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Sample records for single molecular monolayer

  1. Monolayer atomic crystal molecular superlattices

    Science.gov (United States)

    Wang, Chen; He, Qiyuan; Halim, Udayabagya; Liu, Yuanyue; Zhu, Enbo; Lin, Zhaoyang; Xiao, Hai; Duan, Xidong; Feng, Ziying; Cheng, Rui; Weiss, Nathan O.; Ye, Guojun; Huang, Yun-Chiao; Wu, Hao; Cheng, Hung-Chieh; Shakir, Imran; Liao, Lei; Chen, Xianhui; Goddard, William A., III; Huang, Yu; Duan, Xiangfeng

    2018-03-01

    Artificial superlattices, based on van der Waals heterostructures of two-dimensional atomic crystals such as graphene or molybdenum disulfide, offer technological opportunities beyond the reach of existing materials. Typical strategies for creating such artificial superlattices rely on arduous layer-by-layer exfoliation and restacking, with limited yield and reproducibility. The bottom-up approach of using chemical-vapour deposition produces high-quality heterostructures but becomes increasingly difficult for high-order superlattices. The intercalation of selected two-dimensional atomic crystals with alkali metal ions offers an alternative way to superlattice structures, but these usually have poor stability and seriously altered electronic properties. Here we report an electrochemical molecular intercalation approach to a new class of stable superlattices in which monolayer atomic crystals alternate with molecular layers. Using black phosphorus as a model system, we show that intercalation with cetyl-trimethylammonium bromide produces monolayer phosphorene molecular superlattices in which the interlayer distance is more than double that in black phosphorus, effectively isolating the phosphorene monolayers. Electrical transport studies of transistors fabricated from the monolayer phosphorene molecular superlattice show an on/off current ratio exceeding 107, along with excellent mobility and superior stability. We further show that several different two-dimensional atomic crystals, such as molybdenum disulfide and tungsten diselenide, can be intercalated with quaternary ammonium molecules of varying sizes and symmetries to produce a broad class of superlattices with tailored molecular structures, interlayer distances, phase compositions, electronic and optical properties. These studies define a versatile material platform for fundamental studies and potential technological applications.

  2. Molecular diffusion in monolayer and submonolayer nitrogen

    DEFF Research Database (Denmark)

    Hansen, Flemming Yssing; Bruch, Ludwig Walter

    2001-01-01

    The orientational and translational motions in a monolayer fluid of physisorbed molecular nitrogen are treated using molecular dynamics simulations. Dynamical response functions and several approximations to the coefficient of translational diffusion are determined for adsorption on the basal plane...

  3. Langmuir monolayers composed of single and double tail sulfobetaine lipids.

    Science.gov (United States)

    Hazell, Gavin; Gee, Anthony P; Arnold, Thomas; Edler, Karen J; Lewis, Simon E

    2016-07-15

    Owing to structural similarities between sulfobetaine lipids and phospholipids it should be possible to form stable Langmuir monolayers from long tail sulfobetaines. By modification of the density of lipid tail group (number of carbon chains) it should also be possible to modulate the two-dimensional phase behaviour of these lipids and thereby compare with that of equivalent phospholipids. Potentially this could enable the use of such lipids for the wide array of applications that currently use phospholipids. The benefit of using sulfobetaine lipids is that they can be synthesised by a one-step reaction from cheap and readily available starting materials and will degrade via different pathways than natural lipids. The molecular architecture of the lipid can be easily modified allowing the design of lipids for specific purposes. In addition the reversal of the charge within the sulfobetaine head group relative to the charge orientation in phospholipids may modify behaviour and thereby allow for novel uses of these surfactants. Stable Langmuir monolayers were formed composed of single and double tailed sulfobetaine lipids. Surface pressure-area isotherm, Brewster Angle Microscopy and X-ray and neutron reflectometry measurements were conducted to measure the two-dimensional phase behaviour and out-of-plane structure of the monolayers as a function of molecular area. Sulfobetaine lipids are able to form stable Langmuir monolayers with two dimensional phase behaviour analogous to that seen for the well-studied phospholipids. Changing the number of carbon tail groups on the lipid from one to two promotes the existence of a liquid condensed phase due to increased Van der Waals interactions between the tail groups. Thus the structure of the monolayers appears to be defined by the relative sizes of the head and tail groups in a predictable way. However, the presence of sub-phase ions has little effect on the monolayer structure, behaviour that is surprisingly different to

  4. Investigation of the geometrical arrangement and single molecule charge transport in self-assembled monolayers of molecular towers based on tetraphenylmethane tripod

    Czech Academy of Sciences Publication Activity Database

    Sebechlebská, T.; Šebera, Jakub; Kolivoška, Viliam; Lindner, M.; Gasior, Jindřich; Meszáros, G.; Valášek, M.; Mayor, M.; Hromadová, Magdaléna

    2017-01-01

    Roč. 258, DEC 20 (2017), s. 1191-1200 ISSN 0013-4686 R&D Projects: GA ČR GJ16-07460Y Grant - others:AV ČR(CZ) MTA-16-02 Program:Bilaterální spolupráce Institutional support: RVO:61388955 Keywords : molecular electronics * multipodal platforms * reductive desorption of self-assembled monolayers Subject RIV: CG - Electrochemistry OBOR OECD: Electrochemistry (dry cells, batteries, fuel cells, corrosion metals, electrolysis) Impact factor: 4.798, year: 2016

  5. Electronic properties of organic monolayers and molecular devices

    Indian Academy of Sciences (India)

    E-mail: dominique.vuillaume@iemn.univ-lille1.fr. Abstract. We review some of our recent experimental results on charge transport in or- ganic nanostructures such as self-assembled monolayer and monolayers of organic semicon- ductors. We describe a molecular rectifying junction made from a sequential self-assembly.

  6. Unsupported single-atom-thick copper oxide monolayers

    Science.gov (United States)

    Yin, Kuibo; Zhang, Yu-Yang; Zhou, Yilong; Sun, Litao; Chisholm, Matthew F.; Pantelides, Sokrates T.; Zhou, Wu

    2017-03-01

    Oxide monolayers may present unique opportunities because of the great diversity of properties of these materials in bulk form. However, reports on oxide monolayers are still limited. Here we report the formation of single-atom-thick copper oxide layers with a square lattice both in graphene pores and on graphene substrates using aberration-corrected scanning transmission electron microscopy. First-principles calculations find that CuO is energetically stable and its calculated lattice spacing matches well with the measured value. Furthermore, free-standing copper oxide monolayers are predicted to be semiconductors with band gaps ∼3 eV. The new wide-bandgap single-atom-thick copper oxide monolayers usher a new frontier to study the highly diverse family of two-dimensional oxides and explore their properties and their potential for new applications.

  7. Mixed DPPC/POPC Monolayers: All-atom Molecular Dynamics Simulations and Langmuir Monolayer Experiments

    Czech Academy of Sciences Publication Activity Database

    Olžyńska, Agnieszka; Zubek, M.; Roeselová, Martina; Korchowiec, J.; Cwiklik, Lukasz

    2016-01-01

    Roč. 1858, č. 12 (2016), s. 3120-3130 ISSN 0005-2736 R&D Projects: GA ČR GA15-14292S Institutional support: RVO:61388955 ; RVO:61388963 Keywords : phospholipid monolayers * Lung surfactant * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.498, year: 2016

  8. Molecular tilt on monolayer-protected nanoparticles

    KAUST Repository

    Giomi, L.

    2012-02-01

    The structure of the tilted phase of monolayer-protected nanoparticles is investigated by means of a simple Ginzburg-Landau model. The theory contains two dimensionless parameters representing the preferential tilt angle and the ratio ε between the energy cost due to spatial variations in the tilt of the coating molecules and that of the van der Waals interactions which favors the preferential tilt. We analyze the model for both spherical and octahedral particles. On spherical particles, we find a transition from a tilted phase, at small ε, to a phase where the molecules spontaneously align along the surface normal and tilt disappears. Octahedral particles have an additional phase at small ε characterized by the presence of six topological defects. These defective configurations provide preferred sites for the chemical functionalization of monolayer-protected nanoparticles via place-exchange reactions and their consequent linking to form molecules and bulk materials. Copyright © EPLA, 2012.

  9. Functional Molecular Junctions Derived from Double Self-Assembled Monolayers.

    Science.gov (United States)

    Seo, Sohyeon; Hwang, Eunhee; Cho, Yunhee; Lee, Junghyun; Lee, Hyoyoung

    2017-09-25

    Information processing using molecular junctions is becoming more important as devices are miniaturized to the nanoscale. Herein, we report functional molecular junctions derived from double self-assembled monolayers (SAMs) intercalated between soft graphene electrodes. Newly assembled molecular junctions are fabricated by placing a molecular SAM/(top) electrode on another molecular SAM/(bottom) electrode by using a contact-assembly technique. Double SAMs can provide tunneling conjugation across the van der Waals gap between the terminals of each monolayer and exhibit new electrical functions. Robust contact-assembled molecular junctions can act as platforms for the development of equivalent contact molecular junctions between top and bottom electrodes, which can be applied independently to different kinds of molecules to enhance either the structural complexity or the assembly properties of molecules. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Biomembrane modeling: molecular dynamics simulation of phospholipid monolayers

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, T.R.

    1979-01-01

    As a first step toward a computer model of a biomembrane-like bilayer, a dynamic, deterministric model of a phospholipid monolayer has been constructed. The model moves phospholipid-like centers of force according to an integrated law of motion in finite difference form. Forces on each phospholipid analogue are derived from the gradient of the local potential, itself the sum of Coulombic and short-range terms. The Coulombic term is approximated by use of a finite-difference form of Poisson's equation, while the short-range term results from finite-radius, pairwise summation of a Lennard-Jones potential. Boundary potentials are treated in such a way that the model is effectively infinite in extent in the plane of the monolayer. The two-dimensional virial theorem is used to find the surface pressure of the monolayer as a function of molecular area. Pressure-versus-area curves for simulated monolayers are compared to those of real monolayers. Dependence of the simulator's behavior on Lennard-Jones parameters and the specific geometry of the molecular analogue is discussed. Implications for the physical theory of phospholipid monolayers and bilayers are developed.

  11. Synthesis of Triptycene-Based Molecular Rotors for Langmuir-Blodgett Monolayers.

    Science.gov (United States)

    Kaleta, Jiří; Kaletová, Eva; Císařová, Ivana; Teat, Simon J; Michl, Josef

    2015-10-16

    We describe syntheses of six triptycene-containing molecular rotors with several single-crystal X-ray diffraction analyses. These rod-shaped molecules carrying an axial rotator are designed to interleave on an aqueous surface into Langmuir-Blodgett (LB) monolayers containing a two-dimensional trigonal array of dipoles rotatable about an axis normal to the surface. Monolayer formation was verified with the simplest of the rotor structures. On an aqueous subphase containing divalent cations (Mg(2+), Ca(2+), Zn(2+), Sr(2+), or Cd(2+)), the LB isotherm yielded an area of 53 ± 3 Å(2)/molecule (monolayer of type A), compatible with the anticipated triangular packing of axes normal to the surface. On pure water, the area is 30 ± 3 Å(2)/molecule, and it is proposed that in this monolayer (type B), the molecular axes are tilted by 40-45° to a structure similar to those observed in single crystals of related triptycenes. After transfer to a gold surface, ellipsometry and PM IRRAS yield tilt angles of 29 ± 4° (monolayers of type A) and 38 ± 4° (type B). A full-scale examination of monolayers from all the rotors on a subphase and after transfer is underway and will be reported separately.

  12. Impact of Anchoring Groups on Ballistic Transport: Single Molecule vs Monolayer Junctions

    Science.gov (United States)

    2015-01-01

    Tuning the transport properties of molecular junctions by chemically modifying the molecular structure is one of the key challenges for advancing the field of molecular electronics. In the present contribution, we investigate current–voltage characteristics of differently linked metal–molecule–metal systems that comprise either a single molecule or a molecular assembly. This is achieved by employing density functional theory in conjunction with a Green’s function approach. We show that the conductance of a molecular system with a specific anchoring group is fundamentally different depending on whether a single molecule or a continuous monolayer forms the junction. This is a consequence of collective electrostatic effects that arise from dipolar elements contained in the monolayer and from interfacial charge rearrangements. As a consequence of these collective effects, the “ideal” choice for an anchoring group is clearly different for monolayer and single molecule devices. A particularly striking effect is observed for pyridine-docked systems. These are subject to Fermi-level pinning at high molecular packing densities, causing an abrupt increase of the junction current already at small voltages. PMID:26401191

  13. Molecular Electronics of Self-Assembled Monolayers

    DEFF Research Database (Denmark)

    Wang, Xintai

    This thesis deals withmolecular electronic investigations on self-assembledmonolayers. The thesis is divided into seven chapters, as outlined below.Chapter 1 is a general introduction of the history of molecular electronics and its current state.Chapter 2 is separated into three parts. Part I...... providesa brief introduction toself-assembledmonolayers(SAMs), includingits structure, formation, and its role in molecular electronic investigations. Part II is an introduction of different molecular functions, which are interesting for designing real devices. Part III is an introduction of a novel carbon...... material: graphene, and how such material can be incorporated intothe field of molecular electronics.Chapter 3 is a brief introduction of important instruments used in this thesis.Chapter 4, 5 and 6 describe the major experimental work in this thesis. Chapter 4 introduces two novel anchoring...

  14. Doping monolayer graphene with single atom substitutions

    KAUST Repository

    Wang, Hongtao

    2012-01-11

    Functionalized graphene has been extensively studied with the aim of tailoring properties for gas sensors, superconductors, supercapacitors, nanoelectronics, and spintronics. A bottleneck is the capability to control the carrier type and density by doping. We demonstrate that a two-step process is an efficient way to dope graphene: create vacancies by high-energy atom/ion bombardment and fill these vacancies with desired dopants. Different elements (Pt, Co, and In) have been successfully doped in the single-atom form. The high binding energy of the metal-vacancy complex ensures its stability and is consistent with in situ observation by an aberration-corrected and monochromated transmission electron microscope. © 2011 American Chemical Society.

  15. Modulating the electronic and optical properties of monolayer arsenene phases by organic molecular doping

    Science.gov (United States)

    Singh, Deobrat; Gupta, Sanjeev K.; Sonvane, Yogesh; Sahoo, Satyaprakash

    2017-12-01

    Recently, arsenene monolayer structure of the arsenic with two phases has displayed semiconducting behavior. We have systematically investigated the electronic and optical properties of single-layer arsenene with two types of functionalized organic molecules; an electrophilic molecule [tetracyanoquinodimethane (TCNQ)] and a nucleophilic molecule [tetrathiafulvalene (TTF)], as an electron acceptor and electron donor, respectively. The interfacial charge transfer between the arsenene monolayer and TCNQ/TTF molecules extensively reduces the band gap of arsenene and accordingly resulted in a p- or n-type semiconducting behavior, respectively. We have also performed the interfacial charge transfer from organic molecules to monolayer arsenene and vice versa. The interfacial surface molecular modification has established an efficient way to develop the light harvesting of arsenene in different polarization directions. Our theoretical investigation suggests that such n- and p-type arsenene semiconductors would broaden the applications in the field of nanoelectronic and optoelectronic devices such as photodiodes and it is also useful for constructing functional electronic systems.

  16. Simulation of a lipid monolayer using molecular dynamics

    Science.gov (United States)

    Kox, A. J.; Michels, J. P. J.; Wiegel, F. W.

    1980-09-01

    Numerical simulation is often a useful tool f or investigating the behaviour of complex systems with many degrees of freedom. Of the two major methods in this field, the Monte Carlo method and the molecular dynamics method, only the first has been applied to realistic models of lipid monolayers1-5. The term lipid monolayer is used here to describe a class of systems consisting of chain molecules on a liquid substrate, the characteristic properties of which can be summarized as follows. (1) The constituent molecules are amphipathic, that is they consist of a hydrophilic (polar) head group and one or more hydrophobic hydrocarbon chains. (2) Due to the amphipathic character of the molecules, the head groups are constrained to the plane of the substrate, whereas the tails are directed outwards from this plane. (3) The collective properties of the molecules are determined by their short-range repulsive and long-range attractive interactions and by the steric repulsion of the tails. We now present what we believe to be the first molecular dynamics simulation of a realistic model of a lipid monolayer. The model system, which has all three properties enumerated above, shows a first order phase transition from an ordered fluid-like state to a disordered, gas-like state.

  17. Molecular scale energy dissipation in oligothiophene monolayers measured by dynamic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Martinez, Nicolas F; Gomez, Carlos J; Garcia, Ricardo [CSIC-Instituto de Microelectronica de Madrid (IMM), Isaac Newton 8, E-28760 Tres Cantos, Madrid (Spain); Kaminski, Wojciech [Institute of Experimental Physics, University of Wroclaw, plac Maksa Borna 9, PL-50-204 Wroclaw (Poland); Albonetti, Cristiano; Biscarini, Fabio [CNR-Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), Via P Gobetti 101, I-40129 Bologna (Italy); Perez, Ruben, E-mail: ruben.perez@uam.e, E-mail: rgarcia@imm.cnm.csic.e [Departamento de Fisica Teorica de la Materia Condensada, Universidad Autonoma de Madrid, E-28049 Madrid (Spain)

    2009-10-28

    We perform a combined experimental and theoretical approach to establish the atomistic origin of energy dissipation occurring while imaging a molecular surface with an amplitude modulation atomic force microscope. We show that the energy transferred by a single nano-asperity to a sexithiophene monolayer is about 0.15 eV/cycle. The configuration space sampled by the tip depends on whether it approaches or withdraws from the surface. The asymmetry arises because of the presence of energy barriers among different deformations of the molecular geometry. This is the source of the material contrast provided by the phase-shift images.

  18. Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations

    NARCIS (Netherlands)

    Baoukina, Svetlana; Monticelli, Luca; Marrink, Siewert J.; Tieleman, D. Peter

    2007-01-01

    We calculated the pressure-area isotherm of a dipalmitoyl-phosphatidylcholine (DPPC) lipid monolayer from molecular dynamics simulations using a coarse-grained molecular model. We characterized the monolayer structure, geometry, and phases directly from the simulations and compared the calculated

  19. Surface Charge Transfer Doping of Monolayer Phosphorene via Molecular Adsorption.

    Science.gov (United States)

    He, Yuanyuan; Xia, Feifei; Shao, Zhibin; Zhao, Jianwei; Jie, Jiansheng

    2015-12-03

    Monolayer phosphorene has attracted much attention owing to its extraordinary electronic, optical, and structural properties. Rationally tuning the electrical transport characteristics of monolayer phosphorene is essential to its applications in electronic and optoelectronic devices. Herein, we study the electronic transport behaviors of monolayer phosphorene with surface charge transfer doping of electrophilic molecules, including 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ), NO2, and MoO3, using density functional theory combined with the nonequilibrium Green's function formalism. F4TCNQ shows optimal performance in enhancing the p-type conductance of monolayer phosphorene. Static electronic properties indicate that the enhancement is originated from the charge transfer between adsorbed molecule and phosphorene layer. Dynamic transport behaviors demonstrate that additional channels for hole transport in host monolayer phosphorene were generated upon the adsorption of molecule. Our work unveils the great potential of surface charge transfer doping in tuning the electronic properties of monolayer phosphorene and is of significance to its application in high-performance devices.

  20. Molecular modeling of alkyl and alkenyl monolayers on hydrogen-terminated Si(111).

    Science.gov (United States)

    Scheres, Luc; Rijksen, Bart; Giesbers, Marcel; Zuilhof, Han

    2011-02-01

    On H-Si(111) surfaces monolayer formation with 1-alkenes results in alkyl monolayers with a Si-C-C linkage, while 1-alkynes yield alkenyl monolayers with a Si-C═C linkage. Recently, considerable structural differences between both types of monolayers were observed, including an increased thickness, improved packing, and higher surface coverage for the alkenyl monolayers. The precise origin thereof could experimentally not be clarified yet. Therefore, octadecyl and octadecenyl monolayers on Si(111) were studied in detail by molecular modeling via PCFF molecular mechanics calculations on periodically repeated slabs of modified surfaces. After energy minimization the packing energies, structural properties, close contacts, and deformations of the Si surfaces of monolayers structures with various substitution percentages and substitution patterns were analyzed. For the octadecyl monolayers all data pointed to a substitution percentage close to 50-55%, which is due the size of the CH(2) groups near the Si surface. This agrees with literature and the experimentally determined coverage of octadecyl monolayers. For the octadecenyl monolayers the minimum in packing energy per chain is calculated around 60% coverage, i.e., close to the experimentally observed value of 65% [Scheres et al. Langmuir 2010, 26, 4790], and this packing energy is less dependent on the substitution percentage than calculated for alkyl layers. Analysis of the chain conformations, close contacts, and Si surface deformation clarifies this, since even at coverages above 60% a relatively low number of close contacts and a negligible deformation of the Si was observed. In order to evaluate the thermodynamic feasibility of the monolayer structures, we estimated the binding energies of 1-alkenes and 1-alkynes to the hydrogen-terminated Si surface at a range of surface coverages by composite high-quality G3 calculations and determined the total energy of monolayer formation by adding the packing energies

  1. Probing molecular interactions with methylene blue derivatized self-assembled monolayers

    Directory of Open Access Journals (Sweden)

    Eleni Koutsoumpeli

    2015-12-01

    Full Text Available The emergence of stratified and personalised medicine and the associated need for highly multiplexed detection strategies are driving the development of innovative sensor technology. Electronic immunosensor arrays capable of label-free and highly parallel monitoring of ligand binding have emerged as a particularly promising technology capable of meeting these new diagnostic challenges. In this study, we present an approach for interrogating molecular interactions electronically using redox active molecular monolayers. Specifically, we have synthesised self-assembled molecular monolayers assembled from long-chain alkanethiols (LCAT incorporating oligoethyleneglycol (OEG linkers that can be derivatized with a range of functional groups, including the redox active molecule methylene blue. Critically, we show that the electron transport properties of this redox-active monolayer are highly sensitive to the electrochemical environment, including the local concentration of protons and the electrostatic potential at the plane of electron transfer. Using a combination of cyclic voltammetry and QCM-D to study in detail the behaviour of the monolayer during functionalisation and analyte binding, we demonstrate that these redox properties can be exploited for the electrochemical sensing of molecular interactions (biotin–avidin in our case on SAMs. Given the versatility of LCAT-OEG monolayers, in terms of linker lengths, choice of functional group, and ability to create mixed component layers and the straight-forward assembly of mixed SAMs of high quality, our electrochemical sensing approach forms an excellent and generic label-free platform for probing a wide range of molecular interactions.

  2. Binary self-assembled monolayers: Apparent exponential dependence of resistance on average molecular length

    NARCIS (Netherlands)

    Katsouras, I.; Geskin, V.; Kronemeijer, A.J.; Blom, P.W.M.; Leeuw, D.M. de

    2011-01-01

    We investigate the electrical transport through mixed self-assembled monolayers of alkanemonothiols and alkanedithiols in large-area molecular junctions. To disentangle the role of the molecular length and the interfacial composition, monothiol-monothiol, dithiol-dithiol, and monothiol-dithiol

  3. Binary self-assembled monolayers : Apparent exponential dependence of resistance on average molecular length

    NARCIS (Netherlands)

    Katsouras, Ilias; Geskin, Victor; Kronemeijer, Auke J.; Blom, Paul W. M.; de Leeuw, Dago M.

    We investigate the electrical transport through mixed self-assembled monolayers of alkanemonothiols and alkanedithiols in large-area molecular junctions. To disentangle the role of the molecular length and the interfacial composition, monothiol-monothiol, dithiol-dithiol, and monothiol-dithiol

  4. Interpretation of single and competitive adsorption of cadmium and zinc on activated carbon using monolayer and exclusive extended monolayer models.

    Science.gov (United States)

    Sellaoui, Lotfi; Dotto, Guilherme L; Lamine, Abdelmottaleb Ben; Erto, Alessandro

    2017-08-01

    In this work, a modeling analysis based on experimental tests of cadmium/zinc adsorption, in both single-compound and binary systems, was carried out. All the experimental tests were conducted at constant pH (around neutrality) and temperature (20 °C). The experimental results showed that the zinc adsorption capacity was higher than that of cadmium and it does not depend on cadmium presence in binary system. Conversely, cadmium adsorption is affected by zinc presence. In order to provide good understanding of the adsorption process, two statistical physics models were proposed. A monolayer and exclusive extended monolayer models were applied to interpret the single-compound and binary adsorption isotherms of zinc and cadmium on activated carbon. Based on these models, the modeling analysis demonstrated that zinc is dominant in solution and more favorably adsorbed on activated carbon surface. For instance, in single-compound systems, the number of ions bound per each receptor site was n (Zn 2+ ) = 2.12 > n (Cd 2+ ) = 0.98. Thus, the receptor sites of activated carbon are more selective for Zn 2+ than for Cd 2+ . Moreover, the determination of adsorption energy through the adopted models confirmed that zinc is more favored for adsorption in single-compound system (adsorption energies equal to 12.12 and 7.12 kJ/mol for Zn and Cd, respectively) and its adsorption energy does not depend on the cadmium presence in binary system. Finally, the adsorption energy values suggested that single-compound and binary adsorption of zinc and cadmium is a physisorption.

  5. Interactions of phospholipid monolayer with single-walled carbon nanotube wrapped by lysophospholipid

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Siwool; Kim, Hyungsu, E-mail: hkim@dku.edu

    2012-10-01

    In this study, we prepared single-walled carbon nanotubes (SWNTs) wrapped by 1-stearoyl-2-hydroxy-sn-glycero-3-phospho-(1 Prime -rac-glycerol) (LPG), leading to a complex of SWNT-LPG. In an attempt to investigate the interactions of SWNT-LPG with a mimicked cell surface, SWNT-LPG solution was injected into the sub-phase of Langmuir trough to form a mixed monolayer with dipalmitoylphosphatidylcholine (DPPC) and dipalmitoylphosphatidylglycerol (DPPG), respectively. In addition to the measurement of typical surface pressure-area isotherms under compression mode, area changes occurring during insertion of SWNT-LPG into the monolayer were recorded at various surface pressures. Changes in surface potential were also measured for evident tracing of the degree of interactions between sub-phase and monolayer. A systematic comparison of relaxation patterns and insertion behavior along with surface potential data provided a rational basis to distinguish the degree of interactions between SWNT-LPG and the designated monolayer. The observed tendencies were found to be in accordance with the surface topography as revealed by the tapping mode atomic force microscopy. It was consistently observed that SWNT-LPG interacted with DPPC to a greater extent than with DPPG, when the sufficient coverage of nanotube surface by LPG molecules was assured. - Highlights: Black-Right-Pointing-Pointer Complex of single-walled carbon nanotubes and lysophospholipid (SWNT-LPG) is formed. Black-Right-Pointing-Pointer Composite monolayer is formed by inserting SWNT-LPG into the phospholipid monolayer. Black-Right-Pointing-Pointer We measure area-pressure responses and dipole potentials during the insertion process. Black-Right-Pointing-Pointer Properties of composite monolayer depend on the kind of phospholipid and LPG content.

  6. Electron tunneling through alkanedithiol self-assembled monolayers in large-area molecular junctions

    NARCIS (Netherlands)

    Akkerman, Hylke B.; Naber, Ronald C. G.; Jongbloed, Bert; van Hal, Paul A.; Blom, Paul W. M.; de Leeuw, Dago M.; de Boer, Bert

    2007-01-01

    The electrical transport through self-assembled monolayers of alkanedithiols was studied in large-area molecular junctions and described by the Simmons model [Simmons JIG (1963) J Appi Phys 34:1793-1803 and 2581-2590] for tunneling through a practical barrier, i.e., a rectangular barrier with the

  7. Molecular monolayers for electrical passivation and functionalization of silicon-based solar energy devices

    NARCIS (Netherlands)

    Veerbeek, Janneke; Firet, Nienke J.; Vijselaar, Wouter; Elbersen, R.; Gardeniers, Han; Huskens, Jurriaan

    2017-01-01

    Silicon-based solar fuel devices require passivation for optimal performance yet at the same time need functionalization with (photo)catalysts for efficient solar fuel production. Here, we use molecular monolayers to enable electrical passivation and simultaneous functionalization of silicon-based

  8. Molecular structure of dipalmitoylphospatidylcholine Langmuir-Blodgett monolayers studied by atomic force microscopy.

    NARCIS (Netherlands)

    Zhai, X.; Kleijn, J.M.

    1997-01-01

    Monolayers of dipalmitoylphosphatidylcholine (DPPC) on the air-water interface have been transferred at various surface pressures onto quartz substrates using the Langmuir-Blodgett (LB) technique. The topography of these layers, on a molecular scale, has been examined by atomic force microscopy

  9. Linear hydrogen adsorbate structures on graphite induced by self-assembled molecular monolayers

    DEFF Research Database (Denmark)

    Nilsson, Louis; Sljivancanin, Zeljko; Balog, Richard

    2012-01-01

    Combined scanning tunnelling microscopy measurements and density functional theory calculations reveal a method to induce linear structures of hydrogen adsorbates on graphite by covering the surface with a self-assembled molecular monolayer of cyanuric acid and exposing it to atomic hydrogen...

  10. Single-Nanoparticle Plasmonic Electro-optic Modulator Based on MoS2Monolayers.

    Science.gov (United States)

    Li, Bowen; Zu, Shuai; Zhou, Jiadong; Jiang, Qiao; Du, Bowen; Shan, Hangyong; Luo, Yang; Liu, Zheng; Zhu, Xing; Fang, Zheyu

    2017-10-24

    The manipulation of light in an integrated circuit is crucial for the development of high-speed electro-optic devices. Recently, molybdenum disulfide (MoS 2 ) monolayers generated broad interest for the optoelectronics because of their huge exciton binding energy, tunable optical emission, direct electronic band-gap structure, etc. Miniaturization and multifunctionality of electro-optic devices further require the manipulation of light-matter interaction at the single-nanoparticle level. The strong exciton-plasmon interaction that is generated between the MoS 2 monolayers and metallic nanostructures may be a possible solution for compact electro-optic devices at the nanoscale. Here, we demonstrate a nanoplasmonic modulator in the visible spectral region by combining the MoS 2 monolayers with a single Au nanodisk. The narrow MoS 2 excitons coupled with broad Au plasmons result in a deep Fano resonance, which can be switched on and off by applying different gate voltages on the MoS 2 monolayers. A reversible display device that is based on this single-nanoparticle modulator is demonstrated with a heptamer pattern that is actively controlled by the external gates. Our work provides a potential application for electro-optic modulation on the nanoscale and promotes the development of gate-tunable nanoplasmonic devices in the future.

  11. Studies of the surface structures of molecular crystals and of adsorbed molecular monolayers on the (111) crystal faces of platinum and silver by low-energy electron diffraction

    International Nuclear Information System (INIS)

    Firment, L.E.

    1977-01-01

    The structures of molecular crystal surfaces were investigated for the first time by the use of low-energy electron diffraction (LEED). The experimental results from a variety of molecular crystals were examined and compared as a first step towards understanding the properties of these surfaces on a microscopic level. The method of sample preparation employed, vapor deposition onto metal single-crystal substrates at low temperatures in ultrahigh vacuum, allowed concurrent study of the structures of adsorbed monolayers on metal surfaces and of the growth processes of molecular films on metal substrates. The systems investigated were ice, ammonia, naphthalene, benzene, the n-paraffins (C 3 to C 8 ), cyclohexane, trioxane, acetic acid, propionic acid, methanol, and methylamine adsorbed and condensed on both Pt(111) and Ag(111) surfaces. Electron-beam-induced damage of the molecular surfaces was observed after electron exposures of 10 -4 A sec cm -2 at 20 eV. Aromatic molecular crystal samples were more resistant to damage than samples of saturated molecules. The quality and orientation of the grown molecular crystal films were influenced by substrate preparation and growth conditions. Forty ordered monolayer structures were observed. 110 figures, 22 tables, 162 references

  12. Electronic properties of organic monolayers and molecular devices

    Indian Academy of Sciences (India)

    Institut d'Electronique, de Micro-electronique et de Nanotechnologie, CNRS, Molecular Nanostructures and Devices Group, BP69, Avenue Poincaré, 59652 Villeneuve d'Ascq Cedex, France; Centre de Recherche en Sciences et Technologies de l'Information et de la Communication, Université de Reims, BP 1039, 51687 ...

  13. The mechanics-modulated tunneling spectrum and low-pass effect of viscoelastic molecular monolayer

    Science.gov (United States)

    Chen, Yun; Zhang, Xiaoyue; Shao, Jian; Yu, Jing; Wang, Biao; Zheng, Yue

    2017-10-01

    Understanding the force-induced conductance fluctuation in molecules is essential for building molecular devices with high stability. While stiffness of molecule is usually considered to be desirable for stable conductance, we demonstrate mechanical dragging in viscoelastic molecules integrates both noise resistance and mechanical controllability to molecular conductance. Via conductive atomic force microscope measurement and theoretical modeling, it's found that viscoelastic Azurin monolayer has spectrum-like pattern of conductance corresponding to the duration and strength of applied mechanical pulse under low-frequency excitation. Conductance fluctuation is prevented under high-frequency excitation by dragging dissipation, which qualifies molecular junction with electric robustness against mechanical noise.

  14. Tetrairon(III) single-molecule magnet monolayers on gold: insights from ToF-SIMS and isotopic labeling.

    Science.gov (United States)

    Totaro, Pasquale; Poggini, Lorenzo; Favre, Annaick; Mannini, Matteo; Sainctavit, Philippe; Cornia, Andrea; Magnani, Agnese; Sessoli, Roberta

    2014-07-29

    To work as magnetic components in molecular electronics and spintronics, single-molecule magnets (SMMs) must be reliably interfaced with metals. The organization on gold of a Fe4 SMM carrying two acetyl-protected thiol groups has been studied by exploiting the surface sensitivity of time-of-flight secondary ion mass spectrometry (ToF-SIMS), additionally powered by the use of an isotopic labeling strategy. Deposition from millimolar dichloromethane solutions results in a higher surface coverage and better packed monolayers as compared with previous protocols based on more diluted solutions. Fe4 complexes are chemically tethered to the surface via a single Au-S bond while they still contain an intact SAc group.

  15. Oxygen and hydroxyl adsorption on MS{sub 2} (M = Mo, W, Hf) monolayers: a first-principles molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Iordanidou, K.; Houssa, M.; Afanas' ev, V.V.; Stesmans, A. [Department of Physics and Astronomy, University of Leuven (Belgium); Pourtois, G. [IMEC, Leuven (Belgium)

    2016-11-15

    In this paper, we study the oxygen and hydroxyl adsorption on both pristine and S deficient MS{sub 2} (M = Mo, W, Hf) monolayers, using first-principles molecular dynamics calculations. Our simulations reveal that single-layer HfS{sub 2} suffers severely from oxidation, which results in the formation of strong Hf-O bonds, likely degrading the transport properties of the material. Oxygen adsorption on S deficient monolayers acts as a passivation mechanism, both ''structurally'' by saturating the dangling bonds of neighboring metal atoms and ''electronically'' by removing the S vacancy induced gap states. Hydroxyl adsorption on pristine monolayers generates spin-polarized gap states, and for HfS{sub 2} in particular, causes the Fermi level pinning close to the conduction band edge. (copyright 2016 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  16. Single Crystalline Film of Hexagonal Boron Nitride Atomic Monolayer by Controlling Nucleation Seeds and Domains.

    Science.gov (United States)

    Wu, Qinke; Park, Ji-Hoon; Park, Sangwoo; Jung, Seong Jun; Suh, Hwansoo; Park, Noejung; Wongwiriyapan, Winadda; Lee, Sungjoo; Lee, Young Hee; Song, Young Jae

    2015-11-05

    A monolayer hexagonal boron nitride (h-BN) film with controllable domain morphology and domain size (varying from less than 1 μm to more than 100 μm) with uniform crystalline orientation was successfully synthesized by chemical vapor deposition (CVD). The key for this extremely large single crystalline domain size of a h-BN monolayer is a decrease in the density of nucleation seeds by increasing the hydrogen gas flow during the h-BN growth. Moreover, the well-defined shape of h-BN flakes can be selectively grown by controlling Cu-annealing time under argon atmosphere prior to h-BN growth, which provides the h-BN shape varies in triangular, trapezoidal, hexagonal and complex shapes. The uniform crystalline orientation of h-BN from different nucleation seeds can be easily confirmed by polarized optical microscopy (POM) with a liquid crystal coating. Furthermore, seamlessly merged h-BN flakes without structural domain boundaries were evidence by a selective hydrogen etching after a full coverage of a h-BN film was achieved. This seamless large-area and atomic monolayer of single crystalline h-BN film can offer as an ideal and practical template of graphene-based devices or alternative two-dimensional materials for industrial applications with scalability.

  17. The Structures of Self-Assembled Monolayer Films of Organosulfur Compounds Adsorbed on Gold Single Crystals: Electron Diffraction Studies.

    Science.gov (United States)

    1988-01-01

    AD-M193 125 THE STRUCTURES OF SELF-RSSENSLED MOMOLAYER FILMS OF 1/1 ORGANOSULFUR COMPOUND..(U) HRlYARD UNJY CAMBRIDGE MASS DEPT OF CHEMISTRY L STRONG...VV L- ___ THE STRUCTURES OF SELF-ASSEMBLED MONOLAYER FILMS OF ORGANOSULFUR COMPOUNDS ADSORBED ON GOLD SINGLE CRYSTALS: ELECTRON DIFFRACTION STUDIES...true sulfide phase. V V ’A. LA8700876 REVISED The Structures of Self-Assembled Monolayer Films of Organosulfur Compounds Adsorbed on Gold Single

  18. Surface-directed molecular assembly of pentacene on monolayer graphene for high-performance organic transistors.

    Science.gov (United States)

    Lee, Wi Hyoung; Park, Jaesung; Sim, Sung Hyun; Lim, Soojin; Kim, Kwang S; Hong, Byung Hee; Cho, Kilwon

    2011-03-30

    Organic electronic devices that use graphene electrodes have received considerable attention because graphene is regarded as an ideal candidate electrode material. Transfer and lithographic processes during fabrication of patterned graphene electrodes typically leave polymer residues on the graphene surfaces. However, the impact of these residues on the organic semiconductor growth mechanism on graphene surface has not been reported yet. Here, we demonstrate that polymer residues remaining on graphene surfaces induce a stand-up orientation of pentacene, thereby controlling pentacene growth such that the molecular assembly is optimal for charge transport. Thus, pentacene field-effect transistors (FETs) using source/drain monolayer graphene electrodes with polymer residues show a high field-effect mobility of 1.2 cm(2)/V s. In contrast, epitaxial growth of pentacene having molecular assembly of lying-down structure is facilitated by π-π interaction between pentacene and the clean graphene electrode without polymer residues, which adversely affects lateral charge transport at the interface between electrode and channel. Our studies provide that the obtained high field-effect mobility in pentacene FETs using monolayer graphene electrodes arises from the extrinsic effects of polymer residues as well as the intrinsic characteristics of the highly conductive, ultrathin two-dimensional monolayer graphene electrodes.

  19. Electronic structure of monolayer 1T′-MoTe2 grown by molecular beam epitaxy

    Directory of Open Access Journals (Sweden)

    Shujie Tang

    2018-02-01

    Full Text Available Monolayer transition metal dichalcogenides (TMDCs in the 1T′ structural phase have drawn a great deal of attention due to the prediction of quantum spin Hall insulator states. The band inversion and the concomitant changes in the band topology induced by the structural distortion from 1T to 1T′ phases are well established. However, the bandgap opening due to the strong spin-orbit coupling (SOC is only verified for 1T′-WTe2 recently and still debated for other TMDCs. Here we report a successful growth of high-quality monolayer 1T′-MoTe2 on a bilayer graphene substrate through molecular beam epitaxy. Using in situ angle-resolved photoemission spectroscopy (ARPES, we have investigated the low-energy electronic structure and Fermi surface topology. The SOC-induced breaking of the band degeneracy points between the valence and conduction bands is clearly observed by ARPES. However, the strength of SOC is found to be insufficient to open a bandgap, which makes monolayer 1T′-MoTe2 on bilayer graphene a semimetal.

  20. Electronic structure of monolayer 1T'-MoTe2 grown by molecular beam epitaxy

    Science.gov (United States)

    Tang, Shujie; Zhang, Chaofan; Jia, Chunjing; Ryu, Hyejin; Hwang, Choongyu; Hashimoto, Makoto; Lu, Donghui; Liu, Zhi; Devereaux, Thomas P.; Shen, Zhi-Xun; Mo, Sung-Kwan

    2018-02-01

    Monolayer transition metal dichalcogenides (TMDCs) in the 1T' structural phase have drawn a great deal of attention due to the prediction of quantum spin Hall insulator states. The band inversion and the concomitant changes in the band topology induced by the structural distortion from 1T to 1T' phases are well established. However, the bandgap opening due to the strong spin-orbit coupling (SOC) is only verified for 1T'-WTe2 recently and still debated for other TMDCs. Here we report a successful growth of high-quality monolayer 1T'-MoTe2 on a bilayer graphene substrate through molecular beam epitaxy. Using in situ angle-resolved photoemission spectroscopy (ARPES), we have investigated the low-energy electronic structure and Fermi surface topology. The SOC-induced breaking of the band degeneracy points between the valence and conduction bands is clearly observed by ARPES. However, the strength of SOC is found to be insufficient to open a bandgap, which makes monolayer 1T'-MoTe2 on bilayer graphene a semimetal.

  1. X-ray diffraction and molecular-dynamics studies: Structural analysis of phases in diglyceride monolayers

    DEFF Research Database (Denmark)

    Peters, Günther H.J.; Larsen, Niels Bent; Bjørnholm, T.

    1998-01-01

    We report a detailed structural analysis of the phases of 1,2-sn-dipalmitoylglycerol Langmuir monolayers at room temperature. Pressure-induced transitions have been investigated by combination of molecular-dynamics simulations and grazing-incidence x-ray diffraction (XRD). The diglyceride film......; At the lowest pressure the tilt angle reaches approximate to 14 degrees in a direction close to a nearest neighbor direction. Both arrangements of the alkyl chains are confirmed by XRD. For higher order and fractional order Bragg peaks, simulations predict higher intensities than observed with XRD. This may...

  2. Comparative characteristics of membrane-active single-chained ether phospholipids: PAF and lyso-PAF in Langmuir monolayers.

    Science.gov (United States)

    Flasiński, Michał; Broniatowski, Marcin; Wydro, Paweł; Dynarowicz-Łątka, Patrycja

    2012-03-15

    1-O-Octadecyl-2-acetyl-sn-glycero-3-phosphocholine (PAF) and its deacetylated precursor (lyso-PAF) are membrane-active single-chained ether phospholipids, which play an important signaling role in different physiological processes. There is strong evidence that one of the possible mechanisms of PAF and lyso-PAF activity is connected with their direct influence on biomembranes. Although both lipids have very similar structure, their biological activity is very different and in some cases even antagonistic. Unfortunately, there is a lack of the studies correlating these observations with the molecular structure of both compounds. Therefore, we decided to apply model systems and advanced physicochemical methods to explore this subject and look for the reasons of the observed discrepancies. As a model system, we prepared Langmuir monolayers of PAF and lyso-PAF at the air/water interface. The physicochemical characteristic of the model membranes under different experimental conditions was performed with the application of the Langmuir monolayer technique, Brewster angle microscopy, and the methods based on synchrotron radiation scattering (XR and GIXD). Both compounds form stable Langmuir monolayers, in which the lipid molecules are strongly immersed into the water subphase. The monolayers have expanded character, meaning that the hydrophobic tails are considerably tilted and disordered. Similarly to biochemical studies, also in our model systems, profound differences in the properties of PAF and lyso-PAF were observed. Contrary to PAF, the lyso-PAF molecules express the propensity to form organized, periodical structures in the model membranes. It is manifested in the phase transition observed in the course of the lyso-PAF π-A isotherm which was correlated with the diffraction signal registered with the application of the GIXD method. The formation of 2D domains of hexagonal ordering of the film forming molecules was observed only for the lyso precursor. The observed

  3. Molecular packing changes of alkanethiols monolayers on Au(111) under applied pressure

    International Nuclear Information System (INIS)

    Barrena, E.; Ocal, C.; Salmeron, M.

    2000-01-01

    A study of the changes of molecular packing in self-assembled monolayers of alkylthiols on Au(111) induced by external pressure is presented. Atomic force microscopy (AFM) is used to apply pressure and to measure the height of islands of alkanethiols partially covering the gold surface. The islands are made of ordered straight chain alkylthiol molecules tilted from the surface normal. Their height was found to decrease in a stepwise manner as a function of the load applied by the tip. Simultaneous stepwise increases in friction force were observed. A simple geometrical model involving the interlocking of alkyl chains at specific molecular tilt angles can explain the observations. According to the model, tilts in both the nearest neighbor and the next-nearest neighbor directions are necessary. (c) 2000 American Institute of Physics

  4. First-principle study of single TM atoms X (X=Fe, Ru or Os) doped monolayer WS2 systems

    Science.gov (United States)

    Zhu, Yuan-Yan; Zhang, Jian-Min

    2018-05-01

    We report the structural, magnetic and electronic properties of the pristine and single TM atoms X (X = Fe, Ru or Os) doped monolayer WS2 systems based on first-principle calculations. The results show that the W-S bond shows a stronger covalent bond, but the covalency is obviously weakened after the substitution of W atom with single X atoms, especially for Ru (4d75s1) with the easily lost electronic configuration. The smaller total energies of the doped systems reveal that the spin-polarized states are energetically favorable than the non-spin-polarized states, and the smallest total energy of -373.918 eV shows the spin-polarized state of the Os doped monolayer WS2 system is most stable among three doped systems. In addition, although the pristine monolayer WS2 system is a nonmagnetic-semiconductor with a direct band gap of 1.813 eV, single TM atoms Fe and Ru doped monolayer WS2 systems transfer to magnetic-HM with the total moments Mtot of 1.993 and 1.962 μB , while single TM atom Os doped monolayer WS2 systems changes to magnetic-metal with the total moments Mtot of 1.569 μB . Moreover, the impurity states with a positive spin splitting energies of 0.543, 0.276 and 0.1999 eV near the Fermi level EF are mainly contributed by X-dxy and X-dx2-y2 states hybridized with its nearest-neighbor atom W-dz2 states for Fe, Ru and Os doped monolayer WS2 system, respectively. Finally, we hope that the present study on monolayer WS2 will provide a useful theoretical guideline for exploring low-dimensional spintronic materials in future experiments.

  5. Intramolecular diffusive motion in alkane monolayers studied by high-resolution quasielastic neutron scattering and molecular dynamics simulations

    DEFF Research Database (Denmark)

    Hansen, Flemming Yssing; Criswell, L.; Fuhrmann, D

    2004-01-01

    that these relatively slow motions are observable by high-energy-resolution quasielastic neutron scattering (QNS) thus demonstrating QNS as a technique, complementary to nuclear magnetic resonance, for studying conformational dynamics on a nanosecond time scale in molecular monolayers.......Molecular dynamics simulations of a tetracosane (n-C24H50) monolayer adsorbed on a graphite basal-plane surface show that there are diffusive motions associated with the creation and annihilation of gauche defects occurring on a time scale of similar to0.1-4 ns. We present evidence...

  6. Model of self assembled monolayer based molecular diodes made of ferrocenyl-alkanethiols

    Science.gov (United States)

    Duche, David; Planchoke, Ujwol; Dang, Florian-Xuan; Le Rouzo, Judikael; Bescond, Marc; Simon, Jean-Jacques; Balaban, Teodor Silviu; Escoubas, Ludovic

    2017-03-01

    There has been significant work investigating the use of self assembled monolayers (SAMs) made of ferrocenyl terminated alkanethiols for realizing molecular diodes, leading to remarkably large forward-to-reverse current rectification ratios. In this study, we use a multiband barrier tunneling model to examine the electrical properties of SAM-based molecular diodes made of HSC9Fc, HSC11Fc, and HSCiFcC13-i (0 ≤ i ≤ 13). Using our simple physical model, we reproduce the experimental data of charge transport across various ferrocenyl substituted alkanethiols performed by Nijhuis, Reus, and Whitesides [J. Am. Chem. Soc. 132, 18386-184016 (2010)] and Yuan et al. [Nat. Commun. 6, 6324 (2015)]. Especially, the model allows predicting the rectification direction in HSCiFcC13-i (0 ≤ i ≤ 13) based molecular diodes depending on the position of the ferrocenyl (Fc) moiety within the molecules. We show that the asymmetry of the barrier length at both sides of the Highest Occupied Molecular Orbital of the ferrocenyl moiety strongly contributes to the rectifying properties of ferrocenyl-alkanethiol based molecular junctions. Furthermore, our results reveal that bound and quasi-bound states play an important role in the charge transport.

  7. Quasi van der Waals epitaxy of copper thin film on single-crystal graphene monolayer buffer

    Science.gov (United States)

    Lu, Zonghuan; Sun, Xin; Washington, Morris A.; Lu, Toh-Ming

    2018-03-01

    Quasi van der Waals epitaxial growth of face-centered cubic Cu (~100 nm) thin films on single-crystal monolayer graphene is demonstrated using thermal evaporation at an elevated substrate temperature of 250 °C. The single-crystal graphene was transferred to amorphous (glass) and crystalline (quartz) SiO2 substrates for epitaxy study. Raman analysis showed that the thermal evaporation method had minimal damage to the graphene lattice during the Cu deposition. X-ray diffraction and electron backscatter diffraction analyses revealed that both Cu films are single-crystal with (1 1 1) out-of-plane orientation and in-plane Σ3 twin domains of 60° rotation. The crystallinity of the SiO2 substrates has a negligible effect on the Cu crystal orientation during the epitaxial growth, implying the strong screening effect of graphene. We also demonstrate the epitaxial growth of polycrystalline Cu on a commercial polycrystalline monolayer graphene consisting of two orientation domains offset 30° to each other. It confirms that the crystal orientation of the epitaxial Cu film follows that of graphene, i.e. the Cu film consists of two orientation domains offset 30° to each other when deposited on polycrystalline graphene. Finally, on the contrary to the report in the literature, we show that the direct current and radio frequency flip sputtering method causes significant damage to the graphene lattice during the Cu deposition process, and therefore neither is a suitable method for Cu epitaxial growth on graphene.

  8. Neat monolayer tiling of molecularly thin two-dimensional materials in 1 min.

    Science.gov (United States)

    Matsuba, Kazuaki; Wang, Chengxiang; Saruwatari, Kazuko; Uesusuki, Yusuke; Akatsuka, Kosho; Osada, Minoru; Ebina, Yasuo; Ma, Renzhi; Sasaki, Takayoshi

    2017-06-01

    Controlled arrangement of molecularly thin two-dimensional (2D) materials on a substrate, particularly into precisely organized mono- and multilayer structures, is a key to design a nanodevice using their unique and enhanced physical properties. Several techniques such as mechanical transfer process and Langmuir-Blodgett deposition have been applied for this purpose, but they have severe restrictions for large-scale practical applications, for example, limited processable area and long fabrication time, requiring skilled multistep operations. We report a facile one-pot spin-coating method to realize dense monolayer tiling of various 2D materials, such as graphene and metal oxide nanosheets, within 1 min over a wide area (for example, a 30-mmφ substrate). Centrifugal force drives the nanosheets in a thin fluid layer to the substrate edge where they are packed edge to edge all the way to the central region, without forming overlaps. We investigated the relationship between precursor concentration, rotation speed, and ultraviolet-visible absorbance and developed an effective method to optimize the parameters for neat monolayer films. The multilayer buildup is feasible by repeating the spin-coating process combined with a heat treatment at moderate temperature. This versatile solution-based technique will provide both fundamental and practical advancements in the rapid large-scale production of artificial lattice-like films and nanodevices based on 2D materials.

  9. Dip-Pen Nanolithography on (Bio)Reactive Monolayer and Block-Copolymer Platforms: Deposition of Lines of Single Macromolecules

    NARCIS (Netherlands)

    Salazar, Ramon B.; Shovsky, A.; Schönherr, Holger; Vancso, Gyula J.

    2006-01-01

    The application of atomic force microscopy (AFM) tip-mediated molecular transfer (dip-pen nanolithography or DPN) to fabricate nanopatterned (bio)reactive platforms based on dendrimers on reactive self-assembled monolayer (SAM) and polymer thin films is discussed. The transfer of high-molar-mass

  10. Quasielastic neutron scattering and molecular dynamics simulation studies of the melting transition in butane and hexane monolayers adsorbed on graphite

    DEFF Research Database (Denmark)

    Hervig, K.W.; Wu, Z.; Dai, P.

    1997-01-01

    neutron diffraction experiments. Butane melts abruptly to a liquid phase where the molecules in the trans conformation translationally diffuse while rotating about their center of mass. In the case of the hexane monolayer, the MD simulations show that the appearance of quasielastic scattering below T-m...... coincides with transformation of Some molecules from trans to gauche conformations. Furthermore, if gauche molecules are prevented from forming in the simulation, the calculated incoherent scattering function contains no quasielastic component below T-m. Modeling of both the neutron and simulated hexane......Quasielastic neutron scattering experiments and molecular dynamics (MD) simulations have been used to investigate molecular diffusive motion near the melting transition of monolayers of flexible rod-shaped molecules. The experiments were conducted on butane and hexane monolayers adsorbed...

  11. Trapping dynamics of diindenoperylene (DIP) in self-assembled monolayers using molecular simulation

    KAUST Repository

    Kaushik, Ananth P.

    2011-07-01

    All-atom Molecular Dynamics simulation methods employing a well-tested intermolecular potential model, MM3 (Molecular Mechanics 3), demonstrate the propensity for diindenoperylene (DIP) molecules to insert between molecules of a self-assembled monolayer (SAM) during a deposition process intended to grow a thin film of this organic semiconductor molecule onto the surface of self-assembled monolayers. The tendency to insert between SAM molecules is fairly prevalent at normal growth temperatures and conditions, but is most strongly dependent on the density and the nature of the SAM. We posit the existence of an optimal density to favor surface adsorption over insertion for this system. DIP is less likely to insert in fluorinated SAMs, like FOTS (fluorooctatrichlorosilane), than its unfluorinated analog, OTS (octatrichlorosilane). It is also less likely to insert between shorter SAMs (e.g., less insertion in OTS than ODTS (octadecyltrichlorosilane)). Very short length, surface-coating molecules, like HDMS (hexamethyldisilazane), are more likely to scatter energetic incoming DIP molecules with little insertion on first impact (depending on the incident energy of the DIP molecule). Grazing angles of incidence of the depositing molecules generally favor surface adsorption, at least in the limit of low coverage, but are shown to be dependent on the nature of the SAM. The validity of these predictions is confirmed by comparison of the predicted sticking coefficients of DIP at a variety of incident energies on OTS, ODTS, and FOTS SAMs with results obtained experimentally by Desai et al. (2010) [23]. The simulation predictions of the tendency of DIP to insert can be explained, in large part, in terms of binding energies between SAM and DIP molecules. However, we note that entropic and stochastic events play a role in the deposition outcomes. Preliminary studies of multiple deposition events, emulating growth, show an unexpected diffusion of DIP molecules inserted within the

  12. Molecular Dynamics Study of Alkanethiolate Self-Assembled Monolayer Coated Gold Nanoparticle

    Science.gov (United States)

    2007-06-01

    of Organosulfur Compounds on Au( 111). Implications for Molecular Self-Assembly on Gold 21. Plimpton, S.J., "Fast Parallel Algorithms for Short-Range... Organosulfur Compounds SHAKE Algorithm for Molecular Dynamics." Journal of Adsorbed on Gold Single Crystals: Electron Diffraction Computational Physics, 52

  13. On the lipid head group hydration of floating surface monolayers bound to self-assembled molecular protein layers

    DEFF Research Database (Denmark)

    Lösche, M.; Erdelen, C.; Rump, E.

    1994-01-01

    The structure of monomolecular layers of the protein streptavidin, specifically bound to biotin-functionalized lipid monolayers at aqueous surfaces, has been characterized. Neutron and X-ray reflectivity measurements allowed an assessment of the organization of these self-assembled systems...... with molecular resolution. Emphasis here is placed on the hydration of the lipid head groups in the bound state. For three functionalized lipids with spacers of different lengths between the biotin and their chains it was observed that the head groups were dehydrated in monolayers of the pure lipids, which were...... kept at low surface pressure before protein adsorption. The introduction of dipole moments at the interface by the admixture of phospholipids or the application of lateral pressure on the lipid monolayer before protein adsorption were found to impose an extension of the spacer moieties. The biotin...

  14. Synthesis of Large-Scale Single-Crystalline Monolayer WS2 Using a Semi-Sealed Method

    Directory of Open Access Journals (Sweden)

    Feifei Lan

    2018-02-01

    Full Text Available As a two-dimensional semiconductor, WS2 has attracted great attention due to its rich physical properties and potential applications. However, it is still difficult to synthesize monolayer single-crystalline WS2 at larger scale. Here, we report the growth of large-scale triangular single-crystalline WS2 with a semi-sealed installation by chemical vapor deposition (CVD. Through this method, triangular single-crystalline WS2 with an average length of more than 300 µm was obtained. The largest one was about 405 μm in length. WS2 triangles with different sizes and thicknesses were analyzed by optical microscope and atomic force microscope (AFM. Their optical properties were evaluated by Raman and photoluminescence (PL spectra. This report paves the way to fabricating large-scale single-crystalline monolayer WS2, which is useful for the growth of high-quality WS2 and its potential applications in the future.

  15. Molecular-Scale Investigation of Heavy Metal Ions at a Charged Langmuir Monolayer

    Science.gov (United States)

    Rock, William; Qiao, Baofu; Uysal, Ahmet; Bu, Wei; Lin, Binhua

    Solvent extraction - the surfactant-aided preferential transfer of a species from an aqueous to an organic phase - is an important technique used in heavy and precious metal refining and reprocessing. Solvent extraction requires transfer through an oil/water interface, and interfacial interactions are expected to control transfer kinetics and phase stability, yet these key interactions are poorly understood. Langmuir monolayers with charged headgroups atop concentrated salt solutions containing heavy metal ions act as a model of solvent extraction interfaces; studies of ions at a charged surface are also fundamentally important to many other phenomena including protein solvation, mineral surface chemistry, and electrochemistry. We probe these charged interfaces using a variety of surface-sensitive techniques - vibrational sum frequency generation (VSFG) spectroscopy, x-ray reflectivity (XRR), x-ray fluorescence near total reflection (XFNTR), and grazing incidence diffraction (GID). We integrate experiments with Molecular Dynamics (MD) simulations to uncover the molecular-level interfacial structure. This work is supported by the U.S. DOE, BES, Contract DE-AC02-06CH11357. ChemMatCARS is supported by NSF/CHE-1346572.

  16. Molecular dynamics studies of the melting of butane and hexane monolayers adsorbed on the basal-plane surface of graphite

    DEFF Research Database (Denmark)

    Hansen, Flemming Yssing; Newton, J. C.; Taub, H.

    1993-01-01

    The effect of molecular steric properties on the melting of quasi-two-dimensional solids is investigated by comparing results of molecular dynamics simulations of the melting of butane and hexane monolayers adsorbed on the basal-plane surface of graphite. These molecules differ only in their length......, being members of the n-alkane series [CH3(CH2)n−2CH3] where n=4 for butane and n=6 for hexane. The simulations employ a skeletal model, which does not include the hydrogen atoms explicitly, to represent the intermolecular and molecule–substrate interactions. Nearest-neighbor intramolecular bonds...... are fixed in length, but the molecular flexibility is preserved by allowing the bend and dihedral torsion angles to vary. The simulations show a qualitatively different melting behavior for the butane and hexane monolayers consistent with neutron and x-ray scattering experiments. The melting of the low...

  17. Visualization of two-dimensional single chain conformations solubilized in a miscible polymer blend monolayer by atomic force microscopy.

    Science.gov (United States)

    Sugihara, Kouki; Kumaki, Jiro

    2012-06-07

    Polymer Langmuir monolayers spread on a water surface are one of the best models for two-dimensional (2D) polymer and have been extensively studied. However, the most fundamental issue in understanding a 2D film, the polymer chain packing in the film, is still not well-understood, especially from the experimental point of view. Direct observation of the chain packing by microscopy at a molecular level, such as by atomic force microscopy (AFM), might be one of the most promising ways to study this issue; however, because of the limited resolution of the method, the chain packing of polymer cannot be resolved by AFM, except for especially large polymers. Here, we show that a mixed monolayer of vinyl polymers, poly(methyl methacrylate) (PMMA) and poly(n-nonyl acrylate) (PNA), was miscible at a low surface pressure, and if a small amount of PMMA chains was solubilized in a PNA monolayer, the isolated PMMA chains in the PNA monolayer were, for the first time, successfully visualized by AFM with a clear contrast, which originated from a difference of rigidities of the polymers due to their different glass transition temperatures (105 °C(PMMA) and -89 °C(PNA)). The PMMA chains were found to strongly interpenetrate into the PNA monolayer, with a radius of gyration (R(g(PMMA))) that was several times larger than that of the 2D ideal chain (segregated-chain). Furthermore, the radius scaled with the molecular weight of the PMMA (M(PMMA)) as R(g(PMMA)) ∝ M(PMMA)(0.63), which was between the scaling of the 2D ideal chain (segregated chain), R(g) ∝ M(0.5), and the 2D chain in good solvent, R(g) ∝ M(0.75). On the other hand, R(g(PMMA)) was independent of the molecular weight of the PNA matrix over a wide range. These results indicate that the PNA/PMMA monolayer is a strongly miscible system, although the R(g(PMMA)) scaling with M(PMMA) (0.63) is somewhat smaller than that expected for a 2D chain in good solvent systems (0.75). The generation of molecular level information

  18. Plasmonic welded single walled carbon nanotubes on monolayer graphene for sensing target protein

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jangheon; Kim, Soohyun [Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, 373-1 Guseong, Yuseong, Daejeon 305-806 (Korea, Republic of); Kim, Gi Gyu; Jung, Wonsuk, E-mail: wonsuk81@wku.ac.kr [Department of Mechanical and Automotive Engineering, Wonkwang University, Iksan, Jeonbuk 570-749 (Korea, Republic of)

    2016-05-16

    We developed plasmonic welded single walled carbon nanotubes (SWCNTs) on monolayer graphene as a biosensor to detect target antigen molecules, fc fusion protein without any treatment to generate binder groups for linker and antibody. This plasmonic welding induces atomic networks between SWCNTs as junctions containing carboxylic groups and improves the electrical sensitivity of a SWCNTs and the graphene membrane to detect target protein. We investigated generation of the atomic networks between SWCNTs by field-emission scanning electron microscopy and atomic force microscopy after plasmonic welding process. We compared the intensity ratios of D to G peaks from the Raman spectra and electrical sheet resistance of welded SWCNTs with the results of normal SWCNTs, which decreased from 0.115 to 0.086 and from 10.5 to 4.12, respectively. Additionally, we measured the drain current via source/drain voltage after binding of the antigen to the antibody molecules. This electrical sensitivity of the welded SWCNTs was 1.55 times larger than normal SWCNTs.

  19. Molecular simulations of mixed self-assembled monolayer coated gold nanoparticles in water.

    Science.gov (United States)

    J, Meena Devi

    2015-06-01

    Molecular dynamics simulations have been employed to study the hydration of a series of nanoparticles, each of which was coated with a mixed self-assembled monolayer (SAM) comprising methyl- and hydroxy-terminated alkane thiol chains. The mixing ratio of those chains are different for each nanoparticle. The simulations focused on the wetting behavior of the SAM-coated gold nanoparticles and the distribution and structure of their interfacial water molecules. The interactions of the mixed SAM-coated gold nanoparticles with water were analyzed by evaluating the radial distribution function, hydrogen bonds, the dipole orientations of the water molecules, and the water residence time in the interfacial region. The wettability of the mixed SAM-coated gold nanoparticles improved as the concentration of terminal hydroxy moieties was increased. The distribution and dynamics of the interfacial water molecules were found to be influenced by the mixing ratio of the terminal moieties of the SAM chains. The results of our simulations suggest that the surface interactions of the mixed SAM-coated gold nanoparticles with the aqueous medium can be modulated by systematically altering the mixing ratio of the terminal methyl and hydroxy moieties. This work may lead to new biological and technological applications and inspire the development of novel biomimetic materials. Graphical Abstract Mixed SAM-coated gold nanoparticles.

  20. Influence of molecular packing on the corrosion inhibition properties of self-assembled octadecyltrichlorosilane monolayers on silicon

    International Nuclear Information System (INIS)

    Hsieh, Shuchen; Chao, Wei-Jay; Lin, Pei-Ying; Hsieh, Chiung-Wen

    2014-01-01

    Highlights: •Molecular packing plays an important role in determining SAM film properties. •Loose-packed OTS monolayers on silicon were corroded by exposure to KMnO 4 . •Dense-packed OTS SAM films exhibited excellent corrosion protection efficacy. -- Abstract: The corrosion inhibition properties of octadecyltrichlorosilane (OTS) self-assembled monolayers (SAMs) on silicon were investigated. Atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), contact angle (CA), and lateral force microscopy (LFM) were used to determine the OTS film formation time, packing density, and corrosion protection efficacy. The OTS films reached adsorption saturation after 15 s; however, the molecular density continued to increase up to 24 h. The films were exposed to the strong oxidant KMnO 4 , and while 15-s film samples exhibited corrosion after a 1 min exposure, samples with films grown for 24 h were protected even after 24 h

  1. Grafted organic monolayer for single electron transport and for quantum dots solar cells

    Science.gov (United States)

    Caillard, Louis Marie

    Functionalization of oxide-free silicon and silicon oxide surfaces is important for a number of applications. In this work, organic monolayers are grafted (GOM) on oxide-free silicon surfaces using thermal and ultraviolet-activated hydrosilylation of hydrogen-terminated silicon surfaces, primarily using Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy for characterization. The resulting amine-terminated GOM have been used for depositing nanoparticles, selecting the end group for two very specific applications: single electron devices and nano-quantum-dot (NQD) enhanced Si photovoltaic cells. To perform single-electron transport measurements, colloidal gold nanoparticles have been deposited on amine-functionalized silicon surfaces and tunneling measurements performed with a scanning tunneling microscope in an ultra-high vacuum chamber. Using a double-barrier tunneling junction (with the GOM as the first barrier and the vacuum between the scanning tip and the gold nanoparticle as the second one), single-electron transport was observed at 30K through a Coulomb staircase phenomenon. The critical parameters were identified to improve reproducibility. Finally, recently developed advanced modeling, based on traditional "orthodox" theory, was optimized to account for the observations (e.g. I-V dependence on band bending). This work provides a basis for the development of single-electron transistors that are compatible with current silicon based technology. To enhance standard silicon-based solar cells, GOM is also needed to graft strongly absorbing II-VI NQDs and optimize their energy transfer to the silicon substrate. Recent photoluminescence spectroscopy has demonstrated that energy transfer occurs through both radiative and non-radiative mechanisms between NQDs and the substrate. With grafting technology, the aim was to optimize absorption, as probed by photoluminescence, in two ways. First, silicon nanopillars were fabricated to increase the

  2. Structure of a monolayer of molecular rotors on aqueous subphase from grazing-incidence X-ray diffraction.

    Science.gov (United States)

    Kaleta, Jiří; Wen, Jin; Magnera, Thomas F; Dron, Paul I; Zhu, Chenhui; Michl, Josef

    2018-03-23

    In situ grazing-incidence X-ray scattering shows that a monolayer of artificial rod-shaped dipolar molecular rotors produced on the surface of an aqueous subphase in a Langmuir trough has a structure conducive to a 2D ferroelectric phase. The axes of the rotors stand an average of 0.83 nm apart in a triangular grid, perpendicular to the surface within experimental error. They carry 2,3-dichlorophenylene rotators near rod centers, between two decks of interlocked triptycenes installed axially on the rotor axle. The analysis is based first on simultaneous fitting of observed Bragg rods and second on fitting the reflectivity curve with only three adjustable parameters and the calculated rotor electron density, which also revealed the presence of about seven molecules of water near each rotator. Dependent on preparation conditions, a minor and variable amount of a different crystal phase may also be present in the monolayer.

  3. Molecular dynamics simulations of peptide adsorption on self-assembled monolayers

    International Nuclear Information System (INIS)

    Xie Yun; Liu Meifeng; Zhou Jian

    2012-01-01

    All-atom molecular dynamics simulations are performed to investigate the neuromedin-B peptide adsorption on the self-assembled monolayers (SAMs) of SH(CH 2 ) 10 N + (CH 3 ) 2 CH 2 CH(OH)CH 2 SO 3 - (SBT), SH(CH 2 ) 10 OH and SH(CH 2 ) 10 CH 3 . The force-distance profiles show that the surface resistance to peptide adsorption is mainly generated by the water molecules tightly bound to surfaces via hydrogen bonds (hydration water molecules); but surfaces themselves may also set an energy barrier for the approaching peptide. For the SBT-SAM, the surface first exerts a relatively high repulsive force and then a rather week attractive force on the approaching peptide; meanwhile the hydration water molecules exert a strong repulsive force on the peptide. Therefore, SBT-SAM has an excellent performance on resisting protein adsorption. For the OH-SAM and CH 3 -SAM, surfaces show low or little energy barrier but strong affinity to the peptide; and the hydration water molecules apply merely a repulsive force within a much narrower range and with lower intensity compared with the case for the SBT-SAM. The analysis of structural and dynamical properties of the peptide, surface and water indicates that possible factors contributing to surface resistance include the hydrogen-bond formation capability of surfaces, mobility of water molecules near surfaces, surface packing density and chain flexibility of SAMs. There are a large number of hydrogen bonds formed between the hydration water molecules and the functional groups of the SBT-SAM, which greatly lowers the mobility of water molecules near the surface. This tightly-bound water layer effectively reduces the direct contact between the surface and the peptide. Furthermore, the SBT-SAM also has a high flexibility and a low surface packing density, which allows water molecules to penetrate into the surface to form tightly-bound networks and therefore reduces the affinity between the peptide and the surface. The results show that

  4. Sum-frequency generation from molecular monolayers using 14 μm radiation from the FELIX free-electron laser

    International Nuclear Information System (INIS)

    Van der Ham, E.W.M.; Vrehen, Q.H.F.; Eliel, E.R.

    1995-01-01

    Sum-frequency generation (SFG) has developed into a widely applied tool for study of surfaces and interfaces where molecules are present. It combines the surface specificity of a second-order nonlinear optical technique with the power of a spectroscopic method, and it can be used under widely varying experimental conditions ranging from UHV to electrochemical cells. The important characteristic of SFG is that it allows one to study the average spatial orientation of a molecular bond in a monolayer of molecules at an interface. Until recently SFG measurements were confined to the frequency interval Y μ > 1700 cm -1 because of a lack of suitable laser sources at wave-lengths λ > 6 μm. So for most molecules only a few vibrational modes and thus intramolecular bonds can be studied. We have developed a universal sum-frequency spectrometer around the FELIX free-electron law that covers the complete molecular fingerprint since we can generate any IR wavelength between 2.75 and 110 fμ at the FELIX facility. We have used this setup for a series of exploratory SFG experiments in a frequency range that was hitherto unexplored in the study of molecular monolayers. We have studied thiol monolayers chemisorbed on a variety of noble metals (Au, Ag, Pt) where we focussed on the C-S stretch vibration at ν = 702 cm -1 (λ = 14.3 μm). We have found spectroscopic features revealing the presence of both the trane and gauche conformers of the adsorbed molecules. The present measurements open a whole new wavelength range for nonlinear optical studies of interfaces

  5. Average Orientation of a Molecular Rotor Embedded in a Langmuir-Blodgett Monolayer

    Czech Academy of Sciences Publication Activity Database

    Casher, D. L.; Kobr, L.; Michl, Josef

    2012-01-01

    Roč. 28, č. 2 (2012), s. 1625-1637 ISSN 0743-7463 Institutional research plan: CEZ:AV0Z40550506 Keywords : infrared reflection spectroscopy * self-assembled monolayers * electric-field * linear dichroism * fatty-acids Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.187, year: 2012

  6. Covalently Attached Organic Monolayers onto Silicon Carbide from 1-Alkynes: Molecular Structure and Tribological Properties

    NARCIS (Netherlands)

    Pujari, S.P.; Scheres, L.M.W.; Weidner, T.; Baio, J.E.; Cohen Stuart, M.A.; Rijn, van C.J.M.; Zuilhof, H.

