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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. 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.

  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. PMID:25665596

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Hole-trapping in molecularly doped polymers

    NASA Astrophysics Data System (ADS)

    Borsenberger, Paul M.; Gruenbaum, William T.; Lin, Liang-Bih; Visser, Susan A.

    1998-04-01

    Hole mobilities have been measured in tri-p-tolylamine (TTA) doped poly(styrene) containing different concentrations of di- p-tolyl-p-anisylamine (DTA) or tri-p-anisylamine (TAA). DTA and TAA are traps with depths of 0.08 and 0.22 eV, respectively. For low concentrations of DTA or TAA, the transport processes are trap controlled and the mobilities decrease with increasing trap concentration. For high TAA concentrations, however, the transport processes are dominated by trap-to-trap hopping and the mobilities increase with increasing trap concentrations. The threshold concentration for the transition from trap controlled to trap-to-trap transport is approximately 10-1. A transition to trap- to-trap hopping is not observed for TTA containing DTA. The results are discussed within the framework of the Hoesterey- Letson formalism and the recent simulations of Wolf et al. and Borsenberger et al.

  13. 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.

  14. 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

  15. Small Reactor for Semiconductor Production by Neutron Transmutation Doping

    SciTech Connect

    Obara, Toru; Hong, Liem Peng

    2010-06-22

    New concept of small size nuclear reactor is proposed for Neutron Transmutation Doping (NTD). The reactor core consists of conventional PWR type fuel elements with light water moderator/coolant unlike conventional research reactors. Graphite reflector is employed for large neutron irradiation volume. Silicon ingots are put into the reflector region for irradiation. Neutronic analysis results show that this concept has possibility to product large amount of silicon ingots which have large diameter. An optimal reactor design and its performance are shown as a result of analysis in the paper.

  16. Molecular effects of supraphysiological doses of doping agents on health.

    PubMed

    Imperlini, Esther; Mancini, Annamaria; Alfieri, Andreina; Martone, Domenico; Caterino, Marianna; Orrù, Stefania; Buono, Pasqualina

    2015-06-01

    Performance-enhancing drugs (PEDs) gained wide popularity not only among sportsmen but also among specific subsets of population, such as adolescents. Apart from their claimed effects on athletic performance, they are very appealing due to the body shaping effect exerted on fat mass and fat-free mass. Besides the "underestimated" massive misuse of PEDs, the short- as well as long-term consequences of such habits remain largely unrecognized. They have been strictly associated with serious adverse effects, but molecular mechanisms are yet to be elucidated. Here, we analyze the current understanding of the molecular effects of supraphysiological doses of doping agents in healthy biological systems, at genomic and proteomic levels, in order to define the molecular sensors of organ/tissue impairment, determined by their misuse. The focus is put on the anabolic androgenic steroids (AASs), specifically testosterone (T) and its most potent derivative dihydrotestosterone (DHT), and on the peptide hormones, specifically the growth hormone (GH) and the insulin-like growth factor-1 (IGF-1). A map of molecular targets is defined and the risk incidence for human health is taken into account. PMID:25787095

  17. Fe-doped InN layers grown by molecular beam epitaxy

    SciTech Connect

    Wang Xinqiang; Liu Shitao; Ma Dingyu; Zheng Xiantong; Chen Guang; Xu Fujun; Tang Ning; Shen Bo; Zhang Peng; Cao Xingzhong; Wang Baoyi; Huang Sen; Chen, Kevin J.; Zhou Shengqiang; Yoshikawa, Akihiko

    2012-10-22

    Iron(Fe)-doped InN (InN:Fe) layers have been grown by molecular beam epitaxy. It is found that Fe-doping leads to drastic increase of residual electron concentration, which is different from the semi-insulating property of Fe-doped GaN. However, this heavy n-type doping cannot be fully explained by doped Fe-concentration ([Fe]). Further analysis shows that more unintentionally doped impurities such as hydrogen and oxygen are incorporated with increasing [Fe] and the surface is degraded with high density pits, which probably are the main reasons for electron generation and mobility reduction. Photoluminescence of InN is gradually quenched by Fe-doping. This work shows that Fe-doping is one of good choices to control electron density in InN.

  18. 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.

  19. 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.

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

    SciTech Connect

    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.

  1. A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole.

    PubMed

    Fonner, John M; Schmidt, Christine E; Ren, Pengyu

    2010-10-01

    Polypyrrole (PPy) is a biocompatible, electrically conductive polymer that has great potential for battery, sensor, and neural implant applications. Its amorphous structure and insolubility, however, limit the experimental techniques available to study its structure and properties at the atomic level. Previous theoretical studies of PPy in bulk are also scarce. Using ab initio calculations, we have constructed a molecular mechanics force field of chloride-doped PPy (PPyCl) and undoped PPy. This model has been designed to integrate into the OPLS force field, and parameters are available for the Gromacs and TINKER software packages. Molecular dynamics (MD) simulations of bulk PPy and PPyCl have been performed using this force field, and the effects of chain packing and electrostatic scaling on the bulk polymer density have been investigated. The density of flotation of PPyCl films has been measured experimentally. Amorphous X-ray diffraction of PPyCl was obtained and correlated with atomic structures sampled from MD simulations. The force field reported here is foundational for bridging the gap between experimental measurements and theoretical calculations for PPy based materials. PMID:21052521

  2. A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole

    PubMed Central

    Fonner, John M.; Schmidt, Christine E.; Ren, Pengyu

    2010-01-01

    Polypyrrole (PPy) is a biocompatible, electrically conductive polymer that has great potential for battery, sensor, and neural implant applications. Its amorphous structure and insolubility, however, limit the experimental techniques available to study its structure and properties at the atomic level. Previous theoretical studies of PPy in bulk are also scarce. Using ab initio calculations, we have constructed a molecular mechanics force field of chloride-doped PPy (PPyCl) and undoped PPy. This model has been designed to integrate into the OPLS force field, and parameters are available for the Gromacs and TINKER software packages. Molecular dynamics (MD) simulations of bulk PPy and PPyCl have been performed using this force field, and the effects of chain packing and electrostatic scaling on the bulk polymer density have been investigated. The density of flotation of PPyCl films has been measured experimentally. Amorphous X-ray diffraction of PPyCl was obtained and correlated with atomic structures sampled from MD simulations. The force field reported here is foundational for bridging the gap between experimental measurements and theoretical calculations for PPy based materials. PMID:21052521

  3. Mechanisms of molecular doping of graphene: A first-principles study

    NASA Astrophysics Data System (ADS)

    Saha, Srijan Kumar; Chandrakanth, Reddy Ch.; Krishnamurthy, H. R.; Waghmare, U. V.

    2009-10-01

    Doping graphene with electron donating or accepting molecules is an interesting approach to introduce carriers into it, analogous to electrochemical doping accomplished in graphene when used in a field-effect transistor. Here, we use first-principles density-functional theory to determine changes in the electronic-structure and vibrational properties of graphene that arise from the adsorption of aromatic molecules such as aniline and nitrobenzene. Identifying the roles of various mechanisms of chemical interaction between graphene and a molecule, we bring out the contrast between electrochemical and molecular doping of graphene. Our estimates of various contributions to shifts in the Raman-active modes of graphene with molecular doping are fundamental to the possible use of Raman spectroscopy in (a) characterization of the nature and concentration of carriers in graphene with molecular doping, and (b) graphene-based chemical sensors.

  4. 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. PMID:26901192

  5. 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

  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. Electroless Functionalization of Silver Films by Its Molecular Doping.

    PubMed

    Naor, Hadas; Avnir, David

    2015-12-01

    We present a methodology which by far extends the potential applications of thin conductive silver films achieved by an electroless molecular doping process of the metal with any of the endless functional molecules that the large library of organic molecules offer. The resulting metallic films within which the molecule is entrapped--molecule@Ag--carry both the classical chemical and physical properties of silver films, as well as the function of the entrapped molecule. Raman measurements of the organic molecules from within the silver films provide the first spectroscopic observations from within silver, and clearly show that entrapment, a three-dimensional process, and adsorption, a two-dimensional process, on silver films are distinctly different processes. Three organic molecules, the cationic Neutral red, the anionic Congo red, and the antibacterial agent chlorhexidine digluconate (CH), were used to demonstrate the generality of this method for various types of molecules. We studied the sensitivity of the film conductivity to the type of the molecule entrapped within the film, to its concentration, and to temperature. Dual functionality was demonstrated with CH@Ag films, which are both conductive and have prolonged and high antibacterial activity, a combination of properties that has been unknown so far. PMID:26571199

  8. Controlled in situ boron doping of short silicon nanowires grown by molecular beam epitaxy

    SciTech Connect

    Das Kanungo, Pratyush; Zakharov, Nikolai; Bauer, Jan; Breitenstein, Otwin; Werner, Peter; Goesele, Ulrich

    2008-06-30

    Epitaxial silicon nanowires (NWs) of short heights ({approx}280 nm) on Si <111> substrate were grown and doped in situ with boron on a concentration range of 10{sup 15}-10{sup 19} cm{sup -3} by coevaporation of atomic Si and B by molecular beam epitaxy. Transmission electron microscopy revealed a single-crystalline structure of the NWs. Electrical measurements of the individual NWs confirmed the doping. However, the low doped (10{sup 15} cm{sup -3}) and medium doped (3x10{sup 16} and 1x10{sup 17} cm{sup -3}) NWs were heavily depleted by the surface states while the high doped (10{sup 18} and 10{sup 19} cm{sup -3}) ones showed volume conductivities expected for the corresponding intended doping levels.

  9. Precise doping of metals by small gas flows

    NASA Technical Reports Server (NTRS)

    Barrett, C. A.

    1968-01-01

    Simple method was developed for doping refractory metals with oxygen. The metal specimens are heated in a dynamic high-vacuum system. The system can be used for other oxygen absorption processes /such as low-pressure oxidation measurements/ and for gases other than oxygen.

  10. 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

  11. 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

  12. 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.

  13. A highly conducting graphene film with dual-side molecular n-doping.

    PubMed

    Kim, Youngsoo; Park, Jaesung; Kang, Junmo; Yoo, Je Min; Choi, Kyoungjun; Kim, Eun Sun; Choi, Jae-Boong; Hwang, Chanyong; Novoselov, K S; Hong, Byung Hee

    2014-08-21

    Doping is an efficient way to engineer the conductivity and the work function of graphene, which is, however, limited to wet-chemical doping or metal deposition particularly for n-doping, Here, we report a simple method of modulating the electrical conductivity of graphene by dual-side molecular n-doping with diethylenetriamine (DETA) on the top and amine-functionalized self-assembled monolayers (SAMs) at the bottom. The resulting charge carrier density of graphene is as high as -1.7 × 10(13) cm(-2), and the sheet resistance is as low as ∼86 ± 39 Ω sq(-1), which is believed to be the lowest sheet resistance of monolayer graphene reported so far. This facile dual-side n-doping strategy would be very useful to optimize the performance of various graphene-based electronic devices. PMID:24993121

  14. Towards Tunable Band Gap and Tunable Dirac Point in Bilayer Graphene with Molecular Doping

    PubMed Central

    Yu, Woo Jong; Liao, Lei; Chae, Sang Hoon; Lee, Young Hee; Duan, Xiangfeng

    2011-01-01

    The bilayer graphene has attracted considerable attention for potential applications in future electronics and optoelectronics because of the feasibility to tune its band gap with a vertical displacement field to break the inversion symmetry. Surface chemical doping in bilayer graphene can induce an additional offset voltage to fundamentally affect the vertical displacement field and band-gap opening in bilayer graphene. In this study, we investigate the effect of chemical molecular doping on band-gap opening in bilayer graphene devices with single or dual gate modulation. Chemical doping with benzyl viologen molecules modulates the displacement field to allow the opening of a transport band gap and the increase of the on/off ratio in the bilayer graphene transistors. Additionally, Fermi energy level in the opened gap can be rationally controlled by the amount of molecular doping to obtain bilayer graphene transistors with tunable Dirac points, which can be readily configured into functional devices such as complementary inverters. PMID:21985035

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. Improvement of thermoelectric efficiency of the polyaniline molecular junction by the doping process.

    PubMed

    Golsanamlou, Zahra; Tagani, Meysam Bagheri; Soleimani, Hamid Rahimpour

    2015-05-28

    Thermoelectric properties of a polyaniline molecular junction with face centered cubic electrodes are investigated using the Green function formalism in a linear response regime in the presence of the doping process. Doping causes the increase of thermopower and the figure of merit (ZT) and the decrease of electrical conductance as found experimentally in the work of Li et al., (Synthetic. Metals, 2010, 160, 1153-1158). We also find that the ZT increases with the molecular length in short polyanilines. [Golsanamlou et al., Phys. Chem. Chem. Phys., 2000, 35, 3523]. PMID:25929682

  20. High-density Two-Dimensional Small Polaron Gas in a Delta-Doped Mott Insulator

    PubMed Central

    Ouellette, Daniel G.; Moetakef, Pouya; Cain, Tyler A.; Zhang, Jack Y.; Stemmer, Susanne; Emin, David; Allen, S. James

    2013-01-01

    Heterointerfaces in complex oxide systems open new arenas in which to test models of strongly correlated material, explore the role of dimensionality in metal-insulator-transitions (MITs) and small polaron formation. Close to the quantum critical point Mott MITs depend on band filling controlled by random disordered substitutional doping. Delta-doped Mott insulators are potentially free of random disorder and introduce a new arena in which to explore the effect of electron correlations and dimensionality. Epitaxial films of the prototypical Mott insulator GdTiO3 are delta-doped by substituting a single (GdO)+1 plane with a monolayer of charge neutral SrO to produce a two-dimensional system with high planar doping density. Unlike metallic SrTiO3 quantum wells in GdTiO3 the single SrO delta-doped layer exhibits thermally activated DC and optical conductivity that agree in a quantitative manner with predictions of small polaron transport but with an extremely high two-dimensional density of polarons, ~7 × 1014 cm−2. PMID:24257578

  1. Effect of oxygen doping on electrical properties of small radius (2,1) single-walled carbon nanotubes.

    PubMed

    Mashapa, Matete G; Ray, Suprakas Sinha

    2010-07-01

    We investigated the electrical conductivity of the small radius oxygen-doped (2,1) single-walled carbon nanotubes (SWCNTs) using first-principles density functional theory (DFT). We found that introduction of oxygen does not significantly change the global structure of the SWCNT, and thus the bonding mode of the structure is not remarkably altered. The results show that doping enhances the conductivity of the SWCNT. Oxygen doping increases density of states at the Fermi level, thus the conductivity of the doped SWCNT increases when oxygen is introduced, consistent with experimental observations. These observations were further clarified by comparing band structures of pristine and doped nanotubes. PMID:21128405

  2. 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.

  3. 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.

  4. How intermolecular geometrical disorder affects the molecular doping of donor-acceptor copolymers

    NASA Astrophysics Data System (ADS)

    di Nuzzo, Daniele; Fontanesi, Claudio; Jones, Rebecca; Allard, Sybille; Dumsch, Ines; Scherf, Ullrich; von Hauff, Elizabeth; Schumacher, Stefan; da Como, Enrico

    2015-03-01

    Molecular doping of conjugated polymers represents an important strategy for improving organic electronic devices. However, the widely reported low efficiency of doping remains a crucial limitation to obtain high performance. Here we investigate how charge transfer between dopant and donor-acceptor copolymers is affected by the spatial arrangement of the dopant molecule with respect to the copolymer repeat unit. We p-dope a donor-acceptor copolymer and probe its charge-sensitive molecular vibrations in films by infrared spectroscopy. We find that, compared with a related homopolymer, a four times higher dopant/polymer molar ratio is needed to observe signatures of charges. By DFT methods, we simulate the vibrational spectra, moving the dopant along the copolymer backbone and finding that efficient charge transfer occurs only when the dopant is close to the donor moiety. Our results show that the donor-acceptor structure poses an obstacle to efficient doping, with the acceptor moiety being inactive for p-type doping.

  5. Molecular semiconductor-doped insulator (MSDI) heterojunctions as new transducers for chemical sensors

    NASA Astrophysics Data System (ADS)

    Bouvet, M.; Parra, V.; Suisse, J.-M.

    2011-12-01

    This article describes a new principle of transduction involving an heterojunction between a Molecular Semiconductor and a Doped Insulator (MSDI). Herein, we report on an MSDI-based sensor featuring an heterojunction between a lutetium bisphthalocyanine (LuPc2), which acts as Molecular Semiconductor (MS) and a thin film of Doped Insulator (DI) made of substituted or fluorinated copper phthalocyanine (CuFnPc, where n = 0, 8, 16). Previously, we reported the peculiar effect of the heterojunction on the MSDI's electronic behavior, suggesting this device as a new kind of transducer for gas chemosensing. Indeed, of particular significance was the key role of modulator played by the nature of the doped insulator sub-layer. While the MS thin film remains the only layer of the sensor exposed to gas atmosphere, the DI's ability to tune the electronic characteristics of the organic heterojunction allows it to drastically affect the nature of the effective charge carriers. In particular, an increase in fluorination of the doped insulator can cause an inversion of the LuPc2 response toward electron accepting (ozone, ppb level) or donating (ammonia, ppm level) gases. The present work focuses on the structural, electronic and electrical properties of the MSDI heterojunction, which have been studied by UV-vis spectroscopy, atomic force microscopy, current-voltage measurements and chemical doping, in order to shed some light on this phenomenon. The unique ambipolar nature of LuPc2 is suggested to be the main property responsible for the MSDI's unique behavior.

  6. Resonance of graphene nanoribbons doped with nitrogen and boron: a molecular dynamics study.

    PubMed

    Wei, Ye; Zhan, Haifei; Xia, Kang; Zhang, Wendong; Sang, Shengbo; Gu, Yuantong

    2014-01-01

    Based on its enticing properties, graphene has been envisioned with applications in the area of electronics, photonics, sensors, bio-applications and others. To facilitate various applications, doping has been frequently used to manipulate the properties of graphene. Despite a number of studies conducted on doped graphene regarding its electrical and chemical properties, the impact of doping on the mechanical properties of graphene has been rarely discussed. A systematic study of the vibrational properties of graphene doped with nitrogen and boron is performed by means of a molecular dynamics simulation. The influence from different density or species of dopants has been assessed. It is found that the impacts on the quality factor, Q, resulting from different densities of dopants vary greatly, while the influence on the resonance frequency is insignificant. The reduction of the resonance frequency caused by doping with boron only is larger than the reduction caused by doping with both boron and nitrogen. This study gives a fundamental understanding of the resonance of graphene with different dopants, which may benefit their application as resonators. PMID:24991509

  7. 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.

  8. 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.

  9. 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.

  10. Molecular Pairing and Fully Gapped Superconductivity in Yb-doped CeCoIn5

    NASA Astrophysics Data System (ADS)

    Erten, Onur; Flint, Rebecca; Coleman, Piers

    2015-01-01

    The recent observation of fully gapped superconductivity in Yb doped CeCoIn5 poses a paradox, for the disappearance of nodes suggests that they are accidental, yet d -wave symmetry with protected nodes is well established by experiment. Here, we show that composite pairing provides a natural resolution: in this scenario, Yb doping drives a Lifshitz transition of the nodal Fermi surface, forming a fully gapped d -wave molecular superfluid of composite pairs. The T4 dependence of the penetration depth associated with the sound mode of this condensate is in accordance with observation.

  11. 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.

  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. Very high (> 1019 cm-3) in situ n-type doping of silicon during molecular beam epitaxy using supersonic jets of phosphine

    NASA Astrophysics Data System (ADS)

    Malik, R.; Gulari, E.; Bhattacharya, P.; Linder, K. K.; Rieh, J.-S.

    1997-03-01

    The use of supersonically injected pulses of phosphine to achieve uniform and high levels of n-type doping in Si during gas-source molecular beam epitaxy is demonstrated. Uniform n-type doping up to levels of 5×1019 cm-3 is obtained. SiGe/Si junction diodes made with this doping technique show good doping profiles and rectifying characteristics.

  14. 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

  15. 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

  16. 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

  17. Molecular doping for control of gate bias stress in organic thin film transistors

    SciTech Connect

    Hein, Moritz P. Lüssem, Björn; Jankowski, Jens; Tietze, Max L.; Riede, Moritz K.; Zakhidov, Alexander A.; Leo, Karl; Fraunhofer COMEDD, Maria-Reiche-Str. 2, 01109 Dresden

    2014-01-06

    The key active devices of future organic electronic circuits are organic thin film transistors (OTFTs). Reliability of OTFTs remains one of the most challenging obstacles to be overcome for broad commercial applications. In particular, bias stress was identified as the key instability under operation for numerous OTFT devices and interfaces. Despite a multitude of experimental observations, a comprehensive mechanism describing this behavior is still missing. Furthermore, controlled methods to overcome these instabilities are so far lacking. Here, we present the approach to control and significantly alleviate the bias stress effect by using molecular doping at low concentrations. For pentacene and silicon oxide as gate oxide, we are able to reduce the time constant of degradation by three orders of magnitude. The effect of molecular doping on the bias stress behavior is explained in terms of the shift of Fermi Level and, thus, exponentially reduced proton generation at the pentacene/oxide interface.

  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. 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

  20. Coherent quasiparticles with a small Fermi Surface in lightly doped Sr3Ir2O7

    NASA Astrophysics Data System (ADS)

    de la Torre, Alberto; McKeown Walker, Siobhan; Tamai, Anna; Hunter, Emily; Subedi, Alaska; Kim, Timur; Hoesch, Moritz; Perry, Robin; Georges, Antoine; Baumberger, Felix

    2015-03-01

    We characterize the electron doping evolution of (Sr1-xLax)Ir2O7 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 3 x / 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 Sr3Ir2O7, in stark contrast with underdoped cuprates.

  1. Coherent Quasiparticles with a Small Fermi Surface in Lightly Doped Sr3Ir2O7

    NASA Astrophysics Data System (ADS)

    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.

    2014-12-01

    We characterize the electron doping evolution of (Sr1 -xLax)3Ir2O7 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 3 x /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 Sr3Ir2O7 .

  2. 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

  3. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

    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.

  5. Thermodynamic and kinetic studies of laser thermal processing of heavily boron-doped amorphous silicon using molecular dynamics

    NASA Astrophysics Data System (ADS)

    Wang, Liguo; Clancy, Paulette; Thompson, Michael O.; Murthy, Cheruvu S.

    2002-09-01

    Laser thermal processing (LTP) has been proposed as a means to avoid unwanted transient enhanced diffusion and deactivation of dopants, especially boron and arsenic, during the formation of ultrashallow junctions. Although experimental studies have been carried out to determine the efficacy of LTP for pure Si and lightly B-doped junctions, the effects of high concentrations of dopants (above 2% B) on the thermodynamic and kinetic properties of the regrown film are unknown. In this study, a classical interatomic potential model [Stillinger-Weber (SW)] is used with a nonequilibrium molecular dynamics computer simulation technique to study the laser thermal processing of heavily B-doped Si in the range 2-10 at. % B. We observe only a small effect of boron concentration on the congruent melting temperature of the B:Si alloy, and thus the narrowing of the "process window" for LTP is predicted to be small. No significant tendency for boron to segregate was observed at either the regrowth front or the buried c-Si interface during fast regrowth. The B-doped region regrew as defect-free crystal with full activation of the boron atoms at low boron concentrations (2%), in good agreement with experiments. As the concentration of boron increased, the number of intrinsic Si defects and boron interstitials in the regrown materials increased, with a minor amount of boron atoms in clusters (<2%). An instability limit for crystal regrowth was observed at around 8%-10% boron atoms during fast regrowth; systems with 10% B showed partial amorphization during regrowth. Comparison with tight-binding quantum mechanical calculations showed that the SW model gives similar diffusivities in the liquid and tendency to cluster, but the lifetimes of the SW clusters are considerably too long (>150 ps, compared to 5 ps in tight binding). The importance of adequate system size is discussed.

  6. 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.

  7. Characterization of Si volume- and delta-doped InGaAs grown by molecular beam epitaxy

    SciTech Connect

    Fedoryshyn, Y.; Kaspar, P.; Jaeckel, H.; Beck, M.

    2010-05-15

    Bulk InGaAs layers were grown at 400 deg. C lattice-matched to InP semi-insulating substrates by molecular beam epitaxy. Si doping of the layers was performed by applying volume- and delta-doping techniques. The samples were characterized by capacitance-voltage, van der Pauw-Hall, secondary ion mass spectroscopy and photoluminescence measurements. Good agreement in terms of dependence of mobility and Burstein-Moss shift shift on doping concentration in samples doped by the two different techniques was obtained. Amphoteric behavior of Si was observed at doping concentrations higher than {approx}2.9x10{sup 19} cm{sup -3} in both delta- and volume-doped samples. Degradation of InGaAs crystalline quality occurred in samples with Si concentrations higher than {approx}4x10{sup 19} cm{sup -3}.

  8. 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.

  9. 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.

  10. 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.

  11. Elastic properties of polymer-doped dilute lamellar phases: A small-angle neutron scattering study

    NASA Astrophysics Data System (ADS)

    Ficheux, M.-F.; Bellocq, A.-M.; Nallet, F.

    2001-03-01

    We investigate experimentally, using small-angle neutron scattering the elastic properties of polymer-doped dilute lamellar phases. In our system the polymer is water-soluble but nevertheless partially adsorbs onto the negatively charged surfactant bilayers. The effective polymer-mediated interaction between bilayers is less repulsive than the weakly screened electrostatic interaction that prevails at zero polymer content. It even becomes attractive in some regions of the phase diagram. Small-angle neutron scattering allows us to measure directly the Caillé exponent η characterizing the bilayer fluctuations in lamellar (smectic A) phases, and thus indirectly estimate the compression modulus bar{B} as a measure of the strength of the bilayer-bilayer interactions. The compression modulus appears to be vanishing at a point located on the lamellar-lamellar phase separation boundary, a candidate critical point.

  12. 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.

  13. 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 !}.

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

    NASA Astrophysics Data System (ADS)

    Jacox, Marilyn E.

    2015-01-01

    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!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 C2H4 and BF3 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 H2 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 O4+, NH4+, HOCO+, and HCO2!.

  15. NMR of small solutes in liquid crystals and molecular sieves

    NASA Astrophysics Data System (ADS)

    Ylihautala, Mika Petri

    The present thesis deals with the nuclear magnetic resonance (NMR) spectroscopy of small solutes applied to the studies of liquid crystals and molecular sieves. In this method, changes induced by the investigated environment to the static spectral parameters (i.e. nuclear shielding, indirect and direct spin-spin coupling and quadrupole coupling) of the solute are measured. The nuclear shielding of dissolved noble gases is utilized for the studies of thermotropic liquid crystals. The relation between the symmetry properties of mesophases and the nuclear shielding is described. The different interaction mechanisms perturbing the observed noble gas nuclear shielding are discussed, particularly, the role of long-range attractive van der Waals interactions is brought out. The suitability of the noble gas NMR spectroscopy to the studies of Iyotropic liquid crystals is investigated in terms of nuclear shielding and quadrupole coupling interactions. In molecular sieve systems, the effect of inter- and intracrystalline motions of solutes on their NMR spectra is discussed. A novel method for the measurement of the intracrystalline motions is developed. The distinctions in the 13C shielding of methane adsorbed in AlPO4-11 and SAPO-11, two structurally similar molecular sieves differing in composition, are indicated.

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

    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 3HeN clusters with atomic or molecular impurities [J. Chem. Phys. (Communication) 125, 221101 (2006)]. The main difficulty in handling doped 3HeN 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-3HeN clusters. Preliminary results by using the latest version of the FCI-NO computational implementation, to bosonic Cl2(X)-(4He )N clusters, are also shown.

  17. 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.

  18. 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

  19. Theoretical Considerations for the Design of Molecularly-Doped Nanostructures with Tunable Field-Dependent Mobility

    NASA Astrophysics Data System (ADS)

    Kenkre, V. M.; Parris, P. E.; Dunlap, D. H.

    2001-03-01

    Calculations are presented to address the possibility of designing materials and nanostructures with controllable charge transport capabilities. Building upon the current understanding of the relation between the mobility of photoinjected charges in molecularly-doped polymers and the disordered dipolar environment through which they move, we show how the relative alignment of permanent electric dipoles in the nanostructure associated can enhance or reduce the field dependent mobility of carriers injected into the sample. We consider domains which arise in liquid crystals as well as those induced by poling with an external field.

  20. 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

  1. 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

  2. Analysis of plume following ultraviolet laser ablation of doped polymers: Dependence on polymer molecular weight

    SciTech Connect

    Rebollar, Esther; Oujja, Mohamed; Bounos, Giannis; Kolloch, Andreas; Georgiou, Savas; Castillejo, Marta

    2007-02-01

    This work investigates the effect of polymer molecular weight M{sub W} on the plume characteristics of poly(methyl methacrylate) (PMMA) and polystyrene (PS) films doped with iodonaphthalene (NapI) and iodophenanthrene (PhenI) following irradiation in vacuum at 248 nm. Laser-induced fluorescence probing of the plume reveals the presence of ArH products (NapH and PhenH from, respectively, NapI- and PhenI-doped films). While a bimodal translational distribution of these products is observed in all cases, on average, a slower translational distribution is observed in the low M{sub W} system. The extent of the observed dependence is reduced as the optical absorption coefficient of the film increases, i.e., in the sequence NapI/PMMA, PhenI/PMMA, and PS-doped films. Further confirmation of the bimodal translational distributions is provided by monitoring in situ the temporally resolved attenuation by the plume as it expands in vacuum of a continuous wave helium-neon laser propagating parallel to the substrate. Results are discussed in the framework of the bulk photothermal model, according to which ejection requires that a critical number of bonds are broken.

  3. 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.

  4. Arsenic p-Doping of HgCdTe Grown by Molecular Beam Epitaxy (MBE): A Solved Problem?

    NASA Astrophysics Data System (ADS)

    Garland, James W.; Grein, Christoph; Sivananthan, Sivalingam

    2013-11-01

    The goal of achieving well-controlled, reproducibly p-doped mercury cadmium telluride (HgCdTe) with sharp p- n junctions and low Shockley-Read-Hall contribution τ SRH to the minority carrier lifetime τ has been pursued for the past 30 years by the HgCdTe molecular beam epitaxial (MBE) growth community, but remains elusive. On the other hand, n-doping with In avoids the short τ SRH characteristic of arsenic-doped MBE-grown HgCdTe and is well controlled, stable, and reproducibly 100% activated as-grown. However, as discussed herein, because of inherent limitations of n-doped absorber layers, overcoming the challenges of successfully p-doping HgCdTe remains an important problem, especially for long-wavelength infrared detectors. We briefly review the achievements that have been made in p-doping HgCdTe, point out the reasons why achieving well-controlled, reproducibly p-doped MBE-grown HgCdTe with a lifetime τ not limited by τ SRH remains a very important task, discuss the probable origin of the short τ SRH in MBE-grown HgCdTe, and discuss possible ways to achieve much longer values of τ SRH in MBE-grown p-doped HgCdTe.

  5. Small-Molecule Hormones: Molecular Mechanisms of Action

    PubMed Central

    Budzińska, Monika

    2013-01-01

    Small-molecule hormones play crucial roles in the development and in the maintenance of an adult mammalian organism. On the molecular level, they regulate a plethora of biological pathways. Part of their actions depends on their transcription-regulating properties, exerted by highly specific nuclear receptors which are hormone-dependent transcription factors. Nuclear hormone receptors interact with coactivators, corepressors, basal transcription factors, and other transcription factors in order to modulate the activity of target genes in a manner that is dependent on tissue, age and developmental and pathophysiological states. The biological effect of this mechanism becomes apparent not earlier than 30–60 minutes after hormonal stimulus. In addition, small-molecule hormones modify the function of the cell by a number of nongenomic mechanisms, involving interaction with proteins localized in the plasma membrane, in the cytoplasm, as well as with proteins localized in other cellular membranes and in nonnuclear cellular compartments. The identity of such proteins is still under investigation; however, it seems that extranuclear fractions of nuclear hormone receptors commonly serve this function. A direct interaction of small-molecule hormones with membrane phospholipids and with mRNA is also postulated. In these mechanisms, the reaction to hormonal stimulus appears within seconds or minutes. PMID:23533406

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

    PubMed

    Yang, Xiaozhou; Li, Yanxiao

    2016-01-15

    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. PMID:26478986

  7. 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.

  8. 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. PMID:25614208

  9. Molecular orbital model of optical centers in bismuth-doped glasses.

    PubMed

    Kustov, E F; Bulatov, L I; Dvoyrin, V V; Mashinsky, V M

    2009-05-15

    Spectroscopic properties of optical fibers with a bismuth-doped silicate glass core are explained on the basis of molecular orbital theory and a solution of the Schrödinger equation, which takes into account the exchange, the spin-orbital, and the glass field potential interactions of s, p, and d electron shells of bismuth with s(sigma), p(sigma), and p(pi) orbits of oxygen atoms. The approach can explain the IR luminescence properties of other optical centers formed by other atoms with the same structure of electron shells as the bismuth atom. The model of transitions based on intramolecular charge transfer between molecular orbital and metallic states is proposed. PMID:19448817

  10. 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.

  11. Photophysical processes of triplet states and radical ions in pure and molecularly doped polymers. Final report

    SciTech Connect

    Burkhart, R.D.

    1998-01-01

    Both the past and current objectives are to learn how to control the rate and direction of triplet exciton migration in both pure and molecularly doped polymer systems. Since triplet excimers are efficient traps for migrating excitons, a secondary objective has been to characterize these excimers with a view toward their use as rate modifiers or excited state quenchers. Further objectives included those stated above as past and current objectives but with an additional goal. The authors learned that fluid solutions of many of the nitrogen containing chromophores with which they work produce both radical cations and anions upon excimer laser excitation. They also learned that a phosphorus analogue behaves similarly. At this time the mechanism of charge generation in these systems is not well established but they do know that the electronically excited states and radical ions can potentially interconvert. They wanted to find out whether or not the pure or molecularly doped polymer systems could be used in a step-wise sequence involving light absorption followed by charge generation. All of their activities are oriented toward the potential end use of polymeric systems in the conversion of light energy to perform various types of useful work.

  12. Small molecular antibacterial peptoid mimics: the simpler the better!

    PubMed

    Ghosh, Chandradhish; Manjunath, Goutham B; Akkapeddi, Padma; Yarlagadda, Venkateswarlu; Hoque, Jiaul; Uppu, Divakara S S M; Konai, Mohini M; Haldar, Jayanta

    2014-02-27

    The emergence of multidrug resistant bacteria compounded by the depleting arsenal of antibiotics has accelerated efforts toward development of antibiotics with novel mechanisms of action. In this report, we present a series of small molecular antibacterial peptoid mimics which exhibit high in vitro potency against a variety of Gram-positive and Gram-negative bacteria, including drug-resistant species such as methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium. The highlight of these compounds is their superior activity against the major nosocomial pathogen Pseudomonas aeruginosa. Nontoxic toward mammalian cells, these rapidly bactericidal compounds primarily act by permeabilization and depolarization of bacterial membrane. Synthetically simple and selectively antibacterial, these compounds can be developed into a newer class of therapeutic agents against multidrug resistant bacterial species. PMID:24479371

  13. 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

  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. 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.

