nat. Genet. 23 41-6, Houseman et al 2002 Nat. Biotechnol. 20 270-4, Sauer et al 2005 Nat. Rev. Genet. 6 465-76) as well as surface imaging and spectroscopy (Mori et al 2008 Anal. Biochem. 375 223-31, Liu et al 2006 Nat. Nanotechnol. 1 47-52, Liu 2010 IEEE J. Sel. Top. Quantum Electron. 16 662-71). Unfortunately the printed molecular spots on solid surfaces often suffer low distribution uniformity due to the lingering 'coffee stain' (Deegan et al 1997 Nature 389 827-9) problem of molecular accumulations and blotches, especially around the edge of deposition spots caused by solvent evaporation and convection processes. Here we present, without any surface chemistry modification, a unique solid surface of high-aspect-ratio silver-coated silicon nanocone arrays that allows highly uniform molecular deposition and thus subsequent uniform optical imaging and spectroscopic molecular detection. Both fluorescent Rhodamine dye molecules and unlabeled oligopeptides are printed on the metallic nanocone photonic substrate surface as circular spot arrays. In comparison with the printed results on ordinary glass slides and silver-coated glass slides, not only high printing density but uniform molecular distribution in every deposited spot is achieved. The high-uniformity and repeatability of molecular depositions on the 'coffee stain'-free nanocone surface is confirmed by laser scanning fluorescence imaging and surface enhanced Raman imaging experiments. The physical mechanism for the uniform molecular deposition is attributed to the superhydrophobicity and localized pinned liquid-solid-air interface on the silver-coated silicon nanocone surface. The unique surface properties of the presented nanocone surface enabled high-density, high-uniformity probe spotting beneficial

  16. Metallic nanocone array photonic substrate for high-uniformity surface deposition and optical detection of small molecules

    Energy Technology Data Exchange (ETDEWEB)

    Coppe, Jean-Philippe [Kinogea Inc., 2168 Shattuck Ave, Berkeley, CA 94704 (United States); Xu Zhida; Chen Yi; Logan Liu, G, E-mail: loganliu@illinois.edu [Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL (United States)

    2011-06-17

    Molecular probe arrays printed on solid surfaces such as DNA, peptide, and protein microarrays are widely used in chemical and biomedical applications especially genomic and proteomic studies (Pollack et al 1999 Nat. Genet. 23 41-6, Houseman et al 2002 Nat. Biotechnol. 20 270-4, Sauer et al 2005 Nat. Rev. Genet. 6 465-76) as well as surface imaging and spectroscopy (Mori et al 2008 Anal. Biochem. 375 223-31, Liu et al 2006 Nat. Nanotechnol. 1 47-52, Liu 2010 IEEE J. Sel. Top. Quantum Electron. 16 662-71). Unfortunately the printed molecular spots on solid surfaces often suffer low distribution uniformity due to the lingering 'coffee stain' (Deegan et al 1997 Nature 389 827-9) problem of molecular accumulations and blotches, especially around the edge of deposition spots caused by solvent evaporation and convection processes. Here we present, without any surface chemistry modification, a unique solid surface of high-aspect-ratio silver-coated silicon nanocone arrays that allows highly uniform molecular deposition and thus subsequent uniform optical imaging and spectroscopic molecular detection. Both fluorescent Rhodamine dye molecules and unlabeled oligopeptides are printed on the metallic nanocone photonic substrate surface as circular spot arrays. In comparison with the printed results on ordinary glass slides and silver-coated glass slides, not only high printing density but uniform molecular distribution in every deposited spot is achieved. The high-uniformity and repeatability of molecular depositions on the 'coffee stain'-free nanocone surface is confirmed by laser scanning fluorescence imaging and surface enhanced Raman imaging experiments. The physical mechanism for the uniform molecular deposition is attributed to the superhydrophobicity and localized pinned liquid-solid-air interface on the silver-coated silicon nanocone surface. The unique surface properties of the presented nanocone surface enabled high-density, high-uniformity probe

  17. Influence of the water molecules near surface of viral protein on virus activation process

    Energy Technology Data Exchange (ETDEWEB)

