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Sample records for doped small molecular

  1. Stable inverted small molecular organic solar cells using a p-doped optical spacer.

    PubMed

    Lee, Sang-Hoon; Seo, Ji-Won; Lee, Jung-Yong

    2015-01-01

    We report inverted small molecular organic solar cells using a doped window layer as an optical spacer. The optical spacer was used to shift the optical field distribution inside the active layers, generating more charge carriers from sunlight. In this report, N,N,N',N'-tetrakis(4-methoxyphenyl)-benzidine (MeO-TPD) was doped with 2,2-(perfluoronaphthalene-2,6-diylidene)dimalononitrile (F6-TCNNQ), a p-type dopant material. P-doped MeO-TPD was adopted as an optical spacer because it has a large energy band gap, and its conductivity can be increased by several orders of magnitude through a doping process. As a result, a power conversion efficiency of 4.15% was achieved with the doped window layer of optimized thickness. Lastly, we present significantly improved stability of the inverted devices with the MeO-TPD layer. PMID:25407588

  2. The Electric and Optical Properties of Doped Small Molecular Organic Light-Emitting Devices

    SciTech Connect

    Kwang-Ohk Cheon

    2003-08-05

    Organic light-emitting devices (OLEDs) constitute a new and exciting emissive display technology. In general, the basic OLED structure consists of a stack of fluorescent organic layers sandwiched between a transparent conducting-anode and metallic cathode. When an appropriate bias is applied to the device, holes are injected from the anode and electrons from the cathode; some of the recombination events between the holes and electrons result in electroluminescence (EL). Until now, most of the efforts in developing OLEDs have focused on display applications, hence on devices within the visible range. However some organic devices have been developed for ultraviolet or infrared emission. Various aspects of the device physics of doped small molecular OLEDs were described and discussed. The doping layer thickness and concentration were varied systematically to study their effects on device performances, energy transfer, and turn-off dynamics. Low-energy-gap DCM2 guest molecules, in either {alpha}-NPD or DPVBi host layers, are optically efficient fluorophores but also generate deep carrier trap-sites. Since their traps reduce the carrier mobility, the current density decreases with increased doping concentration. At the same time, due to efficient energy transfer, the quantum efficiency of the devices is improved by light doping or thin doping thickness, in comparison with the undoped neat devices. However, heavy doping induces concentration quenching effects. Thus, the doping concentration and doping thickness may be optimized for best performance.

  3. Molecularly doped metals.

    PubMed

    Avnir, David

    2014-02-18

    The many millions of organic, inorganic, and bioorganic molecules represent a very rich library of chemical, biological, and physical properties that do not show up among the approximately 100 metals. The ability to imbue metals with any of these molecular properties would open up tremendous potential for the development of new materials. In addition to their traditional features and their traditional applications, metals would have new traits, which would merge their classical virtues such as conductivity and catalytic activity with the diverse properties of these molecules. In this Account, we describe a new materials methodology, which enables, for the first time, the incorporation and entrapment of small organic molecules, polymers, and biomolecules within metals. These new materials are denoted dopant@metal. The creation of dopant@metal yields new properties that are more than or different from the sum of the individual properties of the two components. So far we have developed methods for the doping of silver, copper, gold, iron, palladium, platinum, and some of their alloys, as well as Hg-Ag amalgams. We have successfully altered classical metal properties (such as conductivity), induced unorthodox properties (such as rendering a metal acidic or basic), used metals as heterogeneous matrices for homogeneous catalysts, and formed new metallic catalysts such as metals doped with organometallic complexes. In addition, we have created materials that straddle the border between polymers and metals, we have entrapped enzymes to form bioactive metals, we have induced chirality within metals, we have made corrosion-resistant iron, we formed efficient biocidal materials, and we demonstrated a new concept for batteries. We have developed a variety of methods for synthesizing dopant@metals including aqueous homogeneous and heterogeneous reductions of the metal cations, reductions in DMF, electrochemical entrapments, thermal decompositions of zerovalent metal carbonyls

  4. Molecularly doped metals.

    PubMed

    Avnir, David

    2014-02-18

    The many millions of organic, inorganic, and bioorganic molecules represent a very rich library of chemical, biological, and physical properties that do not show up among the approximately 100 metals. The ability to imbue metals with any of these molecular properties would open up tremendous potential for the development of new materials. In addition to their traditional features and their traditional applications, metals would have new traits, which would merge their classical virtues such as conductivity and catalytic activity with the diverse properties of these molecules. In this Account, we describe a new materials methodology, which enables, for the first time, the incorporation and entrapment of small organic molecules, polymers, and biomolecules within metals. These new materials are denoted dopant@metal. The creation of dopant@metal yields new properties that are more than or different from the sum of the individual properties of the two components. So far we have developed methods for the doping of silver, copper, gold, iron, palladium, platinum, and some of their alloys, as well as Hg-Ag amalgams. We have successfully altered classical metal properties (such as conductivity), induced unorthodox properties (such as rendering a metal acidic or basic), used metals as heterogeneous matrices for homogeneous catalysts, and formed new metallic catalysts such as metals doped with organometallic complexes. In addition, we have created materials that straddle the border between polymers and metals, we have entrapped enzymes to form bioactive metals, we have induced chirality within metals, we have made corrosion-resistant iron, we formed efficient biocidal materials, and we demonstrated a new concept for batteries. We have developed a variety of methods for synthesizing dopant@metals including aqueous homogeneous and heterogeneous reductions of the metal cations, reductions in DMF, electrochemical entrapments, thermal decompositions of zerovalent metal carbonyls

  5. Small molecules make big differences: molecular doping effects on electronic and optical properties of phosphorene.

    PubMed

    Jing, Yu; Tang, Qing; He, Peng; Zhou, Zhen; Shen, Panwen

    2015-03-01

    Systematical computations on the density functional theory were performed to investigate the adsorption of three typical organic molecules, tetracyanoquinodimethane (TCNQ), tetracyanoethylene (TCNE) and tetrathiafulvalene (TTF), on the surface of phosphorene monolayers and thicker layers. There exist considerable charge transfer and strong non-covalent interaction between these molecules and phosphorene. In particular, the band gap of phosphorene decreases dramatically due to the molecular modification and can be further tuned by applying an external electric field. Meanwhile, surface molecular modification has proven to be an effective way to enhance the light harvesting of phosphorene in different directions. Our results predict a flexible method toward modulating the electronic and optical properties of phosphorene and shed light on its experimental applications.

  6. Small molecules make big differences: molecular doping effects on electronic and optical properties of phosphorene

    NASA Astrophysics Data System (ADS)

    Jing, Yu; Tang, Qing; He, Peng; Zhou, Zhen; Shen, Panwen

    2015-03-01

    Systematical computations on the density functional theory were performed to investigate the adsorption of three typical organic molecules, tetracyanoquinodimethane (TCNQ), tetracyanoethylene (TCNE) and tetrathiafulvalene (TTF), on the surface of phosphorene monolayers and thicker layers. There exist considerable charge transfer and strong non-covalent interaction between these molecules and phosphorene. In particular, the band gap of phosphorene decreases dramatically due to the molecular modification and can be further tuned by applying an external electric field. Meanwhile, surface molecular modification has proven to be an effective way to enhance the light harvesting of phosphorene in different directions. Our results predict a flexible method toward modulating the electronic and optical properties of phosphorene and shed light on its experimental applications.

  7. Small molecules make big differences: molecular doping effects on electronic and optical properties of phosphorene.

    PubMed

    Jing, Yu; Tang, Qing; He, Peng; Zhou, Zhen; Shen, Panwen

    2015-03-01

    Systematical computations on the density functional theory were performed to investigate the adsorption of three typical organic molecules, tetracyanoquinodimethane (TCNQ), tetracyanoethylene (TCNE) and tetrathiafulvalene (TTF), on the surface of phosphorene monolayers and thicker layers. There exist considerable charge transfer and strong non-covalent interaction between these molecules and phosphorene. In particular, the band gap of phosphorene decreases dramatically due to the molecular modification and can be further tuned by applying an external electric field. Meanwhile, surface molecular modification has proven to be an effective way to enhance the light harvesting of phosphorene in different directions. Our results predict a flexible method toward modulating the electronic and optical properties of phosphorene and shed light on its experimental applications. PMID:25665596

  8. Method of making molecularly doped composite polymer material

    DOEpatents

    Affinito, John D [Tucson, AZ; Martin, Peter M [Kennewick, WA; Graff, Gordon L [West Richland, WA; Burrows, Paul E [Kennewick, WA; Gross, Mark E. , Sapochak, Linda S.

    2005-06-21

    A method of making a composite polymer of a molecularly doped polymer. The method includes mixing a liquid polymer precursor with molecular dopant forming a molecularly doped polymer precursor mixture. The molecularly doped polymer precursor mixture is flash evaporated forming a composite vapor. The composite vapor is cryocondensed on a cool substrate forming a composite molecularly doped polymer precursor layer, and the cryocondensed composite molecularly doped polymer precursor layer is cross linked thereby forming a layer of the composite polymer layer of the molecularly doped polymer.

  9. Electrical doping of organic molecular semiconductors

    NASA Astrophysics Data System (ADS)

    Gao, Weiying

    2004-11-01

    Electrical doping is perceived as a key to enhance the performance and versatility of organic molecular devices. Understanding the doping mechanism and the impact of doping on interface electronic structures is very important for better control of the doping. We show that an efficient p-doping is a result of a good energy match between the host ionization energy and the dopant electron affinity, via a study of the electronic structure of host and dopant materials using direct and inverse photoemission spectroscopies (UPS/IPES). The hole transport materials zinc phthalocyanine (ZnPc) and N,N'-diphenyl-N,N '-bis(1-naphthyl)-1,1'-biphenyl-4,4 '-diamine (alpha-NPD) are used as the host materials, and the strong acceptor material tetrafluorotetracyanoquinodimethane (F4 -TCNQ) is the p-type dopant. In p-doped films, EF moves closer to the HOMO, analogous to inorganic semiconductors. The ultimate position of EF with respect to the HOMO in highly doped film is limited by the large polarization and relaxation in molecular solids, especially in 3-D molecules like alpha-NPD. The study of the impact of doping at metal-organic interfaces shows that the interface electronic structure, i.e. interface dipole, ionization energy and EF-HOMO, is nearly independent of doping, although the bulk EF-HOMO of the doped film is determined by the dopant concentration. A depletion region is formed at the interface with its width depending on the dopant concentration similarly as metal-inorganic semiconductor interfaces. This narrow space charge region greatly improves hole injection by several orders of magnitude via tunneling. The impact of doping on the energy alignment at organic-organic heterojunction interfaces is found to be different compared to MO interfaces. Interface dipoles are generally seen upon doping of one organic material at these weakly interacting OO interfaces, and the electron and hole barriers at the interface are correspondingly modified. The interface dipole is found

  10. Self-doped molecular composite battery electrolytes

    DOEpatents

    Harrup, Mason K.; Wertsching, Alan K.; Stewart, Frederick F.

    2003-04-08

    This invention is in solid polymer-based electrolytes for battery applications. It uses molecular composite technology, coupled with unique preparation techniques to render a self-doped, stabilized electrolyte material suitable for inclusion in both primary and secondary batteries. In particular, a salt is incorporated in a nano-composite material formed by the in situ catalyzed condensation of a ceramic precursor in the presence of a solvated polymer material, utilizing a condensation agent comprised of at least one cation amenable to SPE applications. As such, the counterion in the condensation agent used in the formation of the molecular composite is already present as the electrolyte matrix develops. This procedure effectively decouples the cation loading levels required for maximum ionic conductivity from electrolyte physical properties associated with condensation agent loading levels by utilizing the inverse relationship discovered between condensation agent loading and the time domain of the aging step.

  11. Effect of molecular electrical doping on polyfuran based photovoltaic cells

    SciTech Connect

    Yu, Shuwen; Opitz, Andreas; Salzmann, Ingo; Frisch, Johannes; Cohen, Erez; Bendikov, Michael; Koch, Norbert

    2015-05-18

    The electronic, optical, and morphological properties of molecularly p-doped polyfuran (PF) films were investigated over a wide range of doping ratio in order to explore the impact of doping in photovoltaic applications. We find evidence for integer-charge transfer between PF and the prototypical molecular p-dopant tetrafluoro-tetracyanoquinodimethane (F4TCNQ) and employed the doped polymer in bilayer organic solar cells using fullerene as acceptor. The conductivity increase in the PF films at dopant loadings ≤2% significantly enhances the short-circuit current of photovoltaic devices. For higher doping ratios, however, F4TCNQ is found to precipitate at the heterojunction between the doped donor polymer and the fullerene acceptor. Ultraviolet photoelectron spectroscopy reveals that its presence acts beneficial to the energy-level alignment by doubling the open-circuit voltage of solar cells from 0.2 V to ca. 0.4 V, as compared to pristine PF.

  12. Effect of molecular electrical doping on polyfuran based photovoltaic cells

    NASA Astrophysics Data System (ADS)

    Yu, Shuwen; Frisch, Johannes; Opitz, Andreas; Cohen, Erez; Bendikov, Michael; Koch, Norbert; Salzmann, Ingo

    2015-05-01

    The electronic, optical, and morphological properties of molecularly p-doped polyfuran (PF) films were investigated over a wide range of doping ratio in order to explore the impact of doping in photovoltaic applications. We find evidence for integer-charge transfer between PF and the prototypical molecular p-dopant tetrafluoro-tetracyanoquinodimethane (F4TCNQ) and employed the doped polymer in bilayer organic solar cells using fullerene as acceptor. The conductivity increase in the PF films at dopant loadings ≤2% significantly enhances the short-circuit current of photovoltaic devices. For higher doping ratios, however, F4TCNQ is found to precipitate at the heterojunction between the doped donor polymer and the fullerene acceptor. Ultraviolet photoelectron spectroscopy reveals that its presence acts beneficial to the energy-level alignment by doubling the open-circuit voltage of solar cells from 0.2 V to ca. 0.4 V, as compared to pristine PF.

  13. [Gene doping: gene transfer and possible molecular detection].

    PubMed

    Argüelles, Carlos Francisco; Hernández-Zamora, Edgar

    2007-01-01

    The use of illegal substances in sports to enhance athletic performance during competition has caused international sports organizations such as the COI and WADA to take anti doping measures. A new doping method know as gene doping is defined as "the non-therapeutic use of genes, genetic elements and/or cells that have the capacity to enhance athletic performance". However, gene doping in sports is not easily identified and can cause serious consequences. Molecular biology techniques are needed in order to distinguish the difference between a "normal" and an "altered" genome. Further, we need to develop new analytic methods and biological molecular techniques in anti-doping laboratories, and design programs that avoid the non therapeutic use of genes.

  14. Reactions of small molecular systems

    SciTech Connect

    Wittig, C.

    1993-12-01

    This DOE program remains focused on small molecular systems relevant to combustion. Though a number of experimental approaches and machines are available for this research, the authors` activities are centered around the high-n Rydberg time-of-flight (HRTOF) apparatus in this laboratory. One student and one postdoc carry out experiments with this machine and also engage in small intra-group collaborations involving shared equipment. This past year was more productive than the previous two, due to the uninterrupted operation of the HRTOF apparatus. Results were obtained with CH{sub 3}OH, CH{sub 3}SH, Rg-HX complexes, HCOOH, and their deuterated analogs where appropriate. One paper is in print, three have been accepted for publication, and one is under review. Many preliminary results that augur well for the future were obtained with other systems such as HNO{sub 3}, HBr-HI complexes, toluene, etc. Highlights from the past year are presented below that display some of the features of this program.

  15. Molecular behavior in small spaces.

    PubMed

    Rebek, Julius

    2009-10-20

    The study of physical organic chemistry in solution is a mature science, over a century old, but over the last 10 years or so, reversible encapsulation has changed the way researchers view molecular interactions. It is now clear that the behavior of molecules in dilute solution is really quite different from their behavior in capsules. Molecules isolated from bulk media in spaces barely large enough to accommodate them and a few neighbors show new phenomena: their activities resemble those of molecules inside biochemical structures--pockets of enzymes, interiors of chaperones, or the inner space of the ribosome--rather than conventional behavior in solution. In this Account, we recount the behavior of molecules in these small spaces with emphasis on structures and reactivities that have not been, and perhaps cannot be, seen in conventional solution chemistry. The capsules self-assemble through a variety of forces, including hydrogen bonds, metal-ligand interactions, and hydrophobic effects. Their lifetimes range from milliseconds to hours, long enough for NMR spectroscopy to reveal what is going on inside. We describe one particular capsule, the elongated shape of which gives rise to many of the effects and unique phenomena. Molecular guests that are congruent to the space of the host can be tightly packed inside and show reduced mobilities such as rotation and translation within the capsule. These mobilities depend strongly on what else is encapsulated with them. We also relate how asymmetric spaces can be created inside the capsule by using a chiral guest. In contrast to the situation in dilute solution, where rapid exchange of solute partners and free molecular motion average out the steric and magnetic effects of chirality, the long lifetimes of the encounters in the capsules magnify the effects of an asymmetric environment. The capsule remains achiral, but the remaining space is chiral, and coencapsulated molecules respond in an amplified way. We probe the

  16. Surface doping of nitrogen atoms on graphene via molecular precursor

    SciTech Connect

    Hong, Guo; Wu, Qi-Hui; Ren, Jianguo; Xu, Tingting; Wang, Chundong; Zhang, Wenjun; Lee, Shuit-Tong

    2013-02-04

    Surface doping can be a powerful way to modify the electronic properties of graphene with the unique potential to retain the excellent pristine properties of graphene. Here, we report an atomic surface doping method for graphene via dissociation of adsorbed precursor molecules of tetrafluorotetracyanoquinodimethane (F{sub 4}-TCNQ) induced by hydrogen plasma treatment. Significantly, the location of the dopant N atoms can be pre-determined by the location and orientation of the F{sub 4}-TCNQ molecule precursor on graphene, leading in principle to site-selective doping. Furthermore, the molecular precursor is stable under ambient conditions, satisfying an important consideration for patterning processes.

  17. Enhanced sensitivity of graphene ammonia gas sensors using molecular doping

    NASA Astrophysics Data System (ADS)

    Mortazavi Zanjani, Seyedeh Maryam; Sadeghi, Mir Mohammad; Holt, Milo; Chowdhury, Sk. Fahad; Tao, Li; Akinwande, Deji

    2016-01-01

    We report on employing molecular doping to enhance the sensitivity of graphene sensors synthesized via chemical vapor deposition to NH3 molecules at room temperature. We experimentally show that doping an as-fabricated graphene sensor with NO2 gas improves sensitivity of its electrical resistance to adsorption of NH3 molecules by about an order of magnitude. The detection limit of our NO2-doped graphene sensor is found to be ˜200 parts per billion (ppb), compared to ˜1400 ppb before doping. Electrical characterization and Raman spectroscopy measurements on graphene field-effect transistors show that adsorption of NO2 molecules significantly increases hole concentration in graphene, which results in the observed sensitivity enhancement.

  18. Stable doping of carbon nanotubes via molecular self assembly

    SciTech Connect

    Lee, B.; Chen, Y.; Podzorov, V.; Cook, A.; Zakhidov, A.

    2014-10-14

    We report a novel method for stable doping of carbon nanotubes (CNT) based on methods of molecular self assembly. A conformal growth of a self-assembled monolayer of fluoroalkyl trichloro-silane (FTS) at CNT surfaces results in a strong increase of the sheet conductivity of CNT electrodes by 60–300%, depending on the CNT chirality and composition. The charge carrier mobility of undoped partially aligned CNT films was independently estimated in a field-effect transistor geometry (~100 cm²V⁻¹s⁻¹). The hole density induced by the FTS monolayer in CNT sheets is estimated to be ~1.8 ×10¹⁴cm⁻². We also show that FTS doping of CNT anodes greatly improves the performance of organic solar cells. This large and stable doping effect, easily achieved in large-area samples, makes this approach very attractive for applications of CNTs in transparent and flexible electronics.

  19. Superconductivity in oxygen doped iron telluride by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Zheng, Mao

    Iron base superconductor have gained much attention in the research community. They offer great potentials to improve our understanding of the subject of superconductivity by having another family of high temperature superconductors to compare and contrast to the cuprates. Practically, the iron based superconductors seems to be even better candidates for applications in power generation and power transmission. Iron telluride is regarded as the parent compound of the "11" family, the family of iron chalcogenide that has the simplest structure. Iron telluride itself is not a superconductor, by can become one when doped with oxygen. In this investigation, we developed the growth recipe of thin film iron telluride by Molecular Beam Epitaxy (MBE). We found the growth to be self-regulated, similar to that of GaAs. The initial layers of growth seem to experience a spontaneous crystallization, as the film quickly go from the initial polycrystalline phase to highly crystalline in just a few unit cells. We studied oxygen doping to the iron telluride thin films and the resultant superconductivity. We characterized the sample with AFM, XRD, transport, and STEM-EELS, and we found that interfacial strain is not an essential ingredient of superconductivity in this particular case. We investigated the doping conditions for two candidate oxygen doping modes: substitution and interstitial. We found that substitution occurs when the film grown in oxygen, while interstitial oxygen is primarily incorporated during annealing after growth. The substitutional oxygen are concentrated in small local regions where substitution is around 100%, but does not contribute to superconductivity. We estimated substitutional oxygen to be about 5%, and is the proximate cause of superconductivity. Hall experiment on our sample showed a shift of dominant carrier type from holes to electrons around 35 K, but the transition was set in motion as early as the structural phase transition around 70 K. We

  20. Small business development for molecular diagnostics.

    PubMed

    Anagostou, Anthanasia; Liotta, Lance A

    2012-01-01

    Molecular profiling, which is the application of molecular diagnostics technology to tissue and blood -specimens, is an integral element in the new era of molecular medicine and individualized therapy. Molecular diagnostics is a fertile ground for small business development because it can generate products that meet immediate demands in the health-care sector: (a) Detection of disease risk, or early-stage disease, with a higher specificity and sensitivity compared to previous testing methods, and (b) "Companion diagnostics" for stratifying patients to receive a treatment choice optimized to their individual disease. This chapter reviews the promise and challenges of business development in this field. Guidelines are provided for the creation of a business model and the generation of a marketing plan around a candidate molecular diagnostic product. Steps to commercialization are outlined using existing molecular diagnostics companies as learning examples.

  1. Chemistry: Small molecular replicators go organic

    NASA Astrophysics Data System (ADS)

    Taylor, Annette F.

    2016-09-01

    The emergence of complex, dynamic molecular behaviour might have had a role in the origin of life. Such behaviour has now been seen in a reaction network involving small, organic, self-replicating molecules of biological relevance. See Letter p.656

  2. Abnormal behavior of silica doped with small amounts of aluminum

    PubMed Central

    Liu, Jinling; Wang, Yiguang; An, Linan

    2016-01-01

    Silica is the most abundant mineral in the crust of the Earth. It has been demonstrated that the aluminum concentration in silica plays a key role in determining many properties of silica-based components. Although the alumina-silica system has been intensely studied, the effect of very small amounts of aluminum on the structure and properties of silica remains unclear. We report results of first principles calculations showing that small amounts of aluminum could be metastable when located in the center of Si-O rings without breaking the silica network. In contrast, higher aluminum contents will result in the destruction of the Si-O bonds, leading to the formation of triclusters and a 4-, 5-, and 6-fold Al-O coordination, as observed in previous studies. Based on the silica structure obtained through geometric optimization, the properties of silica doped with small amounts of aluminum were calculated. The results can account for many ‘abnormal’ phenomena experimentally observed. The results benefit most areas such as geosciences, microelectronics, glass industry, and ceramic materials. PMID:27752133

  3. Spectroscopic Evidence of Formation of Small Polarons in Doped Manganites

    NASA Astrophysics Data System (ADS)

    Moritomo, Yutaka; Machida, Akihiko; Nakamura, Arao

    1998-03-01

    Temperature dependence of absorption spectra for thin films of doped manganites R_0.6Sr_0.4MnO_3, where R is rare-earth atom, has been investigated systematically changing averaged ionic radius < rA > of perovskite A-site. We have observed a specific absorption band at ~1.5eV due to optical excitations from small polarons (SP)(Machida et al.), submitted.. Spectral weight of the SP band increases with decreasing temperature and eventually disappears at the insulator-metal (IM) transition, indicating that SP in the paramagnetic state (T >= T_C) changes into bare electrons (or large polarons) in the ferromagnetic state due to the enhanced one-electron bandwidth W. We further derived important physical quantities, i.e., W, on-site exchange interaction J and binding energy Ep of SP, and discuss material dependence of stability of SP. This work was supported by a Grant-In-Aid for Scientific Research from the Ministry of Education, Science, Sport and Culture and from PRESTO, Japan Scienece and Technology Corporation (JST), Japan.

  4. Perspective: Extremely fine tuning of doping enabled by combinatorial molecular-beam epitaxy

    NASA Astrophysics Data System (ADS)

    Wu, J.; Božović, I.

    2015-06-01

    Chemical doping provides an effective method to control the electric properties of complex oxides. However, the state-of-art accuracy in controlling doping is limited to about 1%. This hampers elucidation of the precise doping dependences of physical properties and phenomena of interest, such as quantum phase transitions. Using the combinatorial molecular beam epitaxy, we improve the accuracy in tuning the doping level by two orders of magnitude. We illustrate this novel method by two examples: a systematic investigation of the doping dependence of interface superconductivity, and a study of the competing ground states in the vicinity of the insulator-to-superconductor transition.

  5. Lutetium-doped EuO films grown by molecular-beam epitaxy

    SciTech Connect

    Melville, A.; Heeg, T.; Mairoser, T.; Schmehl, A.; Shai, D. E.; Monkman, E. J.; Harter, J. W.; Hollaender, B.; Schubert, J.; Shen, K. M.; Mannhart, J.; Schlom, D. G.

    2012-05-28

    The effect of lutetium doping on the structural, electronic, and magnetic properties of epitaxial EuO thin films grown by reactive molecular-beam epitaxy is experimentally investigated. The behavior of Lu-doped EuO is contrasted with doping by lanthanum and gadolinium. All three dopants are found to behave similarly despite differences in electronic configuration and ionic size. Andreev reflection measurements on Lu-doped EuO reveal a spin-polarization of 96% in the conduction band, despite non-magnetic carriers introduced by 5% lutetium doping.

  6. Analytical and numerical studies of photo-injected charge transport in molecularly-doped polymers

    NASA Astrophysics Data System (ADS)

    Roy Chowdhury, Amrita

    The mobility of photo-injected charge carriers in molecularly-doped polymers (MDPs) exhibits a commonly observed, and nearly universal Poole-Frenkel field dependence, mu exp√(beta0E), that has been shown to arise from the correlated Gaussian energy distribution of transport sites encountered by charges undergoing hopping transport through the material. Analytical and numerical studies of photo-injected charge transport in these materials are presented here with an attempt to understand how specific features of the various models developed to describe these systems depend on the microscopic parameters that define them. Specifically, previously published time-of-flight mobility data for the molecularly doped polymer 30% DEH:PC (polycarbonate doped with 30 wt.% aromatic hydrazone DEH) is compared with direct analytical and numerical predictions of five disorder-based models, the Gaussian disorder model (GDM) of Bassler, and four correlated disorder models introduced by Novikov, et al., and by Parris, et al. In these numerical studies, disorder parameters describing each model were varied from reasonable starting conditions, in order to give the best overall fit. The uncorrelated GDM describes the Poole-Frenkel field dependence of the mobility only at very high fields, but fails for fields lower than about 64 V/mum. The correlated disorder models with small amounts of geometrical disorder do a good over-all job of reproducing a robust Poole-Frenkel field dependence, with correlated disorder theories that employ polaron transition rates showing qualitatively better agreement with experiment than those that employ Miller-Abrahams rates. In a separate study, the heuristic treatment of spatial or geometric disorder incorporated in existing theories is critiqued, and a randomly-diluted lattice gas model is developed to describe the spatial disorder of the transport sites in a more realistic way.

  7. Quantitative Fermi level tuning in amorphous organic semiconductor by molecular doping: Toward full understanding of the doping mechanism

    NASA Astrophysics Data System (ADS)

    Yang, Jin-Peng; Wang, Wen-Qing; Bussolotti, Fabio; Cheng, Li-Wen; Li, Yan-Qing; Kera, Satoshi; Tang, Jian-Xin; Zeng, Xiang-Hua; Ueno, Nobuo

    2016-08-01

    The doping mechanism in organic-semiconductor films has been quantitatively studied via ultrahigh-sensitivity ultraviolet photoelectron spectroscopy of N,N-bis(1-naphthyl)-N,N-diphenyl-1,1-biphenyl-4,4-diamine (α-NPD) films doped with hexaazatriphenylene-hexacarbonitrile [HAT(CN)6]. We observed that HOMO of α-NPD shifts to the Fermi level (EF) in two different rates with the doping concentration of HAT(CN)6, but HOMO distributions of both pristine and doped amorphous α-NPD films are excellently approximated with a same Gaussian distribution without exponential tail states over ˜5 × 1018 cm-3 eV-1. From the theoretical simulation of the HAT(CN)6-concentration dependence of the HOMO in doped films, we show that the passivation of Gaussian-distributed hole traps, which peak at 1.1 eV above the HOMO onset, occurs at ultralow doping [HAT(CN)6 molecular ratio (MR) < 0.01], leading to a strong HOMO shift of ˜0.40 eV towards EF, and MR dependence of HOMO changes abruptly at MR ˜ 0.01 to a weaker dependence for MR > 0.01 due to future of the dopant acceptor level.

  8. Systems Pharmacology in Small Molecular Drug Discovery.

    PubMed

    Zhou, Wei; Wang, Yonghua; Lu, Aiping; Zhang, Ge

    2016-01-01

    Drug discovery is a risky, costly and time-consuming process depending on multidisciplinary methods to create safe and effective medicines. Although considerable progress has been made by high-throughput screening methods in drug design, the cost of developing contemporary approved drugs did not match that in the past decade. The major reason is the late-stage clinical failures in Phases II and III because of the complicated interactions between drug-specific, human body and environmental aspects affecting the safety and efficacy of a drug. There is a growing hope that systems-level consideration may provide a new perspective to overcome such current difficulties of drug discovery and development. The systems pharmacology method emerged as a holistic approach and has attracted more and more attention recently. The applications of systems pharmacology not only provide the pharmacodynamic evaluation and target identification of drug molecules, but also give a systems-level of understanding the interaction mechanism between drugs and complex disease. Therefore, the present review is an attempt to introduce how holistic systems pharmacology that integrated in silico ADME/T (i.e., absorption, distribution, metabolism, excretion and toxicity), target fishing and network pharmacology facilitates the discovery of small molecular drugs at the system level.

  9. Systems Pharmacology in Small Molecular Drug Discovery

    PubMed Central

    Zhou, Wei; Wang, Yonghua; Lu, Aiping; Zhang, Ge

    2016-01-01

    Drug discovery is a risky, costly and time-consuming process depending on multidisciplinary methods to create safe and effective medicines. Although considerable progress has been made by high-throughput screening methods in drug design, the cost of developing contemporary approved drugs did not match that in the past decade. The major reason is the late-stage clinical failures in Phases II and III because of the complicated interactions between drug-specific, human body and environmental aspects affecting the safety and efficacy of a drug. There is a growing hope that systems-level consideration may provide a new perspective to overcome such current difficulties of drug discovery and development. The systems pharmacology method emerged as a holistic approach and has attracted more and more attention recently. The applications of systems pharmacology not only provide the pharmacodynamic evaluation and target identification of drug molecules, but also give a systems-level of understanding the interaction mechanism between drugs and complex disease. Therefore, the present review is an attempt to introduce how holistic systems pharmacology that integrated in silico ADME/T (i.e., absorption, distribution, metabolism, excretion and toxicity), target fishing and network pharmacology facilitates the discovery of small molecular drugs at the system level. PMID:26901192

  10. Gate-Tunable Dirac Point of Molecular Doped Graphene.

    PubMed

    Solís-Fernández, Pablo; Okada, Susumu; Sato, Tohru; Tsuji, Masaharu; Ago, Hiroki

    2016-02-23

    Control of the type and density of charge carriers in graphene is essential for its implementation into various practical applications. Here, we demonstrate the gate-tunable doping effect of adsorbed piperidine on graphene. By gradually increasing the amount of adsorbed piperidine, the graphene doping level can be varied from p- to n-type, with the formation of p-n junctions for intermediate coverages. Moreover, the doping effect of the piperidine can be further tuned by the application of large negative back-gate voltages, which increase the doping level of graphene. In addition, the electronic properties of graphene are well preserved due to the noncovalent nature of the interaction between piperidine and graphene. This gate-tunable doping offers an easy, controllable, and nonintrusive method to alter the electronic structure of graphene. PMID:26812353

  11. Bismuth Interfacial Doping of Organic Small Molecules for High Performance n-type Thermoelectric Materials.

    PubMed

    Huang, Dazhen; Wang, Chao; Zou, Ye; Shen, Xingxing; Zang, Yaping; Shen, Hongguang; Gao, Xike; Yi, Yuanping; Xu, Wei; Di, Chong-An; Zhu, Daoben

    2016-08-26

    Development of chemically doped high performance n-type organic thermoelectric (TE) materials is of vital importance for flexible power generating applications. For the first time, bismuth (Bi) n-type chemical doping of organic semiconductors is described, enabling high performance TE materials. The Bi interfacial doping of thiophene-diketopyrrolopyrrole-based quinoidal (TDPPQ) molecules endows the film with a balanced electrical conductivity of 3.3 S cm(-1) and a Seebeck coefficient of 585 μV K(-1) . The newly developed TE material possesses a maximum power factor of 113 μW m(-1)  K(-2) , which is at the forefront for organic small molecule-based n-type TE materials. These studies reveal that fine-tuning of the heavy metal doping of organic semiconductors opens up a new strategy for exploring high performance organic TE materials. PMID:27496293

  12. Performance Enhancement of Small Molecular Solar Cells by Bilayer Cathode Buffer.

    PubMed

    Sun, Qinjun; Zhao, Huanbin; Zhou, Miao; Gao, Liyan; Hao, Yuying

    2016-04-01

    An effective composite bilayer cathode buffer structure is proposed for use in small molecular solar cells. CsF was doped in Alq3 to form the first cathode buffer, leading to small serial resistances. BCP was used as the second cathode buffer to block the holes to the electrode. The optimized bilayer cathode buffer significantly increased the short circuit and fill factor of devices. By integrating this bilayer cathode buffer, the CuPc/C60 small molecular heterojunction cell exhibited a power conversion efficiency of up to 0.8%, which was an improvement of 56% compared to a device with only the Alq3 cathode buffer. Meanwhile, the bilayer cathode buffer still has a good protective effect on the performance of the device. PMID:27451719

  13. Molecular dynamics investigations of boron doping in a-Si:H

    SciTech Connect

    Fedders, P.A.; Drabold, D.A.

    1997-07-01

    The rather low doping efficiency of B in a-Si:H is almost always explained by the argument that almost all of the B is incorporated into three-fold coordinated sites and that B is inert or non-doping in this configuration. Using ab initio molecular dynamics, the authors have studied the energetics and doping (electronic structure) consequences of B incorporation into a-Si:H both with and without H passivation. Their results suggest that the conventional view is in error and that the low doping efficiency is primarily due to H passivation. These results are consistent with the low doping efficiency of B as well as NMR studies on the large electric field gradients experienced by the B atoms and on NMR double resonance studies of B-H neighboring distances.

  14. Rectifying Properties of a Nitrogen/Boron-Doped Capped-Carbon-Nanotube-Based Molecular Junction

    NASA Astrophysics Data System (ADS)

    Zhao, Peng; Liu, De-Sheng; Zhang, Ying; Wang, Pei-Ji; Zhang, Zhong

    2011-04-01

    Based on the non-equilibrium Green's function method and first-principles density functional theory calculations, we investigate the electronic transport properties of a nitrogen/boron-doped capped-single-walled carbon-nanotube-based molecular junction. Obvious rectifying behavior is observed and it is strongly dependent on the doping site. The best rectifying performance can be carried out when the nitrogen/boron atom dopes at a carbon site in the second layer. Moreover, the rectifying performance can be further improved by adjusting the distance between the C60 nanotube caps.

  15. Tuning dissociation using isoelectronically doped graphene and hexagonal boron nitride: Water and other small molecules

    NASA Astrophysics Data System (ADS)

    Al-Hamdani, Yasmine S.; Alfè, Dario; von Lilienfeld, O. Anatole; Michaelides, Angelos

    2016-04-01

    Novel uses for 2-dimensional materials like graphene and hexagonal boron nitride (h-BN) are being frequently discovered especially for membrane and catalysis applications. Still however, a great deal remains to be understood about the interaction of environmentally and industrially relevant molecules such as water with these materials. Taking inspiration from advances in hybridising graphene and h-BN, we explore using density functional theory, the dissociation of water, hydrogen, methane, and methanol on graphene, h-BN, and their isoelectronic doped counterparts: BN doped graphene and C doped h-BN. We find that doped surfaces are considerably more reactive than their pristine counterparts and by comparing the reactivity of several small molecules, we develop a general framework for dissociative adsorption. From this a particularly attractive consequence of isoelectronic doping emerges: substrates can be doped to enhance their reactivity specifically towards either polar or non-polar adsorbates. As such, these substrates are potentially viable candidates for selective catalysts and membranes, with the implication that a range of tuneable materials can be designed.

  16. A molecular approach to Cu doped ZnO nanorods with tunable dopant content.

    PubMed

    Pashchanka, Mikhail; Hoffmann, Rudolf C; Gurlo, Aleksander; Swarbrick, Janine C; Khanderi, Jayaprakash; Engstler, Jörg; Issanin, Alexander; Schneider, Jörg J

    2011-04-28

    A novel molecular approach to the synthesis of polycrystalline Cu-doped ZnO rod-like nanostructures with variable concentrations of introduced copper ions in ZnO host matrix is presented. Spectroscopic (PLS, variable temperature XRD, XPS, ELNES, HERFD) and microscopic (HRTEM) analysis methods reveal the +II oxidation state of the lattice incorporated Cu ions. Photoluminescence spectra show a systematic narrowing (tuning) of the band gap depending on the amount of Cu(II) doping. The advantage of the template assembly of doped ZnO nanorods is that it offers general access to doped oxide structures under moderate thermal conditions. The doping content of the host structure can be individually tuned by the stoichiometric ratio of the molecular precursor complex of the host metal oxide and the molecular precursor complex of the dopant, Di-aquo-bis[2-(methoxyimino)-propanoato]zinc(II) 1 and -copper(II) 2. Moreover, these keto-dioximato complexes are accessible for a number of transition metal and lanthanide elements, thus allowing this synthetic approach to be expanded into a variety of doped 1D metal oxide structures.

  17. Antimony segregation in Ge and formation of n-type selectively doped Ge films in molecular beam epitaxy

    SciTech Connect

    Yurasov, D. V. Antonov, A. V.; Drozdov, M. N.; Schmagin, V. B.; Novikov, A. V.; Spirin, K. E.

    2015-10-14

    Antimony segregation in Ge(001) films grown by molecular beam epitaxy was studied. A quantitative dependence of the Sb segregation ratio in Ge on growth temperature was revealed experimentally and modeled theoretically taking into account both the terrace-mediated and step-edge-mediated segregation mechanisms. A nearly 5-orders-of-magnitude increase in the Sb segregation ratio in a relatively small temperature range of 180–350 °C was obtained, which allowed to form Ge:Sb doped layers with abrupt boundaries and high crystalline quality using the temperature switching method that was proposed earlier for Si-based structures. This technique was employed for fabrication of different kinds of n-type Ge structures which can be useful for practical applications like heavily doped n{sup +}-Ge films or δ-doped layers. Estimation of the doping profiles sharpness yielded the values of 2–5 nm per decade for the concentration gradient at the leading edge and 2–3 nm for the full-width-half-maximum of the Ge:Sb δ-layers. Electrical characterization of grown Ge:Sb structures revealed nearly full electrical activation of Sb atoms and the two-dimensional nature of charge carrier transport in δ-layers.

  18. Theoretical design of a novel copper doped gold cluster supported on graphene utilizing ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Koizumi, Kenichi; Nobusada, Katsuyuki; Boero, Mauro

    2015-12-01

    Ab initio molecular dynamics simulations have been used to inspect the adsorption of O2 to a small gold-copper alloy cluster supported on graphene. The exposed Cu atom in this cluster acts as a crucial attractive site for the approaching of O2 and consequently widens the reaction channel for the adsorption process. Conversely, a pure Au cluster on the same graphene support is inactive for the O2 adsorption because the corresponding reaction channel for the adsorption is very narrow. These results clearly indicate that doping a different metal to the Au cluster is a way to enhance the oxygen adsorption and to promote catalytic reactions.

  19. Deep levels in Ga-doped ZnSe grown by molecular-beam epitaxy

    NASA Astrophysics Data System (ADS)

    Venkatesan, S.; Pierret, R. F.; Qiu, J.; Kobayashi, M.; Gunshor, R. L.; Kolodziejski, L. A.

    1989-10-01

    Results of a deep-level transient spectroscopy study of Ga-doped ZnSe thin films grown by molecular-beam epitaxy are presented. Two prominent deep levels were observed in all the samples investigated. The concentration of the trap detected at 0.34 eV below the conduction-band edge was essentially independent of the doping concentration and is attributed to native defects arising from Se vacancies in the ZnSe films. The second level with an activation energy of 0.26 eV shows a very strong doping dependence and is tentatively identified as arising from dopant-site (gallium-on-zinc-site) defects complexed with selenium vacancies. Preliminary results also indicate that planar doping of ZnSe significantly reduces the concentration of the Ga-vacancy complex.

  20. Adsorption of molecular oxygen on VIIIB transition metal-doped graphene: A DFT study

    NASA Astrophysics Data System (ADS)

    Nasehnia, F.; Seifi, M.

    2014-12-01

    Adsorption of molecular oxygen with a triplet ground state on Fe-, Co-, Ni-, Ru-, Rh-, Pd-, OS-, Ir- and Pt-doped graphene is studied using density functional theory (DFT) calculations. The calculations show that O2 molecule is chemisorbed on the doped graphene sheets with large adsorption energies ranging from -0.653 eV to -1.851 eV and the adsorption process is irreversible. Mulliken atomic charge analysis of the structure shows that charge transfer from doped graphene sheets to O2 molecule. The amounts of transferred charge are between 0.375e- to 0.650e-, indicating a considerable change in the structures conductance. These results imply that the effect of O2 adsorption on transition metal-doped graphene structures can alter the possibility of using these materials as a toxic-gas (carbon monoxide, hydrogen fluoride, etc.) sensor.

  1. Well-ordered monolayers of alkali-doped coronene and picene: Molecular arrangements and electronic structures

    SciTech Connect

    Yano, M.; Endo, M.; Hasegawa, Y.; Okada, R.; Yamada, Y. Sasaki, M.

    2014-07-21

    Adsorptions of alkali metals (such as K and Li) on monolayers of coronene and picene realize the formation of ordered phases, which serve as well-defined model systems for metal-intercalated aromatic superconductors. Upon alkali-doping of the monolayers of coronene and picene, scanning tunneling microscopy and X-ray absorption spectroscopy revealed the rearrangement of the entire molecular layer. The K-induced reconstruction of both monolayers resulted in the formation of a structure with a herringbone-like arrangement of molecules, suggesting the intercalation of alkali metals between molecular planes. Upon reconstruction, a shift in both the vacuum level and core levels of coronene was observed as a result of a charge transfer from alkali metals to coronene. In addition, a new density of states near the Fermi level was formed in both the doped coronene and the doped picene monolayers. This characteristic electronic feature of the ordered monolayer has been also reported in the multilayer picene films, ensuring that the present monolayer can model the properties of the metal-intercalated aromatic hydrocarbons. It is suggested that the electronic structure near the Fermi level is sensitive to the molecular arrangement, and that both the strict control and determinations of the molecular structure in the doped phase should be important for the determination of the electronic structure of these materials.

  2. Phosphorus and phosphorus-nitrogen doped carbon nanotubes for ultrasensitive and selective molecular detection.

    PubMed

    Cruz-Silva, Eduardo; Lopez-Urias, Florentino; Munoz-Sandoval, Emilio; Sumpter, Bobby G; Terrones, Humberto; Charlier, Jean-Christophe; Meunier, Vincent; Terrones, Mauricio

    2011-03-01

    A first-principles approach is used to establish that substitutional phosphorus atoms within carbon nanotubes strongly modify the chemical properties of the surface, thus creating highly localized sites with specific affinity towards acceptor molecules. Phosphorus-nitrogen co-dopants within the tubes have a similar effect for acceptor molecules, but the P-N bond can also accept charge, resulting in affinity towards donor molecules. This molecular selectivity is illustrated in CO and NH3 adsorbed on PN-doped nanotubes, O2 on P-doped nanotubes, and NO2 and SO2 on both P- and PN-doped nanotubes. The adsorption of different chemical species onto the doped nanotubes modifies the dopant-induced localized states, which subsequently alter the electronic conductance. Although SO2 and CO adsorptions cause minor shifts in electronic conductance, NH3, NO2, and O2 adsorptions induce the suppression of a conductance dip. Conversely, the adsorption of NO2 on PN-doped nanotubes is accompanied with the appearance of an additional dip in conductance, correlated with a shift of the existing ones. Overall these changes in electric conductance provide an efficient way to detect selectively the presence of specific molecules. Additionally, the high oxidation potential of the P-doped nanotubes makes them good candidates for electrode materials in hydrogen fuel cells.

  3. P- and PN-Doped Nanotubes for Ultrasensitive and Selective Molecular Detection

    SciTech Connect

    Cruz Silva, Eduardo; Terrones Maldonado, Humberto; Terrones Maldonado, Mauricio; Charlier, Jean Christophe; Meunier, Vincent; Sumpter, Bobby G; Munoz-Sandoval, Emilio; Lopez, Florentino

    2010-01-01

    A first-principles approach is used to establish that substitutional phosphorus atoms strongly modify the chemical properties of the surface of carbon nanotubes, creating highly-localized sites with specific affinity towards acceptor molecules. Phosphorus-nitrogen co-dopants have a similar effect for acceptor molecules, but the P-N bond can also accept charge, resulting in affinity towards donor molecules. This molecular selectivity is illustrated in CO and NH3 adsorbed on PN doped nanotubes, O2 on P-doped nanotubes, and NO2 and SO2 on both P- and PN-doped nanotubes. The adsorption of different chemical species onto the doped nanotubes modifies the dopant-induced localized states, which subsequently alter electronic conductance. Although SO2 and CO adsorption cause minor shifts in electronic conductance; NH3, NO2, and O2 adsorptions induce the suppression of a conductance dip. Conversely, the adsorption of NO2 on PN-doped nanotubes is accompanied with the appearance of an additional dip in conductance, correlated with a shift of the existing ones. Overall these changes in electric conductance provide an efficient way to detect selectively the presence of specific molecules. Additionally, the high oxidation potential of the P-doped nanotubes makes them good candidates for electrode materials in hydrogen fuel cells.

  4. Phosphorus and phosphorus nitrogen doped carbon nanotubes for ultrasensitive and selective molecular detection

    SciTech Connect

    Cruz Silva, Eduardo; Lopez, Florentino; Munoz-Sandoval, Emilio; Sumpter, Bobby G; Terrones Maldonado, Humberto; Charlier, Jean Christophe; Meunier, Vincent; Terrones Maldonado, Mauricio

    2011-01-01

    A first-principles approach is used to establish that substitutional phosphorus atoms within carbon nanotubes strongly modify the chemical properties of the surface, thus creating highly localized sites with specific affinity towards acceptor molecules. Phosphorus nitrogen co-dopants within the tubes have a similar effect for acceptor molecules, but the P N bond can also accept charge, resulting in affinity towards donor molecules. This molecular selectivity is illustrated in CO and NH3 adsorbed on PN-doped nanotubes, O2 on P-doped nanotubes, and NO2 and SO2 on both P- and PN-doped nanotubes. The adsorption of different chemical species onto the doped nanotubes modifies the dopant-induced localized states, which subsequently alter the electronic conductance. Although SO2 and CO adsorptions cause minor shifts in electronic conductance, NH3, NO2, and O2 adsorptions induce the suppression of a conductance dip. Conversely, the adsorption of NO2 on PN-doped nanotubes is accompanied with the appearance of an additional dip in conductance, correlated with a shift of the existing ones. Overall these changes in electric conductance provide an efficient way to detect selectively the presence of specific molecules. Additionally, the high oxidation potential of the P-doped nanotubes makes them good candidates for electrode materials in hydrogen fuel cells.

  5. Usage of antimony segregation for selective doping of Si in molecular beam epitaxy

    SciTech Connect

    Yurasov, D. V.; Drozdov, M. N.; Murel, A. V.; Shaleev, M. V.; Novikov, A. V.; Zakharov, N. D.

    2011-06-01

    An original approach to selective doping of Si by antimony (Sb) in molecular beam epitaxy (MBE) is proposed and verified experimentally. This approach is based on controllable utilization of the effect of Sb segregation. In particular, the sharp dependence of Sb segregation on growth temperature in the range of 300-550 deg. C is exploited. The growth temperature variations between the kinetically limited and maximum segregation regimes are suggested to be utilized in order to obtain selectively doped structures with abrupt doping profiles. It is demonstrated that the proposed technique allows formation of selectively doped Si:Sb layers, including delta ({delta}-)doped layers in which Sb concentrations can be varied from 5 x 10{sup 15} to 10{sup 20} cm{sup -3}. The obtained doped structures are shown to have a high crystalline quality and the short-term growth interruptions, which are needed to change the substrate temperature, do not lead to any significant accumulation of background impurities in grown samples. Realization of the proposed approach requires neither too low (<300 deg. C), nor too high (>600 deg. C) growth temperatures or any special equipment for the MBE machines.

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

    PubMed

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

    2015-12-01

    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.

  7. n-type doping through tethered functionality: a new paradigm for molecular design of solution-processed organic thermoelectrics

    NASA Astrophysics Data System (ADS)

    Russ, Boris; Robb, Maxwell J.; Popere, Bhooshan C.; Perry, Erin E.; Urban, Jeffrey J.; Chabinyc, Michael L.; Hawker, Craig J.; Segalman, Rachel A.

    2015-03-01

    A scarcity of stable n-type doping mechanisms compatible with facile processing has been a major impediment to the advancement of n-type (electron transporting) organic thermoelectric materials. We recently demonstrated that trimethylammonium functionalization with hydroxide counterions, tethered to a perylene diimide core by alkyl spacers, facilitated solution-processing and resulted in extremely high carrier concentrations (1020carriers/cm3) and best-in-class thermoelectric performance in thin films. In this presentation, we report our recent findings on the underlying mechanism enabling charge carrier generation in these self-doping materials and its influence on material thermoelectric behavior. To draw these conclusions, we complement thermoelectric characterization with insights into chemical, electronic, and structural properties from XPS, optical spectroscopy, EPR, and GIWAXS experiments. Furthermore, we show that doping through tethered functionality can be extended to other n-type small molecule systems of interest, including naphthalene diimides and diketopyrrolopyrroles. Our findings help shape promising molecular design strategies for future enhancements in n-type thermoelectric performance.

  8. Tuning dissociation using isoelectronically doped graphene and hexagonal boron nitride: Water and other small molecules.

    PubMed

    Al-Hamdani, Yasmine S; Alfè, Dario; von Lilienfeld, O Anatole; Michaelides, Angelos

    2016-04-21

    Novel uses for 2-dimensional materials like graphene and hexagonal boron nitride (h-BN) are being frequently discovered especially for membrane and catalysis applications. Still however, a great deal remains to be understood about the interaction of environmentally and industrially relevant molecules such as water with these materials. Taking inspiration from advances in hybridising graphene and h-BN, we explore using density functional theory, the dissociation of water, hydrogen, methane, and methanol on graphene, h-BN, and their isoelectronic doped counterparts: BN dopedgraphene and C doped h-BN. We find that dopedsurfaces are considerably more reactive than their pristine counterparts and by comparing the reactivity of several small molecules, we develop a general framework for dissociative adsorption. From this a particularly attractive consequence of isoelectronic doping emerges: substrates can be doped to enhance their reactivity specifically towards either polar or non-polar adsorbates. As such, these substrates are potentially viable candidates for selective catalysts and membranes, with the implication that a range of tuneable materials can be designed. PMID:27389233

  9. Cu-doped AlN: A possible spinaligner at room-temperature grown by molecular beam epitaxy?

    SciTech Connect

    Ganz, P. R.; Schaadt, D. M.

    2011-12-23

    Cu-doped AlN was prepared by plasma assisted molecular beam epitaxy on C-plane sapphire substrates. The growth conditions were investigated for different Cu to Al flux ratios from 1.0% to 4.0%. The formation of Cu-Al alloys on the surface was observed for all doping level. In contrast to Cu-doped GaN, all samples showed diamagnetic behavior determined by SQUID measurements.

  10. [Small molecular agents against MERS-CoV infection].

    PubMed

    Zeng, Xiao-yun; Lu, Lu; Jiang, Shi-bo; Liu, Shu-wen

    2015-12-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) has caused outbreaks of SARS-like disease with 35% case-fatality rate, mainly in the Middle East. A more severe outbreak of MERS occurred recently in the Republic of Korea, where 186 people contracted the infections, causing great concern worldwide. So far, there has been no clinically available drug for the treatment of MERS-CoV infection. The potential drugs against MERS-CoV mainly consist of monoclonal antibodies, peptides and small molecular agents. Small molecular agents have an advantage of easier synthesis, lower cost in production and relatively higher stability. There is better chance for those candidates to gain a quick development. This article reviews the progress of developing small molecular MERS-CoV agents. PMID:27169271

  11. Advances in simulation study on organic small molecular solar cells

    NASA Astrophysics Data System (ADS)

    Zhang, Xuan; Guo, Wenge; Li, Ming; Ma, Wentao; Meng, Sen

    2015-02-01

    Recently, more focuses have been put on organic semiconductors because of its advantages, such as its flexibility, ease of fabrication and potential low cost, etc. The reasons we pay highlight on small molecular photovoltaic material are its ease of purification, easy to adjust and determine structure, easy to assemble range units and get high carrier mobility, etc. Simulation study on organic small molecular solar cells before the experiment can help the researchers find relationship between the efficiency and structure parameters, properties of material, estimate the performance of the device, bring the optimization of guidance. Also, the applicability of the model used in simulation can be discussed by comparison with experimental data. This paper summaries principle, structure, progress of numerical simulation on organic small molecular solar cells.

  12. Molecular Electrical Doping of Organic Semiconductors: Fundamental Mechanisms and Emerging Dopant Design Rules.

    PubMed

    Salzmann, Ingo; Heimel, Georg; Oehzelt, Martin; Winkler, Stefanie; Koch, Norbert

    2016-03-15

    Today's information society depends on our ability to controllably dope inorganic semiconductors, such as silicon, thereby tuning their electrical properties to application-specific demands. For optoelectronic devices, organic semiconductors, that is, conjugated polymers and molecules, have emerged as superior alternative owing to the ease of tuning their optical gap through chemical variability and their potential for low-cost, large-area processing on flexible substrates. There, the potential of molecular electrical doping for improving the performance of, for example, organic light-emitting devices or organic solar cells has only recently been established. The doping efficiency, however, remains conspicuously low, highlighting the fact that the underlying mechanisms of molecular doping in organic semiconductors are only little understood compared with their inorganic counterparts. Here, we review the broad range of phenomena observed upon molecularly doping organic semiconductors and identify two distinctly different scenarios: the pairwise formation of both organic semiconductor and dopant ions on one hand and the emergence of ground state charge transfer complexes between organic semiconductor and dopant through supramolecular hybridization of their respective frontier molecular orbitals on the other hand. Evidence for the occurrence of these two scenarios is subsequently discussed on the basis of the characteristic and strikingly different signatures of the individual species involved in the respective doping processes in a variety of spectroscopic techniques. The critical importance of a statistical view of doping, rather than a bimolecular picture, is then highlighted by employing numerical simulations, which reveal one of the main differences between inorganic and organic semiconductors to be their respective density of electronic states and the doping induced changes thereof. Engineering the density of states of doped organic semiconductors, the Fermi

  13. Coherent quasiparticles with a small fermi surface in lightly doped Sr(3)Ir(2)O(7).

    PubMed

    de la Torre, A; Hunter, E C; Subedi, A; McKeown Walker, S; Tamai, A; Kim, T K; Hoesch, M; Perry, R S; Georges, A; Baumberger, F

    2014-12-19

    We characterize the electron doping evolution of (Sr_{1-x}La_{x})_{3}Ir_{2}O_{7} by means of angle-resolved photoemission. Concomitant with the metal insulator transition around x≈0.05 we find the emergence of coherent quasiparticle states forming a closed small Fermi surface of volume 3x/2, where x is the independently measured La concentration. The quasiparticle weight Z remains large along the entire Fermi surface, consistent with the moderate renormalization of the low-energy dispersion, and no pseudogap is observed. This indicates a conventional, weakly correlated Fermi liquid state with a momentum independent residue Z≈0.5 in lightly doped Sr_{3}Ir_{2}O_{7}. PMID:25554897

  14. Coherent quasiparticles with a small fermi surface in lightly doped Sr(3)Ir(2)O(7).

    PubMed

    de la Torre, A; Hunter, E C; Subedi, A; McKeown Walker, S; Tamai, A; Kim, T K; Hoesch, M; Perry, R S; Georges, A; Baumberger, F

    2014-12-19

    We characterize the electron doping evolution of (Sr_{1-x}La_{x})_{3}Ir_{2}O_{7} by means of angle-resolved photoemission. Concomitant with the metal insulator transition around x≈0.05 we find the emergence of coherent quasiparticle states forming a closed small Fermi surface of volume 3x/2, where x is the independently measured La concentration. The quasiparticle weight Z remains large along the entire Fermi surface, consistent with the moderate renormalization of the low-energy dispersion, and no pseudogap is observed. This indicates a conventional, weakly correlated Fermi liquid state with a momentum independent residue Z≈0.5 in lightly doped Sr_{3}Ir_{2}O_{7}.

  15. Ultrasensitive molecular sensor using N-doped graphene through enhanced Raman scattering.

    PubMed

    Feng, Simin; Dos Santos, Maria Cristina; Carvalho, Bruno R; Lv, Ruitao; Li, Qing; Fujisawa, Kazunori; Elías, Ana Laura; Lei, Yu; Perea-López, Nestor; Endo, Morinobu; Pan, Minghu; Pimenta, Marcos A; Terrones, Mauricio

    2016-07-01

    As a novel and efficient surface analysis technique, graphene-enhanced Raman scattering (GERS) has attracted increasing research attention in recent years. In particular, chemically doped graphene exhibits improved GERS effects when compared with pristine graphene for certain dyes, and it can be used to efficiently detect trace amounts of molecules. However, the GERS mechanism remains an open question. We present a comprehensive study on the GERS effect of pristine graphene and nitrogen-doped graphene. By controlling nitrogen doping, the Fermi level (E F) of graphene shifts, and if this shift aligns with the lowest unoccupied molecular orbital (LUMO) of a molecule, charge transfer is enhanced, thus significantly amplifying the molecule's vibrational Raman modes. We confirmed these findings using different organic fluorescent molecules: rhodamine B, crystal violet, and methylene blue. The Raman signals from these dye molecules can be detected even for concentrations as low as 10(-11) M, thus providing outstanding molecular sensing capabilities. To explain our results, these nitrogen-doped graphene-molecule systems were modeled using dispersion-corrected density functional theory. Furthermore, we demonstrated that it is possible to determine the gaps between the highest occupied and the lowest unoccupied molecular orbitals (HOMO-LUMO) of different molecules when different laser excitations are used. Our simulated Raman spectra of the molecules also suggest that the measured Raman shifts come from the dyes that have an extra electron. This work demonstrates that nitrogen-doped graphene has enormous potential as a substrate when detecting low concentrations of molecules and could also allow for an effective identification of their HOMO-LUMO gaps. PMID:27532043

  16. Ultrasensitive molecular sensor using N-doped graphene through enhanced Raman scattering

    PubMed Central

    Feng, Simin; dos Santos, Maria Cristina; Carvalho, Bruno R.; Lv, Ruitao; Li, Qing; Fujisawa, Kazunori; Elías, Ana Laura; Lei, Yu; Perea-López, Nestor; Endo, Morinobu; Pan, Minghu; Pimenta, Marcos A.; Terrones, Mauricio

    2016-01-01

    As a novel and efficient surface analysis technique, graphene-enhanced Raman scattering (GERS) has attracted increasing research attention in recent years. In particular, chemically doped graphene exhibits improved GERS effects when compared with pristine graphene for certain dyes, and it can be used to efficiently detect trace amounts of molecules. However, the GERS mechanism remains an open question. We present a comprehensive study on the GERS effect of pristine graphene and nitrogen-doped graphene. By controlling nitrogen doping, the Fermi level (EF) of graphene shifts, and if this shift aligns with the lowest unoccupied molecular orbital (LUMO) of a molecule, charge transfer is enhanced, thus significantly amplifying the molecule’s vibrational Raman modes. We confirmed these findings using different organic fluorescent molecules: rhodamine B, crystal violet, and methylene blue. The Raman signals from these dye molecules can be detected even for concentrations as low as 10−11 M, thus providing outstanding molecular sensing capabilities. To explain our results, these nitrogen-doped graphene-molecule systems were modeled using dispersion-corrected density functional theory. Furthermore, we demonstrated that it is possible to determine the gaps between the highest occupied and the lowest unoccupied molecular orbitals (HOMO-LUMO) of different molecules when different laser excitations are used. Our simulated Raman spectra of the molecules also suggest that the measured Raman shifts come from the dyes that have an extra electron. This work demonstrates that nitrogen-doped graphene has enormous potential as a substrate when detecting low concentrations of molecules and could also allow for an effective identification of their HOMO-LUMO gaps. PMID:27532043

  17. Ultrasensitive molecular sensor using N-doped graphene through enhanced Raman scattering.

    PubMed

    Feng, Simin; Dos Santos, Maria Cristina; Carvalho, Bruno R; Lv, Ruitao; Li, Qing; Fujisawa, Kazunori; Elías, Ana Laura; Lei, Yu; Perea-López, Nestor; Endo, Morinobu; Pan, Minghu; Pimenta, Marcos A; Terrones, Mauricio

    2016-07-01

    As a novel and efficient surface analysis technique, graphene-enhanced Raman scattering (GERS) has attracted increasing research attention in recent years. In particular, chemically doped graphene exhibits improved GERS effects when compared with pristine graphene for certain dyes, and it can be used to efficiently detect trace amounts of molecules. However, the GERS mechanism remains an open question. We present a comprehensive study on the GERS effect of pristine graphene and nitrogen-doped graphene. By controlling nitrogen doping, the Fermi level (E F) of graphene shifts, and if this shift aligns with the lowest unoccupied molecular orbital (LUMO) of a molecule, charge transfer is enhanced, thus significantly amplifying the molecule's vibrational Raman modes. We confirmed these findings using different organic fluorescent molecules: rhodamine B, crystal violet, and methylene blue. The Raman signals from these dye molecules can be detected even for concentrations as low as 10(-11) M, thus providing outstanding molecular sensing capabilities. To explain our results, these nitrogen-doped graphene-molecule systems were modeled using dispersion-corrected density functional theory. Furthermore, we demonstrated that it is possible to determine the gaps between the highest occupied and the lowest unoccupied molecular orbitals (HOMO-LUMO) of different molecules when different laser excitations are used. Our simulated Raman spectra of the molecules also suggest that the measured Raman shifts come from the dyes that have an extra electron. This work demonstrates that nitrogen-doped graphene has enormous potential as a substrate when detecting low concentrations of molecules and could also allow for an effective identification of their HOMO-LUMO gaps.

  18. Couple molecular excitons to surface plasmon polaritons in an organic-dye-doped nanostructured cavity

    NASA Astrophysics Data System (ADS)

    Zhang, Kun; Shi, Wen-Bo; Wang, Di; Xu, Yue; Peng, Ru-Wen; Fan, Ren-Hao; Wang, Qian-Jin; Wang, Mu

    2016-05-01

    In this work, we demonstrate experimentally the hybrid coupling among molecular excitons, surface plasmon polaritons (SPPs), and Fabry-Perot (FP) mode in a nanostructured cavity, where a J-aggregates doped PVA (polyvinyl alcohol) layer is inserted between a silver grating and a thick silver film. By tuning the thickness of the doped PVA layer, the FP cavity mode efficiently couples with the molecular excitons, forming two nearly dispersion-free modes. The dispersive SPPs interact with these two modes while increasing the incident angle, leading to the formation of three hybrid polariton bands. By retrieving the mixing fractions of the polariton band components from the measured angular reflection spectra, we find all these three bands result from the strong coupling among SPPs, FP mode, and excitons. This work may inspire related studies on hybrid light-matter interactions, and achieve potential applications on multimode polariton lasers and optical spectroscopy.

  19. Time domain optical molecular imaging of small animals in vivo

    NASA Astrophysics Data System (ADS)

    Hall, David J.

    2006-03-01

    The advent of optical molecular probes has taken optical imaging beyond approaches limited to intrinsic optical contrast mechanisms. Fluorophores are typically used as the source of contrast for optical molecular probes and the field of optical molecular imaging is concerned with measuring and quantifying their in vivo biodistribution and pharmacokinetics. Most optical molecular imaging systems are based on Continuous Wave (CW) approaches which enable rapid, full-body imaging of small animals and readily yield images of probe location, however quantification of probe concentration is challenging. Time Domain (TD) approaches, although more expensive and complicated than CW, provide more information to assist in determining the probe location and concentration. Moreover, the TD approach permits access to measuring the fluorophore lifetime which can be indicative of the probe's environment. The eXplore Optix TM system, developed by ART (Canada; distributed by GE Healthcare, has enabled TD optical molecular imaging of small animals in vivo and preliminary studies conducted with the system will be presented. In addition, the initial research and development of a full-field TD optical molecular imaging system incorporating a high-power laser for area illumination and a gated-intensified CCD camera for area detection will be presented.

  20. Synthesis of doped graphene nanoribbons from molecular and polymeric precursors

    NASA Astrophysics Data System (ADS)

    Cloke, Ryan Randal

    As electronic devices continue to shrink and energy problems continue to grow, nanoscale materials are becoming increasingly important. Graphene is a material with exceptional promise to complement silicon in next-generation electronics because of its extraordinary charge carrier mobility, while also finding a role in cutting-edge energy solutions due to its high surface area and conductivity. Improving on this material even further by reducing the width of graphene to nanoscale dimensions with atomically-precise dopant patterns is the subject of this thesis. Nanometer-wide strips of graphene, known as graphene nanoribbons (GNRs), offer the advantages of semiconducting behavior, combined with more accessible surface area compared to bulk graphene (Chapter 1). Additionally, it is demonstrated that GNRs can be doped with atomic precision, allowing for intricate modulation of the electronic properties of this material, which was studied by STM, STS, and nc-AFM (Chapter 2). Controlled growth of GNRs on surfaces is still an outstanding challenge within the field, and to this end, a variety of porphyrin-GNR template materials were synthesized (Chapter 3). The GNRs obtained in this work were also synthesized in solution, and it was shown that these materials possess excellent properties for applications in hydrogen storage, carbon dioxide reduction, and Li-ion batteries (Chapter 4). A prerequisite for solution-synthesized GNRs, conjugated aromatic polymers are an important class of materials in their own right. Therefore, Ring-Opening Alkyne Metathesis Polymerization was developed using conjugated, strained diynes (Chapter 5). The resulting conjugated polymers were explored both for their own materials properties due to a remarkable self-assembly process that was discovered, and also as precursors to GNRs (Chapter 6). This work advances the fundamental understanding of carbon-based nanostructures, as well as the large-scale production of GNRs for next-generation energy

  1. Molecular adsorbates as probes of the local properties of doped graphene

    PubMed Central

    Pham, Van Dong; Joucken, Frédéric; Repain, Vincent; Chacon, Cyril; Bellec, Amandine; Girard, Yann; Rousset, Sylvie; Sporken, Robert; Santos, Maria Cristina dos; Lagoute, Jérôme

    2016-01-01

    Graphene-based sensors are among the most promising of graphene’s applications. The ability to signal the presence of molecular species adsorbed on this atomically thin substrate has been explored from electric measurements to light scattering. Here we show that the adsorbed molecules can be used to sense graphene properties. The interaction of porphyrin molecules with nitrogen-doped graphene has been investigated using scanning tunneling microscopy and ab initio calculations. Molecular manipulation was used to reveal the surface below the adsorbed molecules allowing to achieve an atomic-scale measure of the interaction of molecules with doped graphene. The adsorbate’s frontier electronic states are downshifted in energy as the molecule approaches the doping site, with largest effect when the molecule sits over the nitrogen dopant. Theoretical calculations showed that, due to graphene’s high polarizability, the adsorption of porphyrin induces a charge rearrangement on the substrate similar to the image charges on a metal. This charge polarization is enhanced around nitrogen site, leading to an increased interaction of molecules with their image charges on graphene. Consequently, the molecular states are stabilized and shift to lower energies. These findings reveal the local variation of polarizability induced by nitrogen dopant opening new routes towards the electronic tuning of graphene. PMID:27097555

  2. Long-wavelength PtSi infrared detectors fabricated by incorporating a p(+) doping spike grown by molecular beam epitaxy

    NASA Technical Reports Server (NTRS)

    Lin, T. L.; Park, J. S.; George, T.; Jones, E. W.; Fathauer, R. W.; Maserjian, J.

    1993-01-01

    By incorporating a 1-nm-thick p(+) doping spike at the PtSi/Si interface, we have successfully demonstrated extended cutoff wavelengths of PtSi Schottky infrared detectors in the long wavelength infrared (LWIR) regime for the first time. The extended cutoff wavelengths resulted from the combined effects of an increased electric field near the silicide/Si interface due to the p(+) doping spike and the Schottky image force. The p(+) doping spikes were grown by molecular beam epitaxy at 450 C, using elemental boron as the dopant source, with doping concentrations ranging from 5 x 10 exp 19 to 2 x 10 exp 20/cu cm. Transmission electron microscopy indicated good crystalline quality of the doping spikes. The cutoff wavelengths were shown to increase with increasing doping concentrations of the p(+) spikes. Thermionic emission dark current characteristics were observed and photoresponses in the LWIR regime were demonstrated.

  3. Gd(III) doping effect on magnetization and water proton relaxivities in ultra small iron oxide nanoparticles

    NASA Astrophysics Data System (ADS)

    Choi, Eun Sook; Xu, Wenlong; Baek, Myung Ju; Park, Ja Young; Kim, Joo Hyun; Chang, Yongmin; Kim, Tae Jeong; Lee, Gang Ho

    2013-07-01

    Two samples of ultra small Gd(III) doped iron oxide nanoparticles were prepared to investigate Gd(III) doping effect on longitudinal (r1) and transverse (r2) water proton relaxivities. Gd(III) doping mole percents were 0.2 and 0.4 for samples 1 and 2, respectively. Average particle diameters were 2.5 to 2.1 nm for samples 1 and 2, respectively. Reduced r1 and r2 values were observed in both samples. We attributed this to reduced magnetizations arising from opposing effect of Gd(III) to net magnetizations of Fe(III)/Fe(II) in oxide nanoparticles.

  4. Theoretical design of a novel copper doped gold cluster supported on graphene utilizing ab initio molecular dynamics simulations

    SciTech Connect

    Koizumi, Kenichi; Nobusada, Katsuyuki; Boero, Mauro

    2015-12-31

    Ab initio molecular dynamics simulations have been used to inspect the adsorption of O{sub 2} to a small gold-copper alloy cluster supported on graphene. The exposed Cu atom in this cluster acts as a crucial attractive site for the approaching of O{sub 2} and consequently widens the reaction channel for the adsorption process. Conversely, a pure Au cluster on the same graphene support is inactive for the O{sub 2} adsorption because the corresponding reaction channel for the adsorption is very narrow. These results clearly indicate that doping a different metal to the Au cluster is a way to enhance the oxygen adsorption and to promote catalytic reactions.

  5. Carbon doping in molecular beam epitaxy of GaAs from a heated graphite filament

    NASA Technical Reports Server (NTRS)

    Malik, R. J.; Nottenberg, R. N.; Schubert, E. F.; Walker, J. F.; Ryan, R. W.

    1988-01-01

    Carbon doping of GaAs grown by molecular beam epitaxy has been obtained for the first time by use of a heated graphite filament. Controlled carbon acceptor concentrations over the range of 10 to the 17th-10 to the 20th/cu cm were achieved by resistively heating a graphite filament with a direct current power supply. Capacitance-voltage, p/n junction and secondary-ion mass spectrometry measurements indicate that there is negligible diffusion of carbon during growth and with postgrowth rapid thermal annealing. Carbon was used for p-type doping in the base of Npn AlGaAs/GaAs heterojunction bipolar transistors. Current gains greater than 100 and near-ideal emitter heterojunctions were obtained in transistors with a carbon base doping of 1 x 10 to the 19th/cu cm. These preliminary results indicate that carbon doping from a solid graphite source may be an attractive substitute for beryllium, which is known to have a relatively high diffusion coefficient in GaAs.

  6. Electrical and optical properties of Fe doped AlGaN grown by molecular beam epitaxy

    SciTech Connect

    Polyakov, A. Y.; Smirnov, N. B.; Govorkov, A. V.; Kozhukhova, E. A.; Dabiran, A. M.; Chow, P. P.; Wowchak, A. M.; Pearton, S. J.

    2010-01-15

    Electrical and optical properties of AlGaN grown by molecular beam epitaxy were studied in the Al composition range 15%-45%. Undoped films were semi-insulating, with the Fermi level pinned near E{sub c}-0.6-0.7 eV. Si doping to (5-7)x10{sup 17} cm{sup -3} rendered the 15% Al films conducting n-type, but a large portion of the donors were relatively deep (activation energy 95 meV), with a 0.15 eV barrier for capture of electrons giving rise to strong persistent photoconductivity (PPC) effects. The optical threshold of this effect was {approx}1 eV. Doping with Fe to a concentration of {approx}10{sup 17} cm{sup -3} led to decrease in concentration of uncompensated donors, suggesting compensation by Fe acceptors. Addition of Fe strongly suppressed the formation of PPC-active centers in favor of ordinary shallow donors. For higher Al compositions, Si doping of (5-7)x10{sup 17} cm{sup -3} did not lead to n-type conductivity. Fe doping shifted the bandedge luminescence by 25-50 meV depending on Al composition. The dominant defect band in microcathodoluminescence spectra was the blue band near 3 eV, with the energy weakly dependent on composition.

  7. Chloride molecular doping technique on 2D materials: WS2 and MoS2.

    PubMed

    Yang, Lingming; Majumdar, Kausik; Liu, Han; Du, Yuchen; Wu, Heng; Hatzistergos, Michael; Hung, P Y; Tieckelmann, Robert; Tsai, Wilman; Hobbs, Chris; Ye, Peide D

    2014-11-12

    Low-resistivity metal-semiconductor (M-S) contact is one of the urgent challenges in the research of 2D transition metal dichalcogenides (TMDs). Here, we report a chloride molecular doping technique which greatly reduces the contact resistance (Rc) in the few-layer WS2 and MoS2. After doping, the Rc of WS2 and MoS2 have been decreased to 0.7 kΩ·μm and 0.5 kΩ·μm, respectively. The significant reduction of the Rc is attributed to the achieved high electron-doping density, thus a significant reduction of Schottky barrier width. As a proof-of-concept, high-performance few-layer WS2 field-effect transistors (FETs) are demonstrated, exhibiting a high drain current of 380 μA/μm, an on/off ratio of 4 × 10(6), and a peak field-effect mobility of 60 cm(2)/(V·s). This doping technique provides a highly viable route to diminish the Rc in TMDs, paving the way for high-performance 2D nanoelectronic devices.

  8. Molecular doping and band-gap opening of bilayer graphene.

    PubMed

    Samuels, Alexander J; Carey, J David

    2013-03-26

    The ability to induce an energy band gap in bilayer graphene is an important development in graphene science and opens up potential applications in electronics and photonics. Here we report the emergence of permanent electronic and optical band gaps in bilayer graphene upon adsorption of π electron containing molecules. Adsorption of n- or p-type dopant molecules on one layer results in an asymmetric charge distribution between the top and bottom layers and in the formation of an energy gap. The resultant band gap scales linearly with induced carrier density though a slight asymmetry is found between n-type dopants, where the band gap varies as 47 meV/10(13) cm(-2), and p-type dopants where it varies as 40 meV/10(13) cm(-2). Decamethylcobaltocene (DMC, n-type) and 3,6-difluoro-2,5,7,7,8,8-hexacyano-quinodimethane (F2-HCNQ, p-type) are found to be the best molecules at inducing the largest electronic band gaps up to 0.15 eV. Optical adsorption transitions in the 2.8-4 μm region of the spectrum can result between states that are not Pauli blocked. Comparison is made between the band gaps calculated from adsorbate-induced electric fields and from average displacement fields found in dual gate bilayer graphene devices. A key advantage of using molecular adsorption with π electron containing molecules is that the high binding energy can induce a permanent band gap and open up possible uses of bilayer graphene in mid-infrared photonic or electronic device applications.

  9. Tuning the opto-electronic properties of donor-acceptor polymers with molecular doping

    NASA Astrophysics Data System (ADS)

    von Hauff, Elizabeth

    2015-03-01

    Organic semiconductors offer vast potential for low cost, flexible energy production. The photocurrents in organic solar cells, however, are inherently limited by the poor electrical properties of the active layer. In this talk, strategies to increase the power conversion efficiency of polymer:fullerene solar cells by microscopically tuning the transport properties of the donor material are discussed. We observe that molecular doping the active layer of the device leads to increased charge separation efficiency and photocurrents. To investigate the influence of doping on the transport properties, impedance spectroscopy, a powerful, non-destructive technique, was applied. This allows us to probe carrier dynamics at different operational points in the current-voltage characteristics, and thereby correlate material properties with device performance.

  10. Synthesis, Separation, and Characterization of Small and Highly Fluorescent Nitrogen-Doped Carbon NanoDots.

    PubMed

    Arcudi, Francesca; Đorđević, Luka; Prato, Maurizio

    2016-02-01

    A facile bottom-up approach to carbon nanodots (CNDs) is reported, using a microwave-assisted procedure under controlled conditions. The as-prepared nitrogen-doped CNDs (NCNDs) show narrow size-distribution, abundant surface traps and functional groups, resulting in tunable fluorescent emission and excellent solubility in water. Moreover, we present a general method for the separation of NCNDs by low-pressure size-exclusion chromatography, leading to an even narrower size distribution, different surface composition, and optical properties. They display among the smallest size and the highest FLQYs reported so far. (13)C-enriched starting materials produced N(13) CNDs suitable for thorough NMR studies, which gave useful information on their molecular structure. Moreover, they can be easily functionalized and can be used as water-soluble carriers. This work provides an avenue to size- and surface-controllable and structurally defined NCNDs for applications in areas such as optoelectronics, biomedicine, and bioimaging. PMID:26733058

  11. A full-configuration-interaction nuclear orbital approach and application for small doped He clusters

    SciTech Connect

    Lara-Castells, M. P. de Aguirre, N. F. Delgado-Barrio, G. Villarreal, P.; Mitrushchenkov, A. O.

    2015-01-22

    An efficient full-configuration-interaction 'nuclear orbital' treatment was developed as a benchmark quantum-chemistry-like method to calculate, ground and excited, fermionic 'solvent' wave-functions and applied to {sup 3}He{sub N} clusters with atomic or molecular impurities [J. Chem. Phys. (Communication) 125, 221101 (2006)]. The main difficulty in handling doped {sup 3}He{sub N} clusters lies in the Fermi-Dirac nuclear statistics, the wide amplitudes of the He-dopant and He-He motions, and the hard-core He-He interaction at short distances. This paper overviews the theoretical approach and its recent applications to energetic, structural and spectroscopic aspects of different dopant-{sup 3}He{sub N} clusters. Preliminary results by using the latest version of the FCI-NO computational implementation, to bosonic Cl{sub 2}(X)-({sup 4}He){sub N} clusters, are also shown.

  12. Impurity doping of HgTe--CdTe superlattices during growth by molecular-beam epitaxy

    SciTech Connect

    Wroge, M.L.; Peterman, D.J.; Feldman, B.J.; Morris, B.J.; Leopold, D.J.; Broerman, J.G.

    1989-03-01

    We demonstrate the use of In and Ag as n- and p-type dopants, respectively, to controllably dope (100)-oriented HgTe--CdTe superlattices during molecular-beam epitaxial (MBE) growth. When normalized by the superlattice growth rate, the low-temperature Hall-carrier concentrations of both In- and Ag-doped superlattices are shown to have an exponential dependence on the respective effusion-cell temperatures in the electron and hole concentration ranges of approx.10/sup 16/ to 10/sup 18/ cm/sup -3/ . The upper limit on the diffusion coefficient for In at the low MBE growth temperature of approx.160 /sup 0/C is determined to be 5 x 10/sup -15/ cm/sup 2/ /s by use of secondary-ion mass spectrometry. Hall-effect and current--voltage measurements verify that the combination of In and Ag doping allows the formation of p--n electrical junctions. These results provide the first evidence of p--n junction formation in a HgTe--CdTe superlattice.

