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Sample records for doped small molecular

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

    SciTech Connect

    Cheon, Kwang-Ohk

    2003-01-01

    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 α-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.

  2. 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

  3. 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.

  4. Enhanced short-circuit current density in poly(3-hexylthiophene) and 1-(3-methoxycarbonyl)-propyl-1-phenyl-(6,6)C61 based organic solar cells by doping small molecular perylene

    NASA Astrophysics Data System (ADS)

    Lou, Yanhui; Wang, Zhaokui; Naka, Shigeki; Okada, Hiroyuki

    2011-07-01

    The authors investigate the effects of a small molecular dye, perylene, on the performance of organic solar cells based on poly(3-hexylthiophene) (P3HT) and 1-(3-methoxycarbonyl)-propyl-1-phenyl-(6,6)C61 (PCBM) blends. The short-circuit current density is improved, and a maximum 27% enhancement in power conversion efficiency is achieved by doping suitable perylene into P3HT:PCBM blends. It is attributed to be the enhanced absorption of perylene doped P3HT:PCBM blends, which is also confirmed in single-carrier devices. Moreover, the barrier height at the anode/blend is largely lowered from 0.61 eV to 0.28 eV through evaluating temperature dependence of current-voltage characteristics.

  5. Small Molecular as SIRT Modulators.

    PubMed

    Yao, Lei; Xu, Xiangming; Chen, Kai

    2016-06-19

    Sirtuins are class III histone deacetylases, they involve in many important biological functions. Small molecules that can modulate sirtuin activity have been shown to have potential for treating many human diseases. In the article, recent development of small molecular as SIRT modulators has been reviewed.

  6. Unraveling the mechanism of molecular doping in organic semiconductors.

    PubMed

    Mityashin, Alexander; Olivier, Yoann; Van Regemorter, Tanguy; Rolin, Cedric; Verlaak, Stijn; Martinelli, Nicolas G; Beljonne, David; Cornil, Jérôme; Genoe, Jan; Heremans, Paul

    2012-03-22

    The mechanism by which molecular dopants donate free charge carriers to the host organic semiconductor is investigated and is found to be quite different from the one in inorganic semiconductors. In organics, a strong correlation between the doping concentration and its charge donation efficiency is demonstrated. Moreover, there is a threshold doping level below which doping simply has no electrical effect.

  7. Bromine-doped DWNTs: A Molecular Faraday Cage

    NASA Astrophysics Data System (ADS)

    Chen, Gugang; Margine, Roxana; Gupta, Rajeev; Crespi, Vincent; Eklund, Peter; Sumanasekera, Gamini; Bandow, Shunji; Iijima, S.

    2003-03-01

    Raman scattering is used to probe the charge transfer distribution in Bromine-doped double-walled carbon nanotubes (DWNT). Using 1064 nm and 514.5 nm laser excitation we are able to study the charge-transfer sensitive phonons in the inner ( (5,5)) and outer ( (10,10)) tubes of the double-walled pair. The experimental results are compared to our tight binding band structure calculations that include a self-consistent electrostatic term sensitive to the average net charge density on each tube. Upon doping, the nanotube tangential and radial Raman bands from the outer (primary) tubes were observed to shift dramatically to higher frequencies, consistent with a C-C bond contraction driven by the acceptor-doping. The peak intensities of these bands significantly decreased with increasing doping exposure, and they eventually vanished, consistent with a deep depression in the Fermi energy that extinguishes the resonant Raman effect. Interestingly, at the same time, we observed little or no change for the tangential and radial Raman features identified with the inner (secondary) tubes during the bromine doping. Our electronic structure calculations show that the charge distribution between the outer and inner tubes depends on doping level and also, to some extent, on specific tube chirality combinations. In general, in agreement with experiment, the calculations find a very small net charge on the inner tube, consistent with a "Molecular Faraday Effect", e.g., a DWNT of (10, 10)/ (5, 5) configuration that exhibits 0.5 holes/Å total charge transfer, has only 0.04 holes/Å on the inner (secondary) tube.

  8. 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.

  9. Efficient small molecular organic light emitting diode with graphene cathode covered by a Sm layer with nano-hollows and n-doped by Bphen:Cs2CO3 in the hollows

    NASA Astrophysics Data System (ADS)

    Yao, Li; Li, Lei; Qin, Laixiang; Ma, Yaoguang; Wang, Wei; Meng, Hu; Jin, Weifeng; Wang, Yilun; Xu, Wanjin; Ran, Guangzhao; You, Liping; Qin, Guogang

    2017-03-01

    Graphene is a favorable candidate for electrodes of organic light emitting diodes (OLEDs). Graphene has quite a high work function of ∼4.5 eV, and has been extensively studied when used as anodes of OLEDs. In order to use graphene as a cathode, the electron injection barrier between the graphene cathode and the electron transport layer has to be low enough. Using 4,7-diphenyl-1,10-phenanthroline (Bphen):Cs2CO3 to n-dope graphene is a very good method, but the electron injection barrier between the n-doped graphene and Bphen:Cs2CO3 is still too high to be ∼1.0 eV. In this work, in order to further reduce the electron injection barrier, a novel method is suggested. On the graphene cathode, a Sm layer with a lot of nano-hollows, and subsequently a layer of Bphen:Cs2CO3, are deposited. The Bphen:Cs2CO3 can n-dope graphene in the nano-hollows, and the Fermi level of the graphene rises. The nano Sm layer is very easily oxidized. Oxygen adsorbed on the surface of graphene may react with Sm to form an O‑–Sm+ dipole layer. On the areas of the Sm oxide dipole layer without nano-hollows, the electron injection barrier can be further lowered by the dipole layer. Electrons tend to mainly inject through the lower electron barrier where the dipole layer exists. Based on this idea, an effective inverted small molecular OLED with the structure of graphene/1 nm Sm layer with a lot of nano-hollows/Bphen:Cs2CO3/Alq3:C545T/NPB/MoO3/Al is presented. The maximum current efficiency and maximum power efficiency of the OLED with a 1 nm Sm layer are about two and three times of those of the reference OLED without any Sm layer, respectively.

  10. Efficient small molecular organic light emitting diode with graphene cathode covered by a Sm layer with nano-hollows and n-doped by Bphen:Cs2CO3 in the hollows.

    PubMed

    Yao, Li; Li, Lei; Qin, Laixiang; Ma, Yaoguang; Wang, Wei; Meng, Hu; Jin, Weifeng; Wang, Yilun; Xu, Wanjin; Ran, Guangzhao; You, Liping; Qin, Guogang

    2017-03-10

    Graphene is a favorable candidate for electrodes of organic light emitting diodes (OLEDs). Graphene has quite a high work function of ∼4.5 eV, and has been extensively studied when used as anodes of OLEDs. In order to use graphene as a cathode, the electron injection barrier between the graphene cathode and the electron transport layer has to be low enough. Using 4,7-diphenyl-1,10-phenanthroline (Bphen):Cs2CO3 to n-dope graphene is a very good method, but the electron injection barrier between the n-doped graphene and Bphen:Cs2CO3 is still too high to be ∼1.0 eV. In this work, in order to further reduce the electron injection barrier, a novel method is suggested. On the graphene cathode, a Sm layer with a lot of nano-hollows, and subsequently a layer of Bphen:Cs2CO3, are deposited. The Bphen:Cs2CO3 can n-dope graphene in the nano-hollows, and the Fermi level of the graphene rises. The nano Sm layer is very easily oxidized. Oxygen adsorbed on the surface of graphene may react with Sm to form an O(-)-Sm(+) dipole layer. On the areas of the Sm oxide dipole layer without nano-hollows, the electron injection barrier can be further lowered by the dipole layer. Electrons tend to mainly inject through the lower electron barrier where the dipole layer exists. Based on this idea, an effective inverted small molecular OLED with the structure of graphene/1 nm Sm layer with a lot of nano-hollows/Bphen:Cs2CO3/Alq3:C545T/NPB/MoO3/Al is presented. The maximum current efficiency and maximum power efficiency of the OLED with a 1 nm Sm layer are about two and three times of those of the reference OLED without any Sm layer, respectively.

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

    SciTech Connect

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

    2015-05-18

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

  12. 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.

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

    PubMed

    Argüelles, Carlos Francisco; Hernández-Zamora, Edgar

    2007-01-01

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

  14. Origin and structure of polar domains in doped molecular crystals

    PubMed Central

    Meirzadeh, E.; Azuri, I.; Qi, Y.; Ehre, D.; Rappe, A. M.; Lahav, M.; Kronik, L.; Lubomirsky, I.

    2016-01-01

    Doping is a primary tool for the modification of the properties of materials. Occlusion of guest molecules in crystals generally reduces their symmetry by the creation of polar domains, which engender polarization and pyroelectricity in the doped crystals. Here we describe a molecular-level determination of the structure of such polar domains, as created by low dopant concentrations (<0.5%). The approach comprises crystal engineering and pyroelectric measurements, together with dispersion-corrected density functional theory and classical molecular dynamics calculations of the doped crystals, using neutron diffraction data of the host at different temperatures. This approach is illustrated using centrosymmetric α-glycine crystals doped with minute amounts of different L-amino acids. The experimentally determined pyroelectric coefficients are explained by the structure and polarization calculations, thus providing strong support for the local and global understanding of how different dopants influence the properties of molecular crystals. PMID:27824050

  15. Small-polaron theory of doped antiferromagnets

    NASA Astrophysics Data System (ADS)

    Auerbach, Assa; Larson, Brond E.

    1991-04-01

    The spin-hole coherent-state path integral is used to generate a systematic large-spin expansion of the t-J model on the square lattice. The single hole's classical energy is minimized by small polarons with short-ranged interactions. Intersublattice hopping of polarons is forbidden by a tunneling selection rule. We derive the low-energy Lagrangian which reduces to the model of Wiegmann, Wen, Shankar, and Lee of Néel-gauge-field induced superconductivity.

  16. 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.

  17. Contact potential difference measurements of doped organic molecular thin films

    NASA Astrophysics Data System (ADS)

    Chan, Calvin; Gao, Weiying; Kahn, Antoine

    2004-07-01

    The possibility of nonequilibrium conditions in doped organic molecular thin films is investigated using a combination of ultraviolet photoemission spectroscopy (UPS) and contact potential difference measurements. Surface or interface photovoltage is of particular concern in materials with large band gap and appreciable band (or energy level) bending at interfaces. We investigate here zinc phthalocyanine (ZnPc) and N,N'-diphenyl-N,N'-bis(1-naphthyl)-1,1'biphenyl-4,4'' diamine (α-NPD) p-doped with the acceptor molecule, tetrafluorotetracyanoquinodimethane (F4-TCNQ). In both cases, we observe an upward movement of the vacuum level away from the metal interface with respect to the Fermi level, consistent with the formation of a depletion region. We show that photovoltage is not a significant factor in these doped films, under ultraviolet illumination during UPS. We suggest that the carrier recombination rate in organic films is sufficiently fast to exclude any photovoltage effects at room temperature. .

  18. Charge transport in photochemically modified molecularly doped polymers

    NASA Astrophysics Data System (ADS)

    Stasiak, James W.; Storch, Teresa J.; Mao, Erji

    1995-08-01

    Hole mobilities in p-diethylaminobenzaldehyde diphenylhydrazone (DEH) doped polycarbonate films are determined using the time-of-flight transient photocurrent technique. Measurements of hole transport parameters are determined over a range of electric fields before and after the samples are deliberately irradiated with UV light. UV irradiation of the hole transport molecule DEH results in the creation of a photoproduct, 1-phenyl-3-(4- diethylamino-1-phenyl)-1, 3-indazole with moderately high efficiency. Once formed, this photoproduct has been shown to act as a barrier to hole conduction. We exploit this photochemical reaction to examine the hole transport properties in a molecularly doped polymer system containing DEH doped polycarbonate. We propose that the increase in concentration of the photoproduct modifies the intrinsic order of the system and provides a unique probe to distinguish between the disorder formalism of Baessler and coworkers and models which propose polaron formation.

  19. Small business development for molecular diagnostics.

    PubMed

    Anagostou, Anthanasia; Liotta, Lance A

    2012-01-01

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

  20. In vivo Noninvasive Small Animal Molecular Imaging

    PubMed Central

    Youn, Hyewon; Hong, Kee-Jong

    2012-01-01

    The remarkable efforts that are made on molecular imaging technologies demonstrate its potential importance and range of applications. The generation of disease-specific animal models, and the developments of target-specific probes and genetically encoded reporters are another important component. Continued improvements in the instrumentation, the identification of novel targets and genes, and the availability of improved imaging probes should be made. Multimodal imaging probes should provide easier transitions between laboratory studies, including small animal studies and clinical applications. Here, we reviewed basic strategies of noninvasive in vivo imaging methods in small animals to introducing the concept of molecular imaging. PMID:24159487

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

    PubMed Central

    Liu, Jinling; Wang, Yiguang; An, Linan

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Liu, Jinling; Wang, Yiguang; An, Linan

    2016-10-01

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

  3. Indium antimonide doped with manganese grown by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Partin, D. L.; Heremans, J.; Thrush, C. M.