    O, Shepelenko S; S, Salnikov A; V, Rak S; P, Goncharova E; B, Ryzhikov A, E-mail: shep@vector.nsc.r, E-mail: shep@ngs.r [Federal State Research Institution State Research Center of Virology and Biotechnology VECTOR of the Federal Service for Surveillance in Consumer Rights Protection and Human Well-being (FSRI SRC VB VECTOR) Koltsovo, Novosibirsk Region (Russian Federation)

    2009-06-01

    The infection of a cell with influenza virus comprises the stages of receptor binding to the cell membrane, endocytosis of virus particle, and fusion of the virus envelope and cell endosome membrane, which is determined by the conformational changes in hemagglutinin, a virus envelope protein, caused by pH decrease within the endosome. The pH value that induces conformation rearrangements of hemagglutinin molecule considerably varies for different influenza virus strains, first and foremost, due to the differences in amino acid structure of the corresponding proteins. The main goal of this study was to construct a model making it possible to assess the critical pH value characterizing the fusogenic activity of influenza virus hemagglutinin from the data on hemagglutinin structure and experimental verification of this model. Under this model, we assume that when the electrostatic force between interacting hemagglutinin molecules in the virus envelop exceeds a certain value, the hemagglutinin HA1 subunits are arranged so that they form a cavity sufficient for penetration of water molecules. This event leads to an irreversible hydration of the inner fragments of hemagglutinin molecule in a trimer and to the completion of conformational changes. The geometry of electrostatic field in hemagglutinin trimer was calculated taking into account the polarization effects near the interface of two dielectrics, aqueous medium and protein macromolecule. The critical pH values for the conformational changes in hemagglutinin were measured by the erythrocyte hemolysis induced by influenza virus particles when decreasing pH. The critical pH value conditionally separating the pH range into the regions with and without the conformational changes was calculated for several influenza virus H1N1 and H3N2 strains based on the data on the amino acid structure of the corresponding hemagglutinin molecules. Comparison of the theoretical and experimental values of critical pH values for

  18. Photoionization of rare gas clusters

    Science.gov (United States)

    Zhang, Huaizhen

    This thesis concentrates on the study of photoionization of van der Waals clusters with different cluster sizes. The goal of the experimental investigation is to understand the electronic structure of van der Waals clusters and the electronic dynamics. These studies are fundamental to understand the interaction between UV-X rays and clusters. The experiments were performed at the Advanced Light Source at Lawrence Berkeley National Laboratory. The experimental method employs angle-resolved time-of-flight photoelectron spectrometry, one of the most powerful methods for probing the electronic structure of atoms, molecules, clusters and solids. The van der Waals cluster photoionization studies are focused on probing the evolution of the photoelectron angular distribution parameter as a function of photon energy and cluster size. The angular distribution has been known to be a sensitive probe of the electronic structure in atoms and molecules. However, it has not been used in the case of van der Waals clusters. We carried out outer-valence levels, inner-valence levels and core-levels cluster photoionization experiments. Specifically, this work reports on the first quantitative measurements of the angular distribution parameters of rare gas clusters as a function of average cluster sizes. Our findings for xenon clusters is that the overall photon-energy-dependent behavior of the photoelectrons from the clusters is very similar to that of the corresponding free atoms. However, distinct differences in the angular distribution point at cluster-size-dependent effects were found. For krypton clusters, in the photon energy range where atomic photoelectrons have a high angular anisotropy, our measurements show considerably more isotropic angular distributions for the cluster photoelectrons, especially right above the 3d and 4p thresholds. For the valence electrons, a surprising difference between the two spin-orbit components was found. For argon clusters, we found that the

  19. Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems.