  13. Growth and magnetic property of antiperovskite manganese nitride films doped with Cu by molecular beam epitaxy

    SciTech Connect

    Yu, Fengmei; Ren, Lizhu; Meng, Meng; Wang, Yunjia; Yang, Mei; Wu, Shuxiang; Li, Shuwei

    2014-04-07

    Manganese nitrides thin films on MgO (100) substrates with and without Cu-doping have been fabricated by plasma assisted molecular beam epitaxy. Antiperovskite compounds Mn{sub 3.6}Cu{sub 0.4}N have been grown in the case of Cu-doping, and the pure Mn{sub 3}N{sub 2} single crystal has been obtained without Cu-doping. The Mn{sub 3.6}Cu{sub 0.4}N exhibits ferrimagnetism, and the magnetization of Mn{sub 3.6}Cu{sub 0.4}N increases upon the temperature decreasing from 300 K to 5 K, similar to Mn{sub 4}N. The exchange bias (EB) effects emerge in the Mn{sub 3.6}Cu{sub 0.4}N films. The EB behavior is originated from the interfaces between ferrimagnetic Mn{sub 3.6}Cu{sub 0.4}N and antiferromagnetic metal Mn, which is verified to be formed by the data of x-ray photoelectron spectroscopy. The present results not only provide a strategy for producing functional antiperovskite manganese nitrides, but also shed promising light on fabricating the exchange bias part of spintronic devices.

  14. Behavior of phosphorous and contaminants from molecular doping combined with a conventional spike annealing method

    NASA Astrophysics Data System (ADS)

    Shimizu, Yasuo; Takamizawa, Hisashi; Inoue, Koji; Yano, Fumiko; Nagai, Yasuyoshi; Lamagna, Luca; Mazzeo, Giovanni; Perego, Michele; Prati, Enrico

    2013-12-01

    The fabrication of future nanoscale semiconductor devices calls for precise placement of dopant atoms into their crystal lattice. Monolayer doping combined with a conventional spike annealing method provides a bottom-up approach potentially viable for large scale production. While the diffusion of the dopant was demonstrated at the start of the method, more sophisticated techniques are required in order to understand the diffusion, at the near surface, of P and contaminants such as C and O carried by the precursor, not readily accessible to direct time-of-flight secondary ion mass spectrometry measurements. By employing atom probe tomography, we report on the behavior of dopant and contaminants introduced by the molecular monolayer doping method into the first nanometers. The unwanted diffusion of C and O-related molecules is revealed and it is shown that for C and O it is limited to the first monolayers, where Si-C bonding formation is also observed, irrespective of the spike annealing temperature. From the perspective of large scale employment, our results suggest the benefits of adding a further process to the monolayer doping combined with spike annealing method, which consists of removing a sacrificial Si layer to eliminate contaminants.

  15. B/N pair and Si doped ultra-small-diameter single-walled carbon nanotubes: a density functional theory study

    NASA Astrophysics Data System (ADS)

    Huang, Gang; Wang, Yue; Shao, QingYi

    2014-11-01

    The structures and electronic properties of Si-doped ultra-small-diameter single-wall carbon nanotubes (SWCNTs) are studied through the first principle calculations based on density functional theory. To investigate their structural properties, a detailed calculation of bond length is performed for Si-doped (3, 3) armchair and (5, 0) zigzag nanotubes. The total energy and the formation energy show us that the doping configurations are energetically stable structures. The results reveal that Si-doped metallic carbon nanotubes can open their band gap, converting them into semiconductors. In addition, we also discuss the electronic structures of Si and B/N co-doped SWCNTs. B/N pair doping SWCNTs, in which Si has been doped, can increase or decrease their band gaps. For doping atoms, the band gap increases the closer they get to the vertical direction of the nanotube axis.

  16. Geometries, stabilities and electronic properties of small-sized Pd2-doped Sin (n = 1-11) clusters

    NASA Astrophysics Data System (ADS)

    Ji, Xiao-Xu; Li, Jing; Wang, Chong; Zhang, Shuai; Lu, Cheng; Li, Gen-Quan

    2015-11-01

    The geometries, growth patterns, relative stabilities and electronic properties of small-sized Pd2Sin and Sin+2 (n = 1-11) clusters are systematically studied using the hybrid density functional theory method B3LYP. The optimised structures revealed that the lowest energy Pd2Sin clusters are not similar to those of pure Sin clusters. When n = 9, one Pd atom in Pd2Si9 completely falls into the centre of the Si outer frame, forming metal-encapsulated Si cages. On the basis of the optimised structures, the averaged binding energy, fragmentation energy, second-order energy difference and highest occupied-lowest unoccupied molecular orbital energy gap are calculated. It is found that the Pd2Si5 and Pd2Si7 clusters have stronger relative stabilities among the Pd2Sin clusters. Additionally, the stabilities of Sin+2 clusters have been reduced by the doping of Pd impurity. The natural population and natural electronic configuration analysis indicated that the Pd atoms possess negative charges for n = 1-11 and there exist the spd hybridisation in the Pd atom. Finally, the chemical hardness, chemical potential, electrostatic potential and polarisability are discussed.

  17. N-doped carbon networks: alternative materials tracing new routes for activating molecular hydrogen.

    PubMed

    Cortese, Remedios; Ferrante, Francesco; Roggan, Stefan; Duca, Dario

    2015-02-23

    The fragmentation of molecular hydrogen on N-doped carbon networks was investigated by using molecular (polyaromatic macrocycles) as well as truncated and periodic (carbon nanotubes) models. The computational study was focused on the ergonicity analysis of the reaction and on the properties of the transition states involved when constellations of three or four pyridinic nitrogen atom defects are present in the carbon network. Calculations show that whenever N-defects are embedded in species characterized by large conjugated π-systems, either in polyaromatic macrocycles or carbon nanotubes, the corresponding H2 bond cleavage is largely exergonic. The fragmentation Gibbs free energy is affected by the final arrangement of the hydrogen atoms on the defect and by the extension of the π-electron cloud, but it is not influenced by the curvature of the system.

  18. Molecular Design of Doped Polymers for Thermoelectric Systems-Final Technical Report

    SciTech Connect

    Chabinyc, Michael L.; Hawker, Craig J.

    2013-10-09

    The self-assembly of organic semiconducting molecules and polymers is critical for their electrical properties. This project addressed the design of organic semiconductors with novel synthetic building blocks for proton-dopable conducting materials and the molecular order and microstructure of high performance semiconducting polymers blended with charge transfer dopants. Novel azulene donor-acceptor materials were designed and synthesized with unique electronic effects upon protonation to generate charged species in solution. The microstructure and optical properties of these derivatives were examined to develop structure-property relationships. Studies of the microstructure of blends of charge transfer doped semiconducting polymers revealed highly ordered conductive phases in blends. The molecular packing of one blend was studied in detail using a combination of solid-state NMR and x-ray scattering revealing that dopant incorporation is unlikely to be random as assumed in transport models. Studies of the electrical properties of these highly ordered blends revealed a universal trend between the thermopower and electrical conductivity of semiconducting polymers that is independent of the doping mechanism.

  19. A rhenium complex doped in a silica molecular sieve for molecular oxygen sensing: Construction and characterization

    NASA Astrophysics Data System (ADS)

    Yang, Xiaozhou; Li, Yanxiao

    2016-01-01

    This paper reported a diamine ligand and its Re(I) complex for potential application in oxygen sensing. The novelty of this diamine ligand localized at its increased conjugation chain which had a typical electron-withdrawing group of 1,3,4-oxadiazole. Electronic distribution of excited electrons and their lifetime were supposed to be increased, favoring oxygen sensing collision. This hypothesis was confirmed by single crystal analysis, theoretical calculation and photophysical measurement. It was found that this Re(I) complex had a long-lived emission peaking at 545 nm, favoring sensing application. By doping this complex into a silica matrix MCM-41, oxygen sensing performance and mechanism of the resulting composites were discussed in detail. Non-linear Stern-Volmer working curves were observed with maximum sensitivity of 5.54 and short response time of ~ 6 s.

  20. Exploiting molecular dynamics in Nested Sampling simulations of small peptides

    NASA Astrophysics Data System (ADS)

    Burkoff, Nikolas S.; Baldock, Robert J. N.; Várnai, Csilla; Wild, David L.; Csányi, Gábor

    2016-04-01

    Nested Sampling (NS) is a parameter space sampling algorithm which can be used for sampling the equilibrium thermodynamics of atomistic systems. NS has previously been used to explore the potential energy surface of a coarse-grained protein model and has significantly outperformed parallel tempering when calculating heat capacity curves of Lennard-Jones clusters. The original NS algorithm uses Monte Carlo (MC) moves; however, a variant, Galilean NS, has recently been introduced which allows NS to be incorporated into a molecular dynamics framework, so NS can be used for systems which lack efficient prescribed MC moves. In this work we demonstrate the applicability of Galilean NS to atomistic systems. We present an implementation of Galilean NS using the Amber molecular dynamics package and demonstrate its viability by sampling alanine dipeptide, both in vacuo and implicit solvent. Unlike previous studies of this system, we present the heat capacity curves of alanine dipeptide, whose calculation provides a stringent test for sampling algorithms. We also compare our results with those calculated using replica exchange molecular dynamics (REMD) and find good agreement. We show the computational effort required for accurate heat capacity estimation for small peptides. We also calculate the alanine dipeptide Ramachandran free energy surface for a range of temperatures and use it to compare the results using the latest Amber force field with previous theoretical and experimental results.

  1. Infrared spectra of small molecular ions trapped in solid neon

    SciTech Connect

    Jacox, Marilyn E.

    2015-01-22

    The infrared spectrum of a molecular ion provides a unique signature for that species, gives information on its structure, and is amenable to remote sensing. It also serves as a comparison standard for refining ab initio calculations. Experiments in this laboratory trap molecular ions in dilute solid solution in neon at 4.2 K in sufficient concentration for observation of their infrared spectra between 450 and 4000 cm{sup !1}. Discharge-excited neon atoms produce cations by photoionization and/or Penning ionization of the parent molecule. The resulting electrons are captured by other molecules, yielding anions which provide for overall charge neutrality of the deposit. Recent observations of ions produced from C{sub 2}H{sub 4} and BF{sub 3} will be discussed. Because of their relatively large possibility of having low-lying excited electronic states, small, symmetric molecular cations are especially vulnerable to breakdown of the Born-Oppenheimer approximation. Some phenomena which can result from this breakdown will be discussed. Ion-molecule reaction rates are sufficiently high that in some systems absorptions of dimer cations and anions are also observed. When H{sub 2} is introduced into the system, the initially-formed ion may react with it. Among the species resulting from such ion-molecule reactions that have recently been studied are O{sub 4}{sup +}, NH{sub 4}{sup +}, HOCO{sup +}, and HCO{sub 2}{sup !}.

  2. Growth and characterization of Sc-doped EuO thin films

    SciTech Connect

    Altendorf, S. G.; Reisner, A.; Chang, C. F.; Hollmann, N.; Rata, A. D.; Tjeng, L. H.

    2014-02-03

    The preparation of 3d-transition metal-doped EuO thin films by molecular beam epitaxy is investigated using the example of Sc doping. The Sc-doped EuO samples display a good crystalline structure, despite the relatively small ionic radius of the dopant. The Sc doping leads to an enhancement of the Curie temperature to up to 125 K, remarkably similar to previous observations on lanthanide-doped EuO.

  3. Molecular Responses to Small Regulating Molecules against Huanglongbing Disease.

    PubMed

    Martinelli, Federico; Dolan, David; Fileccia, Veronica; Reagan, Russell L; Phu, My; Spann, Timothy M; McCollum, Thomas G; Dandekar, Abhaya M

    2016-01-01

    Huanglongbing (HLB; citrus greening) is the most devastating disease of citrus worldwide. No cure is yet available for this disease and infected trees generally decline after several months. Disease management depends on early detection of symptoms and chemical control of insect vectors. In this work, different combinations of organic compounds were tested for the ability to modulate citrus molecular responses to HLB disease beneficially. Three small-molecule regulating compounds were tested: 1) L-arginine, 2) 6-benzyl-adenine combined with gibberellins, and 3) sucrose combined with atrazine. Each treatment contained K-phite mineral solution and was tested at two different concentrations. Two trials were conducted: one in the greenhouse and the other in the orchard. In the greenhouse study, responses of 42 key genes involved in sugar and starch metabolism, hormone-related pathways, biotic stress responses, and secondary metabolism in treated and untreated mature leaves were analyzed. TGA5 was significantly induced by arginine. Benzyladenine and gibberellins enhanced two important genes involved in biotic stress responses: WRKY54 and WRKY59. Sucrose combined with atrazine mainly upregulated key genes involved in carbohydrate metabolism such as sucrose-phosphate synthase, sucrose synthase, starch synthase, and α-amylase. Atrazine also affected expression of some key genes involved in systemic acquired resistance such as EDS1, TGA6, WRKY33, and MYC2. Several treatments upregulated HSP82, which might help protect protein folding and integrity. A subset of key genes was chosen as biomarkers for molecular responses to treatments under field conditions. GPT2 was downregulated by all small-molecule treatments. Arginine-induced genes involved in systemic acquired resistance included PR1, WRKY70, and EDS1. These molecular data encourage long-term application of treatments that combine these regulating molecules in field trials.

  4. Molecular Responses to Small Regulating Molecules against Huanglongbing Disease

    PubMed Central

    Martinelli, Federico; Dolan, David; Fileccia, Veronica; Reagan, Russell L.; Phu, My; Spann, Timothy M.; McCollum, Thomas G.; Dandekar, Abhaya M.

    2016-01-01

    Huanglongbing (HLB; citrus greening) is the most devastating disease of citrus worldwide. No cure is yet available for this disease and infected trees generally decline after several months. Disease management depends on early detection of symptoms and chemical control of insect vectors. In this work, different combinations of organic compounds were tested for the ability to modulate citrus molecular responses to HLB disease beneficially. Three small-molecule regulating compounds were tested: 1) L-arginine, 2) 6-benzyl-adenine combined with gibberellins, and 3) sucrose combined with atrazine. Each treatment contained K-phite mineral solution and was tested at two different concentrations. Two trials were conducted: one in the greenhouse and the other in the orchard. In the greenhouse study, responses of 42 key genes involved in sugar and starch metabolism, hormone-related pathways, biotic stress responses, and secondary metabolism in treated and untreated mature leaves were analyzed. TGA5 was significantly induced by arginine. Benzyladenine and gibberellins enhanced two important genes involved in biotic stress responses: WRKY54 and WRKY59. Sucrose combined with atrazine mainly upregulated key genes involved in carbohydrate metabolism such as sucrose-phosphate synthase, sucrose synthase, starch synthase, and α-amylase. Atrazine also affected expression of some key genes involved in systemic acquired resistance such as EDS1, TGA6, WRKY33, and MYC2. Several treatments upregulated HSP82, which might help protect protein folding and integrity. A subset of key genes was chosen as biomarkers for molecular responses to treatments under field conditions. GPT2 was downregulated by all small-molecule treatments. Arginine-induced genes involved in systemic acquired resistance included PR1, WRKY70, and EDS1. These molecular data encourage long-term application of treatments that combine these regulating molecules in field trials. PMID:27459099

  5. Molecular Responses to Small Regulating Molecules against Huanglongbing Disease.

    PubMed

    Martinelli, Federico; Dolan, David; Fileccia, Veronica; Reagan, Russell L; Phu, My; Spann, Timothy M; McCollum, Thomas G; Dandekar, Abhaya M

    2016-01-01

    Huanglongbing (HLB; citrus greening) is the most devastating disease of citrus worldwide. No cure is yet available for this disease and infected trees generally decline after several months. Disease management depends on early detection of symptoms and chemical control of insect vectors. In this work, different combinations of organic compounds were tested for the ability to modulate citrus molecular responses to HLB disease beneficially. Three small-molecule regulating compounds were tested: 1) L-arginine, 2) 6-benzyl-adenine combined with gibberellins, and 3) sucrose combined with atrazine. Each treatment contained K-phite mineral solution and was tested at two different concentrations. Two trials were conducted: one in the greenhouse and the other in the orchard. In the greenhouse study, responses of 42 key genes involved in sugar and starch metabolism, hormone-related pathways, biotic stress responses, and secondary metabolism in treated and untreated mature leaves were analyzed. TGA5 was significantly induced by arginine. Benzyladenine and gibberellins enhanced two important genes involved in biotic stress responses: WRKY54 and WRKY59. Sucrose combined with atrazine mainly upregulated key genes involved in carbohydrate metabolism such as sucrose-phosphate synthase, sucrose synthase, starch synthase, and α-amylase. Atrazine also affected expression of some key genes involved in systemic acquired resistance such as EDS1, TGA6, WRKY33, and MYC2. Several treatments upregulated HSP82, which might help protect protein folding and integrity. A subset of key genes was chosen as biomarkers for molecular responses to treatments under field conditions. GPT2 was downregulated by all small-molecule treatments. Arginine-induced genes involved in systemic acquired resistance included PR1, WRKY70, and EDS1. These molecular data encourage long-term application of treatments that combine these regulating molecules in field trials. PMID:27459099

  6. Characteristics and device applications of erbium doped III-V semiconductors grown by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Sethi, S.; Bhattacharya, P. K.

    1996-03-01

    We have studied the properties of molecular beam epitaxially (MBE)-grown Erdoped III-V semiconductors for optoelectronic applications. Optically excited Er3+ in insulating materials exhibits optical emission chiefly around 1.54 μm, in the range of minimum loss in silica fiber. It was thought, therefore, that an electrically pumped Er-doped semiconductor laser would find great applicability in fiber-optic communication systems. Exhaustive photoluminescence (PL) characterization was conducted on several of As-based III-V semiconductors doped with Er, on bulk as well as quantum-well structures. We did not observe any Errelated PL emission at 1.54 μm for any of the materials/structures studied, a phenomenon which renders impractical the realization of an Er-doped III-V semiconductor laser. Deep level transient spectroscopy studies were performed on GaAs and AlGaAs co-doped with Er and Si to investigate the presence of any Er-related deep levels. The lack of band-edge luminescence in the GaAs:Er films led us to perform carrier-lifetime measurements by electro-optic sampling of photoconductive transients generated in these films. We discovered lifetimes in the picosecond regime, tunable by varying the Er concentration in the films. We also found the films to be highly resistive, the resistivity increasing with increasing Er-concentration. Intensive structural characterization (double-crys-tal x-ray and transmission electron microscopy) performed by us on GaAs:Er epilayers indicates the presence of high-density nanometer-sized ErAs precipitates in MBE-grown GaAs:Er. These metallic nanoprecipitates probably form internal Schottky barriers within the GaAs matrix, which give rise to Shockley-Read-Hall recombination centers, thus accounting for both the high resistivities and the ultrashort carrier lifetimes. Optoelectronic devices fabricated included novel tunable (in terms of speed and responsivity) high-speed metal-semiconductor-metal (MSM) photodiodes made with Ga

  7. Glass beads and Ge-doped optical fibres as thermoluminescence dosimeters for small field photon dosimetry

    NASA Astrophysics Data System (ADS)

    Jafari, S. M.; Alalawi, A. I.; Hussein, M.; Alsaleh, W.; Najem, M. A.; Hugtenburg, R. P.; Bradley, D. A.; Spyrou, N. M.; Clark, C. H.; Nisbet, A.

    2014-11-01

    An investigation has been made of glass beads and optical fibres as novel dosimeters for small-field photon radiation therapy dosimetry. Commercially available glass beads of largest dimension 1.5 mm and GeO2-doped SiO2 optical fibres of 5 mm length and 120 µm diameter were characterized as thermoluminescence dosimeters. Results were compared against Monte-Carlo simulations with BEAMnrc/DOSXYZnrc, EBT3 Gafchromic film, and a high-resolution 2D-array of liquid-filled ionization chambers. Measurements included relative output factors and dose profiles for square-field sizes of 1, 2, 3, 4, and 10 cm. A customized Solid-Water® phantom was employed, and the beads and fibres were placed at defined positions along the longitudinal axis to allow accurate beam profile measurement. Output factors and the beam profile parameters were compared against those calculated by BEAMnrc/DOSXYZnrc. The output factors and field width measurements were found to be in agreement with reference measurements to within better than 3.5% for all field sizes down to 2 cm2 for both dosimetric systems, with the beads showing a discrepancy of no more than 2.8% for all field sizes. The results confirm the potential of the beads and fibres as thermoluminescent dosimeters for use in small photon radiation field sizes.

  8. Glass beads and Ge-doped optical fibres as thermoluminescence dosimeters for small field photon dosimetry.

    PubMed

    Jafari, S M; Alalawi, A I; Hussein, M; Alsaleh, W; Najem, M A; Hugtenburg, R P; Bradley, D A; Spyrou, N M; Clark, C H; Nisbet, A

    2014-11-21

    An investigation has been made of glass beads and optical fibres as novel dosimeters for small-field photon radiation therapy dosimetry. Commercially available glass beads of largest dimension 1.5 mm and GeO2-doped SiO2 optical fibres of 5 mm length and 120 µm diameter were characterized as thermoluminescence dosimeters. Results were compared against Monte-Carlo simulations with BEAMnrc/DOSXYZnrc, EBT3 Gafchromic film, and a high-resolution 2D-array of liquid-filled ionization chambers. Measurements included relative output factors and dose profiles for square-field sizes of 1, 2, 3, 4, and 10 cm. A customized Solid-Water® phantom was employed, and the beads and fibres were placed at defined positions along the longitudinal axis to allow accurate beam profile measurement. Output factors and the beam profile parameters were compared against those calculated by BEAMnrc/DOSXYZnrc. The output factors and field width measurements were found to be in agreement with reference measurements to within better than 3.5% for all field sizes down to 2 cm2 for both dosimetric systems, with the beads showing a discrepancy of no more than 2.8% for all field sizes. The results confirm the potential of the beads and fibres as thermoluminescent dosimeters for use in small photon radiation field sizes.

  9. A molecular dynamics study of thermal transport in nanoparticle doped Argon like solid

    NASA Astrophysics Data System (ADS)

    Shahadat, Muhammad Rubayat Bin; Ahmed, Shafkat; Morshed, A. K. M. M.

    2016-07-01

    Interfacial phenomena such as mass and type of the interstitial atom, nano scale material defect influence heat transfer and the effect become very significant with the reduction of the material size. Non Equilibrium Molecular Dynamics (NEMD) simulation was carried out in this study to investigate the effect of the interfacial phenomena on solid. Argon like solid was considered in this study and LJ potential was used for atomic interaction. Nanoparticles of different masses and different molecular defects were inserted inside the solid. From the molecular simulation, it was observed that a large interfacial mismatch due to change in mass in the homogenous solid causes distortion of the phonon frequency causing increase in thermal resistance. Position of the doped nanoparticles have more profound effect on the thermal conductivity of the solid whereas influence of the mass ratio is not very significant. Interstitial atom positioned perpendicular to the heat flow causes sharp reduction in thermal conductivity. Structural defect caused by the molecular defect (void) also observed to significantly affect the thermal conductivity of the solid.

  10. Packaging stiff polymers in small containers: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Rapaport, D. C.

    2016-09-01

    The question of how stiff polymers are able to pack into small containers is particularly relevant to the study of DNA packaging in viruses. A reduced version of the problem based on coarse-grained representations of the main components of the system—the DNA polymer and the spherical viral capsid—has been studied by molecular dynamics simulation. The results, involving longer polymers than in earlier work, show that as polymers become more rigid there is an increasing tendency to self-organize as spools that wrap from the inside out, rather than the inverse direction seen previously. In the final state, a substantial part of the polymer is packed into one or more coaxial spools, concentrically layered with different orientations, a form of packaging achievable without twisting the polymer.

  11. Molecular Doping the Topological Dirac Semimetal Na3Bi across the Charge Neutrality Point with F4-TCNQ.

    PubMed

    Edmonds, Mark T; Hellerstedt, Jack; O'Donnell, Kane M; Tadich, Anton; Fuhrer, Michael S

    2016-06-29

    We perform low-temperature transport and high-resolution photoelectron spectroscopy on 20 nm thin film topological Dirac semimetal Na3Bi grown by molecular beam epitaxy. We demonstrate efficient electron depletion ∼10(13) cm(-2) of Na3Bi via vacuum deposition of molecular F4-TCNQ without degrading the sample mobility. For samples with low as-grown n-type doping (1 × 10(12) cm(-2)), F4-TCNQ doping can achieve charge neutrality and even a net p-type doping. Photoelectron spectroscopy and density functional theory are utilized to investigate the behavior of F4-TCNQ on the Na3Bi surface. PMID:27309858

  12. Minority carrier lifetime in iodine-doped molecular beam epitaxy-grown HgCdTe

    SciTech Connect

    Madni, I.; Umana-Membreno, G. A.; Lei, W.; Gu, R.; Antoszewski, J.; Faraone, L.

    2015-11-02

    The minority carrier lifetime in molecular beam epitaxy grown layers of iodine-doped Hg{sub 1−x}Cd{sub x}Te (x ∼ 0.3) on CdZnTe substrates has been studied. The samples demonstrated extrinsic donor behavior for carrier concentrations in the range from 2 × 10{sup 16} cm{sup −3} to 6 × 10{sup 17} cm{sup −3} without any post-growth annealing. At a temperature of 77 K, the electron mobility was found to vary from 10{sup 4} cm{sup 2}/V s to 7 × 10{sup 3} cm{sup 2}/V s and minority carrier lifetime from 1.6 μs to 790 ns, respectively, as the carrier concentration was increased from 2 × 10{sup 16} cm{sup −3} to 6 × 10{sup 17} cm{sup −3}. The diffusion of iodine is much lower than that of indium and hence a better alternative in heterostructures such as nBn devices. The influence of carrier concentration and temperature on the minority carrier lifetime was studied in order to characterize the carrier recombination mechanisms. Measured lifetimes were also analyzed and compared with the theoretical models of the various recombination processes occurring in these materials, indicating that Auger-1 recombination was predominant at higher doping levels. An increase in deep-level generation-recombination centers was observed with increasing doping level, which suggests that the increase in deep-level trap density is associated with the incorporation of higher concentrations of iodine into the HgCdTe.

  13. Incorporation of small molecular weight active agents into polymeric components.

    PubMed

    Iconomopoulou, Sofia M; Kallitsis, Joannis K; Voyiatzis, George A

    2008-01-01

    The incorporation of small molecular weight active agents into polymeric matrixes bearing controlled release characteristics represents an interesting strategy with numerous useful applications. Antimicrobials, biocides, fungicides or drugs, encapsulated into erodible or non-erodible polymeric micro-spheres, micro-capsules and micro-shells or/and embedded into continuous polymeric matrixes, are controlled released either by particular degradation routes or/and by specific stimuli. Cross-linking, curing or micro-porosity generating agents acting during polymerization impart additional controlled encapsulation characteristics to the active substances. Release modulating agents, like retardants or carrier materials used as vehicles are often encapsulated into microspheres or dispersed within polymeric compositions for the controlled introduction of an active agent into a liquid-based medium. The aim of this review is to reveal relevant strategies reported in recent patents on the encapsulation or incorporation of low molecular weight active agents into the matrix of polymers bearing controlled release characteristics. The inventions described implicate the formation of both erodible and non erodible polymer microparticles that contain active ingredients. Modification of polymer matrix and inorganic porous carriers represent pertinent major strategies that have been also developed and patented.

  14. Integrated molecular portrait of non-small cell lung cancers

    PubMed Central

    2013-01-01

    Background Non-small cell lung cancer (NSCLC), a leading cause of cancer deaths, represents a heterogeneous group of neoplasms, mostly comprising squamous cell carcinoma (SCC), adenocarcinoma (AC) and large-cell carcinoma (LCC). The objectives of this study were to utilize integrated genomic data including copy-number alteration, mRNA, microRNA expression and candidate-gene full sequencing data to characterize the molecular distinctions between AC and SCC. Methods Comparative genomic hybridization followed by mutational analysis, gene expression and miRNA microarray profiling were performed on 123 paired tumor and non-tumor tissue samples from patients with NSCLC. Results At DNA, mRNA and miRNA levels we could identify molecular markers that discriminated significantly between the various histopathological entities of NSCLC. We identified 34 genomic clusters using aCGH data; several genes exhibited a different profile of aberrations between AC and SCC, including PIK3CA, SOX2, THPO, TP63, PDGFB genes. Gene expression profiling analysis identified SPP1, CTHRC1and GREM1 as potential biomarkers for early diagnosis of the cancer, and SPINK1 and BMP7 to distinguish between AC and SCC in small biopsies or in blood samples. Using integrated genomics approach we found in recurrently altered regions a list of three potential driver genes, MRPS22, NDRG1 and RNF7, which were consistently over-expressed in amplified regions, had wide-spread correlation with an average of ~800 genes throughout the genome and highly associated with histological types. Using a network enrichment analysis, the targets of these potential drivers were seen to be involved in DNA replication, cell cycle, mismatch repair, p53 signalling pathway and other lung cancer related signalling pathways, and many immunological pathways. Furthermore, we also identified one potential driver miRNA hsa-miR-944. Conclusions Integrated molecular characterization of AC and SCC helped identify clinically relevant markers

  15. Frequency Domain Fluorescent Molecular Tomography and Molecular Probes for Small Animal Imaging

    NASA Astrophysics Data System (ADS)

    Kujala, Naresh Gandhi

    Fluorescent molecular tomography (FMT) is a noninvasive biomedical optical imaging that enables 3-dimensional quantitative determination of fluorochromes distributed in biological tissues. There are three methods for imaging large volume tissues based on different light sources: (a) using a light source of constant intensity, through a continuous or constant wave, (b) using a light source that is intensity modulated with a radio frequency (RF), and (c) using ultrafast pulses in the femtosecond range. In this study, we have developed a frequency domain fluorescent molecular tomographic system based on the heterodyne technique, using a single source and detector pair that can be used for small animal imaging. In our system, the intensity of the laser source is modulated with a RF frequency to produce a diffuse photon density wave in the tissue. The phase of the diffuse photon density wave is measured by comparing the reference signal with the signal from the tissue using a phasemeter. The data acquisition was performed by using a Labview program. The results suggest that we can measure the phase change from the heterogeneous inside tissue. Combined with fiber optics and filter sets, the system can be used to sensitively image the targeted fluorescent molecular probes, allowing the detection of cancer at an early stage. We used the system to detect the tumor-targeting molecular probe Alexa Fluor 680 and Alexa Fluor 750 bombesin peptide conjugates in phantoms as well as mouse tissues. We also developed and evaluated fluorescent Bombesin (BBN) probes to target gastrin-releasing peptide (GRP) receptors for optical molecular imaging. GRP receptors are over-expressed in several types of human cancer cells, including breast, prostate, small cell lung, and pancreatic cancers. BBN is a 14 amino acid peptide that is an analogue to human gastrin-releasing peptide that binds specifically to GRPr receptors. BBN conjugates are significant in cancer detection and therapy. The

  16. The influence of negative charged centers on the hole transport in a typical molecularly doped polymer

    NASA Astrophysics Data System (ADS)

    Tyutnev, Andrey P.; Ikhsanov, Renat Sh.; Saenko, Vladimir S.; Pozhidaev, Evgenii D.

    2014-03-01

    We have studied effects of the negative charged centers on the time of flight (TOF) curves measured in a typical hole-conducting molecularly doped polymer. The main effects are the unusual TOF (surface generation) current rise in the preflight region (be it a flat plateau or a cusp) due to the accumulated space charge and the current reduction at all times because of the monomolecular recombination. TOF-2 (bulk generation) transients are less sensitive to charged centers. Analysis of these effects has proved that charged centers do not change the carrier mobility provided that the space charge field and bimolecular recombination are properly accounted for in terms of the proposed two-layer MT model. We have shown that combination of TOF, TOF-1a and TOF-2 variants of the electron-gun based technique allows one to establish definitively the character of the charge carrier transport in MDPs.

  17. Large anomalous Hall resistance of pair {delta}-doped GaAs structures grown by molecular-beam epitaxy

    SciTech Connect

    Jung, D. W.; Noh, J. P.; Touhidul Islam, A. Z. M.; Otsuka, N.

    2008-02-15

    Beryllium/silicon pair {delta}-doped GaAs structures grown by molecular-beam epitaxy exhibit a Hall resistance which has a nonlinear dependence on the applied magnetic field and which is strongly correlated to the negative magnetoresistance observed under the applied magnetic field parallel to the {delta}-doped layers. Dependence of the occurrence of the nonlinear Hall resistance on the growth condition is investigated. A significantly large increase in both the magnitude and the nonlinearity of the Hall resistance is observed from samples whose GaAs buffer layers are grown under the condition of a low As/Ga flux ratio. Reflection high energy electron diffraction and electron microscope observations show that a faceted surface develops with the growth and postgrowth annealing of a GaAs buffer layer under the condition of a low As flux. From samples which have only Si {delta}-doped layers and exhibit the n-type conduction, such nonlinear Hall resistance is not observed. The nonlinearity of the Hall resistance of Be/Si pair {delta}-doped structures depends on the single parameter B/T, where B and T are the applied magnetic field and the temperature, respectively. Based on these results, it is suggested that the nonlinear Hall resistance of Be/Si pair {delta}-doped structures is the anomalous Hall effect caused by localized spins in {delta}-doped layers.

  18. Influence of hole transporter doping on electroluminescent property of novel fluorene molecular material

    NASA Astrophysics Data System (ADS)

    Qian, Jincheng; Yu, Junsheng; Lou, Shuangling; Jiang, Yadong; Zhang, Qing

    2009-05-01

    The luminescent characteristics of a novel small molecule fluorene material, 6,6'-(9H-fluoren-9,9-diyl)bis(2,3-bis(9,9-dihexyl-9H-fluoren-2-yl)quinoxaline) (BFLBBFLYQ) for organic light-emitting diode are systemically investigated, especially focusing on the effect of hole transporter doping concentration. Double-layer devices with a structure of indium tin oxide (ITO)/emissive layer (EML)/2,9-dimethyl-4,7-diphenyl-l,10-phenanthroline (BCP)/Mg:Ag are fabricated by spin-coating method, where EML is BFLBBFLYQ and blend of BFLBBFLYQ: N,N'-biphenyl-N,N'-bis-(3-methylphenyl)-1,1'-biphenyl-4,4'-diamine (TPD), respectively. The results show that the performance of the device is improved two magnitudes by doping BFLBBFLYQ with TPD. In the electroluminescent (EL) spectra, the BFLBBFLYQ device show a blue light emission peaking at 485 nm, and the blend device exhibits a broad banded emission with 45 nm red-shifted peaking at 530 nm in green light area. The photoluminescent (PL) spectra of BFLBBFLYQ, TPD and BFLBBFLYQ: TPD blend in xylene solution and spin-coated film is also studied, yielding an evidence that exciplex maybe plays the role for low energy emission.

  19. Peculiarly strong room-temperature ferromagnetism from low Mn-doping in ZnO grown by molecular beam epitaxy

    SciTech Connect

    Zuo Zheng; Morshed, Muhammad; Liu Jianlin; Beyermann, W. P.; Zheng Jianguo; Xin Yan

    2013-03-15

    Strong room-temperature ferromagnetism is demonstrated in single crystalline Mn-doped ZnO thin films grown by molecular beam epitaxy. Very low Mn doping concentration is investigated, and the measured magnetic moment is much larger than what is expected for an isolated ion based on Hund's rules. The ferromagnetic behavior evolves with Mn concentration. Both magnetic anisotropy and anomalous Hall effect confirm the intrinsic nature of ferromagnetism. While the Mn dopant plays a crucial role, another entity in the system is needed to explain the observed large magnetic moments.

  20. Heavily boron-doped Si layers grown below 700 C by molecular beam epitaxy using a HBO2 source

    NASA Technical Reports Server (NTRS)

    Lin, T. L.; Fathauer, R. W.; Grunthaner, P. J.

    1989-01-01

    Boron doping in Si layers grown by molecular beam epitaxy (MBE) at 500-700 C using an HBO2 source has been studied. The maximum boron concentration without detectable oxygen incorporation for a given substrate temperature and Si growth rate has been determined using secondary-ion mass spectrometry analysis. Boron present in the Si MBE layers grown at 550-700 C was found to be electrically active, independent of the amount of oxygen incorporation. By reducing the Si growth rate, highly boron-doped layers have been grown at 600 C without detectable oxygen incorporation.

  1. Major Ampullate Spider Silk with Indistinguishable Spidroin Dope Conformations Leads to Different Fiber Molecular Structures.

    PubMed

    Dionne, Justine; Lefèvre, Thierry; Auger, Michèle

    2016-01-01

    To plentifully benefit from its properties (mechanical, optical, biological) and its potential to manufacture green materials, the structure of spider silk has to be known accurately. To this aim, the major ampullate (MA) silk of Araneus diadematus (AD) and Nephila clavipes (NC) has been compared quantitatively in the liquid and fiber states using Raman spectromicroscopy. The data show that the spidroin conformations of the two dopes are indistinguishable despite their specific amino acid composition. This result suggests that GlyGlyX and GlyProGlyXX amino acid motifs (X = Leu, Glu, Tyr, Ser, etc.) are conformationally equivalent due to the chain flexibility in the aqueous environment. Species-related sequence specificity is expressed more extensively in the fiber: the β-sheet content is lower and width of the orientation distribution of the carbonyl groups is broader for AD (29% and 58°, respectively) as compared to NC (37% and 51°, respectively). β-Sheet content values are close to the proportion of polyalanine segments, suggesting that β-sheet formation is mainly dictated by the spidroin sequence. The extent of molecular alignment seems to be related to the presence of proline (Pro) that may decrease conformational flexibility and inhibit chain extension and alignment upon drawing. It appears that besides the presence of Pro, secondary structure and molecular orientation contribute to the different mechanical properties of MA threads. PMID:27548146

  2. Major Ampullate Spider Silk with Indistinguishable Spidroin Dope Conformations Leads to Different Fiber Molecular Structures

    PubMed Central

    Dionne, Justine; Lefèvre, Thierry; Auger, Michèle

    2016-01-01

    To plentifully benefit from its properties (mechanical, optical, biological) and its potential to manufacture green materials, the structure of spider silk has to be known accurately. To this aim, the major ampullate (MA) silk of Araneus diadematus (AD) and Nephila clavipes (NC) has been compared quantitatively in the liquid and fiber states using Raman spectromicroscopy. The data show that the spidroin conformations of the two dopes are indistinguishable despite their specific amino acid composition. This result suggests that GlyGlyX and GlyProGlyXX amino acid motifs (X = Leu, Glu, Tyr, Ser, etc.) are conformationally equivalent due to the chain flexibility in the aqueous environment. Species-related sequence specificity is expressed more extensively in the fiber: the β-sheet content is lower and width of the orientation distribution of the carbonyl groups is broader for AD (29% and 58°, respectively) as compared to NC (37% and 51°, respectively). β-Sheet content values are close to the proportion of polyalanine segments, suggesting that β-sheet formation is mainly dictated by the spidroin sequence. The extent of molecular alignment seems to be related to the presence of proline (Pro) that may decrease conformational flexibility and inhibit chain extension and alignment upon drawing. It appears that besides the presence of Pro, secondary structure and molecular orientation contribute to the different mechanical properties of MA threads. PMID:27548146

  3. Graphene coated with controllable N-doped carbon layer by molecular layer deposition as electrode materials for supercapacitors

    NASA Astrophysics Data System (ADS)

    Chen, Yao; Gao, Zhe; Zhang, Bin; Zhao, Shichao; Qin, Yong

    2016-05-01

    In this work, graphene is coated with nitrogen-doped carbon layer, which is produced by a carbonization process of aromatic polyimide (PI) films deposited on the surfaces of graphene by molecular layer deposition (MLD). The utilization of MLD not only allows uniform coating of PI layers on the surfaces of pristine graphene without any surface treatment, but also enables homogenous dispersion of doped nitrogen atoms in the carbonized products. The as-prepared N-doped carbon layer coated graphene (NC-G) exhibited remarkable capacitance performance as electrode materials for supercapacitor, showing a high specific capacitance of 290.2 F g-1 at current density of 1 A g-1 in 6 M KOH aqueous electrolyte, meanwhile maintaining good rate performance and stable cycle capability. The NC-G synthesized by this way represents an alternative promising candidate as electrode material for supercapacitors.

  4. Simultaneous direct detection of sub keV molecular and atomic ions with a delta-doped charge-coupled device at the focal plane of a miniature mass spectrometer

    SciTech Connect

    Jewell, April D.; Jones, Todd J.; Sinha, Mahadeva P.; Nikzad, Shouleh

    2006-01-23

    A delta-doped charge-coupled device (CCD) was used for the simultaneous and direct detection of low-energy atomic and molecular ions dispersed along the focal plane of a miniature mass spectrometer (MMS). The measured detection threshold for charged particles with a delta-doped CCD has been extended down to 700 eV, representing over an order of magnitude improvement compared to conventional solid-state detectors. We report the direct detection of 700 eV energy ions by the mass spectral measurements of species such as iron pentacarbonyl. The combination of delta-doped CCD and MMS enables high-speed, precision mass spectrometry of ions and molecules on a small scale suitable for field and space applications.

  5. Photoluminescence study on heavily donor and acceptor impurity doped GaAs layers grown by molecular-beam epitaxy

    SciTech Connect

    Islam, A. Z. M. Touhidul; Jung, D. W.; Noh, J. P.; Otsuka, N.

    2009-05-01

    Gallium arsenide layers doped with high concentrations of Be and Si by molecular-beam epitaxy are studied by photoluminescence (PL) spectroscopy. PL peaks from doped layers are observed at energies significantly lower than the band-gap of GaAs. The growth and doping conditions suggest that the origin of these peaks is different from that of low energy PL peaks, which were observed in earlier studies and attributed to impurity-vacancy complexes. The dependence of the peak energy on the temperature and the annealing is found to differ from that of the peaks attributed to impurity-vacancy complexes. On the basis of these observations, it is suggested that the low energy peaks are attributed to short range ordered arrangements of impurity ions. This possibility is examined by calculations of the PL spectra with models of pairs of acceptor and donor delta-doped layers and PL experiments of a superlattice of pairs of Be and Si delta-doped layers.

  6. Folding of Small Proteins Using Constrained Molecular Dynamics

    PubMed Central

    Balaraman, Gouthaman S.; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan

    2011-01-01

    The focus of this paper is to examine whether conformational search using constrained molecular dynamics (MD) method is more enhanced and enriched towards “native-like” structures compared to all-atom MD for the protein folding as a model problem. Constrained MD methods provide an alternate MD tool for protein structure prediction and structure refinement. It is computationally expensive to perform all-atom simulations of protein folding because the processes occur on a timescale of microseconds. Compared to the all-atom MD simulation, constrained MD methods have the advantage that stable dynamics can be achieved for larger time steps and the number of degrees of freedom is an order of magnitude smaller, leading to a decrease in computational cost. We have developed a generalized constrained MD method that allows the user to “freeze and thaw” torsional degrees of freedom as fit for the problem studied. We have used this method to perform all-torsion constrained MD in implicit solvent coupled with the replica exchange method to study folding of small proteins with various secondary structural motifs such as, α-helix (polyalanine, WALP16), β-turn (1E0Q), and a mixed motif protein (Trp-cage). We demonstrate that constrained MD replica exchange method exhibits a wider conformational search than all-atom MD with increased enrichment of near native structures. “Hierarchical” constrained MD simulations, where the partially formed helical regions in the initial stretch of the all-torsion folding simulation trajectory of Trp-cage were frozen, showed a better sampling of near native structures than all-torsion constrained MD simulations. This is in agreement with the zipping-and-assembly folding model put forth by Dill and coworkers for folding proteins. The use of hierarchical “freeze and thaw” clustering schemes in constrained MD simulation can be used to sample conformations that contribute significantly to folding of proteins. PMID:21591767

  7. Growth of highly doped p-type ZnTe films by pulsed laser ablation in molecular nitrogen

    SciTech Connect

    Lowndes, D.H.; Rouleau, C.M.; Budai, J.D.; Poker, D.B.; Geohegan, D.B.; Zhu, Shen; McCamy, J.W.; Puretzky, A.

    1995-04-01

    Highly p-doped ZnTe films have been grown on semi-insulating GaAs (001) substrates by pulsed-laser ablation (PLA) of a stoichiometric ZnTe target in a high-purity N{sub 2} ambient without the use of any assisting (DC or AC) plasma source. Free hole concentrations in the mid-10{sup 19} cm{sup {minus}3} to > 10{sup 20} cm{sup {minus}3} range were obtained for a range of nitrogen pressures The maximum hole concentration equals the highest hole doping reported to date for any wide band gap II-VI compound. The highest hole mobilities were attained for nitrogen pressures of 50--100 mTorr ({approximately}6.5-13 Pa). Unlike recent experiments in which atomic nitrogen beams, extracted from RF and DC plasma sources, were used to produce p-type doping during molecular beam epitaxy deposition, spectroscopic measurements carried out during PLA of ZnTe in N{sub 2} do not reveal the presence of atomic nitrogen. This suggests that the high hole concentrations in laser ablated ZnTe are produced by a new and different mechanism, possibly energetic beam-induced reactions with excited molecular nitrogen adsorbed on the growing film surface, or transient formation of Zn-N complexes in the energetic ablation plume. This appears to be the first time that any wide band gap (Eg > 2 eV) II-VI compound (or other) semiconductor has been impurity-doped from the gas phase by laser ablation. In combination with the recent discovery that epitaxial ZnSe{sub l-x}S{sub x} films and heterostructures with continuously variable composition can be grown by ablation from a single target of fixed composition, these results appear to open the way to explore PLA growth and doping of compound semiconductors as a possible alternative to molecular beam epitaxy.

  8. Charge carrier transport in molecularly doped polycarbonate as a test case for the dipolar glass model.

    PubMed

    Novikov, S V; Tyutnev, A P

    2013-03-14

    We present the results of Monte Carlo simulations of the charge carrier transport in a disordered molecular system containing spatial and energetic disorders using the dipolar glass model. Model parameters of the material were chosen to fit a typical polar organic photoconductor polycarbonate doped with 30% of aromatic hydrazone, whose transport properties are well documented in literature. Simulated carrier mobility demonstrates a usual Poole-Frenkel field dependence and its slope is very close to the experimental value without using any adjustable parameter. At room temperature transients are universal with respect to the electric field and transport layer thickness. At the same time, carrier mobility does not depend on the layer thickness and transients develop a well-defined plateau where the current does not depend on time, thus demonstrating a non-dispersive transport regime. Tails of the transients decay as power law with the exponent close to -2. This particular feature indicates that transients are close to the boundary between dispersive and non-dispersive transport regimes. Shapes of the simulated transients are in very good agreement with the experimental ones. In summary, we provide a first verification of a self-consistency of the dipolar glass transport model, where major transport parameters, extracted from the experimental transport data, are then used in the transport simulation, and the resulting mobility field dependence and transients are in very good agreement with the initial experimental data.

  9. Charge carrier transport in molecularly doped polycarbonate as a test case for the dipolar glass model

    NASA Astrophysics Data System (ADS)

    Novikov, S. V.; Tyutnev, A. P.

    2013-03-01

    We present the results of Monte Carlo simulations of the charge carrier transport in a disordered molecular system containing spatial and energetic disorders using the dipolar glass model. Model parameters of the material were chosen to fit a typical polar organic photoconductor polycarbonate doped with 30% of aromatic hydrazone, whose transport properties are well documented in literature. Simulated carrier mobility demonstrates a usual Poole-Frenkel field dependence and its slope is very close to the experimental value without using any adjustable parameter. At room temperature transients are universal with respect to the electric field and transport layer thickness. At the same time, carrier mobility does not depend on the layer thickness and transients develop a well-defined plateau where the current does not depend on time, thus demonstrating a non-dispersive transport regime. Tails of the transients decay as power law with the exponent close to -2. This particular feature indicates that transients are close to the boundary between dispersive and non-dispersive transport regimes. Shapes of the simulated transients are in very good agreement with the experimental ones. In summary, we provide a first verification of a self-consistency of the dipolar glass transport model, where major transport parameters, extracted from the experimental transport data, are then used in the transport simulation, and the resulting mobility field dependence and transients are in very good agreement with the initial experimental data.

  10. Molecular materials for organic photovoltaics: small is beautiful.

    PubMed

    Roncali, Jean; Leriche, Philippe; Blanchard, Philippe

    2014-06-18

    An overview of some recent developments of the chemistry of molecular donor materials for organic photovoltaics (OPV) is presented. Although molecular materials have been used for the fabrication of OPV cells from the very beginning of the field, the design of molecular donors specifically designed for OPV is a relatively recent research area. In the past few years, molecular donors have been used in both vacuum-deposited and solution-processed OPV cells and both fields have witnessed impressive progress with power conversion efficiencies crossing the symbolic limit of 10 %. However, this progress has been achieved at the price of an increasing complexity of the chemistry of active materials and of the technology of device fabrication. This evolution probably inherent to the progress of research is difficult to reconcile with the necessity for OPV to demonstrate a decisive economic advantage over existing silicon technology. In this short review various classes of molecular donors are discussed with the aim of defining possible basic molecular structures that can combine structural simplicity, low molecular weight, synthetic accessibility, scalability and that can represent possible starting points for the development of simple and cost-effective OPV materials.

  11. Non-equilibrium Approach to Doping of Wide Bandgap materials by Molecular Beam Epitaxy. Final Report

    SciTech Connect

    Tamargo, M. C.; Neumark, G. F.

    2004-04-19

    It is well known that it has been difficult to obtain good bipolar doping in a wide bandgap semiconductors. Developed a new doping technique, involving use of a standard dopant, together with a ''co-dopant'' used to facilitate the introduction of the dopant, and have vastly alleviated this problem.

  12. Reduction of molecular aggregation and its application to the high-performance blue perylene-doped organic electroluminescent device

    NASA Astrophysics Data System (ADS)

    Mi, B. X.; Gao, Z. Q.; Lee, C. S.; Lee, S. T.; Kwong, H. L.; Wong, N. B.

    1999-12-01

    A nonplanar derivative of perylene, 2,5,8,11-tetra-tertbutylperylene (TBPe), was synthesized via the Friedel-Crafts alkylation reaction. Electroluminescent (EL) devices were made using TBPe or perylene as a dopant in bis(2-methyl-8-quinolinolato)(para-phenylphenolato)aluminum(III) and their EL performance was compared. Similar to the device doped with the parent perylene molecule, the device doped with TBPe also emitted strongly in the blue. As the concentration of TBPe increased from 1% to 5%, the color coordinates in CIE 1931 chromaticity of the TBPe-doped device changed only slightly from (0.168,0.273) to (0.175,0.273), whereas the perylene-doped device exhibited a much larger shift from (0.165,0.196) to (0.178,0.252). The constancy of EL color and efficiency with respect to TBPe dopant concentration is attributable to diminishing molecular aggregation in the nonplanar perylene derivative, TBPe, due to the steric hindrance of the tert-butyl groups.

  13. Low defect densities in molecular beam epitaxial GaAs achieved by isoelectronic In doping

    NASA Technical Reports Server (NTRS)

    Bhattacharya, P. K.; Dhar, S.; Berger, P.; Juang, F.-Y.

    1986-01-01

    A study has been made of the effects of adding small amounts of In (0.2-1.2 pct) to GaAs grown by molecular beam epitaxy. The density of four electron traps decreases in concentration by an order of magnitude, and the peak intensities of prominent emissions in the excitonic spectra are reduced with increase in In content. Based on the higher surface migration rate of In, compared to Ga, at the growth temperatures it is apparent that the traps and the excitonic transitions are related to point defects. This agrees with earlier observations by Briones and Collins (1982) and Skromme et al. (1985).

  14. Molecular mechanism of monodisperse colloidal tin-doped indium oxide nanocrystals by a hot-injection approach

    NASA Astrophysics Data System (ADS)

    Jin, Yizheng; Yi, Qing; Ren, Yuping; Wang, Xin; Ye, Zhizhen

    2013-04-01

    Molecular mechanisms and precursor conversion pathways associated with the reactions that generate colloidal nanocrystals are crucial for the development of rational synthetic protocols. In this study, Fourier transform infrared spectroscopy technique was employed to explore the molecular mechanism associated with the formation of tin-doped indium oxide (ITO) nanocrystals. We found that the reaction pathways of the indium precursor were not consistent with simple ligand replacements proposed in the literature. The resulting understanding inspired us to design a hot-injection approach to separate the ligand replacements of indium acetate and the aminolysis processes, generating quality ITO nanocrystals with decent size distributions. The hot-injection approach was readily applied to the synthesis of ITO nanocrystals with a broad range of tin doping. Structural, chemical, and optical analyses revealed effective doping of Sn4+ ions into the host lattices, leading to characteristic and tunable near-infrared surface plasmon resonance peaks. The size control of ITO nanocrystals by multiple hot-injections of metal precursors was also demonstrated.

  15. Molecular mechanism of monodisperse colloidal tin-doped indium oxide nanocrystals by a hot-injection approach

    PubMed Central

    2013-01-01

    Molecular mechanisms and precursor conversion pathways associated with the reactions that generate colloidal nanocrystals are crucial for the development of rational synthetic protocols. In this study, Fourier transform infrared spectroscopy technique was employed to explore the molecular mechanism associated with the formation of tin-doped indium oxide (ITO) nanocrystals. We found that the reaction pathways of the indium precursor were not consistent with simple ligand replacements proposed in the literature. The resulting understanding inspired us to design a hot-injection approach to separate the ligand replacements of indium acetate and the aminolysis processes, generating quality ITO nanocrystals with decent size distributions. The hot-injection approach was readily applied to the synthesis of ITO nanocrystals with a broad range of tin doping. Structural, chemical, and optical analyses revealed effective doping of Sn4+ ions into the host lattices, leading to characteristic and tunable near-infrared surface plasmon resonance peaks. The size control of ITO nanocrystals by multiple hot-injections of metal precursors was also demonstrated. PMID:23547801

  16. Organic solution-processible electroluminescent molecular glasses for non-doped standard red OLEDs with electrically stable chromaticity

    SciTech Connect

    Bi, Xiaoman; Zuo, Weiwei; Liu, Yingliang Zhang, Zhenru; Zeng, Cen; Xu, Shengang; Cao, Shaokui

    2015-10-15

    Highlights: • The D–A–D electroluminescent molecular glasses are synthesized. • Non-doped red electroluminescent film is fabricated by spin-coating. • Red OLED shows stable wavelength, luminous efficiency and chromaticity. • CIE1931 coordinate is in accord with standard red light in PAL system. - Abstract: Organic light-emitting molecular glasses (OEMGs) are synthesized through the introduction of nonplanar donor and branched aliphatic chain into electroluminescent emitters. The target OEMGs are characterized by {sup 1}H NMR, {sup 13}C NMR, IR, UV–vis and fluorescent spectra as well as elemental analysis, TG and DSC. The results indicated that the optical, electrochemical and electroluminescent properties of OEMGs are adjusted successfully by the replacement of electron-donating group. The non-doped OLED device with a standard red electroluminescent emission is achieved by spin-coating the THF solution of OEMG with a triphenylamine moiety. This non-doped red OLED device takes on an electrically stable electroluminescent performance, including the stable maximum electroluminescent wavelength of 640 nm, the stable luminous efficiency of 2.4 cd/A and the stable CIE1931 coordinate of (x, y) = (0.64, 0.35), which is basically in accord with the CIE1931 coordinate (x, y) = (0.64, 0.33) of standard red light in PAL system.

  17. Unravelling Doping Effects on PEDOT at the Molecular Level: From Geometry to Thermoelectric Transport Properties.

    PubMed

    Shi, Wen; Zhao, Tianqi; Xi, Jinyang; Wang, Dong; Shuai, Zhigang

    2015-10-14

    Tuning carrier concentration via chemical doping is the most successful strategy to optimize the thermoelectric figure of merit. Nevertheless, how the dopants affect charge transport is not completely understood. Here we unravel the doping effects by explicitly including the scattering of charge carriers with dopants on thermoelectric properties of poly(3,4-ethylenedioxythiophene), PEDOT, which is a p-type thermoelectric material with the highest figure of merit reported. We corroborate that the PEDOT exhibits a distinct transition from the aromatic to quinoid-like structure of backbone, and a semiconductor-to-metal transition with an increase in the level of doping. We identify a close-to-unity charge transfer from PEDOT to the dopant, and find that the ionized impurity scattering dominates over the acoustic phonon scattering in the doped PEDOT. By incorporating both scattering mechanisms, the doped PEDOT exhibits mobility, Seebeck coefficient and power factors in very good agreement with the experimental data, and the lightly doped PEDOT exhibits thermoelectric properties superior to the heavily doped one. We reveal that the thermoelectric transport is highly anisotropic in ordered crystals, and suggest to utilize large power factors in the direction of polymer backbone and low lattice thermal conductivity in the stacking and lamellar directions, which is viable in chain-oriented amorphous nanofibers.

  18. Charge Transfer-Induced Molecular Hole Doping into Thin Film of Metal-Organic Frameworks.

    PubMed

    Lee, Deok Yeon; Kim, Eun-Kyung; Shrestha, Nabeen K; Boukhvalov, Danil W; Lee, Joong Kee; Han, Sung-Hwan

    2015-08-26

    Despite the highly porous nature with significantly large surface area, metal-organic frameworks (MOFs) can be hardly used in electronic and optoelectronic devices due to their extremely poor electrical conductivity. Therefore, the study of MOF thin films that require electron transport or conductivity in combination with the everlasting porosity is highly desirable. In the present work, thin films of Co3(NDC)3DMF4 MOFs with improved electronic conductivity are synthesized using layer-by-layer and doctor blade coating techniques followed by iodine doping. The as-prepared and doped films are characterized using FE-SEM, EDX, UV/visible spectroscopy, XPS, current-voltage measurement, photoluminescence spectroscopy, cyclic voltammetry, and incident photon to current efficiency measurements. In addition, the electronic and semiconductor properties of the MOF films are characterized using Hall Effect measurement, which reveals that, in contrast to the insulator behavior of the as-prepared MOFs, the iodine doped MOFs behave as a p-type semiconductor. This is caused by charge transfer-induced hole doping into the frameworks. The observed charge transfer-induced hole doping phenomenon is also confirmed by calculating the densities of states of the as-prepared and iodine doped MOFs based on density functional theory. Photoluminescence spectroscopy demonstrates an efficient interfacial charge transfer between TiO2 and iodine doped MOFs, which can be applied to harvest solar radiations.

  19. Realization of Cu-Doped p-Type ZnO Thin Films by Molecular Beam Epitaxy.

    PubMed

    Suja, Mohammad; Bashar, Sunayna B; Morshed, Muhammad M; Liu, Jianlin

    2015-04-29

    Cu-doped p-type ZnO films are grown on c-sapphire substrates by plasma-assisted molecular beam epitaxy. Photoluminescence (PL) experiments reveal a shallow acceptor state at 0.15 eV above the valence band edge. Hall effect results indicate that a growth condition window is found for the formation of p-type ZnO thin films, and the best conductivity is achieved with a high hole concentration of 1.54 × 10(18) cm(-3), a low resistivity of 0.6 Ω cm, and a moderate mobility of 6.65 cm(2) V(-1) s(-1) at room temperature. Metal oxide semiconductor capacitor devices have been fabricated on the Cu-doped ZnO films, and the characteristics of capacitance-voltage measurements demonstrate that the Cu-doped ZnO thin films under proper growth conditions are p-type. Seebeck measurements on these Cu-doped ZnO samples lead to positive Seebeck coefficients and further confirm the p-type conductivity. Other measurements such as X-ray diffraction, X-ray photoelectron, Raman, and absorption spectroscopies are also performed to elucidate the structural and optical characteristics of the Cu-doped p-type ZnO films. The p-type conductivity is explained to originate from Cu substitution of Zn with a valency of +1 state. However, all p-type samples are converted to n-type over time, which is mostly due to the carrier compensation from extrinsic defects of ZnO.

  20. Realization of Cu-Doped p-Type ZnO Thin Films by Molecular Beam Epitaxy.

    PubMed

    Suja, Mohammad; Bashar, Sunayna B; Morshed, Muhammad M; Liu, Jianlin

    2015-04-29

    Cu-doped p-type ZnO films are grown on c-sapphire substrates by plasma-assisted molecular beam epitaxy. Photoluminescence (PL) experiments reveal a shallow acceptor state at 0.15 eV above the valence band edge. Hall effect results indicate that a growth condition window is found for the formation of p-type ZnO thin films, and the best conductivity is achieved with a high hole concentration of 1.54 × 10(18) cm(-3), a low resistivity of 0.6 Ω cm, and a moderate mobility of 6.65 cm(2) V(-1) s(-1) at room temperature. Metal oxide semiconductor capacitor devices have been fabricated on the Cu-doped ZnO films, and the characteristics of capacitance-voltage measurements demonstrate that the Cu-doped ZnO thin films under proper growth conditions are p-type. Seebeck measurements on these Cu-doped ZnO samples lead to positive Seebeck coefficients and further confirm the p-type conductivity. Other measurements such as X-ray diffraction, X-ray photoelectron, Raman, and absorption spectroscopies are also performed to elucidate the structural and optical characteristics of the Cu-doped p-type ZnO films. The p-type conductivity is explained to originate from Cu substitution of Zn with a valency of +1 state. However, all p-type samples are converted to n-type over time, which is mostly due to the carrier compensation from extrinsic defects of ZnO. PMID:25835032

  1. Nanoclusters of CaSe in calcium-doped Bi2Se3 grown by molecular-beam epitaxy.

    PubMed

    Shang, Panju; Guo, Xin; Zhao, Bao; Dai, Xianqi; Bin, Li; Jia, Jinfeng; Li, Quan; Xie, Maohai

    2016-02-26

    In calcium (Ca) doped Bi2Se3 films grown by molecular beam epitaxy, nanoclusters of CaSe are revealed by high-angle annular dark field imaging and energy dispersive x-ray spectroscopy analysis using a scanning transmission electron microscope. As the interface between the ordinary insulator CaSe and topological insulator, Bi2Se3, can host topological nontrivial interface state, this represents an interesting material system for further studies. We show by first principles total energy calculations that aggregation of Ca atoms in Bi2Se3 is driven by energy minimization and a preferential intercalation of Ca in the van der Waals gap between quintuple layers of Bi2Se3 induces reordering of atomic stacking and causes an increasing amount of stacking faults in film. The above findings also provide an explanation of less-than-expected electrical carrier (hole) concentrations in Ca-doped samples.

  2. p-type ZnO films with solid-source phosphorus doping by molecular-beam epitaxy

    SciTech Connect

    Xiu, F.X.; Yang, Z.; Mandalapu, L.J.; Liu, J.L.; Beyermann, W. P.

    2006-01-30

    Phosphorus-doped p-type ZnO films were grown on r-plane sapphire substrates using molecular-beam epitaxy with a solid-source GaP effusion cell. X-ray diffraction spectra and reflection high-energy electron diffraction patterns indicate that high-quality single crystalline (1120) ZnO films were obtained. Hall and resistivity measurements show that the phosphorus-doped ZnO films have high hole concentrations and low resistivities at room temperature. Photoluminescence (PL) measurements at 8 K reveal a dominant acceptor-bound exciton emission with an energy of 3.317 eV. The acceptor energy level of the phosphorus dopant is estimated to be 0.18 eV above the valence band from PL spectra, which is also consistent with the temperature dependence of PL measurements.

  3. Elemental boron-doped p(+)-SiGe layers grown by molecular beam epitaxy for infrared detector applications

    NASA Technical Reports Server (NTRS)

    Lin, T. L.; George, T.; Jones, E. W.; Ksendzov, A.; Huberman, M. L.

    1992-01-01

    SiGe/Si heterojunction internal photoemission (HIP) detectors have been fabricated utilizing molecular beam epitaxy of p(+)-SiGe layers on p(-)-Si substrates. Elemental boron from a high-temperature effusion cell was used as the dopant source during MBE growth, and high doping concentrations have been achieved. Strong infrared absorption, mainly by free-carrier absorption, was observed for the degenerately doped SiGe layers. The use of elemental boron as the dopant source allows a low MBE growth temperature, resulting in improved crystalline quality and smooth surface morphology of the Si(0.7)Ge(0.3) layers. Nearly ideal thermionic emission dark current characteristics have been obtained. Photoresponse of the HIP detectors in the long-wavelength infrared regime has been demonstrated.

  4. High Conductivity in Molecularly p-Doped Diketopyrrolopyrrole-Based Polymer: The Impact of a High Dopant Strength and Good Structural Order.

    PubMed

    Karpov, Yevhen; Erdmann, Tim; Raguzin, Ivan; Al-Hussein, Mahmoud; Binner, Marcus; Lappan, Uwe; Stamm, Manfred; Gerasimov, Kirill L; Beryozkina, Tetyana; Bakulev, Vasiliy; Anokhin, Denis V; Ivanov, Dimitri A; Günther, Florian; Gemming, Sibylle; Seifert, Gotthard; Voit, Brigitte; Di Pietro, Riccardo; Kiriy, Anton

    2016-07-01

    [3]-Radialene-based dopant CN6-CP studied herein, with its reduction potential of +0.8 versus Fc/Fc+ and the lowest unoccupied molecular orbital level of -5.87 eV, is the strongest molecular p-dopant reported in the open literature, so far. The efficient p-doping of the donor-acceptor dithienyl-diketopyrrolopyrrole-based copolymer having the highest unoccupied molecular orbital level of -5.49 eV is achieved. The doped films exhibit electrical conductivities up to 70 S cm(-1) . PMID:27172371

  5. From Uniplex to Multiplex Molecular Profiling in Advanced Non-Small Cell Lung Carcinoma.

    PubMed

    Ileana, Ecaterina E; Wistuba, Ignacio I; Izzo, Julie G

    2015-01-01

    Non-small cell lung carcinoma is a leading cause of cancer death worldwide. Understanding the molecular biology of survival and proliferation of cancer cells led to a new molecular classification of lung cancer and the development of targeted therapies with promising results. With the advances of image-guided biopsy techniques, tumor samples are becoming smaller, and the molecular testing techniques have to overcome the challenge of integrating the characterization of a panel of abnormalities including gene mutations, copy-number changes, and fusions in a reduced number of assays using only a small amount of genetic material. This article reviews the current knowledge about the most frequent actionable molecular abnormalities in non-small cell lung carcinoma, the new approaches of molecular analysis, and the implications of these findings in the context of clinical practice.

  6. High-mobility Sb-doped p-type ZnO by molecular-beam epitaxy

    SciTech Connect

    Xiu, F.X.; Yang, Z.; Mandalapu, L.J.; Zhao, D.T.; Liu, J.L.; Beyermann, W.P.

    2005-10-10

    Reproducible Sb-doped p-type ZnO films were grown on n-Si (100) by electron-cyclotron-resonance-assisted molecular-beam epitaxy. The existence of Sb in ZnO:Sb films was confirmed by low-temperature photoluminescence measurements. An acceptor-bound exciton (A deg. X) emission was observed at 3.358 eV at 8 K. The acceptor energy level of the Sb dopant is estimated to be 0.2 eV above the valence band. Temperature-dependent Hall measurements were performed on Sb-doped ZnO films. At room temperature, one Sb-doped ZnO sample exhibited a low resistivity of 0.2 {omega} cm, high hole concentration of 1.7x10{sup 18} cm{sup -3} and high mobility of 20.0 cm{sup 2}/V s. This study suggests that Sb is an excellent dopant for reliable and reproducible p-type ZnO fabrication.

  7. Temperature dependence of small polaron population decays in iron-doped lithium niobate by Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Mhaouech, I.; Guilbert, L.

    2016-10-01

    The population decay of light-induced small polarons in iron-doped lithium niobate is simulated by a Monte-Carlo method on the basis of Holstein's theory. The model considers random walks of both bound polarons (NbLi4+) and free polarons (NbNb4+) ending to deep traps (FeLi3+). The thermokinetic interplay between polaron species is introduced by trapping and de-trapping rates at niobium antisites (NbLi). The decay of the NbLi4+ population proceeds by three possible channels: direct trapping at FeLi3+ sites, hopping on niobium antisites and hopping on Nb regular sites after conversion to the free state. Up to three regimes, each one reflecting the predominance of one of these processes, appear with different activation energies in the Arrhenius plots of the decay time. The influence of FeLi and NbLi concentrations on the transition temperatures is evidenced. For both polaron species, the length of the final hop (trapping length) is found much larger than the usual hopping length and decreases at rising temperature. This trap size effect is a natural consequence of Holstein's theory and may explain some unclear features of polaron-related light-induced phenomena, such as the temperature-dependent stretching exponent of light-induced absorption decays and the anomalous increase of the photoconductivity at high doping levels.

  8. Influence of Cr doping on the stability and structure of small cobalt oxide clusters

    SciTech Connect

    Tung, Nguyen Thanh; Lievens, Peter; Janssens, Ewald; Tam, Nguyen Minh; Nguyen, Minh Tho

    2014-07-28

    The stability of mass-selected pure cobalt oxide and chromium doped cobalt oxide cluster cations, Co{sub n}O{sub m}{sup +} and Co{sub n−1}CrO{sub m}{sup +} (n = 2, 3; m = 2–6 and n = 4; m = 3–8), has been investigated using photodissociation mass spectrometry. Oxygen-rich Co{sub n}O{sub m}{sup +} clusters (m ⩾ n + 1 for n = 2, 4 and m ⩾ n + 2 for n = 3) prefer to photodissociate via the loss of an oxygen molecule, whereas oxygen poorer clusters favor the evaporation of oxygen atoms. Substituting a single Co atom by a single Cr atom alters the dissociation behavior. All investigated Co{sub n−1}CrO{sub m}{sup +} clusters, except CoCrO{sub 2}{sup +} and CoCrO{sub 3}{sup +}, prefer to decay by eliminating a neutral oxygen molecule. Co{sub 2}O{sub 2}{sup +}, Co{sub 4}O{sub 3}{sup +}, Co{sub 4}O{sub 4}{sup +}, and CoCrO{sub 2}{sup +} are found to be relatively difficult to dissociate and appear as fragmentation product of several larger clusters, suggesting that they are particularly stable. The geometric structures of pure and Cr doped cobalt oxide species are studied using density functional theory calculations. Dissociation energies for different evaporation channels are calculated and compared with the experimental observations. The influence of the dopant atom on the structure and the stability of the clusters is discussed.

  9. Detecting CO, NO and NO2 gases by Boron-doped graphene nanoribbon molecular devices

    NASA Astrophysics Data System (ADS)

    Xie, Zhen; Zuo, Xi; Zhang, Guang-Ping; Li, Zong-Liang; Wang, Chuan-Kui

    2016-07-01

    Combining nonequilibrium Green's function method and density functional theory, an azulene-like dipole molecule sandwiched between two graphene nanoribbon (GNR) electrodes are explored to gas sensors. Both the pristine zigzag edged GNR and Boron-doped armchair-edged GNR are considered in this study. It shows that certain specific toxic molecules CO, NO and NO2 would adsorb on the doped Boron atoms of the GNR, resulting in a dramatic change in the current-voltage profile. Changes in the subbands of electrodes, induced by gas adsorption, are responsible for the variation of current. The devices are thus demonstrated to be sensitive nanosensors for these toxic gases.

  10. Nanofibers doped with a novel red-emitting Europium complex: Synthesis, characterization, photophysical property and sensing activity toward molecular oxygen

    NASA Astrophysics Data System (ADS)

    Jianliang, SUN; Ge, HU; Qing, SHE; Zhaohong, ZUO; Lei, GUO

    2012-06-01

    In this paper, we synthesize a novel diamine ligand of DIQ-Et and its corresponding Eu(III) complex of Eu(TTA)3DIQ-Et, where DIQ-Et = N-ethyl-10H-dipyrido-[f,h]-indolo-[3,2-b]-quinoxaline, and TTA = 2-thenoyltrifluoroacetonate. The UV-vis absorption, photoluminescence, low temperature phosphorescence, energy transfer mechanism, and excited state lifetime of Eu(TTA)3DIQ-Et are investigated in detail. Data suggest that the emission of Eu(TTA)3DIQ-Et is quenchable by molecular oxygen due to the back-energy transfer process. By doping Eu(TTA)3DIQ-Et into a polymer matrix of poly(vinylpyrrolidone) (PVP), oxygen sensing performance of the resulted nanofibers is investigated. Finally, the 0.7 wt% doped sample exhibits a linear response toward molecular oxygen, with a sensitivity of 2.4 and response/recovery time of 12 s/16 s.

  11. Small RNAs break out: the molecular cell biology of mobile small RNAs.

    PubMed

    Sarkies, Peter; Miska, Eric A

    2014-08-01

    Small RNAs that function in a non-cell autonomous manner are becoming increasingly recognized as regulatory molecules with the potential to transmit information between cells, organisms and species. In plants and nematodes, small RNA mobility can be genetically dissected to provide information about the nature of the mobile RNA species, their distribution in the organism and inside cells, as well as the cellular machinery required for mobility, including channel proteins and cellular trafficking factors. Mobile RNAs function in antiviral defence, cell signalling and gene expression regulation, and might also mediate transgenerational epigenetic inheritance. PMID:25053358

  12. Nitrogen-doped graphene: beyond single substitution and enhanced molecular sensing

    PubMed Central

    Lv, Ruitao; Li, Qing; Botello-Méndez, Andrés R.; Hayashi, Takuya; Wang, Bei; Berkdemir, Ayse; Hao, Qingzhen; Elías, Ana Laura; Cruz-Silva, Rodolfo; Gutiérrez, Humberto R.; Kim, Yoong Ahm; Muramatsu, Hiroyuki; Zhu, Jun; Endo, Morinobu; Terrones, Humberto; Charlier, Jean-Christophe; Pan, Minghu; Terrones, Mauricio

    2012-01-01

    Graphene is a two-dimensional network in which sp2-hybridized carbon atoms are arranged in two different triangular sub-lattices (A and B). By incorporating nitrogen atoms into graphene, its physico-chemical properties could be significantly altered depending on the doping configuration within the sub-lattices. Here, we describe the synthesis of large-area, highly-crystalline monolayer N-doped graphene (NG) sheets via atmospheric-pressure chemical vapor deposition, yielding a unique N-doping site composed of two quasi-adjacent substitutional nitrogen atoms within the same graphene sub-lattice (N2AA). Scanning tunneling microscopy and spectroscopy (STM and STS) of NG revealed the presence of localized states in the conduction band induced by N2AA-doping, which was confirmed by ab initio calculations. Furthermore, we demonstrated for the first time that NG could be used to efficiently probe organic molecules via a highly improved graphene enhanced Raman scattering. PMID:22905317

  13. Effect of Co doping on catalytic activity of small Pt clusters

    NASA Astrophysics Data System (ADS)

    Dhilip Kumar, T. J.; Zhou, Chenggang; Cheng, Hansong; Forrey, Robert C.; Balakrishnan, N.

    2008-03-01

    Platinum is the most widely used catalyst in fuel cell electrodes. Designing improved catalysts with low or no platinum content is one of the grand challenges in fuel cell research. Here, we investigate electronic structures of Pt4 and Pt3Co clusters and report a comparative study of adsorption of H2, O2, and CO molecules on the two clusters using density functional theory. The adsorption studies show that H2 undergoes dissociative chemisorption on the tetrahedral clusters in head on and side on approaches at Pt centers. O2 dissociation occurs primarily in three and four center coordinations and CO prefers to adsorb on Pt or Co atop atoms. The adsorption energy of O2 is found to be higher for the Co doped cluster. For CO, the Pt atop orientation is preferred for both Pt4 and Pt3Co tetrahedral clusters. Adsorption of CO molecule on tetrahedral Pt3Co in side on approach leads to isomerization to planar rhombus geometry. An analysis of Hirshfeld charge distribution shows that the clusters become more polarized after adsorption of the molecules.

  14. Effect of Co doping on catalytic activity of small Pt clusters.

    PubMed

    Dhilip Kumar, T J; Zhou, Chenggang; Cheng, Hansong; Forrey, Robert C; Balakrishnan, N

    2008-03-28

    Platinum is the most widely used catalyst in fuel cell electrodes. Designing improved catalysts with low or no platinum content is one of the grand challenges in fuel cell research. Here, we investigate electronic structures of Pt(4) and Pt(3)Co clusters and report a comparative study of adsorption of H(2), O(2), and CO molecules on the two clusters using density functional theory. The adsorption studies show that H(2) undergoes dissociative chemisorption on the tetrahedral clusters in head on and side on approaches at Pt centers. O(2) dissociation occurs primarily in three and four center coordinations and CO prefers to adsorb on Pt or Co atop atoms. The adsorption energy of O(2) is found to be higher for the Co doped cluster. For CO, the Pt atop orientation is preferred for both Pt(4) and Pt(3)Co tetrahedral clusters. Adsorption of CO molecule on tetrahedral Pt(3)Co in side on approach leads to isomerization to planar rhombus geometry. An analysis of Hirshfeld charge distribution shows that the clusters become more polarized after adsorption of the molecules. PMID:18376957

  15. A density functional study of small sized silver-doped silicon clusters: Ag2Sin (n = 1-13)

    NASA Astrophysics Data System (ADS)

    Yang, Cai; Hao Jia, Song; Ma, Mao Fen; Zhang, Shuai; Lu, Cheng; Li, Gen Quan

    2015-11-01

    The structures and electronic properties for global minimum geometric structures of small-sized neutral Ag2Sin (n = 1-13) clusters have been investigated using the CALYPSO structure searching method coupled with density functional theory calculations. A great deal of low-energy geometric isomers are optimised at the B3LYP / GENECP theory level. The optimised structures suggest that the ground state Ag2Sin clusters are visibly distorted compared with the corresponding pure silicon clusters and favor a three-dimensional configuration. Starting with Ag2Si12, one Ag atom is fully encapsulated by the Si outer cages. Based on the averaged binding energy, fragmentation energy, second-order energy difference and HOMO-LUMO energy gap, it is seen that Ag2Si2 and Ag2Si5 are tested to be the most stable clusters, and the chemical stabilities of pure Sin+2 clusters can be reduced to some extent after doping two Ag atoms. Additionally, natural population and natural electronic configuration are discussed and the results reveal that charges transfer from the Ag atoms to the silicon frames and the spd hybridisations are present in all Ag2Sin clusters. Lastly, the results of natural bonds show that the Ag-Si bond in Ag2Sin clusters is dominated by small ionic character. Supplementary material in the form of one pdf file available from the Journal web page at http://dx.doi.org/10.1140/epjd/e2015-60404-1

  16. Density of states determination in organic donor-acceptor blend layers enabled by molecular doping

    NASA Astrophysics Data System (ADS)

    Fischer, Janine; Ray, Debdutta; Kleemann, Hans; Pahner, Paul; Schwarze, Martin; Koerner, Christian; Vandewal, Koen; Leo, Karl

    2015-06-01

    Charge carrier transport is a key parameter determining the efficiency of organic solar cells, and is closely related to the density of free and trapped states. For trap characterization, impedance spectroscopy is a suitable, non-invasive method, applicable to complete organic semiconductor devices. In order to contribute to the capacitive signal, the traps must be filled with charge carriers. Typically, trap filling is achieved by illuminating the device or by injecting charge carriers through application of a forward bias voltage. However, in both cases, the exact number of charge carriers in the device is not known and depends strongly on the measurement conditions. Here, hole trap states of the model blend layer ZnPc:C60 are filled by weak p-doping, enabling trap characterization in a blend layer at a controlled hole density. We evaluate impedance spectra at different temperatures in order to determine the density of occupied states (DOOS) directly from the capacitance-frequency spectra by assuming a simple energy diagram. The reconstructed DOOS distribution is analyzed at different doping concentrations and device thicknesses and compared to thermally stimulated current measurements performed on the same devices. In both methods, a pronounced Gaussian peak at about 0.4 eV below the transport level is found as well as deep, exponential tail states, providing a deeper insight into the density of states distribution of this donor-acceptor blend layer. Additionally, the effect of doping-induced trap filling on the solar cell characteristics is studied in these devices.