  16. 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.

  17. Detection of small interfering RNA (siRNA) by mass spectrometry procedures in doping controls.

    PubMed

    Thomas, Andreas; Walpurgis, Katja; Delahaut, Philippe; Kohler, Maxie; Schänzer, Wilhelm; Thevis, Mario

    2013-01-01

    Uncovering manipulation of athletic performance via small interfering (si)RNA is an emerging field in sports drug testing. Due to the potential to principally knock down every target gene in the organism by means of the RNA interference pathway, this facet of gene doping has become a realistic scenario. In the present study, two distinct model siRNAs comprising 21 nucleotides were designed as double strands which were perfect counterparts to a sequence of the respective messenger RNA coding the muscle regulator myostatin of Rattus norvegicus. Several modified nucleotides were introduced in both the sense and the antisense strand comprising phosphothioates, 2'-O-methylation, 2'-fluoro-nucleotides, locked nucleic acids and a cholesterol tag at the 3'-end. The model siRNAs were applied to rats at 1 mg/kg (i.v.) and blood as well as urine samples were collected. After isolation of the RNA by means of a RNA purification kit, the target analytes were detected by liquid chromatography - high resolution/high accuracy mass spectrometry (LC-HRMS). Analytes were detected as modified nucleotides after alkaline hydrolysis, as intact oligonucleotide strands (top-down) and by means of denaturing SDS-PAGE analysis. The gel-separated siRNA was further subjected to in-gel hydrolysis with different RNases and subsequent identification of the fragments by untargeted LC-HRMS analysis (bottom-up, 'experimental RNomics'). Combining the results of all approaches, the identification of several 3'-truncated urinary metabolites was accomplished and target analytes were detected up to 24 h after a single administration. Simultaneously collected blood samples yielded no promising results. The methods were validated and found fit-for-purpose for doping controls. PMID:23913913

  18. 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

  19. 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.

  20. 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.

  1. Conducting (Si-doped) aluminum nitride epitaxial films grown by molecular beam epitaxy

    SciTech Connect

    Kim, J.G.; Moorthy, M.; Park, R.M.

    1999-07-01

    As a member of the III-V nitride semiconductor family, AlN, which has a direct energy-gap of 6.2eV, has received much attention as a promising material for many applications. However, despite the promising attributes of AlN for various semiconductor devices, research on AlN has been limited and n-type conducting AlN has not been reported. The objective of this research was to understand the factors impacting the conductivity of AlN and to control the conductivity of this material through intentional doping. Prior to the intentional doping study, growth of undoped AlN epilayers was investigated. Through careful selection of substrate preparation methods and growth parameters, relatively low-temperature molecular beam epitaxial growth of AlN films was established which resulted in insulating material. Intentional Si doping during epilayer growth was found to result in conducting films under specific growth conditions. Above a growth temperature of 900 C, AlN films were insulating, however, below a growth temperature of 900 C, the AlN films were conducting. The magnitude of the conductivity and the growth temperature range over which conducting AlN films could be grown were strongly influenced by the presence of a Ga flux during growth. For instance, conducting, Si-doped, AlN films were grown at a growth temperature of 940 C in the presence of a Ga flux while the films were insulating when grown in the absence of a Ga flux at this particular growth temperature. Also, by appropriate selection of the growth parameters, epilayers with n-type conductivity values as large as 0.2 {Omega}{sup {minus}1} cm{sup {minus}1} for AlN and 17 {Omega}{sup {minus}1} cm{sup {minus}1} for Al{sub 0.75}Ga{sub 0.25}N were grown in this work for the first time.

  2. 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.

  3. Rapid growth of localized nature of carriers in the Kondo semiconductor CeFe2Al10 with nonmagnetic ground state due to small Rh doping

    NASA Astrophysics Data System (ADS)

    Tanida, H.; Nakamura, M.; Sera, M.; Nishioka, T.; Matsumura, M.

    2015-12-01

    We examined the chemical doping effect on the Kondo semiconductor CeFe2Al10 with a nonmagnetic ground state by means of the magnetic susceptibility, specific heat, electrical resistivity, and thermopower. The effect of Ru doping on the ground state is small. On the other hand, by a small amount of Rh doping, the magnetic susceptibility is strongly enhanced along the orthorhombic a axis, and a Curie-Weiss behavior is observed in a wide temperature range. The low-temperature specific heat is also strongly enhanced by the doping, and a metallic ground state is realized at low temperatures. These results suggest the collapse of the spin and charge gap due to the suppression of the c -f hybridization effect. From the results of a crystalline electric field analysis on the magnetic susceptibility of Ce (Fe1 -xRhx )2Al10 , it was revealed that the Rh-doping effect on the c -f hybridization effect is anisotropic, especially for the a axis. Similar doping effects are seen in the Rh-doped CeRu2Al10 , Ir-doped CeOs2Al10 , and Si-doped CeRu2Al10 . From these results, we conclude that the collapse of the spin and charge gap by such an excess electron doping is one of the universal features of the Kondo semiconductor Ce T2Al10 (T = Fe, Ru, and Os).

  4. Effect of ion structure on conductivity in lithium-doped ionic liquid electrolytes: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Liu, Hongjun; Maginn, Edward

    2013-09-01

    Molecular dynamics simulations were performed to examine the role cation and anion structure have on the performance of ionic liquid (IL) electrolytes for lithium conduction over the temperature range of 320-450 K. Two model ionic liquids were studied: 1-butyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide ([bmim][Tf2N]) and 1-butyl-4-methylpyridinium pyrrolide ([bmpyr][pyl]) doped with Li[Tf2N] and Li[pyl], respectively. The results have demonstrated that the Li+ doped IL containing the planar [bmpyr] cation paired with the planar [pyl] anion significantly outperformed the [bmim][Tf2N] IL. The different coordination of Li+ with the [Tf2N]- or [pyl]- anions produces a remarkable change in IL structure with a concomitant effect on the transport of all ions. For the doped [bmim][Tf2N], each Li+ is coordinated by four oxygen atoms from [Tf2N]- anions. Formation of a rigid structure between Li+ and [Tf2N]- induces a decrease in the mobility of all ions. In contrast, for the doped [bmpyr][pyl], each Li+ is coordinated by two nitrogen atoms from [pyl]- anions. The original alternating structure cation|anion|cation in the neat [bmpyr][pyl] is replaced by another alternating structure cation|anion|Li+|anion|cation in the doped [bmpyr][pyl]. Increases of Li+ mole fraction in doped [bmpyr][pyl] affects the dynamics to a much lesser extent compared with [bmim][Tf2N] and leads to reduced diffusivities of cations and anions, but little change in the dynamics of Li+. More importantly, the calculations predict that the Li+ ion conductivity of doped [bmpyr][pyl] is comparable to that observed in organic liquid electrolytes and is about an order of magnitude higher than that of doped [bmim][Tf2N]. Such Li+ conductivity improvement suggests that this and related ILs may be promising candidates for use as electrolytes in lithium ion batteries and capacitors.

  5. 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.

  6. Length dependence of carbon-doped BN nanowires: A-D Rectification and a route to potential molecular devices

    NASA Astrophysics Data System (ADS)

    Qiu, M.; Liew, K. M.

    2013-02-01

    Based on the first-principles approach, electronic transport properties of different lengths of carbon-doped boron-nitrogen nanowires, capped with two thiols as end groups connected to Au electrodes surfaces, are investigated. The results show that rectifying performance and negative differential resistance (NDR) behaviors can be enhanced obviously by increasing the length. Analysis of Mülliken population, transmission spectra, evolutions of frontier orbitals and molecular projected self-consistent Hamiltonian of molecular orbital indicate that electronic transmission strength, charge transfer and distributions of molecular states change are the intrinsic origin of these rectifying performances and NDR behaviors.

  7. 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

  8. 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

  9. 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.

  10. Localized-state distributions in molecularly doped polymers determined from time-of-flight transient photocurrent

    NASA Astrophysics Data System (ADS)

    Nagase, Takashi; Naito, Hiroyoshi

    2000-07-01

    Localized-state distributions have been studied in a molecularly doped polymer (MDP) system of a polymer binder (polycarbonate) doped with charge-transporting [N, N'-diphenyl-N, N'-bis(3-methylphenyl)(1,1'-biphenyl)-4,4'-diamine (TPD)] and trap-forming molecules [1-phenyl-3-(p-diethylaminostyryl)-5-(p-diethylaminophenyl)pyrazoline (PRA)] simultaneously by means of the conventional time-of-flight (TOF) transient photocurrent measurements. The existence of a transport energy in the MDP system is experimentally shown by comparing Gaussian distributions of localized states deduced by the Gaussian disorder model, due to Bässler and co-workers [H. Bässler, Phys. Status Solidi B 175, 15 (1993)], with localized-state distributions determined from the analysis of the TOF transient photocurrent data, based on the trap-controlled band transport [H. Naito, J. Ding, and M. Okuda, Appl. Phys. Lett. 64, 1830 (1994)]. The transport energy is found to be located at the center of the Gaussian distribution due to the host TPD molecules. It is also found that at 0.1 mol % PRA addition, the Gaussian distribution of localized states due to TPD molecules is broadened through the random electrostatic potential generated by dipoles of PRA, and at 1 mol % PRA addition, the localized-state structure due to PRA molecules, as well as the further broadening of the Gaussian distribution, are observed. The energy level of the structure is determined to be 0.54 eV above the transport energy, which is almost equal to the difference in the ionization potential between PRA and TPD.

  11. 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. PMID:24687246

  12. Molecular-beam epitaxy growth and in situ arsenic doping of p-on-n HgCdTe heterojunctions

    NASA Astrophysics Data System (ADS)

    Arias, Jose; Zandian, M.; Pasko, J. G.; Shin, S. H.; Bubulac, L. O.; DeWames, R. E.; Tennant, W. E.

    1991-02-01

    In this paper we present, results on the growth of in situ doped p-on-n heterojunctions on HgCdTe epilayers grown on (211)B GaAs substrates by molecular-beam epitaxy (MBE). Long wavelength infrared (LWIR) photodiodes made with these grown junctions are of high performance. The n-type MBE HgCdTe/GaAs alloy epilayer in these structures was grown at Ts=185 °C and it was doped with indium (high 1014 cm-3 range) atoms. This epilayer was directly followed by the growth, at Ts=165 °C, of an arsenic-doped (1017-1018 cm-3 ) HgTe/CdTe superlattice structure which was necessary to incorporate the arsenic atoms as acceptors. After the structure was grown, a Hg annealing step was needed to interdiffuse the superlattice and obtain the arsenic-doped p-type HgCdTe layer above the indium-doped layer. LWIR mesa diodes made with this material have 77 K R0A values of 5×103, 81, 8.5, and 1.1 Ω cm2 for cutoff wavelengths of 8.0, 10.2, 10.8, and 13.5 μm, respectively; the 77 K quantum efficiency values for these diodes were greater than 55%. These recent results represent a significant step toward the demonstration of MBE as a viable growth technique for the in situ fabrication of large area LWIR focal plane arrays.

  13. 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.

  14. Analysis of the time-of-flight transients in molecularly doped polymers using the Gaussian disorder model

    NASA Astrophysics Data System (ADS)

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

    2011-08-01

    Using published data for four molecularly doped polymers, which exhibit flat plateaus on the time-of-flight transients, we compared theoretical curves with experimental ones. The numerical calculations as well as parameter values were based on the Gaussian disorder model. In no case were flat plateaus predicted to appear. According to theory carrier transit should proceed in the non-equilibrium regime. We saw close agreement for the transit times in weakly polar polymers even at high fields but only at elevated temperatures, while in highly polar polymers similar agreement occurred only at low fields. In addition, the Gaussian disorder model does not account for the current shape universality (regarding field variation) frequently observed experimentally in polar molecularly doped polymers.

  15. Hybrid Modulation-Doping of Solution-Processed Ultrathin Layers of ZnO Using Molecular Dopants.

    PubMed

    Schießl, Stefan P; Faber, Hendrik; Lin, Yen-Hung; Rossbauer, Stephan; Wang, Qingxiao; Zhao, Kui; Amassian, Aram; Zaumseil, Jana; Anthopoulos, Thomas D

    2016-05-01

    An alternative doping approach that exploits the use of organic donor/acceptor molecules for the effective tuning of the free electron concentration in quasi-2D ZnO transistor channel layers is reported. The method relies on the deposition of molecular dopants/formulations directly onto the ultrathin ZnO channels. Through careful choice of materials combinations, electron transfer from the dopant molecule to ZnO and vice versa is demonstrated. PMID:26437002

  16. Non-dispersive carrier transport in molecularly doped polymers and the convection-diffusion equation

    NASA Astrophysics Data System (ADS)

    Tyutnev, A. P.; Parris, P. E.; Saenko, V. S.

    2015-08-01

    We reinvestigate the applicability of the concept of trap-free carrier transport in molecularly doped polymers and the possibility of realistically describing time-of-flight (TOF) current transients in these materials using the classical convection-diffusion equation (CDE). The problem is treated as rigorously as possible using boundary conditions appropriate to conventional time of flight experiments. Two types of pulsed carrier generation are considered. In addition to the traditional case of surface excitation, we also consider the case where carrier generation is spatially uniform. In our analysis, the front electrode is treated as a reflecting boundary, while the counter electrode is assumed to act either as a neutral contact (not disturbing the current flow) or as an absorbing boundary at which the carrier concentration vanishes. As expected, at low fields transient currents exhibit unusual behavior, as diffusion currents overwhelm drift currents to such an extent that it becomes impossible to determine transit times (and hence, carrier mobilities). At high fields, computed transients are more like those typically observed, with well-defined plateaus and sharp transit times. Careful analysis, however, reveals that the non-dispersive picture, and predictions of the CDE contradict both experiment and existing disorder-based theories in important ways, and that the CDE should be applied rather cautiously, and even then only for engineering purposes.

  17. A solution-doped small molecule hole transport layer for efficient ITO-free organic solar cells (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Bormann, Ludwig; Selzer, Franz; Leo, Karl; Mueller-Meskamp, Lars

    2015-10-01

    Indium-tin-oxide-free (ITO-free) organic solar cells are an important, emerging research field because ITO transparent electrodes are a bottleneck for cheap large area devices on flexible substrates. Among highly conductive PEDOT:PSS and metal grids, percolation networks made of silver nanowires (AgNW) with a diameter in the nanoscale show a huge potential due to easy processing (e.g. spray coating), high aspect ratios and excellent electrical and optical properties like 15 Ohm/sq with a transmission of 83.5 % including the substrate. However, the inherent surface roughness of the AgNW film impedes the implementation as bottom electrode in organic devices, especially fully vacuum deposited ones, where often shunts are obtained. Here, we report about the solution processing of a small molecule hole transport layer (s-HTL) comprising N,N'-((Diphenyl-N,N'-bis)9,9,-dimethyl-fluoren-2-yl)-benzidine (BF-DPB, host material) and the proprietary NDP9 (p-dopant) deposited from tetrahydrofuran (THF) as non-halogenated, "green" solvent. We show, that the doping process already takes place in solution and that conductivities, achieved with this process at high doping efficiencies (4 * 10^-4 S/cm at 10 wt% doping concentration), are comparable to thermal co-evaporation of BF-DPB:NDP9 under high vacuum, which is the proven deposition method for doped small molecule films. Applying this s-HTL to AgNW films leads to well smoothened electrodes, ready for application in organic devices. Vacuum-deposited organic p-i-n solar cells with DCV2-5T-Me(3:3):C60 as active layer show a power conversion efficiency of 4.4% and 3.7% on AgNW electrode with 35nm and 90 nm wire diameter, compared to 4.1% on ITO with the s-HTL.

  18. Small molecule recognition of mephedrone using an anthracene molecular clip.

    PubMed

    Kellett, Kathryn; Broome, J Hugh; Zloh, Mire; Kirton, Stewart B; Fergus, Suzanne; Gerhard, Ute; Stair, Jacqueline L; Wallace, Karl J

    2016-06-14

    An anthracene molecular probe has been synthesised and shown to target mephedrone, a stimulant drug from the cathinone class of new psychoactive substances (NPS). A protocol has been developed to detect mephedrone via the probe using NMR spectroscopy in a simulated street sample containing two of the most common cutting agents, benzocaine and caffeine. PMID:27198990

  19. 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).

  20. 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.

  1. 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.

  2. 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. PMID:26226050

  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. Molecular beam epitaxial growth of intermediate-band materials based on GaAs:N δ-doped superlattices

    NASA Astrophysics Data System (ADS)

    Suzuki, Tomoya; Osada, Kazuki; Yagi, Shuhei; Naitoh, Shunya; Shoji, Yasushi; Hijikata, Yasuto; Okada, Yoshitaka; Yaguchi, Hiroyuki

    2015-08-01

    We fabricated GaAs:N δ-doped superlattices (SLs) by molecular beam epitaxy and investigated their potential as an intermediate-band photoabsorber in high-efficiency solar cells. The N area concentration in a N δ-doped layer was well controlled by adjusting the fabrication conditions, and the SLs with the average N composition of up to 1.5% were obtained. The SL minibands related to the N-induced E+ and E- conduction subbands were formed with well-separated bottom energies of up to 0.4 eV, indicating the suitability of this material system for use in intermediate-band solar cells. A two-step photoabsorption process in a solar cell with the SL absorber was successfully demonstrated through external quantum efficiency measurements under additional infrared illumination at room temperature.

  5. 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. PMID:26808586

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

    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.

  7. 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.

  8. 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

  9. 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

  10. Molecular call and response: the physiology of bacterial small RNAs

    PubMed Central

    Richards, Gregory R.; Vanderpool, Carin K.

    2011-01-01

    The vital role of bacterial small RNAs (sRNAs) in cellular regulation is now well-established. Although many diverse mechanisms by which sRNAs effect changes in gene expression have been thoroughly described, comparatively less is known about their biological roles and effects on cell physiology. Nevertheless, for some sRNAs, insight has been gained into the intricate regulatory interplay that is required to sense external environmental and internal metabolic cues and turn them into physiological outcomes. Here, we review examples of regulation by selected sRNAs, emphasizing signals and regulators required for sRNA expression, sRNA regulatory targets, and the resulting consequences for the cell. We highlight sRNAs involved in regulation of the processes of iron homeostasis (RyhB, PrrF, and FsrA) and carbon metabolism (Spot 42, CyaR, and SgrS). PMID:21843668

  11. Molecular call and response: the physiology of bacterial small RNAs.

    PubMed

    Richards, Gregory R; Vanderpool, Carin K

    2011-10-01

    The vital role of bacterial small RNAs (sRNAs) in cellular regulation is now well-established. Although many diverse mechanisms by which sRNAs bring about changes in gene expression have been thoroughly described, comparatively less is known about their biological roles and effects on cell physiology. Nevertheless, for some sRNAs, insight has been gained into the intricate regulatory interplay that is required to sense external environmental and internal metabolic cues and turn them into physiological outcomes. Here, we review examples of regulation by selected sRNAs, emphasizing signals and regulators required for sRNA expression, sRNA regulatory targets, and the resulting consequences for the cell. We highlight sRNAs involved in regulation of the processes of iron homeostasis (RyhB, PrrF, and FsrA) and carbon metabolism (Spot 42, CyaR, and SgrS). PMID:21843668

  12. Evolution in the charge injection efficiency of evaporated Au contacts on a molecularly doped polymer

    NASA Astrophysics Data System (ADS)

    Ioannidis, Andronique; Facci, John S.; Abkowitz, Martin A.

    1998-08-01

    Injection efficiency from evaporated Au contacts on a molecularly doped polymer (MDP) system has been previously observed to evolve from blocking to ohmic over time. In the present article this contact forming phenomenon is analyzed in detail. The initially blocking nature of the Au contact is in contrast with that expected from the relative workfunctions of Au and of the polymer which suggest Au should inject holes efficiently. It is also in apparent contrast to a differently prepared interface of the same materials. The phenomenon is not unique to this interface, having been confirmed also for evaporated Ag and mechanically made liquid Hg contacts on the same MDP. The MDP is a disordered solid state solution of electroactive triarylamine hole transporting TPD molecules in a polycarbonate matrix. The trap-free hole-transport MDP provides a model system for the study of metal/polymer interfaces by enabling the use of a recently developed technique that gives a quantitative measure of contact injection efficiency. The technique combines field-dependent steady state injection current measurements at a contact under test with time-of-flight (TOF) mobility measurements made on the same sample. In the present case, MDP films were prepared with two top vapor-deposited contacts, one of Au (test contact) and one of Al (for TOF), and a bottom carbon-loaded polymer electrode which is known to be ohmic for hole injection. The samples were aged at various temperatures below the glass transition of the MDP (85 °C) and the evolution of current versus field and capacitance versus frequency behaviors are followed in detail over time and analyzed. Control measurements ensure that the evolution of the electrical properties is due to the Au/polymer interface behavior and not the bulk. All evaporated Au contacts eventually achieved ohmic injection. The evaporated Au/MDP interface was also investigated by transmission electron microscopy as a function of time and showed no evidence of

  13. 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.

  14. Effects of Dopant Concentration on the Mobilities of Molecularly Doped Polymers

    NASA Astrophysics Data System (ADS)

    Gruenbaum, W. T.; Lin, L.-B.; Magin, E. H.; Borsenberger, P. M.

    1997-12-01

    Hole mobilities have been measured for poly(styrene) (PS) doped with triphenylmethane (TPM) and triarylamine (TAA) derivatives with the same dipole moment. The results are described by a formalism based on disorder. According to the formalism, charge transport occurs by hopping through a manifold of localized states that are distributed in energy. The key parameter of the formalism is the width of the hopping site energies. For TPM doped PS, the widths decrease with increasing dilution while for TAA doped PS, the widths increase with dilution. The widths are described by a model based on dipolar disorder. The model is based on the assumption that the total width is comprised of a dipolar component and a van der Waals component. The selection of dopant molecules with the same dipole moment provides a method by which the van der Waals component can be determined from an analysis of the total widths of both. For TPM doped PS, the van der Waals component is constant while for TAA doped PS the van der Waals component increases with increasing dilution. The difference is described by a charge delocalization argument.

  15. Ionic conductivity in Gd-doped CeO2: Ab initio color-diffusion nonequilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Nilsson, Johan O.; Vekilova, Olga Yu.; Hellman, Olle; Klarbring, Johan; Simak, Sergei I.; Skorodumova, Natalia V.

    2016-01-01

    A first-principles nonequilibrium molecular dynamics (NEMD) study employing the color-diffusion algorithm has been conducted to obtain the bulk ionic conductivity and the diffusion constant of gadolinium-doped cerium oxide (GDC) in the 850-1150 K temperature range. Being a slow process, ionic diffusion in solids usually requires simulation times that are prohibitively long for ab initio equilibrium molecular dynamics. The use of the color-diffusion algorithm allowed us to substantially speed up the oxygen-ion diffusion. The key parameters of the method, such as field direction and strength as well as color-charge distribution, have been investigated and their optimized values for the considered system have been determined. The calculated ionic conductivity and diffusion constants are in good agreement with available experimental data.

  16. Electron beam evaporated carbon doping of InGaAs layers grown by gas source molecular beam epitaxy

    SciTech Connect

    Salokatve, A.; Toivonen, M.; Asonen, H.; Pessa, M.; Likonen, J.

    1996-12-31

    The authors have studied carbon doping of GaInAs grown by gas-source molecular beam epitaxy. Graphite was used as a source material for carbon evaporation. GaInAs was studied due to its importance as a base layer in InP-based heterojunction bipolar transistors. They show that useful p-type acceptor concentrations can be achieved by evaporation from graphite source for GaInAs grown by gas-source molecular beam epitaxy. Secondary ion mass spectroscopy and Van der Pauw Hall measurements were used to characterize the carbon and net acceptor concentrations of their GaInAs layers. The effect of rapid thermal annealing on acceptor concentrations and Hall mobilities was also studied.

  17. 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.

  18. Molecular stacking character and charge transport properties of tetrabenzoheptacenes derivatives: the effects of nitrogen doping and phenyl substitution.

    PubMed

    Guan, Lin; Wang, Wenliang; Shao, Rong; Liu, Fengyi; Yin, Shiwei

    2015-05-01

    The nitrogen doping and phenyl substitution effects on the geometries, molecular stacking character, electronic, and charge transport properties of tetrabenzoheptacene (TTBH) have been investigated by means of density functional theory (DFT) calculation and incoherent charge hopping model. Our results indicate that the nitrogen doping (TTH) at the 6,8,15,17 positions improves its stability in air and the ability of electron injection and in the meantime slightly changes the molecular stacking due to the C-H···N interaction. For both TTBH and TTH, large hole transport mobility (μh) and electron transport mobility (μe), which are on the same order of magnitude, are given rise by their dense displaced π-stacking in crystal. Comparatively, the phenyl substitution (Ph-TTBH) at the 6,8,15,17 positions adopts a non-planar conformation, adverse to close packing and therefore leads to smaller electron/hole transport mobility (μ) than those of TTBH and TTH. The calculations suggest TTBH and TTH are promising candidates for excellent ambipolar OFET materials. PMID:25910880

  19. Permeability of the small intestine to substances of different molecular weight

    PubMed Central

    Loehry, C. A.; Axon, A. T. R.; Hilton, P. J.; Hider, R. C.; Creamer, B.

    1970-01-01

    The permeability of the rabbit small intestine has been studied by measuring the plasma clearances of water-soluble molecules over the molecular weight range 60-33,000. An inverse relationship has been demonstrated between permeability and molecular weight. The significance of these findings in relation to current concepts of the `pore hypotheses' is discussed, and the possible physiological and pathological implications are considered. PMID:5430371

  20. Scanning tunneling spectroscopy of small Ce-doped endohedral fullerenes on HOPG

    NASA Astrophysics Data System (ADS)

    Klingeler, R.; Breuer, C.; Wirth, I.; Blanchard, A.; Bechthold, P. S.; Neeb, M.; Eberhardt, W.

    2004-03-01

    We report about scanning tunneling spectroscopy (STS) on deposited cerium-doped endohedral fullerenes with ⩽60 carbon atoms, i.e. Ce@C n ( n=36, 44, 50, 60). The clusters have been produced in a laser vaporization source and mass-selected prior to soft-landing onto a highly oriented pyrolytic graphite (HOPG) substrate. The STS spectra of Ce@C 36 and Ce@C 44 reveal a metal-like density of states while the one of Ce@C 50 and Ce@C 60 on HOPG is semiconductor-like. The band gap observed for the two larger fullerenes is interpreted in terms of an on-site Coulomb repulsion within the framework of a Mott-Hubbard picture.

  1. 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

  2. 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.

  3. Efficiency enhancement in small molecular organic photovoltaic devices employing dual anode interfacial layers

    NASA Astrophysics Data System (ADS)

    Fleetham, Tyler; O'Brien, Barry; Mudrick, John P.; Xue, Jiangeng; Li, Jian

    2013-10-01

    We demonstrated enhanced efficiency in small molecule organic photovoltaic devices using dual organic interfacial layers of PEDOT:PSS followed by tetracene between the ITO anode and the organic donor material. The use of a small molecular templating layer, such as tetracene, proved to increase the molecular stacking of the subsequent phthalocyanine (Pc) based donor materials. Upon application in planar heterojunction devices of ZnPc and C60, an enhancement of over 80 percent in the donor contribution to the external quantum efficiency was observed attributed to the combination of exciton blocking by the higher band gap tetracene layer and enhanced exciton diffusion and charge transport resulting from the increased crystallinity.

  4. Small molecular weight protein-protein interaction antagonists: an insurmountable challenge?

    PubMed

    Dömling, Alexander

    2008-06-01

    Several years ago small molecular weight protein-protein interaction (PPI) antagonists were considered as the Mount Everest in drug discovery and generally regarded as too difficult to be targeted. However, recent industrial and academic research has produced a great number of new antagonists of diverse PPIs. This review structurally analyses small molecular weight PPI antagonists and their particular targets as well as tools to discover such compounds. Besides general discussions there will be a focus on the PPI p53/mdm2. PMID:18501203

  5. 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

  6. Molecular doping of regioregular poly(3-hexylthiophene) layers by 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane investigated by infrared spectroscopy and electrical measurements

    NASA Astrophysics Data System (ADS)

    Tadaki, Daisuke; Ma, Teng; Zhang, Jinyu; Iino, Shohei; Hirano-Iwata, Ayumi; Kimura, Yasuo; Niwano, Michio

    2015-09-01

    Molecular doping is a charge-transfer process intended to improve the performance of organic electronic devices such as organic transistors. We have investigated molecular doping of regioregular poly(3-hexylthiophene) (P3HT) layers by 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4-TCNQ) using infrared absorption spectroscopy in the multiple internal reflection geometry (MIR-IRAS) and conductivity measurements. IRAS data confirm that F4-TCNQ acts as an effective p-type dopant for P3HT; highly doped P3HT displayed an intense, broad absorption band due to polaron (“polaron band”) and a high carrier (hole) density which are indicative of the charge transfer between F4-TCNQ and P3HT. We demonstrate that the charge (hole) transferred from the dopant molecule is distributed along the P3HT polymer chain and spreads over at least 10 thiophene monomer units on the chain. From a comparison of the measured conductivity of F4-TCNQ-doped P3HT layers with the carrier density, we show that the carrier mobility is proportional to the concentration of carriers (holes), which suggests that F4-TCNQ doping induces the conformational change of P3HT polymer chains to enhance the mobility of holes in the films of the doped P3HTs.

  7. Molecular dynamic simulation of EuT -doped sodium borate glasses and their fluorescence spectra

    SciTech Connect

    Hirao, K.; Soga, N.

    1985-10-01

    A molecular dynamic simulation was performed for sodium borate glasses containing a small amount of Eu2O3 to investigate the local structures of cations in glass. A new potential V /SUB B-B/ in the form -A exp (-C(r - 0.239)S) was added to the regular modified Born-Mayer-Huggins-type potentials, /PHI/ /SUB B-B/ , /PHI/ /SUB B-O/ , and /PHI/ /SUB O-O/ , to account for the directional tendency of the borate network structure. With this potential added, both the radial distribution of sodium borate glasses observed by smallangle X-ray diffraction and the change in coordination number of boron with sodium content obtained by NMR agreed well with the simulation. The average coordination number of EuT ions in the simulated glasses varied from 7.5 to 8.6, depending on the composition of the host sodium borate glasses. The inhomogeneous line width of the VD0-XF2 emission peak also changed, depending on the sodium content, with a maximum at 18 mol % Na2O content; this result agrees well with experimental data obtained from laser-induced fluorescence spectra.

  8. Controlled current matching in small molecule organic tandem solar cells using doped spacer layers

    NASA Astrophysics Data System (ADS)

    Schueppel, Rico; Timmreck, Ronny; Allinger, Nikola; Mueller, Toni; Furno, Mauro; Uhrich, Christian; Leo, Karl; Riede, Moritz

    2010-02-01

    Current matching of the subcells is crucial to optimize the performance of tandem solar cells. Due to the thin film optics of organic solar cells, the position of the two subcells relative to the reflecting electrode becomes a very important issue. This is demonstrated for an indium tin oxide (ITO)/pin/pii/Al structure with thin intrinsic absorbing layers consisting of zinc-phthalocyanine and fullerene C60 and a metal-free lossless recombination contact between the subcells. By keeping the thickness of the absorbing layers constant and changing only the thickness of the inner p-doped transparent layer in 16 steps from 0to186nm, the distance of the ITO-sided subcell from the reflecting electrode (Al) is systematically varied. Thus, the p-doped layer works as an optical spacer between both subcells. The influence of its thickness on the thin film optics is shown in optical simulations and confirmed with current-voltage measurements. If both subcells are separated only by the recombination contact, they are positioned in the first interference maximum of the incident light and the currents of the individual subcells nearly matches. By increasing the spacer layer thickness, the ITO-sided subcell is moved to the first interference minimum, limiting the measured short circuit current density jsc of the tandem solar cell to about 1/2 of its initial value without spacer. At a spacer thickness of about 140nm, jsc recovers in the second interference maximum to nearly its original value. Within this series, an almost constant high fill factor of about 59% as well as a constant open circuit voltage of 1.06V is observed, showing that the Ohmic losses in the spacer are negligible. The power conversion efficiency of these devices reaches nearly 4% in the first and approximately 3.6% in the second interference maximum, respectively, in an outdoor test at 1sun. Furthermore, it is shown that for thicker absorber layers, an optimized current density cannot be reached in the first

  9. Molecular assembled self-doped polyaniline interlayer for application in polymer light-emitting diode.

    PubMed

    Yang, Chien-Hsin; Chih, Yi-Kai

    2006-10-01

    Self-doped polyaniline (SPANI) ultrathin films were prepared by using a self-assembly process consisting of a self-doping monomer (o-aminobenzenesulfonic acid, SAN) and aniline (AN). SAN-AN copolymerization and film formation were simultaneously performed in aqueous solution. An immersing self-assembly method was developed to build up a SPANI nanofilm on an ITO glass, providing a hole injection layer in a double-layer electroluminescence (EL) device ITO/SPANI nanofilm//MEH-PV//Ca/Al. This device produces an orange EL as compared with a single-layer EL device of ITO//MEH-PV//Ca/Al. A double-layer device demonstrates that a SPANI film is capable of transporting holes in a polymer light-emitting diode (PLED). PMID:17004799

  10. Dark spatial solitons in bulk azo-dye-doped polymer using photoinduced molecular reorientation

    SciTech Connect

    Bian Shaoping; Kuzyk, Mark G.

    2004-08-16

    We report the generation of dark spatial solitons in bulk Disperse Red 1 doped poly(methyl methacrylate) using photoinduced reorientation of azo-dye molecules. Planar solitions are formed when illuminated with a continuous-wave laser at intensities of the order of hundreds of miliwatts per square centimeter. The width of the soliton saturates to a minimum value at high intensity; and when the width of the initial dark notch is reduced, the equilibrium minimum width is unchanged.

  11. 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.

  12. A Novel Mechanism for Small Heat Shock Proteins to Function as Molecular Chaperones

    PubMed Central

    Zhang, Kaiming; Ezemaduka, Anastasia N.; Wang, Zhao; Hu, Hongli; Shi, Xiaodong; Liu, Chuang; Lu, Xinping; Fu, Xinmiao; Chang, Zengyi; Yin, Chang-Cheng

    2015-01-01

    Small heat shock proteins (sHSPs) are molecular chaperones ubiquitously present in all forms of life, but their function mechanisms remain controversial. Here we show by cryo-electron microscopy and single particle 3D reconstruction that, at the low temperatures (4–25°C), CeHSP17 (a sHSP from Caenorhabditis elegans) exists as a 24-subunit spherical oligomer with tetrahedral symmetry. Our studies demonstrate that CeHSP17 forms large sheet-like super-molecular assemblies (SMAs) at the high temperatures (45–60°C), and such SMAs are apparently the form that exhibits chaperone-like activity. Our findings suggest a novel molecular mechanism for sHSPs to function as molecular chaperones. PMID:25744691

  13. Current Concepts on the Molecular Pathology of Non-small Cell Lung Carcinoma

    PubMed Central

    Fujimoto, Junya; Wistuba, Ignacio I.