    Science.gov (United States)

    Send, Robert; Kaila, Ville R I; Sundholm, Dage

    2011-06-07

    We investigate how the reduction of the virtual space affects coupled-cluster excitation energies at the approximate singles and doubles coupled-cluster level (CC2). In this reduced-virtual-space (RVS) approach, all virtual orbitals above a certain energy threshold are omitted in the correlation calculation. The effects of the RVS approach are assessed by calculations on the two lowest excitation energies of 11 biochromophores using different sizes of the virtual space. Our set of biochromophores consists of common model systems for the chromophores of the photoactive yellow protein, the green fluorescent protein, and rhodopsin. The RVS calculations show that most of the high-lying virtual orbitals can be neglected without significantly affecting the accuracy of the obtained excitation energies. Omitting all virtual orbitals above 50 eV in the correlation calculation introduces errors in the excitation energies that are smaller than 0.1 eV. By using a RVS energy threshold of 50 eV, the CC2 calculations using triple-ζ basis sets (TZVP) on protonated Schiff base retinal are accelerated by a factor of 6. We demonstrate the applicability of the RVS approach by performing CC2/TZVP calculations on the lowest singlet excitation energy of a rhodopsin model consisting of 165 atoms using RVS thresholds between 20 eV and 120 eV. The calculations on the rhodopsin model show that the RVS errors determined in the gas-phase are a very good approximation to the RVS errors in the protein environment. The RVS approach thus renders purely quantum mechanical treatments of chromophores in protein environments feasible and offers an ab initio alternative to quantum mechanics/molecular mechanics separation schemes.

  20. Multicolour Emission States from Charge Transfer between Carbon Dots and Surface Molecules

    Directory of Open Access Journals (Sweden)

    Shengliang Hu

    2017-02-01

    Full Text Available The emissive states of carbon dots have been tuned by controlling the charge transfer process. The carbon dots couple with molecules, which are made of a benzene ring and different heteroatom substituents, through amino-carboxylic bonds that are generally identified as charge transfer promoters at the interface. New ways of radiative recombination are created due to the transfer of photo-excited electrons from carbon dots to the lowest unoccupied molecular orbital (LUMO of the grafted molecules. By variation of the molecular orbital energy levels via heteroatom substituents in the benzene ring, the different optical properties and emission colors of the carbon dots were presented. This work opens up new opportunities for the application of carbon dots since different heteroatom substituents could lead to many possibilities for conjugation with drugs and biomolecules.

  1. Gold Cluster Diffusion Kinetics on Stoichiometric and Reduced Surfaces of Rutile TiO 2 (110)

    Energy Technology Data Exchange (ETDEWEB)

    Goldman, Nir; Browning, Nigel D.

    2011-06-16

    Gold clusters on rutile TiO2 are known to serve as efficient oxidation catalysts for pollutants and environmental contaminants. However, the mechanism by which highly mobile small clusters migrate and aggregate into larger species relevant to gold’s catalytic activity remains unresolved. We report herein on ab initio simulations of the diffusion of atomic gold clusters up to the trimer on rutile TiO2(110) surfaces. We show that, on the stoichiometric surface, both the dimer and the trimer can exhibit relatively low surface mobility due to high energetic barriers for diffusion out of their energetic minima coupled with low barriers for the reverse motion. On the reduced surface, these clusters can diffuse relatively quickly between energetic minima within the oxygen vacancy site due to the large degree of vibrational entropy in their transition states. Our computed diffusion times provide a point of comparison for future experiments and will aid in development of models of gold cluster island sintering.

  2. Discharge-nitrate data clustering for characterizing surface-subsurface flow interaction and calibration of a hydrologic model

    Science.gov (United States)

    Shrestha, R. R.; Rode, M.

    2008-12-01

    Concentration of reactive chemicals has different chemical signatures in baseflow and surface runoff. Previous studies on nitrate export from a catchment indicate that the transport processes are driven by subsurface flow. Therefore nitrate signature can be used for understanding the event and pre-event contributions to streamflow and surface-subsurface flow interactions. The study uses flow and nitrate concentration time series data for understanding the relationship between these two variables. Unsupervised artificial neural network based learning method called self organizing map is used for the identification of clusters in the datasets. Based on the cluster results, five different pattern in the datasets are identified which correspond to (i) baseflow, (ii) subsurface flow increase, (iii) surface runoff increase, (iv) surface runoff recession, and (v) subsurface flow decrease regions. The cluster results in combination with a hydrologic model are used for discharge separation. For this purpose, a multi-objective optimization tool NSGA-II is used, where violation of cluster results is used as one of the objective functions. The results show that the use of cluster results as supplementary information for the calibration of a hydrologic model gives a plausible simulation of subsurface flow as well total runoff at the catchment outlet. The study is undertaken using data from the Weida catchment in the North-Eastern Germany, which is a sub-catchment of the Weisse Elster river in the Elbe river basin.