  17. Real-time quantitative nicking endonuclease-mediated isothermal amplification with small molecular beacons.

    PubMed

    Xu, Wentao; Wang, Chenguang; Zhu, Pengyu; Guo, Tianxiao; Xu, Yuancong; Huang, Kunlun; Luo, Yunbo

    2016-04-21

    Techniques of isothermal amplification have recently made great strides, and have generated significant interest in the field of point-of-care detection. Nicking endonuclease-mediated isothermal amplification (NEMA) is an example of simple isothermal technology. In this paper, a real-time quantitative nicking endonuclease-mediated isothermal amplification with small molecular beacons (SMB-NEMA) of improved specificity and sensitivity is described. First, we optimized the prohibition of de novo synthesis by choosing Nt·BstNBI endonuclease. Second, the whole genome was successfully amplified with Nt·BstNBI (6 U), betaine (1 M) and trehalose (60 mM) for the first time. Third, we achieved 10 pg sensitivity for the first time after adding a small molecular beacon that spontaneously undergoes a conformational change when hybridizing to target, and the practical test validated the assay's application. The small molecular beacon has a similar melting temperature to the reaction temperature, but is approximately 10 bp shorter than the length of a traditional molecular beacon. A new threshold regulation was also established for isothermal conditions. Finally, we established a thermodynamic model for designing small molecular beacons. This multistate model is more correct than the traditional algorithm. This theoretical and practical basis will help us to monitor SMB-NEMA in a quantitative way. In summary, our SMB-NEMA method allows the simple, specific and sensitive assessment of isothermal DNA quantification. PMID:27027375

  18. Real-time quantitative nicking endonuclease-mediated isothermal amplification with small molecular beacons.

    PubMed

    Xu, Wentao; Wang, Chenguang; Zhu, Pengyu; Guo, Tianxiao; Xu, Yuancong; Huang, Kunlun; Luo, Yunbo

    2016-04-21

    Techniques of isothermal amplification have recently made great strides, and have generated significant interest in the field of point-of-care detection. Nicking endonuclease-mediated isothermal amplification (NEMA) is an example of simple isothermal technology. In this paper, a real-time quantitative nicking endonuclease-mediated isothermal amplification with small molecular beacons (SMB-NEMA) of improved specificity and sensitivity is described. First, we optimized the prohibition of de novo synthesis by choosing Nt·BstNBI endonuclease. Second, the whole genome was successfully amplified with Nt·BstNBI (6 U), betaine (1 M) and trehalose (60 mM) for the first time. Third, we achieved 10 pg sensitivity for the first time after adding a small molecular beacon that spontaneously undergoes a conformational change when hybridizing to target, and the practical test validated the assay's application. The small molecular beacon has a similar melting temperature to the reaction temperature, but is approximately 10 bp shorter than the length of a traditional molecular beacon. A new threshold regulation was also established for isothermal conditions. Finally, we established a thermodynamic model for designing small molecular beacons. This multistate model is more correct than the traditional algorithm. This theoretical and practical basis will help us to monitor SMB-NEMA in a quantitative way. In summary, our SMB-NEMA method allows the simple, specific and sensitive assessment of isothermal DNA quantification.

  19. Current and future molecular diagnostics in non-small-cell lung cancer.

    PubMed

    Li, Chun Man; Chu, Wing Ying; Wong, Di Lun; Tsang, Hin Fung; Tsui, Nancy Bo Yin; Chan, Charles Ming Lok; Xue, Vivian Wei Wen; Siu, Parco Ming Fai; Yung, Benjamin Yat Ming; Chan, Lawrence Wing Chi; Wong, Sze Chuen Cesar

    2015-01-01

    The molecular investigation of lung cancer has opened up an advanced area for the diagnosis and therapeutic management of lung cancer patients. Gene alterations in cancer initiation and progression provide not only information on molecular changes in lung cancer but also opportunities in advanced therapeutic regime by personalized targeted therapy. EGFR mutations and ALK rearrangement are important predictive biomarkers for the efficiency of tyrosine kinase inhibitor treatment in lung cancer patients. Moreover, epigenetic aberration and microRNA dysregulation are recent advances in the early detection and monitoring of lung cancer. Although a wide range of molecular tests are available, standardization and validation of assay protocols are essential for the quality of the test outcome. In this review, current and new advancements of molecular biomarkers for non-small-cell lung cancer will be discussed. Recommendations on future development of molecular diagnostic services will also be explored.

  20. Current and future molecular diagnostics in non-small-cell lung cancer.

    PubMed

    Li, Chun Man; Chu, Wing Ying; Wong, Di Lun; Tsang, Hin Fung; Tsui, Nancy Bo Yin; Chan, Charles Ming Lok; Xue, Vivian Wei Wen; Siu, Parco Ming Fai; Yung, Benjamin Yat Ming; Chan, Lawrence Wing Chi; Wong, Sze Chuen Cesar

    2015-01-01

    The molecular investigation of lung cancer has opened up an advanced area for the diagnosis and therapeutic management of lung cancer patients. Gene alterations in cancer initiation and progression provide not only information on molecular changes in lung cancer but also opportunities in advanced therapeutic regime by personalized targeted therapy. EGFR mutations and ALK rearrangement are important predictive biomarkers for the efficiency of tyrosine kinase inhibitor treatment in lung cancer patients. Moreover, epigenetic aberration and microRNA dysregulation are recent advances in the early detection and monitoring of lung cancer. Although a wide range of molecular tests are available, standardization and validation of assay protocols are essential for the quality of the test outcome. In this review, current and new advancements of molecular biomarkers for non-small-cell lung cancer will be discussed. Recommendations on future development of molecular diagnostic services will also be explored. PMID:26153330

  1. Gas-source molecular beam epitaxy of SiGe virtual substrates: I. Growth kinetics and doping

    NASA Astrophysics Data System (ADS)

    Hartmann, J. M.; Gallas, B.; Ferguson, R.; Fernàndez, J.; Zhang, J.; Harris, J. J.

    2000-04-01

    We have studied the growth by gas-source molecular beam epitaxy (GS-MBE) of SiGe virtual substrates. We have first determined the relationship existing between the Ge concentration in SiGe thick films and the gas phase ratio of disilane and germane, and its behaviour versus growth temperature. We find that Si atoms are 4.6 times more likely to be incorporated than Ge atoms at 550 °C. This incorporation probability decreases as the growth temperature increases, following a thermally activated law with a 0.082-0.126 eV characteristic energy. The dependence of SiGe growth rate on substrate temperatures has a cross-over point at approximately 8% of Ge, above which the growth rate decreases significantly as the temperature increases . Otherwise, we show what p-type or n-type doping levels are typically achievable in SiGe virtual substrates, and the influence diluted diborane and arsine have on the growth kinetics of SiGe. Additionally, we demonstrate that the `pre-build-up/flash-off' technique originally proposed by Iyer et al for solid-source MBE (1981 J. Appl. Phys. 52 5608) yields abrupt arsenic doping profiles in GS-MBE.

  2. Germanium doping of self-assembled GaN nanowires grown by plasma-assisted molecular beam epitaxy

    SciTech Connect

    Schörmann, Jörg; Hille, Pascal; Schäfer, Markus; Müßener, Jan; Becker, Pascal; Klar, Peter J.; Hofmann, Detlev M.; Teubert, Jörg; Eickhoff, Martin; Kleine-Boymann, Matthias; Rohnke, Marcus; Mata, Maria de la; Arbiol, Jordi

    2013-09-14

    Germanium doping of GaN nanowires grown by plasma-assisted molecular beam epitaxy on Si(111) substrates is studied. Time of flight secondary ion mass spectrometry measurements reveal a constant Ge-concentration along the growth axis. A linear relationship between the applied Ge-flux and the resulting ensemble Ge-concentration with a maximum content of 3.3×10{sup 20} cm{sup −3} is extracted from energy dispersive X-ray spectroscopy measurements and confirmed by a systematic increase of the conductivity with Ge-concentration in single nanowire measurements. Photoluminescence analysis of nanowire ensembles and single nanowires reveals an exciton localization energy of 9.5 meV at the neutral Ge-donor. A Ge-related emission band at energies above 3.475 eV is found that is assigned to a Burstein-Moss shift of the excitonic emission.

  3. Polarity control and transport properties of Mg-doped (0001) InN by plasma-assisted molecular beam epitaxy

    SciTech Connect

    Choi, Soojeong; Wu Feng; Bierwagen, Oliver; Speck, James S.

    2013-05-15

    The authors report on the plasma-assisted molecular beam epitaxy growth and carrier transport of Mg-doped In-face (0001) InN. The 1.2 {mu}m thick InN films were grown on GaN:Fe templates under metal rich conditions with Mg concentration from 1 Multiplication-Sign 10{sup 17}/cm{sup 3} to 3 Multiplication-Sign 10{sup 20}/cm{sup 3}. A morphological transition, associated with the formation of V-shape polarity inversion domains, was observed at Mg concentration over 7 Multiplication-Sign 10{sup 19}/cm{sup 3} by atomic force microscopy and transmission electron microscopy. Seebeck measurements indicated p-type conductivity for Mg-concentrations from 9 Multiplication-Sign 10{sup 17}/cm{sup 3} to 7 Multiplication-Sign 10{sup 19}/cm{sup 3}, i.e., as it exceeded the compensating (unintentional) donor concentration.

  4. Enhanced photoelectrochemical water splitting performance of TiO2 nanotube arrays coated with an ultrathin nitrogen-doped carbon film by molecular layer deposition.

    PubMed

    Tong, Xili; Yang, Peng; Wang, Yunwei; Qin, Yong; Guo, Xiangyun

    2014-06-21

    Vertically oriented TiO2 nanotube arrays (TNTAs) were conformally coated with an ultrathin nitrogen-doped (N-doped) carbon film via the carbonization of a polyimide film deposited by molecular layer deposition and simultaneously hydrogenated, thereby creating a core/shell nanostructure with a precisely controllable shell thickness. The core/shell nanostructure provides a larger heterojunction interface to substantially reduce the recombination of photogenerated electron-hole pairs, and hydrogenation enhances solar absorption of TNTAs. In addition, the N-doped carbon film coating acts as a high catalytic active surface for oxygen evolution reaction, as well as a protective film to prevent hydrogen-treated TiO2 nanotube oxidation by electrolyte or air. As a result, the N-doped carbon film coated TNTAs displayed remarkably improved photocurrent and photostability. The TNTAs with a N-doped carbon film of ∼ 1 nm produces a current density of 3.6 mA cm(-2) at 0 V vs. Ag/AgCl under the illumination of AM 1.5 G (100 mW cm(-2)), which represents one of the highest values achieved with modified TNTAs. Therefore, we propose that ultrathin N-doped carbon film coating on materials is a viable approach to enhance their PEC water splitting performance.

  5. Protein-based fluorescent metal nanoclusters for small molecular drug screening.

    PubMed

    Yu, Yong; New, Siu Yee; Xie, Jianping; Su, Xiaodi; Tan, Yen Nee

    2014-11-18

    A facile drug screening method based on synthesis of fluorescent gold nanoclusters inside albumin proteins loaded with small molecular drugs and comparing the relative fluorescence intensities of the resultant gold nanoclusters has been developed and successfully applied for the quantitative measurement of drug-protein binding constants. PMID:25253537

  6. Multisource Synergistic Electrocatalytic Oxidation Effect of Strongly Coupled PdM (M = Sn, Pb)/N-doped Graphene Nanocomposite on Small Organic Molecules

    NASA Astrophysics Data System (ADS)

    Wu, Peng; Huang, Yiyin; Kang, Longtian; Wu, Maoxiang; Wang, Yaobing

    2015-10-01

    A series of palladium-based catalysts of metal alloying (Sn, Pb) and/or (N-doped) graphene support with regular enhanced electrocatalytic activity were investigated. The peak current density (118.05 mA cm-2) of PdSn/NG is higher than the sum current density (45.63 + 47.59 mA cm-2) of Pd/NG and PdSn/G. It reveals a synergistic electrocatalytic oxidation effect in PdSn/N-doped graphene Nanocomposite. Extend experiments show this multisource synergetic catalytic effect of metal alloying and N-doped graphene support in one catalyst on small organic molecule (methanol, ethanol and Ethylene glycol) oxidation is universal in PdM(M = Sn, Pb)/NG catalysts. Further, The high dispersion of small nanoparticles, the altered electron structure and Pd(0)/Pd(II) ratio of Pd in catalysts induced by strong coupled the metal alloying and N-doped graphene are responsible for the multisource synergistic catalytic effect in PdM(M = Sn, Pb) /NG catalysts. Finally, the catalytic durability and stability are also greatly improved.

  7. Multisource Synergistic Electrocatalytic Oxidation Effect of Strongly Coupled PdM (M = Sn, Pb)/N-doped Graphene Nanocomposite on Small Organic Molecules

    PubMed Central

    Wu, Peng; Huang, Yiyin; Kang, Longtian; Wu, Maoxiang; Wang, Yaobing

    2015-01-01

    A series of palladium-based catalysts of metal alloying (Sn, Pb) and/or (N-doped) graphene support with regular enhanced electrocatalytic activity were investigated. The peak current density (118.05 mA cm−2) of PdSn/NG is higher than the sum current density (45.63 + 47.59 mA cm−2) of Pd/NG and PdSn/G. It reveals a synergistic electrocatalytic oxidation effect in PdSn/N-doped graphene Nanocomposite. Extend experiments show this multisource synergetic catalytic effect of metal alloying and N-doped graphene support in one catalyst on small organic molecule (methanol, ethanol and Ethylene glycol) oxidation is universal in PdM(M = Sn, Pb)/NG catalysts. Further, The high dispersion of small nanoparticles, the altered electron structure and Pd(0)/Pd(II) ratio of Pd in catalysts induced by strong coupled the metal alloying and N-doped graphene are responsible for the multisource synergistic catalytic effect in PdM(M = Sn, Pb) /NG catalysts. Finally, the catalytic durability and stability are also greatly improved. PMID:26434949

  8. A tetraphenylethylene core-based 3D structure small molecular acceptor enabling efficient non-fullerene organic solar cells.

    PubMed

    Liu, Yuhang; Mu, Cheng; Jiang, Kui; Zhao, Jingbo; Li, Yunke; Zhang, Lu; Li, Zhengke; Lai, Joshua Yuk Lin; Hu, Huawei; Ma, Tingxuan; Hu, Rongrong; Yu, Demei; Huang, Xuhui; Tang, Ben Zhong; Yan, He

    2015-02-01

    A tetraphenylethylene core-based small molecular acceptor with a unique 3D molecular structure is developed. Bulk-heterojunction blend films with a small feature size (≈20 nm) are obtained, which lead to non-fullerene organic solar cells (OSCs) with 5.5% power conversion efficiency. The work provides a new molecular design approach to efficient non-fullerene OSCs based on 3D-structured small-molecule acceptors.

  9. An improvement of performance in n-channel organic field effect transistors with N-phenyl[60]fulleropyrrolidines by molecular doping.

    PubMed

    Long, Dang Xuan; Karakawa, Makoto; Noh, Yong-Young

    2016-09-14

    The high performance of soluble [60]fulleropyrrolidine upon its use as the active layer of n-channel organic field-effect transistors (OFETs) is reported. The two materials, N-phenyl derivatives C60-fused-N-phenyl-2-phenylpyrrolidine ([C60]PhNPh) and C60-fused N-phenyl-2-hexylpyrrolidine ([C60]HexNPh), have well-controlled molecular structures with a modification of the pyrrolidine ring, with no increase in the LUMO level, achieving a high mobility and highly ambient stable n-type OFET. The top-gate, bottom-contact device shows a high electron charge-carrier mobility of up to 0.14 and 0.08 cm(2) V(-1) s(-1) for [C60]PhNPh and [C60]HexNPh, respectively, (Ion/Ioff = 10(6)) with the commonly used CYTOP dielectric. Excess carriers introduced by a small amount of chemical doping of polyethyleneimine (PEI) compensate traps by shifting the Fermi level (EF) toward the respective transport energy levels and therefore increase charge-carrier mobility (0.26 and 0.1 cm(2) V(-1) s(-1)) and provide good ambient operational stability compared with pristine devices. PMID:27523163

  10. Challenges in molecular testing in non-small-cell lung cancer patients with advanced disease.

    PubMed

    Hiley, Crispin T; Le Quesne, John; Santis, George; Sharpe, Rowena; de Castro, David Gonzalez; Middleton, Gary; Swanton, Charles

    2016-09-01

    Lung cancer diagnostics have progressed greatly in the previous decade. Development of molecular testing to identify an increasing number of potentially clinically actionable genetic variants, using smaller samples obtained via minimally invasive techniques, is a huge challenge. Tumour heterogeneity and cancer evolution in response to therapy means that repeat biopsies or circulating biomarkers are likely to be increasingly useful to adapt treatment as resistance develops. We highlight some of the current challenges faced in clinical practice for molecular testing of EGFR, ALK, and new biomarkers such as PDL1. Implementation of next generation sequencing platforms for molecular diagnostics in non-small-cell lung cancer is increasingly common, allowing testing of multiple genetic variants from a single sample. The use of next generation sequencing to recruit for molecularly stratified clinical trials is discussed in the context of the UK Stratified Medicine Programme and The UK National Lung Matrix Trial. PMID:27598680

  11. Nonnuclear Nearly Free Electron Conduction Channels Induced by Doping Charge in Nanotube–Molecular Sheet Composites

    SciTech Connect

    Zhao, Jin; Zheng, Qijing; Petek, Hrvoje; Yang, Jinlong

    2014-09-04

    Nearly free electron (NFE) states with density maxima in nonnuclear (NN) voids may have remarkable electron transport properties ranging from suppressed electron–phonon interaction to Wigner crystallization. Such NFE states, however, usually exist near the vacuum level, which makes them unsuitable for transport. Through first principles calculations on nanocomposites consisting of carbon nanotube (CNT) arrays sandwiched between boron nitride (BN) sheets, we describe a stratagem for stabilizing the NN-NFE states to below the Fermi level. By doping the CNTs with negative charge, we establish Coulomb barriers at CNTs walls that, together with the insulating BN sheets, define the transverse potentials of one-dimensional (1D) transport channels, which support the NN-NFE states.

  12. Nonnuclear nearly free electron conduction channels induced by doping charge in nanotube-molecular sheet composites.

    PubMed

    Zhao, Jin; Zheng, Qijing; Petek, Hrvoje; Yang, Jinlong

    2014-09-01

    Nearly free electron (NFE) states with density maxima in nonnuclear (NN) voids may have remarkable electron transport properties ranging from suppressed electron-phonon interaction to Wigner crystallization. Such NFE states, however, usually exist near the vacuum level, which makes them unsuitable for transport. Through first principles calculations on nanocomposites consisting of carbon nanotube (CNT) arrays sandwiched between boron nitride (BN) sheets, we describe a stratagem for stabilizing the NN-NFE states to below the Fermi level. By doping the CNTs with negative charge, we establish Coulomb barriers at CNTs walls that, together with the insulating BN sheets, define the transverse potentials of one-dimensional (1D) transport channels, which support the NN-NFE states. PMID:24401149

  13. Dual origin of defect magnetism in graphene and its reversible switching by molecular doping.

    PubMed

    Nair, R R; Tsai, I-L; Sepioni, M; Lehtinen, O; Keinonen, J; Krasheninnikov, A V; Castro Neto, A H; Katsnelson, M I; Geim, A K; Grigorieva, I V

    2013-01-01

    Control of magnetism by applied voltage is desirable for spintronics applications. Finding a suitable material remains an elusive goal, with only a few candidates found so far. Graphene is one of them and attracts interest because of its weak spin-orbit interaction, the ability to control electronic properties by the electric field effect and the possibility to introduce paramagnetic centres such as vacancies and adatoms. Here we show that the magnetism of adatoms in graphene is itinerant and can be controlled by doping, so that magnetic moments are switched on and off. The much-discussed vacancy magnetism is found to have a dual origin, with two approximately equal contributions; one from itinerant magnetism and the other from dangling bonds. Our work suggests that graphene's spin transport can be controlled by the field effect, similar to its electronic and optical properties, and that spin diffusion can be significantly enhanced above a certain carrier density.

  14. Small unilamellar vesicles: a platform technology for molecular imaging of brain tumors

    NASA Astrophysics Data System (ADS)

    Iqbal, Umar; Albaghdadi, Homam; Nieh, Mu-Ping; Tuor, Ursula I.; Mester, Zoltan; Stanimirovic, Danica; Katsaras, John; Abulrob, Abedelnasser

    2011-05-01

    Molecular imaging enables the non-invasive investigation of cellular and molecular processes. Although there are challenges to overcome, the development of targeted contrast agents to increase the sensitivity of molecular imaging techniques is essential for their clinical translation. In this study, spontaneously forming, small unilamellar vesicles (sULVs) (30 nm diameter) were used as a platform to build a bimodal (i.e., optical and magnetic resonance imaging (MRI)) targeted contrast agent for the molecular imaging of brain tumors. sULVs were loaded with a gadolinium (Gd) chelated lipid (Gd-DPTA-BOA), functionalized with targeting antibodies (anti-EGFR monoclonal and anti-IGFBP7 single domain), and incorporated a near infrared dye (Cy5.5). The resultant sULVs were characterized in vitro using small angle neutron scattering (SANS), phantom MRI and dynamic light scattering (DLS). Antibody targeted and nontargeted Gd loaded sULVs labeled with Cy5.5 were assessed in vivo in a brain tumor model in mice using time domain optical imaging and MRI. The results demonstrated that a spontaneously forming, nanosized ULVs loaded with a high payload of Gd can selectively target and image, using MR and optical imaging, brain tumor vessels when functionalized with anti-IGFBP7 single domain antibodies. The unique features of these targeted sULVs make them promising molecular MRI contrast agents.

  15. Small Unilamellar Vesicles: A Platform Technology for Molecular Imaging of Brain Tumors

    SciTech Connect

    Iqbal, U; Albaghdadi, H; Nieh, Mu-Ping; Tuor, U.I; Mester, Z; Stanimirovic, D; Katsaras, John; Abulrob, A

    2011-01-01

    Molecular imaging enables the non-invasive investigation of cellular and molecular processes. Although there are challenges to overcome, the development of targeted contrast agents to increase the sensitivity of molecular imaging techniques is essential for their clinical translation. In this study, spontaneously forming, small unilamellar vesicles (sULVs) (30 nm diameter) were used as a platform to build a bimodal (i.e., optical and magnetic resonance imaging (MRI)) targeted contrast agent for the molecular imaging of brain tumors. sULVs were loaded with a gadolinium (Gd) chelated lipid (Gd-DPTA-BOA), functionalized with targeting antibodies (anti-EGFR monoclonal and anti-IGFBP7 single domain), and incorporated a near infrared dye (Cy5.5). The resultant sULVs were characterized in vitro using small angle neutron scattering (SANS), phantom MRI and dynamic light scattering (DLS). Antibody targeted and nontargeted Gd loaded sULVs labeled with Cy5.5 were assessed in vivo in a brain tumor model in mice using time domain optical imaging and MRI. The results demonstrated that a spontaneously forming, nanosized ULVs loaded with a high payload of Gd can selectively target and image, using MR and optical imaging, brain tumor vessels when functionalized with anti-IGFBP7 single domain antibodies. The unique features of these targeted sULVs make them promising molecular MRI contrast agents.

  16. Small unilamellar vesicles: a platform technology for molecular imaging of brain tumors.

    PubMed

    Iqbal, Umar; Albaghdadi, Homam; Nieh, Mu-Ping; Tuor, Ursula I; Mester, Zoltan; Stanimirovic, Danica; Katsaras, John; Abulrob, Abedelnasser

    2011-05-13

    Molecular imaging enables the non-invasive investigation of cellular and molecular processes. Although there are challenges to overcome, the development of targeted contrast agents to increase the sensitivity of molecular imaging techniques is essential for their clinical translation. In this study, spontaneously forming, small unilamellar vesicles (sULVs) (30 nm diameter) were used as a platform to build a bimodal (i.e., optical and magnetic resonance imaging (MRI)) targeted contrast agent for the molecular imaging of brain tumors. sULVs were loaded with a gadolinium (Gd) chelated lipid (Gd-DPTA-BOA), functionalized with targeting antibodies (anti-EGFR monoclonal and anti-IGFBP7 single domain), and incorporated a near infrared dye (Cy5.5). The resultant sULVs were characterized in vitro using small angle neutron scattering (SANS), phantom MRI and dynamic light scattering (DLS). Antibody targeted and nontargeted Gd loaded sULVs labeled with Cy5.5 were assessed in vivo in a brain tumor model in mice using time domain optical imaging and MRI. The results demonstrated that a spontaneously forming, nanosized ULVs loaded with a high payload of Gd can selectively target and image, using MR and optical imaging, brain tumor vessels when functionalized with anti-IGFBP7 single domain antibodies. The unique features of these targeted sULVs make them promising molecular MRI contrast agents.

  17. Tellurium n-type doping of highly mismatched amorphous GaN1-xAsx alloys in plasma-assisted molecular beam epitaxy

    DOE PAGESBeta

    Novikov, S. V.; Ting, M.; Yu, K. M.; Sarney, W. L.; Martin, R. W.; Svensson, S. P.; Walukiewicz, W.; Foxon, C. T.

    2014-10-01

    In this paper we report our study on n-type Te doping of amorphous GaN1-xAsx layers grown by plasma-assisted molecular beam epitaxy. We have used a low temperature PbTe source as a source of tellurium. Reproducible and uniform tellurium incorporation in amorphous GaN1-xAsx layers has been successfully achieved with a maximum Te concentration of 9×10²⁰ cm⁻³. Tellurium incorporation resulted in n-doping of GaN1-xAsx layers with Hall carrier concentrations up to 3×10¹⁹ cm⁻³ and mobilities of ~1 cm²/V s. The optimal growth temperature window for efficient Te doping of the amorphous GaN1-xAsx layers has been determined.

  18. Development of Ultra Small Shock Tube for High Energy Molecular Beam Source

    SciTech Connect

    Miyoshi, Nobuya; Nagata, Shuhei; Kinefuchi, Ikuya; Shimizu, Kazuya; Matsumoto, Yoichiro; Takagi, Shu

    2008-12-31

    A molecular beam source exploiting a small shock tube is described for potential generation of high energy beam in a range of 1-5 eV without any undesirable impurities. The performance of a non-diaphragm type shock tube with an inner diameter of 2 mm was evaluated by measuring the acceleration and attenuation process of shock waves. With this shock tube installed in a molecular beam source, we measured the time-of-flight distributions of shock-heated beams, which demonstrated the ability of controlling the beam energy with the initial pressure ratio of the shock tube.

  19. A journey in bioinspired supramolecular chemistry: from molecular tweezers to small molecules that target myotonic dystrophy

    PubMed Central

    2016-01-01

    Summary This review summarizes part of the author’s research in the area of supramolecular chemistry, beginning with his early life influences and early career efforts in molecular recognition, especially molecular tweezers. Although designed to complex DNA, these hosts proved more applicable to the field of host–guest chemistry. This early experience and interest in intercalation ultimately led to the current efforts to develop small molecule therapeutic agents for myotonic dystrophy using a rational design approach that heavily relies on principles of supramolecular chemistry. How this work was influenced by that of others in the field and the evolution of each area of research is highlighted with selected examples. PMID:26877815

  20. CONDENSED MATTER: STRUCTURE, MECHANICAL AND THERMAL PROPERTIES: Structural and Electrical Properties of Single Crystalline Ga-Doped ZnO Thin Films Grown by Molecular Beam Epitaxy

    NASA Astrophysics Data System (ADS)

    Lu, Zhong-Lin; Zou, Wen-Qin; Xu, Ming-Xiang; Zhang, Feng-Ming; Du, You-Wei

    2009-11-01

    High-quality Ga-doped ZnO (ZnO:Ga) single crystalline films with various Ga concentrations are grown on a-plane sapphire substrates using molecular-beam epitaxy. The site configuration of doped Ga atoms is studied by means of x-ray absorption spectroscopy. It is found that nearly all Ga can substitute into ZnO lattice as electrically active donors, a generating high density of free carriers with about one electron per Ga dopant when the Ga concentration is no more than 2%. However, further increasing the Ga doping concentration leads to a decrease of the conductivity due to partial segregation of Ga atoms to the minor phase of the spinel ZnGa2O4 or other intermediate phase. It seems that the maximum solubility of Ga in the ZnO single crystalline film is about 2 at.% and the lowest resistivity can reach 1.92 × 10-4 Ω·cm at room temperature, close to the best value reported. In contrast to ZnO:Ga thin film with 1% or 2% Ga doping, the film with 4% Ga doping exhibits a metal semiconductor transition at 80 K. The scattering mechanism of conducting electrons in single crystalline ZnO:Ga thin film is discussed.

  1. Molecular identification of chlamydial cause of abortion in small ruminants in Jordan.

    PubMed

    Ababneh, Huthaifa Salah; Ababneh, Mustafa Mohammed Kheir; Hananeh, Wael Mahmoud; Alsheyab, Fawzi Mohammad; Jawasreh, Khaleel Ibraheem; Al-Gharaibeh, Moath Ahmad; Ababneh, Mohammed Mahmoud

    2014-12-01

    Chlamydophila abortus (Ch. abortus) is the etiological agent of ovine enzootic abortion (OEA) and one of the most common infectious agents of abortion in small ruminants worldwide. RFLP-PCR analysis of the outer membrane protein gene (OMP2 gene) was used for diagnosis and characterization of chlamydial causes of abortion in small ruminants in Jordan. Sixty-six placental tissues and 15 vaginal swabs were collected from aborted ewes and does to identify cause of abortion in Jordan. Thirty-eight placental samples (58 %) and 13 vaginal swabs (87 %) were positive for chlamydial DNA. Shedding of bacteria in vaginal swabs was detected within 7 days after abortion. The results of this study showed that chlamydiosis is one of the important causes of abortion in small ruminants in Jordan. In addition, vaginal swab is an excellent sample for molecular diagnosis of chlamydiosis. DNA sequencing and RFLP analysis of the OMP2 reveal that all chlamydial cause of abortion in small ruminants in Jordan are due to Ch. abortus. While, Ch. pecorum was not detected in any sample. OMP2 gene of the isolated Jordanian strain was identical (100 %) to Ch. abortus FAS strain. In conclusion, Ch. abortus is an important cause of abortion in Jordan; vaginal swab within 7 days of abortion can be used for molecular diagnosis of chlamydiosis in small ruminants.

  2. An aptazyme-based molecular device that converts a small-molecule input into an RNA output.

    PubMed

    Ayukawa, Shotaro; Sakai, Yoko; Kiga, Daisuke

    2012-08-01

    We describe the construction of an aptazyme-based molecular device that converts, through a cascade of reactions, a small-molecule input into output RNA strands. This device is applicable as an interface between a small molecule and a molecular system that accepts only nucleic acid input.

  3. Molecular dynamics study of the mechanical loss in amorphous pure and doped silica

    SciTech Connect

    Hamdan, Rashid; Trinastic, Jonathan P.; Cheng, H. P.

    2014-08-07

    Gravitational wave detectors and other precision measurement devices are limited by the thermal noise in the oxide coatings on the mirrors of such devices. We have investigated the mechanical loss in amorphous oxides by calculating the internal friction using classical, atomistic molecular dynamics simulations. We have implemented the trajectory bisection method and the non-local ridge method in the DL-POLY molecular dynamics simulation software to carry out those calculations. These methods have been used to locate the local potential energy minima that a system visits during a molecular dynamics trajectory and the transition state between any two consecutive minima. Using the numerically calculated barrier height distributions, barrier asymmetry distributions, relaxation times, and deformation potentials, we have calculated the internal friction of pure amorphous silica and silica mixed with other oxides. The results for silica compare well with experiment. Finally, we use the numerical calculations to comment on the validity of previously used theoretical assumptions.

  4. Following the nanostructural molecular orientation guidelines for sulfur versus thiophene units in small molecule photovoltaic cells

    NASA Astrophysics Data System (ADS)

    Kim, Yu Jin; Park, Chan Eon

    2016-03-01

    In bulk heterojunction (BHJ) organic photovoltaics, particularly those using small molecules, electron donor and/or electron acceptor materials form a distributed network in the photoactive layer where critical photo-physical processes occur. Extensive research has recently focused on the importance of sulfur atoms in the small molecules. Little is known about the three-dimensional orientation of these sulfur atom-containing molecules. Herein, we report on our research concerning the heterojunction textures of the crystalline molecular orientation of small compounds having sulfur-containing units in the side chains, specifically, compounds known as DR3TSBDT that contain the alkylthio group and DR3TBDTT that does not. The improved performance of the DR3TBDTT-based devices, particularly in the photocurrent and the fill factor, was attributed to the large population of donor compound crystallites with a favorable face-on orientation along the perpendicular direction. This orientation resulted in efficient charge transport and a reduction in charge recombination. These findings underscore the great potential of small-molecule solar cells and suggest that even higher efficiencies can be achieved through materials development and molecular orientation control.In bulk heterojunction (BHJ) organic photovoltaics, particularly those using small molecules, electron donor and/or electron acceptor materials form a distributed network in the photoactive layer where critical photo-physical processes occur. Extensive research has recently focused on the importance of sulfur atoms in the small molecules. Little is known about the three-dimensional orientation of these sulfur atom-containing molecules. Herein, we report on our research concerning the heterojunction textures of the crystalline molecular orientation of small compounds having sulfur-containing units in the side chains, specifically, compounds known as DR3TSBDT that contain the alkylthio group and DR3TBDTT that does not

  5. Correlating Molecular Structures with Transport Dynamics in High-Efficiency Small-Molecule Organic Photovoltaics.

    PubMed

    Peng, Jiajun; Chen, Yani; Wu, Xiaohan; Zhang, Qian; Kan, Bin; Chen, Xiaoqing; Chen, Yongsheng; Huang, Jia; Liang, Ziqi

    2015-06-24

    Efficient charge transport is a key step toward high efficiency in small-molecule organic photovoltaics. Here we applied time-of-flight and organic field-effect transistor to complementarily study the influences of molecular structure, trap states, and molecular orientation on charge transport of small-molecule DRCN7T (D1) and its analogue DERHD7T (D2). It is revealed that, despite the subtle difference of the chemical structures, D1 exhibits higher charge mobility, the absence of shallow traps, and better photosensitivity than D2. Moreover, charge transport is favored in the out-of-plane structure within D1-based organic solar cells, while D2 prefers in-plane charge transport.

  6. Small Molecular-Sized Artesunate Attenuates Ocular Neovascularization via VEGFR2, PKCα, and PDGFR Targets.

    PubMed

    Zong, Yao; Yuan, Yongguang; Qian, Xiaobing; Huang, Zhen; Yang, Wei; Lin, Leilei; Zheng, Qishan; Li, Yujie; He, Huining; Gao, Qianying

    2016-08-02

    Ocular neovascularization (NV) is the primary cause of blindness in many ocular diseases. Large molecular weight anti- vascular endothelial growth factor (VEGF) protein drugs, such as Avastin and Lucentis, have saved the vision of millions. However, approximately 20-30% of patients respond poorly to anti-VEGF treatment. We found that artesunate (ART), a small molecular derivative of artemisinin, had a significant inhibitory effect on ocular NV by downregulating the expression of VEGFR2, PKCα, and PDGFR. ART significantly inhibited retinal NV in rabbits and macular edema in monkeys with greater anterior chamber penetrability and more durable efficacy than Avastin. Our pilot study showed that intravitreal injection of 80 μg ART significantly inhibited iris and corneal NV in a severe retinal detachment case. Our results suggest that ART might be a potential persistent small-molecule drug to manage ocular NV via multi-targets.

  7. Correlating Molecular Structures with Transport Dynamics in High-Efficiency Small-Molecule Organic Photovoltaics.

    PubMed

    Peng, Jiajun; Chen, Yani; Wu, Xiaohan; Zhang, Qian; Kan, Bin; Chen, Xiaoqing; Chen, Yongsheng; Huang, Jia; Liang, Ziqi

    2015-06-24

    Efficient charge transport is a key step toward high efficiency in small-molecule organic photovoltaics. Here we applied time-of-flight and organic field-effect transistor to complementarily study the influences of molecular structure, trap states, and molecular orientation on charge transport of small-molecule DRCN7T (D1) and its analogue DERHD7T (D2). It is revealed that, despite the subtle difference of the chemical structures, D1 exhibits higher charge mobility, the absence of shallow traps, and better photosensitivity than D2. Moreover, charge transport is favored in the out-of-plane structure within D1-based organic solar cells, while D2 prefers in-plane charge transport. PMID:26066398

  8. Small Molecular-Sized Artesunate Attenuates Ocular Neovascularization via VEGFR2, PKCα, and PDGFR Targets

    PubMed Central

    Zong, Yao; Yuan, Yongguang; Qian, Xiaobing; Huang, Zhen; Yang, Wei; Lin, Leilei; Zheng, Qishan; Li, Yujie; He, Huining; Gao, Qianying

    2016-01-01

    Ocular neovascularization (NV) is the primary cause of blindness in many ocular diseases. Large molecular weight anti- vascular endothelial growth factor (VEGF) protein drugs, such as Avastin and Lucentis, have saved the vision of millions. However, approximately 20–30% of patients respond poorly to anti-VEGF treatment. We found that artesunate (ART), a small molecular derivative of artemisinin, had a significant inhibitory effect on ocular NV by downregulating the expression of VEGFR2, PKCα, and PDGFR. ART significantly inhibited retinal NV in rabbits and macular edema in monkeys with greater anterior chamber penetrability and more durable efficacy than Avastin. Our pilot study showed that intravitreal injection of 80 μg ART significantly inhibited iris and corneal NV in a severe retinal detachment case. Our results suggest that ART might be a potential persistent small-molecule drug to manage ocular NV via multi-targets. PMID:27480521

  9. Photocatalytic evolution of molecular hydrogen and oxygen over La-doped NaTaO3 particles: Effect of different cocatalysts (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Ivanova, Irina; Kandiel, Tarek; Hakki, Amer; Dillert, Ralf; Bahnemann, Detlef W.

    2015-09-01

    To solve the global energy and environmental issues highly efficient systems for solar energy conversion and storage are needed. One of them involves the photocatalytic conversion of solar energy into the storable fuel molecular hydrogen via the water splitting process utilizing metal-oxide semiconductors as catalysts. Since photocatalytic water splitting is still a rather poorly understood reaction, fundamental research in this field is required. Herein, the photocatalytic activity for water splitting was investigated utilizing La-doped NaTaO3 as a model photocatalyst. The activity of La-doped NaTaO3 was assessed by the determination of the overall quantum yield of molecular hydrogen and molecular oxygen evolution. In pure water La-doped NaTaO3 exhibits rather poor activity for the photocatalytic H2 evolution whereby no O2 was detected. To enhance the photocatalytic activity the surface of La-doped NaTaO3 was modified with various cocatalysts including noble metals (Pt, Au and Rh) and metal oxides (NiO, CuO, CoO, AgO and RuO2). The photocatalytic activity was evaluated in pure water, in aqueous methanol solution, and in aqueous silver nitrate solution. The results reveal that cocatalysts such as RuO2 or CuO exhibiting the highest catalytic activity for H2 evolution from pure water, possess, however, the lowest activity for O2 evolution from aqueous silver nitrate solution. La-doped NaTaO3 modified with Pt shows the highest quantum yield of 33 % with respect to the H2 evolution in the presence of methanol. To clarify the role of methanol in such a photocatalytic system, long-term investigations and isotopic studies were performed. The underlying mechanisms of methanol oxidation were elucidated.

  10. Comprehensive molecular pathology analysis of small bowel adenocarcinoma reveals novel targets with potential for clinical utility

    PubMed Central

    Kelly, Paul; Fuchs, Marc-Aurel; Alderdice, Matthew; McCabe, Clare M.; Bingham, Victoria; McGready, Claire; Tripathi, Shailesh; Emmert-Streib, Frank; Loughrey, Maurice B.; McQuaid, Stephen; Maxwell, Perry; Hamilton, Peter W.; Turkington, Richard; James, Jacqueline A.; Wilson, Richard H.; Salto-Tellez, Manuel

    2015-01-01

    Small bowel accounts for only 0.5% of cancer cases in the US but incidence rates have been rising at 2.4% per year over the past decade. One-third of these are adenocarcinomas but little is known about their molecular pathology and no molecular markers are available for clinical use. Using a retrospective 28 patient matched normal-tumor cohort, next-generation sequencing, gene expression arrays and CpG methylation arrays were used for molecular profiling. Next-generation sequencing identified novel mutations in IDH1, CDH1, KIT, FGFR2, FLT3, NPM1, PTEN, MET, AKT1, RET, NOTCH1 and ERBB4. Array data revealed 17% of CpGs and 5% of RNA transcripts assayed to be differentially methylated and expressed respectively (p < 0.01). Merging gene expression and DNA methylation data revealed CHN2 as consistently hypermethylated and downregulated in this disease (Spearman −0.71, p < 0.001). Mutations in TP53 which were found in more than half of the cohort (15/28) and Kazald1 hypomethylation were both were indicative of poor survival (p = 0.03, HR = 3.2 and p = 0.01, HR = 4.9 respectively). By integrating high-throughput mutational, gene expression and DNA methylation data, this study reveals for the first time the distinct molecular profile of small bowel adenocarcinoma and highlights potential clinically exploitable markers. PMID:26315110

  11. Comprehensive molecular pathology analysis of small bowel adenocarcinoma reveals novel targets with potential for clinical utility.

    PubMed

    Alvi, Muhammad A; McArt, Darragh G; Kelly, Paul; Fuchs, Marc-Aurel; Alderdice, Matthew; McCabe, Clare M; Bingham, Victoria; McGready, Claire; Tripathi, Shailesh; Emmert-Streib, Frank; Loughrey, Maurice B; McQuaid, Stephen; Maxwell, Perry; Hamilton, Peter W; Turkington, Richard; James, Jacqueline A; Wilson, Richard H; Salto-Tellez, Manuel

    2015-08-28

    Small bowel accounts for only 0.5% of cancer cases in the US but incidence rates have been rising at 2.4% per year over the past decade. One-third of these are adenocarcinomas but little is known about their molecular pathology and no molecular markers are available for clinical use. Using a retrospective 28 patient matched normal-tumor cohort, next-generation sequencing, gene expression arrays and CpG methylation arrays were used for molecular profiling. Next-generation sequencing identified novel mutations in IDH1, CDH1, KIT, FGFR2, FLT3, NPM1, PTEN, MET, AKT1, RET, NOTCH1 and ERBB4. Array data revealed 17% of CpGs and 5% of RNA transcripts assayed to be differentially methylated and expressed respectively (p < 0.01). Merging gene expression and DNA methylation data revealed CHN2 as consistently hypermethylated and downregulated in this disease (Spearman -0.71, p < 0.001). Mutations in TP53 which were found in more than half of the cohort (15/28) and Kazald1 hypomethylation were both were indicative of poor survival (p = 0.03, HR = 3.2 and p = 0.01, HR = 4.9 respectively). By integrating high-throughput mutational, gene expression and DNA methylation data, this study reveals for the first time the distinct molecular profile of small bowel adenocarcinoma and highlights potential clinically exploitable markers.

  12. A non-diaphragm type small shock tube for application to a molecular beam source

    NASA Astrophysics Data System (ADS)

    Yoshimoto, Yuta; Osuka, Kenichi; Miyoshi, Nobuya; Kinefuchi, Ikuya; Takagi, Shu; Matsumoto, Yoichiro

    2013-07-01

    A non-diaphragm type small shock tube was developed for application to a molecular beam source, which can generate beams in the energy range from 1 to several electron volts and beams containing dissociated species such as atomic oxygen. Since repetitive high-frequency operation is indispensable for rapid signal acquisition in beam scattering experiments, the dimensions of the shock tube were miniaturized to reduce the evacuation time between shots. The designed shock tube is 2-4 mm in diameter and can operate at 0.5 Hz. Moreover, a high shock Mach number at the tube end is required for high-energy molecular beam generation. To reduce the shock attenuation caused by the wall boundary layer, which becomes significant in small-diameter tubes, we developed a high-speed response valve employing the current-loop mechanism. The response time of this mechanism is about 100 μs, which is shorter than the rupture time of conventional diaphragms. We show that the current-loop valve generates shock waves with shorter formation distances (about 200-300 mm) than those of conventional shock tubes. In addition, the converging geometry efficiently accelerates shock wave in the small-diameter tubes. The optimal geometry of the shock tube yields shock Mach number around 7, which indicates that the translation energy of molecular beams can exceed 1 eV even in the presence of the real gas effect.

  13. Ultra-small Nd3+-doped nanoparticles as near-infrared luminescent biolabels of hemin in bacteria

    NASA Astrophysics Data System (ADS)

    Xi, Yonglan; Chang, Zhizhou; Ye, Xiaomei; Huang, Hongying; Huang, Yanan; Xiao, Qingbo; Lin, Hongzhen

    2016-01-01

    Near-infrared (NIR) luminescent Nd3+-doped nanoparticles (NPs) have attracted considerable attention in bioimaging and biodetection. Here, we demonstrate sub-6 nm NaGdF4:Nd3+,Fe3+ NPs as luminescent biolabels of hemin molecules that act as the exogenous electron carriers in microbial communities. Contrary to the severe quenching of the visible luminescence for either upconverting or downconverting NPs, the Nd3+-doped NPs show superior properties in avoiding the optical absorption of hemin within the UV and visible spectral regions. A detailed examination showed that the Nd3+-doped NPs exhibit no obvious toxic effects on the microbial communities and show scarce influence on the characteristics of labeled hemin molecules in enhancing the reducing power of the fermentation system. More importantly, by monitoring the NIR luminescence of Nd3+-doped NPs, the selective accumulation of exogenous electron carriers in bacteria that are lacking reducing power has been revealed for the first time. The application of Nd3+-doped NPs as biolabels in bacteria would provide new opportunities for further unravelling the role of exogenous electron carriers in anaerobic digestion.Near-infrared (NIR) luminescent Nd3+-doped nanoparticles (NPs) have attracted considerable attention in bioimaging and biodetection. Here, we demonstrate sub-6 nm NaGdF4:Nd3+,Fe3+ NPs as luminescent biolabels of hemin molecules that act as the exogenous electron carriers in microbial communities. Contrary to the severe quenching of the visible luminescence for either upconverting or downconverting NPs, the Nd3+-doped NPs show superior properties in avoiding the optical absorption of hemin within the UV and visible spectral regions. A detailed examination showed that the Nd3+-doped NPs exhibit no obvious toxic effects on the microbial communities and show scarce influence on the characteristics of labeled hemin molecules in enhancing the reducing power of the fermentation system. More importantly, by

  14. Analysis of the electron density features of small boron clusters and the effects of doping with C, P, Al, Si, and Zn: Magic B7P and B8Si clusters

    NASA Astrophysics Data System (ADS)

    Saha, P.; Rahane, A. B.; Kumar, V.; Sukumar, N.

    2016-05-01

    Boron atomic clusters show several interesting and unusual size-dependent features due to the small covalent radius, electron deficiency, and higher coordination number of boron as compared to carbon. These include aromaticity and a diverse array of structures such as quasi-planar, ring or tubular shaped, and fullerene-like. In the present work, we have analyzed features of the computed electron density distributions of small boron clusters having up to 11 boron atoms, and investigated the effect of doping with C, P, Al, Si, and Zn atoms on their structural and physical properties, in order to understand the bonding characteristics and discern trends in bonding and stability. We find that in general there are covalent bonds as well as delocalized charge distribution in these clusters. We associate the strong stability of some of these planar/quasiplanar disc-type clusters with the electronic shell closing with effectively twelve delocalized valence electrons using a disc-shaped jellium model. {{{{B}}}9}-, B10, B7P, and B8Si, in particular, are found to be exceptional with very large gaps between the highest occupied molecular orbital and the lowest unoccupied molecular orbital, and these are suggested to be magic clusters.

  15. Following the nanostructural molecular orientation guidelines for sulfur versus thiophene units in small molecule photovoltaic cells.

    PubMed

    Kim, Yu Jin; Park, Chan Eon

    2016-04-14

    In bulk heterojunction (BHJ) organic photovoltaics, particularly those using small molecules, electron donor and/or electron acceptor materials form a distributed network in the photoactive layer where critical photo-physical processes occur. Extensive research has recently focused on the importance of sulfur atoms in the small molecules. Little is known about the three-dimensional orientation of these sulfur atom-containing molecules. Herein, we report on our research concerning the heterojunction textures of the crystalline molecular orientation of small compounds having sulfur-containing units in the side chains, specifically, compounds known as DR3TSBDT that contain the alkylthio group and DR3TBDTT that does not. The improved performance of the DR3TBDTT-based devices, particularly in the photocurrent and the fill factor, was attributed to the large population of donor compound crystallites with a favorable face-on orientation along the perpendicular direction. This orientation resulted in efficient charge transport and a reduction in charge recombination. These findings underscore the great potential of small-molecule solar cells and suggest that even higher efficiencies can be achieved through materials development and molecular orientation control.

  16. Hyperthermal molecular beam source using a non-diaphragm-type small shock tube

    NASA Astrophysics Data System (ADS)

    Yoshimoto, Yuta; Osuka, Kenichi; Miyoshi, Nobuya; Kinefuchi, Ikuya; Takagi, Shu; Matsumoto, Yoichiro

    2016-10-01

    We have developed a hyperthermal molecular beam source employing a non-diaphragm-type small shock tube for gas-surface interaction studies. Unlike conventional shock-heated beam sources, the capability of repetitive beam generation without the need for replacing a diaphragm makes our beam source suitable for scattering experiments, which require signal accumulation for a large number of beam pulses. The short duration of shock heating alleviates the usual temperature limit due to the nozzle material, enabling the generation of a molecular beam with higher translational energy or that containing dissociated species. The shock-heated beam is substantially free from surface-contaminating impurities that are pronounced in arc-heated beams. We characterize the properties of nitrogen and oxygen molecular beams using the time-of-flight method. When both the timing of beam extraction and the supply quantity of nitrogen gas are appropriately regulated, our beam source can generate a nitrogen molecular beam with translational energy of approximately 1 eV, which corresponds to the typical activation energy of surface reactions. Furthermore, our beam source can generate an oxygen molecular beam containing dissociated oxygen atoms, which can be a useful probe for surface oxidation. The dissociation fraction along with the translational energy can be adjusted through the supply quantity of oxygen gas.

  17. Stopping cancer in its tracks: using small molecular inhibitors to target glioblastoma migrating cells.

    PubMed

    Mattox, Austin K; Li, Jing; Adamson, David C

    2012-12-01

    Glioblastoma multiforme (GBM) represents one of the most common aggressive types of primary brain tumors. Despite advances in surgical resection, novel neuroimaging procedures, and the most recent adjuvant radiotherapy and chemotherapy, the median survival after diagnosis is about 12-14 months. Targeting migrating GBM cells is a key research strategy in the fight against this devastating cancer. Though the vast majority of the primary tumor focus can be surgically resected, these migrating cells are responsible for its universal recurrence. Numerous strategies and technologies are being explored to target migrating glioma cells, with small molecular inhibitors as one of the most commonly studied. Small molecule inhibitors, such as protein kinase inhibitors, phosphorylation site inhibitors, protease inhibitors, and antisense oligonucleotides show promise in slowing the progression of this disease. A better understanding of these small molecule inhibitors and how they target various extra- and intracellular signaling pathways may eventually lead to a cure for GBM.

  18. Enhanced photoelectrochemical water splitting performance of TiO2 nanotube arrays coated with an ultrathin nitrogen-doped carbon film by molecular layer deposition

    NASA Astrophysics Data System (ADS)

    Tong, Xili; Yang, Peng; Wang, Yunwei; Qin, Yong; Guo, Xiangyun

    2014-05-01

    Vertically oriented TiO2 nanotube arrays (TNTAs) were conformally coated with an ultrathin nitrogen-doped (N-doped) carbon film via the carbonization of a polyimide film deposited by molecular layer deposition and simultaneously hydrogenated, thereby creating a core/shell nanostructure with a precisely controllable shell thickness. The core/shell nanostructure provides a larger heterojunction interface to substantially reduce the recombination of photogenerated electron-hole pairs, and hydrogenation enhances solar absorption of TNTAs. In addition, the N-doped carbon film coating acts as a high catalytic active surface for oxygen evolution reaction, as well as a protective film to prevent hydrogen-treated TiO2 nanotube oxidation by electrolyte or air. As a result, the N-doped carbon film coated TNTAs displayed remarkably improved photocurrent and photostability. The TNTAs with a N-doped carbon film of ~1 nm produces a current density of 3.6 mA cm-2 at 0 V vs. Ag/AgCl under the illumination of AM 1.5G (100 mW cm-2), which represents one of the highest values achieved with modified TNTAs. Therefore, we propose that ultrathin N-doped carbon film coating on materials is a viable approach to enhance their PEC water splitting performance.Vertically oriented TiO2 nanotube arrays (TNTAs) were conformally coated with an ultrathin nitrogen-doped (N-doped) carbon film via the carbonization of a polyimide film deposited by molecular layer deposition and simultaneously hydrogenated, thereby creating a core/shell nanostructure with a precisely controllable shell thickness. The core/shell nanostructure provides a larger heterojunction interface to substantially reduce the recombination of photogenerated electron-hole pairs, and hydrogenation enhances solar absorption of TNTAs. In addition, the N-doped carbon film coating acts as a high catalytic active surface for oxygen evolution reaction, as well as a protective film to prevent hydrogen-treated TiO2 nanotube oxidation by

  19. Multiscale Molecular Simulation of Solution Processing of SMDPPEH: PCBM Small-Molecule Organic Solar Cells.

    PubMed

    Lee, Cheng-Kuang; Pao, Chun-Wei

    2016-08-17

    Solution-processed small-molecule organic solar cells are a promising renewable energy source because of their low production cost, mechanical flexibility, and light weight relative to their pure inorganic counterparts. In this work, we developed a coarse-grained (CG) Gay-Berne ellipsoid molecular simulation model based on atomistic trajectories from all-atom molecular dynamics simulations of smaller system sizes to systematically study the nanomorphology of the SMDPPEH/PCBM/solvent ternary blend during solution processing, including the blade-coating process by applying external shear to the solution. With the significantly reduced overall system degrees of freedom and computational acceleration from GPU, we were able to go well beyond the limitation of conventional all-atom molecular simulations with a system size on the order of hundreds of nanometers with mesoscale molecular detail. Our simulations indicate that, similar to polymer solar cells, the optimal blending ratio in small-molecule organic solar cells must provide the highest specific interfacial area for efficient exciton dissociation, while retaining balanced hole/electron transport pathway percolation. We also reveal that blade-coating processes have a significant impact on nanomorphology. For given donor/acceptor blending ratios, applying an external shear force can effectively promote donor/acceptor phase segregation and stacking in the SMDPPEH domains. The present study demonstrated the capability of an ellipsoid-based coarse-grained model for studying the nanomorphology evolution of small-molecule organic solar cells during solution processing/blade-coating and provided links between fabrication protocols and device nanomorphologies.

  20. Multiscale Molecular Simulation of Solution Processing of SMDPPEH: PCBM Small-Molecule Organic Solar Cells.

    PubMed

    Lee, Cheng-Kuang; Pao, Chun-Wei

    2016-08-17

    Solution-processed small-molecule organic solar cells are a promising renewable energy source because of their low production cost, mechanical flexibility, and light weight relative to their pure inorganic counterparts. In this work, we developed a coarse-grained (CG) Gay-Berne ellipsoid molecular simulation model based on atomistic trajectories from all-atom molecular dynamics simulations of smaller system sizes to systematically study the nanomorphology of the SMDPPEH/PCBM/solvent ternary blend during solution processing, including the blade-coating process by applying external shear to the solution. With the significantly reduced overall system degrees of freedom and computational acceleration from GPU, we were able to go well beyond the limitation of conventional all-atom molecular simulations with a system size on the order of hundreds of nanometers with mesoscale molecular detail. Our simulations indicate that, similar to polymer solar cells, the optimal blending ratio in small-molecule organic solar cells must provide the highest specific interfacial area for efficient exciton dissociation, while retaining balanced hole/electron transport pathway percolation. We also reveal that blade-coating processes have a significant impact on nanomorphology. For given donor/acceptor blending ratios, applying an external shear force can effectively promote donor/acceptor phase segregation and stacking in the SMDPPEH domains. The present study demonstrated the capability of an ellipsoid-based coarse-grained model for studying the nanomorphology evolution of small-molecule organic solar cells during solution processing/blade-coating and provided links between fabrication protocols and device nanomorphologies. PMID:27435212

  1. Low-temperature anomalies in the magnetic and thermal properties of molecular cryocrystals doped with oxygen impurity

    NASA Astrophysics Data System (ADS)

    Freiman, Yu. A.; Tretyak, S. M.; JeŻowski, A.

    2000-09-01

    The magnetic properties of oxygen pair clusters are investigated theoretically for different cluster geometries which can be realized by doping molecular cryomatrices with oxygen. Anomalous temperature and pressure behavior of the magnetic susceptibility, heat capacity, and entropy is predicted. It is proposed to use these anomalies for studying the parameters characterizing the oxygen clusters and the parameters of the host matrix: the effective spin-figure interaction constant D for the molecule in the matrix, the exchange parameter J, and the number of pair clusters Np, which can deviate markedly from the purely random value Np=6Nc2 (N is Avogadro's number, and c is the molar concentration of the impurity). The data on the magnetic susceptibility may be used to analyze the character of the positional and orientational short-range order in the solid solution. The value of D contains information about the orientational order parameter; the distance and angular dependence of the exchange interaction parameter are still subject to discussion in the literature. The temperature dependence of Np contains information about diffusion and clusterization processes in the system.

  2. Structural and magnetic characterization of Sm-doped GaN grown by plasma-assisted molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Dehara, Kentaro; Miyazaki, Yuta; Hasegawa, Shigehiko

    2016-05-01

    We have investigated structural, optical and magnetic properties of Sm-doped GaN thin films grown by plasma-assisted molecular beam epitaxy. Reflection high-energy electron diffraction and X-ray diffraction reveal that Ga1- x Sm x N films with a SmN mole fraction of ˜8% or below are grown on GaN templates without segregation of any secondary phases. With increasing SmN mole fraction, the c-axis lattice parameter of the GaSmN films linearly increases. GaSmN films with low Sm concentrations exhibit inner-4f transitions of Sm3+ in photoluminescence spectra. The present findings show that Sm atoms are substituted for some Ga atoms as trivalent ions (Sm3+). The Ga1- x Sm x N films display hysteresis loops in magnetization versus external magnetic field (M-H) curves even at 300 K. We will discuss the origin of these features together with the corresponding temperature dependences of magnetization.

  3. Wear resistance and mechanical properties of highly cross-linked, ultrahigh-molecular weight polyethylene doped with vitamin E.

    PubMed

    Oral, Ebru; Christensen, Steven D; Malhi, Arnaz S; Wannomae, Keith K; Muratoglu, Orhun K

    2006-06-01

    Our hypothesis was that cross-linked, ultrahigh-molecular weight polyethylene (UHMWPE) stabilized with vitamin E (alpha-tocopherol) would be wear-resistant and fatigue-resistant. Acetabular liners were radiation cross-linked, doped with vitamin E, and gamma-sterilized. Hip simulator wear rate of vitamin E-stabilized UHMWPE was approximately 1 and 6 mg/million-cycles in clean serum and in serum with third-body particles, respectively, a 4-fold to 10-fold decrease from that of conventional UHMWPE. The ultimate strength, yield strength, elongation at break, and fatigue resistance of vitamin E-stabilized UHMWPE were significantly higher than that of 100 kGy-irradiated and melted UHMWPE, and were unaffected by accelerated aging. Rim impingement testing with 3.7-mm-thick acetabular liners up to 2 million-cycles showed no significant damage of the cross-linked liners compared with conventional, gamma-sterilized in inert UHMWPE, vitamin E-stabilized liners. The data indicate good in vitro wear properties and improved mechanical and fatigue properties for vitamin E-stabilized, cross-linked UHMWPE.

  4. Effects of growth temperature on Mg-doped GaN grown by ammonia molecular beam epitaxy

    SciTech Connect

    Hurni, Christophe A.; Lang, Jordan R.; Burke, Peter G.; Speck, James S.

    2012-09-03

    The hole concentration p in Mg-doped GaN films grown by ammonia molecular beam epitaxy depends strongly on the growth temperature T{sub GR}. At T{sub GR}=760 Degree-Sign C, GaN:Mg films showed a hole concentration of p=1.2 Multiplication-Sign 10{sup 18} cm{sup -3} for [Mg]=4.5 Multiplication-Sign 10{sup 19} cm{sup -3}, while at T{sub GR}=840 Degree-Sign C, p=4.4 Multiplication-Sign 10{sup 16} cm{sup -3} for [Mg]=7 Multiplication-Sign 10{sup 19} cm{sup -3}. Post-growth annealing did not increase p. The sample grown at 760 Degree-Sign C exhibited a low resistivity of 0.7 {Omega}cm. The mobility for all the samples was around 3-7 cm{sup 2}/V s. Temperature-dependent Hall measurements and secondary ion mass spectroscopy suggest that the samples grown at T{sub GR}>760 Degree-Sign C are compensated by an intrinsic donor rather than hydrogen.

  5. Small animal SPECT and its place in the matrix of molecular imaging technologies.

    PubMed

    Meikle, Steven R; Kench, Peter; Kassiou, Michael; Banati, Richard B

    2005-11-21

    Molecular imaging refers to the use of non-invasive imaging techniques to detect signals that originate from molecules, often in the form of an injected tracer, and observe their interaction with a specific cellular target in vivo. Differences in the underlying physical principles of these measurement techniques determine the sensitivity, specificity and length of possible observation of the signal, characteristics that have to be traded off according to the biological question under study. Here, we describe the specific characteristics of single photon emission computed tomography (SPECT) relative to other molecular imaging technologies. SPECT is based on the tracer principle and external radiation detection. It is capable of measuring the biodistribution of minute (<10(-10) molar) concentrations of radio-labelled biomolecules in vivo with sub-millimetre resolution and quantifying the molecular kinetic processes in which they participate. Like some other imaging techniques, SPECT was originally developed for human use and was subsequently adapted for imaging small laboratory animals at high spatial resolution for basic and translational research. Its unique capabilities include (i) the ability to image endogenous ligands such as peptides and antibodies due to the relative ease of labelling these molecules with technetium or iodine, (ii) the ability to measure relatively slow kinetic processes (compared with positron emission tomography, for example) due to the long half-life of the commonly used isotopes and (iii) the ability to probe two or more molecular pathways simultaneously by detecting isotopes with different emission energies. In this paper, we review the technology developments and design tradeoffs that led to the current state-of-the-art in SPECT small animal scanning and describe the position SPECT occupies within the matrix of molecular imaging technologies.

  6. Investigating molecular interactions and surface morphology of wax-doped asphaltenes.

    PubMed

    Pahlavan, Farideh; Mousavi, Masoumeh; Hung, Albert; Fini, Ellie H

    2016-04-01

    The nature and origin of bee-like microstructures (bees) in asphalt binders and their impact on asphalt oxidation have been the subject of extensive discussions in recent years. While several studies refer to the bees as solely surface features, some others consider them to be bulk microcrystalline components that are formed due to co-precipitation of wax and asphaltene molecules. In this study, we use a rigorous theoretical and experimental approach to investigate the interplay of asphalt components (mainly asphaltene and wax) and their impact on bee formation. In the theoretical section, quantum-mechanical calculations using density functional theory (DFT) are used to evaluate the strength of interactions between asphaltene unit sheets in the presence and absence of a wax component, as well as the mutual interactions between asphaltene molecules (monomers and dimers) and paraffin wax. The results of this section reveal that paraffin waxes not only do not reinforce the interaction between the asphaltene unit sheets, they destabilize asphaltene assembly and dimerization. AIM (Atom in Molecules) analysis shows the destabilizing effect of wax on asphaltene assembly as a reduction in the number of cage and bond critical points between asphaltenes. This destabilization effect among interacting systems (asphaltene-asphaltene and wax-asphaltene) does not support the hypothesis that interaction between paraffin waxes and non-wax components, such as asphaltene, is responsible for their co-precipitation and bee formation. To further examine the effect of wax component on asphalt microstructure experimentally, we used atomic force microscopy (AFM) to study the surface morphology of an asphalt sample doped with 1% to 25% paraffin wax. In agreement with the conclusions drawn from the DFT approach, our experiments indicate that paraffin wax tends to crystallize separately and form lamellar paraffin wax crystal inclusions with 10 nm thickness. Moreover, the addition of 3% wax

  7. Investigating molecular interactions and surface morphology of wax-doped asphaltenes.

    PubMed

    Pahlavan, Farideh; Mousavi, Masoumeh; Hung, Albert; Fini, Ellie H

    2016-04-01

    The nature and origin of bee-like microstructures (bees) in asphalt binders and their impact on asphalt oxidation have been the subject of extensive discussions in recent years. While several studies refer to the bees as solely surface features, some others consider them to be bulk microcrystalline components that are formed due to co-precipitation of wax and asphaltene molecules. In this study, we use a rigorous theoretical and experimental approach to investigate the interplay of asphalt components (mainly asphaltene and wax) and their impact on bee formation. In the theoretical section, quantum-mechanical calculations using density functional theory (DFT) are used to evaluate the strength of interactions between asphaltene unit sheets in the presence and absence of a wax component, as well as the mutual interactions between asphaltene molecules (monomers and dimers) and paraffin wax. The results of this section reveal that paraffin waxes not only do not reinforce the interaction between the asphaltene unit sheets, they destabilize asphaltene assembly and dimerization. AIM (Atom in Molecules) analysis shows the destabilizing effect of wax on asphaltene assembly as a reduction in the number of cage and bond critical points between asphaltenes. This destabilization effect among interacting systems (asphaltene-asphaltene and wax-asphaltene) does not support the hypothesis that interaction between paraffin waxes and non-wax components, such as asphaltene, is responsible for their co-precipitation and bee formation. To further examine the effect of wax component on asphalt microstructure experimentally, we used atomic force microscopy (AFM) to study the surface morphology of an asphalt sample doped with 1% to 25% paraffin wax. In agreement with the conclusions drawn from the DFT approach, our experiments indicate that paraffin wax tends to crystallize separately and form lamellar paraffin wax crystal inclusions with 10 nm thickness. Moreover, the addition of 3% wax

  8. Micropatterning of small molecular weight organic semiconductor thin films using organic vapor phase deposition

    NASA Astrophysics Data System (ADS)

    Shtein, Max; Peumans, Peter; Benziger, Jay B.; Forrest, Stephen R.

    2003-04-01

    Using both analytical and experimental methods, we show that micron scale patterned growth of small molecular weight organic semiconductor thin films can be achieved by the recently demonstrated process of organic vapor phase deposition (OVPD). In contrast to the conventional process of vacuum thermal evaporation, the background gas pressure during OVPD is typically 0.1-10 Torr, resulting in a molecular mean free path (mfp) of from 100 to 1 μm, respectively. Monte Carlo simulations of film growth through apertures at these gas densities indicate that when the mfp is on the order of the mask-to-substrate separation, deposit edges can become diffuse. The simulations and deposition experiments discussed here indicate that the deposited feature shape is controlled by the mfp, the aperture geometry, and the mask-to-substrate separation. Carefully selected process conditions and mask geometries can result in features as small as 1 μm. Furthermore, based on continuum and stochastic models of molecular transport in confined geometries, we propose the in situ direct patterning growth technique of organic vapor jet printing. The high pattern definition obtained by OVPD makes this process attractive for the growth of a wide range of structures employed in modern organic electronic devices.

  9. Disorder effect on conductance in a doped C60 molecular bridge

    NASA Astrophysics Data System (ADS)

    Shokri, Aliasghar

    2013-03-01

    In this work, we study electrical conductance in a C60 molecular nanobridge with randomly point dopants sandwiched between two (5,5) carbon nanotubes (CNTs) in two cases with opened end and closed end. Two different ways of coupling C60 fullerene through one and five carbon atoms to the uncap- and cap-edges are considered in each case. Our calculations are based on the Green's function technique in the tight-binding approximation. The CNT surface self-energy is also obtained, analytically. The effects of contacts, various strengths of random disorder, cage type, and the bond dimerization on the conductance are investigated. Our results indicate that the appearance of conductance resonances is a manifestation of resonant states of CNT caps, which lie within the molecular HOMO-LUMO gap and consequently they change by disorder concentration. By controlling the disorder concentration, bond dimerization, and contact geometries, this kind of system can explain the extended states from the localized states. The numerical results can serve as a base for developments in designing nanoelectronic devices.

  10. Ovarian proteomic study reveals the possible molecular mechanism for hyperprolificacy of Small Tail Han sheep

    PubMed Central

    Miao, Xiangyang; Luo, Qingmiao; Zhao, Huijing; Qin, Xiaoyu

    2016-01-01

    Small Tail Han sheep is a widely bred farm animal in China which has attracted lots of attention due to their high prolificacy and year-round estrus. However, the molecular mechanism of its fecundity remains unrevealed. The FecB gene polymorphism has been found to be associated with the ovulation rate and litter size of sheep. In the present study, we constructed an iTRAQ-based quantitative proteomics analysis to compare the ovarian proteomes of FecB+FecB+ genotype Small Tail Han sheep ewes (Han ++), FecBBFecBB Han ewes (Han BB) and Dorset ewes (Dorset). Hundreds of differentially expressed proteins between each two groups were identified; GO and KEGG pathway analysis indicated that the expressions of those proteins involved in ribosome assembly, protein translation and mTOR pathway between Dorset and both Han groups were highly different. Between Han ++ and Han BB groups, higher level of protein expressions were related to mitochondrial oxidation functions such as oxidoreductase activity, cytochrome-c oxidase activity and electron carrier activity. This was identified in Han BB group, which may contribute to the elevated ovulation rate of Han BB ewes. In conclusion, our work provided a prospective understanding of the molecular mechanism for high prolificacy of Small Tail Han sheep. PMID:27271055

  11. A molecular-beacon-based screen for small molecule inhibitors of miRNA maturation.

    PubMed

    Bose, Debojit; Jayaraj, Gopal Gunanathan; Kumar, Santosh; Maiti, Souvik

    2013-05-17

    miRNAs are small non-coding RNAs that regulate about 60% of mammalian genes by modulating their transcript levels. Network scale studies of miRNA-mediated regulatory circuits demonstrate the central importance of this class of small RNA in the maintenance of biological robustness. More recently, several reports have described the deregulation of numerous miRNA to be causally associated with many diseases, including cancer. These studies have highlighted the potential for development of therapeutic modalities against miRNA. Previous screening protocols, for small molecules targeting miRNA function, are either costly or technically too complex to be applied in a high-throughput manner in standard chemical laboratories. We describe a simple in vitro screening method using a DNA-based molecular beacon that overcomes the limitations associated with earlier screens. We used this method to identify inhibitors of miR-27a function from a library of 14 aminoglycosides as a pilot study. Inhibitory molecules identified were further scrutinized to identify the validity of screen. With this proof of concept we illustrate the utility of a scalable molecular-beacon-based screening strategy for miRNA inhibitors.

  12. High-Energy Molecular Beam Source Using a Non-Diaphragm Type Small Shock Tube

    NASA Astrophysics Data System (ADS)

    Yoshimoto, Yuta; Miyoshi, Nobuya; Kinefuchi, Ikuya; Shimizu, Kazuya; Takagi, Shu; Matsumoto, Yoichiro

    2010-11-01

    The molecular beam technique is one of the powerful tools to analyze gas-surface interactions. In order to generate high-energy molecular beam in a range of 1 - 5 eV, which corresponds to the typical activation energy of surface reactions, we are developing a beam source using a non-diaphragm type shock tube, which can operate at a repetition rate high enough for efficient data acquisition. We made the volume of a tube much smaller than that of conventional ones so that the evacuation time between each shot becomes as short as possible. Our measurement of shock Mach numbers showed that even small diameter (2 or 4 mm) tubes, in which the wall boundary layer has a large influence on the propagation of shock waves, could generate molecular beam with the translational energy of more than 1 eV. This is because the reduction of shock formation distance by rapid opening of the valve, which separates a high pressure room from a low pressure room, weakened the effect of viscous damping on the accelerating shock wave. In addition, the convergent shock tubes of which diameters linearly decrease from 4 to 2 mm exhibited higher Mach numbers than straight ones. This indicates that the application of the convergent tube with the optimized geometry would be promising for generating high-energy molecular beam.

  13. The role of a small-scale cutoff in determining molecular layers at fluid interfaces.

    PubMed

    Sega, Marcello

    2016-08-17

    The existence of molecular layers at liquid/vapour interfaces has been a long debated issue. More than ten years ago it was shown, using computer simulations, that correlations at the liquid/vapour interface resemble those of bulk liquids, even though they can be detected in experiments only in a few cases, where they are so strong that they cannot be concealed by the geometrical smearing of capillary fluctuations. The results of the intrinsic analysis techniques used in computer experiments, however, are still often questioned because of their dependence on a free parameter that usually represents a small-scale cutoff used to determine the interface. In this work I show that there is only one value of the cutoff that can ensure a quantitative explanation of the intrinsic density correlation peaks in terms of successive layer contributions. The value of the cutoff coincides, with a high accuracy, with the molecular diameter. PMID:27499039

  14. HCl-doped conducting Emeraldine polymer studied by ab initio Car-Parrinello molecular dynamics

    NASA Astrophysics Data System (ADS)

    Cavazzoni, Carlo; Colle, Renato; Farchioni, Riccardo; Grosso, Giuseppe

    2006-07-01

    We present a Car-Parrinello molecular dynamics study of the highly conducting Emeraldine salt, which definitely settles the controversy between the polaronic and the bipolaronic lattice models present in the literature. Our treatment is fully microscopic and takes into account interchain interactions, individual chain conformation, and the dynamics of the HCl protonation. We have highlighted the peculiar role of the Cl- counterions both for the polymer structure and for the interpretation of its metallic character. Our study indicates that this metallic character is due to the π electrons along each chain with chlorine counterions in polaronic arrangement and that only the Pc2a lattice symmetry provides an x-ray spectrum in complete agreement with the experiments.

  15. Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules

    PubMed Central

    Cheng, Tiejun; Wang, Yanli; Bryant, Stephen H.

    2010-01-01

    Motivation: Most of the previous data mining studies based on the NCI-60 dataset, due to its intrinsic cell-based nature, can hardly provide insights into the molecular targets for screened compounds. On the other hand, the abundant information of the compound–target associations in PubChem can offer extensive experimental evidence of molecular targets for tested compounds. Therefore, by taking advantages of the data from both public repositories, one may investigate the correlations between the bioactivity profiles of small molecules from the NCI-60 dataset (cellular level) and their patterns of interactions with relevant protein targets from PubChem (molecular level) simultaneously. Results: We investigated a set of 37 small molecules by providing links among their bioactivity profiles, protein targets and chemical structures. Hierarchical clustering of compounds was carried out based on their bioactivity profiles. We found that compounds were clustered into groups with similar mode of actions, which strongly correlated with chemical structures. Furthermore, we observed that compounds similar in bioactivity profiles also shared similar patterns of interactions with relevant protein targets, especially when chemical structures were related. The current work presents a new strategy for combining and data mining the NCI-60 dataset and PubChem. This analysis shows that bioactivity profile comparison can provide insights into the mode of actions at the molecular level, thus will facilitate the knowledge-based discovery of novel compounds with desired pharmacological properties. Availability: The bioactivity profiling data and the target annotation information are publicly available in the PubChem BioAssay database (ftp://ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/). Contact: ywang@ncbi.nlm.nih.gov; bryant@ncbi.nlm.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20947527

  16. Molecular phylogeny of the Heterotrichea (Ciliophora, Postciliodesmatophora) based on small subunit rRNA gene sequences.

    PubMed

    Schmidt, Stephanie L; Foissner, Wilhelm; Schlegel, Martin; Bernhard, Detlef

    2007-01-01

    A comprehensive molecular analysis of the phylogenetic relationships within the Heterotrichea including all described families is still lacking. For this reason, the complete nuclear small subunit (SSU) rDNA was sequenced from further representatives of the Blepharismidae and the Stentoridae. In addition, the SSU rDNA of a new, undescribed species of the genus Condylostomides (Condylostomatidae) was sequenced. The detailed phylogenetic analyses revealed a consistent branching pattern: while the terminal branches are generally well resolved, the basal relationships remain unsolved. Moreover, the data allow some conclusions about the macronuclear evolution within the genera Blepharisma, Stentor, and Spirostomum suggesting that a single, compact macronucleus represents the ancestral state. PMID:17669161

  17. Small metal-organic molecular sandwiches: Versatile units for induced structure manipulation

    NASA Astrophysics Data System (ADS)

    Naumkin, Fedor Y.; Fisher, Kayla

    2013-12-01

    Interfaces between metal atoms and organic molecules are key units of many important metal-organic systems. Presented are results of ab initio calculations for a series of complexes of 2nd-row metal atoms sandwiched between small unsaturated hydrocarbon molecules. Evolution of the system structure and stability is studied for different metal atoms, as well as upon excitation, ionization and electron attachment. Predicted interesting features include cooperative stabilization, unusual geometries, reversible charge- or excitation-governed geometry alterations. The observed variety of properties suggests potential applications of such species as intermolecular junctions and units with charge- or spin-controlled shapes in molecular devices and/or machines.

  18. The skin: target organ in immunotoxicology of small-molecular-weight compounds.

    PubMed

    Merk, H F; Sachs, B; Baron, J

    2001-01-01

    Immunotoxicology studies two different effects of xenobiotics: immunosuppression and dysregulation of immune responses leading to hypersensitivity or autoimmunity. The skin is a major target organ of immunotoxicity which is provoked by small-molecular-weight compounds. Methods may be helpful for immunotoxicological investigations and screenings for adverse effects of xenobiotics which are used for diagnosis or studies on the pathophysiology of skin disorders such as allergic contact dermatitis, cutaneous drug-allergic reactions or autoimmune diseases of the skin. Examples include well-designed patch tests, assays involving antigen-presenting cells such as dendritic cells, but also T lymphocytes, basophiles or keratinocytes.

  19. Communication: Kirkwood-Buff integrals in the thermodynamic limit from small-sized molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Cortes-Huerto, R.; Kremer, K.; Potestio, R.

    2016-10-01

    We present an accurate and efficient method to obtain Kirkwood-Buff (KB) integrals in the thermodynamic limit from small-sized molecular dynamics simulations. By introducing finite size effects into integral equations of statistical mechanics, we derive an analytical expression connecting the KB integrals of the bulk system with the fluctuations of the number of molecules in the corresponding closed system. We validate the method by calculating the activity coefficients of aqueous urea mixtures and the KB integrals of Lennard-Jones fluids. Moreover, our results demonstrate how to identify simulation conditions under which computer simulations reach the thermodynamic limit.

  20. MOLECULARLY TARGETED THERAPIES IN NON-SMALL CELL LUNG CANCER ANNUAL UPDATE 2014

    PubMed Central

    Morgensztern, Daniel; Campo, Meghan J.; Dahlberg, Suzanne E.; Doebele, Robert C.; Garon, Edward; Gerber, David E.; Goldberg, Sarah B.; Hammerman, Peter S.; Heist, Rebecca; Hensing, Thomas; Horn, Leora; Ramalingam, Suresh S.; Rudin, Charles M.; Salgia, Ravi; Sequist, Lecia; Shaw, Alice T.; Simon, George R.; Somaiah, Neeta; Spigel, David R.; Wrangle, John; Johnson, David; Herbst, Roy S.; Bunn, Paul; Govindan, Ramaswamy

    2015-01-01

    There have been significant advances in the understanding of the biology and treatment of non-small cell lung cancer (NSCLC) over the past few years. A number of molecularly targeted agents are in the clinic or in development for patients with advanced NSCLC (Table 1). We are beginning to understand the mechanisms of acquired resistance following exposure to tyrosine kinase inhibitors in patients with oncogene addicted NSCLC. The advent of next generation sequencing has enabled to study comprehensively genomic alterations in lung cancer. Finally, early results from immune checkpoint inhibitors are very encouraging. This review summarizes recent advances in the area of cancer genomics, targeted therapies and immunotherapy. PMID:25535693

  1. Small-angle X-ray scattering method to characterize molecular interactions: Proof of concept.

    PubMed

    Allec, Nicholas; Choi, Mina; Yesupriya, Nikhil; Szychowski, Brian; White, Michael R; Kann, Maricel G; Garcin, Elsa D; Daniel, Marie-Christine; Badano, Aldo

    2015-01-01

    Characterizing biomolecular interactions is crucial to the understanding of biological processes. Existing characterization methods have low spatial resolution, poor specificity, and some lack the capability for deep tissue imaging. We describe a novel technique that relies on small-angle X-ray scattering signatures from high-contrast molecular probes that correlate with the presence of biomolecular interactions. We describe a proof-of-concept study that uses a model system consisting of mixtures of monomer solutions of gold nanoparticles (GNPs) as the non-interacting species and solutions of GNP dimers linked with an organic molecule (dimethyl suberimidate) as the interacting species. We report estimates of the interaction fraction obtained with the proposed small-angle X-ray scattering characterization method exhibiting strong correlation with the known relative concentration of interacting and non-interacting species. PMID:26160052

  2. Detection of Free Radicals in Vitamin E-doped Ultra-High Molecular Weight Polyethylene

    NASA Astrophysics Data System (ADS)

    Walters, Benjamin

    2007-11-01

    Free-radical-induced oxidation of ultra-high molecular weight polyethylene (UHMWPE) liners of the artificial hip- or knee-joint adversely affects the performance of the total joint. [1] To combat oxidation, vitamin E is added to UHMWPE as an antioxidant. [2] In this study, we use 10% by wt. vitamin E (alpha-tocopherol) in UHMWPE powder. Free radicals are produced by irradiating test samples with x-rays and detected using an X-band electron spin resonance (ESR) spectrometer. Test samples for this study are: 1. vitamin E-UHMWPE mixed before irradiation; 2. non-irradiated vitamin E mixed with irradiated UHMWPE; 3. irradiated vitamin E; and 4. irradiated UHMWPE (control). ESR spectra are recorded as a function of time for more than two weeks. While control shows the presence of alkyl/allyl/polyenyl radicals, the vitamin E-mixed powder presents additional signals in the spectrum due to tocopheroxyl radicals. Analyses of the preliminary ESR data will be presented. References: [1] M.S. Jahan et al., Biomed. Mater. Res. 25 (1991) 1005. [2] N. Shibata et al., J. Biomed. Sci. Eng., 1 (2006) 107.