    2014-01-01

    Recent advances in the understanding of the complex biology of non-small cell lung carcinoma (NSCLC), particularly activation of oncogenes by mutation, translocation and amplification, have provided new treatment targets for this disease, and allowed the identification of subsets of NSCLC tumors, mostly with adenocarcinoma histology, having unique molecular profiles that can predict response to targeted therapy. The identification of a specific genetic and molecular targetable abnormalities using tumor tissue and cytology specimens followed by the administration of a specific inhibitor to the target, are the basis of personalized lung cancer treatment. In this new paradigm, the role of a precise pathology diagnosis of lung cancer and the proper handling of tissue and cytology samples for molecular testing is becoming increasingly important. These changes have posed multiple new challenges for pathologists to adequately integrate routine histopathology analysis and molecular testing into the clinical pathology practice for tumor diagnosis and subsequent selection of the most appropriate therapy. PMID:25239274

  14. 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

  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. Precipitation control and activation enhancement in boron-doped p+-BaSi2 films grown by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Khan, M. Ajmal; Nakamura, K.; Du, W.; Toko, K.; Usami, N.; Suemasu, T.

    2014-06-01

    Precipitation free boron (B)-doped as-grown p+-BaSi2 layer is essential for the BaSi2 p-n junction solar cells. In this article, B-doped p-BaSi2 layers were grown by molecular beam epitaxy on Si(111) substrates, and the influence of substrate growth temperature (TS) and B temperature (TB) in the Knudsen cell crucible were investigated on the formation of B precipitates and the activation efficiency. The hole concentration, p, reached 1.0 × 1019 cm-3 at room temperature for TS = 600 and TB = 1550 °C. However, the activation rate of B was only 0.1%. Furthermore, the B precipitates were observed by transmission electron microscopy (TEM). When the TS was raised to 650 °C and the TB was decreased to 1350 °C, the p reached 6.8 × 1019 cm-3, and the activation rate increased to more than 20%. No precipitation of B was also confirmed by TEM.

  17. 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.

  18. Effect of molecular weight on the physicochemical modifications induced in the UV laser ablation of doped polymers

    NASA Astrophysics Data System (ADS)

    Rebollar, E.; Bounos, G.; Oujja, M.; Georgiou, S.; Castillejo, M.

    2007-04-01

    This work investigates the effect of polymer molecular weight MW on the UV ablation of iodo-naphthalene- and iodo-phenanthrene-doped poly(methyl methacrylate) PMMA, and polystyrene PS films following irradiation at 248 nm. For irradiation at weakly absorbed wavelengths, the ablation threshold increases with increasing MW. However, at strongly absorbed wavelengths, the difference in the ablation thresholds is much smaller, or minimal. In parallel, bubble formation due to accumulation of gas produced by polymer and dopant decomposition differs depending on MW. For highly absorbing PS, the differences of behaviour show a less dramatic dependence on MW. These results are explained within the framework of the bulk photothermal model, according to which ejection requires that a critical number of bonds is broken. In all, they are of direct importance for the optimisation of laser processing schemes and applications and provide the first indication of explosive boiling in UV ablation of polymers.

  19. 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.

  20. 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.

  1. 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.

  2. 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

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

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

    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.

  4. 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.

  5. Charge transport in molecularly doped polymers at low dopant concentrations: simulation and experiment

    NASA Astrophysics Data System (ADS)

    Hartenstein, B.; Bässler, H.; Heun, S.; Borsenberger, P.; Van der Auweraer, M.; De Schryver, F. C.

    1995-02-01

    A new computational technique has been developed to simulate charge transport in dilute, energetically random, media. The results predict that in materials containing 15-20% hopping sites, the transition from field-assisted to field-saturated drift occurs within a field range of 10 5-10 6 V/cm, lower values referring to lower degrees of energetic disorder. Experimental results are reported for N,N'-diphenyl-N,N'-bis(3-methylphenyl)-[1,1'-biphenyl]-4,4'-diamine (TPD) and 5'-[4-[bis(4-methylphenyl)amino]-phenyl]-N,N,N',N'-tetrakis (4-ethylphenyl) [1,1':3',1″-terphenyl'-4,rt'-diamine (EFTP) doped in either a polycarbonate (PC) or poly(styrene) (PS). While TPD doped PS fulfills all criteria of disorder controlled hopping, a superposition of disorder and polaron effects has to be invoked for EFTP in both PC or PS, the latter resulting from coupling of the charge transfer process to a torsional mode of the dopant molecule. Criteria to separate disorder and polaron effects in experimental data are briefly outlined.

  6. 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

  7. 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

  8. 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

    2016-01-01

    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. 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

  10. 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

  11. 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.

  12. Effects of gallium doping on properties of a-plane ZnO films on r-plane sapphire substrates by plasma-assisted molecular beam epitaxy

    SciTech Connect

    Han, Seok Kyu; Lee, Hyo Sung; Lim, Dong Seok; Hong, Soon-Ku; Yoon, Nara; Oh, Dong-Cheol; Ahn, Byung Jun; Song, Jung-Hoon; Yao, Takafumi

    2011-05-15

    The authors report on the structural, optical, and electrical properties of Ga-doped a-plane (1120) ZnO films grown by plasma-assisted molecular beam epitaxy. Ga doping level was controlled by changing the Ga cell temperatures from 350 to 470 deg. C with an interval of 30 deg. C. With up to Ga cell temperatures of 440 deg. C, single crystalline Ga-doped a-plane ZnO films were grown; however, the sample with a Ga cell temperature of 470 deg. C showed polycrystalline features. The typical striated surface morphology normally observed from undoped ZnO films disappeared with Ga doping. ZnO films doped with Ga cell temperatures up to 440 deg. C did not show a significant change in full width at half maximum (FWHM) values of (1120) x-ray rocking curves by doping. The smallest FWHM values were 0.433 deg. ({phi}=90 deg.) and 0.522 deg. ({phi}=0 deg. ) for the sample with a Ga cell temperature of 350 deg. C. The polycrystalline ZnO film with excessive Ga doping at the Ga cell temperature of 470 deg. C showed significantly increased FWHM values. Hall measurements at room temperature (RT) revealed that electron concentration began to be saturated at the Ga cell temperature of 440 deg. C and electron mobility was drastically reduced at the Ga cell temperature of 470 deg. C. The carrier concentration of Ga-doped ZnO films were controlled from 7.2x10{sup 18} to 3.6x10{sup 20} cm{sup -3}. Anisotropic electrical properties (carrier concentration and Hall mobility) were observed in measurements by the van der Pauw method depending on the direction (c- or m-direction) for the undoped sample but not observed for the doped samples. RT photoluminescence (PL) spectra from the Ga-doped single crystalline ZnO films showed dominant near band edge (NBE) emissions with negligibly deep level emission. The NBE intensity in PL spectra increases with Ga doping.

  13. Mosaic small supernumerary marker chromosome 1 at amniocentesis: prenatal diagnosis, molecular genetic analysis and literature review.

    PubMed

    Chen, Chih-Ping; Chen, Ming; Su, Yi-Ning; Huang, Jian-Pei; Chern, Schu-Rern; Wu, Peih-Shan; Su, Jun-Wei; Chang, Shun-Ping; Chen, Yu-Ting; Lee, Chen-Chi; Chen, Li-Feng; Pan, Chen-Wen; Wang, Wayseen

    2013-10-15

    We present prenatal diagnosis and molecular cytogenetic analysis of mosaic small supernumerary marker chromosome 1 [sSMC(1)]. We review the literature of sSMC(1) at amniocentesis and chromosome 1p21.1-p12 duplication syndrome. We discuss the genotype-phenotype correlation of the involved genes of ALX3, RBM15, NTNG1, SLC25A24, GPSM2, TBX15 and NOTCH2 in this case. PMID:23933412

  14. Allele-Specific Behavior of Molecular Networks: Understanding Small-Molecule Drug Response in Yeast

    PubMed Central

    Li, Chunquan; Hao, Dapeng; Zhang, Shaojun; Zhou, Meng; Su, Fei; Chen, Xi; Zhi, Hui; Li, Xia

    2013-01-01

    The study of systems genetics is changing the way the genetic and molecular basis of phenotypic variation, such as disease susceptibility and drug response, is being analyzed. Moreover, systems genetics aids in the translation of insights from systems biology into genetics. The use of systems genetics enables greater attention to be focused on the potential impact of genetic perturbations on the molecular states of networks that in turn affects complex traits. In this study, we developed models to detect allele-specific perturbations on interactions, in which a genetic locus with alternative alleles exerted a differing influence on an interaction. We utilized the models to investigate the dynamic behavior of an integrated molecular network undergoing genetic perturbations in yeast. Our results revealed the complexity of regulatory relationships between genetic loci and networks, in which different genetic loci perturb specific network modules. In addition, significant within-module functional coherence was found. We then used the network perturbation model to elucidate the underlying molecular mechanisms of individual differences in response to 100 diverse small molecule drugs. As a result, we identified sub-networks in the integrated network that responded to variations in DNA associated with response to diverse compounds and were significantly enriched for known drug targets. Literature mining results provided strong independent evidence for the effectiveness of these genetic perturbing networks in the elucidation of small-molecule responses in yeast. PMID:23308257

  15. Small-Angle Scattering and Neutron Contrast Variation for Studying Bio-Molecular Complexes

    NASA Astrophysics Data System (ADS)

    Whitten, Andrew E.; Trewhella, Jill

    Structural molecular biology over the past several decades has progressed from studies of the individual proteins, subunits, and domains that accomplish specific biochemistry to seeking to understand the dynamic bio-molecular complexes and assemblies that are responsible for biological function. This progress has led to an expansion of the structural analysis “tool box” to include methods that complement the mainstay techniques of the field: X-ray crystallography, nuclear magnetic resonance (NMR), and cryo-electron microscopy. Small-angle scattering of X-rays or neutrons is one such complementary technique that provides information on the size and shape of scattering particles in solution. This low-resolution structural information can be a powerful complement to high-resolution structural data, especially for the study of bio-molecular interactions with ligands or each other. Further, exploitation of the different neutron-scattering properties of the stable isotopes of hydrogen (1H and 2H) can be used to enrich the information available from the small-angle scattering data, especially for bio-molecular complexes.

  16. 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.

  17. The expression pattern of small nucleolar and small Cajal body-specific RNAs characterizes distinct molecular subtypes of multiple myeloma

    PubMed Central

    Ronchetti, D; Todoerti, K; Tuana, G; Agnelli, L; Mosca, L; Lionetti, M; Fabris, S; Colapietro, P; Miozzo, M; Ferrarini, M; Tassone, P; Neri, A

    2012-01-01

    Small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs) are non-coding RNAs involved in the maturation of other RNA molecules and generally located in the introns of host genes. It is now emerging that altered sno/scaRNAs expression may have a pathological role in cancer. This study elucidates the patterns of sno/scaRNAs expression in multiple myeloma (MM) by profiling purified malignant plasma cells from 55 MMs, 8 secondary plasma cell leukemias (sPCLs) and 4 normal controls. Overall, a global sno/scaRNAs downregulation was found in MMs and, even more, in sPCLs compared with normal plasma cells. Whereas SCARNA22 resulted the only sno/scaRNA characterizing the translocation/cyclin D4 (TC4) MM, TC2 group displayed a distinct sno/scaRNA signature overexpressing members of SNORD115 and SNORD116 families located in a region finely regulated by an imprinting center at 15q11, which, however, resulted overall hypomethylated in MMs independently of the SNORD115 and SNORD116 expression levels. Finally, integrative analyses with available gene expression and genome-wide data revealed the occurrence of significant sno/scaRNAs/host genes co-expression and the putative influence of allelic imbalances on specific snoRNAs expression. Our data extend the current view of sno/scaRNAs deregulation in cancer and add novel information to the bio-molecular complexity of plasma cell dyscrasias. PMID:23178508

  18. Hole Trapping in Molecularly Doped Polymers: The Hoesterey-Letson Formalism

    NASA Astrophysics Data System (ADS)

    Borsenberger, P.; Gruenbaum, W.; Magin, E.; Schildkraut, D.; Visser, S.

    1999-01-01

    Hole trapping has been investigated in di-p-anisyl-p-tolylamine (DAT), tri-p-tolylamine (TTA), di-p-tolylphenylamine (DTP), and diphenyl-p-tolylamine (DPT) doped poly(styrene) containing different concentrations of tri-p-anislyamine (TAA). From oxidation potential measurements, TAA is a trap for DAT, TTA, DTP, and DPT with depths 0.07, 0.22, 0.27, and 0.34 eV, respectively. In such a way, it is possible to investigate the effect of trap depth using the same trap molecule. The mobilities decrease with increasing trap depth and concentration. For a TAA molar concentration of 10-2, the room temperature mobilities are suppressed by as much as four orders of magnitude. The results are compared to predictions of the Hoesterey-Letson formalism and discussed within the framework of the recent simulations of Wolf et al.. [Chem. Phys. 222 (1997) 259] and Borsenbergeret al.. (submitted to Chem. Phys.)

  19. 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.

  20. Hydrogen sulphide doping of GaAs and AlxGa1-xAs grown by molecular beam epitaxy (MBE)

    NASA Astrophysics Data System (ADS)

    Briones, F.; Golmayo, D.; González, L.; de Miguel, J. L.

    1985-03-01

    H2S gas has been used during molecular beam epitaxy (MBE) growth of GaAs and Al x Ga1- x As as sulphur vector for n-type doping. Doping efficiencies are less than 10-3 at usual growth temperatures, and are limited by an incorporation competitive surface process, probably 2Ga+H2S→Ga2S+H2. In AlxGa1- x As for x≧0.2 the doping efficiency is further reduced by carrier freeze-out at deep levels. Measured thermal activation energies depend on growth conditions and remain relatively low even up to the direct-indirect bandgap crossover for substrate temperatures in the 585 645 ‡C range.

  1. InP/InGaAs/InP DHBT structures with high carbon-doped base grown by gas source molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Teng, Teng; Xu, Anhuai; Ai, Likun; Sun, Hao; Qi, Ming

    2013-09-01

    A new InP/InGaAs/InP DHBT structure with high carbon (C)-doped base was optimized and grown successfully by gas source molecular beam epitaxy (GSMBE) in this work. The C-doping concentration is 3×1019 cm-3 with carrier mobility of 66.3 cm2/V s. Characteristics of C-doped InGaAs materials were investigated. High quality InP/InGaAs/InP DHBT structural materials were obtained. The InP/InGaAs/InP DHBT device with emitter area of 100×100 μm2 was fabricated. The open base breakdown voltage (VBCEO) of 4.2 V and current gain of 60 at VCE of 3.0 V were achieved. All these results prove the material is suitable for DHBT device fabrication.

  2. 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.

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

    NASA Astrophysics Data System (ADS)

    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.

  4. In situ doping control for growth of n p n Si/SiGe/Si heterojunction bipolar transistor by gas source molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Gao, F.; Huang, D. D.; Li, J. P.; Liu, C.

    2005-01-01

    N-p-n Si/SiGe/Si heterostructures have been grown by a disilane (Si 2H 6) gas and Ge solid sources molecular beam epitaxy system using phosphine (PH 3) and diborane (B 2H 6) as n- and p-type in situ doping sources, respectively. Adopting an in situ doping control technology, the influence of background B dopant on the growth of n-Si emitter layer was reduced, and an abrupt B dopant distribution from SiGe base to Si emitter layer was obtained. Besides, higher n-type doping in the surface region of emitter to reduce the emitter resist can be realized, and it did not result in the drop of growth rate of Si emitter layer in this technology.

  5. Amphoteric doping of Si in InAlAs/InGaAs/InP(311)A heterostructures grown by molecular-beam epitaxy

    SciTech Connect

    Li, X.; Wang, W.I.; Cho, A.Y.

    1993-05-01

    High-quality InAlAs/InGaAs/InP modulation-doped field effect transistor (MODFET) structures were grown using silicon as an n-type dopant on the (311)A orientation for the first time by the planar-doping technique in molecular-beam epitaxy. An electron mobility as high as 50 000 cm{sup 2}/V s with a sheet carrier concentration of 1.9x10{sup 12}/cm{sup 2} at 77 K is achieved. MODFETs with 1.2 {mu}m gate length exhibit an extrinsic transconductance of 400 mS/mm and a maximum drain current of 485 mA/mm. The results are comparable to that of MODFETs grown on (100) InP substrates. Our results point to the new possibility of making p-n multilayer structures with all-silicon doping. 11 refs., 5 figs.

  6. Molecular modelling on small molecular CDK2 inhibitors: an integrated approach using a combination of molecular docking, 3D-QSAR and pharmacophore modelling.

    PubMed

    Yuan, H; Liu, H; Tai, W; Wang, F; Zhang, Y; Yao, S; Ran, T; Lu, S; Ke, Z; Xiong, X; Xu, J; Chen, Y; Lu, T

    2013-10-01

    Cyclin-dependent kinase 2 (CDK2) has been identified as an important target for developing novel anticancer agents. Molecular docking, three-dimensional quantitative structure-activity relationship (3D-QSAR) and pharmacophore modelling were combined with the ultimate goal of studying the structure-activity relationship of CDK2 inhibitors. The comparative molecular similarity indices analysis (CoMSIA) model constructed based on a set of 3-aminopyrazole derivatives as CDK2 inhibitors gave statistically significant results (q (2) = 0.700; r (2) = 0.982). A HypoGen pharmacophore model, constructed using diverse CDK2 inhibitors, also showed significant statistics ([Formula: see text]Cost = 61.483; RMSD = 0.53; Correlation coefficient = 0.98). The small residues and error values between the estimated and experimental activities of the training and test set compounds proved their strong capability of activity prediction. The structural insights obtained from these two models were consistent with each other. The pharmacophore model summarized the important pharmacophoric features required for protein-ligand binding. The 3D contour maps in combination with the comprehensive pharmacophoric features helped to better interpret the structure-activity relationship. The results will be beneficial for the discovery and design of novel CDK2 inhibitors. The simplicity of this approach provides expansion to its applicability in optimizing other classes of small molecular CDK2 inhibitors. PMID:23941641

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

    PubMed

    Kim, Yu Jin; Park, Chan Eon

    2016-03-31

    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 that contain the alkylthio group and that does not. The improved performance of the -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. PMID:26987868

  8. Molecular transport and phase transition of polycrystalline ice doped with HCl and SO2 near its melting point

    NASA Astrophysics Data System (ADS)

    Lu, H.; McCartney, S.; Sadtchenko, V.

    2007-12-01

    HCl and SO2 are major trace gases in atmosphere, which greatly affects chemical properties of atmospheric ice particles. A particular interest to atmospheric science is the effects of impurities on molecular transport and phase transition at grain boundaries in polycrystalline ice. Effects of doped HCl and SO2 on transport and phase transition at grain boundary of 2-4 micrometer polycrystalline ice were studied using a novel technique - Fast Thermal Desorption Spectroscopy (FTDS) [1] in the temperature range from -2 to -20 deg. C. In these experiments, H2O/D2O/H2O sandwich-like polycrystalline ice films doped with HCl and SO2 were vapor- deposited on the surface of a thin filament positioned in a vacuum chamber and maintained initially at cryogenic temperatures. After the deposition, the temperature of the filament was rapidly raised to a value near ice melting point, thus, initiating rapids H/D exchange reaction at the interface of H2O and D2O layers. Diffusion controlled rate of isotopic exchange in the desorbing film was monitored with a sensitive mass-spectrometer making it possible to gain quantitative information of the extent of diffusion of chemical species along the grain boundaries in polycrystalline ice samples. Comparisons of the experimental results in pure and doped polycrystalline ice show that water self diffusivity at the grain boundaries is significantly enhanced (by at least an order of magnitude) in the presence of HCl or SO2. The strong, non- Arrhenius, dependence of the water self-diffusivity on temperature indicates that this is due to grain boundary premelting [2], which may occur at temperatures as low as 10 deg. below ice melting point. We will discuss implication of this and other results of our FTDS experiments to various environmental phenomena. References: 1. Haiping Lu, Stephanie A. McCartney, M. Chonde, D. Smyla, and Vlad Sadtchenko, Fast thermal desorption spectroscopy study of morphology and vaporization kinetics of polycrystalline

  9. 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.

  10. 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

  11. Molecular beam epitaxy (MBE) growth of rare earth doped gallium nitride for laser diode application

    NASA Astrophysics Data System (ADS)

    Park, Jeongho

    The goal of this dissertation is to demonstrate the visible laser emission from rare earth doped GaN grown on sapphire and silicon substrate. The research presented in this dissertation focused on exploration of RE's physics and laser characteristics and investigating site selective laser emission. In this study, the first visible (red) lasing emission from Eu-doped GaN thin films grown on sapphire substrates was demonstrated. The edge emission fulfills the requirements of stimulated emission properties: super-linear characteristic, spectrum line narrowing, polarization effect, lifetime reduction, and longitudinal modes in a Fabry-Perot cavity. The GaN:Eu active layer has low threshold (˜10kW/cm2) for the onset of lasing. The optical gain and loss are of the order of 50 and 20cm-1, respectively. Growth conditions are investigated for gain enhancement and loss reduction. To obtain the high gain and low loss active layer, N-rich growth conditions are required. Channel waveguide cavities result in 5x increases in gain value compared to planar waveguides. To utilize the performance and flexibility of silicon microelectronics, we used silicon (111) substrate, which incorporated several AlGaN and AIN thin films as buffer, strain compensation and bottom optical cladding layers. With this substrate, we developed the laser structure emitting visible wavelength. We have utilized Eu-doped GaN for the active medium within a structure consisting of a top cladding AlGaN layers grown by MBE on a Si substrate. Stimulated emission (SE) was obtained at room temperature from Eu3+ at 620nm, with a threshold of ˜117kW/cm 2. Values of modal gain and loss of ˜100 and 46 cm-1 were measured. This demonstration indicates that utilizing rare earths a range of lasers on Si can be obtained, covering the UV, visible and IR regions, thus enabling a significant expansion of optoelectronic and microelectronic integration. The dependence of optical modal gain and loss on GaN:Eu growth

  12. 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.

  13. 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.

  14. A new assisted molecular cycloaddition on boron doped silicon surfaces: a predictive DFT-D study.

    PubMed

    Boukari, Khaoula; Duverger, Eric; Stauffer, Louise; Sonnet, Philippe

    2014-06-28

    In the framework of the Density Functional Theory (DFT-D), we investigate the phthalocyanine (H2Pc) molecule adsorption on SiC(0001)3 × 3 and Si(111)√3 × √3R30°-B (SiB) surfaces, and particularly compare the involved molecular adsorptions. In the H2Pc-SiC(0001)3 × 3 system, the molecular adsorption can be ascribed to a [10+2] cycloaddition. The H2Pc-SiB system is considered in three cases: defectless SiB surface (denoted SiB-0D) and SiB surfaces presenting one or two boron defects (denoted SiB-1D and SiB-2D respectively). The SiB-0D surface is passivated by a charge transfer from the Si adatoms to the boron atoms and therefore no chemical bond between the molecule and the substrate is observed. A similar molecular adsorption as already evidenced in the H2Pc-SiC(0001)3 × 3 system is involved in the SiB-2D case. In the case of the SiB-1D surface, two Si-N bonds (Si1-N1 and Si2-N2) are observed. One of them, Si1-N1, is nearly similar to that found in the H2Pc-SiB-2D system, but the Si2-N2 bond is unexpected. The Bader charge analysis suggests that, in the presence of the H2Pc molecule, the boron atoms behave like an electron reservoir whose availability varies following the involved molecular adsorption process. In the SiB-1D case, charges are transferred from the substrate to the molecule, allowing the Si2-N2 bond formation. Such a kind of molecular adsorption, not yet observed, could be designed by "assisted pseudo cycloaddition". PMID:24817040

  15. Molecular chemisorption on passivated and defective boron doped silicon surfaces: a "forced" dative bond.

    PubMed

    Boukari, Khaoula; Duverger, Eric; Sonnet, Philippe

    2014-12-01

    We investigate the adsorption mechanism of a single trans 4-pyridylazobenzene molecule (denoted by PAB) on a doped boron Si(111)√3×√3R30° surface (denoted by SiB) with or without boron-defects, by means of density functional theory calculations. The semiempirical approach proposed by Grimme allows us to take the dispersion correction into account. The role of the van der Waals correction in the adsorption geometries and energies is presented. In particular, two adsorption configurations are electronically studied. In the first one, the molecule is parallel to the surface and interacts with the SiB surface via the -N=N- bond. In the presence of a boron-defect, a Si-N chemical bond between the molecule and the surface is then formed, while electrostatic or/and van der Waals interactions are observed in the defectless surface. In the second adsorption configuration, the molecule presents different orientations with respect to the surface and interacts via the nitrogen atom of the pyridyl part of the PAB molecule. If the molecule is perpendicular to the perfect SiB surface, the lone-pair electrons associated with the heterocyclic nitrogen atom fill the empty dangling bond of a silicon adatom via a dative bond. Finally, in the presence of one boron-defect, the possibility of a "forced" dative bond, corresponding to a chemical bond formation between the PAB molecule and the silicon electron occupied dangling bond, is emphasized. PMID:25318974

  16. Low-temperature hydrothermal synthesis of N-doped TiO2 from small-molecule amine systems and their photocatalytic activity.

    PubMed

    Bao, Nan; Niu, Jun-Jian; Li, Yuan; Wu, Guo-Lin; Yu, Xiao-Hong

    2013-01-01

    Nitrogen-doped TiO2 nanopowders have been successfully synthesized by a one-step hydrothennal route under soft-chemistry conditions (150 degrees, 8 h) without high-temperature calcination using seven different types of nitrogen dopants: methylamine, ethylamine, diethylamine, ethylenediamine, triethylamine, triethanolamine and ammonia. X-ray diffraction, transmission electron microscopy, ultraviolet-visible spectroscopy, X-ray photoelectron spectroscopy, N2 adsorption-desorption isothenns and Fourier transform infrared spectroscopy were used to analyse the as-synthesized TiO2 powders. The results indicated that nitrogen was doped effectively and the structure and morphology of the titania samples were strongly influenced by the nitrogen sources. Among the investigated nitrogen sources, the diethylamine system was clearly superior to the other small-molecule amine or ammonia systems due to the broad-spectrum response (between 400 and 700 nm) of the interstitial nitrogen-doped TiO2 nanopowders. The diethylamine N-doped TiO2 had the largest pore volume (0.39 ml x g(-1)) and showed a well-aligned anatase phase. The visible-light photocatalytic degradation of liquid X-3B used as a probe reaction demonstrated that the removal rate over the diethylamine material reached 99.7% in 90 min. PMID:24617053

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

    PubMed

    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 ++), FecB(B)FecB(B) 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

  18. 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

  19. Ultrasound Biomicroscopy in Small Animal Research: Applications in Molecular and Preclinical Imaging

    PubMed Central

    Greco, A.; Mancini, M.; Gargiulo, S.; Gramanzini, M.; Claudio, P. P.; Brunetti, A.; Salvatore, M.

    2012-01-01

    Ultrasound biomicroscopy (UBM) is a noninvasive multimodality technique that allows high-resolution imaging in mice. It is affordable, widely available, and portable. When it is coupled to Doppler ultrasound with color and power Doppler, it can be used to quantify blood flow and to image microcirculation as well as the response of tumor blood supply to cancer therapy. Target contrast ultrasound combines ultrasound with novel molecular targeted contrast agent to assess biological processes at molecular level. UBM is useful to investigate the growth and differentiation of tumors as well as to detect early molecular expression of cancer-related biomarkers in vivo and to monitor the effects of cancer therapies. It can be also used to visualize the embryological development of mice in uterus or to examine their cardiovascular development. The availability of real-time imaging of mice anatomy allows performing aspiration procedures under ultrasound guidance as well as the microinjection of cells, viruses, or other agents into precise locations. This paper will describe some basic principles of high-resolution imaging equipment, and the most important applications in molecular and preclinical imaging in small animal research. PMID:22163379

  20. Ultrasound biomicroscopy in small animal research: applications in molecular and preclinical imaging.

    PubMed

    Greco, A; Mancini, M; Gargiulo, S; Gramanzini, M; Claudio, P P; Brunetti, A; Salvatore, M

    2012-01-01

    Ultrasound biomicroscopy (UBM) is a noninvasive multimodality technique that allows high-resolution imaging in mice. It is affordable, widely available, and portable. When it is coupled to Doppler ultrasound with color and power Doppler, it can be used to quantify blood flow and to image microcirculation as well as the response of tumor blood supply to cancer therapy. Target contrast ultrasound combines ultrasound with novel molecular targeted contrast agent to assess biological processes at molecular level. UBM is useful to investigate the growth and differentiation of tumors as well as to detect early molecular expression of cancer-related biomarkers in vivo and to monitor the effects of cancer therapies. It can be also used to visualize the embryological development of mice in uterus or to examine their cardiovascular development. The availability of real-time imaging of mice anatomy allows performing aspiration procedures under ultrasound guidance as well as the microinjection of cells, viruses, or other agents into precise locations. This paper will describe some basic principles of high-resolution imaging equipment, and the most important applications in molecular and preclinical imaging in small animal research. PMID:22163379

  1. Screening Molecular Chaperones Similar to Small Heat Shock Proteins in Schizosaccharomyces pombe

    PubMed Central

    Han, Jiyoung; Kim, Kanghwa

    2015-01-01

    To screen molecular chaperones similar to small heat shock proteins (sHsps), but without α-crystalline domain, heat-stable proteins from Schizosaccharomyces pombe were analyzed by 2-dimensional electrophoresis and matrix assisted laser desorption/ionization time-of-flight mass spectrometry. Sixteen proteins were identified, and four recombinant proteins, including cofilin, NTF2, pyridoxin biosynthesis protein (Snz1) and Wos2 that has an α-crystalline domain, were purified. Among these proteins, only Snz1 showed the anti-aggregation activity against thermal denaturation of citrate synthase. However, pre-heating of NTF2 and Wos2 at 70℃ for 30 min, efficiently prevented thermal aggregation of citrate synthase. These results indicate that Snz1 and NTF2 possess molecular chaperone activity similar to sHsps, even though there is no α-crystalline domain in their sequences. PMID:26539043

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. Growth, nucleation, and electrical properties of molecular beam epitaxially grown, As-doped Ge on Si substrates

    SciTech Connect

    Sheldon, P.; Yacobi, B.G.; Asher, S.E.; Jones, K.M.; Hafich, M.J.; Robinson, G.Y.

    1986-05-01

    Epitaxial Ge is grown on (100)Si substrates by molecular beam epitaxy (MBE). The effect of various MBE growth conditions on both the nucleation and morphology of Ge grown on Si is studied by Auger electron spectroscopy (AES), scanning electron microscopy (SEM), and reflection high-energy electron diffraction (RHEED). These studies indicate that, at the substrate temperatures examined (300--600 /sup 0/C), heteroepitaxy of Ge on Si favors three-dimensional growth, which is enhanced by both higher growth temperatures and substrate preparation techniques that leave residual surface contamination. Heavily doped n/sup +/ Ge layers are obtained using an elemental As source. The electrical properties of these films are evaluated by Hall--van der Pauw measurements. Growth temperatures of 250 /sup 0/C and optimum As:Ge flux ratios yield electron concentrations as high as 2.5 x 10/sup 20/ cm/sup -3/. Secondary ion mass spectroscopy (SIMS) and Hall effect data show that for As concentrations which exceed this optimum level, a decrease in both the electron concentration and drift mobility is observed, indicating the presence of electrically inactive As.

  8. 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.

  9. 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.

  10. Role of disorder in characterizing the ubiquitous temperature, concentration, and field dependencies of charge transport in molecularly doped polymers

    NASA Astrophysics Data System (ADS)

    Dunlap, David H.

    1995-08-01

    Over the last two decades, experimental investigations of the mobility of photo-injected charges in a wide variety of molecularly doped, pendant-, and main-chain polymers, and vapor deposited molecular glasses have shown that the mobility at high electric fields is universally described by the Poole-Frenkel law, micrometers equals exp(- (Delta) /kT) exp((gamma) (root)E). With few exceptions, the activation energy (Delta) is about 0.5eV, and the Poole-Frenkel factor (gamma) is a function of temperature which follows the empirical relation (gamma) equals B(1/kT - 1/kT0), where B approximately equals 4 X 10-4(e2Vcm)1/2. The remarkable similarity among experiments suggests a mechanism for these dependencies which is largely based on a feature these materials have in common--lack of a crystal structure. Each material consists of a highly disordered array of active molecules, which is believed in turn to give rise to large energetic fluctuations along the conduction pathways. Computer simulations of hopping transport on a disordered lattice have shown behavior in agreement with many aspects of experiment, lending support to the concept of a disorder-based mechanism. To increase our understanding of the high-field effects of disorder, we have developed a self-consistent algorithm with which the field dependence of the mobility in disordered systems may be calculated analytically. We examine the field dependence within this framework, and suggest that the (root)E- dependence may be understood when the theory of Scher and Montroll is applied to a length scale which the hopping matrix may be considered to be of a lower dimensionality.

  11. 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

  12. DNA translocation through small channels and pores from molecular models. Hydrodynamic, electrostatic, and hybridization considerations.

    NASA Astrophysics Data System (ADS)

    de Pablo, Juan

    2009-03-01

    The flow and translocation of long DNA molecules are of considerable applied and fundamental interest. Design of effective genomic devices requires control of molecular shape and positioning at the level of microns and nanometers, and understanding the manner in which DNA is packaged into small channels and cavities is of interest to biology and medicine. This presentation will present an overview of hierarchical models and computational approaches developed by our research group to investigate the effects of confinement, hydrodynamic interactions, and salt concentration, on the structure and properties of DNA, both at equilibrium and beyond equilibrium. The talk will include a discussion of coarse grain descriptions of the flow of DNA in microfluidic and nanofluidic channels over multiple length and time scales, and a discussion of emerging, detailed models that are capable of describing melting and rehybridization at the single nucleotide level, as well as the packaging of DNA into viral capsids and small pores.

  13. 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

  14. 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

  15. 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.

  16. Ultra-small Nd(3+)-doped nanoparticles as near-infrared luminescent biolabels of hemin in bacteria.

    PubMed

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

    2016-01-21

    Near-infrared (NIR) luminescent Nd(3+)-doped nanoparticles (NPs) have attracted considerable attention in bioimaging and biodetection. Here, we demonstrate sub-6 nm NaGdF4:Nd(3+),Fe(3+) 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 Nd(3+)-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 Nd(3+)-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 Nd(3+)-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 Nd(3+)-doped NPs as biolabels in bacteria would provide new opportunities for further unravelling the role of exogenous electron carriers in anaerobic digestion. PMID:26676549

  17. Pressure Denaturation of Staphylococcal Nuclease Studied by Neutron Small-Angle Scattering and Molecular Simulation

    PubMed Central

    Paliwal, Amit; Asthagiri, Dilipkumar; Bossev, Dobrin P.; Paulaitis, Michael E.