  3. Surface-enhanced photoinduced charge transfer processes in metal-molecule nanoclusters

    OpenAIRE

    Centeno, Silvia P.; Ruano, Cristina; Román-Pérez, Jéssica; López-Tocón, Isabel; Soto, Juan; Otero, Juan Carlos

    2013-01-01

    This work deals with the unexplained efficiency of the electrode potential (EV) in tuning the energy of Charge Transfer (ECT) electronic states of hybrid systems formed by molecules and metal nanostructures. Huge energy gains (G) of up to 5 eV/V observed in electrochemical SERS experiences have been tentatively explained by a local increase of the electric potential at specific adsorption sites.[1] This gain, which is in conflict with the classical picture of the metal-adsorbate CT mechanism ...

  4. A density functional theory for association of fluid molecules with a functionalized surface: fluid-wall single and double bonding

    Science.gov (United States)

    Haghmoradi, Amin; Wang, Le; Chapman, Walter G.

    2017-02-01

    In this manuscript we extend Wertheim’s two-density formalism beyond its first order to model a system of fluid molecules with a single association site close to a planar hard wall with association sites on its surface in a density functional theory framework. The association sites of the fluid molecules are small enough that they can form only one bond, while the wall association sites are large enough to bond with more than one fluid molecule. The effects of temperature and of bulk fluid and wall site densities on the fluid density profile, extent of association, and competition between single and double bonding of fluid segments at the wall sites versus distance from the wall are presented. The theory predictions are compared with new Monte Carlo simulation results and they are in good agreement. The theory captures the surface coverage over wide ranges of temperature and bulk density by introducing the effect of steric hindrance in fluid association at a wall site.

  5. Engineering the magnetic coupling and anisotropy at the molecule-magnetic surface interface in molecular spintronic devices

    Science.gov (United States)

    Campbell, Victoria E.; Tonelli, Monica; Cimatti, Irene; Moussy, Jean-Baptiste; Tortech, Ludovic; Dappe, Yannick J.; Rivière, Eric; Guillot, Régis; Delprat, Sophie; Mattana, Richard; Seneor, Pierre; Ohresser, Philippe; Choueikani, Fadi; Otero, Edwige; Koprowiak, Florian; Chilkuri, Vijay Gopal; Suaud, Nicolas; Guihéry, Nathalie; Galtayries, Anouk; Miserque, Frederic; Arrio, Marie-Anne; Sainctavit, Philippe; Mallah, Talal

    2016-12-01

    A challenge in molecular spintronics is to control the magnetic coupling between magnetic molecules and magnetic electrodes to build efficient devices. Here we show that the nature of the magnetic ion of anchored metal complexes highly impacts the exchange coupling of the molecules with magnetic substrates. Surface anchoring alters the magnetic anisotropy of the cobalt(II)-containing complex (Co(Pyipa)2), and results in blocking of its magnetization due to the presence of a magnetic hysteresis loop. In contrast, no hysteresis loop is observed in the isostructural nickel(II)-containing complex (Ni(Pyipa)2). Through XMCD experiments and theoretical calculations we find that Co(Pyipa)2 is strongly ferromagnetically coupled to the surface, while Ni(Pyipa)2 is either not coupled or weakly antiferromagnetically coupled to the substrate. These results highlight the importance of the synergistic effect that the electronic structure of a metal ion and the organic ligands has on the exchange interaction and anisotropy occurring at the molecule-electrode interface.

  6. Raman and surface enhanced Raman spectroscopic studies of specific, small molecule activator of histone acetyltransferase p300

    Science.gov (United States)

    Kundu, Partha P.; Pavan Kumar, G. V.; Mantelingu, Kempegowda; Kundu, Tapas K.; Narayana, Chandrabhas

    2011-07-01

    We report for the first time, the Raman and surface enhanced Raman scattering (SERS) studies of N-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-benzamide (CTB). This molecule is specific activator of human histone acetyltransferase (HAT), p300, and serves as lead molecule to design anti-neoplastic therapeutics. A detailed Raman and SERS band assignments have been performed for CTB, which are compared with the density functional theory calculations. The observed red shift of N sbnd H stretching frequency from the computed wavenumber indicates the weakening of N sbnd H bond resulting from proton transfer to the neighboring oxygen atom. We observe Ag sbnd N vibrational mode at 234 cm -1 in SERS of CTB. This indicates there is a metal-molecule bond leading to chemical enhancement in SERS. We also observe, enhancement in the modes pertaining to substituted benzene rings and methyl groups. Based on SERS analysis we propose the adsorption sites and the orientation of CTB on silver surface.