    1997-05-01

    Indium antimonide is of interest for infrared detecting and emitting devices and for magnetic field sensors. In this study, indium antimonide doped with manganese and grown by molecular beam epitaxy was investigated. Secondary ion mass spectroscopy (SIMS) was used to show that the incorporation of managenese is near unity over a wide range of manganese concentrations. Manganese is observed to be an acceptor with a dopant efficiency which follows a power law in which the hole density is proportional to the manganese concentration raised to the power α. The power α depends on the growth temperature; at 300°C, α = 0.86 and at 360°C, α = 0.78. Lightly manganese doped samples have transport dominated by electrons at low temperatures due to hole freeze out, followed by holes at intermediate temperatures and finally by intrinsic electrons at high temperatures. Additional SIMS studies showed that manganese diffuses relatively slowly in indium antimonide.

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

    NASA Astrophysics Data System (ADS)

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

    2008-06-01

    Epitaxial silicon nanowires (NWs) of short heights (˜280nm) on Si ⟨111⟩ substrate were grown and doped in situ with boron on a concentration range of 1015-1019cm-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 (1015cm-3) and medium doped (3×1016 and 1×1017cm-3) NWs were heavily depleted by the surface states while the high doped (1018 and 1019cm-3) ones showed volume conductivities expected for the corresponding intended doping levels.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Molecular Interactions and Ordering in Electrically Doped Polymers: Blends of PBTTT and F4TCNQ

    SciTech Connect

    Cochran, Justin E; Junk, Matthias J. N.; Glaudell, Anne M.; Miller, P. L.; Cowart, John S.; Toney, Michael F.; Hawker, Craig J.; Chmelka, Bradley F.; Chabinyc, Michael L.

    2014-09-12

    Identifying how small molecular acceptors pack with polymer donors in thin and thick (bulk) films is critical to understanding the nature of electrical doping by charge transfer. In this study, the packing structure of the molecular acceptor tetrafluorotetracyanoquinodimethane (F4TCNQ) with the semiconducting polymer poly(2,5-bis(3-tetradecylthiophen-2-yl)thieno-[3,2-b]thiophene) (PBTTT-C14) is examined. A combination of solid-state NMR, synchrotron X-ray scattering, and optical spectroscopy was used to determine the packing motif for blends of PBTTT-C14 and F4TCNQ in thin and bulk films. These results indicate that F4TCNQ and PBTTT-C14 order in a cofacial arrangement where charge transfer is near 100% efficient in the solid state. These results provide crucial insights into the structures and compositions of ordered domains in doped semiconducting polymers and suggest a model for the microstructure where the location of the molecular acceptors are correlated rather than randomly dispersed.

  10. 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.

  11. 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

  12. Systems Pharmacology in Small Molecular Drug Discovery.

    PubMed

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

    2016-02-18

    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.

  13. 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.

  14. 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.

  15. Electroless Functionalization of Silver Films by Its Molecular Doping.

    PubMed

    Naor, Hadas; Avnir, David

    2015-12-09

    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.

  16. High-density two-dimensional small polaron gas in a delta-doped Mott insulator.

    PubMed

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

    2013-11-21

    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 × 10(14) cm(-2).

  17. 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

  18. NH3 molecular doping of silicon nanowires grown along the [112], [110], [001], and [111] orientations

    PubMed Central

    2012-01-01

    The possibility that an adsorbed molecule could provide shallow electronic states that could be thermally excited has received less attention than substitutional impurities and could potentially have a high impact in the doping of silicon nanowires (SiNWs). We show that molecular-based ex-situ doping, where NH3 is adsorbed at the sidewall of the SiNW, can be an alternative path to n-type doping. By means of first-principle electronic structure calculations, we show that NH3 is a shallow donor regardless of the growth orientation of the SiNWs. Also, we discuss quantum confinement and its relation with the depth of the NH3 doping state, showing that the widening of the bandgap makes the molecular donor level deeper, thus more difficult to activate. PMID:22709657

  19. Molecular doping and gas sensing in Si nanowires: From charge injection to reduced dielectric mismatch

    NASA Astrophysics Data System (ADS)

    Amato, Giampiero; Cultrera, Alessandro; Boarino, Luca; Lamberti, Carlo; Bordiga, Silvia; Mercuri, Francesco; Cartoixà, Xavier; Rurali, Riccardo

    2013-11-01

    We report experimental and theoretical evidence of the different mechanisms that lead to doping of Si nanowires upon molecular adsorption of two paradigmatic Lewis bases. Pyridine genuinely dopes the nanowires by injecting charge carriers. Ethanol, on the other hand, simply modifies the dielectric screening conditions, allowing the reactivation of preexisting electrically passive impurities, and thus cannot control neither the nature (n- vs p-type) nor the concentration of the carriers.

  20. 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.

  1. Study of fluorescence quenching in aluminum-doped ceria nanoparticles: potential molecular probe for dissolved oxygen.

    PubMed

    Shehata, N; Meehan, K; Leber, D

    2013-05-01

    This work investigates a novel usage of aluminum-doped ceria nanoparticles (ADC-NPs), as the molecular probe in optical fluorescence quenching for sensing the dissolved oxygen (DO). Cerium oxide (ceria) nanoparticles can be considered one of the most unique nanomaterials that are being studied today due to the diffusion and reactivity of oxygen vacancies in ceria, which contributes to its high oxygen storage capability. Aluminum can be considered a promising dopant to increase the oxygen ionic conductivity in ceria nanoparticles which can improve the sensitivity of ceria nanoparticles to DO. The fluorescence intensity of ADC-NPs, synthesized via chemical precipitation, is found to have a strong inverse relationship with the DO concentration in aqueous solutions. Stern-Volmer constant of ADC-NPs at room temperature is determined to be 454.6 M(-1), which indicates that ADC-NPs have a promising sensitivity to dissolved oxygen, compared to many presently used fluorophores. In addition, Stern-Volmer constant is found to have a relatively small dependence on temperature between 25 °C to 50 °C, which shows excellent thermal stability of ADC-NPs sensitivity. Our work suggests that ADC-NPs, at 6 nm, are the smallest diameter DO molecular probes between the currently used optical DO sensors composed of different nanostructures. This investigation can improve the performance of fluorescence-quenching DO sensors for industrial and environmental applications.

  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. Small organic molecular imprinted materials: their preparation and application.

    PubMed

    Jiang, Xiaoman; Jiang, Na; Zhang, Haixia; Liu, Mancang

    2007-09-01

    Molecular imprinting is a technique for preparing polymeric materials that are capable of recognizing and binding the desired molecular target with a high affinity and selectivity. The materials can be applied to a wide range of target molecules, even those for which no natural binder exists or whose antibodies are difficult to raise. The imprinting of small organic molecules (e.g., pharmaceuticals, pesticides, amino acids, steroids, and sugars) is now almost routine. In this review, we pay special attention to the synthesis and application of molecular imprinted polymer (MIPs) imprinted with small organic molecules, including herbicides, pesticides, and drugs. The advantages, applications, and recent developments in small organic molecular imprinted technology are highlighted.

  4. 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.

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

    SciTech Connect

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

    2011-06-01

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

  6. Voltage-Dependent Luminescence Properties of Molecularly Doped Polymer System

    NASA Astrophysics Data System (ADS)

    Mingliang, Wang; Junxiang, Zhang; Juzheng, Liu; Chunxiang, Xu

    2001-05-01

    Single-layer light-emitting diodes (LEDs) are fabricated using a mixture of a blue-emitting polymer and green-emitting 9, 10-bis(phenylethynyl)anthracene as emitting layer. The blend device with these two components in the emitting layer exhibits voltage-induced evolution of the electroluminescence. But when polystyrene is also blended into the emitting layer, the EL spectra show emission bands from both ether-PPV and BPEA in proportion to concentrations of the two materials, and the spectra exhibit no change with applied voltage. This implies that doping inert polymer is helpful in suppressing voltage-induced evolution of electroluminescence in LED blends.

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  8. Ultrasonic spray coating polymer and small molecular organic film for organic light-emitting devices

    NASA Astrophysics Data System (ADS)

    Liu, Shihao; Zhang, Xiang; Zhang, Letian; Xie, Wenfa

    2016-11-01

    Ultrasonic spray coating process (USCP) with high material -utilization, low manufacture costs and compatibility to streamline production has been attractive in researches on photoelectric devices. However, surface tension exists in the solvent is still a huge obstacle to realize smooth organic film for organic light emitting devices (OLEDs) by USCP. Here, high quality polymer anode buffer layer and small molecular emitting layer are successfully realized through USCP by introducing extra-low surface tension diluent and surface tension control method. The introduction of low surface tension methyl alcohol is beneficial to the formation of poly (3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) films and brings obvious phase separation and improved conductivity to PEDOT:PSS film. Besides, a surface tension control method, in which new stable tension equilibrium is built at the border of wetting layer, is proposed to eliminate the effect of surface tension during the solvent evaporation stage of ultrasonic spray coating the film consists of 9,9-Spirobifluoren-2-yl-diphenyl-phosphine oxide doped with 10 wt% tris [2-(p -tolyl) pyridine] iridium (III). A smooth and homogenous small molecular emitting layer without wrinkles is successfully realized. The effectiveness of the ultrasonic spray coating polymer anode buffer layer and small molecular emitting layer are also proved by introducing them in OLEDs.

  9. Ultrasonic spray coating polymer and small molecular organic film for organic light-emitting devices

    PubMed Central

    Liu, Shihao; Zhang, Xiang; Zhang, Letian; Xie, Wenfa

    2016-01-01

    Ultrasonic spray coating process (USCP) with high material -utilization, low manufacture costs and compatibility to streamline production has been attractive in researches on photoelectric devices. However, surface tension exists in the solvent is still a huge obstacle to realize smooth organic film for organic light emitting devices (OLEDs) by USCP. Here, high quality polymer anode buffer layer and small molecular emitting layer are successfully realized through USCP by introducing extra-low surface tension diluent and surface tension control method. The introduction of low surface tension methyl alcohol is beneficial to the formation of poly (3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) films and brings obvious phase separation and improved conductivity to PEDOT:PSS film. Besides, a surface tension control method, in which new stable tension equilibrium is built at the border of wetting layer, is proposed to eliminate the effect of surface tension during the solvent evaporation stage of ultrasonic spray coating the film consists of 9,9-Spirobifluoren-2-yl-diphenyl-phosphine oxide doped with 10 wt% tris [2-(p -tolyl) pyridine] iridium (III). A smooth and homogenous small molecular emitting layer without wrinkles is successfully realized. The effectiveness of the ultrasonic spray coating polymer anode buffer layer and small molecular emitting layer are also proved by introducing them in OLEDs. PMID:27874030

  10. Molecular pairing and fully gapped superconductivity in Yb-doped CeCoIn(5).

    PubMed

    Erten, Onur; Flint, Rebecca; Coleman, Piers

    2015-01-16

    The recent observation of fully gapped superconductivity in Yb doped CeCoIn_{5} 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 T^{4} dependence of the penetration depth associated with the sound mode of this condensate is in accordance with observation.

  11. 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.

  12. Molecular targets for small-molecule modulators of circadian clocks

    PubMed Central

    He, Baokun; Chen, Zheng

    2016-01-01

    Background Circadian clocks are endogenous timing systems that regulate various aspects of mammalian metabolism, physiology and behavior. Traditional chronotherapy refers to the administration of drugs in a defined circadian time window to achieve optimal pharmacokinetic and therapeutic efficacies. In recent years, substantial efforts have been dedicated to developing novel small-molecule modulators of circadian clocks. Methods Here, we review the recent progress in the identification of molecular targets of small-molecule clock modulators and their efficacies in clock-related disorders. Specifically, we examine the clock components and regulatory factors as possible molecular targets of small molecules, and we review several key clock-related disorders as promising venues for testing the preventive/therapeutic efficacies of these small molecules. Finally, we also discuss circadian regulation of drug metabolism. Results Small molecules can modulate the period, phase and/or amplitude of the circadian cycle. Core clock proteins, nuclear hormone receptors, and clock-related kinases and other epigenetic regulators are promising molecular targets for small molecules. Through these targets small molecules exert protective effects against clock-related disorders including the metabolic syndrome, immune disorders, sleep disorders and cancer. Small molecules can also modulate circadian drug metabolism and response to existing therapeutics. Conclusion Small-molecule clock modulators target clock components or diverse cellular pathways that functionally impinge upon the clock. Target identification of new small-molecule modulators will deepen our understanding of key regulatory nodes in the circadian network. Studies of clock modulators will facilitate their therapeutic applications, alone or in combination, for clock-related diseases. PMID:26750111

  13. Optical properties of Si-doped and Be-doped InAlAs lattice-matched to InP grown by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Lumb, M. P.; Yakes, M. K.; González, M.; Tischler, J. G.; Walters, R. J.