  3. Photodiode properties of molecular beam epitaxial InSb on a heavily doped substrate

    NASA Astrophysics Data System (ADS)

    Sun, Weiguo; Fan, Huitao; Peng, Zhenyu; Zhang, Liang; Zhang, Xiaolei; Zhang, Lei; Lu, Zhengxiong; Si, Junjie; Emelyanov, E.; Putyato, M.; Semyagin, B.; Pchelyakov, O.; Preobrazhenskii, V.

    2014-01-01

    Photodiodes of InSb were fabricated on an epitaxial layer grown using molecular beam epitaxy (MBE). Thermal cleaning of the InSb (0 0 1) substrate surface, 2° towards the (1 1 1) B plane, was performed to remove the oxide. Photodiode properties of МВЕ-formed epitaxial InSb were demonstrated. Zero-bias resistance area product (R0A) measurements were taken at 80 K under room temperature background for a pixel size of 100 μm × 100 μm. Values were as high as 4.36 × 104 Ω/cm2, and the average value of R0A was 1.66 × 104 Ω/cm2. The peak response was 2.44 (A/W). The epitaxial InSb photodiodes were fabricated using the same process as bulk crystal InSb diodes with the exception of the junction formation method. These values are comparable to the properties of bulk crystal InSb photodiodes.

  4. Molecular dynamics simulations of interfacial interactions between small nanoparticles during diffusion-limited aggregation

    NASA Astrophysics Data System (ADS)

    Lu, Jing; Liu, Dongmei; Yang, Xiaonan; Zhao, Ying; Liu, Haixing; Tang, Huan; Cui, Fuyi

    2015-12-01

    Due to the limitations of experimental methods at the atomic level, research on the aggregation of small nanoparticles (D < 5 nm) in aqueous solutions is quite rare. The aggregation of small nanoparticles in aqueous solutions is very different than that of normal sized nanoparticles. The interfacial interactions play a dominant role in the aggregation of small nanoparticles. In this paper, molecular dynamics simulations, which can explore the microscopic behavior of nanoparticles during the diffusion-limited aggregation at an atomic level, were employed to reveal the aggregation mechanism of small nanoparticles in aqueous solutions. First, the aggregation processes and aggregate structure were depicted. Second, the particle-particle interaction and surface diffusion of nanoparticles during aggregation were investigated. Third, the water-mediated interactions during aggregation were ascertained. The results indicate that the aggregation of nanoparticle in aqueous solutions is affected by particle size. The strong particle-particle interaction and high surface diffusion result in the formation of particle-particle bonds of 2 nm TiO2 nanoparticles, and the water-mediated interaction plays an important role in the aggregation process of 3 and 4 nm TiO2 nanoparticles.

  5. Application of a continuous-wave tunable erbium-doped fiber laser to molecular spectroscopy in the near infrared

    NASA Astrophysics Data System (ADS)

    Cousin, J.; Masselin, P.; Chen, W.; Boucher, D.; Kassi, S.; Romanini, D.; Szriftgiser, P.

    2006-05-01

    Development of a continuous-wave tunable fiber laser-based spectrometer for applied spectroscopy is reported. Wide wavelength tunability of an erbium-doped fiber laser (EDFL) was investigated in the near-infrared region of 1543-1601 nm. Continuous mode-hop free fine frequency tuning has been accomplished by temperature tuning in conjunction with mechanical tuning. The overall spectroscopic performance of the EDFL was evaluated in terms of frequency tunability along with its suitability for molecular spectroscopy. High-resolution absorption spectra of acetylene (C2H2) were recorded near 1544 nm with a minimum measurable absorption coefficient of about 3.5×10-7 cm-1/Hz1/2 for direct absorption spectroscopy associated with a 100-m long multipass cell. Detections of C2H2 at different concentration levels were performed as well with high dynamic detection range varying from 100% purity to sub ppmv using cavity ring down spectroscopy. A 3σ-detection-limited minimum detectable concentration (MDC) of 400 ppbv has been obtained by using the transition line Pe(22) of the ν1+ν3+ν5 1(Πg)-ν5 1(Πu) hot band near 1543.92 nm with a detection bandwidth of 2.3 Hz. This corresponds to a minimum detectable absorption coefficient of 6.6×10-11 cm-1/Hz1/2. The sensitivity limit could be further improved by almost one order of magnitude (down to ˜60 ppbv) by use of the Pe(27) line of the ν1+ν3(Σu +)-0(Σg +)combination band near 1543.68 nm.

  6. Increased effective barrier heights in Schottky diodes by molecular-beam epitaxy of CoSi2 and Ga-doped Si on Si(111)

    NASA Technical Reports Server (NTRS)

    Fathauer, R. W.; Lin, T. L.; Grunthaner, P. J.; Andersson, P. O.; Iannelli, J. M.

    1988-01-01

    Increasing the effective Schottky-barrier height of epitaxial CoSi2/Si(111) diodes by the use of thin, highly doped Si layers in close proximity to the metal-semiconductor interface has been studied. Intrinsic Si, Si doped by coevaporation of Ga, and epitaxial CoSi2 layers have all been grown in the same molecular-beam epitaxy system. Current-voltage and photoresponse characterization yield barrier heights ranging from 0.61 eV for a sample with no p(+) layer to 0.89 eV for a sample with a 20-nm-thick p(+) layer. These results are compared to theoretical values based on a one-dimensional solution of Poisson's equation under the depletion approximation.

  7. Growth of a delta-doped silicon layer by molecular beam epitaxy on a charge-coupled device for reflection-limited ultraviolet quantum efficiency

    NASA Technical Reports Server (NTRS)

    Hoenk, Michael E.; Grunthaner, Paula J.; Grunthaner, Frank J.; Terhune, R. W.; Fattahi, Masoud; Tseng, Hsin-Fu

    1992-01-01

    Low-temperature silicon molecular beam epitaxy is used to grow a delta-doped silicon layer on a fully processed charge-coupled device (CCD). The measured quantum efficiency of the delta-doped backside-thinned CCD is in agreement with the reflection limit for light incident on the back surface in the spectral range of 260-600 nm. The 2.5 nm silicon layer, grown at 450 C, contained a boron delta-layer with surface density of about 2 x 10 exp 14/sq cm. Passivation of the surface was done by steam oxidation of a nominally undoped 1.5 nm Si cap layer. The UV quantum efficiency was found to be uniform and stable with respect to thermal cycling and illumination conditions.

  8. Molecular aluminum hydrides identified by inelastic neutron scattering during H2 regeneration of catalyst-doped NaAlH4.

    PubMed

    Fu, Qi Jia; Ramirez-Cuesta, A J; Tsang, Shik Chi

    2006-01-19

    Catalyst-doped sodium aluminum hydrides have been intensively studied as solid hydrogen carriers for onboard proton-exchange membrane (PEM) fuel cells. Although the importance of catalyst choice in enhancing kinetics for both hydrogen uptake and release of this hydride material has long been recognized, the nature of the active species and the mechanism of catalytic action are unclear. We have shown by inelastic neutron scattering (INS) spectroscopy that a volatile molecular aluminum hydride is formed during the early stage of H2 regeneration of a depleted, catalyst-doped sodium aluminum hydride. Computational modeling of the INS spectra suggested the formation of AlH3 and oligomers (AlH3)n (Al2H6, Al3H9, and Al4H12 clusters), which are pertinent to the mechanism of hydrogen storage. This paper demonstrates, for the first time, the existence of these volatile species.

  9. Small-molecule inhibitors of cathepsin L incorporating functionalized ring-fused molecular frameworks.

    PubMed

    Song, Jiangli; Jones, Lindsay M; Chavarria, Gustavo E; Charlton-Sevcik, Amanda K; Jantz, Adam; Johansen, Audra; Bayeh, Liela; Soeung, Victoria; Snyder, Lindsey K; Lade, Shawn D; Chaplin, David J; Trawick, Mary Lynn; Pinney, Kevin G

    2013-05-01

    Cathepsin L is a cysteine protease that is upregulated in a variety of malignant tumors and plays a significant role in cancer cell invasion and migration. It is an attractive target for the development of small-molecule inhibitors, which may prove beneficial as treatment agents to limit or arrest cancer metastasis. We have previously identified a structurally diverse series of thiosemicarbazone-based inhibitors that incorporate the benzophenone and thiochromanone molecular scaffolds. Herein we report an important extension of this work designed to explore fused aryl-alkyl ring molecular systems that feature nitrogen atom incorporation (dihydroquinoline-based) and carbon atom exclusivity (tetrahydronaphthalene-based). In addition, analogues that contain oxygen (chromanone-based), sulfur (thiochroman-based), sulfoxide, and sulfone functionalization have been prepared in order to further investigate the structure-activity relationship aspects associated with these compounds and their ability to inhibit cathepsins L and B. From this small-library of 30 compounds, five were found to be strongly inhibitory (IC50 <500 nM) against cathepsin L with the most active compound (7-bromodihydroquinoline thiosemicarbazone 48) demonstrating an IC50=164 nM. All of the compounds evaluated were inactive (IC50 >10,000 nM) as inhibitors of cathepsin B, thus establishing a high degree (>20-fold) of selectivity (cathepsin L vs. cathepsin B) for the most active cathepsin L inhibitors in this series.

  10. Ultrastructural and molecular changes in the developing small intestine of the toad Bufo regularis.

    PubMed

    Sakr, S A; Badawy, G M; El-Borm, H T

    2014-01-01

    The ontogenetic development of the small intestine of the toad Bufo regularis was investigated using twofold approaches, namely, ultrastructural and molecular. The former has been done using transmission electron microscope and utilizing the developmental stages 42, 50, 55, 60, 63, and 66. The most prominent ultrastructural changes were recorded at stage 60 and were more evident at stage 63. These included the appearance of apoptotic bodies/nuclei within the larval epithelium, the presence of macrophages, swollen mitochondria, distorted rough endoplasmic reticulum, chromatin condensation, and irregular nuclear envelop, and the presence of large vacuoles and lysosomes. The molecular investigation involved examining DNA content and fragmentation. The results showed that the DNA content decreased significantly during the metamorphic stages 60 and 63 compared with both larval (50 and 55) and postmetamorphic (66) stages. The metamorphic stages (60 and 63) displayed extensive DNA laddering compared with stages 50, 55, and 66. The percentage of DNA damage was 0.00%, 12.91%, 57.26%, 45.48%, and 4.43% for the developmental stages 50, 55, 60, 63, and 66, respectively. In conclusion, the recorded remodeling of the small intestine represents a model for clarifying the mechanism whereby cell death and proliferation are controlled.

  11. Ultrastructural and Molecular Changes in the Developing Small Intestine of the Toad Bufo regularis

    PubMed Central

    Sakr, S. A.; Badawy, G. M.; El-Borm, H. T.

    2014-01-01

    The ontogenetic development of the small intestine of the toad Bufo regularis was investigated using twofold approaches, namely, ultrastructural and molecular. The former has been done using transmission electron microscope and utilizing the developmental stages 42, 50, 55, 60, 63, and 66. The most prominent ultrastructural changes were recorded at stage 60 and were more evident at stage 63. These included the appearance of apoptotic bodies/nuclei within the larval epithelium, the presence of macrophages, swollen mitochondria, distorted rough endoplasmic reticulum, chromatin condensation, and irregular nuclear envelop, and the presence of large vacuoles and lysosomes. The molecular investigation involved examining DNA content and fragmentation. The results showed that the DNA content decreased significantly during the metamorphic stages 60 and 63 compared with both larval (50 and 55) and postmetamorphic (66) stages. The metamorphic stages (60 and 63) displayed extensive DNA laddering compared with stages 50, 55, and 66. The percentage of DNA damage was 0.00%, 12.91%, 57.26%, 45.48%, and 4.43% for the developmental stages 50, 55, 60, 63, and 66, respectively. In conclusion, the recorded remodeling of the small intestine represents a model for clarifying the mechanism whereby cell death and proliferation are controlled. PMID:24715821

  12. Molecular dynamics investigation of separation of hydrogen sulfide from acidic gas mixtures inside metal-doped graphite micropores.

    PubMed

    Huang, Pei-Hsing

    2015-09-21

    The separation of poisonous compounds from various process fluids has long been highly intractable, motivating the present study on the dynamic separation of H2S in acidic-gas-mixture-filled micropores. The molecular dynamics approach, coupled with the isothermal-isochoric ensemble, was used to model the molecular interactions and adsorption of H2S/CO2/CO/H2O mixtures inside metal-doped graphite slits. Due to the difference in the adsorption characteristics between the two distinct adsorbent materials, the metal dopant in the graphitic micropores leads to competitive adsorption, i.e. the Au and graphite walls compete to capture free adsorbates. The effects of competitive adsorption, coupled with changes in the gas temperature, concentration, constituent ratio and slit width on the constituent separation of mixtures were systematically studied. The molecule-wall binding energies calculated in this work (those of H2S, H2O and CO on Au walls and those of H2O, CO and CO2 on graphite walls) show good agreement with those obtained using density functional theory (DFT) and experimental results. The z-directional self-diffusivities (Dz) for adsorbates inside the slit ranged from 10(-9) to 10(-7) m(2) s(-1) as the temperature was increased from 10 to 500 K. The values are comparable with those for a typical microporous fluid (10(-8)-10(-9) m(2) s(-1) in a condensed phase and 10(-6)-10(-7) m(2) s(-1) in the gaseous state). The formation of H-bonding networks and hydrates of H2S is disadvantageous for the separation of mixtures. The results indicate that H2S can be efficiently separated from acidic gas mixtures onto the Au(111) surface by (i) reducing the mole fraction of H2S and H2O in the mixtures, (ii) raising the gas temperature to the high temperature limit (≥400 K), and (iii) lowering the slit width to below the threshold dimension (≤23.26 Å).

  13. Gene expression profiles of small-cell lung cancers: molecular signatures of lung cancer.

    PubMed

    Taniwaki, Masaya; Daigo, Yataro; Ishikawa, Nobuhisa; Takano, Atsushi; Tsunoda, Tatsuhiko; Yasui, Wataru; Inai, Kouki; Kohno, Nobuoki; Nakamura, Yusuke

    2006-09-01

    To characterize the molecular mechanisms involved in the carcinogenesis and progression of small-cell lung cancer (SCLC) and identify molecules to be applied as novel diagnostic markers and/or for development of molecular-targeted drugs, we applied cDNA microarray profile analysis coupled with purification of cancer cells by laser-microbeam microdissection (LMM). Expression profiles of 32,256 genes in 15 SCLCs identified 252 genes that were commonly up-regulated and 851 transcripts that were down-regulated in SCLC cells compared with non-cancerous lung tissue cells. An unsupervised clustering algorithm applied to the expression data easily distinguished SCLC from the other major histological type of non-small cell lung cancer (NSCLC) and identified 475 genes that may represent distinct molecular features of each of the two histological types. In particular, SCLC was characterized by altered expression of genes related to neuroendocrine cell differentiation and/or growth such as ASCL1, NRCAM, and INSM1. We also identified 68 genes that were abundantly expressed both in advanced SCLCs and advanced adenocarcinomas (ADCs), both of which had been obtained from patients with extensive chemotherapy treatment. Some of them are known to be transcription factors and/or gene expression regulators such as TAF5L, TFCP2L4, PHF20, LMO4, TCF20, RFX2, and DKFZp547I048 as well as those encoding nucleotide-binding proteins such as C9orf76, EHD3, and GIMAP4. Our data provide valuable information for better understanding of lung carcinogenesis and chemoresistance. PMID:16865272

  14. Molecular identification of nanoplanktonic protists based on small subunit ribosomal RNA gene sequences for ecological studies.

    PubMed

    Lim, E L

    1996-01-01

    Nanoplanktonic protists are comprised of a diverse assemblage of species which are responsible for a variety of trophic processes in marine and freshwater ecosystems. Current methods for identifying small protists by electron microscopy do not readily permit both identification and enumeration of nanoplanktonic protists in field samples. Thus, one major goal in the application of molecular approaches in protistan ecology has been the detection and quantification of individual species in natural water samples. Sequences of small subunit ribosomal RNA (SSU rRNA) genes have proven to be useful towards achieving this goal. Comparison of sequences from clone libraries of protistan SSU rRNA genes amplified from natural assemblages of protists by the polymerase chain reaction (PCR) can be used to examine protistan diversity. Furthermore, oligonucleotide probes complementary to short sequence regions unique to species of small protists can be designed by comparative analysis of rRNA gene sequences. These probes may be used to either detect the RNA of particular species of protists in total nucleic acid extracts immobilized on membranes, or the presence of target species in water samples via in situ hybridization of whole cells. Oligonucleotide probes may also serve as primers for the selective amplification of target sequences from total population DNA by PCR. Thus, molecular sequence information is becoming increasingly useful for identifying and enumerating protists, and for studying their spatial and temporal distribution in nature. Knowledge of protistan species composition, abundance and variability in an environment can ultimately be used to relate community structure to various aspects of community function and biogeochemical activity.

  15. Theoretical investigations on enhancing the performance of terminally diketopyrrolopyrrole-based small-molecular donors in organic solar cell applications.

    PubMed

    Liu, Xiaorui; Huang, Chengzhi; Shen, Wei; He, Rongxing; Li, Ming

    2016-01-01

    Diketopyrrolopyrrole (DPP)-based small molecules with acceptor-core-acceptor (A-core-A) type as donor materials have been used successfully in organic solar cells (OSC). In this work, based on the DPP-core-DPP type molecule SM1 consisting of a DPP unit as acceptor and benzene as the core, we replaced the benzene core with more electron-withdrawing groups in SM1 and further designed four new small-molecular donors (SM2-SM5) in order to improve the electrical properties, optical absorption and performance in OSC applications. The calculated results indicate that the designed small-molecular donors SM2-SM5 exhibit better performances in comparison with SM1, such as lower highest occupied molecular orbital (HOMO), narrower energy gap, larger absorption range, better electronic transfer between donor and acceptor and higher hole mobility. Moreover, the decreased HOMO levels and transition energy of small-molecular donors in OSC applications play an important role in the parameters of open-current voltage, fill factor and short-circuit current. Consequently, adjusting the electron-deficient ability of cores in DPP-core-DPP type small-molecular donors is an efficient approach that can be used to obtain high-efficiency DPP-based small-molecular donors for OSC applications. Graphical Abstract The designed small-molecules with good electronic and photophysical properties will act as a promising donor candidate for organic solar cell applications. Moreover, The decreased HOMO levels and transition energy of small-molecular donors in OSC applications play an important role in the parameters of open-current voltage, fill factor and short-circuit current.

  16. Morphological and molecular analysis of Ornithonyssus spp. (Acari: Macronyssidae) from small terrestrial mammals in Brazil.

    PubMed

    Nieri-Bastos, Fernanda A; Labruna, Marcelo B; Marcili, Arlei; Durden, Lance A; Mendoza-Uribe, Leonardo; Barros-Battesti, Darci M

    2011-12-01

    Based on chaetotaxy of the dorsal shield, the taxonomic status of many species of Ornithonyssus has been considered invalid, resulting in the synonymy of all Brazilian Ornithonyssus from small terrestrial wild mammals into one of the following four species: Ornithonyssus bacoti (Hirst, 1913), Ornithonyssus matogrosso (Fonseca, 1954), Ornithonyssus pereirai (Fonseca, 1935) or Ornithonyssus wernecki (Fonseca, 1935). Despite the revision of this genus in 1980, including all known species worldwide, the knowledge of Ornithonyssus in Brazil has not progressed for more than 40 years. Considering the potential importance of these haematophagous mites in transmitting rickettsial disease agents to animals and humans, we have revised Ornithonyssus species collected from small mammals in Brazil by means of morphological and molecular studies. Types and other material deposited in the Acari Collection of the Instituto Butantan (IBSP) were examined in addition to recently collected specimens. Morphological and genetic analysis of the 16S rDNA mitochondrial gene revealed that small terrestrial mammals in Brazil are parasitized by six species of Ornithonyssus mites: Ornithonyssus brasiliensis (Fonseca, 1939), O. matogrosso, O. monteiroi (Fonseca, 1941), O. pereirai, O. vitzthumi (Fonseca, 1941), and O. wernecki. An illustrated key to females of the valid Brazilian species of Ornithonyssus is included, based on optical and scanning electron microscopy. PMID:21786041

  17. Small-molecule G-quadruplex interactions: Systematic exploration of conformational space using multiple molecular dynamics.

    PubMed

    Husby, Jarmila; Todd, Alan K; Platts, James A; Neidle, Stephen

    2013-12-01

    G-quadruplexes are higher-order four-stranded structures formed from repetitive guanine-containing tracts in nucleic acids. They comprise a core of stacked guanine-quartets linked by loops of length and sequence that vary with the context in which the quadruplex sequence occurs. Such sequences can be found in a number of genomic environments; at the telomeric ends of eukaryotic chromosomes, in promoter regions, in untranslated sequences and in open reading frames. Quadruplex formation can inhibit telomere maintenance, transcription and translation, especially when enhanced by quadruplex-binding small molecules, and quadruplex targeting is currently of considerable interest. The available experimental structural data shows that quadruplexes can have high conformational flexibility, especially in loop regions, which has hampered attempts to use high-throughput docking to find quadruplex-binding small-molecules with new scaffolds or to optimize existing ones with structure-based design methods. An approach to overcome the challenge of quadruplex conformational flexibility is presented here, which uses a combined multiple molecular dynamics and sampling approach. Two test small molecules have been used, RHPS4 and pyridostatin, which themselves have contrasting degrees of conformational flexibility.

  18. Investigation of the optical properties of GaAs with δ-Si doping grown by molecular-beam epitaxy at low temperatures

    SciTech Connect

    Lavrukhin, D. V. Yachmenev, A. E.; Bugaev, A. S.; Galiev, G. B.; Klimov, E. A.; Khabibullin, R. A.; Ponomarev, D. S.; Maltsev, P. P.

    2015-07-15

    Molecular-beam epitaxy is used for the preparation of structures based on “low-temperature” grown GaAs with introduced d-Si doping. Specific features in the photon-energy range of 1.28–1.48 eV are observed in the photoluminescence spectrum after structures annealing at temperatures of 520 and 580°C; these features are related to the formation of point defects and their complexes. The “pump–probe” light transmission measurements reveal that the characteristic lifetimes of nonequilibrium carriers in the fabricated structures amount to T{sup c} ≈ 1.2–1.5 ps.

  19. Blue to near-IR energy transfer cascade within a dye-doped polymer matrix, mediated by a photochromic molecular switch.

    PubMed

    Dryza, Viktoras; Smith, Trevor A; Bieske, Evan J

    2016-02-21

    The spectroscopic properties of a poly(methyl methacrylate) matrix doped with a coumarin dye, a cyanine dye, and a photochromic spiropyran dye have been investigated. Before UV irradiation of the matrix, excitation of the coumarin dye results in minimal energy transfer to the cyanine dye. The energy transfer is substantially enhanced following UV irradiation of the matrix, which converts the colourless spiropyran isomer to the coloured merocyanine isomer, which then acts as an intermediate bridge by accepting energy from the coumarin dye and then donating energy to the cyanine dye. This demonstration of a switchable energy transfer cascade should help initiate new research directions in molecular photonics.

  20. Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars.

    PubMed

    Fernandez-Castanon, J; Bomboi, F; Rovigatti, L; Zanatta, M; Paciaroni, A; Comez, L; Porcar, L; Jafta, C J; Fadda, G C; Bellini, T; Sciortino, F

    2016-08-28

    DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed of 196 nucleotides) and to explore the structural signatures of their aggregation process. We report small-angle neutron scattering experiments focused on the evaluation of both the form factor and the temperature evolution of the scattered intensity at a nanostar concentration where the system forms a tetravalent equilibrium gel. We also perform molecular dynamics simulations of one isolated tetramer to evaluate the form factor numerically, without resorting to any approximate shape. The numerical form factor is found to be in very good agreement with the experimental one. Simulations predict an essentially temperature-independent form factor, offering the possibility to extract the effective structure factor and its evolution during the equilibrium gelation. PMID:27586949

  1. Skin: Major target organ of allergic reactions to small molecular weight compounds

    SciTech Connect

    Merk, Hans F. Baron, Jens M.; Neis, Mark M.; Obrigkeit, Daniela Hoeller; Karlberg, Ann-Therese

    2007-11-01

    Skin is a major target organ for allergic reactions to small molecular weight compounds. Drug allergic reactions may be life-threatening such as in the case of anaphylactic reactions or bullous drug reactions and occur in about 5% of all hospitalized patients. Allergic contact dermatitis has an enormous influence on the social life of the patient because it is the most frequent reason for occupational skin diseases and the treatment and prevention of this disease cost approximately Euro 3 billion per year in Germany. The different proposed pathophysiological pathways leading to a drug eruption are discussed in this paper. All major enzymes which are involved in the metabolism of xenobiotica were shown to be present in skin. Evidence supporting the role of metabolism in the development of drug allergy and allergic contact dermatitis is demonstrated in the example of sulphonamides and fragrances.

  2. Skin: major target organ of allergic reactions to small molecular weight compounds.

    PubMed

    Merk, Hans F; Baron, Jens M; Neis, Mark M; Obrigkeit, Daniela Höller; Karlberg, Ann-Therese

    2007-11-01

    Skin is a major target organ for allergic reactions to small molecular weight compounds. Drug allergic reactions may be life-threatening such as in the case of anaphylactic reactions or bullous drug reactions and occur in about 5% of all hospitalized patients. Allergic contact dermatitis has an enormous influence on the social life of the patient because it is the most frequent reason for occupational skin diseases and the treatment and prevention of this disease cost approximately euro 3 billion per year in Germany. The different proposed pathophysiological pathways leading to a drug eruption are discussed in this paper. All major enzymes which are involved in the metabolism of xenobiotica were shown to be present in skin. Evidence supporting the role of metabolism in the development of drug allergy and allergic contact dermatitis is demonstrated in the example of sulphonamides and fragrances.

  3. Transient electroluminescence dynamics in small molecular organic light-emitting diodes

    SciTech Connect

    Gan, Z; Liu, R; Shinar, R; Shinar, J

    2010-09-14

    Intriguing electroluminescence (EL) spikes, following a voltage pulse applied to small molecular OLEDs, are discussed, elucidating carrier and exciton quenching dynamics and their relation to device structure. At low temperatures, all devices exhibit spikes at {approx} 70-300 ns and {mu}s-long tails. At 295 K only those with a hole injection barrier, carrier-trapping guest-host emitting layer, and no strong hole-blocking layer exhibit the spikes. They narrow and appear earlier under post-pulse reverse bias. The spikes and tails are in agreement with a revised model of recombination of correlated charge pairs (CCPs) and initially unpaired charges. Decreased post-pulse field-induced dissociative quenching of singlet excitons and CCPs, and possibly increased post-pulse current of holes that 'turn back' toward the recombination zone after having drifted beyond it are suspected to cause the spikes amplitude, which exceeds the dc EL.

  4. Small molecular donors for organic solar cells obtained by simple and clean synthesis.

    PubMed

    Demeter, Dora; Mohamed, Salma; Diac, Andreea; Grosu, Ion; Roncali, Jean

    2014-04-01

    A small donor-acceptor molecule is synthesized in a two-step procedure involving reaction of N,N-diphenylhydrazine on 2,5-diformylthiophene and Knoevenagel condensation. Results of UV/Vis absorption spectroscopy and cyclic voltammetry show that replacement of the phenyl ring bridge of a reference compound 2 by an azo group produces a slight red-shift of λmax, an enhancement of the molecular absorption coefficient, and a decrease of the energy level of the frontier orbitals. A preliminary evaluation of the potentialities of compound 1 as donor material in a basic bilayer planar heterojunction cell of 28 mm(2) active area using C60 as acceptor gave a short-circuit current density of 6.32 mA cm(-2) and a power conversion efficiency of 2.07 %.

  5. New molecular targeted therapies for advanced non-small-cell lung cancer

    PubMed Central

    Méndez, Míriam; Custodio, Ana; Provencio, Mariano

    2011-01-01

    Non-small-cell lung cancer (NSCLC) is a uniformly fatal disease and most patients will present with advanced stage. Treatment outcomes remain unsatisfactory, with low long-term survival rates. Standard treatment, such as palliative chemotherapy and radiotherapy, offers a median survival not exceeding 1 year. Hence, considerable efforts have started to be made in order to identify new biological agents which may safely and effectively be administered to advanced NSCLC patients. Two cancer cell pathways in particular have been exploited, the epidermal growth factor receptor (EGFR) and the vascular endothelial growth factor receptor (VEGFR) pathways. However, novel targeted therapies that interfere with other dysregulated pathways in lung cancer are already in the clinic. This review outlines the most promising research approaches to the treatment of NSCLC, discussed according to the specific molecular pathway targeted. PMID:22263060

  6. Small Molecule Activators of the Heat Shock Response: Chemical Properties, Molecular Targets, and Therapeutic Promise

    PubMed Central

    West, James D.; Wang, Yanyu; Morano, Kevin A.

    2012-01-01

    All cells have developed various mechanisms to respond and adapt to a variety of environmental challenges, including stresses that damage cellular proteins. One such response, the heat shock response (HSR), leads to the transcriptional activation of a family of molecular chaperone proteins that promote proper folding or clearance of damaged proteins within the cytosol. In addition to its role in protection against acute insults, the HSR also regulates lifespan and protects against protein misfolding that is associated with degenerative diseases of aging. As a result, identifying pharmacological regulators of the HSR has become an active area of research in recent years. Here, we review progress made in identifying small molecule activators of the HSR, what cellular targets these compounds interact with to drive response activation, and how such molecules may ultimately be employed to delay or reverse protein misfolding events that contribute to a number of diseases. PMID:22799889

  7. Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars

    NASA Astrophysics Data System (ADS)

    Fernandez-Castanon, J.; Bomboi, F.; Rovigatti, L.; Zanatta, M.; Paciaroni, A.; Comez, L.; Porcar, L.; Jafta, C. J.; Fadda, G. C.; Bellini, T.; Sciortino, F.

    2016-08-01

    DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed of 196 nucleotides) and to explore the structural signatures of their aggregation process. We report small-angle neutron scattering experiments focused on the evaluation of both the form factor and the temperature evolution of the scattered intensity at a nanostar concentration where the system forms a tetravalent equilibrium gel. We also perform molecular dynamics simulations of one isolated tetramer to evaluate the form factor numerically, without resorting to any approximate shape. The numerical form factor is found to be in very good agreement with the experimental one. Simulations predict an essentially temperature-independent form factor, offering the possibility to extract the effective structure factor and its evolution during the equilibrium gelation.

  8. Elucidating the Molecular Deformation Mechanism of Entangled Polymers in Fast Flow by Small Angle Neutron Scattering

    NASA Astrophysics Data System (ADS)

    Wang, Yangyang; Sanchez-Diaz, Luis; Cheng, Shiwang; Hong, Kunlun; Chen, Wei-Ren; Liu, Jianning; Lin, Panpan; Wang, Shi-Qing

    Understanding the viscoelastic properties of polymers is of fundamental and practical importance because of the vast and ever expanding demand of polymeric materials in daily life. Our current theoretical framework for describing the nonlinear flow behavior of entangled polymers is built upon the tube model pioneered by de Gennes, Doi, and Edwards. In this work, we critically examine the central hypothesis of the tube model for nonlinear rheology using small angle neutron scattering (SANS). While the tube model envisions a unique non-affine elastic deformation mechanism for entangled polymers, our SANS measurements show that the evolution of chain conformation of a well-entangled polystyrene melt closely follows the affine deformation mechanism in uniaxial extension, even when the Rouse Weissenberg number is much smaller than unity. This result provides a key clue for understanding the molecular deformation mechanism of entangled polymers in fast flow. Several implications from our analysis will be discussed in this talk.

  9. Effects of bimetallic doping on small cyclic and tubular boron clusters: B7M2 and B14M2 structures with M = Fe, Co.

    PubMed

    Pham, Hung Tan; Nguyen, Minh Tho

    2015-07-14

    Using density functional theory with the TPSSh functional and the 6-311+G(d) basis set, we extensively searched for the global minima of two metallic atoms doped boron clusters B6M2, B7M2, B12M2 and B14M2 with transition metal element M being Co and Fe. Structural identifications reveal that B7Co2, B7Fe2 and B7CoFe clusters have global minima in a B-cyclic motif, in which a perfectly planar B7 is coordinated with two metallic atoms placed along the C7 axis. The B6 cluster is too small to form a cycle with the presence of two metals. Similarly, the B12 cluster is not large enough to stabilize the metallic dimer within a double ring 2 × B6 tube. The doped B14M2 clusters including B14Co2, B14Fe2 and B14CoFe have a double ring 2 × B7 tubular shape in which one metal atom is encapsulated by the B14 tube and the other is located at an exposed position. Dissociation energies demonstrate that while bimetallic cyclic cluster B7M2 prefers a fragmentation channel that generates the B7 global minimum plus metallic dimer, the tubular structure B14M2 tends to dissociate giving a bimetallic cyclic structure B7M2 and a B@B6 cluster. The enhanced stability of the bimetallic doped boron clusters considered can be understood from the stabilizing interactions between the anti-bonding MOs of metal-metal dimers and the levels of a disk aromatic configuration (for bimetallic cyclic structures), or the eigenstates of the B14 tubular form (in case of bimetallic tubular structure).

  10. Molecular phenotyping of infection-associated small non-coding RNAs.

    PubMed

    Barquist, Lars; Westermann, Alexander J; Vogel, Jörg

    2016-11-01

    Infection is a complicated balance, with both pathogen and host struggling to tilt the result in their favour. Bacterial infection biology has relied on forward genetics for many of its advances, defining phenotype in terms of replication in model systems. However, many known virulence factors fail to produce robust phenotypes, particularly in the systems most amenable to genetic manipulation, such as cell-culture models. This has particularly been limiting for the study of the bacterial regulatory small RNAs (sRNAs) in infection. We argue that new sequencing-based technologies can work around this problem by providing a 'molecular phenotype', defined in terms of the specific transcriptional dysregulation in the infection system induced by gene deletion. We illustrate this using the example of our recent study of the PinT sRNA using dual RNA-seq, that is, simultaneous RNA sequencing of host and pathogen during infection. We additionally discuss how other high-throughput technologies, in particular genetic interaction mapping using transposon insertion sequencing, may be used to further dissect molecular phenotypes. We propose a strategy for how high-throughput technologies can be integrated in the study of non-coding regulators as well as bacterial virulence factors, enhancing our ability to rapidly generate hypotheses with regards to their function.This article is part of the themed issue 'The new bacteriology'.

  11. Molecular chaperone function of the Rana catesbeiana small heat shock protein, hsp30.

    PubMed

    Kaldis, Angelo; Atkinson, Burr G; Heikkila, John J

    2004-10-01

    Eukaryotic small heat shock proteins (shps) act as molecular chaperones by binding to denaturing proteins, preventing their heat-induced aggregation and maintaining their solubility until they can be refolded back to their normal state by other chaperones. In this study we report on the functional characterization of a developmentally regulated shsp, hsp30, from the American bullfrog, Rana catesbeiana. An expression vector containing the open reading frame of the hsp30 gene was expressed in Escherichia coli. Purified recombinant hsp30 was recovered as multimeric complexes and was composed of a mixture of alpha-helical and beta-sheet-like structures as determined by circular dichroism analysis. Hsp30 displayed chaperone activity since it inhibited heat-induced aggregation of citrate synthase. Furthermore hsp30 maintained heat-treated luciferase in a folding competent state. For example, heat denatured luciferase when microinjected into Xenopus oocytes did not regain enzyme activity whereas luciferase heat denatured with hsp30 regained 100% enzyme activity. Finally, hsp30 protected the DNA restriction endonuclease, PstI, from heat inactivation. PstI incubated alone at 42 degrees C lost its enzymatic function after 1 h whereas PstI supplemented with hsp30 accurately digested plasmid DNA after 4 h at the elevated temperature. These results clearly indicate a molecular chaperone role for R. catesbeiana hsp30.

  12. Novel molecular beacons to monitor microRNAs in non-small-cell lung cancer.

    PubMed

    Yao, Quan; Zhang, An-mei; Ma, Hu; Lin, Sheng; Wang, Xin-xin; Sun, Jian-guo; Chen, Zheng-tang

    2012-10-01

    Lung cancer is the leading cause of cancer death worldwide. There is no effective early diagnostic technology for lung cancer. microRNAs (miRNAs) are noncoding RNA molecules which regulate the process of cell growth and differentiation in human cancers. Hsa-miR-155 (miR-155), highly expressed in non-small-cell lung cancer (NSCLC), can be used as a diagnostic marker for NSCLC. Dynamic observation of miR-155 is critical to diagnose NSCLC. A novel molecular beacon (MB) of miR-155 was designed to image the expression of miR-155 in NSCLC. Then miR-155 was detected in vitro by laser confocal microscopy and in vivo by stereomicroscope imaging system, respectively. The present study demonstrated that intracellular miR-155 could be successfully and quickly detected by novel miR-155 MBs. As a noninvasive monitoring approach, MBs could be used to diagnose lung cancer at early stage through molecular imaging.

  13. Molecular phenotyping of infection-associated small non-coding RNAs.

    PubMed

    Barquist, Lars; Westermann, Alexander J; Vogel, Jörg

    2016-11-01

    Infection is a complicated balance, with both pathogen and host struggling to tilt the result in their favour. Bacterial infection biology has relied on forward genetics for many of its advances, defining phenotype in terms of replication in model systems. However, many known virulence factors fail to produce robust phenotypes, particularly in the systems most amenable to genetic manipulation, such as cell-culture models. This has particularly been limiting for the study of the bacterial regulatory small RNAs (sRNAs) in infection. We argue that new sequencing-based technologies can work around this problem by providing a 'molecular phenotype', defined in terms of the specific transcriptional dysregulation in the infection system induced by gene deletion. We illustrate this using the example of our recent study of the PinT sRNA using dual RNA-seq, that is, simultaneous RNA sequencing of host and pathogen during infection. We additionally discuss how other high-throughput technologies, in particular genetic interaction mapping using transposon insertion sequencing, may be used to further dissect molecular phenotypes. We propose a strategy for how high-throughput technologies can be integrated in the study of non-coding regulators as well as bacterial virulence factors, enhancing our ability to rapidly generate hypotheses with regards to their function.This article is part of the themed issue 'The new bacteriology'. PMID:27672158

  14. Arsenic-doped Si(001) gas-source molecular-beam epitaxy: Growth kinetics and transport properties

    SciTech Connect

    Soares, J.A.; Kim, H.; Glass, G.; Desjardins, P.; Greene, J.E.

    1999-03-01

    Arsenic-doped Si(001) layers with concentrations C{sub As} up to 5{times}10{sup 18} cm{sup {minus}3} were grown on Si(001)2{times}1 at temperatures T{sub s}=575{endash}900{degree}C by gas-source molecular-beam epitaxy (GS-MBE) using Si{sub 2}H{sub 6} and AsH{sub 3}. This is almost an order of magnitude higher than the initially reported {open_quotes}maximum attainable{close_quotes} saturated C{sub As} value for GS-MBE from hydride precursors. At constant J{sub AsH{sub 3}}/J{sub Si{sub 2}H{sub 6}}, C{sub As} decreases, while the film growth rate R{sub Si} increases, with T{sub s}. Temperature programmed desorption measurements show that As segregates strongly to the growth surface and that the observed decrease in C{sub As} at high film growth temperatures is primarily due to increasingly rapid arsenic desorption from the segregated layer. Decreasing T{sub s} enhances As incorporation. However, it also results in lower film growth rates due to higher steady-state As surface coverages which, because of the lone-pair electrons associated with each As adatom, decrease the total dangling bond coverage and, hence, the Si{sub 2}H{sub 6} adsorption rate. At constant T{sub s}, C{sub As} increases, while R{sub Si} decreases, with increasing J{sub AsH{sub 3}}/J{sub Si{sub 2}H{sub 6}}. All incorporated As resides at substitutional electrically active sites for concentrations up to 3.8{times}10{sup 18} cm{sup {minus}3}, the highest value yet reported for Si(001):As growth from hydride source gases, and temperature-dependent electron mobilities are equal to those of the best bulk Si:As. {copyright} {ital 1999 American Institute of Physics.}

  15. Ultrahigh density array of vertically aligned small-molecular organic nanowires on arbitrary substrates.

    PubMed

    Starko-Bowes, Ryan; Pramanik, Sandipan

    2013-01-01

    In recent years π-conjugated organic semiconductors have emerged as the active material in a number of diverse applications including large-area, low-cost displays, photovoltaics, printable and flexible electronics and organic spin valves. Organics allow (a) low-cost, low-temperature processing and (b) molecular-level design of electronic, optical and spin transport characteristics. Such features are not readily available for mainstream inorganic semiconductors, which have enabled organics to carve a niche in the silicon-dominated electronics market. The first generation of organic-based devices has focused on thin film geometries, grown by physical vapor deposition or solution processing. However, it has been realized that organic nanostructures can be used to enhance performance of above-mentioned applications and significant effort has been invested in exploring methods for organic nanostructure fabrication. A particularly interesting class of organic nanostructures is the one in which vertically oriented organic nanowires, nanorods or nanotubes are organized in a well-regimented, high-density array. Such structures are highly versatile and are ideal morphological architectures for various applications such as chemical sensors, split-dipole nanoantennas, photovoltaic devices with radially heterostructured "core-shell" nanowires, and memory devices with a cross-point geometry. Such architecture is generally realized by a template-directed approach. In the past this method has been used to grow metal and inorganic semiconductor nanowire arrays. More recently π-conjugated polymer nanowires have been grown within nanoporous templates. However, these approaches have had limited success in growing nanowires of technologically important π-conjugated small molecular weight organics, such as tris-8-hydroxyquinoline aluminum (Alq3), rubrene and methanofullerenes, which are commonly used in diverse areas including organic displays, photovoltaics, thin film transistors

  16. Ultrahigh Density Array of Vertically Aligned Small-molecular Organic Nanowires on Arbitrary Substrates

    PubMed Central

    Starko-Bowes, Ryan; Pramanik, Sandipan

    2013-01-01

    In recent years π-conjugated organic semiconductors have emerged as the active material in a number of diverse applications including large-area, low-cost displays, photovoltaics, printable and flexible electronics and organic spin valves. Organics allow (a) low-cost, low-temperature processing and (b) molecular-level design of electronic, optical and spin transport characteristics. Such features are not readily available for mainstream inorganic semiconductors, which have enabled organics to carve a niche in the silicon-dominated electronics market. The first generation of organic-based devices has focused on thin film geometries, grown by physical vapor deposition or solution processing. However, it has been realized that organic nanostructures can be used to enhance performance of above-mentioned applications and significant effort has been invested in exploring methods for organic nanostructure fabrication. A particularly interesting class of organic nanostructures is the one in which vertically oriented organic nanowires, nanorods or nanotubes are organized in a well-regimented, high-density array. Such structures are highly versatile and are ideal morphological architectures for various applications such as chemical sensors, split-dipole nanoantennas, photovoltaic devices with radially heterostructured "core-shell" nanowires, and memory devices with a cross-point geometry. Such architecture is generally realized by a template-directed approach. In the past this method has been used to grow metal and inorganic semiconductor nanowire arrays. More recently π-conjugated polymer nanowires have been grown within nanoporous templates. However, these approaches have had limited success in growing nanowires of technologically important π-conjugated small molecular weight organics, such as tris-8-hydroxyquinoline aluminum (Alq3), rubrene and methanofullerenes, which are commonly used in diverse areas including organic displays, photovoltaics, thin film transistors

  17. Molecular dynamics study of contact mechanics: contact area and interfacial separation from small to full contact

    NASA Astrophysics Data System (ADS)

    Yang, Chunyan; Persson, Bo

    2008-03-01

    We report a molecular dynamics study of the contact between a rigid solid with a randomly rough surface and an elastic block with a flat surface. We study the contact area and the interfacial separation from small contact (low load) to full contact (high load). For small load the contact area varies linearly with the load and the interfacial separation depends logarithmically on the load [1-4]. For high load the contact area approaches to the nominal contact area (i.e., complete contact), and the interfacial separation approaches to zero. The present results may be very important for soft solids, e.g., rubber, or for very smooth surfaces, where complete contact can be reached at moderate high loads without plastic deformation of the solids. References: [1] C. Yang and B.N.J. Persson, arXiv:0710.0276, (to appear in Phys. Rev. Lett.) [2] B.N.J. Persson, Phys. Rev. Lett. 99, 125502 (2007) [3] L. Pei, S. Hyun, J.F. Molinari and M.O. Robbins, J. Mech. Phys. Sol. 53, 2385 (2005) [4] M. Benz, K.J. Rosenberg, E.J. Kramer and J.N. Israelachvili, J. Phy. Chem. B.110, 11884 (2006)

  18. The molecular nature of very small embryonic-like stem cells in adult tissues.

    PubMed

    Kim, YongHwan; Jeong, Jaeho; Kang, Hyunsook; Lim, Jisun; Heo, Jinbeom; Ratajczak, Janina; Ratajczak, Mariusz Z; Shin, Dong-Myung

    2014-11-01

    Pluripotent stem cells (PSCs) have been considered as the most important cells in regenerative medicine as they are able to differentiate into all types of cells in the human body. PSCs have been established from several sources of embryo tissue or by reprogramming of terminally differentiated adult tissue by transduction of so-called Yamanaka factors (Oct4, Sox2, Klf4, and cMyc). Interestingly, accumulating evidence has demonstrated the residence of PSCs in adult tissue and with the ability to differentiate into multiple types of tissue-committed stem cells (TCSCs). We also recently demonstrated that a population of pluripotent Oct4(+) SSEA-1(+)Sca-1(+)Lin(-)CD45(-) very small embryonic-like stem cells (VSELs) resides in the adult murine bone marrow (BM) and in other murine tissue. These very small (∼3-6 μm) cells express pluripotent markers such as Oct4, Nanog, and SSEA-1. VSELs could be specified into several tissue-residing TCSCs in response to tissue/organ injury, and thus suggesting that these cells have a physiological role in the rejuvenation of a pool of TCSCs under steady-state conditions. In this review article, we discuss the molecular nature of the rare population of VSELs which have a crucial role in regulating the pluripotency, proliferation, differentiation, and aging of these cells. PMID:25473442

  19. Replica exchange molecular dynamics simulations of an α/β-type small acid soluble protein (SASP).

    PubMed

    Ojeda-May, P; Pu, Jingzhi

    2013-12-31

    Small acid soluble proteins (SASPs) of α/β-type play a major role in the resistance of spore DNAs to external assaults. It has been found that α/β-type SASP exhibits intrinsic disorder on isolation, but it acquires a defined native state upon binding to DNA. This disorder to order transition is not yet understood. Other questions related to the role of the thermodynamics and structure of the individual protein in the complex formation remain elusive. Characterization of the unbound state of α/β-type SASP in experiments could be a challenging problem because of the heterogeneous nature of the ensemble. Here, computer simulations can help gain more insights into the unbound state of α/β-type SASP. In the present work, by using replica exchange molecular dynamics (REMD), we simulated an α/β-type SASP on isolation with an implicit solvent. We found that α/β-type SASP undergoes a continuous phase transition with a small free energy barrier, a common feature of intrinsically disordered proteins (IDPs). Additionally, we detected the presence of residual α-helical structures at local level and a high degree of plasticity in the chain which can contribute to the fast disorder to order transition by reducing the fly-casting mechanism.

  20. Probing the conformation of FhaC with small-angle neutron scattering and molecular modeling.

    PubMed

    Gabel, Frank; Lensink, Marc F; Clantin, Bernard; Jacob-Dubuisson, Françoise; Villeret, Vincent; Ebel, Christine

    2014-07-01

    Probing the solution structure of membrane proteins represents a formidable challenge, particularly when using small-angle scattering. Detergent molecules often present residual scattering contributions even at their match point in small-angle neutron scattering (SANS) measurements. Here, we studied the conformation of FhaC, the outer-membrane, β-barrel transporter of the Bordetella pertussis filamentous hemagglutinin adhesin. SANS measurements were performed on homogeneous solutions of FhaC solubilized in n-octyl-d17-βD-glucoside and on a variant devoid of the α helix H1, which critically obstructs the FhaC pore, in two solvent conditions corresponding to the match points of the protein and the detergent, respectively. Protein-bound detergent amounted to 142 ± 10 mol/mol as determined by analytical ultracentrifugation. By using molecular modeling and starting from three distinct conformations of FhaC and its variant embedded in lipid bilayers, we generated ensembles of protein-detergent arrangement models with 120-160 detergent molecules. The scattered curves were back-calculated for each model and compared with experimental data. Good fits were obtained for relatively compact, connected detergent belts, which occasionally displayed small detergent-free patches on the outer surface of the β barrel. The combination of SANS and modeling clearly enabled us to infer the solution structure of FhaC, with H1 inside the pore as in the crystal structure. We believe that our strategy of combining explicit atomic detergent modeling with SANS measurements has significant potential for structural studies of other detergent-solubilized membrane proteins. PMID:24988353

  1. Probing the Conformation of FhaC with Small-Angle Neutron Scattering and Molecular Modeling

    PubMed Central

    Gabel, Frank; Lensink, Marc F.; Clantin, Bernard; Jacob-Dubuisson, Françoise; Villeret, Vincent; Ebel, Christine

    2014-01-01

    Probing the solution structure of membrane proteins represents a formidable challenge, particularly when using small-angle scattering. Detergent molecules often present residual scattering contributions even at their match point in small-angle neutron scattering (SANS) measurements. Here, we studied the conformation of FhaC, the outer-membrane, β-barrel transporter of the Bordetella pertussis filamentous hemagglutinin adhesin. SANS measurements were performed on homogeneous solutions of FhaC solubilized in n-octyl-d17-βD-glucoside and on a variant devoid of the α helix H1, which critically obstructs the FhaC pore, in two solvent conditions corresponding to the match points of the protein and the detergent, respectively. Protein-bound detergent amounted to 142 ± 10 mol/mol as determined by analytical ultracentrifugation. By using molecular modeling and starting from three distinct conformations of FhaC and its variant embedded in lipid bilayers, we generated ensembles of protein-detergent arrangement models with 120–160 detergent molecules. The scattered curves were back-calculated for each model and compared with experimental data. Good fits were obtained for relatively compact, connected detergent belts, which occasionally displayed small detergent-free patches on the outer surface of the β barrel. The combination of SANS and modeling clearly enabled us to infer the solution structure of FhaC, with H1 inside the pore as in the crystal structure. We believe that our strategy of combining explicit atomic detergent modeling with SANS measurements has significant potential for structural studies of other detergent-solubilized membrane proteins. PMID:24988353

  2. Improving biogas separation and methane storage with multilayer graphene nanostructure via layer spacing optimization and lithium doping: a molecular simulation investigation.

    PubMed

    Chen, Jie-Jie; Li, Wen-Wei; Li, Xue-Liang; Yu, Han-Qing

    2012-09-18

    Methane is a desirable alternative to conventional fossil fuels, and also a main component of biogas from anaerobic fermentation of organic wastes. However, its relatively lower purity and poor storage by existing adsorbent materials negatively affect its wide application. Thus, efficient, cost-effective, and safe adsorbent materials for methane purification and storage are highly desired. In this study, multilayer graphene nanostructures (MGNs) with optimized structure are investigated as a potential adsorbent for this purpose. The effects of layer distance and Li doping on MGN performance in terms of methane storage and acid gas (H(2)S and CO(2)) separation from biogas are examined by molecular simulations. The mechanisms for the interactions between gas molecules and substrates are elucidated by analyzing the binding energy, geometric structures, and charge distribution from the first-principles calculations. The results show that nonhydrocarbons in biogas can be effectively separated using Li-doped MGNs with the optimal layer distance of 0.68 nm, and then the pure methane gas can be stored in MGNs with capacity satisfying the DOE target. This work offers a molecular-level insight into the interactions between gas molecules and MGNs and might provide useful information for development of new materials for methane purification and storage.

  3. Noise-like femtosecond pulse in passively mode-locked Tm-doped NALM-based oscillator with small net anomalous dispersion

    NASA Astrophysics Data System (ADS)

    Liu, Shuo; Yan, Feng-Ping; Zhang, Lu-Na; Han, Wen-Guo; Bai, Zhuo-Ya; Zhou, Hong

    2016-01-01

    A passively mode-locked thulium-doped fiber laser (TDFL) based on a nonlinear amplifying loop mirror (NALM) is presented. By adjusting the polarization controllers, stable noise-like (NL) mode-locked femtosecond pulse operation is obtained at the 2 μm band. In the experimental period of 200 min, the output power fluctuation is less than 0.06 dB and the 3 dB spectral bandwidth variation is less than 0.02 nm, indicating that the pulsed TDFL possesses good long-term stability. To the best of our knowledge, this is the first 2 μm band NALM-based TDFL with small net anomalous dispersion for a NL femtosecond pulse. At the maximum pump power of 3.52 W, the emitting laser has a NL pulse width of 460 fs, the repetition rate of 9.1 MHz, and the NL pulse energy of 32.72 nJ.

  4. Tuning the threshold voltage of carbon nanotube transistors by n-type molecular doping for robust and flexible complementary circuits

    PubMed Central

    Wang, Huiliang; Wei, Peng; Li, Yaoxuan; Han, Jeff; Lee, Hye Ryoung; Naab, Benjamin D.; Liu, Nan; Wang, Chenggong; Adijanto, Eric; Tee, Benjamin C.-K.; Morishita, Satoshi; Li, Qiaochu; Gao, Yongli; Cui, Yi; Bao, Zhenan

    2014-01-01

    Tuning the threshold voltage of a transistor is crucial for realizing robust digital circuits. For silicon transistors, the threshold voltage can be accurately controlled by doping. However, it remains challenging to tune the threshold voltage of single-wall nanotube (SWNT) thin-film transistors. Here, we report a facile method to controllably n-dope SWNTs using 1H-benzoimidazole derivatives processed via either solution coating or vacuum deposition. The threshold voltages of our polythiophene-sorted SWNT thin-film transistors can be tuned accurately and continuously over a wide range. Photoelectron spectroscopy measurements confirmed that the SWNT Fermi level shifted to the conduction band edge with increasing doping concentration. Using this doping approach, we proceeded to fabricate SWNT complementary inverters by inkjet printing of the dopants. We observed an unprecedented noise margin of 28 V at VDD = 80 V (70% of 1/2VDD) and a gain of 85. Additionally, robust SWNT complementary metal−oxide−semiconductor inverter (noise margin 72% of 1/2VDD) and logic gates with rail-to-rail output voltage swing and subnanowatt power consumption were fabricated onto a highly flexible substrate. PMID:24639537

  5. POA 02-3 SMALL VESSEL DISEASE AND HYPERTENSION - MOLECULAR MECHANISMS AND CLINICAL IMPLICATIONS.

    PubMed

    Touyz, Rhian M

    2016-09-01

    Pathophysiological mechanisms contributing to hypertension include injury to small arteries, characterised by endothelial dysfunction, vascular remodeling, fibrosis and inflammation, (so called hypertensive vascular phenotype). These changes are initially adaptive but in the long term become maladaptive leading to vascular damage and loss of function, particularly important in small resistance arteries, critically involved in the regulation of peripheral vascular resistance and consequently in blood pressure control. Common to these processes are changes in vascular cells that make up vessels (endothelial cells, vascular smooth muscle cells, adventitial fibroblasts and adipocytes) to a pro-inflammatory, vasoconstrictory, proliferative, pro-fibrotic, pro-migratory phenotype, influenced in large part by oxidative stress (increased bioavailability of reactive oxygen species). Increased reactive oxygen species production, due to activation of NADPH oxidases (Nox), and decreased cellular antioxidant defense mechanisms contribute to oxidative stress, which influences redox-sensitive signaling molecules that impact on endothelial dysfunction and vascular remodeling and inflammation. Our recent studies also elucidate a novel mechanism whereby microparticles may play a role in vascular dysfunction. Clinical studies demonstrate that improved endothelial function, regression of arterial remodeling and decreased vascular inflammation are associated with decreased cardiovascular events and reduced hypertension-related target organ damage. Accordingly strategies to promote vascular health should be a therapeutic priority. Such strategies include drugs (RAAS inhibitors, calcium channel blockers) and lifestyle modifications (exercise, healthy diet, smoking cessation), which reduce oxidative stress and dampen activation of injurious signaling pathways (pro-fibrotic, pro-inflammatory, proliferative pathways). Novel approaches, such as Nox inhibitors, agents that increase antioxidant

  6. Nonadiabatic small-polaron hopping conduction in Li-doped and undoped Bi4Sr3Ca3CuyOx (0<=y<=5)

    NASA Astrophysics Data System (ADS)

    Mollah, S.; Som, K. K.; Bose, K.; Chakravorty, A. K.; Chaudhuri, B. K.

    1992-11-01

    Detailed experimental results of temperature- and CuO-concentration-dependent dc conductivities of semiconducting Bi4Sr3Ca3CuyOx (y=0 to 5) and Li-doped Bi4Sr3Ca3-zLizCu4Ox (z=0.1, 0.5, and 1.0) glasses are reported. The variation of activation energy with glass compositions dominates the conductivity. Unlike many glasses with transition-metal ions, a strong preexponential factor containing the ``small-polaron'' tunneling term [exp(-2αR)] is observed. Nonadiabatic small-polaron hopping mechanism is found to be appropriate for explaining the conductivity data of both glass systems. Addition of alkali-metal ions decreases the conductivities and causes appreciable change of some model parameters obtained from least-squares fittings of the experimental data. The overall thermal behavior of the electrical conductivities of the glasses, however, remains unaltered. This indicates that small (less than 10 wt.%) amount of Li or other alkali-metal ions in these glasses acts as a flux to keep the oxygen content fixed in the corresponding glass-ceramic (superconducting) phases. This in turn helps increase the superconducting transition temperature of the glass ceramics and also lower the sintering and melting temperatures of the glasses.

  7. Stochastic dynamics of small ensembles of non-processive molecular motors: The parallel cluster model

    NASA Astrophysics Data System (ADS)

    Erdmann, Thorsten; Albert, Philipp J.; Schwarz, Ulrich S.

    2013-11-01

    Non-processive molecular motors have to work together in ensembles in order to generate appreciable levels of force or movement. In skeletal muscle, for example, hundreds of myosin II molecules cooperate in thick filaments. In non-muscle cells, by contrast, small groups with few tens of non-muscle myosin II motors contribute to essential cellular processes such as transport, shape changes, or mechanosensing. Here we introduce a detailed and analytically tractable model for this important situation. Using a three-state crossbridge model for the myosin II motor cycle and exploiting the assumptions of fast power stroke kinetics and equal load sharing between motors in equivalent states, we reduce the stochastic reaction network to a one-step master equation for the binding and unbinding dynamics (parallel cluster model) and derive the rules for ensemble movement. We find that for constant external load, ensemble dynamics is strongly shaped by the catch bond character of myosin II, which leads to an increase of the fraction of bound motors under load and thus to firm attachment even for small ensembles. This adaptation to load results in a concave force-velocity relation described by a Hill relation. For external load provided by a linear spring, myosin II ensembles dynamically adjust themselves towards an isometric state with constant average position and load. The dynamics of the ensembles is now determined mainly by the distribution of motors over the different kinds of bound states. For increasing stiffness of the external spring, there is a sharp transition beyond which myosin II can no longer perform the power stroke. Slow unbinding from the pre-power-stroke state protects the ensembles against detachment.

  8. Stochastic dynamics of small ensembles of non-processive molecular motors: The parallel cluster model

    SciTech Connect

    Erdmann, Thorsten; Albert, Philipp J.; Schwarz, Ulrich S.

    2013-11-07

    Non-processive molecular motors have to work together in ensembles in order to generate appreciable levels of force or movement. In skeletal muscle, for example, hundreds of myosin II molecules cooperate in thick filaments. In non-muscle cells, by contrast, small groups with few tens of non-muscle myosin II motors contribute to essential cellular processes such as transport, shape changes, or mechanosensing. Here we introduce a detailed and analytically tractable model for this important situation. Using a three-state crossbridge model for the myosin II motor cycle and exploiting the assumptions of fast power stroke kinetics and equal load sharing between motors in equivalent states, we reduce the stochastic reaction network to a one-step master equation for the binding and unbinding dynamics (parallel cluster model) and derive the rules for ensemble movement. We find that for constant external load, ensemble dynamics is strongly shaped by the catch bond character of myosin II, which leads to an increase of the fraction of bound motors under load and thus to firm attachment even for small ensembles. This adaptation to load results in a concave force-velocity relation described by a Hill relation. For external load provided by a linear spring, myosin II ensembles dynamically adjust themselves towards an isometric state with constant average position and load. The dynamics of the ensembles is now determined mainly by the distribution of motors over the different kinds of bound states. For increasing stiffness of the external spring, there is a sharp transition beyond which myosin II can no longer perform the power stroke. Slow unbinding from the pre-power-stroke state protects the ensembles against detachment.

  9. Small Molecular TRAIL Inducer ONC201 Induces Death in Lung Cancer Cells: A Preclinical Study.

    PubMed

    Feng, Yuan; Zhou, Jihong; Li, Zhanhua; Jiang, Ying; Zhou, Ying

    2016-01-01

    Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) selectively targets cancer cells. The present preclinical study investigated the anti-cancer efficiency of ONC201, a first-in-class small molecule TRAIL inducer, in lung cancer cells. We showed that ONC201 was cytotoxic and anti-proliferative in both established (A549 and H460 lines) and primary human lung cancer cells. It was yet non-cytotoxic to normal lung epithelial cells. Further, ONC201 induced exogenous apoptosis activation in lung cancer cells, which was evidenced by TRAIL/death receptor-5 (DR5) induction and caspase-8 activation. The caspase-8 inhibitor or TRAIL/DR5 siRNA knockdown alleviated ONC201's cytotoxicity against lung cancer cells. Molecularly, ONC201 in-activated Akt-S6K1 and Erk signalings in lung cancer cells, causing Foxo3a nuclear translocation. For the in vivo studies, intraperitoneal injection of ONC201 at well-tolerated doses significantly inhibited xenografted A549 tumor growth in severe combined immunodeficient (SCID) mice. Further, ONC201 administration induced TRAIL/DR5 expression, yet inactivated Akt-S6K1 and Erk in tumor tissues. These results of the study demonstrates the potent anti-lung cancer activity by ONC201. PMID:27626799

  10. Small Molecular TRAIL Inducer ONC201 Induces Death in Lung Cancer Cells: A Preclinical Study

    PubMed Central

    Feng, Yuan; Zhou, Jihong; Li, Zhanhua; Jiang, Ying; Zhou, Ying

    2016-01-01

    Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) selectively targets cancer cells. The present preclinical study investigated the anti-cancer efficiency of ONC201, a first-in-class small molecule TRAIL inducer, in lung cancer cells. We showed that ONC201 was cytotoxic and anti-proliferative in both established (A549 and H460 lines) and primary human lung cancer cells. It was yet non-cytotoxic to normal lung epithelial cells. Further, ONC201 induced exogenous apoptosis activation in lung cancer cells, which was evidenced by TRAIL/death receptor-5 (DR5) induction and caspase-8 activation. The caspase-8 inhibitor or TRAIL/DR5 siRNA knockdown alleviated ONC201’s cytotoxicity against lung cancer cells. Molecularly, ONC201 in-activated Akt-S6K1 and Erk signalings in lung cancer cells, causing Foxo3a nuclear translocation. For the in vivo studies, intraperitoneal injection of ONC201 at well-tolerated doses significantly inhibited xenografted A549 tumor growth in severe combined immunodeficient (SCID) mice. Further, ONC201 administration induced TRAIL/DR5 expression, yet inactivated Akt-S6K1 and Erk in tumor tissues. These results of the study demonstrates the potent anti-lung cancer activity by ONC201. PMID:27626799

  11. Small animal optoacoustic tomography system for molecular imaging of contrast agents

    NASA Astrophysics Data System (ADS)

    Su, Richard; Liopo, Anton; Ermilov, Sergey A.; Oraevsky, Alexander A.

    2016-03-01

    We developed a new and improved Laser Optoacoustic Imaging System, LOIS-3D for preclinical research applications in small animal models. The advancements include (i) a new stabilized imaging module with a more homogeneous illumination of the mouse yielding a better spatial resolution (<0.2 mm) and (ii) a new low noise amplifier incorporated into the ultrasonic probe and providing the noise equivalent pressure around 2 Pa resulting in increased signal-to-noise ratio and the optical absorption sensitivity of about 0.15 cm-1. We also improved scan time and the image reconstruction times. This prototype has been commercialized for a number of biomedical research applications, such as imaging vascularization and measuring hemoglobin / oxyhemoglobin distribution in the organs as well as imaging exogenous or endogenous optoacoustic contrast agents. As examples, we present in vivo experiments using phantoms and mice with and without tumor injected with contrast agents with indocyanine green (ICG). LOIS-3D was capable of detecting ~1-2 pmole of the ICG, in tissues with relatively low blood content. With its high sensitivity and excellent spatial resolution LOIS-3D is an advanced alternative to fluorescence and bioluminescence based modalities for molecular imaging in live mice.

  12. Photoelectric characteristics of organic light-emitting device based on a small molecular fluorene derivative

    NASA Astrophysics Data System (ADS)

    Qian, Jincheng; Yu, Junsheng; Jiang, Yadong; Lou, Shuangling; Zhang, Qing

    2009-11-01

    The performance of organic light-emitting devices (OLEDs) based on a small molecular fluorene material, 6,6'-(9H-fluoren-9,9-diyl)bis(2,3-bis(9,9-dihexyl-9H-fluoren-2-yl)quinoxaline) (BFLBBFLYQ), was investigated. Double-layer devices with a structure of indium tin oxide (ITO)/BFLBBFLYQ/2,9-dimethyl-4,7-diphenyl-l, 10-phenanthroline (BCP)/Mg:Ag were fabricated. To improve the performance of the OLEDs, N,N'-biphenyl-N,N'-bis-(3-methylphenyl)-1, 1'-biphenyl-4,4'-diamine (TPD) was introduced, and triple-layer OLEDs with a configuration of ITO/TPD/BFLBBFLYQ/BCP/Mg:Ag were fabricated. By analyzing the electric and luminescent properties of the devices with two different structures, it was found that the performance of triple-layer devices was higher than that of double-layer device. The electroluminescent (EL) spectra of the devices were also studied, which showed that the EL spectra red-shifted as the vacuum deposition temperature increased.

  13. High Sensitivity Method to Estimate Distribution of Hyaluronan Molecular Sizes in Small Biological Samples Using Gas-Phase Electrophoretic Mobility Molecular Analysis

    PubMed Central

    Do, Lan; Dahl, Christen P.; Kerje, Susanne; Hansell, Peter; Mörner, Stellan; Lindqvist, Ulla; Engström-Laurent, Anna; Larsson, Göran; Hellman, Urban

    2015-01-01

    Hyaluronan is a negatively charged polydisperse polysaccharide where both its size and tissue concentration play an important role in many physiological and pathological processes. The various functions of hyaluronan depend on its molecular size. Up to now, it has been difficult to study the role of hyaluronan in diseases with pathological changes in the extracellular matrix where availability is low or tissue samples are small. Difficulty to obtain large enough biopsies from human diseased tissue or tissue from animal models has also restricted the study of hyaluronan. In this paper, we demonstrate that gas-phase electrophoretic molecular mobility analyzer (GEMMA) can be used to estimate the distribution of hyaluronan molecular sizes in biological samples with a limited amount of hyaluronan. The low detection level of the GEMMA method allows for estimation of hyaluronan molecular sizes from different parts of small organs. Hence, the GEMMA method opens opportunity to attain a profile over the distribution of hyaluronan molecular sizes and estimate changes caused by disease or experimental conditions that has not been possible to obtain before. PMID:26448761

  14. Fe₃O₄@rGO doped molecularly imprinted polymer membrane based on magnetic field directed self-assembly for the determination of amaranth.

    PubMed

    Han, Qing; Wang, Xi; Yang, Zaiyue; Zhu, Wanying; Zhou, Xuemin; Jiang, Huijun

    2014-06-01

    Based on magnetic field directed self-assembly (MDSA) of Fe3O4@rGO composites, a novel magnetic molecularly imprinted electrochemical sensor (MIES) was fabricated and developed for the determination of the azo dye amaranth. Fe3O4@rGO composites were obtained by a one-step approach involving the initial intercalating of iron ions between the graphene oxide layers via the electrostatic interaction, followed by the reduction with hydrazine hydrate to deposit Fe3O4 nanoparticles onto the reduced oxide graphene nanosheets. In molecular imprinting, the complex including the function monomer of aniline, the template of amaranth and Fe3O4@rGO was pre-assembled through π-π stacking and hydrogen bonding interactions, and then was self-assembled on the surface of magnetic glassy carbon electrode (MGCE) with the help of magnetic field induction before electropolymerization. The structures and morphologies of Fe3O4@rGO and the doped molecularly imprinted polymers (MIPs) were investigated by Fourier transform infrared spectrometer (FT-IR), Raman spectra and scanning electron microscope (SEM). Besides, the characterization by differential pulse voltammetry (DPV) showed that Fe3O4@rGO composites promoted the electrical conductivity of the imprinted sensors when doped into the MIPs. The adsorption isotherms and adsorption kinetics were employed to evaluate the performances of MIES. The detection of amaranth was achieved via the redox probe K3[Fe(CN)6] by blocking the imprinted cavities, which avoided the interferences of oxidation products and analogs of amaranth. Furthermore, the prepared MIES exhibited good sensitivity, selectivity, reproducibility and efficiency for detecting amaranth in fruit drinks. The average recoveries were 93.15-100.81% with the RSD <3.0%.

  15. Quantum solvent states and rovibrational spectra of small doped (3)He clusters through the full-configuration-interaction nuclear orbital approach: The ((3)He)(N)-Cl(2)(X) case (N

    PubMed

    de Lara-Castells, María Pilar; Aguirre, Néstor F; Villarreal, Pablo; Barrio, Gerardo Delgado; Mitrushchenkov, Alexander O

    2010-05-21

    A full-configuration-interaction nuclear orbital treatment has been recently developed as a benchmark quantum-chemistry-like method to study small doped (3)He clusters [M. P. de Lara-Castells et al., J. Chem. Phys. 125, 221101 (2006)]. Our objective in this paper is to extend our previous study on ((3)He)(N)-Cl(2)(B) clusters, using an enhanced implementation that allows employing very large one-particle basis sets [M. P. de Lara-Castells et al., J. Chem. Phys. 131, 194101 (2009)], and apply the method to the ((3)He)(N)-Cl(2)(X) case, using both a semiempirical T-shaped and an ab initio He-dopant potential with minima at both T-shaped and linear conformations. Calculations of the ground and low-lying excited solvent states stress the key role played by the anisotropy of the He-dopant interaction in determining the global energies and the structuring of the (3)He atoms around the dopant. Whereas (3)He atoms are localized in a broad belt around the molecular axis in ground-state N-sized complexes with N=1-3, irrespective of using the T-shaped or the ab initio He-dopant potential function, the dopant species becomes fully coated by just four (3)He atoms when the He-dopant potential also has a minimum at linear configurations. However, excited solvent states with a central ring-type clustering of the host molecule are found to be very close in energy with the ground state by using the ab initio potential function. A microscopic analysis of this behavior is provided. Additional simulations of the molecular rovibrational Raman spectra, also including excited solvent states, provide further insights into the importance of proper modeling the anisotropy of the He-dopant interaction in these weakly bound systems and of taking into account the low-lying excitations.

  16. Optical and electrical properties of Mg-doped AlN nanowires grown by molecular beam epitaxy

    SciTech Connect

    Connie, Ashfiqua Tahseen; Zhao, Songrui; Sadaf, Sharif Md.; Shih, Ishiang; Mi, Zetian; Du, Xiaozhang; Lin, Jingyu; Jiang, Hongxing

    2015-05-25

    In this paper, the optical and electrical properties of Mg-doped AlN nanowires are discussed. At room temperature, with the increase of Mg-doping concentration, the Mg-acceptor energy level related optical transition can be clearly measured, which is separated about 0.6 eV from the band-edge transition, consistent with the Mg activation energy in AlN. The electrical conduction measurements indicate an activation energy of 23 meV at 300 K–450 K temperature range, which is significantly smaller than the Mg-ionization energy in AlN, suggesting the p-type conduction being mostly related to hopping conduction. The free hole concentration of AlN:Mg nanowires is estimated to be on the order of 10{sup 16 }cm{sup −3}, or higher.

  17. Structure-based design and synthesis of small molecular inhibitors disturbing the interaction of MLL1-WDR5.

    PubMed

    Li, Dong-Dong; Chen, Wei-Lin; Xu, Xiao-Li; Jiang, Fen; Wang, Lei; Xie, Yi-Yue; Zhang, Xiao-Jin; Guo, Xiao-Ke; You, Qi-Dong; Sun, Hao-Peng

    2016-08-01

    MLL1 complex catalyzes the methylation of H3K4, and plays important roles in the development of acute leukemia harboring MLL fusion proteins. Targeting MLL1-WDR5 protein-protein interaction (PPI) to inhibit the activity of histone methyltransferase of MLL1 complex is a novel strategy for treating of acute leukemia. WDR5-47 (IC50 = 0.3 μM) was defined as a potent small molecule to disturb the interaction of MLL1-WDR5. Here, we described structure-based design and synthesis of small molecular inhibitors to block MLL1-WDR5 PPI. Especially, compound 23 (IC50 = 104 nM) was the most potent small molecular, and about 3-times more potent than WDR5-47. We also discussed the SAR of these series of compounds with docking study, which may stimulate more potent compounds.

  18. Fluorine-doped nanocrystalline SnO{sub 2} powders prepared via a single molecular precursor method as anode materials for Li-ion batteries

    SciTech Connect

    Ha, Hyung-Wook; Kim, Keon . E-mail: kkim@korea.ac.kr; Borniol, Mervyn de; Toupance, Thierry . E-mail: t.toupance@lcoo.u-bordeaux1.fr

    2006-03-15

    Fluorine-doped nanocrystalline tin dioxide materials (F:SnO{sub 2}) have been successfully prepared by the sol-gel process from a single molecular precursor followed by a thermal treatment at 450-650 deg. C. The resulting materials were characterized by FTIR spectroscopy, powder X-ray diffraction, nitrogen adsorption porosimetry (BET) and transmission electron microscopy (TEM). The mean particle size increased from 5 to 20 nm and the specific surface area decreased from 123 to 37 m{sup 2}/g as the temperature of heat treatment was risen from 450 to 650 deg. C. Fluorine-doped nanocrystalline SnO{sub 2} exhibited capacity of 560, 502, and 702 mA h/g with 48%, 50%, and 40% capacity retention after 25 cycles between 1.2 V and 50 mV at the rate of 25 mA/g, respectively. In comparison, commercial SnO{sub 2} showed an initial capacity of 388 mA h/g, with only 23% capacity retention after 25 cycles.

  19. Fluorine-doped nanocrystalline SnO 2 powders prepared via a single molecular precursor method as anode materials for Li-ion batteries

    NASA Astrophysics Data System (ADS)

    Ha, Hyung-Wook; Kim, Keon; Borniol, Mervyn de; Toupance, Thierry

    2006-03-01

    Fluorine-doped nanocrystalline tin dioxide materials (F:SnO 2) have been successfully prepared by the sol-gel process from a single molecular precursor followed by a thermal treatment at 450-650 °C. The resulting materials were characterized by FTIR spectroscopy, powder X-ray diffraction, nitrogen adsorption porosimetry (BET) and transmission electron microscopy (TEM). The mean particle size increased from 5 to 20 nm and the specific surface area decreased from 123 to 37 m 2/g as the temperature of heat treatment was risen from 450 to 650 °C. Fluorine-doped nanocrystalline SnO 2 exhibited capacity of 560, 502, and 702 mA h/g with 48%, 50%, and 40% capacity retention after 25 cycles between 1.2 V and 50 mV at the rate of 25 mA/g, respectively. In comparison, commercial SnO 2 showed an initial capacity of 388 mA h/g, with only 23% capacity retention after 25 cycles.

  20. Structure, electronic and magnetic properties of hexagonal boron nitride sheets doped by 5d transition metal atoms: First-principles calculations and molecular orbital analysis

    NASA Astrophysics Data System (ADS)

    Zhang, Zhaofu; Geng, Zhaohui; Cai, Danyun; Pan, Tongxi; Chen, Yixin; Dong, Liyuan; Zhou, Tiege

    2015-01-01

    A first-principles calculation based on density functional theory is carried out to reveal the geometry, electronic structures and magnetic properties of hexagonal boron nitride sheets (h-BNSs) doped by 5d transitional mental atoms (Lu, Hf, Ta, W, Re, Os, Ir, Pt, Au and Hg) at boron-site (B5d) and nitrogen-site (N5d). Results of pure h-BNS, h-BNS with B vacancy (VB) and N vacancy (VN) are also given for comparison. It is shown that all the h-BNSs doped with 5d atoms possess a C3v local symmetry except for NLu and NHg which have a clear deviation. For the same 5d dopant, the binding energy of B5d is larger than that of N5d, which indicates the substitution of a 5d atom for B is preferred. The total densities of states are presented, where impurity energy levels exist. Besides, the total magnetic moments (TMMs) change regularly with the increment of the 5d atomic number. Theoretical analyses by molecular orbital under C3v symmetry explain the impurity energy levels and TMMs.

  1. Low-Temperature Growth and Doping of Mercury-Based II-Vi Multiple Quantum Well Structures by Molecular Beam Epitaxy

    NASA Astrophysics Data System (ADS)

    Lansari, Yamina

    The growth of Hg-based single layers and multiple quantum well structures by conventional molecular beam epitaxy (MBE) and photoassisted MBE was studied. The use of photoassisted MBE, an epitaxial growth technique developed at NCSU, has resulted in a substantial reduction of the film growth temperature. Indeed, substrate temperatures 50 to 100^circC lower than those customarily used by others for conventional MBE growth of Hg-based layers were successfully employed. Photoassisted MBE allowed the preparation of excellent structural quality HgTe layers (FWHM for the (400) diffraction peak ~ 40 arcsec), HgCdTe layers (FWHM for the (400) diffraction peak ~ 14 arcsec), and HgTeCdTe superlattices (FWHM for the (400) diffraction peak ~ 28 arcsec). In addition, n-type and p-type modulation-doping of Hg-based multilayers was accomplished by photoassisted MBE. This technique has been shown to have a significant effect on the growth process kinetics as well as on the desorption rates of the film species, thereby affecting dopant incorporation mechanisms and allowing for the successful substitutional doping of the multilayer structures. Finally, surface morphology studies were completed using scanning electron microscopy (SEM) and Nomarsky optical microscopy to study the effects of substrate surface preparation, growth initiation, and growth parameters on the density of pyramidal hillocks, a common growth defect plaguing the Hg-based layers grown in the (100) direction. Conditions which minimize the hillock density for (100) film growth have been determined.

  2. Transformation from non-small-cell lung cancer to small-cell lung cancer: molecular drivers and cells of origin.

    PubMed

    Oser, Matthew G; Niederst, Matthew J; Sequist, Lecia V; Engelman, Jeffrey A

    2015-04-01

    Lung cancer is the most common cause of cancer deaths worldwide. The two broad histological subtypes of lung cancer are small-cell lung cancer (SCLC), which is the cause of 15% of cases, and non-small-cell lung cancer (NSCLC), which accounts for 85% of cases and includes adenocarcinoma, squamous-cell carcinoma, and large-cell carcinoma. Although NSCLC and SCLC are commonly thought to be different diseases owing to their distinct biology and genomic abnormalities, the idea that these malignant disorders might share common cells of origin has been gaining support. This idea has been supported by the unexpected findings that a subset of NSCLCs with mutated EGFR return as SCLC when resistance to EGFR tyrosine kinase inhibitors develops. Additionally, other case reports have described the coexistence of NSCLC and SCLC, further challenging the commonly accepted view of their distinct lineages. Here, we summarise the published clinical observations and biology underlying tumours with combined SCLC and NSCLC histology and cancers that transform from adenocarcinoma to SCLC. We also discuss pre-clinical studies pointing to common potential cells of origin, and speculate how the distinct paths of differentiation are determined by the genomics of each disease.