    2004-01-01

    We studied the pressure-induced folding/unfolding transition of staphylococcal nuclease (SN) over a pressure range of ∼1–3 kilobars at 25°C by small-angle neutron scattering and molecular dynamics simulations. We find that applying pressure leads to a twofold increase in the radius of gyration derived from the small-angle neutron scattering spectra, and P(r), the pair distance distribution function, broadens and shows a transition from a unimodal to a bimodal distribution as the protein unfolds. The results indicate that the globular structure of SN is retained across the folding/unfolding transition although this structure is less compact and elongated relative to the native structure. Pressure-induced unfolding is initiated in the molecular dynamics simulations by inserting water molecules into the protein interior and applying pressure. The P(r) calculated from these simulations likewise broadens and shows a similar unimodal-to-bimodal transition with increasing pressure. The simulations also reveal that the bimodal P(r) for the pressure-unfolded state arises as the protein expands and forms two subdomains that effectively diffuse apart during initial stages of unfolding. Hydrophobic contact maps derived from the simulations show that water insertions into the protein interior and the application of pressure together destabilize hydrophobic contacts between these two subdomains. The findings support a mechanism for the pressure-induced unfolding of SN in which water penetration into the hydrophobic core plays a central role. PMID:15347583

  18. Molecular characterisation of the small GTPase CDC42 in the ectomycorrhizal fungus Tuber borchii Vittad.

    PubMed

    Menotta, M; Amicucci, A; Basili, G; Rivero, F; Polidori, E; Sisti, D; Stocchi, V

    2007-01-01

    The small GTPase CDC42 is ubiquitously expressed in eukaryotes, where it participates in the regulation of the cytoskeleton and a wide range of cellular processes, including cytokinesis, gene expression, cell cycle progression, apoptosis, and tumorigenesis. As very little is known on the molecular level about mycorrhizal morphogenesis and development and these events depend on a tightly regulated reorganisation of the cytoskeleton network in filamentous fungi, we focused on the molecular characterisation of the cdc42 gene in Tuber borchii Vittad., an ascomycetous hypogeous fungus forming ectomycorrhizae. The entire gene was isolated from a T. borchii cDNA library and Southern blot analyses showed that only one copy of cdc42 is present in the T. borchii genome. The predicted amino acid sequence is very similar to those of other known small GTPases and the similar domain structures suggest a similar function. Real-time PCR analyses revealed an increased expression of Tbcdc42 during the phase preparative to the instauration of symbiosis, in particular after stimulation with root exudate extracts. Immunolocalisation experiments revealed an accumulation of CDC42 in the apical tips of the growing hyphae. When a constitutively active Tbcdc42 mutant was expressed in Saccharomyces cerevisiae, morphological changes typical of pseudohyphal growth were observed. Our results suggest a fundamental role of CDC42 in cell polarity development in T. borchii. PMID:17762910

  19. 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

  20. Molecular approaches to p- and n-nanoscale doping of Ge 1-ySn y semiconductors: Structural, electrical and transport properties

    NASA Astrophysics Data System (ADS)

    Xie, Junqi; Tolle, J.; D'Costa, V. R.; Weng, C.; Chizmeshya, A. V. G.; Menendez, J.; Kouvetakis, J.

    2009-08-01

    We report the development of practical doping protocols via designer molecular sources to create n- and p-type doped Ge 1-ySn y layers grown directly upon Si(1 0 0). These materials will have applications in the fabrication of advanced PIN devices that are intended to extend the infrared optical response beyond that of Ge by utilizing the Sn composition as an additional design parameter. Highly controlled and efficient n-doping of single-layer structures is achieved using custom built P(GeH 3) 3 and As(GeH 3) 3, precursors containing preformed Ge-As and Ge-P near-tetrahedral bonding arrangements compatible with the structure of the host Ge-Sn lattice. Facile substitution and complete activation of the P and As atoms at levels ˜10 17-10 19 cm -3 is obtained via in situ depositions at low temperatures (350 °C). Acceptor doping is readily achieved using conventional diborane yielding carrier concentrations between 10 17-10 19 cm -3 under similar growth conditions. Full activation of the as-grown dopant concentrations is demonstrated by combined SIMS and Hall experiments, and corroborated using a contactless spectroscopic ellipsometry approach. RTA processing of the samples leads to a significant increase in carrier mobility comparable to that of bulk Ge containing similar doping levels. The alloy scattering contribution appears to be negligible for electron carrier concentrations beyond 10 19 cm -3 in n-type samples and hole concentrations beyond 10 18 cm -3 in p-type samples. A comparative study using the classical lower-order hydrides PH 3 and AsH 3 produced n-doped films with carrier densities (up to 9 × 10 19 cm -3) similar to those afforded by P(GeH 3) 3 and As(GeH 3) 3. However, early results indicate that the simpler PH 3 and AsH 3 sources yield materials with inferior morphology and microstructure. Calculations of surface energetics using bond enthalpies suggest that the latter massive compounds bind to the surface via strong Ge-Ge bonds and likely act as

  1. 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

  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. Molecularly imprinted polymer doped with Hectorite for selective recognition of sinomenine hydrochloride.

    PubMed

    Zhang, W; Fu, H L; Li, X Y; Zhang, H; Wang, N; Li, W; Zhang, X X

    2016-01-01

    In this work, a new and facile method was introduced to prepare molecularly imprinted polymers (MIPs) based on nano clay hectorite (Hec) for sinomenine hydrochloride (SM) analysis. Hec was firstly dissolved in distilled water in order to swell adequately, followed by a common precipitation polymerization with SM as the template, methacrylic acid as monomer, ethylene glycol dimethacrylate as a crosslinker and 2,2-azobisisobutyronitrile as an initiator. Hec@SM-MIPs were characterized by Fourier transform infrared spectrometer, transmission electron microscopy, scanning electron microscopy, energy dispersive X-ray spectroscopy and X-ray diffraction. The maximum binding capacity of Hec@SM-MIPs, SM-MIPs and non-imprinted polymers (NIPs) (Hec@NIPs) was 57.4, 16.8 and 11.6 mg/g, respectively. The reason for this result may be that Hec@SM-MIPs have more binding sites and imprinted cavities for template molecule. Equilibrium data were described by the Langmuir and Freundlich isotherm models. The results showed that the Hec@SM-MIPs adsorption data correlated better with the Langmuir equation than the Freundlich equation under the studied concentration range. In vitro drug release experiment, Hec@SM-MIPs have a better ability to control SM release than SM-MIPs. Therefore, Hec@SM-MIPs were successfully applied to extraction of SM and used as the materials for drug delivery system. PMID:26614052

  4. 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.

  5. 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

  6. Dark electrochemistry and photoelectrochemistry of molecularly doped ion-exchange polymer blends

    SciTech Connect

    Crouch, A.M.; Ordonez, I.; Langford, C.H.; Lawrence, M.F.

    1988-10-20

    Ion-exchange polymer blends have been shown to produce modified electrode surfaces with high affinities for ionic reactants. The main feature of these blends is their spontaneous tendency to segregate into hydrophilic and hydrophobic domains. It is now believed that, when appropriate dye molecules are incorporated into such films and then illuminated, these systems operate under both ionic and dry electronic conduction mechanisms. The dark electrochemical measurements performed on an ion-exchange polymer containing ZnTPPS/sup 4 -/, ZnTPP, ZnPc(OPh)/sub 4/, or CuPcTS/sub 4-/, in contact with a Fe(CN)/sub 6//sup 3-/4-/ redox solution, show that the dye molecules within the film are immobile and that the high ion-exchange capability is maintained. The photoelectrochemical results obtained with the dye-loaded films indicate that electrons may be transferred from the photoexcited dyes to the polymer matrix and transported to the SnO/sub 2/ substrate electrode. The oxidized dye molecules are reduced by accepting electrons from the Fe(CN)/sub 6//sup 4 -/ species. The electronic conduction following charge separation is assumed to be intimately related to the ion-exchange polymer's tendency to segregate into hydrophilic and hydrophobic domains and also the excited-state energetics of the dye. A model which invokes the existence of large distributions of molecular ion states is proposed to explain the conduction of electrons through the hydrophobic domains of the polymer film and a detailed energy level diagram is presented to summarize the overall situation.

  7. Comparison of conventional molecularly doped polymeric photoreceptors and novel liquid-crystalline systems: charge injection and charge transport

    NASA Astrophysics Data System (ADS)

    Adam, Dieter; Swienty, Horst; Pinsler, Heinz; Lutz, Manfred; Bondkowski, Jens; Bleyl, Ingo; Haarer, Dietrich

    1997-10-01

    Charge-carrier transport and charge-carrier injection in mono-layers and two-layer photoreceptors with both "conventional", i. e., molecularly doped polymeric (MDP) transport layers and novel liquid-crystalline (LC) transport systems have been investigated by time-of-flight (TOF) experiments. As compared to the MDP materials, the LC model compounds showed a considerable potential towards high-speed xerographic application due to a charge-carrier mobility as high as 0,1 cm2/V s for the hexa(hexyltho)triphenylene (HHTT). In two-layer systems with MDP CTL, the formation of a sharp and well-defined interface between CGL and TL is impossible, a bulky intermediate layer is inevitable due to the wet-coating process. This results in a delayed charge-carrier injection due to space-charge effects originating from the intermediate layer. Two-layer systems with a LC CTL allow to investigate two novel aspects: (i) Since preparation of a LC CU is feasible in a solvent-free process, the formation of an ideal, i.e., sharp interface between CU and CGL is possible. Hence, charge-carrier injection from a well-defined interface can be studied. The results can be explained (i) by taking into account the different extrinsic charge-generation mechanisms for azo pigments (Azo) and phthalocyanine pigments and (ii) the different HOMO levels of Azo and phthalocyanine as compared to the HOMO-level of HHTT (ii) Due to the high charge carrier mobility, the LC CU is a "fast enough probe" to monitor time resolved injection phenomena.

  8. 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.

  9. Electrical properties of C-doped p-type GaP and GaPN grown by molecular beam epitaxy

    SciTech Connect

    Liu Zhengxin; Kawanami, Hitoshi; Sakata, Isao

    2010-01-18

    The electrical properties of C-doped p-type GaP and GaPN epilayers grown by molecular beam epitaxy using CBr{sub 4} as a doping source have been investigated. C is shown to be a relatively shallow acceptor both in GaP and GaPN, with the activation energy in the regions of 16-33 and 18-35 meV, respectively. GaP demonstrates ordinary conduction characteristics, whereas GaPN has a typical mixed conduction effect and the impurity conduction becomes dominant at low temperatures. It is conjectured that impurity conduction and ionized impurity scattering mechanisms in GaPN may be related to the inactivated C and N radicals.

  10. 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). PMID:26256825

  11. 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

  12. 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

  13. 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.

  14. Solution-Processed Small Molecular Organic Light-Emitting Devices with a Mixed Single Layer

    NASA Astrophysics Data System (ADS)

    Wang, Zhaokui; Naka, Shigeki; Okada, Hiroyuki

    2011-01-01

    We investigated the characteristics of solution-processed mixed-single-layer organic light-emitting devices (OLEDs) by mixing an electron injection material, a hole transport material, and a dopant material based on 5,6,11,12-tetraphenylnaphthacene (rubrene). The mixed-single-layer OLEDs showed better performance by optimizing the solution concentration and mixing ratio of organic materials. The performance was further improved by mixing chloroform (95 wt %) and toluene (5 wt %) as a solvent. The maximum luminance and power efficiency obtained were 12,400 cd/m2 and 1.1 lm/W, respectively. The mixed-single-layer OLEDs by solution process can be expected as an alternative route to the fabrication of small-molecular OLEDs with reduced cost of devices and avoiding the complexities of the co-evaporation of multiple organic materials in the vacuum deposition process.

  15. Small molecular phosphorescent organic light-emitting diodes using a spin-coated hole blocking layer

    NASA Astrophysics Data System (ADS)

    Zhao, Yan; Duan, Lian; Zhang, Deqiang; Hou, Liudong; Qiao, Juan; Wang, Liduo; Qiu, Yong

    2012-02-01

    Small molecular green phosphorescent organic light-emitting diodes (OLEDs) have been studied using a solution processed polyethyleneoxide (PEO) hole blocking layer (HBL) and a Cs2CO3/Al cathode. PEO is soluable in alcoholic solvents and allows the fabrication of multilayer OLEDs by successive spin-coating. The current efficiency of the optimized OLED with the PEO HBL increases from 18.8 cd/A to 32.1 cd/A, and the turn-on voltage reduces from 4.8 V to 3.4 V, compared with the device without the PEO HBL. Photovoltaic measurements indicate that the injection barrier for electron is reduced by inserting the PEO layer. X-ray photoelectron spectroscopy measurements further reveal that improvement in device performance is due to the partial penetration of Cs into the PEO layer.

  16. 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.

  17. Molecular conformations of triton X 114 in the presence of a small amount of water

    NASA Astrophysics Data System (ADS)

    Zheliaskova, A.; Blinc, R.; Zupancic, I.; Sepe, A.; Derzhanski, A.

    1989-04-01

    The viscosity of the binary system Triton X 114-water and the self-diffusion of the detergent molecules of Triton X 114 have been determined experimentally in the region of small water concentrations (0-10 wt% of water). The temperature was varied from 10 to 50°C in steps of 5°C. The self-diffusion was measured by means of the NMR method. The viscosity of the samples was determined by an efflux viscosimeter. A deviation of the experimentally obtained temperature trend of the viscosity and of the molecular mobility from the theoretical expected exponential dependence was found. This may be due to the building of dimers from the detergent molecules, whose number increases in the low temperature interval.

  18. Molecularly targeted therapies for advanced or metastatic non-small-cell lung carcinoma

    PubMed Central

    Bayraktar, Soley; Rocha-Lima, Caio M

    2013-01-01

    Non-small-cell lung cancer (NSCLC) remains the leading cause of cancer-related death in both men and women in the United States. Platinum-based doublet chemotherapy has been a standard for patients with advanced stage disease. Improvements in overall survival and quality of life have been modest. Improved knowledge of the aberrant molecular signaling pathways found in NSCLC has led to the development of biomarkers with associated targeted therapeutics, thus changing the treatment paradigm for many NSCLC patients. In this review, we present a summary of many of the currently investigated biologic targets in NSCLC, discuss their current clinical trial status, and also discuss the potential for development of other targeted agents. PMID:23696960

  19. 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

  20. Toxoplasma gondii in free-ranging wild small felids from Brazil: molecular detection and genotypic characterization.

    PubMed

    Cañón-Franco, W A; Araújo, F A P; López-Orozco, N; Jardim, M M A; Keid, L B; Dalla-Rosa, C; Cabral, A D; Pena, H F J; Gennari, S M

    2013-11-01

    Brazil harbors the largest number of wild Neotropical felid species, with ten of the twelve species recorded in the American continent. Although these animals are considered to be definitive hosts for Toxoplasma gondii, there are few descriptions of the parasite in these species. Here, we performed a molecular detection of T. gondii by amplification of the marker ITS-1 from tissue samples obtained from 90 free-ranging wild small Neotropical felids from Rio Grande do Sul - Brazil. Of the sampled animals, 34.4% (n=31) were positive including the species Puma yagouaroundi - jaguarondi (9/22), Leopardus geoffroyi - Geoffroy's cat (6/22), Leopardus tigrinus - oncilla (8/28), Leopardus wiedii - margay (6/10), Leopardus pardalis - ocelot (1/1) and Leopardus colocolo - Pampas cat (1/7). Toxoplasma DNA was detected with a frequency of 14.6% (63/433) in primary samples of tongue (16/56), brain (8/43), skeletal muscle (15/83), heart (7/63), diaphragm (3/56), vitreous humor (2/44), eye muscle (6/44) and eyeball (6/44). Multilocus PCR-RFLP genotyping of eleven small Neotropical felids using the molecular markers SAG1, 5'3'SAG2, alt. SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, Apico and CS3 allowed the partial characterization of eight genotypes. We fully characterized two new genotypes that have not been described previously in Brazil (Lw#31Tn from L. wiedii and Py#21Sm from P. yagouaroundi) and one genotype Py#56Br from P. yagouaroundi that has been described previously in isolates from cats, dogs and capybaras from São Paulo state. This study constitutes the first detection and genotypic characterization of T. gondii in free-ranging felids in Brazil, demonstrating the occurrence of the parasite in wild populations and suggesting its potential transmissibility to humans and other domestic and wild animals. PMID:23932730

  1. All-optical anatomical co-registration for molecular imaging of small animals using dynamic contrast

    NASA Astrophysics Data System (ADS)

    Hillman, Elizabeth M. C.; Moore, Anna

    2007-09-01

    Optical molecular imaging in small animals harnesses the power of highly specific and biocompatible contrast agents for drug development and disease research. However, the widespread adoption of in vivo optical imaging has been inhibited by its inability to clearly resolve and identify targeted internal organs. Optical tomography and combined X-ray and micro-computed tomography (micro-CT) approaches developed to address this problem are generally expensive, complex or incapable of true anatomical co-registration. Here, we present a remarkably simple all-optical method that can generate co-registered anatomical maps of a mouse's internal organs, while also acquiring in vivo molecular imaging data. The technique uses a time series of images acquired after injection of an inert dye. Differences in the dye's in vivo biodistribution dynamics allow precise delineation and identification of major organs. Such co-registered anatomical maps permit longitudinal organ identification irrespective of repositioning or weight gain, thereby promising greatly improved accuracy and versatility for studies of orthotopic disease, diagnostics and therapies.

  2. Development of molecularly targeted agents and immunotherapies in small cell lung cancer.

    PubMed

    Sharp, Adam; Bhosle, Jaishree; Abdelraouf, Fatma; Popat, Sanjay; O'Brien, Mary; Yap, Timothy A

    2016-06-01

    Small cell lung cancer (SCLC) is a smoking-induced malignancy with multiple toxin-associated mutations, which accounts for 15% of all lung cancers. It remains a clinical challenge with a rapid doubling time, early dissemination and poor prognosis. Despite multiple clinical trials in SCLC, platinum-based chemotherapy remains the mainstay of treatment in the first line advanced disease setting; good initial responses are nevertheless inevitably followed by disease relapse and survival ultimately remains poor. There are currently no molecularly targeted agents licenced for use in SCLC. Advances in sequencing the cancer genome and other high-throughput profiling technologies have identified aberrant pathways and mechanisms implicated in SCLC development and progression. Novel anti-tumour therapeutics that impact these putative targets are now being developed and investigated in SCLC. In this review, we discuss novel anti-tumour agents assessed in SCLC with reference to the complex molecular mechanisms implicated in SCLC development and progression. We focus on novel DNA damage response inhibitors, immune checkpoint modulators and antibody-drug conjugates that have shown promise in SCLC, and which may potentially transform treatment strategies in this disease. Finally, we envision the future management of SCLC and propose a biomarker-driven translational treatment paradigm for SCLC that incorporates next generation sequencing studies with patient tumours, circulating plasma DNA and functional imaging. Such modern strategies have the potential to transform the management and improve patient outcomes in SCLC. PMID:27060747

  3. Molecular dynamics of glycine ions in alanine doped TGS single crystal as probed by polarized laser raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Bajpai, P. K.; Verma, A. L.

    2012-10-01

    Polarized Raman spectra of pure and alanine doped tri-glycine sulfate (TGS) single crystals at 12 K in different scattering geometries are analyzed. Sub species modes due to three crystallographically distinguishable glycine ions G (I), G (II) and G (III) are assigned. It is observed that alanine doping does not change the crystalline field and acts as local perturbation only. The major changes due to doping are observed in the relative intensities of different modes; most of the modes associated with G (I) and SO42- ions show reversal behavior in relative intensity at high doping concentration. The observed spectral changes are analyzed in terms of reorientation of G (I) ions with sub species modes of G (II)/ G (III) following the reorientation due to complex hydrogen bonding network.

  4. Hydrogenation of undoped and nitrogen doped CdTe and ZnSe grown by molecular beam epitaxy

    SciTech Connect

    Hirsch, L.S.; Setzler, S.D.; Ptak, A.J.; Giles, N.C.; Myers, T.H.

    1998-12-31

    Hydrogen incorporation in both undoped and nitrogen-doped CdTe and ZnSe is investigated. Evidence for a strong nitrogen-hydrogen interaction is presented. Preliminary data indicate that the growth of CdTe and ZnSe under an atomic hydrogen flux results in a significant concentration of paramagnetic defects possibly accompanied by enhanced auto-doping from residual impurities.

  5. 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

  6. A modular molecular framework for utility in small-molecule solution-processed organic photovoltaic devices

    SciTech Connect

    Welch, Gregory C.; Perez, Louis A.; Hoven, Corey V.; Zhang, Yuan; Dang, Xuan-Dung; Sharenko, Alexander; Toney, Michael F.; Kramer, Edward J.; Nguyen, Thuc-Quyen; Bazan, Guillermo C.

    2011-07-22

    We report on the design, synthesis and characterization of light harvesting small molecules for use in solution-processed small molecule bulk heterojunction (SM-BHJ) solar cell devices. These molecular materials are based upon an acceptor/donor/acceptor (A/D/A) core with donor endcapping units. Utilization of a dithieno(3,2-b;2',3'-d)silole (DTS) donor and pyridal[2,1,3]thiadiazole (PT) acceptor leads to strong charge transfer characteristics, resulting in broad optical absorption spectra extending well beyond 700 nm. SM-BHJ solar cell devices fabricated with the specific example 5,5'-bis{7-(4-(5-hexylthiophen-2-yl)thiophen-2-yl)-[1,2,5]thiadiazolo[3,4-c]pyridine}-3,3'-di-2-ethylhexylsilylene-2,2'-bithiophene (6) as the donor and [6,6]-phenyl-C71-butyric acid methyl ester (PC71BM) as the acceptor component showed short circuit currents above -10 mA cm-2 and power conversion efficiencies (PCEs) over 3%. Thermal processing is a critical factor in obtaining favorable active layer morphologies and high PCE values. A combination of UV-visible spectroscopy, conductive and photo-conductive atomic force microscopies, dynamic secondary mass ion spectrometry (DSIMS), and grazing incident wide angle X-ray scattering (GIWAXS) experiments were carried out to characterize how thermal treatment influences the active layer structure and organization.

  7. Molecular breast imaging: advantages and limitations of a scintimammographic technique in patients with small breast tumors.

    PubMed

    O'Connor, Michael K; Phillips, Stephen W; Hruska, Carrie B; Rhodes, Deborah J; Collins, Douglas A

    2007-01-01

    Preliminary studies from our laboratory showed that molecular breast imaging (MBI) can reliably detect tumors <2 cm in diameter. This study extends our work to a larger patient population and examines the technical factors that influence the ability of MBI to detect small breast tumors. Following injection of 740 MBq Tc-99m sestamibi, MBI was performed on 100 patients scheduled for biopsy of a lesion suspicious for malignancy that measured <2 cm on mammography or sonography. Using a small field of view gamma camera, patients were imaged in the standard mammographic views using light pain-free compression. Subjective discomfort, breast thickness, the amount of breast tissue in the detector field of view, and breast counts per unit area were measured and recorded. Follow-up was obtained in 99 patients; 53 patients had 67 malignant tumors confirmed at surgery. Of these, 57 of 67 were detected by MBI (sensitivity 85%). Sensitivity was 29%, 86%, and 97% for tumors <5, 6-10, and > or =11 mm in diameter, respectively. In seven patients, MBI identified eight additional mammographically occult tumors. Of 47 patients with no evidence of cancer at biopsy or surgery, there were 36 true negative and 11 false positive scans on MBI. MBI has potential for the regular detection of malignant breast tumors less than 2 cm in diameter. Work in progress to optimize the imaging parameters and technique may further improve sensitivity and specificity. PMID:17214787

  8. 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

  9. The Molecular Nature of Very Small Embryonic-Like Stem Cells in Adult Tissues

    PubMed Central

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

    2014-01-01

    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

  10. 1,8-Naphthalimide-Based Planar Small Molecular Acceptor for Organic Solar Cells.

    PubMed

    Zhang, Jicheng; Zhang, Xuejuan; Xiao, Hongmei; Li, Guangwu; Liu, Yahui; Li, Cuihong; Huang, Hui; Chen, Xuebo; Bo, Zhishan

    2016-03-01

    Four small molecular acceptors (SM1-4) comprising a central benzene core, two thiophene bridges and two 1,8-naphthalimide (NI) terminal groups were designed and synthesized by direct C-H activation. SM1 has a planar chemical structure and forms H-aggregation as films. By attachment of different substituents on the central benzene ring, the dihedral angles between the two NI end groups of SM1-4 gradually increased, leading to a gradual decrease of planarity. SM1-4 all possess a high-lying LUMO level, matching with wide band gap (WBG) polymer donors which usually have a high-lying LUMO level. When used in OSCs, devices based on SM1 and WBG donor PCDTBT-C12 gave higher electron mobility, superior film morphology and better photovoltaic performance. After optimization, a PCE of 2.78% with a V(oc) of 1.04 V was achieved for SM1 based devices, which is among the highest PCEs with a V(oc) higher than 1 V. Our results have demonstrated that NI based planar small molecules are potential acceptors for WBG polymer based OSCs. PMID:26845638

  11. Predicting Molecular Targets for Small-Molecule Drugs with a Ligand-Based Interaction Fingerprint Approach.

    PubMed

    Cao, Ran; Wang, Yanli

    2016-06-20

    The computational prediction of molecular targets for small-molecule drugs remains a great challenge. Herein we describe a ligand-based interaction fingerprint (LIFt) approach for target prediction. Together with physics-based docking and sampling methods, we assessed the performance systematically by modeling the polypharmacology of 12 kinase inhibitors in three stages. First, we examined the capacity of this approach to differentiate true targets from false targets with the promiscuous binder staurosporine, based on native complex structures. Second, we performed large-scale profiling of kinase selectivity on the clinical drug sunitinib by means of computational simulation. Third, we extended the study beyond kinases by modeling the cross-inhibition of bromodomain-containing protein 4 (BRD4) for 10 well-established kinase inhibitors. On this basis, we made prospective predictions by exploring new kinase targets for the anticancer drug candidate TN-16, originally known as a colchicine site binder and microtubule disruptor. As a result, p38α was highlighted from a panel of 187 different kinases. Encouragingly, our prediction was validated by an in vitro kinase assay, which showed TN-16 as a low-micromolar p38α inhibitor. Collectively, our results suggest the promise of the LIFt approach in predicting potential targets for small-molecule drugs. PMID:26222196

  12. 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)

  13. 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

  14. 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.

  15. A high quantum efficiency in situ doped mid-wavelength infrared p-on-n homojunction superlattice detector grown by photoassisted molecular-beam epitaxy

    NASA Astrophysics Data System (ADS)

    Harris, K. A.; Myers, T. H.; Yanka, R. W.; Mohnkern, L. M.; Otsuka, N.

    1991-10-01

    HgTe/CdTe superlattices in infrared (IR) detector structures have been theoretically shown to allow for better control over cutoff wavelength, minimize diffusion currents, and greatly reduce band-to-band tunneling currents as compared with the corresponding HgCdTe alloy. However, the few HgTe/CdTe superlattice detectors that have been fabricated exhibit little or no quantum efficiency. In this paper, we report the first high quantum efficiency mid-wavelength infrared (MWIR) detectors based on HgTe/CdTe superlattices. This result is significant because it represents the first experimental verification that IR detectors with useful characteristics can in fact be fabricated from HgTe/CdTe superlattices. The MWIR detectors were fabricated from an in situ doped p-on-n MWIR homojunction superlattice epilayer grown by photoassisted molecular-beam epitaxy (PAMBE). This growth technique produces low defect growth of superlattice material, as is described in this paper. Our development of an extrinsic doping technology using indium and arsenic as the n-type and p-type dopants, respectively, led to the successful doping of the superlattice and is also discussed.

  16. Revisiting the Stӧber method: Design of nitrogen-doped porous carbon spheres from molecular precursors of different chemical structures.

    PubMed

    Tian, Hao; Liu, Jian; O'Donnell, Kane; Liu, Tingting; Liu, Xinmei; Yan, Zifeng; Liu, Shaomin; Jaroniec, Mietek

    2016-08-15

    Porous polymer resins and carbon spheres have been successfully prepared by an extended Stӧber method using phenol derivatives of different functionality. Herein, the Stӧber method is revised and used for the preparation of phenolic resin spheres from a series of hetero-atoms containing phenol derivatives (such as nitrophenol, aminophenol and halide-substituted phenols), which upon carbonization are converted to heteroatom-doped carbon spheres. The use of 4-amino-3-nitrophenol affords monodispersed carbon spheres with unprecedentedly high nitrogen content of about 11.9wt%. In this synthesis phenolic resin is initially formed by polymerizing formaldehyde with one of the aforementioned phenol derivatives, which acts as a resin precursor and source of heteroatoms to be doped. When amino group in aminophenol is in meta position the monodisperse phenolic resin and subsequently converted-doped carbon spheres are obtained. The resultant carbon spheres were examined as potential CO2 adsorbents and electrode materials for supercapacitors, reaching CO2 uptake of 89cm(3) STP/g (at 273K and 1.0bar), and the electrochemical capacitance of 127 F/g under basic conditions, respectively. This study provides some guidelines for design of carbon spheres by selecting phenolic resin precursors with desired molecular structures and functionalities for specific applications. PMID:27208436

  17. Toward the use of a molecularly imprinted polymer in doping analysis: selective preconcentration and analysis of testosterone and epitestosterone in human urine.

    PubMed

    Tse Sum Bui, Bernadette; Merlier, Franck; Haupt, Karsten

    2010-06-01

    A molecularly imprinted polymer (MIP), templated with methyltestosterone, has been synthesized for the cleanup of hydrolyzed urine samples for subsequent testosterone (T) quantification by LC-MS/MS. A concentration of 2 ng/mL testosterone could be quantified after a single step extraction on the MIP. The limit of detection and quantification with the criteria of a signal-to-noise ratio of 3 and 5 were 0.3 and 2 ng/mL, respectively. These values meet the conditions set by the World Anti-Doping Agency for the minimum required performance limits for doping controls, between 2 and 10 ng/mL. Epitestosterone (E) was also separated on this polymer and could be detected at concentrations down to 0.3 ng/mL. The quantification of T and E gives access to the determination of the T/E ratio, essential in doping analysis. Hence, our polymers can offer a more specific extraction procedure, resulting in increased sensitivity with limits of detection 10 times lower than the ones achieved by the standard SPE C(18) sorbents employed in official testing laboratories. PMID:20438053

  18. Investigating the dopaminergic synapse in vivo. II. Molecular imaging studies in small laboratory animals.

    PubMed

    Nikolaus, Susanne; Larisch, Rolf; Beu, Markus; Antke, Christina; Kley, Konstantin; Forutan, Farhad; Wirrwar, Andreas; Müller, Hans-Wilhelm

    2007-01-01

    Dopaminergic synaptic function may be assessed either at the presynaptic terminal or at the postsynaptic binding sites using molecular in vivo imaging methods. Apart from the density of binding sites, parameters such as alterations in dopamine synthesis, dopamine storage or dopamine release can be quantified either by application of specific radiotracers or by assessing the competition between the exogenous radioligand and endogenous dopamine. The performance of animal studies allows the induction of specific short-term or long-term synaptic conditions via pharmacological challenges or infliction of neurotoxic lesions. Therefore, small laboratory animals such as rats and mice have become invaluable models for a variety of human disorders. This article gives an overview of those small animal studies which have been performed so far on dopaminergic neurotransmission using in vivo imaging methods, with a special focus on the relevance of findings within the functional entity of the dopaminergic synapse. Taken together, in vivo investigations on animal models of Parkinson's disease showed decreases of dopamine storage, dopamine release and dopamine transporter binding, no alterations of dopamine synthesis and DA release, and either increases or no alterations of D2 receptor binding, while in vivo investigations of animal models of Huntington's disease. showed decreases of DAT and D1 receptor binding. For D2 receptor binding, both decreases and increases have been reported, dependent on the radioligand employed. Substances of abuse, such as alcohol, amphetamine and methylphenidate, led to an increase of dopamine release in striatal regions. This held for the acute application of substances to both healthy animals and animal models of drug abuse. Findings also showed that chronic application of cocaine induced long-term reductions of both D1 and D2 receptor binding, which disappeared after several weeks of withdrawal. Finally, preliminary results yielded the first

  19. Progress in the development of immunoanalytical methods incorporating recombinant antibodies to small molecular weight biotoxins.

    PubMed

    Kavanagh, Owen; Elliott, Christopher T; Campbell, Katrina

    2015-04-01

    Rapid immunoanalytical screening of food and environmental samples for small molecular weight (hapten) biotoxin contaminations requires the production of antibody reagents that possess the requisite sensitivity and specificity. To date animal-derived polyclonal (pAb) and monoclonal (mAb) antibodies have provided the binding element of the majority of these assays but recombinant antibodies (rAb) isolated from in vitro combinatorial phage display libraries are an exciting alternative due to (1) circumventing the need for experimental animals, (2) speed of production in commonly used in vitro expression systems and (3) subsequent molecular enhancement of binder performance. Short chain variable fragments (scFv) have been the most commonly employed rAb reagents for hapten biotoxin detection over the last two decades but antibody binding fragments (Fab) and single domain antibodies (sdAb) are increasing in popularity due to increased expression efficiency of functional binders and superior resistance to solvents. rAb-based immunochromatographic assays and surface plasmon resonance (SPR) biosensors have been reported to detect sub-regulatory levels of fungal (mycotoxins), marine (phycotoxins) and aquatic biotoxins in a wide range of food and environmental matrices, however this technology has yet to surpass the performances of the equivalent mAb- and pAb-based formats. As such the full potential of rAb technology in hapten biotoxin detection has yet to be achieved, but in time the inherent advantages of engineered rAb are set to provide the next generation of ultra-high performing binder reagents for the rapid and specific detection of hapten biotoxins. PMID:25716465

  20. Electrostatic Interactions Mediate Binding of Obscurin to Small Ankyrin 1: Biochemical and Molecular Modeling Studies

    PubMed Central

    Busby, Ben; Oashi, Taiji; Willis, Chris D.; Ackermann, Maegen A.; Kontrogianni-Konstantopoulos, Aikaterini; MacKerell, Alexander D.; Bloch, Robert J.