  7. GAS SURFACE DENSITY, STAR FORMATION RATE SURFACE DENSITY, AND THE MAXIMUM MASS OF YOUNG STAR CLUSTERS IN A DISK GALAXY. II. THE GRAND-DESIGN GALAXY M51

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez-Lopezlira, Rosa A. [On sabbatical leave from the Centro de Radioastronomia y Astrofisica, UNAM, Campus Morelia, Michoacan, C.P. 58089, Mexico. (Mexico); Pflamm-Altenburg, Jan; Kroupa, Pavel, E-mail: r.gonzalez@crya.unam.mx [Argelander Institut fuer Astronomie, Universitaet Bonn, Auf dem Huegel 71, D-53121 Bonn (Germany)

    2013-06-20

    We analyze the relationship between maximum cluster mass and surface densities of total gas ({Sigma}{sub gas}), molecular gas ({Sigma}{sub H{sub 2}}), neutral gas ({Sigma}{sub H{sub I}}), and star formation rate ({Sigma}{sub SFR}) in the grand-design galaxy M51, using published gas data and a catalog of masses, ages, and reddenings of more than 1800 star clusters in its disk, of which 223 are above the cluster mass distribution function completeness limit. By comparing the two-dimensional distribution of cluster masses and gas surface densities, we find for clusters older than 25 Myr that M{sub 3rd}{proportional_to}{Sigma}{sub H{sub I}{sup 0.4{+-}0.2}}, whereM{sub 3rd} is the median of the five most massive clusters. There is no correlation with{Sigma}{sub gas},{Sigma}{sub H2}, or{Sigma}{sub SFR}. For clusters younger than 10 Myr, M{sub 3rd}{proportional_to}{Sigma}{sub H{sub I}{sup 0.6{+-}0.1}} and M{sub 3rd}{proportional_to}{Sigma}{sub gas}{sup 0.5{+-}0.2}; there is no correlation with either {Sigma}{sub H{sub 2}} or{Sigma}{sub SFR}. The results could hardly be more different from those found for clusters younger than 25 Myr in M33. For the flocculent galaxy M33, there is no correlation between maximum cluster mass and neutral gas, but we have determined M{sub 3rd}{proportional_to}{Sigma}{sub gas}{sup 3.8{+-}0.3}, M{sub 3rd}{proportional_to}{Sigma}{sub H{sub 2}{sup 1.2{+-}0.1}}, and M{sub 3rd}{proportional_to}{Sigma}{sub SFR}{sup 0.9{+-}0.1}. For the older sample in M51, the lack of tight correlations is probably due to the combination of strong azimuthal variations in the surface densities of gas and star formation rate, and the cluster ages. These two facts mean that neither the azimuthal average of the surface densities at a given radius nor the surface densities at the present-day location of a stellar cluster represent the true surface densities at the place and time of cluster formation. In the case of the younger sample, even if the clusters have not yet

  8. Interaction of Biologically Active Molecules with Sulfur-modified Gold Surface

    Institute of Scientific and Technical Information of China (English)

    DING Xue-feng; YANG Gui-fu; WANG Xiao; WANG Zi-chen; LIN Hai-bo

    2007-01-01

    The immobilization of cytochrome c or horseradish peroxidase at the sulfur-modified gold electrode exhibits a ra-pid electron transfer behavior because of its specific orientation on the electrode surface and the interaction between cytochrome c or horseradish peroxidase and sulfur-modified on the surface of the Au electrode.

  9. Decomposition of SnH4 molecules on metal and metal-oxide surfaces

    NARCIS (Netherlands)

    Ugur, D.; Storm, A.J.; Verberk, R.; Brouwer, J.C.; Sloof, W.G.