    2013-09-01

    In this paper, we determine the optical constants and carrier mobilities of Si-doped and Be-doped InAlAs lattice matched to InP. The samples were grown using molecular beam epitaxy and characterized using Hall measurements, variable angle spectroscopic ellipsometry, and room temperature photoluminescence spectroscopy. A Moss-Burstein shift in the fundamental absorption edge was observed in both Si-doped and Be-doped materials. We fitted a multiple-oscillator, critical point model to the dielectric function of the materials extracted using the spectroscopic ellipsometry. The tabulated input parameters of this model allow for accurate calculations of the dielectric function of doped InAlAs to be made, which is useful information for simulating a variety of InP-based optoelectronic devices.

  14. 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.

  15. Effect of polymer matrices on hopping charge transport in molecularly doped polymers

    NASA Astrophysics Data System (ADS)

    Kanemitsu, Yoshihiko; Einami, Jiro

    1990-08-01

    We have studied the effect of polymer matrices on time-of-flight (TOF) photocurrent pulse shape and the drift mobility of holes in polymers doped with 2-(p-dipropylaminophenyl)-4-(p-dimethylaminophenyl)-5-(o-chlorophenyl)-1, 3-oxazole in order to understand the nature of hopping charge transport in molecularly doped polymers (MDPs). The TOF pulse shapes in oxazole-doped polymers are classed into two groups: near rectangular or dispersive shapes. The drift mobility of holes in MDPs exhibiting near-rectangular TOF shape is large compared with that exhibiting dispersive. Moreover, the drift mobility of holes depends on the dielectric constant and the glass transition temperature of polymers. These results show that the polarization and phonon mode of polymers play an important role in hopping charge transport in MDPs.

  16. 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

  17. 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

  18. Chemically doped double-walled carbon nanotubes: cylindrical molecular capacitors.

    PubMed

    Chen, Gugang; Bandow, S; Margine, E R; Nisoli, C; Kolmogorov, A N; Crespi, Vincent H; Gupta, R; Sumanasekera, G U; Iijima, S; Eklund, P C

    2003-06-27

    A double-walled carbon nanotube is used to study the radial charge distribution on the positive inner electrode of a cylindrical molecular capacitor. The outer electrode is a shell of bromine anions. Resonant Raman scattering from phonons on each carbon shell reveals the radial charge distribution. A self-consistent tight-binding model confirms the observed molecular Faraday cage effect, i.e., most of the charge resides on the outer wall, even when this wall was originally semiconducting and the inner wall was metallic.

  19. Chemically Doped Double-Walled Carbon Nanotubes: Cylindrical Molecular Capacitors

    NASA Astrophysics Data System (ADS)

    Chen, Gugang; Bandow, S.; Margine, E. R.; Nisoli, C.; Kolmogorov, A. N.; Crespi, Vincent H.; Gupta, R.; Sumanasekera, G. U.; Iijima, S.; Eklund, P. C.

    2003-06-01

    A double-walled carbon nanotube is used to study the radial charge distribution on the positive inner electrode of a cylindrical molecular capacitor. The outer electrode is a shell of bromine anions. Resonant Raman scattering from phonons on each carbon shell reveals the radial charge distribution. A self-consistent tight-binding model confirms the observed molecular Faraday cage effect, i.e., most of the charge resides on the outer wall, even when this wall was originally semiconducting and the inner wall was metallic.

  20. Poole-Frenkel mobility field dependence in molecularly doped polymers revisited

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

    We have examined the Poole-Frenkel mobility field dependence in a molecularly doped polymer (MDP) both experimentally and theoretically trying to separate two physically different contributions to this phenomenon, one constituting a real physical effect and the other arising from the fact that the charge carrier transport in MDP is not fully equilibrated. The former is ascribed to the influence of an electric field on the transport process itself affecting at least one of the model parameters. The latter should be associated with the mobility field effect under conditions when neither model parameter is field sensitive. Numerical calculations have been used to achieve their deconvolution. On the experimental front, we relied on the time of flight technique specifically modified to suit this task. Both approaches show that the contribution of the second (operational) field effect in the investigated MDP is quite appreciable. This result is compared with the traditional interpretation of the Poole-Frenkel effect in molecularly doped polymers.

  1. Recent Advance of Biological Molecular Imaging Based on Lanthanide-Doped Upconversion-Luminescent Nanomaterials

    PubMed Central

    Min, Yuanzeng; Li, Jinming; Liu, Fang; Padmanabhan, Parasuraman; Yeow, Edwin K. L.; Xing, Bengang

    2014-01-01

    Lanthanide-doped upconversion-luminescent nanoparticles (UCNPs), which can be excited by near-infrared (NIR) laser irradiation to emit multiplex light, have been proven to be very useful for in vitro and in vivo molecular imaging studies. In comparison with the conventionally used down-conversion fluorescence imaging strategies, the NIR light excited luminescence of UCNPs displays high photostability, low cytotoxicity, little background auto-fluorescence, which allows for deep tissue penetration, making them attractive as contrast agents for biomedical imaging applications. In this review, we will mainly focus on the latest development of a new type of lanthanide-doped UCNP material and its main applications for in vitro and in vivo molecular imaging and we will also discuss the challenges and future perspectives.

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

    NASA Astrophysics Data System (ADS)

    Hein, Moritz P.; Zakhidov, Alexander A.; Lüssem, Björn; Jankowski, Jens; Tietze, Max L.; Riede, Moritz K.; Leo, Karl

    2014-01-01

    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.

  3. 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.

  4. 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

  5. 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}.

  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. 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

  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. Molecular doping of single-walled carbon nanotube transistors: optoelectronic study

    NASA Astrophysics Data System (ADS)

    Zhang, Jiangbin; Emelianov, Aleksei V.; Bakulin, Artem A.; Bobrinetskiy, Ivan I.

    2016-09-01

    Single-walled carbon nanotubes (SWCNT) are a promising material for future optoelectronic applications, including flexible electrodes and field-effect transistors. Molecular doping of carbon nanotube surface can be an effective way to control the electronic structure and charge dynamics of these material systems. Herein, two organic semiconductors with different energy level alignment in respect to SWCNT are used to dope the channel of the SWCNT-based transistor. The effects of doping on the device performance are studied with a set of optoelectronic measurements. For the studied system, we observed an opposite change in photo-resistance, depending on the type (electron donor vs electron acceptor) of the dopants. We attribute this effect to interplay between two effects: (i) the change in the carrier concentration and (ii) the formation of trapping states at the SWCNT surface. We also observed a modest 4 pA photocurrent generation in the doped systems, which indicates that the studied system could be used as a platform for multi-pulse optoelectronic experiments with photocurrent detection.

  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. Switchable Multiple Spin States in the Kondo description of Doped Molecular Magnets.

    PubMed

    Ray, Rajyavardhan; Kumar, Sanjeev

    2017-02-08

    We show that introducing electrons in magnetic clusters and molecular magnets lead to rich phase diagrams with a variety of low-spin and high-spin states allowing for multiple switchability. The analysis is carried out for a quantum spin-fermion model using the exact diagonalization, and the cluster mean-field approach. The model is relevant for a number of molecular magnets with triangular motifs consisting of transition metal ions such as Cr, Cu and V. Re-entrant spin-state behavior and chirality on-off transitions exist over a wide parameter regime. A subtle competition among geometrical frustration effects, electron itinerancy, and Kondo coupling at the molecular level is highlighted. Our results demonstrate that electron doping provides a viable mean to tame the magnetic properties of molecular magnets towards potential technological applications.

  12. Switchable Multiple Spin States in the Kondo description of Doped Molecular Magnets

    PubMed Central

    Ray, Rajyavardhan; Kumar, Sanjeev

    2017-01-01

    We show that introducing electrons in magnetic clusters and molecular magnets lead to rich phase diagrams with a variety of low-spin and high-spin states allowing for multiple switchability. The analysis is carried out for a quantum spin-fermion model using the exact diagonalization, and the cluster mean-field approach. The model is relevant for a number of molecular magnets with triangular motifs consisting of transition metal ions such as Cr, Cu and V. Re-entrant spin-state behavior and chirality on-off transitions exist over a wide parameter regime. A subtle competition among geometrical frustration effects, electron itinerancy, and Kondo coupling at the molecular level is highlighted. Our results demonstrate that electron doping provides a viable mean to tame the magnetic properties of molecular magnets towards potential technological applications. PMID:28176869

  13. Switchable Multiple Spin States in the Kondo description of Doped Molecular Magnets

    NASA Astrophysics Data System (ADS)

    Ray, Rajyavardhan; Kumar, Sanjeev

    2017-02-01

    We show that introducing electrons in magnetic clusters and molecular magnets lead to rich phase diagrams with a variety of low-spin and high-spin states allowing for multiple switchability. The analysis is carried out for a quantum spin-fermion model using the exact diagonalization, and the cluster mean-field approach. The model is relevant for a number of molecular magnets with triangular motifs consisting of transition metal ions such as Cr, Cu and V. Re-entrant spin-state behavior and chirality on-off transitions exist over a wide parameter regime. A subtle competition among geometrical frustration effects, electron itinerancy, and Kondo coupling at the molecular level is highlighted. Our results demonstrate that electron doping provides a viable mean to tame the magnetic properties of molecular magnets towards potential technological applications.

  14. 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.

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

    PubMed

    Samuels, Alexander J; Carey, J David

    2013-03-26

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

  16. Nitrogen doping and vacancy effects on the mechanical properties of graphene: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Mortazavi, Bohayra; Ahzi, Said; Toniazzo, Valérie; Rémond, Yves

    2012-02-01

    In this Letter, we used classical Molecular Dynamics (MD) simulations to investigate the tensile behavior of graphene. The validity of the proposed MD architecture is verified by comparing the simulation results with the available experimental results. By performing uniaxial tension simulations, we studied the effects of strain rate, chirality, nanoribbons width and number of atomic planes on the mechanical properties of graphene. We particularly investigated the effects of doped nitrogen atoms and point vacancies concentrations on the Young's modulus and tensile strength of graphene. By plotting the deformation process of graphene at various strain levels, the failure behavior is discussed.

  17. On the structure of biomedical silver-doped phosphate-based glasses from molecular dynamics simulations.

    PubMed

    Ainsworth, Richard I; Christie, Jamieson K; de Leeuw, Nora H

    2014-10-21

    First-principles and classical molecular dynamics simulations of undoped and silver-doped phosphate-based glasses with 50 mol% P2O5, 0-20 mol% Ag2O, and varying amounts of Na2O and CaO have been carried out. Ag occupies a distorted local coordination with a mean Ag-O bond length of 2.5 Å and an ill-defined first coordination shell. This environment is shown to be distorted octahedral/trigonal bipyramidal. Ag-O coordination numbers of 5.42 and 5.54-5.71 are calculated for first-principles and classical methodologies respectively. A disproportionation in the medium-range phosphorus Q(n) distribution is explicitly displayed upon silver-doping via CaO substitution, approximating 2Q(2)→Q(1) + Q(3), but not on silver-doping via Na2O substitution. An accompanying increase in FWHM of the phosphorus to bridging oxygen partial pair-correlation function is strong evidence for a bulk structural mechanism associated with decreased dissolution rates with increased silver content. Experimentally, Ag2O ↔ Na2O substitution is known to decrease dissolution and we show this to be a result of Ag's local bonding.

  18. 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 !}.

  19. 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.

  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. 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.

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

    PubMed

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

    2014-11-21

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

  3. 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.

  4. 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

  5. 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.

  6. 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.

  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. Quantum-chemical investigations of small molecular anions

    NASA Astrophysics Data System (ADS)

    Botschwina, P.; Seeger, S.; Mladenović, M.; Schulz, B.; Horn, M.; Schmatz, S.; Flügge, J.; Oswald, R.

    Dedicated to Dr Gerhard Herzberg on the occasion of his 90th birthday Recent large-scale ab initio calculations for small negative molecular ions are reviewed. Accurate equilibrium geometries are established for several species like NH2-, HCC-, NO2-, CH2N- C5- and C6-. Predictions are made for various spectroscopic properties like vibrational frequencies, rotational constants and infrared intensities. The effects of a shallow energy minimum in the T-shaped configuration on the rovibrational term energies of HCC - are investigated. The calculated vibrational structures of the photoelectron spectra of SiH3- and CH2N - are in very good agreement with the experiment. The present calculations support the assignment of an absorption observed at 608 nm in a neon matrix to the

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

    NASA Astrophysics Data System (ADS)

    Rapaport, D. C.