    2013-01-01

    In order to achieve improved tribological and wear properties at semiconductor interfaces, we have investigated the thermal grafting of both alkylated and fluorine-containing ((CxF2x+1)–(CH2)n-) 1-alkynes and 1-alkenes onto silicon carbide (SiC). The resulting monolayers display static water contact

  7. Potential of Transition Metal Atoms Embedded in Buckled Monolayer g-C3N4 as Single-Atom Catalysts

    KAUST Repository

    Li, Shu-Long

    2017-10-27

    We use first-principles calculations to systematically explore the potential of transition metal atoms (Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Ru, Rh, Pd, Ag, Ir, Pt, and Au) embedded in buckled monolayer g-C3N4 as single-atom catalysts. We show that clustering of Sc and Ti on g-C3N4 is thermodynamically impeded and that V, Cr, Mn, and Cu are much less susceptible to clustering than the other TM atoms under investigation. Strong bonding of the transition metal atoms in the cavities of g-C3N4 and high diffusion barriers together are responsible for single-atom fixation. Analysis of the CO oxidation process indicates that embedding of Cr and Mn in g-C3N4 gives rise to promising single-atom catalysts at low temperature.

  8. Two-dimensional iron-phthalocyanine (Fe-Pc) monolayer as a promising single-atom-catalyst for oxygen reduction reaction: a computational study

    Science.gov (United States)

    Wang, Yu; Yuan, Hao; Li, Yafei; Chen, Zhongfang

    2015-07-01

    Searching for low-cost non-Pt catalysts for oxygen reduction reaction (ORR) has been a key scientific issue in the development of fuel cells. In this work, the potential of utilizing the experimentally available two-dimensional (2D) Fe-phthalocyanine (Fe-Pc) monolayer with precisely-controlled distribution of Fe atoms as a catalyst of ORR was systematically explored by means of comprehensive density functional theory computations. The computations revealed that O2 molecules can be sufficiently activated on the surface of the Fe-Pc monolayer, and the subsequent ORR steps prefer to proceed on the Fe-Pc monolayer through a more efficient 4e pathway with a considerable limiting potential of 0.68 V. Especially, the Fe-Pc monolayer is more stable than the Fe-Pc molecule in acidic medium, and can present good catalytic performance for ORR on the addition of axial ligands. Therefore, the Fe-Pc monolayer is quite a promising single-atom-catalyst with high efficiency for ORR in fuel cells.Searching for low-cost non-Pt catalysts for oxygen reduction reaction (ORR) has been a key scientific issue in the development of fuel cells. In this work, the potential of utilizing the experimentally available two-dimensional (2D) Fe-phthalocyanine (Fe-Pc) monolayer with precisely-controlled distribution of Fe atoms as a catalyst of ORR was systematically explored by means of comprehensive density functional theory computations. The computations revealed that O2 molecules can be sufficiently activated on the surface of the Fe-Pc monolayer, and the subsequent ORR steps prefer to proceed on the Fe-Pc monolayer through a more efficient 4e pathway with a considerable limiting potential of 0.68 V. Especially, the Fe-Pc monolayer is more stable than the Fe-Pc molecule in acidic medium, and can present good catalytic performance for ORR on the addition of axial ligands. Therefore, the Fe-Pc monolayer is quite a promising single-atom-catalyst with high efficiency for ORR in fuel cells. Electronic

  9. Electrochemical characterization of a 1,8-octanedithiol self-assembled monolayer (ODT-SAM) on a Au(1 1 1) single crystal electrode

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Raya, Daniel; Madueno, Rafael; Sevilla, Jose Manuel; Blazquez, Manuel [Departamento de Quimica Fisica y Termodinamica Aplicada, Universidad de Cordoba, Campus de Rabanales, Ed. Marie Curie, E-14071 Cordoba (Spain); Pineda, Teresa [Departamento de Quimica Fisica y Termodinamica Aplicada, Universidad de Cordoba, Campus de Rabanales, Ed. Marie Curie, E-14071 Cordoba (Spain)], E-mail: tpineda@uco.es

    2008-11-15

    Recently, it has becoming increasingly important to control the organization of self-assembled monolayers (SAMs) of {omega}-functionalized thiols for its potential applications in the construction of more complex molecular architectures. In this paper, we report on the spontaneous formation of a SAM of octanedithiol (ODT) as a function of the modification time. Electrochemical techniques such as cyclic voltammetry, double layer capacitance and electrochemical impedance spectroscopy are used for the characterization of this monolayer. The increase in modification time brings about changes in the octanedithiol self-assembled monolayer (ODT-SAM) reductive desorption voltammograms that indicate an evolution toward a more ordered and compact monolayer. This trend has also been found by following the changes in the electron transfer processes of the redox probe K{sub 3}Fe(CN){sub 6}. In fact, the ODT-SAM formed at low-modification time does not significantly perturb the electrochemical response as it is typical of either a low coverage or of the presence of large defects in the layer. Upon increasing the modification time, the voltammograms of the redox probe adopt a sigmoidal shape indicating the existence of pinholes in the monolayer distributed as an array of microelectrodes. The surface coverage as well as the size and distribution of these pinholes have been determined by the impedance technique that gives a more reliable evaluation of these monolayer structural parameters.

  10. Electrochemical characterization of a 1,8-octanedithiol self-assembled monolayer (ODT-SAM) on a Au(111) single crystal electrode

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Raya, Daniel; Madueno, Rafael; Sevilla, Jose Manuel; Blazquez, Manuel; Pineda, Teresa [Departamento de Quimica Fisica y Termodinamica Aplicada, Universidad de Cordoba, Campus de Rabanales, Cordoba (Spain)

    2008-11-15

    Recently, it has becoming increasingly important to control the organization of self-assembled monolayers (SAMs) of {omega}-functionalized thiols for its potential applications in the construction of more complex molecular architectures. In this paper, we report on the spontaneous formation of a SAM of octanedithiol (ODT) as a function of the modification time. Electrochemical techniques such as cyclic voltammetry, double layer capacitance and electrochemical impedance spectroscopy are used for the characterization of this monolayer. The increase in modification time brings about changes in the octanedithiol self-assembled monolayer (ODT-SAM) reductive desorption voltammograms that indicate an evolution toward a more ordered and compact monolayer. This trend has also been found by following the changes in the electron transfer processes of the redox probe K{sub 3}Fe(CN){sub 6}. In fact, the ODT-SAM formed at low-modification time does not significantly perturb the electrochemical response as it is typical of either a low coverage or of the presence of large defects in the layer. Upon increasing the modification time, the voltammograms of the redox probe adopt a sigmoidal shape indicating the existence of pinholes in the monolayer distributed as an array of microelectrodes. The surface coverage as well as the size and distribution of these pinholes have been determined by the impedance technique that gives a more reliable evaluation of these monolayer structural parameters. (author)

  11. Perforated monolayers

    Energy Technology Data Exchange (ETDEWEB)

    Regen, S.L.

    1992-12-01

    Goal of this research program is to create ultrathin organic membranes that possess uniform and adjustable pores ( < 7[angstrom] diameter). Such membranes are expected to possess high permeation selectivity (permselectivity) and high permeability, and to provide the basis for energy-efficient methods of molecular separation. Work carried out has demonstrated feasibility of using perforated monolayer''-based composites as molecular sieve membranes. Specifically, composite membranes derived from Langmuir-Blodgett multilayers of the calix[6]arene-based surfactant shown below plus poly[l-(trimethylsilyl)-l-propyne] (PTMSP) were found to exhibit sieving behavior towards He, N[sub 2] and SF[sub 6]. Results of derivative studies that have also been completed are also described in this report.

  12. Molecular beam epitaxy of quasi-freestanding transition metal disulphide monolayers on van der Waals substrates: a growth study

    Science.gov (United States)

    Hall, Joshua; Pielić, Borna; Murray, Clifford; Jolie, Wouter; Wekking, Tobias; Busse, Carsten; Kralj, Marko; Michely, Thomas

    2018-04-01

    Based on an ultra-high vacuum compatible two-step molecular beam epitaxy synthesis with elemental sulphur, we grow clean, well-oriented, and almost defect-free monolayer islands and layers of the transition metal disulphides MoS2, TaS2 and WS2. Using scanning tunneling microscopy and low energy electron diffraction we investigate systematically how to optimise the growth process, and provide insight into the growth and annealing mechanisms. A large band gap of 2.55 eV and the ability to move flakes with the scanning tunneling microscope tip both document the weak interaction of MoS2 with its substrate consisting of graphene grown on Ir(1 1 1). As the method works for the synthesis of a variety of transition metal disulphides on different substrates, we speculate that it could be of great use for providing hitherto unattainable high quality monolayers of transition metal disulphides for fundamental spectroscopic investigations.

  13. Structure of solid monolayers and multilayers of n-hexane on graphite

    Indian Academy of Sciences (India)

    Unknown

    Abstract. We present all-atom molecular dynamics simulations of n-hexane on the basal plane of graphite at monolayer and multilayer coverages. In keeping with experimental data, we find the presence of ordered adsorbed layers both at single monolayer coverage and when the adsorbed layer coexists with excess liquid.

  14. Molecular Fin Effect from Heterogeneous Self-Assembled Monolayer Enhances Thermal Conductance across Hard-Soft Interfaces.

    Science.gov (United States)

    Wei, Xingfei; Zhang, Teng; Luo, Tengfei

    2017-10-04

    Thermal transport across hard-soft interfaces is critical to many modern applications, such as composite materials, thermal management in microelectronics, solar-thermal phase transition, and nanoparticle-assisted hyperthermia therapeutics. In this study, we use equilibrium molecular dynamics (EMD) simulations combined with the Green-Kubo method to study how molecularly heterogeneous structures of the self-assembled monolayer (SAM) affect the thermal transport across the interfaces between the SAM-functionalized gold and organic liquids (hexylamine, propylamine and hexane). We focus on a practically synthesizable heterogeneous SAM featuring alternating short and long molecular chains. Such a structure is found to improve the thermal conductance across the hard-soft interface by 46-68% compared to a homogeneous nonpolar SAM. Through a series of further simulations and analyses, it is found that the root reason for this enhancement is the penetration of the liquid molecules into the spaces between the long SAM molecule chains, which increase the effective contact area. Such an effect is similar to the fins used in macroscopic heat exchanger. This "molecular fin" structure from the heterogeneous SAM studied in this work provides a new general route for enhancing thermal transport across hard-soft material interfaces.

  15. Thermal grafting of fluorinated molecular monolayers on doped amorphous silicon surfaces

    International Nuclear Information System (INIS)

    Sabbah, H.; Zebda, A.; Ababou-Girard, S.; Solal, F.; Godet, C.; Conde, J. P.; Chu, V.

    2009-01-01

    Thermally induced (160-300 deg. C) gas phase grafting of linear alkene molecules (perfluorodecene) was performed on hydrogenated amorphous silicon (a-Si:H) films, either nominally undoped or doped with different boron and phosphorus concentrations. Dense and smooth a-Si:H films were grown using plasma decomposition of silane. Quantitative analysis of in situ x-ray photoelectron spectroscopy indicates the grafting of a single layer of organic molecules. The hydrophobic properties of perfluorodecene-modified surfaces were studied as a function of surface coverage. Annealing experiments in ultrahigh vacuum show the covalent binding and the thermal stability of these immobilized layers up to 370 deg. C; this temperature corresponds to the Si-C bond cleavage temperature. In contrast with hydrogenated crystalline Si(111):H, no heavy wet chemistry surface preparation is required for thermal grafting of alkene molecules on a-Si:H films. A threshold grafting temperature is observed, with a strong dependence on the doping level which produces a large contrast in the molecular coverage for grafting performed at 230 deg. C

  16. Molecular suction pads: self-assembled monolayers of subphthalocyaninatoboron complexes on gold.

    Science.gov (United States)

    Glebe, Ulrich; Baio, Joe E; Árnadóttir, Líney; Siemeling, Ulrich; Weidner, Tobias

    2013-04-15

    Subphthalocyaninatoboron complexes with six long-chain alkylthio substituents in their periphery are applicable for the formation of self-assembled monolayers (SAMs) on gold. Such films are prepared from solution with the axially chlorido-substituted derivatives and characterised by near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). The results are in accord with the formation of SAMs assembled by the chemisorption of both covalently bound thiolate-type as well as coordinatively bound thioether units. The adsorbate molecules adopt an essentially flat adsorption geometry on the substrate, resembling a suction pad on a surface. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Control of the molecular density in a chemically adsorbed thiophene system monolayer

    Directory of Open Access Journals (Sweden)

    Tanaka Yosuke

    2013-08-01

    Full Text Available Chemically absorbed monolayers (CAM of thienyl functionalized n-alkyltrichlorosilane 11-(3-thienyl undecyltrichlorosilane (TUTS have been prepared with two methods which are the standard technique (TUTS-STD and the twice adsorption method (TUTS-TAM. The existence of TUTS-CAM was confirmed with water contact angle measurements, calculation of thickness with ellipsometry, fourier transform infrared reflection adsorption spectroscopy (FTIR-RAS. Here are described is the comparison of TUTS-STD and TUTS-TAM characterized by using Electron Spectroscopy for Chemical Analysis (ESCA and ultraviolet visible (UV-vis absorption spectroscopy. TUTS-TAM showed more densely packing than TUTS-STD by these measurements. Moreover, these TUTS-CAM polymerized by chemical oxidative polymerization and UV-Vis absorption spectra was measured to confirm the conjugated bond length of the polymerized thienyl groups. UV-vis spectra of the polymerized TUTS-CAM showed a new broad absorbance band at longer wavelength than 700nm.

  18. Defect properties of InGaAsN layers grown as sub-monolayer digital alloys by molecular beam epitaxy

    Science.gov (United States)

    Baranov, Artem I.; Gudovskikh, Alexander S.; Kudryashov, Dmitry A.; Lazarenko, Alexandra A.; Morozov, Ivan A.; Mozharov, Alexey M.; Nikitina, Ekaterina V.; Pirogov, Evgeny V.; Sobolev, Maxim S.; Zelentsov, Kirill S.; Egorov, Anton Yu.; Darga, Arouna; Le Gall, Sylvain; Kleider, Jean-Paul

    2018-04-01

    The defect properties of InGaAsN dilute nitrides grown as sub-monolayer digital alloys (SDAs) by molecular beam epitaxy for photovoltaic application were studied by space charge capacitance spectroscopy. Alloys of i-InGaAsN (Eg = 1.03 eV) were lattice-matched grown on GaAs wafers as a superlattice of InAs/GaAsN with one monolayer of InAs (solar cells. Low p-type background doping was demonstrated at room temperature in samples with InGaAsN layers 900 nm and 1200 nm thick (less 1 × 1015 cm-3). According to admittance spectroscopy and deep-level transient spectroscopy measurements, the SDA approach leads to defect-free growth up to a thickness of 900 nm. An increase in thickness to 1200 nm leads to the formation of non-radiative recombination centers with an activation energy of 0.5 eV (NT = 8.4 × 1014 cm-3) and a shallow defect level at 0.20 eV. The last one leads to the appearance of additional doping, but its concentration is low (NT = 5 × 1014 cm-3) so it does not affect the photoelectric properties. However, further increase in thickness to 1600 nm, leads to significant growth of its concentration to (3-5) × 1015 cm-3, while the concentration of deep levels becomes 1.3 × 1015 cm-3. Therefore, additional free charge carriers appearing due to ionization of the shallow level change the band diagram from p-i-n to p-n junction at room temperature. It leads to a drop of the external quantum efficiency due to the effect of pulling electric field decrease in the p-n junction and an increased number of non-radiative recombination centers that negatively impact lifetimes in InGaAsN.

  19. Single-Residue Sensitivity in Neutron Reflectivity and Resonant X-ray Reflectivity from Langmuir Monolayers of Synthetic Peptides

    Science.gov (United States)

    Strzalka, Joseph; Satija, Sushil; Dimasi, Elaine; Kuzmenko, Ivan; Gog, Thomas; Blasie, J. Kent

    2004-03-01

    Labeling groups with ^2H to distinguish them in the scattering length density (SLD) profile constitutes the chief advantage of neutron reflectivity (NR) in studying Langmuir monolayers (LM) of lipids and proteins. Solid phase synthesis (SPPS) permits the labeling of a single residue in a peptide. Recent work demonstrates the sensitivity of NR to single ^2H-labeled residues in LM of vectorially oriented α -helical bundle peptides. NR requires comparison of isomorphic samples of all-^1H and ^2H-labeled peptides. Alternately, resonant x-ray reflectivity (RXR) uses only one sample. RXR exploits energy-dependent changes in the scattering factor from heavy atoms to distinguish them within the SLD profile. Peptides may be labeled by SPPS (e.g. Br-Phe), or may have inherent labels (e.g. Fe in heme proteins). As test cases, we studied LM of Br-labeled lipids and peptides with RXR. Both approaches require a model-independent means of obtaining SLD profiles from the reflectivity data. We have applied box-refinement to obtain the gradient SLD profile. This is fit uniquely with a sum of Gaussians and integrated analytically [Blasie et al., PRB 67 224201 (2003)] to provide the SLD profile. Label positions can then be determined to sub-Ångstrom accuracy. This work supported by the NIH (GM55876).

  20. Organic layers at metal/electrolyte interfaces: molecular structure and reactivity of viologen monolayers

    International Nuclear Information System (INIS)

    Breuer, Stephan; Pham, Duc T; Huemann, Sascha; Gentz, Knud; Zoerlein, Caroline; Wandelt, Klaus; Broekmann, Peter; Hunger, Ralf

    2008-01-01

    The adsorption of viologens (1,1'-disubstituted-4,4'-bipyridinium molecules) on a chloride-modified copper electrode has been studied using a combination of cyclic voltammetry (CV), in-situ scanning tunneling microscopy (STM) and ex-situ photoemission spectroscopy (XPS). Two prototypes of viologens could be identified with respect to their redox behavior upon adsorption, namely those which retain (non-reactive adsorption) and those which change their redox state (reactive adsorption) upon interaction with the chloride-modified copper surface at given potential. The first class of viologens represented by 1,1'-dibenzyl-4,4'-bipyridinium molecules (dibenzyl-viologens, abbreviated as DBV) can be adsorbed and stabilized on this electrode surface in their di-cationic state at potentials more positive than the reduction potential of the solution species. XPS N1s core level shifts verify that the adsorbed DBV molecules on the electrode are in their oxidized di-cationic state. Electrostatic attraction between the partially solvated viologen di-cations and the anionic chloride layer is discussed as the main driving force for the DBV stabilization on the electrode surface. Analysis of the N1s and O1s core level shifts points to a non-reactive DBV adsorption leaving the DBV ads 2+ solvation shell partly intact. The laterally ordered DBV ads 2+ monolayer turns out to be hydrophilic with at least four water molecules per viologen present within this cationic organic film. The analysis of the Cl2p core level reveals that no further chloride species are present at the surface besides those which are specifically adsorbed, i.e. which are in direct contact with the metallic copper surface underneath the organic layer. The reduction of these adsorbed DBV ads 2+ surface species takes place only in the same potential regime where the solvated DBV aq 2+ bulk solution species react and is accompanied by a pronounced structural change from the di-cationic 'cavitand'-structure to a

  1. Organic layers at metal/electrolyte interfaces: molecular structure and reactivity of viologen monolayers

    Energy Technology Data Exchange (ETDEWEB)

    Breuer, Stephan; Pham, Duc T; Huemann, Sascha; Gentz, Knud; Zoerlein, Caroline; Wandelt, Klaus; Broekmann, Peter [Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstreet 14, 53115 Bonn (Germany); Hunger, Ralf [Department of Material Science, Technical University of Darmstadt, Petersenstreet 43, 64484 Darmstadt (Germany)], E-mail: k.wandelt@pc.uni-bonn.de

    2008-12-15

    The adsorption of viologens (1,1'-disubstituted-4,4'-bipyridinium molecules) on a chloride-modified copper electrode has been studied using a combination of cyclic voltammetry (CV), in-situ scanning tunneling microscopy (STM) and ex-situ photoemission spectroscopy (XPS). Two prototypes of viologens could be identified with respect to their redox behavior upon adsorption, namely those which retain (non-reactive adsorption) and those which change their redox state (reactive adsorption) upon interaction with the chloride-modified copper surface at given potential. The first class of viologens represented by 1,1'-dibenzyl-4,4'-bipyridinium molecules (dibenzyl-viologens, abbreviated as DBV) can be adsorbed and stabilized on this electrode surface in their di-cationic state at potentials more positive than the reduction potential of the solution species. XPS N1s core level shifts verify that the adsorbed DBV molecules on the electrode are in their oxidized di-cationic state. Electrostatic attraction between the partially solvated viologen di-cations and the anionic chloride layer is discussed as the main driving force for the DBV stabilization on the electrode surface. Analysis of the N1s and O1s core level shifts points to a non-reactive DBV adsorption leaving the DBV{sub ads}{sup 2+} solvation shell partly intact. The laterally ordered DBV{sub ads}{sup 2+} monolayer turns out to be hydrophilic with at least four water molecules per viologen present within this cationic organic film. The analysis of the Cl2p core level reveals that no further chloride species are present at the surface besides those which are specifically adsorbed, i.e. which are in direct contact with the metallic copper surface underneath the organic layer. The reduction of these adsorbed DBV{sub ads}{sup 2+} surface species takes place only in the same potential regime where the solvated DBV{sub aq}{sup 2+} bulk solution species react and is accompanied by a pronounced structural

  2. Photoelectron spectroscopy of self-assembled monolayers of molecular switches on noble metal surfaces; Photoelektronenspektroskopie selbstorganisierter Adsorbatschichten aus molekularen Schaltern auf Edelmetalloberflaechen

    Energy Technology Data Exchange (ETDEWEB)

    Heinemann, Nils

    2012-09-12

    Self-assembled monolayers (SAMs) of butanethiolate (C4) on single crystalline Au(111) surfaces were prepared by adsorption from solution. The thermally activated desorption behaviour of the C4 molecules from the gold substrate was examined by qualitative thermal desorption measurements (TDM), through this a desorption temperature T{sub Des}=473 K could be determined. With this knowledge, it was possible to produce samples of very good surface quality, by thermal treatment T{sub Sample}molecular switch 3-(4-(4-Hexyl-phenylazo)-phenoxy)-propane-1-thiol (ABT), deposited by self-assembly from solution on Au(111), was examined using laser-based photoelectron spectroscopy. Differences in the molecular dipole moment characteristic for the trans and the cis isomer of ABT were observed via changes in the sample work function, accessible by detection of the threshold energy for photoemission. A quantitative

  3. Influence of molecular distortion on the exciton quenching for quaterthiophene-terminated self-assembled monolayers on Au(111)

    Science.gov (United States)

    Kato, Hiroyuki S.; Murakami, Yoshinari; Saitoh, Riyo; Osumi, Yuji; Okaue, Daijiro; Kiriyama, Yoshiaki; Ueba, Takahiro; Yamada, Takashi; Ie, Yutaka; Aso, Yoshio; Munakata, Toshiaki

    2018-03-01

    We have studied the dynamics of photoexcited electronic states for structure-specific alkanethiolate-based self-assembled monolayers (SAMs) on Au(111). At the even numbers of methylene units (n) in the alkylene chain, a molecular distortion due to strong interference between the end substituents is expected. Focused on this geometrical perturbation, here, we examine the influence of the molecular distortion on the quenching process of photoexcited quaterthiophene (4T)-terminated alkanethiolate SAMs (4TCnS-SAMs) for even n (= 6 and 8). The occupied and unoccupied electronic levels of 4TCnS-SAMs are specified by ultraviolet photoelectron spectroscopy (UPS) and two-photon photoemission (2PPE) spectroscopy, respectively. The quenching rate, i.e., lifetime (τn), of the photoexcited state for 4TCnS-SAMs is evaluated by the time-resolved 2PPE measurements. In comparison to the previously reported results for odd n [J. Phys. Chem. C 119 (2015) 7400-7407], we find that τn for even n is not in the middle of those for n ± 1 but close to that for n - 1, i.e., τ6 ≈ τ5 and τ8 ≈ τ7, in contrast to the negligible difference in the electronic levels for all n. By the examination of molecular configurations using scanning tunneling microscopy (STM) and infrared reflection absorption spectroscopy (IRAS), we elucidate the weak n dependence of the 4T group orientation and the n-parity-dependent conformation change of alkylene chain. We conclude that the n parity dependence of τn results from a structural distortion of the aliphatic alkylene chain, in which a skewed alkylene chain appears for even n, rather than the electronic modification of the aromatic 4T groups.

  4. Molecular dynamics and electrochemical investigations of a pH-responsive peptide monolayer

    Czech Academy of Sciences Publication Activity Database

    Doneux, T.; Bouffier, L.; Mello, L.V.; Rigden, D.J.; Kejnovská, Iva; Fernig, D.G.; Higgins, S.J.; Nichols, R.J.

    2009-01-01

    Roč. 113, č. 16 (2009), s. 6792-6799 ISSN 1932-7447 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : peptide * molecular dynamics simulation * cyclic voltammetry Subject RIV: BO - Biophysics Impact factor: 4.224, year: 2009

  5. Single-layer ionic conduction on carboxyl-terminated silane monolayers patterned by constructive lithography.

    Science.gov (United States)

    Berson, Jonathan; Burshtain, Doron; Zeira, Assaf; Yoffe, Alexander; Maoz, Rivka; Sagiv, Jacob

    2015-06-01

    Ionic transport plays a central role in key technologies relevant to energy, and information processing and storage, as well as in the implementation of biological functions in living organisms. Here, we introduce a supramolecular strategy based on the non-destructive chemical patterning of a highly ordered self-assembled monolayer that allows the reproducible fabrication of ion-conducting surface patterns (ion-conducting channels) with top -COOH functional groups precisely definable over the full range of length scales from nanometre to centimetre. The transport of a single layer of selected metal ions and the electrochemical processes related to their motion may thus be confined to predefined surface paths. As a generic solid ionic conductor that can accommodate different mobile ions in the absence of any added electrolyte, these ion-conducting channels exhibit bias-induced competitive transport of different ionic species. This approach offers unprecedented opportunities for the realization of designed ion-conducting systems with nanoscale control, beyond the inherent limitations posed by available ionic materials.

  6. Interfacial shear stress between single-walled carbon nanotubes and gold surfaces with and without an alkanethiol monolayer.

    Science.gov (United States)

    Pan, Huiyan; Wu, Yu-Chiao; Adams, George G; Miller, Glen P; McGruer, Nicol E

    2013-10-01

    A novel and effective technique is developed to make the first determination of shear stress between dielectrophoretically assembled single-walled carbon nanotubes (SWNTs) and surfaces. The results demonstrate that we can vary the shear stress by a factor of 20 by functionalizing a gold surface with different alkanethiols. The interfacial shear stress between a small bundle of SWNTs and a gold surface with and without self-assembled monolayers of alkanethiol (2-phenylethanethiol or 2-aminoethanethiol) is determined. The measurements are based on simple NEMS cantilever beams, a nanomanipulator, and a scanning electron microscope (SEM). It is emphasized that the measured quantity is the slack in the nanotube (not the shear stress) induced by the nanomanipulation. The shear stress is determined from the slack through a mechanics model. An average shear stress of 87 MPa between SWNTs and gold surfaces is obtained. For the tests on the self-assembled 2-aminoethanethiol surface, an average shear stress of 142 MPa is obtained. For the self-assembled 2-phenylethanethiol surface, the shear stress is determined to be around 7.2 MPa with an estimated work of adhesion of 0.5 J/m(2). Copyright © 2013 Elsevier Inc. All rights reserved.

  7. Molecular dynamics based simulations to study the fracture strength of monolayer graphene oxide

    Science.gov (United States)

    Verma, Akarsh; Parashar, Avinash

    2018-03-01

    The aim of this article is to study the effects of functional groups such as hydroxyl, epoxide and carboxyl on the fracture toughness of graphene. These functional groups form the backbone of the intrinsic atomic structure of graphene oxide (GO). Molecular dynamics based simulations were performed in conjunction with reactive force field parameters to capture the Mode-I fracture toughness of functionalised graphene. Simulations were performed in stages, to study the effect of these functional groups, individually as well as all together on the fracture toughness of GO nanosheets. The molecular dynamics based simulations performed in this article helps us to conclude that the spatial distribution and concentration of functional groups significantly affects the fracture behavior of GO nanosheets.

  8. Elastic properties of surfactant monolayers at liquid-liquid interfaces: A molecular dynamics study

    DEFF Research Database (Denmark)

    Laradji, Mohamed; Mouritsen, Ole G.

    2000-01-01

    Using a simple molecular model based on the Lennard-Jones potential, we systematically study the elastic properties of liquid-liquid interfaces containing surfactant molecules by means of extensive and large-scale molecular dynamics simulations. The main elastic constants of the interface...... is further increased. Using a Gaussian theory on an interfacial Ginzburg-Landau model of surfactants, we find that the initial decrease of the bending rigidity is attributed to coupling between fluctuations of the surfactant orientation field to those in the interfacial height. (C) 2000 American Institute......, corresponding to the interfacial tension and the mean bending modulus are determined from the analyses of the long-wavelength behavior of the structure factor of the capillary waves. We found that the interfacial tension decreases with increasing surfactant interfacial coverage and/or surfactant chain length...

  9. Monolayer Superconductivity in WS2

    NARCIS (Netherlands)

    Zheliuk, Oleksandr; Lu, Jianming; Yang, Jie; Ye, Jianting

    Superconductivity in monolayer tungsten disulfide (2H-WS2) is achieved by strong electrostatic electron doping of an electric double-layer transistor (EDLT). Single crystals of WS2 are grown by a scalable method - chemical vapor deposition (CVD) on standard Si/SiO2 substrate. The monolayers are

  10. Molecular mechanics applied to single-walled carbon nanotubes

    OpenAIRE

    Ávila,Antonio Ferreira; Lacerda,Guilherme Silveira Rachid

    2008-01-01

    Single-walled carbon nanotubes, with stiffness of 1.0 TPa and strength of 60 GPa, are a natural choice for high strength materials. A problem, however, arises when experimental data are compiled. The large variability of experimental data leads to the development of numerical models denominated molecular mechanics, which is a "symbiotic" association of molecular dynamics and solid mechanics. This paper deals with molecular mechanics simulations of single-walled carbon nanotubes. To be able to...

  11. Direct imaging of hexaamine-ruthenium(III) in domain boundaries in monolayers of single-stranded DNA

    DEFF Research Database (Denmark)

    Grubb, Mikala; Wackerbarth, Hainer; Wengel, J.

    2007-01-01

    We describe adsorption and identification of the binding sites of [Ru(NH3)(6)](3+) (RuHex) molecules in a closely packed monolayer of a 13-base ss-DNA on Au(111) electrodes by electrochemical in situ scanning tunneling microscopy (STM), cyclic voltammetry and interfacial capacitance data. In situ...

  12. Charge Transport Across Insulating Self-Assembled Monolayers: Non-equilibrium Approaches and Modeling To Relate Current and Molecular Structure

    NARCIS (Netherlands)

    Mirjani, F.; Thijssen, J.M.; Whitesides, G.M.; Ratner, M.A.

    2014-01-01

    This paper examines charge transport by tunneling across a series of electrically insulating molecules with the structure HS(CH2)4CONH(CH2)2R) in the form of self-assembled monolayers (SAMs), supported on silver. The molecules examined were studied experimentally by Yoon et al. (Angew. Chem. Int.

  13. Formation of hydroxyl-functionalized stilbenoid molecular sieves at the liquid/solid interface on top of a 1-decanol monolayer

    Science.gov (United States)

    Bellec, Amandine; Arrigoni, Claire; Douillard, Ludovic; Fiorini-Debuisschert, Céline; Mathevet, Fabrice; Kreher, David; Attias, André-Jean; Charra, Fabrice

    2014-10-01

    Specific molecular tectons can be designed to form molecular sieves through self-assembly at the solid-liquid interface. After demonstrating a model tecton bearing apolar alkyl chains, we then focus on a modified structure involving asymmetric functionalization of some alkyl chains with polar hydroxyl groups in order to get chemical selectivity in the sieving. As the formation of supramolecular self-assembled networks strongly depends on molecule-molecule, molecule-substrate and molecule-solvent interactions, we compared the tectons’ self-assembly on graphite for two types of solvent. We demonstrate the possibility to create hydroxylated stilbenoid molecular sieves by using 1-decanol as a solvent. Interestingly, with this solvent, the porous network is developed on top of a 1-decanol monolayer.

  14. BRCA Testing by Single-Molecule Molecular Inversion Probes

    NARCIS (Netherlands)

    Neveling, K.; Mensenkamp, A.R.; Derks, R; Kwint, M.P.; Ouchene, H.; Steehouwer, M.; Lier, L.A. van; Bosgoed, E.A.J.; Rikken, A.; Tychon, M.W.J.; Zafeiropoulou, D.; Castelein, S.; Hehir-Kwa, J.Y.; Thung, G.W.; Hofste, T.; Lelieveld, S.H.; Bertens, S.M.; Adan, I.B.; Eijkelenboom, A.; Tops, B.B.J.; Yntema, H.G.; Stokowy, T.; Knappskog, P.M.; Hoberg-Vetti, H.; Steen, V.M.; Boyle, E.; Martin, B.; Ligtenberg, M.J.L.; Shendure, J.; Nelen, M.R.; Hoischen, A.

    2017-01-01

    BACKGROUND: Despite advances in next generation DNA sequencing (NGS), NGS-based single gene tests for diagnostic purposes require improvements in terms of completeness, quality, speed, and cost. Single-molecule molecular inversion probes (smMIPs) are a technology with unrealized potential in the

  15. Single Atomically Sharp Lateral Monolayer p-n Heterojunction Solar Cells with Extraordinarily High Power Conversion Efficiency.

    Science.gov (United States)

    Tsai, Meng-Lin; Li, Ming-Yang; Retamal, José Ramón Durán; Lam, Kai-Tak; Lin, Yung-Chang; Suenaga, Kazu; Chen, Lih-Juann; Liang, Gengchiau; Li, Lain-Jong; He, Jr-Hau

    2017-08-01

    The recent development of 2D monolayer lateral semiconductor has created new paradigm to develop p-n heterojunctions. Albeit, the growth methods of these heterostructures typically result in alloy structures at the interface, limiting the development for high-efficiency photovoltaic (PV) devices. Here, the PV properties of sequentially grown alloy-free 2D monolayer WSe 2 -MoS 2 lateral p-n heterojunction are explores. The PV devices show an extraordinary power conversion efficiency of 2.56% under AM 1.5G illumination. The large surface active area enables the full exposure of the depletion region, leading to excellent omnidirectional light harvesting characteristic with only 5% reduction of efficiency at incident angles up to 75°. Modeling studies demonstrate the PV devices comply with typical principles, increasing the feasibility for further development. Furthermore, the appropriate electrode-spacing design can lead to environment-independent PV properties. These robust PV properties deriving from the atomically sharp lateral p-n interface can help develop the next-generation photovoltaics. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Single Atomically Sharp Lateral Monolayer p-n Heterojunction Solar Cells with Extraordinarily High Power Conversion Efficiency

    KAUST Repository

    Tsai, Meng-Lin

    2017-06-26

    The recent development of 2D monolayer lateral semiconductor has created new paradigm to develop p-n heterojunctions. Albeit, the growth methods of these heterostructures typically result in alloy structures at the interface, limiting the development for high-efficiency photovoltaic (PV) devices. Here, the PV properties of sequentially grown alloy-free 2D monolayer WSe-MoS lateral p-n heterojunction are explores. The PV devices show an extraordinary power conversion efficiency of 2.56% under AM 1.5G illumination. The large surface active area enables the full exposure of the depletion region, leading to excellent omnidirectional light harvesting characteristic with only 5% reduction of efficiency at incident angles up to 75°. Modeling studies demonstrate the PV devices comply with typical principles, increasing the feasibility for further development. Furthermore, the appropriate electrode-spacing design can lead to environment-independent PV properties. These robust PV properties deriving from the atomically sharp lateral p-n interface can help develop the next-generation photovoltaics.

  17. Temperature-dependent Raman spectroscopy studies of the interface coupling effect of monolayer ReSe2 single crystals on Au foils

    Science.gov (United States)

    Jiang, Shaolong; Zhao, Liyun; Shi, Yuping; Xie, Chunyu; Zhang, Na; Zhang, Zhepeng; Huan, Yahuan; Yang, Pengfei; Hong, Min; Zhou, Xiebo; Shi, Jianping; Zhang, Qing; Zhang, Yanfeng

    2018-05-01

    Rhenium diselenide (ReSe2), which bears in-plane anisotropic optical and electrical properties, is of considerable interest for its excellent applications in novel devices, such as polarization-sensitive photodetectors and integrated polarization-controllers. However, great challenges to date in the controllable synthesis of high-quality ReSe2 have hindered its in-depth investigations and practical applications. Herein, we report a feasible synthesis of monolayer single-crystal ReSe2 flakes on the Au foil substrate by using a chemical vapor deposition route. Particularly, we focus on the temperature-dependent Raman spectroscopy investigations of monolayer ReSe2 grown on Au foils, which present concurrent red shifts of Eg-like and Ag-like modes with increasing measurement temperature from 77–290 K. Linear temperature dependences of both modes are revealed and explained from the anharmonic vibration of the ReSe2 lattice. More importantly, the strong interaction of ReSe2 with Au, with respect to that with SiO2/Si, is further confirmed by temperature-dependent Raman characterization. This work is thus proposed to shed light on the optical and thermal properties of such anisotropic two-dimensional three-atom-thick materials.

  18. Luminescent Organic Semiconducting Langmuir Monolayers.

    Science.gov (United States)

    Agina, Elena V; Mannanov, Artur A; Sizov, Alexey S; Vechter, Olga; Borshchev, Oleg V; Bakirov, Artem V; Shcherbina, Maxim A; Chvalun, Sergei N; Konstantinov, Vladislav G; Bruevich, Vladimir V; Kozlov, Oleg V; Pshenichnikov, Maxim S; Paraschuk, Dmitry Yu; Ponomarenko, Sergei A

    2017-05-31

    In recent years, monolayer organic field-effect devices such as transistors and sensors have demonstrated their high potential. In contrast, monolayer electroluminescent organic field-effect devices are still in their infancy. One of the key challenges here is to create an organic material that self-organizes in a monolayer and combines efficient charge transport with luminescence. Herein, we report a novel organosilicon derivative of oligothiophene-phenylene dimer D2-Und-PTTP-TMS (D2, tetramethyldisiloxane; Und, undecylenic spacer; P, 1,4-phenylene; T, 2,5-thiophene; TMS, trimethylsilyl) that meets these requirements. The self-assembled Langmuir monolayers of the dimer were investigated by steady-state and time-resolved photoluminescence spectroscopy, atomic force microscopy, X-ray reflectometry, and grazing-incidence X-ray diffraction, and their semiconducting properties were evaluated in organic field-effect transistors. We found that the best uniform, fully covered, highly ordered monolayers were semiconducting. Thus, the ordered two-dimensional (2D) packing of conjugated organic molecules in the semiconducting Langmuir monolayer is compatible with its high-yield luminescence, so that 2D molecular aggregation per se does not preclude highly luminescent properties. Our findings pave the way to the rational design of functional materials for monolayer organic light-emitting transistors and other optoelectronic devices.

  19. Controlling single-molecule junction conductance by molecular interactions

    Science.gov (United States)

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

    2015-01-01

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

  20. Kinetic energy distributions of molecular and cluster ions sputtered from self-assembled monolayers of octanethiol on gold

    International Nuclear Information System (INIS)

    Arezki, Bahia; Delcorte, Arnaud; Bertrand, Patrick

    2002-01-01

    Self-assembled monolayers (SAMs) of alkanethiols are an ideal model system to study the mechanisms that lead to emission of organic species under keV ion bombardment. In this contribution, we focus on the emission processes of gold-molecule cluster ions, which are not fully understood yet. To gain insights into these processes, monolayers of octanethiol CH 3 (CH 2 ) 7 SH adsorbed on gold are investigated using time-of-flight secondary ion mass spectrometry (ToF-SIMS). First, the static SIMS conditions are verified using the degradation of the SAM signals as a function of ion fluence. Second, the kinetic energy distributions (KEDs) of fragment, parent and cluster ions ejected upon 15 keV Ga + ion bombardment are measured. The peak maxima, FWHMs and high energy tails of the distributions are analyzed for Au-thiolate clusters, as well as thiol fragments. After calibration of the energy spectra using monoatomic ions, we find that the KEDs of all the clusters containing the thiolate molecule peak at about 1.2 eV. Besides, the distributions of the gold-molecule cluster ions including Au(M-H) 2 - , the most intense cluster peak in the spectrum, are significantly narrower than that of the hydrocarbon fragments

  1. Molecular-scale observation of YD2-o-C8 self-assembled monolayer on TiO2 (1 1 0)

    Science.gov (United States)

    Li, Ya-Juan; Sun, Lei; Jiang, Lei; Zhou, Qin; Ma, Zhi-Bo; Yang, Xue-Ming; Deng, Wei-Qiao

    2017-11-01

    The self-assembled monolayer (SAM) on TiO2 nanocrystal surface plays an important role in the processes of photoelectric conversion in dye sensitized solar cells (DSSCs). The SAM of dye YD2-o-C8, which was the best dye for DSSCs, has been observed by scanning tunneling microscope (STM) at molecular scale for the first time. The observation results showed that different morphologies of YD2-o-C8 SAM can be formed with or without chenodeoxycholic acid (cheno), which determined their corresponding photovoltaic cell efficiencies. The density functional theory (DFT) calculations explored the reason that was caused by the reduced electron coupling between side-to-side dimers separated by cheno molecules.

  2. Highly-Oriented Molecular Assembly on Monolayer Graphene for Boosting Photon Harvesting in Bilayer Organic Solar Cells

    Science.gov (United States)

    Cho, Kilwon

    2015-03-01

    A novel approach to dramatically enhance the photon harvesting in organic solar cells was demonstrated by utilizing a graphene-organic heterointerface. A large area, residue-free monolayer graphene was inserted at anodic interface to serve as an atomically thin, transparent and highly conductive epitaxial template for organic crystal growth with specific orientation. The anisotropic nature of optoelectronic properties of organic semiconductor molecules provided a significant enhancement in exciton diffusion length, optical absorption, charge carrier lifetime as well as the energy level alignment at metal-organic and organic-organic interfaces. Especially, the exciton diffusion length increases up to nearly 100 nm, which allows the device thickness to be doubled to yield 5 times higher power conversion efficiency in comparison to conventional planar heterojunction organic photovoltaic cells. Theoretical simulations as well as systematic studies on the film structure and optoelectrical properties were performed to corroborate our new findings.

  3. Excitons and trions in monolayer transition metal dichalcogenides: A comparative study between the multiband model and the quadratic single-band model

    Science.gov (United States)

    Van der Donck, M.; Zarenia, M.; Peeters, F. M.

    2017-07-01

    The electronic and structural properties of excitons and trions in monolayer transition metal dichalcogenides are investigated using both a multiband and a single-band model. In the multiband model we construct the excitonic Hamiltonian in the product base of the single-particle states at the conduction and valence band edges. We decouple the corresponding energy eigenvalue equation and solve the resulting differential equation self-consistently, using the finite element method (FEM), to determine the energy eigenvalues and the wave functions. As a comparison, we also consider the simple single-band model which is often used in numerical studies. We solve the energy eigenvalue equation using the FEM as well as with the stochastic variational method (SVM) in which a variational wave function is expanded in a basis of a large number of correlated Gaussians. We find good agreement between the results of both methods, as well as with other theoretical works for excitons, and we also compare with available experimental data. For trions the agreement between both methods is not as good due to our neglect of angular correlations when using the FEM. Finally, when comparing the two models, we see that the presence of the valence bands in the mutiband model leads to differences with the single-band model when (interband) interactions are strong.

  4. Reducing leakage currents in n-channel organic field-effect transistors using molecular dipole monolayers on nanoscale oxides.

    Science.gov (United States)

    Martínez Hardigree, Josué F; Dawidczyk, Thomas J; Ireland, Robert M; Johns, Gary L; Jung, Byung-Jun; Nyman, Mathias; Osterbacka, Ronald; Marković, Nina; Katz, Howard E

    2013-08-14

    Leakage currents through the gate dielectric of thin film transistors remain a roadblock to the fabrication of organic field-effect transistors (OFETs) on ultrathin dielectrics. We report the first investigation of a self-assembled monolayer (SAM) dipole as an electrostatic barrier to reduce leakage currents in n-channel OFETs fabricated on a minimal, leaky ∼10 nm SiO2 dielectric on highly doped Si. The electric field associated with 1H,1H,2H,2H-perfluoro-octyltriethoxysilane (FOTS) and octyltriethoxysilane (OTS) dipolar chains affixed to the oxide surface of n-Si gave an order of magnitude decrease in gate leakage current and subthreshold leakage and a two order-of-magnitude increase in ON/OFF ratio for a naphthalenetetracarboxylic diimide (NTCDI) transistor. Identically fabricated devices on p-Si showed similarly reduced leakage and improved performance for oxides treated with the larger dipole FOTS monolayer, while OTS devices showed poorer transfer characteristics than those on bare oxide. Comparison of OFETs on both substrates revealed that relative device performance from OTS and FOTS treatments was dictated primarily by the organosilane chain and not the underlying siloxane-substrate bond. This conclusion is supported by the similar threshold voltages (VT) extrapolated for SAM-treated devices, which display positive relative VT shifts for FOTS on either substrate but opposite VT shifts for OTS treatment on n-Si and p-Si. Our results highlight the potential of dipolar SAMs as performance-enhancing layers for marginal quality dielectrics, broadening the material spectrum for low power, ultrathin organic electronics.

  5. Poly(glycidyl ether)-Based Monolayers on Gold Surfaces: Control of Grafting Density and Chain Conformation by Grafting Procedure, Surface Anchor, and Molecular Weight.

    Science.gov (United States)

    Heinen, Silke; Weinhart, Marie

    2017-03-07

    For a meaningful correlation of surface coatings with their respective biological response reproducible coating procedures, well-defined surface coatings, and thorough surface characterization with respect to layer thickness and grafting density are indispensable. The same applies to polymeric monolayer coatings which are intended to be used for, e.g., fundamental studies on the volume phase transition of surface end-tethered thermoresponsive polymer chains. Planar gold surfaces are frequently used as model substrates, since they allow a variety of straightforward surface characterization methods. Herein we present reproducible grafting-to procedures performed with thermoresponsive poly(glycidyl ether) copolymers composed of glycidyl methyl ether (GME) and ethyl glycidyl ether (EGE). The copolymers feature different molecular weights (2 kDa, 9 kDa, 24 kDa) and are equipped with varying sulfur-containing anchor groups in order to achieve adjustable grafting densities on gold surfaces and hence control the tethered polymers' chain conformation. We determined "wet" and "dry" thicknesses of these coatings by QCM-D and ellipsometry measurements and deduced anchor distances and degrees of chain overlap of the polymer chains assembled on gold. Grafting under cloud point conditions allowed for higher degrees of chain overlap compared to grafting from a good solvent like ethanol, independent of the used sulfur-containing anchor group for polymers with low (2 kDa) and medium (9 kDa) molecular weights. By contrast, the achieved grafting densities and thus chain overlaps of surface-tethered polymers with high (24 kDa) molecular weights were identical for both grafting methods. Monolayers prepared from an ethanolic solution of poly(glycidyl ether)s equipped with sterically demanding disulfide-containing anchors revealed the lowest degrees of chain overlap. The ratio of the radius of gyration to the anchor distance (2 R g /l) of the latter coating was found to be lower than 1

  6. Lateral pressure profiles in lipid monolayers

    NARCIS (Netherlands)

    Baoukina, Svetlana; Marrink, Siewert J.; Tieleman, D. Peter

    2010-01-01

    We have used molecular dynamics simulations with coarse-grained and atomistic models to study the lateral pressure profiles in lipid monolayers. We first consider simple oil/air and oil/water interfaces, and then proceed to lipid monolayers at air/water and oil/water interfaces. The results are

  7. Mechanical Model of Geometric Cell and Topological Algorithm for Cell Dynamics from Single-Cell to Formation of Monolayered Tissues with Pattern

    KAUST Repository

    Kachalo, Sëma

    2015-05-14

    Geometric and mechanical properties of individual cells and interactions among neighboring cells are the basis of formation of tissue patterns. Understanding the complex interplay of cells is essential for gaining insight into embryogenesis, tissue development, and other emerging behavior. Here we describe a cell model and an efficient geometric algorithm for studying the dynamic process of tissue formation in 2D (e.g. epithelial tissues). Our approach improves upon previous methods by incorporating properties of individual cells as well as detailed description of the dynamic growth process, with all topological changes accounted for. Cell size, shape, and division plane orientation are modeled realistically. In addition, cell birth, cell growth, cell shrinkage, cell death, cell division, cell collision, and cell rearrangements are now fully accounted for. Different models of cell-cell interactions, such as lateral inhibition during the process of growth, can be studied in detail. Cellular pattern formation for monolayered tissues from arbitrary initial conditions, including that of a single cell, can also be studied in detail. Computational efficiency is achieved through the employment of a special data structure that ensures access to neighboring cells in constant time, without additional space requirement. We have successfully generated tissues consisting of more than 20,000 cells starting from 2 cells within 1 hour. We show that our model can be used to study embryogenesis, tissue fusion, and cell apoptosis. We give detailed study of the classical developmental process of bristle formation on the epidermis of D. melanogaster and the fundamental problem of homeostatic size control in epithelial tissues. Simulation results reveal significant roles of solubility of secreted factors in both the bristle formation and the homeostatic control of tissue size. Our method can be used to study broad problems in monolayered tissue formation. Our software is publicly

  8. Mechanical model of geometric cell and topological algorithm for cell dynamics from single-cell to formation of monolayered tissues with pattern.

    Directory of Open Access Journals (Sweden)

    Sëma Kachalo

    Full Text Available Geometric and mechanical properties of individual cells and interactions among neighboring cells are the basis of formation of tissue patterns. Understanding the complex interplay of cells is essential for gaining insight into embryogenesis, tissue development, and other emerging behavior. Here we describe a cell model and an efficient geometric algorithm for studying the dynamic process of tissue formation in 2D (e.g. epithelial tissues. Our approach improves upon previous methods by incorporating properties of individual cells as well as detailed description of the dynamic growth process, with all topological changes accounted for. Cell size, shape, and division plane orientation are modeled realistically. In addition, cell birth, cell growth, cell shrinkage, cell death, cell division, cell collision, and cell rearrangements are now fully accounted for. Different models of cell-cell interactions, such as lateral inhibition during the process of growth, can be studied in detail. Cellular pattern formation for monolayered tissues from arbitrary initial conditions, including that of a single cell, can also be studied in detail. Computational efficiency is achieved through the employment of a special data structure that ensures access to neighboring cells in constant time, without additional space requirement. We have successfully generated tissues consisting of more than 20,000 cells starting from 2 cells within 1 hour. We show that our model can be used to study embryogenesis, tissue fusion, and cell apoptosis. We give detailed study of the classical developmental process of bristle formation on the epidermis of D. melanogaster and the fundamental problem of homeostatic size control in epithelial tissues. Simulation results reveal significant roles of solubility of secreted factors in both the bristle formation and the homeostatic control of tissue size. Our method can be used to study broad problems in monolayered tissue formation. Our software

  9. Probing single nanometer-scale pores with polymeric molecular rulers

    Science.gov (United States)

    Henrickson, Sarah E.; DiMarzio, Edmund A.; Wang, Qian; Stanford, Vincent M.; Kasianowicz, John J.

    2010-04-01

    We previously demonstrated that individual molecules of single-stranded DNA can be driven electrophoretically through a single Staphylococcus aureus α-hemolysin ion channel. Polynucleotides thread through the channel as extended chains and the polymer-induced ionic current blockades exhibit stable modes during the interactions. We show here that polynucleotides can be used to probe structural features of the α-hemolysin channel itself. Specifically, both the pore length and channel aperture profile can be estimated. The results are consistent with the channel crystal structure and suggest that polymer-based "molecular rulers" may prove useful in deducing the structures of nanometer-scale pores in general.

  10. Optofluidic lasers with a single molecular layer of gain

    Science.gov (United States)

    Chen, Qiushu; Ritt, Michael; Sivaramakrishnan, Sivaraj; Sun, Yuze; Fan, Xudong

    2014-01-01

    We achieve optofluidic lasers with a single molecular layer of gain, in which green fluorescent protein, dye-labeled bovine serum albumin, and dye-labeled DNA are respectively used as the gain medium and attached to the surface of a ring resonator via surface immobilization biochemical methods. It is estimated that the surface density of the gain molecules is on the order of 1012/cm2, sufficient for lasing under pulsed optical excitation. It is further shown that the optofluidic laser can be tuned by energy transfer mechanisms through biomolecular interactions. This work not only opens a door to novel photonic devices that can be controlled at the level of a single molecular layer, but also provides a promising sensing platform to analyze biochemical processes at the solid-liquid interface. PMID:25312306

  11. In silico modelling of permeation enhancement potency in Caco-2 monolayers based on molecular descriptors and random forest

    DEFF Research Database (Denmark)

    Welling, Søren Havelund; Clemmensen, Line Katrine Harder; Buckley, Stephen T.

    2015-01-01

    has been developed.The random forest-QSAR model was based upon Caco-2 data for 41 surfactant-like permeation enhancers from Whitehead et al. (2008) and molecular descriptors calculated from their structure.The QSAR model was validated by two test-sets: (i) an eleven compound experimental set with Caco......-2 data and (ii) nine compounds with Caco-2 data from literature. Feature contributions, a recent developed diagnostic tool, was applied to elucidate the contribution of individual molecular descriptors to the predicted potency. Feature contributions provided easy interpretable suggestions...

  12. Single orientation graphene synthesized on iridium thin films grown by molecular beam epitaxy

    OpenAIRE

    Dangwal Pandey, A.; Krausert, Konstantin; Franz, D.; Grånäs, E.; Shayduk, R.; Müller, P.; Keller, Thomas F.; Noei, H.; Vonk, V.; Stierle, A.

    2016-01-01

    Heteroepitaxial iridium thin films were deposited on (0001) sapphire substrates by means of molecular beam epitaxy, and subsequently, one monolayer of graphene was synthesized by chemical vapor deposition. The influence of the growth parameters on the quality of the Ir films, as well as of graphene, was investigated system atically by means of low energy electron diffraction, x-ray reflectivity, x-ray diffraction, Auger electron spectroscopy, scanning electron microscopy, and atomic force mic...

  13. A single molecular marker to distinguish between species of Dioscorea.

    Science.gov (United States)

    Techen, Natascha; Parveen, Iffat; Khan, Ikhlas A

    2017-03-01

    Yams are species of the genus Dioscorea (family Dioscoreaceae), which consists of approximately 630 species. The majority of the world production of yams occurs in Africa with 58.8 million t annually, but they are also produced in the Americas and Asia. The saponins in yams have been reported to possess various properties to improve health. The tuber and aerial parts of various species often share morphological similarities, which can cause problems in the proper identification of sample material. For example, the rootstocks and aerial parts of Dioscorea villosa L. share similarities with Dioscorea polystachia Turcz. Dioscorea bulbifera L. may be mistaken for Dioscorea alata L. owing to similar morphologies. Various molecular analyses have been published to help with the identification of species and varieties within the genus Dioscorea. The multi-loci or single-locus analysis has resulted in varying success, some with only a limited discrimination rate. In the present study, a single nuclear genomic region, biparentally inherited, was analyzed for its usefulness as a molecular marker for species identification and discrimination between D. bulbifera, D. villosa, D. nipponica, D. alata, D. caucasica, and D. deltoidea samples. The results of this study show that the LFY genomic region can be useful as a molecular marker to distinguish between samples.

  14. Molecular single photon double K-shell ionization

    International Nuclear Information System (INIS)

    Penent, F.; Nakano, M.; Tashiro, M.; Grozdanov, T.P.; Žitnik, M.; Carniato, S.; Selles, P.; Andric, L.; Lablanquie, P.; Palaudoux, J.; Shigemasa, E.; Iwayama, H.; Hikosaka, Y.; Soejima, K.; Suzuki, I.H.; Kouchi, N.; Ito, K.

    2014-01-01

    We have studied single photon double K-shell ionization of small molecules (N 2 , CO, C 2 H 2n (n = 1–3), …) and the Auger decay of the resulting double core hole (DCH) molecular ions thanks to multi-electron coincidence spectroscopy using a magnetic bottle time-of-flight spectrometer. The relative cross-sections for single-site (K −2 ) and two-site (K −1 K −1 ) double K-shell ionization with respect to single K-shell (K −1 ) ionization have been measured that gives important information on the mechanisms of single photon double ionization. The spectroscopy of two-site (K −1 K −1 ) DCH states in the C 2 H 2n (n = 1–3) series shows important chemical shifts due to a strong dependence on the C-C bond length. In addition, the complete cascade Auger decay following single site (K −2 ) ionization has been obtained

  15. Molecular dynamics study of the effect of calcium ions on the monolayer of SDC and SDSn surfactants at the vapor/liquid interface.

    Science.gov (United States)

    Yan, Hui; Guo, Xin-Li; Yuan, Shi-Ling; Liu, Cheng-Bu

    2011-05-17

    The effect of Ca(2+) ions on the hydration shell of sodium dodecyl carboxylate (SDC) and sodium dodecyl sulfonate (SDSn) monolayer at vapor/liquid interfaces was studied using molecular dynamics simulations. For each surfactant, two different surface concentrations were used to perform the simulations, and the aggregation morphologies and structural details have been reported. The results showed that the aggregation structures relate to both the surface coverage and the calcium ions. The divalent ions can screen the interaction between the polar head and Na(+) ions. Thus, Ca(2+) ions locate near the vapor/liquid interface to bind to the headgroup, making the aggregations much more compact via the salt bridge. The potential of mean force (PMF) between Ca(2+) and the headgroups shows that the interaction is decided by a stabilizing solvent-separated minimum in the PMF. To bind to the headgroup, Ca(2+) should overcome the energy barrier. Among contributions to the PMF, the major repulsive interaction was due to the rearrangement of the hydration shell after the calcium ions entered into the hydration shell of the headgroup. The PMFs between the headgroup and Ca(2+) in the SDSn systems showed higher energy barriers than those in the SDC systems. This result indicated that SDSn binds the divalent ions with more difficulty compared with SDC, so the ions have a strong effect on the hydration shell of SDC. That is why sulfonate surfactants have better efficiency in salt solutions with Ca(2+) ions for enhanced oil recovery.

  16. Manipulating localized molecular orbitals by single-atom contacts.

    Science.gov (United States)

    Wang, Weihua; Shi, Xingqiang; Lin, Chensheng; Zhang, Rui Qin; Minot, Christian; Van Hove, Michel A; Hong, Yuning; Tang, Ben Zhong; Lin, Nian

    2010-09-17

    We have fabricated atom-molecule contacts by attachment of single Cu atoms to terpyridine side groups of bis-terpyridine tetra-phenyl ethylene molecules on a Cu(111) surface. By means of scanning tunneling microscopy, spectroscopy, and density functional calculations, we have found that, due to the localization characteristics of molecular orbitals, the Cu-atom contact modifies the state localized at the terpyridine side group which is in contact with the Cu atom but does not affect the states localized at other parts of the molecule. These results illustrate the contact effects at individual orbitals and offer possibilities to manipulate orbital alignments within molecules.

  17. Patterning the molecular printboard: patterning cyclodextrin monolayers on silicon oxide using nanoimprint lithography and its application in 3D multilayer nanostructuring

    International Nuclear Information System (INIS)

    Maury, Pascale; Peter, Maria; Crespo-Biel, Olga; Ling, Xing Yi; Reinhoudt, David N; Huskens, Jurriaan

    2007-01-01

    An accurate and versatile process for the fabrication of high-resolution 3D nanostructures combining top-down and bottom-up nanofabrication schemes is described here. The method is based on layer-by-layer (LBL) assembly of functionalized nanoparticles (NPs) bound together by means of supramolecular interactions between a layer of adamantyl-functionalized dendrimers, the guest, and cyclodextrin (CD)-functionalized nanoparticles, the host. First, a self-assembled CD monolayer (CD SAM) was patterned using nanoimprint lithography (NIL) and later used to anchor supramolecular LBL assemblies onto it. The versatility of the process was demonstrated by using NPs of different size and nature. Two types of LBL assemblies were fabricated based on (i) 2.8 nm CD-functionalized Au NPs, which allow an accurate height control and (ii) 60 nm CD-functionalized SiO 2 particles, which permit the fabrication of nanostructures. In one of the cases vertical deposition was used to obtain high particle ordering. Both types of NP were used to produce nanostructured LBL assemblies with lateral sizes below 100 nm. Physical confinement was observed when using 60 nm CD-functionalized SiO 2 particles in the sub-300 nm scale on the first and second bilayers. Finally, periodic patterns of single nanoparticles were achieved

  18. Single molecular biology: coming of age in DNA replication.

    Science.gov (United States)

    Liu, Xiao-Jing; Lou, Hui-Qiang

    2017-09-20

    DNA replication is an essential process of the living organisms. To achieve precise and reliable replication, DNA polymerases play a central role in DNA synthesis. Previous investigations have shown that the average rates of DNA synthesis on the leading and lagging strands in a replisome must be similar to avoid the formation of significant gaps in the nascent strands. The underlying mechanism has been assumed to be coordination between leading- and lagging-strand polymerases. However, Kowalczykowski's lab members recently performed single molecule techniques in E. coli and showed the real-time behavior of a replisome. The leading- and lagging-strand polymerases function stochastically and independently. Furthermore, when a DNA polymerase is paused, the helicase slows down in a self-regulating fail-safe mechanism, akin to a ''dead-man's switch''. Based on the real-time single-molecular observation, the authors propose that leading- and lagging-strand polymerases synthesize DNA stochastically within a Gaussian distribution. Along with the development and application of single-molecule techniques, we will witness a new age of DNA replication and other biological researches.

  19. High-Performance n-Channel Organic Transistors Using High-Molecular-Weight Electron-Deficient Copolymers and Amine-Tailed Self-Assembled Monolayers.

    Science.gov (United States)

    Wang, Yang; Hasegawa, Tsukasa; Matsumoto, Hidetoshi; Mori, Takehiko; Michinobu, Tsuyoshi

    2018-03-01

    While high-performance p-type semiconducting polymers are widely reported, their n-type counterparts are still rare in terms of quantity and quality. Here, an improved Stille polymerization protocol using chlorobenzene as the solvent and palladium(0)/copper(I) as the catalyst is developed to synthesize high-quality n-type polymers with number-average molecular weight up to 10 5 g mol -1 . Furthermore, by sp 2 -nitrogen atoms (sp 2 -N) substitution, three new n-type polymers, namely, pBTTz, pPPT, and pSNT, are synthesized, and the effect of different sp 2 -N substitution positions on the device performances is studied for the first time. It is found that the incorporation of sp 2 -N into the acceptor units rather than the donor units results in superior crystalline microstructures and higher electron mobilities. Furthermore, an amine-tailed self-assembled monolayer (SAM) is smoothly formed on a Si/SiO 2 substrate by a simple spin-coating technique, which can facilitate the accumulation of electrons and lead to more perfect unipolar n-type transistor performances. Therefore, a remarkably high unipolar electron mobility up to 5.35 cm 2 V -1 s -1 with a low threshold voltage (≈1 V) and high on/off current ratio of ≈10 7 is demonstrated for the pSNT-based devices, which are among the highest values for unipolar n-type semiconducting polymers. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Spin models for the single molecular magnet Mn12-AC

    Science.gov (United States)

    Al-Saqer, Mohamad A.

    2005-11-01

    The single molecular magnet (SMM) Mn12-AC attracted the attention of scientists since the discovery of its magnetic hystereses which are accompanied by sudden jumps in magnetic moments at low temperature. Unlike conventional bulk magnets, hysteresis in SMMs is of molecular origin. This qualifies them as candidates for next generation of high density storage media where a molecule which is at most few nanometers in size can be used to store a bit of information. However, the jumps in these hystereses, due to spin tunneling, can lead to undesired loss of information. Mn12-AC molecule contains twelve magnetic ions antiferromagnetically coupled by exchanges leading to S = 10 ground state manifold. The magnetic ions are surrounded by ligands which isolate them magnetically from neighboring molecules. The lowest state of S = 9 manifold is believed to lie at about 40 K above the ground state. Therefore, at low temperatures, the molecule is considered as a single uncoupled moment of spin S = 10. Such model has been used widely to understand phenomena exhibited by the molecule at low temperatures including the tunneling of its spin, while a little attention has been paid for the multi-spin nature of the molecule. Using the 8-spin model, we demonstrate that in order to understand the phenomena of tunneling, a full spin description of the molecule is required. We utilized a calculation scheme where a fraction of energy levels are used in the calculations and the influence of levels having higher energy is neglected. From the dependence of tunnel splittings on the number of states include, we conclude that models based on restricting the number of energy levels (single-spin and 8-spin models) lead to unreliable results of tunnel splitting calculations. To attack the full 12-spin model, we employed the Davidson algorithm to calculated lowest energy levels produced by exchange interactions and single ion anisotropies. The model reproduces the anisotropy properties at low

  1. Nonlinear and Nonsymmetric Single-Molecule Electronic Properties Towards Molecular Information Processing.

    Science.gov (United States)

    Tamaki, Takashi; Ogawa, Takuji

    2017-09-05

    This review highlights molecular design for nonlinear and nonsymmetric single-molecule electronic properties such as rectification, negative differential resistance, and switching, which are important components of future single-molecule information processing devices. Perspectives on integrated "molecular circuits" are also provided. Nonlinear and nonsymmetric single-molecule electronics can be designed by utilizing (1) asymmetric molecular cores, (2) asymmetric anchoring groups, (3) an asymmetric junction environment, and (4) asymmetric electrode materials. This review mainly focuses on the design of molecular cores.

  2. Molecular Etiology of Hereditary Single-Side Deafness

    Science.gov (United States)

    Kim, Shin Hye; Kim, Ah Reum; Choi, Hyun Seok; Kim, Min Young; Chun, Eun Hi; Oh, Seung-Ha; Choi, Byung Yoon

    2015-01-01

    Abstract Unilateral sensorineural hearing loss (USNHL)/single-side deafness (SSD) is a frequently encountered disability in children. The etiology of a substantial portion of USNHL/SSD still remains unknown, and genetic causes have not been clearly elucidated. In this study, the authors evaluated the heritability of USNHL/SSD. The authors sequentially recruited 50 unrelated children with SSD. For an etiologic diagnosis, we performed a rigorous review on the phenotypes of family members of all children and conducted, if necessary, molecular genetic tests including targeted exome sequencing of 129 deafness genes. Among the 50 SSD children cohort, the authors identify 4 (8%) unrelated SSD probands from 4 families (SH136, SB173, SB177, and SB199) with another hearing impaired family members. Notably, all 4 probands in our cohort with a familial history of SSD also have pigmentary abnormalities such as brown freckles or premature gray hair within first degree relatives, which may indicate that genes whose products are involved with pigmentary disorder could be candidates for heritable SSD. Indeed, SH136 and SB199 turned out to segregate a mutation in MITF and PAX3, respectively, leading to a molecular diagnosis of Waardenburg syndrome (WS). We report, for the first time in the literature, a significant heritability of pediatric SSD. There is a strong association between the heritability of USNHL/SSD and the pigmentary abnormality, shedding a new light on the understanding of the molecular basis of heritable USNHL/SSD. In case of children with congenital SSD, it would be mandatory to rigorously screen pigmentary abnormalities. WS should also be included in the differential diagnosis of children with USNHL/SSD, especially in a familial form. PMID:26512583

  3. Atomically precise graphene nanoribbon heterojunctions from a single molecular precursor

    Science.gov (United States)

    Nguyen, Giang D.; Tsai, Hsin-Zon; Omrani, Arash A.; Marangoni, Tomas; Wu, Meng; Rizzo, Daniel J.; Rodgers, Griffin F.; Cloke, Ryan R.; Durr, Rebecca A.; Sakai, Yuki; Liou, Franklin; Aikawa, Andrew S.; Chelikowsky, James R.; Louie, Steven G.; Fischer, Felix R.; Crommie, Michael F.

    2017-11-01

    The rational bottom-up synthesis of atomically defined graphene nanoribbon (GNR) heterojunctions represents an enabling technology for the design of nanoscale electronic devices. Synthetic strategies used thus far have relied on the random copolymerization of two electronically distinct molecular precursors to yield GNR heterojunctions. Here we report the fabrication and electronic characterization of atomically precise GNR heterojunctions prepared through late-stage functionalization of chevron GNRs obtained from a single precursor. Post-growth excitation of fully cyclized GNRs induces cleavage of sacrificial carbonyl groups, resulting in atomically well-defined heterojunctions within a single GNR. The GNR heterojunction structure was characterized using bond-resolved scanning tunnelling microscopy, which enables chemical bond imaging at T = 4.5 K. Scanning tunnelling spectroscopy reveals that band alignment across the heterojunction interface yields a type II heterojunction, in agreement with first-principles calculations. GNR heterojunction band realignment proceeds over a distance less than 1 nm, leading to extremely large effective fields.

  4. Polymorphic transitions in single crystals: A new molecular dynamics method

    Energy Technology Data Exchange (ETDEWEB)

    Parrinello, M.; Rahman, A.

    1981-12-01

    A new Lagrangian formulation is introduced. It can be used to make molecular dynamics (MD) calculations on systems under the most general, externally applied, conditions of stress. In this formulation the MD cell shape and size can change according to dynamical equations given by this Lagrangian. This new MD technique is well suited to the study of structural transformations in solids under external stress and at finite temperature. As an example of the use of this technique we show how a single crystal of Ni behaves under uniform uniaxial compressive and tensile loads. This work confirms some of the results of static (i.e., zero temperature) calculations reported in the literature. We also show that some results regarding the stress-strain relation obtained by static calculations are invalid at finite temperature. We find that, under compressive loading, our model of Ni shows a bifurcation in its stress-strain relation; this bifurcation provides a link in configuration space between cubic and hexagonal close packing. It is suggested that such a transformation could perhaps be observed experimentally under extreme conditions of shock.