    2012-01-01

    Small ankyrin 1 (sAnk1; also Ank1.5) is an integral protein of the sarcoplasmic reticulum in skeletal and cardiac muscle cells, where it is thought to bind to the C-terminal region of obscurin, a large modular protein that surrounds the contractile apparatus. Using fusion proteins in vitro, in combination with site directed mutagenesis and surface plasmon resonance measurements, we previously showed that the binding site on sAnk1 for obscurin consists in part of six lysine and arginine residues. Here we show that four charged residues in the high affinity binding site on obscurin for sAnk1, between residues 6316-6345, consisting of three glutamates and a lysine, are necessary, but not sufficient, for this site on obscurin to bind with high affinity to sAnk1. We also identify specific complementary mutations in sAnk1 that can partially or completely compensate for the changes in binding caused by charge-switching mutations in obscurin. We used molecular modeling to develop structural models of residues 6322-6339 of obscurin bound to sAnk1. The models, based on a combination of Brownian and molecular dynamics simulations, predict that the binding site on sAnk1 for obscurin is organized as two ankyrin-like repeats, with the last α-helical segment oriented at an angle to the nearby helices, allowing lysine-6338 of obscurin to form an ionic interaction with aspartate-111 of sAnk1. This prediction was validated by double mutant cycle experiments. Our results are consistent with a model in which electrostatic interactions between specific pairs of side chains on obscurin and sAnk1 promote binding and complex formation. PMID:21333652

  1. 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.

  2. Long-Term Retention of Small, Volatile Molecular Species within Metallic Microcapsules.

    PubMed

    Hitchcock, James P; Tasker, Alison L; Baxter, Elaine A; Biggs, Simon; Cayre, Olivier J

    2015-07-15

    Encapsulation and full retention of small molecular weight active ingredients is a challenging task that remains unsolved by current technologies used in industry and academia. In particular, certain everyday product formulations provide difficult environments in which preventing active leakage through capsule walls is not feasible. For example, a continuous phase that can fully dissolve an encapsulated active will typically force full release over a fraction of the intended lifetime of a product. This is due to the inherent porosity of polymeric membranes typically used as capsule wall material in current technologies. In this study, we demonstrate a method for preventing undesired loss of encapsulated actives under these extreme conditions using a simple threestep process. Our developed methodology, which forms an impermeable metal film around polymer microcapsules, prevents loss of small, volatile oils within an ethanol continuous phase for at least 21 days while polymeric capsules lose their entire content in less than 30 min under the same conditions. Polymer shell-oil core microcapsules are produced using a well-known cosolvent extraction method to precipitate a polymeric shell around the oil core. Subsequently, metallic catalytic nanoparticles are physically adsorbed onto the microcapsule polymeric shells. Finally, this nanoparticle coating is used to catalyze the growth of a secondary metallic film. Specifically, this work shows that it is possible to coat polymeric microcapsules containing a model oil system or a typical fragrance oil with a continuous metal shell. It also shows that the coverage of nanoparticles on the capsule surface can be controlled, which is paramount for obtaining a continuous impermeable metal film. In addition, control over the metal shell thickness is demonstrated without altering the capability of the metal film to retain the encapsulated oils. PMID:26079485

  3. 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.

  4. Culture phenotypes and molecular characterization of Mycobacterium avium subsp. paratuberculosis isolates from small ruminants.

    PubMed

    Dimareli-Malli, Z; Mazaraki, K; Stevenson, K; Tsakos, P; Zdragas, A; Giantzi, V; Petridou, E; Heron, I; Vafeas, G

    2013-08-01

    In this study the suitability of different solid media was investigated for the isolation of Mycobacterium avium subsp. paratuberculosis (Map) in order to identify the optimum single or combination of media to permit the isolation of all strain types from small ruminants. A subset of these Map strains was then further characterized by molecular typing methods to assess the genetic diversity of Map strains in the study area (Northern Greece). Map strains were isolated from tissues and faeces of infected goats (n=52) and sheep (n=8) and were analysed for polymorphisms in IS1311 to classify the strain type as Type C or S. The study found that M7H11 supplemented with mycobactin j, OADC and new born calf serum (M7H11+Mj) is the best single choice of medium for the primary isolation of Map of both Type C and S from small ruminants. The combination of M7H11+Mj and Herrolds egg yolk medium supplemented with mycobactin j and sodium pyruvate allowed the detection of all Map isolates in this study. Nineteen Map isolates were characterised by pulsed-field gel electrophoresis and the isolates demonstrated significant genetic diversity. Twelve different SnaBI and 16 distinct SpeI profiles were detected of which 25 have not been described previously and are new profiles. The combination of both enzyme profiles gave 13 different multiplex profiles. Ten different multiplex profiles were detected in goats and three in sheep. One ovine isolate gave the same multiplex profile as a caprine isolate and two different profiles were found within a single goat herd. PMID:23587160

  5. Survivability of Silicon-Doped Diamond-Like Carbon Films in Energetic Atomic/Molecular Oxygen Beam Environments

    NASA Astrophysics Data System (ADS)

    Tagawa, Masahito; Kishida, Kazuhiro; Yokota, Kumiko; Matsumoto, Koji; Yoshigoe, Akitaka; Teraoka, Yuden; Zhang, Jianming; Minton, Timothy K.

    Volatile products were measured from two types of diamond-like carbon films under the hyperthermal atomic oxygen (AO) beam bombardment. It was clearly observed that CO and CO2 were formed at the conventional hydrogenated DLC surface when exposed to hyperthermal AO beam. Desorption rates of CO and CO2 are constant with AO fluence which reflects the constant erosion rate of the hydrogenated DLC. In contrast, Si-doped DLC shows decrease in amount of CO and CO2 with increasing AO fluence. Oxidation of Si atoms at the DLC surface was detected by X-ray photoelectron spectroscopy, confirming the formation of SiO2 film formed at the DLC surface that could prevent AO reaction with C atoms in DLC which leads to loss of DLC. Since a self-healing capability can be expected on Si-doped DLC, metal doping is a promising technology for space application of DLC.

  6. 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

  7. Doping dependence and anisotropy of minority electron mobility in molecular beam epitaxy-grown p type GaInP

    SciTech Connect

    Haegel, N. M.; Christian, T.; Norman, A. G.; Mascarenhas, A.; Scandrett, C.; Misra, Pranob; Liu, Ting; Sukiasyan, Arsen; Pickett, Evan; Yuen, Homan

    2014-11-17

    Direct imaging of minority electron transport via the spatially resolved recombination luminescence signature has been used to determine carrier diffusion lengths in GaInP as a function of doping. Minority electron mobility values are determined by performing time resolved photoluminescence measurements of carrier lifetime on the same samples. Values at 300 K vary from ∼2000 to 400 cm{sup 2}/V s and decrease with increasing doping. Anisotropic diffusion lengths and strongly polarized photoluminescence are observed, resulting from lateral composition modulation along the [110] direction. We report anisotropic mobility values associated with carrier transport parallel and perpendicular to the modulation direction.

  8. Magnetic field effects in singlet-polaron quenching in molecularly doped fluorescence organic light-emitting diodes

    NASA Astrophysics Data System (ADS)

    Xu, Kai; Ma, Dongge

    2014-08-01

    The magnetic field effects of electroluminescence (MEL) in 4-[dicyanomethylene]-2-t-butyl-6-(1,1,7,7-tetramethyljulolidyl-9-enyl)-4H-pyran(DCJTB) doped tri-(8-hydroxyquinoline)-aluminum (Alq3) based organic light-emitting diodes were investigated. A linear decrease in MEL with the increase of magnetic field was observed at high magnetic field (>20 mT) in this doping devices, which has been attributed to the singlet-polaron quenching effect. It was found that the singlet-polaron quenching is magnetic field dependent. Our results showed that singlet-polaron quenching commonly exists in fluorescence OLEDs and induces the linear decrease in MEL.

  9. Monitoring the Spatiotemporal Activities of miRNAs in Small Animal Models Using Molecular Imaging Modalities

    PubMed Central

    Baril, Patrick; Ezzine, Safia; Pichon, Chantal

    2015-01-01

    MicroRNAs (miRNAs) are a class of small non-coding RNAs that regulate gene expression by binding mRNA targets via sequence complementary inducing translational repression and/or mRNA degradation. A current challenge in the field of miRNA biology is to understand the functionality of miRNAs under physiopathological conditions. Recent evidence indicates that miRNA expression is more complex than simple regulation at the transcriptional level. MiRNAs undergo complex post-transcriptional regulations such miRNA processing, editing, accumulation and re-cycling within P-bodies. They are dynamically regulated and have a well-orchestrated spatiotemporal localization pattern. Real-time and spatio-temporal analyses of miRNA expression are difficult to evaluate and often underestimated. Therefore, important information connecting miRNA expression and function can be lost. Conventional miRNA profiling methods such as Northern blot, real-time PCR, microarray, in situ hybridization and deep sequencing continue to contribute to our knowledge of miRNA biology. However, these methods can seldom shed light on the spatiotemporal organization and function of miRNAs in real-time. Non-invasive molecular imaging methods have the potential to address these issues and are thus attracting increasing attention. This paper reviews the state-of-the-art of methods used to detect miRNAs and discusses their contribution in the emerging field of miRNA biology and therapy. PMID:25749473

  10. 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.

  11. Some tentative models of molecular motion applied to water in small reversed micelles

    SciTech Connect

    Llor, A.; Rigny, P.

    1986-11-26

    The molecular dynamics of water in small, swollen, reversed micelles of sodium bis(2-ethyl-1-hexyl)sulfosuccinate (AOT) in cyclohexane has been investigated using proton NMR relaxation methods. When the water content drops from 15 to 3 molecules per AOT molecule, the /sup 1/H NMR relaxation time T/sub 1/ is considerably reduced. This is due in part to slower motions of water molecules and also to the increased influence of external relaxation processes, such as the dipolar interactions with the surfactant protons. By progressive substitution of the micellized water by heavy water, the dipolar water-water effects have been distinguished from other relaxation processes. Using standard models of motion, this substitution has shown the water movements to be slower than in pure water by at most a factor of 5. This somewhat unusual result is in agreement with data from concentrated ionic solutions. The external relaxation effects displayed a frequency dependence which is typically induced by slow motions. Some dynamical models have been discussed to explain them, but the main effects seem to be induced by the dipole-dipole interaction with the protons of the AOT polar heads. The complex modulation of this interaction could not be described precisely, and a simplified model was used to deduce qualitative dynamical information from the experimental data. The water-polar head movements were then found to be in the range of 5 x 10/sup -10/ s.

  12. 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

  13. Predicting Adsorption Affinities of Small Molecules on Carbon Nanotubes Using Molecular Dynamics Simulation.

    PubMed

    Comer, Jeffrey; Chen, Ran; Poblete, Horacio; Vergara-Jaque, Ariela; Riviere, Jim E

    2015-12-22

    Computational techniques have the potential to accelerate the design and optimization of nanomaterials for applications such as drug delivery and contaminant removal; however, the success of such techniques requires reliable models of nanomaterial surfaces as well as accurate descriptions of their interactions with relevant solutes. In the present work, we evaluate the ability of selected models of naked and hydroxylated carbon nanotubes to predict adsorption equilibrium constants for about 30 small aromatic compounds with a variety of functional groups. The equilibrium constants determined using molecular dynamics coupled with free-energy calculation techniques are directly compared to those derived from experimental measurements. The calculations are highly predictive of the relative adsorption affinities of the compounds, with excellent correlation (r ≥ 0.9) between calculated and measured values of the logarithm of the adsorption equilibrium constant. Moreover, the agreement in absolute terms is also reasonable, with average errors of less than one decade. We also explore possible effects of surface loading, although we demonstrate that they are negligible for the experimental conditions considered. Given the degree of reliability demonstrated, we move on to employing the in silico techniques in the design of nanomaterials, using the optimization of adsorption affinity for the herbacide atrazine as an example. Our simulations suggest that, compared to other modifications of graphenic carbon, polyvinylpyrrolidone conjugation gives the highest affinity for atrazine-substantially greater than that of graphenic carbon alone-and may be useful as a nanomaterial for delivery or sequestration of atrazine. PMID:26506132

  14. XAV939, a small molecular inhibitor, provides neuroprotective effects on oligodentrocytes.

    PubMed

    Chen, Jing; Li, Jizhen; Miao, Zhigang; Xu, Xingshun; Liu, Chun-Feng

    2014-10-01

    White matter tracts are composed of axons and myelinating oligodendrocytes. Oligodendrocytes are the myelinating cells in the central nervous system that allow formation of myelin and saltatory nerve conduction. Cerebral white matter is highly vulnerable to ischemic injury in adults and neonates. White matter injury in newborn brains results in cerebral palsy and cognitive disability. In this study, we found that XAV939, a small-molecular inhibitor that stimulated β-catenin degradation by stabilizing axin, protected against serum and glucose deprivation (SGD)-induced cell death in oligodentrocyte cell line OLN-93 cells in a concentration-dependent manner. We further showed that XAV939 reduced caspase-3 and caspase-8 levels and increased the expression of phosphorylated Akt in SGD-induced OLN-93 cells. Our data demonstrate that XAV939 protects against neonatal hypoxic/ischemic injury. In summary, our results demonstrate that XAV939 confers neuroprotection against SGD-induced injury in OLN-93 cells via its antiapoptotic activity and the loss of oligodendrocytes and neurons in neonatal hypoxic/ischemic injury. PMID:24861203

  15. Sequential Molecular Changes during Multistage Pathogenesis of Small Peripheral Adenocarcinomas of the Lung

    PubMed Central

    Soh, Junichi; Toyooka, Shinichi; Ichihara, Shuji; Asano, Hiroaki; Kobayashi, Naruyuki; Suehisa, Hiroshi; Otani, Hiroki; Yamamoto, Hiromasa; Ichimura, Kouichi; Kiura, Katsuyuki; Gazdar, Adi F.; Date, Hiroshi

    2009-01-01

    Introduction We investigated EGFR and KRAS alterations among atypical adenomatous hyperplasia and small lung adenocarcinomas with bronchioloalveolar features to understand their role during multistage pathogenesis. Methods Sixty lesions measuring 2 cm or less were studied, including 38 noninvasive lesions (4 atypical adenomatous hyperplasias, 19 Noguchi type A and 15 type B) and 22 invasive lesions (type C) based on the World Health Organization classification and Noguchi’s criteria. EGFR and KRAS mutations were examined using PCR-based assays. EGFR copy number was evaluated using fluorescence in situ hybridization. Results EGFR and KRAS mutations were found in 26 (43.3%) and 5 (8.3%) lesions, respectively. Increased EGFR copy number status was identified in 10 lesions (16.7%), both mutant and wild type. EGFR or KRAS mutations were present in 39.5% and 7.9% (respectively) of noninvasive lesions and 50% or 9.1% (respectively) of invasive lesions. EGFR copy number was increased in 7.9% and 31.8% of noninvasive and invasive lesions (P = 0.029). Multivariate analysis revealed that increased EGFR copy number was the only significant factor to associate with invasive lesions (P = 0.035). Conclusions EGFR and KRAS mutations occur early during the multistage pathogenesis of peripheral lung adenocarcinomas. By contrast, increased EGFR copy number is a late event during tumor development and plays a role in the progression of lung adenocarcinoma independent of the initiating molecular events. PMID:18379350

  16. Ex vivo inhibition of Clostridium botulinum neurotoxin types B, C, E, and F by small molecular weight inhibitors.

    PubMed

    Montgomery, Vicki A; Ahmed, S Ashraf; Olson, Mark A; Mizanur, Rahman M; Stafford, Robert G; Roxas-Duncan, Virginia I; Smith, Leonard A

    2015-05-01

    Two small molecular weight inhibitors, compounds CB7969312 and CB7967495, that displayed inhibition of botulinum neurotoxin serotype A in a previous study, were evaluated for inhibition of botulinum neurotoxin serotypes B, C, E, and F. The small molecular weight inhibitors were assessed by molecular modeling, UPLC-based peptide cleavage assay; and an ex vivo assay, the mouse phrenic nerve - hemidiaphragm assay (MPNHDA). While both compounds were inhibitors of botulinum neurotoxin (BoNT) serotypes B, C, and F in the MPNHDA, compound CB7969312 was effective at lower molar concentrations than compound CB7967495. However, compound CB7967495 was significantly more effective at preventing BoNTE intoxication than compound CB7969312. In the UPLC-based peptide cleavage assay, CB7969312 was also more effective against LcC. Both compounds inhibited BoNTE, but not BoNTF, LcE, or LcF in the UPLC-based peptide cleavage assay. Molecular modeling studies predicted that both compounds would be effective inhibitors of BoNTs B, C, E, and F. But CB7967495 was predicted to be a more effective inhibitor of the four serotypes (B, C, E, and F) than CB7969312. This is the first report of a small molecular weight compound that inhibits serotypes B, C, E, and F in the ex vivo assay. PMID:25707753

  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. PMID:27116709

  18. 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.

  19. 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

  20. Photochemical processes in doped argon-neon core-shell clusters: the effect of cage size on the dissociation of molecular oxygen.

    PubMed

    Laarmann, T; Wabnitz, H; von Haeften, K; Möller, T

    2008-01-01

    The caging effect of the host environment on photochemical reactions of molecular oxygen is investigated using monochromatic synchrotron radiation and spectrally resolved fluorescence. Oxygen doped clusters are formed by coexpansion of argon and oxygen, by pickup of molecular oxygen or by multiple pickup of argon and oxygen by neon clusters. Sequential pickup provides radially ordered core-shell structures in which a central oxygen molecule is surrounded by argon layers of variable thickness inside large neon clusters. Pure argon and core-shell argon-neon clusters excited with approximately 12 eV monochromatic synchrotron radiation show strong fluorescence in the vacuum ultraviolet (vuv) spectral range. When the clusters are doped with O2, fluorescence in the visible (vis) spectral range is observed and the vuv radiation is found to be quenched. Energy-resolved vis fluorescence spectra show the 2 1Sigma+-->1 1Sigma+(ArO(1S)-->ArO(1D)) transition from argon oxide as well as the vibrational progression A '3Delta u(nu'=0)-->X 3Sigmag*(nu") of O2 indicating that molecular oxygen dissociates and occasionally recombines depending on the experimental conditions. Both the emission from ArO and O2 as well the vuv quenching by oxygen are found to depend on the excitation energy, providing evidence that the energy transfer from the photoexcited cluster to the embedded oxygen proceeds via the O2+ ground state. The O2+ decays via dissociative recombination and either reacts with Ar resulting in electronically excited ArO or it recombines to O2 within the Ar cage. Variation of the Ar layer thickness in O2-Ar-Ne core-shell clusters shows that a stable cage is formed by two solvation layers. PMID:18190199

  1. 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.

  2. Inhibition of non-small cell lung cancer (NSCLC) growth by a novel small molecular inhibitor of EGFR

    PubMed Central

    Fang, Yuanzhang; Vaughn, Amanda; Cai, Xiaopan; Xu, Leqin; Wan, Wei; Li, Zhenxi; Chen, Shijie; Yang, Xinghai; Wu, Song; Xiao, Jianru

    2015-01-01

    The epidermal growth factor receptor (EGFR) is a therapeutic target (oncotarget) in NSCLC. Using in vitro EGFR kinase activity system, we identified a novel small molecule, WB-308, as an inhibitor of EGFR. WB-308 decreased NSCLC cell proliferation and colony formation, by causing G2/M arrest and apoptosis. Furthermore, WB-308 inhibited the engraft tumor growths in two animal models in vivo (lung orthotopic transplantation model and patient-derived engraft mouse model). WB-308 impaired the phosphorylation of EGFR, AKT, and ERK1/2 protein. WB-308 was less cytotoxic than Gefitinib. Our study suggests that WB-308 is a novel EGFR-TKI and may be considered to substitute for Gefitinib in clinical therapy for NSCLC. PMID:25730907

  3. Near-edge x-ray absorption studies of Na-doped tetracyanoethylene films: A model system for the V(TCNE)x room-temperature molecular magnet

    NASA Astrophysics Data System (ADS)

    Carlegrim, E.; Gao, B.; Kanciurzewska, A.; de Jong, M. P.; Wu, Z.; Luo, Y.; Fahlman, M.

    2008-02-01

    V(TCNE)x , with TCNE=tetracyanoethylene and xtilde 2 , is an organic-based molecular magnet with potential to be used in spintronic devices. With the aim of shedding light on the unoccupied frontier electronic structure of V(TCNE)x we have studied pristine TCNE and sodium-intercalated TCNE by near edge x-ray absorption fine structure (NEXAFS) spectroscopy as well as with theoretical calculations. Sodium-intercalated TCNE was used as a model system of the more complex V(TCNE)x and both experimental and theoretical results of the model compound have been used to interpret the NEXAFS spectra of V(TCNE)x . By comparing the experimental and theoretical C K -edge of pristine TCNE, the contributions from the various carbon species (cyano and vinyl) could be disentangled. Upon fully sodium intercalation, TCNE is n doped with one electron per molecule and the features in the C and N K -edge spectra of pristine TCNE undergo strong modification caused by partially filling the TCNE lowest unoccupied molecular orbital (LUMO). When comparing the C and N K -edge NEXAFS spectra of fully sodium-doped TCNE with V(TCNE)x , the spectra are similar except for broadening of the features which originates from structural disorder of the V(TCNE)x films. The combined results from the model system and V(TCNE)x suggest that the lowest unoccupied molecular orbital with density on the nitrogen atoms in V(TCNE)x has no significant hybridization with vanadium and is similar to the so-called singly occupied molecular orbital of the TCNE anion. This suggests that the LUMO of V(TCNE)x is TCNE- or vanadiumlike, in contrast to the frontier occupied electronic structure where the highest occupied molecular orbital is a hybridization between V(3d) and cyano carbons. The completely different nature of the unoccupied and occupied frontier electronic structure of the material will most likely affect both charge injection and transport properties of a spintronic device featuring V(TCNE)x .

  4. 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.

  5. 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.

  6. Vacancy-type defects in Mg-doped GaN grown by ammonia-based molecular beam epitaxy probed using a monoenergetic positron beam

    NASA Astrophysics Data System (ADS)

    Uedono, Akira; Malinverni, Marco; Martin, Denis; Okumura, Hironori; Ishibashi, Shoji; Grandjean, Nicolas

    2016-06-01

    Vacancy-type defects in Mg-doped GaN were probed using a monoenergetic positron beam. GaN films with a thickness of 0.5-0.7 μm were grown on GaN/sapphire templates using ammonia-based molecular beam epitaxy and characterized by measuring Doppler broadening spectra. Although no vacancies were detected in samples with a Mg concentration [Mg] below 7 × 1019 cm-3, vacancy-type defects were introduced starting at above [Mg] = 1 × 1020 cm-3. The major defect species was identified as a complex between Ga vacancy (VGa) and multiple nitrogen vacancies (VNs). The introduction of vacancy complexes was found to correlate with a decrease in the net acceptor concentration, suggesting that the defect introduction is closely related to the carrier compensation. We also investigated Mg-doped GaN layers grown using In as the surfactant. The formation of vacancy complexes was suppressed in the subsurface region (≤80 nm). The observed depth distribution of defects was attributed to the thermal instability of the defects, which resulted in the introduction of vacancy complexes during the deposition process.

  7. Synthesis and characterization of novel molecularly imprinted polymer - coated Mn-doped ZnS quantum dots for specific fluorescent recognition of cocaine.

    PubMed

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

    2016-01-15

    Mn-doped ZnS quantum dots (QDs) coated with a molecularly imprinted polymer (MIP) material selective toward cocaine and its metabolites have been prepared and applied to cocaine (COC) and metabolites assessment by spectrofluorimetry. Ultrasound irradiation (37kHz) was novelty used for performing the Mn-doped ZnS QDs synthesis as well as for preparing the QD based MIP-coated composite by precipitation polymerization (imprinting process). This fact allowed the synthesis to be accomplished in four hours. In addition, the use of ultrasound irradiation during MIP-QDs synthesis increased the homogeneity of the QDs size, and reduced nanoparticles agglomeration. MIP was synthesized using COC as a template molecule, ethylene dimethacrylate (EDMA) as a functional monomer, divinylbenzene (DVB) as a cross-linker, and 2,2'-azobisisobutyronitrile (AIBN) as an initiator. The fluorescence of MIP-coated QDs was quenched by the template (COC) and also by metabolites from COC such as benzoylecgonine (BZE), and ecgonine methyl ester (EME). Quenching was not observed when performing experiments with non-imprinted polymer (NIP)-coated QDs; and also, fluorescence quenching of MIP-coated QDs was not observed by other drugs of abuse and metabolites (heroin and cannabis abuse). This fact indicates that the prepared material recognize only COC (template) and metabolites. PMID:26319164

  8. 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.

  9. Displacement-type quartz crystal microbalance immunosensing platform for ultrasensitive monitoring of small molecular toxins.

    PubMed

    Tang, Dianping; Zhang, Bing; Tang, Juan; Hou, Li; Chen, Guonan

    2013-07-16

    A novel displacement-type quartz crystal microbalance (QCM) immunosensing strategy, based on glucose and its analogue dextran for concanavalin A (ConA) binding sites, was designed for ultrasensitive monitoring of small molecular biotoxins (brevetoxin B, PbTx-2, used as a model) with signal amplification on a graphene-functionalized sensing interface. To construct such a QCM immunosensing platform, phenoxy-functionalized dextran (DexP) was initially assembled onto the surface of graphene-coated QCM probe via the π-stacking interaction, and ConA-labeled monoclonal mouse anti-PbTx-2 capture antibody was then immobilized on the DexP-modified probe by dextran-ConA binding. Gold nanoparticle heavily functionalized with glucoamylase and bovine serum albumin-PbTx-2 (PbTx-2-BSA) conjugate was employed as the trace tag. A competitive-type immunoassay format was adopted for the online monitoring of PbTx-2 between anti-PbTx-2 antibody immobilized on the QCM probe and PbTx-2-BSA labeled on the gold nanoparticle. Accompanying the gold nanoparticle, the carried glucoamylase could hydrolyze amylopectin in glucose. The produced glucose competed with dextran for ConA and displaced the ConA-streptavidin-anti-PbTx-2 complex from the QCM probe, resulting in the frequency change. Under optimal conditions, the frequency of the QCM immunosensor was indirectly proportional to the concentration of target PbTx-2 in the sample and exhibited a dynamic range from 1.0 pg·mL(-1) to 10 ng·mL(-1) with a detection limit (LOD) of 0.6 pg·mL(-1) at the 3Sblank level. Intra- and interassay coefficients of variation were below 7.5% and 9.5%, respectively. In addition, the methodology was evaluated for analysis of PbTx-2 in 15 spiked seafood samples and showed good accordance between results obtained by the displacement-type QCM immunosensor and a commercialized enzyme-linked immunosorbent assay (ELISA) method. PMID:23789727

  10. Small molecular weight organic thin-film photodetectors and solar cells

    NASA Astrophysics Data System (ADS)

    Peumans, Peter; Yakimov, Aharon; Forrest, Stephen R.

    2003-04-01

    In this review, we discuss the physics underlying the operation of single and multiple heterojunction, vacuum-deposited organic solar cells based on small molecular weight thin films. For single heterojunction cells, we find that the need for direct contact between the deposited electrode and the active organics leads to quenching of excitons. An improved device architecture, the double heterojunction, is shown to confine excitons within the active layers, allowing substantially higher internal efficiencies to be achieved. A full optical and electrical analysis of the double heterostructure architecture leads to optimal cell design as a function of the optical properties and exciton diffusion lengths of the photoactive materials. Combining the double heterostructure with novel light trapping schemes, devices with external efficiencies approaching their internal efficiency are obtained. When applied to an organic photovoltaic cell with a power conversion efficiency of 1.0%±0.1% under 1 sun AM1.5 illumination, devices with external power conversion efficiencies of 2.4%±0.3% are reported. In addition, we show that by using materials with extended exciton diffusion lengths LD, highly efficient double heterojunction photovoltaic cells are obtained, even in the absence of a light trapping geometry. Using C60 as an acceptor material, double heterostructure external power conversion efficiencies of 3.6%±0.4% under 1 sun AM1.5 illumination are obtained. Stacking of single heterojunction devices leads to thin film multiple heterojunction photovoltaic and photodetector structures. Thin bilayer photovoltaic cells can be stacked with ultrathin (˜5 Å), discontinuous Ag layers between adjacent cells serving as efficient recombination sites for electrons and holes generated in the neighboring cells. Such stacked cells have open circuit voltages that are n times the open circuit voltage of a single cell, where n is the number of cells in the stack. In optimized structures, the

  11. Nucleation and growth of GaN nanorods on Si (111) surfaces by plasma-assisted molecular beam epitaxy - The influence of Si- and Mg-doping

    SciTech Connect

    Furtmayr, Florian; Vielemeyer, Martin; Stutzmann, Martin; Eickhoff, Martin; Arbiol, Jordi

    2008-08-01

    The self-assembled growth of GaN nanorods on Si (111) substrates by plasma-assisted molecular beam epitaxy under nitrogen-rich conditions is investigated. An amorphous silicon nitride layer is formed in the initial stage of growth that prevents the formation of a GaN wetting layer. The nucleation time was found to be strongly influenced by the substrate temperature and was more than 30 min for the applied growth conditions. The observed tapering and reduced length of silicon-doped nanorods is explained by enhanced nucleation on nonpolar facets and proves Ga-adatom diffusion on nanorod sidewalls as one contribution to the axial growth. The presence of Mg leads to an increased radial growth rate with a simultaneous decrease of the nanorod length and reduces the nucleation time for high Mg concentrations.

  12. Growth of Cr-doped TiO₂ Films in the Rutile and Anatase Structures by Oxygen Plasma Assisted Molecular Beam Epitaxy

    SciTech Connect

    Osterwalder, Juerg; Droubay, Timothy C.; Kaspar, Tiffany C.; Williams, Josh R.; Wang, Chong M.; Chambers, Scott A.

    2005-07-22

    As part of a search for new spintronic materials, highly ordered films of CrxTi₁-xO₂ in both rutile and anatase structure and for several Cr concentrations ranging from x=0.02 to 0.16 were grown by oxygen-plasma assisted molecular beam epitaxy. X-ray photoelectron diffraction data of the Cr 2p level exhibit the same patterns and the same modulation amplitudes as those observed for Ti 2p, providing a strong indication that a large fraction of the Cr atoms occupy substitutional lattice sites in both structures. The Cr 2p core-level spectra as well as a Cr 3d related dopant signal above the valence band of TiO₂ are characteristic of Cr³⁺ ions. At room temperature, Cr-doped anatase films exhibit ferromagnetic order with a saturation magnetization of ~0.6 µB per Cr atom and strong in-lane anisotropy.

  13. Doping driven small-to-large Fermi surface transition and d-wave superconductivity in a two-dimensional Kondo lattice

    NASA Astrophysics Data System (ADS)

    Eder, R.; Wróbel, P.

    2011-07-01

    We study the two-dimensional Kondo lattice model with an additional Heisenberg exchange between localized spins. In a first step, we use mean-field theory with two order parameters. The first order parameter is a complex pairing amplitude between conduction electrons and localized spins that describes condensation of Kondo (or Zhang-Rice) singlets. A nonvanishing value implies that the localized spins contribute to the Fermi surface volume. The second-order parameter describes singlet pairing between the localized spins and competes with the Kondo-pairing order parameter. Reduction of the carrier density in the conduction band reduces the energy gain due to the formation of the large Fermi surface and induces a phase transition to a state with strong singlet correlations between the localized spins and a Fermi surface that comprises only the conduction electrons. The model thus shows a doping driven change of its Fermi surface volume. At intermediate doping and low temperature, there is a phase where both order parameters coexist, which has a gapped large Fermi surface and dx2-y2 superconductivity. The theory thus qualitatively reproduces the phase diagram of cuprate superconductors. In the second part of this paper, we show how the two phases with different Fermi surface volume emerge in a strong-coupling theory applicable in the limit of large Kondo exchange. The large Fermi surface phase corresponds to a “vacuum” of localized Kondo singlets with uniform phase, and the quasiparticles are spin-1/2 charge fluctuations around this fully paired state. In the small Fermi surface phase, the quasiparticles correspond to propagating Kondo singlets or triplets whereby the phase of a given Kondo singlet corresponds to its momentum. In this picture, a phase transition occurs for low filling of the conduction band as well.

  14. First small molecular inhibitors of T. brucei dolicholphosphate mannose synthase (DPMS), a validated drug target in African sleeping sickness

    PubMed Central

    Smith, Terry K.; Young, Benjamin L.; Denton, Helen; Hughes, David L.; Wagner, Gerd K.

    2013-01-01

    Drug-like molecules with activity against Trypanosoma brucei are urgently required as potential therapeutics for the treatment of African sleeping sickness. Starting from known inhibitors of other glycosyltransferases, we have developed the first small molecular inhibitors of dolicholphosphate mannose synthase (DPMS), a mannosyltransferase critically involved in glycoconjugate biosynthesis in T. brucei. We show that these DPMS inhibitors prevent the biosynthesis of glycosylphosphatidylinositol (GPI) anchors, and possess trypanocidal activity against live trypanosomes. PMID:19217283

  15. The Molecular Evolution of the Small Heat-Shock Proteins in Plants

    PubMed Central

    Waters, E. R.

    1995-01-01

    The small heat-shock proteins have undergone a tremendous diversification in plants; whereas only a single small heat-shock protein is found in fungi and many animals, over 20 different small heat-shock proteins are found in higher plants. The small heat-shock proteins in plants have diversified in both sequence and cellular localization and are encoded by at least five gene families. In this study, 44 small heat-shock protein DNA and amino acid sequences were examined, using both phylogenetic analysis and analysis of nucleotide substitution patterns to elucidate the evolutionary history of the small heat-shock proteins. The phylogenetic relationships of the small heat-shock proteins, estimated using parsimony and distance methods, reveal that gene duplication, sequence divergence and gene conversion have all played a role in the evolution of the small heat-shock proteins. Analysis of nonsynonymous substitutions and conservative and radical replacement substitutions (in relation to hydrophobicity) indicates that the small heat-shock protein gene families are evolving at different rates. This suggests that the small heat-shock proteins may have diversified in function as well as in sequence and cellular localization. PMID:8647410

  16. Templating effects in molecular growth of blended films for efficient small-molecule photovoltaics.

    PubMed

    Wang, Zhiping; Miyadera, Tetsuhiko; Yamanari, Toshihiro; Yoshida, Yuji

    2014-05-14

    A strategy to control the molecular growth of coevaporated zinc phthalocyanine (ZnPc) and fullerene (C60) blended films for efficient organic photovoltaic (OPV) cells was demonstrated. Introduction of a 2,5-bis(4-biphenylyl)-bithiophene (BP2T) film or a ZnPc film on BP2T as nanostructured templates not only results in phase-separated domains in blended films with clear interpenetrating networks but also improves the crystallinity of ZnPc domains, both of which enhance photocurrent generation and charge carrier transport. Such morphology is strongly associated with the molecular growth of the templating layers. Roughness and adhesion of the templating layers are of great importance for the molecular growth of the blended films and in turn for cell characteristics. By carefully regulating the molecular growth of the blended films, the power conversion efficiency was improved by 125%, from 1.85 to 4.15% under 1 sun. PMID:24712371

  17. 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.

  18. Informatics calibration of a molecular descriptors database to predict solid dispersion potential of small molecule organic solids.