    2016-09-01

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

  10. Tyrosine kinase inhibitors - small molecular weight compounds inhibiting EGFR.

    PubMed

    Hegymegi-Barakonyi, Bálint; Eros, Dániel; Szántai-Kis, Csaba; Breza, Nóra; Bánhegyi, Péter; Szabó, Gábor Viktor; Várkondi, Edit; Peták, István; Orfi, László; Kéri, György

    2009-06-01

    Abnormally elevated EGFR kinase activity can lead to various pathological states, including proliferative diseases such as cancer. The development of selective protein kinase inhibitors has become an important area of drug discovery for the potential treatment of a variety of solid tumors such as breast, ovarian and colorectal cancers, NSCLC, and carcinoma of the head and neck. There are three small molecule EGFR kinase inhibitor drugs in clinical use (gefitinib, erlotinib and lapatinib), and several others are currently undergoing clinical development. This review summarizes the development of EGFR kinase inhibitors, and includes descriptions of the binding modes, the importance of a multiple-targets strategy, the effects of sensitizing and resistance mutations in the EGFR, and molecular diagnostic approaches. In addition, the use of target fishing for selectivity profiling, off-target identification and quantitative structure-activity relationship modeling for the prediction of EGFR inhibition is discussed.

  11. How does the isomerization rate affect the photoisomerization-induced transport properties of a doped molecular glass-former?

    NASA Astrophysics Data System (ADS)

    Accary, J.-B.; Teboul, V.

    2013-07-01

    We investigate the effect of the isomerization rate f on the microscopic mechanisms at the origin of the massive mass transport found in glass-formers doped with isomerizing azobenzene molecules that result in surface relief gratings formation. To this end we simulate the isomerization of dispersed probe molecules embedded into a molecular host glass-former. The host diffusion coefficient first increases linearly with f and then saturates. The saturated value of the diffusion coefficient and of the viscosity does not depend on f but increases with temperature while the linear response for these transport coefficients depends only slightly on the temperature. We interpret this saturation as arising from the appearance of increasingly soft regions around the probes for high isomerization rates, a result in qualitative agreement with experiments. These two different physical behaviors, linear response and saturation, are reminiscent of the two different unexplained mass transport mechanisms observed for small or large light intensities (for small intensities the molecules move towards the dark regions while for large intensities they move towards the illuminated regions).

  12. Doping ZnO with Water/Alcohol-Soluble Small Molecules as Electron Transport Layers for Inverted Polymer Solar Cells.

    PubMed

    Liu, Chang; Zhang, Lin; Xiao, Liangang; Peng, Xiaobin; Cao, Yong

    2016-10-03

    By doping ZnO with porphyrin small molecules (FNEZnP-OE and FNEZnP-T) as cathode electron transport layers (ETLs), the inverted polymer solar cells (i-PSC) with PTB7:PC71BM (PTB7: polythieno[3,4-b]-thiophene-co-benzodithiophene, PC71BM: [6, 6]-phenyl-C71-butyric acid methyl ester) as the active materials exhibit enhanced device performance. While the power conversion efficiency (PCE) of the PSCs with pure ZnO ETL is 7.52%, that of the devices with FNEZnP-T-doped ZnO ETL shows a slightly improved PCE of 8.09%, and that of the PSCs with FNEZnP-OE-doped ZnO ETL is further enhanced up to 9.24% with an over 20% improvement compared to that with pure ZnO ETL. The better performance is contributed by the better interfacial contact and reduced work function induced by 9,9-bis(30-(N,N-dimethylamino)propyl)-2,7-fluorenes and 3,4-bis-(2-(2-methoxy-ethoxy)-ethoxy)-phenyls in the porphyrin small molecules. More importantly, the PCE is still higher than 8% even when the thickness of FNEZnP-OE-doped ZnO ETL is up to 110 nm, which are important criteria for eventually making organic photovoltaic modules with roll-to-roll coat processing.

  13. Surface ionisation of molecular H2 and atomic H Rydberg states at doped silicon surfaces

    NASA Astrophysics Data System (ADS)

    Sashikesh, G.; So, E.; Ford, M. S.; Softley, T. P.

    2014-09-01

    The detection of ions or electrons from the surface ionisation of molecular H2 and atomic H Rydberg states incident at doped Si surfaces is investigated experimentally to analyse the effect of the dopant charge distribution on the surface-ionisation processes. In both experimental studies, the molecular H2 and atomic H Rydberg states are generated via two-colour vacuum ultraviolet--ultraviolet (VUV-UV) resonant excitation. For H2, various Stark states of the N+ = 2, n = 17 manifold are populated in the presence of an electric field. The variation of the observed surface-ionisation signal with surface dopant concentration and type, shows similar characteristics for all the Stark states. A comparison is made between these ion-detected surface-ionisation profiles and those obtained via electron detection. Different trends as a function of dopant concentration and type are observed for the two cases, explained by the greater effect of surface charges on the post-ionisation ion trajectory compared to the electron trajectory. For the atomic-H Rydberg states with principal quantum number ? populated in the absence of a Stark field, the observed behaviour is similar to the interaction of molecular H2 Rydberg states at the same surfaces, and these measurements confirm that the observed effects are attributable to the nature of the target surface rather than the specific atomic or molecular Rydberg species.

  14. 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

  15. 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.

  16. Transient space-charge-limited current pulse shapes in molecularly doped polymers

    NASA Astrophysics Data System (ADS)

    Goldie, D. M.

    1999-12-01

    The transient current response of molecularly doped polymers have been numerically modelled under space-charge-limited (SCL) conditions for the situation in which a step potential is applied to an ideal injecting contact. Under trap-free conditions, the transient SCL current pulse shape is found to be sensitive not only to the underlying field dependence of the injected carrier mobilities and diffusivities, but also to the magnitude of the applied step potential. A progressive reduction in the ratio of the peak current density jp to the final steady-state magnitude jss is obtained by increasing either the field strength of the mobility or the relative amount of diffusion. It is demonstrated, however, that for times preceding the location tp of the current peak, the rate of current increase displays a gradual transition from a super-linear to linear time dependence upon the introduction of diffusion. The diminishing observability of jp/jss is accompanied by a shift in the position of tp relative to the space-charge-free carrier transit time t0. The classical fixed-mobility value tp/t0 = 0.786 is modestly reduced as the field strength of the mobility or amount of carrier diffusion is enhanced. The numerical predictions are compared with experimental SCL current transients obtained from hydrazone doped polyester samples fitted with gold contacts.

  17. Pervasive small-scale structure in molecular clouds

    NASA Technical Reports Server (NTRS)

    Martin, B.; Lada, E.

    1986-01-01

    An unbiased CO survey of molecular cloud cores was completed, and the profiles were analyzed within the context of a model for emission from clumpy clouds. It was found that all sources observed contain a significant amount of structure that is not resolved with our 2.3-arcmin beam, and that the parameters which describe the degree of clumping span a remarkably narrow range of the possible values. We studied two separate samples of cloud cores: a large sample of warm cores from the Massachusetts-Stony Brook 12CO survey of the first galactic quadrant, and a sample of cool cores in the Taurus dark clouds chosen primarily on the basis of H2CO emission. We observed all sources in the 1-0 transition of 12CO and 13CO with the 5-m telescope of the Millimeter Wave Observatory. The 12CO/13CO ratios can be explained if there is unresolved structure giving rise to significant variations of opacity across the beam. Our model cloud consists of a large number of identical clumps distributed randomly in the beam. These clumps have velocity widths v small compared to the width of the observed profile, which is determined by the relative motion of the clumps. The entire cloud is isothermal and in local thermodynamic equilibrium. With these assumptions the intensity and linewidth ratios depend on three parameters: the abundance ratio; the peak 13CO opacity through a single clump, tau(0); and the average number of clumps on a line of sight N. Small tau(0) and large N correspond to the microturbulent limit, which is indistinguishable from a uniform gas distribution. In the other extreme, large tau(0) and snall N, at a given velocity at most one clump contributes to the profile on each line of sight. A figure is presented which shows the model parameters which reproduce the measured intensity and linewidth ratios for the sample of warm cores, assuming an abundance ratio of 75.

  18. Indium antimonide doped with lead telluride grown by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Partin, D. L.; Heremans, J.; Trush, C. M.

    1991-05-01

    A PbTe dopant source has been used to grow n-type InSb using the molecular beam epitaxy growth technique. From Auger electron spectroscopy studies, no surface segregation of tellurium or lead is observed up to ∽ 10 19 cm -3 doping levels. The correlation between the PbTe flux used during growth and the electron density in the grown films is very good, suggesting that the incorporation of tellurium is near unity. Six-probe Hall measurements of carrier transport gave room temperature mobilities as high as 51,300 cm 2 V -1 s -1 at an electron density of 2.9×10 16 cm -3 (54,300 at an electron density of 1.9×10 16 cm -3 at 110 K) for a film of 4.0 μm thickness on an InP substrate.

  19. 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.

  20. Inhomogeneous Si-doping of gold-seeded InAs nanowires grown by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Rolland, Chloé; Caroff, Philippe; Coinon, Christophe; Wallart, Xavier; Leturcq, Renaud

    2013-06-01

    We have investigated in situ Si doping of InAs nanowires grown by molecular beam epitaxy from gold seeds. The effectiveness of n-type doping is confirmed by electrical measurements showing an increase of the electron density with the Si flux. We also observe an increase of the electron density along the nanowires from the tip to the base, attributed to the dopant incorporation on the nanowire facets whereas no detectable incorporation occurs through the seed. Furthermore, the Si incorporation strongly influences the lateral growth of the nanowires without giving rise to significant tapering, revealing the complex interplay between axial and lateral growth.

  1. Folding of Small Proteins Using Constrained Molecular Dynamics

    PubMed Central

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

    2011-01-01

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

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

    PubMed Central

    Dionne, Justine; Lefèvre, Thierry; Auger, Michèle

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  4. 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.

  5. Energy level alignment at planar organic heterojunctions: influence of contact doping and molecular orientation.

    PubMed

    Opitz, Andreas

    2017-04-05

    Planar organic heterojunctions are widely used in photovoltaic cells, light-emitting diodes, and bilayer field-effect transistors. The energy level alignment in the devices plays an important role in obtaining the aspired gap arrangement. Additionally, the π-orbital overlap between the involved molecules defines e.g. the charge-separation efficiency in solar cells due to charge-transfer effects. To account for both aspects, direct/inverse photoemission spectroscopy and near edge x-ray absorption fine structure spectroscopy were used to determine the energy level landscape and the molecular orientation at prototypical planar organic heterojunctions. The combined experimental approach results in a comprehensive model for the electronic and morphological characteristics of the interface between the two investigated molecular semiconductors. Following an introduction on heterojunctions used in devices and on energy levels of organic materials, the energy level alignment of planar organic heterojunctions will be discussed. The observed energy landscape is always determined by the individual arrangement between the energy levels of the molecules and the work function of the electrode. This might result in contact doping due to Fermi level pinning at the electrode for donor/acceptor heterojunctions, which also improves the solar cell efficiency. This pinning behaviour can be observed across an unpinned interlayer and results in charge accumulation at the donor/acceptor interface, depending on the transport levels of the respective organic semiconductors. Moreover, molecular orientation will affect the energy levels because of the anisotropy in ionisation energy and electron affinity and is influenced by the structural compatibility of the involved molecules at the heterojunction. High structural compatibility leads to π-orbital stacking between different molecules at a heterojunction, which is of additional interest for photovoltaic active interfaces and for ground

  6. Energy level alignment at planar organic heterojunctions: influence of contact doping and molecular orientation

    NASA Astrophysics Data System (ADS)

    Opitz, Andreas

    2017-04-01

    Planar organic heterojunctions are widely used in photovoltaic cells, light-emitting diodes, and bilayer field-effect transistors. The energy level alignment in the devices plays an important role in obtaining the aspired gap arrangement. Additionally, the π-orbital overlap between the involved molecules defines e.g. the charge-separation efficiency in solar cells due to charge-transfer effects. To account for both aspects, direct/inverse photoemission spectroscopy and near edge x-ray absorption fine structure spectroscopy were used to determine the energy level landscape and the molecular orientation at prototypical planar organic heterojunctions. The combined experimental approach results in a comprehensive model for the electronic and morphological characteristics of the interface between the two investigated molecular semiconductors. Following an introduction on heterojunctions used in devices and on energy levels of organic materials, the energy level alignment of planar organic heterojunctions will be discussed. The observed energy landscape is always determined by the individual arrangement between the energy levels of the molecules and the work function of the electrode. This might result in contact doping due to Fermi level pinning at the electrode for donor/acceptor heterojunctions, which also improves the solar cell efficiency. This pinning behaviour can be observed across an unpinned interlayer and results in charge accumulation at the donor/acceptor interface, depending on the transport levels of the respective organic semiconductors. Moreover, molecular orientation will affect the energy levels because of the anisotropy in ionisation energy and electron affinity and is influenced by the structural compatibility of the involved molecules at the heterojunction. High structural compatibility leads to π-orbital stacking between different molecules at a heterojunction, which is of additional interest for photovoltaic active interfaces and for ground

  7. High performance carbon molecular sieving membranes derived from pyrolysis of metal-organic framework ZIF-108 doped polyimide matrices.