  5. I. Enabling Single-Chain Surfactants to Form Vesicles by Nonamphiphilic Liquid Crystals in Water II. Controlling Attachment and Ligand-Mediated Adherence of Candida albicans on Monolayers

    Science.gov (United States)

    Varghese, Nisha

    This dissertation describes a fundamental study of weak noncovalent interactions and surface forces that exist at the interfaces of various interacting moieties (small molecules or microbes), and its relevance to colloidal and material chemistry. Chapter 1 presents an emulsion system that enables single-chain anionic or nonionic surfactants to sequester and encapsulate certain water-soluble organic salts, leading to the formation of vesicles in water. The water-soluble organic salt in the system comprises of disodium cromoglycate crystals that are emulsified by surfactants in water to form stable liquid crystal droplets. The work provides an exception to the rule of geometric packing factor that dictates formation of micelles by the surfactants in water. Chapter 2 shows that the odd or even number of carbon atoms present in the aliphatic chain of surfactants affect the ability of surfactants to emulsify aqueous-based liquid crystals of disodium cromoglycate. Such an odd-even effect is frequently observed for solid state properties like melting point, heat of fusion and refractive index but is rarely observed for molecules present in solution. When mixed in water, anionic single-chain surfactants with odd number of carbon atoms emulsifies disodium cromoglycate to form liquid crystal droplets, while surfactants with even number of carbon atoms fail to emulsify disodium cromoglycate. Chapter 3 Bolaamphiphiles usually form vesicles only in extreme conditions or in the presence of surfactants. Here, we explore the co-assembly system of synthesized bolaamphiphiles and disodium cromoglycate in water. The combination of the self-assembly forces of the bolaamphiphile and self-associating property of disodium cromoglycate liquid crystals act together at the interface form a unique microemulsion of liquid crystal droplets of disodium cromoglycate embedded in liquid crystal phase. Chapter 4 describes a key event (adhesion) that precedes infections caused by Candida albicans

  6. Coexistence of type-I and type-II band line-ups in 1-2 monolayer thick GaN/AlN single quantum wells

    Science.gov (United States)

    Evropeytsev, E. A.; Jmerik, V. N.; Nechaev, D. V.; Rouvimov, S.; Shubina, T. V.; Kaibyshev, V. Kh; Pozina, G.; Ivanov, S. V.; Toropov, A. A.

    2017-11-01

    GaN/AlN quantum wells (QWs) with varied nominal thickness of 0.5-4 monolayers have been studied by time-resolved photoluminescence (PL) spectroscopy. The structures demonstrate an emission peak with the thickness-dependent wavelength in the range 225-320 nm. The observed temporal behavior of PL between 225 and 280 nm can be described as a superposition of fast and slow decaying components with characteristic decay time constants of the order of 0.1-0.7 ns and 7-30 ns, respectively. The fast PL component with the decay time smaller than 1 ns dominates in the thicker GaN insertions and tends to vanish in the thinnest ones, where the slow PL component becomes progressively longer. These observations imply formation in the GaN/AlN monolayer-thick layers of an inhomogeneous excitonic system involving both direct and indirect in space excitons.

  7. Molecular Assembly of Hemin on Single-Crystal Au(111)-electrode Surfaces

    DEFF Research Database (Denmark)

    Zhang, Ling; Ulstrup, Jens; Zhang, Jingdong

    also acts as catalyst in electrochemical reduction of dioxygen and other small inert molecules such as nitrogen monoxide, and in electrochemiluminescent detection of dioxygen, peroxide, DNA, and proteins. л-л interactions of hemin with carbon materials have been broadly studied. Hemin onnoble metal......-defined single-crystal Au(111)-electrodesurfaces using electrochemistry combined with scanning tunnelling microscopy under electrochemical control. Hemin gives two voltammetric peaks assigned to adsorbed monomers and dimmers (Fig. 1A). In situ STM shows that hemin self-assembles in ordered monolayers through non...

  8. Light and Redox Switchable Molecular Components for Molecular Electronics

    NARCIS (Netherlands)

    Browne, Wesley R.; Feringa, Bernard

    2010-01-01

    The field of molecular and organic electronics has seen rapid progress in recent years, developing from concept and design to actual demonstration devices in which both single molecules and self-assembled monolayers are employed as light-responsive components. Research in this field has seen

  9. Characterization of heterojunctions via x-ray and uv photoemission spectroscopy: energy level implications for single and mixed monolayer SAMs, cadmium selenide nanoparticle films, and organic semiconductor depositions

    Science.gov (United States)

    Graham, Amy L.

    This work has centered on the interface dipoles arising at heterojunctions between metals, semiconductor nanoparticles, self-assembled monolayers, and organic semiconductor materials. Alkanethiol self-assembled monolayers, CdSe nanocrystals, and the organic semiconductors zinc phthalocyanine (ZnPc) and Buckminster fullerene (C60) were the basis of these investigations. UV photoemission spectroscopy has proven to be an invaluable tool to observe the vacuum level shifts for these analyses while using XPS to corroborate surface structure. With a full evaluation of these surfaces, the shifts in the vacuum level, valence ionizations, and core ionizations, the impact of these interfaces, as well as their influence on the subsequent deposition of organic semiconductor layers is established. Alkanethiols possessing varying dipole moments were examined on gold and silver substrates. The viability of these alkanethiols was demonstrated to predictively adjust the work function of these metals as a function of their intrinsic dipole moments projected to surface normal, and established differences between Ag---S and Au---S bonds. The capability of the SAMs to modify the work function of gold provided an opportunity for mixed monolayers of the alkanethiols to produce a precise range of work functions by minimal adjustments of solution concentration, which were examined with a simple point dipole model. Photoemission spectroscopy offers a thorough analysis of CdSe nanoparticle films. Despite a plethora of research on these nanocrystals, there still is controversy on the magnitude of the shift in the valence band with diameter. In our research we found the majority of the valence band shift could be attributed to the interface dipole, ignored previously. Meanwhile, the valence band tethered films was obscured by the sulfur of the thiol tether. Finally, organic semiconductor layers deposited on SAMs on gold exhibited various interface dipole effects at these heterojunctions. Charge

  10. Exploring the electron density localization in single MoS2 monolayers by means of a localize-electrons detector and the quantum theory of atoms in molecules

    Directory of Open Access Journals (Sweden)

    Yosslen Aray

    2017-11-01

    Full Text Available The nature of the electron density localization in a MoS2 monolayer under 0 % to 11% tensile strain has been systematically studied by means of a localized electron detector function and the Quantum Theory of atoms in molecules. At 10% tensile strain, this monolayer become metallic. It was found that for less than 6.5% of applied stress, the same atomic structure of the equilibrium geometry (0% strain is maintained; while over 6.5% strain induces a transformation to a structure where the sulfur atoms placed on the top and bottom layer form S2 groups. The localized electron detector function shows the presence of zones of highly electron delocalization extending throughout the Mo central layer. For less than 10% tensile strain, these zones comprise the BCPs and the remainder CPs in separates regions of the space; while for the structures beyond 10% strain, all the critical points are involved in a region of highly delocalized electrons that extends throughout the material. This dissimilar electron localization pattern is like to that previously reported for semiconductors such as Ge bulk and metallic systems such as transition metals bulk.

  11. Molecular electronics: the single molecule switch and transistor

    NARCIS (Netherlands)

    Sotthewes, Kai; Geskin, Victor; Heimbuch, Rene; Kumar, Avijit; Zandvliet, Henricus J.W.

    2014-01-01

    In order to design and realize single-molecule devices it is essential to have a good understanding of the properties of an individual molecule. For electronic applications, the most important property of a molecule is its conductance. Here we show how a single octanethiol molecule can be connected

  12. Nanotubes based on monolayer blue phosphorus

    KAUST Repository

    Montes Muñoz, Enrique

    2016-07-08

    We demonstrate structural stability of monolayer zigzag and armchair blue phosphorus nanotubes by means of molecular dynamics simulations. The vibrational spectrum and electronic band structure are determined and analyzed as functions of the tube diameter and axial strain. The nanotubes are found to be semiconductors with a sensitive indirect band gap that allows flexible tuning.

  13. Perforated monolayers. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Regen. Steven L.

    2000-06-01

    This STI is a final report for a DOE-supported program, ''Perforated Monolayers,'' which focused on the fabrication of ultrathin membranes for gas separations based on Langmuir-Blodgett chemistry.

  14. Monolayer-by-monolayer growth of platinum films on complex carbon fiber paper structure

    Energy Technology Data Exchange (ETDEWEB)

    Pang, Liuqing; Zhang, Yunxia [Key Laboratory of Applied Surface and Colloid Chemistry, National Ministry of Education, Shaanxi Key Laboratory for Advanced Energy Devices, Shaanxi Engineering Lab for Advanced Energy Technology, School of Materials Science and Engineering, Shaanxi Normal University, Xi’an 710119 (China); Liu, Shengzhong, E-mail: szliu@dicp.ac.cn [Key Laboratory of Applied Surface and Colloid Chemistry, National Ministry of Education, Shaanxi Key Laboratory for Advanced Energy Devices, Shaanxi Engineering Lab for Advanced Energy Technology, School of Materials Science and Engineering, Shaanxi Normal University, Xi’an 710119 (China); Dalian National Laboratory for Clean Energy, iChEM, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China)

    2017-06-15

    Graphical abstract: A controlled monolayer-by-monolayer deposition process has been developed to fabricate Pt coating on carbon fiber paper with complex network structures using a dual buffer strategy. This development may pave a way to fabricate superior Pt catalysts with the minimal Pt usage. In fact, the present Pt group metal loading is 25 times lower than the U.S. DOE 2017 target value. - Highlights: • Developed a controlled monolayer-by-monolayer Pt deposition using a dual buffer strategy. • The present Pt group metal loading is 25 times lower than the U.S. DOE 2017 target value. • This development may pave a way to fabricate superior Pt catalysts with the minimal Pt usage. - Abstract: A controlled monolayer-by-monolayer deposition process has been developed to fabricate Pt coating on carbon fiber paper with complex network structures using a dual buffer (Au/Ni) strategy. The X-ray diffraction, electrochemical quartz crystal microbalance, current density analyses, and X-ray photoelectron spectroscopy results conclude that the monolayer deposition process accomplishes full coverage on the substrate and that the thickness of the deposition layer can be controlled on a single atom scale. This development may pave a way to fabricate superior Pt catalysts with the minimal Pt usage. In fact, the present Pt group metal loading is 25 times lower than the U.S. DOE 2017 target value.

  15. Coexistence of multiple conformations in cysteamine monolayers on Au(111)

    DEFF Research Database (Denmark)

    Zhang, Jingdong; Bilic, A; Reimers, JR

    2005-01-01

    The structural organization, catalytic function, and electronic properties of cysteamine monolayers on Au(111) have been addressed comprehensively by voltammetry, in situ scanning tunneling microscopy (STM) in anaerobic environment, and a priori molecular dynamics (MD) simulation and STM image si...

  16. Molecular analysis of desmoid tumors with a high-density single-nucleotide polymorphism array identifies new molecular candidate lesions

    OpenAIRE

    Erben, Philipp; Nowak, Daniel; Sauer, Christian; Ströbel, Philipp; Hofmann, Wolf-Karsten; Hofheinz, Ralf-Dieter; Hohenberger, Peter; Kasper, Bernd

    2012-01-01

    Background: Desmoid tumors are neoplastic proliferations of connective tissues. The mutation status of the gene coding for catenin (cadherin-associated protein) beta 1 (CTNNB1) and trisomy 8 on the chromosomal level have been described to have prognostic relevance. Patients and Methods: In order to elucidate new molecular mechanisms underlying these tumors, we carried out a molecular analysis with a genome-wide human high-density single-nucleotide polymorphism (SNP) array, in 9 patients. Resu...

  17. Toward Molecular 4f Single-Ion Magnet Qubits.

    Science.gov (United States)

    Pedersen, Kasper S; Ariciu, Ana-Maria; McAdams, Simon; Weihe, Høgni; Bendix, Jesper; Tuna, Floriana; Piligkos, Stergios

    2016-05-11

    Quantum coherence is detected in the 4f single-ion magnet (SIM) Yb(trensal), by isotope selective pulsed EPR spectroscopy on an oriented single crystal. At X-band, the spin-lattice relaxation (T1) and phase memory (Tm) times are found to be independent of the nuclei bearing, or not, a nuclear spin. The observation of Rabi oscillations of the spin echo demonstrates the possibility to coherently manipulate the system for more than 70 rotations. This renders Yb(trensal), a sublimable and chemically modifiable SIM, an excellent candidate for quantum information processing.

  18. Manipulation resolves non-trivial structure of corrole monolayer on Ag(111)

    International Nuclear Information System (INIS)

    Tebi, Stefano; Serrano, Giulia; Koch, Reinhold; Müllegger, Stefan; Aldahhak, Hazem; Rauls, Eva; Schmidt, Wolf Gero; Schöfberger, Wolfgang

    2016-01-01

    Non-trivial arrangement of molecules within a molecular network complicates structure determination due to interdigitation, partial overlap, or stacking. We demonstrate that combined imaging and lateral manipulation with a scanning tunneling microscope resolves the intricate structure of a molecular network in two-dimensions in a straightforward manner. The network, formed by a monolayer of 5,10,15-tris(pentafluorophenyl)-corrole molecules on Ag(111), is manipulated for the first time with single-molecule precision. Our results reveal a shingle-like packing of partially overlapping corrole molecules. Density functional theory calculations support our findings. (paper)

  19. Electrochemistry of single molecules and biomolecules, molecular scale nanostructures, and low-dimensional systems

    DEFF Research Database (Denmark)

    Nazmutdinov, Renat R.; Zinkicheva, Tamara T.; Zinkicheva, Tamara T.

    2018-01-01

    Electrochemistry at ultra-small scales, where even the single molecule or biomolecule can be characterized and manipulated, is on the way to a consolidated status. At the same time molecular electrochemistry is expanding into other areas of sophisticated nano- and molecular scale systems including...

  20. Molecular beam epitaxy of single crystal colossal magnetoresistive material

    International Nuclear Information System (INIS)

    Eckstein, J.N.; Bozovic, I.; Rzchowski, M.; O'Donnell, J.; Hinaus, B.; Onellion, M.

    1996-01-01

    The authors have grown films of (LaSr)MnO 3 (LSMO) and (LaCa)MnO 3 (LCMO) using atomic layer-by-layer molecular beam epitaxy (ALL-MBE). Depending on growth conditions, substrate lattice constant and the exact cation stoichiometry, the films are either pseudomorphic or strain relaxed. The pseudomorphic films show atomically flat surfaces, with a unit cell terrace structure that is a replica of that observed on the slightly vicinal substrates, while the strain relaxed films show bumpy surfaces correlated with a dislocation network. All films show tetragonal structure and exhibit anisotropic magnetoresistance, with a low field response, (1/R)(dR/dH) as large as 5 T -1

  1. Imaging and Force Recognition of Single Molecular Behaviors Using Atomic Force Microscopy

    Directory of Open Access Journals (Sweden)

    Mi Li

    2017-01-01

    Full Text Available The advent of atomic force microscopy (AFM has provided a powerful tool for investigating the behaviors of single native biological molecules under physiological conditions. AFM can not only image the conformational changes of single biological molecules at work with sub-nanometer resolution, but also sense the specific interactions of individual molecular pair with piconewton force sensitivity. In the past decade, the performance of AFM has been greatly improved, which makes it widely used in biology to address diverse biomedical issues. Characterizing the behaviors of single molecules by AFM provides considerable novel insights into the underlying mechanisms guiding life activities, contributing much to cell and molecular biology. In this article, we review the recent developments of AFM studies in single-molecule assay. The related techniques involved in AFM single-molecule assay were firstly presented, and then the progress in several aspects (including molecular imaging, molecular mechanics, molecular recognition, and molecular activities on cell surface was summarized. The challenges and future directions were also discussed.

  2. Effect of Perfluoroalkyl Endgroups on the Interactions of Tri-Block Copolymers with Monofluorinated F-DPPC Monolayers

    Directory of Open Access Journals (Sweden)

    Syed W. H. Shah

    2017-10-01

    Full Text Available We studied the interaction of amphiphilic and triphilic polymers with monolayers prepared from F-DPPC (1-palmitoyl-2-(16-fluoropalmitoyl-sn-glycero-3-phosphocholine, a phospholipid with a single fluorine atom at the terminus of the sn-2 chain, an analogue of dipalmitoyl-phosphatidylcholine (DPPC. The amphiphilic block copolymers contained a hydrophobic poly(propylene oxide block flanked by hydrophilic poly(glycerol monomethacrylate blocks (GP. F-GP was derived from GP by capping both termini with perfluoro-n-nonyl segments. We first studied the adsorption of GP and F-GP to lipid monolayers of F-DPPC. F-GP was inserted into the monolayer up to a surface pressure Π of 42.4 mN m−1, much higher than GP (32.5 mN m−1. We then studied isotherms of lipid-polymer mixtures co-spread at the air-water interface. With increasing polymer content in the mixture a continuous shift of the onset of the liquid-expanded (LE to liquid-condensed (LC transition towards higher molecular and higher area per lipid molecule was observed. F-GP had a larger effect than GP indicating that it needed more space. At a Π-value of 32 mN m−1, GP was excluded from the mixed monolayer, whereas F-GP stayed in F-DPPC monolayers up to 42 mN m−1. F-GP is thus more stably anchored in the monolayer up to higher surface pressures. Images of mixed monolayers were acquired using different fluorescent probes and showed the presence of perfluorinated segments of F-GP at LE-LC domain boundaries.

  3. Novel tailor-made externally triggerable single-molecular switches for molecular electronics

    OpenAIRE

    Harzmann, Gero

    2015-01-01

    Molecular electronics marks a highly interdisciplinary scientific field, in which physicists, chemists, and biologist jointly investigate electronic phenomena on a molecular level. Herein, the foremost task of the chemist is the design and synthesis of novel, tailor-made model compounds bearing externally addressable or controllable functions, which are predominantly of electronic nature. This present PhD thesis mainly focusses on the synthetic aspects towards innovative metalorga...

  4. Microcavity single virus detection and sizing with molecular sensitivity

    Science.gov (United States)

    Dantham, V. R.; Holler, S.; Kolchenko, V.; Wan, Z.; Arnold, S.

    2013-02-01

    We report the label-free detection and sizing of the smallest individual RNA virus, MS2 by a spherical microcavity. Mass of this virus is ~6 ag and produces a theoretical resonance shift ~0.25 fm upon adsorbing an individual virus at the equator of the bare microcavity, which is well below the r.m.s background noise of 2 fm. However, detection was accomplished with ease (S/N = 8, Q = 4x105) using a single dipole stimulated plasmonic-nanoshell as a microcavity wavelength shift enhancer. Analytical expressions based on the "reactive sensing principle" are developed to extract the radius of the virus from the measured signals. Estimated limit of detection for these experiments was ~0.4 ag or 240 kDa below the size of all known viruses, largest globular and elongated proteins [Phosphofructokinase (345 kDa) and Fibrinogen (390 kDa), respectively].

  5. Single-cell technologies in molecular marine studies

    KAUST Repository

    Kodzius, Rimantas

    2015-01-24

    Middle Eastern countries are experiencing a renaissance, with heavy investment in both in infrastructure and science. King Abdullah University of Science and Technology (KAUST) is a new and modern university in Saudi Arabia. At the Computational Bioscience Research Center (CBRC) we are working on exploring the Red Sea and beyond, collaborating with Japanese and other research centers. We are using the environment to collect and analyze the microorganisms present. The platform being established at CBRC allows to process samples in a pipeline. The pipeline components consist of sample collection, processing and sequencing, following the in silico analysis, determining the gene functions, identifying the organisms. The genomes of microorganisms of interest are targeted modified by genome editing technology such as CRISPR and desired properties are selected by single cell instrumentation. The final output is to identify valuable microorganisms with production of bio-energy, nutrients, the food and fine chemicals.

  6. Defect Structure of Localized Excitons in a WSe2 Monolayer

    KAUST Repository

    Zhang, Shuai

    2017-07-26

    The atomic and electronic structure of intrinsic defects in a WSe2 monolayer grown on graphite was revealed by low temperature scanning tunneling microscopy and spectroscopy. Instead of chalcogen vacancies that prevail in other transition metal dichalcogenide materials, intrinsic defects in WSe2 arise surprisingly from single tungsten vacancies, leading to the hole (p-type) doping. Furthermore, we found these defects to dominate the excitonic emission of the WSe2 monolayer at low temperature. Our work provided the first atomic-scale understanding of defect excitons and paved the way toward deciphering the defect structure of single quantum emitters previously discovered in the WSe2 monolayer.

  7. Equilibrium electrostatics of responsive polyelectrolyte monolayers.

    Science.gov (United States)

    Wang, Kang; Zangmeister, Rebecca A; Levicky, Rastislav

    2009-01-14

    The physical behavior of polyelectrolytes at solid-liquid interfaces presents challenges both in measurement and in interpretation. An informative, yet often overlooked, property that characterizes the equilibrium organization of these systems is their membrane or rest potential. Here a general classification scheme is presented of the relationship between the rest potential and structural response of polyelectrolyte films to salt concentration. A numerical lattice theory, adapted from the polymer community, is used to analyze the rest potential response of end-tethered polyelectrolyte layers in which electrostatics and short-range contact interactions conspire to bring about different structural states. As an experimental quantity the rest potential is a readily accessible, nonperturbing metric of the equilibrium structure of a polyelectrolyte layer. A first set of measurements is reported on monolayers of end-tethered, single-stranded DNA in monovalent (NaCl) and divalent (MgCl(2)) counterion environments. Intriguingly, in NaCl electrolyte at least two different mechanisms appear by which the DNA layers can structurally relax in response to changing salt conditions. In MgCl(2) the layers appear to collapse. The possible molecular mechanisms behind these behaviors are discussed. These studies provide insight into phenomena more generally underlying polyelectrolyte applications in the chemical, environmental, and biotechnological fields.

  8. Structure of cholesterol/ceramide monolayer mixtures

    DEFF Research Database (Denmark)

    Scheffer, L.; Solomonov, I.; Weygand, M.J.

    2005-01-01

    The structure of monolayers of cholesterol/ ceramide mixtures was investigated using grazing incidence x-ray diffraction, immunofluorescence, and atomic force microscopy techniques. Grazing incidence x-ray diffraction measurements showed the existence of a crystalline mixed phase of the two....... As ceramide incorporates the lipid backbone common to all sphingolipids, this arrangement may be relevant to the understanding of the molecular organization of lipid rafts....

  9. Surface-enhanced Raman scattering from a single molecularly bridged silver nanoparticle aggregate

    Czech Academy of Sciences Publication Activity Database

    Sládková, M.; Vlčková, B.; Pavel, I.; Šišková, Karolína; Šlouf, Miroslav

    924-26, SI (2009), s. 567-570 ISSN 0022-2860. [European Congress on Molecular Spectroscopy /29./. Opatija, 31.08.2008-05.09.2008] R&D Projects: GA ČR GA203/07/0717; GA AV ČR KAN100500652 Institutional research plan: CEZ:AV0Z40500505 Keywords : single molecule SERS * 4,4"-diaminoterphenyl * molecularly bridget Ag nanoparticle aggregates Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.551, year: 2009

  10. Cleavage and formation of molecular dinitrogen in a single system assisted by molybdenum complexes bearing ferrocenyldiphosphine.

    Science.gov (United States)

    Miyazaki, Takamasa; Tanaka, Hiromasa; Tanabe, Yoshiaki; Yuki, Masahiro; Nakajima, Kazunari; Yoshizawa, Kazunari; Nishibayashi, Yoshiaki

    2014-10-20

    The N≡N bond of molecular dinitrogen bridging two molybdenum atoms in the pentamethylcyclopentadienyl molybdenum complexes that bear ferrocenyldiphosphine as an auxiliary ligand is homolytically cleaved under visible light irradiation at room temperature to afford two molar molybdenum nitride complexes. Conversely, the bridging molecular dinitrogen is reformed by the oxidation of the molybdenum nitride complex at room temperature. This result provides a successful example of the cleavage and formation of molecular dinitrogen induced by a pair of two different external stimuli using a single system assisted by molybdenum complexes bearing ferrocenyldiphosphine under ambient conditions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Single orientation graphene synthesized on iridium thin films grown by molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Dangwal Pandey, A., E-mail: arti.pandey@desy.de; Grånäs, E.; Shayduk, R.; Noei, H.; Vonk, V. [Deutsches Elektronen-Synchrotron (DESY), D-22607 Hamburg (Germany); Krausert, K.; Franz, D.; Müller, P.; Keller, T. F.; Stierle, A., E-mail: andreas.stierle@desy.de [Deutsches Elektronen-Synchrotron (DESY), D-22607 Hamburg (Germany); Fachbereich Physik, Universität Hamburg, D-22607 Hamburg (Germany)

    2016-08-21

    Heteroepitaxial iridium thin films were deposited on (0001) sapphire substrates by means of molecular beam epitaxy, and subsequently, one monolayer of graphene was synthesized by chemical vapor deposition. The influence of the growth parameters on the quality of the Ir films, as well as of graphene, was investigated systematically by means of low energy electron diffraction, x-ray reflectivity, x-ray diffraction, Auger electron spectroscopy, scanning electron microscopy, and atomic force microscopy. Our study reveals (111) oriented iridium films with high crystalline quality and extremely low surface roughness, on which the formation of large-area epitaxial graphene is achieved. The presence of defects, like dislocations, twins, and 30° rotated domains in the iridium films is also discussed. The coverage of graphene was found to be influenced by the presence of 30° rotated domains in the Ir films. Low iridium deposition rates suppress these rotated domains and an almost complete coverage of graphene was obtained. This synthesis route yields inexpensive, air-stable, and large-area graphene with a well-defined orientation, making it accessible to a wider community of researchers for numerous experiments or applications, including those which use destructive analysis techniques or irreversible processes. Moreover, this approach can be used to tune the structural quality of graphene, allowing a systematic study of the influence of defects in various processes like intercalation below graphene.

  12. Diffusion of Supercritical Fluids through Single-Layer Nanoporous Solids: Theory and Molecular Simulations.

    Science.gov (United States)

    Oulebsir, Fouad; Vermorel, Romain; Galliero, Guillaume

    2018-01-16

    With the advent of graphene material, membranes based on single-layer nanoporous solids appear as promising devices for fluid separation, be it liquid or gaseous mixtures. The design of such architectured porous materials would greatly benefit from accurate models that can predict their transport and separation properties. More specifically, there is no universal understanding of how parameters such as temperature, fluid loading conditions, or the ratio of the pore size to the fluid molecular diameter influence the permeation process. In this study, we address the problem of pure supercritical fluids diffusing through simplified models of single-layer porous materials. Basically, we investigate a toy model that consists of a single-layer lattice of Lennard-Jones interaction sites with a slit gap of controllable width. We performed extensive equilibrium and biased molecular dynamics simulations to document the physical mechanisms involved at the molecular scale. We propose a general constitutive equation for the diffusional transport coefficient derived from classical statistical mechanics and kinetic theory, which can be further simplified in the ideal gas limit. This transport coefficient relates the molecular flux to the fluid density jump across the single-layer membrane. It is found to be proportional to the accessible surface porosity of the single-layer porous solid and to a thermodynamic factor accounting for the inhomogeneity of the fluid close to the pore entrance. Both quantities directly depend on the potential of mean force that results from molecular interactions between solid and fluid atoms. Comparisons with the simulations data show that the kinetic model captures how narrowing the pore size below the fluid molecular diameter lowers dramatically the value of the transport coefficient. Furthermore, we demonstrate that our general constitutive equation allows for a consistent interpretation of the intricate effects of temperature and fluid loading

  13. Active cell-matrix coupling regulates cellular force landscapes of cohesive epithelial monolayers

    Science.gov (United States)

    Zhao, Tiankai; Zhang, Yao; Wei, Qiong; Shi, Xuechen; Zhao, Peng; Chen, Long-Qing; Zhang, Sulin

    2018-03-01

    Epithelial cells can assemble into cohesive monolayers with rich morphologies on substrates due to competition between elastic, edge, and interfacial effects. Here we present a molecularly based thermodynamic model, integrating monolayer and substrate elasticity, and force-mediated focal adhesion formation, to elucidate the active biochemical regulation over the cellular force landscapes in cohesive epithelial monolayers, corroborated by microscopy and immunofluorescence studies. The predicted extracellular traction and intercellular tension are both monolayer size and substrate stiffness dependent, suggestive of cross-talks between intercellular and extracellular activities. Our model sets a firm ground toward a versatile computational framework to uncover the molecular origins of morphogenesis and disease in multicellular epithelia.

  14. Single particle and molecular assembly analysis of polyribosomes by single- and double-tilt cryo electron tomography

    Energy Technology Data Exchange (ETDEWEB)

    Myasnikov, Alexander G. [IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Department of Integrative Structural Biology, Centre National de la Recherche Scientifique (CNRS) UMR 7104/ Institut National de la Santé de la Recherche Médicale INSERM U964/ Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch (France); Afonina, Zhanna A. [Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region (Russian Federation); Klaholz, Bruno P., E-mail: klaholz@igbmc.fr [IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Department of Integrative Structural Biology, Centre National de la Recherche Scientifique (CNRS) UMR 7104/ Institut National de la Santé de la Recherche Médicale INSERM U964/ Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch (France)

    2013-03-15

    Cryo electron tomography (cryo-ET) can provide cellular and molecular structural information on various biological samples. However, the detailed interpretation of tomograms reconstructed from single-tilt data tends to suffer from low signal-to-noise ratio and artefacts caused by some systematically missing angular views. While these can be overcome by sub-tomogram averaging, they remain limiting for the analysis of unique structures. Double-tilt ET can improve the tomogram quality by acquiring a second tilt series after an in-plane rotation, but its usage is not widespread yet because it is considered technically demanding and it is rarely used under cryo conditions. Here we show that double-tilt cryo-ET improves the quality of 3D reconstructions so significantly that even single particle analysis can be envisaged despite of the intrinsically low image contrast obtained from frozen-hydrated specimens. This is illustrated by the analysis of eukaryotic polyribosomes in which individual ribosomes were reconstructed using single-tilt, partial and full double-tilt geometries. The improved tomograms favour the faster convergence of iterative sub-tomogram averaging and allow a better 3D classification using multivariate statistical analysis. Our study of single particles and molecular assemblies within polysomes illustrates that the dual-axis approach is particularly useful for cryo applications of ET, both for unique objects and for structures that can be classified and averaged. - Highlights: ► Double-tilt cryo-ET improves 3D reconstructions thus making single particle analysis possible. ► Dual-axis cryo-ET data favour a faster convergence of iterative sub-tomogram averaging. ► Individual ribosomes were reconstructed from single-tilt, partial/ full double-tilt geometries. ► Double-tilt cryo-ET facilitates analysis of larger molecular assemblies such as in cell sections. ► Dual-axis cryo-ET is applicable to unique objects and to structures that can be

  15. Research Update: Molecular electronics: The single-molecule switch and transistor

    Directory of Open Access Journals (Sweden)

    Kai Sotthewes

    2014-01-01

    Full Text Available In order to design and realize single-molecule devices it is essential to have a good understanding of the properties of an individual molecule. For electronic applications, the most important property of a molecule is its conductance. Here we show how a single octanethiol molecule can be connected to macroscopic leads and how the transport properties of the molecule can be measured. Based on this knowledge we have realized two single-molecule devices: a molecular switch and a molecular transistor. The switch can be opened and closed at will by carefully adjusting the separation between the electrical contacts and the voltage drop across the contacts. This single-molecular switch operates in a broad temperature range from cryogenic temperatures all the way up to room temperature. Via mechanical gating, i.e., compressing or stretching of the octanethiol molecule, by varying the contact's interspace, we are able to systematically adjust the conductance of the electrode-octanethiol-electrode junction. This two-terminal single-molecule transistor is very robust, but the amplification factor is rather limited.

  16. Electronic structure of surface-supported bis(phthalocyaninato) terbium(III) single molecular magnets.

    Science.gov (United States)

    Vitali, Lucia; Fabris, Stefano; Conte, Adriano Mosca; Brink, Susan; Ruben, Mario; Baroni, Stefano; Kern, Klaus

    2008-10-01

    The electronic structure of isolated bis(phthalocyaninato) terbium(III) molecules, a novel single-molecular-magnet (SMM), supported on the Cu(111) surface has been characterized by density functional theory and scanning tunneling spectroscopy. These studies reveal that the interaction with the metal surface preserves both the molecular structure and the large spin magnetic moment of the metal center. The 4f electron states are not perturbed by the adsorption while a strong molecular/metal interaction can induce the suppression of the minor spin contribution delocalized over the molecular ligands. The calculations show that the inherent spin magnetic moment of the molecule is only weakly affected by the interaction with the surface and suggest that the SMM character might be preserved.

  17. Possibility designing half-wave and full-wave molecular rectifiers by using single benzene molecule

    Science.gov (United States)

    Abbas, Mohammed A.; Hanoon, Falah H.; Al-Badry, Lafy F.

    2018-02-01

    This work focused on possibility designing half-wave and full-wave molecular rectifiers by using single and two benzene rings, respectively. The benzene rings were threaded by a magnetic flux that changes over time. The quantum interference effect was considered as the basic idea in the rectification action, the para and meta configurations were investigated. All the calculations are performed by using steady-state theoretical model, which is based on the time-dependent Hamiltonian model. The electrical conductance and the electric current are considered as DC output signals of half-wave and full-wave molecular rectifiers. The finding in this work opens up the exciting potential to use these molecular rectifiers in molecular electronics.

  18. Acyclic cucurbit[n]uril molecular containers selectively solubilize single-walled carbon nanotubes in water.

    Science.gov (United States)

    Shen, Cai; Ma, Da; Meany, Brendan; Isaacs, Lyle; Wang, YuHuang

    2012-05-02

    Making single-walled carbon nanotubes (SWNTs) soluble in water is a challenging first step to use their remarkable electronic and optical properties in a variety of applications. We report that acyclic cucurbit[n]uril molecular containers 1 and 2 selectively solubilize small-diameter and low chiral angle SWNTs. The selectivity is tunable by increasing the concentration of the molecular containers or by adjusting the ionic strength of the solution. Even at a concentration 1000 times lower than typically required for surfactants, the molecular containers render SWNTs soluble in water. Molecular mechanics simulations suggest that these C-shaped acyclic molecules complex the SWNTs such that a large portion of nanotube sidewalls are exposed to the external environment. These "naked" nanotubes fluoresce upon patching the exposed surface with sodium dodecylbenzene sulfonate. © 2012 American Chemical Society

  19. Variable contact gap single-molecule conductance determination for a series of conjugated molecular bridges

    DEFF Research Database (Denmark)

    Haiss, W.; Wang, Christian; Jitchati, R.

    2008-01-01

    It is now becoming clear that the characteristics of the whole junction are important in determining the conductance of single molecules bound between two metal contacts. This paper shows through measurements on a series of seven conjugated molecular bridges that contact separation is an important...... that conductance increases rather dramatically at higher tilt angle away from the normal for conformationally rigid molecular wires and that this increase in conductance arises from increased electronic coupling between the molecular bridge and the gold contacts.......-distance curves and knowledge of the terminal to terminal length of the molecular wire. The contact gap separation dependence is interpreted as arising from tilting of these molecules in the junction and this model is underpinned by ab initio transport computations. In this respect we make the general observation...

  20. Experimental study of thermal rectification in suspended monolayer graphene

    Science.gov (United States)

    Wang, Haidong; Hu, Shiqian; Takahashi, Koji; Zhang, Xing; Takamatsu, Hiroshi; Chen, Jie

    2017-06-01

    Thermal rectification is a fundamental phenomenon for active heat flow control. Significant thermal rectification is expected to exist in the asymmetric nanostructures, such as nanowires and thin films. As a one-atom-thick membrane, graphene has attracted much attention for realizing thermal rectification as shown by many molecular dynamics simulations. Here, we experimentally demonstrate thermal rectification in various asymmetric monolayer graphene nanostructures. A large thermal rectification factor of 26% is achieved in a defect-engineered monolayer graphene with nanopores on one side. A thermal rectification factor of 10% is achieved in a pristine monolayer graphene with nanoparticles deposited on one side or with a tapered width. The results indicate that the monolayer graphene has great potential to be used for designing high-performance thermal rectifiers for heat flow control and energy harvesting.

  1. Molecular investigation of evaporation of biodroplets containing single-strand DNA on graphene surface.

    Science.gov (United States)

    Akbari, Fahimeh; Foroutan, Masumeh

    2018-02-14

    In this study, the water droplet behaviour of four different types of single-strand DNA with homogeneous base sequence on a graphene substrate during evaporation of the droplet was investigated using molecular dynamics (MD) simulation. The simulation results indicated that the evaporation depended on the DNA sequence. The observed changes can be divided into four parts: (i) vaporization mode, (ii) evaporation flux, (iii) mechanism of single-strand placement on the surface, and (iv) consideration of remaining single strands after evaporation. Our simulation observations indicated different evaporation modes for thymine biodroplets as compared to those for other biodroplets. The evaporation of the thymine biodroplets occurred with an increase in the contact angle, while that of the other biodroplets occur in a constant contact angle mode. Moreover, thymine biodroplets generate the lowest contact line compared to other single strands, and it is always placed far away from the centre of the droplets during evaporation. Investigating variations in the evaporation flux shows that thymine has the highest evaporation flux and guanine has the lowest. Moreover, during initial evaporation, the flux of evaporation increases at the triple point of the biodroplets containing thymine single strands, while it decreases in the other biodroplets. The following observation was obtained from the study of the placement of single strands on the substrate: guanine and thymine interacted slower than other single strands during evaporation with graphene, adenine single strand had a higher folding during evaporation, and guanine single strand showed the lowest end-to-end distance. The investigation of single-strand DNA after evaporation shows that adenine produces the most stable structure at the end of evaporation. In addition, cytosine is the most stretched single-strand DNA due to its lack of internal π-π stacking and hydrogen bonding. Therefore, cytosine single strand is more

  2. Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants.

    Science.gov (United States)

    Li, Zhen; De La Torre, Amanda R; Sterck, Lieven; Cánovas, Francisco M; Avila, Concepción; Merino, Irene; Cabezas, José Antonio; Cervera, María Teresa; Ingvarsson, Pär K; Van de Peer, Yves

    2017-05-01

    Phylogenetic relationships among seed plant taxa, especially within the gymnosperms, remain contested. In contrast to angiosperms, for which several genomic, transcriptomic and phylogenetic resources are available, there are few, if any, molecular markers that allow broad comparisons among gymnosperm species. With few gymnosperm genomes available, recently obtained transcriptomes in gymnosperms are a great addition to identifying single-copy gene families as molecular markers for phylogenomic analysis in seed plants. Taking advantage of an increasing number of available genomes and transcriptomes, we identified single-copy genes in a broad collection of seed plants and used these to infer phylogenetic relationships between major seed plant taxa. This study aims at extending the current phylogenetic toolkit for seed plants, assessing its ability for resolving seed plant phylogeny, and discussing potential factors affecting phylogenetic reconstruction. In total, we identified 3,072 single-copy genes in 31 gymnosperms and 2,156 single-copy genes in 34 angiosperms. All studied seed plants shared 1,469 single-copy genes, which are generally involved in functions like DNA metabolism, cell cycle, and photosynthesis. A selected set of 106 single-copy genes provided good resolution for the seed plant phylogeny except for gnetophytes. Although some of our analyses support a sister relationship between gnetophytes and other gymnosperms, phylogenetic trees from concatenated alignments without 3rd codon positions and amino acid alignments under the CAT + GTR model, support gnetophytes as a sister group to Pinaceae. Our phylogenomic analyses demonstrate that, in general, single-copy genes can uncover both recent and deep divergences of seed plant phylogeny. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  3. Nanoscale heterostructures with molecular-scale single-crystal metal wires.

    Science.gov (United States)

    Kundu, Paromita; Halder, Aditi; Viswanath, B; Kundu, Dipan; Ramanath, Ganpati; Ravishankar, N

    2010-01-13

    Creating nanoscale heterostructures with molecular-scale (synthesis of nanoscale heterostructures with single-crystal molecular-scale Au nanowires attached to different nanostructure substrates. Our method involves the formation of Au nanoparticle seeds by the reduction of rocksalt AuCl nanocubes heterogeneously nucleated on the substrates and subsequent nanowire growth by oriented attachment of Au nanoparticles from the solution phase. Nanoscale heterostructures fabricated by such site-specific nucleation and growth are attractive for many applications including nanoelectronic device wiring, catalysis, and sensing.

  4. Molecular analysis of desmoid tumors with a high-density single-nucleotide polymorphism array identifies new molecular candidate lesions.

    Science.gov (United States)

    Erben, Philipp; Nowak, Daniel; Sauer, Christian; Ströbel, Philipp; Hofmann, Wolf-Karsten; Hofheinz, Ralf-Dieter; Hohenberger, Peter; Kasper, Bernd

    2012-01-01

    Desmoid tumors are neoplastic proliferations of connective tissues. The mutation status of the gene coding for catenin (cadherin-associated protein) beta 1 (CTNNB1) and trisomy 8 on the chromosomal level have been described to have prognostic relevance. In order to elucidate new molecular mechanisms underlying these tumors, we carried out a molecular analysis with a genome-wide human high-density single-nucleotide polymorphism (SNP) array, in 9 patients. Single samples showed numerical aberrations on chromosomes (Chrs) 20 and 6 with either trisomy 20 or monosomy 6. No trisomy 8 could be detected. Recurrent heterozygous deletions were found in Chr 5q (including the APC gene locus, n = 3) and Chr 8p23 (n = 4, containing coding regions for the potential tumor suppressor gene CSMD1). This novel deletion in 8p23 showed an association with local recurrence. In addition, structural chromosomal changes (gain of Chrs 8 and 20) were found in a minority of cases. The genomic alteration affecting the candidate gene CSMD1 could be important in the development of desmoid tumors.

  5. Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics

    Science.gov (United States)

    Dupuis, Nicholas F.; Holmstrom, Erik D.; Nesbitt, David J.

    2014-01-01

    The effects of “molecular crowding” on elementary biochemical processes due to high solute concentrations are poorly understood and yet clearly essential to the folding of nucleic acids and proteins into correct, native structures. The present work presents, to our knowledge, first results on the single-molecule kinetics of solute molecular crowding, specifically focusing on GAAA tetraloop–receptor folding to isolate a single RNA tertiary interaction using time-correlated single-photon counting and confocal single-molecule FRET microscopy. The impact of crowding by high–molecular-weight polyethylene glycol on the RNA folding thermodynamics is dramatic, with up to ΔΔG° ∼ −2.5 kcal/mol changes in free energy and thus >60-fold increase in the folding equilibrium constant (Keq) for excluded volume fractions of 15%. Most importantly, time-correlated single-molecule methods permit crowding effects on the kinetics of RNA folding/unfolding to be explored for the first time (to our knowledge), which reveal that this large jump in Keq is dominated by a 35-fold increase in tetraloop–receptor folding rate, with only a modest decrease in the corresponding unfolding rate. This is further explored with temperature-dependent single-molecule RNA folding measurements, which identify that crowding effects are dominated by entropic rather than enthalpic contributions to the overall free energy change. Finally, a simple “hard-sphere” treatment of the solute excluded volume is invoked to model the observed kinetic trends, and which predict ΔΔG° ∼ −5 kcal/mol free-energy stabilization at excluded volume fractions of 30%. PMID:24850865

  6. A Comprehensive Experiment for Molecular Biology: Determination of Single Nucleotide Polymorphism in Human REV3 Gene Using PCR-RFLP

    Science.gov (United States)

    Zhang, Xu; Shao, Meng; Gao, Lu; Zhao, Yuanyuan; Sun, Zixuan; Zhou, Liping; Yan, Yongmin; Shao, Qixiang; Xu, Wenrong; Qian, Hui

    2017-01-01

    Laboratory exercise is helpful for medical students to understand the basic principles of molecular biology and to learn about the practical applications of molecular biology. We have designed a lab course on molecular biology about the determination of single nucleotide polymorphism (SNP) in human REV3 gene, the product of which is a subunit of…

  7. A molecular ruler based on plasmon coupling of single gold andsilver nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Sonnichsen, Carsten; Reinhard, Bjorn M.; Liphardt, Jan; Alivisatos, A. Paul

    2005-05-22

    Molecular rulers based on Foerster Resonance Energy Transfer (FRET) that report conformational changes and intramolecular distances of single biomolecules have helped to understand important biological processes. However, these rulers suffer from low and fluctuating signal intensities from single dyes and limited observation time due to photobleaching. The plasmon resonance in noble metal particles has been suggested as an alternative probe to overcome the limitations of organic fluorophores and the coupling of plasmons in nearby particles has been exploited to detect particle aggregation by a distinct color change in bulk experiments. Here we demonstrate that plasmon coupling can be used to monitor distances between single pairs of gold and silver nanoparticles. We use this effect to follow the directed assembly of gold and silver nanoparticle dimers in real time and to study the time dynamics of single DNA hybridization events. These ''plasmon rulers'' allowed us to continuously monitor separations of up to 70 nm for more than 3000 seconds. Single molecule in vitro studies of biological processes previously inaccessible with fluorescence based molecular rulers are enabled with plasmon rulers with extended time and distance range.

  8. Mn-Promoted Growth and Photoluminescence of Molybdenum Disulphide Monolayer

    Directory of Open Access Journals (Sweden)

    Shengzhong Jin

    2017-06-01

    Full Text Available Molybdenum disulphide (MoS2 monolayer is a two-dimensional semiconductor material with potential applications in nano electronic devices. However, it is still a challenge to reproducibly synthesize single layer MoS2 in high quality. Herein, we report the growth of monolayer of MoS2 on the SiO2/Si substrate with manganese heterogeneous nucleation. It was shown that the Mn promotes the growth of monolayer MoS2 via heterogeneous nucleation. The growth temperature range expanded two-fold, the nucleation density increased as well. The monolayer prepared in the presence of Mn exhibits a unique red emission peak at 732 nm at room temperature compared to the sample in the absence of Mn.

  9. Macroscopic quantum coherence in a single molecular magnet and Kondo effect of electron transport

    International Nuclear Information System (INIS)

    Chang, Bo; Wang, Qiang; Xie, Haiqing; Liang, J.-Q.

    2011-01-01

    We report a Kondo-effect study of electron transport through a quantum dot with embedded biaxial single-molecule magnet based on slave boson mean-field theory and non-equilibrium Green-function technique. It is found the macroscopic quantum coherence of molecule-magnet results in the Kondo peak split of differential conductance due to interaction between electron and molecular magnet. It is also demonstrated that both the peak height and position can be controlled by the sweeping magnetic field and polarization of ferromagnetic electrodes. The characteristic peak split may be used to identify the macroscopic quantum coherence and develop molecule devices. -- Highlights: → Splits of Kondo peak are induced by the single molecular magnet. → Kondo effect can be controlled by magnetic field and its sweeping speed in our model. → The suppression and broadening of Kondo peaks is also observed with increase of temperature. → The peaks height and position is sensitive to polarization of the electrode.

  10. Molecular scale buckling mechanics in individual aligned single-wall carbon nanotubes on elastomeric substrates.

    Science.gov (United States)

    Khang, Dahl-Young; Xiao, Jianliang; Kocabas, Coskun; MacLaren, Scott; Banks, Tony; Jiang, Hanqing; Huang, Yonggang Y; Rogers, John A

    2008-01-01

    We have studied the scaling of controlled nonlinear buckling processes in materials with dimensions in the molecular range (i.e., approximately 1 nm) through experimental and theoretical studies of buckling in individual single-wall carbon nanotubes on substrates of poly(dimethylsiloxane). The results show not only the ability to create and manipulate patterns of buckling at these molecular scales, but also, that analytical continuum mechanics theory can explain, quantitatively, all measurable aspects of this system. Inverse calculation applied to measurements of diameter-dependent buckling wavelengths yields accurate values of the Young's moduli of individual SWNTs. As an example of the value of this system beyond its use in this type of molecular scale metrology, we implement parallel arrays of buckled SWNTs as a class of mechanically stretchable conductor.

  11. Single and double charge transfer in Be/sup 4+/+He collisions: A molecular (Feshbach) approach

    Energy Technology Data Exchange (ETDEWEB)

    Martin, F.; Riera, A.; Yaez, M.

    1986-12-01

    In recent articles, we pointed out the fundamental difference between the molecular treatment of processes involving a multicharged ion and hydrogen or helium atoms, which is the (formal) autoionizing character of the molecular channels, and we reported a (new) implementation of the Feshbach method to calculate the molecular energies and couplings. In the present work we use the wave functions calculated with this Feshbach method for the BeHe/sup 4+/ quasimolecule, introduce a common translation factor in the formalism, and calculate the single and double charge-exchange cross sections in Be/sup 4+/+He(1s/sup 2/) collisions for impact energies 0.2--20 keV/amu. The mechanisms of the processes are discussed in detail.

  12. Quantum Tunneling of Magnetization in Single Molecular Magnets Coupled to Ferromagnetic Reservoirs

    OpenAIRE

    Misiorny, Maciej; Barnas, Józef

    2006-01-01

    The role of spin polarized reservoirs in quantum tunneling of magnetization and relaxation processes in a single molecular magnet (SMM) is investigated theoretically. The SMM is exchange-coupled to the reservoirs and also subjected to a magnetic field varying in time, which enables the quantum tunneling of magnetization (QTM). The spin relaxation times are calculated from the Fermi golden rule. The exchange interaction with tunneling electrons is shown to affect the spin reversal due to QTM. ...

  13. Magnetic Switching of a Single Molecular Magnet due to Spin-Polarized Current

    OpenAIRE

    Misiorny, Maciej; Barnas, Józef

    2006-01-01

    Magnetic switching of a single molecular magnet (SMM) due to spin-polarized current flowing between ferromagnetic metallic electrodes is investigated theoretically. Magnetic moments of the electrodes are assumed to be collinear and parallel to the magnetic easy axis of the molecule. Electrons tunneling through a barrier between magnetic leads are coupled to the SMM via exchange interaction. The current flowing through the system as well as the spin relaxation times of the SMM are calculated f...

  14. Pumping $ac$ Josephson current in the Single Molecular Magnets by spin nutation

    OpenAIRE

    Abdollahipour, B.; Abouie, J.; Rostami, A. A.

    2012-01-01

    We demonstrate that an {\\it ac} Josephson current is pumped through the Single Molecular Magnets (SMM) by the spin nutation. The spin nutation is generated by applying a time dependent magnetic field to the SMM. We obtain the flowing charge current through the junction by working in the tunneling limit and employing Green's function technique. At the resonance conditions some discontinuities and divergencies are appeared in the normal and Josephson currents, respectively. Such discontinuities...

  15. Deuteron NMR resolved mesogen vs. crosslinker molecular order and reorientational exchange in liquid single crystal elastomers

    Czech Academy of Sciences Publication Activity Database

    Milavec, J.; Domenici, V.; Zupančič, B.; Rešetič, A.; Bubnov, Alexej; Zalar, B.

    2016-01-01

    Roč. 18, č. 5 (2016), s. 4071-4077 ISSN 1463-9076 R&D Projects: GA ČR GA15-02843S; GA MŠk(CZ) LD14007 Grant - others:EU - ICT(XE) COST Action IC1208 Institutional support: RVO:68378271 Keywords : liquid single crystal elastomer * NMR * liquid crystal * molecular order * monomers Subject RIV: JJ - Other Materials Impact factor: 4.123, year: 2016

  16. Intramolecular and Lattice Melting in n-Alkane Monolayers: An Analog of Melting in Lipid Bilayers

    DEFF Research Database (Denmark)

    Hansen, Flemming Yssing; Herwig, K.W.; Matthies, B.

    1999-01-01

    Molecular dynamics (MD) simulations and neutron diffraction experiments have been performed on n-dotriacontane (n-C32D66) monolayers adsorbed on a graphite basal-plane surface. The diffraction experiments show little change in the crystalline monolayer structure up to a temperature of similar...

  17. Single-molecule chemical reaction reveals molecular reaction kinetics and dynamics.

    Science.gov (United States)

    Zhang, Yuwei; Song, Ping; Fu, Qiang; Ruan, Mingbo; Xu, Weilin

    2014-06-25

    Understanding the microscopic elementary process of chemical reactions, especially in condensed phase, is highly desirable for improvement of efficiencies in industrial chemical processes. Here we show an approach to gaining new insights into elementary reactions in condensed phase by combining quantum chemical calculations with a single-molecule analysis. Elementary chemical reactions in liquid-phase, revealed from quantum chemical calculations, are studied by tracking the fluorescence of single dye molecules undergoing a reversible redox process. Statistical analyses of single-molecule trajectories reveal molecular reaction kinetics and dynamics of elementary reactions. The reactivity dynamic fluctuations of single molecules are evidenced and probably arise from either or both of the low-frequency approach of the molecule to the internal surface of the SiO2 nanosphere or the molecule diffusion-induced memory effect. This new approach could be applied to other chemical reactions in liquid phase to gain more insight into their molecular reaction kinetics and the dynamics of elementary steps.

  18. Estimating single molecule conductance from spontaneous evolution of a molecular contact

    Science.gov (United States)

    Gil, M.; Malinowski, T.; Iazykov, M.; Klein, H. R.

    2018-03-01

    We present an original method to estimate the conductivity of a single molecule anchored to nanometric-sized metallic electrodes, using a Mechanically Controlled Break Junction operated at room temperature in the liquid. We record the conductance through the metal/molecules/metal nanocontact while keeping the metallic electrodes at a fixed distance. Taking advantage of thermal diffusion and electromigration, we let the contact naturally explore the more stable configurations around a chosen conductance value. The conductance of a single molecule is estimated from a statistical analysis of raw conductance and conductance standard deviation data for molecular contacts containing up to 14 molecules. The single molecule conductance values are interpreted as time-averaged conductance of an ensemble of conformers at thermal equilibrium.

  19. DNA detection and single nucleotide mutation identification using SERS for molecular diagnostics and global health

    Science.gov (United States)

    Ngo, Hoan T.; Gandra, Naveen; Fales, Andrew M.; Taylor, Steve M.; Vo-Dinh, Tuan

    2017-02-01

    Nucleic acid-based molecular diagnostics at the point-of-care (POC) and in resource-limited settings is still a challenge. We present a sensitive yet simple DNA detection method with single nucleotide polymorphism (SNP) identification capability. The detection scheme involves sandwich hybridization of magnetic beads conjugated with capture probes, target sequences, and ultrabright surface-enhanced Raman Scattering (SERS) nanorattles conjugated with reporter probes. Upon hybridization, the sandwich probes are concentrated at the detection focus controlled by a magnetic system for SERS measurements. The ultrabright SERS nanorattles, consisting of a core and a shell with resonance Raman reporters loaded in the gap space between the core and the shell, serve as SERS tags for ultrasensitive signal detection. Specific DNA sequences of the malaria parasite Plasmodium falciparum and dengue virus 1 (DENV1) were used as the model marker system. Detection limit of approximately 100 attomoles was achieved. Single nucleotide polymorphism (SNP) discrimination of wild type malaria DNA and mutant malaria DNA, which confers resistance to artemisinin drugs, was also demonstrated. The results demonstrate the molecular diagnostic potential of the nanorattle-based method to both detect and genotype infectious pathogens. The method's simplicity makes it a suitable candidate for molecular diagnosis at the POC and in resource-limited settings.

  20. A Failure Criterion for Single-Walled Carbon Nanotubes Based on Molecular Mechanics

    Science.gov (United States)

    Avila, Antonio; Lacerda, Guilherme

    2008-03-01

    Single-walled carbon nanotubes (SWNT) are the natural choice for high performance materials. The problem, however, rises when the experimental data are compared against each other. The large variability of experimental data lead to development of a new set of numerical simulations called molecular mechanics, which is a ``symbiotic'' association of molecular dynamics and solid mechanics. This papers deals with a molecular mechanics simulations of single-walled carbon nanotubes. Three SWNT configurations and its combinations were simulated, i.e. armchair, zigzag and chiral. The failure criterion introduced is based on modified Morse's potential with dissociation energy of 124 Kcal/mol and an inflection point considered is around 13% of strain. The numerical data are in good agreement with data from Belytschko et al. (2002) where the failure occurred at 10.6% strain at 65.2 GPa of stress. To be able to identify the highest stress concentration region, one end of the SWNT all degrees-of-freedom were fixed and a prescribed axial displacement was applied at the opposite end. The Sadoc (chiral-chiral) configuration had the highest stress at the smallest chiral SWNT. For the Dunlap configuration (chiral-zigzag) the highest stress occurred at chiral part close to the pentagon location.

  1. The thinnest molecular separation sheet by graphene gates of single-walled carbon nanohorns.

    Science.gov (United States)

    Ohba, Tomonori

    2014-11-25

    Graphene is possibly the thinnest membrane that could be used as a molecular separation gate. Several techniques including absorption, cryogenic distillation, adsorption, and membrane separation have been adopted for constructing separation systems. Molecular separation using graphene as the membrane has been studied because large area synthesis of graphene is possible by chemical vapor deposition. Control of the gate sizes is necessary to achieve high separation performances in graphene membranes. The separation of molecules and ions using graphene and graphene oxide layers could be achieved by the intrinsic defects and defect donation of graphene. However, the controllability of the graphene gates is still under debate because gate size control at the picometer level is inevitable for the fabrication of the thinnest graphene membranes. In this paper, the controlled gate size in the graphene sheets in single-walled carbon nanohorns (NHs) is studied and the molecular separation ability of the graphene sheets is assessed by molecular probing with CO2, O2, N2, CH4, and SF6. Graphene sheets in NHs with different sized gates of 310, 370, and >500 pm were prepared and assessed by molecular probing. The 310 pm-gates in the graphene sheets could separate the molecules tested, whereas weak separation properties were observed for 370 pm-gates. The amount of CO2 that penetrated the 310 pm-gates was more than 35 times larger than that of CH4. These results were supported by molecular dynamics simulations of the penetration of molecules through 300, 400, and 700 pm-gates in graphene sheets. Therefore, a gas separation membrane using a 340-pm-thick graphene sheet has high potential. These findings provide unambiguous evidence of the importance of graphene gates on the picometer level. Control of the gates is the primary challenge for high-performance separation membranes made of graphene.

  2. Melting mechanism in monolayers of flexible rod-shaped molecules

    DEFF Research Database (Denmark)

    Hansen, Flemming Yssing; Taub, H.

    1992-01-01

    The melting of butane and hexane monolayers adsorbed on a graphite basal-plane surface has been studied by molecular-dynamics simulations and experimentally by neutron diffraction. The simulation results are qualitatively consistent with the observed diffraction patterns and suggest a general...

  3. Computational exploration of single-protein mechanics by steered molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Sotomayor, Marcos [Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio (United States)

    2015-12-31

    Hair cell mechanotransduction happens in tens of microseconds, involves forces of a few picoNewtons, and is mediated by nanometer-scale molecular conformational changes. As proteins involved in this process become identified and their high resolution structures become available, multiple tools are being used to explore their “single-molecule responses” to force. Optical tweezers and atomic force microscopy offer exquisite force and extension resolution, but cannot reach the high loading rates expected for high frequency auditory stimuli. Molecular dynamics (MD) simulations can reach these fast time scales, and also provide a unique view of the molecular events underlying protein mechanics, but its predictions must be experimentally verified. Thus a combination of simulations and experiments might be appropriate to study the molecular mechanics of hearing. Here I review the basics of MD simulations and the different methods used to apply force and study protein mechanics in silico. Simulations of tip link proteins are used to illustrate the advantages and limitations of this method.

  4. Monitoring the hydration of DNA self-assembled monolayers using an extensional nanomechanical resonator

    DEFF Research Database (Denmark)

    Cagliani, Alberto; Kosaka, Priscila; Tamayo, Javier

    2012-01-01

    We have fabricated an ultrasensitive nanomechanical resonator based on the extensional vibration mode to weigh the adsorbed water on self-assembled monolayers of DNA as a function of the relative humidity. The water adsorption isotherms provide the number of adsorbed water molecules per nucleotide...... for monolayers of single stranded (ss) DNA and after hybridization with the complementary DNA strand. Our results differ from previous data obtained with bulk samples, showing the genuine behavior of these self-assembled monolayers. The hybridization cannot be inferred from the water adsorption isotherms due...... on the interaction between water and self-assembled monolayers of nucleic acids....

  5. Interaction of molecular oxygen with single wall nanotubes: Role of surfactant contamination

    International Nuclear Information System (INIS)

    Larciprete, R.; Goldoni, A.; Lizzit, S.

    2003-01-01

    The interaction of molecular oxygen with single wall nanotubes in the form of a commercial bucky paper was investigated by high resolution photoemission spectroscopy. Sodium contamination was found in the sample, which was completely removed only after prolonged heating at 1250 K. The C 1s core level spectrum measured on the sample annealed to 1020 K dramatically changed upon exposure to molecular oxygen. On the contrary, when exposing the Na-free SWNTs to several KL of O 2 , the sample remained oxygen free and no modification in the C 1s core level was observed. Therefore the observed sensitivity of the sample to O 2 was due to a Na mediated oxidation, determining a charge transfer from the C tubes to the Na-O complex

  6. Phase transitions in surfactant monolayers

    International Nuclear Information System (INIS)

    Casson, B.D.

    1998-01-01

    Two-dimensional phase transitions have been studied in surfactant monolayers at the air/water interface by sum-frequency spectroscopy and ellipsometry. In equilibrium monolayers of medium-chain alcohols C n H 2n+1 OH (n = 9-14) a transition from a two-dimensional crystalline phase to a liquid was observed at temperatures above the bulk melting point. The small population of gauche defects in the solid phase increased only slightly at the phase transition. A model of the hydrocarbon chains as freely rotating rigid rods allowed the area per molecule and chain tilt in the liquid phase to be determined. The area per molecule, chain tilt and density of the liquid phase all increased with increasing chain length, but for each chain length the density was higher than in a bulk liquid hydrocarbon. In a monolayer of decanol adsorbed at the air/water interface a transition from a two-dimensional liquid to a gas was observed. A clear discontinuity in the coefficient of ellipticity as a function of temperature showed that the transition is first-order. This result suggests that liquid-gas phase transitions in surfactant monolayers may be more widespread than once thought. A solid-liquid phase transition has also been studied in mixed monolayers of dodecanol with an anionic surfactant (sodium dodecyl sulphate) and with a homologous series of cationic surfactants (alkyltrimethylammonium bromides: C n TABs, n = 12, 14, 16). The composition and structure of the mixed monolayers was studied above and below the phase transition. At low temperatures the mixed monolayers were as densely packed as a monolayer of pure dodecanol in its solid phase. At a fixed temperature the monolayers under-went a first-order phase transition to form a phase that was less dense and more conformationally disordered. The proportion of ionic surfactant in the mixed monolayer was greatest in the high temperature phase. As the chain length of the C n TAB increased the number of conformational defects

  7. Molecular Rotors as Switches

    Directory of Open Access Journals (Sweden)

    Kang L. Wang

    2012-08-01

    Full Text Available The use of a functional molecular unit acting as a state variable provides an attractive alternative for the next generations of nanoscale electronics. It may help overcome the limits of conventional MOSFETd due to their potential scalability, low-cost, low variability, and highly integratable characteristics as well as the capability to exploit bottom-up self-assembly processes. This bottom-up construction and the operation of nanoscale machines/devices, in which the molecular motion can be controlled to perform functions, have been studied for their functionalities. Being triggered by external stimuli such as light, electricity or chemical reagents, these devices have shown various functions including those of diodes, rectifiers, memories, resonant tunnel junctions and single settable molecular switches that can be electronically configured for logic gates. Molecule-specific electronic switching has also been reported for several of these device structures, including nanopores containing oligo(phenylene ethynylene monolayers, and planar junctions incorporating rotaxane and catenane monolayers for the construction and operation of complex molecular machines. A specific electrically driven surface mounted molecular rotor is described in detail in this review. The rotor is comprised of a monolayer of redox-active ligated copper compounds sandwiched between a gold electrode and a highly-doped P+ Si. This electrically driven sandwich-type monolayer molecular rotor device showed an on/off ratio of approximately 104, a read window of about 2.5 V, and a retention time of greater than 104 s. The rotation speed of this type of molecular rotor has been reported to be in the picosecond timescale, which provides a potential of high switching speed applications. Current-voltage spectroscopy (I-V revealed a temperature-dependent negative differential resistance (NDR associated with the device. The analysis of the device

  8. Formation of single-walled aluminosilicate nanotubes from molecular precursors and curved nanoscale intermediates.

    Science.gov (United States)

    Yucelen, G Ipek; Choudhury, Rudra Prosad; Vyalikh, Anastasia; Scheler, Ulrich; Beckham, Haskell W; Nair, Sankar

    2011-04-13

    We report the identification and elucidation of the mechanistic role of molecular precursors and nanoscale (1-3 nm) intermediates with intrinsic curvature in the formation of single-walled aluminosilicate nanotubes. We characterize the structural and compositional evolution of molecular and nanoscale species over a length scale of 0.1-100 nm by electrospray ionization mass spectrometry, nuclear magnetic resonance spectroscopy ((27)Al liquid-state, (27)Al and (29)Si solid-state MAS), and dynamic light scattering. Together with structural optimization of key experimentally identified species by solvated density functional theory calculations, this study reveals the existence of intermediates with bonding environments, as well as intrinsic curvature, similar to the structure of the final nanotube product. We show that "proto-nanotube-like" intermediates with inherent curvature form in aqueous synthesis solutions immediately after initial hydrolysis of reactants, disappear from the solution upon heating to 95 °C due to condensation accompanied by an abrupt pH decrease, and finally form ordered single-walled aluminosilicate nanotubes. Detailed quantitative analysis of NMR and ESI-MS spectra from the relevant aluminosilicate, aluminate, and silicate solutions reveals the presence of a variety of monomeric and polymeric aluminate and aluminosilicate species (Al(1)Si(x)-Al(13)Si(x)), such as Keggin ions [AlO(4)Al(12)(OH)(24)(H(2)O)(12)](7+) and polynuclear species with a six-membered Al oxide ring unit. Our study also directly reveals the complexation of aluminate and aluminosilicate species with perchlorate species that most likely inhibit the formation of larger condensates or nontubular structures. Integration of all of our results leads to the construction of the first molecular-level mechanism of single-walled metal oxide nanotube formation, incorporating the role of monomeric and polymeric aluminosilicate species as well as larger nanoparticles. © 2011 American

  9. Quantum tunneling of magnetization in single molecular magnets coupled to ferromagnetic reservoirs

    Science.gov (United States)

    Misiorny, M.; Barnas, J.

    2007-04-01

    The role of spin polarized reservoirs in quantum tunneling of magnetization and relaxation processes in a single molecular magnet (SMM) is investigated theoretically. The SMM is exchange-coupled to the reservoirs and also subjected to a magnetic field varying in time, which enables the quantum tunneling of magnetization. The spin relaxation times are calculated from the Fermi golden rule. The exchange interaction of SMM and electrons in the leads is shown to affect the spin reversal due to quantum tunneling of magnetization. It is shown that the switching is associated with transfer of a certain charge between the leads.

  10. An improved method for the molecular identification of single dinoflagellate cysts

    Directory of Open Access Journals (Sweden)

    Yangchun Gao

    2017-04-01

    Full Text Available Background Dinoflagellate cysts (i.e., dinocysts are biologically and ecologically important as they can help dinoflagellate species survive harsh environments, facilitate their dispersal and serve as seeds for harmful algal blooms. In addition, dinocysts derived from some species can produce more toxins than vegetative forms, largely affecting species through their food webs and even human health. Consequently, accurate identification of dinocysts represents the first crucial step in many ecological studies. As dinocysts have limited or even no available taxonomic keys, molecular methods have become the first priority for dinocyst identification. However, molecular identification of dinocysts, particularly when using single cells, poses technical challenges. The most serious is the low success rate of PCR, especially for heterotrophic species. Methods In this study, we aim to improve the success rate of single dinocyst identification for the chosen dinocyst species (Gonyaulax spinifera, Polykrikos kofoidii, Lingulodinium polyedrum, Pyrophacus steinii, Protoperidinium leonis and Protoperidinium oblongum distributed in the South China Sea. We worked on two major technical issues: cleaning possible PCR inhibitors attached on the cyst surface and designing new dinoflagellate-specific PCR primers to improve the success of PCR amplification. Results For the cleaning of single dinocysts separated from marine sediments, we used ultrasonic wave-based cleaning and optimized cleaning parameters. Our results showed that the optimized ultrasonic wave-based cleaning method largely improved the identification success rate and accuracy of both molecular and morphological identifications. For the molecular identification with the newly designed dinoflagellate-specific primers (18S634F-18S634R, the success ratio was as high as 86.7% for single dinocysts across multiple taxa when using the optimized ultrasonic wave-based cleaning method, and much higher than that

  11. Super-Resolution Imaging of Molecular Emission Spectra and Single Molecule Spectral Fluctuations.

    Science.gov (United States)

    Mlodzianoski, Michael J; Curthoys, Nikki M; Gunewardene, Mudalige S; Carter, Sean; Hess, Samuel T

    2016-01-01

    Localization microscopy can image nanoscale cellular details. To address biological questions, the ability to distinguish multiple molecular species simultaneously is invaluable. Here, we present a new version of fluorescence photoactivation localization microscopy (FPALM) which detects the emission spectrum of each localized molecule, and can quantify changes in emission spectrum of individual molecules over time. This information can allow for a dramatic increase in the number of different species simultaneously imaged in a sample, and can create super-resolution maps showing how single molecule emission spectra vary with position and time in a sample.

  12. Molecular Field Calculation of Magnetization on NdRh2Ge2 Single Crystal

    Directory of Open Access Journals (Sweden)

    A. Himori

    2008-01-01

    Full Text Available Calculation of magnetization of the ternary single crystal compound NdRh2Ge2 has been carried out by using the wave-like molecular field model to explain the complex magnetic behavior. The field-induced magnetic structures having the propagation vectors, 2=(0,0,39/40, 3=(0,0,35/40, 4=(0,0,31/40, and 5=(0,0,0/40 (= the field-induced ferromagnetic phase were proposed. Calculation on the basis of these structures and the antiferromagnetic phase with 1=(0,0,1 well reproduces the experimental magnetization processes and - magnetic phase diagram.

  13. Direct and enantioselective α-allylation of ketones via singly occupied molecular orbital (SOMO) catalysis

    Science.gov (United States)

    Mastracchio, Anthony; Warkentin, Alexander A.; Walji, Abbas M.; MacMillan, David W. C.

    2010-01-01

    The first enantioselective organocatalytic α-allylation of cyclic ketones has been accomplished via singly occupied molecular orbital catalysis. Geometrically constrained radical cations, forged from the one-electron oxidation of transiently generated enamines, readily undergo allylic alkylation with a variety of commercially available allyl silanes. A reasonable latitude in both the ketone and allyl silane components is readily accommodated in this new transformation. Moreover, three new oxidatively stable imidazolidinone catalysts have been developed that allow cyclic ketones to successfully participate in this transformation. The new catalyst platform has also been exploited in the first catalytic enantioselective α-enolation and α-carbooxidation of ketones. PMID:20921367

  14. [Prediction of the molecular response to pertubations from single cell measurements].

    Science.gov (United States)

    Remacle, Françoise; Levine, Raphael D

    2014-12-01

    The response of protein signalization networks to perturbations is analysed from single cell measurements. This experimental approach allows characterizing the fluctuations in protein expression levels from cell to cell. The analysis is based on an information theoretic approach grounded in thermodynamics leading to a quantitative version of Le Chatelier principle which allows to predict the molecular response. Two systems are investigated: human macrophages subjected to lipopolysaccharide challenge, analogous to the immune response against Gram-negative bacteria and the response of the proteins involved in the mTOR signalizing network of GBM cancer cells to changes in partial oxygen pressure. © 2014 médecine/sciences – Inserm.

  15. Molecular dynamic simulation for nanometric cutting of single-crystal face-centered cubic metals.

    Science.gov (United States)

    Huang, Yanhua; Zong, Wenjun

    2014-01-01

    In this work, molecular dynamics simulations are performed to investigate the influence of material properties on the nanometric cutting of single crystal copper and aluminum with a diamond cutting tool. The atomic interactions in the two metallic materials are modeled by two sets of embedded atom method (EAM) potential parameters. Simulation results show that although the plastic deformation of the two materials is achieved by dislocation activities, the deformation behavior and related physical phenomena, such as the machining forces, machined surface quality, and chip morphology, are significantly different for different materials. Furthermore, the influence of material properties on the nanometric cutting has a strong dependence on the operating temperature.