  3. Molecular alterations in non-small cell lung carcinomas of the young.

    PubMed

    VandenBussche, Christopher J; Illei, Peter B; Lin, Ming-Tseh; Ettinger, David S; Maleki, Zahra

    2014-12-01

    Lung cancer is the leading cause of cancer death in the United States. Gene alterations are significant in lung tumorigenesis, with certain genes (Kristen rat sarcoma viral oncogene homolog (KRAS), epidermal growth factor receptor [EGFR], anaplastic lymphoma kinase [ALK], and B-Raf proto-oncogene, serine/threonine kinase (BRAF)) possessing alterations important in the prognosis and treatment of lung adenocarcinoma. Mutation frequencies are affected by different patient factors, such as smoking history, age, and race. Because most lung cancers occur in patients older than age of 50 years, few studies have examined molecular alterations present in these younger patients. The pathology database was searched for patients age of 50 years or younger with non-small cell lung carcinomas (NSCLCs) tested for EGFR, ALK, KRAS, and/or BRAF alterations. A total of 53 cases were identified. The mean patient age was 44.4 years old, and there were 19 men and 34 women. Of the tumors, 11.6% had ALK rearrangements, 25.5% had KRAS mutations, and 20.0% had EGFR mutations. No BRAF mutations were identified in the 28 cases tested. All but 1 (92% [12/13]) tumor with KRAS mutation were from women patients. A smoking history of greater than 5 pack-years was associated with KRAS mutations and negatively associated with EGFR mutations and ALK translocation. The frequencies of EGFR mutation and ALK translocation in the study cohort are greater than the reported frequencies among NSCLC from adults of all ages in the United States but less than the reported frequencies among NSCLC from East Asian young adults. The frequency of KRAS mutation is significantly greater than what was previously found in young Japanese patients.

  4. Molecular Characterisation of Small Molecule Agonists Effect on the Human Glucagon Like Peptide-1 Receptor Internalisation

    PubMed Central

    Thompson, Aiysha; Stephens, Jeffrey W.; Bain, Stephen C.

    2016-01-01

    The glucagon-like peptide receptor (GLP-1R), which is a G-protein coupled receptor (GPCR), signals through both Gαs and Gαq coupled pathways and ERK phosphorylation to stimulate insulin secretion. The aim of this study was to determine molecular details of the effect of small molecule agonists, compounds 2 and B, on GLP-1R mediated cAMP production, intracellular Ca2+ accumulation, ERK phosphorylation and its internalisation. In human GLP-1R (hGLP-1R) expressing cells, compounds 2 and B induced cAMP production but caused no intracellular Ca2+ accumulation, ERK phosphorylation or hGLP-1R internalisation. GLP-1 antagonists Ex(9–39) and JANT-4 and the orthosteric binding site mutation (V36A) in hGLP-1R failed to inhibit compounds 2 and B induced cAMP production, confirming that their binding site distinct from the GLP-1 binding site on GLP-1R. However, K334A mutation of hGLP-1R, which affects Gαs coupling, inhibited GLP-1 as well as compounds 2 and B induced cAMP production, indicating that GLP-1, compounds 2 and B binding induce similar conformational changes in the GLP-1R for Gαs coupling. Additionally, compound 2 or B binding to the hGLP-1R had significantly reduced GLP-1 induced intracellular Ca2+ accumulation, ERK phosphorylation and hGLP-1R internalisation. This study illustrates pharmacology of differential activation of GLP-1R by GLP-1 and compounds 2 and B. PMID:27100083

  5. Potentiometric sensors doped with biomolecules as a new approach to small molecule/biomolecule binding kinetics analysis.

    PubMed

    Daems, D; De Wael, K; Vissenberg, K; Van Camp, G; Nagels, L

    2014-04-15

    The most successful binding kinetics analysis systems at this moment include surface plasmon resonance (SPR), quartz microcrystal balance (QMB) and surface acoustic wave (SAW). Although these are powerful methods, they generally are complex, expensive and require the use of monolayers. Here, we report on potentiometric sensors as an inexpensive and simple alternative to do binding kinetics analysis between small molecules in solution and biomolecules (covalently) attached in a biopolymer sensor coating layer. As an example, dopamine and an anti-dopamine aptamer were used as the small molecule and the biomolecule respectively. Binding between both follows a Langmuir adsorption type model and creates a surface potential. The system operates in Flow Injection Analysis mode (FIA). Besides being an interesting new binding kinetics tool, the approach allows systematic design of potentiometric biosensors (in the present study a dopamine sensor), and gives new insights into the functioning of ion-selective electrodes (ISE's).

  6. The improved efficiency of low molecular weight organic solar cells doped with a Cu(I) triplet material

    NASA Astrophysics Data System (ADS)

    Su, Bin; Gao, Lin; Li, Xiuying; Che, Guangbo; Zhu, Enwei; Wang, Bo; Yan, Yongsheng

    2016-08-01

    We developed a method to improve the performance of the copper phthalocyanine (CuPc)/fullerene (C60) organic solar cells (OSCs) by doping CuPc with a long triplet lifetime material. By doping [Cu(bis[2-(diphenylphosphino)phenyl]ether)(benzo[i]dipyrido[3,2-a:2',3'-c]phenazine)]BF4 (CuDB) into CuPc, the enhanced short-circuit current density ( J SC) of 6.213 mA/cm2, open-circuit voltage ( V OC) of 0.39 V and a peak power conversion efficiency (PCE) of 0.92% compared to 0.79% of the standard CuPc/C60 OSCs are achieved under 1 sun AM 1.5 G illumination at an intensity of 100 mW/cm2. The performance improvement is mainly attributed to the long triplet lifetime of CuDB (τ = 70.05 μs) which leads to more effective exciton dissociation.

  7. Molecular ecology of Listeria monocytogenes and other Listeria species in small and very small ready-to-eat meat processing plants.

    PubMed

    Williams, Shanna K; Roof, Sherry; Boyle, Elizabeth A; Burson, Dennis; Thippareddi, Harshavardhan; Geornaras, Ifigenia; Sofos, John N; Wiedmann, Martin; Nightingale, Kendra

    2011-01-01

    A longitudinal study was conducted to track Listeria contamination patterns in ready-to-eat meats from six small or very small meat processing plants located in three states over 1 year. A total of 688 environmental sponge samples were collected from nonfood contact surfaces during bimonthly visits to each plant. Overall, L. monocytogenes was isolated from 42 (6.1%) environmental samples, and its prevalence ranged from 1.7 to 10.8% across different plants. Listeria spp., other than L. monocytogenes, were isolated from 9.5% of samples overall, with the prevalence ranging from 1.5 to 18.3% across different plants. The prevalence of L. monocytogenes correlated well with that of other Listeria spp. for some but not all plants. One L. monocytogenes isolate representing each positive sample was characterized by molecular serotyping, EcoRI ribotyping, and pulsed-field gel electrophoresis typing. Seven sample sites tested positive for L. monocytogenes on more than one occasion, and the same ribotype was detected more than once at five of these sites. Partial sigB sequencing was used to speciate other Listeria spp. isolates and assign an allelic type to each isolate. Other Listeria spp. were isolated more than once from 14 sample sites, and the same sigB allelic type was recovered at least twice from seven of these sites. One plant was colonized by an atypical hemolytic L. innocua strain. Our findings indicate that small and very small meat processing plants that produce ready-to-eat meat products are characterized by a varied prevalence of Listeria, inconsistent correlation between contamination by L. monocytogenes and other Listeria spp., and a unique Listeria molecular ecology.

  8. High-T c superconductivity in potassium-doped fullerene, K xC 60, via coupled C 60 (pπ) cluster molecular orbitals and dynamic Jahn-Teller coupling

    NASA Astrophysics Data System (ADS)

    Johnson, K. H.; McHenry, M. E.; Clougherty, D. P.

    1991-11-01

    Recently observed superconductivity at 18 K in potassium-doped fullerene, K xC 60, may be due to Cooper pairing of partially occupied icosahedral C 60 cluster t 1u (pπ) molecular orbitals, induced by cooperative dynamic Jahn-Teller coupling of these orbitals to “soft-mode” vibrations of the C 60 molecules, leading to a BCS-like mechanism. Predicted are a nonvanishing isotope effect and Tc increasing to 30 K or more with optimization of doping, and significant effects with pressure.

  9. Small molecular glasses based on multiposition encapsulated phenyl benzimidazole iridium(III) complexes: toward efficient solution-processable host-free electrophosphorescent diodes.

    PubMed

    Xu, Hui; Yu, Dong-Hui; Liu, Le-Le; Yan, Peng-Fei; Jia, Li-Wei; Li, Guang-Ming; Yue, Zheng-Yu

    2010-01-14

    Three electrophosphorescent small molecular Ir(3+) complexes, Ir(HexPhBI)(3) 1 (HexPhBI = 1-Hexyl-2-phenyl-1H-benzo[d]imidazole), Ir(CzPhBI)(3) 2 (CzPhBI = 9-(6-(2-phenyl-1H-benzo[d]imidazol-1-yl)hexyl)-9H-carbazole), and Ir(Cz(2)PhBI)(3) 3 (Cz(2)PhBI = 9-(6-(4-(1-(6-(9H-carbazol-9-yl)hexyl)-1H-benzo[d]imidazol-2-yl)phenoxy)hexyl)-9H-carbazole), were synthesized in which 3 was designed with the structure of multiposition encapsulation. Compared to the hexyl-substituted 1, 2 and 3 end-capped with the conjugated carbazole moieties have improved thermal stability. X-ray diffraction analysis proved the amorphous state of 2 and 3. High-photoluminescent efficiencies of 3 are achieved as 72% in solution and 61% in solid. It indicates that the peripheral carbazoles not only facilitate the separation of triplet-emission cores and reduce the intermolecular aggregation but also supply a routine for the intermolecular energy transfer. Electrochemical analysis showed the more oxidation states of 3, which might be anticipated to make it superior to 1 and 2 in hole injection and transporting. The important role of the peripheral carbazole moieties in carrier injection/transporting and the optical properties of the complexes were further investigated by Gaussian simulation. A dramatic electroluminescent (EL) performance, including external quantum efficiency of nearly 6%, low turn-on voltage of 2.5 V, and high brightness over 6000 cd m(-2), from the host-free spin-coated device of 3 was achieved. The superiority of multiencapsulation in EL was proved by comparing the EL performance of 2 and 3. By making comparison between the host-free and phosphor-doping devices, it indicated that the combined modification of the aliphatic chains and functional groups in multipositions is a feasible approach to realize the high-efficiency small molecular phosphorescent materials. PMID:19954149

  10. Molecular dynamics simulation analysis of small-angle neutron scattering by a solution of stearic acid in benzene

    NASA Astrophysics Data System (ADS)

    Eremin, R. A.; Kholmurodov, Kh. T.; Petrenko, V. I.; Rosta, L.; Avdeev, M. V.

    2014-01-01

    Data of small-angle neutron scattering by a diluted solution of stearic acid in deuterated benzene have been analyzed using the results of molecular dynamics simulation. The molecular dynamics simulation approach has been used to calculate the time-averaged distribution of the neutron scattering length density at the interface between the acid molecule and the solvent. It has been shown that the organization of the solvent at the interface with the acid molecule leads to a modulation of the neutron scattering length density and makes a significant contribution to the scattering. This contribution should be taken into account when interpreting the experimental small-angle neutron scattering curves for both the considered system and its analogues.

  11. Molecular diagnostics for infectious disease in small animal medicine: an overview from the laboratory.

    PubMed

    Daniels, Joshua B

    2013-11-01

    Molecular diagnostic tests have augmented the way in which veterinary practitioners approach the diagnosis of infectious disease. The technical bases of these tests are explained in addition to the general clinical applications for which they are most aptly suited, as individual assays are best discussed in the context of their respective diseases. In this article, an emphasis is placed on validation of molecular tests so that practitioners can be educated consumers of molecular diagnostics. The relationships between disease prevalence and positive and negative predictive values are discussed. Finally, examples of the pitfalls of multiplex polymerase chain reaction testing are illustrated.

  12. Measurement of Small Molecular Dopant F4TCNQ and C60F36 Diffusion in Organic Bilayer Architectures.

    PubMed

    Li, Jun; Rochester, Chris W; Jacobs, Ian E; Friedrich, Stephan; Stroeve, Pieter; Riede, Moritz; Moulé, Adam J

    2015-12-30

    The diffusion of molecules through and between organic layers is a serious stability concern in organic electronic devices. In this work, the temperature-dependent diffusion of molecular dopants through small molecule hole transport layers is observed. Specifically we investigate bilayer stacks of small molecules used for hole transport (MeO-TPD) and p-type dopants (F4TCNQ and C60F36) used in hole injection layers for organic light emitting diodes and hole collection electrodes for organic photovoltaics. With the use of absorbance spectroscopy, photoluminescence spectroscopy, neutron reflectometry, and near-edge X-ray absorption fine structure spectroscopy, we are able to obtain a comprehensive picture of the diffusion of fluorinated small molecules through MeO-TPD layers. F4TCNQ spontaneously diffuses into the MeO-TPD material even at room temperature, while C60F36, a much bulkier molecule, is shown to have a substantially higher morphological stability. This study highlights that the differences in size/geometry and thermal properties of small molecular dopants can have a significant impact on their diffusion in organic device architectures. PMID:26673846

  13. Simple and Sensitive Molecularly Imprinted Polymer - Mn-Doped ZnS Quantum Dots Based Fluorescence Probe for Cocaine and Metabolites Determination in Urine.

    PubMed

    Chantada-Vázquez, María Pilar; Sánchez-González, Juan; Peña-Vázquez, Elena; Tabernero, María Jesús; Bermejo, Ana María; Bermejo-Barrera, Pilar; Moreda-Piñeiro, Antonio

    2016-03-01

    A new molecularly imprinted polymer (MIP)-based fluorescent artificial receptor has been prepared by anchoring a selective MIP for cocaine (COC) on the surface of polyethylene glycol (PEG) modified Mn-doped ZnS quantum dots (QDs). The prepared material combines the high selectivity attributed to MIPs and the sensitive fluorescent property of the Mn-doped ZnS QDs. Simple and low cost methods have therefore been optimized for assessing cocaine abuse in urine by monitoring the fluorescence quenching when the template (COC) and also metabolites from COC [benzoylecgonine (BZE) and ecgonine methyl ester (EME)] are present. Fluorescence quenching was not observed when performing experiments with other drugs of abuse (and their metabolites) or when using nonimprinted polymer (NIP)-coated QDs. Under optimized operating conditions (1.5 mL of 200 mg L(-1) MIP-coated QDs solution, pH 5.5, and 15 min before fluorescence scanning) two analytical methods were developed/validated. One of the procedures (direct method) consisted of urine sample 1:20 dilution before fluorescence measurements. The method has been found to be fast, precise, and accurate, but the standard addition technique for performing the analysis was required because of the existence of matrix effect. The second procedure performed a solid phase extraction (SPE) first, avoiding matrix effect and allowing external calibration. The limits of detection of the methods were 0.076 mg L(-1) (direct method) and 0.0042 mg L(-1) (SPE based method), which are lower than the cutoff values for confirmative conclusions regarding cocaine abuse. PMID:26857857

  14. A new molecular precursor route for the synthesis of Bi-Y, Y-Nb and Bi-doped Y-Nb oxides at moderate temperatures

    SciTech Connect

    Bayot, D.A.; Dupont, A.M.; Devillers, Michel M.

    2007-03-15

    Yttrium-based multimetallic oxides containing bismuth and/or niobium were prepared by a method starting from pre-isolated stable water-soluble precursors which are complexes with the ethylenediaminetetraacetate ligand (edta). The cubic Bi{sub 1-} {sub x} Y {sub x} O{sub 1.5} (x=0.22, 0.25 and 0.3) and Y{sub 3}NbO{sub 7} oxides were obtained in a pure form in a range of moderate temperatures (600-650 deg. C). This preparation method also allowed to stabilize at room temperature, without quenching, the tetragonal YNbO{sub 4} oxide in a distorted form (T'-phase) by calcining the precursor at 800 deg. C. When heated up to 1000 deg. C, this metastable T'-phase transforms into the metastable 'high-temperature' T oxide, which converts on cooling down to room temperature into the thermodynamically stable monoclinic M oxide. Doping the YNbO{sub 4} oxide with Bi{sup 3+} cations (0.5% and 1% Bi with respect to total Bi+Y amount) led at 800 deg. C to a mixture of the T'-phase and the thermodynamically stable monoclinic one. At 900 deg. C, the almost pure monoclinic structure was obtained. - Graphical abstract: Bi-Y, Nb-Y and Bi-doped Nb-Y oxides were prepared by a molecular precursors method from pre-isolated water-soluble edta-based complexes. The cubic Bi{sub 1-} {sub x} Y {sub x} O{sub 1.5} and Y{sub 3}NbO{sub 7} oxides were obtained in a pure form at the moderate temperature of 650 deg. C. A distorted tetragonal YNbO{sub 4} phase was also stabilized at room temperature by calcining the precursor at 800 deg. C, and the pure corresponding monoclinic oxide has been obtained near 1100 deg. C.

  15. Structural Evolution of Polylactide Molecular Bottlebrushes: Kinetics Study by Size Exclusion Chromatography, Small Angle Neutron Scattering and Simulations

    SciTech Connect

    Pickel, Deanna L; Kilbey, II, S Michael; Uhrig, David; Hong, Kunlun; Carrillo, Jan-Michael Y; Sumpter, Bobby G; Ahn, Suk-Kyun; Han, Youngkyu; Kim, Dr. Tae-Hwan; Smith, Gregory Scott; Do, Changwoo

    2014-01-01

    Structural evolution from poly(lactide) (PLA) macromonomer to resultant PLA molecular bottlebrush during ring opening metathesis polymerization (ROMP) was investigated for the first time by combining size exclusion chromatography (SEC), small-angle neutron scattering (SANS) and coarse-grained molecular dynamics (CG-MD) simulations. Multiple aliquots were collected at various reaction times during ROMP, and subsequently analyzed by SEC and SANS. The two complementary techniques enable the understanding of systematic changes in conversion, molecular weight and dispersity as well as structural details of PLA molecular bottlebrushes. CG-MD simulation not only predicts the experimental observations, but it also provides further insight into the analysis and interpretation of data obtained in SEC and SANS experiments. We find that PLA molecular bottlebrushes undergo three conformational transitions with increasing conversion (i.e., increasing the backbone length): (1) from an elongated to a globular shape due to longer side chain at lower conversion, (2) from a globular to an elongated shape at intermediate conversion caused by excluded volume of PLA side chain, and (3) the saturation of contour length at higher conversion due to chain transfer reactions.

  16. Fabrication of water-dispersible and highly conductive PSS-doped PANI/graphene nanocomposites using a high-molecular weight PSS dopant and their application in H2S detection.

    PubMed

    Cho, Sunghun; Lee, Jun Seop; Jun, Jaemoon; Kim, Sung Gun; Jang, Jyongsik

    2014-12-21

    This work describes the fabrication of poly(4-styrenesulfonic acid)-doped polyaniline/graphene (PSS-doped PANI/graphene) nanocomposites and their use as sensing elements for hydrogen sulfide (H2S) detection. PSS with a weight-average molecular weight (Mw) of 1.96 × 10(6) was synthesized using low-temperature free-radical polymerization. The PSS was used as both a doping agent and a binding agent for the polymerization of aniline monomers in a biphasic system (water-chloroform) at -50 °C. The high Mw of PSS resulted in relatively large particle sizes and smooth surfaces of the PSS-doped PANI. These physical characteristics, in turn, resulted in low interparticle resistance and high conductivity. In addition, the PSS allowed homogeneous dispersion of reduced graphene sheets through electrostatic repulsion. The prepared PSS-doped PANI/graphene solutions showed good compatibility with flexible poly(ethylene terephthalate) (PET) substrates, making them suitable for flexible sensor electrodes. Changes in the charge-transport properties, such as protonation level, conjugation length, crystalline structure, and charge-transfer resistance, of the electrode materials were the main factors influencing the electrical and sensor performance of the PSS-doped PANI-based electrodes. PSS-doped PANI/graphene composites containing 30 wt% graphene showed the highest conductivity (168.4 S cm(-1)) and the lowest minimum detection level (MDL) for H2S gas (1 ppm). This result is consistent with the observed improvements in charge transport in the electrode materials via strong π-π stacking interactions between the PANI and the graphene sheets.

  17. Molecular Origin of Properties of Organic-Inorganic Hybrid Perovskites: The Big Picture from Small Clusters.

    PubMed

    Fang, Hong; Jena, Puru

    2016-04-21

    We show that the electronic properties, including the band gap, the gap deformation potential, and the exciton binding energy as well as the chemical stability of organic-inorganic hybrid perovskites can be traced back to their corresponding molecular motifs. This understanding allows one to quickly estimate the properties of the bulk semiconductors from their corresponding molecular building blocks. New hybrid perovskite admixtures are proposed by replacing halogens with superhalogens having compatible ionic radii. The mechanism of the boron-hydride based hybrid perovskite reacting with water is investigated by using a cluster model. PMID:27064550

  18. Infrared absorption spectra of molecular crystals: Possible evidence for small-polaron formation?

    NASA Astrophysics Data System (ADS)

    Pržulj, Željko; Čevizović, Dalibor; Zeković, Slobodan; Ivić, Zoran

    2008-09-01

    The temperature dependence of the position of the so-called anomalous band peaked at 1650cm in the IR-absorption spectrum of crystalline acetanilide (ACN) is theoretically investigated within the small-polaron theory. Its pronounced shift towards the position of the normal band is predicted with the rise of temperature. Interpretation of the IR-absorption spectra in terms of small-polaron model has been critically assessed on the basis of these results.

  19. Methods for Doping Detection.

    PubMed

    Ponzetto, Federico; Giraud, Sylvain; Leuenberger, Nicolas; Boccard, Julien; Nicoli, Raul; Baume, Norbert; Rudaz, Serge; Saugy, Martial

    2016-01-01

    Over the past few years, the World Anti-Doping Agency (WADA) has focused its efforts on detecting not only small prohibited molecules, but also larger endogenous molecules such as hormones, in the view of implementing an endocrinological module in the Athlete Biological Passport (ABP). In this chapter, the detection of two major types of hormones used for doping, growth hormone (GH) and endogenous anabolic androgenic steroids (EAASs), will be discussed: a brief historical background followed by a description of state-of-the-art methods applied by accredited anti-doping laboratories will be provided and then current research trends outlined. In addition, microRNAs (miRNAs) will also be presented as a new class of biomarkers for doping detection. PMID:27348309

  20. Molecular aptamer beacon tuned DNA strand displacement to transform small molecules into DNA logic outputs.

    PubMed

    Zhu, Jinbo; Zhang, Libing; Zhou, Zhixue; Dong, Shaojun; Wang, Erkang

    2014-03-28

    A molecular aptamer beacon tuned DNA strand displacement reaction was introduced in this work. This strand displacement mode can be used to transform the adenosine triphosphate (ATP) input into a DNA strand output signal for the downstream gates to process. A simple logic circuit was built on the basis of this mechanism.

  1. The small contribution of molecular Bremsstrahlung radiation to the air-fluorescence yield of cosmic ray shower particles

    NASA Astrophysics Data System (ADS)

    Al Samarai, Imen; Deligny, Olivier; Rosado, Jaime

    2016-10-01

    A small contribution of molecular Bremsstrahlung radiation to the air-fluorescence yield in the UV range is estimated based on an approach previously developed in the framework of the radio-detection of showers in the gigahertz frequency range. First, this approach is shown to provide an estimate of the main contribution of the fluorescence yield due to the de-excitation of the C 3Πu electronic level of nitrogen molecules to the B 3Πg one amounting to Y[ 337 ] =(6.05 ± 1.50) MeV-1 at 800 hPa pressure and 293 K temperature conditions, which compares well to previous dedicated works and to experimental results. Then, under the same pressure and temperature conditions, the fluorescence yield induced by molecular Bremsstrahlung radiation is found to be Y[330-400]MBR = 0.10 MeV-1 in the wavelength range of interest for the air-fluorescence detectors used to detect extensive air showers induced in the atmosphere by ultra-high energy cosmic rays. This means that out of ≃175 photons with wavelength between 330 and 400 nm detected by fluorescence detectors, one of them has been produced by molecular Bremsstrahlung radiation. Although small, this contribution is not negligible in regards to the total budget of systematic uncertainties when considering the absolute energy scale of fluorescence detectors.

  2. Correlation between molecular structure and self-healing in a series of Anthraquinone derivatives doped in PMMA polymer

    NASA Astrophysics Data System (ADS)

    Dhakal, P.; Ramini, S. K.; Kuzyk, Mark G.

    2012-10-01

    We observe that many different derivatives of anthraquinone chromophores doped in PMMA self heal after undergoing photodegradation. We are interested to know the mechanisms that are responsible for photodegradation and photorecovery, which are not yet fully understood. We used fluorescence and absorption spectroscopy as a probe of the photodegradation and recovery process while the temperature dependence is used to determine the energies of the species involved. We hypothesize that the host polymer mediates the formation of a quasi-stable state. In this scenario, once photo - damaged by intense pump laser, the molecules non radiatively decay into a tautomer state by intra molecule proton transfer, which subsequently leads to the formation of a damaged species - leading to decay of the fluorescence intensity. This hypothesis is consistent with our observation. The temperature dependent fluorescence decay and recovery studies give an insight about the different energy levels participating in optical excitation, decay and recovery. Comparing the experimental parameters such as decay and recovery rates of the fluorescence signal associated with the evolution of peaks in the fluorescence and absorbance spectrum helps us understand correlations between the efficiency of the recovery process and the structures of the dye molecules. Based on the temperature and the time-dependent observations of fluorescence and absorption, we validate qualitatively a new theoretical model which qualitatively takes into account the observed behavior and sheds light on the underlying mechanism. Preliminary measurements show good agreement with the theoretical model. More careful experiments and calculations are in process for further validation of the model.

  3. Effects of nitrogen-doped multi-walled carbon nanotubes compared to pristine multi-walled carbon nanotubes on human small airway epithelial cells.

    PubMed

    Mihalchik, Amy L; Ding, Weiqiang; Porter, Dale W; McLoughlin, Colleen; Schwegler-Berry, Diane; Sisler, Jennifer D; Stefaniak, Aleksandr B; Snyder-Talkington, Brandi N; Cruz-Silva, Rodolfo; Terrones, Mauricio; Tsuruoka, Shuji; Endo, Morinobu; Castranova, Vincent; Qian, Yong

    2015-07-01

    Nitrogen-doped multi-walled carbon nanotubes (ND-MWCNTs) are modified multi-walled carbon nanotubes (MWCNTs) with enhanced electrical properties that are used in a variety of applications, including fuel cells and sensors; however, the mode of toxic action of ND-MWCNT has yet to be fully elucidated. In the present study, we compared the interaction of ND-MWCNT or pristine MWCNT-7 with human small airway epithelial cells (SAEC) and evaluated their subsequent bioactive effects. Transmission electron microscopy, X-ray photoelectron spectroscopy, Raman spectroscopy, and X-ray diffraction suggested the presence of N-containing defects in the lattice of the nanotube. The ND-MWCNTs were determined to be 93.3% carbon, 3.8% oxygen, and 2.9% nitrogen. A dose-response cell proliferation assay showed that low doses of ND-MWCNT (1.2μg/ml) or MWCNT-7 (0.12μg/ml) increased cellular proliferation, while the highest dose of 120μg/ml of either material decreased proliferation. ND-MWCNT and MWCNT-7 appeared to interact with SAEC at 6h and were internalized by 24h. ROS were elevated at 6 and 24h in ND-MWCNT exposed cells, but only at 6h in MWCNT-7 exposed cells. Significant alterations to the cell cycle were observed in SAEC exposed to either 1.2μg/ml of ND-MWCNT or MWCNT-7 in a time and material-dependent manner, possibly suggesting potential damage or alterations to cell cycle machinery. Our results indicate that ND-MWCNT induce effects in SAEC over a time and dose-related manner which differ from MWCNT-7. Therefore, the physicochemical characteristics of the materials appear to alter their biological effects.

  4. Effects of nitrogen-doped multi-walled carbon nanotubes compared to pristine multi-walled carbon nanotubes on human small airway epithelial cells

    PubMed Central

    Mihalchik, Amy L.; Ding, Weiqiang; Porter, Dale W.; McLoughlin, Colleen; Schwegler-Berry, Diane; Sisler, Jennifer D.; Stefaniak, Aleksandr B.; Snyder-Talkington, Brandi N.; Cruz-Silva, Rodolfo; Terrones, Mauricio; Tsuruoka, Shuji; Endo, Morinobu; Castranova, Vincent; Qian, Yong

    2015-01-01

    Nitrogen-doped multi-walled carbon nanotubes (ND-MWCNTs) are modified multi-walled carbon nanotubes (MWCNTs) with enhanced electrical properties that are used in a variety of applications, including fuel cells and sensors; however, the mode of toxic action of ND-MWCNT has yet to be fully elucidated. In the present study, we compared the interaction of ND-MWCNT or pristine MWCNT-7 with human small airway epithelial cells (SAEC) and evaluated their subsequent bioactive effects. Transmission electron microscopy, X-ray photoelectron spectroscopy, Raman spectroscopy, and X-ray diffraction suggested the presence of N-containing defects in the lattice of the nanotube. The ND-MWCNTs were determined to be 93.3% carbon, 3.8% oxygen, and 2.9% nitrogen. A dose–response cell proliferation assay showed that low doses of ND-MWCNT (1.2 mg/ml) or MWCNT-7 (0.1 mg/ml) increased cellular proliferation, while the highest dose of 120 mg/ml of either material decreased proliferation. ND-MWCNT and MWCNT-7 appeared to interact with SAEC at 6 h and were internalized by 24 h. ROS were elevated at 6 and 24 h in ND-MWCNT exposed cells, but only at 6 h in MWCNT-7 exposed cells. Significant alterations to the cell cycle were observed in SAEC exposed to either 1.2 mg/ml of ND-MWCNT or MWCNT-7 in a time and material-dependent manner, possibly suggesting potential damage or alterations to cell cycle machinery. Our results indicate that ND-MWCNT induce effects in SAEC over a time and dose-related manner which differ from MWCNT-7. Therefore, the physicochemical characteristics of the materials appear to alter their biological effects. PMID:25797581

  5. Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches.

    PubMed

    Mills, Jeffrey D; Ben-Nun, Michal; Rollin, Kyle; Bromley, Michael W J; Li, Jiabo; Hinde, Robert J; Winstead, Carl L; Sheehy, Jeffrey A; Boatz, Jerry A; Langhoff, Peter W

    2016-08-25

    Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an "ex-post-facto" method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions. The general theory in its various forms incorporates the early semiempirical atoms- and diatomics-in-molecules approaches of Moffitt, Ellison, Tully, Kuntz, and others in a comprehensive mathematical setting, and generalizes the developments of Eisenschitz, London, Claverie, and others addressing electron permutation symmetry adaptation issues, completing these early attempts to treat van der Waals and chemical forces on a common basis. Exact expressions are obtained for molecular Hamiltonian matrices and for associated energy eigenvalues as sums of separate atomic and interaction-energy terms, similar in this respect to the forms of classical force fields. The latter representation is seen to also provide a long-missing general definition of the energies of individual atoms and of their interactions within molecules and matter free from subjective additional constraints. A computer code suite is described for calculations of the many-electron atomic eigenspectra and

  6. Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches.

    PubMed

    Mills, Jeffrey D; Ben-Nun, Michal; Rollin, Kyle; Bromley, Michael W J; Li, Jiabo; Hinde, Robert J; Winstead, Carl L; Sheehy, Jeffrey A; Boatz, Jerry A; Langhoff, Peter W

    2016-08-25

    Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an "ex-post-facto" method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions. The general theory in its various forms incorporates the early semiempirical atoms- and diatomics-in-molecules approaches of Moffitt, Ellison, Tully, Kuntz, and others in a comprehensive mathematical setting, and generalizes the developments of Eisenschitz, London, Claverie, and others addressing electron permutation symmetry adaptation issues, completing these early attempts to treat van der Waals and chemical forces on a common basis. Exact expressions are obtained for molecular Hamiltonian matrices and for associated energy eigenvalues as sums of separate atomic and interaction-energy terms, similar in this respect to the forms of classical force fields. The latter representation is seen to also provide a long-missing general definition of the energies of individual atoms and of their interactions within molecules and matter free from subjective additional constraints. A computer code suite is described for calculations of the many-electron atomic eigenspectra and

  7. A Biphasic Pleural Tumor with Features of an Epithelioid and Small Cell Mesothelioma: Morphologic and Molecular Findings

    PubMed Central

    2016-01-01

    Malignant mesotheliomas are generally classified into epithelioid, sarcomatoid, desmoplastic, and biphasic types with rare reports of a small cell form. These small cell variants display some morphologic overlap with desmoplastic small round cell tumors (DSRCTs) which generally occur within the abdominal cavity of young males and are defined by a characteristic t(11;22)(p13;q12) translocation. However, there are rare reports of DSRCTs lacking this translocation. We present a 78-year-old man with a pleura-based biphasic neoplasm with features of both epithelioid mesothelioma and a small cell blastema-like neoplasm. The epithelioid portion showed IHC reactivity for pan cytokeratin, CK5/6, D2-40, and calretinin and the small cell portion marked with CD99, pan cytokeratin, WT1, FLI1, S100, CD200, MyoD1, and CD15. Fluorescence in situ hybridization testing for the t(11;22)(p13;q12) translocation disclosed loss of the EWSR1 gene in 94% of tumor cell nuclei, but there was no evidence of the classic translocation. Array based-comparative genomic hybridization (a-CGH) confirmed the tumor had numerous chromosome copy number losses, including 11p15.5-p11.12 and 22q12.1-q13.33, with loss of the EWSR1 and WT1 gene regions. Herein, we report novel complex CGH findings in a biphasic tumor and review the molecular genetic alterations in both mesothelioma and DSRCTs. PMID:27403364

  8. Syntheses of D-A-A Type Small Molecular Donor Materials Having Various Electron Accepting Moiety for Organic Photovoltaic Application.

    PubMed

    Kim, Nahyeon; Park, Sangman; Lee, Myong-Hoon; Lee, Jaemin; Lee, Changjin; Yoon, Sung Cheol

    2016-03-01

    Small molecular donor, DTDCTB achieved a high power conversion efficiency (PCE) value of 6.6 ± 0.2% in vacuum-deposited planar mixed heterojunction (PMHJ) structure. However, the same material just recorded PCE of 0.34% in solution processed small molecule based bulk heterjunction (BHJ) organic photovoltaic cells. For the improvement of organic photovoltaic cells (OPVs), In this study, we designed and synthesized several D-A-A (donor-acceptor-acceptor) type molecular electron donating materials. Ditolylaminothienyl moiety as an electron donating group connected to 1,2,5-benzothiadiazole as a conjugated electron accepting unit, simultaneously with an electron accepting terminal group such as cyano alkyl acetate and N-alkyl rhodanine. The thermal, photophysical, and electrochemical properties of prepared small molecules were investigated by DSC, UV/Vis spectroscopy and Cyclic Voltametry, respectively. As a result, 0.89% of PCE can be obtained from OPV using a mixture of DTATBTER and PCBM as an active layer with a Voc of 0.87 V, a Jsc of 3.20 mA/cm2, and a fill factor of 31.9%. PMID:27455734

  9. Molecular genetics of pediatric brain stem gliomas. Application of PCR techniques to small and archival brain tumor specimens

    SciTech Connect

    Louis, D.N.; Rubio, M.P.; Correa, K.M.; Gusella, J.F.; Deimling, A. von )

    1993-09-01

    Brain stem gliomas are pediatric astrocytomas that histologically resemble adult supratentorial astrocytomas such as gliobastomas multiforme (GBM). The molecular genetic studies have suggested that adult GBM can be divided into two genetic subsets: Tumors with p53 tumor suppressor gene mutations and chromosome 17p loss that occur more commonly in younger patients; and tumors with epidermal growth factor receptor (EGFR) gene amplification that occur more commonly in older patients. Brain stem gliomas have not been studied since biopsies of these tumors are rare and extremely small. The authors investigated the molecular genetic composition of seven brain stem glioblastomas (two small biopsies, five autopsies) using polymerase chain reaction (PCR) assays for chromosomal loss, gene mutation and gene amplification. Four cases lost portions of chromosome 17p that included the 53p gene. These four cases and one additional case had mutations in the p53 gene. None of the cases showed amplification of the EGFR gene. Allelic losses of the long arm of chromosome 10 were noted in four cases. These results suggest similarities between pediatric brain stem glioblastomas and those GBM that occur in younger adult patients, and confirm the utility of PCR-based means of studying small and archival brain tumor specimens. 47 refs., 7 figs., 2 tabs.

  10. Syntheses of D-A-A Type Small Molecular Donor Materials Having Various Electron Accepting Moiety for Organic Photovoltaic Application.

    PubMed

    Kim, Nahyeon; Park, Sangman; Lee, Myong-Hoon; Lee, Jaemin; Lee, Changjin; Yoon, Sung Cheol

    2016-03-01

    Small molecular donor, DTDCTB achieved a high power conversion efficiency (PCE) value of 6.6 ± 0.2% in vacuum-deposited planar mixed heterojunction (PMHJ) structure. However, the same material just recorded PCE of 0.34% in solution processed small molecule based bulk heterjunction (BHJ) organic photovoltaic cells. For the improvement of organic photovoltaic cells (OPVs), In this study, we designed and synthesized several D-A-A (donor-acceptor-acceptor) type molecular electron donating materials. Ditolylaminothienyl moiety as an electron donating group connected to 1,2,5-benzothiadiazole as a conjugated electron accepting unit, simultaneously with an electron accepting terminal group such as cyano alkyl acetate and N-alkyl rhodanine. The thermal, photophysical, and electrochemical properties of prepared small molecules were investigated by DSC, UV/Vis spectroscopy and Cyclic Voltametry, respectively. As a result, 0.89% of PCE can be obtained from OPV using a mixture of DTATBTER and PCBM as an active layer with a Voc of 0.87 V, a Jsc of 3.20 mA/cm2, and a fill factor of 31.9%.

  11. Molecular overlap in the regulation of SK channels by small molecules and phosphoinositides

    PubMed Central

    Zhang, Miao; Meng, Xuan-Yu; Zhang, Ji-fang; Cui, Meng; Logothetis, Diomedes E.

    2015-01-01

    Phosphatidylinositol 4,5-bisphosphate (PIP2) directly interacts with the small-conductance Ca2+-activated K+ 2-a (SK2-a) channel/calmodulin complex, serving as a critical element in the regulation of channel activity. We report that changes of protein conformation in close proximity to the PIP2 binding site induced by a small-molecule SK channel modulator, NS309, can effectively enhance the interaction between the protein and PIP2 to potentiate channel activity. This novel modulation of PIP2 sensitivity by small-molecule drugs is likely not to be limited in its application to SK channels, representing an intriguing strategy to develop drugs controlling the activity of the large number of PIP2-dependent proteins. PMID:26366439

  12. Molecular imaging of small animals with a triple-head SPECT system using pinhole collimation.

    PubMed

    Metzler, S D; Jaszczak, R J; Patil, N H; Vemulapalli, S; Akabani, G; Chin, B B

    2005-07-01

    Pinhole collimation yields high sensitivity when the distance from the object to the aperture is small, as in the case of imaging small animals. Fine-resolution images may be obtained when the magnification is large since this mitigates the effect of detector resolution. Large magnifications in pinhole single-photon emission computed tomography (SPECT) may be obtained by using a collimator whose focal length is many times the radius of rotation. This may be achieved without truncation if the gamma camera is large. We describe a commercially available clinical scanner mated with pinhole collimation and an external linear stage. The pinhole collimation gives high magnification. The linear stage allows for helical pinhole SPECT. We have used the system to image radiolabeled molecules in phantoms and small animals.

  13. Molecular targets in the treatment of non-small-cell lung cancer: is there hope on the horizon?

    PubMed

    Carter, Corey A; Nations, Joel Anthony; Lazarus, Angeline

    2014-11-01

    Non-small-cell lung cancer (NSCLC) is a growing concern worldwide, and its incidence continues to increase in developing countries. It has a strong association with smoking. Lung cancer remains the leading cause of cancer-related deaths in most industrialized countries and in the United States. In the last 10 years, there have been significant advancements in the understanding of molecular oncogenes and how they play a role in driving lung cancer to both grow and metastasize. Understanding this rapidly expanding field has the potential to extend life, and it is an important field for all providers to conceptualize if they are treating patients with lung cancer. Currently, > 50% of all NSCLC is linked to 1 of several known genetic driver mutations. Using online databases, expert opinion, and practice-changing trials, we review the current standards of molecular testing of NSCLC and the expanding evidence of oncogenic drivers in nonsquamous NSCLC.

  14. Molecular docking studies of Traditional Chinese Medicinal compounds against known protein targets to treat non-small cell lung carcinomas

    PubMed Central

    Zhao, Guo-Fang; Huang, Zuo-An; Du, Xue-Kui; Yang, Ming-Lei; Huang, Dan-Dan; Zhang, Shun

    2016-01-01

    In silico drug design using virtual screening, absorption, distribution, metabolism and excretion (ADME)/Tox data analysis, automated docking and molecular dynamics simulations for the determination of lead compounds for further in vitro analysis is a cost effective strategy. The present study used this strategy to discover novel lead compounds from an in-house database of Traditional Chinese Medicinal (TCM) compounds against epithelial growth factor receptor (EGFR) protein for targeting non-small cell lung cancer (NSCLC). After virtual screening of an initial dataset of 2,242 TCM compounds, leads were identified based on binding energy and ADME/Tox data and subjected to automated docking followed by molecular dynamics simulation. Triptolide, a top compound identified by this vigorous in silico screening, was then tested in vitro on the H2347 cell line carrying wild-type EGFR, revealing an anti-proliferative potency similar to that of known drugs against NSCLC. PMID:27279494

  15. Molecular analysis of lungworms from European bison (Bison bonasus) on the basis of small subunit ribosomal RNA gene (SSU).

    PubMed

    Pyziel, Anna M

    2014-03-01

    Dictyocaulosis (Nematoda: Trichostrongyloidea) is a widespread parasitosis of the European bison (Bison bonasus) inhabiting Bialowieza Primeval Forest. Bearing in mind the current coexistence of bison with wild cervids, and with domestic ruminants in the 19th and 20th century, the need arose for molecular identification of lungworm species. Molecular analysis was done on adult lungworms that were obtained from the respiratory track of four free-roaming bison euthanized as a part of the population health control program. As the result of the study four identical small subunit-ribosomal RNA gene sequences from the lungworms were obtained and deposited in GenBank as sequence, 1708 bp long (GenBank KC771250). Comparative analysis of the SSU rRNA sequences revealed the European bison to be a host for the bovine lungworm Dictyocaulus viviparus.

  16. Small-scale structure and chemical differentiation in the central region of the Sagittarius B2 molecular cloud

    SciTech Connect

    Goldsmith, P.F.; Snell, R.L.; Hasegawa, T.; Ukita, N.

    1987-03-01

    Fifteen arcsec angular resolution observations of a number of molecular species in the center of the Sgr B2 molecular cloud, including HC3N in the ground and v7 = 1 vibrational states, SO, OCS,l and HNCO, have been performed. Emission from HC3N is fairly uniformly distributed over the region studied; SO and OCS have a spatially extended component but are strongly centrally peaked. HNCO and vibrationally excited HC/sub 3/N emission are essentially restricted to a very small region around the center of activity in the north. The difference between the spatial distributions are attributed to variation in the chemical abundances of the various clumps. The excitation requirements of the vibrationally excited HC/sub 3/N imply the presence of dust and gas at high temperatures. The results further heighten the apparent contradiction presented by the lack of infrared emission from this source. 53 references.

  17. A highly efficient molecular cloning platform that utilises a small bacterial toxin gene.

    PubMed

    Mok, Wendy W K; Li, Yingfu

    2013-04-15

    Molecular cloning technologies that have emerged in recent years are more efficient and simpler to use than traditional strategies, but many have the disadvantages of requiring multiple steps and expensive proprietary enzymes. We have engineered cloning vectors containing variants of IbsC, a 19-residue toxin from Escherichia coli K-12. These toxic peptides offer selectivity to minimise the background, labour, and cost associated with conventional molecular cloning. As demonstrated with the cloning of reporter genes, this "detox cloning" system consistently produced over 95 % positive clones. Purification steps between digestion and ligation are not necessary, and the total time between digestion and plating of transformants can be as little as three hours. Thus, these IbsC-based cloning vectors are as reliable and amenable to high-throughput cloning as commercially available systems, and have the advantage of being more time-efficient and cost-effective. PMID:23512843

  18. Molecular Testing for Treatment of Metastatic Non-Small Cell Lung Cancer: How to Implement Evidence-Based Recommendations

    PubMed Central

    Chioda, Marc D.; Herndon, Dana; Longshore, John W.; Mohamed, Mohamed; Ou, Sai-Hong Ignatius; Reynolds, Craig; Singh, Jaspal; Wistuba, Ignacio I.; Bunn, Paul A.; Hirsch, Fred R.

    2015-01-01

    The recent discovery of relevant biomarkers has reshaped our approach to therapy selection for patients with non-small cell lung cancer. The unprecedented outcomes demonstrated with tyrosine kinase inhibitors in molecularly defined cohorts of patients has underscored the importance of genetic profiling in this disease. Despite published guidelines on biomarker testing, successful tumor genotyping faces significant hurdles at both academic and community-based practices. Oncologists are now faced with interpreting large-scale genomic data from multiple tumor types, possibly making it difficult to stay current with practice standards in lung cancer. In addition, physicians’ lack of time, resources, and face-to-face opportunities can interfere with the multidisciplinary approach that is essential to delivery of care. Finally, several challenges exist in optimizing the amount and quality of tissue for molecular testing. Recognizing the importance of biomarker testing, a series of advisory boards were recently convened to address these hurdles and clarify best practices. We reviewed these challenges and established recommendations to help optimize tissue acquisition, processing, and testing within the framework of a multidisciplinary approach. Implications for Practice: Although several professional societies have incorporated biomarker testing recommendations into clinical practice guidelines for the diagnosis and management of non-small cell lung cancer (NSCLC), health care providers still face considerable challenges when establishing and implementing these standards. Developing and instituting protocols to ensure that all appropriate patients are tested for molecular biomarkers requires communication among the various specialists involved in the care of patients with NSCLC. This report provides insights into key challenges and recommendations for molecular testing of patients with metastatic NSCLC, summarized from a multidisciplinary team of experts spanning

  19. Molecular phylogeny of Stentor (Ciliophora: Heterotrichea) based on small subunit ribosomal RNA sequences.

    PubMed

    Gong, Ying-Chun; Yu, Yu-He; Zhu, Fei-Yun; Feng, Wei-Song

    2007-01-01

    To determine the phylogenetic position of Stentor within the Class Heterotrichea, the complete small subunit rRNA genes of three Stentor species, namely Stentor polymorphus, Stentor coeruleus, and Stentor roeseli, were sequenced and used to construct phylogenetic trees using the maximum parsimony, neighbor joining, and Bayesian analysis. With all phylogenetic methods, the genus Stentor was monophyletic, with S. roeseli branching basally. PMID:17300519

  20. Molecular characterization and pathogenicity of fungal isolates for use against the small hive beetle (Aethina tumida)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The analysis of DNA sequences from fungal pathogens obtained from cadavers of the small hive beetle (SHB) collected from several apiaries in Florida revealed a mixture of saprobes and two potential primary entomopathogens, Metarhizium anisopliae and Beauveria bassiana. Spray tower bioassays indicate...

  1. Molecular Signature of Pseudomonas aeruginosa with Simultaneous Nanomolar Detection of Quorum Sensing Signaling Molecules at a Boron-Doped Diamond Electrode.

    PubMed

    Buzid, Alyah; Shang, Fengjun; Reen, F Jerry; Muimhneacháin, Eoin Ó; Clarke, Sarah L; Zhou, Lin; Luong, John H T; O'Gara, Fergal; McGlacken, Gerard P; Glennon, Jeremy D

    2016-01-01

    Electroanalysis was performed using a boron-doped diamond (BDD) electrode for the simultaneous detection of 2-heptyl-3-hydroxy-4-quinolone (PQS), 2-heptyl-4-hydroxyquinoline (HHQ) and pyocyanin (PYO). PQS and its precursor HHQ are two important signal molecules produced by Pseudomonas aeruginosa, while PYO is a redox active toxin involved in virulence and pathogenesis. This Gram-negative and opportunistic human pathogen is associated with a hospital-acquired infection particularly in patients with compromised immunity and is the primary cause of morbidity and mortality in cystic fibrosis (CF) patients. Early detection is crucial in the clinical management of this pathogen, with established infections entering a biofilm lifestyle that is refractory to conventional antibiotic therapies. Herein, a detection procedure was optimized and proven for the simultaneous detection of PYO, HHQ and PQS in standard mixtures, biological samples, and P. aeruginosa spiked CF sputum samples with remarkable sensitivity, down to nanomolar levels. Differential pulse voltammetry (DPV) scans were also applicable for monitoring the production of PYO, HHQ and PQS in P. aeruginosa PA14 over 8 h of cultivation. The simultaneous detection of these three compounds represents a molecular signature specific to this pathogen. PMID:27427496

  2. Molecular Signature of Pseudomonas aeruginosa with Simultaneous Nanomolar Detection of Quorum Sensing Signaling Molecules at a Boron-Doped Diamond Electrode

    NASA Astrophysics Data System (ADS)

    Buzid, Alyah; Shang, Fengjun; Reen, F. Jerry; Muimhneacháin, Eoin Ó.; Clarke, Sarah L.; Zhou, Lin; Luong, John H. T.; O’Gara, Fergal; McGlacken, Gerard P.; Glennon, Jeremy D.

    2016-07-01

    Electroanalysis was performed using a boron-doped diamond (BDD) electrode for the simultaneous detection of 2-heptyl-3-hydroxy-4-quinolone (PQS), 2-heptyl-4-hydroxyquinoline (HHQ) and pyocyanin (PYO). PQS and its precursor HHQ are two important signal molecules produced by Pseudomonas aeruginosa, while PYO is a redox active toxin involved in virulence and pathogenesis. This Gram-negative and opportunistic human pathogen is associated with a hospital-acquired infection particularly in patients with compromised immunity and is the primary cause of morbidity and mortality in cystic fibrosis (CF) patients. Early detection is crucial in the clinical management of this pathogen, with established infections entering a biofilm lifestyle that is refractory to conventional antibiotic therapies. Herein, a detection procedure was optimized and proven for the simultaneous detection of PYO, HHQ and PQS in standard mixtures, biological samples, and P. aeruginosa spiked CF sputum samples with remarkable sensitivity, down to nanomolar levels. Differential pulse voltammetry (DPV) scans were also applicable for monitoring the production of PYO, HHQ and PQS in P. aeruginosa PA14 over 8 h of cultivation. The simultaneous detection of these three compounds represents a molecular signature specific to this pathogen.

  3. Molecular Signature of Pseudomonas aeruginosa with Simultaneous Nanomolar Detection of Quorum Sensing Signaling Molecules at a Boron-Doped Diamond Electrode

    PubMed Central

    Buzid, Alyah; Shang, Fengjun; Reen, F. Jerry; Muimhneacháin, Eoin Ó; Clarke, Sarah L.; Zhou, Lin; Luong, John H. T.; O’Gara, Fergal; McGlacken, Gerard P.; Glennon, Jeremy D.

    2016-01-01

    Electroanalysis was performed using a boron-doped diamond (BDD) electrode for the simultaneous detection of 2-heptyl-3-hydroxy-4-quinolone (PQS), 2-heptyl-4-hydroxyquinoline (HHQ) and pyocyanin (PYO). PQS and its precursor HHQ are two important signal molecules produced by Pseudomonas aeruginosa, while PYO is a redox active toxin involved in virulence and pathogenesis. This Gram-negative and opportunistic human pathogen is associated with a hospital-acquired infection particularly in patients with compromised immunity and is the primary cause of morbidity and mortality in cystic fibrosis (CF) patients. Early detection is crucial in the clinical management of this pathogen, with established infections entering a biofilm lifestyle that is refractory to conventional antibiotic therapies. Herein, a detection procedure was optimized and proven for the simultaneous detection of PYO, HHQ and PQS in standard mixtures, biological samples, and P. aeruginosa spiked CF sputum samples with remarkable sensitivity, down to nanomolar levels. Differential pulse voltammetry (DPV) scans were also applicable for monitoring the production of PYO, HHQ and PQS in P. aeruginosa PA14 over 8 h of cultivation. The simultaneous detection of these three compounds represents a molecular signature specific to this pathogen. PMID:27427496

  4. Molecular-beam epitaxial growth and characterization of modulation-doped field-effect transistor heterostructures using InAs/GaAs superlattice channels

    SciTech Connect

    Baeta Moreira, M.V.; Py, M.A.; Ilegems, M.

    1993-05-01

    The molecular-beam epitaxial growth conditions of (N + 1)(InAs){sub m}/N(GaAsw){sub n} short period superlattices (SPSs) on GaAs substrates have been optimized. Hall electrical properties measured by the van der Pauw method were compared to low-temperature photoluminescence (77 K PL) spectra of GaAs/SPS/AlGaAs modulation-doped field-effect transistor-type heterostructures. By using these two characterization methods, the influences of the growth temperature T{sub s}, of the SPS channel thickness d{sub ch} and of its average indium composition y{sub m} were studied. Interesting correlations were established between their optical and their transport properties measured at 77 K either in the dark or under white-light illumination. The thickness m of the InAs layers was varied in the range 0.57 to 1.7 and sharp optimum properties were obtained slightly above m=1 monolayer.

  5. The development of a new optical sensor based on the Mn doped ZnS quantum dots modified with the molecularly imprinted polymers for sensitive recognition of florfenicol.

    PubMed

    Sadeghi, Susan; Jahani, Moslem; Belador, Foroogh

    2016-04-15

    The Mn doped ZnS quantum dots (Mn:ZnS QDs) capped with the florfenicol molecularly imprinted polymer (Mn:ZnS QDs@MIP) were prepared via the sol-gel surface imprinting approach using 3-aminopropyltriethoxysilane (APTES) as the functional monomer and tetraethoxysilane (TEOS) as the cross-linker for the optosensing of the florfenicol. Transmission electron microscopy (TEM), X-ray diffractometer, IR spectroscopy, UV-Vis absorption spectrophotometry, and spectrofluorometry were used to elucidate the formation, morphology, and identification of the products. To illustrate the usefulness of the new imprinted material, the non-imprinted coated Mn:ZnS QDs (Mn:ZnS QDs@NIP) were synthesized without the presence of the florfenicol. It was revealed that the fluorescence (FL) intensity of the Mn:ZnS QDs@MIP increased with increasing the FF concentration. Under the optimal conditions, changes in the FL intensity in the presence of the target molecule showed a linear response in the concentration range of 30-700 μmol L(-1) with a detection limit of 24 μmol L(-1). The developed method was finally applied successfully to the determination of FF in different meat samples with satisfactory recoveries.

  6. The development of a new optical sensor based on the Mn doped ZnS quantum dots modified with the molecularly imprinted polymers for sensitive recognition of florfenicol

    NASA Astrophysics Data System (ADS)

    Sadeghi, Susan; Jahani, Moslem; Belador, Foroogh

    2016-04-01

    The Mn doped ZnS quantum dots (Mn:ZnS QDs) capped with the florfenicol molecularly imprinted polymer (Mn:ZnS QDs@MIP) were prepared via the sol-gel surface imprinting approach using 3-aminopropyltriethoxysilane (APTES) as the functional monomer and tetraethoxysilane (TEOS) as the cross-linker for the optosensing of the florfenicol. Transmission electron microscopy (TEM), X-ray diffractometer, IR spectroscopy, UV-Vis absorption spectrophotometry, and spectrofluorometry were used to elucidate the formation, morphology, and identification of the products. To illustrate the usefulness of the new imprinted material, the non-imprinted coated Mn:ZnS QDs (Mn:ZnS QDs@NIP) were synthesized without the presence of the florfenicol. It was revealed that the fluorescence (FL) intensity of the Mn:ZnS QDs@MIP increased with increasing the FF concentration. Under the optimal conditions, changes in the FL intensity in the presence of the target molecule showed a linear response in the concentration range of 30-700 μmol L- 1 with a detection limit of 24 μmol L- 1. The developed method was finally applied successfully to the determination of FF in different meat samples with satisfactory recoveries.

  7. Efficient new ribozyme mimics: direct mapping of molecular design principles from small molecules to macromolecular, biomimetic catalysts.

    PubMed

    Putnam, W C; Daniher, A T; Trawick, B N; Bashkin, J K

    2001-05-15

    Dramatic improvements in ribozyme mimics have been achieved by employing the principles of small molecule catalysis to the design of macromolecular, biomimetic reagents. Ribozyme mimics derived from the ligand 2,9-dimethylphenanthroline (neocuproine) show at least 30-fold improvements in efficiency at sequence-specific RNA cleavage when compared with analogous o-phenanthroline- and terpyridine-derived reagents. The suppression of hydroxide-bridged dimers and the greater activation of coordinated water by Cu(II) neocuproine (compared with the o-phenanthroline and terpyridine complexes) better allow Cu(II) to reach its catalytic potential as a biomimetic RNA cleavage agent. This work demonstrates the direct mapping of molecular design principles from small-molecule cleavage to macromolecular cleavage events, generating enhanced biomimetic, sequence-specific RNA cleavage agents.

  8. Alkaline Earth Metal Zirconate Perovskites MZrO3 (M=Ba(2+), Sr(2+), Ca(2+)) Derived from Molecular Precursors and Doped with Eu(3+) Ions.

    PubMed

    Drąg-Jarząbek, Anna; John, Łukasz; Petrus, Rafał; Kosińska-Klähn, Magdalena; Sobota, Piotr

    2016-03-24

    The effect of alkaline earth metal alkoxides on the protonation of zirconocene dichloride was investigated. This approach enabled the design of compounds with preset molecular structures for generating high-purity binary metal oxide perovskites MZrO3 (M=Ba(2+), Sr(2+), Ca(2+)). Single-source molecular precursors [Ba4 Zr2 (μ6 -O)(μ3 ,η(2)-OR)8 (OR)2(η(2) -HOR)2 (HOR)2 Cl4], [Sr4 Zr2 (μ6 -O)(μ3 ,η(2)-OR)8 (OR)2 (HOR)4 Cl4], [Ca4 Zr2 (μ6-O)(μ3 ,η(2)-OR)8 (OR)2 Cl4], and [Ca6 Zr2 (μ2 ,η(2)-OR)12 (μ-Cl)2 (η(2) -HOR)4 Cl6 ]⋅8 CH2 Cl2 were prepared via elimination of the cyclopentadienyl ring from Cp2 ZrCl2 as CpH in the presence of M(OR)2 and alcohol ROH (ROH=CH3OCH2 CH2OH) as a source of protons. The resulting complexes were characterized by elemental analysis, IR and NMR spectroscopy, and single-crystal X-ray diffraction. The compounds were then thermally decomposed to MCl2 /MZrO3 mixtures. Leaching of MCl2 from the raw powder with deionized water produced highly pure perovskite-like oxide particles of 40-80 nm in size. Luminescence studies on Eu(3+)-doped MZrO3 revealed that the perovskites are attractive host lattices for potential applications in display technology. PMID:26891039

  9. Small molecule interactions with lipid bilayers: a molecular dynamics study of chlorhexidine

    NASA Astrophysics Data System (ADS)

    van Oosten, Brad; Marquardt, Drew; Sternin, Edward; Harroun, Thad

    2013-03-01

    Chlorhexidine presents an interesting modelling challenge with a hydrophobic hexane connecting two biguanides (arginine analogues) and two aromatic rings. We conducted molecular dynamic simulations using the GROMACS simulation software to reproduce the experimental environment of chlorhexidine in a 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC) bilayer to produce atomic-level information. We constructed an all-atom force field of chlorhexidine from the CHARMM36 force field using well established parameters of certain amino acids. Partial charges were treated differently, which were calculated using GAUSSIAN software. We will compare and contrast the results of our model to that of our neutron scattering experiments previously done in our lab.

  10. RET-targeting molecular stratified non-small-cell lung cancers

    PubMed Central

    2013-01-01

    Recent advances in lung cancer genomics have successfully characterized therapeutic targets of lung cancer. RET fusion gene products are among the newest target molecules for lung adenocarcinoma. Preclinical findings and preliminary reports regarding potential tumor control by RET-targeting multi-kinase inhibitors encourage further clinical trials. The infrequent prevalence of RET fusion gene-positive cases may be a major obstacle hindering the development of RET-targeted therapy. Thus, it is necessary to recruit appropriate participants for trials to develop an efficient RET fusion gene detection system to achieve targeted therapy for lung adenocarcinomas stratified by this molecular target. PMID:25806272

  11. Note: Molecular diffusivity in a small pore zeolite measured by a variable pressure (piezometric) uptake method

    NASA Astrophysics Data System (ADS)

    Wang, Fei; Kobayashi, Yasukazu; Muhammad, Usman; Wang, Dezheng; Wang, Yao

    2016-03-01

    The use of numerical analysis to solve the diffusion equation in the uptake method allowed the measurement of molecular diffusivity in a zeolite with a variable pressure around it. The diffusivity was obtained from the data in the measurement of the adsorption isotherm, which means that the diffusivity measurement now needs neither a special instrument nor procedure. The diffusivities of all the gases are readily available from the measurement of their adsorption isotherms and these data include how the diffusivity changes versus adsorbed concentration. The modeling introduced can also be used for a zeolite with a surface barrier.

  12. Molecular Identification of Echinococcus multilocularis Infection in Small Mammals from Northeast, Iran

    PubMed Central

    Beiromvand, Molouk; Akhlaghi, Lame; Fattahi Massom, Seyed Hossein; Meamar, Ahmad Reza; Darvish, Jamshid; Razmjou, Elham

    2013-01-01

    Background Alveolar echinococcosis is a zoonotic disease caused by the metacestode of Echinococcus multilocularis. Many species of small mammals, including arvicolid rodents or Ochotona spp., are natural intermediate hosts of the cestode. The main aim of this study was to identify natural intermediate hosts of E. multilocularis in Chenaran County, Razavi Khorasan Province, northeastern Iran, where the prevalence of infected wild and domestic carnivores is high. Methodology/Principal Findings A program of trapping was carried out in five villages in which this cestode was reported in carnivores. The livers of 85 small mammals were investigated for the presence of E. multilocularis infection using multiplex PCR of mitochondrial genes. Infections were identified in 30 specimens: 23 Microtus transcaspicus, three Ochotona rufescens, two Mus musculus, one Crocidura gmelini, and one Apodemus witherbyi. Conclusions/Significance A range of small mammals therefore act as natural intermediate hosts for the transmission of E. multilocularis in Chenaran County, and the prevalence suggested that E. multilocularis infection is endemic in this region. The existence of the life cycle of this potentially lethal cestode in the vicinity of human habitats provides a significant risk of human infection. PMID:23875048

  13. First molecular survey of Anaplasma bovis in small ruminants from Tunisia.

    PubMed

    Ben Said, Mourad; Belkahia, Hanène; Karaoud, Maroua; Bousrih, Maha; Yahiaoui, Mouna; Daaloul-Jedidi, Monia; Messadi, Lilia

    2015-09-30

    To date, no information is available regarding the presence of Anaplasma bovis in the South Mediterranean area. In this study, prevalence, risk factors, and genetic diversity of A. bovis were assessed in small ruminants. A total of 563 healthy small ruminants (260 sheep and 303 goats), from 25 randomly selected flocks located in 5 localities from two bioclimatic areas in Tunisia, were investigated for the detection of A. bovis in blood by nested polymerase chain reaction (nPCR) assay. The overall infection rates of A. bovis were 42.7 and 23.8% in sheep and goats, respectively. Goats located in a sub-humid area were statistically more infected than those located in a humid area. A. bovis prevalence rate varied significantly according to sheep and goat flocks, and to the sheep breed. Infection with A. bovis was validated by sequencing. Sequence analysis based on the 16S rRNA gene showed that A. bovis from Tunisian goats and sheep clustered with other strain sequences detected from wild and domestic animals and published in GenBank. This study gives the first insight of presence of A. bovis DNA in small ruminants in Tunisia and suggests that these animal species may be playing an important role in the bovine anaplasmosis natural cycle caused by A. bovis in the South Mediterranean ecosystem. PMID:26088935

  14. First molecular survey of Anaplasma bovis in small ruminants from Tunisia.

    PubMed

    Ben Said, Mourad; Belkahia, Hanène; Karaoud, Maroua; Bousrih, Maha; Yahiaoui, Mouna; Daaloul-Jedidi, Monia; Messadi, Lilia

    2015-09-30

    To date, no information is available regarding the presence of Anaplasma bovis in the South Mediterranean area. In this study, prevalence, risk factors, and genetic diversity of A. bovis were assessed in small ruminants. A total of 563 healthy small ruminants (260 sheep and 303 goats), from 25 randomly selected flocks located in 5 localities from two bioclimatic areas in Tunisia, were investigated for the detection of A. bovis in blood by nested polymerase chain reaction (nPCR) assay. The overall infection rates of A. bovis were 42.7 and 23.8% in sheep and goats, respectively. Goats located in a sub-humid area were statistically more infected than those located in a humid area. A. bovis prevalence rate varied significantly according to sheep and goat flocks, and to the sheep breed. Infection with A. bovis was validated by sequencing. Sequence analysis based on the 16S rRNA gene showed that A. bovis from Tunisian goats and sheep clustered with other strain sequences detected from wild and domestic animals and published in GenBank. This study gives the first insight of presence of A. bovis DNA in small ruminants in Tunisia and suggests that these animal species may be playing an important role in the bovine anaplasmosis natural cycle caused by A. bovis in the South Mediterranean ecosystem.

  15. Molecular dynamics simulation studies of hyperbranched polyglycerols and their encapsulation behaviors of small drug molecules.

    PubMed

    Yu, Chunyang; Ma, Li; Li, Ke; Li, Shanlong; Liu, Yannan; Zhou, Yongfeng; Yan, Deyue

    2016-08-10

    Hyperbranched polyglycerol (HPG) is one of the most important hyperbranched polymers (HBPs) due to its interesting properties and applications. Herein, the conformation of HPGs depending on the degree of polymerization (DP) and the degree of branching (DB) is investigated explicitly by molecular dynamics simulations. This study shows that the radius of gyration (Rg) scales as Rg ∼ DP(1/3), which is in close agreement with the result of the SANS experiment. For HPGs with the same DP, the radius of gyration, asphericities and solvent accessible surface area all monotonically decrease with the increase of DB; while for HPGs with the same DB, the molecular anisotropy decreases with the increase of DP. The radial density investigation discloses that the cavities are randomly distributed in the interior of the HPG core to support the "dendritic box effect", which can be used to encapsulate the guest molecules. Interestingly, the terminal groups of HPGs with a high Wiener index (WI) are more favorable to fold back into the interiors than those with the low WI when in water. For the hyperbranched multi-arm copolymer with a HPG core and many polyethylene glycol (PEG) arms, drug encapsulation studies show that the PEG caps can not only effectively prevent tamoxifen from leaving the HPG core, but also encapsulate tamoxifen inside the PEG chains. These simulation results have provided more details for understanding the structure-property relationships of HPGs in water. PMID:27465863

  16. A comparative study on the molecular descriptors for predicting drug-likeness of small molecules

    PubMed Central

    Mishra, Hrishikesh; Singh, Nitya; Lahiri, Tapobrata; Misra, Krishna

    2009-01-01

    Screening of “ drug-like” molecule from the molecular database produced through high throughput techniques and their large repositories requires robust classification. In our work, a set of heuristically chosen nine molecular descriptors including four from Lipinski's rule, were used as classification parameter for screening “drug-like” molecules. The robustness of classification was compared with four fundamental descriptors of Lipinski. Back propagation neural network based classifier was applied on a database of 60000 molecules for classification of, “ drug-like” and “non drug-like” molecules. Classification result using nine descriptors showed high classification accuracy of 96.1% in comparison to that using four Lipinski's descriptors which yielded an accuracy of 82.48%. Also a significant decrease of false positives resulted while using nine descriptors causing a sharp 18% increase of specificity of classification. From this study it appeared that Lipinski's descriptors which mainly deal with pharmacokinetic properties of molecules form the basis for identification of “drug-like” molecules that can be substantially improved by adding more descriptors representing pharmaco­dynamics properties of molecules. PMID:19707563

  17. Conserved molecular mechanisms underlying the effects of small molecule xenobiotic chemotherapeutics on cells

    PubMed Central

    SARIN, HEMANT

    2016-01-01

    For proper determination of the apoptotic potential of chemoxenobiotics in synergism, it is important to understand the modes, levels and character of interactions of chemoxenobiotics with cells in the context of predicted conserved biophysical properties. Chemoxenobiotic structures are studied with respect to atom distribution over molecular space, the predicted overall octanol-to-water partition coefficient (Log OWPC; unitless) and molecular size viz a viz van der Waals diameter (vdWD). The Log OWPC-to-vdWD (nm−1) parameter is determined, and where applicable, hydrophilic interacting moiety/core-to-vdWD (nm−1) and lipophilic incorporating hydrophobic moiety/core-to-vdWD (nm−1) parameters of their part-structures are determined. The cellular and sub-cellular level interactions of the spectrum of xenobiotic chemotherapies have been characterized, for which a classification system has been developed based on predicted conserved biophysical properties with respect to the mode of chemotherapeutic effect. The findings of this study are applicable towards improving the effectiveness of existing combination chemotherapy regimens and the predictive accuracy of personalized cancer treatment algorithms as well as towards the selection of appropriate novel xenobiotics with the potential to be potent chemotherapeutics for dendrimer nanoparticle-based effective transvascular delivery. PMID:26998284

  18. CO near the Pleiades: Encounter of a star cluster with a small molecular cloud

    NASA Technical Reports Server (NTRS)

    Bally, J.; White, R. E.

    1986-01-01

    Although there is a large amount of interstellar matter near the Pleiades star cluster, the observed dust and gas is not a remnant of the placental molecular cloud from which the star cluster was formed. Carbon monoxide (CO) associated with the visible reflection nebulae was discovered by Cohen (1975). Its radial velocity differs from that of the cluster by many times the cluster escape velocity, which implies that the cloud-cluster association is the result of a chance encounter. This circumstance and the proximity of the Pleiades to the sun creates an unique opportunity for study of interstellar processes at high spatial resolution. To study the molecular component of the gas, a 1.7 square degree field was mapped with the AT&T Bell Laboratories 7-meter antenna (1.7' beam) on a 1' grid in the J=1.0 C(12)O line, obtaining over 6,000 spectra with 50 kHz resolution. The cloud core was mapped in the J=1-0 line of C(13)O. Further observations include an unsuccessful search for CS (J=2-1) at AT&T BL, and some C(12)O J=2-1 spectra obtained at the Millimeter Wave Observatory of the University of Texas.

  19. 7,7,8,8-Tetracyanoquinodimethane based molecular dopants for p-type doping of OLEDs: A theoretical investigation

    SciTech Connect

    Cosimbescu, Lelia; Padmaperuma, Asanga B.; Gaspar, Daniel J.

    2011-11-15

    The array of organic conductivity dopants used for organic light emitting devices (OLED) to reduce the operating voltage and improve power efficiency is extremely limited. Here we report a comparative theoretical study between newly proposed analogs and the standard state-of-the-art conductivity dopant 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ). We used density functional theory to determine the bond lengths, bond angles and electronic properties, such as the energy of the highest occupied molecular orbital (E{sub HOMO}) and lowest occupied molecular orbital (E{sub LUMO}) states, as well as the triplet energies of the novel structures (ET). The ground state structures of the proposed molecules were optimized at the B3LYP/6-31G* level. The results show that substitution of one or two fluorine groups in the F4-TCNQ core with a substituted phenyl ring or other electron withdrawing moieties, will not substantially affect the geometry of the molecule or its electronic ability to accept electrons. The most significant finding was that the phenyl substitutions onto the TCNQ core are nearly perpendicular to the TCNQ plane, and thus there is no electronic communication between the two rings. This is extremely important, as such extension of the {pi} conjugated system would negatively affect the E{sub LUMO} and thus the electron affinity of the molecule.

  20. Fabrication of water-dispersible and highly conductive PSS-doped PANI/graphene nanocomposites using a high-molecular weight PSS dopant and their application in H2S detection

    NASA Astrophysics Data System (ADS)

    Cho, Sunghun; Lee, Jun Seop; Jun, Jaemoon; Kim, Sung Gun; Jang, Jyongsik

    2014-11-01

    This work describes the fabrication of poly(4-styrenesulfonic acid)-doped polyaniline/graphene (PSS-doped PANI/graphene) nanocomposites and their use as sensing elements for hydrogen sulfide (H2S) detection. PSS with a weight-average molecular weight (Mw) of 1.96 × 106 was synthesized using low-temperature free-radical polymerization. The PSS was used as both a doping agent and a binding agent for the polymerization of aniline monomers in a biphasic system (water-chloroform) at -50 °C. The high Mw of PSS resulted in relatively large particle sizes and smooth surfaces of the PSS-doped PANI. These physical characteristics, in turn, resulted in low interparticle resistance and high conductivity. In addition, the PSS allowed homogeneous dispersion of reduced graphene sheets through electrostatic repulsion. The prepared PSS-doped PANI/graphene solutions showed good compatibility with flexible poly(ethylene terephthalate) (PET) substrates, making them suitable for flexible sensor electrodes. Changes in the charge-transport properties, such as protonation level, conjugation length, crystalline structure, and charge-transfer resistance, of the electrode materials were the main factors influencing the electrical and sensor performance of the PSS-doped PANI-based electrodes. PSS-doped PANI/graphene composites containing 30 wt% graphene showed the highest conductivity (168.4 S cm-1) and the lowest minimum detection level (MDL) for H2S gas (1 ppm). This result is consistent with the observed improvements in charge transport in the electrode materials via strong π-π stacking interactions between the PANI and the graphene sheets.This work describes the fabrication of poly(4-styrenesulfonic acid)-doped polyaniline/graphene (PSS-doped PANI/graphene) nanocomposites and their use as sensing elements for hydrogen sulfide (H2S) detection. PSS with a weight-average molecular weight (Mw) of 1.96 × 106 was synthesized using low-temperature free-radical polymerization. The PSS was

  1. Advances in molecular biology of lung disease: aiming for precision therapy in non-small cell lung cancer.

    PubMed

    Rooney, Claire; Sethi, Tariq

    2015-10-01

    Lung cancer is the principal cause of cancer-related mortality in the developed world, accounting for almost one-quarter of all cancer deaths. Traditional treatment algorithms have largely relied on histologic subtype and have comprised pragmatic chemotherapy regimens with limited efficacy. However, because our understanding of the molecular basis of disease in non-small cell lung cancer (NSCLC) has improved exponentially, it has become apparent that NSCLC can be radically subdivided, or molecularly characterized, based on recurrent driver mutations occurring in specific oncogenes. We know that the presence of such mutations leads to constitutive activation of aberrant signaling proteins that initiate, progress, and sustain tumorigenesis. This persistence of the malignant phenotype is referred to as "oncogene addiction." On this basis, a paradigm shift in treatment approach has occurred. Rational, targeted therapies have been developed, the first being tyrosine kinase inhibitors (TKIs), which entered the clinical arena > 10 years ago. These were tremendously successful, significantly affecting the natural history of NSCLC and improving patient outcomes. However, the benefits of these drugs are somewhat limited by the emergence of adaptive resistance mechanisms, and efforts to tackle this phenomenon are ongoing. A better understanding of all types of oncogene-driven NSCLC and the occurrence of TKI resistance will help us to further develop second- and third-generation small molecule inhibitors and will expand our range of precision therapies for this disease.

  2. Molecular characterization and phylogenetic analysis of the causative agent of hemoplasma infection in small Indian Mongoose (Herpestes Javanicus).

    PubMed

    Sharifiyazdi, Hassan; Nazifi, Saeed; Shirzad Aski, Hesamaddin; Shayegh, Hossein

    2014-09-01

    Hemoplasmas are the trivial name for a group of erythrocyte-parasitizing bacteria of the genus Mycoplasma. This study is the first report of hemoplasma infection in Small Indian Mongoose (Herpestes Javanicus) based on molecular analysis of 16S rDNA. Whole blood samples were collected by sterile methods, from 14 live captured mongooses, in the south of Iran. Candidatus Mycoplasma turicensis (CMt)-like hemoplasma was detected in blood samples from one animal tested. BLAST search and phylogenetic analysis of partial 16S rDNA sequence (933bp) of the hemoplasma from Small Indian mongoose (KJ530704) revealed only 96-97% identity to the previously described CMt followed by 95% and 91% similarity with Mycoplasma coccoides and Mycoplasma haemomuris, respectively. Accordingly, the Iranian mongoose CMt isolate showed a high intra-specific genetic variation compared to all previously reported CMt strains in GenBank. Further molecular studies using multiple phylogenetic markers are required to characterize the exact species of Mongoose-derived hemoplasma. PMID:25097036

  3. Aptamer sandwich-based carbon nanotube sensors for single-carbon-atomic-resolution detection of non-polar small molecular species.

    PubMed

    Lee, Joohyung; Jo, Minjoung; Kim, Tae Hyun; Ahn, Ji-Young; Lee, Dong-ki; Kim, Soyoun; Hong, Seunghun

    2011-01-01

    A portable sensor platform for the detection of small molecular species is crucial for the on-site monitoring of environmental pollutants, food toxicants, and disease-related metabolites. However, it is still extremely difficult to find highly selective and sensitive sensor platforms for general small molecular detection. Herein, we report aptamer sandwich-based carbon nanotube sensor strategy for small molecular detection, where aptamers were utilized to capture target molecules as well as to enhance the sensor signals. We successfully demonstrated the detection of non-polar bisphenol A molecules with a 1 pM sensitivity. Significantly, our sensors were able to distinguish between similar small molecular species with single-carbon-atomic resolution. Furthermore, using the additional biotin modification on labeling aptamer, we enhanced the detection limit of our sensors down to 10 fM. This strategy allowed us to detect non-polar small molecular species using carbon nanotube transistors, thus overcoming the fundamental limitation of field effect transistor-based sensors. Considering the extensive applications of sandwich assay for the detection of rather large biomolecules, our results should open up completely new dimension in small molecular detection technology and should enable a broad range of applications such as environmental protection and food safety.

  4. Airplane dopes and doping

    NASA Technical Reports Server (NTRS)

    Smith, W H

    1919-01-01

    Cellulose acetate and cellulose nitrate are the important constituents of airplane dopes in use at the present time, but planes were treated with other materials in the experimental stages of flying. The above compounds belong to the class of colloids and are of value because they produce a shrinking action on the fabric when drying out of solution, rendering it drum tight. Other colloids possessing the same property have been proposed and tried. In the first stages of the development of dope, however, shrinkage was not considered. The fabric was treated merely to render it waterproof. The first airplanes constructed were covered with cotton fabric stretched as tightly as possible over the winds, fuselage, etc., and flying was possible only in fine weather. The necessity of an airplane which would fly under all weather conditions at once became apparent. Then followed experiments with rubberized fabrics, fabrics treated with glue rendered insoluble by formaldehyde or bichromate, fabrics treated with drying and nondrying oils, shellac, casein, etc. It was found that fabrics treated as above lost their tension in damp weather, and the oil from the motor penetrated the proofing material and weakened the fabric. For the most part the film of material lacked durability. Cellulose nitrate lacquers, however were found to be more satisfactory under varying weather conditions, added less weight to the planes, and were easily applied. On the other hand, they were highly inflammable, and oil from the motor penetrated the film of cellulose nitrate, causing the tension of the fabric to be relaxed.

  5. Small renal masses: The molecular markers associated with outcome of patients with kidney tumors 7 cm or less

    NASA Astrophysics Data System (ADS)

    Spirina, L. V.; Usynin, Y. A.; Kondakova, I. V.; Yurmazov, Z. A.; Slonimskaya, E. M.; Pikalova, L. V.

    2016-08-01

    The investigation of molecular mechanisms of tumor cell behavior in small renal masses is required to achieve the better cancer survival. The aim of the study is to find molecular markers associated with outcome of patients with kidney tumors 7 cm or less. A homogenous group of 20 patients T1N0M0-1 (mean age 57.6 ± 2.2 years) with kidney cancer was selected for the present analysis. The content of transcription and growth factors was determined by ELISA. The levels of AKT-mTOR signaling pathway components were measured by Western blotting analysis. The molecular markers associated with unfavorable outcome of patients with kidney tumors 7 cm or less were high levels of NF-kB p50, NF-kB p65, HIF-1, HIF-2, VEGF and CAIX. AKT activation with PTEN loss also correlated with the unfavorable outcome of kidney cancer patients with tumor size 7 cm or less. It is observed that the biological features of kidney cancer could predict the outcome of patients.