    PubMed

    Moore, Michael D; Wildfong, Peter L D

    2011-10-14

    The use of a novel, in silico method for making an intelligent polymer selection to physically stabilize small molecule organic (SMO) solid compounds formulated as amorphous molecular solid dispersions is reported. 12 compounds (75%, w/w) were individually co-solidified with polyvinyl pyrrolidone:vinyl acetate (PVPva) copolymer by melt-quenching. Co-solidified products were analyzed intact using differential scanning calorimetry (DSC) and the pair distribution function (PDF) transform of powder X-ray diffraction (PXRD) data to assess miscibility. Molecular descriptor indices were calculated for all twelve compounds using their reported crystallographic structures. Logistic regression was used to assess correlation between molecular descriptors and amorphous molecular solid dispersion potential. The final model was challenged with three compounds. Of the 12 compounds, 6 were miscible with PVPva (i.e. successful formation) and 6 were phase separated (i.e. unsuccessful formation). 2 of the 6 unsuccessful compounds exhibited detectable phase-separation using the PDF method, where DSC indicated miscibility. Logistic regression identified 7 molecular descriptors correlated to solid dispersion potential (α=0.001). The atomic mass-weighted third-order R autocorrelation index (R3m) was the only significant descriptor to provide completely accurate predictions of dispersion potential. The three compounds used to challenge the R3m model were also successfully predicted. PMID:21756988

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. Effective ionic charge polarization using typical supporting electrolyte and charge injection phenomena in molecularly doped polymer light-emitting diodes

    NASA Astrophysics Data System (ADS)

    Itoh, Eiji; Yamashita, Takanori; Miyairi, Keiichi

    2002-11-01

    An effective method of enhancing charge injection and electroluminescence efficiency of polymer-based light-emitting diodes is introduced. Spin-coated films of poly (N-vinylcarbazole) blended with electron-transport material (Bu-PBD), laser dye (Coumarin6), and the typical supporting electrolyte [tetraethylammonium perchlorate (TEAP)] were examined and it was found that the injection current and luminance of the light emitting diodes doped with TEAP were enhanced dramatically after heat treatment at 80 degC and appropriate biasing in an external electric field of 1.5 x108 V/m at this temperature. A charge injection model based on Fowler-Nordheim tunneling is proposed, taking into account electric field distortion due to the accumulation of ionic space charges at the electrode/film interface. The relaxation time of ionic polarization is found to be related to the cation size of the electrolyte.

  5. Optically recorded tunable microlenses based on dye-doped liquid crystal cells

    NASA Astrophysics Data System (ADS)

    Lucchetti, Liana; Tasseva, Jordanka

    2012-04-01

    We report on optically recorded microlenses in conventional liquid crystal cells doped with the azo-dye methyl-red. The focal length can be tuned electrically and changed in a wide range with just a small variation of the applied dc voltage. No patterned electrodes, built-in polymeric lens, or patterned molecular reorientation are required.

  6. Design rules for rational control of polymer glass formation behavior and mechanical properties with small molecular additives

    NASA Astrophysics Data System (ADS)

    Mangalara, Jayachandra Hari; Simmons, David

    Small molecule additives have long been employed to tune polymers' glass formation, mechanical and transport properties. For example, plasticizers are commonly employed to suppress polymer Tg and soften the glassy state, while antiplasticizers, which stiffen the glassy state of a polymer while suppressing its Tg, are employed to enhance protein and tissue preservation in sugar glasses. Recent literature indicates that additives can have a wide range of possible effects, but all of these have not been clearly understood and well appreciated. Here we employ molecular dynamics simulations to establish design rules for the selection of small molecule additives with size, molecular stiffness, and interaction energy chosen to achieve targeted effects on polymer properties. We furthermore find that a given additive's effect on a polymer's Tg can be predicted from its Debye-Waller factor via a function previously found to describe nanoconfinement effects on the glass transition. These results emphasize the potential for a new generation of targeted molecular additives to contribute to more targeted rational design of polymers. We acknowledge the Keck Foundation and the Ohio Supercomputing Center for financial and computational support of this effort, respectively.

  7. Correlation between molecular structure and self healing in a series of anthraquinone derivatives doped in poly(methyl methacrylate)

    NASA Astrophysics Data System (ADS)

    Dhakal, Prabodh

    Using absorbance spectroscopy and fluorescence spectroscopy as a probe, we studied photodegradation and recovery of a series of anthraquinone derivatives doped in (poly)methyl methacrylate (PMMA) thin films. We observed that many anthraquinone derivatives recover their optical properties after they are photodamaged. The mechanism that is responsible for their recovery is not well understood. Previous research, which uses non-linear methods such as Amplified spontaneous emission (ASE), two photon absorption, and indirect linear methods such as transmittance imaging, have focussed on one of the derivatives of the anthraquinone class named dispersed orange 11 (DO11) dye doped in PMMA. Since no direct measurements have yet been reported on a variety of anthraquinone derivatives, we have extended our research on a series of anthraquinone derivatives using direct measurement techniques such as linear absorption spectroscopy, fluorescence spectroscopy and photochroism measurements as a function of dye concentration and sample temperature. The data obtained from temperature-dependent photodecay and recovery as well as concentration-dependent photodecay are found to be in qualitative agreement with the Correlated Chromophore Domain Model (CCrDM). We also applied the depth dependent absorption model to estimate the degree of self-absorption of the fluorescence signal emitted by the sample. This analysis allows us to determine the depth dependent damage profile and time dependence of the damage profile. Our results show that damage decreases as a function of depth into the sample and increases as a function of time of exposure of the pump beam. The degree of self-absorption is found to increase with sample thickness. We also did a numerical analysis to find the intensity dependent decay rate constant alpha and the recovery rate beta for fluorescence. We then used the data to test the CCrDM to find the average number of molecules in a domain, number density of molecules and

  8. 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

  9. Small Molecular White Organic Light Emitting Devices with Single Emission Zone

    NASA Astrophysics Data System (ADS)

    Duan, Yu; Jiang, Wenlong; Li, Jiang; Chen, Gang; Zhao, Yi; Hou, Jingying; Liu, Shiyong

    2004-11-01

    An organic white-light-emitting device has been demonstrated by mixing two colors from a single emissive layer. The device structure included indium tin oxide glass (ITO) substrate/30 nm 4,4',4''-tris{N,-(3-methylphenyl)-N-phenylamino}triphenylamine (m-MTDATA) as hole injection layer/10 nm N,N-diphenyl-N,N-bis1-naphthy l-1,1-biphenyl-4,4-diamine (NPB) as hole transparent layer/30 nm bis [2-(2-hydroxyphenyl)-pyridine]beryllium (Bepp2) doped with 0.2% rubrene as emitting layer/40 nm tris-8-hydroxyquinoline aluminum (Alq3) as electron transport layer/0.8 nm LiF/aluminum (Al). A stable white emission Commission Internationale de 1’Eclairage (CIE) chromaticity coordinate range from (0.38, 0.36) to (0.31, 0.31) for forward bias voltage which changing from 6 to 17 V has been achieved. Its maximum luminance was 29000 cd/m2 at 15v, and the maximum power and current efficiencies were 3.0 lm/W at 5 V and 6.3 cd/A at 7 V, respectively.

  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%. PMID:27455734

  11. 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

  12. 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.

  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. Molecular entrapment of small molecules within the interior of horse spleen ferritin.

    PubMed

    Webb, B; Frame, J; Zhao, Z; Lee, M L; Watt, G D

    1994-02-15

    A procedure for trapping small molecules inside the interior of horse spleen ferritin (HoSF) and methods for characterizing HoSF and its small entrapped molecules are described. HoSF is first dissociated into subunits by adjustment to pH 2 in the presence of the small molecules to be trapped. The pH of the dissociated HoSF is then increased to 7 at which time the dissociated subunits reassemble reforming the 24-mer HoSF, thereby trapping solvent within its interior. HoSF is then separated from unbound molecules by dialysis, ultrafiltration, and/or ammonium sulfate precipitation. Sephadex G-25 and DEAE chromatographic methods were also used to separate HoSF from unbound small molecules. Capillary electrophoresis (CE) was used to demonstrate the association of small molecules with HoSF after the pH-induced unfolding-refolding process. The pH indicator neutral red was clearly associated with HoSF and presumed trapped within the ferritin interior. Acid/base titrations suggested that the trapped indicator had a different pKa than the free indicator, a result which indicates that the ferritin interior is different than the external solution. The utility of using trapped molecules for gaining information on ferritin function is proposed and discussed. PMID:8117106

  15. 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

  16. Assessing the accuracy of the van der Waals density functionals for rare-gas and small molecular systems

    NASA Astrophysics Data System (ADS)

    Callsen, Martin; Hamada, Ikutaro

    2015-05-01

    The precise description of chemical bonds with different natures is a prerequisite for an accurate electronic structure method. The van der Waals density functional is a promising approach that meets such a requirement. Nevertheless, the accuracy should be assessed for a variety of materials to test the robustness of the method. We present benchmark calculations for weakly interacting molecular complexes and rare-gas systems as well as covalently bound molecular systems, in order to assess the accuracy and applicability of rev-vdW-DF2, a recently proposed variant [I. Hamada, Phys. Rev. B 89, 121103 (2014), 10.1103/PhysRevB.89.121103] of the van der Waals density functional. It is shown that although the calculated atomization energies for small molecules are less accurate rev-vdW-DF2 describes the interaction energy curves for the weakly interacting molecules and rare-gas complexes, as well as the bond lengths of diatomic molecules, reasonably well.

  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. Determining the Energetics of Small β-Sheet Peptides using Adaptive Steered Molecular Dynamics.

    PubMed

    Bureau, Hailey R; Hershkovits, Eli; Quirk, Stephen; Hernandez, Rigoberto

    2016-04-12

    Mechanically driven unfolding is a useful computational tool for extracting the energetics and stretching pathway of peptides. In this work, two representative β-hairpin peptides, chignolin (PDB: 1UAO ) and trpzip1 (PDB: 1LE0 ), were investigated using an adaptive variant of the original steered molecular dynamics method called adaptive steered molecular dynamics (ASMD). The ASMD method makes it possible to perform energetic calculations on increasingly complex biological systems. Although the two peptides are similar in length and have similar secondary structures, their unfolding energetics are quite different. The hydrogen bonding profile and specific residue pair interaction energies provide insight into the differing stabilities of these peptides and reveal which of the pairs provides the most significant stabilization. PMID:26930270

  19. n-Type transparent conducting films of small molecule and polymer amine doped single-walled carbon nanotubes.

    PubMed

    Mistry, Kevin S; Larsen, Brian A; Bergeson, Jeremy D; Barnes, Teresa M; Teeter, Glenn; Engtrakul, Chaiwat; Blackburn, Jeffrey L

    2011-05-24

    In this report, we investigate the electrical and optical properties of thin conducting films of SWNTs after treatment with small molecule and polymeric amines. Among those tested, we find hydrazine to be the most effective n-type dopant. We use absorbance, Raman, X-ray photoelectron, and nuclear magnetic resonance spectroscopies on thin conducting films and opaque buckypapers treated with hydrazine to study fundamental properties and spectroscopic signatures of n-type SWNTs and compare them to SWNTs treated with nitric acid, a well-characterized p-type dopant. We find that hydrazine physisorbs to the surface of semiconducting and metallic SWNTs and injects large electron concentrations, raising the Fermi level as much as 0.7 eV above that of intrinsic SWNTs. Hydrazine-treated transparent SWNT films display sheet resistances nearly as low as p-type nitric-acid-treated films at similar optical transmittances, demonstrating their potential for use in photovoltaic devices as low work function transparent electron-collecting electrodes. PMID:21388221

  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. Efficient new ribozyme mimics: direct mapping of molecular design principles from small molecules to macromolecular, biomimetic catalysts

    PubMed Central

    Putnam, William C.; Daniher, Andrew T.; Trawick, Bobby N.; Bashkin, James K.

    2001-01-01

    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-phananthroline 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. PMID:11353090

  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. 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.

  4. 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

  5. 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.

  6. The Development of Protein Chips for High Throughput Screening (HTS) of Chemically Labeling Small Molecular Drugs.

    PubMed

    Feng, Yingzhu; Wang, Bochu; Chu, Xinxin; Wang, Yazhou; Zhu, Liancai

    2016-01-01

    How to construct protein chips and chemically labeling drug molecules without disrupting structures for HTS is still a challenging area. There are two main obstacles, one is that human multitrans membrane receptors, which are major drug targets, exhibit distinct motifs, and fold structures, and they will collapse unfold without membrane support in vitro; another one is that there still lack effective chemical labeling method for small drugs for detection. Therefore, how to acquire high detecting sensitivity for small molecules and to immobilize membrane protein receptors in native conformation with uniform direction on the chip, need to be solved for drug HTS. This paper reviews drug HTS trends in recent years, proposed a new virion-chip model and a feasible C-H activation method for CY-5 labeling drugs. It is expected to provide a good platform for future drug HTS. PMID:25963567

  7. GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes

    PubMed Central

    2014-01-01

    Background Interpretation of binding modes of protein–small ligand complexes from 3D structure data is essential for understanding selective ligand recognition by proteins. It is often performed by visual inspection and sometimes largely depends on a priori knowledge about typical interactions such as hydrogen bonds and π-π stacking. Because it can introduce some biases due to scientists’ subjective perspectives, more objective viewpoints considering a wide range of interactions are required. Description In this paper, we present a web server for analyzing protein–small ligand interactions on the basis of patterns of atomic contacts, or “interaction patterns” obtained from the statistical analyses of 3D structures of protein–ligand complexes in our previous study. This server can guide visual inspection by providing information about interaction patterns for each atomic contact in 3D structures. Users can visually investigate what atomic contacts in user-specified 3D structures of protein–small ligand complexes are statistically overrepresented. This server consists of two main components: “Complex Analyzer”, and “Pattern Viewer”. The former provides a 3D structure viewer with annotations of interacting amino acid residues, ligand atoms, and interacting pairs of these. In the annotations of interacting pairs, assignment to an interaction pattern of each contact and statistical preferences of the patterns are presented. The “Pattern Viewer” provides details of each interaction pattern. Users can see visual representations of probability density functions of interactions, and a list of protein–ligand complexes showing similar interactions. Conclusions Users can interactively analyze protein–small ligand binding modes with statistically determined interaction patterns rather than relying on a priori knowledge of the users, by using our new web server named GIANT that is freely available at http://giant.hgc.jp/. PMID:24423161

  8. New Neurons in Aging Brains: Molecular Control by Small Non-Coding RNAs

    PubMed Central

    Schouten, Marijn; Buijink, M. Renate; Lucassen, Paul J.; Fitzsimons, Carlos P.

    2012-01-01

    Adult neurogenesis generates functional neurons from neural stem cells present in specific brain regions. It is largely confined to two main regions: the subventricular zone of the lateral ventricle, and the subgranular zone of the dentate gyrus (DG), in the hippocampus. With age, the function of the hippocampus and particularly the DG is impaired. For instance, adult neurogenesis is decreased with aging, in both proliferating and differentiation of newborn cells, while in parallel an age-associated decline in cognitive performance is often seen. Surprisingly, the synaptogenic potential of adult-born neurons is only marginally influenced by aging. Therefore, although proliferation, differentiation, and synaptogenesis of adult-born new neurons in the DG are closely related to each other, they are differentially affected by aging. In this review we discuss the crucial roles of a novel class of recently discovered modulators of gene expression, the small non-coding RNAs, in the regulation of adult neurogenesis. Multiple small non-coding RNAs are differentially expressed in the hippocampus. In particular a subgroup of the small non-coding RNAs, the microRNAs, fine-tune the progression of adult neurogenesis. This makes small non-coding RNAs appealing candidates to orchestrate the functional alterations in adult neurogenesis and cognition associated with aging. Finally, we summarize observations that link changes in circulating levels of steroid hormones with alterations in adult neurogenesis, cognitive decline, and vulnerability to psychopathology in advanced age, and discuss a potential interplay between steroid hormone receptors and microRNAs in cognitive decline in aging individuals. PMID:22363255

  9. 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

  10. Mechanism of Mcl-1 Conformational Regulation Upon Small Molecule Binding Revealed by Molecular Dynamic Simulation.

    PubMed

    Wang, Anhui; Song, Ting; Wang, Ziqian; Liu, Yubo; Fan, Yudan; Zhang, Yahui; Zhang, Zhichao

    2016-04-01

    Inhibition of interactions between Mcl-1 and proapoptotic proteins is considered to be a therapeutic strategy to induce apoptosis in cancer cells. Here, we adopted molecular dynamics simulation with molecular mechanics-Poisson Boltzmann/surface area method (MM-PB/SA) to study the inhibition mechanism of three Mcl-1 inhibitors, compounds 1, 2 and 3. Analysis of energy components shows that the better binding free energy of compound 3 than compounds 1 and 2 is attributable to the van der Waals energy (ΔEvdw ) and non-polar solvation energy (ΔGnp ) upon binding. In addition to the excellent agreement with previous experimentally determined affinities, our simulation results further show a bend of helix 4 on Mcl-1 upon compound 3 binding, which is driven by hydrophobic interaction with residue Val(253) , leading to a narrowed BH3-binding groove to impede Puma(BH) (3) binding. The computational result is consistent with our competitive isothermal titration calorimetry (ITC) assays, which shows that the competitive ability of compound 3 toward Mcl-1/Puma(BH) (3) complex is improved beyond its direct binding affinity toward Mcl-1 itself, and compound 3 exhibits much more efficiency to compete with Puma(BH) (3) than compound 2. Our study provides a new strategy to improve inhibitory activity on Mcl-1 based on the conformational dynamic change. PMID:26518611

  11. 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.

  12. 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

  13. A Molecular Imaging Paradigm to Rapidly Profile Response to Angiogenesis-directed Therapy in Small Animals

    PubMed Central

    Virostko, John; Xie, Jingping; Hallahan, Dennis E.; Arteaga, Carlos L.; Gore, John C.; Manning, H. Charles

    2009-01-01

    Purpose The development of novel angiogenesis-directed therapeutics is hampered by the lack of non-invasive imaging metrics capable of assessing treatment response. We report the development and validation of a novel molecular imaging paradigm to rapidly assess response to angiogenesis-directed therapeutics in preclinical animal models. Procedures A monoclonal antibody-based optical imaging probe targeting vascular endothelial growth factor receptor-2 (VEGFR2) expression was synthesized and evaluated in vitro and in vivo via multispectral fluorescence imaging. Results The optical imaging agent demonstrated specificity for the target receptor in cultured endothelial cells and in vivo. The agent exhibited significant accumulation within 4T1 xenograft tumors. Mice bearing 4T1 xenografts and treated with sunitinib exhibited both tumor growth arrest and decreased accumulation of NIR800-αVEGFR2ab compared to untreated cohorts (p=0.0021). Conclusions Molecular imaging of VEGFR2 expression is a promising non-invasive biomarker for assessing angiogenesis and evaluating the efficacy of angiogenesis-directed therapies. PMID:19130143

  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. PMID:26088935

  15. 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

  16. 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. PMID:26182407

  17. 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

  18. 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.

  19. Molecular Dynamics Simulations on Parallel Computers: a Study of Polar Versus Nonpolar Media Effects in Small Molecule Solvation.

    NASA Astrophysics Data System (ADS)

    Debolt, Stephen Edward

    Solvent effects were studied and described via molecular dynamics (MD) and free energy perturbation (FEP) simulations using the molecular mechanics program AMBER. The following specific topics were explored:. Polar solvents cause a blue shift of the rm nto pi^* transition band of simple alkyl carbonyl compounds. The ground- versus excited-state solvation effects responsible for the observed solvatochromism are described in terms of the molecular level details of solute-solvent interactions in several modeled solvents spanning the range from polar to nonpolar, including water, methanol, and carbon tetrachloride. The structure and dynamics of octanol media were studied to explore the question: "why is octanol/water media such a good biophase analog?". The formation of linear and cyclic polymers of hydrogen-bonded solvent molecules, micelle-like clusters, and the effects of saturating waters are described. Two small drug-sized molecules, benzene and phenol, were solvated in water-saturated octanol. The solute-solvent structure and dynamics were analysed. The difference in their partitioning free energies was calculated. MD and FEP calculations were adapted for parallel computation, increasing their "speed" or the time span accessible by a simulation. The non-cyclic polyether ionophore salinomycin was studied in methanol solvent via parallel FEP. The path of binding and release for a potassium ion was investigated by calculating the potential of mean force along the "exit vector".

  20. Molecular conformation of the full-length tumor suppressor NF2/Merlin—a small angle neutron scattering study

    PubMed Central

    Khajeh, Jahan Ali; Ju, Jeong Ho; Atchiba, Moussoubaou; Allaire, Marc; Stanley, Christopher; Heller, William T.; Callaway, David J.E.; Bu, Zimei

    2014-01-01

    Summary The tumor suppressor protein Merlin inhibits cell proliferation upon establishing cell-cell contacts. Because Merlin has high sequence similarity to the Ezrin-Radixin-Moesin (ERM) family of proteins, the structural model of ERM protein autoinhibition and cycling between closed/resting and open/active conformational states is often employed to explain Merlin function. However, recent biochemical studies suggest alternative molecular models of Merlin function. Here, we have determined the low resolution molecular structure and binding activity of Merlin and a Merlin(S518D) mutant that mimics the inactivating phosphorylation at S518 using small angle neutron scattering (SANS) and binding experiments. SANS shows that in solution both Merlin and Merlin(S518D) adopt a closed conformation, but binding experiments indicate that a significant fraction of either Merlin or Merlin(S518D) is capable of binding to the target protein NHERF1. Upon binding to the phosphatidylinositol 4,5-bisphosphate lipid, the wild-type Merlin adopts a more open conformation than in solution, but Merlin(S518D) remains in a closed conformation. This study supports a rheostat model of Merlin in NHERF1 binding, and contributes to resolve a controversy about the molecular conformation and binding activity of Merlin. PMID:24882693

  1. 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.

  2. Resolving the Transition from Molecular to Atomic at 1/5 Solar Metallicity in the Small Magellanic Cloud

    NASA Astrophysics Data System (ADS)

    Jameson, Katherine; Bolatto, Alberto; Warren, Steven; Wolfire, Mark; Rubio, Monica; Herrera Camus, Rodrigo

    2015-08-01

    At a distance of 61 kpc, the Small Magellanic Cloud (SMC) affords an absolutely unique view of the low metallicity star-forming interstellar medium, providing the nearest laboratory to study processes relevant to star formation at high redshifts. We present new ALMA maps of 12CO and 13CO in 4 regions in the Southwest Bar of the SMC. These maps are the first high-resolution (1.6" ~ 0.6 pc) images of CO in a molecular cloud at 1/5 Solar metallicity. We show the structure of photodissociation regions for the first time at 1/5 Solar metallicity by combining the new ALMA data with Herschel maps of [CII], dust-based estimates of H2, NEWFIRM NIR 2 micron warm H2 images, and HI. We compare the data to recent 3D simulations by Glover & Mac Low (2011) and Shetty et al. (2011) to determine whether the equilibrium model of the HI to H2 transition breaks down. We present measures of the fraction of molecular gas traced by CO at low metallicity by combinging this study with the existing dust-based H2 estimates (Bolatto et al. 2011), which is needed to infer the molecular mass of any high-z ALMA CO observation.

  3. Interference free detection for small molecules: probing the Mn2+-doped effect and cysteine capped effect on the ZnS nanoparticles for coccidiostats and peptide analysis in SALDI-TOF MS.

    PubMed

    Kailasa, Suresh Kumar; Wu, Hui-Fen

    2010-05-01

    For the first time, we report the applications of Mn(2+)-doped ZnS@cysteine nanoparticles (NPs) as matrices for analysis of coccidiostats (lasalocid, monensin, salinomycin and narasin) and peptide mixtures (Met-enk, Leu-enk, HW6 and gramicidin) in surface-assisted laser desorption/ionization time-of-flight mass spectrometry (SALDI-TOF MS). The Mn(2+)-doped ZnS@cysteine NPs have been successfully synthesized in aqueous phase and characterized by SEM, TEM and FT-IR spectroscopy. Comparison with the bare ZnS NPs, ZnS@cysteine NPs and CHCA to serve as matrices, we found that using Mn(2+)-doped ZnS@cysteine NPs as matrices offer better detection sensitivity and less background interferences for small molecule analysis. Current approach has been successfully applied for the analysis of peptide mixtures in urine samples and coccidiostats from egg samples by SALDI-TOF MS. The Mn(2+) ions doped in ZnS@cysteine NPs play a significant role for enhancing the detection sensitivity of analytes in SALDI-TOF MS. We believe that this approach is a promising tool to solve the low mass interference problems in MALDI-MS for complex mixture analysis of peptides and drugs. PMID:20419264

  4. UCLA's Molecular Screening Shared Resource: enhancing small molecule discovery with functional genomics and new technology.

    PubMed

    Damoiseaux, Robert

    2014-05-01

    The Molecular Screening Shared Resource (MSSR) offers a comprehensive range of leading-edge high throughput screening (HTS) services including drug discovery, chemical and functional genomics, and novel methods for nano and environmental toxicology. The MSSR is an open access environment with investigators from UCLA as well as from the entire globe. Industrial clients are equally welcome as are non-profit entities. The MSSR is a fee-for-service entity and does not retain intellectual property. In conjunction with the Center for Environmental Implications of Nanotechnology, the MSSR is unique in its dedicated and ongoing efforts towards high throughput toxicity testing of nanomaterials. In addition, the MSSR engages in technology development eliminating bottlenecks from the HTS workflow and enabling novel assays and readouts currently not available. PMID:24661210

  5. Molecular Evidence for Gender Differences in the Migratory Behaviour of a Small Seabird

    PubMed Central

    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

  6. 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

  7. 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

  8. Proton Fingerprints Portray Molecular Structures: Enhanced Description of the 1H NMR Spectra of Small Molecules

    PubMed Central

    Napolitano, José G.; Lankin, David C.; McAlpine, James B.; Niemitz, Matthias; Korhonen, Samuli-Petrus; Chen, Shao-Nong; Pauli, Guido F.

    2013-01-01

    The characteristic signals observed in NMR spectra encode essential information on the structure of small molecules. However, extracting all of this information from complex signal patterns is not trivial. This report demonstrates how computer-aided spectral analysis enables the complete interpretation of 1D 1H NMR data. The effectiveness of this approach is illustrated with a set of organic molecules, for which replicas of their 1H NMR spectra were generated. The potential impact of this methodology on organic chemistry research is discussed. PMID:24007197

  9. 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

  10. Sampling small-scale and large-scale conformational changes in proteins and molecular complexes

    NASA Astrophysics Data System (ADS)

    Yun, Mi-Ran; Mousseau, N.; Derreumaux, P.

    2007-03-01

    Sampling of small-scale and large-scale motions is important in various computational tasks, such as protein-protein docking and ligand binding. Here, we report further development and applications of the activation-relaxation technique for internal coordinate space trajectories (ARTIST). This method generates conformational moves of any complexity and size by identifying and crossing well-defined saddle points connecting energy minima. Simulations on two all-atom proteins and three protein complexes containing between 70 and 300 amino acids indicate that ARTIST opens the door to the full treatment of all degrees of freedom in dense systems such as protein-protein complexes.

  11. Calculation of the fourth-rank molecular hypermagnetizability of some small molecules.

    PubMed

    Pagola, G I; Caputo, M C; Ferraro, M B; Lazzeretti, P

    2004-05-22

    A computational scheme has been developed within the framework of Rayleigh-Schrödinger perturbation theory to evaluate nonlinear interaction energy contributions for a molecule in the presence of an external spatially uniform, time-independent magnetic field. Terms connected with the fourth power of the perturbing field, representing the fourth-rank hypermagnetizabilities of five small molecules, have been evaluated at the coupled Hartree-Fock level of accuracy within the conventional common-origin approach. Gaugeless basis sets of increasing size and flexibility have been employed in a numerical test, adopting two different coordinate systems to estimate the degree of convergence of theoretical tensor components. PMID:15267967

  12. Calculation of the fourth-rank molecular hypermagnetizability of some small molecules

    NASA Astrophysics Data System (ADS)

    Pagola, G. I.; Caputo, M. C.; Ferraro, M. B.; Lazzeretti, P.

    2004-05-01

    A computational scheme has been developed within the framework of Rayleigh-Schrödinger perturbation theory to evaluate nonlinear interaction energy contributions for a molecule in the presence of an external spatially uniform, time-independent magnetic field. Terms connected with the fourth power of the perturbing field, representing the fourth-rank hypermagnetizabilities of five small molecules, have been evaluated at the coupled Hartree-Fock level of accuracy within the conventional common-origin approach. Gaugeless basis sets of increasing size and flexibility have been employed in a numerical test, adopting two different coordinate systems to estimate the degree of convergence of theoretical tensor components.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. The properties of samarium-doped zinc oxide/phthalocyanine structure for optoelectronics prepared by pulsed laser deposition and organic molecular evaporation

    NASA Astrophysics Data System (ADS)

    Novotný, M.; Marešová, E.; Fitl, P.; Vlček, J.; Bergmann, M.; Vondráček, M.; Yatskiv, R.; Bulíř, J.; Hubík, P.; Hruška, P.; Drahokoupil, J.; Abdellaoui, N.; Vrňata, M.; Lančok, J.

    2016-03-01

    Samarium-doped zinc oxide (ZnO:Sm)/zinc phthalocyanine (ZnPc) thin film multilayer structure was prepared by combination of pulsed laser deposition (PLD) and organic molecular evaporation (OME). ZnO:Sm thin film was grown by PLD (Nd:YAG, λ = 266 nm, τ = 6 ns) from Sm2O3:ZnO (1 % Sm) target in oxygen ambient at pressure of 10 and 20 Pa at room temperature on fused silica and Si(100) substrates. ZnPc thin film was deposited on ZnO:Sm layer by OME. ZnO:Sm films of c-axis-oriented hexagonal wurtzite structure and α-form ZnPc were obtained. Emission of intra-4f transition in Sm3+ ions and photoluminescence enhancement of near-band-edge emission of ZnO in ZnO:Sm/ZnPc were observed. Electrical properties were not affected by Sm3+ dopant as ZnO:Sm film exhibited high electrical resistivity ~5 × 104 Ω cm.

  18. Raman and photoluminescence spectroscopic detection of surface-bound Li(+)O2(-) defect sites in Li-doped ZnO nanocrystals derived from molecular precursors.

    PubMed

    Kirste, Ronny; Aksu, Yilmaz; Wagner, Markus R; Khachadorian, Sevak; Jana, Surajit; Driess, Matthias; Thomsen, Christian; Hoffmann, Axel

    2011-04-18

    We present a detailed study of Raman spectroscopy and photoluminescence measurements on Li-doped ZnO nanocrystals with varying lithium concentrations. The samples were prepared starting from molecular precursors at low temperature. The Raman spectra revealed several sharp lines in the range of 100-200 cm(-1), which are attributed to acoustical phonons. In the high-energy range two peaks were observed at 735 cm(-1) and 1090 cm(-1). Excitation-dependent Raman spectroscopy of the 1090 cm(-1) mode revealed resonance enhancement at excitation energies around 2.2 eV. This energy coincides with an emission band in the photoluminescence spectra. The emission is attributed to the deep lithium acceptor and intrinsic point defects such as oxygen vacancies. Based on the combined Raman and PL results, we introduce a model of surface-bound LiO(2) defect sites, that is, the presence of Li(+)O(2)(-) superoxide. Accordingly, the observed Raman peaks at 735 cm(-1) and 1090 cm(-1) are assigned to Li-O and O-O vibrations of LiO(2). PMID:21433242

  19. 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 30-700μmolL(-1) with a detection limit of 24μmolL(-1). The developed method was finally applied successfully to the determination of FF in different meat samples with satisfactory recoveries. PMID:26828536

  20. 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

  1. 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

  2. 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

  3. Molecular Probing of the HPV-16 E6 Protein Alpha Helix Binding Groove with Small Molecule Inhibitors.

    PubMed

    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

  4. Molecular investigation of Cryptosporidium in small caged pets in northeast China: host specificity and zoonotic implications.

    PubMed

    Li, Qiao; Li, Lu; Tao, Wei; Jiang, Yanxue; Wan, Qiang; Lin, Yongchao; Li, Wei

    2016-07-01

    This study screened 151 pet-derived fecal specimens randomly collected from four commercial markets in northeast China for the presence of Cryptosporidium by genus-specific nested PCRs of the small subunit rRNA gene. Of these, 14 specimens (9.3 %) from nine species of birds, two types of rodents, and a hedgehog were positive for Cryptosporidium. Sequence analysis on the PCR-positive isolates facilitated identification of three Cryptosporidium species (C. baileyi, C. galli, and C. ubiquitum) and two Cryptosporidium genotypes (ferret genotype and avian genotype V). The study birds were affected predominantly with bird-specific C. baileyi (Atlantic canary, budgerigar, crested myna, rock dove, and silky fowl), C. galli (Chinese hwamei), and Cryptosporidium avian genotype V (Fischer's lovebird and rosy-faced lovebird). Cryptosporidium ferret genotype previously considered rodent-adapted was identified in three specimens from budgerigar, chipmunk, and red squirrel. Two specimens collected from common hill myna and hedgehog were positive for C. ubiquitum. The species of birds that can be colonized by Cryptosporidium were extended. Moreover, the data expanded the host range of Cryptosporidium ferret genotype and C. ubiquitum, especially the birds. The carriage of zoonotic C. ubiquitum in small caged pets is of public health importance. PMID:27107987

  5. 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

  6. 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

  7. 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.

  8. 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

  9. Expression of molecular factors correlated with metastasis in small cell lung cancer and their significance

    PubMed Central

    Li, Xiao-Xia; Li, Rui-Jian; Zhao, Lu-Jun; Liu, Ning-Bo; Wang, Ping

    2015-01-01

    Distant metastasis continues to be a fatal threat to quality of life in patients with small cell lung caner (SCLC). The purpose of this work is to analyze the expressions of chemokine receptor four (CXCR4), matrix metalloproteinase-9 (MMP-9), transforming growth factor-b1 (TGF-β1), N-cadherin and vascular endothelial growth factor (VEGF) in small cell lung caner (SCLC), and to explore their correlations with the prognosis and metastasis. Sixty-five consecutive patients with stage I-III SCLC who received operation in our hospital from Jan 2003 to Oct 2009 were retrospectively analyzed. The expression of CXCR4 was found significantly correlated with bone metastasis (P = 0.004), and were marginally correlated with brain metastasis (P = 0.068) and lymph node metastasis (P = 0.085). The expression of MMP-9 was significantly associated with pathological staging (P = 0.048). Univariate analysis suggested surgical approach, clinical stage, lymph node metastasis were significantly associated with OS and PFS (P < 0.05), high expression of CXCR4 was significantly correlated with worse OS (P = 0.004) and PFS (P = 0.005). Multivariate analysis suggested surgical approach, TGF-β1, CXCR4 and lymph node metastasis were independent prognostic factor for PFS. In conclusion, High expression of CXCR4, MMP-9, TGF-β1 and VEGF were found in SCLC. High expression of MMP-9 was significantly associated with pathological staging, and high expression of CXCR4 was correlated with bone metastasis and also might correlate with brain metastasis. CXCR4 were independent prognostic factor for survival in SCLC and expanded samples should be further explored in the future. PMID:26823791

  10. 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

  11. 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

  12. 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. PMID:26835966

  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. PMID:25518984

  14. 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

  15. Novel Strategy for Biofilm Inhibition by Using Small Molecules Targeting Molecular Chaperone DnaK

    PubMed Central

    Arita-Morioka, Ken-ichi; Yamanaka, Kunitoshi; Mizunoe, Yoshimitsu; Ogura, Teru

    2014-01-01

    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

  16. 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

  17. Molecular dynamics simulation of fast particle irradiation to the Gd2O3-doped CeO2

    NASA Astrophysics Data System (ADS)

    Sasajima, Y.; Ajima, N.; Osada, T.; Ishikawa, N.; Iwase, A.