    PubMed

    Jiao, Wenmei; Ban, Yujie; Shi, Zixing; Jiang, Xuesong; Li, Yanshuo; Yang, Weishen

    2016-12-11

    Carbon molecular sieve membranes (CMSMs) were fabricated by pyrolysis of MOF-doped polyimide mixed matrix membranes. ZIF-108 (Zn(2-nitroimidazolate)2) was used as a dopant to tailor the micropores of the as-prepared CMSMs into narrow ultramicropores, providing a remarkable combination of permeability and selectivity of membranes in CO2/CH4, O2/N2 and N2/CH4 separation.

  8. Photoacoustic molecular imaging of small animals in vivo

    NASA Astrophysics Data System (ADS)

    Xie, Xueyi; Li, Meng-Lin; Oh, Jung-Taek; Ku, Geng; Wang, Wei; Li, Chun; Similache, Sergiu; Lungu, Gina F.; Stoica, George; Wang, Lihong V.

    2006-02-01

    Molecular imaging is a newly emerging field in which the modern tools of molecular and cell biology have been married to state-of-the-art technologies for noninvasive imaging. The study of molecular imaging will lead to better methods for understanding biological processes as well as diagnosing and managing disease. Here we present noninvasive in vivo spectroscopic photoacoustic tomography (PAT)-based molecular imaging of αvβ3 integrin in a nude mouse U87 brain tumor. PAT combines high optical absorption contrast and high ultrasonic resolution by employing short laser pulses to generate acoustic waves in biological tissues through thermoelastic expansion. Spectroscopic PAT-based molecular imaging offers the separation of the contributions from different absorbers based on the differences in optical absorption spectra among those absorbers. In our case, in the near infrared (NIR) range, oxy-heamoglobin (O2Hb), deoxy-heamoglobin (HHb) and the injected αvβ3-targeted peptide-ICG conjugated NIR fluorescent contrast agent are the three main absorbers. Therefore, with the excitation by multiple wavelength laser pulses, spectroscopic PAT-based molecular imaging not only provides the level of the contrast agent accumulation in the U87 glioblastoma tumor, which is related to the metabolism and angiogenesis of the tumor, but also offers the information on tumor angiogenesis and tumor hypoxia.

  9. Optically generated small electron and hole polarons in nominally undoped and Fe-doped KNbO3 investigated by transient absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Torbrügge, S.; Imlau, M.; Schoke, B.; Merschjann, C.; Schirmer, O. F.; Vernay, S.; Gross, A.; Wesemann, V.; Rytz, D.

    2008-09-01

    Transient light-induced absorption in nominally undoped and Fe-doped KNbO3 crystals is observed in the visible and infrared spectral ranges after single pulse illumination with λ=532nm . For nominally undoped KNbO3 the decay of the light-induced absorption in a single step can be explained by incoherent hopping transport of optically generated small bound O- hole and small free Nb4+ electron polarons and their mutual recombination. Iron doping causes an additional slow decay component and, remarkably, accelerates the initial decay process. A consistent model for the formation, hopping, and recombination paths of hole and electron polarons is deduced from the experimental data set for both nominally undoped and Fe-doped KNbO3 . The decrease in the polaron hopping-transport length in Fe-doped samples is attributed to the increased number densities of optically generated hole polarons by additional one-quantum excitations.

  10. 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.

  11. Highly p-doped regions in silicon solar cells quantitatively analyzed by small angle beveling and micro-Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Becker, M.; Gösele, U.; Hofmann, A.; Christiansen, S.

    2009-10-01

    Highly p-doped regions in multicrystalline silicon solar cells, such as the back surface field region, are analyzed by means of small angle beveling and micro-Raman spectroscopy. Small angle beveling and subsequent Secco etching are used to enhance the lateral resolution of the micro-Raman spectroscopic measurements and to investigate the microstructure of the back surface field region in detail. The position-dependent analysis of the free carrier concentrations within the back surface field region is based on the Raman specific Fano resonances. The Raman spectroscopic measurement results are compared to results obtained from electrochemical capacitance-voltage measurements, which allows a subsequent calibration of the Raman data for the quantitative analysis of the free carrier concentrations within the highly p-doped regions of silicon solar cells and other devices. Our investigations show that the free carrier as well as the dopant concentration profiles within the back surface field region exhibit a nearly step-functional shape instead of the extended gradient shape which the electrochemical capacitance-voltage measurements suggest. Moreover, we show that the shape of the back surface field is often influenced by grain boundaries and other defects that occur in multicrystalline silicon wafers.

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

    1999-12-01

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

  14. [Advances in the study of natural small molecular antibody].

    PubMed

    Zhu, Lei; Zhang, Da-peng

    2012-10-01

    Small molecule antibodies are naturally existed and well functioned but not structurally related to the conventional antibodies. They are only composed of heavy protein chains or light chains, much smaller than common antibody. The first small molecule antibody, called Nanobody was engineered from heavy-chain antibodies found in camelids. Cartilaginous fishes also have heavy-chain antibodies (IgNAR, "immunoglobulin new antigen receptor"), from which single-domain antibodies called Vnar fragments can be obtained. In addition, free light chain (FLC) antibodies in human bodies are being developed as therapeutic and diagnostic agents. Comparing to intact antibodies, common advantages of small molecule antibodies are with better solubility, tissue penetration, stability towards heat and enzymes, and comparatively low production costs. This article reviews the structural characteristics and mechanism of action of the Nanobody, IgNAR and FLC.

  15. 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).

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

    SciTech Connect

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

    2015-10-15

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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Ge doping of β-Ga2O3 films grown by plasma-assisted molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Ahmadi, Elaheh; Koksaldi, Onur S.; Kaun, Stephen W.; Oshima, Yuichi; Short, Dane B.; Mishra, Umesh K.; Speck, James S.

    2017-04-01

    The Ge doping of β-Ga2O3(010) films was investigated using plasma-assisted molecular beam epitaxy as the growth method. The dependences of the amount of Ge incorporated on the substrate temperature, Ge-cell temperature, and growth regime were studied by secondary ion mass spectrometry. The electron concentration and mobility were investigated using Van der Pauw Hall patterns. Hall measurement confirmed that Ge acts as an n-dopant in β-Ga2O3(010) films. These results were compared with similar films doped by Sn. The Hall data showed an improved electron mobility for the same electron concentration when Ge is used instead of Sn as the dopant.

  2. Ultra-low resistance ohmic contacts to GaN with high Si doping concentrations grown by molecular beam epitaxy

    SciTech Connect

    Afroz Faria, Faiza; Guo Jia; Zhao Pei; Li Guowang; Kumar Kandaswamy, Prem; Wistey, Mark; Xing Huili; Jena, Debdeep

    2012-07-16

    Ti/Al/Ni/Au ohmic contacts were formed on heavily doped n{sup +} metal-polar GaN samples with various Si doping concentrations grown by molecular beam epitaxy. The contact resistivity (R{sub C}) and sheet resistance (R{sub sh}) as a function of corresponding GaN free carrier concentration (n) were measured. Very low R{sub C} values (<0.09 {Omega} mm) were obtained, with a minimum R{sub C} of 0.035 {Omega} mm on a sample with a room temperature carrier concentration of {approx}5 Multiplication-Sign 10{sup 19} cm{sup -3}. Based on the systematic study, the role of R{sub C} and R{sub sh} is discussed in the context of regrown n{sup +} GaN ohmic contacts for GaN based high electron mobility transistors.

  3. Fast synthesis and bioconjugation of (68) Ga core-doped extremely small iron oxide nanoparticles for PET/MR imaging.

    PubMed

    Pellico, Juan; Ruiz-Cabello, Jesús; Saiz-Alía, Marina; Del Rosario, Gilberto; Caja, Sergio; Montoya, María; Fernández de Manuel, Laura; Morales, M Puerto; Gutiérrez, Lucia; Galiana, Beatriz; Enríquez, Jose A; Herranz, Fernando

    2016-05-01

    Combination of complementary imaging techniques, like hybrid PET/MRI, allows protocols to be developed that exploit the best features of both. In order to get the best of these combinations the use of dual probes is highly desirable. On this sense the combination of biocompatible iron oxide nanoparticles and 68Ga isotope is a powerful development for the new generation of hybrid systems and multimodality approaches. Our objective was the synthesis and application of a chelator-free 68Ga-iron oxide nanotracer with improved stability, radiolabeling yield and in vivo performance in dual PET/MRI. We carried out the core doping of iron oxide nanoparticles, without the use of any chelator, by a microwave-driven protocol. The synthesis allowed the production of extremely small (2.5 nm) 68Ga core-doped iron oxide nanoparticles. The microwave approach allowed an extremely fast synthesis with a 90% radiolabeling yield and T1 contrast in MRI. With the same microwave approach the nano-radiotracer was functionalized in a fast and efficient way. We finally evaluated these dual targeting nanoparticles in an angiogenesis murine model by PET/MR imaging. Copyright © 2016 John Wiley & Sons, Ltd.

  4. Small interfering RNA-based molecular therapy of cancers

    PubMed Central

    Guo, Wei; Chen, Wangbing; Yu, Wendan; Huang, Wenlin; Deng, Wuguo

    2013-01-01

    RNA interference (RNAi) has become a gold standard for validating gene function in basic life science research and provides a promising therapeutic modality for cancer and other diseases. This mini-review focuses on the potential of small interfering RNAs (siRNAs) in anticancer treatment, including the establishment and screening of cancer-associated siRNA libraries and their applications in anticancer drug target discovery and cancer therapy. This article also describes the current delivery approaches of siRNAs using lipids, polymers, and, in particular, gold nanoparticles to induce significant gene silencing and tumor growth regression. PMID:23327796

  5. Conformational Changes of Doped Polyaniline as Characterized by Small-Angle Neutron Scattering (SANS)

    DTIC Science & Technology

    2007-11-02

    analyze the weight average molecular weight, Mw, radius of gyration, Rg, and the second virial coefficient , A2. The conformation of polyaniline was...an expanded conformation and allowed for an increase in the second virial coefficient .

  6. First molecular detection and characterization of Akabane virus in small ruminants in Turkey.

    PubMed

    Oğuzoğlu, T Ç; Toplu, N; Koç, B T; Doğan, F; Epikmen, E T; İpek, E; Akkoç, A N

    2015-10-01

    Abortion outbreaks associated with congenital malformations in two distinct small-ruminant flocks were reported in Turkey in 2013-2014. This paper describes the first molecular characterization of Turkish Akabane virus strains in small-ruminant flocks using partial sequence analysis of the S segment and pathological findings.

  7. 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.

  8. Solid-state tellurium doping of AlInP and its application to photovoltaic devices grown by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Dai, P.; Tan, M.; Wu, Y. Y.; Ji, L.; Bian, L. F.; Lu, S. L.; Yang, H.

    2015-03-01

    Solid-state tellurium (Te) is used as an n-type dopant of AlInP grown by molecular beam epitaxy (MBE). The carrier concentration proportionally increases with increasing Te beam equivalent pressure (BEP) up to a high doping density of 1×1019 cm-3. The incorporation of Te into AlInP results in a mirror-like surface at a moderate doping density due to its surfactant effect, while the surface roughness increased with a further rising of Te doping concentration. Furthermore, for the same In and Al flux ratio, the increase of the Te flux leads to a decreased In-content, but little effect on the alloy's disorder is observed. The highly Te-doped AlInP was used in a GaAs solar cell as a window layer. As compared with the solar cell with the Si-doped AlInP window layer, the device with the Te-doped AlInP window layer exhibits the higher efficiency and an extended increase under concentrated solar illumination, due to the benefits of the higher doping density in the Te-doped epilayer.

  9. Upconversion fluorescence imaging of cells and small animals using lanthanide doped nanocrystals.

    PubMed

    Chatterjee, Dev K; Rufaihah, Abdul J; Zhang, Yong

    2008-03-01

    Upconversion fluorescence imaging technique with excitation in the near-infrared (NIR) region has been used for imaging of biological cells and tissues. This has several advantages, including absence of photo-damage to living organisms, very low auto-fluorescence, high detection sensitivity, and high light penetration depth in biological tissues. In this report we demonstrate the use of a new upconversion fluorophore, lanthanide doped nanocrystals, for imaging of cells and some deep tissues in animal. Polyethyleneimine (PEI) coated NaYF(4):Yb,Er nanoparticles were synthesized, which produce very strong upconversion fluorescence when excited at 980 nm by a NIR laser. The nanoparticles were shown to be stable in physiologic buffered saline (PBS), non-toxic to bone marrow stem cells, and resistant to photo-bleaching. The nanoparticles delivered into some cell lines or injected intradermally and intramuscularly into some tissues either near the body surface or deep in the body of rats showed visible fluorescence, when exposed to a 980 nm NIR laser. To the best of our knowledge, this represents the first demonstration of use of upconversion fluorophores for cellular and tissue imaging.