  6. Pick-up, transport and release of a molecular cargo using a small-molecule robotic arm

    NASA Astrophysics Data System (ADS)

    Kassem, Salma; Lee, Alan T. L.; Leigh, David A.; Markevicius, Augustinas; Solà, Jordi

    2016-02-01

    Modern-day factory assembly lines often feature robots that pick up, reposition and connect components in a programmed manner. The idea of manipulating molecular fragments in a similar way has to date only been explored using biological building blocks (specifically DNA). Here, we report on a wholly artificial small-molecule robotic arm capable of selectively transporting a molecular cargo in either direction between two spatially distinct, chemically similar, sites on a molecular platform. The arm picks up/releases a 3-mercaptopropanehydrazide cargo by formation/breakage of a disulfide bond, while dynamic hydrazone chemistry controls the cargo binding to the platform. Transport is controlled by selectively inducing conformational and configurational changes within an embedded hydrazone rotary switch that steers the robotic arm. In a three-stage operation, 79-85% of 3-mercaptopropanehydrazide molecules are transported in either (chosen) direction between the two platform sites, without the cargo at any time fully dissociating from the machine nor exchanging with other molecules in the bulk.

  7. Pick-up, transport and release of a molecular cargo using a small-molecule robotic arm.

    PubMed

    Kassem, Salma; Lee, Alan T L; Leigh, David A; Markevicius, Augustinas; Solà, Jordi

    2016-02-01

    Modern-day factory assembly lines often feature robots that pick up, reposition and connect components in a programmed manner. The idea of manipulating molecular fragments in a similar way has to date only been explored using biological building blocks (specifically DNA). Here, we report on a wholly artificial small-molecule robotic arm capable of selectively transporting a molecular cargo in either direction between two spatially distinct, chemically similar, sites on a molecular platform. The arm picks up/releases a 3-mercaptopropanehydrazide cargo by formation/breakage of a disulfide bond, while dynamic hydrazone chemistry controls the cargo binding to the platform. Transport is controlled by selectively inducing conformational and configurational changes within an embedded hydrazone rotary switch that steers the robotic arm. In a three-stage operation, 79-85% of 3-mercaptopropanehydrazide molecules are transported in either (chosen) direction between the two platform sites, without the cargo at any time fully dissociating from the machine nor exchanging with other molecules in the bulk.

  8. Water activity and mobility in solutions of glycerol and small molecular weight sugars: Implication for cryo- and lyopreservation

    NASA Astrophysics Data System (ADS)

    He, Xiaoming; Fowler, Alex; Toner, Mehmet

    2006-10-01

    In this study, the free volume models, originally developed for large molecular weight polymer-solvent systems, were used to study the water activity and mobility in solutions of four small molecular weight cryo-/lyoprotectants, viz., glycerol, a monosaccharide (fructose), and two disaccharides (sucrose and trehalose). The free volume model parameters were determined by fitting the models to available experimental data using a nonlinear optimization procedure. It was found that free volume models could accurately predict the available experimental data, which suggests that the free volume models might be generally applicable to aqueous solutions of small molecular weight cryo-/lyoprotectants. Furthermore, several models for estimating the mutual diffusion coefficient were tested using available experimental data for aqueous solutions of glycerol and a better method to estimate the mutual diffusion coefficient was proposed. Free volume models were used to predict and analyze the water activity and mobility in solutions of four cryo-/lyoprotectants under conditions frequently encountered in cryo-/lyopreservation applications. It was found that the water mobility in the glassy state of the above four solutions is essentially negligible in the case of cryopreservation with storage temperature lower than -110°C. However, the water mobility in a glass at higher temperature (>-80°C) may be significant. As a result, a subcooling of up to 50°C may be necessary for the long-term cryo-/lyopreservation of biomaterials depending on the water content and the type of cryo-/lyoprotectants. It was further shown that trehalose might be the best of the four protectants studied for lyopreservation (water mass fraction ⩽0.1) when the storage temperature is above the room temperature. The results from this study might be useful for the development of more effective protocols for both cryopreservation and lyopreservation of living cells and other biomaterials.

  9. Molecular Dynamics simulations of Inhibitor of Apoptosis Proteins and identification of potential small molecule inhibitors.

    PubMed

    Jayakumar, Jayanthi; Anishetty, Sharmila

    2014-05-01

    Chemotherapeutic resistance due to over expression of Inhibitor of Apoptosis Proteins (IAPs) XIAP, survivin and livin has been observed in various cancers. In the current study, Molecular Dynamics (MD) simulations were carried out for all three IAPs and a common ligand binding scaffold was identified. Further, a novel sequence based motif specific to these IAPs was designed. SMAC is an endogenous inhibitor of IAPs. Screening of ChemBank for compounds similar to lead SMAC-non-peptidomimetics yielded a cemadotin related compound NCIMech_000654. Cemadotin is a derivative of natural anti-tumor peptide dolastatin-15; hence these compounds were docked against all three IAPs. Based on our analysis, we propose that NCIMech_000654/dolastatin-15/cemadotin derivatives may be investigated for their potential in inhibiting XIAP, survivin and livin.

  10. Selective-area growth of heavily n-doped GaAs nanostubs on Si(001) by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Chang, Yoon Jung; Simmonds, Paul J.; Beekley, Brett; Goorsky, Mark S.; Woo, Jason C. S.

    2016-04-01

    Using an aspect ratio trapping technique, we demonstrate molecular beam epitaxy of GaAs nanostubs on Si(001) substrates. Nanoholes in a SiO2 mask act as a template for GaAs-on-Si selective-area growth (SAG) of nanostubs 120 nm tall and ≤100 nm in diameter. We investigate the influence of growth parameters including substrate temperature and growth rate on SAG. Optimizing these parameters results in complete selectivity with GaAs growth only on the exposed Si(001). Due to the confined-geometry, strain and defects in the GaAs nanostubs are restricted in lateral dimensions, and surface energy is further minimized. We assess the electrical properties of the selectively grown GaAs nanostubs by fabricating heterogeneous p+-Si/n+-GaAs p-n diodes.

  11. Cellular and molecular biology of small cell lung cancer: an overview.

    PubMed

    Karachaliou, Niki; Pilotto, Sara; Lazzari, Chiara; Bria, Emilio; de Marinis, Filippo; Rosell, Rafael

    2016-02-01

    Although the incidence of small cell lung cancer (SCLC) has declined during the past 30 years, it remains a frustrating disease to research and treat. Numerous attempts to enhance the anti-tumor effects of traditional chemotherapy for SCLC have not been successful. For any tumor to become cancerous, various genetic mutations and biologic alterations must occur in the cell that, when combined, render it a malignant neoplasm. New and novel therapies based on understanding these mechanisms of transformation are needed. Herein we provide an in-depth view of some of the genomic alterations in SCLC that have emerged as potential targets for therapeutic intervention.

  12. Molecular theory for the phase equilibria and cluster distribution of associating fluids with small bond angles.

    PubMed

    Marshall, Bennett D; Chapman, Walter G

    2013-08-01

    We develop a new theory for associating fluids with multiple association sites. The theory accounts for small bond angle effects such as steric hindrance, ring formation, and double bonding. The theory is validated against Monte Carlo simulations for the case of a fluid of patchy colloid particles with three patches and is found to be very accurate. Once validated, the theory is applied to study the phase diagram of a fluid composed of three patch colloids. It is found that bond angle has a significant effect on the phase diagram and the very existence of a liquid-vapor transition.

  13. Cellular and molecular biology of small cell lung cancer: an overview

    PubMed Central

    Karachaliou, Niki; Pilotto, Sara; Lazzari, Chiara; Bria, Emilio; de Marinis, Filippo

    2016-01-01

    Although the incidence of small cell lung cancer (SCLC) has declined during the past 30 years, it remains a frustrating disease to research and treat. Numerous attempts to enhance the anti-tumor effects of traditional chemotherapy for SCLC have not been successful. For any tumor to become cancerous, various genetic mutations and biologic alterations must occur in the cell that, when combined, render it a malignant neoplasm. New and novel therapies based on understanding these mechanisms of transformation are needed. Herein we provide an in-depth view of some of the genomic alterations in SCLC that have emerged as potential targets for therapeutic intervention. PMID:26958489

  14. Molecular evidence for gender differences in the migratory behaviour of a small seabird.

    PubMed

    Medeiros, Renata J; King, R Andrew; Symondson, William O C; Cadiou, Bernard; Zonfrillo, Bernard; Bolton, Mark; Morton, Rab; Howell, Stephen; Clinton, Anthony; Felgueiras, Marcial; Thomas, Robert J

    2012-01-01

    Molecular sexing revealed an unexpectedly strong female bias in the sex ratio of pre-breeding European Storm Petrels (Hydrobates pelagicus), attracted to playback of conspecific calls during their northwards migration past SW Europe. This bias was consistent across seven years, ranging from 80.8% to 89.7% female (mean annual sex ratio ± SD = 85.5% female ±4.1%). The sex ratio did not differ significantly from unity (i.e., 50% female) among (i) Storm Petrel chicks at a breeding colony in NW France, (ii) adults found dead on beaches in Southern Portugal, (iii) breeding birds attending nest burrows in the UK, captured by hand, and (iv) adults captured near a breeding colony in the UK using copies of the same sound recordings as used in Southern Europe, indicating that females are not inherently more strongly attracted to playback calls than males. A morphological discriminant function analysis failed to provide a good separation of the sexes, showing the importance of molecular sexing for this species. We found no sex difference in the seasonal or nocturnal timing of migration past Southern Europe, but there was a significant tendency for birds to be caught in sex-specific aggregations. The preponderance of females captured in Southern Europe suggests that the sexes may differ in migration route or in their colony-prospecting behaviour during migration, at sites far away from their natal colonies. Such differences in migration behaviour between males and females are poorly understood but have implications for the vulnerability of seabirds to pollution and environmental change at sea during the non-breeding season. PMID:23029481

  15. Small copper-doped silicon clusters CuSin (n = 4-10) and their anions: structures, thermochemistry, and electron affinities.

    PubMed

    Lin, Lin; Yang, Jucai

    2015-06-01

    The structures and energies of copper-doped small silicon clusters CuSi n (n = 4-10) and their anions were investigated systematically using CCSD(T)/aug-cc-pVTZ-DK//MP2/6-31G(2df,p), G4//MP2/6-31G(2df,p), and the B3LYP/6-311+G* basis set. The performance of the methods used for the prediction of energetic and thermodynamic properties was evaluated. Comparing experimental [Xu et al. (2012) J Chem Phys 136:104308] and theoretical calculations, it was concluded that the CCSD(T) results are very accurate and exhibit the best performance; the mean absolute deviation from experimental data was 0.043 eV. The excellent agreement of vertical detachment energy (VDE) between experimental results and CCSD(T) calculations indicates that the ground state structures of CuSi n (-) (n = 4-10) presented in this paper are reliable. For CuSi10, assigning 2.90±0.08 eV to the experimental adiabatic electron affinity (AEA) and 3.90±0.08 eV to the VDE is more reasonable than to 3.46±0.08 eV and 3.62±0.08 eV, respectively, based on the CCSD(T) calculations and the previous photoelectron spectrum of CuSi10 (-) (Xu et al., op. cit.). The AEAs of CuSi n (n = 4-10), excluding CuSi7, are in excellent agreement with experimental data, showing that the ground state structures of CuSi n (n = 4-6, 8-10) reported in this paper are reliable. CuSi10 is suggested to be the smallest endohedral ground state structure. However, adding an additional electron to CuSi10 pulls out the Cu atom from the center location, forming an exohedral ground state structure of CuSi10 (-). The charge transfer and dissociation energy of Cu from CuSi n and their anions determined to examine the nature of bonding and their relative stabilities. PMID:26003428

  16. Small copper-doped silicon clusters CuSin (n = 4-10) and their anions: structures, thermochemistry, and electron affinities.

    PubMed

    Lin, Lin; Yang, Jucai

    2015-06-01

    The structures and energies of copper-doped small silicon clusters CuSi n (n = 4-10) and their anions were investigated systematically using CCSD(T)/aug-cc-pVTZ-DK//MP2/6-31G(2df,p), G4//MP2/6-31G(2df,p), and the B3LYP/6-311+G* basis set. The performance of the methods used for the prediction of energetic and thermodynamic properties was evaluated. Comparing experimental [Xu et al. (2012) J Chem Phys 136:104308] and theoretical calculations, it was concluded that the CCSD(T) results are very accurate and exhibit the best performance; the mean absolute deviation from experimental data was 0.043 eV. The excellent agreement of vertical detachment energy (VDE) between experimental results and CCSD(T) calculations indicates that the ground state structures of CuSi n (-) (n = 4-10) presented in this paper are reliable. For CuSi10, assigning 2.90±0.08 eV to the experimental adiabatic electron affinity (AEA) and 3.90±0.08 eV to the VDE is more reasonable than to 3.46±0.08 eV and 3.62±0.08 eV, respectively, based on the CCSD(T) calculations and the previous photoelectron spectrum of CuSi10 (-) (Xu et al., op. cit.). The AEAs of CuSi n (n = 4-10), excluding CuSi7, are in excellent agreement with experimental data, showing that the ground state structures of CuSi n (n = 4-6, 8-10) reported in this paper are reliable. CuSi10 is suggested to be the smallest endohedral ground state structure. However, adding an additional electron to CuSi10 pulls out the Cu atom from the center location, forming an exohedral ground state structure of CuSi10 (-). The charge transfer and dissociation energy of Cu from CuSi n and their anions determined to examine the nature of bonding and their relative stabilities.

  17. Energy Storage: Nitrogen-Doped Ordered Mesoporous Anatase TiO2 Nanofibers as Anode Materials for High Performance Sodium-Ion Batteries (Small 26/2016).

    PubMed

    Wu, Ying; Liu, Xiaowu; Yang, Zhenzhong; Gu, Lin; Yu, Yan

    2016-07-01

    On page 3522, Y. Yu and co-workers fabricate nitrogen-doped ordered mesoporous TiO2 nanofibers (denoted as N-MTO) by electrospinning and subsequent nitridation treatment. Nitrogen atoms are successfully doped into the TiO2 lattice, accompanied by the formation of Ti(3+) and oxygen vacancies, contributing to the improvement of electronic conductivity of TiO2 . When used as an anode for a sodium-ion battery, the N-MTO demonstrates excellent rate capability and superior long cycling performance. PMID:27383035

  18. Energy Storage: Nitrogen-Doped Ordered Mesoporous Anatase TiO2 Nanofibers as Anode Materials for High Performance Sodium-Ion Batteries (Small 26/2016).

    PubMed

    Wu, Ying; Liu, Xiaowu; Yang, Zhenzhong; Gu, Lin; Yu, Yan

    2016-07-01

    On page 3522, Y. Yu and co-workers fabricate nitrogen-doped ordered mesoporous TiO2 nanofibers (denoted as N-MTO) by electrospinning and subsequent nitridation treatment. Nitrogen atoms are successfully doped into the TiO2 lattice, accompanied by the formation of Ti(3+) and oxygen vacancies, contributing to the improvement of electronic conductivity of TiO2 . When used as an anode for a sodium-ion battery, the N-MTO demonstrates excellent rate capability and superior long cycling performance.

  19. Molecular Probing of the HPV-16 E6 Protein Alpha Helix Binding Groove with Small Molecule Inhibitors

    PubMed Central

    Rietz, Anne; Petrov, Dino P.; Bartolowits, Matthew; DeSmet, Marsha; Davisson, V. Jo; Androphy, Elliot J.

    2016-01-01

    The human papillomavirus (HPV) HPV E6 protein has emerged as a central oncoprotein in HPV-associated cancers in which sustained expression is required for tumor progression. A majority of the E6 protein interactions within the human proteome use an alpha-helix groove interface for binding. The UBE3A/E6AP HECT domain ubiquitin ligase binds E6 at this helix-groove interface. This enables formation of a trimeric complex with p53, resulting in destruction of this tumor suppressor. While recent x-ray crystal structures are useful, examples of small molecule probes that can modulate protein interactions at this interface are limited. To develop insights useful for potential structure-based design of ligands for HPV E6, a series of 2,6-disubstituted benzopyranones were prepared and tested as competitive antagonists of E6-E6AP helix-groove interactions. These small molecule probes were used in both binding and functional assays to evaluate recognition features of the E6 protein. Evidence for an ionic functional group interaction within the helix groove was implicated by the structure-activity among the highest affinity ligands. The molecular topographies of these protein-ligand interactions were evaluated by comparing the binding and activities of single amino acid E6 mutants with the results of molecular dynamic simulations. A group of arginine residues that form a rim-cap over the E6 helix groove offer compensatory roles in binding and recognition of the small molecule probes. The flexibility and impact on the overall helix-groove shape dictated by these residues offer new insights for structure-based targeting of HPV E6. PMID:26915086

  20. Molecular characterization of the gene encoding an 18-kilodalton small heat shock protein associated with the membrane of Leuconostoc oenos.

    PubMed Central

    Jobin, M P; Delmas, F; Garmyn, D; Diviès, C; Guzzo, J

    1997-01-01

    In Leuconostoc oenos, different stresses such as heat, ethanol, and acid shocks dramatically induce the expression of an 18-kDa small heat shock protein called Lo 18. The corresponding gene (hsp18) was cloned from a genomic library of L. oenos constructed in Escherichia coli. A 2.3-kb DNA fragment carrying the hsp18 gene was sequenced. The hsp18 gene encodes a polypeptide of 148 amino acids with a calculated molecular mass of 16,938 Da. The Lo18 protein has a significant identity with small heat shock proteins of the alpha-crystallin family. The transcriptional start site was determined by primer extension. This experiment allowed us to identify the promoter region exhibiting high similarity to consensus promoter sequences of gram-positive bacteria, as well as E. coli. Northern blot analysis showed that hsp18 consists of a unique transcription unit of 0.6 kb. Moreover, hsp18 expression seemed to be controlled at the transcriptional level. This small heat shock protein was found to be peripherally associated with the membrane of L. oenos. PMID:9023938

  1. Molecular characterization of the small nonstructural proteins of parvovirus Aleutian mink disease virus (AMDV) during infection.

    PubMed

    Huang, Qinfeng; Luo, Yong; Cheng, Fang; Best, Sonja M; Bloom, Marshall E; Qiu, Jianming

    2014-03-01

    Aleutian mink disease virus (AMDV) is the only member in genus Amdovirus of the family Parvoviridae. During AMDV infection, six species of viral transcripts are generated from one precursor mRNA through alternative splicing and alternative polyadenylation. In addition to the large non-structural protein NS1, two small non-structural proteins, NS2 and NS3, are putatively encoded (Qiu J, et al., 2006. J. Virol. 80 654-662). However, these two proteins have not been experimentally demonstrated during virus infection, and nothing is known about their function. Here, we studied the nonstructural protein expression profile of AMDV, and for the first time, confirmed expression of NS2 and NS3 during infection, and identified their intracellular localization. More importantly, we provided evidence that both NS2 and NS3 are necessary for AMDV replication. PMID:24606679

  2. Molecular Characterization of the Small Nonstructural Proteins of Parvovirus Aleutian Mink Disease Virus (AMDV) During Infection

    PubMed Central

    Huang, Qinfeng; Luo, Yong; Cheng, Fang; Best, Sonja M.; Bloom, Marshall E.; Qiu, Jianming

    2014-01-01

    Aleutian mink disease virus (AMDV) is the only member in genus Amdovirus of the family Parvoviridae. During AMDV infection, six species of viral transcripts are generated from one precursor mRNA through alternative splicing and alternative polyadenylation. In addition to the large non-structural protein NS1, two small non-structural proteins, NS2 and NS3, are putatively encoded (Qiu J, et al: Journal of Virology, 80:654–62, 2006). However, these two proteins have not been experimentally demonstrated during virus infection, and nothing is known about their function. Here, we studied the nonstructural protein expression profile of AMDV, and for the first time, confirmed expression of NS2 and NS3 during infection, and identified their intracellular localization. More importantly, we provided evidence that both NS2 and NS3 are necessary for AMDV replication. PMID:24606679

  3. Biomolecular Crowding Arising from Small Molecules, Molecular Constraints, Surface Packing, and Nano-Confinement

    PubMed Central

    Hilaire, Mary Rose; Abaskharon, Rachel M.; Gai, Feng

    2015-01-01

    The effect of macromolecular crowding on the structure, dynamics, and reactivity of biomolecules is well-established and the relevant research has been extensively reviewed. Herein, we focus our discussion on crowding effects arising from small co-solvent molecules and densely packed surface conditions. In addition, we highlight recent efforts that capitalize on the excluded volume effect for various tailored biochemical and biophysical applications. Specifically, we discuss how a targeted increase in local mass density can be exploited to gain insight into the folding dynamics of the protein of interest and how confinement via reverse micelles can be used to study a range of biophysical questions, from protein hydration dynamics to amyloid formation. PMID:26266732

  4. Human, rat and chicken small intestinal Na+-Cl−-creatine transporter: functional, molecular characterization and localization

    PubMed Central

    Peral, M J; García-Delgado, M; Calonge, M L; Durán, J M; De La Horra, M C; Wallimann, T; Speer, O; Ilundáin, A A

    2002-01-01

    In spite of all the fascinating properties of oral creatine supplementation, the mechanism(s) mediating its intestinal absorption has(have) not been investigated. The purpose of this study was to characterize intestinal creatine transport. [14C]Creatine uptake was measured in chicken enterocytes and rat ileum, and expression of the creatine transporter CRT was examined in human, rat and chicken small intestine by reverse transcription-polymerase chain reaction, Northern blot, in situ hybridization, immunoblotting and immunohistochemistry. Results show that enterocytes accumulate creatine against its concentration gradient. This accumulation was electrogenic, Na+- and Cl−-dependent, with a probable stoichiometry of 2 Na+: 1 Cl−: 1 creatine, and inhibited by ouabain and iodoacetic acid. The kinetic study revealed a Km for creatine of 29 μm. [14C]Creatine uptake was efficiently antagonized by non-labelled creatine, guanidinopropionic acid and cyclocreatine. More distant structural analogues of creatine, such as GABA, choline, glycine, β-alanine, taurine and betaine, had no effect on intestinal creatine uptake, indicating a high substrate specificity of the creatine transporter. Consistent with these functional data, messenger RNA for CRT was detected only in the cells lining the intestinal villus. The sequences of partial clones, and of the full-length cDNA clone, isolated from human and rat small intestine were identical to previously cloned CRT cDNAs. Immunological analysis revealed that CRT protein was mainly associated with the apical membrane of the enterocytes. This study reports for the first time that mammalian and avian enterocytes express CRT along the villus, where it mediates high-affinity, Na+- and Cl−-dependent, apical creatine uptake. PMID:12433955

  5. Molecular locks and keys: the role of small molecules in phytohormone research

    PubMed Central

    Fonseca, Sandra; Rosado, Abel; Vaughan-Hirsch, John; Bishopp, Anthony; Chini, Andrea

    2014-01-01

    Plant adaptation, growth and development rely on the integration of many environmental and endogenous signals that collectively determine the overall plant phenotypic plasticity. Plant signaling molecules, also known as phytohormones, are fundamental to this process. These molecules act at low concentrations and regulate multiple aspects of plant fitness and development via complex signaling networks. By its nature, phytohormone research lies at the interface between chemistry and biology. Classically, the scientific community has always used synthetic phytohormones and analogs to study hormone functions and responses. However, recent advances in synthetic and combinational chemistry, have allowed a new field, plant chemical biology, to emerge and this has provided a powerful tool with which to study phytohormone function. Plant chemical biology is helping to address some of the most enduring questions in phytohormone research such as: Are there still undiscovered plant hormones? How can we identify novel signaling molecules? How can plants activate specific hormone responses in a tissue-specific manner? How can we modulate hormone responses in one developmental context without inducing detrimental effects on other processes? The chemical genomics approaches rely on the identification of small molecules modulating different biological processes and have recently identified active forms of plant hormones and molecules regulating many aspects of hormone synthesis, transport and response. We envision that the field of chemical genomics will continue to provide novel molecules able to elucidate specific aspects of hormone-mediated mechanisms. In addition, compounds blocking specific responses could uncover how complex biological responses are regulated. As we gain information about such compounds we can design small alterations to the chemical structure to further alter specificity, enhance affinity or modulate the activity of these compounds. PMID:25566283

  6. Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: calibration of the molecular clock.

    PubMed

    Van de Peer, Y; Neefs, J M; De Rijk, P; De Wachter, R

    1993-08-01

    The detailed descriptions now available for the secondary structure of small-ribosomal-subunit RNA, including areas of highly variable primary structure, facilitate the alignment of nucleotide sequences. However, for optimal exploitation of the information contained in the alignment, a method must be available that takes into account the local sequence variability in the computation of evolutionary distance. A quantitative definition for the variability of an alignment position is proposed in this study. It is a parameter in an equation which expresses the probability that the alignment position contains a different nucleotide in two sequences, as a function of the distance separating these sequences, i.e., the number of substitutions per nucleotide that occurred during their divergence. This parameter can be estimated from the distance matrix resulting from the conversion of pairwise sequence dissimilarities into pairwise distances. Alignment positions can then be subdivided into a number of sets of matching variability, and the average variability of each set can be derived. Next, the conversion of dissimilarity into distance can be recalculated for each set of alignment positions separately, using a modified version of the equation that corrects for multiple substitutions and changing for each set the parameter that reflects its average variability. The distances computed for each set are finally averaged, giving a more precise distance estimation. Trees constructed by the algorithm based on variability calibration have a topology markedly different from that of trees constructed from the same alignments in the absence of calibration. This is illustrated by means of trees constructed from small-ribosomal-subunit RNA sequences of Metazoa. A reconstruction of vertebrate evolution based on calibrated alignments matches the consensus view of paleontologists, contrary to trees based on uncalibrated alignments. In trees derived from sequences covering several metazoan

  7. Molecular locks and keys: the role of small molecules in phytohormone research.

    PubMed

    Fonseca, Sandra; Rosado, Abel; Vaughan-Hirsch, John; Bishopp, Anthony; Chini, Andrea

    2014-01-01

    Plant adaptation, growth and development rely on the integration of many environmental and endogenous signals that collectively determine the overall plant phenotypic plasticity. Plant signaling molecules, also known as phytohormones, are fundamental to this process. These molecules act at low concentrations and regulate multiple aspects of plant fitness and development via complex signaling networks. By its nature, phytohormone research lies at the interface between chemistry and biology. Classically, the scientific community has always used synthetic phytohormones and analogs to study hormone functions and responses. However, recent advances in synthetic and combinational chemistry, have allowed a new field, plant chemical biology, to emerge and this has provided a powerful tool with which to study phytohormone function. Plant chemical biology is helping to address some of the most enduring questions in phytohormone research such as: Are there still undiscovered plant hormones? How can we identify novel signaling molecules? How can plants activate specific hormone responses in a tissue-specific manner? How can we modulate hormone responses in one developmental context without inducing detrimental effects on other processes? The chemical genomics approaches rely on the identification of small molecules modulating different biological processes and have recently identified active forms of plant hormones and molecules regulating many aspects of hormone synthesis, transport and response. We envision that the field of chemical genomics will continue to provide novel molecules able to elucidate specific aspects of hormone-mediated mechanisms. In addition, compounds blocking specific responses could uncover how complex biological responses are regulated. As we gain information about such compounds we can design small alterations to the chemical structure to further alter specificity, enhance affinity or modulate the activity of these compounds.

  8. Ultra-small-sample molecular structure detection using microslot waveguide nuclear spin resonance.

    PubMed

    Maguire, Yael; Chuang, Isaac L; Zhang, Shuguang; Gershenfeld, Neil

    2007-05-29

    We here report on the design of a planar microslot waveguide NMR probe with an induction element that can be fabricated at scales from centimeters to nanometers to allow analysis of biomolecules at nano- or picomole quantities, reducing the required amount of materials by several orders of magnitude. This device demonstrates the highest signal-to-noise ratio for a planar detector to date, measured by using the anomeric proton signal from a 15.6-nmol sample of sucrose. This probe had a linewidth of 1.1 Hz for pure water without susceptibility matching. Analysis of 1.57 nmol of ribonuclease-A shows high sensitivity in one- and two-dimensional NMR spectra. Along with reducing required sample volumes, this integrated geometry can be packed in parallel arrays and combined with microfluidic systems. Further development of this device may have broad implications not only for advancing our understanding of many intractable protein structures and their folding, molecular interactions, and dynamic behaviors, but also for high-sensitivity diagnosis of a number of protein conformational diseases. PMID:17517654

  9. Molecular Dynamics Simulations of Small Clusters and Liquid Hydrogen Sulfide at Different Thermodynamic Conditions.

    PubMed

    Albertí, M; Amat, A; Aguilar, A; Pirani, F

    2016-07-14

    A new force field for the intermolecular H2S-H2S interaction has been used to study the most relevant properties of the hydrogen sulfide system from gaseous to liquid phases by means of molecular dynamics (MD) simulations. In order to check the validity of the interaction formulation, ab initio CCSD(T)/aug-cc-pVTZ calculations, including the counterpoise correction on the H2S, (H2S)2, and (H2S)3 structures optimized at the MP2/aug-cc-pVDZ level, have been performed. The (H2S)2,3 systems have been characterized by performing NVE MD simulations at decreasing values of the temperature, while the liquid sulfide behavior has been investigated considering a NpT ensemble of 512 molecules at several thermodynamic states, defined by different pressure and temperature values. Additional calculations using an ensemble of 2197 molecules at two different temperatures have been performed to investigate the liquid/vapor interface of the system. The S-S, S-H, and H-H radial distribution functions and the coordination number, calculated at the same conditions used in X-ray and neutron diffraction experiments, and the evaluated thermodynamic and structural properties have been compared successfully with experimental data, thus confirming the reliability of the force field formulation and of the MD predictions.

  10. Simple pair-wise interactions for hybrid Monte Carlo-molecular dynamics simulations of titania/yttria-doped iron.

    PubMed

    Hammond, Karl D; Voigt, Hyon-Jee Lee; Marus, Lauren A; Juslin, Niklas; Wirth, Brian D

    2013-02-01

    We present pair-wise, charge-neutral model potentials for an iron-titanium-yttrium-oxygen system. These simple models are designed to provide a tractable method of simulating nanostructured ferritic alloys (NFAs) using off-lattice Monte Carlo and molecular dynamics techniques without deviating significantly from the formalism employed in existing Monte Carlo simulations. The model is fitted to diamagnetic density functional theory (DFT) calculations of the various species over a range of densities and concentrations. The resulting model potentials provide reasonable and in some cases even excellent mechanical and thermodynamic properties for the pure metals. The model replicates the qualitative trends in formation energy predicted by DFT, though the energies of formation do not agree as well for dilute systems as they do for more concentrated systems. We find that on-lattice models will consistently favor tetrahedral oxygen interstitial sites over octahedral interstitial sites, while relaxed systems typically favor octahedral sites. This emphasizes the need for the off-lattice simulations for which this potential was designed. PMID:23288578

  11. Novel strategy for biofilm inhibition by using small molecules targeting molecular chaperone DnaK.

    PubMed

    Arita-Morioka, Ken-ichi; Yamanaka, Kunitoshi; Mizunoe, Yoshimitsu; Ogura, Teru; Sugimoto, Shinya

    2015-01-01

    Biofilms are complex communities of microorganisms that attach to surfaces and are embedded in a self-produced extracellular matrix. Since these cells acquire increased tolerance against antimicrobial agents and host immune systems, biofilm-associated infectious diseases tend to become chronic. We show here that the molecular chaperone DnaK is important for biofilm formation and that chemical inhibition of DnaK cellular functions is effective in preventing biofilm development. Genetic, microbial, and microscopic analyses revealed that deletion of the dnaK gene markedly reduced the production of the extracellular functional amyloid curli, which contributes to the robustness of Escherichia coli biofilms. We tested the ability of DnaK inhibitors myricetin (Myr), telmisartan, pancuronium bromide, and zafirlukast to prevent biofilm formation of E. coli. Only Myr, a flavonol widely distributed in plants, inhibited biofilm formation in a concentration-dependent manner (50% inhibitory concentration [IC50] = 46.2 μM); however, it did not affect growth. Transmission electron microscopy demonstrated that Myr inhibited the production of curli. Phenotypic analyses of thermosensitivity, cell division, intracellular level of RNA polymerase sigma factor RpoH, and vulnerability to vancomycin revealed that Myr altered the phenotype of E. coli wild-type cells to make them resemble those of the isogenic dnaK deletion mutant, indicating that Myr inhibits cellular functions of DnaK. These findings provide insights into the significance of DnaK in curli-dependent biofilm formation and indicate that DnaK is an ideal target for antibiofilm drugs. PMID:25403660

  12. Evaluation of Three Small Molecular Drugs for Targeted Therapy to Treat Nonsmall Cell Lung Cancer

    PubMed Central

    Ni, Jun; Zhang, Li

    2016-01-01

    Objective: To guide the optimal selection among first-generation epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) in clinical practice. This review attempted to provide a thorough comparison among three first-generation EGFR-TKIs, namely icotinib, erlotinib, and gefitinib, with regard to their molecular structure, pharmacokinetic parameters, clinical data, adverse reactions, and contraindications. Data Sources: An electronic literature search of the PubMed database and Google Scholar for all the available articles regarding gefitinib, icotinib, and erlotinib in the English language from January 2005 to December 2014 was used. Study Selection: The search terms or keywords included but not limited to “lung cancer”, “nonsmall cell lung cancer (NSCLC)”, “epidemiology”, “EGFR”, “TKIs”, and “optimal selection”. Results: As suggested by this review, even though the three first-generation EGFR-TKIs share the quinazoline structure, erlotinib had the strongest apoptosis induction activity because of its use of a different side-chain. The pharmacokinetic parameters indicated that both erlotinib and icotinib are affected by food. The therapeutic window of erlotinib is narrow, and the recommended dosage is close to the maximum tolerable dosage. Icotinib enjoys a wider therapeutic window, and its concentration in the blood is within a safe dosage range even if it is administered with food. Based on multiple large-scale clinical trials, erlotinib is universally applied as the first-line treatment. In marked contrast, icotinib is available only in China as the second- or third-line therapeutic approach for treating advanced lung cancer. In addition, it exhibits a similar efficacy but better safety profile than gefitinib. Conclusions: Although there is a paucity of literature regarding whether icotinib is superior to erlotinib, its superior toxicity profile, noninferior efficacy, and lower cost indicate that it is a better alternative

  13. Reducing THMFP by H2O2/UV oxidation for humic acid of small molecular weight.

    PubMed

    Yen, Hsing Yuan; Yen, Li Shuang

    2015-01-01

    In this study, the merits of using H2O2/UV oxidation for reducing trihalomethane formation potential (THMFP), colour, and dissolved organic carbon (DOC) of smaller molecular humic acid were investigated, especially the energy consumption based on EEO. The results show that THMFP decreases by increasing oxidation time, H2O2 dose and UV intensity. The reaction constant in descending order is kColour>kDOC>kTHMFP. Furthermore, EEO shows three trends. First, it decreases as H2O2 dose increases. That is, by increasing the amount of H2O2 dose, the electrical energy efficiency becomes better. Second, EEO,9 W>EEO,13 W, implying that higher UV power would result in a higher electrical energy efficiency. Third, EEO,THMFP>EEO,DOC>EEO,colour. That is, the electric energy efficiency is the best for colour removal, second for DOC removal, and third for THMFP reduction. The operation costs for 90% removal of colour, DOC, and THMFP are from 0.31 to 0.69, from 0.78 to 1.72, and from 1.11 to 2.29 US$/m3, respectively. However, reducing THMs to Taiwan's drinking water standard of 80 µg/L needs only 0.25-0.60 US$/m3. Therefore, the condition with UV of 9 W, H2O2 of 50 mg/L, and oxidation time of 23 min can be applied for THMs reduction as the cost is the smallest of 0.25 US$/m3, even lower than current Taiwan's drinking water price of 0.3 US$/m3.

  14. Low temperature p-type doping of (Al)GaN layers using ammonia molecular beam epitaxy for InGaN laser diodes

    SciTech Connect

    Malinverni, M. Lamy, J.-M.; Martin, D.; Grandjean, N.; Feltin, E.; Dorsaz, J.; Castiglia, A.; Rossetti, M.; Duelk, M.; Vélez, C.

    2014-12-15

    We demonstrate state-of-the-art p-type (Al)GaN layers deposited at low temperature (740 °C) by ammonia molecular beam epitaxy (NH{sub 3}-MBE) to be used as top cladding of laser diodes (LDs) with the aim of further reducing the thermal budget on the InGaN quantum well active region. Typical p-type GaN resistivities and contact resistances are 0.4 Ω cm and 5 × 10{sup −4} Ω cm{sup 2}, respectively. As a test bed, we fabricated a hybrid laser structure emitting at 400 nm combining n-type AlGaN cladding and InGaN active region grown by metal-organic vapor phase epitaxy, with the p-doped waveguide and cladding layers grown by NH{sub 3}-MBE. Single-mode ridge-waveguide LD exhibits a threshold voltage as low as 4.3 V for an 800 × 2 μm{sup 2} ridge dimension and a threshold current density of ∼5 kA cm{sup −2} in continuous wave operation. The series resistance of the device is 6 Ω and the resistivity is 1.5 Ω cm, confirming thereby the excellent electrical properties of p-type Al{sub 0.06}Ga{sub 0.94}N:Mg despite the low growth temperature.

  15. Molecular Survey of Zoonotic Agents in Rodents and Other Small Mammals in Croatia.

    PubMed

    Tadin, Ante; Tokarz, Rafal; Markotić, Alemka; Margaletić, Josip; Turk, Nenad; Habuš, Josipa; Svoboda, Petra; Vucelja, Marko; Desai, Aaloki; Jain, Komal; Lipkin, W Ian

    2016-02-01

    Croatia is a focus for many rodent-borne zoonosis. Here, we report a survey of 242 rodents and small mammals, including 43 Myodes glareolus, 131 Apodemus flavicollis, 53 Apodemus agrarius, three Apodemus sylvaticus, six Sorex araneus, four Microtus arvalis, one Microtus agrestis, and one Muscardinus avellanarius, collected at eight sites in Croatia over an 8-year period. Multiplex MassTag polymerase chain reaction (PCR) was used for detection of Borrelia, Rickettsia, Bartonella, Babesia, Ehrlichia, Anaplasma, Francisella tularensis, and Coxiella burnetii. Individual PCR assays were used for detection of Leptospira, lymphocytic choriomeningitis virus, orthopoxviruses, flaviviruses, hantaviruses, and Toxoplasma gondii. Of the rodents, 52 (21.5%) were infected with Leptospira, 9 (3.7%) with Borrelia miyamotoi, 5 (2%) with Borrelia afzelii, 29 (12.0%) with Bartonella, 8 (3.3%) with Babesia microti, 2 (0.8%) with Ehrlichia, 4 (1.7%) with Anaplasma, 2 (0.8%) with F. tularensis, 43 (17.8%) with hantaviruses, and 1 (0.4%) with an orthopoxvirus. Other agents were not detected. Multiple infections were found in 32 rodents (13.2%): dual infections in 26 rodents (10.7%), triple infections in four rodents (2.9%), and quadruple infections in two rodents (0.8%). Our findings indicate that rodents in Croatia harbor a wide range of bacteria and viruses that are pathogenic to humans.

  16. Serological and molecular evidence of Q fever among small ruminant flocks in Algeria.

    PubMed

    Khaled, H; Sidi-Boumedine, K; Merdja, S; Dufour, P; Dahmani, A; Thiéry, R; Rousset, E; Bouyoucef, A

    2016-08-01

    Q fever, a commonly reported zoonosis worldwide, is caused by infection with Coxiella burnetii, an obligate intracellular bacterium. The infection is often asymptomatic in ruminants, but it can lead to reproductive disorders with bacterial shedding into the environment. Between 2011 and 2013, a study was undertaken in small ruminant flocks in different regions of Algeria. A total of 35 flocks were visited and 227 sera and 267 genital swabs were collected from females after abortions or the lambing period to investigate Q fever infection. Indirect ELISA was used to detect specific antibodies against C. burnetii and real-time PCR for detecting bacterial DNA. Our survey indicated that 58% (95% CI=40-76%) of flocks had at least one positive animal (17 seropositive flocks) and individual seroprevalence was estimated at 14.1% (95% CI=11.8-16.4%) (32 seropositive animals). Bacterial excretion was observed in 21 flocks (60%), and 57 females showed evidence of C. burnetii shedding (21.3%). These results suggest that C. burnetii distribution is high at the flock level and that seropositive and infected (shedder) animals can be found all over the country. Further studies are needed in other regions and on different animal species to better understand the distribution and incidence of Q fever, as well as human exposure, and to develop an adequate prophylaxis program. PMID:27477503

  17. Molecular targeted therapy to improve radiotherapeutic outcomes for non-small cell lung carcinoma

    PubMed Central

    Bhardwaj, Bhaskar; Bhardwaj, Himanshu; Balusu, Sree; Shwaiki, Ali

    2016-01-01

    Effective treatments for non-small cell lung carcinoma (NSCLC) remain elusive. The use of concurrent chemotherapy with radiotherapy (RT) has improved outcomes, but a significant proportion of NSCLC patients are too frail to be able to tolerate an intense course of concurrent chemoradiotherapy. The development of targeted therapies ignited new hope in enhancing radiotherapeutic outcomes. The use of targeted therapies against the epidermal growth factor receptor (EGFR) has offered slight but significant benefits in concurrent use with RT for certain patients in certain situations. However, despite theoretical promise, the use of anti-angiogenics, such as bevacizumab and endostatin, has not proven clinically safe or useful in combination with RT. However, many new targeted agents against new targets are being experimented for combined use with RT. It is hoped that these agents may provide a significant breakthrough in the radiotherapeutic management of NSCLC. The current review provides a brief discussion about the targets, the targeted therapies, the rationale for the use of targeted therapies in combination with RT, and a brief review of the existing data on the subject. PMID:26904572

  18. The Molecular Basis for the Endocytosis of Small R-SNAREs by the Clathrin Adaptor CALM

    PubMed Central

    Miller, Sharon E.; Sahlender, Daniela A.; Graham, Stephen C.; Höning, Stefan; Robinson, Margaret S.; Peden, Andrew A.; Owen, David J.

    2011-01-01

    Summary SNAREs provide a large part of the specificity and energy needed for membrane fusion and, to do so, must be localized to their correct membranes. Here, we show that the R-SNAREs VAMP8, VAMP3, and VAMP2, which cycle between the plasma membrane and endosomes, bind directly to the ubiquitously expressed, PtdIns4,5P2-binding, endocytic clathrin adaptor CALM/PICALM. X-ray crystallography shows that the N-terminal halves of their SNARE motifs bind the CALMANTH domain as helices in a manner that mimics SNARE complex formation. Mutation of residues in the CALM:SNARE interface inhibits binding in vitro and prevents R-SNARE endocytosis in vivo. Thus, CALM:R-SNARE interactions ensure that R-SNAREs, required for the fusion of endocytic clathrin-coated vesicles with endosomes and also for subsequent postendosomal trafficking, are sorted into endocytic vesicles. CALM's role in directing the endocytosis of small R-SNAREs may provide insight into the association of CALM/PICALM mutations with growth retardation, cognitive defects, and Alzheimer's disease. PMID:22118466

  19. Molecular mechanisms of glucose-stimulated GLP-1 secretion from perfused rat small intestine.

    PubMed

    Kuhre, Rune E; Frost, Charlotte R; Svendsen, Berit; Holst, Jens J

    2015-02-01

    Glucose is an important stimulus for glucagon-like peptide 1 (GLP-1) secretion, but the mechanisms of secretion have not been investigated in integrated physiological models. We studied glucose-stimulated GLP-1 secretion from isolated perfused rat small intestine. Luminal glucose (5% and 20% w/v) stimulated the secretion dose dependently, but vascular glucose was without significant effect at 5, 10, 15, and 25 mmol/L. GLP-1 stimulation by luminal glucose (20%) secretion was blocked by the voltage-gated Ca channel inhibitor, nifedipine, or by hyperpolarization with diazoxide. Luminal administration (20%) of the nonmetabolizable sodium-glucose transporter 1 (SGLT1) substrate, methyl-α-D-glucopyranoside (α-MGP), stimulated release, whereas the SGLT1 inhibitor phloridzin (luminally) abolished responses to α-MGP and glucose. Furthermore, in the absence of luminal NaCl, luminal glucose (20%) did not stimulate a response. Luminal glucose-stimulated GLP-1 secretion was also sensitive to luminal GLUT2 inhibition (phloretin), but in contrast to SGLT1 inhibition, phloretin did not eliminate the response, and luminal glucose (20%) stimulated larger GLP-1 responses than luminal α-MGP in matched concentrations. Glucose transported by GLUT2 may act after metabolization, closing KATP channels similar to sulfonylureas, which also stimulated secretion. Our data indicate that SGLT1 activity is the driving force for glucose-stimulated GLP-1 secretion and that KATP-channel closure is required to stimulate a full-blown glucose-induced response.

  20. Lymphatic drainage, CTV and molecular imaging in non-small cell lung cancer.

    PubMed

    Trodella, Lucio; Ciresa, Marzia; D'Angelillo, Rolando; Ramella, Sara

    2003-01-01

    Prognosis for non-small cell lung cancer (NSCLC) patients who have locally advanced unresectable disease is poor for persistent thoracic disease and development of distant metastasis. In view of the poor rate of local control following conventional radiation therapy, there is a great need for methods to improve its efficacy. Three-dimensional conformal radiation therapy (3DCRT) is a high precision radiotherapy able to deliver higher doses with smaller doses to the surrounding normal tissues. However, the real problem is: "what do I want to treat?" This question is addressed based on the clinical and biological target volume definition. Selection of the CTV is therefore basically the clinical compromise between the most radical possible CTV and the critical normal tissue tolerance. The clinical target volume includes the GTV plus a margin to encompass subclinical or microscopic malignant disease immediately adjacent to it. Standard radiation therapy consists of a dose of 40 Gy to the entire mediastinum, supraclavicular fossa, and ipsilateral hilum, even if there is no evidence of disease in these areas. Despite the high risk of nodal spread in lung cancer, the benefit of additional elective nodal irradiation (ENI) is not proven while it seems to significantly increase the rate of radiation morbidity. Several studies have been published where ENI was systematically omitted. The main arguments for omitting ENI and the principal clinical experiences, are discussed. PMID:15018317

  1. A microcomputed tomography guided fluorescence tomography system for small animal molecular imaging

    SciTech Connect

    Kepshire, Dax; Gruber, Josiah; Hypnarowski, Justin; Leblond, Frederic; Pogue, Brian W.; Mincu, Niculae; Hutchins, Michael; Khayat, Mario; Dehghani, Hamid

    2009-04-15

    A prototype small animal imaging system was created for coupling fluorescence tomography (FT) with x-ray microcomputed tomography (microCT). The FT system has the potential to provide synergistic information content resultant from using microCT images as prior spatial information and then allows overlay of the FT image onto the original microCT image. The FT system was designed to use single photon counting to provide maximal sensitivity measurements in a noncontact geometry. Five parallel detector locations are used, each allowing simultaneous sampling of the fluorescence and transmitted excitation signals through the tissue. The calibration and linearity range performance of the system are outlined in a series of basic performance tests and phantom studies. The ability to image protoporphyrin IX in mouse phantoms was assessed and the system is ready for in vivo use to study biological production of this endogenous marker of tumors. This multimodality imaging system will have a wide range of applications in preclinical cancer research ranging from studies of the tumor microenvironment and treatment efficacy for emerging cancer therapeutics.

  2. Structural investigations of E. Coli dihydrolipoamide dehydrogenase in solution: Small-angle X-ray scattering and molecular docking

    NASA Astrophysics Data System (ADS)

    Dadinova, L. A.; Rodina, E. V.; Vorobyeva, N. N.; Kurilova, S. A.; Nazarova, T. I.; Shtykova, E. V.

    2016-05-01

    Dihydrolipoamide dehydrogenase from Escherichia coli (LpD) is a bacterial enzyme that is involved in the central metabolism and shared in common between the pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase complexes. In the crystal structure, E. coli LpD is known to exist as a dimer. The present work is focused on analyzing the solution structure of LpD by small-angle X-ray scattering, molecular docking, and analytical ultracentrifugation. It was shown that in solution LpD exists as an equilibrium mixture of a dimer and a tetramer. The presence of oligomeric forms is determined by the multifunctionality of LpD in the cell, in particular, the required stoichiometry in the complexes.

  3. The Effect of Small Cosolutes that Mimic Molecular Crowding Conditions on the Stability of Triplexes Involving Duplex DNA

    PubMed Central

    Aviñó, Anna; Mazzini, Stefania; Gargallo, Raimundo; Eritja, Ramon

    2016-01-01

    Triplex stability is studied in crowding conditions using small cosolutes (ethanol, acetonitrile and dimethylsulfoxide) by ultraviolet (UV), circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopies. The results indicate that the triplex is formed preferentially when the triplex forming oligonucleotide (TFO) is RNA. In addition, DNA triplexes (D:D·D) are clearly less stable in cosolute solutions while the stability of the RNA triplexes (R:D·D) is only slightly decreased. The kinetic of triplex formation with RNA-TFO is slower than with DNA-TFO and the thermal stability of the triplex is increased with the salt concentration in EtOH-water solutions. Accordingly, RNA could be considered a potential molecule to form a stable triplex for regulatory purposes in molecular crowding conditions. PMID:26861295

  4. Tuning of EAG K(+) channel inactivation: molecular determinants of amplification by mutations and a small molecule.

    PubMed

    Garg, Vivek; Sachse, Frank B; Sanguinetti, Michael C

    2012-09-01

    Ether-à-go-go (EAG) and EAG-related gene (ERG) K(+) channels are close homologues but differ markedly in their gating properties. ERG1 channels are characterized by rapid and extensive C-type inactivation, whereas mammalian EAG1 channels were previously considered noninactivating. Here, we show that human EAG1 channels exhibit an intrinsic voltage-dependent slow inactivation that is markedly enhanced in rate and extent by 1-10 µM 3-nitro-N-(4-phenoxyphenyl) benzamide, or ICA105574 (ICA). This compound was previously reported to have the opposite effect on ERG1 channels, causing an increase in current magnitude by inhibition of C-type inactivation. The voltage dependence of 2 µM ICA-induced inhibition of EAG1 current was half-maximal at -73 mV, 62 mV negative to the half-point for channel activation. This finding suggests that current inhibition by the drug is mediated by enhanced inactivation and not open-channel block, where the voltage half-points for current inhibition and channel activation are predicted to overlap, as we demonstrate for clofilium and astemizole. The mutation Y464A in the S6 segment also induced inactivation of EAG1, with a time course and voltage dependence similar to that caused by 2 µM ICA. Several Markov models were investigated to describe gating effects induced by multiple concentrations of the drug and the Y464A mutation. Models with the smallest fit error required both closed- and open-state inactivation. Unlike typical C-type inactivation, the rate of Y464A- and ICA-induced inactivation was not decreased by external tetraethylammonium or elevated [K(+)](e). EAG1 channel inactivation introduced by Y464A was prevented by additional mutation of a nearby residue located in the S5 segment (F359A) or pore helix (L434A), suggesting a tripartite molecular model where interactions between single residues in S5, S6, and the pore helix modulate inactivation of EAG1 channels. PMID:22930803

  5. Molecular and biochemical characterization of human galactokinase and its small molecule inhibitors.

    PubMed

    Tang, M; Wierenga, K; Elsas, L J; Lai, K

    2010-12-01

    Human galactokinase (GALK) is the first enzyme in the Leloir pathway, converting α-d-galactose into galactose-1-phosphate (Gal-1-P). Recently, there is increasing interest in targeting GALK as a novel therapy to ameliorate the disease manifestations in patients with Classic Galactosemia as it would, in combination with (ga-)lactose restriction reduce accumulation of Gal-1-P, a cytotoxic agent. Previously, we identified 34 small molecule compounds that inhibited GALK in vitro using experimental high-throughput screening. In order to isolate useful lead compounds, we characterized these hits with regards to their kinase selectivity profiles, potency and capability to reduce Gal-1-P accumulation in patient cell lines, and their modes of action. We found that the majority of these compounds had IC(50)s ranging from 0.7μM to 33.3μM. When tested against other members of the GHMP kinase family, three compounds (1, 4, and 24) selectively inhibited GALK with high potency. Through alignment of GALK and mevalonate kinase (MVK) crystal structures, we identified that eight amino acid residues and an L1 loop were different within the ATP-binding pockets of these two closely related kinases. By site-directed mutagenesis experiments, we identified one amino acid residue required for the inhibitory function of two of the three selective compounds. Based on these results, we generated binding models of these two compounds using a high-precision docking program. Compounds 4 and 24 inhibited GALK in a mixed model, while compound 1 exhibited parabolic competitive inhibition. Most importantly, using cells from galactosemic patients we found that selected compounds lowered Gal-1-P concentrations.

  6. In vivo application of a small molecular weight antifungal protein of Penicillium chrysogenum (PAF)

    SciTech Connect

    Palicz, Zoltán; Jenes, Ágnes; Gáll, Tamás; Miszti-Blasius, Kornél; Kollár, Sándor; Kovács, Ilona; Emri, Miklós; Márián, Teréz; Leiter, Éva; Pócsi, István; Csősz, Éva; Kalló, Gergő; Hegedűs, Csaba; Virág, László; Csernoch, László; Szentesi, Péter

    2013-05-15

    The antifungal protein of Penicillium chrysogenum (PAF) inhibits the growth of important pathogenic filamentous fungi, including members of the Aspergillus family and some dermatophytes. Furthermore, PAF was proven to have no toxic effects on mammalian cells in vitro. To prove that PAF could be safely used in therapy, experiments were carried out to investigate its in vivo effects. Adult mice were inoculated with PAF intranasally in different concentrations, up to 2700 μg·kg{sup −1} daily, for 2 weeks. Even at the highest concentration – a concentration highly toxic in vitro for all affected molds – used, animals neither died due to the treatment nor were any side effects observed. Histological examinations did not find pathological reactions in the liver, in the kidney, and in the lungs. Mass spectrometry confirmed that a measurable amount of PAF was accumulated in the lungs after the treatment. Lung tissue extracts from PAF treated mice exerted significant antifungal activity. Small-animal positron emission tomography revealed that neither the application of physiological saline nor that of PAF induced any inflammation while the positive control lipopolysaccharide did. The effect of the drug on the skin was examined in an irritative dermatitis model where the change in the thickness of the ears following PAF application was found to be the same as in control and significantly less than when treated with phorbol-12-myristate-13-acetate used as positive control. Since no toxic effects of PAF were found in intranasal application, our result is the first step for introducing PAF as potential antifungal drug in therapy. - Highlights: • PAF, the antifungal protein of Penicillium chrysogenum, was not toxic in mice. • Its intranasal application didn't induce pathological reactions in the lung. • PAF retained its antifungal activity in lung extracts. • Its application on the skin did not cause inflammation.

  7. Investigation of potential molecular biomarkers and small molecule drugs for hepatocellular carcinoma transformed from cirrhosis

    PubMed Central

    XIE, FENG; ZHU, FANG; LU, ZAIMING; LIU, ZHENGRONG; WANG, HONGYAN

    2016-01-01

    Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in China and the third leading cause of cancer-associated morality. The aim of the present study was to investigate and analyze differentially-expressed genes (DEGs) between cirrhosis and HCC, in order to screen the key genes involved in the transformation from cirrhosis to HCC and provide novel targets for the diagnosis and treatment of HCC in patients with cirrhosis. The gene expression profile, GSE17548, was obtained from Gene Expression Omnibus database and the DEGs were identified by LIMMA package in R language. Kyoto Encyclopedia of Genes and Genomes and gene ontology biology process analysis were performed for the DEGs. Differential co-expression network (DEN) analysis was conducted and the network was visualized using Cytoscape. Small molecule drugs were also screened from the Comparative Toxicogenomics Database for higher degree DEGs. A total of 95 DEGs were obtained, including 46 upregulated and 49 downregulated genes. The upregulated DEGs were primarily involved in biological processes and pathways associated with the cell cycle, while the downregulated DEGs were primarily involved in immune-associated biological processes. A total of 22 key DEGs were identified by DEN analysis, which distinguished HCC from cirrhosis samples. Furthermore, estradiol, benzo(a)pyrene, acetaminophen, copper sulfate and bisphenol A were identified as the five most associated chemicals to these 22 DEGs. In conclusion, the hub genes and chemicals identified by the present study may provide a theoretical basis for additional research on diagnosis and treatment of HCC transformed from cirrhosis. PMID:27347171

  8. Dosimetry for spectral molecular imaging of small animals with MARS-CT

    NASA Astrophysics Data System (ADS)

    Ganet, Noémie; Anderson, Nigel; Bell, Stephen; Butler, Anthony; Butler, Phil; Carbonez, Pierre; Cook, Nicholas; Cotterill, Tony; Marsh, Steven; Panta, Raj Kumar; Laban, John; Walker, Sophie; Yeabsley, Adam; Damet, Jérôme

    2015-03-01

    The Medipix All Resolution Scanner (MARS) spectral CT is intended for small animal, pre-clinical imaging and uses an x-ray detector (Medipix) operating in single photon counting mode. The MARS system provides spectrometric information to facilitate differentiation of tissue types and bio-markers. For longitudinal studies of disease models, it is desirable to characterise the system's dosimetry. This dosimetry study is performed using three phantoms each consisting of a 30 mm diameter homogeneous PMMA cylinder simulating a mouse. The imaging parameters used for this study are derived from those used for gold nanoparticle identification in mouse kidneys. Dosimetry measurement are obtained with thermo-luminescent Lithium Fluoride (LiF:CuMgP) detectors, calibrated in terms of air kerma and placed at different depths and orientations in the phantoms. Central axis TLD air kerma rates of 17.2 (± 0.71) mGy/min and 18.2 (± 0.75) mGy/min were obtained for different phantoms and TLD orientations. Validation measurements were acquired with a pencil ionization chamber, giving an air-kerma rate of 20.3 (±1) mGy/min and an estimated total air kerma of 81.2 (± 4) mGy for a 720 projection acquisition. It is anticipated that scanner design improvements will significantly decrease future dose requirements. The procedures developed in this work will be used for further dosimetry calculations when optimizing image acquisition for the MARS system as it undergoes development towards human clinical applications.

  9. Microbial Abundances in Salt Marsh Soils: A Molecular Approach for Small Spatial Scales

    NASA Astrophysics Data System (ADS)

    Granse, Dirk; Mueller, Peter; Weingartner, Magdalena; Hoth, Stefan; Jensen, Kai

    2016-04-01

    The rate of biological decomposition greatly determines the carbon sequestration capacity of salt marshes. Microorganisms are involved in the decomposition of biomass and the rate of decomposition is supposed to be related to microbial abundance. Recent studies quantified microbial abundance by means of quantitative polymerase chain reaction (QPCR), a method that also allows determining the microbial community structure by applying specific primers. The main microbial community structure can be determined by using primers specific for 16S rRNA (Bacteria) and 18S rRNA (Fungi) of the microbial DNA. However, the investigation of microbial abundance pattern at small spatial scales, such as locally varying abiotic conditions within a salt-marsh system, requires high accuracy in DNA extraction and QPCR methods. Furthermore, there is evidence that a single extraction may not be sufficient to reliably quantify rRNA gene copies. The aim of this study was to establish a suitable DNA extraction method and stable QPCR conditions for the measurement of microbial abundances in semi-terrestrial environments. DNA was extracted from two soil samples (top WE{5}{cm}) by using the PowerSoil DNA Extraction Kit (Mo Bio Laboratories, Inc., Carlsbad, CA) and applying a modified extraction protocol. The DNA extraction was conducted in four consecutive DNA extraction loops from three biological replicates per soil sample by reusing the PowerSoil bead tube. The number of Fungi and Bacteria rRNA gene copies of each DNA extraction loop and a pooled DNA solution (extraction loop 1 - 4) was measured by using the QPCR method with taxa specific primer pairs (Bacteria: B341F, B805R; Fungi: FR1, FF390). The DNA yield of the replicates varied at DNA extraction loop 1 between WE{25 and 85}{ng

  10. INFRARED AND RADIO OBSERVATIONS OF A SMALL GROUP OF PROTOSTELLAR OBJECTS IN THE MOLECULAR CORE, L1251-C

    SciTech Connect

    Kim, Jungha; Lee, Jeong-Eun; Choi, Minho; Kang, Miju; Bourke, Tyler L.; II, Neal J. Evans; Francesco, James Di; Cieza, Lucas A.; Dunham, Michael M.

    2015-05-15

    We present a multi-wavelength observational study of a low-mass star-forming region, L1251-C, with observational results at wavelengths from the near-infrared to the millimeter. Spitzer Space Telescope observations confirmed that IRAS 22343+7501 is a small group of protostellar objects. The extended emission in the east–west direction with its intensity peak at the center of L1251A has been detected at 350 and 850 μm with the Caltech Submillimeter Observatory and James Clerk Maxwell telescopes, tracing dense envelope material around L1251A. The single-dish data from the Korean VLBI Network and TRAO telescopes show inconsistencies between the intensity peaks of several molecular emission lines and that of the continuum emission, suggesting complex distributions of molecular abundances around L1251A. The Submillimeter Array interferometer data, however, show intensity peaks of CO 2–1 and {sup 13}CO 2–1 located at the position of IRS 1, which is both the brightest source in the Infrared Array Camera image and the weakest source in the 1.3 mm dust-continuum map. IRS 1 is the strongest candidate for the driving source of the newly detected compact CO 2–1 outflow. Over the entire region (14′ × 14′) of L125l-C, 3 Class I and 16 Class II sources have been detected, including three young stellar objects (YSOs) in L1251A. A comparison between the average projected distance among the 19 YSOs in L1251-C and that among the 3 YSOs in L1251A suggests that L1251-C is an example of low-mass cluster formation where protostellar objects form in a small group.

  11. Infrared and Radio Observations of a Small Group of Protostellar Objects in the Molecular Core, L1251-C

    NASA Astrophysics Data System (ADS)

    Kim, Jungha; Lee, Jeong-Eun; Choi, Minho; Bourke, Tyler L.; Evans, Neal J., II; Di Francesco, James; Cieza, Lucas A.; Dunham, Michael M.; Kang, Miju

    2015-05-01

    We present a multi-wavelength observational study of a low-mass star-forming region, L1251-C, with observational results at wavelengths from the near-infrared to the millimeter. Spitzer Space Telescope observations confirmed that IRAS 22343+7501 is a small group of protostellar objects. The extended emission in the east-west direction with its intensity peak at the center of L1251A has been detected at 350 and 850 μm with the Caltech Submillimeter Observatory and James Clerk Maxwell telescopes, tracing dense envelope material around L1251A. The single-dish data from the Korean VLBI Network and TRAO telescopes show inconsistencies between the intensity peaks of several molecular emission lines and that of the continuum emission, suggesting complex distributions of molecular abundances around L1251A. The Submillimeter Array interferometer data, however, show intensity peaks of CO 2-1 and 13CO 2-1 located at the position of IRS 1, which is both the brightest source in the Infrared Array Camera image and the weakest source in the 1.3 mm dust-continuum map. IRS 1 is the strongest candidate for the driving source of the newly detected compact CO 2-1 outflow. Over the entire region (14‧ × 14‧) of L125l-C, 3 Class I and 16 Class II sources have been detected, including three young stellar objects (YSOs) in L1251A. A comparison between the average projected distance among the 19 YSOs in L1251-C and that among the 3 YSOs in L1251A suggests that L1251-C is an example of low-mass cluster formation where protostellar objects form in a small group.

  12. A molecular insight into the electro-transfer of small molecules through electropores driven by electric fields.

    PubMed

    Casciola, Maura; Tarek, Mounir

    2016-10-01

    The transport of chemical compounds across the plasma membrane into the cell is relevant for several biological and medical applications. One of the most efficient techniques to enhance this uptake is reversible electroporation. Nevertheless, the detailed molecular mechanism of transport of chemical species (dyes, drugs, genetic materials, …) following the application of electric pulses is not yet fully elucidated. In the past decade, molecular dynamics (MD) simulations have been conducted to model the effect of pulsed electric fields on membranes, describing several aspects of this phenomenon. Here, we first present a comprehensive review of the results obtained so far modeling the electroporation of lipid membranes, then we extend these findings to study the electrotransfer across lipid bilayers subject to microsecond pulsed electric fields of Tat11, a small hydrophilic charged peptide, and of siRNA. We use in particular a MD simulation protocol that allows to characterize the transport of charged species through stable pores. Unexpectedly, our results show that for an electroporated bilayer subject to transmembrane voltages in the order of 500mV, i.e. consistent with experimental conditions, both Tat11 and siRNA can translocate through nanoelectropores within tens of ns. We discuss these results in comparison to experiments in order to rationalize the mechanism of drug uptake by cells. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. PMID:27018309

  13. Taurine Boosts Cellular Uptake of Small d-Peptides for Enzyme-Instructed Intracellular Molecular Self-Assembly

    PubMed Central

    2016-01-01

    Due to their biostability, d-peptides are emerging as an important molecular platform for biomedical applications. Being proteolytically resistant, d-peptides lack interactions with endogenous transporters and hardly enter cells. Here we show that taurine, a natural amino acid, drastically boosts the cellular uptake of small d-peptides in mammalian cells by >10-fold, from 118 μM (without conjugating taurine) to >1.6 mM (after conjugating taurine). The uptake of a large amount of the ester conjugate of taurine and d-peptide allows intracellular esterase to trigger intracellular self-assembly of the d-peptide derivative, further enhancing their cellular accumulation. The study on the mechanism of the uptake reveals that the conjugates enter cells via both dynamin-dependent endocytosis and macropinocytosis, but likely not relying on taurine transporters. Differing fundamentally from the positively charged cell-penetrating peptides, the biocompatibility, stability, and simplicity of the enzyme-cleavable taurine motif promise new ways to promote the uptake of bioactive molecules for countering the action of efflux pump and contributing to intracellular molecular self-assembly. PMID:26235707

  14. Molecular docking studies of Traditional Chinese Medicinal compounds against known protein targets to treat non-small cell lung carcinomas.

    PubMed

    Zhao, Guo-Fang; Huang, Zuo-An; Du, Xue-Kui; Yang, Ming-Lei; Huang, Dan-Dan; Zhang, Shun

    2016-08-01

    In silico drug design using virtual screening, absorption, distribution, metabolism and excretion (ADME)/Tox data analysis, automated docking and molecular dynamics simulations for the determination of lead compounds for further in vitro analysis is a cost effective strategy. The present study used this strategy to discover novel lead compounds from an in-house database of Traditional Chinese Medicinal (TCM) compounds against epithelial growth factor receptor (EGFR) protein for targeting non-small cell lung cancer (NSCLC). After virtual screening of an initial dataset of 2,242 TCM compounds, leads were identified based on binding energy and ADME/Tox data and subjected to automated docking followed by molecular dynamics simulation. Triptolide, a top compound identified by this vigorous in silico screening, was then tested in vitro on the H2347 cell line carrying wild-type EGFR, revealing an anti-proliferative potency similar to that of known drugs against NSCLC. PMID:27279494

  15. Taurine Boosts Cellular Uptake of Small D-Peptides for Enzyme-Instructed Intracellular Molecular Self-Assembly.

    PubMed

    Zhou, Jie; Du, Xuewen; Li, Jie; Yamagata, Natsuko; Xu, Bing

    2015-08-19

    Due to their biostability, D-peptides are emerging as an important molecular platform for biomedical applications. Being proteolytically resistant, D-peptides lack interactions with endogenous transporters and hardly enter cells. Here we show that taurine, a natural amino acid, drastically boosts the cellular uptake of small D-peptides in mammalian cells by >10-fold, from 118 μM (without conjugating taurine) to >1.6 mM (after conjugating taurine). The uptake of a large amount of the ester conjugate of taurine and D-peptide allows intracellular esterase to trigger intracellular self-assembly of the D-peptide derivative, further enhancing their cellular accumulation. The study on the mechanism of the uptake reveals that the conjugates enter cells via both dynamin-dependent endocytosis and macropinocytosis, but likely not relying on taurine transporters. Differing fundamentally from the positively charged cell-penetrating peptides, the biocompatibility, stability, and simplicity of the enzyme-cleavable taurine motif promise new ways to promote the uptake of bioactive molecules for countering the action of efflux pump and contributing to intracellular molecular self-assembly.

  16. Molecular Testing for Treatment of Metastatic Non-Small Cell Lung Cancer: How to Implement Evidence-Based Recommendations.

    PubMed

    Levy, Benjamin P; Chioda, Marc D; Herndon, Dana; Longshore, John W; Mohamed, Mohamed; Ou, Sai-Hong Ignatius; Reynolds, Craig; Singh, Jaspal; Wistuba, Ignacio I; Bunn, Paul A; Hirsch, Fred R

    2015-10-01

    The recent discovery of relevant biomarkers has reshaped our approach to therapy selection for patients with non-small cell lung cancer. The unprecedented outcomes demonstrated with tyrosine kinase inhibitors in molecularly defined cohorts of patients has underscored the importance of genetic profiling in this disease. Despite published guidelines on biomarker testing, successful tumor genotyping faces significant hurdles at both academic and community-based practices. Oncologists are now faced with interpreting large-scale genomic data from multiple tumor types, possibly making it difficult to stay current with practice standards in lung cancer. In addition, physicians' lack of time, resources, and face-to-face opportunities can interfere with the multidisciplinary approach that is essential to delivery of care. Finally, several challenges exist in optimizing the amount and quality of tissue for molecular testing. Recognizing the importance of biomarker testing, a series of advisory boards were recently convened to address these hurdles and clarify best practices. We reviewed these challenges and established recommendations to help optimize tissue acquisition, processing, and testing within the framework of a multidisciplinary approach. PMID:26330460

  17. Surface treatment by binary solvents induces the crystallization of a small molecular donor for enhanced photovoltaic performance.

    PubMed

    Zhou, Weihua; Xie, Yuanpeng; Hu, Xiaotian; Zhang, Lin; Meng, Xiangchuan; Zhang, Yong; Ma, Wei; Chen, Yiwang

    2016-01-14

    The surface treatment of the active layer with binary solvents composed of methanol (MeOH) and 1-chloronaphthalene (CN), was demonstrated to effectively improve the power conversion efficiency (PCE) from 2.4% to 6.5% for p-DTS(FBTTh2)2:PC71BM based small molecular solar cells. The optical properties and morphology of the p-DTS(FBTTh2)2:PC71BM films were carefully investigated. The results indicate that treatment with MeOH:CN binary solvents could significantly enhance the absorption of the active layer, due to the formation of more p-DTS(FBTTh2)2 nanofibrils associated with higher crystallinity as revealed by atomic force microscopy (AFM) and transmission electron microscopy (TEM). The two-dimensional grazing incidence wide-angle X-ray scattering (GIWAXS) results further demonstrate that the molecular packing of p-DTS(FBTTh2)2 molecules could be strongly enhanced after treatment with the binary solvents. In contrast, pristine methanol shows no significant influence on the crystalline structure, phase separation or the photovoltaic properties of the p-DTS(FBTTh2)2:PC71BM system, showing that the CN solvent plays the main role in inducing the crystallization of p-DTS(FBTTh2)2 molecules. PMID:26660911

  18. Taurine Boosts Cellular Uptake of Small D-Peptides for Enzyme-Instructed Intracellular Molecular Self-Assembly.

    PubMed

    Zhou, Jie; Du, Xuewen; Li, Jie; Yamagata, Natsuko; Xu, Bing

    2015-08-19

    Due to their biostability, D-peptides are emerging as an important molecular platform for biomedical applications. Being proteolytically resistant, D-peptides lack interactions with endogenous transporters and hardly enter cells. Here we show that taurine, a natural amino acid, drastically boosts the cellular uptake of small D-peptides in mammalian cells by >10-fold, from 118 μM (without conjugating taurine) to >1.6 mM (after conjugating taurine). The uptake of a large amount of the ester conjugate of taurine and D-peptide allows intracellular esterase to trigger intracellular self-assembly of the D-peptide derivative, further enhancing their cellular accumulation. The study on the mechanism of the uptake reveals that the conjugates enter cells via both dynamin-dependent endocytosis and macropinocytosis, but likely not relying on taurine transporters. Differing fundamentally from the positively charged cell-penetrating peptides, the biocompatibility, stability, and simplicity of the enzyme-cleavable taurine motif promise new ways to promote the uptake of bioactive molecules for countering the action of efflux pump and contributing to intracellular molecular self-assembly. PMID:26235707

  19. Vicinage forces between molecular and atomic fragments dissociated from small hydrogen clusters and their effects on energy distributions

    SciTech Connect

    Barriga-Carrasco, Manuel D.; Garcia-Molina, Rafael

    2003-12-01

    In this paper we analyze the dynamic evolution of molecular and atomic fragments of small hydrogen clusters interacting with thin solid foils. We compare the vicinage forces, calculated within the dielectric formalism, for H{sup +}, H{sup 0}, and H{sub 2}{sup +} fragments. Using a molecular dynamics numerical code we determine the energy distribution of the fragments after interacting with the target. This distribution is compared to experimental results for protons coming from the fragmentation of v=2.02 a.u. H{sub 2}{sup +} ions impinging on an aluminum foil; a fraction of neutral H{sup 0} is needed to be included in the simulation to get a good agreement with the experimental results. The H{sub 2}{sup +} energy spectra for v=5.42 a.u. H{sub 3}{sup +} interacting with amorphous carbon is also determined. The asymmetry in the Coulomb peaks appearing in the energy spectra both experimentally and in our calculation is opposite for H{sub 2}{sup +} than in H{sup +}; kinematic effects and differences in the electronic stopping are enough to reproduce the difference in the alignment of H{sub 2}{sup +} and H{sup +} fragments.

  20. Spatial distribution of intra-molecular water and polymeric components in polyelectrolyte dendrimers revealed by small angle scattering investigations

    SciTech Connect

    Chen, Chun-Yu; Chen, Wei-Ren; Herwig, Kenneth W; Hong, Kunlun; Li, Xin; Liu, Emily; Liu, Yun; Smith, Gregory Scott; Wu, Bin; Yang, Jun; Do, Changwoo

    2011-01-01

    An experimental scheme using contrast variation small angle neutron scattering technique (SANS), is developed to investigate the structural characteristics of amine-terminated poly(amidoamine) dendrimers (PAMAM) solutions. The focus is placed on understanding the dependence of intra-dendrimer water and polymer distribution on molecular protonation, which can be precisely adjusted by tuning the pH value of solution. Assuming the spherical symmetry in the spatial arrangement of the constituent component of dendrimer, and the atomic ratio of hydrogen-to-deuterium for the solvent residing within the cavities of dendrimer is identical to that for the solvent outside dendrimer, the intra-dendrimer water distribution along the radial direction can be determined based on the model of coherent scattering cross section developed in this work. Moreover, our result clearly reveals an outward relocation of the peripheral groups, as well as the enhanced intra-dendrimer hydration, upon increasing the molecular protonation and therefore allows the determination of segmental backfolding in a quantitative manner. The connection between these charge-induced structural changes and our recently observed progressively active segmental dynamics is also discussed.

  1. Array formatting of the heat-transfer method (HTM) for the detection of small organic molecules by molecularly imprinted polymers.

    PubMed

    Wackers, Gideon; Vandenryt, Thijs; Cornelis, Peter; Kellens, Evelien; Thoelen, Ronald; De Ceuninck, Ward; Losada-Pérez, Patricia; van Grinsven, Bart; Peeters, Marloes; Wagner, Patrick

    2014-06-20

    In this work we present the first steps towards a molecularly imprinted polymer (MIP)-based biomimetic sensor array for the detection of small organic molecules via the heat-transfer method (HTM). HTM relies on the change in thermal resistance upon binding of the target molecule to the MIP-type receptor. A flow-through sensor cell was developed, which is segmented into four quadrants with a volume of 2.5 μL each, allowing four measurements to be done simultaneously on a single substrate. Verification measurements were conducted, in which all quadrants received a uniform treatment and all four channels exhibited a similar response. Subsequently, measurements were performed in quadrants, which were functionalized with different MIP particles. Each of these quadrants was exposed to the same buffer solution, spiked with different molecules, according to the MIP under analysis. With the flow cell design we could discriminate between similar small organic molecules and observed no significant cross-selectivity. Therefore, the MIP array sensor platform with HTM as a readout technique, has the potential to become a low-cost analysis tool for bioanalytical applications.

  2. Isomers of small Pbn clusters (n=2-15) : Geometric and electronic structures based on ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Rajesh, C.; Majumder, C.; Rajan, M. G. R.; Kulshreshtha, S. K.

    2005-12-01

    The geometric and electronic structure of the Pbn clusters (n=2-15) has been calculated to elucidate its structural evolution and compared with other group-IV elemental clusters. The search for several low-lying isomers was carried out using the ab initio molecular dynamics simulations under the framework of the density functional theory formalism. The results suggest that unlike Si, Ge, and Sn clusters, which favor less compact prolate shape in the small size range, Pb clusters favor compact spherical structures consisting of fivefold or sixfold symmetries. The difference in the growth motif can be attributed to their bulk crystal structure, which is diamond-like for Si, Ge, and Sn but fcc for Pb. The relative stability of Pbn clusters is analyzed based on the calculated binding energies and second difference in energy. The results suggest that n=4 , 7, 10, and 13 clusters are more stable than their respective neighbors, reflecting good agreement with experimental observation. Based on the fragmentation pattern it is seen that small clusters up to n=12 favor monomer evaporation, larger ones fragment into two stable daughter products. The experimental observation of large abundance for n=7 and lowest abundance of n=14 have been demonstrated from their fragmentation pattern. Finally a good agreement of our theoretical results with that of the experimental findings reported earlier implies accurate predictions of the ground state geometries of these clusters.

  3. Array Formatting of the Heat-Transfer Method (HTM) for the Detection of Small Organic Molecules by Molecularly Imprinted Polymers

    PubMed Central

    Wackers, Gideon; Vandenryt, Thijs; Cornelis, Peter; Kellens, Evelien; Thoelen, Ronald; De Ceuninck, Ward; Losada-Pérez, Patricia; van Grinsven, Bart; Peeters, Marloes; Wagner, Patrick

    2014-01-01

    In this work we present the first steps towards a molecularly imprinted polymer (MIP)-based biomimetic sensor array for the detection of small organic molecules via the heat-transfer method (HTM). HTM relies on the change in thermal resistance upon binding of the target molecule to the MIP-type receptor. A flow-through sensor cell was developed, which is segmented into four quadrants with a volume of 2.5 μL each, allowing four measurements to be done simultaneously on a single substrate. Verification measurements were conducted, in which all quadrants received a uniform treatment and all four channels exhibited a similar response. Subsequently, measurements were performed in quadrants, which were functionalized with different MIP particles. Each of these quadrants was exposed to the same buffer solution, spiked with different molecules, according to the MIP under analysis. With the flow cell design we could discriminate between similar small organic molecules and observed no significant cross-selectivity. Therefore, the MIP array sensor platform with HTM as a readout technique, has the potential to become a low-cost analysis tool for bioanalytical applications. PMID:24955945

  4. The reaction enthalpy of hydrogen dissociation calculated with the Small System Method from simulation of molecular fluctuations.

    PubMed

    Skorpa, Ragnhild; Simon, Jean-Marc; Bedeaux, Dick; Kjelstrup, Signe

    2014-09-28

    We show how we can find the enthalpy of a chemical reaction under non-ideal conditions using the Small System Method to sample molecular dynamics simulation data for fluctuating variables. This method, created with Hill's thermodynamic analysis, is used to find properties in the thermodynamic limit, such as thermodynamic correction factors, partial enthalpies, volumes, heat capacities and compressibility. The values in the thermodynamic limit at (T,V, μj) are then easily transformed into other ensembles, (T,V,Nj) and (T,P,Nj), where the last ensemble gives the partial molar properties which are of interest to chemists. The dissociation of hydrogen from molecules to atoms was used as a convenient model system. Molecular dynamics simulations were performed with three densities; ρ = 0.0052 g cm(-3) (gas), ρ = 0.0191 g cm(-3) (compressed gas) and ρ = 0.0695 g cm(-3) (liquid), and temperatures in the range; T = 3640-20,800 K. The enthalpy of reaction was observed to follow a quadratic trend as a function of temperature for all densities. The enthalpy of reaction was observed to only have a small pressure dependence. With a reference point close to an ideal state (T = 3640 K and ρ = 0.0052 g cm(-3)), we were able to calculate the thermodynamic equilibrium constant, and thus the deviation from ideal conditions for the lowest density. We found the thermodynamic equilibrium constant to increase with increasing temperature, and to have a negligible pressure dependence. Taking the enthalpy variation into account in the calculation of the thermodynamic equilibrium constant, we found the ratio of activity coefficients to be in the order of 0.7-1.0 for the lowest density, indicating repulsive forces between H and H2. This study shows that the compressed gas- and liquid density values at higher temperatures are far from those calculated under ideal conditions. It is important to have a method that can give access to partial molar properties, independent of the ideality of

  5. Measurements of free radical in vitamin E-doped ultra-high molecular weight polyethylene: Dependence on materials processing and irradiation environments

    NASA Astrophysics Data System (ADS)

    Ridley, M. D.; Jahan, M. S.