    2014-01-01

    Atomic hydrogen cleaning is a promising method for EUV lithography systems, to recover from surface oxidation and to remove carbon and tin contaminants. Earlier studies showed, however, that tin may redeposit on nearby surfaces due to SnH4 decomposition. This phenomenon of SnH4 decomposition during

  10. Synthesis and structure of an "iron-doped" copper selenide cluster molecule: [Cu30Fe2Se6(SePh)24(dppm)4].

    Science.gov (United States)

    Eichhöfer, Andreas; Olkowska-Oetzel, Jolanta; Fenske, Dieter; Fink, Karin; Mereacre, Valeriu; Powell, Annie K; Buth, Gernot

    2009-09-21

    CuCl and bis(diphenylphosphanyl)methane (dppm) react in the presence of small amounts of FeCl(3) with PhSeSiMe(3) and Se(SiMe(3))(2) to yield [Cu(30)Fe(2)Se(6)(SePh)(24)(dppm)(4)]. The crystal structure of the compound was determined by single-crystal X-ray analysis to give a mixed copper selenide/selenolate cluster molecule of a new structural type incorporating two central iron atoms. The formal oxidation state of the iron atoms was determined by Mössbauer spectroscopy to be +3, in agreement with quantum chemical calculations and modeling of the magnetic data. In addition, Mössbauer studies show no magnetic hyperfine structure in zero field, and the magnetically perturbed spectrum displays a pattern typical for a diamagnetic species in a transverse field, suggesting a singlet ground state. However, the inclusion of the iron atoms has a distinct influence on the optical properties of the compound compared to similar clusters containing only copper and selenium atoms.

  11. On the widths of Stokes lines in Raman scattering from molecules adsorbed at metal surfaces and in molecular conduction junctions

    Science.gov (United States)

    Gao, Yi; Galperin, Michael; Nitzan, Abraham

    2016-06-01

    Within a generic model we analyze the Stokes linewidth in surface enhanced Raman scattering (SERS) from molecules embedded as bridges in molecular junctions. We identify four main contributions to the off-resonant Stokes signal and show that under zero voltage bias (a situation pertaining also to standard SERS experiments) and at low bias junctions only one of these contributions is pronounced. The linewidth of this component is determined by the molecular vibrational relaxation rate, which is dominated by interactions with the essentially bosonic thermal environment when the relevant molecular electronic energy is far from the metal(s) Fermi energy(ies). It increases when the molecular electronic level is close to the metal Fermi level so that an additional vibrational relaxation channel due to electron-hole (eh) exciton in the molecule opens. Other contributions to the Raman signal, of considerably broader linewidths, can become important at larger junction bias.

  12. A proposal and a theoretical analysis of an enhanced surface plasmon coupled emission structure for single molecule detection

    Science.gov (United States)

    Uddin, Shiekh Zia; Tanvir, Mukhlasur Rahman; Talukder, Muhammad Anisuzzaman

    2016-05-01

    We propose a structure that can be used for enhanced single molecule detection using surface plasmon coupled emission (SPCE). In the proposed structure, instead of a single metal layer on the glass prism of a typical SPCE structure for fluorescence microscopy, a metal-dielectric-metal structure is used. We theoretically show that the proposed structure significantly decreases the excitation volume of the fluorescently labeled sample, and simultaneously increases the peak SPCE intensity and SPCE power. Therefore, the signal-to-noise ratio and sensitivity of an SPCE based fluorescence microscopy system can be significantly increased using the proposed structure, which will be helpful for enhanced single molecule detection, especially, in a less pure biological sample.

  13. Quantitative Single-Molecule Surface-Enhanced Raman Scattering by Optothermal Tuning of DNA Origami-Assembled Plasmonic Nanoantennas.