  16. In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element Specific for Bromacil

    Directory of Open Access Journals (Sweden)

    Ryan M. Williams

    2014-01-01

    Full Text Available Bromacil is a widely used herbicide that is known to contaminate environmental systems. Due to the hazards it presents and inefficient detection methods, it is necessary to create a rapid and efficient sensing device. Towards this end, we have utilized a stringent in vitro selection method to identify single-stranded DNA molecular recognition elements (MRE specific for bromacil. We have identified one MRE with high affinity (Kd=9.6 nM and specificity for bromacil compared to negative targets of selection and other pesticides. The selected ssDNA MRE will be useful as the sensing element in a field-deployable bromacil detection device.

  17. Infrared spectroscopy of self-assembled monolayer films on silicon

    Science.gov (United States)

    Rowell, N. L.; Tay, Lilin; Boukherroub, R.; Lockwood, D. J.

    2007-07-01

    Infrared vibrational spectroscopy in an attenuated total reflection (ATR) geometry has been employed to investigate the presence of organic thin layers on Si-wafer surfaces. The phenomena have been simulated to show there can be a field enhancement with the presented single-reflection ATR (SR-ATR) approach which is substantially larger than for conventional ATR or specular reflection. In SR-ATR, a discontinuity of the field normal to the film contributes a field enhancement in the lower index thin film causing a two order of magnitude increase in sensitivity. SR-ATR was employed to characterize a single monolayer of undecylenic acid self-assembled on Si(1 1 1) and to investigate a two monolayer system obtained by adding a monolayer of bovine serum albumin protein.

  18. Strong exciton-photon coupling in organic single crystal microcavity with high molecular orientation

    Energy Technology Data Exchange (ETDEWEB)

    Goto, Kaname [Department of Electronics, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585 (Japan); Yamashita, Kenichi, E-mail: yamasita@kit.ac.jp [Faculty of Electrical Engineering and Electronics, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585 (Japan); Yanagi, Hisao [Graduate School of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192 (Japan); Yamao, Takeshi; Hotta, Shu [Faculty of Materials Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585 (Japan)

    2016-08-08

    Strong exciton-photon coupling has been observed in a highly oriented organic single crystal microcavity. This microcavity consists of a thiophene/phenylene co-oligomer (TPCO) single crystal laminated on a high-reflection distributed Bragg reflector. In the TPCO crystal, molecular transition dipole was strongly polarized along a certain horizontal directions with respect to the main crystal plane. This dipole polarization causes significantly large anisotropies in the exciton transition and optical constants. Especially the anisotropic exciton transition was found to provide the strong enhancement in the coupling with the cavity mode, which was demonstrated by a Rabi splitting energy as large as ∼100 meV even in the “half-vertical cavity surface emitting lasing” microcavity structure.

  19. Structural modeling of dahlia-type single-walled carbon nanohorn aggregates by molecular dynamics.

    Science.gov (United States)

    Hawelek, L; Brodka, A; Dore, John C; Hannon, Alex C; Iijima, S; Yudasaka, M; Ohba, T; Kaneko, K; Burian, A

    2013-09-19

    The structure of dahlia-type single-walled carbon nanohorn aggregates has been modeled by classical molecular dynamics simulations, and the validity of the model has been verified by neutron diffraction. Computer-generated models consisted of an outer part formed from single-walled carbon nanohorns with diameters of 20-50 Å and a length of 400 Å and an inner turbostratic graphite-like core with a diameter of 130 Å. The diffracted intensity and the pair correlation function computed for such a constructed model are in good agreement with the neutron diffraction experimental data. The proposed turbostratic inner core explains the occurrence of the additional (002) and (004) graphitic peaks in the diffraction pattern of the studied sample and provides information about the interior structure of the dahlia-type aggregates.

  20. A visualization method for probing grain boundaries of single layer graphene via molecular beam epitaxy

    Science.gov (United States)

    Zhan, Linjie; Wan, Wen; Zhu, Zhenwei; Zhao, Zhijuan; Zhang, Zhenhan; Shih, Tien-Mo; Cai, Weiwei

    2017-07-01

    Graphene, a member of layered two-dimensional (2D) materials, possesses high carrier mobility, mechanical flexibility, and optical transparency, as well as enjoying a wide range of promising applications in electronics. Adopting the chemical vaporization deposition method, the majority of investigators have ubiquitously grown single layer graphene (SLG), which inevitably involves polycrystalline properties. Here we demonstrate a simple method for the direct visualization of arbitrarily large-size SLG domains by synthesizing one-hundred-nm-scale MoS2 single crystals via a high-vacuum molecular beam epitaxy process. The present study based on epitaxial growth provides a guide for probing the grain boundaries of various 2D materials and implements higher potentials for the next-generation electronic devices.

  1. Molecular beam epitaxy of single crystalline GaN nanowires on a flexible Ti foil

    Science.gov (United States)

    Calabrese, Gabriele; Corfdir, Pierre; Gao, Guanhui; Pfüller, Carsten; Trampert, Achim; Brandt, Oliver; Geelhaar, Lutz; Fernández-Garrido, Sergio

    2016-05-01

    We demonstrate the self-assembled growth of vertically aligned GaN nanowire ensembles on a flexible Ti foil by plasma-assisted molecular beam epitaxy. The analysis of single nanowires by transmission electron microscopy reveals that they are single crystalline. Low-temperature photoluminescence spectroscopy demonstrates that in comparison to standard GaN nanowires grown on Si, the nanowires prepared on the Ti foil exhibit an equivalent crystalline perfection, a higher density of basal-plane stacking faults, but a reduced density of inversion domain boundaries. The room-temperature photoluminescence spectrum of the nanowire ensemble is not influenced or degraded by the bending of the substrate. The present results pave the way for the fabrication of flexible optoelectronic devices based on GaN nanowires on metal foils.

  2. Molecular beam epitaxy of single crystalline GaN nanowires on a flexible Ti foil

    International Nuclear Information System (INIS)

    Calabrese, Gabriele; Corfdir, Pierre; Gao, Guanhui; Pfüller, Carsten; Trampert, Achim; Brandt, Oliver; Geelhaar, Lutz; Fernández-Garrido, Sergio

    2016-01-01

    We demonstrate the self-assembled growth of vertically aligned GaN nanowire ensembles on a flexible Ti foil by plasma-assisted molecular beam epitaxy. The analysis of single nanowires by transmission electron microscopy reveals that they are single crystalline. Low-temperature photoluminescence spectroscopy demonstrates that in comparison to standard GaN nanowires grown on Si, the nanowires prepared on the Ti foil exhibit an equivalent crystalline perfection, a higher density of basal-plane stacking faults, but a reduced density of inversion domain boundaries. The room-temperature photoluminescence spectrum of the nanowire ensemble is not influenced or degraded by the bending of the substrate. The present results pave the way for the fabrication of flexible optoelectronic devices based on GaN nanowires on metal foils.

  3. Innovative molecular-based fluorescent nanoparticles for multicolor single particle tracking in cells

    International Nuclear Information System (INIS)

    Daniel, Jonathan; Blanchard-Desce, Mireille; Godin, Antoine G; Palayret, Matthieu; Lounis, Brahim; Cognet, Laurent

    2016-01-01

    Based on an original molecular-based design, we present bright and photostable fluorescent organic nanoparticles (FONs) showing excellent colloidal stability in various aqueous environments. Complementary near-infrared emitting and green emitting FONs were prepared using a simple, fast and robust protocol. Both types of FONs could be simultaneously imaged at the single-particle level in solution as well as in biological environments using a monochromatic excitation and a dual-color fluorescence microscope. No evidence of acute cytotoxicity was found upon incubation of live cells with mixed solutions of FONs, and both types of nanoparticles were found internalized in the cells where their motion could be simultaneously tracked at video-rate up to minutes. These fluorescent organic nanoparticles open a novel non-toxic alternative to existing nanoparticles for imaging biological structures, compatible with live-cell experiments and specially fitted for multicolor single particle tracking. (paper)

  4. Solid-state molecular organometallic chemistry. Single-crystal to single-crystal reactivity and catalysis with light hydrocarbon substrates.

    Science.gov (United States)

    Chadwick, F Mark; McKay, Alasdair I; Martinez-Martinez, Antonio J; Rees, Nicholas H; Krämer, Tobias; Macgregor, Stuart A; Weller, Andrew S

    2017-08-01

    0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 CHCD 3 , using [Rh(Cy 2 PCH 2 CH 2 PCy 2 )(η 2 η 2 -NBA)][BAr F 4 ] scrambles the D-label into all possible positions of the propene, as shown by isotopic perturbation of equilibrium measurements for the agostic interaction. Periodic DFT calculations show a low barrier to H/D exchange (10.9 kcal mol -1 , PBE-D3 level), and GIPAW chemical shift calculations guide the assignment of the experimental data. When synthesized using solution routes a bis-propene complex, [Rh(Cy 2 PCH 2 CH 2 PCy 2 )(propene) 2 ][BAr F 4 ] , is formed. [Rh(Cy 2 PCH 2 CH 2 PCy 2 )(butene)][BAr F 4 ] ( x = 1) is characterized as having 2-butene bound as the cis -isomer and a single Rh···H 3 C agostic interaction. In the solid-state two low-energy fluxional processes are proposed. The first is a simple libration of the 2-butene that exchanges the agostic interaction, and the second is a butene isomerization process that proceeds via an allyl-hydride intermediate with a low computed barrier of 14.5 kcal mol -1 . [Rh(Cy 2 PCH 2 CH 2 PCy 2 )(η 2 η 2 -NBA)][BAr F 4 ] and the polymorphs of [Rh(Cy 2 PCH 2 CH 2 PCy 2 )(ethene) 2 ][BAr F 4 ] are shown to be effective in solid-state molecular organometallic catalysis (SMOM-Cat) for the isomerization of 1-butene to a mixture of cis - and trans -2-butene at 298 K and 1 atm, and studies suggest that catalysis is likely dominated by surface-active species. [Rh(Cy 2 PCH 2 CH 2 PCy 2 )(η 2 η 2 -NBA

  5. Ion assisted structural collapse of a single stranded DNA: A molecular dynamics approach

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Soumadwip; Dixit, Himanshu; Chakrabarti, Rajarshi, E-mail: rajarshi@chem.iitb.ac.in

    2015-09-28

    Highlights: • The dynamics of a single-stranded DNA in presence of different concentrations of Mg{sup 2+} is investigated. • The initial DNA chain collapse is characterized by the formation of non-sequentially stacked base pairs. • The DNA chain re-swells at high concentrations of Mg{sup 2+} as a consequence of overcharging. - Abstract: The structure and dynamics of negatively charged nucleic acids strongly correlate with the concentration and charge of the oppositely charged counterions. It is well known that the structural collapse of DNA is favoured in the presence of additional salt, a source of excess oppositely charged ions. Under such conditions single stranded DNA adopts a collapsed coil like conformation, typically characterized by stacking base pairs. Using atomistic molecular dynamics simulation, we demonstrate that in the presence of additional divalent salt (MgCl{sub 2}) single stranded DNA with base sequence 5′-CGCGAATTCGCG-3′ (Dickerson Drew dodecamer) initially collapses and then expands with increasing salt concentration. This is due to the overcharging induced DNA chain swelling, a dominant factor at a higher divalent salt concentration. In a nutshell, our simulations show how in the presence of divalent salt, non-sequential base stacking and overcharging competes and affect single stranded DNA dynamics unlike a monovalent salt.

  6. Latent Membrane Protein 1 as a molecular adjuvant for single-cycle lentiviral vaccines

    Directory of Open Access Journals (Sweden)

    Rahmberg Andrew R

    2011-05-01

    Full Text Available Abstract Background Molecular adjuvants are a promising method to enhance virus-specific immune responses and protect against HIV-1 infection. Immune activation by ligands for receptors such as CD40 can induce dendritic cell activation and maturation. Here we explore the incorporation of two CD40 mimics, Epstein Barr Virus gene LMP1 or an LMP1-CD40 chimera, into a strain of SIV that was engineered to be limited to a single cycle of infection. Results Full length LMP1 or the chimeric protein LMP1-CD40 was cloned into the nef-locus of single-cycle SIV. Human and Macaque monocyte derived macrophages and DC were infected with these viruses. Infected cells were analyzed for activation surface markers by flow cytometry. Cells were also analyzed for secretion of pro-inflammatory cytokines IL-1β, IL-6, IL-8, IL-12p70 and TNF by cytometric bead array. Conclusions Overall, single-cycle SIV expressing LMP1 and LMP1-CD40 produced a broad and potent TH1-biased immune response in human as well as rhesus macaque macrophages and DC when compared with control virus. Single-cycle SIV-LMP1 also enhanced antigen presentation by lentiviral vector vaccines, suggesting that LMP1-mediated immune activation may enhance lentiviral vector vaccines against HIV-1.

  7. Nonequilibrium Chemical Effects in Single-Molecule SERS Revealed by Ab Initio Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, Sean A.; Apra, Edoardo; Govind, Niranjan; Hess, Wayne P.; El-Khoury, Patrick Z.

    2017-02-03

    Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single molecule SERS spectra and selection rules is a challenging task, and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4’-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag20). This affects our simulated single molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.

  8. Monolayers of a De Novo Designed 4-Alpha-Helix Bundle Carboprotein and Partial Structures on Au(111)-Surfaces

    DEFF Research Database (Denmark)

    Brask, Jesper; Wackerbarth, Hainer; Jensen, Knud Jørgen

    2002-01-01

    on a galactopyranoside derivative with a thiol anchor aglycon suitable for surface immobilization on gold. The galactopyranoside with thiol anchor and the thiol anchor alone were prepared for comparison. Voltammetry of the three molecules on Au(111) showed reductive desorption peaks caused by monolayer adsorption via...... thiolate-Au bonding. In situ STM of the thiol anchor disclosed an ordered adlayer with clear domains and molecular features. This holds promise, broadly for single-molecule voltammetry and the SPM and scanning tunnelling microscopy (STM) of natural and synthetic proteins....

  9. Single-site Lennard-Jones models via polynomial chaos surrogates of Monte Carlo molecular simulation

    KAUST Repository

    Kadoura, Ahmad Salim

    2016-06-01

    In this work, two Polynomial Chaos (PC) surrogates were generated to reproduce Monte Carlo (MC) molecular simulation results of the canonical (single-phase) and the NVT-Gibbs (two-phase) ensembles for a system of normalized structureless Lennard-Jones (LJ) particles. The main advantage of such surrogates, once generated, is the capability of accurately computing the needed thermodynamic quantities in a few seconds, thus efficiently replacing the computationally expensive MC molecular simulations. Benefiting from the tremendous computational time reduction, the PC surrogates were used to conduct large-scale optimization in order to propose single-site LJ models for several simple molecules. Experimental data, a set of supercritical isotherms, and part of the two-phase envelope, of several pure components were used for tuning the LJ parameters (ε, σ). Based on the conducted optimization, excellent fit was obtained for different noble gases (Ar, Kr, and Xe) and other small molecules (CH4, N2, and CO). On the other hand, due to the simplicity of the LJ model used, dramatic deviations between simulation and experimental data were observed, especially in the two-phase region, for more complex molecules such as CO2 and C2 H6.

  10. VNAR single-domain antibodies specific for BAFF inhibit B cell development by molecular mimicry.

    Science.gov (United States)

    Häsler, Julien; Flajnik, Martin F; Williams, Gareth; Walsh, Frank S; Rutkowski, J Lynn

    2016-07-01

    B cell-activating factor (BAFF) plays a dominant role in the B cell homeostasis. However, excessive BAFF promotes the development of autoreactive B-cells and several antibodies have been developed to block its activity. Bispecific antibodies with added functionality represent the next wave of biologics that may be more effective in the treatment of complex autoimmune disease. The single variable domain from the immunoglobulin new antigen receptor (VNAR) is one of the smallest antibody recognition units that could be combined with monospecific antibodies to develop bispecific agents. We isolated a panel of BAFF-binding VNARs with low nM potency from a semi-synthetic phage display library and examined their functional activity. The anti-BAFF VNARs blocked the binding of BAFF to all three of its receptors (BR3, TACI and BCMA) and the presence of the conserved DXL receptor motif found in the CDR3 regions suggests molecular mimicry as the mechanism of antagonism. One clone was formatted as an Fc fusion for functional testing and it was found to inhibit both mouse and human BAFF with equal potency ex vivo in a splenocyte proliferation assay. In mice, subchronic administration reduced the number of immature and transitional intermediates B cells and mature B cell subsets. These results indicate that VNAR single domain antibodies function as selective B-cell inhibitors and offer an alternative molecular format for targeting B-cell disorders. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Single intra-articular injection of high molecular weight hyaluronic acid for hip osteoarthritis.

    Science.gov (United States)

    Rivera, Fabrizio

    2016-03-01

    Intra-articular (IA) injection of hyaluronic acid (HA) into the hip joint appears to be safe and well tolerated but only a small number of randomized clinical trials in humans has been published. The objective of this prospective study was to evaluate the efficacy and safety of a single IA injection of high-molecular-weight (2800 kDa) HA (Coxarthrum) for hip osteoarthritis. All patients received a single IA administration of 2.5 % sodium hyaluronate (75 mg/3 mL) of high molecular weight. Fluoroscopy requires an iodized contrast medium (iopamidol, 1 ml) which highlights the capsule before administering HA. Patients were evaluated before IA injection (T0), after 3 months, after 6 months and after 1 year from injection. Results were evaluated by the Brief Pain Inventory (BPI II), Harris Hip Score and a visual analog scale of pain (pain VAS). All treated patients were considered for statistical analysis. Two hundred seven patients were included at T0. The mean age was 67 years (range 46-81). Regarding BPI severity score, changes in pain between T0 and the three following visits were statistically highly significant (p injection of Coxarthrum is effective from the third month and that the results are stable or continue to improve up to 1 year. IV.

  12. Scattering of atomic and molecular ions from single crystal surfaces of Cu, Ag and Fe

    International Nuclear Information System (INIS)

    Zoest, J.M. van.

    1986-01-01

    This thesis deals with analysis of crystal surfaces of Cu, Ag and Fe with Low Energy Ion scattering Spectroscopy (LEIS). Different atomic and molecular ions with fixed energies below 7 keV are scattered by a metal single crystal (with adsorbates). The energy and direction of the scattered particles are analysed for different selected charge states. In that way information can be obtained concerning the composition and atomic and electronic structure of the single crystal surface. Energy spectra contain information on the composition of the surface, while structural atomic information is obtained by direction measurements (photograms). In Ch.1 a description is given of the experimental equipment, in Ch.2 a characterization of the LEIS method. Ch.3 deals with the neutralization of keV-ions in surface scattering. Two different ways of data interpretation are presented. First a model is treated in which the observed directional dependence of neutralization action of the first atom layer of the surface is presented by a laterally varying thickness of the neutralizing layer. Secondly it is shown that the data can be reproduced by a more realistic, physical model based on atomic transition matrix elements. In Ch.4 the low energy hydrogen scattering is described. The study of the dissociation of H 2 + at an Ag surface r0230ted in a model based on electronic dissociation, initialized by electron capture into a repulsive (molecular) state. In Ch.5 finally the method is applied to the investigation of the surface structure of oxidized Fe. (Auth.)

  13. Synthetic lethality between gene defects affecting a single non-essential molecular pathway with reversible steps.

    Directory of Open Access Journals (Sweden)

    Andrei Zinovyev

    2013-04-01

    Full Text Available Systematic analysis of synthetic lethality (SL constitutes a critical tool for systems biology to decipher molecular pathways. The most accepted mechanistic explanation of SL is that the two genes function in parallel, mutually compensatory pathways, known as between-pathway SL. However, recent genome-wide analyses in yeast identified a significant number of within-pathway negative genetic interactions. The molecular mechanisms leading to within-pathway SL are not fully understood. Here, we propose a novel mechanism leading to within-pathway SL involving two genes functioning in a single non-essential pathway. This type of SL termed within-reversible-pathway SL involves reversible pathway steps, catalyzed by different enzymes in the forward and backward directions, and kinetic trapping of a potentially toxic intermediate. Experimental data with recombinational DNA repair genes validate the concept. Mathematical modeling recapitulates the possibility of kinetic trapping and revealed the potential contributions of synthetic, dosage-lethal interactions in such a genetic system as well as the possibility of within-pathway positive masking interactions. Analysis of yeast gene interaction and pathway data suggests broad applicability of this novel concept. These observations extend the canonical interpretation of synthetic-lethal or synthetic-sick interactions with direct implications to reconstruct molecular pathways and improve therapeutic approaches to diseases such as cancer.

  14. Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity

    Science.gov (United States)

    Chiu, Isaac M; Barrett, Lee B; Williams, Erika K; Strochlic, David E; Lee, Seungkyu; Weyer, Andy D; Lou, Shan; Bryman, Gregory S; Roberson, David P; Ghasemlou, Nader; Piccoli, Cara; Ahat, Ezgi; Wang, Victor; Cobos, Enrique J; Stucky, Cheryl L; Ma, Qiufu; Liberles, Stephen D; Woolf, Clifford J

    2014-01-01

    The somatosensory nervous system is critical for the organism's ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1) IB4+SNS-Cre/TdTomato+, 2) IB4−SNS-Cre/TdTomato+, and 3) Parv-Cre/TdTomato+ cells, encompassing the majority of nociceptive, pruriceptive, and proprioceptive neurons. These neurons displayed distinct expression patterns of ion channels, transcription factors, and GPCRs. Highly parallel qRT-PCR analysis of 334 single neurons selected by membership of the three populations demonstrated further diversity, with unbiased clustering analysis identifying six distinct subgroups. These data significantly increase our knowledge of the molecular identities of known DRG populations and uncover potentially novel subsets, revealing the complexity and diversity of those neurons underlying somatosensation. DOI: http://dx.doi.org/10.7554/eLife.04660.001 PMID:25525749

  15. Molecular dynamics simulations on aqueous two-phase systems - Single PEG-molecules in solution

    Directory of Open Access Journals (Sweden)

    Oelmeier Stefan A

    2012-08-01

    Full Text Available Abstract Background Molecular Dynamics (MD simulations are a promising tool to generate molecular understanding of processes related to the purification of proteins. Polyethylene glycols (PEG of various length are commonly used in the production and purification of proteins. The molecular mechanisms behind PEG driven precipitation, aqueous two-phase formation or the effects of PEGylation are however still poorly understood. Results In this paper, we ran MD simulations of single PEG molecules of variable length in explicitly simulated water. The resulting structures are in good agreement with experimentally determined 3D structures of PEG. The increase in surface hydrophobicity of PEG of longer chain length could be explained on an atomic scale. PEG-water interactions as well as aqueous two-phase formation in the presence of PO4 were found to be correlated to PEG surface hydrophobicity. Conclusions We were able to show that the taken MD simulation approach is capable of generating both structural data as well as molecule descriptors in agreement with experimental data. Thus, we are confident of having a good in silico representation of PEG.

  16. Nanomechanical resonators based on group IV element monolayers

    Science.gov (United States)

    He, Ji-Dong; Sun, Jia-Sheng; Jiang, Jin-Wu

    2018-04-01

    We perform molecular dynamics simulations to investigate the energy dissipation of the resonant oscillation for the group IV monolayers of puckered configuration, in which the oscillation is driven with different actuation velocities. We find that, in the moderate actuation velocity regime, the nonlinear coupling between the resonant oscillation mode and other high-frequency modes will lead to the non-resonant motion of the system. For the larger actuation velocity, the effective strain generated during the resonant oscillating causes a structural transition from the puckered configuration into the planar configuration, which is a characteristic energy dissipation mechanism for the resonant oscillation of these group IV puckered monolayers. Our findings shed light on mechanical applications of the group IV monolayers in the nanomechanical resonator field.

  17. Photo-induced travelling waves in condensed Langmuir monolayers

    CERN Document Server

    Tabe, Y; Yokoyama, H

    2003-01-01

    We report the detailed properties of photo-induced travelling waves in liquid crystalline Langmuir monolayers composed of azobenzene derivatives. When the monolayer, in which the constituent rodlike molecules are coherently tilted from the layer normal, is weakly illuminated to undergo the trans-cis photo-isomerization, spatio-temporal periodic oscillations of the molecular azimuth begin over the entire excited area and propagate as a two-dimensional orientational wave. The wave formation takes place only when the film is formed at an asymmetric interface with broken up-down symmetry and when the chromophores are continuously excited near the long-wavelength edge of absorption to induce repeated photo-isomerizations between the trans and cis forms. Under proper illumination conditions, Langmuir monolayers composed of a wide variety of azobenzene derivatives have been confirmed to exhibit similar travelling waves with velocity proportional to the excitation power irrespective of the degree of amphiphilicity. T...

  18. Multi-scale Modeling of Compressible Single-phase Flow in Porous Media using Molecular Simulation

    KAUST Repository

    Saad, Ahmed Mohamed

    2016-05-01

    In this study, an efficient coupling between Monte Carlo (MC) molecular simulation and Darcy-scale flow in porous media is presented. The cell-centered finite difference method with a non-uniform rectangular mesh were used to discretize the simulation domain and solve the governing equations. To speed up the MC simulations, we implemented a recently developed scheme that quickly generates MC Markov chains out of pre-computed ones, based on the reweighting and reconstruction algorithm. This method astonishingly reduces the required computational time by MC simulations from hours to seconds. In addition, the reweighting and reconstruction scheme, which was originally designed to work with the LJ potential model, is extended to work with a potential model that accounts for the molecular quadrupole moment of fluids with non-spherical molecules such as CO2. The potential model was used to simulate the thermodynamic equilibrium properties for single-phase and two-phase systems using the canonical ensemble and the Gibbs ensemble, respectively. Comparing the simulation results with the experimental data showed that the implemented model has an excellent fit outperforming the standard LJ model. To demonstrate the strength of the proposed coupling in terms of computational time efficiency and numerical accuracy in fluid properties, various numerical experiments covering different compressible single-phase flow scenarios were conducted. The novelty in the introduced scheme is in allowing an efficient coupling of the molecular scale and Darcy scale in reservoir simulators. This leads to an accurate description of the thermodynamic behavior of the simulated reservoir fluids; consequently enhancing the confidence in the flow predictions in porous media.

  19. Structure and function evolution of thiolate monolayers on gold

    Energy Technology Data Exchange (ETDEWEB)

    Edwards, Grant Alvin [Iowa State Univ., Ames, IA (United States)

    2006-01-01

    The use of n-alkanethiolate self-assembled monolayers on gold has blossomed in the past few years. These systems have functioned as models for common interfaces. Thiolate monolayers are ideal because they are easily modified before or after deposition. The works contained within this dissertation include interfacial characterization (infrared reflection absorption spectroscopy, ellipsometry, contact angle, scanning probe microscopy, and heterogeneous electron-transfer kinetics) and various modeling scenarios. The results of these characterizations present ground-breaking insights into the structure, function, and reproducible preparation of these monolayers. Surprisingly, three interfacial properties (electron-transfer, contact angle, and ellipsometry) were discovered to depend directly on the odd-even character of the monolayer components. Molecular modeling was utilized to investigate adlayer orientation, and suggests that these effects are adlayer structure specific. Finally, the electric force microscopy and theoretical modeling investigations of monolayer samples are presented, which show that the film dielectric constant, thickness, and dipole moment directly affect image contrast. In addition, the prospects for utilization of this emerging technique are outlined.

  20. Structure and Function Evolution of Thiolate Monolayers on Gold

    Energy Technology Data Exchange (ETDEWEB)

    Edwards, Grant Alvin [Iowa State Univ., Ames, IA (United States)

    2006-01-01

    The use of n-alkanethiolate self-assembled monolayers on gold has blossomed in the past few years. These systems have functioned as models for common interfaces. Thiolate monolayers are ideal because they are easily modified before or after deposition. The works contained within this dissertation include interfacial characterization (inbred reflection absorption spectroscopy, ellipsometry, contact angle, scanning probe microscopy, and heterogeneous electron-transfer kinetics) and various modeling scenarios. The results of these characterizations present ground-breaking insights into the structure, function, and reproducible preparation of these monolayers. Surprisingly, three interfacial properties (electron-transfer, contact angle, and ellipsometry) were discovered to depend directly on the odd-even character of the monolayer components. Molecular modeling was utilized to investigate adlayer orientation, and suggests that these effects are adlayer structure specific. Finally, the electric force microscopy and theoretical modeling investigations of monolayer samples are presented, which show that the film dielectric constant, thickness, and dipole moment directly affect image contrast. In addition, the prospects for utilization of this emerging technique are outlined.

  1. Thermal conductivity of a h-BCN monolayer.

    Science.gov (United States)

    Zhang, Ying-Yan; Pei, Qing-Xiang; Liu, Hong-Yuan; Wei, Ning

    2017-10-18

    A hexagonal graphene-like boron-carbon-nitrogen (h-BCN) monolayer, a new two-dimensional (2D) material, has been synthesized recently. Herein we investigate for the first time the thermal conductivity of this novel 2D material. Using molecular dynamics simulations based on the optimized Tersoff potential, we found that the h-BCN monolayers are isotropic in the basal plane with close thermal conductivity magnitudes. Though h-BCN has the same hexagonal lattice as graphene and hexagonal boron nitride (h-BN), it exhibits a much lower thermal conductivity than the latter two materials. In addition, the thermal conductivity of h-BCN monolayers is found to be size-dependent but less temperature-dependent. Modulation of the thermal conductivity of h-BCN monolayers can also be realized by strain engineering. Compressive strain leads to a monotonic decrease in the thermal conductivity while the tensile strain induces an up-then-down trend in the thermal conductivity. Surprisingly, the small tensile strain can facilitate the heat transport of the h-BCN monolayers.

  2. Piezoelectric effect on the thermal conductivity of monolayer gallium nitride

    Science.gov (United States)

    Zhang, Jin

    2018-01-01

    Using molecular dynamics and density functional theory simulations, in this work, we find that the heat transport property of the monolayer gallium nitride (GaN) can be efficiently tailored by external electric field due to its unique piezoelectric characteristic. As the monolayer GaN possesses different piezoelectric properties in armchair and zigzag directions, different effects of the external electric field on thermal conductivity are observed when it is applied in the armchair and zigzag directions. Our further study reveals that due to the elastoelectric effect in the monolayer GaN, the external electric field changes the Young's modulus and therefore changes the phonon group velocity. Also, due to the inverse piezoelectric effect, the applied electric field induces in-plane stress in the monolayer GaN subject to a length constraint, which results in the change in the lattice anharmonicity and therefore affects the phonon mean free path. Furthermore, for relatively long GaN monolayers, the in-plane stress may trigger the buckling instability, which can significantly reduce the phonon mean free path.

  3. Self-assemblies of meso-tetraphenylporphine ligand on surfaces of highly oriented pyrolytic graphite and single-walled carbon nanotubes: insights from scanning tunneling microscopy and molecular modeling.

    Science.gov (United States)

    Bassiouk, Maria; Alvarez-Zauco, Edgar; Basiuk, Vladimir A

    2011-06-01

    The self-assembly of porphyrins into highly organized functional arrays supported on appropriate solid substrates is an area of research with multiple potential applications in the "bottom-up" approach to manufacturing. In order to analyze the self-assembly of meso-tetraphenylporphine (H2TPP) on the surfaces of highly oriented pyrolytic graphite (HOPG) and single-walled carbon nanotubes (SWNTs), we performed molecular mechanics modeling (by MM+ force field) and scanning tunneling microscopy (STM) imaging. Molecular modeling predicted an energetic preference of the H2TPP molecules to adsorb in monolayers on the surfaces of graphite and SWNT sidewall, rather than their stacking or separation. On graphite, the most favorable arrays were predicted to be ribbons composed of interacting parallel chains of H2TPP molecules. On the SWNT sidewall, the energetic preference pointed toward the formation of parallel and interacting long-period helixes, resulting in an almost full coverage of the SWNT surface. These preferable arrays on both carbon materials assure the interaction of every porphyrin unit with as many neighbors as possible, thus lowering the potential energy of the adsorption complexes. STM imaging results are in good agreement with molecular modeling predictions. The formation of self-assembled ribbons was a frequently observed phenomenon on the HOPG surface, while on the SWNT surface a full coverage of the exposed portion of the sidewalls was observed, suggesting the formation of interacting long-period helixes. A preferential adsorption of H2TPP molecules near graphite topographic defects was also observed.

  4. Drift correction for single-molecule imaging by molecular constraint field, a distance minimum metric

    International Nuclear Information System (INIS)

    Han, Renmin; Wang, Liansan; Xu, Fan; Zhang, Yongdeng; Zhang, Mingshu; Liu, Zhiyong; Ren, Fei; Zhang, Fa

    2015-01-01

    The recent developments of far-field optical microscopy (single molecule imaging techniques) have overcome the diffraction barrier of light and improve image resolution by a factor of ten compared with conventional light microscopy. These techniques utilize the stochastic switching of probe molecules to overcome the diffraction limit and determine the precise localizations of molecules, which often requires a long image acquisition time. However, long acquisition times increase the risk of sample drift. In the case of high resolution microscopy, sample drift would decrease the image resolution. In this paper, we propose a novel metric based on the distance between molecules to solve the drift correction. The proposed metric directly uses the position information of molecules to estimate the frame drift. We also designed an algorithm to implement the metric for the general application of drift correction. There are two advantages of our method: First, because our method does not require space binning of positions of molecules but directly operates on the positions, it is more natural for single molecule imaging techniques. Second, our method can estimate drift with a small number of positions in each temporal bin, which may extend its potential application. The effectiveness of our method has been demonstrated by both simulated data and experiments on single molecular images

  5. Reverse engineering of an affinity-switchable molecular interaction characterized by atomic force microscopy single-molecule force spectroscopy.

    Science.gov (United States)

    Anselmetti, Dario; Bartels, Frank Wilco; Becker, Anke; Decker, Björn; Eckel, Rainer; McIntosh, Matthew; Mattay, Jochen; Plattner, Patrik; Ros, Robert; Schäfer, Christian; Sewald, Norbert

    2008-02-19

    Tunable and switchable interaction between molecules is a key for regulation and control of cellular processes. The translation of the underlying physicochemical principles to synthetic and switchable functional entities and molecules that can mimic the corresponding molecular functions is called reverse molecular engineering. We quantitatively investigated autoinducer-regulated DNA-protein interaction in bacterial gene regulation processes with single atomic force microscopy (AFM) molecule force spectroscopy in vitro, and developed an artificial bistable molecular host-guest system that can be controlled and regulated by external signals (UV light exposure and thermal energy). The intermolecular binding functionality (affinity) and its reproducible and reversible switching has been proven by AFM force spectroscopy at the single-molecule level. This affinity-tunable optomechanical switch will allow novel applications with respect to molecular manipulation, nanoscale rewritable molecular memories, and/or artificial ion channels, which will serve for the controlled transport and release of ions and neutral compounds in the future.

  6. Collapse of Langmuir monolayer at lower surface pressure: Effect of hydrophobic chain length

    Energy Technology Data Exchange (ETDEWEB)

    Das, Kaushik, E-mail: kaushikdas2089@gmail.com; Kundu, Sarathi [Physical Sciences Division, Institute of Advanced Study in Science and Technology, Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, Assam 781035 (India)

    2016-05-23

    Long chain fatty acid molecules (e.g., stearic and behenic acids) form a monolayer on water surface in the presence of Ba{sup 2+} ions at low subphase pH (≈ 5.5) and remain as a monolayer before collapse generally occurs at higher surface pressure (π{sub c} > 50 mN/m). Monolayer formation is verified from the surface pressure vs. area per molecule (π-A) isotherms and also from the atomic force microscopy (AFM) analysis of the films deposited by single upstroke of hydrophilic Si (001) substrate through the monolayer covered water surface. At high subphase pH (≈ 9.5), barium stearate molecules form multilayer structure at lower surface pressure which is verified from the π-A isotherms and AFM analysis of the film deposited at 25 mN/m. Such monolayer to multilayer structure formation or monolayer collapse at lower surface pressure is unusual as at this surface pressure generally fatty acid salt molecules form a monolayer on the water surface. Formation of bidentate chelate coordination in the metal containing headgroups is the reason for such monolayer to multilayer transition. However, for longer chain barium behenate molecules only monolayer structure is maintained at that high subphase pH (≈ 9.5) due to the presence of relatively more tail-tail hydrophobic interaction.

  7. Self Assembled Monolayers

    Indian Academy of Sciences (India)

    one paper he discussed the effect of olive oil films on the surface tension of water and concluded that the films of olive oil are. 10-20 A in thickness. Rayleigh appeared to have the belief that oil spreads on the water surface to such an extent that the film thickness approaches molecular dimensions. Direct measure- ments of ...

  8. Nitro Stretch Probing of a Single Molecular Layer to Monitor Shock Compression with Picosecond Time-Resolution

    Science.gov (United States)

    Berg, Christopher; Lagutchev, Alexei; Fu, Yuanxi; Dlott, Dana

    2011-06-01

    To obtain maximum possible temporal resolution, laser-driven shock compression of a molecular monolayer was studied using vibrational spectroscopy. The stretching transitions of nitro groups bound to aromatic rings was monitored using a nonlinear coherent infrared spectroscopy termed sum-frequency generation, which produced high-quality signals from this very thin layer. To overcome the shock opacity problem, a novel polymer overcoat method allowed us to make the observation window (witness plate) a few micrometers thick. The high signal-to-noise ratios (>100:1) obtained via this spectroscopy allowed us to study detailed behavior of the shocked molecules. To help interpret these vibrational spectra, additional spectra were obtained under conditions of static pressures up to 10 GPa and static temperatures up to 1000 C. Consequently, this experiment represents a significant step in resolving molecular dynamics during shock compression and unloading with both high spatial and temporal resolution. Supported by the Stewardship Sciences Academic Alliance Program from the Carnegie-DOE Alliance Center under grant number DOE CIW 4-3253-13 and the US Air Force Office of Scientific Research under award number FAA9550-09-1-0163.

  9. The rise of 3-d single-ion magnets in molecular magnetism: towards materials from molecules?

    Science.gov (United States)

    Frost, Jamie M; Harriman, Katie L M; Murugesu, Muralee

    2016-04-21

    Single-molecule magnets (SMMs) that contain one spin centre (so-called single-ion magnets) theoretically represent the smallest possible unit for spin-based electronic devices. The realisation of this and related technologies, depends on first being able to design systems with sufficiently large energy barriers to magnetisation reversal, U eff , and secondly, on being able to organise these molecules into addressable arrays. In recent years, significant progress has been made towards the former goal - principally as a result of efforts which have been directed towards studying complexes based on highly anisotropic lanthanide ions, such as Tb(iii) and Dy(iii). Since 2013 however, and the remarkable report by Long and co-workers of a linear Fe(i) system exhibiting U eff = 325 K, single-ion systems of transition metals have undergone something of a renaissance in the literature. Not only do they have important lessons to teach us about anisotropy and relaxation dynamics in the quest to enhance U eff , the ability to create strongly coupled spin systems potentially offers access to a whole of host of 1, 2 and 3-dimensional materials with interesting structural and physical properties. This perspective summarises recent progress in this rapidly expanding sub-genre of molecular magnetism from the viewpoint of the synthetic chemist, with a particular focus on the lessons that have so far been learned from single-ion magnets of the d-block, and, the future research directions which we feel are likely to emerge in the coming years.

  10. Single particle tracking-based reaction progress kinetic analysis reveals a series of molecular mechanisms of cetuximab-induced EGFR processes in a single living cell.

    Science.gov (United States)

    Kim, Do-Hyeon; Kim, Dong-Kyun; Zhou, Kai; Park, Soyeon; Kwon, Yonghoon; Jeong, Min Gyu; Lee, Nam Ki; Ryu, Sung Ho

    2017-07-01

    Cellular processes occur through the orchestration of multi-step molecular reactions. Reaction progress kinetic analysis (RPKA) can provide the mechanistic details to elucidate the multi-step molecular reactions. However, current tools have limited ability to simultaneously monitor dynamic variations in multiple complex states at the single molecule level to apply RPKA in living cells. In this research, a single particle tracking-based reaction progress kinetic analysis (sptRPKA) was developed to simultaneously determine the kinetics of multiple states of protein complexes in the membrane of a single living cell. The subpopulation ratios of different states were quantitatively (and statistically) reliably extracted from the diffusion coefficient distribution rapidly acquired by single particle tracking at constant and high density over a long period of time using super-resolution microscopy. Using sptRPKA, a series of molecular mechanisms of epidermal growth factor receptor (EGFR) cellular processing induced by cetuximab were investigated. By comprehensively measuring the rate constants and cooperativity of the molecular reactions involving four EGFR complex states, a previously unknown intermediate state was identified that represents the rate limiting step responsible for the selectivity of cetuximab-induced EGFR endocytosis to cancer cells.

  11. Magnetic switching of a single molecular magnet due to spin-polarized current

    Science.gov (United States)

    Misiorny, Maciej; Barnaś, Józef

    2007-04-01

    Magnetic switching of a single molecular magnet (SMM) due to spin-polarized current flowing between ferromagnetic metallic leads (electrodes) is investigated theoretically. Magnetic moments of the leads are assumed to be collinear and parallel to the magnetic easy axis of the molecule. Electrons tunneling through the barrier between magnetic leads are coupled to the SMM via exchange interaction. The current flowing through the system, as well as the spin relaxation times of the SMM, are calculated from the Fermi golden rule. It is shown that spin of the SMM can be reversed by applying a certain voltage between the two magnetic electrodes. Moreover, the switching may be visible in the corresponding current-voltage characteristics.

  12. Direct monolithic integration of vertical single crystalline octahedral molecular sieve nanowires on silicon

    Energy Technology Data Exchange (ETDEWEB)

    Carretero-Genevrier, Adrian [Institut des Nanotechnologies de Lyon (INL), UMR-CNRS 5270, Ecole Central de Lyon, Ecully (France); Institut de Ciencia de Materials de Barcelona ICMAB, Catalonia (Spain); Sorbonne Univ., UPMC Univ. Paris 06, CNRS, College de France, Paris (France); Oro-Sole, Judith [Institut de Ciencia de Materials de Barcelona ICMAB, Catalonia (Spain); Gazquez, Jaume [Institut de Ciencia de Materials de Barcelona ICMAB, Catalonia (Spain); Magen, Cesar [Univ. de Zaragoza, Zaragoza (Spain); Miranda, Laura [Sorbonne Univ., UPMC Univ. Paris 06, CNRS, College de France, Paris (France); Puig, Teresa [Institut de Ciencia de Materials de Barcelona ICMAB, Catalonia (Spain); Obradors, Xavier [Institut de Ciencia de Materials de Barcelona ICMAB, Catalonia (Spain); Ferain, Etienne [Univ. Catholique de Louvain, Louvain-la-Neuve (Belgium); Sanchez, Clement [Sorbonne Univ., UPMC Univ. Paris 06, CNRS, College de France, Paris (France); Rodriguez-Carvajal, Juan [Institut Laue-Langevin, Grenoble Cedex (France); Mestres, Narcis [Institut de Ciencia de Materials de Barcelona ICMAB, Catalonia (Spain)

    2013-12-13

    We developed an original strategy to produce vertical epitaxial single crystalline manganese oxide octahedral molecular sieve (OMS) nanowires with tunable pore sizes and compositions on silicon substrates by using a chemical solution deposition approach. The nanowire growth mechanism involves the use of track-etched nanoporous polymer templates combined with the controlled growth of quartz thin films at the silicon surface, which allowed OMS nanowires to stabilize and crystallize. α-quartz thin films were obtained after thermal activated crystallization of the native amorphous silica surface layer assisted by Sr2+- or Ba2+-mediated heterogeneous catalysis in the air at 800 °C. These α-quartz thin films work as a selective template for the epitaxial growth of randomly oriented vertical OMS nanowires. Furthermore, the combination of soft chemistry and epitaxial growth opens new opportunities for the effective integration of novel technological functional tunneled complex oxides nanomaterials on Si substrates.

  13. Failure of single electron descriptions of molecular orbital collision processes. [Electron promotion mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Elston, S.B.

    1978-01-01

    Inner-shell excitation occurring in low and moderate (keV range) energy collisions between light atomic and ionic systems is frequently describable in terms of molecular promotion mechanisms, which were extensively explored both theoretically and experimentally. The bulk of such studies have concentrated on processes understandable through the use of single- and independent-electron models. Nonetheless, it is possible to find cases of inner-shell excitation in relatively simple collision systems which involve nearly simultaneous multiple-electron transitions and transitions induced by inherently two-electron interactions. Evidence for these many- and nonindependent-electron phenomena in inner-shell excitation processes and the importance of considering such effects in the interpretation of collisionally induced excitation spectra is discussed. 13 references.

  14. Kondo peak splitting and Kondo dip in single molecular magnet junctions

    Energy Technology Data Exchange (ETDEWEB)

    Niu, Pengbin, E-mail: 120233951@qq.com [Institute of Solid State Physics, Shanxi Datong University, Datong 037009 (China); Shi, Yunlong; Sun, Zhu [Institute of Solid State Physics, Shanxi Datong University, Datong 037009 (China); Nie, Yi-Hang [Institute of Theoretical Physics, Shanxi University, Taiyuan 030006 (China); Luo, Hong-Gang [Center for Interdisciplinary Studies & Key Laboratory for Magnetism and Magnetic Materials of the MoE, Lanzhou University, Lanzhou 730000 (China); Beijing Computational Science Research Center, Beijing 100084 (China)

    2016-01-15

    Many factors containing bias, spin–orbit coupling, magnetic fields applied, and so on can strongly influence the Kondo effect, and one of the consequences is Kondo peak splitting (KPS). It is natural that KPS should also appear when another spin degree of freedom is involved. In this work we study the KPS effects of single molecular magnets (SMM) coupled with two metallic leads in low-temperature regime. It is found that the Kondo transport properties are strongly influenced by the exchange coupling and anisotropy of the magnetic core. By employing Green's function method in Hubbard operator representation, we give an analytical expression for local retarded Green's function of SMM and discussed its low-temperature transport properties. We find that the anisotropy term behaves as a magnetic field and the splitting behavior of exchange coupling is quite similar to the spin–orbit coupling. These splitting behaviors are explained by introducing inter-level or intra-level transitions, which account for the seven-peak splitting structure. Moreover, we find a Kondo dip at Fermi level under proper parameters. These Kondo peak splitting behaviors in SMM deepen our understanding to Kondo physics and should be observed in the future experiments. - Highlights: • We study Kondo peak splitting in single molecular magnets. • We study Kondo effect by Hubbard operator Green's function method. • We find Kondo peak splitting structures and a Kondo dip at Fermi level. • The exchange coupling and magnetic anisotropy induce fine splitting structure. • The splitting structures are explained by inter-level or intra-level transitions.

  15. Molecular Etiology of Hereditary Single-Side Deafness: Its Association With Pigmentary Disorders and Waardenburg Syndrome.

    Science.gov (United States)

    Kim, Shin Hye; Kim, Ah Reum; Choi, Hyun Seok; Kim, Min Young; Chun, Eun Hi; Oh, Seung-Ha; Choi, Byung Yoon

    2015-10-01

    Unilateral sensorineural hearing loss (USNHL)/single-side deafness (SSD) is a frequently encountered disability in children. The etiology of a substantial portion of USNHL/SSD still remains unknown, and genetic causes have not been clearly elucidated. In this study, the authors evaluated the heritability of USNHL/SSD.The authors sequentially recruited 50 unrelated children with SSD. For an etiologic diagnosis, we performed a rigorous review on the phenotypes of family members of all children and conducted, if necessary, molecular genetic tests including targeted exome sequencing of 129 deafness genes.Among the 50 SSD children cohort, the authors identify 4 (8%) unrelated SSD probands from 4 families (SH136, SB173, SB177, and SB199) with another hearing impaired family members. Notably, all 4 probands in our cohort with a familial history of SSD also have pigmentary abnormalities such as brown freckles or premature gray hair within first degree relatives, which may indicate that genes whose products are involved with pigmentary disorder could be candidates for heritable SSD. Indeed, SH136 and SB199 turned out to segregate a mutation in MITF and PAX3, respectively, leading to a molecular diagnosis of Waardenburg syndrome (WS).We report, for the first time in the literature, a significant heritability of pediatric SSD. There is a strong association between the heritability of USNHL/SSD and the pigmentary abnormality, shedding a new light on the understanding of the molecular basis of heritable USNHL/SSD. In case of children with congenital SSD, it would be mandatory to rigorously screen pigmentary abnormalities. WS should also be included in the differential diagnosis of children with USNHL/SSD, especially in a familial form.

  16. Single-molecule study of molecular mobility in the cytoplasm of Escherichia coli

    Science.gov (United States)

    Lill, Yoriko; Kaserer, Wallace A.; Newton, Salete M.; Lill, Markus; Klebba, Phillip E.; Ritchie, Ken

    2012-08-01

    The cytoplasm of bacterial cells is filled with individual molecules and molecular complexes that rely on diffusion to bring them together for interaction. The mobility of molecules in the cytoplasm has been characterized by several techniques mainly using fluorescent probes and ensemble methods. In order to probe the microenvrionment inside the cytoplasm as viewed by an individual molecule, we have studied single green fluorescent proteins (GFPs) diffusing in the cytoplasm of Escherichia coli cells at observation at rates ranging from 60 to 1000 Hz. Over long times the diffusion shows confinement due to the geometry of the cells themselves. A simulation in model cells using the actual distribution of cell sizes found in the experiments describes accurately the experimental results as well as reveals a short time diffusion coefficient that agrees well with that determined by ensemble methods. Higher short time diffusion coefficients can be obtained by filling the simulated cell with small spheres modeling cytoplasmic molecules and, depending on the density of particles included in the modeled cytoplasm, can approach the diffusion coefficient of GFPs found in water. Thus, single-molecule tracking combined with analysis using simple simulation of Brownian motion is able to reveal the main contributors to the GFP mobility in the cytoplasm of E. coli.

  17. Structures and shear response of lipid monolayers

    International Nuclear Information System (INIS)

    Dutta, P.; Ketterson, J.B.

    1993-02-01

    This report discusses our work during the last 3 years using x-ray diffraction and shear measurements to study lipid monolayers (membranes). The report is divided into: (1) structure: phase diagram of saturated fatty acid Langmuir monolayers, effect of head group interactions, studies of transferred monolayers (LB films); (2) mechanical properties: fiber=optic capillary wave probe and centrosymmetric trough, mechanical behavior of heneicosanoic acid monolayer phases

  18. Effect of lipid composition and packing on the adsorption of apolipoproteins to lipid monolayers

    International Nuclear Information System (INIS)

    Ibdah, J.A.; Lund-Katz, S.; Phillips, M.C.

    1987-01-01

    The monolayer system has been used to study the effects of lipoprotein surface lipid composition and packing on the affinities of apolipoproteins for the surfaces of lipoprotein particles. The adsorption of apolipoproteins injected beneath lipid monolayers prepared with pure lipids or lipoprotein surface lipids is evaluated by monitoring the surface pressure of the film and the surface concentration (Gamma) of 14 C-labelled apolipoprotein. At a given initial film pressure (π/sub i/) there is a higher adsorption of human apo A-I to unsaturated phosphatidylcholine (PC) monolayers compared to saturated PC monolayers (e.g., at π/sub i/ = 10 mN/m, Gamma = 0.35 and 0.06 mg/m 2 for egg PC and distearoyl PC, respectively, with 3 x 10 -4 mg/ml apo A-I in the subphase). In addition, adsorption of apo A-I is less to an egg sphingomyelin monolayer than to an egg PC monolayer. The adsorption of apo A-I to PC monolayers is decreased by addition of cholesterol. Generally, apo A-I adsorption diminishes as the lipid molecular area decreases. Apo A-I adsorbs more to monolayers prepared with HDL 3 surface lipids than with LDL surface lipids. These studies suggest that lipoprotein surface lipid composition and packing are crucial factors influencing the transfer and exchange of apolipoproteins among various lipoprotein classes during metabolism of lipoprotein particles

  19. Thin Film Behavior of Poly(methyl methacrylates). 9. Crystallization of Isotactic Poly(methyl methacrylate) in Mixed Monolayers

    NARCIS (Netherlands)

    Brinkhuis, R.H.G.; Schouten, A.J.

    1992-01-01

    The crystallization behavior of isotactic poly(methyl methacrylate) (i-PMMA) in monolayers of mixtures with a noncrystallizable component was investigated. The monolayer crystallization process in mixtures with high molecular weight condensed type polymers such as syndiotactic poly(methyl

  20. Fibrinogen monolayer characterization by colloid deposition.

    Science.gov (United States)

    Nattich-Rak, Małgorzata; Adamczyk, Zbigniew; Wasilewska, Monika; Sadowska, Marta

    2013-09-24

    Colloid particle deposition was applied to characterize bovine and human fibrinogen (Fb) monolayers on mica produced by controlled adsorption under diffusion transport at pH 3.5. The surface concentration of Fb was determined by AFM enumeration of single molecules adsorbed over the substrate surface. The electrokinetic properties of Fb monolayers for various ionic strength were studied using the in situ streaming potential measurements. It was shown that Fb adsorbs irreversibly on mica for a broad range of ionic strength of 4 × 10(-4) to 0.15 M, NaCl. The overcharging of initially negative mica surface occurred for fibrinogen surface concentrations higher than 1400 μm(-2). The orientation of fibrinogen molecules in the monolayers was evaluated by the colloid deposition method involving negatively charged polystyrene latex microspheres, 820 nm in diameter. An anomalous deposition of negative latex particles on substrates exhibiting a negative zeta potential was observed, which contradicts the mean-field DLVO predictions. Measurable deposition was observed even at low ionic strength where the minimum approach distance of latex particles to the interface exceeds 70 nm (for 6 × 10(-4) M NaCl). This confirms that, at this pH, fibrinogen molecules adsorb end-on on mica assuming extended conformations with the positive charge located mostly in the end part of the αA chains. This agrees with previous experimental and theoretical results discussed in the literature (Santore, M. M.; Wertz Ch. F. Protein spreading kinetics at liquid-solid interfaces via an adsorption probe method. Langmuir 2005, 21, 10172-10178 (experimental); Adamczyk, Z.; Barbasz, J.; Cieśla, M.; Mechanisms of fibrinogen adsorption at solid substrates. Langmuir, 2011, 25, 6868-6878 (theoretical)). This unusual latex deposition on Fb monolayers was quantitatively interpreted in terms of the model developed in ref 55 (Jin, X.; Wang, N. H. L.; Tarjus, G.; Talbot, J. Irreversible adsorption on nonuniform

  1. Molecular Processes Studied at a Single-Molecule Level Using DNA Origami Nanostructures and Atomic Force Microscopy

    Directory of Open Access Journals (Sweden)

    Ilko Bald

    2014-09-01

    Full Text Available DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.

  2. Crystallization behavior of single isotactic poly(methyl methacrylate) chains visualized by atomic force microscopy.

    Science.gov (United States)

    Anzai, Takahiro; Kawauchi, Mariko; Kawauchi, Takehiro; Kumaki, Jiro

    2015-01-08

    We have, for the first time, successfully visualized the crystallization behavior of a single isolated polymer chain at the molecular level by atomic force microscopy (AFM). Previously, we found that isotactic poly(methyl methacrylate) (it-PMMA) formed two-dimensional folded chain crystals composed of double-stranded helices upon compression of its Langmuir monolayer on a water surface, and the molecular images of the crystals deposited on mica were clearly visualized by AFM (Kumaki, J.; et al. J. Am. Chem. Soc. 2005, 127, 5788). In the present study, a high-molecular-weight it-PMMA was diluted in a monolayer of an it-PMMA oligomer which cannot crystallize at the experimental temperature due to its low molecular weight. At a low surface pressure, isolated amorphous chains of the high-molecular-weight it-PMMA solubilized in the oligomer monolayer were observed. On compression, the isolated chains converted to crystals composed of a single chain, typically some small crystallites linked by an amorphous chain like a necklace. Detailed AFM observations of the crystals indicated that the crystalline nuclei preferentially formed at the ends of the chains, and the size of the nuclei was almost independent of the molecular weight of it-PMMA over a wide range. At an extremely slow compression, crystallization was promoted, resulting in crystallization of the whole chain. The crystallization behavior of a single isolated chain provides new insights in understanding the polymer crystallization process.

  3. Study of the helium cross-section of unsymmetric disulfide self-assembled monolayers on Au(111)

    Energy Technology Data Exchange (ETDEWEB)

    Albayrak, Erol [Department of Materials and Metallurgical Engineering, Ahi Evran University, Kırşehir 40000 (Turkey); Karabuga, Semistan [Department of Chemistry, Kahramanmaraş Sütçü İmam University, Kahramanmaraş 46030 (Turkey); Bracco, Gianangelo [CNR-IMEM and Department of Physics, University of Genoa, Via Dodecaneso 33, Genoa 16146 (Italy); Danışman, M. Fatih, E-mail: danisman@metu.edu.tr [Department of Chemistry, Middle East Technical University, Ankara 06800 (Turkey)

    2016-12-30

    Highlights: • Unsymmetrtic disulfide (HDD and HOD) self assembled monolayers were grown on Au(111) by supersonic molecular beam deposition. • Helium scattering cross sections for these two different unsymmetric disulfides were determined. • A common low temperature film phase was observed for the studied disulfides. - Abstract: We have investigated the formation of self-assembled monolayers (SAMs) of 11-hydroxyundecyl decyl disulfide (CH{sub 3}-(CH{sub 2}){sub 9}-S-S-(CH{sub 2}){sub 11}-OH, HDD) and 11-hydroxyundecyl octadecyl disulfide (CH{sub 3}-(CH{sub 2}){sub 17}-S-S-(CH{sub 2}){sub 11}-OH, HOD) produced by supersonic molecular beam deposition (SMBD). The study has been carried out by means of helium diffraction at very low film coverage. In this regime helium single molecule cross sections have been estimated in a temperature range between 100 K and 450 K. The results show a different behavior above 300 K that has been interpreted as the starting of mobility with the formation of two thiolate moieties either linked by a gold adatom or distant enough to prevent cross section overlapping. Finally, helium diffraction patterns measured at 80 K for the SAMs grown at 200 K are discussed and the results support the proposed hypothesis of molecular dissociation based on the cross section data.

  4. Surface investigation of chitosan film with fatty acid monolayers

    Directory of Open Access Journals (Sweden)

    Esam A. El-hefian

    2009-05-01

    Full Text Available The surface pressure- molecular area (-A isotherm curves of two fatty acids of different chain lengths, i.e. stearic (C18 and arachidic (C20 acids, were obtained by using Langmuir-Blodgett (LB technique. Results showed clear isotherm plots with limiting mean molecular area around 21 Å2 for both acids. However, the monolayer was found to collapse at higher than 33 mN m-1 and 21 mN m-1 for stearic acid and arachidic acid respectively. The effect of Langmuir-Blodgett monolayers of the acids was investigated by atomic force microscopy (AFM. Chitosan film, before and after dipping in water, was also studied by means of AFM so that it could be used for comparison. It was found that the surface of chitosan was more homogeneous and smoother after dipping in water. In addition, more homogeneous surfaces were achieved after transferring a layer of the fatty acid onto the substrate.

  5. UV-Induced Reaction Kinetics of Dilinoleoylphosphatidylethanolamine Monolayers

    OpenAIRE

    Viitala, Tapani; Peltonen, Jouko

    1999-01-01

    The UV-induced reactivity of dilinoleoylphosphatidylethanolamine (DLiPE) Langmuir and Langmuir-Blodgett films has been studied by in situ measurements of the changes in the mean molecular area, UV-vis and Fourier transform infrared spectroscopy, and atomic force microscopy (AFM). Optimum orientation and packing density of the DLiPE molecules in the monolayer were achieved by adding uranyl acetate to the subphase. A first-order reaction kinetic model was successfully fitted to the experimental...

  6. Molecular-dynamic simulations of the thermophysical properties of hexanitrohexaazaisowurtzitane single crystal at high pressures and temperatures

    Science.gov (United States)

    Kozlova, S. A.; Gubin, S. A.; Maklashova, I. V.; Selezenev, A. A.

    2017-11-01

    Molecular dynamic simulations of isothermal compression parameters are performed for a hexanitrohexaazaisowurtzitane single crystal (C6H6O12N12) using a modified ReaxFF-log reactive force field. It is shown that the pressure-compression ratio curve for a single C6H6O12N12 crystal at constant temperature T = 300 K in pressure range P = 0.05-40 GPa is in satisfactory agreement with experimental compression isotherms obtained for a single C6H6O12N12 crystal. Hugoniot molecular-dynamic simulations of the shock-wave hydrostatic compression of a single C6H6O12N12 crystal are performed. Along with Hugoniot temperature-pressure curves, calculated shock-wave pressure-compression ratios for a single C6H6O12N12 crystal are obtained for a wide pressure range of P = 1-40 GPa. It is established that the percussive adiabat obtained for a single C6H6O12N12 crystal is in a good agreement with the experimental data. All calculations are performed using a LAMMPS molecular dynamics simulation software package that provides a ReaxFF-lg reactive force field to support the approach.

  7. Coherent manipulation of three-qubit states in a molecular single-ion magnet

    Science.gov (United States)

    Jenkins, M. D.; Duan, Y.; Diosdado, B.; García-Ripoll, J. J.; Gaita-Ariño, A.; Giménez-Saiz, C.; Alonso, P. J.; Coronado, E.; Luis, F.

    2017-02-01

    We study the quantum spin dynamics of nearly isotropic Gd3 + ions entrapped in polyoxometalate molecules and diluted in crystals of a diamagnetic Y3 + derivative. The full energy-level spectrum and the orientations of the magnetic anisotropy axes have been determined by means of continuous-wave electron paramagnetic resonance experiments, using X-band (9-10 GHz) cavities and on-chip superconducting waveguides and 1.5-GHz resonators. The results show that seven allowed transitions between the 2 S +1 spin states can be separately addressed. Spin coherence T2 and spin-lattice relaxation T1 rates have been measured for each of these transitions in properly oriented single crystals. The results suggest that quantum spin coherence is limited by residual dipolar interactions with neighbor electronic spins. Coherent Rabi oscillations have been observed for all transitions. The Rabi frequencies increase with microwave power and agree quantitatively with predictions based on the spin Hamiltonian of the molecular spin. We argue that the spin states of each Gd3 + ion can be mapped onto the states of three addressable qubits (or, alternatively, of a d =8 -level "qudit"), for which the seven allowed transitions form a universal set of operations. Within this scheme, one of the coherent oscillations observed experimentally provides an implementation of a controlled-controlled-NOT (or Toffoli) three-qubit gate.

  8. A Single Molecular Diels-Alder Crosslinker for Achieving Recyclable Cross-Linked Polymers.

    Science.gov (United States)

    Chen, Shengli; Wang, Fenfen; Peng, Yongjin; Chen, Tiehong; Wu, Qiang; Sun, Pingchuan

    2015-09-01

    A triol-functional crosslinker combining the thermoreversible properties of Diels-Alder (DA) adducts in one molecule is designed, synthesized, and used as an ideal substitute of a traditional crosslinker to prepare thermal recyclable cross-linked polyurethanes with excellent mechanical properties and recyclability in a very simple and efficient way. The recycle property of these materials achieved by the DA/retro-DA reaction at a suitable temperature is verified by differential scanning calorimetry and in situ variable temperature solid-state NMR experiments during the cyclic heating and cooling processes. The thermal recyclability and remending ability of the bulk polyurethanes is demonstrated by three polymer processing methods, including hot-press molding, injection molding, and solution casting. It is notable that all the recycled cross-linked polymers display nearly invariable elongation/stress at break compared to the as-synthesized samples. Further end-group functionalization of this single molecular DA crosslinker provides the potential in preparing a wide range of recyclable cross-linked polymers. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. A molecular beacon microarray based on a quantum dot label for detecting single nucleotide polymorphisms.

    Science.gov (United States)

    Guo, Qingsheng; Bai, Zhixiong; Liu, Yuqian; Sun, Qingjiang

    2016-03-15

    In this work, we report the application of streptavidin-coated quantum dot (strAV-QD) in molecular beacon (MB) microarray assays by using the strAV-QD to label the immobilized MB, avoiding target labeling and meanwhile obviating the use of amplification. The MBs are stem-loop structured oligodeoxynucleotides, modified with a thiol and a biotin at two terminals of the stem. With the strAV-QD labeling an "opened" MB rather than a "closed" MB via streptavidin-biotin reaction, a sensitive and specific detection of label-free target DNA sequence is demonstrated by the MB microarray, with a signal-to-background ratio of 8. The immobilized MBs can be perfectly regenerated, allowing the reuse of the microarray. The MB microarray also is able to detect single nucleotide polymorphisms, exhibiting genotype-dependent fluorescence signals. It is demonstrated that the MB microarray can perform as a 4-to-2 encoder, compressing the genotype information into two outputs. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Integrative Single-Cell Transcriptomics Reveals Molecular Networks Defining Neuronal Maturation During Postnatal Neurogenesis.

    Science.gov (United States)

    Gao, Yu; Wang, Feifei; Eisinger, Brian E; Kelnhofer, Laurel E; Jobe, Emily M; Zhao, Xinyu

    2017-03-01

    In mammalian hippocampus, new neurons are continuously produced from neural stem cells throughout life. This postnatal neurogenesis may contribute to information processing critical for cognition, adaptation, learning, and memory, and is implicated in numerous neurological disorders. During neurogenesis, the immature neuron stage defined by doublecortin (DCX) expression is the most sensitive to regulation by extrinsic factors. However, little is known about the dynamic biology within this critical interval that drives maturation and confers susceptibility to regulatory signals. This study aims to test the hypothesis that DCX-expressing immature neurons progress through developmental stages via activity of specific transcriptional networks. Using single-cell RNA-seq combined with a novel integrative bioinformatics approach, we discovered that individual immature neurons can be classified into distinct developmental subgroups based on characteristic gene expression profiles and subgroup-specific markers. Comparisons between immature and more mature subgroups revealed novel pathways involved in neuronal maturation. Genes enriched in less mature cells shared significant overlap with genes implicated in neurodegenerative diseases, while genes positively associated with neuronal maturation were enriched for autism-related gene sets. Our study thus discovers molecular signatures of individual immature neurons and unveils potential novel targets for therapeutic approaches to treat neurodevelopmental and neurological diseases. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  11. Molecular Modeling of PEGylated Peptides, Dendrimers, and Single-Walled Carbon Nanotubes for Biomedical Applications

    Directory of Open Access Journals (Sweden)

    Hwankyu Lee

    2014-03-01

    Full Text Available Polyethylene glycol (PEG has been conjugated to many drugs or drug carriers to increase their solubility and circulating lifetime, and reduce toxicity. This has motivated many experimental studies to understand the effect of PEGylation on delivery efficiency. To complement the experimental findings and uncover the mechanism that cannot be captured by experiments, all-atom and coarse-grained molecular dynamics (MD simulations have been performed. This has become possible, due to recent advances in simulation methodologies and computational power. Simulations of PEGylated peptides show that PEG chains wrap antimicrobial peptides and weaken their binding interactions with lipid bilayers. PEGylation also influences the helical stability and tertiary structure of coiled-coil peptides. PEGylated dendrimers and single-walled carbon nanotubes (SWNTs were simulated, showing that the PEG size and grafting density significantly modulate the conformation and structure of the PEGylated complex, the interparticle aggregation, and the interaction with lipid bilayers. In particular, simulations predicted the structural transition between the dense core and dense shell of PEGylated dendrimers, the phase behavior of self-assembled complexes of lipids, PEGylated lipids, and SWNTs, which all favorably compared with experiments. Overall, these new findings indicate that simulations can now predict the experimentally observed structure and dynamics, as well as provide atomic-scale insights into the interactions of PEGylated complexes with other molecules.

  12. Molecular basis of proton uptake in single and double mutants of cytochrome c oxidase

    Energy Technology Data Exchange (ETDEWEB)

    Henry, Rowan M; Caplan, David; Pomes, Regis [Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, M5G 1X8 (Canada); Fadda, Elisa, E-mail: pomes@sickkids.ca [Department of Chemistry, University of Galway (Ireland)

    2011-06-15

    Cytochrome c oxidase, the terminal enzyme of the respiratory chain, utilizes the reduction of dioxygen into water to pump protons across the mitochondrial inner membrane. The principal pathway of proton uptake into the enzyme, the D channel, is a 2.5 nm long channel-like cavity named after a conserved, negatively charged aspartic acid (D) residue thought to help recruiting protons to its entrance (D132 in the first subunit of the S. sphaeroides enzyme). The single-point mutation of D132 to asparagine (N), a neutral residue, abolishes enzyme activity. Conversely, replacing conserved N139, one-third into the D channel, by D, induces a decoupled phenotype, whereby oxygen reduction proceeds but not proton pumping. Intriguingly, the double mutant D132N/N139D, which conserves the charge of the D channel, restores the wild-type phenotype. We use molecular dynamics simulations and electrostatic calculations to examine the structural and physical basis for the coupling of proton pumping and oxygen chemistry in single and double N139D mutants. The potential of mean force for the conformational isomerization of N139 and N139D side chains reveals the presence of three rotamers, one of which faces the channel entrance. This out-facing conformer is metastable in the wild-type and in the N139D single mutant, but predominant in the double mutant thanks to the loss of electrostatic repulsion with the carboxylate group of D132. The effects of mutations and conformational isomerization on the pKa of E286, an essential proton-shuttling residue located at the top of the D channel, are shown to be consistent with the electrostatic control of proton pumping proposed recently (Fadda et al 2008 Biochim. Biophys. Acta 1777 277-84). Taken together, these results suggest that preserving the spatial distribution of charges at the entrance of the D channel is necessary to guarantee both the uptake and the relay of protons to the active site of the enzyme. These findings highlight the interplay

  13. Monolayer adsorption of noble gases on graphene

    Science.gov (United States)

    Maiga, Sidi M.; Gatica, Silvina M.

    2018-02-01

    We report our results of simulations of the adsorption of noble gases (Kr, Ar, Xe) on graphene. For Kr, we consider two configurations: supported and free-standing graphene, where atoms are adsorbed only on one or two sides of the graphene. For Ar and Xe, we studied only the case of supported graphene. For the single-side adsorption, we calculated the two-dimensional gas-liquid critical temperature for each adsorbate. We determined the different phases of the monolayers and constructed the phase diagrams. We found two-dimensional incommensurate solid phases for krypton, argon and xenon, and a two-dimensional commensurate solid phase for krypton. For double side adsorption of Kr, we do not see evidence of an ordering transition driven by the interlayer forces.

  14. Vector assembly of colloids on monolayer substrates

    Science.gov (United States)

    Jiang, Lingxiang; Yang, Shenyu; Tsang, Boyce; Tu, Mei; Granick, Steve

    2017-06-01

    The key to spontaneous and directed assembly is to encode the desired assembly information to building blocks in a programmable and efficient way. In computer graphics, raster graphics encodes images on a single-pixel level, conferring fine details at the expense of large file sizes, whereas vector graphics encrypts shape information into vectors that allow small file sizes and operational transformations. Here, we adapt this raster/vector concept to a 2D colloidal system and realize `vector assembly' by manipulating particles on a colloidal monolayer substrate with optical tweezers. In contrast to raster assembly that assigns optical tweezers to each particle, vector assembly requires a minimal number of optical tweezers that allow operations like chain elongation and shortening. This vector approach enables simple uniform particles to form a vast collection of colloidal arenes and colloidenes, the spontaneous dissociation of which is achieved with precision and stage-by-stage complexity by simply removing the optical tweezers.

  15. Ion beam analysis with monolayer depth resolution

    Science.gov (United States)

    Carstanjen, H. D.