    2013-12-01

    The structural relaxation caused by the high-energy-ion irradiation of CeO2 with Gd2O3 addition was simulated by the molecular dynamics method. The amount of Gd2O3 was changed from 0 to 25 mol% by 5 mol%. As the initial condition, high thermal energy was supplied to the individual atoms within a cylindrical region of nanometer-order radius located in the center of the specimen. The potential proposed by Inaba et al. was utilized to calculate interaction between atoms [H. Inaba, R. Sagawa, H. Hayashi, K. Kawamura, Solid State Ionics 122 (1999) 95-103]. The supplied thermal energy was first spent to change the crystal structure into an amorphous one within a short period of about 0.3 ps, then it dissipated in the specimen. By increasing the concentration of Gd2O3, more structural disorder was observed in the sample, which is consistent to the actual experiment.

  18. 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.

  19. 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

  20. Properties of small molecular drug loading and diffusion in a fluorinated PEG hydrogel studied by H molecular diffusion NMR and F spin diffusion NMR.

    PubMed

    Mathias, Errol V; Aponte, Julia; Kornfield, Julia A; Ba, Yong

    2010-12-01

    R(f)-PEG (fluoroalkyl double-ended poly(ethylene glycol)) hydrogel is potentially useful as a drug delivery depot due to its advanced properties of sol-gel two-phase coexistence and low surface erosion. In this study, (1)H molecular diffusion nuclear magnetic resonance (NMR) and (19)F spin diffusion NMR were used to probe the drug loading and diffusion properties of the R(f)-PEG hydrogel for small anticancer drugs, 5-fluorouracil (FU) and its hydrophobic analog, 1,3-dimethyl-5-fluorouracil (DMFU). It was found that FU has a larger apparent diffusion coefficient than that of DMFU, and the diffusion of the latter was more hindered. The result of (19)F spin diffusion NMR for the corresponding freeze-dried samples indicates that a larger portion of DMFU resided in the R(f) core/IPDU intermediate-layer region (where IPDU refers to isophorone diurethane, as a linker to interconnect the R(f) group and the PEG chain) than that of FU while the opposite is true in the PEG-water phase. To understand the experimental data, a diffusion model was proposed to include: (1) hindered diffusion of the drug molecules in the R(f) core/IPDU-intermediate-layer region; (2) relatively free diffusion of the drug molecules in the PEG-water phase (or region); and (3) diffusive exchange of the probe molecules between the above two regions. This study also shows that molecular diffusion NMR combined with spin diffusion NMR is useful in studying the drug loading and diffusion properties in hydrogels for the purpose of drug delivery applications. PMID:21170115

  1. A microcomputed tomography guided fluorescence tomography system for small animal molecular imaging

    NASA Astrophysics Data System (ADS)

    Kepshire, Dax; Mincu, Niculae; Hutchins, Michael; Gruber, Josiah; Dehghani, Hamid; Hypnarowski, Justin; Leblond, Frederic; Khayat, Mario; Pogue, Brian W.

    2009-04-01

    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. 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. PMID:26711522

  3. High Resolution, High Sensitivity Detectors for Molecular Imaging of Small Animals and Tumor Detection

    NASA Astrophysics Data System (ADS)

    Magliozzi, M. L.; Cisbani, E.; Colilli, S.; Cusanno, F.; Fratoni, R.; Garibaldi, F.; Giuliani, F.; Gricia, M.; Lo Meo, S.; Lucentini, M.; Santavenere, F.; Veneroni, P.; Schillaci, O.; Simonetti, G.; Majewsky, S.; Cinti, M. N.; de Vincentis, G.; Pani, R.; Pellegrini, R.; Scopinaro, F.

    2006-04-01

    Imaging techniques with radionuclides provide very sensitive measures of a wide range of specific processes underying disease in the body. Detection of very small tumors with high specificity is therefore possible but the tecnique requires both high spatial resolution and high sensitivity. We present the first simulations, performed by means of GEANT4 code, of breast tumors, imaged by different configurations of a compact discrete gamma camera, in order to optimize the performances of dedicated detectors for these tasks. Simulated planar images from 6 to 10 mm diameter tumors, placed at 5 mm from the collimator, were generated for NaI scintillator pixel sizes of 1.0×1.0 and 1.2×1.2 mm2, hexagonal hole Pb collimators with hole size of 1.5 and 1.9 mm. The generated photons have been sampled by two modelled Hamamatsu H8500 and H9500 PMT. Tumor to background uptake ratio from 1:6 to 1:12 has been considered. The preliminary results in terms of spatial resolution and SNR show a slightly better performance of the high efficiency collimator, larger crystal size and H9500 combination.

  4. 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.

  5. Molecular analysis of human papillomavirus in never-smokers with non-small cell lung cancer

    PubMed Central

    ISA, SHUN-ICHI; KURAHARA, YU; YAMAMOTO, SATOMI; TAMIYA, AKIHIRO; OMACHI, NAOKI; ASAMI, KAZUHIRO; OKISHIO, KYOICHI; UTSUMI, TOMOKI; ITO, NORIMASA; YOON, HYUNG-EUN; MATSUMURA, AKIHIDE; ATAGI, SHINJI; KAWAGUCHI, TOMOYA

    2015-01-01

    The causes of lung cancer in never-smokers remain unclear. The potential contribution of human papillomavirus (HPV) to the carcinogenesis of non-small cell lung cancer (NSCLC) has been reported. In 2008, a prospective registry of never-smokers with NSCLC was established at the Kinki-Chuo Chest Medical Center, Sakai, Osaka, Japan. Never-smokers with NSCLC were consecutively enrolled onto the registry. Of these patients, 114 with large tumor specimens, the majority of which were surgical tissues, were selected. In total, 23 of the most clinically relevant HPV types were assayed using polymerase chain reaction amplification of the viral genome. Following exclusion of samples with suboptimal quality, DNA was extracted from 96 formalin-fixed paraffin-embedded samples. These 96 cases consisted of 82 females (85.4%) and 14 males (14.6%), with a median age of 67 years (range, 29–83). Almost all cases (93.8%) were of the adenocarcinoma histological subtype. Despite confirmation of the quality and amount of DNA, HPV type 6 was detected in only one case (1.1%). Furthermore, no other samples examined were positive for any other HPV types. The results therefore suggest that HPV does not play a major role as the driving oncogenic event in never-smokers with NSCLC. PMID:25621070

  6. 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

  7. 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

  8. 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

  9. Molecular characterization of geminivirus-derived small RNAs in different plant species.

    PubMed

    Akbergenov, Rashid; Si-Ammour, Azeddine; Blevins, Todd; Amin, Imran; Kutter, Claudia; Vanderschuren, Herve; Zhang, Peng; Gruissem, Wilhelm; Meins, Frederick; Hohn, Thomas; Pooggin, Mikhail M

    2006-01-01

    DNA geminiviruses are thought to be targets of RNA silencing. Here, we characterize small interfering (si) RNAs-the hallmarks of silencing-associated with Cabbage leaf curl begomovirus in Arabidopsis and African cassava mosaic begomovirus in Nicotiana benthamiana and cassava. We detected 21, 22 and 24 nt siRNAs of both polarities, derived from both the coding and the intergenic regions of these geminiviruses. Genetic evidence showed that all the 24 nt and a substantial fraction of the 22 nt viral siRNAs are generated by the dicer-like proteins DCL3 and DCL2, respectively. The viral siRNAs were 5' end phosphorylated, as shown by phosphatase treatments, and methylated at the 3'-nucleotide, as shown by HEN1 miRNA methylase-dependent resistance to beta-elimination. Similar modifications were found in all types of endogenous and transgene-derived siRNAs tested, but not in a major fraction of siRNAs from a cytoplasmic RNA tobamovirus. We conclude that several distinct silencing pathways are involved in DNA virus-plant interactions. PMID:16421273

  10. 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

  11. The Effect of Small Cosolutes that Mimic Molecular Crowding Conditions on the Stability of Triplexes Involving Duplex DNA.

    PubMed

    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

  12. Discovery of non-peptide small molecular CXCR4 antagonists as anti-HIV agents: Recent advances and future opportunities.

    PubMed

    Zhang, Heng; Kang, Dongwei; Huang, Boshi; Liu, Na; Zhao, Fabao; Zhan, Peng; Liu, Xinyong

    2016-05-23

    CXCR4 plays vital roles in HIV-1 life cycle for it's essential in mediating the interaction of host and virus and completing the entry process in the lifecycle of HIV-1 infection. Compared with some traditional targets, CXCR4 provides a novel and less mutated drug target in the battle against AIDS. Its antagonists have no cross resistance with other antagonists. Great achievements have been made recent years and a number of small molecular CXCR4 antagonists with diversity scaffolds have been discovered. In this review, recent advances in the discovery of CXCR4 antagonists with special attentions on their evolution and structure-activity relationships of representative CXCR4 antagonists are described. Moreover, some classical medicinal chemistry strategies and novel methodologies are also introduced. PMID:26974376

  13. Small-Pore Molecular Sieves SAPO-34 with Chabazite Structure: Theoretical Study of Silicon Incorporation and Interrelated Catalytic Activity

    NASA Astrophysics Data System (ADS)

    Wang, Hong; Lewis, James; Liu, Zhongmin

    2011-03-01

    The catalytic conversion of methonal to olefin (MTO) has attracted attention both in industrial and academic fields. Strong evidence shows that small-pore molecular sieves with certain amount silicon incorporated (SAPO) present promising high catalytic activity in MTO conversion. Using DFT, we study the structural and electronic properties of chabazite SAPO-34. Although there are extensively experimental results show that silicon incorporation does not change the overall structure as the original AlPO structure, local structural changes are still created by silicon substitution, which probably accounted for the high catalytic activity. It is noted that the catalytic activity of SAPO-34 presents increasing trend along with the silicon incorporation amount increasing and maintain a flat peak even with more silicon incorporated. Hence, there is an optimal silicon incorporation amount which possibly yields the highest catalytic MTO conversion.

  14. 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.

  15. Tuning of EAG K+ channel inactivation: Molecular determinants of amplification by mutations and a small molecule

    PubMed Central

    Garg, Vivek; Sachse, Frank B.

    2012-01-01

    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

  16. 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

  17. Polarization induced hole doping in graded Al{sub x}Ga{sub 1-x}N (x = 0.7 {approx} 1) layer grown by molecular beam epitaxy

    SciTech Connect

    Li, Shibin; Zhang, Ting; Wu, Jiang; Yang, Yajie; Wang, Zhiming; Wu, Zhiming; Chen, Zhi; Jiang, Yadong

    2013-02-11

    Polarization induced hole doping on the order of {approx}10{sup 18} cm{sup -3} is achieved in linearly graded Al{sub x}Ga{sub 1-x}N (x = 0.7 {approx} 1) layer grown by molecular beam epitaxy. Graded Al{sub x}Ga{sub 1-x}N and conventional Al{sub 0.7}Ga{sub 0.3}N layers grown on AlN are beryllium (Be) doped via epitaxial growth. The hole concentration in graded Al{sub x}Ga{sub 1-x}N:Be (x = 0.7 {approx} 1) layers demonstrates that polarization generates hole charges from Be dopant. The Al{sub 0.7}Ga{sub 0.3}N layer is not conductive owing to the absence of carriers generated from the Be dopant without the inducement of polarization. Polarization doping provides an approach to high efficiency p-type doping in high Al composition AlGaN.

  18. 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.

  19. Genetic aberrations in small B-cell lymphomas and leukemias: molecular pathology, clinical relevance and therapeutic targets.

    PubMed

    Bogusz, Agata M; Bagg, Adam

    2016-09-01

    Small B-cell lymphomas and leukemias (SBCLs) are a clinically, morphologically, immunophenotypically and genetically heterogeneous group of clonal lymphoid neoplasms, including entities such as chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), mantle cell lymphoma (MCL), follicular lymphoma (FL), lymphoplasmacytic lymphoma (LPL), marginal zone lymphoma (MZL) and hairy cell leukemia (HCL). The pathogenesis of some of these lymphoid malignancies is characterized by distinct translocations, for example t(11;14) in the majority of cases of MCL and t(14;18) in most cases of FL, whereas other entities are associated with a variety of recurrent but nonspecific numeric chromosomal abnormalities, as exemplified by del(13q14), del(11q22), and +12 in CLL, and yet others such as LPL and HCL that lack recurrent or specific cytogenetic aberrations. The recent surge in next generation sequencing (NGS) technology has shed more light on the genetic landscape of SBCLs through characterization of numerous driver mutations including SF3B1 and NOTCH1 in CLL, ATM and CCND1 in MCL, KMT2D and EPHA7 in FL, MYD88 (L265P) in LPL, KLF2 and NOTCH2 in splenic MZL (SMZL) and BRAF (V600E) in HCL. The identification of distinct genetic lesions not only provides greater insight into the molecular pathogenesis of these disorders but also identifies potential valuable biomarkers for prognostic stratification, as well as specific targets for directed therapy. This review discusses the well-established and recently identified molecular lesions underlying the pathogenesis of SBCLs, highlights their clinical relevance and summarizes novel targeted therapies. PMID:27121112

  20. 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

  1. RET-rearranged non-small-cell lung carcinoma: a clinicopathological and molecular analysis

    PubMed Central

    Tsuta, K; Kohno, T; Yoshida, A; Shimada, Y; Asamura, H; Furuta, K; Kushima, R

    2014-01-01

    Background: To elucidate clinicopathological characteristics of non-small-cell lung carcinoma (NSCLC) cases carrying RET rearrangements causing oncogenic fusions to identify responders to therapy with RET tyrosine kinase inhibitors. Methods: We investigated 1874 patients with carcinomas, including 1620 adenocarcinomas (ADCs), 203 squamous cell carcinomas (SCCs), 8 large cell carcinomas, and 43 sarcomatoid carcinomas (SACs). Fluorescence in situ hybridisation (FISH) and/or reverse transcription–PCR (RT–PCR) were performed to detect RET gene rearrangement. Results: In all, 22 cases (1.2%) showed RET rearrangements; all cases were of ADC histology. Of the 22 patients, 19 possessed KIF5B–RET fusion genes, whereas 3 possessed CCDC6–RET fusion genes. The RET-rearranged tumours were significantly more common in younger patients (P=0.038) and tended to occur in patients with no history of smoking (P=0.051). In addition, RET rearrangements were not associated with gender, occupational history (particularly radioactive exposure), tumour size, lymph node status, tumour stage, or patient survival. The predominant growth pattern in RET-rearranged ADCs was lepidic in 6 cases, papillary in 9 cases, acinar in 2 cases, micropapillary in 1 case, and solid in 4 cases. Cells with cytoplasmic mucin production were at least focally present in 12 of the 22 (54.5%) RET-rearranged ADC cases. Among the 21 analysed RET-rearranged tumours, RET immunopositivity was observed in 15 cases (71.4%), and was significantly associated with RET rearrangement (P<0.001). Conclusions: The RET rearrangements were observed in 1.2% of NSCLCs. All cases of RET rearrangement were ADCs. The RET rearrangements were more likely to be observed in younger patients. Although cytoplasmic mucin production was at least focally present in 54.5% of RET-rearranged ADCs, specific histological features were not detected. PMID:24504365

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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

  8. 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

  9. Oncogenic roles of TOPK and MELK, and effective growth suppression by small molecular inhibitors in kidney cancer cells

    PubMed Central

    Kato, Taigo; Inoue, Hiroyuki; Imoto, Seiya; Tamada, Yoshinori; Miyamoto, Takashi; Matsuo, Yo; Nakamura, Yusuke; Park, Jae-Hyun

    2016-01-01

    T–lymphokine-activated killer cell–originated protein kinase (TOPK) and maternal embryonic leucine zipper kinase (MELK) have been reported to play critical roles in cancer cell proliferation and maintenance of stemness. In this study, we investigated possible roles of TOPK and MELK in kidney cancer cells and found their growth promotive effect as well as some feedback mechanism between these two molecules. Interestingly, the blockade of either of these two kinases effectively caused downregulation of forkhead box protein M1 (FOXM1) activity which is known as an oncogenic transcriptional factor in various types of cancer cells. Small molecular compound inhibitors against TOPK (OTS514) and MELK (OTS167) effectively suppressed the kidney cancer cell growth, and the combination of these two compounds additively worked and showed the very strong growth suppressive effect on kidney cancer cells. Collectively, our results suggest that both TOPK and MELK are promising molecular targets for kidney cancer treatment and that dual blockade of OTS514 and OTS167 may bring additive anti-tumor effects with low risk of side effects. PMID:26933922

  10. 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.

  11. The role of molecular pathology in non-small-cell lung carcinoma—now and in the future

    PubMed Central

    Brandao, G.D.A.; Brega, E.F.; Spatz, A.

    2012-01-01

    In recent years, better understanding of the molecular biology of non-small-cell lung carcinoma (nsclc) has led to a revolution in the work-up of these neoplasms. As a pathology diagnosis, “nsclc” without further attempt at subclassification is no longer accepted as a standard of care; separating squamous cell carcinoma from adenocarcinoma and large-cell carcinoma carries implications for prognosis and treatment decisions. Currently, detection of the presence in nsclc of mutations involving the epidermal growth factor receptor (EGFR) gene and fusion of the N-terminal portion of the protein encoded by EML4 (echinoderm microtubule-associated protein-like 4 gene) with the intracellular signaling portion of the receptor tyrosine kinase encoded by ALK (anaplastic lymphoma kinase gene)—that is, EML4–ALK—and variants has become routine in many centres because patients having tumours harbouring such alterations might benefit from tyrosine kinase inhibitors as part of their treatment regimen. The purpose of the present review is to highlight important aspects of the screening for molecular derangements in nsclc and to briefly discuss the emergence of possible future biomarkers. PMID:22787408

  12. The impact on the multidisciplinary team of molecular profiling for personalized therapy in non-small cell lung cancer.

    PubMed

    Blackhall, Fiona; Thatcher, Nick; Booton, Richard; Kerr, Keith

    2013-02-01

    The composition of the multidisciplinary team (MDT) that treats lung cancer varies by region and practice setting but generally includes a thoracic medical oncologist, a thoracic surgeon, a thoracic radiation oncologist, and an interventional radiologist, as well as a pathologist, pulmonologist, and specialist nurses. Growing clinical evidence supports a personalized approach to non-small cell lung cancer (NSCLC) treatment, and clinical trials in advanced disease have shown the value of testing for epidermal growth factor receptor gene (EGFR) mutations prior to first-line therapy with erlotinib or gefitinib and testing for anaplastic lymphoma kinase gene (ALK) rearrangements prior to therapy with crizotinib. The most recent National Comprehensive Cancer Network (NCCN) guidelines also recommend sequential EGFR and ALK testing for patients with a diagnosis of recurrent or metastatic adenocarcinoma, large cell carcinoma, or not otherwise specified histology, and simultaneous molecular screening has also been proposed. Here, we explore potential challenges for the MDT implied by the move toward personalized therapy in NSCLC and the increasing need for molecular diagnoses, and anticipate how the working roles and responsibilities of team members may develop to accommodate them. PMID:23182148

  13. Tear fluid small molecular antioxidants profiling shows lowered glutathione in keratoconus.

    PubMed

    Saijyothi, Aluru Venkata; Fowjana, Jenofar; Madhumathi, Subramanian; Rajeshwari, Mahadevan; Thennarasu, Maruthamuthu; Prema, Padmanaban; Angayarkanni, Narayanasamy

    2012-10-01

    Keratoconus (KC) is a non-inflammatory disease of the cornea involving structural changes. Oxidative stress is reported to be parts of its pathology, yet the tear antioxidant status contributed by smaller molecule antioxidants can be indicative of the disease. Therefore this study is an attempt to present the status of small molecule antioxidants in KC condition as well as the influence of contact lens wear (CLW) in KC as evaluated in the tear specimen. Tear fluid was collected using schirmer strips from KC with and without CLW (n = 40) with age matched controls (n = 29). Tear fluid antioxidants cysteine, ascorbic acid, glutathione, uric acid and tyrosine were determined by HPLC electrochemical detection. Tear reactive oxygen species was estimated by fluorescence detection using dichlorodihydrofluorescein diacetate (DCF-DA) method. The corneal epithelial mRNA expression of the enzymes, gamma-glutamine cysteinyl synthase (γ-GCS) and gamma-glutamyl transpeptidase (γ-GT) by semiquantitative RT-PCR. Among the five antioxidant molecules estimated, GSH decreased significantly 50.9 ± 9.4 μM in control and 16 ± 5.7 μM in KC (p = 0.015) with increase in tyrosine 13.9 ± 2.6 μM in control, 30 ± 6.4 μM in KC cases (p = 0.022) and uric acid 162 ± 18 μM in control and 210 ± 32 μM (p < 0.00) in KC compared to the controls. The ROS levels were increased significantly, 55.7 ± 16.7 AU in KC and 23.2 ± 5.8 AU in controls (p = 0.023). No significant change in the tear antioxidants studied was observed in KC cases with and without CL wear. However tyrosine levels were increased significantly in CL wear amongst healthy controls compared to controls (p < 0.000). γ-GCS and γ-GT showed no significant change in KC epithelial cells. Though variations were seen in other antioxidants analysed, they had no statistical significance. Tear specimen in KC can indicate the antioxidant status. KC is associated with increased tear levels of tyrosine, uric acid and decrease in GSH

  14. 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

  15. Constant pH Molecular Dynamics Reveals pH-Modulated Binding of Two Small-Molecule BACE1 Inhibitors.

    PubMed

    Ellis, Christopher R; Tsai, Cheng-Chieh; Hou, Xinjun; Shen, Jana

    2016-03-17

    Targeting β-secretase (BACE1) with small-molecule inhibitors offers a promising route for treatment of Alzheimer's disease. However, the intricate pH dependence of BACE1 function and inhibitor efficacy has posed major challenges for structure-based drug design. Here we investigate two structurally similar BACE1 inhibitors that have dramatically different inhibitory activity using continuous constant pH molecular dynamics (CpHMD). At high pH, both inhibitors are stably bound to BACE1; however, within the enzyme active pH range, only the iminopyrimidinone-based inhibitor remains bound, while the aminothiazine-based inhibitor becomes partially dissociated following the loss of hydrogen bonding with the active site and change of the 10s loop conformation. The drastically lower activity of the second inhibitor is due to the protonation of a catalytic aspartate and the lack of a propyne tail. This work demonstrates that CpHMD can be used for screening pH-dependent binding profiles of small-molecule inhibitors, providing a new tool for structure-based drug design and optimization. PMID:26905811

  16. 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

    2014-01-01

    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

  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. 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.

  19. Design, Synthesis and Characterization of Novel Small Molecular Inhibitors of Ephrin-B2 Binding to EphB4

    PubMed Central

    Duggineni, Srinivas; Mitra, Sayantan; Noberini, Roberta; Han, Xiaofeng; Lin, Nan; Xu, Yan; Tian, Wang; An, Jing; Pasquale, Elena B.; Huang, Ziwei

    2013-01-01

    EphB4 is a member of the large Eph receptor tyrosine kinase family. By interacting with its preferred ligand ephrin-B2, which is also a transmembrane protein, EphB4 plays a role in a variety of physiological and pathological processes ranging from bone remodeling to cancer malignancy. EphB4-ephrin-B2 binding occurs at sites of contact between cells. Ephrin-B2 causes EphB4 clustering and increased kinase activity to generate downstream signals that affect cell behavior. Previous work identified a high-affinity antagonistic peptide that targets EphB4, named TNYL-RAW. This peptide is 15 amino acid long, has a molecular weight of ~1,700 Da and binds to the ephrin-binding pocket of EphB4. Here we report the structure-based design and chemical synthesis of two novel small molecules of ~600–700 Da, which were designed starting from the small and functionally critical C-terminal portion of the TNYL-RAW peptide. These compounds inhibit ephrin-B2 binding to EphB4 at low micromolar concentrations. Additionally, although the ephrin-B2 ligand can interact with multiple other Eph receptors besides EphB4, the two compounds retain the high selectivity of the TNYL-RAW peptide in targeting EphB4. TNYL-RAW peptide displacement experiments using the more potent of the two compounds, compound 5, suggest a competitive mode of inhibition. These EphB4 antagonistic compounds can serve as promising templates for the further development of small molecule drugs targeting EphB4. PMID:23253822

  20. 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.

  1. 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

  2. Preliminary Evidence on the Diagnostic and Molecular Role of Circulating Soluble EGFR in Non-Small Cell Lung Cancer

    PubMed Central

    Lococo, Filippo; Paci, Massimiliano; Rapicetta, Cristian; Rossi, Teresa; Sancisi, Valentina; Braglia, Luca; Cavuto, Silvio; Bisagni, Alessandra; Bongarzone, Italia; Noonan, Douglas M.; Albini, Adriana; Maramotti, Sally

    2015-01-01

    Assessment of biological diagnostic factors providing clinically-relevant information to guide physician decision-making are still needed for diseases with poor outcomes, such as non-small cell lung cancer (NSCLC). Epidermal growth factor receptor (EGFR) is a promising molecule in the clinical management of NSCLC. While the EGFR transmembrane form has been extensively investigated in large clinical trials, the soluble, circulating EGFR isoform (sEGFR), which may have a potential clinical use, has rarely been considered. This study investigates the use of sEGFR as a potential diagnostic biomarker for NSCLC and also characterizes the biological function of sEGFR to clarify the molecular mechanisms involved in the course of action of this protein. Plasma sEGFR levels from a heterogeneous cohort of 37 non-advanced NSCLC patients and 54 healthy subjects were analyzed by using an enzyme-linked immunosorbent assay. The biological function of sEGFR was analyzed in vitro using NSCLC cell lines, investigating effects on cell proliferation and migration. We found that plasma sEGFR was significantly decreased in the NSCLC patient group as compared to the control group (median value: 48.6 vs. 55.6 ng/mL respectively; p = 0.0002). Moreover, we demonstrated that sEGFR inhibits growth and migration of NSCLC cells in vitro through molecular mechanisms that included perturbation of EGF/EGFR cell signaling and holoreceptor internalization. These data show that sEGFR is a potential circulating biomarker with a physiological protective role, providing a first approach to the functional role of the soluble isoform of EGFR. However, the impact of these data on daily clinical practice needs to be further investigated in larger prospective studies. PMID:26295387

  3. 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

  4. 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

  5. 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

  6. Characterization of small HSPs from Anemonia viridis reveals insights into molecular evolution of alpha crystallin genes among cnidarians.

    PubMed

    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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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.

  13. Intra-molecular Structural Change of PAMAM Dendrimers in Aqueous Solutions Revealed by Small Angle Neutron Scattering

    SciTech Connect

    Porcar, L.; Hong, Kunlun; Butler, Paul D; Herwig, Kenneth W; Smith, Gregory Scott; Liu, Yun; Chen, Wei-Ren

    2010-01-01

    Small-angle neutron scattering (SANS) experiments were carried out to investigate the structure of aqueous (D2O) G4 PAMAM dendrimer solutions as a function of molecular protonation and dendrimer concentration. Our results indicate unambiguously that, although the radius of gyration RG remains nearly invariant, the dendrimer radial density profile (r) decreases in the dendrimer core with a continuous increase in protonation. This discovery also suggests that RG, which is commonly adopted by numerous simulation and experimental works in describing the global dendrimer size, is not suitable as the index parameter to characterize the dendrimer conformation change. We also found that RG and (r), for dendrimers dissolved in both neutral and acidified solutions, remain nearly constant over the studied concentration range. We further demonstrate that the outcome of the widely used Guinier method is questionable for extracting RG in the concentration range studied. Our results reveal the polymer colloid structural duality as benchmarks for future experimental and theoretical studies and provide a critical step toward understanding drug encapsulation by ionic bonds.

  14. Assessment of cytology based molecular analysis to guide targeted therapy in advanced non-small-cell lung cancer

    PubMed Central

    Guo, Lei; Qiu, Tian; Ling, Yun; Cao, Jian; Guo, Huiqin; Zhao, Huan; Li, Lin; Ying, Jianming

    2016-01-01

    To investigate the use of molecular testing on cytological specimens in selecting advanced non-small cell lung cancer (NSCLC) patients who are adequate for targeted treatment, a total of 137 NSCLC cases were analyzed by fluorescence in situ hybridization (FISH) for anaplastic lymphoma kinase (ALK) rearrangements, and Epidermal growth factor receptor (EGFR), kirsten rat sarcoma viral oncogene homolog (KRAS) mutations were evaluated by quantitative real-time PCR (qRT-PCR) platform combining amplification refractory mutation system (ARMS) primers and TaqMan probes. Cytological specimens included 91 fine-needle aspirates, 5 fibreoptic bronchoscopic derived samples and 41 pleural effusions. Among 137 NSCLCs analyzed for ALK FISH, 16 (11.7%, of 137) were detected to harbor ALK rearrangement. FISH positive cases were all defined as adenocarcinoma (ADC) histologic subtype and the FNA samples showed the highest ALK positive rate (13.2%, 12/91). Of the 9 ALK FISH positive patients who received crizotinib treatment, 8 (88.9%) patients exhibited tumor regression. In addition, 60 (44.8%, of 134) cases were found to harbor EGFR mutations and 22 patients with EGFR sensitive mutations who received gefitinib or erlotinib treatment showed a median PFS of 16.0 months. Mutations of KRAS occurred in 8 (6.0%, of 134) cases and this was mutually exclusive from EGFR mutation. Our results demonstrated that ALK FISH and EGFR, KRAS mutational analysis on cytological specimens are sensitive methods for screening advanced stage NSCLC patients who are adequate for targeted treatment. PMID:26789109

  15. 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

  16. Development of small molecule non-peptide formyl peptide receptor (FPR) ligands and molecular modeling of their recognition.

    PubMed

    Schepetkin, I A; Khlebnikov, A I; Giovannoni, M P; Kirpotina, L N; Cilibrizzi, A; Quinn, M T

    2014-01-01

    Formyl peptide receptors (FPRs) are G protein-coupled receptors (GPCRs) expressed on a variety of cell types. These receptors play an important role in the regulation of inflammatory reactions and sensing cellular damage. They have also been implicated in the pathogenesis of various diseases, including neurodegenerative diseases, cataract formation, and atherogenesis. Thus, FPR ligands, both agonists and antagonists, may represent novel therapeutics for modulating host defense and innate immunity. A variety of molecules have been identified as receptor subtype-selective and mixed FPR agonists with potential therapeutic value during last decade. This review describes our efforts along with recent advances in the identification, optimization, biological evaluation, and structure-activity relationship (SAR) analysis of small molecule non-peptide FPR agonists and antagonists, including chiral molecules. Questions regarding the interaction at the molecular level of benzimidazoles, pyrazolones, pyridazin-3(2H)-ones, N-phenylureas and other derivatives with FPR1 and FPR2 are discussed. Application of computational models for virtual screening and design of FPR ligands is also considered. PMID:24350845

  17. Molecular beam epitaxy growth of high quality p-doped SnS van der Waals epitaxy on a graphene buffer layer

    SciTech Connect

    Wang, W.; Leung, K. K.; Fong, W. K.; Wang, S. F.; Surya, C.; Hui, Y. Y.; Lau, S. P.; Chen, Z.; Shi, L. J.; Cao, C. B.

    2012-05-01

    We report on the systematic investigation of optoelectronic properties of tin (IV) sulfide (SnS) van der Waals epitaxies (vdWEs) grown by molecular beam epitaxy (MBE) technique. Energy band simulation using commercial CASTEP code indicates that SnS has an indirect bandgap of size 0.982 eV. Furthermore, our simulation shows that elemental Cu can be used as a p-type dopant for the material. Growth of high quality SnS thin films is accomplished by MBE technique using graphene as the buffer layer. We observed significant reduction in the rocking curve FWHM over the existing published values. Crystallite size in the range of 2-3 {mu}m is observed which is also significantly better than the existing results. Measurement of the absorption coefficient, {alpha}, is performed using a Hitachi U-4100 Spectrophotometer system which demonstrate large values of {alpha} of the order of 10{sup 4} cm{sup -1}. Sharp cutoff in the values of {alpha}, as a function of energy, is observed for the films grown using a graphene buffer layer indicating low concentration of localized states in the bandgap. Cu-doping is achieved by co-evaporation technique. It is demonstrated that the hole concentration of the films can be controlled between 10{sup 16} cm{sup -3} and 5 x 10{sup 17}cm{sup -3} by varying the temperature of the Cu K-cell. Hole mobility as high as 81 cm{sup 2}V{sup -1}s{sup -1} is observed for SnS films on graphene/GaAs(100) substrates. The improvements in the physical properties of the films are attributed to the unique layered structure and chemically saturated bonds at the surface for both SnS and the graphene buffer layer. Consequently, the interaction between the SnS thin films and the graphene buffer layer is dominated by van der Waals force and structural defects at the interface, such as dangling bonds or dislocations, are substantially reduced.

  18. Investigation on non-polar m-plane ZnO and Na-doped p-type ZnO films grown by plasma-assisted molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Chen, W.; Pan, X. H.; Chen, S. S.; He, H. P.; Huang, J. Y.; Lu, B.; Ye, Z. Z.

    2015-10-01

    Non-polar ZnO and Na-doped ZnO films were epitaxially grown on m-plane sapphire substrates by plasma-assisted molecular beam epitaxy. The films exhibit dominant () ( m-plane) orientation as identified by the X-ray diffraction pattern. The quality of the obtained m-plane ZnO film is evidenced by X-ray diffraction rocking curves full width at half maximum of 1125 arcsec for the () reflection and 1427 arcsec for the () reflection, respectively. Hall-effect measurements show that the m-plane Na-doped ZnO film exhibits p-type conductivity with a hole concentration of 2.50 × 1017 cm-3, while the m-plane ZnO film exhibits compensatory conductivity. Na atoms substituting for Zn atoms are believed to be the origin of p-type conductivity. The Na-related acceptor level is deduced to be ~120 meV by temperature-dependent photoluminescence, indicating the superiority of m-plane ZnO film in p-type doping compared with the polar ZnO film.

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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.

  5. Elucidation of direct competition and allosteric modulation of small-molecular-weight protein ligands using surface plasmon resonance methods.