    Science.gov (United States)

    Simoncelli, Sabrina; Roller, Eva-Maria; Urban, Patrick; Schreiber, Robert; Turberfield, Andrew J; Liedl, Tim; Lohmüller, Theobald

    2016-11-22

    DNA origami is a powerful approach for assembling plasmonic nanoparticle dimers and Raman dyes with high yields and excellent positioning control. Here we show how optothermal-induced shrinking of a DNA origami template can be employed to control the gap sizes between two 40 nm gold nanoparticles in a range from 1 to 2 nm. The high field confinement achieved with this optothermal approach was demonstrated by detection of surface-enhanced Raman spectroscopy (SERS) signals from single molecules that are precisely placed within the DNA origami template that spans the nanoparticle gap. By comparing the SERS intensity with respect to the field enhancement in the plasmonic hot-spot region, we found good agreement between measurement and theory. Our straightforward approach for the fabrication of addressable plasmonic nanosensors by DNA origami demonstrates a path toward future sensing applications with single-molecule resolution.

  14. Platinum vapor deposition surface-assisted laser desorption/ionization for imaging mass spectrometry of small molecules.

    Science.gov (United States)

    Kawasaki, Hideya; Ozawa, Tomoyuki; Hisatomi, Hirotaka; Arakawa, Ryuichi

    2012-08-30

    Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) allows for the simultaneous detection and imaging of several molecules in a sample. However, when using an organic matrix in the MALDI-IMS of small molecules, inhomogeneous matrix crystallization may yield poorly reproducible peaks in the mass spectra. We describe a solvent-free approach that employs a homogeneously deposited metal nanoparticle layer (or film) for small-molecule detection. Platinum vapor deposition surface-assisted laser desorption/ionization imaging mass spectrometry (Pt vapor deposition SALDI-IMS) of small molecules was performed as a solvent-free and organic-matrix-free method. A commercially available magnetron sputtering device was used for Pt deposition. Vapor deposition of Pt produced a homogenous layer of nanoparticles over the surface of the target imaging sample. The effectiveness of Pt vapor deposition SALDI-IMS was demonstrated for the direct detection of small analytes of inkjet ink on printed paper as well as for various other analytes (saccharides, pigments, and drugs) separated by thin-layer chromatography (TLC), without the need for extraction or concentration processes. The advantage of choosing Pt instead of Au in SALDI-IMS was also shown. A solvent-free approach involving the direct deposition of Pt on samples (SALDI-IMS) is effective for the analysis of inkjet-printed papers and various analytes separated by TLC. This method would be useful in imaging analyses of various insulating materials such as polymers and biological materials. Copyright © 2012 John Wiley & Sons, Ltd.

  15. Testing the Universality of the TIS Model on Cluster Scales from the X-ray Surface Brightness Profiles

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The truncated isothermal sphere (TIS) model has been recently suggested as an alternative for virialized dark halos (Shapiro et al. 1999). Both its profound theoretical motivation and its successful explanations for the galactic rotation curves and the gravitational scaling laws of clusters indicate that the TIS model is a promising candidate among other prevailing models such as the NFW profile and the Burkert profile. This promotes us to re-examine the universality of the TIS model on cluster scales from a different angle. Using an ensemble of X-ray surface brightness profiles of 45 clusters, we test the goodness of fit of the TIS predicted gas distributions to the X-ray data under the assumption of isothermal, hydrostatic equilibrium. Unlike the conventional β model or the NFW/Burkert profile, for which about half of the clusters have the reduced x2v values smaller than 2,the TIS model fails in the fitting of the X-ray surface brightness profiles of clusters in the sense that 38 out of the 45 clusters show x2v > 2. This may constitute a challenge for the universality of the TIS model unless the present analysis is seriously contaminated by other uncertainties including the negligence of non-gravitational heating processes and the unconventional sampling of the X-ray data.

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

    Energy Technology Data Exchange (ETDEWEB)

    Sun, X. [Hefei National Laboratory for Physical Sciences at Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); National Institute for Materials Science, 1-2-1 Sengen, Tsukuba 305-0047 (Japan); Wang, B. [Hefei National Laboratory for Physical Sciences at Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Pratt, A. [National Institute for Materials Science, 1-2-1 Sengen, Tsukuba 305-0047 (Japan); Department of Physics, University of York, York YO10 5DD (United Kingdom); Yamauchi, Y. [National Institute for Materials Science, 1-2-1 Sengen, Tsukuba 305-0047 (Japan)