    1998-03-01

    The paper is concerned with the analysis of surfaces and near-surface layers with monolayer depth resolution by means of high resolution Rutherford backscattering (HRBS) and elastic recoil detection (HERDA) of ions with an energy of a few MeV, in combination with an electrostatic spectrometer. With this instrument, which has recently been set up at the 6 MV Pelletron accelerator of the Max-Planck-Institut für Metallforschung in Stuttgart, depth resolutions of 0.1 nm are obtained in HRBS and 0.3 nm in HERDA experiments. This paper gives a short outline of the design and performance of the spectrometer followed by various examples of applications. These comprise examples showing the analyzing power of the instrument, the analysis of an X-ray mirror by HRBS, the study of the initial oxidation of surfaces of aluminum single crystals by HERDA and recent results concerning charge exchange in ion backscattering.

  16. Defect-Mediated Lithium Adsorption and Diffusion on Monolayer Molybdenum Disulfide

    OpenAIRE

    Sun, Xiaoli; Wang, Zhiguo; Fu, Yong Qing

    2015-01-01

    Monolayer Molybdenum Disulfide (MoS2) is a promising anode material for lithium ion batteries because of its high capacities. In this work, first principle calculations based on spin density functional theory were performed to investigate adsorption and diffusion of lithium on monolayer MoS2 with defects, such as single- and few-atom vacancies, antisite, and grain boundary. The values of adsorption energies on the monolayer MoS2 with the defects were increased compared to those on the pristin...

  17. On the Hopping Efficiency of Nanoparticles in the Electron Transfer across Self‐Assembled Monolayers

    DEFF Research Database (Denmark)

    Liu, Feng; Khan, Kamran; Liang, Jing‐Hong

    2013-01-01

    Redox reactions of solvated molecular species at gold‐electrode surfaces modified by electrochemically inactive self‐assembled molecular monolayers (SAMs) are found to be activated by introducing Au nanoparticles (NPs) covalently bound to the SAM to form a reactive Au–alkanedithiol–NP–molecule hy...

  18. Overcrowding drives the unjamming transition of gap-free monolayers

    Science.gov (United States)

    Lan, Ganhui; Su, Tao

    Collective cell motility plays central roles in various biological phenomena such as wound healing, cancer metastasis and embryogenesis. These are demonstrations of the unjamming transition in biology. However, contradictory to the typical density-driven jamming in particulate assemblies, cellular systems often get unjammed in highly packed, sometimes overcrowding environments. Here, we investigate monolayers' collective behaviors when cell number changes under the gap-free constraint. We report that overcrowding can unjam gap-free monolayers through increasing isotropic compression. We show that the transition boundary is determined by the isotropic compression and the cell-cell adhesion. Furthermore, we construct the free energy landscape for the T1 topological transition during monolayer rearrangement, and discover that the landscape evolves from single-barrier W shape to double-barrier M shape during the unjamming process. We also discover a distributed-to-disordered morphological transition of cells' geometry, coinciding with the unjamming transition. Our analyses reveal that the overcrowding and adhesion induced unjamming reflects the mechanical yielding of the highly deformable monolayer, suggesting an alternative mechanism that cells may robustly gain collective mobility through proliferation in confined environments, which differs from those caused by loosing up a packed particulate assembly. This work is supported by the GWU College Facilitating Funds.

  19. Engineering monolayer poration for rapid exfoliation of microbial membranes† †Electronic supplementary information (ESI) available: Materials and methods, microscopy, spectroscopy, molecular dynamics and spectrometry data. See DOI: 10.1039/c6sc02925f Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file.

    Science.gov (United States)

    Pyne, Alice; Pfeil, Marc-Philipp; Bennett, Isabel; Ravi, Jascindra; Iavicoli, Patrizia; Lamarre, Baptiste; Roethke, Anita; Ray, Santanu; Jiang, Haibo; Bella, Angelo; Reisinger, Bernd; Yin, Daniel; Little, Benjamin; Muñoz-García, Juan C.; Cerasoli, Eleonora; Judge, Peter J.; Faruqui, Nilofar; Calzolai, Luigi; Henrion, Andre; Martyna, Glenn J.; Grovenor, Chris R. M.; Crain, Jason; Hoogenboom, Bart W.; Watts, Anthony

    2017-01-01

    The spread of bacterial resistance to traditional antibiotics continues to stimulate the search for alternative antimicrobial strategies. All forms of life, from bacteria to humans, are postulated to rely on a fundamental host defense mechanism, which exploits the formation of open pores in microbial phospholipid bilayers. Here we predict that transmembrane poration is not necessary for antimicrobial activity and reveal a distinct poration mechanism that targets the outer leaflet of phospholipid bilayers. Using a combination of molecular-scale and real-time imaging, spectroscopy and spectrometry approaches, we introduce a structural motif with a universal insertion mode in reconstituted membranes and live bacteria. We demonstrate that this motif rapidly assembles into monolayer pits that coalesce during progressive membrane exfoliation, leading to bacterial cell death within minutes. The findings offer a new physical basis for designing effective antibiotics. PMID:28451250

  20. Single Molecular Level Probing of Structure and Dynamics of Papain Under Denaturation.

    Science.gov (United States)

    Sengupta, Bhaswati; Chaudhury, Apala; Das, Nilimesh; Sen, Pratik

    2017-01-01

    Papain is a cysteine protease enzyme present in papaya and known to help in digesting peptide. Thus the structure and function of the active site of papain is of interest. The objective of present study is to unveil the overall structural transformation and the local structural change around the active site of papain as a function of chemical denaturant. Papain has been tagged at Cys-25 with a thiol specific fluorescence probe N-(7- dimethylamino-4-methylcoumarin-3-yl) iodoacetamide (DACIA). Guanidine hydrochloride (GnHCl) has been used as the chemical denaturant. Steady state, time-resolved, and single molecular level fluorescence techniques was applied to map the change in the local environment. It is found that papain undergoes a two-step denaturation in the presence of GnHCl. Fluorescence correlation spectroscopic (FCS) data indicate that the size (hydrodynamic diameter) of native papain is ~36.8 Å, which steadily increases to ~53 Å in the presence of 6M GnHCl. FCS study also reveals that the conformational fluctuation time of papain is 6.3 µs in its native state, which decreased to 2.7 µs in the presence of 0.75 M GnHCl. Upon further increase in GnHCl concentration the conformational fluctuation time increase monotonically till 6 M GnHCl, where the time constant is measured as 14 µs. On the other hand, the measurement of ellipticity, hence the helical structure, by circular dichroism spectroscopy is found to be incapable to capture such structural transformation. It is concluded that in the presence of small amount of GnHCl the active site of papain takes up a more compact structure (although the overall size increases) than in the native state, which has been designated as the intermediate state. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  1. Molecular asymmetry in the 8-cell stage Xenopus tropicalis embryo described by single blastomere transcript sequencing.

    Science.gov (United States)

    De Domenico, Elena; Owens, Nick D L; Grant, Ian M; Gomes-Faria, Rosa; Gilchrist, Michael J

    2015-12-15

    Correct development of the vertebrate body plan requires the early definition of two asymmetric, perpendicular axes. The first axis is established during oocyte maturation, and the second is established by symmetry breaking shortly after fertilization. The physical processes generating the second asymmetric, or dorsal-ventral, axis are well understood, but the specific molecular determinants, presumed to be maternal gene products, are poorly characterized. Whilst enrichment of maternal mRNAs at the animal and vegetal poles in both the oocyte and the early embryo has been studied, little is known about the distribution of maternal mRNAs along either the dorsal-ventral or left-right axes during the early cleavage stages. Here we report an unbiased analysis of the distribution of maternal mRNA on all axes of the Xenopus tropicalis 8-cell stage embryo, based on sequencing of single blastomeres whose positions within the embryo are known. Analysis of pooled data from complete sets of blastomeres from four embryos has identified 908 mRNAs enriched in either the animal or vegetal blastomeres, of which 793 are not previously reported as enriched. In contrast, we find no evidence for asymmetric distribution along either the dorsal-ventral or left-right axes. We confirm that animal pole enrichment is on average distinctly lower than vegetal pole enrichment, and that considerable variation is found between reported enrichment levels in different studies. We use publicly available data to show that there is a significant association between genes with human disease annotation and enrichment at the animal pole. Mutations in the human ortholog of the most animally enriched novel gene, Slc35d1, are causative for Schneckenbecken dysplasia, and we show that a similar phenotype is produced by depletion of the orthologous protein in Xenopus embryos. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  2. A Biofunctional Molecular Beacon for Detecting Single Base Mutations in Cancer Cells

    Directory of Open Access Journals (Sweden)

    Haiyan Dong

    2016-01-01

    Full Text Available The development of a convenient and sensitive biosensing system to detect specific DNA sequences is an important issue in the field of genetic disease therapy. As a classic DNA detection technique, molecular beacon (MB is often used in the biosensing system. However, it has intrinsic drawbacks, including high assay cost, complicated chemical modification, and operational complexity. In this study, we developed a simple and cost-effective label-free multifunctional MB (LMMB by integrating elements of polymerization primer, template, target recognition, and G-quadruplex into one entity to detect target DNA. The core technique was accomplished by introducing a G-hairpin that features fragments of both G-quadruplex and target DNA recognition in the G-hairpin stem. Hybridization between LMMB and target DNA triggered conformational change between the G-hairpin and the common C-hairpin, resulting in significant SYBR-green signal amplification. The hybridization continues to the isothermal circular strand-displacement polymerization and accumulation of the double-stranded fragments, causing the uninterrupted extension of the LMMB without a need of chemical modification and other assistant DNA sequences. The novel and programmable LMMB could detect target DNA with sensitivity at 250 pmol/l with a linear range from 2 to 100 nmol/l and the relative standard deviation of 7.98%. The LMMB could sense a single base mutation from the normal DNA, and polymerase chain reaction (PCR amplicons of the mutant-type cell line from the wild-type one. The total time required for preparation and assaying was only 25 minutes. Apparently, the LMMB shows great potential for detecting DNA and its mutations in biosamples, and therefore it opens up a new prospect for genetic disease therapy.

  3. Quantitative Molecular Imaging with a Single Gd-Based Contrast Agent Reveals Specific Tumor Binding and Retention in Vivo.

    Science.gov (United States)

    Johansen, Mette L; Gao, Ying; Hutnick, Melanie A; Craig, Sonya E L; Pokorski, Jonathan K; Flask, Chris A; Brady-Kalnay, Susann M

    2017-06-06

    Magnetic resonance imaging (MRI) has become an indispensable tool in the diagnosis and treatment of many diseases, especially cancer. However, the poor sensitivity of MRI relative to other imaging modalities, such as PET, has hindered the development and clinical use of molecular MRI contrast agents that could provide vital diagnostic information by specifically locating a molecular target altered in the disease process. This work describes the specific and sustained in vivo binding and retention of a protein tyrosine phosphatase mu (PTPμ)-targeted, molecular magnetic resonance (MR) contrast agent with a single gadolinium (Gd) chelate using a quantitative MRI T 1 mapping technique in glioma xenografts. Quantitative T 1 mapping is an imaging method used to measure the longitudinal relaxation time, the T 1 relaxation time, of protons in a magnetic field after excitation by a radiofrequency pulse. T 1 relaxation times can in turn be used to calculate the concentration of a gadolinium-containing contrast agent in a region of interest, thereby allowing the retention or clearance of an agent to be quantified. In this context, retention is a measure of molecular contrast agent binding. Using conventional peptide chemistry, a PTPμ-targeted peptide was linked to a chelator that had been conjugated to a lysine residue. Following complexation with Gd, this PTPμ-targeted molecular contrast agent containing a single Gd ion showed significant tumor enhancement and a sustained increase in Gd concentration in both heterotopic and orthotopic tumors using dynamic quantitative MRI. This single Gd-containing PTPμ agent was more effective than our previous version with three Gd ions. Differences between nonspecific and specific agents, due to specific tumor binding, can be determined within the first 30 min after agent administration by examining clearance rates. This more facile chemistry, when combined with quantitative MR techniques, allows for widespread adoption by academic

  4. A trough for improved SFG spectroscopy of lipid monolayers

    Science.gov (United States)

    Franz, Johannes; van Zadel, Marc-Jan; Weidner, Tobias

    2017-05-01

    Lipid monolayers are indispensable model systems for biological membranes. The main advantage over bilayer model systems is that the surface pressure within the layer can be directly and reliably controlled. The sensitive interplay between surface pressure and temperature determines the molecular order within a model membrane and consequently determines the membrane phase behavior. The lipid phase is of crucial importance for a range of membrane functions such as protein interactions and membrane permeability. A very reliable method to probe the structure of lipid monolayers is sum frequency generation (SFG) vibrational spectroscopy. Not only is SFG extremely surface sensitive but it can also directly access critical parameters such as lipid order and orientation, and it can provide valuable information about protein interactions along with interfacial hydration. However, recent studies have shown that temperature gradients caused by high power laser beams perturb the lipid layers and potentially obscure the spectroscopic results. Here we demonstrate how the local heating problem can be effectively reduced by spatially distributing the laser pulses on the sample surface using a translating Langmuir trough for SFG experiments at lipid monolayers. The efficiency of the trough is illustrated by the detection of enhanced molecular order due to reduced heat load.

  5. Gold nanoparticles with patterned surface monolayers for nanomedicine: current perspectives.

    Science.gov (United States)

    Pengo, Paolo; Şologan, Maria; Pasquato, Lucia; Guida, Filomena; Pacor, Sabrina; Tossi, Alessandro; Stellacci, Francesco; Marson, Domenico; Boccardo, Silvia; Pricl, Sabrina; Posocco, Paola

    2017-12-01

    Molecular self-assembly is a topic attracting intense scientific interest. Various strategies have been developed for construction of molecular aggregates with rationally designed properties, geometries, and dimensions that promise to provide solutions to both theoretical and practical problems in areas such as drug delivery, medical diagnostics, and biosensors, to name but a few. In this respect, gold nanoparticles covered with self-assembled monolayers presenting nanoscale surface patterns-typically patched, striped or Janus-like domains-represent an emerging field. These systems are particularly intriguing for use in bio-nanotechnology applications, as presence of such monolayers with three-dimensional (3D) morphology provides nanoparticles with surface-dependent properties that, in turn, affect their biological behavior. Comprehensive understanding of the physicochemical interactions occurring at the interface between these versatile nanomaterials and biological systems is therefore crucial to fully exploit their potential. This review aims to explore the current state of development of such patterned, self-assembled monolayer-protected gold nanoparticles, through step-by-step analysis of their conceptual design, synthetic procedures, predicted and determined surface characteristics, interactions with and performance in biological environments, and experimental and computational methods currently employed for their investigation.

  6. Specific Ion Effects in Cholesterol Monolayers

    Directory of Open Access Journals (Sweden)

    Teresa Del Castillo-Santaella

    2016-05-01

    Full Text Available The interaction of ions with interfaces and, in particular, the high specificity of these interactions to the particular ions considered, are central questions in the field of surface forces. Here we study the effect of different salts (NaI, NaCl, CaCl2 and MgCl2 on monolayers made of cholesterol molecules, both experimentally (surface area vs. lateral pressure isotherms measured by a Langmuir Film Balance and theoretically (molecular dynamics (MD all-atomic simulations. We found that surface isotherms depend, both quantitatively and qualitatively, on the nature of the ions by altering the shape and features of the isotherm. In line with the experiments, MD simulations show clear evidences of specific ionic effects and also provide molecular level details on ion specific interactions with cholesterol. More importantly, MD simulations show that the interaction of a particular ion with the surface depends strongly on its counterion, a feature ignored so far in most theories of specific ionic effects in surface forces.

  7. Towards optimised drug delivery: structure and composition of testosterone enanthate in sodium dodecyl sulfate monolayers.

    Science.gov (United States)

    Saaka, Yussif; Allen, Daniel T; Luangwitchajaroen, Yuvared; Shao, Yanan; Campbell, Richard A; Lorenz, Christian D; Lawrence, M Jayne

    2018-04-09

    Surface tension and specular neutron reflectivity measurements have been used, for the first time to systematically study both the interfacial structure and composition of monolayers of the soluble surfactant, sodium dodecyl sulfate containing a low-dose, poorly water soluble drug, testosterone enanthate. Modelling of the specular neutron reflectivity data suggests that the hydrophobic testosterone enanthate was adsorbed in the C12 hydrophobic tail region of the surfactant monolayer, regardless of the concentration of surfactant at the interface and whether or not additional drug was added to the interface. The location of the hydrophobic drug in the tail region of the surfactant monolayer is supported by the results of classical, large-scale molecular dynamics simulations. The thickness of the surfactant monolayer obtained, in the presence and absence of drug, using molecular dynamics simulations was in good agreement with the corresponding values obtained from the specular neutron reflectivity measurements. The stoichiometry of surfactant:drug at the air-water interface at sodium dodecyl sulfate concentrations above the critical micelle concentration was determined from specular neutron reflectivity measurements to be approximately 3 : 1, and remained constant after the spreading of further testosterone enanthate at the interface. Significantly, this stoichiometry was the same as that obtained in the micelles from bulk solubilisation studies. Important insights into the preferred location of drug in surfactant monolayers at the air-water interface as well as its effect on the structure of the monolayer have been obtained from our combined use of experimental and simulation techniques.

  8. Functional regulation of an immobilized redox protein on an oriented metal coordinated peptide monolayer as an electron mediator.

    Science.gov (United States)

    Wang, Xinxin; Nagata, Kenji; Higuchi, Masahiro

    2011-10-18

    We fabricated a vertically and unidirectionally oriented metal coordinated α-helical peptide monolayer, Leu(2)Ala(Pyri)(Co(II))Leu(6)Ala(4-Pyri)(Co(II))Leu(6), by stepwise polymerization on a mixed self-assembled monolayer consisting of amino-alkanethiol, dialkyl disulfide, and ferrocenyl alkanethiol acted as a photoresponsive electron donor. Redox-active protein, nitrate reductase (NR), was fixed on the surface of the peptide monolayer. By contrast, we fixed NR on the mixed self-assembled monolayer directly. Upon photoirradiation, electron flow occurred from the excited ferrocenyl group on the substrate to the electron acceptor, NR, on the surface of the molecular layers. The activated NR on the molecular layers reduced the nitrate to nitrite. The amount of the bioelectrocatalytic product, nitrite, generated by the immobilized NR on the peptide monolayer was larger than that produced by the immobilized NR on the mixed self-assembled monolayer directly. That is to say, the NR on the peptide monolayer has been more activated rather than that on the peptide absent monolayer by photoirradiation. The effective activation of the NR on the peptide monolayer can be explained in terms of enhancement of the vectorial electron flow along the macro-dipole moment of the α-helical peptide that arranged unidirectionally. It suggested that the ordered metal coordinated α-helical peptide monolayer acted as an efficient electron mediator to achieve a communication between the electron donor and the redox-active moiety. Such a hybrid molecular system looks promising for novel nanodevices, such as nano-photoreactors. © 2011 American Chemical Society

  9. Organosilicon derivatives of BTBT for monolayer organic field effect transistors

    Science.gov (United States)

    Agina, Elena V.; Polinskaya, Marina S.; Trul, Askold A.; Chekusova, Viktoria P.; Sizov, Alexey S.; Borshchev, Oleg V.; Ponomarenko, Sergey A.

    2017-08-01

    Synthesis of novel organosilicon derivatives of [1]benzothieno[3,2-b][1]-benzothiophene (BTBT) linked though flexible aliphatic spacers to a disiloxane anchor group is reported. They were successfully used in monolayer OFETs with the charge carrier mobilities up to 0.02 cm2 /Vs, threshold voltage close to 0 V and On/Off ratio up to 10,000. Influence of the chemical structure of the molecules synthesized on the morphology, molecular 2D ordering in the monolayers and their semiconducting properties is considered. The effect of different methods of the ultrathin semiconducting layer preparation, such as Langmuir-Blodgett, Langmuir-Schaefer, spin coating or doctor blade, on the OFET performance is discussed.

  10. Liquid-Phase Exfoliation into Monolayered BiOBr Nanosheets for Photocatalytic Oxidation and Reduction

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Hongjian [Beijing; Huang, Hongwei [Beijing; Xu, Kang [Center; Hao, Weichang [Center; Guo, Yuxi [Beijing; Wang, Shuobo [Beijing; Shen, Xiulin [Beijing; Pan, Shaofeng [Beijing; Zhang, Yihe [Beijing

    2017-09-26

    Monolayered photocatalytic materials have attracted huge research interests in terms of their large specific surface area and ample active sites. Sillén-structured layered BiOX (X = Cl, Br, I) casts great prospects owing to their strong photo-oxidation ability and high stability. Fabrication of monolayered BiOX by a facile, low-cost, and scalable approach is highly challenging and anticipated. Herein, we describe the large-scale preparation of monolayered BiOBr nanosheets with a thickness of ~0.85 nm via a readily achievable liquid-phase exfoliation strategy with assistance of formamide at ambient conditions. The as-obtained monolayered BiOBr nanosheets are allowed diverse superiorities, such as enhanced specific surface area, promoted band structure, and strengthened charge separation. Profiting from these benefits, the advanced BiOBr monolayers not only show excellent adsorption and photodegradation performance for treating contaminants, but also demonstrate a greatly promoted photocatalytic activity for CO2 reduction into CO and CH4. Additionally, monolayered BiOI nanosheets have also been obtained by the same synthetic approach. Our work offers a mild and general approach for preparation of monolayered BiOX, and may have huge potential to be extended to the synthesis of other single-layer two-dimensional materials.

  11. Imatinib (Gleevec@) conformations observed in single crystals, protein-Imatinib co-crystals and molecular dynamics: Implications for drug selectivity

    Science.gov (United States)

    Golzarroshan, B.; Siddegowda, M. S.; Li, Hong qi; Yathirajan, H. S.; Narayana, B.; Rathore, R. S.

    2012-06-01

    Structure and dynamics of the Leukemia drug, Imatinib, were examined using X-ray crystallography and molecular dynamics studies. Comparison of conformations observed in single crystals with several reported co-crystals of protein-drug complexes suggests existence of two conserved conformations of Imatinib, extended and compact (or folded), corresponding to two binding modes of interaction with the receptor. Furthermore, these conformations are conserved throughout a dynamics simulation. The present study attempts to draw a parallel on conformations and binding patterns of interactions, obtained from small-molecule single-crystal and macromolecule co-crystal studies, and provides structural insights for understanding the high selectivity of this drug molecule.

  12. The long tail of molecular alterations in non-small cell lung cancer: a single-institution experience of next-generation sequencing in clinical molecular diagnostics.

    Science.gov (United States)

    Fumagalli, Caterina; Vacirca, Davide; Rappa, Alessandra; Passaro, Antonio; Guarize, Juliana; Rafaniello Raviele, Paola; de Marinis, Filippo; Spaggiari, Lorenzo; Casadio, Chiara; Viale, Giuseppe; Barberis, Massimo; Guerini-Rocco, Elena

    2018-03-13

    Molecular profiling of advanced non-small cell lung cancers (NSCLC) is essential to identify patients who may benefit from targeted treatments. In the last years, the number of potentially actionable molecular alterations has rapidly increased. Next-generation sequencing allows for the analysis of multiple genes simultaneously. To evaluate the feasibility and the throughput of next-generation sequencing in clinical molecular diagnostics of advanced NSCLC. A single-institution cohort of 535 non-squamous NSCLC was profiled using a next-generation sequencing panel targeting 22 actionable and cancer-related genes. 441 non-squamous NSCLC (82.4%) harboured at least one gene alteration, including 340 cases (63.6%) with clinically relevant molecular aberrations. Mutations have been detected in all but one gene ( FGFR1 ) of the panel. Recurrent alterations were observed in KRAS , TP53 , EGFR , STK11 and MET genes, whereas the remaining genes were mutated in <5% of the cases. Concurrent mutations were detected in 183 tumours (34.2%), mostly impairing KRAS or EGFR in association with TP53 alterations. The study highlights the feasibility of targeted next-generation sequencing in clinical setting. The majority of NSCLC harboured mutations in clinically relevant genes, thus identifying patients who might benefit from different targeted therapies. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  13. Single-Molecule Nanomagnets

    Science.gov (United States)

    Friedman, Jonathan R.; Sarachik, Myriam P.

    2010-04-01

    Single-molecule magnets straddle the classical and quantum mechanical worlds, displaying many fascinating phenomena. They may have important technological applications in information storage and quantum computation. We review the physical properties of two prototypical molecular nanomagnets, Mn12-acetate and Fe8: Each behaves as a rigid, spin-10 object and exhibits tunneling between up and down directions. As temperature is lowered, the spin-reversal process evolves from thermal activation to pure quantum tunneling. At low temperatures, magnetic avalanches occur in which the magnetization of an entire sample rapidly reverses. We discuss the important role that symmetry-breaking fields play in driving tunneling and in producing Berry-phase interference. Recent experimental advances indicate that quantum coherence can be maintained on timescales sufficient to allow a meaningful number of quantum computing operations to be performed. Efforts are under way to create monolayers and to address and manipulate individual molecules.

  14. Heterointerface Screening Effects between Organic Monolayers and Monolayer Transition Metal Dichalcogenides

    KAUST Repository

    Zheng, Yu Jie

    2016-01-21

    © 2016 American Chemical Society. The nature and extent of electronic screening at heterointerfaces and their consequences on energy level alignment are of profound importance in numerous applications, such as solar cells, electronics etc. The increasing availability of two-dimensional (2D) transition metal dichalcogenides (TMDs) brings additional opportunities for them to be used as interlayers in "van der Waals (vdW) heterostructures" and organic/inorganic flexible devices. These innovations raise the question of the extent to which the 2D TMDs participate actively in dielectric screening at the interface. Here we study perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA) monolayers adsorbed on single-layer tungsten diselenide (WSe2), bare graphite, and Au(111) surfaces, revealing a strong dependence of the PTCDA HOMO-LUMO gap on the electronic screening effects from the substrate. The monolayer WSe2 interlayer provides substantial, but not complete, screening at the organic/inorganic interface. Our results lay a foundation for the exploitation of the complex interfacial properties of hybrid systems based on TMD materials.

  15. Spatially Extended and High-Velocity Dispersion Molecular Component in Spiral Galaxies: Single-Dish Versus Interferometric Observations

    Science.gov (United States)

    Caldú-Primo, Anahi; Schruba, Andreas; Walter, Fabian; Leroy, Adam; Bolatto, Alberto D.; Vogel, Stuart

    2015-02-01

    Recent studies of the molecular medium in nearby galaxies have provided mounting evidence that the molecular gas can exist in two phases: one that is clumpy and organized as molecular clouds and another one that is more diffuse. This last component has a higher velocity dispersion than the clumpy one. In order to investigate these two molecular components further, we compare the fluxes and line widths of CO in NGC 4736 and NGC 5055, two nearby spiral galaxies for which high-quality interferometric as well as single-dish data sets are available. Our analysis leads to two main results: (1) employing three different methods, we determine the flux recovery of the interferometer as compared to the single-dish to be within a range of 35%-74% for NGC 4736 and 81%-92% for NGC 5055, and (2) when focusing on high (S/N ≥ 5) lines of sight (LOSs), the single-dish line widths are larger by ˜(40 ± 20)% than the ones derived from interferometric data, which is in agreement with stacking all LOSs. These results point to a molecular gas component that is distributed over spatial scales larger than 30″(˜1 kpc), and is therefore filtered out by the interferometer. The available observations do not allow us to distinguish between a truly diffuse gas morphology and a uniform distribution of small clouds that are separated by less than the synthesized beam size (˜3″ or ˜100 pc), as they would both be invisible for the interferometer. This high velocity dispersion component has a dispersion similar to what is found in the atomic medium, as traced through observations of the H i line.

  16. Spatially extended and high-velocity dispersion molecular component in spiral galaxies: Single-dish versus interferometric observations

    International Nuclear Information System (INIS)

    Caldú-Primo, Anahi; Walter, Fabian; Schruba, Andreas; Leroy, Adam; Bolatto, Alberto D.; Vogel, Stuart

    2015-01-01

    Recent studies of the molecular medium in nearby galaxies have provided mounting evidence that the molecular gas can exist in two phases: one that is clumpy and organized as molecular clouds and another one that is more diffuse. This last component has a higher velocity dispersion than the clumpy one. In order to investigate these two molecular components further, we compare the fluxes and line widths of CO in NGC 4736 and NGC 5055, two nearby spiral galaxies for which high-quality interferometric as well as single-dish data sets are available. Our analysis leads to two main results: (1) employing three different methods, we determine the flux recovery of the interferometer as compared to the single-dish to be within a range of 35%–74% for NGC 4736 and 81%–92% for NGC 5055, and (2) when focusing on high (S/N ≥ 5) lines of sight (LOSs), the single-dish line widths are larger by ∼(40 ± 20)% than the ones derived from interferometric data, which is in agreement with stacking all LOSs. These results point to a molecular gas component that is distributed over spatial scales larger than 30″(∼1 kpc), and is therefore filtered out by the interferometer. The available observations do not allow us to distinguish between a truly diffuse gas morphology and a uniform distribution of small clouds that are separated by less than the synthesized beam size (∼3″ or ∼100 pc), as they would both be invisible for the interferometer. This high velocity dispersion component has a dispersion similar to what is found in the atomic medium, as traced through observations of the H i line.

  17. A Continuous Molecular Roadmap to iPSC Reprogramming through Progression Analysis of Single-Cell Mass Cytometry

    OpenAIRE

    Zunder, Eli R.; Lujan, Ernesto; Goltsev, Yury; Wernig, Marius; Nolan, Garry P.

    2015-01-01

    To analyze cellular reprogramming at the single-cell level, mass cytometry was used to simultaneously measure markers of pluripotency, differentiation, cell-cycle status, and cellular signaling throughout the reprogramming process. Time-resolved progression analysis of the resulting data sets was used to construct a continuous molecular roadmap for three independent reprogramming systems. Although these systems varied substantially in Oct4, Sox2, Klf4, and c-Myc stoichiometry, they presented ...

  18. Influence of temperature on the anisotropic cutting behaviour of single crystal silicon: A molecular dynamics simulation investigation

    OpenAIRE

    Chavoshi, Saeed Zare; Goel, Saurav; Luo, Xichun

    2016-01-01

    Using molecular dynamics (MD) simulation, this paper investigates anisotropic cutting behaviour of single crystal silicon in vacuum under a wide range of substrate temperatures (300 K, 500 K, 750 K, 850 K, 1173 K and 1500 K). Specific cutting energy, force ratio, stress in the cutting zone and cutting temperature were the indicators used to quantify the differences in the cutting behaviour of silicon. A key observation was that the specific cutting energy required to cut the (1 1 1) surface o...

  19. Single Molecule Electronics and Devices

    Science.gov (United States)

    Tsutsui, Makusu; Taniguchi, Masateru

    2012-01-01

    The manufacture of integrated circuits with single-molecule building blocks is a goal of molecular electronics. While research in the past has been limited to bulk experiments on self-assembled monolayers, advances in technology have now enabled us to fabricate single-molecule junctions. This has led to significant progress in understanding electron transport in molecular systems at the single-molecule level and the concomitant emergence of new device concepts. Here, we review recent developments in this field. We summarize the methods currently used to form metal-molecule-metal structures and some single-molecule techniques essential for characterizing molecular junctions such as inelastic electron tunnelling spectroscopy. We then highlight several important achievements, including demonstration of single-molecule diodes, transistors, and switches that make use of electrical, photo, and mechanical stimulation to control the electron transport. We also discuss intriguing issues to be addressed further in the future such as heat and thermoelectric transport in an individual molecule. PMID:22969345

  20. Electronic properties of single-molecule junction: Effect of the molecular distortion

    International Nuclear Information System (INIS)

    Gao, W.; Zhao, M.; Jiang, Q.

    2009-01-01

    For a model system consisting of a benzenedithio (BDT) molecule sandwiched between two Au plates, the electronic properties as a function of different BDT geometry are investigated using density functional theory. The distorted BDT structures are got through stretching the electrode distance. The corresponding electronic properties, including the spatial distribution of the frontier orbits, the gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital levels and density of states at the Fermi energy are determined. It reveals that the molecular distortion essentially determines electronic structures. The result should be beneficial to understand the stress-dependent or structure-dependent transport mechanism of electrons of the BDT junction.

  1. Antibiotic interaction with phospholipid monolayers

    Energy Technology Data Exchange (ETDEWEB)

    Gambinossi, F.; Mecheri, B.; Caminati, G.; Nocentini, M.; Puggelli, M.; Gabrielli, G

    2002-12-01

    We studied the interactions of tetracycline (TC) antibiotic molecules with phospholipid monolayers with the two-fold aim of elucidating the mechanism of action and providing a first step for the realization of bio-mimetic sensors for such drugs by means of the Langmuir-Blodgett technique. We examined spreading monolayers of three phospholipids in the presence of tetracycline in the subphase by means of surface pressure-area and surface potential-area isotherms as a function of bulk pH. We selected phospholipids with hydrophobic chains of the same length but polar head groups differing either in dimensions and protonation equilibria, i.e. dipalmitoylphosphatidylcholine (DPPC), dipalmitoylphosphatidylethanolamine (DPPE) and dipalmitoylphosphatidic acid (DPPA). The interaction of tetracycline with the three phospholipids was found to be highly dependent on the electric charge of the antibiotic and on the ionization state of the lipid. Significant interactions are established between the negatively charged form of dipalmitoylphosphatidic acid and the zwitterionic form of tetracycline. The drug was found to migrate at the interface where it is adsorbed underneath or/and among the head groups, depending on the surface pressure of the film, whereas penetration through the hydrophobic layer was excluded for all the three phospholipids.

  2. Single asperity nanocontacts: Comparison between molecular dynamics simulations and continuum mechanics models

    NARCIS (Netherlands)

    Solhjoo, Soheil; Vakis, Antonis I.

    Abstract Using classical molecular dynamics, atomic scale simulations of normal contact between a nominally flat substrate and different atomistic and non-atomistic spherical particles were performed to investigate the applicability of classical contact theories at the nanoscale, and further

  3. Measurement of Exciton Binding Energy of Monolayer WS2

    Science.gov (United States)

    Chen, Xi; Zhu, Bairen; Cui, Xiaodong

    Excitonic effects are prominent in monolayer crystal of transition metal dichalcogenides (TMDCs) because of spatial confinement and reduced Coulomb screening. Here we use linear differential transmission spectroscopy and two-photon photoluminescence excitation spectroscopy (TP-PLE) to measure the exciton binding energy of monolayer WS2. Peaks for excitonic absorptions of the direct gap located at K valley of the Brillouin zone and transitions from multiple points near Γ point of the Brillouin zone, as well as trion side band are shown in the linear absorption spectra of WS2. But there is no gap between distinct excitons and the continuum of the interband transitions. Strong electron-phonon scattering, overlap of excitons around Γ point and the transfer of the oscillator strength from interband continuum to exciton states make it difficult to resolve the electronic interband transition edge even down to 10K. The gap between excited states of the band-edge exciton and the single-particle band is probed by TP-PLE measurements. And the energy difference between 1s exciton and the single-particle gap gives the exciton binding energy of monolayer WS2 to be about 0.71eV. The work is supported by Area of excellency (AoE/P-04/08), CRF of Hong Kong Research Grant Council (HKU9/CRF/13G) and SRT on New Materials of The University of Hong Kong.

  4. Nanocomposite Materials of Alternately Stacked C60 Monolayer and Graphene

    International Nuclear Information System (INIS)

    Ishikawa, M.; Miura, K.; Kamiya, S.; Yoshimoto, S.; Suzuki, M.; Kuwahara, D.; Sasaki, N.

    2010-01-01

    We synthesized the novel nanocomposite consisting alternately of a stacked single graphene sheet and a C 60 monolayer by using the graphite intercalation technique in which alkylamine molecules help intercalate large C 60 molecules into the graphite. Moreover, it is found that the intercalated C 60 molecules can rotate in between single graphene sheets by using C 13 NMR measurements. This preparation method provides a general way for intercalating huge fullerene molecules into graphite, which will lead to promising materials with novel mechanical, physical, and electrical properties.

  5. Nanocomposite Materials of Alternately Stacked C60 Monolayer and Graphene

    Directory of Open Access Journals (Sweden)

    Makoto Ishikawa

    2010-01-01

    Full Text Available We synthesized the novel nanocomposite consisting alternately of a stacked single graphene sheet and a C60 monolayer by using the graphite intercalation technique in which alkylamine molecules help intercalate large C60 molecules into the graphite. Moreover, it is found that the intercalated C60 molecules can rotate in between single graphene sheets by using C13 NMR measurements. This preparation method provides a general way for intercalating huge fullerene molecules into graphite, which will lead to promising materials with novel mechanical, physical, and electrical properties.

  6. On the elastic properties of single-walled carbon nanotubes/poly(ethylene oxide) nanocomposites using molecular dynamics simulations.

    Science.gov (United States)

    Rouhi, S; Alizadeh, Y; Ansari, R

    2016-01-01

    Molecular dynamics simulations are used to study the physical and mechanical properties of single-walled carbon nanotubes/poly(ethylene oxide) nanocomposites. The effects of nanotube atomic structure, diameter, and volume fraction on the polymer density distribution, polymer atom distribution, stress-strain curves of nanocomposites and Young's, and shear moduli of single-walled carbon nanotubes/poly(ethylene oxide) nanocomposites are explored. It is shown that the density of polymer, surrounding the nanotube surface, has a peak near the nanotube surface. However, increasing distance leads to dropping it to the value near the density of pure polymer. It is seen that for armchair nanotubes, the average polymer atoms distances from the single-walled carbon nanotubes are larger than the polymer atom distance from zigzag nanotubes. It further is shown that zigzag nanotubes are better candidates to reinforce poly (ethylene oxide) than their armchair counterparts.

  7. Lipid monolayers and adsorbed polyelectrolytes with different degrees of polymerization.

    Science.gov (United States)

    Ortmann, Thomas; Ahrens, Heiko; Lawrenz, Frank; Gröning, Andreas; Nestler, Peter; Günther, Jens-Uwe; Helm, Christiane A

    2014-06-17

    Polystyrene sulfonate (PSS) of different molecular weight M(w) is adsorbed to oppositely charged DODAB monolayers from dilute solutions (0.01 mmol/L). PSS adsorbs flatly in a lamellar manner, as is shown by X-ray reflectivity and grazing incidence diffraction (exception: PSS with M(w) below 7 kDa adsorbs flatly disordered to the liquid expanded phase). The surface coverage and the separation of the PSS chains are independent of PSS M(w). On monolayer compression, the surface charge density increases by a factor of 2, and the separation of the PSS chains decreases by the same factor. Isotherms show that on increase of PSS M(w) the transition pressure of the LE/LC (liquid expanded/liquid condensed) phase transition decreases. When the contour length exceeds the persistence length (21 nm), the transition pressure is low and constant. For low-M(w) PSS (<7 kDa) the LE/LC transition of the lipids and the disordered/ordered transition of adsorbed PSS occur simultaneously, leading to a maximum in the contour length dependence of the transition enthalpy. These findings show that lipid monolayers at the air/water interface are a suitable model substrate with adjustable surface charge density to study the equilibrium conformation of adsorbed polyelectrolytes as well as their interactions with a model membrane.

  8. Photo-induced travelling waves in condensed Langmuir monolayers

    Energy Technology Data Exchange (ETDEWEB)

    Tabe, Y [Yokoyama Nano-Structured Liquid Crystal Project, ERATO, Japan Science and Technology Corporation, 5-9-9 Tokodai, Tsukuba, Ibaraki 300-2635, Japan (Japan); Yamamoto, T [Yokoyama Nano-Structured Liquid Crystal Project, ERATO, Japan Science and Technology Corporation, 5-9-9 Tokodai, Tsukuba, Ibaraki 300-2635, Japan (Japan); Yokoyama, H [Yokoyama Nano-Structured Liquid Crystal Project, ERATO, Japan Science and Technology Corporation, 5-9-9 Tokodai, Tsukuba, Ibaraki 300-2635, Japan (Japan)

    2003-06-01

    We report the detailed properties of photo-induced travelling waves in liquid crystalline Langmuir monolayers composed of azobenzene derivatives. When the monolayer, in which the constituent rodlike molecules are coherently tilted from the layer normal, is weakly illuminated to undergo the trans-cis photo-isomerization, spatio-temporal periodic oscillations of the molecular azimuth begin over the entire excited area and propagate as a two-dimensional orientational wave. The wave formation takes place only when the film is formed at an asymmetric interface with broken up-down symmetry and when the chromophores are continuously excited near the long-wavelength edge of absorption to induce repeated photo-isomerizations between the trans and cis forms. Under proper illumination conditions, Langmuir monolayers composed of a wide variety of azobenzene derivatives have been confirmed to exhibit similar travelling waves with velocity proportional to the excitation power irrespective of the degree of amphiphilicity. The dynamics can be qualitatively explained by the modified reaction-diffusion model proposed by Reigada, Sagues and Mikhailov.

  9. Phase diagram of the CF₄ monolayer and bilayer on graphite.

    Science.gov (United States)

    Thomas, Petros; Hess, George B

    2014-05-21

    We report an experimental study of physisorbed monolayers and bilayers of CF4 on graphite using infrared reflection absorption spectroscopy supplemented by ellipsometry. The symmetric C-F stretch mode ν3 near 1283 cm(-1) in the gas is strongly blue shifted in the film by dynamic dipole coupling. This blue shift provides a very sensitive measure of the inter-molecular spacing in the monolayer and, less directly, in the bilayer. We find that important corrections are necessary to the volumetric coverage scales used in previous heat capacity and x-ray diffraction studies of this system. This requires quantitative and some qualitative changes to the previously proposed phase diagram. We find evidence for a new phase transition in the middle of the hexagonal incommensurate region and construct new phase diagrams in both the variables coverage-temperature and chemical potential-temperature. We determine the compressibility and thermal expansion in the low-pressure hexagonal incommensurate phase and values for the entropy change in several phase transitions. Below about 55 K there is evidence of solution of up to 7% of an impurity, most likely CO, in our monolayer but not the bilayer film.

  10. Self-Assembled Monolayers for Dental Implants

    Directory of Open Access Journals (Sweden)

    Sidónio C. Freitas

    2018-01-01

    Full Text Available Implant-based therapy is a mature approach to recover the health conditions of patients affected by edentulism. Thousands of dental implants are placed each year since their introduction in the 80s. However, implantology faces challenges that require more research strategies such as new support therapies for a world population with a continuous increase of life expectancy, to control periodontal status and new bioactive surfaces for implants. The present review is focused on self-assembled monolayers (SAMs for dental implant materials as a nanoscale-processing approach to modify titanium surfaces. SAMs represent an easy, accurate, and precise approach to modify surface properties. These are stable, well-defined, and well-organized organic structures that allow to control the chemical properties of the interface at the molecular scale. The ability to control the composition and properties of SAMs precisely through synthesis (i.e., the synthetic chemistry of organic compounds with a wide range of functional groups is well established and in general very simple, being commercially available, combined with the simple methods to pattern their functional groups on complex geometry appliances, makes them a good system for fundamental studies regarding the interaction between surfaces, proteins, and cells, as well as to engineering surfaces in order to develop new biomaterials.

  11. Development and Characterization of a Human and Mouse Intestinal Epithelial Cell Monolayer Platform

    Directory of Open Access Journals (Sweden)

    Kenji Kozuka

    2017-12-01

    Full Text Available Summary: We describe the development and characterization of a mouse and human epithelial cell monolayer platform of the small and large intestines, with a broad range of potential applications including the discovery and development of minimally systemic drug candidates. Culture conditions for each intestinal segment were optimized by correlating monolayer global gene expression with the corresponding tissue segment. The monolayers polarized, formed tight junctions, and contained a diversity of intestinal epithelial cell lineages. Ion transport phenotypes of monolayers from the proximal and distal colon and small intestine matched the known and unique physiology of these intestinal segments. The cultures secreted serotonin, GLP-1, and FGF19 and upregulated the epithelial sodium channel in response to known biologically active agents, suggesting intact secretory and absorptive functions. A screen of over 2,000 pharmacologically active compounds for inhibition of potassium ion transport in the mouse distal colon cultures led to the identification of a tool compound. : Siegel and colleagues describe their development of a human and mouse intestinal epithelial cell monolayer platform that maintains the cellular, molecular, and functional characteristics of tissue for each intestinal segment. They demonstrate the platform's application to drug discovery by screening a library of over 2,000 compounds to identify an inhibitor of potassium ion transport in the mouse distal colon. Keywords: intestinal epithelium, organoids, monolayer, colon, small intestine, phenotype screening assays, enteroid, colonoid

  12. Effects of monolayer Bi on the self-assembly of DBBA on Au(111)

    Science.gov (United States)

    Tian, Guo; Shen, Yixian; He, Bingchen; Yu, Zhengqing; Song, Fei; Lu, Yunhao; Wang, Pingshan; Gao, Yongli; Huang, Han

    2017-11-01

    The initial growth behaviors of nonplanar 10,10‧-dibromo-9,9‧-bianthryl (DBBA) molecules on the Au(111) substrates, which is either pristine or Bi-3 × √3-Au(111), at low deposition rates have been systematically investigated using low temperature scanning tunneling microscopy (LT-STM) and density functional theories (DFT) calculations. The effects of such substrates on the subsequent graphene nanoribbons (GNRs) formation are addressed. On clean Au(111), DBBA molecules self-assemble into highly ordered commensurate single-molecule chains along Au at a coverage of 0.8 monolayer (ML), and collectively transit into long-range ordered commensurate double-molecule chains along Au but with many single-molecule vacancies at a coverage of 1.2 ML, revealing the delicate competing between intermolecular interactions and molecule-substrate interfacial interactions. The interfacial interactions are further tuned by introducing bismuth to form a Bi-3 × √3-Au(111)surface, where DBBA molecules self-assemble into an unique hexamer phase due to the enhanced intermolecular interactions via Csbnd H…π and halogen bonds. DFT calculations confirm the proposed molecular configuration change of single DBBA molecule when adsorbed on different substrates. The calculated difference in Csbnd Br bond gives further insight into why no GNRs formed on Bi-3 × √3-Au(111).

  13. Comparative study of normal and branched alkane monolayer films adsorbed on a solid surface. I. Structure

    DEFF Research Database (Denmark)

    Enevoldsen, Ann Dorrit; Hansen, Flemming Yssing; Diama, A.

    2007-01-01

    their backbone and squalane has, in addition, six methyl side groups. Upon adsorption, there are significant differences as well as similarities in the behavior of these molecular films. Both molecules form ordered structures at low temperatures; however, while the melting point of the two-dimensional (2D......The structure of a monolayer film of the branched alkane squalane (C30H62) adsorbed on graphite has been studied by neutron diffraction and molecular dynamics (MD) simulations and compared with a similar study of the n-alkane tetracosane (n-C24H52). Both molecules have 24 carbon atoms along...... temperature. The neutron diffraction data show that the translational order in the squalane monolayer is significantly less than in the tetracosane monolayer. The authors' MD simulations suggest that this is caused by a distortion of the squalane molecules upon adsorption on the graphite surface. When...

  14. Controlled synthesis of high-quality crystals of monolayer MoS2 for nanoelectronic device application

    DEFF Research Database (Denmark)

    Yang, Xiaonian; Li, Qiang; Hu, Guofeng

    2016-01-01

    . Monolayer MoS2 so far can be obtained by mechanical exfoliation or chemical vapor deposition (CVD). However, controllable synthesis of large area monolayer MoS2 with high quality needs to be improved and their growth mechanism requires more studies. Here we report a systematical study on controlled...... synthesis of high-quality monolayer MoS2 single crystals using low pressure CVD. Large-size monolayer MoS2 triangles with an edge length up to 405 mu m were successfully synthesized. The Raman and photoluminescence spectroscopy studies indicate high homogenous optical characteristic of the synthesized......) V-1 s(-1), indicating excellent electronic property comparing with previously reported CVD grown MoS2 monolayer. The MoS2 FETs also show a high photoresponsivity of 7 A W-1, as well as a fast photo-response time of 20 ms. The improved synthesis method recommended here, which makes material...

  15. Influence of calcium on ceramide-1-phosphate monolayers

    Directory of Open Access Journals (Sweden)

    Joana S. L. Oliveira

    2016-02-01

    Full Text Available Ceramide-1-phosphate (C1P plays an important role in several biological processes, being identified as a key regulator of many protein functions. For instance, it acts as a mediator of inflammatory responses. The mediation of the inflammation process happens due to the interaction of C1P with the C2 domain of cPLA2α, an effector protein that needs the presence of submicromolar concentrations of calcium ions. The aim of this study was to determine the phase behaviour and structural properties of C1P in the presence and absence of millimolar quantities of calcium in a well-defined pH environment. For that purpose, we used monomolecular films of C1P at the soft air/liquid interface with calcium ions in the subphase. The pH was varied to change the protonation degree of the C1P head group. We used surface pressure versus molecular area isotherms coupled with other monolayer techniques as Brewster angle microscopy (BAM, infrared reflection–absorption spectroscopy (IRRAS and grazing incidence X-ray diffraction (GIXD. The isotherms indicate that C1P monolayers are in a condensed state in the presence of calcium ions, regardless of the pH. At higher pH without calcium ions, the monolayer is in a liquid-expanded state due to repulsion between the negatively charged phosphate groups of the C1P molecules. When divalent calcium ions are added, they are able to bridge the highly charged phosphate groups, enhancing the regular arrangement of the head groups. Similar solidification of the monolayer structure can be seen in the presence of a 150 times larger concentration of monovalent sodium ions. Therefore, calcium ions have clearly a strong affinity for the phosphomonoester of C1P.

  16. Conductance of Alkanedithiol Single-Molecule Junctions: A Molecular Dynamics Study

    DEFF Research Database (Denmark)

    Paulsson, Magnus; Krag, Casper; Frederiksen, Thomas

    2009-01-01

    We study formation and conductance of alkanedithiol junctions using density functional based molecular dynamics. The formation involves straightening of the molecule, migration of thiol end-groups, and pulling out Au atoms. Plateaus are found in the low-bias conductance traces which decrease by 1...

  17. Extracting physics of life at the molecular level: A review of single-molecule data analyses.

    Science.gov (United States)

    Colomb, Warren; Sarkar, Susanta K

    2015-06-01

    Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Temperature effects in a nonlinear model of monolayer Scheibe aggregates

    DEFF Research Database (Denmark)

    Bang, Ole; Christiansen, Peter Leth; If, F.

    1994-01-01

    of the complicated spectrum of the noise are considered: time independent, spatially white noise, simply corresponding to disorder in the arrangement of the molecules, and pure white noise. Parameter values are found by comparison with experiments by Mobius and Kuhn [Isr. J. Chem. 18, 375 (1979)] and order......A nonlinear dynamical model of molecular monolayers arranged in Scheibe aggregates is derived from a proper Hamiltonian. Thermal fluctuations of the phonons are included. The resulting equation for the excitons is the two dimensional nonlinear Schrodinger equation with noise. Two limits...

  19. Monolayer MoS{sub 2} self-switching diodes

    Energy Technology Data Exchange (ETDEWEB)

    Al-Dirini, Feras, E-mail: alf@unimelb.edu.au; Hossain, Md Sharafat [Department of Electrical and Electronic Engineering, University of Melbourne, Victoria (Australia); Centre for Neural Engineering, University of Melbourne, Victoria (Australia); Victorian Research Laboratory, National ICT Australia, West Melbourne, Victoria (Australia); Hossain, Faruque M.; Skafidas, Efstratios [Department of Electrical and Electronic Engineering, University of Melbourne, Victoria (Australia); Centre for Neural Engineering, University of Melbourne, Victoria (Australia); Mohammed, Mahmood A. [Princess Sumaya University for Technology, Amman (Jordan); Nirmalathas, Ampalavanapillai [Department of Electrical and Electronic Engineering, University of Melbourne, Victoria (Australia); Melbourne Networked Society Institute (MNSI), University of Melbourne, Victoria (Australia)

    2016-01-28

    This paper presents a new molybdenum disulphide (MoS{sub 2}) nanodevice that acts as a two-terminal field-effect rectifier. The device is an atomically-thin two-dimensional self-switching diode (SSD) that can be realized within a single MoS{sub 2} monolayer with very minimal process steps. Quantum simulation results are presented confirming the device's operation as a diode and showing strong non-linear I-V characteristics. Interestingly, the device shows p-type behavior, in which conduction is dominated by holes as majority charge carriers and the flow of reverse current is enhanced, while the flow of forward current is suppressed, in contrast to monolayer graphene SSDs, which behave as n-type devices. The presence of a large bandgap in monolayer MoS{sub 2} results in strong control over the channel, showing complete channel pinch-off in forward conduction, which was confirmed with transmission pathways plots. The device exhibited large leakage tunnelling current through the insulating trenches, which may have been due to the lack of passivation; nevertheless, reverse current remained to be 6 times higher than forward current, showing strong rectification. The effect of p-type substitutional channel doping of sulphur with phosphorus was investigated and showed that it greatly enhances the performance of the device, increasing the reverse-to-forward current rectification ratio more than an order of magnitude, up to a value of 70.

  20. Monolayer MoS2 self-switching diodes

    International Nuclear Information System (INIS)

    Al-Dirini, Feras; Hossain, Md Sharafat; Hossain, Faruque M.; Skafidas, Efstratios; Mohammed, Mahmood A.; Nirmalathas, Ampalavanapillai

    2016-01-01

    This paper presents a new molybdenum disulphide (MoS 2 ) nanodevice that acts as a two-terminal field-effect rectifier. The device is an atomically-thin two-dimensional self-switching diode (SSD) that can be realized within a single MoS 2 monolayer with very minimal process steps. Quantum simulation results are presented confirming the device's operation as a diode and showing strong non-linear I-V characteristics. Interestingly, the device shows p-type behavior, in which conduction is dominated by holes as majority charge carriers and the flow of reverse current is enhanced, while the flow of forward current is suppressed, in contrast to monolayer graphene SSDs, which behave as n-type devices. The presence of a large bandgap in monolayer MoS 2 results in strong control over the channel, showing complete channel pinch-off in forward conduction, which was confirmed with transmission pathways plots. The device exhibited large leakage tunnelling current through the insulating trenches, which may have been due to the lack of passivation; nevertheless, reverse current remained to be 6 times higher than forward current, showing strong rectification. The effect of p-type substitutional channel doping of sulphur with phosphorus was investigated and showed that it greatly enhances the performance of the device, increasing the reverse-to-forward current rectification ratio more than an order of magnitude, up to a value of 70

  1. On the influence of the aliphatic linker on fabrication of highly ordered and orientated self-assembled monolayers of aromatic selenols on AU(111)

    KAUST Repository

    Azzam, Waleed

    2014-03-06

    Self-assembled monolayers (SAMs) formed by adsorption of 1,2-dibenzyldiselenide (DPMSe) and 1,2-diphenyldiselenide (DBSe) on Au(111) substrates at room temperature have been characterized using scanning tunnelling microscopy, X-ray photoelectron spectroscopy, infrared reflection absorption spectroscopy, near-edge X-ray absorption fine structure spectroscopy, and low-energy electron diffraction. Upon adsorption, the Se-Se bonds in DPMSe and DBSe were cleaved on the gold surface to form phenylmethaneselenolate (PMSe) and benzeneselenolate (BSe) species, respectively. Although both PMSe and BSe molecular entities only differ in their structure (an additional methyl group in PMSe), the resulting monolayer films revealed noteworthy dissimilarities regarding their adlayer SAM structure and surface morphology. The molecular adlayer structure and orientation of PMSe and BSe species were found to vary significantly with the immersion time (IT). The resulting PMSe films were poorly organized, and the structure was described by a (4√3 × 2) rectangular unit cell for the SAMs prepared with 24 h of IT. Moreover, the PMSe-SAMs were found to be unstable upon exposure to air for a long time. Our results showed that exposure to air for 48 h results in the formation of small bright ad-islands, which have a height corresponding to that of a single atomic step on the Au(111). Contrary, BSe-SAMs exhibited densely packed and well-ordered monolayers, and two different structural phases were resolved at short and long ITs. The most densely packed structure was obtained for SAMs prepared with very short ITs (10 min). Upon increasing the IT, the SAMs exhibited structural changes to a lower density of molecular packing structure. The spectroscopic data also confirmed this structural transformation by suggesting an upright orientation for BSe-SAMs prepared after short ITs and strongly inclined adsorption geometry for SAMs prepared after long ITs. © 2014 American Chemical Society.

  2. Waterborne polyurethane single-ion electrolyte from aliphatic diisocyanate and various molecular length of polyethylene glycol

    Directory of Open Access Journals (Sweden)

    2007-03-01

    Full Text Available The waterborne polyurethane (WPU dispersions from the reaction of cycloaliphatic diisocyanates [4,4’-methylenebis(cyclohexyl isocyanate (H12MDI and isophorone diisocyanate (IPDI] and polyethylene glycol (PEG with various molecular lengths were synthesized using our modified acetone process. Differetial scanning calorimeter (DSC and Fourier transform infrared spectroscopy (FTIR were utilized to characterize WPU films for the behavior of their crystallinity and H-bonding of WPU films. The Tg value of WPU increases with increasing the molecular length of PEG, whereas the Tm of WPU decreases with increasing PEG length. Alternating current (AC impedance experiments were performed to determine the ionic conductivities of WPU films. The WPU gel electrolytes exhibits an ionic conductivity as high as ~ 10-5 S/cm at room temperature.

  3. Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules.

    Science.gov (United States)

    Mayjonade, Baptiste; Gouzy, Jérôme; Donnadieu, Cécile; Pouilly, Nicolas; Marande, William; Callot, Caroline; Langlade, Nicolas; Muños, Stéphane

    2016-10-01

    De novo sequencing of complex genomes is one of the main challenges for researchers seeking high-quality reference sequences. Many de novo assemblies are based on short reads, producing fragmented genome sequences. Third-generation sequencing, with read lengths >10 kb, will improve the assembly of complex genomes, but these techniques require high-molecular-weight genomic DNA (gDNA), and gDNA extraction protocols used for obtaining smaller fragments for short-read sequencing are not suitable for this purpose. Methods of preparing gDNA for bacterial artificial chromosome (BAC) libraries could be adapted, but these approaches are time-consuming, and commercial kits for these methods are expensive. Here, we present a protocol for rapid, inexpensive extraction of high-molecular-weight gDNA from bacteria, plants, and animals. Our technique was validated using sunflower leaf samples, producing a mean read length of 12.6 kb and a maximum read length of 80 kb.

  4. Solvothermal synthesis of uniform hexagonal-phase ZnS nanorods using a single-source molecular precursor

    International Nuclear Information System (INIS)

    Zhang Yongcai; Wang Guiyun; Hu Xiaoya; Chen Weiwei

    2006-01-01

    Pure and uniform hexagonal-phase ZnS nanorods with quantum confinement effect were synthesized by solvothermal decomposition of an air-stable, easily obtained single-source molecular precursor (zinc diethyldithiocarbamate, Zn-(DDTC) 2 ) in hydrazine hydrate aqueous solutions at 150-200 deg. C, and characterized by powder X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), selected area electron diffraction (SAED) and UV-vis absorption spectra. The possible formation mechanism of one-dimensional ZnS nanostructure in the present system was also briefly discussed

  5. Molecular Sieving Across Centimeter-Scale Single-Layer Nanoporous Graphene Membranes.

    Science.gov (United States)

    Boutilier, Michael S H; Jang, Doojoon; Idrobo, Juan-Carlos; Kidambi, Piran R; Hadjiconstantinou, Nicolas G; Karnik, Rohit

    2017-06-27

    Molecular sieving across atomically thin nanoporous graphene is predicted to enable superior gas separation performance compared to conventional membranes. Although molecular sieving has been demonstrated across a few pores in microscale graphene membranes, leakage through nonselective defects presents a major challenge toward realizing selective membranes with high densities of pores over macroscopic areas. Guided by multiscale gas transport modeling of nanoporous graphene membranes, we designed the porous support beneath the graphene to isolate small defects and minimize leakage through larger defects. Ion bombardment followed by oxygen plasma etching was used to produce subnanometer pores in graphene at a density of ∼10 11 cm -2 . Gas permeance measurements demonstrate selectivity that exceeds the Knudsen effusion ratio and scales with the kinetic diameter of the gas molecules, providing evidence of molecular sieving across centimeter-scale nanoporous graphene. The extracted nanoporous graphene performance is comparable to or exceeds the Robeson limit for polymeric gas separation membranes, confirming the potential of nanoporous graphene membranes for gas separations.

  6. Electrochemical gate-controlled electron transport of redox-active single perylene bisimide molecular junctions

    International Nuclear Information System (INIS)

    Li, C; Mishchenko, A; Li, Z; Pobelov, I; Wandlowski, Th; Li, X Q; Wuerthner, F; Bagrets, A; Evers, F

    2008-01-01

    We report a scanning tunneling microscopy (STM) experiment in an electrochemical environment which studies a prototype molecular switch. The target molecules were perylene tetracarboxylic acid bisimides modified with pyridine (P-PBI) and methylthiol (T-PBI) linker groups and with bulky tert-butyl-phenoxy substituents in the bay area. At a fixed bias voltage, we can control the transport current through a symmetric molecular wire Au|P-PBI(T-PBI)|Au by variation of the electrochemical 'gate' potential. The current increases by up to two orders of magnitude. The conductances of the P-PBI junctions are typically a factor 3 larger than those of T-PBI. A theoretical analysis explains this effect as a consequence of shifting the lowest unoccupied perylene level (LUMO) in or out of the bias window when tuning the electrochemical gate potential VG. The difference in on/off ratios reflects the variation of hybridization of the LUMO with the electrode states with the anchor groups. I T -E S(T) curves of asymmetric molecular junctions formed between a bare Au STM tip and a T-PBI (P-PBI) modified Au(111) electrode in an aqueous electrolyte exhibit a pronounced maximum in the tunneling current at -0.740, which is close to the formal potential of the surface-confined molecules. The experimental data were explained by a sequential two-step electron transfer process

  7. The electronic structures and optical properties of light-element atom adsorbed SnSe monolayers

    Science.gov (United States)

    Cai, Xiaoyu; Luo, Jia; Zhang, Xi; Xiang, Gang

    2018-03-01

    The effect of adsorption of different light-element atoms on the electronic structures and optical properties of single-layered SnSe sheets are investigated using density-functional theory. The optimized structures of SnSe monolayers with the adatoms (H, Li, B, C, N, O and F) are calculated by full optimization method. We found that depending on the nature of the adatoms, SnSe monolayers can be designed to be either metal or semiconductor. With the decoration of H, Li, B, N or F adatoms, SnSe monolayers become metallic, either resulted from the formation of impurity bands (H, B and N) or the shifts of energy bands (Li and F). With the decoration of C or O adatoms, SnSe monolayers remain semiconducting, but the band structures change evidently, resulting in robust modulation of effective masses of charge carriers near band edges and optical absorption properties of the monolayers. Our calculated results demonstrate that the electronic and optical properties of SnSe monolayers can be tuned by adsorption of light-element adatoms which may be used in electrical and optical applications.

  8. Defect-Mediated Lithium Adsorption and Diffusion on Monolayer Molybdenum Disulfide.

    Science.gov (United States)

    Sun, Xiaoli; Wang, Zhiguo; Fu, Y Q

    2015-12-22

    Monolayer Molybdenum Disulfide (MoS2) is a promising anode material for lithium ion batteries because of its high capacities. In this work, first principle calculations based on spin density functional theory were performed to investigate adsorption and diffusion of lithium on monolayer MoS2 with defects, such as single- and few-atom vacancies, antisite, and grain boundary. The values of adsorption energies on the monolayer MoS2 with the defects were increased compared to those on the pristine MoS2. The presence of defects causes that the Li is strongly bound to the monolayer MoS2 with adsorption energies in the range between 2.81 and 3.80 eV. The donation of Li 2s electron to the defects causes an enhancement of adsorption of Li on the monolayer MoS2. At the same time, the presence of defects does not apparently affect the diffusion of Li, and the energy barriers are in the range of 0.25-0.42 eV. The presence of the defects can enhance the energy storage capacity, suggesting that the monolayer MoS2 with defects is a suitable anode material for the Li-ion batteries.

  9. Revealing deposition mechanism of colloid particles on human serum albumin monolayers.

    Science.gov (United States)

    Nattich-Rak, Małgorzata; Adamczyk, Zbigniew; Kujda, Marta

    2016-01-01

    Colloid particle deposition was applied in order to characterize human serum albumin (HSA) monolayers on mica adsorbed under diffusion transport at pH 3.5. The surface concentration of HSA was determined by a direct AFM imaging of single molecules. The electrokinetic characteristics of the monolayers for various ionic strength were done by in situ streaming potential measurements. In this way the mean-field zeta potential of monolayers was determined. It was shown that the initially negative potential changed its sign for HSA surface concentrations above 2800μm(-2) that was interpreted as overcharging effect. The monolayers were also characterized by the colloid deposition method where negatively charged polystyrene particles, 810nm in diameter were used. The kinetics of particle deposition and their maximum coverage were determined as a function of the HSA monolayer surface concentration. An anomalous deposition of particles on substrates exhibiting a negative zeta potential was observed, which contradicts the mean-field theoretical predictions. This effect was quantitatively interpreted in terms of the random site sequential adsorption model. It was shown that efficient immobilization of particles only occurs at adsorption sites formed by three and more closely adsorbed HSA molecules. These results can be exploited as useful reference data for the analysis of deposition phenomena of bioparticles at protein monolayers that has practical significance for the regulation of the bioadhesive properties of surfaces. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Single-order laser high harmonics in XUV for ultrafast photoelectron spectroscopy of molecular wavepacket dynamics

    Directory of Open Access Journals (Sweden)

    Mizuho Fushitani

    2016-11-01

    Full Text Available We present applications of extreme ultraviolet (XUV single-order laser harmonics to gas-phase ultrafast photoelectron spectroscopy. Ultrashort XUV pulses at 80 nm are obtained as the 5th order harmonics of the fundamental laser at 400 nm by using Xe or Kr as the nonlinear medium and separated from other harmonic orders by using an indium foil. The single-order laser harmonics is applied for real-time probing of vibrational wavepacket dynamics of I2 molecules in the bound and dissociating low-lying electronic states and electronic-vibrational wavepacket dynamics of highly excited Rydberg N2 molecules.

  11. Single-order laser high harmonics in XUV for ultrafast photoelectron spectroscopy of molecular wavepacket dynamics.

    Science.gov (United States)

    Fushitani, Mizuho; Hishikawa, Akiyoshi

    2016-11-01

    We present applications of extreme ultraviolet (XUV) single-order laser harmonics to gas-phase ultrafast photoelectron spectroscopy. Ultrashort XUV pulses at 80 nm are obtained as the 5th order harmonics of the fundamental laser at 400 nm by using Xe or Kr as the nonlinear medium and separated from other harmonic orders by using an indium foil. The single-order laser harmonics is applied for real-time probing of vibrational wavepacket dynamics of I 2 molecules in the bound and dissociating low-lying electronic states and electronic-vibrational wavepacket dynamics of highly excited Rydberg N 2 molecules.

  12. GaN Schottky diodes with single-crystal aluminum barriers grown by plasma-assisted molecular beam epitaxy

    Science.gov (United States)

    Tseng, H. Y.; Yang, W. C.; Lee, P. Y.; Lin, C. W.; Cheng, Kai-Yuan; Hsieh, K. C.; Cheng, K. Y.; Hsu, C.-H.

    2016-08-01

    GaN-based Schottky barrier diodes (SBDs) with single-crystal Al barriers grown by plasma-assisted molecular beam epitaxy are fabricated. Examined using in-situ reflection high-energy electron diffractions, ex-situ high-resolution x-ray diffractions, and high-resolution transmission electron microscopy, it is determined that epitaxial Al grows with its [111] axis coincident with the [0001] axis of the GaN substrate without rotation. In fabricated SBDs, a 0.2 V barrier height enhancement and 2 orders of magnitude reduction in leakage current are observed in single crystal Al/GaN SBDs compared to conventional thermal deposited Al/GaN SBDs. The strain induced piezoelectric field is determined to be the major source of the observed device performance enhancements.

  13. GaN Schottky diodes with single-crystal aluminum barriers grown by plasma-assisted molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Tseng, H. Y.; Yang, W. C.; Lee, P. Y.; Lin, C. W.; Cheng, Kai-Yuan; Hsieh, K. C.; Cheng, K. Y., E-mail: kycheng@ee.nthu.edu.tw [Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Hsu, C.-H. [Division of Scientific Research, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan (China)

    2016-08-22

    GaN-based Schottky barrier diodes (SBDs) with single-crystal Al barriers grown by plasma-assisted molecular beam epitaxy are fabricated. Examined using in-situ reflection high-energy electron diffractions, ex-situ high-resolution x-ray diffractions, and high-resolution transmission electron microscopy, it is determined that epitaxial Al grows with its [111] axis coincident with the [0001] axis of the GaN substrate without rotation. In fabricated SBDs, a 0.2 V barrier height enhancement and 2 orders of magnitude reduction in leakage current are observed in single crystal Al/GaN SBDs compared to conventional thermal deposited Al/GaN SBDs. The strain induced piezoelectric field is determined to be the major source of the observed device performance enhancements.

  14. Multiple breast cancer cell-lines derived from a single tumor differ in their molecular characteristics and tumorigenic potential.

    Directory of Open Access Journals (Sweden)

    Goar Mosoyan

    Full Text Available BACKGROUND: Breast cancer cell lines are widely used tools to investigate breast cancer biology and to develop new therapies. Breast cancer tissue contains molecularly heterogeneous cell populations. Thus, it is important to understand which cell lines best represent the primary tumor and have similarly diverse phenotype. Here, we describe the development of five breast cancer cell lines from a single patient's breast cancer tissue. We characterize the molecular profiles, tumorigenicity and metastatic ability in vivo of all five cell lines and compare their responsiveness to 4-hydroxytamoxifen (4-OHT treatment. METHODS: Five breast cancer cell lines were derived from a single patient's primary breast cancer tissue. Expression of different antigens including HER2, estrogen receptor (ER, CK8/18, CD44 and CD24 was determined by flow cytometry, western blotting and immunohistochemistry (IHC. In addition, a Fluorescent In Situ Hybridization (FISH assay for HER2 gene amplification and p53 genotyping was performed on all cell lines. A xenograft model in nude mice was utilized to assess the tumorigenic and metastatic abilities of the breast cancer cells. RESULTS: We have isolated, cloned and established five new breast cancer cell lines with different tumorigenicity and metastatic abilities from a single primary breast cancer. Although all the cell lines expressed low levels of ER, their growth was estrogen-independent and all had high-levels of expression of mutated non-functional p53. The HER2 gene was rearranged in all cell lines. Low doses of 4-OHT induced proliferation of these breast cancer cell lines. CONCLUSIONS: All five breast cancer cell lines have different antigenic expression profiles, tumorigenicity and organ specific metastatic abilities although they derive from a single tumor. None of the studied markers correlated with tumorigenic potential. These new cell lines could serve as a model for detailed genomic and proteomic analyses to

  15. Quantifying the Assembly of Multicomponent Molecular Machines by Single-Molecule Total Internal Reflection Fluorescence Microscopy.

    Science.gov (United States)

    Boehm, E M; Subramanyam, S; Ghoneim, M; Washington, M Todd; Spies, M

    2016-01-01

    Large, dynamic macromolecular complexes play essential roles in many cellular processes. Knowing how the components of these complexes associate with one another and undergo structural rearrangements is critical to understanding how they function. Single-molecule total internal reflection fluorescence (TIRF) microscopy is a powerful approach for addressing these fundamental issues. In this article, we first discuss single-molecule TIRF microscopes and strategies to immobilize and fluorescently label macromolecules. We then review the use of single-molecule TIRF microscopy to study the formation of binary macromolecular complexes using one-color imaging and inhibitors. We conclude with a discussion of the use of TIRF microscopy to examine the formation of higher-order (i.e., ternary) complexes using multicolor setups. The focus throughout this article is on experimental design, controls, data acquisition, and data analysis. We hope that single-molecule TIRF microscopy, which has largely been the province of specialists, will soon become as common in the tool box of biophysicists and biochemists as structural approaches have become today. © 2016 Elsevier Inc. All rights reserved.