    PubMed

    Huber, Walter; Sinopoli, Alessandro; Kohler, Josiane; Hug, Melanie; Ruf, Armin; Huber, Sylwia

    2015-08-01

    The present work introduces a surface plasmon resonance-based method for the discrimination of direct competition and allosteric effects that occur in ternary systems comprising a receptor protein and two small-molecular-weight ligands that bind to it. Fatty acid binding protein 4, fructose-1,6-bisphosphatase and human serum albumin were used as model receptor molecules to demonstrate the performance of the method. For each of the receptor molecules, pairs of ligand molecules were selected for which either direct competition or an allosteric effect had already been determined by other methods. The method of discrimination introduced here is based on the surface plasmon resonance responses observed at equilibrium when an immobilized receptor protein is brought into contact with binary mixtures of interacting ligands. These experimentally determined responses are compared with the responses calculated using a theoretical model that considers both direct competition and allosteric ligand interaction modes. This study demonstrates that the allosteric ternary complex model, which enables calculation of the fractional occupancy of the protein by each ligand in such ternary systems, is well suited for the theoretical calculation of these types of responses. For all of the ternary systems considered in this work, the experimental and calculated responses in the chosen concentration ratio range were identical within a five-σ confidence interval when the calculations considered the correct interaction mode of the ligands (direct competition or different types of allosteric regulation), and in case of allosteric modulation, also the correct strength of this effect. This study also demonstrates that the allosteric ternary complex model-based calculations are well suited to predict the ideal concentration ratio range or even single concentration ratios that can serve as hot spots for discrimination, and such hot spots can drastically reduce the numbers of measurements needed

  6. Alternative splice isoforms of small conductance calcium-activated SK2 channels differ in molecular interactions and surface levels

    PubMed Central

    Scholl, Elizabeth Storer; Pirone, Antonella; Cox, Daniel H; Duncan, R Keith; Jacob, Michele H

    2014-01-01

    Small conductance Ca2+-sensitive potassium (SK2) channels are voltage-independent, Ca2+-activated ion channels that conduct potassium cations and thereby modulate the intrinsic excitability and synaptic transmission of neurons and sensory hair cells. In the cochlea, SK2 channels are functionally coupled to the highly Ca2+ permeant α9/10-nicotinic acetylcholine receptors (nAChRs) at olivocochlear postsynaptic sites. SK2 activation leads to outer hair cell hyperpolarization and frequency-selective suppression of afferent sound transmission. These inhibitory responses are essential for normal regulation of sound sensitivity, frequency selectivity, and suppression of background noise. However, little is known about the molecular interactions of these key functional channels. Here we show that SK2 channels co-precipitate with α9/10-nAChRs and with the actin-binding protein α-actinin-1. SK2 alternative splicing, resulting in a 3 amino acid insertion in the intracellular 3′ terminus, modulates these interactions. Further, relative abundance of the SK2 splice variants changes during developmental stages of synapse maturation in both the avian cochlea and the mammalian forebrain. Using heterologous cell expression to separately study the 2 distinct isoforms, we show that the variants differ in protein interactions and surface expression levels, and that Ca2+ and Ca2+-bound calmodulin differentially regulate their protein interactions. Our findings suggest that the SK2 isoforms may be distinctly modulated by activity-induced Ca2+ influx. Alternative splicing of SK2 may serve as a novel mechanism to differentially regulate the maturation and function of olivocochlear and neuronal synapses. PMID:24394769

  7. Molecular characterization and expression analysis of the small GTPase ROP members expressed in laticifers of the rubber tree (Hevea brasiliensis).

    PubMed

    Qin, Yunxia; Huang, Yacheng; Fang, Yongjun; Qi, Jiyan; Tang, Chaorong

    2014-01-01

    ROP (Rho of plants) proteins are plant-specific Rho-type small GTPases which play important roles in cellular processes and stress responses. This study explores the characteristics and possible functions of ROPs that are expressed primarily in laticifers of the rubber tree (Hevea brasiliensis). The work serves as a preliminary step to determining their involvement in latex flow and regeneration, laticifers formation and tapping panel dryness (TPD, a physiological disorder in rubber trees that result in the stoppage of latex flow). In this connection, we (i) identified five HbROPs (HbROP1-HbROP5) by searching latex transcripts database and the genome databases, (ii) characterized molecular and phylogenic aspects of the HbROPs and examined the cis-regulatory elements in their promoter regions; (iii) analyzed by Real-time Quantitative PCR (QPCR) the tissue specificity of the HbROPs and their expression patterns in response to tapping, bark wounding and growth regulator treatments. All five HbROP genes were strongly expressed in the latex, with HbROP1, 3, 4 and 5 showing the highest expression among the six Hevea tissues examined, viz. latex, bud, mature leaf, bark, male flower and seed. When tapping was initiated on previously untapped trees, HbROP3 transcription was substantially down-regulated whereas HbROP5 expression was markedly up-regulated. Transcripts of HbROP3 rose gradually with the development of TPD. Except for the cytokinin 6-benzyl aminopurine that induced a rise in HbROP5 transcripts by more than 2-fold, the other growth regulators tested had little effect on HbROPs expression. The roles of HbROPs in rubber tree are discussed in relation to the diverse functions of ROP homologs reported in other plant species. PMID:24308989

  8. 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

  9. 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

  10. Localization of small heat shock proteins to the higher plant endomembrane system. [Low-molecular-weight heat shock proteins

    SciTech Connect

    Helm, K.W.; Vierling, E. ); LaFayette, P.R.; Nagao, R.T.; Key, J.L. )

    1993-01-01

    Most eukaryotic cells respond to high temperature and other stresses with the production of heat shock proteins, which aid in cell survival. There are four major classes of heat shock proteins HSP90, HSP70, HSP60 and low-molecular weight HSP. The data from this research indicate that members of the low-molecular weight heat shock proteins are most likely resident endoplasmic reticulum (ER) proteins and may be similar in function to related low-molecular weight heat shock proteins in the cytoplasm. The low-molecular weight heat shock proteins, the HSP90 and the HSP70 all appear to localize to the endoplasmic reticulum. Since the ER-localized low-molecular weight heat shock proteins are physically separated from their counterparts in other cell compartments, investigations of the ER-localized heat shock proteins provides a simplified model system for determining the functions of low-molecular weight heat shock proteins in eukaryotes.

  11. 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

  12. 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.

  13. 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. PMID:26954555

  14. Structures and stabilities of small silicon clusters: Ab initio molecular-orbital calculations of Si7-Si11

    NASA Astrophysics Data System (ADS)

    Zhu, Xiaolei; Zeng, X. C.

    2003-02-01

    Ab initio all-electron molecular-orbital calculations have been carried out to study the structure and relative stability of small silicon clusters (Sin, n=7-11). A number of low-energy geometric isomers are optimized at the second-order Møller-Plesset (MP2) MP2/6-31G(d) level. Harmonic vibrational analysis has been performed to assure that the optimized geometries are stable. The total energies of stable isomers are computed at the coupled-cluster single and double substitutions (including triple excitations) [CCSD(T)] CCSD(T)/6-31G(d) level. The calculated binding energies per atom at both the MP2/6-31G(d) and CCSD(T)/6-31G(d) levels agree with the experiments. For Si7, Si8, and Si10, the lowest-energy structures are the same as those predicted previously from the all-electron optimization at the Hartree-Fock (HF) HF/6-31G(d) level [Raghavachari and Rohlfing, J. Chem. Phys. 89, 2219 (1988)]. For Si9, the lowest-energy isomer is same as that predicted based on density-functional plane-wave pseudopotential method [Vasiliev, Ogut, and Chelikowsky, Phys. Rev. Lett. 78, 4805 (1997)]. Particular attention has been given to Si11 because several low-energy geometric isomers were found nearly isoenergetic. On the basis of MP2/6-311G(2d)//CCSD(T)/6-311G(2d) calculation, we identified that the C2v isomer, a tricapped trigonal prism with two additional caps on side trigonal faces, is most likely the global-minimum structure. However, another competitive geometric isomer for the global minimum is also found on basis of the MP2/6-311G(2d)//CCSD(T)/6-311G(2d) calculation. Additionally, calculations of the binding energy and the cluster polarizability offer more insights into relatively strong stability of two magic-number clusters Si6 and Si10.

  15. Molecular predictors of response to tyrosine kinase inhibitors in patients with Non-Small-Cell Lung Cancer

    PubMed Central

    2012-01-01

    Introduction Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) have become a treatment option in non-small-cell lung cancer (NSCLC) patients. However, despite their use in this disease, a significant number of patients will eventually develop resistance and relapse. In this study, we aimed to characterize several molecular events involved in potential resistance mechanisms to anti-EGFR treatment and correlate our findings with clinical outcome. Material and methods The medical records of patients with NSCLC who received anti-EGFR TKIs in any line within the participating centers were reviewed and available paraffin embedded tissue was retrieved. Mutational analysis for EGFR, KRAS, BRAF and intron-exon 14 deletions of MET; FISH analysis for chromosomal gain or amplification for EGFR, MET and the deletion marker D7S486 were performed. Furthermore, the expression of EGFR and MET were analysed by immunohistochemistry. All results were correlated with treatment outcomes. Results Between 10/2001 and 12/2009 from an initial cohort of 72 treated patients, 59 cases (28 gefitinib/ 31 erlotinib) were included in the analysis. The majority had adenocarcinoma histology (68%), and received treatment in the second line setting (56%). Disease control rate (DCR) was 25.4% for all patients. EGFR and RAS mutational rates were 33% and 10% respectively, no other mutations were identified. High EGFR expressing tumors were found in 7 of 45 cases and pEGFR positivity (IHC) was found in 56% of the cases; MET expression was found in 48% of tumors. EGFR gene amplification was found in 4 cases, two cases showed high polysomy; overall, 13% cases were FISH positive for EGFR. High polysomy of MET gene was detected in 1/43 cases tested. D7S486 locus deletion was detected in 15/37 (40%) of cases. EGFR mutational status and gene gain were both associated with more favorable DCR. No other associations between examined biomarkers and DCR or survival were noted. Conclusions

  16. 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

  17. Zero-dark-counting high-speed X-ray photon detection using a cerium-doped yttrium aluminum perovskite crystal and a small photomultiplier tube and its application to gadolinium imaging

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Satoshi; Sato, Eiichi; Oda, Yasuyuki; Nakamura, Ryuji; Oikawa, Hirobumi; Yabuushi, Tomonori; Ariga, Hisanori; Ehara, Shigeru

    2014-04-01

    X-ray photons are detected using a cerium-doped yttrium aluminum perovskite [YAP(Ce)] single-crystal scintillator with a decay time of 30 ns and a small-sized photomultiplier tube (SPMT). The negative output pulse from the SPMT is amplified by a high-speed inverse amplifier, and the event pulses are sent to a multichannel analyzer to measure X-ray spectra. The energy resolution of the spectrometer was 15% at 59.5 keV. We carried out photon-counting computed tomography using gadolinium media with a maximum rate of 650 kilo counts per second and confirmed the energy-dispersive effect with changes in the description voltage of event pulses using a high-speed comparator.

  18. 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.

  19. What parameters to consider and which software tools to use for target selection and molecular design of small interfering RNAs.

    PubMed

    Matveeva, Olga

    2013-01-01

    The design of small gene silencing RNAs with a high probability of being efficient still has some elements of an art, especially when the lowest concentration of small molecules needs to be utilized. The design of highly target-specific small interfering RNAs or short hairpin RNAs is even a greater challenging task. Some logical schemes and software tools that can be used for simplifying both tasks are presented here. In addition, sequence motifs and sequence composition biases of small interfering RNAs that have to be avoided because of specificity concerns are also detailed. PMID:23027043

  20. Conformation of one- and two-chain high molecular weight urokinase analyzed by small-angle neutron scattering and vacuum ultraviolet circular dichroism

    SciTech Connect

    Mangel, W.F.; Lin, B.H.; Ramakrishnan, V. )

    1991-05-25

    The structures of one- and two-chain high molecular weight human urokinase were analyzed by small-angle neutron scattering and vacuum ultraviolet circular dichroism. Both one- and two-chain high molecular weight urokinases exhibited a radius of gyration of 31 A and a maximum dimension of 90 A. Neither parameter was affected by the presence of lysine sufficient to saturate all the lysine-binding sites in human plasminogen. These physical parameters are consistent with the sedimentation coefficient of high molecular weight urokinase and indicate that both proteins are highly asymmetric. Neither protein contained much alpha-helix or parallel beta-sheet. Most of the secondary structure was in the form of antiparallel beta-sheet and beta-turns, very similar to the secondary structure of plasminogen. The macroscopic kinetic constants, Km and kcat, for the hydrolysis of (pyroGlu-Gly-Arg-NH)2-rhodamine by two-chain high molecular weight urokinase and low molecular weight urokinase which lacks the epidermal growth factor and kringle domains were similar. These structural and kinetic data are consistent with the domains in both forms of urokinase being independent structural and functional units.

  1. Molecular dynamics characterization of the conformational landscape of small peptides: A series of hands-on collaborative practical sessions for undergraduate students.

    PubMed

    Rodrigues, João P G L M; Melquiond, Adrien S J; Bonvin, Alexandre M J J

    2016-01-01

    Molecular modelling and simulations are nowadays an integral part of research in areas ranging from physics to chemistry to structural biology, as well as pharmaceutical drug design. This popularity is due to the development of high-performance hardware and of accurate and efficient molecular mechanics algorithms by the scientific community. These improvements are also benefitting scientific education. Molecular simulations, their underlying theory, and their applications are particularly difficult to grasp for undergraduate students. Having hands-on experience with the methods contributes to a better understanding and solidification of the concepts taught during the lectures. To this end, we have created a computer practical class, which has been running for the past five years, composed of several sessions where students characterize the conformational landscape of small peptides using molecular dynamics simulations in order to gain insights on their binding to protein receptors. In this report, we detail the ingredients and recipe necessary to establish and carry out this practical, as well as some of the questions posed to the students and their expected results. Further, we cite some examples of the students' written reports, provide statistics, and share their feedbacks on the structure and execution of the sessions. These sessions were implemented alongside a theoretical molecular modelling course but have also been used successfully as a standalone tutorial during specialized workshops. The availability of the material on our web page also facilitates this integration and dissemination and lends strength to the thesis of open-source science and education. PMID:26751257

  2. 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

  3. Boiling Points of the Family of Small Molecules CHwFxClyBrz: How Are They Related to Molecular Mass?

    NASA Astrophysics Data System (ADS)

    Laing, Michael

    2001-11-01

    A plot of boiling point versus molecular mass for the family of tetrahedral molecular compounds CHw Fx Cly Brz is not linear, but yields a two-dimensional array with the data for molecules of similar formulae lying on straight lines. A plot of boiling point versus molar refraction (polarizability) of the compounds gives three near-parallel straight lines. The highest is for the family of compounds CH2XY; the lowest is for the all-halogen compounds CFxCyBrz; the compounds CHXxYyZz and CH3X lie intermediate. The boiling points of the compounds containing hydrogen are enhanced relative to what their molecular refraction suggests (excepting CH4). Boiling point is related to the macroscopic properties of refractive index and density of the liquid and to the molecular properties of molar refraction and dipole moment. These are connected by the molecular mass, which, with the density, determines the molar volume and thus the polarizability.

    See Letter re: this article.

    See Second Letter re: this article.

  4. 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

  5. Effects of molybdenum oxide molecular doping on the chemical structure of poly(3,4-ethylenedioxythiophene):poly(stylenesulfonate) and on carrier collection efficiency of silicon/poly(3,4-ethylenedioxythiophene):poly(stylenesulfonate) heterojunction solar cells

    NASA Astrophysics Data System (ADS)

    Liu, Q.; Khatri, I.; Ishikawa, R.; Ueno, K.; Shirai, H.

    2013-05-01

    The effects of MoO3 molecular doping in poly(3,4-ethylenedioxythiophene):poly(stylenesulfonate) (PEDOT:PSS) on the chemical structure and, in turn, on the carrier collection efficiency of c-Si/PEDOT:PSS heterojunction solar cells are demonstrated. Scanning electron microscopy revealed that the hydrophilic PSS polymer chain was intercalated into the interlayer van der Waals gap of MoO3 flake sheets, which modified the chemical structure of PEDOT:PSS. MoO3 exhibited intense photoluminescence in the 350-550 nm region, which enhanced the carrier collection efficiency of c-Si/PEDOT:PSS heterojunction solar cells with no significant changes. These findings suggest that the intense photoluminescence of MoO3 and its light wavelength conversion contribute to the increased carrier collection efficiency.

  6. 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.

  7. 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.

  8. 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

  9. 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,...

  10. On the growth mechanism of Li- and Na-doped Zn chalcogenides on GaAs(001) by means of molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Ohishi, M.; Yoneta, M.; Ishii, S.; Ohura, M.; Hiroe, Y.; Saito, H.

    1996-02-01

    Sharp and semicircular patterns were observed in RHEED during the MBE growth of Li- or Na-acceptor doped ZnSe and ZnS on GaAs(001). The radius and the separation between the diffraction circles vary with the change of the azimuth of the incident electron beam. Calculated diffraction patterns assuming that Li or Na atoms are arrayed one-dimensionally along the [110] direction of the crystal axis are in good agreement with the experimental results. We conclude that Li or Na atoms are incorporated at the [110] terrace steps, which prevents the further growth from the step edge.

  11. 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.

  12. 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

  13. 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

  14. On structural features of fullerene C60 dissolved in carbon disulfide: complementary study by small-angle neutron scattering and molecular dynamic simulations.

    PubMed

    Avdeev, M V; Tropin, T V; Bodnarchuk, I A; Yaradaikin, S P; Rosta, L; Aksenov, V L; Bulavin, L A

    2010-04-28

    The parameters of fullerene C(60) dissolved in carbon disulfide CS(2) are analyzed by small-angle neutron scattering (SANS) in a wide interval of momentum transfer. To exclude the influence of nonequilibrium conditions, the solutions are prepared without applying shaking, stirring or ultrasound. No indication of the equilibrium cluster state of C(60) (with the cluster size below 60 nm) in the final solutions is revealed. Molecular dynamic simulations are complementary used to find out the partial volume of C(60) in CS(2) and the scattering contribution of the solvent organization at the interface with the fullerene molecule, which is shown to be small. Among several approaches for describing SANS data the preference is given to the model, which takes into account the presence of stable C(60) dimers (comprising 10% of the total particle number density) in the solution. PMID:20441296

  15. 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

  16. 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

  17. Identification of a small molecule inhibitor of serine 276 phosphorylation of the p65 subunit of NF-κB using in silico molecular docking

    PubMed Central

    Law, Mary; Corsino, Patrick; Parker, Nicole Teoh; Law, Brian K.

    2009-01-01

    NF-κB is activated in many types of cancer. Phosphorylation of p65 at serine 276 is required for the expression of a subset of NF-κB regulated genes, including vascular cell adhesion molecule-1 (VCAM-1) and interleukin-8 (IL-8). Thus, inhibition of serine 276 phosphorylation may prevent metastasis and angiogenesis in certain tumor types. Using in silico molecular docking, small molecules that are predicted to bind to a structural pocket near serine 276 were identified. One compound, NSC-127102, hinders serine 276 phosphorylation and the expression of IL-8 and VCAM-1. Small molecules such as NSC-127102 may be optimized for the future treatment of cancer. PMID:19910110

  18. Fuzzy ARTMAP prediction of biological activities for potential HIV-1 protease inhibitors using a small molecular data set.

    PubMed

    Andonie, Răzvan; Fabry-Asztalos, Levente; Abdul-Wahid, Christopher Badi'; Abdul-Wahid, Sarah; Barker, Grant I; Magill, Lukas C

    2011-01-01

    Obtaining satisfactory results with neural networks depends on the availability of large data samples. The use of small training sets generally reduces performance. Most classical Quantitative Structure-Activity Relationship (QSAR) studies for a specific enzyme system have been performed on small data sets. We focus on the neuro-fuzzy prediction of biological activities of HIV-1 protease inhibitory compounds when inferring from small training sets. We propose two computational intelligence prediction techniques which are suitable for small training sets, at the expense of some computational overhead. Both techniques are based on the FAMR model. The FAMR is a Fuzzy ARTMAP (FAM) incremental learning system used for classification and probability estimation. During the learning phase, each sample pair is assigned a relevance factor proportional to the importance of that pair. The two proposed algorithms in this paper are: 1) The GA-FAMR algorithm, which is new, consists of two stages: a) During the first stage, we use a genetic algorithm (GA) to optimize the relevances assigned to the training data. This improves the generalization capability of the FAMR. b) In the second stage, we use the optimized relevances to train the FAMR. 2) The Ordered FAMR is derived from a known algorithm. Instead of optimizing relevances, it optimizes the order of data presentation using the algorithm of Dagher et al. In our experiments, we compare these two algorithms with an algorithm not based on the FAM, the FS-GA-FNN introduced in [4], [5]. We conclude that when inferring from small training sets, both techniques are efficient, in terms of generalization capability and execution time. The computational overhead introduced is compensated by better accuracy. Finally, the proposed techniques are used to predict the biological activities of newly designed potential HIV-1 protease inhibitors. PMID:21071799

  19. 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.

  20. Electron transfer modifies chemical properties of C70 fullerene surface: An ab initio molecular dynamics study of C70O3 molozonides doped with light atoms

    NASA Astrophysics Data System (ADS)

    Bil, Andrzej; Hutter, Jürg; Morrison, Carole A.

    2014-06-01

    Light metal atoms such as Li, K (electronic state 2S1/2) or Ca (1S0) encapsulated in a C70 cage considerably modifies the chemical properties of the fullerene surface due to metal-to-cage electron transfer. H-doped and anion ozonide systems were also considered to validate the electron transfer hypothesis. The relative stabilities of the eight isomers of the C70O3 molozonide series at room temperature depend on the identity of the endohedral guest, as was the preferred channel for thermal decomposition. No electron transfer was observed for the complex N@C70 where the fullerene acts as an inert container for the 4S3/2 radical.

  1. Universal scaling behavior of molecular electronic stopping cross section for protons colliding with small molecules and nucleobases

    NASA Astrophysics Data System (ADS)

    Trujillo-López, L. N.; Martínez-Flores, C.; Cabrera-Trujillo, R.

    2013-10-01

    The electronic stopping cross section and mean excitation energy for molecules and 5 nucleobases have been calculated within the first Born approximation in terms of an orbital decomposition to take into account the molecular structure. The harmonic oscillator (HO) description of the stopping cross section together with a Floating Spherical Gaussian Orbital (FSGO) model is implemented to account for the chemical composition of the target. This approach allows us to use bonds, cores, and lone pairs as HO basis to describe the ground state molecular structure. In the HO model, the orbital angular frequency is the only parameter that connects naturally with the mean excitation energy. As a result, we obtain a simple expression for the equivalent mean excitation energy in terms of the orbital radius parameter, as well as an analytical expression of the stopping cross section. For gas phase molecular targets, we provide HO based orbital mean excitation energies to describe any molecule containing C, N, O, H, and P atoms. We present results for protons colliding with H2, N2, O2, H2O, CO2, propylene (C3H6), methane (CH4), ethylene (C2H4) and the nucleobases - guanine (C5H5N5O), cytosine (C4H5N2O2), thymine (C5H6N2O2), adenine (C5H5N5) and uracil (C4H4N2O2). The results for the stopping cross section are compared with available experimental and theoretical data showing good to excellent agreement in the region of validity of the model. The HO approach allows us to obtain a universal stopping cross section formula to describe a universal scaling behavior for the energy loss process. The universal scaled curve is confirmed by the experimental data.

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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

    2016-01-01

    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 180(°). PMID:26846891

  7. 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. PMID:26430156

  8. Development of a small-scale bioreactor method to monitor the molecular diversity and environmental impacts of bacterial biofilm communities from an acid mine drainage impacted creek.

    PubMed

    Cole, Michael; Wrubel, Joshua; Henegan, Patricia; Janzen, Christopher; Holt, Jack; Tobin, Tammy

    2011-10-01

    Shamokin Creek is a tributary of the Susquehanna River in central Pennsylvania that is heavily impacted by the acid mine drainage (AMD) caused by the oxidation of pyrite from the region's extensive anthracite coal mining industry. Recent studies have begun to characterize the microbial communities present in this and other AMD-impacted waters, but varying environmental conditions have complicated attempts to determine the ecological impacts of individual bacterial species within these communities. This study developed a small-scale biofilm reactor protocol that allowed us to simultaneously monitor the development of bacterial biofilm communities in AMD-impacted creek collected water using terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes, while assessing the impacts that the developing biofilms were having on water quality. Our analysis confirmed that the diversity and composition of these small in situ biofilm communities could be monitored using molecular methods, and indicated the possible presence of many taxa frequently found in AMD environments, including Sulfobacillus, Nitrospira, Desulfovibrio, Geobacter, and Leptothrix species. A significant increase in the total sulfate was observed in the bioreactor, and as most likely due to the accumulation of sulfur-oxidizing bacteria such as Sulfobacillus in the biofilms. This system will allow us to study the microbial ecology of Shamokin Creek through controlled experiments that will ultimately integrate microscopic, molecular, physiological and chemical analyses, and that can be utilized to develop more effective and cost-efficient environmental remediation techniques for AMD-impacted areas. PMID:21821067

  9. 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

  10. 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

  11. Nitrogen and phosphorus co-doped graphene quantum dots: synthesis from adenosine triphosphate, optical properties, and cellular imaging

    NASA Astrophysics Data System (ADS)

    Ananthanarayanan, Arundithi; Wang, Yue; Routh, Parimal; Sk, Mahasin Alam; Than, Aung; Lin, Ming; Zhang, Jie; Chen, Jie; Sun, Handong; Chen, Peng

    2015-04-01

    Graphene quantum dots (GQDs) are emerging zero-dimensional materials promising a wide spectrum of applications, particularly, as superior fluorescent reporters for bio-imaging and optical sensing. Heteroatom doping can endow GQDs with new or improved photoluminescence properties. Here, we demonstrate a simple strategy for the synthesis of nitrogen and phosphorus co-doped GQDs from a single biomolecule precursor (adenosine triphosphate - ATP). Such ATP-GQDs exhibit high fluorescence quantum yield, strong two-photon upconversion, small molecular weight, high photostability, and good biocompatibility. Furthermore, transferrin conjugated ATP-GQDs have been used for imaging and real-time tracking of transferrin receptors in live cells.Graphene quantum dots (GQDs) are emerging zero-dimensional materials promising a wide spectrum of applications, particularly, as superior fluorescent reporters for bio-imaging and optical sensing. Heteroatom doping can endow GQDs with new or improved photoluminescence properties. Here, we demonstrate a simple strategy for the synthesis of nitrogen and phosphorus co-doped GQDs from a single biomolecule precursor (adenosine triphosphate - ATP). Such ATP-GQDs exhibit high fluorescence quantum yield, strong two-photon upconversion, small molecular weight, high photostability, and good biocompatibility. Furthermore, transferrin conjugated ATP-GQDs have been used for imaging and real-time tracking of transferrin receptors in live cells. Electronic supplementary information (ESI) available: Supplementary figures related to characterization, computational studies and protein conjugation. See DOI: 10.1039/c5nr01519g

  12. Electron mobilities and quantum Hall effect in modulation-doped HgTe-CdTe superlattices

    NASA Astrophysics Data System (ADS)

    Hoffman, C. A.; Meyer, J. R.; Bartoli, F. J.; Lansari, Y.; Cook, J. W., Jr.; Schetzina, J. F.

    1991-10-01

    Photoassisted molecular-beam epitaxy and controlled modulation doping have been used to grow HgTe-CdTe superlattices with n-type carrier concentrations of up to 3×1017 cm-3. It is found that in contrast to Hg1-xCdxTe alloys where the electron mobility decreases strongly with donor concentration, μn in the modulation-doped superlattices is nearly independent of ND at large ND. We also discuss an observation of the quantum Hall effect associated with carriers distributed throughout the interior of a HgTe-CdTe superlattice. Whereas previous reports of quantized steps in the Hall conductivity have involved a small number of conduction channels (hence a small fraction of the superlattice periods), we observe plateaus at multiples of ~=200e2/h in a number of 200-period superlattices with high doping levels. This indicates participation by nearly all wells in the superlattice, and implies that the controlled doping is extremely uniform.

  13. 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

  14. A molecular phylogeny of Asian species of the genus Metagonimus (Digenea)--small intestinal flukes--based on representative Japanese populations.

    PubMed

    Pornruseetairatn, Siritavee; Kino, Hideto; Shimazu, Takeshi; Nawa, Yukifumi; Scholz, Tomáš; Ruangsittichai, Jiraporn; Saralamba, Naowarat Tanomsing; Thaenkham, Urusa

    2016-03-01

    Metagonimus Katsurada, 1912 is a genus of small intestinal parasites. The genus comprises eight species, primarily from far-eastern Asia, with two exceptions reported from Europe. Metagonimus yokogawai, the most widespread species, is the main agent responsible for the intestinal disease, metagonimiasis, in Japan and some other East Asian countries. On the basis of the ratio of the size of the ventral and oral suckers, Metagonimus has traditionally been morphologically divided into two groups; however, the genus has not been extensively studied using molecular data. To reveal phylogenetic relationships within Metagonimus based on molecular data, we analyzed six of the seven species present in Asia using samples collected in central Japan. Maximum likelihood and Bayesian analyses of a combined 28S ribosomal DNA (rDNA), internal transcribed spacer 2 (ITS2), and mitochondrial cox1 gene sequence dataset separated the six species into two well-supported clades. One clade comprised M. yokogawai, M. takahashii, M. miyatai, and M. hakubaensis, whereas the other consisted of M. otsurui and M. katsuradai. Genetic distances calculated from 28S rDNA and ITS2 nucleotide sequences and a comparison of the predicted amino acid sequences of cox1 gene suggested that M. otsurui and M. katsuradai may have diverged recently. None of the four main morphological characters used to delimit species of Metagonimus (i.e., sucker ratio, positions of the uterus and testes, and distribution of vitelline follicles) was consistent with the distribution of species in the molecular tree. PMID:26614357

  15. 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.

  16. Molecular adsorption on graphene

    NASA Astrophysics Data System (ADS)

    Kong, Lingmei; Enders, Axel; Rahman, Talat S.; Dowben, Peter A.

    2014-11-01

    Current studies addressing the engineering of charge carrier concentration and the electronic band gap in epitaxial graphene using molecular adsorbates are reviewed. The focus here is on interactions between the graphene surface and the adsorbed molecules, including small gas molecules (H2O, H2, O2, CO, NO2, NO, and NH3), aromatic, and non-aromatic molecules (F4-TCNQ, PTCDA, TPA, Na-NH2, An-CH3, An-Br, Poly (ethylene imine) (PEI), and diazonium salts), and various biomolecules such as peptides, DNA fragments, and other derivatives. This is followed by a discussion on graphene-based gas sensor concepts. In reviewing the studies of the effects of molecular adsorption on graphene, it is evident that the strong manipulation of graphene’s electronic structure, including p- and n-doping, is not only possible with molecular adsorbates, but that this approach appears to be superior compared to these exploiting edge effects, local defects, or strain. However, graphene-based gas sensors, albeit feasible because huge adsorbate-induced variations in the relative conductivity are possible, generally suffer from the lack of chemical selectivity.

  17. Molecular adsorption on graphene.

    PubMed

    Kong, Lingmei; Enders, Axel; Rahman, Talat S; Dowben, Peter A

    2014-11-01

    Current studies addressing the engineering of charge carrier concentration and the electronic band gap in epitaxial graphene using molecular adsorbates are reviewed. The focus here is on interactions between the graphene surface and the adsorbed molecules, including small gas molecules (H(2)O, H(2), O(2), CO, NO(2), NO, and NH(3)), aromatic, and non-aromatic molecules (F4-TCNQ, PTCDA, TPA, Na-NH(2), An-CH(3), An-Br, Poly (ethylene imine) (PEI), and diazonium salts), and various biomolecules such as peptides, DNA fragments, and other derivatives. This is followed by a discussion on graphene-based gas sensor concepts. In reviewing the studies of the effects of molecular adsorption on graphene, it is evident that the strong manipulation of graphene's electronic structure, including p- and n-doping, is not only possible with molecular adsorbates, but that this approach appears to be superior compared to these exploiting edge effects, local defects, or strain. However, graphene-based gas sensors, albeit feasible because huge adsorbate-induced variations in the relative conductivity are possible, generally suffer from the lack of chemical selectivity. PMID:25287516

  18. Choline molecular imaging with small-animal PET for monitoring tumor cellular response to photodynamic therapy of cancer

    NASA Astrophysics Data System (ADS)

    Fei, Baowei; Wang, Hesheng; Wu, Chunying; Meyers, Joseph; Xue, Liang-Yan; MacLennan, Gregory; Schluchter, Mark

    2009-02-01

    We are developing and evaluating choline molecular imaging with positron emission tomography (PET) for monitoring tumor response to photodynamic therapy (PDT) in animal models. Human prostate cancer (PC-3) was studied in athymic nude mice. A second-generation photosensitizer Pc 4 was used for PDT in tumor-bearing mice. MicroPET images with 11C-choline were acquired before PDT and 48 h after PDT. Time-activity curves of 11C-choline uptake were analyzed before and after PDT. For treated tumors, normalized choline uptake decreased significantly 48 h after PDT, compared to the same tumors pre-PDT (p <~ 0.001). However, for the control tumors, normalized choline uptake increased significantly (p <~ 0.001). PET imaging with 11C-choline is sensitive to detect early tumor response to PDT in the animal model of human prostate cancer.

  19. 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).

  20. Primary small cell carcinoma of the stomach: a case report with an immunohistochemical and molecular genetic analysis.

    PubMed

    Terada, Tadashi

    2013-01-01

    Small cell carcinoma (SCC) of the stomach is extremely rare; about 110 cases have been reported in the world literature. Immunohistochemical studies of various antigens and genetic studies of KIT and platelet-derived growth factor-α (PDGFRA) have not been performed in gastric SCC. An 84-year-old man consulted our hospital because of epigastralgia and weakness. Blood test showed anemia and increased CA19-9 (233 U/ml). Endoscopic examination revealed a large Borrmann type III tumor measuring 6x8 cm in the stomach. Biopsies from the tumor revealed typical small cell carcinoma with very scant cytoplasm, hyperchromatic nuclei, absent nucleoli, molded nuclei, and increased nucleo-cytoplasmic ratio. Immunohistochemically, the tumor cells were positive for pancytokeratin (PCK) WSS, PCK MNF-116, PCK AE1/3, PCK CAM5.2, cytokeratin (CK) 34BE12, CK 5/6, CK7, CK8, CK18, vimentin, EMA, KIT (CD117), CD56, synaptophysin, chromogranin, NSE, CA19-9, CEA, p53 protein, and Ki67 antigen (Ki-67 labeling = 60%). The tumor cells were negative for CK14, CK19, CK20, PDGFRA, CD45, CD45RO, CD3, CD20, CD30, and CD79a. A retrospective genetic analysis using PCR-direct sequencing method in paraffin sections identified no mutations of KIT (exons 9, 11, 13 and 17) and PDGFRA (exons 12 and 18) genes. Various imaging modalities including CT and MRI showed multiple small metastases in the liver, bilateral lungs, and perigastric lymph nodes. The patient was thus inoperative. The patient is now treated by cisplatin-based chemotherapy four months after the first manifestation. PMID:23411939