  10. Improved understanding and control of magnesium-doped gallium nitride by plasma assisted molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Burnham, Shawn D.

    By an improved understanding of Mg-doped GaN through an exhaustive review of current limitations, increased control over the material was achieved by addressing several of these issues. To address the issues of the memory effect, low sticking coefficient and high vapor pressure of Mg, a new Mg dopant source was implemented, characterized and modeled for p-type doping of GaN. The device enhanced the sticking coefficient of Mg by energizing the outgoing Mg flux, and also allowed the first reported demonstration of an abrupt junction between two non-zero Mg concentrations and a graded Mg-doped GaN film. The significant compensation of Mg acceptors at high dopant concentrations was used advantageously to develop a new ex situ resistivity analysis technique using the energy distributions of SIMS to characterize doping of buried layers. The new technique was used to identify the barrier between conductive and resistive Mg doping for increased Mg concentration, which was then used to optimize Mg-doped GaN. Because Mg doping exhibits a dependence upon the growth regime, a new growth and regime characterization technique was developed using specific RHEED intensity responses to repeat growth conditions. During the development of this technique, a new surface kinetics growth model for III-nitrides was discovered based on DMS observations, which suggests preferential buildup of the metal bilayer before growth begins with an unfamiliar cation-anion exchange process initially upon metal shutter opening. Using the new RHEED growth and regime characterization technique, a new growth technique called metal modulated epitaxy (MME) was developed to increase repeatability, uniformity and smoothness. The MME technique was enhanced with a closed-loop control using real-time feedback from RHEED transients to control shutter transitions. This enhancement, called "smart shuttering," led to improved growth rate and further improvement of surface roughness and grain size, which were

  11. 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

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

    PubMed Central

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

    2012-01-01

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

  13. Molecular doping of MoS2 transistors by self-assembled oleylamine networks

    NASA Astrophysics Data System (ADS)

    Lockhart de la Rosa, César J.; Phillipson, Roald; Teyssandier, Joan; Adisoejoso, Jinne; Balaji, Yashwanth; Huyghebaert, Cedric; Radu, Iuliana; Heyns, Marc; De Feyter, Steven; De Gendt, Stefan

    2016-12-01

    Thin MoS2 films continue to be of key interest for numerous applications; however, effective doping and high metal to MoS2 contact resistance are challenges for future applications. We report on the self-assembly of oleylamine on top of MoS2 thin-films and the effective doping of MoS2 thin-film field effect transistors by oleylamine. Atomic force microscopy revealed that oleylamine organizes in lamellae domains on MoS2 thin films with similar characteristics of those previously observed on highly ordered pyrolytic graphite. A carrier concentration increase from 7.1 × 1011 cm-2 up to 1.9 × 1013 cm-2 at 0 V gate voltage is achieved together with a reduction of the contact resistance by a factor of 5 when using gold as metal contact. Furthermore, this non-covalent doping proves to be removable and reproducible among different flakes and does not degrade the electron mobility. Thus, this work opens the path for future works on controlling the doping of MoS2 by proper selection of the self-assembled species.

  14. Molecular statistical theory of small bodies and their thermophysical and thermodynamic characteristics

    NASA Astrophysics Data System (ADS)

    Tovbin, Yu. K.

    2015-03-01

    The constraints of classical thermodynamics on analyzing nanosized objects are considered. It is shown that it is essential to separate the thermodynamic concepts of a cluster and a drop. Using the lattice gas model, a molecular statistical theory of small multicomponent mixtures is developed that considers inter-particle interactions in several coordination spheres and the effects of size equilibrium fluctuations. Kinetic equations describing the particle redistribution dynamics inside small bodies and the problems of allowing for size fluctuations in them are discussed. The principles of the molecular statistical theory are compared to results from applying molecular dynamics to modeling the states of small clusters and the surface states of metal atoms during their adsorption and diffusion on graphene.

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

    PubMed

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

    2015-01-01

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

  16. Importance of Molecular Features of Non–Small Cell Lung Cancer for Choice of Treatment

    PubMed Central

    Moran, Cesar

    2011-01-01

    Lung cancer is the leading cause of cancer-related deaths in the United States. Approximately 85% of lung cancer is categorized as non–small cell lung cancer, and traditionally, non–small cell lung cancer has been treated with surgery, radiation, and chemotherapy. Targeted agents that inhibit the epidermal growth factor receptor pathway have been developed and integrated into the treatment regimens in non–small cell lung cancer. Currently, approved epidermal growth factor receptor inhibitors include the tyrosine kinase inhibitors erlotinib and gefitinib. Molecular determinants, such as epidermal growth factor receptor–activating mutations, have been associated with response to epidermal growth factor receptor tyrosine kinase inhibitors and may be used to guide treatment choices in patients with non–small cell lung cancer. Thus, treatment choice for patients with non–small cell lung cancer depends on molecular features of tumors; however, improved techniques are required to increase the specificity and efficiency of molecular profiling so that these methods can be incorporated into routine clinical practice. This review provides an overview of how genetic analysis is currently used to direct treatment choices in non–small cell lung cancer. PMID:21514411

  17. 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.

  18. 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

  19. Responsive small molecular hydrogels based on adamantane-peptides for cell culture.

    PubMed

    Yang, Cuihong; Li, Dongxia; Liu, Zheng; Hong, Ge; Zhang, Jun; Kong, Deling; Yang, Zhimou

    2012-01-12

    The development of responsive small molecular hydrogels that can be applied for recovery of cells postculture attract extensive interests for researchers in fields of cell biology, stem cell differentiation, and tissue engineering. We report in this study several responsive small molecular hydrogels based on adamantane-peptides whose gel to clear solution phase transition can be achieved by addition of β-cyclodextrin (β-CD) derivatives. The small molecular hydrogels are formed by our recently developed method of disulfide bond cleavage by glutathione (GSH). Mouse fibroblast 3T3 cells attach and grow well at the surface of hydrogels. Furthermore, 3T3 cells postculture can be recovered from the gels by the addition of a β-CD derivative due to formation of clear solutions by the adamantane-β-CD interaction. The culture on hydrogels and recovery process do not cause obvious effects on behaviors of 3T3 cells. The results shown in this study indicate that small molecular hydrogels based on adamantane-peptides have great potentials in research fields where further analysis of cells is needed.

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

    PubMed

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

    2015-02-01

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

  1. Ag/N-doped reduced graphene oxide incorporated with molecularly imprinted polymer: An advanced electrochemical sensing platform for salbutamol determination.

    PubMed

    Li, Junhua; Xu, Zhifeng; Liu, Mengqin; Deng, Peihong; Tang, Siping; Jiang, Jianbo; Feng, Haibo; Qian, Dong; He, Lingzhi

    2017-04-15

    In this work, the metallic silver and non-metallic nitrogen co-doped reduced graphene oxide (Ag-N-RGO) was first synthesized by a simple and cost-effective strategy, and then a molecularly imprinted polymer (MIP) was formed in situ at the surface of the prepared composite via electropolymerization of o-phenylenediamine in the presence of salbutamol as the template molecule. The electrochemical characterizations demonstrate that the bifunctional graphene-based composite shows improved catalytic performance than that of pristine graphene doped with one-component or none. The MIP sensor based on Ag-N-RGO owns high porous surface structure, resulting in the increased current response and enhanced recognition capacity than that of non-imprinted sensor. The outstanding performance of the developed sensor derives from the combined advantages of Ag-N-RGO with effective catalytic property and MIP with excellent selectivity. Under the optimal conditions, the electrochemical response of the developed sensor is linearly proportional to the concentration of salbutamol in the range of 0.03-20.00µmolL(-1) with a low detection limit of 7 nmol L(-1). The designed sensor has exhibited the multiple advantages such as low cost, simple manufacture, convenient use, excellent selectivity and good reproducibility. Finally, the proposed method has been extended for the determinations of salbutamol in human urine and pork samples, and the satisfactory recoveries between 98.9-105.3% are achieved.

  2. Atomic and Molecular Hydrogen Interaction with Ti-Doped Al (100): Hydrogen Dissociation and Surface Alane Formation

    NASA Astrophysics Data System (ADS)

    Muller, Erik; Sutter, Peter; Zahl, Percy; Chaudhuri, Santanu; Muckerman, James

    2006-03-01

    A comprehensive research effort on the atomistic mechanisms underlying hydrogen storage in Ti-doped NaAlH4 is aimed at deriving a knowledge base for the rational optimization of this and other related complex hydride materials. Our investigation focuses on the role of the Ti dopants in promoting reversible hydrogenation, a key requirement for any practical hydrogen storage material. The re-hydrogenation reaction proceeds from the crucial initial step of dissociative adsorption of molecular hydrogen on Al or NaH. A specific Al:Ti complex was recently predicted as an active site for H2 dissociation on extended Al(100) surfaces [1]. Combining high-resolution surface imaging experiments (scanning tunneling microscopy, low-energy electron microscopy) with density functional theory, we are investigating the dissociative adsorption of H2 on Ti-doped Al(100) prepared in ultrahigh vacuum. We will discuss our progress toward identifying catalytically active sites for H2 dissociation on this surface, as well as pathways toward the formation of mobile Al-species. [1] S. Chaudhuri and J.T. Muckerman, J. Phys. Chem. B 109, 6952 (2005).

  3. Amperometric detection of dopamine in human serum by electrochemical sensor based on gold nanoparticles doped molecularly imprinted polymers.

    PubMed

    Xue, Cheng; Han, Qing; Wang, Yang; Wu, Jinhua; Wen, Tingting; Wang, Ruoyu; Hong, Junli; Zhou, Xuemin; Jiang, Huijun

    2013-11-15

    In this work, a highly sensitive and selective biomimetic electrochemical sensor for the amperometric detection of trace dopamine (DA) in human serums was achieved by gold nanoparticles (AuNPs) doped molecularly imprinted polymers (MIPs). Functionalized AuNPs (F-AuNPs), a novel functional monomer bearing aniline moieties on the surface of the AuNPs, were prepared via a direct synthesis method and then used to fabricate the conductive MIPs film on the modified electrode by electropolymerization method in the presence of DA and p-aminobenzenethiol (p-ATP). The obtained electrochemical sensor based on the conductive film of AuNPs doped MIPs (AuNPs@MIPs) could effectively minimize the interferences caused by ascorbic acid (AA) and uric acid (UA). The linear range for amperometric detection of DA was from 0.02 μmol L(-1) to 0.54 μmol L(-1) with the detection limit of 7.8 nmol L(-1) (S/N=3). Furthermore, the AuNPs@MIPs modified electrode (AuNPs@MIES) was successfully employed to detect trace DA in different human serums.

  4. Small Gold Nanoparticles Interfaced to Electrodes through Molecular Linkers: A Platform to Enhance Electron Transfer and Increase Electrochemically Active Surface Area.

    PubMed

    Young, Samantha L; Kellon, Jaclyn E; Hutchison, James E

    2016-10-17

    For the smallest nanostructures (<5 nm), small changes in structure can lead to significant changes in properties and reactivity. In the case of nanoparticle (NP)-functionalized electrodes, NP structure and composition, and the nature of the NP-electrode interface have a strong influence upon electrochemical properties that are critical in applications such as amperometric sensing, photocatalysis and electrocatalysis. Existing methods to fabricate NP-functionalized electrodes do not allow for precise control over all these variables, especially the NP-electrode interface, making it difficult to understand and predict how structural changes influence NP activity. We investigated the electrochemical properties of small (dcore < 2.5 nm) gold nanoparticles (AuNPs) on boron doped diamond electrodes using three different electrode fabrication techniques with varying degrees of nanoparticle-electrode interface definition. Two methods to attach AuNPs to the electrode through a covalently bound molecular linker were developed and compared to NP-functionalized electrodes fabricated using solution deposition methods (drop-casting and physiadsorption of a monolayer). In each case, a ferrocene redox probe was tethered to the AuNP surface to evaluate electron transfer through the AuNPs. The AuNPs that were molecularly interfaced with the electrode exhibited nearly ideal, reproducible electrochemical behavior with narrow redox peaks and small peak separations, whereas the solution deposited NPs had broader redox peaks with large peak separations. These data suggest that the molecular tether facilitates AuNP-mediated electron transfer. Interestingly, the molecularly tethered NPs also had significantly more electrochemically active surface area than the solution deposited NPs. The enhanced electrochemical behavior of the molecularly interfaced NPs demonstrates the significant influence of the interface on NP-mediated electron transfer and suggests that similar modified electrodes

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

    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 3.3×1020 cm-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.