  16. Lattice and Molecular Vibrations in Single Crystal I2 at 77 K by Inelastic Neutron Scattering

    DEFF Research Database (Denmark)

    Smith, H. G.; Nielsen, Mourits; Clark, C. B.

    1975-01-01

    Phonon dispersion curves of single crystal iodine at 77 K have been measured by one-phonon coherent inelastic neutron scattering techniques. The data are analysed in terms of two Buckingham-six intermolecular potentials; one to represent the shortest intermolecular interaction (3.5 Å) and the other...

  17. Distinctive interactions of oleic acid covered magnetic nanoparticles with saturated and unsaturated phospholipids in Langmuir monolayers.

    Science.gov (United States)

    Matshaya, Thabo J; Lanterna, Anabel E; Granados, Alejandro M; Krause, Rui W M; Maggio, Bruno; Vico, Raquel V

    2014-05-27

    The growing number of innovations in nanomedicine and nanobiotechnology are posing new challenges in understanding the full spectrum of interactions between nanomateriales and biomolecules at nano-biointerfaces. Although considerable achievements have been accomplished by in vivo applications, many issues regarding the molecular nature of these interactions are far from being well-understood. In this work, we evaluate the interaction of hydrophobic magnetic nanoparticles (MNP) covered with a single layer of oleic acid with saturated and unsaturated phospholipids found in biomembranes through the use of Langmuir monolayers. We find distinctive interactions among the MNP with saturated and unsaturated phospholipids that are reflected by both, the compression isotherms and the surface topography of the films. The interaction between MNP and saturated lipids causes a noticeable reduction of the mean molecular area in the interfacial plane, while the interaction with unsaturated lipids promotes area expansion compared to the ideally mixed films. Moreover, when liquid expanded and liquid condensed phases of the phospholipid(s) coexist, the MNP preferably partition to the liquid-expanded phase, thus hindering the coalescence of the condensed domains with increasing surface pressure. In consequence organizational information on long-range order is attained. These results evidence the existence of a sensitive composition-dependent surface regulation given by phospholipid-nanoparticle interactions which enhance the biophysical relevance of understanding nanoparticle surface functionalization in relation to its interactions in biointerfaces constituted by defined types of biomolecules.

  18. Large Friction Anisotropy of a Polydiacetylene Monolayer

    International Nuclear Information System (INIS)

    Burns, A.R.; Carpick, R.W.; Sasaki, D.Y.

    1999-01-01

    Friction force microscopy measurements of a polydiacetylene monolayer film reveal a 300% friction anisotropy that is correlated with the film structure. The film consists of a monolayer of the red form of N-(2-ethanol)- 10,12 pentacosadiynamide, prepared on a Langmuir trough and deposited on a mica substrate. As confirmed by atomic force microscopy and fluorescence microscopy, the monolayer consists of domains of linearly oriented conjugated backbones with pendant hydrocarbon side chains above and below the backbones. Maximum friction occurs when the sliding direction is perpendicular to the backbone. We propose that the backbones impose anisotropic packing of the hydrocarbon side chains which leads to the observed friction anisotropy. Friction anisotropy is therefore a sensitive, optically-independent indicator of polymer backbone direction and monolayer structural properties

  19. Packing of ganglioside-phospholipid monolayers

    DEFF Research Database (Denmark)

    Majewski, J.; Kuhl, T.L.; Kjær, K.

    2001-01-01

    Using synchrotron grazing-incidence x-ray diffraction (GIXD) and reflectivity, the in-plane and out-of-plane structure of mixed ganglioside-phospholipid monolayers was investigated at the air-water interface. Mixed monolayers of 0, 5, 10, 20, and 100 mol% ganglioside GM, and the phospholipid...... dipaimitoylphosphatidylethanolamine (DPPE) were studied in the solid phase at 23 degreesC and a surface pressure of 45 mN/m. At these concentrations and conditions the two components do not phase-separate and no evidence for domain formation was observed. X-ray scattering measurements reveal that GM, is accommodated within the host...... monolayers did not affect hydrocarbon tail packing (fluidization or condensation of the hydrocarbon region). This is in contrast to previous investigations of lipopolymer-lipid mixtures, where the packing structure of phospholipid monolayers was greatly altered by the inclusion of lipids bearing hydrophilic...

  20. Single NdPc2 molecules on surfaces. Adsorption, interaction, and molecular magnetism

    International Nuclear Information System (INIS)

    Fahrendorf, Sarah

    2013-01-01

    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 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 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 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 spin

  1. 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

  2. Charge Transport Processes in Molecular Junctions

    Science.gov (United States)

    Smith, Christopher Eugene

    Molecular electronics (ME) has evolved into a rich area of exploration that combines the fields of chemistry, materials, electronic engineering and computational modeling to explore the physics behind electronic conduction at the molecular level. Through studying charge transport properties of single molecules and nanoscale molecular materials the field has gained the potential to bring about new avenues for the miniaturization of electrical components where quantum phenomena are utilized to achieve solid state molecular device functionality. Molecular junctions are platforms that enable these studies and consist of a single molecule or a small group of molecules directly connected to electrodes. The work presented in this thesis has built upon the current understanding of the mechanisms of charge transport in ordered junctions using self-assembled monolayer (SAM) molecular thin films. Donor and acceptor compounds were synthesized and incorporated into SAMs grown on metal substrates then the transport properties were measured with conducting probe atomic force microscopy (CP-AFM). In addition to experimentally measured current-voltage (I-V) curves, the transport properties were addressed computationally and modeled theoretically. The key objectives of this project were to 1) investigate the impact of molecular structure on hole and electron charge transport, 2) understand the nature of the charge carriers and their structure-transport properties through long (films, and open opportunities to engineer improved electronic functionality into molecular devices.

  3. Epitaxial growth and new phase of single crystal Dy by molecular beam epitaxy

    International Nuclear Information System (INIS)

    Yang, Kai-Yueh; Homma, Hitoshi; Schuller, I.K.

    1987-09-01

    We have grown two novel epitaxial phases of dysprosium (Dy) on vanadium (V) by molecular beam epitaxy technique. Surface and bulk structures are studied by in-situ reflection high energy electron diffraction (RHEED) and x-ray diffraction techniques. The new hcp phases are ∼4% expanded uniformly in-plane (0001), and ∼9% and ∼4% expanded out of plane along the c-axes for non-interrupted and interrupted deposition case, respectively. We also observed (2 x 2), (3 x 3), and (4 x 4) Dy surface reconstruction patterns and a series of transitions as the Dy film thickness increases. 12 refs., 3 figs

  4. Molecular dynamics simulations of RNA: An in silico single molecule approach

    Czech Academy of Sciences Publication Activity Database

    McDowell, S.E.; Špačková, Naďa; Šponer, Jiří; Walter, N.G.

    2006-01-01

    Roč. 85, č. 2 (2006), s. 169-184 ISSN 0006-3525 R&D Projects: GA ČR(CZ) GA203/05/0009; GA ČR(CZ) GA203/05/0388; GA AV ČR(CZ) 1QS500040581; GA MŠk(CZ) LC06030; GA MŠk(CZ) LC512 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z40550506 Keywords : hydration and cation binding * molecular dynamics * RNA Subject RIV: BO - Biophysics Impact factor: 2.480, year: 2006

  5. Single-asperity contributions to multi-asperity wear simulated with molecular dynamics

    International Nuclear Information System (INIS)

    Eder, S J; Cihak-Bayr, U; Bianchi, D

    2016-01-01

    We use a molecular dynamics approach to simulate the wear of a rough ferrite surface due to multiple hard, abrasive particles under variation of normal pressure, grinding direction, and particle geometry. By employing a clustering algorithm that incorporates some knowledge about the grinding process such as the main grinding direction, we can break down the total wear volume into contributions from the individual abrasive particles in a time-resolved fashion. The resulting analysis of the simulated grinding process allows statements on wear particle generation, distribution, and stability depending on the initial topography, the grinding angle, the normal pressure, as well as the abrasive shape and orientation with respect to the surface. (paper)

  6. Molecular Genetic Characterization of Individual Cancer Cells Isolated via Single-Cell Printing.

    Directory of Open Access Journals (Sweden)

    Julian Riba

    Full Text Available Intratumoral genetic heterogeneity may impact disease outcome. Gold standard for dissecting clonal heterogeneity are single-cell analyses. Here, we present an efficient workflow based on an advanced Single-Cell Printer (SCP device for the study of gene variants in single cancer cells. To allow for precise cell deposition into microwells the SCP was equipped with an automatic dispenser offset compensation, and the 384-microwell plates were electrostatically neutralized. The ejection efficiency was 99.7% for fluorescent beads (n = 2304 and 98.7% for human cells (U-2 OS or Kasumi-1 cancer cell line, acute myeloid leukemia [AML] patient; n = 150. Per fluorescence microscopy, 98.8% of beads were correctly delivered into the wells. A subset of single cells (n = 81 was subjected to whole genome amplification (WGA, which was successful in all cells. On empty droplets, a PCR on LINE1 retrotransposons yielded no product after WGA, verifying the absence of free-floating DNA in SCP-generated droplets. Representative gene variants identified in bulk specimens were sequenced in single-cell WGA DNA. In U-2 OS, 22 of 25 cells yielded results for both an SLC34A2 and TET2 mutation site, including cells harboring the SLC34A2 but not the TET2 mutation. In one cell, the TET2 mutation analysis was inconclusive due to allelic dropout, as assessed via polymorphisms located close to the mutation. Of Kasumi-1, 23 of 33 cells with data on both the KIT and TP53 mutation site harbored both mutations. In the AML patient, 21 of 23 cells were informative for a TP53 polymorphism; the identified alleles matched the loss of chromosome arm 17p. The advanced SCP allows efficient, precise and gentle isolation of individual cells for subsequent WGA and routine PCR/sequencing-based analyses of gene variants. This makes single-cell information readily accessible to a wide range of applications and can provide insights into clonal heterogeneity that were indeterminable solely by

  7. Exciton Binding Energy of Monolayer WS2

    Science.gov (United States)

    Zhu, Bairen; Chen, Xi; Cui, Xiaodong

    2015-03-01

    The optical properties of monolayer transition metal dichalcogenides (TMDC) feature prominent excitonic natures. Here we report an experimental approach to measuring the exciton binding energy of monolayer WS2 with linear differential transmission spectroscopy and two-photon photoluminescence excitation spectroscopy (TP-PLE). TP-PLE measurements show the exciton binding energy of 0.71 +/- 0.01 eV around K valley in the Brillouin zone.

  8. STM studies of synthetic peptide monolayers

    Science.gov (United States)

    Bergeron, David J.; Clauss, Wilfried; Pilloud, Denis L.; Leslie Dutton, P.; Johnson, Alan T.

    1998-08-01

    We have used scanning probe microscopy to investigate self-assembled monolayers of chemically synthesized peptides. We find that the peptides form a dense uniform monolayer, above which is found a sparse additional layer. Using scanning tunneling microscopy, submolecular resolution can be obtained, revealing the alpha helices which constitute the peptide. The nature of the images is not significantly affected by the incorporation of redox cofactors (hemes) in the peptides.

  9. Synthesis of a molecularly defined single-active site heterogeneous catalyst for selective oxidation of N-heterocycles.

    Science.gov (United States)

    Zhang, Yujing; Pang, Shaofeng; Wei, Zhihong; Jiao, Haijun; Dai, Xingchao; Wang, Hongli; Shi, Feng

    2018-04-13

    Generally, a homogeneous catalyst exhibits good activity and defined active sites but it is difficult to recycle. Meanwhile, a heterogeneous catalyst can easily be reused but its active site is difficult to reveal. It is interesting to bridge the gap between homogeneous and heterogeneous catalysis via controllable construction of a heterogeneous catalyst containing defined active sites. Here, we report that a molecularly defined, single-active site heterogeneous catalyst has been designed and prepared via the oxidative polymerization of maleimide derivatives. These polymaleimide derivatives can be active catalysts for the selective oxidation of heterocyclic compounds to quinoline and indole via the recycling of -C=O and -C-OH groups, which was confirmed by tracing the reaction with GC-MS using maleimide as the catalyst and by FT-IR analysis with polymaleimide as the catalyst. These results might promote the development of heterogeneous catalysts with molecularly defined single active sites exhibiting a comparable activity to homogeneous catalysts.

  10. Insight into a Novel p53 Single Point Mutation (G389E by Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Maria Cristina De Rosa

    2010-12-01

    Full Text Available The majority of inactivating mutations of p53 reside in the central core DNA binding domain of the protein. In this computational study, we investigated the structural effects of a novel p53 mutation (G389E, identified in a patient with congenital adrenal hyperplasia, which is located within the extreme C-terminal domain (CTD of p53, an unstructured, flexible region (residues 367–393 of major importance for the regulation of the protein. Based on the three-dimensional structure of a carboxyl-terminal peptide of p53 in complex with the S100B protein, which is involved in regulation of the tumor suppressor activity, a model of wild type (WT and mutant extreme CTD was developed by molecular modeling and molecular dynamics simulation. It was found that the G389E amino acid replacement has negligible effects on free p53 in solution whereas it significantly affects the interactions of p53 with the S100B protein. The results suggest that the observed mutation may interfere with p53 transcription activation and provide useful information for site-directed mutagenesis experiments.

  11. Mass spectrometric analysis of monolayer protected nanoparticles

    Science.gov (United States)

    Zhu, Zhengjiang

    Monolayer protected nanoparticles (NPs) include an inorganic core and a monolayer of organic ligands. The wide variety of core materials and the tunable surface monolayers make NPs promising materials for numerous applications. Concerns related to unforeseen human health and environmental impacts of NPs have also been raised. In this thesis, new analytical methods based on mass spectrometry are developed to understand the fate, transport, and biodistributions of NPs in the complex biological systems. A laser desorption/ionization mass spectrometry (LDI-MS) method has been developed to characterize the monolayers on NP surface. LDI-MS allows multiple NPs taken up by cells to be measured and quantified in a multiplexed fashion. The correlations between surface properties of NPs and cellular uptake have also been explored. LDI-MS is further coupled with inductively coupled plasma mass spectrometry (ICP-MS) to quantitatively measure monolayer stability of gold NPs (AuNPs) and quantum dots (QDs), respectively, in live cells. This label-free approach allows correlating monolayer structure and particle size with NP stability in various cellular environments. Finally, uptake, distribution, accumulation, and excretion of NPs in higher order organisms, such as fish and plants, have been investigated to understand the environmental impact of nanomaterials. The results indicate that surface chemistry is a primary determinant. NPs with hydrophilic surfaces are substantially less toxic and present a lower degree of bioaccumulation, making these nanomaterials attractive for sustainable nanotechnology.

  12. Reversible photoswitching of azobenzene-based monolayers physisorbed on a mica surface.

    Science.gov (United States)

    El Garah, Mohamed; Palmino, Frank; Cherioux, Frederic

    2010-01-19

    The formation of compact and large-scale self-assembled monolayers (SAMs) adsorbed on a mica surface has been achieved by insertion of alkyl chains on azobenzene derivatives, leading to strong intermolecular van der Waals interactions and hydrogen bonding. The reversible photoswitching of monolayers was investigated by monitoring the variation of the thickness of the SAMs during the cis-trans isomerization of the azobenzene cores with an atomic force microscope (AFM). The absence of covalent bonds between molecules and substrate induces a molecular diffusion which leads to the complete isomerization of the molecules constituting the SAMs.

  13. UV-induced reaction kinetics in dilinoleoylphosphatidylcholine monolayers with incorporated photosensitizers

    Directory of Open Access Journals (Sweden)

    DEJAN MARKOVIC

    2006-04-01

    Full Text Available Mixed insoluble monolayers (Langmuir films of 1,2-di-O-linoleoyl-3-sn-phosphatidylcholine (1,2-DLPC and incorporated benzophenone-type photosensitizers at an air-water interface were exposed to prolonged UV-irradiation. The irradiation was initiated at a particular fixed molecular packing value. Changes of the surface pressure during the UV-induced photolysis of the sensitizers were plotted against the irradiation time and the results were interpreted in terms of themolecular lipid / sensitizer ratios inside the monolayers.

  14. Perspective: Thermal and thermoelectric transport in molecular junctions

    Science.gov (United States)

    Cui, Longji; Miao, Ruijiao; Jiang, Chang; Meyhofer, Edgar; Reddy, Pramod

    2017-03-01

    With the advent of molecular electronics, tremendous attention has been paid towards understanding the structure-function relationship of molecular junctions. Understanding how heat is transported, dissipated, and converted into electricity in molecular junctions is of great importance for designing thermally robust molecular circuits and high-performance energy conversion devices. Further, the study of thermal and thermoelectric phenomena in molecular junctions provides novel insights into the limits of applicability of classical laws. Here, we present a review of the computational and experimental progress made in probing thermoelectric effects, thermal conduction, heat dissipation, and local heating/cooling in self-assembled monolayer and single molecule junctions. We also discuss some outstanding challenges and potential future directions.

  15. Clinical and molecular characterization of 112 single-center patients with Neurofibromatosis type 1.

    Science.gov (United States)

    Corsello, Giovanni; Antona, Vincenzo; Serra, Gregorio; Zara, Federico; Giambrone, Clara; Lagalla, Luca; Piccione, Maria; Piro, Ettore

    2018-04-04

    The aim of this retrospective study was to define clinical and molecular characteristics of a large sample of neurofibromatosis type 1 (NF1) patients, as well as to evaluate mutational spectrum and genotype-phenotype correlation. NF1 is a relatively common neurogenetic disorder (1:2500-1:3000 individuals). It is caused by mutations of the NF1 gene on chromosome 17ql1.2, with autosomal dominant pattern of inheritance and wide phenotypical variability. Café-au-lait spots (CALs), cutaneous and/or subcutaneous neurofibromas (CNFs/SCNFs), skinfold freckling, skeletal abnormalities, Lisch nodules of the iris and increased risk of learning and intellectual disabilities, as well as tumors of the nervous system and other organs are its main clinical features. The preliminary group collected 168 subjects with clinical suspicion of NF1. They were evaluated following the National Institutes of Health (NIH) criteria for NF1, revised by Gutmann et al. 1997, integrated for 67 of them by molecular testing. According to these references, 112 of 168 patients were diagnosed as NF1. The sample was characterized by an equal sex ratio (57 males, 55 females) and age distribution ranging from 10 days to 60 years of age (mean age, 13 years). A wide spectrum of clinical features has been observed in our patients. Mutational analysis resulted positive in 51 cases (76%). Twenty-four mutations detected in our cohort have not been reported to date. This study may contribute to a better definition of genotypic and phenotypic features of NF1 patients, with respect to further insights into the clinical characterization of the disease. In addition, an amplification of the spectrum of mutations in the NF1 gene has been documented.

  16. Molecular identification of broomrape species from a single seed by High Resolution Melting analysis

    Directory of Open Access Journals (Sweden)

    Mathieu Rolland

    2016-12-01

    Full Text Available Broomrapes are holoparasitic plants spreading through seeds. Each plant produces hundreds of thousands of seeds which remain viable in the soils for decades. To limit their spread, drastic measures are being taken and the contamination of a commercial seed lot by a single broomrape seed can lead to its rejection. Considering that broomrapes species identification from a single seed is extremely difficult even for trained botanists and that among all the described species, only a few are really noxious for the crops, numerous seed lots are rejected because of the contamination by seeds of non-noxious broomrape species. The aim of this study was to develop and evaluate a High Resolution Melting assay identifying the eight most noxious and common broomrape species (P. aegyptiaca, O. cernua, O. crenata, O. cumana, O. foetida, O. hederae, O. minor, and P. ramosa from a single seed. Based on trnL and rbcL plastidial genes amplification, the designed assay successfully identifies O. cumana, O. cernua, O. crenata, O. minor, O. hederae, and O. foetida; P. ramosa and P. aegyptiaca can be differentiated from other species but not from each other. Tested on 50 seed lots, obtained results perfectly matched identifications performed by sequencing. Through the analysis of common seed lots by different analysts, the reproducibility of the assay was evaluated at 90 %. Despite an original sample preparation process it was not possible to extract enough DNA from some seeds (10% of the samples. The described assay fulfils its objectives and allows an accurate identification of the targeted broomrape species. It can be used to identify contaminants in commercial seed lots or for any other purpose. The assay might be extended to vegetative material.

  17. Molecular Identification of Broomrape Species from a Single Seed by High Resolution Melting Analysis.

    Science.gov (United States)

    Rolland, Mathieu; Dupuy, Aurélie; Pelleray, Aude; Delavault, Philippe

    2016-01-01

    Broomrapes are holoparasitic plants spreading through seeds. Each plant produces hundreds of thousands of seeds which remain viable in the soils for decades. To limit their spread, drastic measures are being taken and the contamination of a commercial seed lot by a single broomrape seed can lead to its rejection. Considering that broomrapes species identification from a single seed is extremely difficult even for trained botanists and that among all the described species, only a few are really noxious for the crops, numerous seed lots are rejected because of the contamination by seeds of non-noxious broomrape species. The aim of this study was to develop and evaluate a High Resolution Melting assay identifying the eight most noxious and common broomrape species ( Phelipanche aegyptiaca , Orobanche cernua , O. crenata, O. cumana , O. foetida , O. hederae , O. minor , and P. ramosa ) from a single seed. Based on trn L and rbc L plastidial genes amplification, the designed assay successfully identifies O. cumana , O. cernua , O. crenata , O. minor , O. hederae , and O. foetida ; P. ramosa , and P. aegyptiaca can be differentiated from other species but not from each other. Tested on 50 seed lots, obtained results perfectly matched identifications performed by sequencing. Through the analysis of common seed lots by different analysts, the reproducibility of the assay was evaluated at 90%. Despite an original sample preparation process it was not possible to extract enough DNA from some seeds (10% of the samples). The described assay fulfills its objectives and allows an accurate identification of the targeted broomrape species. It can be used to identify contaminants in commercial seed lots or for any other purpose. The assay might be extended to vegetative material.

  18. Molecular adsorption study of nicotine and caffeine on single-walled carbon nanotubes from first principles

    Science.gov (United States)

    Lee, Hyung-June; Kim, Gunn; Kwon, Young-Kyun

    2013-08-01

    Using first-principles calculations, we investigate the electronic structures and binding properties of nicotine and caffeine adsorbed on single-walled carbon nanotubes to determine whether CNTs are appropriate for filtering or sensing nicotine and caffeine molecules. We find that caffeine adsorbs more strongly than nicotine. The different binding characteristics are discussed by analyzing the modification of the electronic structure of the molecule-adsorbed CNTs. We also calculate the quantum conductance of the CNTs in the presence of nicotine or caffeine adsorbates and demonstrate that the influence of caffeine is stronger than nicotine on the conductance of the host CNT.

  19. Highly simplified small molecular phosphorescent organic light emitting devices with a solution-processed single layer

    Directory of Open Access Journals (Sweden)

    Zhaokui Wang

    2011-09-01

    Full Text Available A highly simplified single layer solution-processed phosphorescent organic light emitting device (PHOLED with the maximum ηP 11.5 lm/W corresponding to EQE 9.6% has been demonstrated. The solution-processed device is shown having comparable even exceeding device performance to vacuum-processed PHOLED. The simplified device design strategy represents a pathway toward large area, low cost and high efficiency OLEDs in the future. The charge injection and conduction mechanisms in two solution- and vacuum-processed devices are also investigated by evaluating the temperature dependence of current density – voltage characteristics.

  20. Effect of Structure on the Interactions between Five Natural Antimicrobial Compounds and Phospholipids of Bacterial Cell Membrane on Model Monolayers

    Directory of Open Access Journals (Sweden)

    Stella W. Nowotarska

    2014-06-01

    Full Text Available Monolayers composed of bacterial phospholipids were used as model membranes to study interactions of the naturally occurring phenolic compounds 2,5-dihydroxybenzaldehyde and 2-hydroxy-5-methoxybenzaldehyde, and the plant essential oil compounds carvacrol, cinnamaldehyde, and geraniol, previously found to be active against both Gram-positive and Gram-negative pathogenic microorganisms. The lipid monolayers consist of 1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine (DPPE, 1,2-dihexa- decanoyl-sn-glycero-3-phospho-(1'-rac-glycerol (DPPG, and 1,1',2,2'-tetratetradecanoyl cardiolipin (cardiolipin. Surface pressure–area (π-A and surface potential–area (Δψ-A isotherms were measured to monitor changes in the thermodynamic and physical properties of the lipid monolayers. Results of the study indicated that the five compounds modified the three lipid monolayer structures by integrating into the monolayer, forming aggregates of antimicrobial –lipid complexes, reducing the packing effectiveness of the lipids, increasing the membrane fluidity, and altering the total dipole moment in the monolayer membrane model. The interactions of the five antimicrobial compounds with bacterial phospholipids depended on both the structure of the antimicrobials and the composition of the monolayers. The observed experimental results provide insight into the mechanism of the molecular interactions between naturally-occurring antimicrobial compounds and phospholipids of the bacterial cell membrane that govern activities.

  1. Humidity-controlled rectification switching in ruthenium-complex molecular junctions

    Science.gov (United States)

    Atesci, Huseyin; Kaliginedi, Veerabhadrarao; Celis Gil, Jose A.; Ozawa, Hiroaki; Thijssen, Joseph M.; Broekmann, Peter; Haga, Masa-aki; van der Molen, Sense Jan

    2018-02-01

    Although molecular rectifiers were proposed over four decades ago1,2, until recently reported rectification ratios (RR) were rather moderate2-11 (RR 101). This ceiling was convincingly broken using a eutectic GaIn top contact12 to probe molecular monolayers of coupled ferrocene groups (RR 105), as well as using scanning tunnelling microscopy-break junctions13-16 and mechanically controlled break junctions17 to probe single molecules (RR 102-103). Here, we demonstrate a device based on a molecular monolayer in which the RR can be switched by more than three orders of magnitude (between RR 100 and RR ≥ 103) in response to humidity. As the relative humidity is toggled between 5% and 60%, the current-voltage (I-V) characteristics of a monolayer of di-nuclear Ru-complex molecules reversibly change from symmetric to strongly asymmetric (diode-like). Key to this behaviour is the presence of two localized molecular orbitals in series, which are nearly degenerate in dry circumstances but become misaligned under high humidity conditions, due to the displacement of counter ions (PF6-). This asymmetric gating of the two relevant localized molecular orbital levels results in humidity-controlled diode-like behaviour.

  2. Single-electron capture collisions of ground and metastable Ne2+ ions with molecular gases

    Science.gov (United States)

    Hasan, A.; Abu-Haija, O.; Harris, J.; Elkafrawy, T.; Kayani, A.; Kamber, E. Y.

    2013-09-01

    Using the translational energy-gain spectroscopy technique, we have measured the energy-gain spectra and absolute total cross sections for single-electron capture in collisions of Ne2+ with N2, CO2 and H2O at laboratory impact energies between 50 and 400 eV and 0° scattering angles. In all the collision systems studied here, reaction channels have been observed which indicate the presence of the long-lived metastable states of (2s2 2p4 1D and 1S) in the Ne2+ incident beam. These measurements also indicate that capture from the metastable states into excited states of the projectile product ions is the most important inelastic process. Contributions from capture accompanied by the excitation and ionization of the target product are also detected. In addition, the energy dependence of the total single-electron capture cross sections is studied and found to slowly increase with increasing impact energy. The present data are compared with the theoretical calculations of the classical over the barrier, extended classical over the barrier and Landau-Zener models.

  3. Elucidation of polymer induced DNA condensation. Visualisation at the single molecular level

    International Nuclear Information System (INIS)

    Martin, Alison Laura

    2002-01-01

    DNA condensation is a phenomenon that has stimulated interest from biologists, physicists, and polymer chemists for decades. At the cellular level, this process is key to the packing of DNA within the nuclear envelope, and the exposure of the appropriate nucleic acid sequences in order for transcription to occur, and proteins to be produced. The advent of gene therapy has led to an invigoration of this subject area. In order to successfully deliver to, and transfect target cells, many delivery vectors condense the therapeutic DNA into small compact particles. The nature of these particles have a considerable influence on the ultimate expression of the administered nucleic acid material. In addition, at its most fundamental, DNA itself is a classical polyelectrolyte polymer, the behaviour of which has applicability to other charged polymeric systems. There are two core interwound themes to this investigation; the visualisation of DNA condensate morphology at ultra-resolution, and the elucidation of the mechanisms of formation of these structures. The technique of atomic force microscopy is central to these investigations. Methodologies have been devised allowing the visualisation of the tertiary structure and conformational behaviour of individual DNA condensates in near in situ conditions. Condensation of the nucleic acid material has been induced by two classes of cation; small molecular cations, like those found within eukaryotic cells, and a range of cationic polymers. The cationic polymers investigated all have considerable potential as gene delivery vectors. The resultant DNA condensates have been assessed and contrasted in terms of their tertiary morphology, lateral dimensions, and structural volume. Assessments have also been made regarding the influence of the molecular architecture of the cationic moiety and the nature of the input nucleic acid material on the resultant DNA condensates. With regard to the elucidation of the mechanisms of DNA condensate

  4. Graphene growth by conversion of aromatic self-assembled monolayers

    Energy Technology Data Exchange (ETDEWEB)

    Turchanin, Andrey [Institute of Physical Chemistry, Friedrich Schiller University Jena (Germany); Jena Center for Soft Matter (JCSM), Jena (Germany); Center for Energy and Environmental Chemistry Jena (CEEC), Jena (Germany); Abbe Center of Photonics (ACP), Jena (Germany)

    2017-11-15

    Despite present diversity of graphene production methods there is still a high demand for improvement of the existing production schemes or development of new. Here a method is reviewed to produce graphene employing aromatic self-assembled monolayers (SAMs) as molecular precursors. This method is based on electron irradiation induced crosslinking of aromatic SAMs resulting in their conversion into carbon nanomembranes (CNMs) with high thermal stability and subsequent pyrolysis of CNMs into graphene in vacuum or in the inert atmosphere. Depending on the production conditions, such as chemical structure of molecular precursors, irradiation and annealing parameters, various properties of the produced graphene sheets including shape, crystallinity, thickness, optical properties and electric transport can be adjusted. The assembly of CNM/graphene van der Waals heterostructures opens a flexible route to non-destructive chemical functionalization of graphene for a variety of applications in electronic and photonic devices. (copyright 2017 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  5. Perforated monolayers. Progress report, July 1, 1990--December 31, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Regen, S.L.

    1992-12-01

    Goal of this research program is to create ultrathin organic membranes that possess uniform and adjustable pores ( < 7{angstrom} diameter). Such membranes are expected to possess high permeation selectivity (permselectivity) and high permeability, and to provide the basis for energy-efficient methods of molecular separation. Work carried out has demonstrated feasibility of using ``perforated monolayer``-based composites as molecular sieve membranes. Specifically, composite membranes derived from Langmuir-Blodgett multilayers of the calix[6]arene-based surfactant shown below plus poly[l-(trimethylsilyl)-l-propyne] (PTMSP) were found to exhibit sieving behavior towards He, N{sub 2} and SF{sub 6}. Results of derivative studies that have also been completed are also described in this report.

  6. Temperature-dependent surface density of alkylthiol monolayers on gold nanocrystals

    Science.gov (United States)

    Liu, Xuepeng; Lu, Pin; Zhai, Hua; Wu, Yucheng

    2018-03-01

    Atomistic molecular dynamics (MD) simulations are performed to study the surface density of passivating monolayers of alkylthiol chains on gold nanocrystals at temperatures ranging from 1 to 800 K. The results show that the surface density of alkylthiol monolayer reaches a maximum value at near room temperature (200-300 K), while significantly decreases with increasing temperature in the higher temperature region (> 300 {{K}}), and slightly decreases with decreasing temperature at low temperature (< 200 {{K}}). We find that the temperature dependence of surface ligand density in the higher temperature region is attributed to the substantial ligand desorption induced by the thermal fluctuation, while that at low temperature results from the reduction in entropy caused by the change in the ordering of passivating monolayer. These results are expected helpful to understand the temperature-dependent surface coverage of gold nanocrystals.

  7. Determining molecular orientation via single molecule SERS in a plasmonic nano-gap.

    Science.gov (United States)

    Marshall, Addison R L; Stokes, Jamie; Viscomi, Francesco N; Proctor, John E; Gierschner, Johannes; Bouillard, Jean-Sebastien G; Adawi, Ali M

    2017-11-16

    In this work, plasmonic nano-gaps consisting of a silver nanoparticle coupled to an extended silver film have been fully optimized for single molecule Surface-Enhanced Raman Scattering (SERS) spectroscopy. The SERS signal was found to be strongly dependent on the particle size and the molecule orientation with respect to the field inside the nano-gap. Using Finite Difference Time Domain (FDTD) simulations to complement the experimental measurements, the complex interplay between the excitation enhancement and the emission enhancement of the system as a function of particle size were highlighted. Additionally, in conjunction with Density Functional Theory (DFT), the well-defined field direction in the nano-gap enables to recover the orientation of individual molecules.

  8. A molecular phylogeny shows the single origin of the Pyrenean subterranean Trechini ground beetles (Coleoptera: Carabidae).

    Science.gov (United States)

    Faille, A; Ribera, I; Deharveng, L; Bourdeau, C; Garnery, L; Quéinnec, E; Deuve, T

    2010-01-01

    Trechini ground beetles include some of the most spectacular radiations of cave and endogean Coleoptera, but the origin of the subterranean taxa and their typical morphological adaptations (loss of eyes and wings, depigmentation, elongation of body and appendages) have never been studied in a formal phylogenetic framework. We provide here a molecular phylogeny of the Pyrenean subterranean Trechini based on a combination of mitochondrial (cox1, cyb, rrnL, tRNA-Leu, nad1) and nuclear (SSU, LSU) markers of 102 specimens of 90 species. We found all Pyrenean highly modified subterranean taxa to be monophyletic, to the exclusion of all epigean and all subterranean species from other geographical areas (Cantabrian and Iberian mountains, Alps). Within the Pyrenean subterranean clade the three genera (Geotrechus, Aphaenops and Hydraphaenops) were polyphyletic, indicating multiple origins of their special adaptations to different ways of life (endogean, troglobitic or living in deep fissures). Diversification followed a geographical pattern, with two main clades in the western and central-eastern Pyrenees respectively, and several smaller lineages of more restricted range. Based on a Bayesian relaxed-clock approach, and using as an approximation a standard mitochondrial mutation rate of 2.3% MY, we estimate the origin of the subterranean clade at ca. 10 MY. Cladogenetic events in the Pliocene and Pleistocene were almost exclusively within the same geographical area and involving species of the same morphological type.

  9. Structural and chemical characterization of monofluoro-substituted oligo(phenylene-ethynylene) thiolate self-assembled monolayers on gold.

    Science.gov (United States)

    Hacker, Christina A; Batteas, James D; Garno, Jayne C; Marquez, Manuel; Richter, Curt A; Richter, Lee J; van Zee, Roger D; Zangmeister, Christopher D

    2004-07-20

    Monolayers of oligo(phenylene-ethynylene) (OPE) molecules have exhibited promise in molecular electronic test structures. This paper discusses films formed from a novel molecule within this class, 2-fluoro-4-phenylethynyl-1-[(4-acetylthio)phenylethynyl]benzene (F-OPE). The conditions of self-assembled monolayer (SAM) formation were systematically altered to fabricate reproducible high-quality molecular monolayers from the acetate-protected F-OPE molecule. Detailed characterization of the F-OPE monolayers was performed by using an array of surface probes, including reflection absorbance infrared spectroscopy (RAIRS), contact angle (CA) measurements, spectroscopic ellipsometry (SE), X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), and atomic force microscopy (AFM). XPS and RAIRS established that the SAM formed without removal of the F substituent and without oxidation of the thiol. The monolayer thickness, determined from SE and AFM based nanolithography, was consistent with the formation of a densely packed monolayer. The valence electronic structure of the SAM was consistent with an aromatic structure shifted by the electron-withdrawing fluorine substituent and intermolecular coupling within an oriented array of molecules. Copyright 2004 American Chemical Society

  10. Theoretical Prediction of an Antimony-Silicon Monolayer (penta-Sb2Si): Band Gap Engineering by Strain Effect

    Science.gov (United States)

    Morshedi, Hosein; Naseri, Mosayeb; Hantehzadeh, Mohammad Reza; Elahi, Seyed Mohammad

    2018-04-01

    In this paper, using a first principles calculation, a two-dimensional structure of silicon-antimony named penta-Sb2Si is predicted. The structural, kinetic, and thermal stabilities of the predicted monolayer are confirmed by the cohesive energy calculation, phonon dispersion analysis, and first principles molecular dynamic simulation, respectively. The electronic properties investigation shows that the pentagonal Sb2Si monolayer is a semiconductor with an indirect band gap of about 1.53 eV (2.1 eV) from GGA-PBE (PBE0 hybrid functional) calculations which can be effectively engineered by employing external biaxial compressive and tensile strain. Furthermore, the optical characteristics calculation indicates that the predicted monolayer has considerable optical absorption and reflectivity in the ultraviolet region. The results suggest that a Sb2Si monolayer has very good potential applications in new nano-optoelectronic devices.

  11. Combined single cell AFM manipulation and TIRFM for probing the molecular stability of multilayer fibrinogen matrices

    Energy Technology Data Exchange (ETDEWEB)

    Christenson, W. [Department of Physics, Arizona State University, Tempe, AZ 85287 (United States); Center for Biological Physics, Arizona State University, Tempe, AZ 85287 (United States); Yermolenko, I. [Department of Physics, Arizona State University, Tempe, AZ 85287 (United States); School of Life Sciences, Arizona State University, Tempe, AZ 85287 (United States); Plochberger, B. [Department of Physics, Arizona State University, Tempe, AZ 85287 (United States); Camacho-Alanis, F.; Ros, A. [Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287 (United States); Ugarova, T.P. [School of Life Sciences, Arizona State University, Tempe, AZ 85287 (United States); Ros, R., E-mail: Robert.Ros@asu.edu [Department of Physics, Arizona State University, Tempe, AZ 85287 (United States); Center for Biological Physics, Arizona State University, Tempe, AZ 85287 (United States)

    2014-01-15

    Adsorption of fibrinogen on various surfaces produces a nanoscale multilayer matrix, which strongly reduces the adhesion of platelets and leukocytes with implications for hemostasis and blood compatibility of biomaterials. The nonadhesive properties of fibrinogen matrices are based on their extensibility, ensuing the inability to transduce strong mechanical forces via cellular integrins and resulting in weak intracellular signaling. In addition, reduced cell adhesion may arise from the weaker associations between fibrinogen molecules in the superficial layers of the matrix. Such reduced stability would allow integrins to pull fibrinogen molecules out of the matrix with comparable or smaller forces than required to break integrin–fibrinogen bonds. To examine this possibility, we developed a method based on the combination of total internal reflection fluorescence microscopy, single cell manipulation with an atomic force microscope and microcontact printing to study the transfer of fibrinogen molecules out of a matrix onto cells. We calculated the average fluorescence intensities per pixel for wild-type HEK 293 (HEK WT) and HEK 293 cells expressing leukocyte integrin Mac-1 (HEK Mac-1) before and after contact with multilayered matrices of fluorescently labeled fibrinogen. For contact times of 500 s, HEK Mac-1 cells show a median increase of 57% of the fluorescence intensity compared to 6% for HEK WT cells. The results suggest that the integrin Mac-1-fibrinogen interactions are stronger than the intermolecular fibrinogen interactions in the superficial layer of the matrix. The low mechanical stability of the multilayer fibrinogen surface may contribute to the reduced cell adhesive properties of fibrinogen-coated substrates. We anticipate that the described method can be applied to various cell types to examine their integrin-mediated adhesion to the extracellular matrices with a variable protein composition. - Highlights: • We present a method combining

  12. Synthesis, XRD single crystal structure analysis, vibrational spectral analysis, molecular dynamics and molecular docking studies of 2-(3-methoxy-4-hydroxyphenyl) benzothiazole

    Science.gov (United States)

    Sarau Devi, A.; Aswathy, V. V.; Sheena Mary, Y.; Yohannan Panicker, C.; Armaković, Stevan; Armaković, Sanja J.; Ravindran, Reena; Van Alsenoy, C.

    2017-11-01

    The vibrational spectra and corresponding vibrational assignments of 2-(3-methoxy-4-hydroxyphenyl)benzothiazole is reported. Single crystal XRD data of the title compound is reported and the orientation of methoxy group is cis to nitrogen atom of the thiazole ring. The phenyl ring breathing modes of the title compound are assigned at 1042 and 731 cm-1 theoretically. The charge transfer within the molecule is studied using frontier molecular orbital analysis. The chemical reactivity descriptors are calculated theoretically. The NMR spectral data predicted theoretically are in good agreement with the experimental data. The strong negative region spread over the phenyl rings, nitrogen atom and oxygen atom of the hydroxyl group in the MEP plot is due to the immense conjugative and hyper conjugative resonance charge delocalization of π-electrons. Molecule sites prone to electrophilic attacks have been determined by analysis of ALIE surfaces, while Fukui functions provided further insight into the local reactivity properties of title molecule. Autoxidation properties have been investigated by calculation of bond dissociation energies (BDEs) of hydrogen abstraction, while BDEs of the rest of the single acyclic bonds were valuable for the further investigation of degradation properties. Calculation of radial distribution functions was performed in order to determine which atoms of the title molecule have pronounced interactions with water molecules. The title compound forms a stable complex with aryl hydrocarbon receptor and can be a lead compound for developing new anti-tumor drug. Antimicrobial properties of the title compound was screened against one bacterial culture Escherchia coli and four fungal cultures viz., Aspergillus niger, Pencillum chrysogenum, Saccharomyces cerevisiae and Rhyzopus stolonifer.

  13. Shock-induced plasticity in tantalum single crystals: Interatomic potentials and large-scale molecular-dynamics simulations

    Science.gov (United States)

    Ravelo, R.; Germann, T. C.; Guerrero, O.; An, Q.; Holian, B. L.

    2013-10-01

    We report on large-scale nonequilibrium molecular dynamics simulations of shock wave compression in tantalum single crystals. Two new embedded atom method interatomic potentials of Ta have been developed and optimized by fitting to experimental and density functional theory data. The potentials reproduce the isothermal equation of state of Ta up to 300 GPa. We examined the nature of the plastic deformation and elastic limits as functions of crystal orientation. Shock waves along (100), (110), and (111) exhibit elastic-plastic two-wave structures. Plastic deformation in shock compression along (110) is due primarily to the formation of twins that nucleate at the shock front. The strain-rate dependence of the flow stress is found to be orientation dependent, with (110) shocks exhibiting the weaker dependence. Premelting at a temperature much below that of thermodynamic melting at the shock front is observed in all three directions for shock pressures above about 180 GPa.

  14. Electronic readout of a single nuclear spin using a molecular spin transistor

    Science.gov (United States)

    Vincent, R.; Klyastskaya, S.; Ruben, M.; Wernsdorfer, W.; Balestro, F.

    2012-02-01

    Quantum control of individual spins in condensed matter devices is an emerging field with a wide range of applications ranging from nanospintronics to quantum computing [1,2]. The electron, with its spin and orbital degrees of freedom, is conventionally used as carrier of the quantum information in the devices proposed so far. However, electrons exhibit a strong coupling to the environment leading to reduced relaxation and coherence times. Indeed quantum coherence and stable entanglement of electron spins are extremely difficult to achieve. We propose a new approach using the nuclear spin of an individual metal atom embedded in a single-molecule magnet (SMM). In order to perform the readout of the nuclear spin, the quantum tunneling of the magnetization (QTM) of the magnetic moment of the SMM in a transitor-like set-up is electronically detected. Long spin lifetimes of an individual nuclear spin were observed and the relaxation characteristics were studied. The manipulation of the nuclear spin state of individual atoms embedded in magnetic molecules opens a completely new world, where quantum logic may be integrated.[4pt] [1] L. Bogani, W. Wernsdorfer, Nature Mat. 7, 179 (2008).[0pt] [2] M. Urdampilleta, S. Klyatskaya, J.P. Cleuziou, M. Ruben, W. Wernsdorfer, Nature Mat. 10, 502 (2011).

  15. Inelastic tunneling of electrons through a quantum dot with an embedded single molecular magnet

    Science.gov (United States)

    Chang, Bo; Liang, J.-Q.

    2010-06-01

    We report a theoretical analysis of electron transport through a quantum dot with an embedded biaxial single-molecule magnet (SMM) based on mapping of the many-body interaction-system onto a one-body problem by means of the non-equilibrium Green function technique. It is found that the conducting current exhibits a stepwise behavior and the nonlinear differential conductance displays additional peaks with variation of the sweeping speed and the magnitude of magnetic field. This observation can be interpreted by the interaction of electron-spin with the SMM and the quantum tunneling of magnetization. The inelastic conductance and the corresponding tunneling processes are investigated with normal as well as ferromagnetic electrodes. In the case of ferromagnetic configuration, the coupling to the SMM leads to an asymmetric tunneling magnetoresistance (TMR), which can be enhanced or suppressed greatly in certain regions. Moreover, a sudden TMR-switch with the variation of magnetic field is observed, which is seen to be caused by the inelastic tunneling.

  16. Inelastic tunneling of electrons through a quantum dot with an embedded single molecular magnet

    Energy Technology Data Exchange (ETDEWEB)

    Chang Bo [Institute of Theoretical Physics and Department of Physics, Shanxi University, Taiyuan, Shanxi 030006 (China); Liang, J.-Q., E-mail: jqliang@sxu.edu.c [Institute of Theoretical Physics and Department of Physics, Shanxi University, Taiyuan, Shanxi 030006 (China)

    2010-06-28

    We report a theoretical analysis of electron transport through a quantum dot with an embedded biaxial single-molecule magnet (SMM) based on mapping of the many-body interaction-system onto a one-body problem by means of the non-equilibrium Green function technique. It is found that the conducting current exhibits a stepwise behavior and the nonlinear differential conductance displays additional peaks with variation of the sweeping speed and the magnitude of magnetic field. This observation can be interpreted by the interaction of electron-spin with the SMM and the quantum tunneling of magnetization. The inelastic conductance and the corresponding tunneling processes are investigated with normal as well as ferromagnetic electrodes. In the case of ferromagnetic configuration, the coupling to the SMM leads to an asymmetric tunneling magnetoresistance (TMR), which can be enhanced or suppressed greatly in certain regions. Moreover, a sudden TMR-switch with the variation of magnetic field is observed, which is seen to be caused by the inelastic tunneling.

  17. Sweeter and stronger: enhancing sweetness and stability of the single chain monellin MNEI through molecular design

    Science.gov (United States)

    Leone, Serena; Pica, Andrea; Merlino, Antonello; Sannino, Filomena; Temussi, Piero Andrea; Picone, Delia

    2016-09-01

    Sweet proteins are a family of proteins with no structure or sequence homology, able to elicit a sweet sensation in humans through their interaction with the dimeric T1R2-T1R3 sweet receptor. In particular, monellin and its single chain derivative (MNEI) are among the sweetest proteins known to men. Starting from a careful analysis of the surface electrostatic potentials, we have designed new mutants of MNEI with enhanced sweetness. Then, we have included in the most promising variant the stabilising mutation E23Q, obtaining a construct with enhanced performances, which combines extreme sweetness to high, pH-independent, thermal stability. The resulting mutant, with a sweetness threshold of only 0.28 mg/L (25 nM) is the strongest sweetener known to date. All the new proteins have been produced and purified and the structures of the most powerful mutants have been solved by X-ray crystallography. Docking studies have then confirmed the rationale of their interaction with the human sweet receptor, hinting at a previously unpredicted role of plasticity in said interaction.

  18. Thermal conductivities of single- and multi-layer phosphorene: a molecular dynamics study.

    Science.gov (United States)

    Zhang, Ying-Yan; Pei, Qing-Xiang; Jiang, Jin-Wu; Wei, Ning; Zhang, Yong-Wei

    2016-01-07

    As a new two-dimensional (2D) material, phosphorene has drawn growing attention owing to its novel electronic properties, such as layer-dependent direct bandgaps and high carrier mobility. Herein we investigate the in-plane and cross-plane thermal conductivities of single- and multi-layer phosphorene, focusing on geometrical (sample size, orientation and layer number) and strain (compression and tension) effects. A strong anisotropy is found in the in-plane thermal conductivity with its value along the zigzag direction being much higher than that along the armchair direction. Interestingly, the in-plane thermal conductivity of multi-layer phosphorene is insensitive to the layer number, which is in strong contrast to that of graphene where the interlayer interactions strongly influence the thermal transport. Surprisingly, tensile strain leads to an anomalous increase in the in-plane thermal conductivity of phosphorene, in particular in the armchair direction. Both the in-plane and cross-plane thermal conductivities can be modulated by external strain; however, the strain modulation along the cross-plane direction is more effective and thus more tunable than that along the in-plane direction. Our findings here are of great importance for the thermal management in phosphorene-based nanoelectronic devices and for thermoelectric applications of phosphorene.

  19. Single walled carbon nanotube-based stochastic resonance device with molecular self-noise source

    Science.gov (United States)

    Fujii, Hayato; Setiadi, Agung; Kuwahara, Yuji; Akai-Kasaya, Megumi

    2017-09-01

    Stochastic resonance (SR) is an intrinsic noise usage system for small-signal sensing found in various living creatures. The noise-enhanced signal transmission and detection system, which is probabilistic but consumes low power, has not been used in modern electronics. We demonstrated SR in a summing network based on a single-walled carbon nanotube (SWNT) device that detects small subthreshold signals with very low current flow. The nonlinear current-voltage characteristics of this SWNT device, which incorporated Cr electrodes, were used as the threshold level of signal detection. The adsorption of redox-active polyoxometalate molecules on SWNTs generated additional noise, which was utilized as a self-noise source. To form a summing network SR device, a large number of SWNTs were aligned parallel to each other between the electrodes, which increased the signal detection ability. The functional capabilities of the present small-size summing network SR device, which rely on dense nanomaterials and exploit intrinsic spontaneous noise at room temperature, offer a glimpse of future bio-inspired electronic devices.

  20. Structure-based molecular simulations reveal the enhancement of biased Brownian motions in single-headed kinesin.

    Science.gov (United States)

    Kanada, Ryo; Kuwata, Takeshi; Kenzaki, Hiroo; Takada, Shoji

    2013-01-01

    Kinesin is a family of molecular motors that move unidirectionally along microtubules (MT) using ATP hydrolysis free energy. In the family, the conventional two-headed kinesin was experimentally characterized to move unidirectionally through "walking" in a hand-over-hand fashion by coordinated motions of the two heads. Interestingly a single-headed kinesin, a truncated KIF1A, still can generate a biased Brownian movement along MT, as observed by in vitro single molecule experiments. Thus, KIF1A must use a different mechanism from the conventional kinesin to achieve the unidirectional motions. Based on the energy landscape view of proteins, for the first time, we conducted a set of molecular simulations of the truncated KIF1A movements over an ATP hydrolysis cycle and found a mechanism exhibiting and enhancing stochastic forward-biased movements in a similar way to those in experiments. First, simulating stand-alone KIF1A, we did not find any biased movements, while we found that KIF1A with a large friction cargo-analog attached to the C-terminus can generate clearly biased Brownian movements upon an ATP hydrolysis cycle. The linked cargo-analog enhanced the detachment of the KIF1A from MT. Once detached, diffusion of the KIF1A head was restricted around the large cargo which was located in front of the head at the time of detachment, thus generating a forward bias of the diffusion. The cargo plays the role of a diffusional anchor, or cane, in KIF1A "walking."

  1. Structure-based molecular simulations reveal the enhancement of biased Brownian motions in single-headed kinesin.

    Directory of Open Access Journals (Sweden)

    Ryo Kanada

    Full Text Available Kinesin is a family of molecular motors that move unidirectionally along microtubules (MT using ATP hydrolysis free energy. In the family, the conventional two-headed kinesin was experimentally characterized to move unidirectionally through "walking" in a hand-over-hand fashion by coordinated motions of the two heads. Interestingly a single-headed kinesin, a truncated KIF1A, still can generate a biased Brownian movement along MT, as observed by in vitro single molecule experiments. Thus, KIF1A must use a different mechanism from the conventional kinesin to achieve the unidirectional motions. Based on the energy landscape view of proteins, for the first time, we conducted a set of molecular simulations of the truncated KIF1A movements over an ATP hydrolysis cycle and found a mechanism exhibiting and enhancing stochastic forward-biased movements in a similar way to those in experiments. First, simulating stand-alone KIF1A, we did not find any biased movements, while we found that KIF1A with a large friction cargo-analog attached to the C-terminus can generate clearly biased Brownian movements upon an ATP hydrolysis cycle. The linked cargo-analog enhanced the detachment of the KIF1A from MT. Once detached, diffusion of the KIF1A head was restricted around the large cargo which was located in front of the head at the time of detachment, thus generating a forward bias of the diffusion. The cargo plays the role of a diffusional anchor, or cane, in KIF1A "walking."

  2. Molecular simulation of flavin adenine dinucleotide immobilized on charged single-walled carbon nanotubes for biosensor applications.

    Science.gov (United States)

    Yang, Guang; Kang, Zhengzhong; Ye, Xuesong; Wu, Tao; Zhu, Qin

    2012-12-01

    The reconstitution of apo-glucose oxidase (apo-GOx) on single-walled carbon nanotubes (SWNTs) functionalized with the cofactor, flavin adenine dinucleotide (FAD), greatly improved electron transfer turnover rate of the redox reactions in glucose sensing with glucose sensors. The research reported here is aimed to better understand molecular details of affection of the charging SWNT to the conformational changes of FAD, in order to find a rational design and selection scheme of SWNT which is suitable for the FAD and apo-GOx to perform their reconstitution. In this report, molecular simulations of FAD functionalized differently charged SWNTs were carried outin an aqueous environment, with counterions to maintain total charge neutrality. The conformation and orientation changes were observed by both trajectory and quantitative analyses. The simulation results showed that in both uncharged and positively charged SWNT situations, FAD adsorbed onto SWNT at the end of the simulations, which increased the steric resistance of molecules and hindered the reconstitution of apo-GOx and FAD to some degree. By contrast, FAD functionalized negatively charged SWNT maintained its original conformation largely. In addition, negatively charged SWNT may be the best choice for electron transfer mediator for the reconstitution of apo-GOx on relay-cofactor units associated with electrodes. Copyright © 2012 Elsevier Ltd. All rights reserved.

  3. Dark excitations in monolayer transition metal dichalcogenides

    DEFF Research Database (Denmark)

    Deilmann, Thorsten; Thygesen, Kristian Sommer

    2017-01-01

    Monolayers of transition metal dichalcogenides (TMDCs) possess unique optoelectronic properties, including strongly bound excitons and trions. To date, most studies have focused on optically active excitations, but recent experiments have highlighted the existence of dark states, which are equally...... important in many respects. Here, we use ab initio many-body calculations to unravel the nature of the dark excitations in monolayer MoSe2, MoS2, WSe2, andWS(2). Our results show that all these monolayer TMDCs host dark states as their lowest neutral and charged excitations. We further show that dark...... excitons possess larger binding energies than their bright counterparts while the opposite holds for trions....

  4. Analytical and molecular dynamics studies on the impact loading of single-layered graphene sheet by fullerene

    Science.gov (United States)

    Hosseini-Hashemi, Shahrokh; Sepahi-Boroujeni, Amin; Sepahi-Boroujeni, Saeid

    2018-04-01

    Normal impact performance of a system including a fullerene molecule and a single-layered graphene sheet is studied in the present paper. Firstly, through a mathematical approach, a new contact law is derived to describe the overall non-bonding interaction forces of the "hollow indenter-target" system. Preliminary verifications show that the derived contact law gives a reliable picture of force field of the system which is in good agreements with the results of molecular dynamics (MD) simulations. Afterwards, equation of the transversal motion of graphene sheet is utilized on the basis of both the nonlocal theory of elasticity and the assumptions of classical plate theory. Then, to derive dynamic behavior of the system, a set including the proposed contact law and the equations of motion of both graphene sheet and fullerene molecule is solved numerically. In order to evaluate outcomes of this method, the problem is modeled by MD simulation. Despite intrinsic differences between analytical and MD methods as well as various errors arise due to transient nature of the problem, acceptable agreements are established between analytical and MD outcomes. As a result, the proposed analytical method can be reliably used to address similar impact problems. Furthermore, it is found that a single-layered graphene sheet is capable of trapping fullerenes approaching with low velocities. Otherwise, in case of rebound, the sheet effectively absorbs predominant portion of fullerene energy.

  5. Molecular dynamics study on the evolution of interfacial dislocation network and mechanical properties of Ni-based single crystal superalloys

    Science.gov (United States)

    Li, Nan-Lin; Wu, Wen-Ping; Nie, Kai

    2018-05-01

    The evolution of misfit dislocation network at γ /γ‧ phase interface and tensile mechanical properties of Ni-based single crystal superalloys at various temperatures and strain rates are studied by using molecular dynamics (MD) simulations. From the simulations, it is found that with the increase of loading, the dislocation network effectively inhibits dislocations emitted in the γ matrix cutting into the γ‧ phase and absorbs the matrix dislocations to strengthen itself which increases the stability of structure. Under the influence of the temperature, the initial mosaic structure of dislocation network gradually becomes irregular, and the initial misfit stress and the elastic modulus slowly decline as temperature increasing. On the other hand, with the increase of the strain rate, it almost has no effect on the elastic modulus and the way of evolution of dislocation network, but contributes to the increases of the yield stress and tensile strength. Moreover, tension-compression asymmetry of Ni-based single crystal superalloys is also presented based on MD simulations.

  6. Insight into the wetting of a graphene-mica slit pore with a monolayer of water

    Science.gov (United States)

    Lin, Hu; Schilo, Andre; Kamoka, A. Rauf; Severin, Nikolai; Sokolov, Igor M.; Rabe, Jürgen P.

    2017-05-01

    Scanning force microscopy (SFM) and Raman spectroscopy allow the unraveling of charge doping and strain effects upon wetting and dewetting of a graphene-mica slit pore with water. SFM reveals a wetting monolayer of water, slightly thinner than a single layer of graphene. The Raman spectrum of the dry pore exhibits the D' peak of graphene, which practically disappears upon wetting, and recurs when the water layer dewets the pore. Based on the 2 D - and G -peak positions, the corresponding peak intensities, and the widths, we conclude that graphene on dry mica is charge-doped and variably strained. A monolayer of water in between graphene and mica removes the doping and reduces the strain. We attribute the D' peak to direct contact of the graphene with the ionic mica surface in dry conditions, and we conclude that a complete monolayer of water wetting the slit pore decouples the graphene from the mica substrate both mechanically and electronically.

  7. Point defects and composition in hexagonal group-III nitride monolayers: A first-principles calculation

    Science.gov (United States)

    Gao, Han; Ye, Han; Yu, Zhongyuan; Zhang, Yunzhen; Liu, Yumin; Li, Yinfeng

    2017-12-01

    In this paper, we systematically investigate the structural, electronic and magnetic properties of hexagonal group-III nitride monolayers with point defects and alloying on the basis of first-principles calculations. Six typical point defects including three vacancies and three antisites are modeled in pure AlN, GaN and InN monolayers. The defect-induced modifications of band gaps and magnetic properties are demonstrated. The vacancy of nitrogen, with lowest formation energy, metalizes the semiconducting nitride monolayers. The defects losing single group-III atom introduce net magnetic moment to the systems, while others maintain non-magnetic. For ordered alloy monolayers, the AlGaN and InGaN systems are taken into consideration. The compositional variation is achieved by atomic substitution in supercells with different sizes. We find that the lattice constant and cohesive energy follow good linear relation with concentration while a slight bowing effect is observed for the band gap. These results provide a development in defective and alloy nitride monolayers and extend the potential applications.

  8. Sub-THz Characterisation of Monolayer Graphene

    Directory of Open Access Journals (Sweden)

    Ehsan Dadrasnia

    2014-01-01

    Full Text Available We explore the optical and electrical characteristics of monolayer graphene by using pulsed optoelectronic terahertz time-domain spectroscopy in the frequency range of 325–500 GHz based on fast direct measurements of phase and amplitude. We also show that these parameters can, however, be measured with higher resolution using a free space continuous wave measurement technique associated with a vector network analyzer that offers a good dynamic range. All the scattering parameters (both magnitude and phase are measured simultaneously. The Nicholson-Ross-Weir method is implemented to extract the monolayer graphene parameters at the aforementioned frequency range.

  9. Nonlinear optical studies of organic monolayers

    International Nuclear Information System (INIS)

    Shen, Y.R.

    1988-02-01

    Second-order nonlinear optical effects are forbidden in a medium with inversion symmetry, but are necessarily allowed at a surface where the inversion summary is broken. They are often sufficiently strong so that a submonolayer perturbation of the surface can be readily detected. They can therefore be used as effective tools to study monolayers adsorbed at various interfaces. We discuss here a number of recent experiments in which optical second harmonic generation (SHG) and sum-frequency generation (SFG) are employed to probe and characterize organic monolayers. 15 refs., 5 figs

  10. Investigating phosphonate monolayer stability on ALD oxide surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Branch, Brittany [Nanoscience and Microsystems Engineering and Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131 (United States); Dubey, Manish [Lujan Center, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Anderson, Aaron S. [Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Artyushkova, Kateryna [Nanoscience and Microsystems Engineering and Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131 (United States); Baldwin, J. Kevin [Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Petsev, Dimiter [Nanoscience and Microsystems Engineering and Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131 (United States); Dattelbaum, Andrew M., E-mail: amdattel@lanl.gov [Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)

    2014-01-01

    We report a series of studies aimed at investigating the stability of phosphonate self-assembled monolayers (SAMs) made from octadecylphosphonic acid (ODPA) or a perfluorinated phosphonic acid (PFPA) on hafnium and aluminum oxide surfaces deposited by atomic layer deposition (ALD). The monolayers were deposited by a series of techniques including self-assembly from solution, tethering by aggregation and growth, and the Langmuir–Blodgett (LB) method. SAMs prepared by LB method were primarily used in our stability investigations because they were found to be the most uniform and reproducible. All films deposited on ALD oxide-coated substrates were characterized by means of water contact angle measurements, spectroscopic ellipsometry, X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). XPS data conclusively showed covalent phosphonate formation on both substrates. SAMs formed on both Al{sub 2}O{sub 3} and HfO{sub 2} were stable upon exposure to water. PFPA SAMs on HfO{sub 2} were found to be the most stable SAMs studied here in either water or phosphate buffer (PBS) at room temperature. We also show that similar silane-based SAMs made from octadecyltrichlorosilane (OTS) on silicon oxide (SiO{sub 2}) are less stable in PBS than phosphonate SAMs on atomic layer deposited HfO{sub 2} substrates. These data suggest that phosphonate SAMs should be considered for use in (bio)molecular sensing and actuator devices that utilize ALD and require longer-term stability under aqueous conditions.

  11. Molecular chains and carpets of sexithiophenes on Au(111)

    Science.gov (United States)

    Glowatzki, H.; Duhm, S.; Braun, K.-F.; Rabe, J. P.; Koch, N.

    2007-09-01

    The two organic molecular materials α -sexithiophene (6T) and α,ω -dihexylsexithiophene (DH6T) adsorbed on Au(111) in the (sub)monolayer range were investigated by scanning tunneling microscopy (STM) in order to explore the effect of alkyl substitution on the self-assembly at surfaces. Metal substrate step edges are identified as preferred nucleation sites for 6T, while stable nucleus formation for DH6T occurs at kinks of the Au(111) herringbone reconstruction. At low coverage, 6T forms continuous chains of single-molecular width along Au step edges, involving molecular conformation changes by rotations around C-C bonds of neighboring thiophene units. In contrast, DH6T exhibits no ordered structures in the submonolayer range. At monolayer coverage, substantially different structures were observed for the two molecules. 6T forms rows of molecules with parallel long molecular axes, whereas DH6T forms lines along these axes, where the conjugated cores are embedded in a matrix of hexyl chains. Because of different preferred nucleation sites, 6T forms a continuous molecular carpet on extended Au(111) terraces, whereas DH6T resembles a patchworklike carpet as domain boundaries are induced by the Au(111) herringbone surface structure, leading to reduced domain sizes. Alkylation of 6T thus drastically changes the adsorption behavior and the resulting layer structure on the Au surface. These results should be valuable for developing new directed self-assembly schemes on prepatterned surfaces.

  12. Controlling the formation process and atomic structures of single pyrazine molecular junction by tuning the strength of the metal-molecule interaction.

    Science.gov (United States)

    Kaneko, Satoshi; Takahashi, Ryoji; Fujii, Shintaro; Nishino, Tomoaki; Kiguchi, Manabu

    2017-04-12

    The formation process and atomic structures were investigated for single pyrazine molecular junctions sandwiched by three different Au, Ag, and Cu electrodes using a mechanically controllable break junction technique in ultrahigh vacuum conditions at 300 K. We demonstrated that the formation process of the single-molecule junction crucially depended on the choice of the metal electrodes. While single-molecule junction showing two distinct conductance states were found for the Au electrodes, only the single conductance state was evident for the Ag electrodes, and there was no junction formation for the Cu electrodes. These results suggested that metal-molecule interaction dominates the formation process and probability of the single-molecule junction. In addition to the metal-molecule interaction, temperature affected the formation process of the single-molecule junction. The single pyrazine molecular junction formed between Au electrodes exhibited significant temperature dependence where the junction-formation probability was about 8% at 300 K, while there was no junction-formation at 100 K. Instead of the junction formation, an Au atomic wire was formed at the low temperature. This study provides insight into the tuning of the junction-forming process for single-molecule junctions, which is needed to construct device structures on a single molecule scale.

  13. Photocatalytic oxidation of the organic monolayers on TiO2 surface investigated by in-situ sum frequency generation spectroscopy

    Directory of Open Access Journals (Sweden)

    Yujin Tong

    2015-10-01

    Full Text Available In-situ vibrational sum frequency generation (SFG spectroscopy has been employed to investigate the photocatalytic oxidation of two types of well-ordered organic monolayers, namely, an arachidic acid (AA monolayer prepared by the Langmuir-Blodgett method and an octadecyltrichlorosilane (OTS monolayer prepared by the self-assembling method, on a TiO2 surface under ultraviolet (UV irradiation. The extremely high sensitivity and unique selectivity of the SFG spectroscopy enabled us to directly probe the structural changes in these monolayers during the surface photocatalytic oxidation and further elucidate their reaction mechanisms at a molecular level. It was revealed that the ordering of the monolayers during the photocatalytic reaction is strongly dependent on their interaction with the substrate; the AA monolayer maintains its ordered conformation until the final oxidation stage, while the OTS monolayer shows a large increase in disordering during the initial oxidation stage, indicating a different photocatalytic reaction mechanism of the two monolayers on the TiO2 surface.

  14. Photocatalytic oxidation of the organic monolayers on TiO{sub 2} surface investigated by in-situ sum frequency generation spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Tong, Yujin; Peng, Qiling; Ma, Tongsen; Nishida, Takuma; Ye, Shen, E-mail: ye@cat.hokudai.ac.jp [Catalysis Research Center, Hokkaido University, Sapporo 060-0811 (Japan)

    2015-10-01

    In-situ vibrational sum frequency generation (SFG) spectroscopy has been employed to investigate the photocatalytic oxidation of two types of well-ordered organic monolayers, namely, an arachidic acid (AA) monolayer prepared by the Langmuir-Blodgett method and an octadecyltrichlorosilane (OTS) monolayer prepared by the self-assembling method, on a TiO{sub 2} surface under ultraviolet (UV) irradiation. The extremely high sensitivity and unique selectivity of the SFG spectroscopy enabled us to directly probe the structural changes in these monolayers during the surface photocatalytic oxidation and further elucidate their reaction mechanisms at a molecular level. It was revealed that the ordering of the monolayers during the photocatalytic reaction is strongly dependent on their interaction with the substrate; the AA monolayer maintains its ordered conformation until the final oxidation stage, while the OTS monolayer shows a large increase in disordering during the initial oxidation stage, indicating a different photocatalytic reaction mechanism of the two monolayers on the TiO{sub 2} surface.

  15. Determining the thickness of aliphatic alcohol monolayers covalently attached to silicon oxide surfaces using angle-resolved X-ray photoelectron spectroscopy

    Science.gov (United States)

    Lee, Austin W. H.; Kim, Dongho; Gates, Byron D.

    2018-04-01

    The thickness of alcohol based monolayers on silicon oxide surfaces were investigated using angle-resolved X-ray photoelectron spectroscopy (ARXPS). Advantages of using alcohols as building blocks for the formation of monolayers include their widespread availability, ease of handling, and stability against side reactions. Recent progress in microwave assisted reactions demonstrated the ease of forming uniform monolayers with alcohol based reagents. The studies shown herein provide a detailed investigation of the thickness of monolayers prepared from a series of aliphatic alcohols of different chain lengths. Monolayers of 1-butanol, 1-hexanol, 1-octanol, 1-decanol, and 1-dodecanol were each successfully formed through microwave assisted reactions and characterized by ARXPS techniques. The thickness of these monolayers consistently increased by ∼1.0 Å for every additional methylene (CH2) within the hydrocarbon chain of the reagents. Tilt angles of the molecules covalently attached to silicon oxide surfaces were estimated to be ∼35° for each type of reagent. These results were consistent with the observations reported for thiol based or silane based monolayers on either gold or silicon oxide surfaces, respectively. The results of this study also suggest that the alcohol based monolayers are uniform at a molecular level.

  16. Interaction of plasma apolipoproteins with lipid monolayers

    NARCIS (Netherlands)

    Jackson, R.L.; Pattus, F.; Demel, R.A.

    1979-01-01

    The monolayer technique has been used to study the interaction of lipids with plasma apolipoproteins. Apolipoprotein C-II and C-III from human very low density lipoproteins, apolipoprotein A-I from human high density lipoproteins and arginine-rich protein from swine very low density lipoproteins

  17. Semiconductor monolayer assemblies with oriented crystal faces

    KAUST Repository

    Ma, Guijun

    2012-01-01

    Fabrication of two-dimensional monolayers of crystalline oxide and oxynitride particles was attempted on glass plate substrates. X-Ray diffraction patterns of the assemblies show only specific crystal facets, indicative of the uniform orientation of the particles on the substrate. The selectivity afforded by this immobilization technique enables the organization of randomly distributed polycrystalline powders in a controlled manner.

  18. Shadow mask evaporation through monolayer modified nanostencils

    NARCIS (Netherlands)

    Kolbel, M.; Tjerkstra, R.W.; Brugger, J.P.; van Rijn, C.J.M.; Nijdam, W.; Huskens, Jurriaan; Reinhoudt, David

    2002-01-01

    Gradual clogging of the apertures of nanostencils used as miniature shadow masks in metal evaporations can be reduced by coating the stencil with self-assembled monolayers (SAM). This is quantified by the dimensions (height and volume) of gold features obtained by nanostencil evaporation as measured

  19. Compressibility study of quaternary phospholipid blend monolayers.

    Science.gov (United States)

    Cavalcanti, Leide P; Tho, Ingunn; Konovalov, Oleg; Fossheim, Sigrid; Brandl, Martin

    2011-07-01

    The mechanical properties of liposome membranes are strongly dependent on type and ratio of lipid compounds, which can have important role in drug targeting and release processes when liposome is used as drug carrier. In this work we have used Brewster's angle microscopy to monitor the lateral compression process of lipid monolayers containing as helper lipids either distearoyl phosphatidylethanolamine (DSPE) or dioleoyl phophatidylethanolamine (DOPE) molecules on the Langmuir trough. The compressibility coefficient was determined for lipid blend monolayers containing the helper lipids above, cholesterol, distearoyl phosphatidylcholine (DSPC) and pegylated-DSPE at room temperature. Two variables, the cholesterol fraction and the ratio ρ between the helper lipid (either DSPE or DOPE) and the reference lipid DSPC, were studied by multivariate analysis to evaluate their impact on the compressibility coefficient of the monolayers. The cholesterol level was found to be the most significant variable for DSPE blends while the ratio ρ was the most significant one for DOPE blend monolayers. It was also found that these two variables can exhibit positive interaction and the same compressibility value can be obtained with different blend compositions. Copyright © 2011 Elsevier B.V. All rights reserved.