    2007-12-01

    Ultra-high molecular weight polyethylene (UHMWPE), doped with vitamin E (α-tocopherol (α-T)), was irradiated with gamma rays in nitrogen (N 2) or air, and the resulting free radicals were detected in air using an electron spin resonance (ESR) technique. Two groups of samples were investigated. In one group, samples were prepared from blends of α-T (20 wt%) and UHMWPE powder (PPE-α-T) and, in the other, from compression molded blocks (CMPE-α-T). The CMPE-α-T blocks contained 0% (control), 0.5%, 1.0%, 10.0%, 15.0%, 20.0% and 25.0% α-T by weight. When irradiation was performed in air, the ESR spectrum of powder samples showed the presence of only vitamin E radical (tocopheroxyl, α-T-O rad ), and there was no detectable signal due to PE radicals (alkyl/allyl). Most likely, all PE radicals were quenched by vitamin E during irradiation in air. However, when irradiation was performed in N 2, composite ESR spectra showed the presence of both PE and α-T-O rad radicals. Compared to the control (PPE, 0% α-T) PE radicals in PPE-20% α-T were found to be significantly reduced or quenched by α-T. The presence of α-T in powder samples, however, did not affect the long-term (71 days in this study) oxidation behavior of the PE radicals. Compression molded samples, with and without α-T, produced identical ESR spectra irrespective of their irradiation environment N 2 or air. However, radical concentration, measured immediately after irradiation, was found to be an order of magnitude less in CMPE-α-T than in the control (CMPE-0% α-T). They also evidenced identical structural changes in the respective ESR spectra during subsequent oxidation for 24 days in open air. These observations suggest that α-T can effectively quench a significant fraction of PE radicals during irradiation, but has no measurable effect on subsequent reactions. No significant difference was found in the ESR spectra of samples containing different α-T concentration.

  6. Solution Processed Organic Photovoltaic Cells Using D-A-D-A-D Type Small Molecular Donor Materials with Benzodithiophene and Diketopyrrolopyrrole Units.

    PubMed

    Park, Sangman; Nam, So Yeon; Suh, Dong Hack; Lee, Jaemin; Lee, Changjin; Yoon, Sung Cheol

    2016-03-01

    Organic photovoltaic Cells (OPVs) have been considered to be a next-generation energy source to overcome exhaustion of resources. Currently, OPVs are developed based on two types of donor material with polymer and small molecule. Polymeric donor materials have shown better power conversion efficiency (PCE) than small molecular donor materials, since it's easy to control the morphology of photoactive film. However, the difficulty in synthetic reproducibility and purification of polymeric donor were main drawback to overcome. And then, recently small molecule donor materials have been overcome bad morphology of OPVs film by using appropriate alkyl substituents and relatively long conjugation system. In this study, we designed and synthesized D-A-D-A-D type small molecular donor materials containing alternatively linked benzodithiophene (BDT) and diketopyrrolopyrrole (DPP) units. Also, we studied on the effect of photovoltaic performance of prepared small molecular D-A-D-A-D type donor with variation of thiophene links and with/without hexyl substituent. Our small molecular donors showed HOMO energy levels from -5.26 to -5.34 eV and optical bandgaps from 1.70 to 1.87 eV by CV (cyclic voltammetry) and UV/Vis spectroscopy, respectively. Finally, 3.4% of PCE can be obtained using a mixture of BDT(DPP)2-T2 and PCBM as an active layer with a Voc of 0.78 V, a Jsc of 9.72 mA/cm2, and a fill factor of 0.44 under 100 mW/cm2 AM 1.5G simulated light. We will discuss the performance of D-A-D-A-D type small molecular donor based OPVs with variation of both terminal substituents.

  7. Solution Processed Organic Photovoltaic Cells Using D-A-D-A-D Type Small Molecular Donor Materials with Benzodithiophene and Diketopyrrolopyrrole Units.

    PubMed

    Park, Sangman; Nam, So Yeon; Suh, Dong Hack; Lee, Jaemin; Lee, Changjin; Yoon, Sung Cheol

    2016-03-01

    Organic photovoltaic Cells (OPVs) have been considered to be a next-generation energy source to overcome exhaustion of resources. Currently, OPVs are developed based on two types of donor material with polymer and small molecule. Polymeric donor materials have shown better power conversion efficiency (PCE) than small molecular donor materials, since it's easy to control the morphology of photoactive film. However, the difficulty in synthetic reproducibility and purification of polymeric donor were main drawback to overcome. And then, recently small molecule donor materials have been overcome bad morphology of OPVs film by using appropriate alkyl substituents and relatively long conjugation system. In this study, we designed and synthesized D-A-D-A-D type small molecular donor materials containing alternatively linked benzodithiophene (BDT) and diketopyrrolopyrrole (DPP) units. Also, we studied on the effect of photovoltaic performance of prepared small molecular D-A-D-A-D type donor with variation of thiophene links and with/without hexyl substituent. Our small molecular donors showed HOMO energy levels from -5.26 to -5.34 eV and optical bandgaps from 1.70 to 1.87 eV by CV (cyclic voltammetry) and UV/Vis spectroscopy, respectively. Finally, 3.4% of PCE can be obtained using a mixture of BDT(DPP)2-T2 and PCBM as an active layer with a Voc of 0.78 V, a Jsc of 9.72 mA/cm2, and a fill factor of 0.44 under 100 mW/cm2 AM 1.5G simulated light. We will discuss the performance of D-A-D-A-D type small molecular donor based OPVs with variation of both terminal substituents. PMID:27455709

  8. Structural properties of archaeal lipid bilayers: small-angle X-ray scattering and molecular dynamics simulation study.

    PubMed

    Polak, Andraž; Tarek, Mounir; Tomšič, Matija; Valant, Janez; Ulrih, Nataša Poklar; Jamnik, Andrej; Kramar, Peter; Miklavčič, Damijan

    2014-07-22

    Aeropyrum pernix is an aerobic hyperthermophilic archaeon that grows in harsh environmental conditions and as such possesses unique structural and metabolic features. Its membrane interfaces with the extreme environment and is the first line of defense from external factors. Therefore, lipids composing this membrane have special moieties that increase its stability. The membrane of A. pernix is composed predominantly of two polar lipids 2,3-di-O-sesterterpanyl-sn-glicerol-1-phospho-1'(2'-O-α-D-glucosyl)-myo-inositol (AGI) and 2,3-di-O-sesterterpanyl-sn-glicerol-1-phospho-myo-inositol (AI). Both have methyl branches in their lipid tails and ether linkages and carbohydrates in their headgroup. These moieties significantly affect the structure and dynamics of the bilayer. To provide a molecular level insight into these characteristics, we used here Molecular Dynamics (MD) simulations of lipid bilayers of composition similar to those of the archaeal membranes. First, we show that the electron density profiles along the normal to the bilayers derived from the simulations are in good agreement with the profiles obtained by the small-angle X-ray scattering (SAXS) technique, which provides confidence in the force fields used. Analyses of the simulation data show that the archaeal lipid bilayers are less hydrated than conventional phosphatidylcholine (PC) lipids and that their structure is not affected by the salt present in the surrounding solution. Furthermore, the lateral pressure in their hydrophobic core, due to the presence of the branched tails, is much higher than that at PC-based lipid bilayers. Both the methyl branched tails and the special headgroup moieties contribute to slow drastically the lateral diffusion of the lipids. Furthermore, we found that the lipid head groups associate via hydrogen bonding, which affects their reorientational dynamics. All together, our data provide links between the microscopic properties of these membranes and their overall

  9. Molecular basis of polyspecificity of the Small Multidrug Resistance Efflux Pump AbeS from Acinetobacter baumannii.

    PubMed

    Lytvynenko, Iryna; Brill, Shlomo; Oswald, Christine; Pos, Klaas M

    2016-02-13

    Secondary multidrug efflux transporters play a key role in the bacterial resistance phenotype. One of the major questions concerns the polyspecific recognition of substrates by these efflux pumps. To understand the molecular basis of this promiscuous recognition, we compared the substrate specificity of the well-studied Escherichia coli small multidrug resistance protein EmrE with that of the poorly studied Acinetobacter baumannii homologue AbeS. The latter drug/H(+) antiporter is a 109-amino-acid membrane protein with predicted four transmembrane helices. It effectively confers resistance toward ethidium, acriflavine and benzalkonium in an E. coli ΔemrEΔmdfA background. Purified AbeS and the substrate-specific hyperactive variant A16G bind tetraphenylphosphonium with nanomolar affinity and exhibit electrogenic transport of 1-methyl-4-phenylpyridinium after reconstitution into liposomes. A16G hyperactivity was apparent toward acriflavine and ethidium, resulting in 7- to 10-fold higher normalized IC50 values, respectively, but not toward substrates 1-methyl-4-phenylpyridinium and benzalkonium. Substitution of Y3 and A42 with Ala or Ser, respectively, also displayed a substrate-dependent phenotype, as these variants were strongly affected in their properties to confer resistance against acriflavine and ethidium, but not against benzalkonium. The size and planarity of the conjugated aromatic moieties appear to be a critical and subtle criterion for substrate recognition by these transporters. Rather moderate changes in the property of side chains postulated to be part of the substrate binding site result in a large phenotypical difference. These observations provide indications for the molecular basis of specificity within the binding pocket of polyspecific transporters. PMID:26707198

  10. MO-G-BRF-07: Optical Characterization of Novel Terbium-Doped Nanophosphors Excited by Clinical Electron and Photon Beams for Potential Use in Molecular Imaging Or Photodynamic Therapy

    SciTech Connect

    Darafsheh, A; Paik, T; Tenuto, M; Najmr, S; Friedberg, J; Murray, C; Finlay, J

    2014-06-15

    Purpose: Optical properties of terbium (Tb3+)-doped gadolinium trifluoride (GdF3) nanoplates irradiated by electron and photon beams were investigated for their potential as optical probes. The contribution of induced Cerenkov radiation in exciting the nanophosphors was investigated as well. Methods: The emission spectra of Terbium-doped GdF3 dispersed in hexane, embedded in tissue mimicking phantoms were collected by an optical fiber connected to a CCD-coupled spectrograph, while the samples were irradiated by a medical linear accelerator with electron beams of energies 6, 9, 12, 16, and 20 MeV or X-ray beams of energies of 6, and 15 MV. The contribution of induced Cerenkov radiation in exciting the nanophosphores was investigated in a dedicated experimental apparatus through optical isolation of the samples and also by using 125 kVp X-ray beams whose energy is below the threshold for generating Cerenkov radiation in that medium. Results: Terbium-doped GdF3 nanoplates show characteristic cathodoluminescence emission peaks at 488, 543, 586, and 619 nm, which are responsible for the characteristic f-f transition of terbium ion. In a series of experiments, the contribution of Cerenkov radiation in the luminescence of such nanophosphors was ruled out. Conclusion: We have characterized the optical properties of Terbium-doped GdF3 nanoplates. Such nanocrystals with emission tunability and high surface area that facilitates attachment with targeting reagents are promising in situ light source candidates for molecular imaging or exciting a photosensitizer for ultralow fluence photodynamic therapy. This work is supported by the Department of Radiation Oncology at the University of Pennsylvania, the American Cancer Society through IRG-78-002-28, and the University of Pennsylvania's Nano/Bio Interface Center through NSEC DMR08-32802.

  11. Characterization of Small HSPs from Anemonia viridis Reveals Insights into Molecular Evolution of Alpha Crystallin Genes among Cnidarians

    PubMed Central

    Nicosia, Aldo; Maggio, Teresa; Mazzola, Salvatore; Gianguzza, Fabrizio; Cuttitta, Angela; Costa, Salvatore

    2014-01-01

    Gene family encoding small Heat-Shock Proteins (sHSPs containing α-crystallin domain) are found both in prokaryotic and eukaryotic organisms; however, there is limited knowledge of their evolution. In this study, two small HSP genes termed AvHSP28.6 and AvHSP27, both organized in one intron and two exons, were characterised in the Mediterranean snakelocks anemone Anemonia viridis. The release of the genome sequence of Hydra magnipapillata and Nematostella vectensis enabled a comprehensive study of the molecular evolution of α-crystallin gene family among cnidarians. Most of the H. magnipapillata sHSP genes share the same gene organization described for AvHSP28.6 and AvHSP27, differing from the sHSP genes of N. vectensis which mainly show an intronless architecture. The different genomic organization of sHSPs, the phylogenetic analyses based on protein sequences, and the relationships among Cnidarians, suggest that the A.viridis sHSPs represent the common ancestor from which H. magnipapillata genes directly evolved through segmental genome duplication. Additionally retroposition events may be considered responsible for the divergence of sHSP genes of N. vectensis from A. viridis. Analyses of transcriptional expression profile showed that AvHSP28.6 was constitutively expressed among different tissues from both ectodermal and endodermal layers of the adult sea anemones, under normal physiological conditions and also under different stress condition. Specifically, we profiled the transcriptional activation of AvHSP28.6 after challenges with different abiotic/biotic stresses showing induction by extreme temperatures, heavy metals exposure and immune stimulation. Conversely, no AvHSP27 transcript was detected in such dissected tissues, in adult whole body cDNA library or under stress conditions. Hence, the involvement of AvHSP28.6 gene in the sea anemone defensome is strongly suggested. PMID:25251681

  12. The Physiological and Molecular Characterization of a Small Colony Variant of Escherichia coli and Its Phenotypic Rescue

    PubMed Central

    Hirshfield, Irvin

    2016-01-01

    Small colony variants (SCVs) can be defined as a naturally occurring sub-population of bacteria characterized by their reduced colony size and distinct biochemical properties. SCVs of Staphylococcus aureus have been studied extensively over the past two decades due to their role in recurrent human infections. However, little work has been done on SCVs of Escherichia coli, and this work has focused on the physiology and morphology that define these colonies of E. coli, such as small size and slow growth. E. coli strain JW0623, has a null lipA mutation in the lipoic acid synthase gene (lipA), and is a lipoic acid auxotroph. When the mutant was grown in LB medium to log phase, it showed remarkable resistance to acid (pH 3), hydrogen peroxide, heat and osmotic stress compared to its parent BW25113. Using RT-PCR and real time RT-PCR, the expression of certain genes was compared in the two strains in an attempt to create a molecular profile of Escherichia coli SCVs. These include genes involved in glycolysis, TCA cycle, electron transport, iron acquisition, biofilm formation and cyclopropane fatty acid synthesis. It was also demonstrated that the addition of 5 μg/ml of lipoic acid to LB medium allows for the phenotypic rescue of the mutant; reversing its slow growth, its resistance characteristics, and elevated gene expression. These results indicate that the mutation in lipA leads to an E. coli SCV that resembles an electron transport defective SCV of S. aureus These strains are typically auxotrophs, and are phenotypically rescued by adding the missing metabolite to rich medium. There are global shifts in gene expression which are reversible and depend on whether the auxotrophic molecule is absent or present. Looking at the E. coli SCV from an evolutionary point of view, it becomes evident that its path to survival is to express genes that confer stress resistance. PMID:27310825

  13. Monitoring intermediate filament assembly by small-angle x-ray scattering reveals the molecular architecture of assembly intermediates

    PubMed Central

    Sokolova, Anna V.; Kreplak, Laurent; Wedig, Tatjana; Mücke, Norbert; Svergun, Dmitri I.; Herrmann, Harald; Aebi, Ueli; Strelkov, Sergei V.

    2006-01-01

    Intermediate filaments (IFs), along with microtubules, microfilaments, and associated cross-bridging proteins, constitute the cytoskeleton of metazoan cells. While crystallographic data on the dimer representing the elementary IF “building block” have recently become available, little structural detail is known about both the mature IF architecture and its assembly pathway. Here, we have applied solution small-angle x-ray scattering to investigate the in vitro assembly of a 53-kDa human IF protein vimentin at pH 8.4 by systematically varying the ionic strength conditions, and complemented these experiments by electron microscopy and analytical ultracentrifugation. While a vimentin solution in 5 mM Tris·HCl (pH 8.4) contains predominantly tetramers, addition of 20 mM NaCl induces further lateral assembly evidenced by the shift of the sedimentation coeficient and yields a distinct octameric intermediate. Four octamers eventually associate into unit-length filaments (ULFs) that anneal longitudinally. Based on the small-angle x-ray scattering experiments supplemented by crystallographic data and additional structural constraints, 3D molecular models of the vimentin tetramer, octamer, and ULF were constructed. Within each of the three oligomers, the adjacent dimers are aligned exclusively in an approximately half-staggered antiparallel A11 mode with a distance of 3.2–3.4 nm between their axes. The ULF appears to be a dynamic and a relatively loosely packed structure with a roughly even mass distribution over its cross-section. PMID:17050693

  14. Molecular cloning and expression analysis of GABA(A) receptor-associated protein (GABARAP) from small abalone, Haliotis diversicolor.

    PubMed

    Bai, Rongyao; You, Weiwei; Chen, Jun; Huang, Heqing; Ke, Caihuan

    2012-10-01

    GABA(A) receptor-associated protein (GABARAP), a multifunctional protein participating in autophagy process, is evolutionarily conserved and involves in innate immunity in eukaryotic cells, but currently there is no research on the relationship between GABARAP and innate immunity in mollusc. In the present study, the GABARAP full-length cDNA and its genomic DNA were firstly cloned from small abalone (Haliotis diversicolor), which was named as saGABARAP. Its full-length cDNA is 963 bp with a 354 bp open reading frame encoding a protein of 117 aa, a 276 bp 5'-UTR, and a 333 bp 3'-UTR including a poly(A) tail, two typical polyadenylation signals (AATAA) and two RNA instability motifs (ATTTA). The deduced protein has an estimated molecular weight of 13.9 kDa and a predicted PI of 8.73. Its genomic DNA comprises 4352 bp, containing three exons and two introns. Quantitative real-time PCR analysis revealed that saGABARAP was constitutively expressed in all examined tissues, with the highest expression level in hepatopancreas, and was upregulated in hepatopancreas and hemocytes after bacterial challenge. In addition, saGABARAP was ubiquitously expressed at all examined embryonic and larval development stages. These results suggested that saGABARAP could respond to bacteria challenge and may play a vital role in the adult innate immune system against pathogens and the development process of abalone embryo and larvae.

  15. Investigating the significance of zero-point motion in small molecular clusters of sulphuric acid and water

    SciTech Connect

    Stinson, Jake L. Ford, Ian J.; Kathmann, Shawn M.

    2014-01-14

    The nucleation of particles from trace gases in the atmosphere is an important source of cloud condensation nuclei, and these are vital for the formation of clouds in view of the high supersaturations required for homogeneous water droplet nucleation. The methods of quantum chemistry have increasingly been employed to model nucleation due to their high accuracy and efficiency in calculating configurational energies; and nucleation rates can be obtained from the associated free energies of particle formation. However, even in such advanced approaches, it is typically assumed that the nuclei have a classical nature, which is questionable for some systems. The importance of zero-point motion (also known as quantum nuclear dynamics) in modelling small clusters of sulphuric acid and water is tested here using the path integral molecular dynamics method at the density functional level of theory. The general effect of zero-point motion is to distort the mean structure slightly, and to promote the extent of proton transfer with respect to classical behaviour. In a particular configuration of one sulphuric acid molecule with three waters, the range of positions explored by a proton between a sulphuric acid and a water molecule at 300 K (a broad range in contrast to the confinement suggested by geometry optimisation at 0 K) is clearly affected by the inclusion of zero point motion, and similar effects are observed for other configurations.

  16. Molecular Phylogeny Supports Repeated Adaptation to Burrowing within Small-Eared Shrews Genus of Cryptotis (Eulipotyphla, Soricidae).

    PubMed

    He, Kai; Woodman, Neal; Boaglio, Sean; Roberts, Mariel; Supekar, Sunjana; Maldonado, Jesús E

    2015-01-01

    Small-eared shrews of the New World genus Cryptotis (Eulipotyphla, Soricidae) comprise at least 42 species that traditionally have been partitioned among four or more species groups based on morphological characters. The Cryptotis mexicana species group is of particular interest, because its member species inhibit a subtly graded series of forelimb adaptations that appear to correspond to locomotory behaviors that range from more ambulatory to more fossorial. Unfortunately, the evolutionary relationships both among species in the C. mexicana group and among the species groups remain unclear. To better understand the phylogeny of this group of shrews, we sequenced two mitochondrial and two nuclear genes. To help interpret the pattern and direction of morphological changes, we also generated a matrix of morphological characters focused on the evolutionarily plastic humerus. We found significant discordant between the resulting molecular and morphological trees, suggesting considerable convergence in the evolution of the humerus. Our results indicate that adaptations for increased burrowing ability evolved repeatedly within the genus Cryptotis. PMID:26489020

  17. Investigating the significance of zero-point motion in small molecular clusters of sulphuric acid and water.

    PubMed

    Stinson, Jake L; Kathmann, Shawn M; Ford, Ian J

    2014-01-14

    The nucleation of particles from trace gases in the atmosphere is an important source of cloud condensation nuclei, and these are vital for the formation of clouds in view of the high supersaturations required for homogeneous water droplet nucleation. The methods of quantum chemistry have increasingly been employed to model nucleation due to their high accuracy and efficiency in calculating configurational energies; and nucleation rates can be obtained from the associated free energies of particle formation. However, even in such advanced approaches, it is typically assumed that the nuclei have a classical nature, which is questionable for some systems. The importance of zero-point motion (also known as quantum nuclear dynamics) in modelling small clusters of sulphuric acid and water is tested here using the path integral molecular dynamics method at the density functional level of theory. The general effect of zero-point motion is to distort the mean structure slightly, and to promote the extent of proton transfer with respect to classical behaviour. In a particular configuration of one sulphuric acid molecule with three waters, the range of positions explored by a proton between a sulphuric acid and a water molecule at 300 K (a broad range in contrast to the confinement suggested by geometry optimisation at 0 K) is clearly affected by the inclusion of zero point motion, and similar effects are observed for other configurations.

  18. Biomarkers and molecular profiling in non-small cell lung cancer: an expanding role and its managed care implications.

    PubMed

    Adamson, Robert T

    2013-12-01

    Lung cancer is the leading cause of cancerrelated mortality in the world. The American Cancer Society estimated that in 2013, the disease will account for almost 159,500 deaths in the United States, or approximately 27% of all cancer deaths in the country. Lung cancer accounts for about 14% and 12% of all new cancer diagnoses in males and females, respectively, and nearly 70% of patients with lung cancer will present with locally advanced or metastatic disease at initial diagnosis. Despite evidence-based recommendations and clinical guidelines that support the utility of epidermal growth factor receptor (EGFR) mutation testing in improving targeted therapy in non-small cell lung cancer (NSCLC), the most common form of lung cancer, EGFR testing continues to be underutilized, as the procedure may cost up to $1000 and require up to 2 weeks for results. Additional research and data collection will be needed to ascertain the costeffectiveness and role of molecular testing and targeted therapies in the management of NSCLC. This article reviews the current testing strategy and treatment guidelines, and provides a pharmacoeconomic evaluation of the use of EGFR testing to guide the management of NSCLC in today's cost-constrained healthcare environment. PMID:24494721

  19. Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

    PubMed Central

    Boldon, Lauren; Laliberte, Fallon; Liu, Li

    2015-01-01

    In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics’ equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques. PMID:25721341

  20. Ab initio nonadiabatic molecular dynamics of the ultrafast excitation energy transfer in small semiconducting carbon nanotube aggregates

    NASA Astrophysics Data System (ADS)

    Postupna, Olena; Long, Run; Prezhdo, Oleg

    2012-02-01

    Outstanding physical properties of carbon nanotubes (CNTs), such as well-defined optical resonance and ultrafast nonlinear response, result in CNTs gaining popularity in academic and industrial endeavors as potential effective energy generating devices. Following recent experiments on ultrafast excitation energy transfer in small semiconducting carbon nanotube aggregates [1], we report results of ab initio nonadiabatic molecular dynamics simulation of the energy transfer taking place in two carbon nanotube systems. We investigate the energy transfer between (8,4) and (10,0) CNTs, as well as (8,4) and (13,0) CNTs. In both cases, the CNTs are orthogonal to each other. Luer et al. in [1] elucidate the second excitonic transitions followed by fast intratube relaxation and energy transfer from the (8,4) CNT toward other acceptor tubes. Our project aims to provide a better understanding of the energy transfer mechanism in the given systems, which should foster development of a theory for the electronic structure and dynamics of CNT networks, hence enhancing their tailoring and application in the future. References 1.Larry Luer, Jared Crochet, Tobias Hertel, Giulio Cerullo, Gugliermo Lanzani. ACSNano. Vol.4, No. 7, 4265-4273

  1. Toward chelerythrine optimization: Analogues designed by molecular simplification exhibit selective growth inhibition in non-small-cell lung cancer cells.

    PubMed

    Yang, Rosania; Tavares, Maurício T; Teixeira, Sarah F; Azevedo, Ricardo A; C Pietro, Diego; Fernandes, Thais B; Ferreira, Adilson K; Trossini, Gustavo H G; Barbuto, José A M; Parise-Filho, Roberto

    2016-10-01

    A series of novel chelerythrine analogues was designed and synthesized. Antitumor activity was evaluated against A549, NCI-H1299, NCI-H292, and NCI-H460 non-small-cell lung cancer (NSCLC) cell lines in vitro. The selectivity of the most active analogues and chelerythrine was also evaluated, and we compared their cytotoxicity in NSCLC cells and non-tumorigenic cell lines, including human umbilical vein endothelial cells (HUVECs) and LL24 human lung fibroblasts. In silico studies were performed to establish structure-activity relationships between chelerythrine and the analogues. The results showed that analogue compound 3f induced significant dose-dependent G0/G1 cell cycle arrest in A549 and NCI-H1299 cells. Theoretical studies indicated that the molecular arrangement and electron characteristics of compound 3f were closely related to the profile of chelerythrine, supporting its activity. The present study presents a new and simplified chelerythrinoid scaffold with enhanced selectivity against NSCLC tumor cells for further optimization. PMID:27561984

  2. Molecular Phylogeny Supports Repeated Adaptation to Burrowing within Small-Eared Shrews Genus of Cryptotis (Eulipotyphla, Soricidae)

    PubMed Central

    He, Kai; Woodman, Neal; Boaglio, Sean; Roberts, Mariel; Supekar, Sunjana; Maldonado, Jesús E.

    2015-01-01

    Small-eared shrews of the New World genus Cryptotis (Eulipotyphla, Soricidae) comprise at least 42 species that traditionally have been partitioned among four or more species groups based on morphological characters. The Cryptotis mexicana species group is of particular interest, because its member species inhibit a subtly graded series of forelimb adaptations that appear to correspond to locomotory behaviors that range from more ambulatory to more fossorial. Unfortunately, the evolutionary relationships both among species in the C. mexicana group and among the species groups remain unclear. To better understand the phylogeny of this group of shrews, we sequenced two mitochondrial and two nuclear genes. To help interpret the pattern and direction of morphological changes, we also generated a matrix of morphological characters focused on the evolutionarily plastic humerus. We found significant discordant between the resulting molecular and morphological trees, suggesting considerable convergence in the evolution of the humerus. Our results indicate that adaptations for increased burrowing ability evolved repeatedly within the genus Cryptotis. PMID:26489020

  3. Doping To Reduce Base Resistances Of Bipolar Transistors

    NASA Technical Reports Server (NTRS)

    Lin, True-Lon

    1991-01-01

    Modified doping profile proposed to reduce base resistance of bipolar transistors. A p/p+ base-doping profile reduces base resistance without reducing current gain. Proposed low/high base-doping profile realized by such low-temperature deposition techniques as molecular-beam epitaxy, ultra-high-vacuum chemical-vapor deposition, and limited-reaction epitaxy. Produces desired doping profiles without excessive diffusion of dopant.

  4. Infrared absorption spectra of various doping states in cuprate superconductors

    SciTech Connect

    Yonemitsu, K.; Bishop, A.R.; Lorenzana, J.

    1992-02-01

    Doping states in a two-dimensional three-band extended Peierls-Hubbard model was investigated within inhomogeneous Hartree-Fock and random phase approximation. They are very sensitive to small changes of interaction parameters and their distinct vibrational and optical absorption spectra can be used to identify different doping states. For electronic parameters relevant to cuprate superconductors, as intersite electron-phonon interaction strength increases, the doping state changes from a Zhang-Rice state to a covalent molecular singlet state accompanied by local quenching of the Cu magnetic moment and large local lattice distortion in an otherwise undistorted antiferromagnetic background. In a region where both intersite electron-phonon interaction and on-site electron-electron repulsion are large, we obtain new stable global phases including a bond-order-wave state and a mixed state of spin-Peierls bonds and antiferromagnetic Cu spins, as well as many metastable states. Doping in the bond-order-wave region induces separation of spin and charge. 9 refs.

  5. Infrared absorption spectra of various doping states in cuprate superconductors

    SciTech Connect

    Yonemitsu, K.; Bishop, A.R. ); Lorenzana, J. )

    1992-01-01

    Doping states in a two-dimensional three-band extended Peierls-Hubbard model was investigated within inhomogeneous Hartree-Fock and random phase approximation. They are very sensitive to small changes of interaction parameters and their distinct vibrational and optical absorption spectra can be used to identify different doping states. For electronic parameters relevant to cuprate superconductors, as intersite electron-phonon interaction strength increases, the doping state changes from a Zhang-Rice state to a covalent molecular singlet state accompanied by local quenching of the Cu magnetic moment and large local lattice distortion in an otherwise undistorted antiferromagnetic background. In a region where both intersite electron-phonon interaction and on-site electron-electron repulsion are large, we obtain new stable global phases including a bond-order-wave state and a mixed state of spin-Peierls bonds and antiferromagnetic Cu spins, as well as many metastable states. Doping in the bond-order-wave region induces separation of spin and charge. 9 refs.

  6. Controlled Doping of Vacancy-Containing Few-Layer MoS2 via Highly Stable Thiol-Based Molecular Chemisorption.

    PubMed

    Sim, Dong Min; Kim, Mincheol; Yim, Soonmin; Choi, Min-Jae; Choi, Jaesuk; Yoo, Seunghyup; Jung, Yeon Sik

    2015-12-22

    MoS2 is considered a promising two-dimensional active channel material for future nanoelectronics. However, the development of a facile, reliable, and controllable doping methodology is still critical for extending the applicability of MoS2. Here, we report surface charge transfer doping via thiol-based binding chemistry for modulating the electrical properties of vacancy-containing MoS2 (v-MoS2). Although vacancies present in 2D materials are generally regarded as undesirable components, we show that the electrical properties of MoS2 can be systematically engineered by exploiting the tight binding between the thiol group and sulfur vacancies and by choosing different functional groups. For example, we demonstrate that NH2-containing thiol molecules with lone electron pairs can serve as an n-dopant and achieve a substantial increase of electron density (Δn = 3.7 × 10(12) cm(-2)). On the other hand, fluorine-rich molecules can provide a p-doping effect (Δn = -7.0 × 10(11) cm(-2)) due to its high electronegativity. Moreover, the n- and p-doping effects were systematically evaluated by photoluminescence (PL), X-ray photoelectron spectroscopy (XPS), and electrical measurement results. The excellent binding stability of thiol molecules and recovery properties by thermal annealing will enable broader applicability of ultrathin MoS2 to various devices. PMID:26503105

  7. Molecular cloning and expression analysis of small ubiquitin-like modifier (SUMO) genes from grouper (Epinephelus coioides).

    PubMed

    Xu, Meng; Wei, Jingguang; Chen, Xiuli; Gao, Pin; Zhou, Yongcan; Qin, Qiwei

    2016-01-01

    Small ubiquitin-like modifier (SUMO) is a group of proteins binding to lysine residues of target proteins and thereby modifying their stability, activity and subcellular localization. In the present study, two SUMO homolog genes (EcSUMO1 and EcSUMO2) from grouper (Epinephelus coioides) were cloned and characterized. The full-length sequence of EcSUMO1 was 749 bp in length and contained a predicted open reading frame of 306 bp encoding 101 amino acids with a molecular mass of 11.34 kDa. The full-length sequence of EcSUMO2 was 822 bp in length and contained a predicted open reading frame of 291 bp encoding 96 amino acids with a molecular mass of 10.88 kDa EcSUMO1 shares 44.55% identity with EcSUMO2. EcSUMO1 shares 99%, 90%, and 88% identity with those from Oreochromis niloticus, Danio rerio, and Homo sapiens, respectively. EcSUMO2 shares 98%, 93%, and 96% identity with those from Anoplopoma fimbria, D.rerio, and H. sapiens, respectively. Quantitative real-time PCR analysis indicated that EcSUMO1 and EcSUMO2 were constitutively expressed in all of the analyzed tissues in healthy grouper, but the expression of EcSUMO2 was higher than that of EcSUMO1. EcSUMO1 and EcSUMO2 were identified as a remarkably (P < 0.01) up-regulated responding to poly(I:C) and Singapore grouper iridovirus (SGIV) stimulation in head kidney of groupers. EcSUMO1 and EcSUMO2 were distributed in both cytoplasm and nucleus in GS cells. Over-expressed EcSUMO1 and EcSUMO2 enhanced SGIV and Red-spotted grouper nervous necrosis virus (RGNNV) replication during viral infection in vitro. Our study was an important attempt to understand the SUMO pathway in fish, which may provide insights into the regulatory mechanism of viral infection in E.coioides under farmed conditions. PMID:26616235

  8. Molecular cloning and expression analysis of small ubiquitin-like modifier (SUMO) genes from grouper (Epinephelus coioides).

    PubMed

    Xu, Meng; Wei, Jingguang; Chen, Xiuli; Gao, Pin; Zhou, Yongcan; Qin, Qiwei

    2016-01-01

    Small ubiquitin-like modifier (SUMO) is a group of proteins binding to lysine residues of target proteins and thereby modifying their stability, activity and subcellular localization. In the present study, two SUMO homolog genes (EcSUMO1 and EcSUMO2) from grouper (Epinephelus coioides) were cloned and characterized. The full-length sequence of EcSUMO1 was 749 bp in length and contained a predicted open reading frame of 306 bp encoding 101 amino acids with a molecular mass of 11.34 kDa. The full-length sequence of EcSUMO2 was 822 bp in length and contained a predicted open reading frame of 291 bp encoding 96 amino acids with a molecular mass of 10.88 kDa EcSUMO1 shares 44.55% identity with EcSUMO2. EcSUMO1 shares 99%, 90%, and 88% identity with those from Oreochromis niloticus, Danio rerio, and Homo sapiens, respectively. EcSUMO2 shares 98%, 93%, and 96% identity with those from Anoplopoma fimbria, D.rerio, and H. sapiens, respectively. Quantitative real-time PCR analysis indicated that EcSUMO1 and EcSUMO2 were constitutively expressed in all of the analyzed tissues in healthy grouper, but the expression of EcSUMO2 was higher than that of EcSUMO1. EcSUMO1 and EcSUMO2 were identified as a remarkably (P < 0.01) up-regulated responding to poly(I:C) and Singapore grouper iridovirus (SGIV) stimulation in head kidney of groupers. EcSUMO1 and EcSUMO2 were distributed in both cytoplasm and nucleus in GS cells. Over-expressed EcSUMO1 and EcSUMO2 enhanced SGIV and Red-spotted grouper nervous necrosis virus (RGNNV) replication during viral infection in vitro. Our study was an important attempt to understand the SUMO pathway in fish, which may provide insights into the regulatory mechanism of viral infection in E.coioides under farmed conditions.

  9. Effects of endogenous small molecular compounds on the rheological properties, texture and microstructure of soymilk coagulum: Removal of phytate using ultrafiltration.

    PubMed

    Wang, Ruican; Guo, Shuntang

    2016-11-15

    This study aims to clarify the roles played by endogenous small molecular components in soymilk coagulation process and the properties of gels. Soymilk samples with decreasing levels of small molecules were prepared by ultrafiltration, to reduce the amount of phytate and salts. CaSO4-induced coagulation process was analyzed using rheological methods. Results showed that removal of free small molecules decreased the activation energy of protein coagulation, resulting in accelerated reaction and increased gel strength. However, too fast a reaction led to the drop in storage modulus (G'). Microscopic observation suggested that accelerated coagulation generated a coarse and non-uniform gel network with large pores. This network could not hold much water, leading to serious syneresis. Endogenous small molecules in soymilk were vital in the fine gel structure. Coagulation rate could be controlled by adjusting the amount of small molecules to obtain tofu products with the optimal texture. PMID:27283662

  10. Gene doping.

    PubMed

    Harridge, Stephen D R; Velloso, Cristiana P

    2008-01-01

    Gene doping is the misuse of gene therapy to enhance athletic performance. It has recently been recognised as a potential threat and subsequently been prohibited by the World Anti-Doping Agency. Despite concerns with safety and efficacy of gene therapy, the technology is progressing steadily. Many of the genes/proteins which are involved in determining key components of athletic performance have been identified. Naturally occurring mutations in humans as well as gene-transfer experiments in adult animals have shown that altered expression of these genes does indeed affect physical performance. For athletes, however, the gains in performance must be weighed against the health risks associated with the gene-transfer process, whereas the detection of such practices will provide new challenges for the anti-doping authorities.

  11. Simulation of polymer translocation through small channels: A molecular dynamics study and a new Monte Carlo approach

    NASA Astrophysics Data System (ADS)

    Gauthier, Michel G.

    With the recent completion of the Human Genome Project and the announcement of the $1000 Genome Race in 2003, the interest for developing faster and cheaper sequencing technologies is continuously growing. Nanopore sequencing offers one of the most promising new ideas. This method consists in reading DNA as it passes through a small aperture perforated through a membrane; a technique similar to decoding a magnetic tape in a tape player. The process of linearly moving a flexible chain from one side of a small channel to the other is called polymer translocation. However, the physics behind this process is still not well understood. During the last ten years, theorists proposed several scaling laws in order to describe this problem and explain experimental observations. The goal of this thesis is to shed light on some of these interesting theoretical predictions. One of the most important questions addressed in this thesis is the role of the hydrodynamic interactions in the polymer translocation process. Even though the impact of such interactions have been theoretically considered, they are neglected in most simulation models. One of our aims in this thesis is to look at the implications of increasing the pore diameter in the presence of hydrodynamic interactions. We use Molecular Dynamics simulations with explicit solvent particles to generate unbiased translocation events in order to characterize the screening of the hydrodynamic interactions by the membrane and to test the hypothesis that polymer translocation is a quasi-equilibrium process. The latter question is quite fundamental since this assumption is at the origin of most theoretical approaches. Another major goal of this thesis is to clarify the nature of the transition between the two translocation regimes dominated by the pore-polymer friction and the hydrodynamic drag of the subchains outside the channel, respectively. However, such an investigation requires the ability to simulate translocation events

  12. Investigating the significance of zero-point motion in small molecular clusters of sulphuric acid and water

    SciTech Connect

    Stinson, Jake L.; Kathmann, Shawn M.; Ford, Ian J.

    2014-01-14

    The nucleation of particles from trace gases in the atmosphere is an important source of cloud condensation nuclei (CCN), and these are vital for the formation of clouds in view of the high supersaturations required for homogeneous water droplet nucleation. The methods of quantum chemistry have increasingly been employed to model nucleation due to their high accuracy and efficiency in calculating configurational energies; and nucleation rates can be obtained from the associated free energies of particle formation. However, even in such advanced approaches, it is typically assumed that the nuclei have a classical nature, which is questionable for some systems. The importance of zero-point motion (also known as quantum nuclear dynamics) in modelling small clusters of sulphuric acid and water is tested here using the path integral molecular dynamics (PIMD) method at the density functional theory (DFT) level of theory. We observe a small zero-point effect on the the equilibrium structures of certain clusters. One configuration is found to display a bimodal behaviour at 300 K in contrast to the stable ionised state suggested from a zero temperature classical geometry optimisation. The general effect of zero-point motion is to promote the extent of proton transfer with respect to classical behaviour. We thank Prof. Angelos Michaelides and his group in University College London (UCL) for practical advice and helpful discussions. This work benefited from interactions with the Thomas Young Centre through seminar and discussions involving the PIMD method. SMK was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. JLS and IJF were supported by the IMPACT scheme at UCL and by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. We are grateful for use of the UCL Legion High Performance Computing Facility and the

  13. The chimeric EWS-WT1 gene product in the desmoplastic small round cell tumor: Molecular detection and alternative transcripts

    SciTech Connect

    Gerald, W.; Alava, E. de; Ladanyi, M.

    1994-09-01

    The desmoplastic small round cell tumor (DSRCT) is a recently recognized aggressive type of primitive sarcoma occurring mainly in young males. Previous cytogenetic reports have identified a recurrent translocation in DSRCT, t(11;22)(p13;q12). We have recently shown that this translocation represents a rearrangement between the EWS and WT1 genes, normally located at 22q12 and 11p13, respectively, generating a fusion gene which encodes a chimeric RNA resulting from an in-frame junction of EWS exon 7 to WT1 exon 8. Thus, this chimeric RNA encodes a putative protein in which the RNA-binding domain of EWS is replaced by the three C-terminal zinc fingers of the WT1 DNA-binding domain. We have now assessed the molecular detection of this rearrangement in a panel of 7 DSRCTs and 38 other small round cell tumors, and we have examined the WT1 portion of the chimeric RNA for the presence of the previously reported splice variants of the zinc-finger DNA-binding domain of WT1. Reverse transcriptase PCR (RT-PCR) revealed a single identical product in 4/5 cases tested, including a case in which a t(11;22)(p13;q12) by karyotyping. By Southern blotting, rearrangement of both EWS and WT1 was detectable in 3/6 cases, EWS alone in 1/6, and neither in 2/6. Histologically, the sole sample negative by both methods contained very scanty viable tumor. EWS-WT1 RT-PCR was negative in 16 Wilms` tumors, 12 rhadomyosarcomas, and 10 Ewing`s sarcomas. RT-PCR with splice site-specific primers showed the chimeric EWS-WT1 transcripts to include both splice variants of the zinc-finger domain of WT1, {open_quotes}+KTS{close_quotes} and {open_quotes}-KTS{close_quotes}. The t(11;22)(p13;q12) of DSRCT is most reliably detected by RT-PCR, and results in a specific and structurally highly consistent EWS-WT1 chimeric transcript which may interact with the normal targets of both splice variants of WT1.

  14. Discovery and validation of small-molecule heat-shock protein 90 inhibitors through multimodality molecular imaging in living subjects.

    PubMed

    Chan, Carmel T; Reeves, Robert E; Geller, Ron; Yaghoubi, Shahriar S; Hoehne, Aileen; Solow-Cordero, David E; Chiosis, Gabriela; Massoud, Tarik F; Paulmurugan, Ramasamy; Gambhir, Sanjiv S

    2012-09-11

    Up-regulation of the folding machinery of the heat-shock protein 90 (Hsp90) chaperone protein is crucial for cancer progression. The two Hsp90 isoforms (α and β) play different roles in response to chemotherapy. To identify isoform-selective inhibitors of Hsp90(α/β)/cochaperone p23 interactions, we developed a dual-luciferase (Renilla and Firefly) reporter system for high-throughput screening (HTS) and monitoring the efficacy of Hsp90 inhibitors in cell culture and live mice. HTS of a 30,176 small-molecule chemical library in cell culture identified a compound, N-(5-methylisoxazol-3-yl)-2-[4-(thiophen-2-yl)-6-(trifluoromethyl)pyrimidin-2-ylthio]acetamide (CP9), that binds to Hsp90(α/β) and displays characteristics of Hsp90 inhibitors, i.e., degradation of Hsp90 client proteins and inhibition of cell proliferation, glucose metabolism, and thymidine kinase activity, in multiple cancer cell lines. The efficacy of CP9 in disrupting Hsp90(α/β)/p23 interactions and cell proliferation in tumor xenografts was evaluated by non-invasive, repetitive Renilla luciferase and Firefly luciferase imaging, respectively. At 38 h posttreatment (80 mg/kg × 3, i.p.), CP9 led to selective disruption of Hsp90α/p23 as compared with Hsp90β/p23 interactions. Small-animal PET/CT in the same cohort of mice showed that CP9 treatment (43 h) led to a 40% decrease in (18)F-fluorodeoxyglucose uptake in tumors relative to carrier control-treated mice. However, CP9 did not lead to significant degradation of Hsp90 client proteins in tumors. We performed a structural activity relationship study with 62 analogs of CP9 and identified A17 as the lead compound that outperformed CP9 in inhibiting Hsp90(α/β)/p23 interactions in cell culture. Our efforts demonstrated the power of coupling of HTS with multimodality molecular imaging and led to identification of Hsp90 inhibitors.

  15. Molecular characterization of two small heat shock protein genes in rice: their expression patterns, localizations, networks, and heterogeneous overexpressions.

    PubMed

    Ham, Deok-Jae; Moon, Jun-Chul; Hwang, Sun-Goo; Jang, Cheol Seong

    2013-09-28

    Heat stress is an example of a severe abiotic stress that plants can suffer in the field, causing a significant detrimental effect on their growth and productivity. Understanding the mechanism of plant response to heat stress is important for improving the productivity of crop plants under global warming. We used a microarray dataset that is deposited in the public database to evaluate plant responses to heat stress, and we selected the top 10 genes that are highly expressed under heat stress in rice. Two genes, OsSHSP1 (Os03g16030) and OsSHSP2 (Os01g04380), were selected for further study. These genes were highly induced in response to salt and drought but not in response to cold. In addition, OsSHSP1 and OsSHSP2 gene transcripts were induced under abscisic acid and salicylic acid but not under jasmonic acid and ethylene. Subcellular localization of proteins of 35S::OsSHSP1 were associated with the cytosol, whereas those of and 35S::OsSHSP2 were associated with the cytosol and nucleus. Heterogeneous overexpression of both genes exhibited higher germination rates than those of wild-type plants under the salt treatment, but not under heat or drought stress, supporting a hypothesis regarding functional specialization of members of small heat-shock protein family over evolutionary time. The network of both genes harboring nine sHSPs as well as at least 13 other chaperone genes might support the idea of a role for sHSPs in the chaperone network. Our findings might provide clues to shed light on the molecular functions of OsSHSP1 and OsSHSP2 in response to abiotic stresses, especially heat stress.

  16. Molecular profiling of thin-prep FNA samples in assisting clinical management of non-small-cell lung cancer.

    PubMed

    Petriella, Daniela; Galetta, Domenico; Rubini, Vincenza; Savino, Eufemia; Paradiso, Angelo; Simone, Giovanni; Tommasi, Stefania

    2013-07-01

    The discovery of new target treatments for NSCLC has led to a search for new genetic and epigenetic markers able to selectively predict response to these new drugs. Somatic mutations in EGFR and KRAS genes are routinely analyzed to predict response to tyrosine kinase inhibitors (TKIs), used in the treatment of NSCLC patients, whose efficacy depend on the presence or the absence of specific mutations. MicroRNA (miRNA) expression evaluation has been recently analyzed because of the involvement of these molecules in lung cancer pathogenesis and in drug resistance. Only 30 % of NSCLC patients present a resectable stage at time of diagnosis so tissue samples cannot be the only starting material for genetic and epigenetic analysis. Therefore, the possibility to use cytological sampling already used for diagnosis also for molecular testing is emerging. The aim of this study was to evaluate for the first time in lung cancer the use of liquid-based cytology both for EGFR and KRAS mutational testing and for the expression trend of some miRNAs involved in lung cancer pathogenesis: miR-21, miR-155, miR-7, and let7a. We enrolled 20 fine-needle aspirate (FNA) samples diagnosed as NSCLC, 10 FNAs without neoplastic cells, and tissue samples coming from 5 of the 20 patients who underwent surgery after FNA NSCLC diagnosis. All Thin-Prep processed FNA samples were evaluable for DNA and RNA analysis and results were compared with those of the small group of patients whose matched tumor histology was available. The mutational status of the EGFR and KRAS genes and the expression profile of the selected miRNA showed comparable results between FNA samples and histological tissues. Our results underline that cytological samples could give the same genetic information as that obtained from histological specimens and so could be collected to create a nucleic acids bank.

  17. Genetic diversity and molecular characterization of Babesia motasi-like in small ruminants and ixodid ticks from China.

    PubMed

    Niu, Qingli; Liu, Zhijie; Yang, Jifei; Yu, Peifa; Pan, Yuping; Zhai, Bintao; Luo, Jianxun; Yin, Hong

    2016-07-01

    Ovine babesioses, an important tick-borne disease of sheep and goats in China, is caused by the reproduction of intraerythrocytic protozoa of the Babesia genus. Babesia motasi-like is a Babesia parasite that infects small ruminant in China, and two sub-groups of B. motasi-like can be subdivided based on differences in the rhoptry-associated-protein-1 gene. This study aimed to characterize the distribution, epidemiology and genetics of B. motasi-like in animals and ticks. A molecular investigation was carried out from 2009 to 2015 in 16 provinces in China. In total, 1081 blood samples were collected from sheep and goats originating from 27 different regions, and 778 ixodid tick samples were collected from 8 regions; the samples were tested for the presence of B. motasi-like using a specific nested PCR assay based on the rap-1b gene. The results indicated that 139 (12.9%), 91 (8.4%), 48 (4.4%) and 6 (0.7%) of the blood samples were positive for general B. motasi-like, Babesia sp. BQ1 (Lintan and Ningxian), Babesia sp. Tianzhu and Babesia sp. Hebei sub-groups, mixed infections, respectively. Among the collected 778 ixodid ticks (including Haemaphysalis longicornis, Haemaphysalis qinghaiensis, Dermacentor silvarum, Ixodes persulcatus, Rhipicephalus sanguineus and Rhipicephalus (Boophilus) microplus), the most frequently infected with Babesia were D. silvarum and I. persulcatus (35.7%), followed by H. longicornis (26.8%), H. qinghaiensis (24.8%) and R. sanguineus (9.3%). The PCR results were confirmed by DNA sequencing. The positive rates of B. motasi-like infection in ticks were found to be higher in China, compared with previous studies in other countries. B. motasi-like infections have not previously been reported in D. silvarum, I. persulcatus or R. sanguineus. The findings obtained in this study could be used for planning effective control strategies against babesiosis in China. PMID:26976477

  18. Physical Properties of the 1.1 mm selected Giant Molecular Clouds in the Small Magellanic Cloud

    NASA Astrophysics Data System (ADS)

    Takekoshi, Tatsuya

    2015-08-01

    The first 1.1 mm continuum survey toward the Small Magellanic Cloud (SMC) is performed with the AzTEC instrument installed on the ASTE 10 m telescope. This survey covers 4.5 square degrees of the SMC, and achieves the 1σ noise levels of 5-13 mJy beam-1. As a result of the analysis, 44 extended objects are identified. The 1.1 mm extended emission has good spatial correlation with 160 μm, indicating that the origin of the 1.1 mm continuum is thermal emission from cold dust component. Spectral energy distribution analysis are performed assuming single-temperature thermal emission from the cold dust component. Assuming a gas-to-dust ratio of 1000, the 1.1 mm objects have gas mass ranges from 7×103 to 4×105 M⊙, which is typical mass range of giant molecular clouds (GMCs), implying that the detected objects are dust-selected GMCs. The 1.1 mm objects show good spatial correlation with the 24 μm and CO emission, and the physical properties are very similar to that of our Galaxy and the Large Magellanic Cloud. The existences of star formation activity or CO detection provide the information about the evolutionary sequence. Comparisions with signs of star-formation and CO emission provide information about the evolutionary sequence. We found 2, 8, 13, and 21 samples of the starless/CO-detected, starless/CO-dark, star-forming/CO-dark, and star-forming/CO-detected objects, respectively. This result implies the existence of three main evolutionary phases, and the starless/CO-dark samples can be explained as the youngest evolution phase of GMCs. The deficiency of the starless/CO-detected samples suggests that the detectable amount of CO forms after the onset of star formation in the low metallicity environment of the SMC.

  19. A Novel Small Molecular STAT3 Inhibitor, LY5, Inhibits Cell Viability, Cell Migration, and Angiogenesis in Medulloblastoma Cells*

    PubMed Central

    Xiao, Hui; Bid, Hemant Kumar; Jou, David; Wu, Xiaojuan; Yu, Wenying; Li, Chenglong; Houghton, Peter J.; Lin, Jiayuh

    2015-01-01

    Signal transducers and activators of transcription 3 (STAT3) signaling is persistently activated and could contribute to tumorigenesis of medulloblastoma. Numerous studies have demonstrated that inhibition of the persistent STAT3 signaling pathway results in decreased proliferation and increased apoptosis in human cancer cells, indicating that STAT3 is a viable molecular target for cancer therapy. In this study, we investigated a novel non-peptide, cell-permeable small molecule, named LY5, to target STAT3 in medulloblastoma cells. LY5 inhibited persistent STAT3 phosphorylation and induced apoptosis in human medulloblastoma cell lines expressing constitutive STAT3 phosphorylation. The inhibition of STAT3 signaling by LY5 was confirmed by down-regulating the expression of the downstream targets of STAT3, including cyclin D1, bcl-XL, survivin, and micro-RNA-21. LY5 also inhibited the induction of STAT3 phosphorylation by interleukin-6 (IL-6), insulin-like growth factor (IGF)-1, IGF-2, and leukemia inhibitory factor in medulloblastoma cells, but did not inhibit STAT1 and STAT5 phosphorylation stimulated by interferon-γ (IFN-γ) and EGF, respectively. In addition, LY5 blocked the STAT3 nuclear localization induced by IL-6, but did not block STAT1 and STAT5 nuclear translocation mediated by IFN-γ and EGF, respectively. A combination of LY5 with cisplatin or x-ray radiation also showed more potent effects than single treatment alone in the inhibition of cell viability in human medulloblastoma cells. Furthermore, LY5 demonstrated a potent inhibitory activity on cell migration and angiogenesis. Taken together, these findings indicate LY5 inhibits persistent and inducible STAT3 phosphorylation and suggest that LY5 is a promising therapeutic drug candidate for medulloblastoma by inhibiting persistent STAT3 signaling. PMID:25313399

  20. Ultrahigh B doping ({<=}10{sup 22} cm{sup -3}) during Si(001) gas-source molecular-beam epitaxy: B incorporation, electrical activation, and hole transport

    SciTech Connect

    Glass, G.; Kim, H.; Desjardins, P.; Taylor, N.; Spila, T.; Lu, Q.; Greene, J. E.

    2000-03-15

    Si(001) layers doped with B concentrations C{sub B} between 1x10{sup 17} and 1.2x10{sup 22} cm{sup -3} (24 at %) were grown on Si(001)2x1 at temperatures T{sub s}=500-850 degree sign C by gas-source molecular-beam epitaxy from Si{sub 2}H{sub 6} and B{sub 2}H{sub 6}. C{sub B} increases linearly with the incident precursor flux ratio J{sub B{sub 2}}{sub H{sub 6}}/J{sub Si{sub 2}}{sub H{sub 6}} and B is incorporated into substitutional electrically active sites at concentrations up to C{sub B}{sup *}(T{sub s}) which, for T{sub s}=600 degree sign C, is 2.5x10{sup 20} cm{sup -3}. At higher B concentrations, C{sub B} increases faster than J{sub B{sub 2}}{sub H{sub 6}}/J{sub Si{sub 2}}{sub H{sub 6}} and there is a large and discontinuous decrease in the activated fraction of incorporated B. However, the total activated B concentration continues to increase and reaches a value of N{sub B}=1.3x10{sup 21} cm{sup -3} with C{sub B}=1.2x10{sup 22} cm{sup -3}. High-resolution x-ray diffraction (HR-XRD) and reciprocal space mapping measurements show that all films, irrespective of C{sub B} and T{sub s}, are fully strained. No B precipitates or misfit dislocations were detected by HR-XRD or transmission electron microscopy. The lattice constant in the film growth direction a{sub (perpendicular} {sub sign)} decreases linearly with increasing C{sub B} up to the limit of full electrical activation and continues to decrease, but nonlinearly, with C{sub B}>C{sub B}{sup *}. Room-temperature resistivity and conductivity mobility values are in good agreement with theoretical values for B concentrations up to C{sub B}=2.5x10{sup 20} and 2x10{sup 21} cm{sup -3}, respectively. All results can be explained on the basis of a model which accounts for strong B surface segregation to the second-layer with a saturation coverage {theta}{sub B,sat} of 0.5 ML (corresponding to C{sub B}=C{sub B}{sup *}). At higher C{sub B} (i.e., {theta}{sub B}>{theta}{sub B,sat}), B accumulates in the upper layer as

  1. Enclathration and Confinement of Small Gases by the Intrinsically 0D Porous Molecular Solid, Me,H,SiMe2.

    PubMed

    Kane, Christopher M; Banisafar, Arash; Dougherty, Timothy P; Barbour, Leonard J; Holman, K Travis

    2016-04-01

    The stable, guest-free crystal form of the simple molecular cavitand, Me,H,SiMe2, is shown to be intrinsically porous, possessing discrete, zero-dimensional (0D) pores/microcavities of about 28 Å(3). The incollapsible 0D pores of Me,H,SiMe2 have been exploited for the enclathration and room temperature (and higher) confinement of a wide range of small gases. Over 20 isostructural x(gas/guest)@Me,H,SiMe2 (x ≤ 1) clathrates (guest = H2O, N2, Ar, CH4, Kr, Xe, C2H4, C2H6, CH3F, CO2, H2S, CH3Cl, CH3OCH3, CH3Br, CH3SH, CH3CH2Cl, CH2Cl2, CH3I, CH3OH, BrCH2Cl, CH3CH2OH, CH3CN, CH3NO2, I2), and a propyne clathrate (CH3CCH@Me,H,SiMe2·2CHCl3), have been prepared and characterized, and their single crystal structures determined. Gas enclathration is found to be highly selective for gases that can be accommodated by the predefined, though slightly flexible 0D pore. The structure determinations provide valuable insight, at subangstrom resolution, into the factors that govern inclusion selectivity, gas accommodation, and the kinetic stability of the clathrates, which has been probed by thermal gravimetric analysis. The activation (emptying) of several clathrates (guest = H2O, N2, CO2, Kr, CH3F) is shown to occur in a single-crystal-to-single-crystal (SC → SC) fashion, often requiring elevated temperatures. Akin to open pore materials, water vapor and CO2 gas are shown to be taken up by single crystals of empty Me,H,SiMe2 at room temperature, but sorption rates are slow, occurring over weeks to months. Thus, Me,H,SiMe2 exhibits very low, but measurable, gas permeability, despite there being no obvious dynamic mechanism to facilitate gas uptake. The unusually slow exchange kinetics has allowed the rates of gas (water vapor and CO2) sorption to be quantified by single crystal X-ray diffraction. The data are well fit to a simple three-dimensional diffusion model.

  2. Direct label-free measurement of the distribution of small molecular weight compound inside thick biological tissue using coherent Raman microspectroscopy

    PubMed Central

    Kawagishi, Masahiko; Obara, Yuki; Suzuki, Takayuki; Hayashi, Masumi; Misawa, Kazuhiko; Terada, Sumio

    2015-01-01

    Distributions of small molecular weight (less than 300 Da) compounds inside biological tissue have been obscure because of the lack of appropriate methods to measure them. Although fluorescence techniques are widely used to characterise the localisation of large biomolecules, they cannot be easily applied to the cases with small molecule compounds. We used CARS spectroscopy to detect and identify a label-free small molecule compound. To facilitate detection in aqueous environment, we utilised time-resolved and phase-sensitive techniques to reduce non-resonant background generated from water. We applied this technique to detect small molecular weight compound, taurine, inside mouse cornea tissue immersed in taurine solution as an initial model experiment. We detected a Raman peak of taurine near wavenumber 1033 cm−1 inside cornea and successfully characterised its depth profile in the tissue. Our CARS spectra measurement can be a promising method to measure and visualise the distribution of small bio-related compounds in biological background without using any labeling, paving the way for new cell biological analysis in various disciplines. PMID:26353981

  3. Positron-attachment to small molecules: Vibrational enhancement of positron affinities with configuration interaction level of multi-component molecular orbital approach

    SciTech Connect

    Tachikawa, Masanori

    2015-12-31

    To theoretically demonstrate the binding of a positron to small polarized molecules, we have calculated the vibrational averaged positron affinity (PA) values along the local vibrational contribution with the configuration interaction level of multi-component molecular orbital method. This method can take the electron-positron correlation contribution into account through single electronic - single positronic excitation configurations. The PA values are enhanced by including the local vibrational contribution from vertical PA values due to the anharmonicity of the potential.

  4. Rapid detection of the epidermal growth factor receptor mutation in non-small-cell lung cancer for analysis of acquired resistance using molecular beacons.

    PubMed

    Oh, Young-Hee; Kim, Youngwook; Kim, Young-Pil; Seo, Soo-Won; Mitsudomi, Tetsuya; Ahn, Myung-Ju; Park, Keunchil; Kim, Hak-Sung

    2010-09-01

    A secondary mutation (T790M) in epidermal growth factor receptor (EGFR) is a hallmark of acquired resistance to EGFR inhibitors used to treat non-small-cell lung cancer (NSCLC). Therefore, identifying the T790M mutation is crucial to guide treatment decisions. Given that DNA sequencing methods are time-consuming and insensitive, we developed and investigated the feasibility of using molecular beacons for the detection of the T790M mutation in EGFR. A molecular beacon complementary to the region of the secondary EGFR mutation (T790M) was designed and used in NSCLC samples bearing drug-sensitive and -resistant EGFR mutations. For a rapid and simple assay, we attempted to use the molecular beacon with real-time PCR and in situ fluorescence imaging. The ability of the designed molecular beacon to specifically detect the T790M mutation of EGFR was tested for samples from two patients with drug resistance and compared with conventional DNA sequencing methods. The molecular beacon successfully detected the T790M mutation in patient samples with drug resistance. The sensitivity of the molecular beacon, which detected as little as 2% of genomic DNA from the drug-resistant cells (H1975), was much higher than direct sequencing. Furthermore, in situ fluorescence imaging with the molecular beacon gave rise to a distinguishable signal for the T790M mutation in drug-resistant cells. The molecular beacon-based approach enabled rapid and sensitive detection of the EGFR mutation (T790M) in NSCLC with in situ fluorescence imaging, which can be directed to determine various treatment options in patients with cancer.

  5. Energy stabilization of the s -symmetry superatom molecular orbital by endohedral doping of C 82 fullerene with a lanthanum atom

    SciTech Connect

    Feng, Min; Shi, Yongliang; Lin, Chungwei; Zhao, Jin; Liu, Fupin; Yang, Shangfeng; Petek, Hrvoje

    2013-08-01

    Energy stabilization of the superatom molecular orbitals (SAMOs) in fullerenes is investigated with the goal of involving their nearly free-electron bands in practical charge transport applications. Combining low-temperature scanning tunneling microscopy-based spectroscopic methods and density functional theory calculations on an endohedral metallofullerene La@C82, we confirm that the s-SAMO of C82 fullerene is stabilized by as much as 2 eV with respect to that of C60 by endohedral doping with the La atom. On the copper metal substrate, the s-SAMO energy is further lowered to just 1 eV above the Fermi level, making the applications of s-SAMO state in transport more plausible. We conclude that in an endohedral metallofullerene, the s-SAMO state is stabilized through the hybridization with the s-symmetry valence state of the metal atom and the stabilization energy correlates with the ionization potential of the free atom.

  6. Functional and molecular structural analysis of dentine interfaces promoted by a Zn-doped self-etching adhesive and an in vitro load cycling model.

    PubMed

    Toledano, Manuel; Aguilera, Fátima S; Osorio, Estrella; Cabello, Inmaculada; Toledano-Osorio, Manuel; Osorio, Raquel

    2015-10-01

    The aim of this study was to evaluate if mechanical cycling influences bioactivity and bond strength of resin-dentine interface after bonding with Zn-doped self-etching adhesives. Sound dentine surfaces were bonded with Clearfil SE Bond (SEB), 10 wt% ZnO microparticles or 2 wt% ZnCl2 were added into the SEB primer (P) or bonding (Bd) for Zn-doping. Bonded interfaces were stored in simulated body fluid (24h), and then tested or submitted to mechanical loading. Microtensile bond strength testing was performed. Debonded dentine surfaces were studied by scanning electron microscopy. Remineralisation of the bonded interfaces was assessed by nano-indentation, Raman spectroscopy, and Masson׳s trichrome staining. Load cycling (LC) increased the percentage of adhesive failures in all groups. LC increased the Young׳s modulus (Ei) at the hybrid layer (HL) when SEB, SEB·P-ZnO and SEB·P-ZnCl2 were applied, but decreased when both ZnO and ZnCl2 were incorporated into the bonding. Ei was higher when Zn compounds were incorporated into the primer (SEB·P). ZnO promoted an increase, and ZnCl2 a decrease, of both the relative presence of minerals and crystallinity, after LC. LC increased collagen crosslinking with both SEB·P-ZnO and SEB·P-ZnCl2. The ratios which reflect the nature of collagen increased, in general, at both HL and BHL after LC, confirming recovery, better organisation, improved structural differences and collagen quality. After loading, trichrome staining reflected a deeper demineralised dentine fringe when Zn-doped compounds were incorporated into SEB·Bd. Multiple Zn-rich phosphate deposits and salt formations were detected. Mineral precipitates nucleated in multilayered platforms or globular formations on peritubular and intertubular dentine.

  7. Functional and molecular structural analysis of dentine interfaces promoted by a Zn-doped self-etching adhesive and an in vitro load cycling model.

    PubMed

    Toledano, Manuel; Aguilera, Fátima S; Osorio, Estrella; Cabello, Inmaculada; Toledano-Osorio, Manuel; Osorio, Raquel

    2015-10-01

    The aim of this study was to evaluate if mechanical cycling influences bioactivity and bond strength of resin-dentine interface after bonding with Zn-doped self-etching adhesives. Sound dentine surfaces were bonded with Clearfil SE Bond (SEB), 10 wt% ZnO microparticles or 2 wt% ZnCl2 were added into the SEB primer (P) or bonding (Bd) for Zn-doping. Bonded interfaces were stored in simulated body fluid (24h), and then tested or submitted to mechanical loading. Microtensile bond strength testing was performed. Debonded dentine surfaces were studied by scanning electron microscopy. Remineralisation of the bonded interfaces was assessed by nano-indentation, Raman spectroscopy, and Masson׳s trichrome staining. Load cycling (LC) increased the percentage of adhesive failures in all groups. LC increased the Young׳s modulus (Ei) at the hybrid layer (HL) when SEB, SEB·P-ZnO and SEB·P-ZnCl2 were applied, but decreased when both ZnO and ZnCl2 were incorporated into the bonding. Ei was higher when Zn compounds were incorporated into the primer (SEB·P). ZnO promoted an increase, and ZnCl2 a decrease, of both the relative presence of minerals and crystallinity, after LC. LC increased collagen crosslinking with both SEB·P-ZnO and SEB·P-ZnCl2. The ratios which reflect the nature of collagen increased, in general, at both HL and BHL after LC, confirming recovery, better organisation, improved structural differences and collagen quality. After loading, trichrome staining reflected a deeper demineralised dentine fringe when Zn-doped compounds were incorporated into SEB·Bd. Multiple Zn-rich phosphate deposits and salt formations were detected. Mineral precipitates nucleated in multilayered platforms or globular formations on peritubular and intertubular dentine. PMID:26122790

  8. Heteroatom-Containing Porous Carbons Derived from Ionic Liquid-Doped Alkali Organic Salts for Supercapacitors.

    PubMed

    Zhu, Jingyue; Xu, Dan; Qian, Wenjing; Zhang, Jinyu; Yan, Feng

    2016-04-13

    A simple strategy for the synthesis of heteroatom-doped porous carbon materials (CMs) via using ionic liquid (IL)-doped alkali organic salts as small molecular precursors is developed. Doping of alkali organic salts (such as sodium glutamate, sodium tartrate, and sodium citrate) with heteroatoms containing ILs (including 1-butyl-3-methylimidazolium chlorine and 3-butyl-4-methythiazolebromination) not only incorporates the heteroatoms into the carbon frameworks but also highly improves the carbonization yield, as compared with that of either alkali organic salts or ILs as precursors. The porous structure of CMs can be tuned by adjusting the feed ratio of ILs. The porous CMs derived from 1-butyl-3-methylimidazolium chlorine-doped sodium glutamate exhibit high charge storage capacity with a specific capacitance of 287 F g(-1) and good stability over 5000 cycles in 6 m KOH at a current density of 1 A g(-1) for supercapacitors. This strategy opens a simple and efficient method for the synthesis of heteroatom-doped porous CMs. PMID:26869577

  9. Measuring the molecular dimensions of wine tannins: comparison of small-angle X-ray scattering, gel-permeation chromatography and mean degree of polymerization.

    PubMed

    McRae, Jacqui M; Kirby, Nigel; Mertens, Haydyn D T; Kassara, Stella; Smith, Paul A

    2014-07-23

    The molecular size of wine tannins can influence astringency, and yet it has been unclear as to whether the standard methods for determining average tannin molecular weight (MW), including gel-permeation chromatography (GPC) and depolymerization reactions, are actually related to the size of the tannin in wine-like conditions. Small-angle X-ray scattering (SAXS) was therefore used to determine the molecular sizes and corresponding MWs of wine tannin samples from 3 and 7 year old Cabernet Sauvignon wine in a variety of wine-like matrixes: 5-15% and 100% ethanol; 0-200 mM NaCl and pH 3.0-4.0, and compared to those measured using the standard methods. The SAXS results indicated that the tannin samples from the older wine were larger than those of the younger wine and that wine composition did not greatly impact on tannin molecular size. The average tannin MWs as determined by GPC correlated strongly with the SAXS results, suggesting that this method does give a good indication of tannin molecular size in wine-like conditions. The MW as determined from the depolymerization reactions did not correlate as strongly with the SAXS results. To our knowledge, SAXS measurements have not previously been attempted for wine tannins.

  10. Chemical approaches for doping nanodevice architectures.

    PubMed

    O'Connell, John; Biswas, Subhajit; Duffy, Ray; Holmes, Justin D

    2016-08-26

    Advanced doping technologies are key for the continued scaling of semiconductor devices and the maintenance of device performance beyond the 14 nm technology node. Due to limitations of conventional ion-beam implantation with thin body and 3D device geometries, techniques which allow precise control over dopant diffusion and concentration, in addition to excellent conformality on 3D device surfaces, are required. Spin-on doping has shown promise as a conventional technique for doping new materials, particularly through application with other dopant methods, but may not be suitable for conformal doping of nanostructures. Additionally, residues remain after most spin-on-doping processes which are often difficult to remove. In situ doping of nanostructures is especially common for bottom-up grown nanostructures but problems associated with concentration gradients and morphology changes are commonly experienced. Monolayer doping has been shown to satisfy the requirements for extended defect-free, conformal and controllable doping on many materials ranging from traditional silicon and germanium devices to emerging replacement materials such as III-V compounds but challenges still remain, especially with regard to metrology and surface chemistry at such small feature sizes. This article summarises and critically assesses developments over the last number of years regarding the application of gas and solution phase techniques to dope silicon-, germanium- and III-V-based materials and nanostructures to obtain shallow diffusion depths coupled with high carrier concentrations and abrupt junctions. PMID:27418239

  11. Chemical approaches for doping nanodevice architectures

    NASA Astrophysics Data System (ADS)

    O’Connell, John; Biswas, Subhajit; Duffy, Ray; Holmes, Justin D.

    2016-08-01

    Advanced doping technologies are key for the continued scaling of semiconductor devices and the maintenance of device performance beyond the 14 nm technology node. Due to limitations of conventional ion-beam implantation with thin body and 3D device geometries, techniques which allow precise control over dopant diffusion and concentration, in addition to excellent conformality on 3D device surfaces, are required. Spin-on doping has shown promise as a conventional technique for doping new materials, particularly through application with other dopant methods, but may not be suitable for conformal doping of nanostructures. Additionally, residues remain after most spin-on-doping processes which are often difficult to remove. In situ doping of nanostructures is especially common for bottom-up grown nanostructures but problems associated with concentration gradients and morphology changes are commonly experienced. Monolayer doping has been shown to satisfy the requirements for extended defect-free, conformal and controllable doping on many materials ranging from traditional silicon and germanium devices to emerging replacement materials such as III–V compounds but challenges still remain, especially with regard to metrology and surface chemistry at such small feature sizes. This article summarises and critically assesses developments over the last number of years regarding the application of gas and solution phase techniques to dope silicon-, germanium- and III–V-based materials and nanostructures to obtain shallow diffusion depths coupled with high carrier concentrations and abrupt junctions.

  12. Chemical approaches for doping nanodevice architectures

    NASA Astrophysics Data System (ADS)

    O'Connell, John; Biswas, Subhajit; Duffy, Ray; Holmes, Justin D.

    2016-08-01

    Advanced doping technologies are key for the continued scaling of semiconductor devices and the maintenance of device performance beyond the 14 nm technology node. Due to limitations of conventional ion-beam implantation with thin body and 3D device geometries, techniques which allow precise control over dopant diffusion and concentration, in addition to excellent conformality on 3D device surfaces, are required. Spin-on doping has shown promise as a conventional technique for doping new materials, particularly through application with other dopant methods, but may not be suitable for conformal doping of nanostructures. Additionally, residues remain after most spin-on-doping processes which are often difficult to remove. In situ doping of nanostructures is especially common for bottom-up grown nanostructures but problems associated with concentration gradients and morphology changes are commonly experienced. Monolayer doping has been shown to satisfy the requirements for extended defect-free, conformal and controllable doping on many materials ranging from traditional silicon and germanium devices to emerging replacement materials such as III-V compounds but challenges still remain, especially with regard to metrology and surface chemistry at such small feature sizes. This article summarises and critically assesses developments over the last number of years regarding the application of gas and solution phase techniques to dope silicon-, germanium- and III-V-based materials and nanostructures to obtain shallow diffusion depths coupled with high carrier concentrations and abrupt junctions.

  13. The chemistry and spatial distribution of small hydrocarbons in UV-irradiated molecular clouds: the Orion Bar PDR

    NASA Astrophysics Data System (ADS)

    Cuadrado, S.; Goicoechea, J. R.; Pilleri, P.; Cernicharo, J.; Fuente, A.; Joblin, C.

    2015-03-01

    Context. Carbon chemistry plays a pivotal role in the interstellar medium (ISM) but even the synthesis of the simplest hydrocarbons and how they relate to polycyclic aromatic hydrocarbons (PAHs) and grains is not well understood. Aims: We study the spatial distribution and chemistry of small hydrocarbons in the Orion Bar photodissociation region (PDR), a prototypical environment in which to investigate molecular gas irradiated by strong UV fields. Methods: We used the IRAM 30 m telescope to carry out a millimetre line survey towards the Orion Bar edge, complemented with ~2' × 2' maps of the C2H and c-C3H2 emission. We analyse the excitation of the detected hydrocarbons and constrain the physical conditions of the emitting regions with non-LTE radiative transfer models. We compare the inferred column densities with updated gas-phase photochemical models including 13CCH and C13CH isotopomer fractionation. Results: Approximately 40% of the lines in the survey arise from hydrocarbons (C2H, C4H, c-C3H2, c-C3H, C13CH, 13CCH, l-C3H, and l-H2C3 in decreasing order of abundance). We detect new lines from l-C3H+ and improve its rotational spectroscopic constants. Anions or deuterated hydrocarbons are not detected, but we provide accurate upper limit abundances: [C2D]/[C2H] < 0.2%, [C2H-]/[C2H] < 0.007%, and [C4H-]/[C4H] < 0.05%. Conclusions: Our models can reasonably match the observed column densities of most hydrocarbons (within factors of <3). Since the observed spatial distribution of the C2H and c-C3H2 emission is similar but does not follow the PAH emission, we conclude that, in high UV-flux PDRs, photodestruction of PAHs is not a necessary requirement to explain the observed abundances of the smallest hydrocarbons. Instead, gas-phase endothermic reactions (or with barriers) between C+, radicals, and H2 enhance the formation of simple hydrocarbons. Observations and models suggest that the [C2H]/[c-C3H2] ratio (~32 at the PDR edge) decreases with the UV field

  14. Rare Earth Doped Magnetic Clusters of Gold for Medical Application

    NASA Astrophysics Data System (ADS)

    Yadav, Brahm Deo; Kumar, Vijay

    2011-03-01

    In recent years gold clusters have been studied extensively due to their unusual properties and applications in cancer treatment and catalysis. Small gold clusters having up to 15 atoms are planar as shown in figure 1. Thereafter a transition occurs to 3D structures but the atomic structures continue to have high dispersion. Doping of these clusters could transform them in to new structures and affect the properties. Gold clusters with cage structures such as W@Au12 can be prepared with large highest occupied-lowest unoccupied molecular orbital (HOMO-LUMO) gap by doping with a transition metal atom such as W. By changing the transition metal atom, cage structures of different sizes as well as different HOMO-LUMO gaps can be formed which could be useful in different optical applications. In these structures gold clusters are generally non-magnetic. However, it is also possible to form magnetic clusters of gold such as Gold clusters have been found to be good for cancer treatment. We have performed ab initio calculations on doping of rare earths in small gold clusters to obtain magnetic clusters using projector augmented wave pseudopotential method within generalized gradient approximation for the exchange-correlation energy. Elemental gold clusters having up to 15 atoms are planar and thereafter 3D structures become favorable. We have explored the changes in the growth behavior when a rare earth atom is doped and studied the variation in the magnetic behavior as a function of size. Our results suggest that gold clusters may have twin advantage of treating cancer as well as be helful in magnetic imaging such as by MRI.

  15. Continuously adjustable, molecular-sieving “gate” on 5A zeolite for distinguishing small organic molecules by size

    DOE PAGESBeta

    Song, Zhuonan; Huang, Yi; Xu, Weiwei L.; Wang, Lei; Bao, Yu; Li, Shiguang; Yu, Miao

    2015-09-11

    Zeolites/molecular sieves with uniform, molecular-sized pores are important for many adsorption-based separation processes. Pore size gaps, however, exist in the current zeolite family. This leads to a great challenge of separating molecules with size differences at ~0.01 nm level. Here, we report a novel concept, pore misalignment, to form a continuously adjustable, molecular-sieving “gate” at the 5A zeolite pore entrance without sacrificing the internal capacity. Misalignment of the micropores of the alumina coating with the 5A zeolite pores was related with and facilely adjusted by the coating thickness. For the first time, organic molecules with sub-0.01 nm size differences weremore » effectively distinguished via appropriate misalignment. Lastly, this novel concept may have great potential to fill the pore size gaps of the zeolite family and realize size-selective adsorption separation.« less

  16. Continuously adjustable, molecular-sieving “gate” on 5A zeolite for distinguishing small organic molecules by size

    SciTech Connect

    Song, Zhuonan; Huang, Yi; Xu, Weiwei L.; Wang, Lei; Bao, Yu; Li, Shiguang; Yu, Miao

    2015-09-11

    Zeolites/molecular sieves with uniform, molecular-sized pores are important for many adsorption-based separation processes. Pore size gaps, however, exist in the current zeolite family. This leads to a great challenge of separating molecules with size differences at ~0.01 nm level. Here, we report a novel concept, pore misalignment, to form a continuously adjustable, molecular-sieving “gate” at the 5A zeolite pore entrance without sacrificing the internal capacity. Misalignment of the micropores of the alumina coating with the 5A zeolite pores was related with and facilely adjusted by the coating thickness. For the first time, organic molecules with sub-0.01 nm size differences were effectively distinguished via appropriate misalignment. Lastly, this novel concept may have great potential to fill the pore size gaps of the zeolite family and realize size-selective adsorption separation.

  17. Continuously Adjustable, Molecular-Sieving “Gate” on 5A Zeolite for Distinguishing Small Organic Molecules by Size

    PubMed Central

    Song, Zhuonan; Huang, Yi; Xu, Weiwei L.; Wang, Lei; Bao, Yu; Li, Shiguang; Yu, Miao

    2015-01-01

    Zeolites/molecular sieves with uniform, molecular-sized pores are important for many adsorption-based separation processes. Pore size gaps, however, exist in the current zeolite family. This leads to a great challenge of separating molecules with size differences at ~0.01 nm level. Here, we report a novel concept, pore misalignment, to form a continuously adjustable, molecular-sieving “gate” at the 5A zeolite pore entrance without sacrificing the internal capacity. Misalignment of the micropores of the alumina coating with the 5A zeolite pores was related with and facilely adjusted by the coating thickness. For the first time, organic molecules with sub-0.01 nm size differences were effectively distinguished via appropriate misalignment. This novel concept may have great potential to fill the pore size gaps of the zeolite family and realize size-selective adsorption separation. PMID:26358480

  18. Quasiequilibrium unfolding thermodynamics of a small protein studied by molecular dynamics simulation with an explicit water model

    NASA Astrophysics Data System (ADS)

    Wang, Jihua; Zhang, Zhiyong; Liu, Haiyan; Shi, Yunyu

    2003-06-01

    The 124 independent molecular dynamics simulations are completed with total time of 196.8 ns. The calculated unfolding quasiequilibrium thermodynamics of G-IgG-binding domain B1 (GB1) shows the experimentally observed protein transitions: a coil to disordered globule transition, a disordered globule to molten globule transition, a molten globule to nativelike transition, and a nativelike to solidlike state transition. The first protein unfolding phase diagram has been constructed from molecular dynamics simulations with an explicit water model. The calculated melting temperature of GB1 agrees with early experiment. The results also agree with the recent experiment result in which GB1 has more than one intermediate.