  7. Al- and Cu-doped BaSi2 films on Si(111) substrate by molecular beam epitaxy and evaluation of depth profiles of Al and Cu atoms

    NASA Astrophysics Data System (ADS)

    Ajmal Khan, M.; Takeishi, M.; Matsumoto, Y.; Saito, T.; Suemasu, T.

    The main objective of the present work is to evaluate and compare the depth profiles of Al and Cu atoms in in-situ doped BaSi2. Furthermore, it is also desired to investigate and compare the carrier concentration of Al-doped as well as Cu-doped BaSi2 films and qualify as a potential dopant-candidate for more efficient solar cells of BaSi2. During the experiment, reactive deposition epitaxy and molecular beam epitaxy were used to develop the samples. X-ray diffraction (XRD) measurements and secondary ion mass spectroscopy (SIMS), were used to determine the structure, depth profile and composition of the already grown films. The electrical properties were characterized by Hall measurement using the van der Pauw method. In case of Al-doped BaSi2 films, it was not encouraging result due to diffusion and segregation of Al in both the surface and BaSi2/ Si interface regions. On the other hand, those phenomena were not observed for Cu-doped BaS2 films. Heavily Cu-doped BaSi2 showed n+ conductivity, differently from our prediction.

  8. Molecular targeted therapy in the treatment of advanced stage non-small cell lung cancer (NSCLC).

    PubMed

    Kumarakulasinghe, Nesaretnam Barr; van Zanwijk, Nico; Soo, Ross A

    2015-04-01

    Historically, patients with advanced stage non-small cell lung cancer (NSCLC) were treated with chemotherapy alone, but a therapeutic plateau has been reached. Advances in the understanding of molecular genetics have led to the recognition of multiple molecularly distinct subsets of NSCLC. This in turn has led to the development of rationally directed molecular targeted therapy, leading to improved clinical outcomes. Tumour genotyping for EGFR mutations and ALK rearrangement has meant chemotherapy is no longer given automatically as first-line treatment but reserved for when patients do not have a 'druggable' driver oncogene. In this review, we will address the current status of clinically relevant driver mutations and emerging new molecular subsets in lung adenocarcinoma and squamous cell carcinoma, and the role of targeted therapy and mechanisms of acquired resistance to targeted therapy.

  9. Tuning the charge carriers in epitaxial graphene on SiC(0001) from electron to hole via molecular doping with C60F48

    NASA Astrophysics Data System (ADS)

    Tadich, A.; Edmonds, M. T.; Ley, L.; Fromm, F.; Smets, Y.; Mazej, Z.; Riley, J.; Pakes, C. I.; Seyller, Th.; Wanke, M.

    2013-06-01

    We demonstrate that the intrinsic electron doping of monolayer epitaxial graphene on SiC(0001) can be tuned in a controlled fashion to holes via molecular doping with the fluorinated fullerene C60F48. In situ angle-resolved photoemission is used to measure an upward shift of (0.6 ± 0.05) eV in the Dirac point from -0.43 eV to +0.17 eV relative to the Fermi level. The carrier density is observed to change from n ˜ (1 × 1013 ± 0.1 × 1013) cm-2 to p ˜ (2 × 1012 ± 1 × 1012) cm-2. We introduce a doping model employing Fermi-Dirac statistics which explicitly takes temperature and the highly correlated nature of molecular orbitals into account. The model describes the observed doping behaviour in our experiment and readily explains why net p-type doping was not achieved in a previous study [Coletti et al., Phys. Rev. B 81, 8 (2010)] which used tetrafluorotetra-cyanoquinodimethane (F4-TCNQ).

  10. Impurity distribution and microstructure of Ga-doped ZnO films grown by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Kvit, A. V.; Yankovich, A. B.; Avrutin, V.; Liu, H.; Izyumskaya, N.; Özgür, Ü.; Morkoç, H.; Voyles, P. M.

    2012-12-01

    We report microstructural characterization of heavily Ga-doped ZnO (GZO) thin films on GaN and sapphire by aberration-corrected scanning transmission electron microscopy. Growth under oxygen-rich and metal-rich growth conditions leads to changes in the GZO polarity and different extended defects. For GZO layers on sapphire, the primary extended defects are voids, inversion domain boundaries, and low-angle grain boundaries. Ga doping of ZnO grown under metal-rich conditions causes a switch from pure oxygen polarity to mixed oxygen and zinc polarity in small domains. Electron energy loss spectroscopy and energy dispersive spectroscopy spectrum imaging show that Ga is homogeneous, but other residual impurities tend to accumulate at the GZO surface and at extended defects. GZO grown on GaN on c-plane sapphire has Zn polarity and no voids. There are misfit dislocations at the interfaces between GZO and an undoped ZnO buffer layer and at the buffer/GaN interface. Low-angle grain boundaries are the only threading microstructural defects. The potential effects of different extended defects and impurity distributions on free carrier scattering are discussed.

  11. Hopping charge transport in molecularly doped polymers: Polymer matrix dependence of the hole drift mobility

    NASA Astrophysics Data System (ADS)

    Kanemitsu, Yoshihiko

    1992-03-01

    Effects of the polymer matrix on the drift mobility of holes in polymers doped with 2-(p-dipropylaminophenyl)-4-(p-dimethylaminophenyl)-5-(o-chlorophenyl)-1, 3-oxazole were studied by means of time-of-flight photoconductivity measurements. The drift mobility at zero field, the activation energy for hopping, and the electric field dependence of the mobility strongly depend on the polymer composition. These polymer matrix dependence of the drift mobility are largely related to energetic disorder of hopping sites in binary solid solution.

  12. Efficient Triplet Exciton Fusion in Molecularly Doped Polymer Light-Emitting Diodes.

    PubMed

    Di, Dawei; Yang, Le; Richter, Johannes M; Meraldi, Lorenzo; Altamimi, Rashid M; Alyamani, Ahmed Y; Credgington, Dan; Musselman, Kevin P; MacManus-Driscoll, Judith L; Friend, Richard H

    2017-04-01

    Solution-processed polymer organic light-emitting diodes (OLEDs) doped with triplet-triplet annihilation (TTA)-upconversion molecules, including 9,10-diphenylanthracene, perylene, rubrene and TIPS-pentacene, are reported. The fraction of triplet-generated electroluminescence approaches the theoretical limit. Record-high efficiencies in solution-processed OLEDs based on these materials are achieved. Unprecedented solid-state TTA-upconversion quantum yield of 23% (TTA-upconversion reaction efficiency of 70%) at electrical excitation well below one-sun equivalent is observed.

  13. 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.

  14. 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.

  15. Fe-doped semi-insulating GaN with solid Fe source grown on (110) Si substrates by NH3 molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Noh, Young Kyun; Lee, Sang Tae; Kim, Moon Deock; Oh, Jae Eung

    2017-02-01

    Iron doped GaN layers were grown on (110) Si substrates by ammonia molecular beam epitaxy (MBE) using solid elemental iron as a source. Specular films with concentrations up to 1×1020 cm-3, as determined by secondary ion mass spectroscopy, were grown, unlike a limited incorporation of Fe into GaN by metal-rich rf plasma MBE. The Fe concentration in the film showed an exponential dependence on the inverse of source temperature with an activation energy of 3.4 eV, which agrees well to the reported value for the sublimation of Fe. A 1.5 μm thick GaN film with a sheet resistance of 1 GΩ/sq. was obtained by compensating unintentional residual donors with a small Fe concentration of 1×1017 cm-3. X-ray diffraction rocking curves indicated high crystalline quality, very similar to an undoped film, showing that the Fe incorporation required to obtain the semi-insulating film properties did not affect the structural properties of the film. The low-temperature PL spectra of highly resistive and semi-insulating Fe:GaN in the range of 1017 1018 cm-3 show dominant exciton emissions and enhanced donor-acceptor-pair (DAP) emissions, implying that Fe ions contribute to the DAP transition between donor levels and Fe-related acceptor levels, possibly compensating the residual donors to achieve the semi-insulating electrical properties.

  16. Linearly and circularly polarized laser photoinduced molecular order in azo dye doped polymer films

    NASA Astrophysics Data System (ADS)

    Saad, Bendaoud

    2017-03-01

    Photo-induced behavior of Azo Disperse one (AZD1) doped Poly(Methyl MethAcrylate) (PMMA) using both linear and circular polarized light is studied. The anisotropy is not erased by the circular polarization light. The circular polarization light combined with relatively long lifetime of the cis state in azo dye doped polymers activate all transverse directions of the angular hole burning through the spot in the film inducing anisotropy. Under circular polarized light, there is no orientation perpendicularly to the helex described by the rotating electric field vector, trans molecules reorients in the propagation direction of the pump beam. The polarization state of the probe beam after propagation through the pumped spot depends strongly on the angle of incidence of both pump and probe beams on the input face. In the case where circular polarized pump and probe beams are under the same angle of incidence, the probe beam "sees" anisotropic film as if it is isotropic. Results of this work shows the possibility to reorient azobenzene-type molecules in two orthogonal directions using alternately linearly and circularly polarized beams.

  17. 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

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

    SciTech Connect

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

    2008-12-31

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

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

    PubMed

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

    2014-12-01

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

  20. 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

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

    PubMed

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

    2015-06-24

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

  2. 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.

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

    PubMed

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

    2013-01-01

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

  4. Boron doped graphene wrapped silver nanowires as an efficient electrocatalyst for molecular oxygen reduction

    NASA Astrophysics Data System (ADS)

    Nair, Anju K.; Thazhe Veettil, Vineesh; Kalarikkal, Nandakumar; Thomas, Sabu; Kala, M. S.; Sahajwalla, Veena; Joshi, Rakesh K.; Alwarappan, Subbiah

    2016-12-01

    Metal nanowires exhibit unusually high catalytic activity towards oxygen reduction reaction (ORR) due to their inherent electronic structures. However, controllable synthesis of stable nanowires still remains as a daunting challenge. Herein, we report the in situ synthesis of silver nanowires (AgNWs) over boron doped graphene sheets (BG) and demonstrated its efficient electrocatalytic activity towards ORR for the first time. The electrocatalytic ORR efficacy of BG-AgNW is studied using various voltammetric techniques. The BG wrapped AgNWs shows excellent ORR activity, with very high onset potential and current density and it followed four electron transfer mechanism with high methanol tolerance and stability towards ORR. The results are comparable to the commercially available 20% Pt/C in terms of performance.

  5. Boron doped graphene wrapped silver nanowires as an efficient electrocatalyst for molecular oxygen reduction

    PubMed Central

    Nair, Anju K.; Thazhe veettil, Vineesh; Kalarikkal, Nandakumar; Thomas, Sabu; Kala, M. S.; Sahajwalla, Veena; Joshi, Rakesh K.; Alwarappan, Subbiah

    2016-01-01

    Metal nanowires exhibit unusually high catalytic activity towards oxygen reduction reaction (ORR) due to their inherent electronic structures. However, controllable synthesis of stable nanowires still remains as a daunting challenge. Herein, we report the in situ synthesis of silver nanowires (AgNWs) over boron doped graphene sheets (BG) and demonstrated its efficient electrocatalytic activity towards ORR for the first time. The electrocatalytic ORR efficacy of BG-AgNW is studied using various voltammetric techniques. The BG wrapped AgNWs shows excellent ORR activity, with very high onset potential and current density and it followed four electron transfer mechanism with high methanol tolerance and stability towards ORR. The results are comparable to the commercially available 20% Pt/C in terms of performance. PMID:27941954

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

    DOE PAGES

    Novikov, S. V.; Ting, M.; Yu, K. M.; ...

    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.

  7. 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.

  8. 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

  9. 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.

  10. Efficient bulk heterojunction photovoltaic cells using small-molecular-weight organic thin films.

    PubMed

    Peumans, Peter; Uchida, Soichi; Forrest, Stephen R

    2003-09-11

    The power conversion efficiency of small-molecular-weight and polymer organic photovoltaic cells has increased steadily over the past decade. This progress is chiefly attributable to the introduction of the donor-acceptor heterojunction that functions as a dissociation site for the strongly bound photogenerated excitons. Further progress was realized in polymer devices through use of blends of the donor and acceptor materials: phase separation during spin-coating leads to a bulk heterojunction that removes the exciton diffusion bottleneck by creating an interpenetrating network of the donor and acceptor materials. The realization of bulk heterojunctions using mixtures of vacuum-deposited small-molecular-weight materials has, on the other hand, posed elusive: phase separation induced by elevating the substrate temperature inevitably leads to a significant roughening of the film surface and to short-circuited devices. Here, we demonstrate that the use of a metal cap to confine the organic materials during annealing prevents the formation of a rough surface morphology while allowing for the formation of an interpenetrating donor-acceptor network. This method results in a power conversion efficiency 50 per cent higher than the best values reported for comparable bilayer devices, suggesting that this strained annealing process could allow for the formation of low-cost and high-efficiency thin film organic solar cells based on vacuum-deposited small-molecular-weight organic materials.