    2014-07-21

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

  17. Gas surface density, star formation rate surface density, and the maximum mass of young star clusters in a disk galaxy. I. The flocculent galaxy M33

    CERN Document Server

    Gonzalez-Lopezlira, Rosa A; Kroupa, Pavel

    2012-01-01

    We analyze the relationship between maximum cluster mass, M_max, and surface densities of total gas (Sigma_gas), molecular gas (Sigma_H2) and star formation rate (Sigma_SFR) in the flocculent galaxy M33, using published gas data and a catalog of more than 600 young star clusters in its disk. By comparing the radial distributions of gas and most massive cluster masses, we find that M_max is proportional to Sigma_gas^4.7, M_max is proportional Sigma_H2^1.3, and M_max is proportional to Sigma_SFR^1.0. We rule out that these correlations result from the size of sample; hence, the change of the maximum cluster mass must be due to physical causes.

  18. The properties of Irn (n = 2-10) clusters and their nucleation on γ-Al₂O₃ and MgO surfaces: from ab initio studies.

    Science.gov (United States)

    Chen, Yongchang; Huo, Miao; Chen, Tong; Li, Qiang; Sun, Zhaolin; Song, Lijuan

    2015-01-21

    The structural stability and magnetic properties of iridium clusters Irn (n = 2-10) and their interaction on γ-Al2O3(001) and MgO(100) surfaces have been investigated from first principles calculations. It is found that the adsorption energy of Irn (n = 2-10)/γ-Al2O3(001) is lower than that of Irn/MgO(100); meanwhile, the strongest adsorption energy cluster for γ-Al2O3(001) is the tetrahedral Ir4 cluster, while for MgO(100) is a cubic Ir8 cluster. On the other hand, the nucleation of Irn (n = 2-10) clusters on both surfaces is thermodynamically favorable and exothermic. Moreover, the nucleation energy of Irn (n = 2-10) clusters on the γ-Al2O3(001) surface is close to the corresponding energy on the MgO(100) surface, except for Ir3, Ir4 and Ir6 clusters. Interestingly, the nucleation of Ir3 and Ir6 clusters on the MgO(100) surface is more favorable than that on the γ-Al2O3(001) surface, while the nucleation of the Ir4 cluster is reverse and very close to the gas phase Ir4 cluster. More importantly, deformation energy and charge density analysis show that the adsorbed Ir4 cluster on the γ-Al2O3(001) surface has obviously charge transfer between Ir atoms and surface Al, O atoms with negligible deformation. However, for the MgO(100) surface, the Ir4 cluster connects directly to three surface O atoms with severe distortion, which inhibits the activity of the tetrahedral Ir4 cluster as a catalyst.

  19. Surface Density of dark matter haloes on galactic and cluster scales

    CERN Document Server

    Del Popolo, A; Belvedere, G

    2013-01-01

    In this paper, in the framework of the secondary infall model, the correlation between the central surface density and the halo core radius of galaxy, and cluster of galaxies, dark matter haloes was analyzed, this having recently been studied on a wide range of scales. We used Del Popolo (2009) secondary infall model taking into account ordered and random angular momentum, dynamical friction, and dark matter (DM) adiabatic contraction to calculate the density profile of haloes, and then these profiles are used to determine the surface density of DM haloes. The main result is that $r_\\ast$ (the halo characteristic radius) is not an universal quantity as claimed by Donato et al. (2009) and Gentile et al. (2009). On the contrary, we find a correlation with the halo mass $M_{200}$ in agreement with Cardone & Tortora (2010), Boyarsky at al. (2009) and Napolitano et al. (2010), but with a significantly smaller scatter, namely $0.16 \\pm 0.05$. We also consider the baryon column density finding this latter being ...

  20. Role of different Skyrme forces and surface corrections in exotic cluster decay

    Indian Academy of Sciences (India)

    Narinder K Dhiman; Ishwar Dutt

    2011-03-01

    We present cluster-decay studies of 56Ni∗ formed in heavy-ion collisions using different Skyrme forces. Our study reveals that different Skyrme forces do not alter the transfer structure of fractional yields significantly. The cluster decay half-lives of different clusters lie within ± 10% for preformed cluster models (PCM) and ± 15% for unified fission models (UFM)