  19. Molecular identification of Emericella echinulata as a cause of Cerebral Aspergillosis in a patient following small bowel and liver transplantation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular methods are now more commonly used for identification of the aspergilli and their teleomorphs and have led to reports of species not previously recognized as causing human disease. We report the first case of cerebral aspergillosis in a compromised patient caused by Emericella echinulata,...

  20. Observation of positive and small electron affinity of Si-doped AlN films grown by metalorganic chemical vapor deposition on n-type 6H–SiC

    NASA Astrophysics Data System (ADS)

    Feng, Liang; Ping, Chen; De-Gang, Zhao; De-Sheng, Jiang; Zhi-Juan, Zhao; Zong-Shun, Liu; Jian-Jun, Zhu; Jing, Yang; Wei, Liu; Xiao-Guang, He; Xiao-Jing, Li; Xiang, Li; Shuang-Tao, Liu; Hui, Yang; Li-Qun, Zhang; Jian-Ping, Liu; Yuan-Tao, Zhang; Guo-Tong, Du

    2016-05-01

    We have investigated the electron affinity of Si-doped AlN films (N Si = 1.0 × 1018–1.0 × 1019 cm‑3) with thicknesses of 50, 200, and 400 nm, synthesized by metalorganic chemical vapor deposition (MOCVD) under low pressure on the n-type (001)6H–SiC substrates. The positive and small electron affinity of AlN films was observed through the ultraviolet photoelectron spectroscopy (UPS) analysis, where an increase in electron affinity appears with the thickness of AlN films increasing, i.e., 0.36 eV for the 50-nm-thick one, 0.58 eV for the 200-nm-thick one, and 0.97 eV for the 400-nm-thick one. Accompanying the x-ray photoelectron spectroscopy (XPS) analysis on the surface contaminations, it suggests that the difference of electron affinity between our three samples may result from the discrepancy of surface impurity contaminations. Project supported by the National Natural Science Foundation of China (Grant Nos. 61574135, 61574134, 61474142, 61474110, 61377020, 61376089, 61223005, and 61321063), the One Hundred Person Project of the Chinese Academy of Sciences, and the Basic Research Project of Jiangsu Province, China (Grant No. BK20130362).

  1. A Bio-Inspired Two-Layer Sensing Structure of Polypeptide and Multiple-Walled Carbon Nanotube to Sense Small Molecular Gases

    PubMed Central

    Wang, Li-Chun; Su, Tseng-Hsiung; Ho, Cheng-Long; Yang, Shang-Ren; Chiu, Shih-Wen; Kuo, Han-Wen; Tang, Kea-Tiong

    2015-01-01

    In this paper, we propose a bio-inspired, two-layer, multiple-walled carbon nanotube (MWCNT)-polypeptide composite sensing device. The MWCNT serves as a responsive and conductive layer, and the nonselective polypeptide (40 mer) coating the top of the MWCNT acts as a filter into which small molecular gases pass. Instead of using selective peptides to sense specific odorants, we propose using nonselective, peptide-based sensors to monitor various types of volatile organic compounds. In this study, depending on gas interaction and molecular sizes, the randomly selected polypeptide enabled the recognition of certain polar volatile chemical vapors, such as amines, and the improved discernment of low-concentration gases. The results of our investigation demonstrated that the polypeptide-coated sensors can detect ammonia at a level of several hundred ppm and barely responded to triethylamine. PMID:25751078

  2. A bio-inspired two-layer sensing structure of polypeptide and multiple-walled carbon nanotube to sense small molecular gases.

    PubMed

    Wang, Li-Chun; Su, Tseng-Hsiung; Ho, Cheng-Long; Yang, Shang-Ren; Chiu, Shih-Wen; Kuo, Han-Wen; Tang, Kea-Tiong

    2015-03-05

    In this paper, we propose a bio-inspired, two-layer, multiple-walled carbon nanotube (MWCNT)-polypeptide composite sensing device. The MWCNT serves as a responsive and conductive layer, and the nonselective polypeptide (40 mer) coating the top of the MWCNT acts as a filter into which small molecular gases pass. Instead of using selective peptides to sense specific odorants, we propose using nonselective, peptide-based sensors to monitor various types of volatile organic compounds. In this study, depending on gas interaction and molecular sizes, the randomly selected polypeptide enabled the recognition of certain polar volatile chemical vapors, such as amines, and the improved discernment of low-concentration gases. The results of our investigation demonstrated that the polypeptide-coated sensors can detect ammonia at a level of several hundred ppm and barely responded to triethylamine.

  3. A bio-inspired two-layer sensing structure of polypeptide and multiple-walled carbon nanotube to sense small molecular gases.

    PubMed

    Wang, Li-Chun; Su, Tseng-Hsiung; Ho, Cheng-Long; Yang, Shang-Ren; Chiu, Shih-Wen; Kuo, Han-Wen; Tang, Kea-Tiong

    2015-01-01

    In this paper, we propose a bio-inspired, two-layer, multiple-walled carbon nanotube (MWCNT)-polypeptide composite sensing device. The MWCNT serves as a responsive and conductive layer, and the nonselective polypeptide (40 mer) coating the top of the MWCNT acts as a filter into which small molecular gases pass. Instead of using selective peptides to sense specific odorants, we propose using nonselective, peptide-based sensors to monitor various types of volatile organic compounds. In this study, depending on gas interaction and molecular sizes, the randomly selected polypeptide enabled the recognition of certain polar volatile chemical vapors, such as amines, and the improved discernment of low-concentration gases. The results of our investigation demonstrated that the polypeptide-coated sensors can detect ammonia at a level of several hundred ppm and barely responded to triethylamine. PMID:25751078

  4. High-resolution emission tomography of small laboratory animals: physics and gamma-astronomy meet molecular biology

    NASA Astrophysics Data System (ADS)

    Beekman, F. J.; Colijn, A. P.; Vastenhouw, B.; Wiegant, V. M.; Gerrits, M. A. F. M.

    2003-08-01

    Molecular imaging can be defined as the characterization and measurement of biological processes in living animals, model systems and humans at the cellular and molecular level using remote imaging detectors. An example concerns the mapping of the distributions of radioactively labeled molecules in laboratory animals which is of crucial importance for life sciences. Tomographic methods like Single Photon Emission Computed Tomography (SPECT) offer a possibility to visualize distributions of radioactively labeled molecules in living animals. Miniature tomography systems, derived from their clinical counterparts, but with a much higher image resolution are under development in several institutes. An example is U-SPECT that will be discussed in the present paper. Such systems are expected to accelerate several biomedical research procedures, the understanding of gene and protein function, as well as pharmaceutical development.

  5. Molecular Profiling to Optimize Treatment in Non-Small Cell Lung Cancer: A Review of Potential Molecular Targets for Radiation Therapy by the Translational Research Program of the Radiation Therapy Oncology Group

    SciTech Connect

    Ausborn, Natalie L.; Le, Quynh Thu; Bradley, Jeffrey D.; Choy, Hak; Dicker, Adam P.; Saha, Debabrata; Simko, Jeff; Story, Michael D.; Torossian, Artour; Lu, Bo

    2012-07-15

    Therapeutic decisions in non-small cell lung cancer (NSCLC) have been mainly based on disease stage, performance status, and co-morbidities, and rarely on histological or molecular classification. Rather than applying broad treatments to unselected patients that may result in survival increase of only weeks to months, research efforts should be, and are being, focused on identifying predictive markers for molecularly targeted therapy and determining genomic signatures that predict survival and response to specific therapies. The availability of such targeted biologics requires their use to be matched to tumors of corresponding molecular vulnerability for maximum efficacy. Molecular markers such as epidermal growth factor receptor (EGFR), K-ras, vascular endothelial growth factor (VEGF), mammalian target of rapamycin (mTOR), and anaplastic lymphoma kinase (ALK) represent potential parameters guide treatment decisions. Ultimately, identifying patients who will respond to specific therapies will allow optimal efficacy with minimal toxicity, which will result in more judicious and effective application of expensive targeted therapy as the new paradigm of personalized medicine develops.

  6. A Delicate Balance When Substituting a Small Hydrophobe onto Low Molecular Weight Polyethylenimine to Improve Its Nucleic Acid Delivery Efficiency.

    PubMed

    Meneksedag-Erol, Deniz; KC, Remant Bahadur; Tang, Tian; Uludağ, Hasan

    2015-11-11

    High molecular weight (HMW) polyethylenimine (PEI) is one of the most versatile nonviral gene vectors that was extensively investigated over the past two decades. The cytotoxic profile of HMW PEI, however, encouraged a search for safer alternatives. Because of lack of cytotoxicity of low molecular weight (LMW) PEI, enhancing its performance via hydrophobic modifications has been pursued to this end. Since the performance of modified PEIs depends on the nature and extent of substituents, we systematically investigated the effect of hydrophobic modification of LMW (1.2 kDa) PEI with a short propionic acid (PrA). Moderate enhancements in PEI hydrophobicity resulted in enhanced cellular uptake of polyplexes and siRNA-induced silencing efficacy, whereas further increase in PrA substitution abolished the uptake as well as the silencing. We performed all-atom molecular dynamics simulations to elucidate the mechanistic details behind these observations. A new assembly mechanism was observed by the presence of hydrophobic PrA moieties, where PrA migrated to core of the polyplex. This phenomenon caused higher surface hydrophobicity and surface charge density at low substitutions, and it caused deleterious effects on surface hydrophobicity and cationic charge at higher substitutions. It is evident that an optimal balance of hydrophobicity/hydrophilicity is needed to achieve the desired polyplex properties for an efficient siRNA delivery, and our mechanistic findings should provide valuable insights for the design of improved substituents on nonviral carriers.

  7. High Resolution Laboratory Spectroscopy in Support of Herschel and SOFIA: From Small Molecular Ions to PAHs and Fullerenes

    NASA Astrophysics Data System (ADS)

    McCall, Benjamin

    The spectral lines of molecules serve as essential tools for astronomers, allowing them to probe the physical and chemical conditions of diverse environments, ranging from the diffuse interstellar medium to quiescent molecular clouds to star- and planet-forming regions to nebulae and circumstellar shells. This use of molecules as astronomical probes is only possible because of decades of work by laboratory spectroscopists, who have measured the frequencies of molecular spectral lines and determined the energy levels from which they originate. Ground-based astronomical spectroscopy has been mostly limited to frequencies below ~1 THz or above ~60 THz (below ~5 1/4m) due to the opacity of Earth s atmosphere, but new NASA missions (Herschel and SOFIA) are enabling high resolution spectroscopy in the no-man s land between 1-60 THz. However, comparatively little laboratory spectroscopy has been performed in this region, jeopardizing the scientific return from these missions. There is therefore a critical need to measure THz/far-IR spectral line frequencies of astrophysically important molecules. Two particularly important classes of such molecules are molecular ions and large neutral molecules. The objective of this particular proposal is to perform spectroscopy of astrophysically important molecular cations and large molecules with unprecedented precision and accuracy, to determine their transition frequencies in the THz/far-IR region. The rationale for the proposed research is that it will enable the study of these species with Herschel and SOFIA, thereby improving our understanding of interstellar clouds, star- forming regions, and other astronomical environments. The specific objectives of the proposed research is to measure high-precision infrared spectra of astrophysically important molecular cations, and determine their THz/far-IR frequencies to support Herschel and SOFIA. Using our newly discovered technique NICE-OHVMS (noise-immune cavity-enhanced optical

  8. Small Atomic Orbital Basis Set First-Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources.

    PubMed

    Sure, Rebecca; Brandenburg, Jan Gerit; Grimme, Stefan

    2016-04-01

    In quantum chemical computations the combination of Hartree-Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double-zeta quality is still widely used, for example, in the popular B3LYP/6-31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean-field methods. PMID:27308221

  9. Small Atomic Orbital Basis Set First-Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources.

    PubMed

    Sure, Rebecca; Brandenburg, Jan Gerit; Grimme, Stefan

    2016-04-01

    In quantum chemical computations the combination of Hartree-Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double-zeta quality is still widely used, for example, in the popular B3LYP/6-31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean-field methods.

  10. Small Atomic Orbital Basis Set First‐Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources

    PubMed Central

    Sure, Rebecca; Brandenburg, Jan Gerit

    2015-01-01

    Abstract In quantum chemical computations the combination of Hartree–Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double‐zeta quality is still widely used, for example, in the popular B3LYP/6‐31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean‐field methods. PMID:27308221

  11. Metal-doped organic foam

    DOEpatents

    Rinde, James A.

    1982-01-01

    Organic foams having a low density and very small cell size and method for producing same in either a metal-loaded or unloaded (nonmetal loaded) form are described. Metal-doped foams are produced by soaking a polymer gel in an aqueous solution of desired metal salt, soaking the gel successively in a solvent series of decreasing polarity to remove water from the gel and replace it with a solvent of lower polarity with each successive solvent in the series being miscible with the solvents on each side and being saturated with the desired metal salt, and removing the last of the solvents from the gel to produce the desired metal-doped foam having desired density cell size, and metal loading. The unloaded or metal-doped foams can be utilized in a variety of applications requiring low density, small cell size foam. For example, rubidium-doped foam made in accordance with the invention has utility in special applications, such as in x-ray lasers.

  12. Simulations of the dissociation of small helium clusters with ab initio molecular dynamics in electronically excited states

    SciTech Connect

    Closser, Kristina D.; Head-Gordon, Martin; Gessner, Oliver

    2014-04-07

    The dynamics resulting from electronic excitations of helium clusters were explored using ab initio molecular dynamics. The simulations were performed with configuration interaction singles and adiabatic classical dynamics coupled to a state-following algorithm. 100 different configurations of He{sub 7} were excited into the 2s and 2p manifold for a total of 2800 trajectories. While the most common outcome (90%) was complete fragmentation to 6 ground state atoms and 1 excited state atom, 3% of trajectories yielded bound, He {sub 2}{sup *}, and <0.5% yielded an excited helium trimer. The nature of the dynamics, kinetic energy release, and connections to experiments are discussed.

  13. DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening

    PubMed Central

    2009-01-01

    Background Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats. Results Here, we describe the new open source program DG-AMMOS which allows the generation of the 3D conformation of small molecules using Distance Geometry and their energy minimization via Automated Molecular Mechanics Optimization. The program is validated on the Astex dataset, the ChemBridge Diversity database and on a number of small molecules with known crystal structures extracted from the Cambridge Structural Database. A comparison with the free program Balloon and the well-known commercial program Omega generating the 3D of small molecules is carried out. The results show that the new free program DG-AMMOS is a very efficient 3D structure generator engine. Conclusion DG-AMMOS provides fast, automated and reliable access to the generation of 3D conformation of small molecules and facilitates the preparation of a compound collection prior to high-throughput virtual screening computations. The validation of DG-AMMOS on several different datasets proves that generated structures are generally of equal quality or sometimes better than structures obtained by other tested methods. PMID:19912625

  14. Proton irradiation effects on deep level states in Mg-doped p-type GaN grown by ammonia-based molecular beam epitaxy

    SciTech Connect

    Zhang, Z.; Arehart, A. R.; Ringel, S. A.; Kyle, E. C. H.; Speck, J. S.; Chen, J.; Zhang, E. X.; Fleetwood, D. M.; Schrimpf, R. D.

    2015-01-12

    The impact of proton irradiation on the deep level states throughout the Mg-doped p-type GaN bandgap is investigated using deep level transient and optical spectroscopies. Exposure to 1.8 MeV protons of 1 × 10{sup 13 }cm{sup −2} and 3 × 10{sup 13 }cm{sup −2} fluences not only introduces a trap with an E{sub V} + 1.02 eV activation energy but also brings monotonic increases in concentration for as-grown deep states at E{sub V} + 0.48 eV, E{sub V} + 2.42 eV, E{sub V} + 3.00 eV, and E{sub V} + 3.28 eV. The non-uniform sensitivities for individual states suggest different physical sources and/or defect generation mechanisms. Comparing with prior theoretical calculations reveals that several traps are consistent with associations to nitrogen vacancy, nitrogen interstitial, and gallium vacancy origins, and thus are likely generated through displacing nitrogen and gallium atoms from the crystal lattice in proton irradiation environment.

  15. Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another?

    PubMed Central

    Mellis, Ian A.; Raj, Arjun

    2015-01-01

    Small-scale molecular systems biology, by which we mean the understanding of a how a few parts work together to control a particular biological process, is predicated on the assumption that cellular regulation is arranged in a circuit-like structure. Results from the omics revolution have upset this vision to varying degrees by revealing a high degree of interconnectivity, making it difficult to develop a simple, circuit-like understanding of regulatory processes. We here outline the limitations of the small-scale systems biology approach with examples from research into genetic algorithms, genetics, transcriptional network analysis, and genomics. We also discuss the difficulties associated with deriving true understanding from the analysis of large data sets and propose that the development of new, intelligent, computational tools may point to a way forward. Throughout, we intentionally oversimplify and talk about things in which we have little expertise, and it is likely that many of our arguments are wrong on one level or another. We do believe, however, that developing a true understanding via molecular systems biology will require a fundamental rethinking of our approach, and our goal is to provoke thought along these lines. PMID:26430156

  16. Strong Photo-Amplification Effects in Flexible Organic Capacitors with Small Molecular Solid-State Electrolyte Layers Sandwiched between Photo-Sensitive Conjugated Polymer Nanolayers

    PubMed Central

    Lee, Hyena; Kim, Jungnam; Kim, Hwajeong; Kim, Youngkyoo

    2016-01-01

    We demonstrate strong photo-amplification effects in flexible organic capacitors which consist of small molecular solid-state electrolyte layers sandwiched between light-sensitive conjugated polymer nanolayers. The small molecular electrolyte layers were prepared from aqueous solutions of tris(8-hydroxyquinoline-5-sulfonic acid) aluminum (ALQSA3), while poly(3-hexylthiophene) (P3HT) was employed as the light-sensitive polymer nanolayer that is spin-coated on the indium-tin oxide (ITO)-coated poly(ethylene terephthalate) (PET) film substrates. The resulting capacitors feature a multilayer device structure of PET/ITO/P3HT/ALQSA3/P3HT/ITO/PET, which were mechanically robust due to good adhesion between the ALQSA3 layers and the P3HT nanolayers. Results showed that the specific capacitance was increased by ca. 3-fold when a white light was illuminated to the flexible organic multilayer capacitors. In particular, the capacity of charge storage was remarkably (ca. 250-fold) enhanced by a white light illumination in the potentiostatic charge/discharge operation, and the photo-amplification functions were well maintained even after bending for 300 times at a bending angle of 180o. PMID:26846891

  17. Strong Photo-Amplification Effects in Flexible Organic Capacitors with Small Molecular Solid-State Electrolyte Layers Sandwiched between Photo-Sensitive Conjugated Polymer Nanolayers

    NASA Astrophysics Data System (ADS)

    Lee, Hyena; Kim, Jungnam; Kim, Hwajeong; Kim, Youngkyoo

    2016-02-01

    We demonstrate strong photo-amplification effects in flexible organic capacitors which consist of small molecular solid-state electrolyte layers sandwiched between light-sensitive conjugated polymer nanolayers. The small molecular electrolyte layers were prepared from aqueous solutions of tris(8-hydroxyquinoline-5-sulfonic acid) aluminum (ALQSA3), while poly(3-hexylthiophene) (P3HT) was employed as the light-sensitive polymer nanolayer that is spin-coated on the indium-tin oxide (ITO)-coated poly(ethylene terephthalate) (PET) film substrates. The resulting capacitors feature a multilayer device structure of PET/ITO/P3HT/ALQSA3/P3HT/ITO/PET, which were mechanically robust due to good adhesion between the ALQSA3 layers and the P3HT nanolayers. Results showed that the specific capacitance was increased by ca. 3-fold when a white light was illuminated to the flexible organic multilayer capacitors. In particular, the capacity of charge storage was remarkably (ca. 250-fold) enhanced by a white light illumination in the potentiostatic charge/discharge operation, and the photo-amplification functions were well maintained even after bending for 300 times at a bending angle of 180o.

  18. Strong Photo-Amplification Effects in Flexible Organic Capacitors with Small Molecular Solid-State Electrolyte Layers Sandwiched between Photo-Sensitive Conjugated Polymer Nanolayers.

    PubMed

    Lee, Hyena; Kim, Jungnam; Kim, Hwajeong; Kim, Youngkyoo

    2016-02-05

    We demonstrate strong photo-amplification effects in flexible organic capacitors which consist of small molecular solid-state electrolyte layers sandwiched between light-sensitive conjugated polymer nanolayers. The small molecular electrolyte layers were prepared from aqueous solutions of tris(8-hydroxyquinoline-5-sulfonic acid) aluminum (ALQSA3), while poly(3-hexylthiophene) (P3HT) was employed as the light-sensitive polymer nanolayer that is spin-coated on the indium-tin oxide (ITO)-coated poly(ethylene terephthalate) (PET) film substrates. The resulting capacitors feature a multilayer device structure of PET/ITO/P3HT/ALQSA3/P3HT/ITO/PET, which were mechanically robust due to good adhesion between the ALQSA3 layers and the P3HT nanolayers. Results showed that the specific capacitance was increased by ca. 3-fold when a white light was illuminated to the flexible organic multilayer capacitors. In particular, the capacity of charge storage was remarkably (ca. 250-fold) enhanced by a white light illumination in the potentiostatic charge/discharge operation, and the photo-amplification functions were well maintained even after bending for 300 times at a bending angle of 180(°).

  19. Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another?

    PubMed

    Mellis, Ian A; Raj, Arjun

    2015-10-01

    Small-scale molecular systems biology, by which we mean the understanding of a how a few parts work together to control a particular biological process, is predicated on the assumption that cellular regulation is arranged in a circuit-like structure. Results from the omics revolution have upset this vision to varying degrees by revealing a high degree of interconnectivity, making it difficult to develop a simple, circuit-like understanding of regulatory processes. We here outline the limitations of the small-scale systems biology approach with examples from research into genetic algorithms, genetics, transcriptional network analysis, and genomics. We also discuss the difficulties associated with deriving true understanding from the analysis of large data sets and propose that the development of new, intelligent, computational tools may point to a way forward. Throughout, we intentionally oversimplify and talk about things in which we have little expertise, and it is likely that many of our arguments are wrong on one level or another. We do believe, however, that developing a true understanding via molecular systems biology will require a fundamental rethinking of our approach, and our goal is to provoke thought along these lines.

  20. Molecular evolution inferred from small subunit rRNA sequences: what does it tell us about phylogenetic relationships and taxonomy of the parabasalids?

    NASA Technical Reports Server (NTRS)

    Viscogliosi, E.; Edgcomb, V. P.; Gerbod, D.; Noel, C.; Delgado-Viscogliosi, P.; Sogin, M. L. (Principal Investigator)

    1999-01-01

    The Parabasala are a primitive group of protists divided into two classes: the trichomonads and the hypermastigids. Until recently, phylogeny and taxonomy of parabasalids were mainly based on the comparative analysis of morphological characters primarily linked to the development of their cytoskeleton. Recent use of molecular markers, such as small subunit (SSU) rRNA has led to now insights into the systematics of the Parabasala and other groups of prolists. An updated phylogeny based on SSU rRNA is provided and compared to that inferred from ultrastructural data. The SSU rRNA phylogeny contradicts the dogma equating simple characters with pumitive characters. Hypermastigids, possessing a hyperdeveloped cytoskeleton, exhibit the most basal emergence in the parabasalid lineage. Other observations emerge from the SSU rRNA analysis, such as the secondary loss of some cytoskeleton structures in all representatives of the Monocercomonadidae, the existence of secondarily free living taxa (reversibility of parasitism) and the evidence against the co-evolution of the endobiotic parabasalids and their animal hosts. According to phylogenies based on SSU rRNA, all the trichomonad families are not monophyletic groups, putting into question the validity of current taxonomic assignments. The precise branching order of some taxa remains unclear, but this issue can possibly be addressed by the molecular analysis of additional parabasalids. The goal of such additional analyses would be to propose, in a near future, a revision of the taxonomy of this group of protists that takes into account both molecular and morphological data.

  1. Molecular evolution inferred from small subunit rRNA sequences: what does it tell us about phylogenetic relationships and taxonomy of the parabasalids?

    PubMed

    Viscogliosi, E; Edgcomb, V P; Gerbod, D; Noël, C; Delgado-Viscogliosi, P

    1999-12-01

    The Parabasala are a primitive group of protists divided into two classes: the trichomonads and the hypermastigids. Until recently, phylogeny and taxonomy of parabasalids were mainly based on the comparative analysis of morphological characters primarily linked to the development of their cytoskeleton. Recent use of molecular markers, such as small subunit (SSU) rRNA has led to now insights into the systematics of the Parabasala and other groups of prolists. An updated phylogeny based on SSU rRNA is provided and compared to that inferred from ultrastructural data. The SSU rRNA phylogeny contradicts the dogma equating simple characters with pumitive characters. Hypermastigids, possessing a hyperdeveloped cytoskeleton, exhibit the most basal emergence in the parabasalid lineage. Other observations emerge from the SSU rRNA analysis, such as the secondary loss of some cytoskeleton structures in all representatives of the Monocercomonadidae, the existence of secondarily free living taxa (reversibility of parasitism) and the evidence against the co-evolution of the endobiotic parabasalids and their animal hosts. According to phylogenies based on SSU rRNA, all the trichomonad families are not monophyletic groups, putting into question the validity of current taxonomic assignments. The precise branching order of some taxa remains unclear, but this issue can possibly be addressed by the molecular analysis of additional parabasalids. The goal of such additional analyses would be to propose, in a near future, a revision of the taxonomy of this group of protists that takes into account both molecular and morphological data.

  2. Advances in molecular-based personalized non-small-cell lung cancer therapy: targeting epidermal growth factor receptor and mechanisms of resistance

    PubMed Central

    Jotte, Robert M; Spigel, David R

    2015-01-01

    Molecularly targeted therapies, directed against the features of a given tumor, have allowed for a personalized approach to the treatment of advanced non-small-cell lung cancer (NSCLC). The reversible epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) gefitinib and erlotinib had undergone turbulent clinical development until it was discovered that these agents have preferential activity in patients with NSCLC harboring activating EGFR mutations. Since then, a number of phase 3 clinical trials have collectively shown that EGFR-TKI monotherapy is more effective than combination chemotherapy as first-line therapy for EGFR mutation-positive advanced NSCLC. The next generation of EGFR-directed agents for EGFR mutation-positive advanced NSCLC is irreversible TKIs against EGFR and other ErbB family members, including afatinib, which was recently approved, and dacomitinib, which is currently being tested in phase 3 trials. As research efforts continue to explore the various proposed mechanisms of acquired resistance to EGFR-TKI therapy, agents that target signaling pathways downstream of EGFR are being studied in combination with EGFR TKIs in molecularly selected advanced NSCLC. Overall, the results of numerous ongoing phase 3 trials involving the EGFR TKIs will be instrumental in determining whether further gains in personalized therapy for advanced NSCLC are attainable with newer agents and combinations. This article reviews key clinical trial data for personalized NSCLC therapy with agents that target the EGFR and related pathways, specifically based on molecular characteristics of individual tumors, and mechanisms of resistance. PMID:26310719

  3. Stem Cell-Mediated Accelerated Bone Healing Observed with In Vivo Molecular and Small Animal Imaging Technologies in a Model of Skeletal Injury

    PubMed Central

    Lee, Sheen-Woo; Padmanabhan, Parasuraman; Ray, Pritha; Gambhir, Sanjiv Sam; Doyle, Timothy; Contag, Christopher; Goodman, Stuart B.; Biswal, Sandip

    2014-01-01

    Adult stem cells are promising therapeutic reagents for skeletal regeneration. We hope to validate by molecular imaging technologies the in vivo life cycle of adipose-derived multipotent cells (ADMCs) in an animal model of skeletal injury. Primary ADMCs were lentivirally transfected with a fusion reporter gene and injected intravenously into mice with bone injury or sham operation. Bioluminescence imaging (BLI), [18F]FHBG (9-(fluoro-hydroxy-methyl-butyl-guanine)-micro-PET, [18F]Fluoride ion micro-PET and micro-CT were performed to monitor stem cells and their effect. Bioluminescence microscopy and immunohistochemistry were done for histological confirmation. BLI showed ADMC’s traffic from the lungs then to the injury site. BLI microscopy and immunohistochemistry confirmed the ADMCs in the bone defect. Micro-CT measurements showed increased bone healing in the cell-injected group compared to the noninjected group at postoperative day 7 (p <0.05). Systemically administered ADMC’s traffic to the site of skeletal injury and facilitate bone healing, as demonstrated by molecular and small animal imaging. Molecular imaging technologies can validate the usage of adult adipose tissue-derived multipotent cells to promote fracture healing. Imaging can in the future help establish therapeutic strategies including dosage and administration route. PMID:18752273

  4. Advances in molecular-based personalized non-small-cell lung cancer therapy: targeting epidermal growth factor receptor and mechanisms of resistance.

    PubMed

    Jotte, Robert M; Spigel, David R

    2015-11-01

    Molecularly targeted therapies, directed against the features of a given tumor, have allowed for a personalized approach to the treatment of advanced non-small-cell lung cancer (NSCLC). The reversible epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) gefitinib and erlotinib had undergone turbulent clinical development until it was discovered that these agents have preferential activity in patients with NSCLC harboring activating EGFR mutations. Since then, a number of phase 3 clinical trials have collectively shown that EGFR-TKI monotherapy is more effective than combination chemotherapy as first-line therapy for EGFR mutation-positive advanced NSCLC. The next generation of EGFR-directed agents for EGFR mutation-positive advanced NSCLC is irreversible TKIs against EGFR and other ErbB family members, including afatinib, which was recently approved, and dacomitinib, which is currently being tested in phase 3 trials. As research efforts continue to explore the various proposed mechanisms of acquired resistance to EGFR-TKI therapy, agents that target signaling pathways downstream of EGFR are being studied in combination with EGFR TKIs in molecularly selected advanced NSCLC. Overall, the results of numerous ongoing phase 3 trials involving the EGFR TKIs will be instrumental in determining whether further gains in personalized therapy for advanced NSCLC are attainable with newer agents and combinations. This article reviews key clinical trial data for personalized NSCLC therapy with agents that target the EGFR and related pathways, specifically based on molecular characteristics of individual tumors, and mechanisms of resistance. PMID:26310719

  5. Recent advances in small molecular, non-polymeric organic hole transporting materials for solid-state DSSC

    NASA Astrophysics Data System (ADS)

    Bui, Thanh-Tuan; Goubard, Fabrice

    2013-10-01

    Issue from thin-film technologies, dye-sensitized solar cells have become one of the most promising technologies in the field of renewable energies. Their success is not only due to their low weight, the possibility of making large flexible surfaces, but also to their photovoltaic efficiency which are found to be more and more significant (>12% with a liquid electrolyte, >7% with a solid organic hole conductor). This short review highlights recent advances in the characteristics and use of low-molecular-weight glass-forming organic materials as hole transporters in all solid-state dye-sensitized solar cells. These materials must feature specific physical and chemical properties that will ensure both the operation of a photovoltaic cell and the easy implementation. This review is an english extended version based on our recent article published in Matériaux & Techniques 101, 102 (2013).

  6. Molecular, cellular and medical aspects of the action of nutraceuticals and small molecules therapeutics: from chemoprevention to new drug development.

    PubMed

    Colic, M; Pavelic, K

    2002-01-01

    Dietary supplements, functional foods and their concentrated, sometimes purified, active forms, the so-called nutraceuticals, are becoming increasingly popular throughout the world. Small molecules that regulate signal transduction cascades and gene expression are being tested by many pharmaceutical companies. A rapidly and exponentially growing industry (close to $30 billion in 1999 worldwide) exists to commercialize and exploit this interest. However, the scientific basis of the action of such unproved products is in the very early stages of development. While supporters claim they produce miracle cures, opponents argue that such unproved agents do more harm than good.

  7. Hormones as doping in sports.

    PubMed

    Duntas, Leonidas H; Popovic, Vera

    2013-04-01

    Though we may still sing today, as did Pindar in his eighth Olympian Victory Ode, "… of no contest greater than Olympia, Mother of Games, gold-wreathed Olympia…", we must sadly admit that today, besides blatant over-commercialization, there is no more ominous threat to the Olympic games than doping. Drug-use methods are steadily becoming more sophisticated and ever harder to detect, increasingly demanding the use of complex analytical procedures of biotechnology and molecular medicine. Special emphasis is thus given to anabolic androgenic steroids, recombinant growth hormone and erythropoietin as well as to gene doping, the newly developed mode of hormones abuse which, for its detection, necessitates high-tech methodology but also multidisciplinary individual measures incorporating educational and psychological methods. In this Olympic year, the present review offers an update on the current technologically advanced endocrine methods of doping while outlining the latest procedures applied-including both the successes and pitfalls of proteomics and metabolomics-to detect doping while contributing to combating this scourge.

  8. The structure of human apolipoprotein A-IV as revealed by stable isotope-assisted cross-linking, molecular dynamics, and small angle x-ray scattering.

    PubMed

    Walker, Ryan G; Deng, Xiaodi; Melchior, John T; Morris, Jamie; Tso, Patrick; Jones, Martin K; Segrest, Jere P; Thompson, Thomas B; Davidson, W Sean

    2014-02-28

    Apolipoprotein (apo)A-IV plays important roles in dietary lipid and glucose metabolism, and knowledge of its structure is required to fully understand the molecular basis of these functions. However, typical of the entire class of exchangeable apolipoproteins, its dynamic nature and affinity for lipid has posed challenges to traditional high resolution structural approaches. We previously reported an x-ray crystal structure of a dimeric truncation mutant of apoA-IV, which showed a unique helix-swapping molecular interface. Unfortunately, the structures of the N and C termini that are important for lipid binding were not visualized. To build a more complete model, we used chemical cross-linking to derive distance constraints across the full-length protein. The approach was enhanced with stable isotope labeling to overcome ambiguities in determining molecular span of the cross-links given the remarkable similarities in the monomeric and dimeric apoA-IV structures. Using 51 distance constraints, we created a starting model for full-length monomeric apoA-IV and then subjected it to two modeling approaches: (i) molecular dynamics simulations and (ii) fitting to small angle x-ray scattering data. This resulted in the most detailed models yet for lipid-free monomeric or dimeric apoA-IV. Importantly, these models were of sufficient detail to direct the experimental identification of new functional residues that participate in a "clasp" mechanism to modulate apoA-IV lipid affinity. The isotope-assisted cross-linking approach should prove useful for further study of this family of apolipoproteins in both the lipid-free and -bound states. PMID:24425874

  9. A small difference in the molecular structure of angiotensin II receptor blockers induces AT1 receptor-dependent and -independent beneficial effects

    PubMed Central

    Fujino, Masahiro; Miura, Shin-ichiro; Kiya, Yoshihiro; Tominaga, Yukio; Matsuo, Yoshino; Karnik, Sadashiva S; Saku, Keijiro

    2013-01-01

    Angiotensin II (Ang II) type 1 (AT1) receptor blockers (ARBs) induce multiple pharmacological beneficial effects, but not all ARBs have the same effects and the molecular mechanisms underlying their actions are not certain. In this study, irbesartan and losartan were examined because of their different molecular structures (irbesartan has a cyclopentyl group whereas losartan has a chloride group). We analyzed the binding affinity and production of inositol phosphate (IP), monocyte chemoattractant protein-1 (MCP-1) and adiponectin. Compared with losartan, irbesartan showed a significantly higher binding affinity and slower dissociation rate from the AT1 receptor and a significantly higher degree of inverse agonism and insurmountability toward IP production. These effects of irbesartan were not seen with the AT1-Y113A mutant receptor. On the basis of the molecular modeling of the ARBs–AT1 receptor complex and a mutagenesis study, the phenyl group at Tyr113 in the AT1 receptor and the cyclopentyl group of irbesartan may form a hydrophobic interaction that is stronger than the losartan–AT1 receptor interaction. Interestingly, irbesartan inhibited MCP-1 production more strongly than losartan. This effect was mediated by the inhibition of nuclear factor-kappa B activation that was independent of the AT1 receptor in the human coronary endothelial cells. In addition, irbesartan, but not losartan, induced significant adiponectin production that was mediated by peroxisome proliferator-activated receptor-γ activation in 3T3-L1 adipocytes, and this effect was not mediated by the AT1 receptor. In conclusion, irbesartan induced greater beneficial effects than losartan due to small differences between their molecular structures, and these differential effects were both dependent on and independent of the AT1 receptor. PMID:20668453

  10. Molecular Phenotyping Small (Asian) versus Large (Western) Plaque Psoriasis Shows Common Activation of IL-17 Pathway Genes, but Different Regulatory Gene Sets

    PubMed Central

    Kim, Jaehwan; Oh, Chil-Hwan; Jeon, Jiehyun; Baek, Yoosang; Ahn, Jaewoo; Kim, Dong Joo; Lee, Hyun-Soo; da Rosa, Joel Correa; Suárez-Fariñas, Mayte; Lowes, Michelle A.; Krueger, James G.

    2015-01-01

    Psoriasis is present in all racial groups, but in varying frequencies and severity. Considering that small plaque psoriasis is specific to the Asian population and severe psoriasis is more predominant in the Western population, we defined Asian small and intermediate plaque psoriasis as psoriasis subtypes, and compared their molecular signatures with classic subtype of Western large plaque psoriasis. Two different characteristics of psoriatic spreading—vertical growth and radial expansion—were contrasted between subtypes, and genomic data were correlated to histologic and clinical measurements. Compared to Western large plaque psoriasis, Asian small plaque psoriasis revealed limited psoriasis spreading, but IL-17A and IL-17-regulated pro-inflammatory cytokines were highly expressed. Paradoxically, IL-17A and IL-17-regulated pro-inflammatory cytokines were lower in Western large plaque psoriasis, while T cells and dendritic cells in total psoriatic skin area were exponentially increased. Negative immune regulators, such as CD69 and FAS, were decreased in both Western large plaque psoriasis and psoriasis with accompanying arthritis or obesity, and their expression was correlated with psoriasis severity index. Based on the disease subtype comparisons, we propose that dysregulation of T cell expansion enabled by downregulation of immune negative regulators is the main mechanism for development of large plaque psoriasis subtypes. PMID:26763436

  11. Molecular Phenotyping Small (Asian) versus Large (Western) Plaque Psoriasis Shows Common Activation of IL-17 Pathway Genes but Different Regulatory Gene Sets.

    PubMed

    Kim, Jaehwan; Oh, Chil-Hwan; Jeon, Jiehyun; Baek, Yoosang; Ahn, Jaewoo; Kim, Dong Joo; Lee, Hyun-Soo; Correa da Rosa, Joel; Suárez-Fariñas, Mayte; Lowes, Michelle A; Krueger, James G

    2016-01-01

    Psoriasis is present in all racial groups, but in varying frequencies and severity. Considering that small plaque psoriasis is specific to the Asian population and severe psoriasis is more predominant in the Western population, we defined Asian small and intermediate plaque psoriasis as psoriasis subtypes and compared their molecular signatures with the classic subtype of Western large plaque psoriasis. Two different characteristics of psoriatic spreading-vertical growth and radial expansion-were contrasted between subtypes, and genomic data were correlated to histologic and clinical measurements. Compared with Western large plaque psoriasis, Asian small plaque psoriasis revealed limited psoriasis spreading, but IL-17A and IL-17-regulated proinflammatory cytokines were highly expressed. Paradoxically, IL-17A and IL-17-regulated proinflammatory cytokines were lower in Western large plaque psoriasis, whereas T cells and dendritic cells in total psoriatic skin area were exponentially increased. Negative immune regulators, such as CD69 and FAS, were decreased in both Western large plaque psoriasis and psoriasis with accompanying arthritis or obesity, and their expression was correlated with psoriasis severity index. Based on the disease subtype comparisons, we propose that dysregulation of T-cell expansion enabled by downregulation of immune negative regulators is the main mechanism for development of large plaque psoriasis subtypes. PMID:26763436

  12. Molecular Phenotyping Small (Asian) versus Large (Western) Plaque Psoriasis Shows Common Activation of IL-17 Pathway Genes but Different Regulatory Gene Sets.

    PubMed

    Kim, Jaehwan; Oh, Chil-Hwan; Jeon, Jiehyun; Baek, Yoosang; Ahn, Jaewoo; Kim, Dong Joo; Lee, Hyun-Soo; Correa da Rosa, Joel; Suárez-Fariñas, Mayte; Lowes, Michelle A; Krueger, James G

    2016-01-01

    Psoriasis is present in all racial groups, but in varying frequencies and severity. Considering that small plaque psoriasis is specific to the Asian population and severe psoriasis is more predominant in the Western population, we defined Asian small and intermediate plaque psoriasis as psoriasis subtypes and compared their molecular signatures with the classic subtype of Western large plaque psoriasis. Two different characteristics of psoriatic spreading-vertical growth and radial expansion-were contrasted between subtypes, and genomic data were correlated to histologic and clinical measurements. Compared with Western large plaque psoriasis, Asian small plaque psoriasis revealed limited psoriasis spreading, but IL-17A and IL-17-regulated proinflammatory cytokines were highly expressed. Paradoxically, IL-17A and IL-17-regulated proinflammatory cytokines were lower in Western large plaque psoriasis, whereas T cells and dendritic cells in total psoriatic skin area were exponentially increased. Negative immune regulators, such as CD69 and FAS, were decreased in both Western large plaque psoriasis and psoriasis with accompanying arthritis or obesity, and their expression was correlated with psoriasis severity index. Based on the disease subtype comparisons, we propose that dysregulation of T-cell expansion enabled by downregulation of immune negative regulators is the main mechanism for development of large plaque psoriasis subtypes.

  13. The Small Molecule Nobiletin Targets the Molecular Oscillator to Enhance Circadian Rhythms and Protect against Metabolic Syndrome.

    PubMed

    He, Baokun; Nohara, Kazunari; Park, Noheon; Park, Yong-Sung; Guillory, Bobby; Zhao, Zhaoyang; Garcia, Jose M; Koike, Nobuya; Lee, Cheng Chi; Takahashi, Joseph S; Yoo, Seung-Hee; Chen, Zheng

    2016-04-12

    Dysregulation of circadian rhythms is associated with metabolic dysfunction, yet it is unclear whether enhancing clock function can ameliorate metabolic disorders. In an unbiased chemical screen using fibroblasts expressing PER2::Luc, we identified Nobiletin (NOB), a natural polymethoxylated flavone, as a clock amplitude-enhancing small molecule. When administered to diet-induced obese (DIO) mice, NOB strongly counteracted metabolic syndrome and augmented energy expenditure and locomotor activity in a Clock gene-dependent manner. In db/db mutant mice, the clock is also required for the mitigating effects of NOB on metabolic disorders. In DIO mouse liver, NOB enhanced clock protein levels and elicited pronounced gene expression remodeling. We identified retinoid acid receptor-related orphan receptors as direct targets of NOB, revealing a pharmacological intervention that enhances circadian rhythms to combat metabolic disease via the circadian gene network.

  14. Elucidation by NMR solution of neurotensin in small unilamellar vesicle environment: molecular surveys for neurotensin receptor recognition.

    PubMed

    Da Costa, Grégory; Bondon, Arnaud; Delalande, Olivier; Mouret, Liza; Monti, Jean-Pierre

    2013-01-01

    Neurotensin (NT) is a tridecapeptide, hormone in the periphery and neurotransmitter in the brain. We used high-resolution nuclear magnetic resonance (NMR) to resolve the three-dimensional structure of NT in a small unilamellar vesicle (SUV) environment. We demonstrate that if the dynamic of the association-dissociation processes of peptide to SUV binding is rapid enough, structural determination can be obtained by solution NMR experiments. Thus, according to the global dynamic of the system, SUVs seem to be an effective model to mimic biological membranes, especially since the lipid composition can be modified or sterols may be added to closely mimic the biological membranes studied. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:2. PMID:22928939

  15. Composite mantle cell lymphoma and chronic lymphocytic leukemia/small lymphocytic lymphoma: a clinicopathologic and molecular study.

    PubMed

    Hoeller, Sylvia; Zhou, Yi; Kanagal-Shamanna, Rashmi; Xu-Monette, Zijun Y; Hoehn, Daniela; Bihl, Michel; Swerdlow, Steven H; Rosenwald, Andreas; Ott, German; Said, Jonathan; Dunphy, Cherie H; Bueso-Ramos, Carlos E; Lin, Pei; Wang, Michael; Miranda, Roberto N; Tzankov, Alexander; Medeiros, L Jeffrey; Young, Ken H

    2013-01-01

    Mantle cell lymphoma (MCL) and chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL) share many features and both arise from CD5+ B-cells; their distinction is critical as MCL is a more aggressive neoplasm. Rarely, cases of composite MCL and CLL/SLL have been reported. Little is known about the nature of these cases and, in particular, the clonal relationship of the 2 lymphomas. Eleven composite MCL and CLL/SLL cases were identified. The clinical, morphologic and immunophenotypic features of the MCL and CLL/SLL were characterized. IGH (immunoglobulin heavy chain) gene analysis was performed on microdissected MCL and CLL/SLL components to assess their clonal relationship. Ten patients had lymphadenopathy, and 7 patients had bone marrow involvement. The MCL component had the following growth patterns: in situ (n = 1), mantle zone (n = 3), nodular and diffuse (n = 3), diffuse (n = 3), and interstitial in the bone marrow (the only patient without lymphadenopathy) (n = 1); 6 MCLs had blastoid or pleomorphic and 5 small lymphocytic features. The CLL/SLL component was nodular (n = 9) or diffuse (n = 2). All MCL were CD5(+) and cyclin D1(+) with t(11;14) translocation. All CLL/SLL were CD5(+), CD23(+) and negative for cyclin D1 or t(11;14). IGH gene analysis showed that the MCL and CLL/SLL components displayed different sized fragments, indicating that the MCL and CLL/SLL are likely derived from different neoplastic B-cell clones. The lack of a clonal relationship between the MCL and CLL/SLL components suggests that MCL and CLL/SLL components represent distinct disease processes and do not share a common progenitor B-cell.

  16. Honokiol: a promising small molecular weight natural agent for the growth inhibition of oral squamous cell carcinoma cells.

    PubMed

    Chen, Xi-Rui; Lu, Rui; Dan, Hong-Xia; Liao, Ga; Zhou, Min; Li, Xiao-Yu; Ji, Ning

    2011-01-01

    Honokiol (HNK) is a small organic molecule purified from magnolia species and has demonstrated anticancer activities in a variety of cancer cell lines; however, its effect on oral squamous cell carcinoma (OSCC) cells is unknown. We investigated the antitumor activities of HNK on OSCC cells in vitro for the first time. The inhibitory effects of HNK on the growth and proliferation of OSCC cells were demonstrated via in vitro 3-(4,5-dimethyl thiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and propidium iodide (PI) assays, and the apoptotic cells were investigated by the observation of morphological changes and detection of DNA fragmentation via PI, TdT-mediated dUTP-biotin nick end labeling (TUNEL), and DNA ladder assays, as well as flow cytometry assay. The results showed that HNK inhibited the growth and proliferation of OSCC cells in vitro in a time and dose-dependent manner. The inhibitory effect was associated with the cell apoptosis induced by HNK, evidenced by the morphological features of apoptotic cells, TUNEL-positive cells and a degradation of chromosomal DNA into small internucleosomal fragments. The study also demonstrated here that the inhibition or apoptosis mediated by 15 microg x mL(-1) or 20 microg x mL(-1) of HNK were more stronger compared with those of 20 microg x mL(-1) 5-fluorouracil (5-Fu, the control) applied to OSCC cells, when the ratio of OSCC cell numbers were measured between the treatment of different concentrations of HNK to the 5-Fu treatment for 48 h. HNK is a promising compound that can be potentially used as a novel treatment agent for human OSCC. PMID:21449214

  17. The cryptic Y-autosome translocation in the small Indian mongoose, Herpestes auropunctatus, revealed by molecular cytogenetic approaches.

    PubMed

    Murata, Chie; Sawaya, Hirohito; Nakata, Katsushi; Yamada, Fumio; Imoto, Issei; Kuroiwa, Asato

    2016-09-01

    In initial studies of the eutherian small Indian mongoose (Herpestes auropunctatus), the Y chromosome could not be identified in somatic cells. The male chromosome number is uniquely odd, 2n = 35, whereas that of females is 2n = 36. Previous reports indicated that this unique karyotype resulted from a translocation of the ancestral Y chromosome to an autosome. However, it has been difficult to identify the chromosomes that harbor the translocated Y chromosomal segment because it is an extremely small euchromatic region. Using a Southern blot analysis, we detected four conserved Y-linked genes, SRY, EIF2S3Y, KDM5D, and ZFY, in the male genome. We cloned homologues of these genes and determined their sequences, which showed high homology to genes in two carnivore species, cat and dog. To unambiguously identify the Y-bearing autosome, we performed immunostaining of pachytene spermatocytes using antibodies against SYCP3, γH2AX, and the centromere. We observed trivalent chromosomes, and the associations between the distal ends of the chromosomes were consistent with those of Y and X1 chromosomes. The centromere of the Y chromosome was located on the ancestral Y chromosomal segment. We mapped the complementary DNA (cDNA) clones of these genes to the male chromosomes using fluorescence in situ hybridization (FISH), and the linear localization of all genes was confirmed by two-colored FISH. These Y-linked genes were localized to the proximal region of the long arm of a single telomeric chromosome, and we successfully identified the chromosome harboring the ancestral Y chromosomal segment.

  18. The cryptic Y-autosome translocation in the small Indian mongoose, Herpestes auropunctatus, revealed by molecular cytogenetic approaches.

    PubMed

    Murata, Chie; Sawaya, Hirohito; Nakata, Katsushi; Yamada, Fumio; Imoto, Issei; Kuroiwa, Asato

    2016-09-01

    In initial studies of the eutherian small Indian mongoose (Herpestes auropunctatus), the Y chromosome could not be identified in somatic cells. The male chromosome number is uniquely odd, 2n = 35, whereas that of females is 2n = 36. Previous reports indicated that this unique karyotype resulted from a translocation of the ancestral Y chromosome to an autosome. However, it has been difficult to identify the chromosomes that harbor the translocated Y chromosomal segment because it is an extremely small euchromatic region. Using a Southern blot analysis, we detected four conserved Y-linked genes, SRY, EIF2S3Y, KDM5D, and ZFY, in the male genome. We cloned homologues of these genes and determined their sequences, which showed high homology to genes in two carnivore species, cat and dog. To unambiguously identify the Y-bearing autosome, we performed immunostaining of pachytene spermatocytes using antibodies against SYCP3, γH2AX, and the centromere. We observed trivalent chromosomes, and the associations between the distal ends of the chromosomes were consistent with those of Y and X1 chromosomes. The centromere of the Y chromosome was located on the ancestral Y chromosomal segment. We mapped the complementary DNA (cDNA) clones of these genes to the male chromosomes using fluorescence in situ hybridization (FISH), and the linear localization of all genes was confirmed by two-colored FISH. These Y-linked genes were localized to the proximal region of the long arm of a single telomeric chromosome, and we successfully identified the chromosome harboring the ancestral Y chromosomal segment. PMID:26743516

  19. Molecular characterization of peste des petits ruminants viruses from outbreaks caused by unrestricted movements of small ruminants in pakistan.

    PubMed

    Munir, M; Saeed, A; Abubakar, M; Kanwal, S; Berg, M

    2015-02-01

    Peste des petits ruminants (PPR) is an endemic disease of small ruminants, and vaccination has been the method of control but outbreaks are continuously occurring in Pakistan. The following study presents a detailed investigation of an outbreak, suspected to be PPR, probably introduced by PPRV-infected sheep and goats from Sindh Province (north-west) to Punjab Province (central) of Pakistan during the flood relief campaign in 2011. A total of 70 serum samples from 28 different flocks were tested with competitive ELISA (H antibodies), which detected 24 (34.2%) samples positive for PPRV antibodies. Nasal swabs and faeces were tested with immunocapture ELISA (N antigen), which detected 18 (25.7%) samples positive for PPRV antigen. The RNA detected positive (n = 28, 40%) using real-time PCR was subjected to conventional PCR for the amplification of the fusion and nucleoprotein genes. Sequencing of both genes and subsequent phylogenetic analysis indicated the grouping of all the sequences to be in lineage IV along with other Asian isolates of PPRV. However, sequences of both genes were divided into two groups within lineage IV. One group of viruses clustered with previously characterized Pakistani isolates, whereas the other group was distinctly clustered with isolates from the Middle East or India. The sequence identity indicated the introduction of at least one population of PPRV from a different source and circulation in the local flocks of small ruminants, which emphasized the need to obtain health clearance certificate before movement of animals. The results of this study provide baseline data for the genetic characterization of different PPRV populations in Pakistan.

  20. A molecular study of tick-borne haemoprotozoan parasites (Theileria and Babesia) in small ruminants in Northern Tunisia.

    PubMed

    M'ghirbi, Youmna; Ros-García, Amaia; Iribar, Pilar; Rhaim, Adel; Hurtado, Ana; Bouattour, Ali

    2013-11-15

    In this study, the frequency of Theileria and Babesia species in sheep and goats was assessed via reverse line blotting (RLB). A total of 263 apparently healthy sheep and goats, from 16 randomly selected flocks located in 9 localities situated in 3 bioclimatic zones in Tunisia, were investigated for the blood protozoans. RLB hybridization with polymerase chain reaction detected only Theileria ovis in sheep and goats, accounting for 22.4% (95% confidence interval [CI]: 17.6-27.1%) positive samples. The infection rate in sheep (28.1%; 95% CI: 23.8-32.3%) was higher than in goats (4.7%; 95% CI: -10.9 to 20.4%). Neither Babesia nor mixed infections were detected. Only two Ixodid tick species (Rhipicephalus turanicus and Rhipicephalus bursa) were collected from the examined sheep and goats in 5 localities. R. turanicus was the dominant species (95.5%) collected mainly in the humid zone, while apparently rare in the sub-humid zone. R. bursa was the only species collected in the semi-arid area. RLB analysis identified six different piroplasms in ticks, with an overall prevalence of 31.5% (95% CI: 28.1-34.9%). Twenty percent (95% CI: 14.4-25.5%) of the collected ticks tested positive for Theileria spp., 3% (95% CI: -5.6 to 11.6%) for Babesia spp. and 0.9% (95% CI: -8.1 to 9.9%) of the ticks harbored both genera; several of these species are not known to occur in small ruminants. This is the first report on the detection of Theileria and Babesia species DNA in small ruminants and ticks in Tunisia.

  1. Nanocrystal doped matrixes

    SciTech Connect

    Parce, J. Wallace; Bernatis, Paul; Dubrow, Robert; Freeman, William P.; Gamoras, Joel; Kan, Shihai; Meisel, Andreas; Qian, Baixin; Whiteford, Jeffery A.; Ziebarth, Jonathan

    2010-01-12

    Matrixes doped with semiconductor nanocrystals are provided. In certain embodiments, the semiconductor nanocrystals have a size and composition such that they absorb or emit light at particular wavelengths. The nanocrystals can comprise ligands that allow for mixing with various matrix materials, including polymers, such that a minimal portion of light is scattered by the matrixes. The matrixes of the present invention can also be utilized in refractive index matching applications. In other embodiments, semiconductor nanocrystals are embedded within matrixes to form a nanocrystal density gradient, thereby creating an effective refractive index gradient. The matrixes of the present invention can also be used as filters and antireflective coatings on optical devices and as down-converting layers. Processes for producing matrixes comprising semiconductor nanocrystals are also provided. Nanostructures having high quantum efficiency, small size, and/or a narrow size distribution are also described, as are methods of producing indium phosphide nanostructures and core-shell nanostructures with Group II-VI shells.

  2. Refinement of causative genes in monosomy 1p36 through clinical and molecular cytogenetic characterization of small interstitial deletions.

    PubMed

    Rosenfeld, Jill A; Crolla, John A; Tomkins, Susan; Bader, Patricia; Morrow, Bernice; Gorski, Jerome; Troxell, Robin; Forster-Gibson, Cynthia; Cilliers, Deirdre; Hislop, R Gordon; Lamb, Allen; Torchia, Beth; Ballif, Blake C; Shaffer, Lisa G

    2010-08-01

    Monosomy 1p36 is the most common terminal deletion syndrome seen in humans, occurring in approximately 1 in 5,000 live births. Common features include mental retardation, characteristic dysmorphic features, hypotonia, seizures, hearing loss, heart defects, cardiomyopathy, and behavior abnormalities. Similar phenotypes are seen among patients with a variety of deletion sizes, including terminal and interstitial deletions, complex rearrangements, and unbalanced translocations. Consequently, critical regions harboring causative genes for each of these features have been difficult to identify. Here we report on five individuals with 200-823 kb overlapping deletions of proximal 1p36.33, four of which are apparently de novo. They present with features of monosomy 1p36, including developmental delay and mental retardation, dysmorphic features, hypotonia, behavioral abnormalities including hyperphagia, and seizures. The smallest region of deletion overlap is 174 kb and contains five genes; these genes are likely candidates for some of the phenotypic features in monosomy 1p36. Other genes deleted in a subset of the patients likely play a contributory role in the phenotypes, including GABRD and seizures, PRKCZ and neurologic features, and SKI and dysmorphic and neurologic features. Characterization of small deletions is important for narrowing critical intervals and for the identification of causative or candidate genes for features of monosomy 1p36 syndrome.

  3. Structural basis of molecular recognition of the Leishmania small hydrophilic endoplasmic reticulum-associated protein (SHERP) at membrane surfaces.

    PubMed

    Moore, Benjamin; Miles, Andrew J; Guerra-Giraldez, Cristina; Simpson, Peter; Iwata, Momi; Wallace, B A; Matthews, Stephen J; Smith, Deborah F; Brown, Katherine A

    2011-03-18

    The 57-residue small hydrophilic endoplasmic reticulum-associated protein (SHERP) shows highly specific, stage-regulated expression in the non-replicative vector-transmitted stages of the kinetoplastid parasite, Leishmania major, the causative agent of human cutaneous leishmaniasis. Previous studies have demonstrated that SHERP localizes as a peripheral membrane protein on the cytosolic face of the endoplasmic reticulum and on outer mitochondrial membranes, whereas its high copy number suggests a critical function in vivo. However, the absence of defined domains or identifiable orthologues, together with lack of a clear phenotype in transgenic parasites lacking SHERP, has limited functional understanding of this protein. Here, we use a combination of biophysical and biochemical methods to demonstrate that SHERP can be induced to adopt a globular fold in the presence of anionic lipids or SDS. Cross-linking and binding studies suggest that SHERP has the potential to form a complex with the vacuolar type H(+)-ATPase. Taken together, these results suggest that SHERP may function in modulating cellular processes related to membrane organization and/or acidification during vector transmission of infective Leishmania. PMID:21106528

  4. Molecular characterization of nuclear small subunit (18S)-rDNA pseudogenes in a symbiotic dinoflagellate (Symbiodinium, Dinophyta).

    PubMed

    Santos, Scott R; Kinzie, Robert A; Sakai, Kazuhiko; Coffroth, Mary Alice

    2003-01-01

    For the dinoflagellates, an important group of single-cell protists, some nuclear rDNA phylogenetic studies have reported the discovery of rDNA pseudogenes. However, it is unknown if these aberrant molecules are confined to free-living taxa or occur in other members of the group. We have cultured a strain of symbiotic dinoflagellate, belonging to the genus Symbiodinium, which produces three distinct amplicons following PCR for nuclear small subunit (18S) rDNA genes. These amplicons contribute to a unique restriction fragment length polymorphism pattern diagnostic for this particular strain. Sequence analyses revealed that the largest amplicon was the expected region of 18S-rDNA, while the two smaller amplicons are Symbiodinium nuclear 18S-rDNA genes that contain single long tracts of nucleotide deletions. Reverse transcription (RT)-PCR experiments did not detect RNA transcripts of these latter genes, suggesting that these molecules represent the first report of nuclear 18S-rDNA pseudogenes from the genome of Symbiodinium. As in the free-living dinoflagellates, nuclear rDNA pseudogenes are effective indicators of unique Symbiodinium strains. Furthermore, the evolutionary pattern of dinoflagellate nuclear rDNA pseudogenes appears to be unique among organisms studied to date, and future studies of these unusual molecules will provide insight on the cellular biology and genomic evolution of these protists.

  5. On the microstructure of organic solutions of mono-carboxylic acids: Combined study by infrared spectroscopy, small-angle neutron scattering and molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Eremin, Roman A.; Kholmurodov, Kholmirzo T.; Petrenko, Viktor I.; Rosta, László; Grigoryeva, Natalia A.; Avdeev, Mikhail V.

    2015-11-01

    The data of infrared spectroscopy (IR), molecular dynamics (MD) simulations and small-angle neutron scattering (SANS) have been combined to conclude about the nanoscale structural organization of organic non-polar solutions of saturated mono-carboxylic acids with different alkyl chain lengths for diluted solutions of saturated myristic (C14) and stearic (C18) acids in benzene and decalin. In particular, the degree of dimerization was found from the IR spectra. The structural anisotropy of the acids and their dimers was used in the treatment of the data of MD simulations to describe the solute-solvent interface in a cylindrical approximation and show its rather strong influence on SANS. The corresponding scattering length density profiles were used to fit the experimental SANS data comprising the information about the acid molecule isomerization. The SANS data from concentrated solutions showed a partial self-assembling of the acids within the nematic transition is different for two solvents due to lyophobic peculiarities.

  6. The importance of molecular profiling in predicting response to epidermal growth factor receptor family inhibitors in non-small-cell lung cancer: focus on clinical trial results.

    PubMed

    Tsao, Anne S; Papadimitrakopoulou, Vassiliki

    2013-07-01

    In recent years, the epidermal growth factor receptor (EGFR) family has become a key focus of non-small-cell lung cancer biology and targeted therapies, such as the reversible EGFR tyrosine kinase inhibitors erlotinib and gefitinib. Initially, response to these agents was associated with certain demographic and clinical characteristics; subsequently, it was discovered that these subgroups were more likely to harbor specific mutations in the EGFR gene that enhanced tumor response. However, the presence of these mutations does not equate to therapeutic success. Other aspects of EGFR family signaling, including other types of EGFR mutations, EGFR protein expression, EGFR gene amplification, mediators of downstream signaling, and other receptors with similar downstream pathways may all play a role in response or resistance to treatment. The identification of these and other molecular determinants is driving the development of novel therapies designed to achieve improved clinical outcomes in patients.

  7. SASSIM: a method for calculating small-angle X-ray and neutron scattering and the associated molecular envelope from explicit-atom models of solvated proteins.

    PubMed

    Merzel, Franci; Smith, Jeremy C

    2002-02-01

    A method is presented to calculate efficiently small-angle neutron and X-ray solution scattering intensities from explicit-atom models of macromolecules and the surrounding solvent. The method is based on a multipole expansion of the scattering amplitude. It is particularly appropriate for extensive configurational averaging, as is required for calculations based on computer-simulation results. In test calculations, excellent agreement with experiment is found between neutron and X-ray scattering profiles calculated from a molecular-dynamics simulation of lysozyme in water. The question of definition of the protein surface is also addressed. For comparison with the continuum model, an analytical envelope around the protein is defined in terms of spherical harmonics and is calculated using a Lebedev grid. The analytical surface thus defined is shown to reproduce well the scattering profile calculated from the explicit-atom model of the protein.

  8. Molecular cloning and characterization of the putative Halloween gene Phantom from the small brown planthopper Laodelphax striatellus.

    PubMed

    Jia, Shuang; Wan, Pin-Jun; Li, Guo-Qing

    2015-12-01

    Ecdysteroid hormone 20-hydroxyecdysone plays fundamental roles in insect postembryonic development and reproduction. Several cytochrome P450 mono-oxygenases (CYPs), encoded by the Halloween genes, have been documented to be involved in ecdysteroidogenesis in representative insects in Diptera, Lepidoptera and Orthoptera. Here the putative Halloween gene Phantom (Phm, cyp306a1) from a hemipteran insect species, the small brown planthopper Laodelphax striatellus, was cloned. LsPHM shows five insect conserved P450 motifs, that is, Helix-C, Helix-I, Helix-K, PERF and heme-binding motifs. Temporal and spatial expression patterns of LsPhm were evaluated by quantitative polymerase chain reaction. Through the fourth-instar and the early fifth-instar stages, LsPhm showed two expression peaks in day 2 and days 4-5 fourth-instar nymphs, and three troughs in day 1 and 3 fourth instars and day 1 fifth instars. On day 5 of the fourth-instar nymphs, LsPhm clearly had a high transcript level in the thorax where the prothoracic glands were located. Dietary introduction of double-stranded RNA (dsRNA) of LsPhm at the nymph stage successfully knocked down the target gene, decreased expression level of ecdysone receptor (LsEcR) gene and caused a higher nymphal mortality rate and delayed development. Ingestion of 20-hydroxyecdysone on LsPhm-dsRNA-exposed nymphs did not increase LsPhm expression level, but almost completely rescued the LsEcR mRNA level, and relieved the negative effects on survival and development. Thus, our data suggest that the putative LsPhm encodes a functional 25-hydroxylase that catalyzes the biosynthesis of ecdysteroids in L. striatellus. PMID:24954278

  9. Molecular characterization and evolution of the SPRR family of keratinocyte differentiation markers encoding small proline-rich proteins

    SciTech Connect

    Gibbs, S.; Fijneman, R.; Wiegant, J.; Van De Putte, P.; Backendorf, C. ); Van Kessel, A.D. )

    1993-06-01

    SPRR genes (formerly SPR) encode a novel class of polypeptides (small proline rich proteins) that are strongly induced during differentiation of human epidermal keratinocytes in vitro and in vivo. Recently the authors found that the N- and C-terminal domains of these proteins show strong sequence homology to loricrin and involucrin, suggesting that SPRR proteins constitute a new class of cornified envelope precursor proteins. Here they show that SPRR proteins are encoded by closely related members of a gene family, consisting of two genes for SPRR1, approximately seven genes for SPRR2, and a single gene for SPRR3. All SPRR genes are closely linked within a 300-kb DNA segment on human chromosome 1 band q21-q22, a region where the related loricrin and involucrin genes have also been mapped. The most characteristic feature of the SPRR gene family resides in the structure of the central segments of the encoded polypeptides that are built up from tandemly repeated units of either eight (SPRR1 and SPRR3) or nine (SPRR2) amino acids with the general consensus *K*PEP**. Sequencing data of the different members, together with their clustered chromosomal organization, strongly suggest that this gene family has evolved from a single progenitor gene by multiple intra- and intergenic duplications. Analysis of the different SPRR subfamilies reveals a gene-specific bias to either intra- or intergenic duplication. The authors propose that a process of homogenization has acted on the different members of one subfamily, whereas the different subfamilies appear to have diverged from each other, at the levels of both protein structure and gene regulation. 25 refs., 7 figs., 2 tab.

  10. Clinical and Molecular Characteristics of Infections with CO2-Dependent Small-Colony Variants of Staphylococcus aureus▿

    PubMed Central

    Gómez-González, Carmen; Acosta, Joshi; Villa, Jennifer; Barrado, Laura; Sanz, Francisca; Orellana, M. Ángeles; Otero, Joaquín R.; Chaves, Fernando

    2010-01-01

    Most Staphylococcus aureus small-colony variants (SCVs) are auxotrophs for menadione, hemin, or thymidine but rarely for CO2. We conducted a prospective investigation of all clinical cases of CO2-dependent S. aureus during a 3-year period. We found 14 CO2-dependent isolates of S. aureus from 14 patients that fulfilled all requirements to be considered SCVs, 9 of which were methicillin resistant. The clinical presentations included four cases of catheter-related bacteremia, one complicated by endocarditis; two deep infections (mediastinitis and spondylodiscitis); four wound infections; two respiratory infections; and two cases of nasal colonization. Pulsed-field gel electrophoresis typing showed that the 14 isolates were distributed into 4 types corresponding to sequence types ST125-agr group II (agrII), ST30-agrIII, ST34-agrIII, and ST45-agrI. An array hybridization technique performed on the 14 CO2-dependent isolates and 20 S. aureus isolates with normal phenotype and representing the same sequence types showed that all possessed the enterotoxin gene cluster egc, as well as the genes for α-hemolysin and δ-hemolysin; biofilm genes icaA, icaC, and icaD; several microbial surface components recognizing adhesive matrix molecules (MSCRAMM) genes (clfA, clfB, ebh, eno, fib, ebpS, sdrC, and vw); and the isaB gene. Our study confirms the importance of CO2-dependent SCVs of S. aureus as significant pathogens. Clinical microbiologists should be aware of this kind of auxotrophy because recovery and identification are challenging and not routine. Further studies are necessary to determine the incidence of CO2 auxotrophs of S. aureus, the factors that select these strains in the host, and the genetic basis of this type of auxotrophy. PMID:20554819

  11. Molecular analysis of central feeding regulation by neuropeptide Y (NPY) neurons with NPY receptor small interfering RNAs (siRNAs).

    PubMed

    Higuchi, Hiroshi

    2012-11-01

    Hypothalamic neuropeptides play important roles in central feeding behavior. Among them, neuropeptide Y (NPY) has the strongest orexigenic action. It is synthesized in NPY-expressing neurons in the arcuate nucleus (ARC), which projects to other nuclei, mainly to the paraventricular nucleus (PVN). PVN, which possesses NPY-Y1, -Y2 and -Y4, -Y5 receptors, is considered as feeding center for central feeding behavior. Herein I review recent results on feeding behavior obtained by gene knockdown technologies. The small interfering RNA (siRNA) plasmid-based vectors, which drive transcription of siRNA by U6 RNA polymerase III promoter to produce knockdown of the NPY and its receptor (Y1, Y2, Y4 and Y5) genes, were stereotaxically injected into mouse ARC and PVN. Feeding behaviors were measured for 6days after siRNA vector injection. NPY and its receptor mRNA levels were decreased, which were measured by RT-PCR and in situ hybridization, and simultaneous decrease in their proteins was also detected in separate nuclei by immunohistochemistry. In the NPY system, decrease in NPY, Y1 and Y5 expressions in specialized nuclei diminished central feeding behavior, whereas decrease in Y2 or Y4 expression in both ARC or PVN did not affect feeding behavior. Thus, specialized change in expressions of NPY and its receptors (especially Y1 and Y5) are important for regulation of endogenous feeding behavior in central regulation. Further analysis of NPY receptors may provide better understanding of feeding behavior and of potential therapeutic targets.

  12. Molecular cloning and characterization of the putative Halloween gene Phantom from the small brown planthopper Laodelphax striatellus.

    PubMed

    Jia, Shuang; Wan, Pin-Jun; Li, Guo-Qing

    2015-12-01

    Ecdysteroid hormone 20-hydroxyecdysone plays fundamental roles in insect postembryonic development and reproduction. Several cytochrome P450 mono-oxygenases (CYPs), encoded by the Halloween genes, have been documented to be involved in ecdysteroidogenesis in representative insects in Diptera, Lepidoptera and Orthoptera. Here the putative Halloween gene Phantom (Phm, cyp306a1) from a hemipteran insect species, the small brown planthopper Laodelphax striatellus, was cloned. LsPHM shows five insect conserved P450 motifs, that is, Helix-C, Helix-I, Helix-K, PERF and heme-binding motifs. Temporal and spatial expression patterns of LsPhm were evaluated by quantitative polymerase chain reaction. Through the fourth-instar and the early fifth-instar stages, LsPhm showed two expression peaks in day 2 and days 4-5 fourth-instar nymphs, and three troughs in day 1 and 3 fourth instars and day 1 fifth instars. On day 5 of the fourth-instar nymphs, LsPhm clearly had a high transcript level in the thorax where the prothoracic glands were located. Dietary introduction of double-stranded RNA (dsRNA) of LsPhm at the nymph stage successfully knocked down the target gene, decreased expression level of ecdysone receptor (LsEcR) gene and caused a higher nymphal mortality rate and delayed development. Ingestion of 20-hydroxyecdysone on LsPhm-dsRNA-exposed nymphs did not increase LsPhm expression level, but almost completely rescued the LsEcR mRNA level, and relieved the negative effects on survival and development. Thus, our data suggest that the putative LsPhm encodes a functional 25-hydroxylase that catalyzes the biosynthesis of ecdysteroids in L. striatellus.

  13. Clinical and molecular characteristics of infections with CO2-dependent small-colony variants of Staphylococcus aureus.

    PubMed

    Gómez-González, Carmen; Acosta, Joshi; Villa, Jennifer; Barrado, Laura; Sanz, Francisca; Orellana, M Angeles; Otero, Joaquín R; Chaves, Fernando

    2010-08-01

    Most Staphylococcus aureus small-colony variants (SCVs) are auxotrophs for menadione, hemin, or thymidine but rarely for CO(2). We conducted a prospective investigation of all clinical cases of CO(2)-dependent S. aureus during a 3-year period. We found 14 CO(2)-dependent isolates of S. aureus from 14 patients that fulfilled all requirements to be considered SCVs, 9 of which were methicillin resistant. The clinical presentations included four cases of catheter-related bacteremia, one complicated by endocarditis; two deep infections (mediastinitis and spondylodiscitis); four wound infections; two respiratory infections; and two cases of nasal colonization. Pulsed-field gel electrophoresis typing showed that the 14 isolates were distributed into 4 types corresponding to sequence types ST125-agr group II (agrII), ST30-agrIII, ST34-agrIII, and ST45-agrI. An array hybridization technique performed on the 14 CO(2)-dependent isolates and 20 S. aureus isolates with normal phenotype and representing the same sequence types showed that all possessed the enterotoxin gene cluster egc, as well as the genes for alpha-hemolysin and delta-hemolysin; biofilm genes icaA, icaC, and icaD; several microbial surface components recognizing adhesive matrix molecules (MSCRAMM) genes (clfA, clfB, ebh, eno, fib, ebpS, sdrC, and vw); and the isaB gene. Our study confirms the importance of CO(2)-dependent SCVs of S. aureus as significant pathogens. Clinical microbiologists should be aware of this kind of auxotrophy because recovery and identification are challenging and not routine. Further studies are necessary to determine the incidence of CO(2) auxotrophs of S. aureus, the factors that select these strains in the host, and the genetic basis of this type of auxotrophy.

  14. Structures of Human Cyctochrome P450 2E1: Insights Into the Binding of Inhibitors And Both Small Molecular Weight And Fatty Acid Substrates

    SciTech Connect

    Porubsky, P.R.; Meneely, K.M.; Scott, E.E.

    2009-05-21

    Human microsomal cytochrome P-450 2E1 (CYP2E1) monooxygenates >70 low molecular weight xenobiotic compounds, as well as much larger endogenous fatty acid signaling molecules such as arachidonic acid. In the process, CYP2E1 can generate toxic or carcinogenic compounds, as occurs with acetaminophen overdose, nitrosamines in cigarette smoke, and reactive oxygen species from uncoupled catalysis. Thus, the diverse roles that CYP2E1 has in normal physiology, toxicity, and drug metabolism are related to its ability to metabolize diverse classes of ligands, but the structural basis for this was previously unknown. Structures of human CYP2E1 have been solved to 2.2 {angstrom} for an indazole complex and 2.6 {angstrom} for a 4-methylpyrazole complex. Both inhibitors bind to the heme iron and hydrogen bond to Thr{sup 303} within the active site. Complementing its small molecular weight substrates, the hydrophobic CYP2E1 active site is the smallest yet observed for a human cytochrome P-450. The CYP2E1 active site also has two adjacent voids: one enclosed above the I helix and the other forming a channel to the protein surface. Minor repositioning of the Phe{sup 478} aromatic ring that separates the active site and access channel would allow the carboxylate of fatty acid substrates to interact with conserved {sup 216}QXXNN{sup 220} residues in the access channel while positioning the hydrocarbon terminus in the active site, consistent with experimentally observed {omega}-1 hydroxylation of saturated fatty acids. Thus, these structures provide insights into the ability of CYP2E1 to effectively bind and metabolize both small molecule substrates and fatty acids.

  15. Molecular weight growth in Titan's atmosphere: branching pathways for the reaction of 1-propynyl radical (H3CC≡C˙) with small alkenes and alkynes.

    PubMed

    Kirk, Benjamin B; Savee, John D; Trevitt, Adam J; Osborn, David L; Wilson, Kevin R

    2015-08-28

    The reaction of small hydrocarbon radicals (i.e.˙CN, ˙C2H) with trace alkenes and alkynes is believed to play an important role in molecular weight growth and ultimately the formation of Titan's characteristic haze. Current photochemical models of Titan's atmosphere largely assume hydrogen atom abstraction or unimolecular hydrogen elimination reactions dominate the mechanism, in contrast to recent experiments that reveal significant alkyl radical loss pathways during reaction of ethynyl radical (˙C2H) with alkenes and alkynes. In this study, the trend is explored for the case of a larger ethynyl radical analogue, the 1-propynyl radical (H3CC[triple bond, length as m-dash]C˙), a likely product from the high-energy photolysis of propyne in Titan's atmosphere. Using synchrotron vacuum ultraviolet photoionization mass spectrometry, product branching ratios are measured for the reactions of 1-propynyl radical with a suite of small alkenes (ethylene and propene) and alkynes (acetylene and d4-propyne) at 4 Torr and 300 K. Reactions of 1-propynyl radical with acetylene and ethylene form single products, identified as penta-1,3-diyne and pent-1-en-3-yne, respectively. These products form by hydrogen atom loss from the radical-adduct intermediates. The reactions of 1-propynyl radical with d4-propyne and propene form products from both hydrogen atom and methyl loss, (-H = 27%, -CH3 = 73%) and (-H = 14%, -CH3 = 86%), respectively. Together, these results indicate that reactions of ethynyl radical analogues with alkenes and alkynes form significant quantities of products by alkyl loss channels, suggesting that current photochemical models of Titan over predict both hydrogen atom production as well as the efficiency of molecular weight growth in these reactions.

  16. Molecular weight growth in Titan's atmosphere: Branching pathways for the reaction of 1-propynyl radical (H3CC≡C˙) with small alkenes and alkynes

    DOE PAGESBeta

    Kirk, Benjamin B.; Savee, John D.; Trevitt, Adam J.; Osborn, David L.; Wilson, Kevin R.

    2015-07-16

    The reaction of small hydrocarbon radicals (i.e. ˙CN, ˙C2H) with trace alkenes and alkynes is believed to play an important role in molecular weight growth and ultimately the formation of Titan's characteristic haze. Current photochemical models of Titan's atmosphere largely assume hydrogen atom abstraction or unimolecular hydrogen elimination reactions dominate the mechanism, in contrast to recent experiments that reveal significant alkyl radical loss pathways during reaction of ethynyl radical (˙C2H) with alkenes and alkynes. In this study, the trend is explored for the case of a larger ethynyl radical analogue, the 1-propynyl radical (H3CC≡C˙), a likely product from the high-energymore » photolysis of propyne in Titan's atmosphere. Using synchrotron vacuum ultraviolet photoionization mass spectrometry, product branching ratios are measured for the reactions of 1-propynyl radical with a suite of small alkenes (ethylene and propene) and alkynes (acetylene and d4-propyne) at 4 Torr and 300 K. Reactions of 1-propynyl radical with acetylene and ethylene form single products, identified as penta-1,3-diyne and pent-1-en-3-yne, respectively. These products form by hydrogen atom loss from the radical-adduct intermediates. The reactions of 1-propynyl radical with d4-propyne and propene form products from both hydrogen atom and methyl loss, (–H = 27%, –CH3 = 73%) and (–H = 14%, –CH3 = 86%), respectively. Altogether, these results indicate that reactions of ethynyl radical analogues with alkenes and alkynes form significant quantities of products by alkyl loss channels, suggesting that current photochemical models of Titan over predict both hydrogen atom production as well as the efficiency of molecular weight growth in these reactions.« less

  17. Molecular weight growth in Titan's atmosphere: Branching pathways for the reaction of 1-propynyl radical (H3CC≡C˙) with small alkenes and alkynes

    SciTech Connect

    Kirk, Benjamin B.; Savee, John D.; Trevitt, Adam J.; Osborn, David L.; Wilson, Kevin R.

    2015-07-16

    The reaction