  20. Mode damping in a commensurate monolayer solid

    DEFF Research Database (Denmark)

    Bruch, Ludwig Walter; Hansen, Flemming Yssing

    1997-01-01

    The normal modes of a commensurate monolayer solid may be damped by mixing with elastic waves of the substrate. This was shown by Hall, Mills, and Black [Phys. Rev. B 32, 4932 (1985)], for perpendicular adsorbate vibrations in the presence of an isotropic elastic medium. That work is generalized...

  1. Imidazolide monolayers for versatile reactive microcontact printing

    NARCIS (Netherlands)

    Hsu, S.H.; Reinhoudt, David; Huskens, Jurriaan; Velders, Aldrik

    2008-01-01

    Imidazolide monolayers prepared from the reaction of amino SAMs with N,N-carbonyldiimidazole (CDI) are used as a versatile platform for surface patterning with amino-, carboxyl- and alcohol-containing compounds through reactive microcontact printing (µCP). To demonstrate the surface reactivity of

  2. Patterned monolayers of nitronyl nitroxide radicals

    NARCIS (Netherlands)

    Mannini, Matteo; Rovai, Donella; Sorace, Lorenzo; Perl, A.; Ravoo, B.J.; Reinhoudt, David

    2008-01-01

    We report here the results of the preliminary characterization of the monolayer obtained both by self-assembling and microcontact printing of a di-alkyl sulfide nitronyl nitroxide derivative, 11-decyl sulfanyl-undecanyl nitronyl nitroxide of which we describe the synthesis. The sulfide unit has been

  3. Fullerene monolayer formation by spray coating

    Czech Academy of Sciences Publication Activity Database

    Červenka, Jiří; Flipse, C.F.J.

    2010-01-01

    Roč. 21, č. 6 (2010), 065302/1-065302/7 ISSN 0957-4484 Institutional research plan: CEZ:AV0Z10100521 Keywords : monolayer * spray coating * fullerene * atomic force microscopy * scanning tunnelling microscopy * electronic structure * graphite * gold Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.644, year: 2010

  4. Elasticity of a quantum monolayer solid

    DEFF Research Database (Denmark)

    Bruch, Ludwig Walter

    1992-01-01

    A perturbation-theory formulation of the zero-temperature elastic constants is used to verify symmetry relations for a (monolayer) triangluar lattice. A generalization of the Cauchy relation between the two elastic constants of the triangular lattice with central-pair-potential interactions...

  5. Monolayer graphene dispersion and radiative cooling for high power LED

    Science.gov (United States)

    Hsiao, Tun-Jen; Eyassu, Tsehaye; Henderson, Kimberly; Kim, Taesam; Lin, Chhiu-Tsu

    2013-10-01

    Molecular fan, a radiative cooling by thin film, has been developed and its application for compact electronic devices has been evaluated. The enhanced surface emissivity and heat dissipation efficiency of the molecular fan coating are shown to correlate with the quantization of lattice modes in active nanomaterials. The highly quantized G and 2D bands in graphene are achieved by our dispersion technique, and then incorporated in an organic-inorganic acrylate emulsion to form a coating assembly on heat sinks (for LED and CPU). This water-based dielectric layer coating has been formulated and applied on metal core printed circuit boards. The heat dissipation efficiency and breakdown voltage are evaluated by a temperature-monitoring system and a high-voltage breakdown tester. The molecular fan coating on heat dissipation units is able to decrease the equilibrium junction temperature by 29.1 ° C, while functioning as a dielectric layer with a high breakdown voltage (>5 kV). The heat dissipation performance of the molecular fan coating applied on LED devices shows that the coated 50 W LED gives an enhanced cooling of 20% at constant light brightness. The schematics of monolayer graphene dispersion, undispersed graphene platelet, and continuous graphene sheet are illustrated and discussed to explain the mechanisms of radiative cooling, radiative/non-radiative, and non-radiative heat re-accumulation.

  6. a Molecular Approach to Electrolyte Solutions: Predicting Phase Behavior and Thermodynamic Properties of Single and Binary-Solvent Systems

    Science.gov (United States)

    Gering, Kevin Leslie

    A molecular formulation based on modern liquid state theory is applied to the properties and phase behavior of electrolyte systems containing volatile species. An electrolyte model based on the exponential modification of the Mean Spherical Approximation (EXP-MSA) is used to describe the cation-cation, cation-anion, and anion-anion distributions of the ionic species. This theory represents an improvement over the nonmodified MSA approach, and goes beyond the usual Debye-Huckel theory and Pitzer correlation for treating concentrated solutions. Electrolyte solutions such as water-salt, ammonia-salt, mixed salts, and mixed -solvent systems are investigated over a wide range of temperatures, pressures, and compositions. The usual salt properties, such as osmotic and mean activity coefficients and other thermodynamic properties (enthalpies), are calculated. The predictions are accurate to saturation limits. In addition, an iterative method is presented that is used to predict vapor-liquid equilibria (VLE) and thermodynamic properties of single-salt multisolvent electrolytes of the form solvent-cosolvent-salt. In this method, a local composition model (LCM) and EXP-MSA theory are combined with traditional phase equilibria relations to estimate the pressures and compositions of a vapor phase in equilibrium with a binary-solvent electrolyte. Also, a pseudo-solvent model is proposed as a means of obtaining a variety of averaged liquid phase electrolyte properties. To predict preferential solvation in mixed solvents, a general framework is developed that is based on predicted solvation numbers of each solvent. Preferential solvation will be shown to influence VLE. Results show that phase equilibria is accurately predicted by the above iterative method. Three mixed-solvent electrolyte systems are investigated: water -ethylene glycol-LiBr, ammonia-water-LiBr, and methanol -water-LiCl. Finally, the above electrolyte model is utilized in predicting design criteria for a single

  7. Shear rheology of lipid monolayers and insights on membrane fluidity

    Science.gov (United States)

    Espinosa, Gabriel; López-Montero, Iván; Monroy, Francisco; Langevin, Dominique

    2011-01-01

    The concept of membrane fluidity usually refers to a high molecular mobility inside the lipid bilayer which enables lateral diffusion of embedded proteins. Fluids have the ability to flow under an applied shear stress whereas solids resist shear deformations. Biological membranes require both properties for their function: high lateral fluidity and structural rigidity. Consequently, an adequate account must include, in addition to viscosity, the possibility for a nonzero shear modulus. This knowledge is still lacking as measurements of membrane shear properties have remained incomplete so far. In the present contribution we report a surface shear rheology study of different lipid monolayers that model distinct biologically relevant situations. The results evidence a large variety of mechanical behavior under lateral shear flow. PMID:21444777

  8. Engineering monolayer poration for rapid exfoliation of microbial membranes.

    Science.gov (United States)

    Pyne, Alice; Pfeil, Marc-Philipp; Bennett, Isabel; Ravi, Jascindra; Iavicoli, Patrizia; Lamarre, Baptiste; Roethke, Anita; Ray, Santanu; Jiang, Haibo; Bella, Angelo; Reisinger, Bernd; Yin, Daniel; Little, Benjamin; Muñoz-García, Juan C; Cerasoli, Eleonora; Judge, Peter J; Faruqui, Nilofar; Calzolai, Luigi; Henrion, Andre; Martyna, Glenn J; Grovenor, Chris R M; Crain, Jason; Hoogenboom, Bart W; Watts, Anthony; Ryadnov, Maxim G

    2017-02-01

    The spread of bacterial resistance to traditional antibiotics continues to stimulate the search for alternative antimicrobial strategies. All forms of life, from bacteria to humans, are postulated to rely on a fundamental host defense mechanism, which exploits the formation of open pores in microbial phospholipid bilayers. Here we predict that transmembrane poration is not necessary for antimicrobial activity and reveal a distinct poration mechanism that targets the outer leaflet of phospholipid bilayers. Using a combination of molecular-scale and real-time imaging, spectroscopy and spectrometry approaches, we introduce a structural motif with a universal insertion mode in reconstituted membranes and live bacteria. We demonstrate that this motif rapidly assembles into monolayer pits that coalesce during progressive membrane exfoliation, leading to bacterial cell death within minutes. The findings offer a new physical basis for designing effective antibiotics.

  9. Evaluating polymeric biomaterial-environment interfaces by Langmuir monolayer techniques.

    Science.gov (United States)

    Schöne, Anne-Christin; Roch, Toralf; Schulz, Burkhard; Lendlein, Andreas

    2017-05-01

    Polymeric biomaterials are of specific relevance in medical and pharmaceutical applications due to their wide range of tailorable properties and functionalities. The knowledge about interactions of biomaterials with their biological environment is of crucial importance for developing highly sophisticated medical devices. To achieve optimal in vivo performance, a description at the molecular level is required to gain better understanding about the surface of synthetic materials for tailoring their properties. This is still challenging and requires the comprehensive characterization of morphological structures, polymer chain arrangements and degradation behaviour. The review discusses selected aspects for evaluating polymeric biomaterial-environment interfaces by Langmuir monolayer methods as powerful techniques for studying interfacial properties, such as morphological and degradation processes. The combination of spectroscopic, microscopic and scattering methods with the Langmuir techniques adapted to polymers can substantially improve the understanding of their in vivo behaviour. © 2017 The Author(s).

  10. Acamprosate permeability across Caco-2 cell monolayer is predominantly paracellular

    DEFF Research Database (Denmark)

    Antonescu, Irina-Elena; Steffansen, Bente

    was mathematically accounting for the unstirred boundary layer permeability (PUBL), the filter permeability (Pf), the intrinsic passive transcellular permeability (Ptrans,0) and Ppara (1-3). The mathematical model thereby accounted for (i) the physical-chemical properties of acamprosate and mannitol (molecular...... role in acamprosate permeability, as only a very low fraction of acamprosate is in the neutral form at pH 7.4. The estimated acamprosate Ppara accounts for nearly 100% of the mathematically determined acamprosate Papp, calc (0.20 ± 0.10 x 10-6 cm/s), which matches well with the experimentally...... in the different regions of the rodent small intestine and colon. Biopharm Drug Dispos. 2017;38(2):94-114. 2. Avdeef A. Leakiness and size exclusion of paracellular channels in cultured epithelial cell monolayers-interlaboratory comparison. Pharm Res. 2010;27(3):480-9. 3. Avdeef A. Absorption and Drug Development...

  11. Quantification of stromal vascular cell mechanics with a linear cell monolayer rheometer

    Energy Technology Data Exchange (ETDEWEB)

    Elkins, Claire M., E-mail: cma9@stanford.edu; Fuller, Gerald G. [Department of Chemical Engineering, Stanford University, Stanford, California 94305 (United States); Shen, Wen-Jun; Khor, Victor K.; Kraemer, Fredric B. [Division of Endocrinology, Gerontology and Metabolism, Stanford University, Stanford, California 94305 and Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304 (United States)

    2015-01-15

    Over the past few decades researchers have developed a variety of methods for measuring the mechanical properties of whole cells, including traction force microscopy, atomic force microscopy (AFM), and single-cell tensile testing. Though each of these techniques provides insight into cell mechanics, most also involve some nonideal conditions for acquiring live cell data, such as probing only one portion of a cell at a time, or placing the cell in a nonrepresentative geometry during testing. In the present work, we describe the development of a linear cell monolayer rheometer (LCMR) and its application to measure the mechanics of a live, confluent monolayer of stromal vascular cells. In the LCMR, a monolayer of cells is contacted on both top and bottom by two collagen-coated plates and allowed to adhere. The top plate then shears the monolayer by stepping forward to induce a predetermined step strain, while a force transducer attached to the top plate collects stress information. The stress and strain data are then used to determine the maximum relaxation modulus recorded after step-strain, G{sub r}{sup 0}, referred to as the zero-time relaxation modulus of the cell monolayer. The present study validates the ability of the LCMR to quantify cell mechanics by measuring the change in G{sub r}{sup 0} of a confluent cell monolayer upon the selective inhibition of three major cytoskeletal components (actin microfilaments, vimentin intermediate filaments, and microtubules). The LCMR results indicate that both actin- and vimentin-deficient cells had ∼50% lower G{sub r}{sup 0} values than wild-type, whereas tubulin deficiency resulted in ∼100% higher G{sub r}{sup 0} values. These findings constitute the first use of a cell monolayer rheometer to quantitatively distinguish the roles of different cytoskeletal elements in maintaining cell stiffness and structure. Significantly, they are consistent with results obtained using single-cell mechanical testing methods

  12. An alternative to the search for single polymorphisms: toward molecular personality scales for the five-factor model.

    Science.gov (United States)

    McCrae, Robert R; Scally, Matthew; Terracciano, Antonio; Abecasis, Gonçalo R; Costa, Paul T

    2010-12-01

    There is growing evidence that personality traits are affected by many genes, all of which have very small effects. As an alternative to the largely unsuccessful search for individual polymorphisms associated with personality traits, the authors identified large sets of potentially related single nucleotide polymorphisms (SNPs) and summed them to form molecular personality scales (MPSs) with from 4 to 2,497 SNPs. Scales were derived from two thirds of a large (N = 3,972) sample of individuals from Sardinia who completed the Revised NEO Personality Inventory (P. T. Costa, Jr., & R. R. McCrae, 1992) and were assessed in a genomewide association scan. When MPSs were correlated with the phenotype in the remaining one third of the sample, very small but significant associations were found for 4 of the 5e personality factors when the longest scales were examined. These data suggest that MPSs for Neuroticism, Openness to Experience, Agreeableness, and Conscientiousness (but not Extraversion) contain genetic information that can be refined in future studies, and the procedures described here should be applicable to other quantitative traits. PsycINFO Database Record (c) 2010 APA, all rights reserved.

  13. Molecular dynamics study of radiation damage and microstructure evolution of zigzag single-walled carbon nanotubes under carbon ion incidence

    Science.gov (United States)

    Li, Huan; Tang, Xiaobin; Chen, Feida; Huang, Hai; Liu, Jian; Chen, Da

    2016-07-01

    The radiation damage and microstructure evolution of different zigzag single-walled carbon nanotubes (SWCNTs) were investigated under incident carbon ion by molecular dynamics (MD) simulations. The radiation damage of SWCNTs under incident carbon ion with energy ranging from 25 eV to 1 keV at 300 K showed many differences at different incident sites, and the defect production increased to the maximum value with the increase in incident ion energy, and slightly decreased but stayed fairly stable within the majority of the energy range. The maximum damage of SWCNTs appeared when the incident ion energy reached 200 eV and the level of damage was directly proportional to incident ion fluence. The radiation damage was also studied at 100 K and 700 K and the defect production decreased distinctly with rising temperature because radiation-induced defects would anneal and recombine by saturating dangling bonds and reconstructing carbon network at the higher temperature. Furthermore, the stability of a large-diameter tube surpassed that of a thin one under the same radiation environments.

  14. A molecular dynamics study on the thermal conductivity of endohedrally functionalized single-walled carbon nanotubes with gold nanowires

    Science.gov (United States)

    Ajori, Shahram; Haghighi, Samieh; Ansari, Reza

    2018-02-01

    The thermal conductivity of endohedrally functionalized single-walled carbon nanotubes (SWCNTs) with gold nanowires (GNWs) is studied by using a series of molecular dynamics (MD) simulations. The effect of geometrical parameters, i.e. length and radius of pure SWCNTs/GNWs/SWCNTs filled with GNWs on the thermal conductivity are investigated. Also, the influence of various structures of GNWs such as pentagonal and multishell-GNWs on the thermal conductivity of the system is explored. The results indicate that as the length of the system rises, the thermal conductivity increases. It is also found that the thermal conductivity of GNWs is considerably lower than that of pure SWCNTs and GNWs@SWCNTs at a constant length of SWCNT or GNWs. For long pure SWCNTs, by increasing the radii of nanotubes, the thermal conductivity increases. Moreover, the thermal conductivity of the multishell-GNWs@SWCNTs is obtained higher than that of pentagonal configurations for the same lengths of SWCNTs. Through inserting the GNWs inside the SWCNTs, by maintaining the natural properties of NWs due to endohedral functionalization, the thermal conductivity is increased. This finding can be used as a benchmark for more efficient design of NEMS based on metallic NWs.

  15. Molecular dynamics for lateral surface adhesion and peeling behavior of single-walled carbon nanotubes on gold surfaces

    International Nuclear Information System (INIS)

    Huang, Pei-Hsing

    2011-01-01

    Highlights: ► Adhesion and peeling behaviors of SWCNTs are investigated by detailed, fully atomistic MD simulations. ► Adhesion energy of SWCNTs are discussed. ► Dynamical behaviors of SWCNTs in low temperature adhesion are analyzed. ► Adhesion strengths of SWCNTs obtained from MD simulations are compared with the predictions of Hamaker theory and JKR model. - Abstract: Functional gecko-inspired adhesives have attracted a lot of research attention in the last decade. In this work, the lateral surface adhesion and normal peeling-off behavior of single-walled carbon nanotubes (SWCNTs) on gold substrates are investigated by performing detailed, fully atomistic molecular dynamics (MD) simulations. The effects of the diameter and adhered length of CNTs on the adhesive properties were systematically examined. The simulation results indicate that adhesion energies between the SWCNTs and the Au surface varied from 220 to 320 mJ m −2 over the reported chirality range. The adhesion forces on the lateral surface and the tip of the nanotubes obtained from MD simulations agree very well with the predictions of Hamaker theory and Johnson–Kendall–Roberts (JKR) model. The analyses of covalent bonds indicate that the SWCNTs exhibited excellent flexibility and extensibility when adhering at low temperatures (∼100 K). This mechanism substantially increases adhesion time compared to that obtained at higher temperatures (300–700 K), which makes SWCNTs promising for biomimetic adhesives in ultra-low temperature surroundings.

  16. Interactions of gaseous HNO3 and water with individual and mixed alkyl self-assembled monolayers at room temperature.

    Science.gov (United States)

    Nishino, Noriko; Hollingsworth, Scott A; Stern, Abraham C; Roeselová, Martina; Tobias, Douglas J; Finlayson-Pitts, Barbara J

    2014-02-14

    The major removal processes for gaseous nitric acid (HNO3) in the atmosphere are dry and wet deposition onto various surfaces. The surface in the boundary layer is often covered with organic films, but the interaction of gaseous HNO3 with them is not well understood. To better understand the factors controlling the uptake of gaseous nitric acid and its dissociation in organic films, studies were carried out using single component and mixtures of C8 and C18 alkyl self-assembled monolayers (SAMs) attached to a germanium (Ge) attenuated total reflectance (ATR) crystal upon which a thin layer of SiOx had been deposited. For comparison, diffuse reflectance infrared Fourier transform spectrometry (DRIFTS) studies were also carried out using a C18 SAM attached to the native oxide layer on the surface of silicon powder. These studies show that the alkyl chain length and order/disorder of the SAMs does not significantly affect the uptake or dissociation/recombination of molecular HNO3. Thus, independent of the nature of the SAM, molecular HNO3 is observed up to 70-90% relative humidity. After dissociation, molecular HNO3 is regenerated on all SAM surfaces when water is removed. Results of molecular dynamics simulations are consistent with experiments and show that defects and pores on the surfaces control the uptake, dissociation and recombination of molecular HNO3. Organic films on surfaces in the boundary layer will certainly be more irregular and less ordered than SAMs studied here, therefore undissociated HNO3 may be present on surfaces in the boundary layer to a greater extent than previously thought. The combination of this observation with the results of recent studies showing enhanced photolysis of nitric acid on surfaces suggests that renoxification of deposited nitric acid may need to be taken into account in atmospheric models.

  17. Voltammetry and Molecular Assembly of G-quadruplex DNAzyme on Single-crystal Au(111)-electrode Surfaces – Hemin as an Electrochemical Intercalator

    DEFF Research Database (Denmark)

    Zhang, Ling; Ulstrup, Jens; Zhang, Jingdong

    2016-01-01

    ). The target DNZyme is formed from a single-strand OGN with 12 guanines and iron (III) porphyrin IX (hemin), and assembles on Au(111) by the mercapto alkyl linker. The DNAzyme monolayers exhibit a strong pair of redox peaks at 0.0 V (NHE) at pH 7 in acetate buffer, shifted positively by about 50 mV compared......DNA quadruplexes (qs’s) are a class of “non-canonical” oligonucleotides (OGNs) composed of stacked guanine (G) quartets generally stabilized by monovalent cations. Metal porphyrins selectively bind to G-qs complexes to form DNAzyme, which can exhibit peroxidase and other catalytic activity similar...... to free hemin physisorbed on the Au(111). The voltammetric signal of DNZyme is enhanced 15 times, indicative that hemin is strongly bound to the immobilized 12G-qs and in well-defined orientation favorable for interfacial ET with a rate constant of 6.0 s−1. The G-quartet structures with a size of 1.6 ± 0...

  18. Formation of n-Alkyl Monolayers by Organomercury Deposition on Gold

    Czech Academy of Sciences Publication Activity Database

    Scholz, F.; Kaletová, Eva; Stensrud, Elizabeth; Ford, W. E.; Kohutová, Anna; Mucha, Malgorzata; Stibor, Ivan; Michl, Josef; Wrochem von, F.

    2013-01-01

    Roč. 4, č. 16 (2013), s. 2624-2629 ISSN 1948-7185 R&D Projects: GA ČR GA203/07/1619; GA ČR GA203/09/0705 EU Projects: European Commission(XE) 213382 - FUNMOL; European Commission(XE) 227756 - DIPOLAR ROTOR ARRAY Institutional support: RVO:61388963 Keywords : self-assembled monolayers * ray photoelectron-spectroscopy * altitudinal molecular rotors Subject RIV: CC - Organic Chemistry Impact factor: 6.687, year: 2013

  19. Dominant effects of first monolayer energetics at donor/acceptor interfaces on organic photovoltaics.

    Science.gov (United States)

    Izawa, Seiichiro; Nakano, Kyohei; Suzuki, Kaori; Hashimoto, Kazuhito; Tajima, Keisuke

    2015-05-20

    Energy levels of the first monolayer are manipulated at donor/acceptor interfaces in planar heterojunction organic photovoltaics by using molecular self-organization. A "cascade" energy landscape allows thermal-activation-free charge generation by photoirradiation, destabilizes the energy of the interfacial charge-transfer state, and suppresses bimolecular charge recombination, resulting in a higher open-circuit voltage and fill factor. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Electronic properties of organic monolayers and molecular devices

    Indian Academy of Sciences (India)

    ... 59652 Villeneuve d'Ascq Cedex, France; Centre de Recherche en Sciences et Technologies de l'Information et de la Communication, Université de Reims, BP 1039, 51687 Reims Cedex 2, France; Laboratoire de Microscopies et d'Etudes de Nanostructures, Université de Reims, BP 1039, 51687 Reims Cedex 2, France ...

  1. Properties of oxidized phospholipid monolayers: An atomistic molecular dynamics study

    Czech Academy of Sciences Publication Activity Database

    Khabiri, Morteza; Roeselová, Martina; Cwiklik, Lukasz

    519-520, 5 Jan (2012), s. 93-99 ISSN 0009-2614 R&D Projects: GA MŠk ME09064; GA MŠk LC512 Grant - others:ESF EUROMEMBRANE(XE) MEM/09/E006 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z40400503 Keywords : dioleoylphosphatidylcholine (DOPC) * pulmonary surfactant * oxidative stress Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.145, year: 2012

  2. Electronic properties of organic monolayers and molecular devices

    Indian Academy of Sciences (India)

    34, 433 (2001). [14] Y Chen, G-Y Jung, D A A Ohlberg, X Li, D R Stewart, J O Jeppesen, K A Nielsen,. J F Stoddart and R S Williams, Nanotechnology 14, 462 (2003). [15] Y Chen, D A A Ohlberg, X Li, D R Stewart, R S Williams, J O Jeppesen, K A. Nielsen, J F Stoddart, D L Olynick and E Anderson, Appl. Phys. Lett. 82, 1610.

  3. Orientation modulation of a synthetic polypeptide in self-assembled monolayers: a TOF-SIMS study.

    Science.gov (United States)

    Leufgen, Kirsten; Mutter, Manfred; Vogel, Horst; Szymczak, Wilfried

    2003-07-23

    Structure and orientation of molecules are key properties of functionalized surfaces. Using time-of-flight secondary ion mass spectrometry (TOF-SIMS), here we investigate how to modulate these parameters upon the immobilization process varying the conditions of self-assembly. The molecule of interest, a template-assembled synthetic protein (TASP), consists of a central peptide ring with orthogonally arranged residues. Thioalkane chains allow the directed self-assembly of the molecule on a gold surface; four serine residues on the opposite side of the ring can be used as anchoring sites for various functional sensing molecules. The TASP conformation and its orientation in self-assembled monolayers (SAMs) play a central role for the accessibility of these serine residues. To study the influence of the self-assembly conditions, two series of samples were prepared. Pure TASP monolayers of different surface densities are compared to mixed TASP/alkanethiol monolayers prepared by sequential adsorption varying sequence and particular incubation times as well as by coadsorption modifying incubation times and TASP/alkanethiol mass ratios. Switching the TASP orientation from a state where the molecules are lying flat on the surface to an upright orientation turned out to be possible by inserting the TASP into a preformed alkanethiol monolayer of an appropriate surface density. This study demonstrates that TOF-SIMS is an excellent tool not only to investigate the surface composition, but also the molecular structure of functionalized surfaces.

  4. Effect of density and structure on dynamics within self-assembled monolayers

    Science.gov (United States)

    Stevens, Derrick; Scott, Mary; Bochinski, Jason; Clarke, Laura

    2009-03-01

    Previously, we have observed interacting dynamics within self-assembled alkylsiloxane monolayers, and characterized this motion via sensitive dielectric spectroscopy (along with more traditional techniques such as ellipsometry, contact angle, and force microscopy). In these monolayers, molecules are covalently bound to the surface and thus cannot spontaneously change density, as in an adsorbate system. We identified this relaxation as akin to the polyethylene-like glass transition observed in polymers with phase-segregated alkyl side chains [1]. As a next step, we deliberately manipulated the physical structure of the monolayers (via different film growth procedures and/or post-deposition heat treating) and the monolayer density (from ˜10% to full coverage), and observed the resultant changes in dynamics. This experimental system may prove a useful model for more complex materials, such as glassy polymers or traditional molecular glasses, where density cannot be explicitly tuned. As density increases, the steepness index increases, indicating a more complex or fragile relaxation. At low densities, the motion has an almost-Arrhenius dependence on temperature. [1] M.C. Scott, D.R. Stevens, J.R. Bochinski, L.I. Clarke, ACS Nano. DOI: 10.1021/nn800543j.

  5. Aggregation of Puroindoline in Phospholipid Monolayers Spread at the Air-Liquid Interface

    Science.gov (United States)

    Dubreil, L.; Vié, V.; Beaufils, S.; Marion, D.; Renault, A.

    2003-01-01

    Puroindolines, cationic and cystine-rich low molecular weight lipid binding proteins from wheat seeds, display unique foaming properties and antimicrobial activity. To unravel the mechanism involved in these properties, the interaction of puroindoline-a (PIN-a) with dipalmitoylphosphatidylcholine (DPPC) and dipalmitoylphosphatidylglycerol (DPPG) monolayers was studied by coupling Langmuir-Blodgett and imaging techniques. Compression isotherms of PIN-a/phospholipid monolayers and adsorption of PIN-a to lipid monolayers showed that the protein interacted strongly with phospholipids, especially with the anionic DPPG. The electrostatic contribution led to the formation of a highly stable lipoprotein monolayer. Confocal laser scanning microscopy and atomic force microscopy showed that PIN-a was mainly inserted in the liquid-expanded phase of the DPPC, where it formed an aggregated protein network and induced the fusion of liquid-condensed domains. For DPPG, the protein partitioned in both the liquid-expanded and liquid-condensed phases, where it was aggregated. The extent of protein aggregation was related both to the physical state of phospholipids, i.e., condensed or expanded, and to the electrostatic interactions between lipids and PIN-a. Aggregation of PIN-a at air-liquid and lipid interfaces could account for the biological and technological properties of this wheat lipid binding protein. PMID:14507728

  6. Electrochemistry and bioelectrochemistry towards the single-molecule level: Theoretical notions and systems

    International Nuclear Information System (INIS)

    Zhang Jingdong; Chi Qijin; Albrecht, Tim; Kuznetsov, Alexander M.; Grubb, Mikala; Hansen, Allan G.; Wackerbarth, Hainer; Welinder, Anne C.; Ulstrup, Jens

    2005-01-01

    Surface structures controlled at the nanometer and single-molecule levels, with functions crucially determined by interfacial electron transfer (ET) are broadly reported in recent years, with different kinds of electrochemically controlled nanoscale/single molecule systems. One is the broad class of metallic and semiconductor-based nanoparticles, nano-arrays, nanotubes, and nanopits. Others are based on self-assembled molecular monolayers. The latter extend to bioelectrochemical systems with redox metalloproteins and DNA-based molecules as targets. We overview here some recent achievements in areas of interfacial electrochemical ET systems, mapped to the nanoscale and single-molecule levels. Focus is on both experimental and theoretical studies in our group. Systems addressed are organized monolayers of redox active transition metal complexes, and metalloproteins and metalloenzymes on single-crystal Au(1 1 1)-electrode surfaces. These systems have been investigated by voltammetry, spectroscopy, microcantilever technology, and scanning probe microscopy. A class of Os-complexes has shown suitable as targets for electrochemical in situ scanning tunnelling microscopy (STM), with close to single-molecule scanning tunnelling spectroscopic (STS) features. Mapping of redox metalloproteins from the three major classes, i.e. blue copper proteins, heme proteins, and iron-sulfur proteins, at the monolayer and single-molecule levels have also been achieved. In situ STM and spectroscopy of redox molecules and biomolecules have been supported by new theoretical frames, which extend established theory of interfacial electrochemical ET. The electrochemical nanoscale and single-molecule systems discussed are compared with other recent nanoscale and single-molecule systems with conspicuous device-like properties, particularly unimolecular rectifiers and single-molecule transistors. Both of these show analogies to electrochemical in situ STM features of redox molecules and

  7. Laccase immobilized on a mixed thiol monolayer on Au(111) – structure-dependent activity towards oxygen reduction

    International Nuclear Information System (INIS)

    Traunsteiner, Christoph; Sek, Slawomir; Huber, Veronika; Valero-Vidal, Carlos; Kunze-Liebhäuser, Julia

    2016-01-01

    Immobilization of high-potential multicopper oxidases like laccase from Trametes versicolor (TvLc) on cathode surfaces in an orientation that enables direct electron transfer (DET) to the active center allows to profit from the enzyme’s low overpotential towards the oxygen reduction reaction (ORR). In this work, TvLc is immobilized on mixed self-assembled monolayers (SAMs) of thiolates on Au(111). The SAMs consist of two species, a linker molecule, thiolated veratric acid (tVA) with a moiety similar to the enzyme’s natural substrates, and a diluent molecule, 3-mercaptopropionic acid (MPA), which increases the lateral distance between neighboring tVA molecules when incorporated between the linkers. In this work we study the effect of linker separation on enzyme activity. Electrochemical scanning tunneling microscopy (EC-STM) is used to determine the molecular arrangement of the two species in two different SAMs. After enzyme immobilization, negligible enzymatic activity is found on a monolayer, where a separation between tVA and MPA phases is observed. This is explained by the close packing of tVA linkers, which prevents access to the enzyme’s active center. Maximum bioelectrocatalytic currents at low overpotentials are measured on a SAM, where tVA and MPA homogeneously mix in a single phase. The increased distance between isolated linkers allows for induced-fit binding of TvLc to the linker moiety, which leads to a proper orientation of the enzyme and allows for DET from the electrode through the linker molecule to the enzyme’s active center.

  8. A primary battery-on-a-chip using monolayer graphene

    Science.gov (United States)

    Iost, Rodrigo M.; Crespilho, Frank N.; Kern, Klaus; Balasubramanian, Kannan

    2016-07-01

    We present here a bottom-up approach for realizing on-chip on-demand batteries starting out with chemical vapor deposition-grown graphene. Single graphene monolayers contacted by electrode lines on a silicon chip serve as electrodes. The anode and cathode are realized by electrodeposition of zinc and copper respectively onto graphene, leading to the realization of a miniature graphene-based Daniell cell on a chip. The electrolyte is housed partly in a gel and partly in liquid form in an on-chip enclosure molded using a 3d printer or made out of poly(dimethylsiloxane). The realized batteries provide a stable voltage (∼1.1 V) for many hours and exhibit capacities as high as 15 μAh, providing enough power to operate a pocket calculator. The realized batteries show promise for deployment as on-chip power sources for autonomous systems in lab-on-a-chip or biomedical applications.

  9. Miscibility of dl-α-tocopherol β-glucoside in DPPC monolayer at air/water and air/solid interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Neunert, G. [Department of Physics and Biophysics, Poznan University of Life Sciences, 60-637 Poznan (Poland); Makowiecki, J.; Piosik, E.; Hertmanowski, R. [Faculty of Technical Physics, Poznan University of Technology, 60-965 Poznan (Poland); Polewski, K. [Department of Physics and Biophysics, Poznan University of Life Sciences, 60-637 Poznan (Poland); Martynski, T., E-mail: tomasz.martynski@put.poznan.pl [Faculty of Technical Physics, Poznan University of Technology, 60-965 Poznan (Poland)

    2016-10-01

    The role of newly synthesized tocopherol glycosidic derivative in modifying molecular organization and phase transitions of phospholipid monolayer at the air/water interface has been investigated. Two-component Langmuir films of dl-α-tocopheryl β-D-glucopyranoside (BG) mixed with dipalmitoyl phosphatidylcholine (DPPC) in the whole range of mole fractions were formed at the water surface. An analysis of surface pressure versus mean molecular area (π-A) isotherms and Brewster angle microscope images showed that the presence of BG molecules changes the structure and packing of the DPPC monolayer in a BG concentration dependent manner. BG molecules incorporated into DPPC monolayer inhibit its liquid expanded to liquid condensed phase transition proportionally to the BG concentration. The monolayers were also transferred onto solid substrates and visualized using an atomic force microscope. The results obtained indicate almost complete miscibility of BG and DPPC in the monolayers at surface pressures present in the biological cell membrane (30-35·10{sup -3} N·m{sup -1}) for a BG mole fraction as high as 0.3. This makes the monolayer less packed and more disordered, leading to an increased permeability. The results support our previous molecular dynamics simulation data. - Highlights: • Langmuir films of α-tocopherol derivative with DPPC was studied thermodynamically. • Mixed DPPC/BG films were transferred onto mica substrates for topography imaging by using AFM. • Miscibility of BG/DPPC films at surface pressures present in membranes was observed up to MF = 0.3.

  10. Molecular dynamics simulations of the structure and single-particle dynamics of mixtures of divalent salts and ionic liquids

    Science.gov (United States)

    Gómez-González, Víctor; Docampo-Álvarez, Borja; Cabeza, Oscar; Fedorov, Maxim; Lynden-Bell, Ruth M.; Gallego, Luis J.; Varela, Luis M.

    2015-09-01

    We report a molecular dynamics study of the structure and single-particle dynamics of mixtures of a protic (ethylammonium nitrate) and an aprotic (1-butyl-3-methylimidazolium hexaflurophosphate [BMIM][PF6]) room-temperature ionic liquids doped with magnesium and calcium salts with a common anion at 298.15 K and 1 atm. The solvation of these divalent cations in dense ionic environments is analyzed by means of apparent molar volumes of the mixtures, radial distribution functions, and coordination numbers. For the protic mixtures, the effect of salt concentration on the network of hydrogen bonds is also considered. Moreover, single-particle dynamics of the salt cations is studied by means of their velocity autocorrelation functions and vibrational densities of states, explicitly analyzing the influence of salt concentration, and cation charge and mass on these magnitudes. The effect of the valency of the salt cation on these properties is considered comparing the results with those for the corresponding mixtures with lithium salts. We found that the main structural and dynamic features of the local solvation of divalent cations in ionic liquids are similar to those of monovalent salts, with cations being localized in the polar nanoregions of the bulk mixture coordinated in monodentate and bidentate coordination modes by the [NO3]- and [PF6]- anions. However, stronger electrostatic correlations of these polar nanoregions than in mixtures with salts with monovalent cations are found. The vibrational modes of the ionic liquid (IL) are seen to be scarcely affected by the addition of the salt, and the effect of mass and charge on the vibrational densities of states of the dissolved cations is reported. Cation mass is seen to exert a deeper influence than charge on the low-frequency vibrational spectra, giving a red shift of the vibrational modes and a virtual suppression of the higher energy vibrational modes for the heavier Ca2+ cations. No qualitative difference with

  11. Epitaxial growth by monolayer restricted galvanic displacement

    Directory of Open Access Journals (Sweden)

    Vasilić Rastko

    2012-01-01

    Full Text Available The development of a new method for epitaxial growth of metals in solution by galvanic displacement of layers pre-deposited by underpotential deposition (UPD was discussed and experimentally illustrated throughout the lecture. Cyclic voltammetry (CV and scanning tunneling microscopy (STM are employed to carry out and monitor a “quasi-perfect”, two-dimensional growth of Ag on Au(111, Cu on Ag(111, and Cu on Au(111 by repetitive galvanic displacement of underpotentially deposited monolayers. A comparative study emphasizes the displacement stoichiometry as an efficient tool for thickness control during the deposition process and as a key parameter that affects the deposit morphology. The excellent quality of layers deposited by monolayer-restricted galvanic displacement is manifested by a steady UPD voltammetry and ascertained by a flat and uniform surface morphology maintained during the entire growth process.

  12. Kinetic proofreading at single molecular level: aminoacylation of tRNA(Ile and the role of water as an editor.

    Directory of Open Access Journals (Sweden)

    Mantu Santra

    Full Text Available Proofreading/editing in protein synthesis is essential for accurate translation of information from the genetic code. In this article we present a theoretical investigation of efficiency of a kinetic proofreading mechanism that employs hydrolysis of the wrong substrate as the discriminatory step in enzyme catalytic reactions. We consider aminoacylation of tRNA(Ile which is a crucial step in protein synthesis and for which experimental results are now available. We present an augmented kinetic scheme and then employ methods of stochastic simulation algorithm to obtain time dependent concentrations of different substances involved in the reaction and their rates of formation. We obtain the rates of product formation and ATP hydrolysis for both correct and wrong substrates (isoleucine and valine in our case, respectively, in single molecular enzyme as well as ensemble enzyme kinetics. The present theoretical scheme correctly reproduces (i the amplitude of the discrimination factor in the overall rates between isoleucine and valine which is obtained as (1.8×10(2.(4.33×10(2 = 7.8×10(4, (ii the rates of ATP hydrolysis for both Ile and Val at different substrate concentrations in the aminoacylation of tRNA(Ile. The present study shows a non-michaelis type dependence of rate of reaction on tRNA(Ile concentration in case of valine. The overall editing in steady state is found to be independent of amino acid concentration. Interestingly, the computed ATP hydrolysis rate for valine at high substrate concentration is same as the rate of formation of Ile-tRNA(Ile whereas at intermediate substrate concentration the ATP hydrolysis rate is relatively low. We find that the presence of additional editing domain in class I editing enzyme makes the kinetic proofreading more efficient through enhanced hydrolysis of wrong product at the editing CP1 domain.

  13. Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in AMPLE.

    Science.gov (United States)

    Rigden, Daniel J; Thomas, Jens M H; Simkovic, Felix; Simpkin, Adam; Winn, Martyn D; Mayans, Olga; Keegan, Ronan M

    2018-03-01

    Molecular replacement (MR) is the predominant route to solution of the phase problem in macromolecular crystallography. Although routine in many cases, it becomes more effortful and often impossible when the available experimental structures typically used as search models are only distantly homologous to the target. Nevertheless, with current powerful MR software, relatively small core structures shared between the target and known structure, of 20-40% of the overall structure for example, can succeed as search models where they can be isolated. Manual sculpting of such small structural cores is rarely attempted and is dependent on the crystallographer's expertise and understanding of the protein family in question. Automated search-model editing has previously been performed on the basis of sequence alignment, in order to eliminate, for example, side chains or loops that are not present in the target, or on the basis of structural features (e.g. solvent accessibility) or crystallographic parameters (e.g. B factors). Here, based on recent work demonstrating a correlation between evolutionary conservation and protein rigidity/packing, novel automated ways to derive edited search models from a given distant homologue over a range of sizes are presented. A variety of structure-based metrics, many readily obtained from online webservers, can be fed to the MR pipeline AMPLE to produce search models that succeed with a set of test cases where expertly manually edited comparators, further processed in diverse ways with MrBUMP, fail. Further significant performance gains result when the structure-based distance geometry method CONCOORD is used to generate ensembles from the distant homologue. To our knowledge, this is the first such approach whereby a single structure is meaningfully transformed into an ensemble for the purposes of MR. Additional cases further demonstrate the advantages of the approach. CONCOORD is freely available and computationally inexpensive, so

  14. Wilhelmy plate artifacts in elastic monolayers

    Science.gov (United States)

    Witten, T. A.; Wang, Jin; Pocivavsek, L.; Lee, K. Y. C.

    2010-01-01

    A recent article [L. Pocivavsek et al., Soft Matter4, 2019 (2008)] by some of us pointed out difficulties in interpreting Wilhelmy plate measurements on elastic Langmuir monolayers that support anisotropic stress. Using a simplified geometry it showed conditions in which the Wilhelmy plate measures significantly different stress from the ambient stress. We correct a serious error in this analysis and strengthen its conclusion, showing that the Wilhelmy stress and the ambient stress can have opposite signs.

  15. Molecular boxes on a molecular printboard: encapsulation of anionic dyes in immobilized dendrimers

    NARCIS (Netherlands)

    Onclin, S.; Huskens, Jurriaan; Ravoo, B.J.; Reinhoudt, David

    2005-01-01

    Fifth-generation poly(propylene imine) dendrimers, modified with 64 apolar adamantyl groups, have been immobilized on cyclodextrin host monolayers (molecular printboards) on glass by supramolecular microcontact printing. The immobilized dendrimers retain their guest-binding properties and function

  16. Janus monolayers of transition metal dichalcogenides

    KAUST Repository

    Lu, Ang-Yu

    2017-05-15

    Structural symmetry-breaking plays a crucial role in determining the electronic band structures of two-dimensional materials. Tremendous efforts have been devoted to breaking the in-plane symmetry of graphene with electric fields on AB-stacked bilayers or stacked van der Waals heterostructures. In contrast, transition metal dichalcogenide monolayers are semiconductors with intrinsic in-plane asymmetry, leading to direct electronic bandgaps, distinctive optical properties and great potential in optoelectronics. Apart from their in-plane inversion asymmetry, an additional degree of freedom allowing spin manipulation can be induced by breaking the out-of-plane mirror symmetry with external electric fields or, as theoretically proposed, with an asymmetric out-of-plane structural configuration. Here, we report a synthetic strategy to grow Janus monolayers of transition metal dichalcogenides breaking the out-of-plane structural symmetry. In particular, based on a MoS2 monolayer, we fully replace the top-layer S with Se atoms. We confirm the Janus structure of MoSSe directly by means of scanning transmission electron microscopy and energy-dependent X-ray photoelectron spectroscopy, and prove the existence of vertical dipoles by second harmonic generation and piezoresponse force microscopy measurements.

  17. Diffusive spreading and mixing of fluid monolayers

    International Nuclear Information System (INIS)

    Popescu, M N; Dietrich, S; Oshanin, G

    2005-01-01

    The use of ultra-thin, i.e. monolayer, films plays an important role in the emerging field of nano-fluidics. Since the dynamics of such films is governed by the interplay between substrate-fluid and fluid-fluid interactions, the transport of matter in nanoscale devices may eventually be efficiently controlled by substrate engineering. For such films, the dynamics is expected to be captured by two-dimensional lattice-gas models with interacting particles. Using a lattice-gas model and the non-linear diffusion equation derived from the microscopic dynamics in the continuum limit, we study two problems of relevance in the context of nano-fluidics. The first one is the case in which along the spreading direction of a monolayer a mesoscopic-sized obstacle is present, with a particular focus on the relaxation of the fluid density profile upon encountering and passing the obstacle. The second one is the mixing of two monolayers of different particle species which spread side by side following the merger of two chemical lanes, here defined as domains of high affinity for fluid adsorption surrounded by domains of low affinity for fluid adsorption

  18. Exploring atomic defects in molybdenum disulphide monolayers

    KAUST Repository

    Hong, Jinhua

    2015-02-19

    Defects usually play an important role in tailoring various properties of two-dimensional materials. Defects in two-dimensional monolayer molybdenum disulphide may be responsible for large variation of electric and optical properties. Here we present a comprehensive joint experiment-theory investigation of point defects in monolayer molybdenum disulphide prepared by mechanical exfoliation, physical and chemical vapour deposition. Defect species are systematically identified and their concentrations determined by aberration-corrected scanning transmission electron microscopy, and also studied by ab-initio calculation. Defect density up to 3.5 × 10 13 cm \\'2 is found and the dominant category of defects changes from sulphur vacancy in mechanical exfoliation and chemical vapour deposition samples to molybdenum antisite in physical vapour deposition samples. Influence of defects on electronic structure and charge-carrier mobility are predicted by calculation and observed by electric transport measurement. In light of these results, the growth of ultra-high-quality monolayer molybdenum disulphide appears a primary task for the community pursuing high-performance electronic devices.

  19. Simultaneous optimization of monolayer formation factors, including temperature, to significantly improve nucleic acid hybridization efficiency on gold substrates.

    Science.gov (United States)

    Pris, Andrew D; Ostrowski, Sara G; Garaas, Sarah D

    2010-04-20

    Past literature investigations have optimized various single factors used in the formation of thiolated, single stranded DNA (ss-DNA) monolayers on gold. In this study a more comprehensive approach is taken, where a design of experiment (DOE) is employed to simultaneously optimize all of the factors involved in construction of the capture monolayer used in a fluorescence-based hybridization assay. Statistical analysis of the fluorescent intensities resulting from the DOE provides empirical evidence for the importance and the optimal levels of traditional and novel factors included in this investigation. We report on the statistical importance of a novel factor, temperature of the system during monolayer formation of the capture molecule and lateral spacer molecule, and how proper usage of this temperature factor increased the hybridization signal 50%. An initial theory of how the physical factor of heat is mechanistically supplementing the function of the lateral spacer molecule is provided.

  20. Molecular level computational studies of polyethylene and polyacrylonitrile composites containing single walled carbon nanotubes: effect of carboxylic acid functionalization on nanotube-polymer interfacial properties.

    Science.gov (United States)

    Haghighatpanah, Shayesteh; Bohlén, Martin; Bolton, Kim

    2014-01-01

    Molecular dynamics (MD) and molecular mechanics (MM) methods have been used to investigate additive-polymer interfacial properties in single walled carbon nanotube (SWNT)-polyethylene and SWNT-polyacrylonitrile composites. Properties such as the interfacial shear stress and bonding energy are similar for the two composites. In contrast, functionalizing the SWNT with carboxylic acid groups leads to an increase in these properties, with a larger increase for the polar polyacrylonitrile composite. Increasing the percentage of carbon atoms that were functionalized from 1 to 5% also leads to an increase in the interfacial properties. In addition, the interfacial properties depend on the location of the functional groups on the SWNT wall.

  1. Characterization of zinc (Zn) transport across Caco-2 cell monolayers

    Energy Technology Data Exchange (ETDEWEB)

    Wapnir, R.A.; Raffaniello, R.; Shihyu Lee (North Shore Univ. Hospital, Manhasset, NY (United States))

    1991-03-15

    Colonic carcinoma Caco-2 cells grown as a monolayer exhibit many of the characteristics of the small intestine including inducibility of metallothionein by Zn. The authors have now characterized the transport of Zn across confluent, 14 day in vitro Caco-2 monolayers grown on polycarbonate support membranes. Both uptake and transport across the cells were linear for at least 10 min. Zn cell uptake in the mucosa-to-serosa (m-s) direction was saturable, with a K{sub t} = 23.8 {plus minus} 7.8 {mu}M. J{sub max} was 0.46 {plus minus} 0.08 {mu}mol/cm{sup 2} {times} 10 min. Transcellular passage was concentration dependent. In the (s-m) direction, the K{sub t} of Zn cell uptake was 59 {plus minus} 13 {mu}M and that of the transcellular transport was 103 {plus minus} 53 {mu}M. Cell uptake J{sub max} was 0.98 {plus minus} 0.11 {mu}mol/cm{sup 2} {times} 10 min, and transcellular transport J{sub max} was 2.90 {plus minus} 0.47 {mu}mol/cm{sup 2} {times} 10 min. Low molecular weight ligands (histidine, cysteine, proline or glutathione at 1 mM each), added to the mucosal side, did not alter Zn cell uptake or transmembrane passage. Potential transport inhibitors such as ouabain or vanadate, or metabolic inhibitors also had no effect. Zn transport and cell uptake by Caco-2 cells are kinetically comparable to those of in vivo systems and could serve as a valid model for Zn absorption studies.

  2. Conductance switching in a molecular device: The role of side groups and intermolecular interactions

    DEFF Research Database (Denmark)

    Taylor, Jeremy Philip; Brandbyge, Mads; Stokbro, Kurt

    2003-01-01

    flow through the monolayer. However, functionalization has a significant effect on the interactions within the monolayer, so that monolayers with NO2 side groups exhibit local minima associated with twisted conformations of the molecules. We use our results to interpret observations of negative......We report first-principles studies of electronic transport in monolayers of Tour wires functionalized with different side groups. An analysis of the scattering states and transmission eigenchannels suggests that the functionalization does not strongly affect the resonances responsible for current...... differential resistance and molecular memory in monolayers of NO2 functionalized molecules in terms of a twisting of the central ring induced by an applied bias potential....

  3. Interactions between an anticancer drug - edelfosine - and cholesterol in Langmuir monolayers

    International Nuclear Information System (INIS)

    Wiecek, Agata; Dynarowicz-Latka, Patrycja; Minones, J.; Conde, Olga; Casas, Matilde

    2008-01-01

    Edelfosine (1-O-octadecyl-2-O-methyl-rac-glycero-3-phosphocholine, abbr. Et-18-OCH 3 ) is a new generation anticancer drug based on a phospholipids-like structure. Since its mechanism of action is believed to be related to the lipids of cellular membrane, we have investigated the interactions between edelfosine and main mammalian sterol: cholesterol, using the Langmuir monolayer technique. The interactions have been analyzed by comparing the experimental curves with theoretical ones, obtained basing on the additivity rule. The observed contraction together with negative deviations from ideality observed on the mean molecular area (A 12 ) vs film composition plots proves the existence of strong attractive forces between edelfosine and cholesterol, which have been quantified with the excess free energy of mixing (ΔG exc ) values, calculated from the surface pressure-area isotherms datapoints. The most negative values of ΔG exc have been found for the mixture of equimolar composition, proving its highest thermodynamic stability and the existence of the strongest interactions between film components. Thus, it has been postulated that at the surface edelfosine and cholesterol form stable complexes of 1:1 stoichiometry. The analysis of the collapse pressure values for the investigated mixed monolayers proves that films of edelfosine mole fraction ≤ 0.5 are miscible within the whole range of surface pressures, while monolayers richer in edelfosine mix in the pressure region below ca. 37.6 mN/m, which corresponds to the collapse of pure edelfosine monolayer. At this very surface pressure, edelfosine is expelled from the mixed monolayer and the remaining film is composed by surface complexes of high stability. The hypothesis of complex formation explains the results performed in vitro on cell cultures, indicating that the increase of cholesterol content significantly reduces the uptake of edelfosine

  4. Implications of lipid monolayer charge characteristics on their selective interactions with a short antimicrobial peptide.

    Science.gov (United States)

    Ciumac, Daniela; Campbell, Richard A; Xu, Hai; Clifton, Luke A; Hughes, Arwel V; Webster, John R P; Lu, Jian R

    2017-02-01

    Many antimicrobial peptides (AMPs) target bacterial membranes and they kill bacteria by causing structural disruptions. One of the fundamental issues however lies in the selective responses of AMPs to different cell membranes as a lack of selectivity can elicit toxic side effects to mammalian host cells. A key difference between the outer surfaces of bacterial and mammalian cells is the charge characteristics. We report a careful study of the binding of one of the representative AMPs, with the general sequence G(IIKK) 4 I-NH 2 (G 4 ), to the spread lipid monolayers of DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) and DPPG (1,2-dipalmitoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (sodium salt)) mimicking the charge difference between them, using the combined measurements from Langmuir trough, Brewster angle microscopy (BAM) and neutron reflection (NR). The difference in pressure rise upon peptide addition into the subphase clearly demonstrated the different interactions arising from different lipid charge features. Morphological changes from the BAM imaging confirmed the association of the peptide into the lipid monolayers, but there was little difference between them. However, NR studies revealed that the peptide bound 4 times more onto the DPPG monolayer than onto the DPPC monolayer. Importantly, whilst the peptide could only be associated with the head groups of DPPC it was well penetrated into the entire DPPG monolayer, showing that the electrostatic interaction strengthened the hydrophobic interaction and that the combined molecular interactive processes increased the power of G 4 in disrupting the charged membranes. The results are discussed in the context of general antibacterial actions as observed from other AMPs and membrane lytic actions. Copyright © 2016. Published by Elsevier B.V.

  5. Structural properties of iron nitride on Cu(100): An ab-initio molecular dynamics study

    KAUST Repository

    Heryadi, Dodi

    2011-01-01

    Due to their potential applications in magnetic storage devices, iron nitrides have been a subject of numerous experimental and theoretical investigations. Thin films of iron nitride have been successfully grown on different substrates. To study the structural properties of a single monolayer film of FeN we have performed an ab-initio molecular dynamics simulation of its formation on a Cu(100) substrate. The iron nitride layer formed in our simulation shows a p4gm(2x2) reconstructed surface, in agreement with experimental results. In addition to its structural properties, we are also able to determine the magnetization of this thin film. Our results show that one monolayer of iron nitride on Cu(100) is ferromagnetic with a magnetic moment of 1.67 μ B. © 2011 Materials Research Society.

  6. A New Extension of Cauchy–Born Rule for Monolayer Crystal Films

    Directory of Open Access Journals (Sweden)

    Lu Sheng

    2010-01-01

    Full Text Available Abstract By combining with the physical concept of inscribed surface, the standard Cauchy–Born rule (CBR is straightly extended to have a rigorous and accurate atomistic continuum theory for the monolayer crystal films. Resorting to using Tersoff–Brenner potential, the present theory to graphite sheet and single-walled carbon nanotubes (SWCNTs is applied to evaluate the mechanical properties. The results are validated by the comparison with previously reported studies.

  7. Synthesis, Characterization, and Properties of the Two-Dimensional Chalcogenides: Monolayers, Alloys, and Heterostructures

    Science.gov (United States)

    Cain, Jeffrey D.

    Inspired by the triumphs of graphene, and motivated by its limitations, the science and engineering community is rapidly exploring the landscape of other layered materials in their atomically-thin forms. Dominating this landscape are the layered chalcogenides; diverse in chemistry, crystal structure, and properties, there are well over 100 primary members of this material family. Driven by quantum confinement, single layers (or few, in some cases) of these materials exhibit electronic, optical, and mechanical properties that diverge dramatically from their bulk counterparts. While initially isolated in monolayer form via mechanical exfoliation, the field of two-dimensional (2D) materials is being forced evolve to more scalable and reliable methods. Focusing on the chalcogenides (e.g. MoS2, Bi 2Se3, etc.), this dissertation introduces and mechanistically examines multiple novel synthetic approaches for the direct growth of monolayers, heterostructures, and alloys with the desired quality, reproducibility and generality. The first methods described in this thesis are physical vapor transport (PVT) and evaporative thinning (ET): a facile, top-down synthesis approach for creating ultrathin specimens of layered materials down to the two-dimensional limit. Evaporative thinning, applied in this study to the fabrication of A2X3 (Bi2Se3 and Sb2Te3) monolayers, is based on the controlled evaporation of material from initially thick specimens until the 2D limit is reached. The resultant flakes are characterized with a suite of imaging and spectroscopic techniques and the mechanism of ET is investigated via in-situ heating within a transmission electron microscope. Additionally, the basic transport properties of the resultant flakes are probed. The growth of ultrathin GeSe flakes is explored using PVT and the material's basic structure, properties, and stability are addressed. Second, oxide precursor based chemical vapor deposition (CVD) is presented for the direct growth of

  8. Mixed 2D molecular systems: Mechanic, thermodynamic and dielectric properties

    Energy Technology Data Exchange (ETDEWEB)

    Beno, Juraj [Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19-SK Bratislava (Slovakia); Weis, Martin [Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19-SK Bratislava (Slovakia)], E-mail: Martin.Weis@stuba.sk; Dobrocka, Edmund [Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19-SK Bratislava (Slovakia); Institute of Electrical Engineering, Slovak Academy of Sciences, Dubravska cesta 9, 841 04-SK Bratislava (Slovakia); Hasko, Daniel [International Laser Centre, Ilkovicova 3, 812 19-SK Bratislava (Slovakia)

    2008-08-15

    Study of Langmuir monolayers consisting of stearic acid (SA) and dipalmitoylphosphatidylcholine (DPPC) molecules was done by surface pressure-area isotherms ({pi}-A), the Maxwell displacement current (MDC) measurement, X-ray reflectivity (XRR) and atomic force microscopy (AFM) to investigate the selected mechanic, thermodynamic and dielectric properties based on orientational structure of monolayers. On the base of {pi}-A isotherms analysis we explain the creation of stable structures and found optimal monolayer composition. The dielectric properties represented by MDC generated monolayers were analyzed in terms of excess dipole moment, proposing the effect of dipole-dipole interaction. XRR and AFM results illustrate deposited film structure and molecular ordering.

  9. Effects of single nucleotide polymorphisms on human N-acetyltransferase 2 structure and dynamics by molecular dynamics simulation.

    Directory of Open Access Journals (Sweden)

    M Rajasekaran

    Full Text Available BACKGROUND: Arylamine N-acetyltransferase 2 (NAT2 is an important catalytic enzyme that metabolizes the carcinogenic arylamines, hydrazine drugs and chemicals. This enzyme is highly polymorphic in different human populations. Several polymorphisms of NAT2, including the single amino acid substitutions R64Q, I114T, D122N, L137F, Q145P, R197Q, and G286E, are classified as slow acetylators, whereas the wild-type NAT2 is classified as a fast acetylator. The slow acetylators are often associated with drug toxicity and efficacy as well as cancer susceptibility. The biological functions of these 7 mutations have previously been characterized, but the structural basis behind the reduced catalytic activity and reduced protein level is not clear. METHODOLOGY/PRINCIPAL FINDINGS: We performed multiple molecular dynamics simulations of these mutants as well as NAT2 to investigate the structural and dynamical effects throughout the protein structure, specifically the catalytic triad, cofactor binding site, and the substrate binding pocket. None of these mutations induced unfolding; instead, their effects were confined to the inter-domain, domain 3 and 17-residue insert region, where the flexibility was significantly reduced relative to the wild-type. Structural effects of these mutations propagate through space and cause a change in catalytic triad conformation, cofactor binding site, substrate binding pocket size/shape and electrostatic potential. CONCLUSIONS/SIGNIFICANCE: Our results showed that the dynamical properties of all the mutant structures, especially in inter-domain, domain 3 and 17-residue insert region were affected in the same manner. Similarly, the electrostatic potential of all the mutants were altered and also the functionally important regions such as catalytic triad, cofactor binding site, and substrate binding pocket adopted different orientation and/or conformation relative to the wild-type that may affect the functions of the mutants

  10. Monoatomic and cluster beam effect on ToF-SIMS spectra of self-assembled monolayers on gold

    International Nuclear Information System (INIS)

    Tuccitto, N.; Torrisi, V.; Delfanti, I.; Licciardello, A.

    2008-01-01

    Self-assembled monolayers represent well-defined systems that is a good model surface to study the effect of primary ion beams used in secondary ion mass spectrometry. The effect of polyatomic primary beams on both aliphatic and aromatic self-assembled monolayers has been studied. In particular, we analysed the variation of the relative secondary ion yield of both substrate metal-cluster (Au n - ) in comparison with the molecular ions (M - ) and clusters (M x Au y - ) by using Bi + , Bi 3 + , Bi 5 + beams. Moreover, the differences in the secondary ion generation efficiency are discussed. The main effect of the cluster beams is related to an increased formation of low-mass fragments and to the enhancement of the substrate related gold-clusters. The results show that, at variance of many other cases, the static SIMS of self-assembled monolayers does not benefit of the use of polyatomic primary ions.

  11. Formation and Characterization of Self-Assembled Phenylboronic Acid Derivative Monolayers toward Developing Monosaccaride Sensing-Interface

    Directory of Open Access Journals (Sweden)

    Kwangnak Koh

    2007-08-01

    Full Text Available We designed and synthesized phenylboronic acid as a molecular recognitionmodel system for saccharide detection. The phenylboronic acid derivatives that haveboronic acid moiety are well known to interact with saccharides in aqueous solution; thus,they can be applied to a functional interface of saccharide sensing through the formation ofself-assembled monolayer (SAM. In this study, self-assembled phenylboronic acidderivative monolayers were formed on Au surface and carefully characterized by atomicforce microscopy (AFM, Fourier transform infrared reflection absorption spectroscopy(FTIR-RAS, surface enhanced Raman spectroscopy (SERS, and surface electrochemicalmeasurements. The saccharide sensing application was investigated using surface plasmonresonance (SPR spectroscopy. The phenylboronic acid monolayers showed goodsensitivity of monosaccharide sensing even at the low concentration range (1.0 × 10-12 M.The SPR angle shift derived from interaction between phenylboronic acid andmonosaccharide was increased with increasing the alkyl spacer length of synthesizedphenylboronic acid derivatives.

  12. A comparison of the packing behavior of egg phosphatidylcholine with cholesterol and biogenically related sterols in Langmuir monolayer films.

    Science.gov (United States)

    Lintker, Kimberly Borrenpohl; Kpere-Daibo, Peter; Fliesler, Steven J; Serfis, Alexa Barnoski

    2009-09-01

    Cholesterol and selected derivatives were studied as mixed Langmuir monolayers with egg phosphatidylcholine (PC). As an extension of our earlier work, which employed binary sterol/PC mixtures, here we examined ternary mixed monolayers containing cholesterol along with an alternate sterol and PC in different molar ratios, using pressure-area isotherms. The ternary systems behaved similarly to the binary sterol/PC systems reported previously, with similar condensation noted for the sterol/PC films. To better understand how variations in sterol structure affect sterol packing in such membrane monolayers, binary mixtures containing cholestenone, cholestanol, and lanosterol with PC were also studied. Cholestanol behaved similarly to cholesterol when incorporated with PC, while cholestenone and lanosterol did not cause as much film condensation. The observed differences in molecular packing, and attributed sterol structural differences, are considered within the context of sterol/phospholipid mixtures in biological membranes.

  13. C60-propylamine adduct monolayers at the gas/water interface: A Brewster angle microscopy and x-ray scattering study

    International Nuclear Information System (INIS)

    Fukuto, M.; Penanen, K.; Heilmann, R.K.; Pershan, P.S.; Vaknin, D.

    1997-01-01

    Brewster angle microscopy (BAM), x-ray specular reflectivity and grazing-incidence x-ray diffraction (GID) studies of C 60 -propylamine adduct monolayers at the gas/water interface as a function of molecular area are reported. At large molecular areas (A>∼150 Angstrom 2 /molecule), BAM images reveal macroscopic heterogeneity in the film, consisting of the coexistence between regions covered with uniform solidlike monolayer and bare water surface. After compression to a limiting molecular area of 150 Angstrom 2 /molecule, the film is observed to be homogeneous, with the uniform monolayer covering the entire available surface. Both the x-ray reflectivity results and the GID patterns are consistent with the formation of a uniform monolayer at A∼150 Angstrom 2 /molecule, while the little dependence that the GID patterns have on the molecular area for A>∼150 Angstrom 2 /molecule is consistent with the heterogeneity in the film. Upon further compression to higher densities (A 2 /molecule), the x-ray reflectivity results suggest the formation of a partial layer either at the molecule/gas interface or at the molecule/water interface. In this high density regime, the shift in the observed GID pattern with molecular area is much smaller than would be expected if the film were to remain a homogeneous monolayer, also consistent with the formation of an inhomogeneous partial layer. The analysis of the broad GID pattern observed from a uniform monolayer in terms of a model 2D radial distribution function, implies a short range positional correlation, extending to only a few molecular distances. The average nearest neighbor distance (d∼13 Angstrom), extracted from the GID analysis, is consistent with the limiting molecular area (A∼150 Angstrom 2 /molecule) assuming local hexagonal packing. (Abstract Truncated)

  14. Seeing phenomena in flatland: studies of monolayers by fluorescence microscopy.

    Science.gov (United States)

    Knobler, C M

    1990-08-24

    Monolayers formed at the interface between air and water can be seen with fluorescence microscopy. This allows the phase behavior of these monolayers to be determined by direct observation and opens up the possibility of following the kinetics of phase transformations in two-dimensional systems. Some unexpected morphologies have been discovered that provide information about the nature of monolayer phases and have connections to pattern formation in other systems.

  15. Oxygen adsorption and dissociation during the oxidation of monolayer Ti2C

    KAUST Repository

    Gan, Liyong

    2013-08-20

    Exfoliated two-dimensional early transition metal carbides and carbonitrides are usually not terminated by metal atoms but saturated by O, OH, and/or F, thus making it difficult to understand the surface structure evolution and the induced electronic modifications. To fill this gap, density functional theory and molecular dynamics simulations are performed to capture the initial stage of the oxidation process of Ti2C, a prototypical example from the recently fabricated class of two-dimensional carbides and carbonitrides. It is shown that the unsaturated Ti 3d orbitals of the pristine Ti2C surface interact strongly with the approaching O2 molecules, resulting in barrierless O2 dissociation. The diffusion of the dissociated O atoms is also found to be very facile. Molecular dynamics simulations suggest that both dissociation and diffusion are enhanced as the O2 coverage increases to 0.25 monolayer. For a coverage of less than 0.11 monolayer, the adsorbates lead to a minor modification of the electronic properties of Ti2C, while the modification is remarkable at 0.25 monolayer. The formed Ti2CO2 after O saturation is an indirect narrow gap semiconductor (0.33 eV) with high intrinsic carrier concentration at room temperature and high thermodynamic stability at intermediate temperature (e.g., 550 °C).

  16. Piezoelectricity enhancement and bandstructure modification of atomic defect-mediated MoS2 monolayer.

    Science.gov (United States)

    Yu, Sheng; Rice, Quinton; Neupane, Tikaram; Tabibi, Bagher; Li, Qiliang; Seo, Felix Jaetae

    2017-09-13

    Piezoelectricity appears in the inversion asymmetric crystal that converts mechanical deformation to electricity. Two-dimensional transition metal dichalcolgenide (TMDC) monolayers exhibit the piezoelectric effect due to inversion asymmetry. The intrinsic piezoelectric coefficient (e 11 ) of MoS 2 is ∼298 pC m -1 . For the single atomic shift of Mo of 20% along the armchair direction, the piezoelectric coefficient (e 11 ) of MoS 2 with 5 × 5 unit cells was enhanced up to 18%, and significantly modified the band structure. The single atomic shift in the MoS 2 monolayer also induced new energy levels inside the forbidden bandgap. The defect-induced energy levels for a Mo atom shift along the armchair direction are relatively deeper than that for a S atom shift along the same direction. This indicates that the piezoelectricity and band structure of MoS 2 can be engineered by a single atomic shift in the monolayer with multi unit cells for piezo- and opto-electric applications.

  17. MOLECULAR-DYNAMICS SIMULATIONS OF CARBOHYDRATE-BASED SURFACTANTS IN SURFACTANT WATER OIL SYSTEMS

    NARCIS (Netherlands)

    VANBUUREN, AR; BERENDSEN, HJC

    Molecular dynamics simulations of two monolayers of carbohydrate-based surfactants (decyl alpha-glucoside and decyl beta-glucoside) at the interface between liquid decane and liquid water have been performed with the purpose to study the properties of these monolayers on a molecular and atomic

  18. The ice-like water monolayer near the wall makes inner water shells diffuse faster inside a charged nanotube.

    Science.gov (United States)

    Zhou, Xiaoyan; Wang, Chunlei; Wu, Fengmin; Feng, Mei; Li, Jingyuan; Lu, Hangjun; Zhou, Ruhong

    2013-05-28

    Using molecular dynamics simulations, we have investigated the impact of the ice-like water monolayer inside the tube and nearest to the tube wall on the diffusion properties of other inner water shells confined within a charged nanotube. We find that the axial diffusion coefficient of the first water monolayer near the wall monotonously decreases with the charge size on the nanotube, indicating a tighter control of the first monolayer from the larger sized charge. However, for the other water shells, the diffusion coefficients increase when the charge is larger than a critical value qc (~1.0 e). This unexpected phenomenon is attributed to the decreased number of hydrogen bonds between the first monolayer and other inner water shells caused by the very unique hydrogen-bond network patterns in the first ice-like monolayer, which makes it behave like a "hydrophobic water layer." Our findings may have implications for water treatment, non-fouling surfaces, catalysis engine, and biological sensor.

  19. Interfacial properties in Langmuir monolayers and LB films of DPPC with partially fluorinated alcohol (F8H7OH).

    Science.gov (United States)

    Nakahara, Hiromichi; Hirano, Chikayo; Fujita, Ichiro; Shibata, Osamu

    2013-01-01

    Two-component interactions between (perfluorooctyl) heptanol (F8H7OH) and dipalmitoylphosphatidylcholine (DPPC), which is a major component of pulmonary surfactants in mammals, were systematically elucidated using Langmuir monolayers and Langmuir-Blodgett (LB) films of the compounds. The interactions such as the miscibility of the compounds and their phase behavior were examined from thermodynamic and morphological perspectives. The surface pressure (π)-molecular area (A) and surface potential (ΔV)-A isotherms of the binary monolayers containing F8H7OH in different mole fractions (XF8H7OH) were measured simultaneously. The excess Gibbs free energy of mixing of the two components was calculated from the π-A isotherms. The resulting isotherm data were employed to construct a two-dimensional (2D) phase diagram of the system. The phase diagram revealed that the transition pressure as well as the monolayer collapse pressure change with changes in XF8H7OH. These thermodynamic analyses suggested that the miscibility of the two components and the solidification of DPPC monolayers can be induced by the addition of F8H7OH. The phase behavior upon monolayer compression was observed morphologically in situ using Brewster angle microscopy (BAM) and fluorescence microscopy (FM), as well as ex situ using atomic force microscopy (AFM). Interestingly, the AFM-based analysis revealed the formation of monodispersed 2D micelles consisting of F8H7OH at low surface pressures.

  20. Zitterbewegung in monolayer silicene in a magnetic field

    Energy Technology Data Exchange (ETDEWEB)

    Romera, E. [Departamento de Física Atómica, Molecular y Nuclear and Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Fuentenueva s/n, 18071 Granada (Spain); Roldán, J.B. [Departamento de Electrónica y Tecnología de Computadores and CITIC, Universidad de Granada, Fuentenueva s/n, 18071 Granada (Spain); Santos, F. de los [Departamento de Electromagnetismo y Física de la Materia, and Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Fuentenueva s/n, 18071 Granada (Spain)

    2014-07-04

    We study the Zitterbewegung in monolayer silicene under a perpendicular magnetic field. Using an effective Hamiltonian, we have investigated the autocorrelation function and the density currents in this material. Moreover, we have analyzed other types of periodicities of the system (classical and revival times). Finally, the above results are compared with their counterparts in two other monolayer materials subject to a magnetic field: graphene and MoS{sub 2}. - Highlights: • We study Zitterbewegung in monolayer silicene in a magnetic field. • We have analyzed other types of periodicities in silicene. • The above results are compared with other monolayer materials (graphene and MoS{sub 2})

  1. Construction of mixed mercaptopropionic acid/alkanethiol monolayers of controlled composition by structural control of a gold substrate with underpotentially deposited lead atoms.

    Science.gov (United States)

    Shimazu, Katsuaki; Kawaguchi, Toshikazu; Isomura, Takao

    2002-01-30

    Mixed monolayers of 3-mercaptopropionic acid (MPA) and alkanethiols of various chain lengths have been constructed on Au based on a novel concept, namely, control of the composition of the component thiols in mixed monolayers by controlling the surface structure of the substrate. The Au substrate surface was first modified with underpotentially deposited Pb (UPD Pb) atoms, followed by the formation of a self-assembled monolayer (SAM) of alkanethiol. The UPD Pb atoms were then oxidatively stripped from the surface to create vacant site, on which MPA was adsorbed to finally form the mixed monolayers. The surface coverages of Pb, alkanethiol and MPA, and the total numbers of thiols were determined using an electrochemical quartz crystal microbalance, X-ray photoelectron spectroscopy, and reductive desorption voltammetry. These results demonstrate that the surface coverage of MPA in the mixed monolayers is determined by the initial coverage of UPD Pb. Fourier transform infrared spectra also support this conclusion. The observed single peak in the cyclic voltammogram for the reductive desorption shows that MPA and alkanethiol do not form their single-component domains. Scanning tunneling microscopy revealed the single-row pinstripe structure for all the thiol adlayers formed during each step of the preparation. This shows that the surface structure of the mixed monolayers is determined by the structure of the initially formed SAM on Au partially covered with UPD Pb.

  2. Tracing the 4000 year history of organic thin films: From monolayers on liquids to multilayers on solidsa)

    Science.gov (United States)

    Greene, J. E.

    2015-03-01

    The recorded history of organic monolayer and multilayer thin films spans approximately 4000 years. Fatty-acid-based monolayers were deposited on water by the ancients for applications ranging from fortune telling in King Hammurabi's time (˜1800 BC, Mesopotamia) to stilling choppy waters for sailors and divers as reported by the Roman philosopher Pliny the Elder in ˜78 AD, and then much later (1774) by the peripatetic American statesman and natural philosopher Benjamin Franklin, to Japanese "floating-ink" art (suminagashi) developed ˜1000 years ago. The modern science of organic monolayers began in the late-1800s/early-1900s with experiments by Lord Rayleigh and the important development by Agnes Pockels, followed two decades later by Irving Langmuir, of the tools and technology to measure the surface tension of liquids, the surface pressure of organic monolayers deposited on water, interfacial properties, molecular conformation of the organic layers, and phase transitions which occur upon compressing the monolayers. In 1935, Katherine Blodgett published a landmark paper showing that multilayers can be synthesized on solid substrates, with controlled thickness and composition, using an apparatus now known as the Langmuir-Blodgett (L-B) trough. A disadvantage of LB films for some applications is that they form weak physisorbed bonds to the substrate. In 1946, Bigelow, Pickett, and Zisman demonstrated, in another seminal paper, the growth of organic self-assembled monolayers (SAMs) via spontaneous adsorption from solution, rather than from the water/air interface, onto SiO2 and metal substrates. SAMs are close-packed two-dimensional organic crystals which exhibit strong covalent bonding to the substrate. The first multicomponent adsorbed monolayers and multilayer SAMs were produced in the early 1980s. Langmuir monolayers, L-B multilayers, and self-assembled mono- and multilayers have found an extraordinarily broad range of applications including controlled wetting

  3. Tracing the 4000 year history of organic thin films: From monolayers on liquids to multilayers on solids

    Energy Technology Data Exchange (ETDEWEB)

    Greene, J. E. [University of Illinois, Urbana, Illinois 61801 (United States); Linköping University, 581 83 Linköping (Sweden); National Taiwan University of Science and Technology, Taipei 10607, Taiwan (China)

    2015-03-15

    The recorded history of organic monolayer and multilayer thin films spans approximately 4000 years. Fatty-acid-based monolayers were deposited on water by the ancients for applications ranging from fortune telling in King Hammurabi's time (∼1800 BC, Mesopotamia) to stilling choppy waters for sailors and divers as reported by the Roman philosopher Pliny the Elder in ∼78 AD, and then much later (1774) by the peripatetic American statesman and natural philosopher Benjamin Franklin, to Japanese “floating-ink” art (suminagashi) developed ∼1000 years ago. The modern science of organic monolayers began in the late-1800s/early-1900s with experiments by Lord Rayleigh and the important development by Agnes Pockels, followed two decades later by Irving Langmuir, of the tools and technology to measure the surface tension of liquids, the surface pressure of organic monolayers deposited on water, interfacial properties, molecular conformation of the organic layers, and phase transitions which occur upon compressing the monolayers. In 1935, Katherine Blodgett published a landmark paper showing that multilayers can be synthesized on solid substrates, with controlled thickness and composition, using an apparatus now known as the Langmuir-Blodgett (L-B) trough. A disadvantage of LB films for some applications is that they form weak physisorbed bonds to the substrate. In 1946, Bigelow, Pickett, and Zisman demonstrated, in another seminal paper, the growth of organic self-assembled monolayers (SAMs) via spontaneous adsorption from solution, rather than from the water/air interface, onto SiO{sub 2} and metal substrates. SAMs are close-packed two-dimensional organic crystals which exhibit strong covalent bonding to the substrate. The first multicomponent adsorbed monolayers and multilayer SAMs were produced in the early 1980s. Langmuir monolayers, L-B multilayers, and self-assembled mono- and multilayers have found an extraordinarily broad range of applications including

  4. Catalytic monolayer voltammetry and in situ scanning tunneling microscopy of copper nitrite reductase on cysteamine-modified Au(111) electrodes

    DEFF Research Database (Denmark)

    Zhang, Jingdong; Welinder, A.C.; Hansen, Allan Glargaard

    2003-01-01

    We have studied the adsorption and electrocatalysis of the redox metalloenzyme blue copper nitrite reductase from Achromobacter xylosoxidans (AxCuNiR) on single-crystal Au(111)-electrode surfaces modified by a self-assembled monolayer of cysteamine. A combination of cyclic voltammetry and in situ...

  5. Slow Diffusive Motions in a Monolayer of Tetracosane Molecules Adsorbed on Graphite

    DEFF Research Database (Denmark)

    Taub, H.; Hansen, Flemming Yssing; Criswell, L.

    2004-01-01

    Monolayers of intermediate-length alkane molecules such as tetracosane (n-C24H50 or C24) serve as prototypes for studying the interfacial dynamics of more complex polymers, including bilayer lipid membranes. Using high-resolution quasielastic neutron scattering (QNS) and exfoliated graphite...... to a temperature of similar to230 K, we observe the QNS energy width to be dispersionless, consistent with molecular dynamics simulations showing rotational motion of the molecules about their long axis. At 260 K, the QNS energy width begins to increase with wave vector transfer, suggesting onset of nonuniaxial...... rotational motion and bounded translational motion. We continue to observe QNS up to the monolayer melting temperature at similar to340 K where our simulations indicate that the only motion slow enough to be visible within our energy window results from the creation of gauche defects in the molecules....

  6. Anomalously fast kinetics of lipid monolayer buckling

    Science.gov (United States)

    Oppenheimer, Naomi; Diamant, Haim; Witten, Thomas A.

    2013-08-01

    We reexamine previous observations of folding kinetics of compressed lipid monolayers in light of the accepted mechanical buckling mechanism recently proposed by L. Pocivavsek [ScienceSCIEAS0036-807510.1126/science.1154069 320, 912 (2008)]. Using simple models, we set conservative limits on (a) the energy released in the mechanical buckling process and (b) the kinetic energy entailed by the observed folding motion. These limits imply a kinetic energy at least 30 times greater than the energy supplied by the buckling instability. We discuss possible extensions of the accepted picture that might resolve this discrepancy.

  7. Defect-Tolerant Monolayer Transition Metal Dichalcogenides

    DEFF Research Database (Denmark)

    Pandey, Mohnish; Rasmussen, Filip Anselm; Kuhar, Korina

    2016-01-01

    -principles investigation of defect tolerance in 29 monolayer transition metal dichalcogenides (TMDs) of interest for nanoscale optoelectronics. We find that the TMDs based on group VI and X metals form deep gap states upon creation of a chalcogen (S, Se, Te) vacancy, while the TMDs based on group IV metals form only...... shallow defect levels and are thus predicted to be defect-tolerant. Interestingly, all the defect sensitive TMDs have valence and conduction bands with a very similar orbital composition. This indicates a bonding/antibonding nature of the gap, which in turn suggests that dangling bonds will fall inside...

  8. Template-Directed Self-Assembly of Alkanethiol Monolayers: Selective Growth on Preexisting Monolayer Edges

    NARCIS (Netherlands)

    Sharpe, R.B.A.; Burdinski, Dirk; Huskens, Jurriaan; Zandvliet, Henricus J.W.; Reinhoudt, David; Poelsema, Bene

    2007-01-01

    Self-assembled monolayers were investigated for their suitability as two-dimensional scaffolds for the selective growth of alkanethiol edge structures. Heterostructures with chemical contrast could be grown, whose dimensions were governed by both the initial pattern sizes and the process time.

  9. Relationships among North American and Japanese Laetiporus isolates inferred from molecular phylogenetics and single-spore incompatibility reactions

    Science.gov (United States)

    Mark T. Banik; Daniel L. Lindner; Yuko Ota; Tsutomu. Hattori

    2010-01-01

    Relationships were investigated among North American and Japanese isolates of Laetiporus using phylogenetic analysis of ITS sequences and single-spore isolate incompatibility. Single-spore isolate pairings revealed no significant compatibility between North American and Japanese isolates. ITS analysis revealed 12 clades within the core ...

  10. Compositional and structural characterization of monolayers and bilayers composed of native pulmonary surfactant from wild type mice

    DEFF Research Database (Denmark)

    Bernardino de la Serna, Jorge; Hansen, Soren; Berzina, Zane

    2013-01-01

    This work comprises a structural and dynamical study of monolayers and bilayers composed of native pulmonary surfactant from mice. Spatially resolved information was obtained using fluorescence (confocal, wide field and two photon excitation) and atomic force microscopy methods. Lipid mass...... spectrometry experiments were also performed in order to obtain relevant information on the lipid composition of this material. Bilayers composed of mice pulmonary surfactant showed coexistence of distinct domains at room temperature, with morphologies and lateral packing resembling the coexistence of liquid...... between mono- and bi-layers composed of mice pulmonary surfactant were observed when the monolayers reach a surface pressure of 30 mN/m. This value is in line with theoretically predicted and recently measured surface pressures, where the monolayer-bilayer equivalence occurs in samples composed of single...

  11. Cavity plasmon polaritons in monolayer graphene

    International Nuclear Information System (INIS)

    Kotov, O.V.; Lozovik, Yu.E.

    2011-01-01

    Plasmon polaritons in a new system, a monolayer doped graphene embedded in optical microcavity, are studied here. The dispersion law for lower and upper cavity plasmon polaritons is obtained. Peculiarities of Rabi splitting for the system are analyzed; particularly, role of Dirac-like spinor (envelope) wave functions in graphene and corresponding angle factors are considered. Typical Rabi frequencies for maximal (acceptable for Dirac-like electron spectra) Fermi energy and frequencies of polaritons near polariton gap are estimated. The plasmon polaritons in considered system can be used for high-speed information transfer in the THz region. -- Highlights: → Plasmon polaritons in a monolayer doped graphene embedded in optical microcavity, are studied here. → The dispersion law for lower and upper cavity plasmon polaritons is obtained. → Peculiarities of Rabi splitting for the system are analyzed. → Role of Dirac-like wave functions in graphene and corresponding angle factors are considered. → Typical Rabi frequencies and frequencies of polaritons near polariton gap are estimated.

  12. Strictly monolayer large continuous MoS{sub 2} films on diverse substrates and their luminescence properties

    Energy Technology Data Exchange (ETDEWEB)

    Mohapatra, P. K.; Deb, S.; Singh, B. P.; Vasa, P.; Dhar, S., E-mail: dhar@phy.iitb.ac.in [Department of Physics, Indian Institute of Technology Bombay, Mumbai 400076 (India)

    2016-01-25

    Despite a tremendous interest on molybdenum disulfide as a thinnest direct band gap semiconductor, single step synthesis of a large area purely monolayer MoS{sub 2} film has not yet been reported. Here, we report a CVD route to synthesize a continuous film of strictly monolayer MoS{sub 2} covering an area as large as a few cm{sup 2} on a variety of different substrates without using any seeding material or any elaborate pretreatment of the substrate. This is achieved by allowing the growth to take place in the naturally formed gap between a piece of SiO{sub 2} coated Si wafer and the substrate, when the latter is placed on top of the former inside a CVD reactor. We propose a qualitative model to explain why the MoS{sub 2} films are always strictly monolayer in this method. The photoluminescence study of these monolayers shows the characteristic excitonic and trionic features associated with monolayer MoS{sub 2}. In addition, a broad defect related luminescence band appears at ∼1.7 eV. As temperature decreases, the intensity of this broad feature increases, while the band edge luminescence reduces.

  13. Surface structures of normal paraffins and cyclohexane monolayers and thin crystals grown on the (111) crystal face of platinum. A low-energy electron diffraction study

    International Nuclear Information System (INIS)

    Firment, L.E.; Somorjai, G.A.

    1977-01-01

    The surfaces of the normal paraffins (C 3 --C 8 ) and cyclohexane have been studied using low-energy electron diffraction (LEED). The samples were prepared by vapor deposition on the (111) face of a platinum single crystal in ultrahigh vacuum, and were studied both as thick films and as adsorbed monolayers. These molecules form ordered monolayers on the clean metal surface in the temperature range 100--220 K and at a vapor flux corresponding to 10 -7 Torr. In the adsorbed monolayers of the normal paraffins (C 4 --C 8 ), the molecules lie with their chain axes parallel to the Pt surface and Pt[110]. The paraffin monolayer structures undergo order--disorder transitions as a function of temperature. Multilayers condensed upon the ordered monolayers maintained the same orientation and packing as found in the monolayers. The surface structures of the growing organic crystals do not corresond to planes in their reported bulk crystal structures and are evidence for epitaxial growth of pseudomorphic crystal forms. Multilayers of n-octane and n-heptane condensed upon disordered monolayers have also grown with the (001) plane of the triclinic bulk crystal structures parallel to the surface. n-Butane has three monolayer structures on Pt(111) and one of the three is maintained during growth of the crystal. Cyclohexane forms an ordered monolayer, upon which a multilayer of cyclohexane grows exhibiting the (001) surface orientation of the monoclinic bulk crystal structure. Surface structures of saturated hydrocarbons are found to be very susceptible to electron beam induced damage. Surface charging interferes with LEED only at sample thicknesses greater than 200 A

  14. Mismatch in mechanical and adhesive properties induces pulsating cancer cell migration in epithelial monolayer.

    Science.gov (United States)

    Lee, Meng-Horng; Wu, Pei-Hsun; Staunton, Jack Rory; Ros, Robert; Longmore, Gregory D; Wirtz, Denis

    2012-06-20

    The mechanical and adhesive properties of cancer cells significantly change during tumor progression. Here we assess the functional consequences of mismatched stiffness and adhesive properties between neighboring normal cells on cancer cell migration in an epithelial-like cell monolayer. Using an in vitro coculture system and live-cell imaging, we find that the speed of single, mechanically soft breast carcinoma cells is dramatically enhanced by surrounding stiff nontransformed cells compared with single cells or a monolayer of carcinoma cells. Soft tumor cells undergo a mode of pulsating migration that is distinct from conventional mesenchymal and amoeboid migration, whereby long-lived episodes of slow, random migration are interlaced with short-lived episodes of extremely fast, directed migration, whereas the surrounding stiff cells show little net migration. This bursty migration is induced by the intermittent, myosin II-mediated deformation of the soft nucleus of the cancer cell, which is induced by the transient crowding of the stiff nuclei of the surrounding nontransformed cells, whose movements depend directly on the cadherin-mediated mismatched adhesion between normal and cancer cells as well as α-catenin-based intercellular adhesion of the normal cells. These results suggest that a mechanical and adhesive mismatch between transformed and nontransformed cells in a cell monolayer can trigger enhanced pulsating migration. These results shed light on the role of stiff epithelial cells that neighbor individual cancer cells in early steps of cancer dissemination. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  15. Sphingomyelin distribution in lipid rafts of artificial monolayer membranes visualized by Raman microscopy.

    Science.gov (United States)

    Ando, Jun; Kinoshita, Masanao; Cui, Jin; Yamakoshi, Hiroyuki; Dodo, Kosuke; Fujita, Katsumasa; Murata, Michio; Sodeoka, Mikiko

    2015-04-14

    Sphingomyelin (SM) and cholesterol (chol)-rich domains in cell membranes, called lipid rafts, are thought to have important biological functions related to membrane signaling and protein trafficking. To visualize the distribution of SM in lipid rafts by means of Raman microscopy, we designed and synthesized an SM analog tagged with a Raman-active diyne moiety (diyne-SM). Diyne-SM showed a strong peak in a Raman silent region that is free of interference from intrinsic vibrational modes of lipids and did not appear to alter the properties of SM-containing monolayers. Therefore, we used Raman microscopy to directly visualize the distribution of diyne-SM in raft-mimicking domains formed in SM/dioleoylphosphatidylcholine/chol ternary monolayers. Raman images visualized a heterogeneous distribution of diyne-SM, which showed marked variation, even within a single ordered domain. Specifically, diyne-SM was enriched in the central area of raft domains compared with the peripheral area. These results seem incompatible with the generally accepted raft model, in which the raft and nonraft phases show a clear biphasic separation. One of the possible reasons is that gradual changes of SM concentration occur between SM-rich and -poor regions to minimize hydrophobic mismatch. We believe that our technique of hyperspectral Raman imaging of a single lipid monolayer opens the door to quantitative analysis of lipid membranes by providing both chemical information and spatial distribution with high (diffraction-limited) spatial resolution.

  16. Dendritic functionalization of monolayer-protected gold nanoparticles

    International Nuclear Information System (INIS)

    Cutler, Erin C.; Lundin, Erik; Garabato, B. Davis; Choi, Daeock; Shon, Young-Seok

    2007-01-01

    This paper describes the facile synthesis of nanoparticle-cored dendrimers (NCDs) and nanoparticle megamers from monolayer-protected gold clusters using either single or multi-step reactions. First, 11-mercaptoundecanoic acid/hexanethiolate-protected gold clusters were synthesized using the Schiffrin reaction followed by the ligand place-exchange reaction. A convergent approach for the synthesis of nanoparticle-cored dendrimers uses a single step reaction that is an ester coupling reaction of hydroxy-functionalized dendrons with carboxylic acid-functionalized gold clusters. A divergent approach, which is based on multi-step reactions, employs the repetition of an amide coupling reaction and a Michael addition reaction to build polyamidoamine dendritic architectures around a nanoparticle core. Nanoparticle megamers, which are large dendrimer-induced nanoparticle aggregates with an average diameter of more than 300 nm, were prepared by the amide coupling reaction between polyamiodoamine [G-2] dendrimers and carboxylic acid-functionalized gold clusters. 1 H NMR spectroscopy, FT-IR spectroscopy, thermogravimetric analysis (TGA), and transmission electron microscopy (TEM) were used for the characterization of these hybrid nanoparticles

  17. Self-assembled monolayers of metallosalophenes on gold

    NARCIS (Netherlands)

    Beulen, M.W.J.; van Veggel, F.C.J.M.; Reinhoudt, David

    2000-01-01

    Salophene complexes of transition metals exhibit a reversible electro- chemistry. We have synthesized salophene complexes with sulfur-containing substituents aimed at the formation of self-assembled monolayers on a gold surface. Such monolayers have interesting cation complexating properties. The

  18. Computational screening and molecular dynamic simulation of breast cancer associated deleterious non-synonymous single nucleotide polymorphisms in TP53 gene.

    Directory of Open Access Journals (Sweden)

    Kumaraswamy Naidu Chitrala

    Full Text Available Breast cancer is one of the most common cancers among the women around the world. Several genes are known to be responsible for conferring the susceptibility to breast cancer. Among them, TP53 is one of the major genetic risk factor which is known to be mutated in many of the breast tumor types. TP53 mutations in breast cancer are known to be related to a poor prognosis and chemo resistance. This renders them as a promising molecular target for the treatment of breast cancer. In this study, we present a computational based screening and molecular dynamic simulation of breast cancer associated deleterious non-synonymous single nucleotide polymorphisms in TP53. We have predicted three deleterious coding non-synonymous single nucleotide polymorphisms rs11540654 (R110P, rs17849781 (P278A and rs28934874 (P151T in TP53 with a phenotype in breast tumors using computational tools SIFT, Polyphen-2 and MutDB. We have performed molecular dynamics simulations to study the structural and dynamic effects of these TP53 mutations in comparison to the wild-type protein. Results from our simulations revealed a detailed consequence of the mutations on the p53 DNA-binding core domain that may provide insight for therapeutic approaches in breast cancer.

  19. Structural confirmation, single X-ray crystallographic behavior, molecular docking and other physico-chemical properties of gerberinol, a natural dimethyl dicoumarol from Gerbera lanuginosa Benth. (Compositae)

    Science.gov (United States)

    Brahmachari, Goutam; Das, Saktipada; Kumar, Abhishek; Misra, Neeraj; Sharma, Sakshi; Gupta, Vivek K.

    2017-05-01

    The proposed structure of gerberinol (1), a naturally occurring dimethyl dicoumarol, has been conclusively established on the basis of its detailed spectral and single crystal X-ray analyses. The compound, C21H16O6, crystallizes in the monoclinic space group P21/c with the following unit-cell parameters: a = 14.0884(14), b = 15.1746(15), c = 7.6392(8)Å, α = 90.00°, β = 98.949(4)°, γ = 90.00° and Z = 4. The crystal structure was solved by direct methods using single-crystal X-ray diffraction data collected at room temperature and refined by full-matrix least-squares procedures to a final R-value of 11.43 for 2377 observed reflections. Exhaustive theoretical studies on the molecular structure, vibrational spectra, HOMO, LUMO, MESP surfaces, and molecular docking of this plant-derived natural molecule have also been performed. The equilibrium geometry of the title compound has been obtained and analyzed using DFT-B3LYP/6-311 + G(d,p) method. Molecular docking study of the molecule for predicting its possible biological activities revealed that the compound might be a potent antimicrobial, neurodegenerative and anticancer agent as evidenced from its excellent FF (full fitness) score for 1FUJ and 1ZX1 enzymes.

  20. Cantilever measurements of surface stress, surface reconstruction, film stress and magnetoelastic stress of monolayers.

    Science.gov (United States)

    Sander, Dirk; Tian, Zhen; Kirschner, Jürgen

    2008-07-29

    We review the application of cantilever-based stress measurements in surface science and magnetism. The application of thin (thickness appr. 0.1 mm) single crystalline substrates as cantilevers has been used successfully to measure adsorbate-induced surface stress changes, lattice misfit induced film stress, and magneto-elastic stress of ferromagnetic monolayers. Surface stress changes as small as 0.01 N/m can be readily measured, and this translates into a sensitivity for adsorbate-coverage well below 0.01 of one layer. Stress as large as several GPa, beyond the elasticity limits of high strength materials, is measured, and it is ascribed to the lattice misfit between film and substrate. Our results point at the intimate relation between surface stress and surface reconstruction, stress-induced structural changes in epitaxially strained films, and strain-induced modifications of the magneto-elastic coupling in ferromagnetic monolayers.

  1. Electrical control of neutral and charged excitons in a monolayer semiconductor.

    Science.gov (United States)

    Ross, Jason S; Wu, Sanfeng; Yu, Hongyi; Ghimire, Nirmal J; Jones, Aaron M; Aivazian, Grant; Yan, Jiaqiang; Mandrus, David G; Xiao, Di; Yao, Wang; Xu, Xiaodong

    2013-01-01

    Monolayer group-VI transition metal dichalcogenides have recently emerged as semiconducting alternatives to graphene in which the true two-dimensionality is expected to illuminate new semiconducting physics. Here we investigate excitons and trions (their singly charged counterparts), which have thus far been challenging to generate and control in the ultimate two-dimensional limit. Utilizing high-quality monolayer molybdenum diselenide, we report the unambiguous observation and electrostatic tunability of charging effects in positively charged (X(+)), neutral (X(o)) and negatively charged (X(-)) excitons in field-effect transistors via photoluminescence. The trion charging energy is large (30 meV), enhanced by strong confinement and heavy effective masses, whereas the linewidth is narrow (5 meV) at temperatures charging energies for X(+) and X(-) to be nearly identical implying the same effective mass for electrons and holes.

  2. Chemical hole doping into large-area transition metal dichalcogenide monolayers using boron-based oxidant

    KAUST Repository

    Matsuoka, Hirofumi

    2018-01-18

    Hole carrier doping into single-crystalline transition metal dichalcogenide (TMDC) films can be achieved with various chemical reagents. However, large-area polycrystalline TMDC monolayers produced by a chemical vapor deposition (CVD) growth method have yet to be chemically doped. Here, we report that a salt of a two-coordinate boron cation, Mes2B+ (Mes: 2,4,6-trimethylphenyl group), with a chemically stable tetrakis(pentafluorophenyl)borate anion, [(C6F5)4B]−, can serve as an efficient hole-doping reagent for large-area CVD-grown tungsten diselenide (WSe2) films. Upon doping, the sheet resistance of large-area polycrystalline WSe2 monolayers decreased from 90 GΩ/sq to 3.2 kΩ/sq.

  3. Chemical hole doping into large-area transition metal dichalcogenide monolayers using boron-based oxidant

    Science.gov (United States)

    Matsuoka, Hirofumi; Kanahashi, Kaito; Tanaka, Naoki; Shoji, Yoshiaki; Li, Lain-Jong; Pu, Jiang; Ito, Hiroshi; Ohta, Hiromichi; Fukushima, Takanori; Takenobu, Taishi

    2018-02-01

    Hole carrier doping into single-crystalline transition metal dichalcogenide (TMDC) films can be achieved with various chemical reagents. However, large-area polycrystalline TMDC monolayers produced by a chemical vapor deposition (CVD) growth method have yet to be chemically doped. Here, we report that a salt of a two-coordinate boron cation, Mes2B+ (Mes: 2,4,6-trimethylphenyl group), with a chemically stable tetrakis(pentafluorophenyl)borate anion, [(C6F5)4B]‑, can serve as an efficient hole-doping reagent for large-area CVD-grown tungsten diselenide (WSe2) films. Upon doping, the sheet resistance of large-area polycrystalline WSe2 monolayers decreased from 90 GΩ/sq to 3.2 kΩ/sq.

  4. Spontaneous spheroid budding from monolayers: a potential contribution to ovarian cancer dissemination.

    Science.gov (United States)

    Pease, Jillian C; Brewer, Molly; Tirnauer, Jennifer S

    2012-07-15

    Ovarian cancer is the most lethal gynaecologic cancer, in large part because of its early dissemination and rapid development of chemotherapy resistance. Spheroids are clusters of tumor cells found in the peritoneal fluid of patients that are thought to promote this dissemination. Current models suggest that spheroids form by aggregation of single tumor cells shed from the primary tumor. Here, we demonstrate that spheroids can also form by budding directly as adherent clusters from a monolayer. Formation of budded spheroids correlated with expression of vimentin and lack of cortical E-cadherin. We also found that compared to cells grown in monolayers, cells grown as spheroids acquired progressive resistance to the chemotherapy drugs Paclitaxel and Cisplatin. This resistance could be completely reversed by dissociating the spheroids. Our observations highlight a previously unappreciated mode of spheroid formation that might have implications for tumor dissemination and chemotherapy resistance in patients, and suggest that this resistance might be reversed by spheroid dissociation.

  5. Large-area and bright pulsed electroluminescence in monolayer semiconductors

    KAUST Repository

    Lien, Der-Hsien

    2018-04-04

    Transition-metal dichalcogenide monolayers have naturally terminated surfaces and can exhibit a near-unity photoluminescence quantum yield in the presence of suitable defect passivation. To date, steady-state monolayer light-emitting devices suffer from Schottky contacts or require complex heterostructures. We demonstrate a transient-mode electroluminescent device based on transition-metal dichalcogenide monolayers (MoS, WS, MoSe, and WSe) to overcome these problems. Electroluminescence from this dopant-free two-terminal device is obtained by applying an AC voltage between the gate and the semiconductor. Notably, the electroluminescence intensity is weakly dependent on the Schottky barrier height or polarity of the contact. We fabricate a monolayer seven-segment display and achieve the first transparent and bright millimeter-scale light-emitting monolayer semiconductor device.

  6. Defining the risk of toxicity in phase I oncology trials of novel molecularly targeted agents: A single-center experience

    NARCIS (Netherlands)

    Fehrmann, Rudolf

    2010-01-01

    Background: Phase I oncology trials are designed to define the maximum tolerated dose and toxicity of new drugs. This study aims to define the risk of toxicity in phase I trials of novel molecularly targeted agents (MTA), as this therapeutic approach is becoming increasingly relevant. Methods: We

  7. Electrochemical control of the single molecule conductance of a conjugated bis(pyrrolo)tetrathiafulvalene based molecular switch

    DEFF Research Database (Denmark)

    O'Driscoll, Luke J.; Hamill, Joseph M.; Grace, Iain

    2017-01-01

    (pyrrolo)tetrathiafulvalene (BPTTF) has been designed, synthesised and investigated using scanning tunnelling microscopy break junction (STM-BJ) studies and quantum transport calculations. Oxidising the BPTTF unit increases its conjugation, which was anticipated to increase the molecular conductance of 1. By changing the redox...

  8. Defining the risk of toxicity in phase I oncology trials of novel molecularly targeted agents : a single centre experience

    NARCIS (Netherlands)

    Molife, L R; Alam, S; Olmos, D; Puglisi, M; Shah, K; Fehrmann, Rudolf; Trani, L; Tjokrowidjaja, A; de Bono, J S; Banerji, U; Kaye, S B

    BACKGROUND: This study defined the risk of serious toxicity in phase I trials of molecularly targeted agents (MTA). PATIENTS AND METHODS: A retrospective analysis of toxicity data from patients treated in phase I trials of MTAs was carried out to define the rate of treatment-related grade 3/4 toxic

  9. Evaluation of digital real-time PCR assay as a molecular diagnostic tool for single-cell analysis.

    Science.gov (United States)

    Chang, Chia-Hao; Mau-Hsu, Daxen; Chen, Ke-Cheng; Wei, Cheng-Wey; Chiu, Chiung-Ying; Young, Tai-Horng

    2018-02-21

    In a single-cell study, isolating and identifying single cells are essential, but these processes often require a large investment of time or money. The aim of this study was to isolate and analyse single cells using a novel platform, the PanelChip™ Analysis System, which includes 2500 microwells chip and a digital real-time polymerase chain reaction (dqPCR) assay, in comparison with a standard PCR (qPCR) assay. Through the serial dilution of a known concentration standard, namely pUC19, the accuracy and sensitivity levels of two methodologies were compared. The two systems were tested on the basis of expression levels of the genetic markers vimentin, E-cadherin, N-cadherin and GAPDH in A549 lung carcinoma cells at two known concentrations. Furthermore, the influence of a known PCR inhibitor commonly found in blood samples, heparin, was evaluated in both methodologies. Finally, mathematical models were proposed and separation method of single cells was verified; moreover, gene expression levels during epithelial-mesenchymal transition in single cells under TGFβ1 treatment were measured. The drawn conclusion is that dqPCR performed using PanelChip™ is superior to the standard qPCR in terms of sensitivity, precision, and heparin tolerance. The dqPCR assay is a potential tool for clinical diagnosis and single-cell applications.

  10. The validity of sedimentation data from high molecular weight DNA and the effects of additives on radiation-induced single-strand breakage

    International Nuclear Information System (INIS)

    Dugle, D.L.

    1979-10-01

    The optimization of many of the factors governing reproducible sedimentation behaviour of high molecular weight single-strand DNA in a particular alkaline sucrose density gradient system is described. A range of angular momenta is defined for which a constant strand breakage efficiency is required, despite a rotor speed effect which increases the measured molecular weights at decreasing rotor speeds for larger DNA molecules. The possibility is discussed that the bimodal control DNA profiles obtained after sedimentation at 11 500 rev/min (12 400 g) or less represent structural subunits of the chromatid. The random induction of single-strand DNA breaks by ionizing radiation is demonstrated by the computer-derived fits to the experimental profiles. The enhancement of single-strand break (SSB) yields in hypoxic cells by oxygen, para-nitroacetophenone (PNAP), or any of the three nitrofuran derivatives used was well correlated with increased cell killing. Furthermore, reductions in SSB yields for known hydroxyl radical (OH.) scavengers correlates with the reactivities of these compounds toward OH.. This supports the contention that some type of OH.-induced initial lesion, which may ultimately be expressed as an unrepaired or misrepaired double-strand break, constitutes a lethal event. (author)

  11. Ordered array of CoPc-vacancies filled with single-molecule rotors

    Science.gov (United States)

    Xie, Zheng-Bo; Wang, Ya-Li; Tao, Min-Long; Sun, Kai; Tu, Yu-Bing; Yuan, Hong-Kuan; Wang, Jun-Zhong

    2018-05-01

    We report the highly ordered array of CoPc-vacancies and the single-molecule rotors inside the vacancies. When CoPc molecules are deposited on Cd(0001) at low-temperature, three types of molecular vacancies appeared randomly in the CoPc monolayer. Annealing the sample to higher temperature leads to the spontaneous phase separation and self-organized arrangement of the vacancies. Highly ordered arrays of two-molecule vacancies and single-molecule vacancies have been obtained. In particular, there is a rotating CoPc molecule inside each single-molecule vacancy, which constitutes the array of single-molecule rotors. These results provide a new routine to fabricate the nano-machines on a large scale.

  12. Chemical surface reactions by click chemistry: coumarin dye modification of 11-bromoundecyltrichlorosilane monolayers

    International Nuclear Information System (INIS)

    Haensch, Claudia; Hoeppener, Stephanie; Schubert, Ulrich S

    2008-01-01

    The functionalization of surfaces and the ability to tailor their properties with desired physico-chemical functions is an important field of research with a broad spectrum of applications. These applications range from the modification of wetting properties, over the alteration of optical properties, to the fabrication of molecular electronic devices. In each of these fields, it is of specific importance to be able to control the quality of the layers with high precision. The present study demonstrates an approach that utilizes the 1,3-dipolar cycloaddition of terminal acetylenes to prepare triazole-terminated monolayers on different substrates. The characterization of the precursor monolayers, the optimization of the chemical surface reactions as well as the clicking of a fluorescent dye molecule on such azide-terminated monolayers was carried out. A coumarin 343 derivative was utilized to discuss the aspects of the functionalization approach. Based on this approach, a number of potential surface reactions, facilitated via the acetylene-substituted functional molecules, for a broad range of applications is at hand, thus leading to numerous possibilities where surface modifications are concerned. These modifications can be applied on non-structured surfaces of silicon or glass or can be used on structured surfaces. Various possibilities are discussed

  13. Ising Superconductivity and Quantum Phase Transition in Macro-Size Monolayer NbSe2.

    Science.gov (United States)

    Xing, Ying; Zhao, Kun; Shan, Pujia; Zheng, Feipeng; Zhang, Yangwei; Fu, Hailong; Liu, Yi; Tian, Mingliang; Xi, Chuanying; Liu, Haiwen; Feng, Ji; Lin, Xi; Ji, Shuaihua; Chen, Xi; Xue, Qi-Kun; Wang, Jian

    2017-11-08

    Two-dimensional (2D) transition metal dichalcogenides (TMDs) have a range of unique physics properties and could be used in the development of electronics, photonics, spintronics, and quantum computing devices. The mechanical exfoliation technique of microsize TMD flakes has attracted particular interest due to its simplicity and cost effectiveness. However, for most applications, large-area and high-quality films are preferred. Furthermore, when the thickness of crystalline films is down to the 2D limit (monolayer), exotic properties can be expected due to the quantum confinement and symmetry breaking. In this paper, we have successfully prepared macro-size atomically flat monolayer NbSe 2 films on bilayer graphene terminated surface of 6H-SiC(0001) substrates by a molecular beam epitaxy (MBE) method. The films exhibit an onset superconducting critical transition temperature (T c onset ) above 6 K and the zero resistance superconducting critical transition temperature (T c zero ) up to 2.40 K. Simultaneously, the transport measurements at high magnetic fields and low temperatures reveal that the parallel characteristic field B c// (T = 0) is above 5 times of the paramagnetic limiting field, consistent with Zeeman-protected Ising superconductivity mechanism. Besides, by ultralow temperature electrical transport measurements, the monolayer NbSe 2 film shows the signature of quantum Griffiths singularity (QGS) when approaching the zero-temperature quantum critical point.

  14. Cholesterol-Induced Buckling in Physisorbed Polymer-Tethered Lipid Monolayers

    Directory of Open Access Journals (Sweden)

    Christoph A. Naumann

    2013-04-01

    Full Text Available The influence of cholesterol concentration on the formation of buckling structures is studied in a physisorbed polymer-tethered lipid monolayer system using epifluorescence microscopy (EPI and atomic force microscopy (AFM. The monolayer system, built using the Langmuir-Blodgett (LB technique, consists of 3 mol % poly(ethylene glycol (PEG lipopolymers and various concentrations of the phospholipid, 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine (SOPC, and cholesterol (CHOL. In the absence of CHOL, AFM micrographs show only occasional buckling structures, which is caused by the presence of the lipopolymers in the monolayer. In contrast, a gradual increase of CHOL concentration in the range of 0–40 mol % leads to fascinating film stress relaxation phenomena in the form of enhanced membrane buckling. Buckling structures are moderately deficient in CHOL, but do not cause any notable phospholipid-lipopolymer phase separation. Our experiments demonstrate that membrane buckling in physisorbed polymer-tethered membranes can be controlled through CHOL-mediated adjustment of membrane elastic properties. They further show that CHOL may have a notable impact on molecular confinement in the presence of crowding agents, such as lipopolymers. Our results are significant, because they offer an intriguing prospective on the role of CHOL on the material properties in complex membrane architecture.

  15. Pressure induced structure formation in Langmuir monolayers of amphiphilic metallocene diblock copolymers.

    Science.gov (United States)

    Kraska, Martin; Gallei, Markus; Stühn, Bernd; Rehahn, Matthias

    2013-07-02

    We present in situ structural investigations of a metal-containing diblock copolymer on a water surface. Monolayers of poly(vinylferrocene-b-(2-vinylpyridine)) (PVFc-b-P2VP) block copolymers are studied in a wide range of compositions by varying molar masses of P2VP with two different molecular weights of PVFc. We focus on the role of the respective block partners, PVFc and P2VP, when compressing the layer on the water surface. Compression isotherms are presented and interpreted in terms of the classical gaseous, expanded, and condensed phases. We calculate isothermal compressibilities, which reveal a minimum value independent of the molar masses of the respective block partners. We find the isotherms to be dominated by P2VP while PVFc barely contribute to the compression behavior due to its rather compact coil structure. We consider the diblock copolymer monolayers as a two-dimensional model system, which is reflected by two-dimensional scaling behavior in the semi dilute and condensed regime. By X-ray reflectometry (XR), we monitor in situ the monolayer structure change with increasing surface pressure Π and observe the PVFc-b-P2VP separation at high Π.

  16. Water adsorption beyond monolayer coverage on ZnO surfaces and nanoclusters

    Science.gov (United States)

    Raymand, David; Edvinsson, Tomas; Spångberg, Daniel; van Duin, Adri; Hermansson, Kersti

    2008-08-01

    The surface structures of ZnO surfaces and ZnO nanoparticles, with and without water, were studied with a reactive force field (FF) within the ReaxFF framework, and molecular dynamics (MD) simulations. The force field parameters were fitted to a training set of data points (energies, geometries, charges) derived from quantum-mechanical B3LYP calculations. The ReaxFF model predicts structures and reactions paths at a fraction of the computational cost of the quantum-mechanical calculations. Our simulations give the following results for the (10-10) surface. (i) The alternating H-bond pattern of Meyer et al. for one monolayer coverage is reproduced and maintained at higher temperatures. (ii) Coverages beyond one water monolayer enhances ZnO hydroxylation at the expense of ZnO hydration. (iii) This is achieved through an entirely new H-bond pattern mediated via the water molecules in the second layer above the ZnO surface. (iv) During a desorption process, the desorption rate slows significantly when two monolayers remain. Simulations of nanoparticles in water suggest that these conclusions are relevant also in the nano case.

  17. Electrical resistivity of monolayers and bilayers of alkanethiols in tunnel junction with gate electrode

    International Nuclear Information System (INIS)

    York, Roger L.; Nacionales, David; Slowinski, Krzysztof

    2005-01-01

    The tunneling resistances of monolayers and bilayers of n-alkanethiols in macroscopic Hg-Hg junctions with an electrochemical gate are reported. The resistances near zero bias calculated per 1 hydrocarbon chain vary from (5 ± 4) x 10 12 Ω for n-nonanethiol to (4 ± 2) x 10 16 Ω for n-octadecanethiol. These values indicate that monolayers of hydrocarbons in Hg-Hg junctions are substantially more resistive as compared to measurements employing microscopic tunnel junctions. The tunneling resistances of monolayer junctions are approximately 1 order of magnitude larger than those of bilayer junctions containing the same number of atoms indicating inefficient electronic coupling across the non-bonded -CH 3 |Hg interface. The symmetric current-voltage curves observed for the asymmetric junctions of Hg-S-(CH 2 ) n -CH 3 |Hg type suggest that these junctions do not behave as molecular diodes. Additional experimental evidence for the nature of the -CH 3 |Hg interface in the Hg-S-(CH 2 ) n -CH 3 |Hg junction is also presented

  18. The role of terminations and coordination atoms on the pseudocapacitance of titanium carbonitride monolayers.

    Science.gov (United States)

    Zhang, Wenqiang; Cheng, Chuan; Fang, Peilin; Tang, Bin; Zhang, Jindou; Huang, Guoming; Cong, Xin; Zhang, Bao; Ji, Xiao; Miao, Ling

    2016-02-14

    Nowadays, MXenes have received extensive concern as a prominent electrode material of electrochemical capacitors. As two important factors to the capacitance, the influence of the intrinsical terminations (F, O and OH) and coordination atoms (C and N) is investigated using first-principles calculations. According to the density of states aligned with the standard hydrogen electrode, it turns out that a Ti3CNO2 monolayer is proven to show an obvious pseudocapacitive behavior, while the bare, F and OH terminated Ti3CN monolayers may only present electrochemical double layer characters in an aqueous electrolyte. Moreover, the illustration of molecular orbitals over the Fermi level are mainly contributed by the d-orbitals of Ti atoms coordinated with O and N atoms, indicating that the redox pseudocapacitance of the Ti3CNO2 monolayer is promoted by the coordination N atoms. Then the superiority of N bonded Ti atoms in accepting charges can be visualized through the charge population. Further, the larger ratio of C/N in the coordination environment of Ti atoms indicates that more electrons can be stored. Our investigation can give an instructional advice in the MXenes-electrode production.

  19. The search for the most stable structures of silicon-carbon monolayer compounds.

    Science.gov (United States)

    Li, Pengfei; Zhou, Rulong; Zeng, Xiao Cheng

    2014-10-21

    The most stable structures of two-dimensional (2D) silicon-carbon monolayer compounds with different stoichiometric compositions (i.e., Si : C ratio = 2 : 3, 1 : 3 and 1 : 4) are predicted for the first time based on the particle-swarm optimization (PSO) technique combined with density functional theory optimization. Although the 2D Si-C monolayer compounds considered here are rich in carbon, many of the low-energy metastable and the lowest-energy silicon-carbon structures are not graphene (carbon monolayer) like. Phonon-spectrum calculations and ab initio molecular dynamics simulations were also performed to confirm the dynamical stability of the predicted most stable 2D silicon-carbon structures as well their thermal stability at elevated temperature. The computed electronic band structures show that all three predicted silicon-carbon compounds are semiconductors with direct or indirect bandgaps. Importantly, their bandgaps are predicted to be close to those of bulk silicon or bulk germanium. If confirmed in the laboratory, these 2D silicon-carbon compounds with different stoichiometric compositions may be exploited for future applications in nanoelectronic devices.

  20. High-performance organic complementary inverters using monolayer graphene electrodes.

    Science.gov (United States)

    Jeong, Yong Jin; Jang, Jaeyoung; Nam, Sooji; Kim, Kyunghun; Kim, Lae Ho; Park, Seonuk; An, Tae Kyu; Park, Chan Eon

    2014-05-14

    Chemical vapor deposition-grown graphene has been an attractive electrode material for organic electronic devices, such as organic field-effect transistors (OFETs), because it is highly conductive and provides good oxidation and thermal stability properties. However, it still remains a challenge to demonstrate organic complementary circuits using graphene electrodes because of the relatively poor performance of n-type OFETs. Here, we report the development of high-performance organic complementary inverters using graphene as source/drain electrodes and N, N'-ditridecyl-3,4,9,10-perylenetetracarboxylic diimide (PTCDI-C13) and pentacene as n- and p-type organic semiconductors, respectively. Graphene electrodes were n-doped via the formation of NH2-terminated self-assembled monolayers that lowered the work function and the electron injection barrier between the graphene and PTCDI-C13. Thermal annealing improved the molecular packing among PTCDI-C13 groups on the graphene surface, thereby increasing the crystallinity and grain size. The thermally annealed PTCDI-C13 OFETs prepared using n-doped graphene electrodes exhibited a good field-effect mobility of up to 0.43 cm2/(V s), which was comparable to the values obtained from other p-type pentacene OFETs. By integrating p- and n-type OFETs, we successfully fabricated organic complementary inverters that exhibited highly symmetric operation with an excellent voltage gain of up to 124 and good noise margin.

  1. Effect of Intrinsic Ripples on Elasticity of the Graphene Monolayer.

    Science.gov (United States)

    Lee, Seungjun

    2015-12-01

    The effect of intrinsic ripples on the mechanical response of the graphene monolayer is investigated under uniaxial loading using molecular dynamics (MD) simulations with a focus on nonlinear behavior at a small strain. The calculated stress-strain response shows a nonlinear relation through the entire range without constant slopes as a result of the competition between ripple softening and bond stretching hardening. For a small strain, entropic contribution is dominant due to intrinsic ripples, leading to elasticity softening. As the ripples flatten at increasing strain, the energetic term due to C-C bonds stretching competes with the entropic contribution, followed by energetic dominant deformation. Elasticity softening is enhanced at increased temperature as the ripple amplitude increases. The study shows that the intrinsic ripple of graphene affects elasticity. This result suggests that a change of ripple amplitudes due to various environmental conditions such as temperature, and substrate interactions can lead to a change of the mechanical properties of graphene. The understanding of the rippling effect on the mechanical behavior of 2D materials is useful for strain-based ripple manipulation for their engineering applications.

  2. Clinical and molecular analysis of 49 patients with X-linked agammaglobulinemia from a single center in Argentina.

    Science.gov (United States)

    Basile, Natalia; Danielian, Silvia; Oleastro, Matias; Rosenzweig, Sergio; Prieto, Emma; Rossi, Jorge; Roy, Adriana; Zelazko, Marta

    2009-01-01

    Argentina has a large number of patients with definite diagnosis of X-linked agammaglobulinemia reported in the Latin-American registry. Forty-nine of them were seen in our referral pediatric hospital, between 1987 and 2005. A retrospective study of clinical, laboratory, and molecular data showed that respiratory tract infections were the most frequent initial clinical presentation and the most common among all manifestations prior to diagnosis (69%). Up to diagnosis, we found a high frequency of severe infections (sepsis, 14% and meningitis, 16%) and a high proportion of patients with chronic lung disease. During follow-up, the development of chronic lung disease was significantly related with age at diagnosis and inappropriate treatment. Although molecular diagnosis has been available in our center for the past 10 years, there is no doubt that awareness for early recognition of immunodeficiency should be improved through broader and more comprehensive education programs emphasizing characteristics of patients with immunodeficiencies.

  3. Packing stress reduction in polymer-lipid monolayers at the air-water interface: An X-ray grazing-incidence diffraction and reflectivity study

    Energy Technology Data Exchange (ETDEWEB)

    Kuhl, T.L.; Majewski, J.; Howes, P.B.; Kjaer, K.; Nahmen, A. von; Lee, K.Y.C.; Ocko, B.; Israelachvili, J.N.; Smith, G.S.

    1999-08-25

    Using synchrotron grazing-incidence X-ray diffraction (GIXD) and reflectivity (XR), the authors have determined the in-plane and out-of-plane structure of phospholipid monolayers at the air-water interface as a function of hydrophilic lipid headgroup size. Di-stearoyl-phosphatidyl-ethanolamine (DSPE) lipid monolayers were systematically modified by chemically grafting hydrophilic poly(ethylene glycol) (PEG) chains of MW = 90 g/mol (2 ethylene oxide, EO, units), MW = 350 g/mol (8 EO units), and MW = 750 g/mol (17 EO units) to the lipid headgroups. The monolayers were studied in the solid phase at a surface pressure of 42 mN/m. At these high lipid packing densities, the PEG chains are submerged in the water subphase. The increased packing stresses from these bulky polymer headgroups distort the unit cell and the in-plane packing modes of the monolayers, leading to large out-of-plane alterations and staggering of the lipid molecules. Surprisingly, a change in the molecular packing of the monolayer toward higher packing densities (lower area per molecule) was observed on increasing the PEG MW to 750 g/mol (17 EO units). This rearrangement of the monolayer structure may be due to a conformational change in the PEG chains.

  4. Accurate determination of genetic identity for a single cacao bean, using molecular markers with a nanofluidic system, ensures cocoa authentication.

    Science.gov (United States)

    Fang, Wanping; Meinhardt, Lyndel W; Mischke, Sue; Bellato, Cláudia M; Motilal, Lambert; Zhang, Dapeng

    2014-01-15

    Cacao (Theobroma cacao L.), the source of cocoa, is an economically important tropical crop. One problem with the premium cacao market is contamination with off-types adulterating raw premium material. Accurate determination of the genetic identity of single cacao beans is essential for ensuring cocoa authentication. Using nanofluidic single nucleotide polymorphism (SNP) genotyping with 48 SNP markers, we generated SNP fingerprints for small quantities of DNA extracted from the seed coat of single cacao beans. On the basis of the SNP profiles, we identified an assumed adulterant variety, which was unambiguously distinguished from the authentic beans by multilocus matching. Assignment tests based on both Bayesian clustering analysis and allele frequency clearly separated all 30 authentic samples from the non-authentic samples. Distance-based principle coordinate analysis further supported these results. The nanofluidic SNP protocol, together with forensic statistical tools, is sufficiently robust to establish authentication and to verify gourmet cacao varieties. This method shows significant potential for practical application.

  5. Clinical, endocrinological, and molecular characterization of Kallmann syndrome and normosmic idiopathic hypogonadotropic hypogonadism: a single center experience

    Directory of Open Access Journals (Sweden)

    Sun-Jeong Shin

    2015-03-01

    Full Text Available PurposeIsolated gonadotropin-releasing hormone (GnRH deficiency (IGD is classified as Kallmann syndrome (KS with anosmia and normosmic idiopathic hypogonadotropic hypogonadism (nIHH. This study was undertaken to investigate the clinical, endocrinological, and molecular characteristics in Korean patients with KS and nIHH.MethodsTwenty-six patients from 25 unrelated families were included. Their clinical, endocrinological, and radiological findings were analyzed retrospectively. Mutation analysis of the GNRH1, GNRHR, KISS1, KISS1R, PROK2, PROKR2, TAC3, TACR3, FGF8, FGFR1, and KAL1 genes was performed in all patients. CHD7 and SOX10 were analyzed in patients with CHARGE (Coloboma, Heart defects, choanae Atresia, Growth retardation, Genitourinary abnormality, Ear abnormality features or deafness.ResultsOf the 26 patients, 16 had KS and 10 had nIHH. At diagnosis, mean chronologic age was 18.1 years in males and 18.0 years in females; height SDS were -0.67±1.35 in males, -1.12±1.86 in females; testis volume was 2.0±1.3 mL; and Tanner stage was 1.5. There were associated anomalies in some of the KS patients: hearing loss (n=6 and congenital heart disease (n=4. Absence or hypoplasia of the olfactory bulb/sulci was found in 84.62% of patients with KS. Molecular defects in KAL1, SOX10, and CHD7 were identified in 5 patients from 4 families (16.0%, 4/25 pedigrees. After sex hormone replacement therapy, there were improvement in sexual characteristics and the sexual function.ConclusionThis study described the clinical, endocrinological, and molecular genetic features in IGD patients in Korea. Although the mutation screening was performed in 10 genes that cause IGD, molecular defects were identified in relatively small proportions of the cohort.

  6. Clinical, endocrinological, and molecular characterization of Kallmann syndrome and normosmic idiopathic hypogonadotropic hypogonadism: a single center experience.

    Science.gov (United States)

    Shin, Sun-Jeong; Sul, Yeonah; Kim, Ja Hye; Cho, Ja Hyang; Kim, Gu-Hwan; Kim, Jae Hyun; Choi, Jin-Ho; Yoo, Han-Wook

    2015-03-01

    Isolated gonadotropin-releasing hormone (GnRH) deficiency (IGD) is classified as Kallmann syndrome (KS) with anosmia and normosmic idiopathic hypogonadotropic hypogonadism (nIHH). This study was undertaken to investigate the clinical, endocrinological, and molecular characteristics in Korean patients with KS and nIHH. Twenty-six patients from 25 unrelated families were included. Their clinical, endocrinological, and radiological findings were analyzed retrospectively. Mutation analysis of the GNRH1, GNRHR, KISS1, KISS1R, PROK2, PROKR2, TAC3, TACR3, FGF8, FGFR1, and KAL1 genes was performed in all patients. CHD7 and SOX10 were analyzed in patients with CHARGE (Coloboma, Heart defects, choanae Atresia, Growth retardation, Genitourinary abnormality, Ear abnormality) features or deafness. Of the 26 patients, 16 had KS and 10 had nIHH. At diagnosis, mean chronologic age was 18.1 years in males and 18.0 years in females; height SDS were -0.67±1.35 in males, -1.12±1.86 in females; testis volume was 2.0±1.3 mL; and Tanner stage was 1.5. There were associated anomalies in some of the KS patients: hearing loss (n=6) and congenital heart disease (n=4). Absence or hypoplasia of the olfactory bulb/sulci was found in 84.62% of patients with KS. Molecular defects in KAL1, SOX10, and CHD7 were identified in 5 patients from 4 families (16.0%, 4/25 pedigrees). After sex hormone replacement therapy, there were improvement in sexual characteristics and the sexual function. This study described the clinical, endocrinological, and molecular genetic features in IGD patients in Korea. Although the mutation screening was performed in 10 genes that cause IGD, molecular defects were identified in relatively small proportions of the cohort.

  7. Acid monolayer functionalized iron oxide nanoparticle catalysts

    Science.gov (United States)

    Ikenberry, Myles

    Superparamagnetic iron oxide nanoparticle functionalization is an area of intensely active research, with applications across disciplines such as biomedical science and heterogeneous catalysis. This work demonstrates the functionalization of iron oxide nanoparticles with a quasi-monolayer of 11-sulfoundecanoic acid, 10-phosphono-1-decanesulfonic acid, and 11-aminoundecanoic acid. The carboxylic and phosphonic moieties form bonds to the iron oxide particle core, while the sulfonic acid groups face outward where they are available for catalysis. The particles were characterized by thermogravimetric analysis (TGA), transmission electron microscopy (TEM), potentiometric titration, diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), inductively coupled plasma optical emission spectrometry (ICP-OES), X-ray photoelectron spectrometry (XPS), and dynamic light scattering (DLS). The sulfonic acid functionalized particles were used to catalyze the hydrolysis of sucrose at 80° and starch at 130°, showing a higher activity per acid site than the traditional solid acid catalyst Amberlyst-15, and comparing well against results reported in the literature for sulfonic acid functionalized mesoporous silicas. In sucrose catalysis reactions, the phosphonic-sulfonic nanoparticles (PSNPs) were seen to be incompletely recovered by an external magnetic field, while the carboxylic-sulfonic nanoparticles (CSNPs) showed a trend of increasing activity over the first four recycle runs. Between the two sulfonic ligands, the phosphonates produced a more tightly packed monolayer, which corresponded to a higher sulfonic acid loading, lower agglomeration, lower recoverability through application of an external magnetic field, and higher activity per acid site for the hydrolysis of starch. Functionalizations with 11-aminoundecanoic acid resulted in some amine groups binding to the surfaces of iron oxide nanoparticles. This amine binding is commonly ignored in iron oxide

  8. On the Wrapping of Polyglycolide, Poly(Ethylene Oxide), and Polyketone Polymer Chains Around Single-Walled Carbon Nanotubes Using Molecular Dynamics Simulations

    Science.gov (United States)

    Rouhi, S.; Alizadeh, Y.; Ansari, R.

    2015-02-01

    By using molecular dynamics simulations, the interaction between a single-walled carbon nanotube and three different polymers has been studied in this work. The effects of various parameters such as the nanotube geometry and temperature on the interaction energy and radius of gyration of polymers have been explored. By studying the snapshots of polymers along the single-walled carbon nanotube, it has been shown that 50 ps can be considered as a suitable time after which the shape of polymer chains around the nanotube remains almost unchanged. It is revealed that the effect of temperature on the interaction energy and radius of gyration of polymers in the range of 250 to 500 K is not significant Also, it is shown that the interaction energy depends on the nanotube diameter.

  9. Photon emission statistics and photon tracking in single-molecule spectroscopy of molecular aggregates : Dimers and trimers

    NARCIS (Netherlands)

    Bloemsma, E. A.; Knoester, J.

    2012-01-01

    Based on the generating function formalism, we investigate broadband photon statistics of emission for single dimers and trimers driven by a continuous monochromatic laser field. In particular, we study the first and second moments of the emission statistics, which are the fluorescence excitation

  10. Towards single molecule biosensors using super-resolution fluorescence microscopy.

    Science.gov (United States)

    Lu, Xun; Nicovich, Philip R; Gaus, Katharina; Gooding, J Justin

    2017-07-15

    Conventional immunosensors require many binding events to give a single transducer output which represents the concentration of the analyte in the sample. Because of the requirements to selectively detect species in complex samples, immunosensing interfaces must allow immobilisation of antibodies while repelling nonspecific adsorption of other species. These requirements lead to quite sophisticated interfacial design, often with molecular level control, but we have no tools to characterise how well these interfaces work at the molecular level. The work reported herein is an initial feasibility study to show that antibody-antigen binding events can be monitored at the single molecule level using single molecule localisation microscopy (SMLM). The steps to achieve this first requires showing that indium tin oxide surfaces can be used for SMLM, then that these surfaces can be modified with self-assembled monolayers using organophosphonic acid derivatives, that the amount of antigens and antibodies on the surface can be controlled and monitored at the single molecule level and finally antibody binding to antigen modified surfaces can be monitored. The results show the amount of antibody that binds to an antigen modified surface is dependent on both the concentration of antigen on the surface and the concentration of antibody in solution. This study demonstrates the potential of SMLM for characterising biosensing interfaces and as the transducer in a massively parallel, wide field, single molecule detection scheme for quantitative analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Dynamics of ordered-domain formation of DNA fragments on Au(111) with molecular resolution

    DEFF Research Database (Denmark)

    Wackerbarth, Hainer; Ulstrup, Jens

    2004-01-01

    KeyWords Plus: SCANNING-TUNNELING-MICROSCOPY; PSEUDOMONAS-AERUGINOSA AZURIN; INTERFACIAL ELECTRON-TRANSFER; SELF-ASSEMBLED MONOLAYERS; SINGLE-CRYSTAL; THIN-FILMS; SURFACES; ELECTROCHEMISTRY; VOLTAMMETRY; ADSORPTION......KeyWords Plus: SCANNING-TUNNELING-MICROSCOPY; PSEUDOMONAS-AERUGINOSA AZURIN; INTERFACIAL ELECTRON-TRANSFER; SELF-ASSEMBLED MONOLAYERS; SINGLE-CRYSTAL; THIN-FILMS; SURFACES; ELECTROCHEMISTRY; VOLTAMMETRY; ADSORPTION...

  12. Method for selective immobilization of macromolecules on self assembled monolayer surfaces

    Science.gov (United States)

    Laskin, Julia [Richland, WA; Wang, Peng [Billerica, MA

    2011-11-29

    Disclosed is a method for selective chemical binding and immobilization of macromolecules on solid supports in conjunction with self-assembled monolayer (SAM) surfaces. Immobilization involves selective binding of peptides and other macromolecules to SAM surfaces using reactive landing (RL) of mass-selected, gas phase ions. SAM surfaces provide a simple and convenient platform for tailoring chemical properties of a variety of substrates. The invention finds applications in biochemistry ranging from characterization of molecular recognition events at the amino acid level and identification of biologically active motifs in proteins, to development of novel biosensors and substrates for stimulated protein and cell adhesion.

  13. Synthesis of Novel Amphiphilic Azobenzenes and X-ray Scattering Studies of Their Langmuir Monolayers

    DEFF Research Database (Denmark)

    Sørensen, Thomas Just; Kjær, Kristian; Breiby, Dag Werner

    2008-01-01

    . At the air-water interface, the amphiphilic azobenzenes form noncrystalline but stable Langmuir films that display an unusual reversible monolayer collapse close to 35 mN/m. The structures and phase transitions were studied by X-ray reflectivity (XR) and grazing-incidence X-ray diffraction, both utilizing...... synchrotron radiation. Compression beyond the collapse point does not change the XR data, showing that the film is unchanged at the molecular level, even at areas less than half of that of the collapse. This leads to the conclusion that few macroscopic collapse sites are responsible for reversibly removing...

  14. Site accessibility tailors DNA cleavage by restriction enzymes in DNA confined monolayers.

    Science.gov (United States)

    Rotella, Chiara; Doni, Giovanni; Bosco, Alessandro; Castronovo, Matteo; De Vita, Alessandro; Casalis, Loredana; Pavan, Giovanni M; Parisse, Pietro

    2017-05-18

    Density-tunable nanografted monolayers (NAMs) of short oligonucleotide sequences on gold surfaces show novel properties that make them suitable for advanced biosensing applications, and in particular to study the effects of crowding and confinement on biomolecular interactions. Here, combining atomic force microscopy nanolithography, topography measurements and coarse-grained molecular dynamics simulations, we investigated restriction enzyme reaction mechanisms within confined DNA brushes highlighting the role played by the DNA sequence conformation and restriction site position along the chain, respectively, in determining the accessibility of the enzyme, and its consequent cleavage efficiency.

  15. Reflection and extinction of light by self-assembled monolayers of a quinque-thiophene derivative: A coherent scattering approach.

    Science.gov (United States)

    Gholamrezaie, Fatemeh; de Leeuw, Dago M; Meskers, Stefan C J

    2016-06-07

    Scattering matrix theory is used to describe resonant optical properties of molecular monolayers. Three types of coupling are included: exciton-exciton, exciton-photon, and exciton-phonon coupling. We use the K-matrix formalism, developed originally to describe neutron scattering spectra in nuclear physics to compute the scattering of polaritons by phonons. This perturbation approach takes into account the three couplings and allows one to go beyond molecular exciton theory without the need of introducing additional boundary conditions for the polariton. We demonstrate that reflection, absorption, and extinction of light by 2D self-assembled monolayers of molecules containing quinque-thiophene chromophoric groups can be calculated. The extracted coherence length of the Frenkel exciton is discussed.

  16. Reflection and extinction of light by self-assembled monolayers of a quinque-thiophene derivative: A coherent scattering approach

    Energy Technology Data Exchange (ETDEWEB)

    Gholamrezaie, Fatemeh; Meskers, Stefan C. J., E-mail: s.c.j.meskers@tue.nl [Molecular Materials and Nanosystems and Institute of Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven (Netherlands); Leeuw, Dago M. de [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany)

    2016-06-07

    Scattering matrix theory is used to describe resonant optical properties of molecular monolayers. Three types of coupling are included: exciton-exciton, exciton-photon, and exciton-phonon coupling. We use the K-matrix formalism, developed originally to describe neutron scattering spectra in nuclear physics to compute the scattering of polaritons by phonons. This perturbation approach takes into account the three couplings and allows one to go beyond molecular exciton theory without the need of introducing additional boundary conditions for the polariton. We demonstrate that reflection, absorption, and extinction of light by 2D self-assembled monolayers of molecules containing quinque-thiophene chromophoric groups can be calculated. The extracted coherence length of the Frenkel exciton is discussed.

  17. Near-Edge X-ray Absorption Fine Structure Spectroscopy of Diamondoid Thiol Monolayers on Gold

    Energy Technology Data Exchange (ETDEWEB)

    Willey, T M; Fabbri, J; Lee, J I; Schreiner, P; Fokin, A A; Tkachenko, B A; Fokina, N A; Dahl, J; Carlson, B; Vance, A L; Yang, W; Terminello, L J; van Buuren, T; Melosh, N

    2007-11-27

    Diamondoids, hydrocarbon molecules with cubic-diamond-cage structures, have unique properties with potential value for nanotechnology. The availability and ability to selectively functionalize this special class of nanodiamond materials opens new possibilities for surface-modification, for high-efficiency field emitters in molecular electronics, as seed crystals for diamond growth, or as robust mechanical coatings. The properties of self-assembled monolayers (SAMs) of diamondoids are thus of fundamental interest for a variety of emerging applications. This paper presents the effects of thiol substitution position and polymantane order on diamondoid SAMs on gold using near-edge X-ray absorption fine structure spectroscopy (NEXAFS) and X-ray photoelectron spectroscopy (XPS). A framework to determine both molecular tilt and twist through NEXAFS is presented and reveals highly ordered diamondoid SAMs, with the molecular orientation controlled by the thiol location. C 1s and S 2p binding energies are lower in adamantane thiol than alkane thiols on gold by 0.67 {+-} 0.05 eV and 0.16 {+-} 0.04 eV respectively. These binding energies vary with diamondoid monolayer structure and thiol substitution position, consistent with different amounts of steric strain and electronic interaction with the substrate. This work demonstrates control over the assembly, in particular the orientational and electronic structure, providing a flexible design of surface properties with this exciting new class of diamond clusters.

  18. Fabrication of Silicon nanostructures by UHV-STM lithography in Self-Assembled Monolayers

    International Nuclear Information System (INIS)

    Sundermann, M.; Brechling, A.; Rott, K.; Meyners, D.; Kleineberg, U.; Heinzmann, U.; Knueller, A.; Eck, W.; Goelzhueuser, A.; Grunze, M.

    2002-01-01

    Our approach utilizes UHV-STM writing in Self-Assembled Monolayers (SAM). SAMs form highly-ordered ultrathin (∼2-3 nm) monomolecular layers on top of pre-activated Si(100) or Si(111) surfaces. After patterning by UHV-STM writing in constant-current mode at different write parameters (gap voltage, electron dose) the modified Self-Assembled Monolayer serves as an etch mask for an anisotropic wet etch transfer (two-step etch process in aqueous solutions of 5 % HF and 1 M KOH), of the write structure into the silicon substrate. The corresponding silicon nano-structures have been analyzed afterwards by AFM or SEM to characterize the pattern accuracy. We have studied the suitability of three different types of SAMs on silicon single-crystals. Alkyl-chain-type SAMs like Octadecylsilane (ODS) monolayer have been formed by immersion of hydroxylated Si(100) in Octadecyltrichlorosilane (CH 3 (CH 27 SiCl 3 ) while SAMs with aromatic spacer groups such as Hydroxybiphenyl (HBP, (C 6 H 6 ) 2 OH) and Ethoxybiphenyl silane (EBP, (C 6 H 6 ) 2 O(CH 2 ) 3 Si(OCH 3 ) 3 ) are formed on Si(111). (Authors)

  19. Cascaded exciton energy transfer in a monolayer semiconductor lateral heterostructure assisted by surface plasmon polariton.

    Science.gov (United States)

    Shi, Jinwei; Lin, Meng-Hsien; Chen, I-Tung; Mohammadi Estakhri, Nasim; Zhang, Xin-Quan; Wang, Yanrong; Chen, Hung-Ying; Chen, Chun-An; Shih, Chih-Kang; Alù, Andrea; Li, Xiaoqin; Lee, Yi-Hsien; Gwo, Shangjr

    2017-06-26

    Atomically thin lateral heterostructures based on transition metal dichalcogenides have recently been demonstrated. In monolayer transition metal dichalcogenides, exciton energy transfer is typically limited to a short range (~1 μm), and additional losses may be incurred at the interfacial regions of a lateral heterostructure. To overcome these challenges, here we experimentally implement a planar metal-oxide-semiconductor structure by placing a WS 2 /MoS 2 monolayer heterostructure on top of an Al 2 O 3 -capped Ag single-crystalline plate. We find that the exciton energy transfer range can be extended to tens of microns in the hybrid structure mediated by an exciton-surface plasmon polariton-exciton conversion mechanism, allowing cascaded exciton energy transfer from one transition metal dichalcogenides region supporting high-energy exciton resonance to a different transition metal dichalcogenides region in the lateral heterostructure with low-energy exciton resonance. The realized planar hybrid structure combines two-dimensional light-emitting materials with planar plasmonic waveguides and offers great potential for developing integrated photonic and plasmonic devices.Exciton energy transfer in monolayer transition metal dichalcogenides is limited to short distances. Here, Shi et al. fabricate a planar metal-oxide-semiconductor structure and show that exciton energy transfer can be extended to tens of microns, mediated by an exciton-surface-plasmon-polariton-exciton conversion mechanism.

  20. Probing protein: DNA interactions using a uniform monolayer of DNA and surface plasmon resonance

    Science.gov (United States)

    Shumaker-Parry, Jennifer S.; Campbell, Charles T.; Stormo, Gary D.; Silbaq, Fauzi S.; Aebersold, Rudolf H.

    2000-04-01

    A method is described for immobilizing double-stranded DNAs to a planar gold surface with high density and uniform spacing. This is accomplished by adsorbing biotinylated DNAs onto a nearly close-packed monolayer of the protein streptavidin. This streptavidin monolayer, which offers approximately 5 X 1012 biotin sites per cm2, is prepared first by adsorbing it onto a mixed self-assembled monolayer on gold which contains biotin-terminated and oligo-terminated alkylthiolates in a 3/7 ratio. This DNA- functionalized surface resists non-specific protein adsorption and is useful for probing the kinetics and equilibrium binding of proteins to DNA with surface plasmon resonance. This is demonstrated with the Mnt protein, which is found to bind in 3.8:1 ratio to its immobilized DNA operator sequence. This is consistent with its behavior in homogeneous solution, where it binds as a tetramer to its DNA. A sequence with a single base-pair mutation shows nearly as much Mnt binding, but a completely random DNA sequence shows only 5 percent of this binding. This proves that DNA-binding proteins bind sequence-specifically to double-stranded DNAs which are immobilized to gold with this streptavidin linker layer.