  11. An anchor-dependent molecular docking process for docking small flexible molecules into rigid protein receptors.

    PubMed

    Lin, Thy-Hou; Lin, Guan-Liang

    2008-08-01

    A molecular docking method designated as ADDock, anchor-dependent molecular docking process for docking small flexible molecules into rigid protein receptors, is presented in this article. ADDock makes the bond connection lists for atoms based on anchors chosen for building molecular structures for docking small flexible molecules or ligands into rigid active sites of protein receptors. ADDock employs an extended version of piecewise linear potential for scoring the docked structures. Since no translational motion for small molecules is implemented during the docking process, ADDock searches the best docking result by systematically changing the anchors chosen, which are usually the single-edge connected nodes or terminal hydrogen atoms of ligands. ADDock takes intact ligand structures generated during the docking process for computing the docked scores; therefore, no energy minimization is required in the evaluation phase of docking. The docking accuracy by ADDock for 92 receptor-ligand complexes docked is 91.3%. All these complexes have been docked by other groups using other docking methods. The receptor-ligand steric interaction energies computed by ADDock for some sets of active and inactive compounds selected and docked into the same receptor active sites are apparently separated. These results show that based on the steric interaction energies computed between the docked structures and receptor active sites, ADDock is able to separate active from inactive compounds for both being docked into the same receptor.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-08-28

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

  14. [Effects of UV radiation on the aggregation performance of small molecular organic acids].

    PubMed

    Wang, Wen-Dong; Wang, Ya-Bo; Fan, Qing-Hai; Ding, Zhen-Zhen; Wang, Wen; Song, Shan; Zhang, Yin-Ting

    2014-10-01

    This study systematically investigated the effects of UV radiation on the aggregation of small molecular aliphatic carboxylic acids and phenolic acids by jar test. Experimental results show that solution pH has little effect on the coagulation of small molecular aliphatic carboxylic acids including citric acid, oxalic acid, tartaric acid, and succinic acid. For the solutions pretreated with UV light, the removal rates of the selected aliphatic carboxylic acids in coagulation are higher than that without UV radiation. Further study shows that photochemical reactions occur during UV radiation which decreases the negative charge in aliphatic carboxylic acids, and thereby increases their aggregation properties. Different from aliphatic carboxylic acids, phenol, salicylic acid, and benzoic acid have poor coagulation properties, and UV radiation does not have notable effects on their aggregation in the coagulation process. The coagulation performance of tannic acid is better than the other phenolic acids. At pH = 6, its removal rate is above 90%, which may be contributed to the aliphatic carboxylic acid structure in its molecular. Meanwhile, the large molecular of tannic acid is also easier to be adsorbed by the hydrolysis products of PAC1.

  15. Tri-iodide reduction activity of ultra-small size PtFe nanoparticles supported nitrogen-doped graphene as counter electrode for dye-sensitized solar cell.

    PubMed

    Nechiyil, Divya; Vinayan, B P; Ramaprabhu, S

    2017-02-15

    Efficient and cost effective counter electrode (CE) is pre-requisite for the commercialization of dye-sensitized solar cell (DSSC). Present work investigates ultra small size platinum-iron alloy nanoparticles dispersed over nitrogen-doped graphene (PtFe/NG) as an effective counter electrode for DSSC. Hereby we achieve low loading of Pt by alloying with Fe accompanied by superior electrocatalytic activity towards the iodide-triiodide (I(-)/I3(-)) mechanism. Enhancement in electrocatalytic performance of PtFe/NG has been shown by cyclic voltammetry, electrochemical impedance spectroscopy and Tafel polarization analysis. PtFe/NG counter electrode exhibits higher power conversion efficiency (∼6.12%) with lower charge transfer resistance, which helps in faster diffusion of I(-)/I3(-) ions as compared to NG and Pt/NG counter electrodes. The increased electrocatalytic activity of PtFe/NG is due to the collective effect of intrinsic electronic effects by alloying, uniform dispersion of small PtFe alloy nanoparticles over nitrogen doped graphene, and additional catalytic sites offered by nitrogen-doped graphene.

  16. Studies of arsenic incorporation and P-type doping in epitaxial mercury cadmium telluride thin films grown by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Zandian, Majid

    Doped layer semiconductor structures provide possibilities for novel electronic devices. Growth of Hg1-xCdxTe by molecular beam epitaxy (MBE) allows precise control over the doping profile and position of heterojunctions as well as structural properties of this ternary alloy. Even though n-type doping using indium is well established, little is known about p-type doping in this material system by MBE. Several elements such as Ag, Au, Sb, Bi and P have been previously used, however high diffusion coefficient and amphoteric behavior of these atoms in HgCdTe has restricted their use in heterojunction devices where control over doping profiles and concentrations is needed. We investigated arsenic incorporation efficiency as a function of As 4 flux and growth temperature. The sticking coefficient of As is substantially higher at lower growth temperature compared to growth at 190°C. For samples grown at 170°C, the etch pit density (EPD) is higher compared to p-type As doped samples grown at 190°C. Higher EPD is associated with columnar twin defects observed in transmission electron microscopy (TEM) studies of low growth temperature samples. Growth at low temperature of 170°C causes Hg rich condition promoting twin formation. Therefore, growth of p-type layers doped with As at low temperatures require optimization of II/VI flux ratio to eliminate columnar twin defects. It is possible to incorporate As at normal MBE growth temperature of 190°C but very high flux of As has to used to overcome low sticking coefficient of As at these temperatures. We proposed a mechanism for the activation of As involving Hg vacancies (VHg··) where Te is moved to a Hg vacancy, leaving behind a Te vacancy, which is then filled by an As atom. The Te that is now on a Hg site (i.e., Te antisite) migrates to the surface and leaves the crystal.

  17. 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.

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

    PubMed

    Kim, Yu Jin; Park, Chan Eon

    2016-04-14

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

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

    PubMed

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

    2012-12-01

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

  20. 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.

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  4. 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.

  5. STM Observation of Molecular Adsorption on Graphene and Nitrogen Doped Graphene

    NASA Astrophysics Data System (ADS)

    Obata, Seiji; Saiki, Koichiro

    2014-03-01

    Carbon alloy catalyst (CAC) shows catalytic activity to oxygen reduction reaction (ORR) and it is expected as a substitution of Pt in fuel cells due to its catalytic property. At present CAC are synthesized by burning organic compounds which contain nitrogen atoms such as phthalocyanine. The catalytic activity of CAC is lower than Pt. Since catalytic sites and oxygen reduction process is still unknown, elucidation of catalytic sites of CAC helps to synthesize high performance CAC. STM is a useful tool to investigate adsorption and reaction at atomic level. However, disordered structure of CAC makes it difficult to use STM for catalytic site observation. To overcome this difficulty, we synthesized nitrogen doped graphene (NG) and and pristine graphene (PG) on Pt (111) and used it as model catalyst to study the catalytic property of CAC. Oxygen adsorption is the first step of oxygen reduction reaction. Therefore we investigated the oxygen adsorption to NG and PG by STM. Oxygen adsorbed at domain boundary (DB) of NG?According to XPS measurement nitrogen atoms exist at edge site preferably. These results indicate that nitrogen atom enhances oxygen adsorption activity. In addition, actual reaction process occurs in H2O. Thus we also investigated H2O adsorption on NG.

  6. TOPICAL REVIEW: Small animal SPECT and its place in the matrix of molecular imaging technologies

    NASA Astrophysics Data System (ADS)

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

    2005-11-01

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

  7. In Situ Selected Area Doping of GaAs by Molecular Beam Epitaxy.

    DTIC Science & Technology

    1985-07-01

    several Sn-containing molecules (tetramethyltin, tetrabutyltin, dibutyltin dibromide and stannic chloride) as gas phase sources of Sn for use in molecular... Dibutyltin Dibromide A brief screening experiment with DBTB was performed. DBTB adsorbed, but similar to the above organometallic compounds, it...surfaces from a variety of tin containing compounds (tetramethyltin, tetrabutyltin, dibutyltin dibromide, stannic chloride, hexamethylditin

  8. 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

  9. In vitro synthesis of high molecular weight rubber by Hevea small rubber particles.

    PubMed

    Rojruthai, Porntip; Sakdapipanich, Jitladda Tangpakdee; Takahashi, Seiji; Hyegin, Lee; Noike, Motoyoshi; Koyama, Tanetoshi; Tanaka, Yasuyuki

    2010-02-01

    Hevea brasiliensis is one of few higher plants producing the commercial natural rubber used in many significant applications. The biosynthesis of high molecular weight rubber molecules by the higher plants has not been clarified yet. Here, the in vitro rubber biosynthesis was performed by using enzymatically active small rubber particles (SRP) from Hevea. The mechanism of the in vitro rubber synthesis was investigated by the molecular weight distribution (MWD). The highly purified SRP prepared by gel filtration and centrifugation in the presence of Triton((R)) X-100 showed the low isopentenyl diphosphate (IPP) incorporation for the chain extension mechanism of pre-existing rubber. The MWD of in vitro rubber elongated from the pre-existing rubber chains in SRP was analyzed for the first time in the case of H. brasiliensis by incubating without the addition of any initiator. The rubber transferase activity of 70% incorporation of the added IPP (w/w) was obtained when farnesyl diphosphate was present as the allylic diphosphate initiator. The in vitro synthesized rubber showed a typical bimodal MWD of high and low molecular weight fractions in GPC analysis, which was similar to that of the in vivo rubber with peaks at around 10(6) and 10(5) Da or lower. The reaction time independence and dependence of molecular weight of high and low molecular weight fractions, respectively, indicated that the high molecular weight rubber was synthesized from the chain extension of pre-existing rubber molecules whereas the lower one was from the chain elongation of rubber molecules newly synthesized from the added allylic substrates.

  10. Molecular-targeted therapy for elderly patients with advanced non-small cell lung cancer

    PubMed Central

    ANTONELLI, GIOVANNA; LIBRA, MASSIMO; PANEBIANCO, VINCENZO; RUSSO, ALESSIA ERIKA; VITALE, FELICE VITO; COLINA, PAOLO; D'ANGELO, ALESSANDRO; ROSSELLO, ROSALBA; FERRAÙ, FRANCESCO

    2016-01-01

    Lung cancer is the most common cause of cancer-related mortality in men and women. Non-small cell lung cancer (NSCLC) represents close to 90% of all lung cancers. When diagnosed, >50% of patients are >65 years old. Through an improved understanding of the molecular mechanisms involved in lung oncogenesis, molecular-targeted approaches have become an essential element for the treatment of patients with NSCLC. As the toxicity profiles of the techniques are definitely more favorable compared with chemotherapy, they are particularly attractive for use in elderly patients, who are potentially more susceptible to the toxicity of systemic oncological therapies. However, studies on the activity of molecular-targeted agents in this aged patient setting are much more limited compared with those in their younger counterparts. In the present review, the literature on molecular-targeted therapy for elderly patients with advanced NSCLC is discussed. It is concluded that bevacizumab should be reserved only for highly select elderly patients with advanced NSCLC when the clinician deems it useful in the face of acceptable toxicities. In elderly patients with advanced epidermal growth factor receptor mutation-positive NSCLC, erlotinib and gefitinib appear to repeat the same favorable performance as that documented on a larger scale in the overall population of patients with activating mutations. A good toxicity profile is also confirmed for active molecules on different pathways, such as crizotinib. PMID:26870160

  11. Molecular-targeted therapy for elderly patients with advanced non-small cell lung cancer.

    PubMed

    Antonelli, Giovanna; Libra, Massimo; Panebianco, Vincenzo; Russo, Alessia Erika; Vitale, Felice Vito; Colina, Paolo; D'Angelo, Alessandro; Rossello, Rosalba; Ferraù, Francesco

    2016-01-01

    Lung cancer is the most common cause of cancer-related mortality in men and women. Non-small cell lung cancer (NSCLC) represents close to 90% of all lung cancers. When diagnosed, >50% of patients are >65 years old. Through an improved understanding of the molecular mechanisms involved in lung oncogenesis, molecular-targeted approaches have become an essential element for the treatment of patients with NSCLC. As the toxicity profiles of the techniques are definitely more favorable compared with chemotherapy, they are particularly attractive for use in elderly patients, who are potentially more susceptible to the toxicity of systemic oncological therapies. However, studies on the activity of molecular-targeted agents in this aged patient setting are much more limited compared with those in their younger counterparts. In the present review, the literature on molecular-targeted therapy for elderly patients with advanced NSCLC is discussed. It is concluded that bevacizumab should be reserved only for highly select elderly patients with advanced NSCLC when the clinician deems it useful in the face of acceptable toxicities. In elderly patients with advanced epidermal growth factor receptor mutation-positive NSCLC, erlotinib and gefitinib appear to repeat the same favorable performance as that documented on a larger scale in the overall population of patients with activating mutations. A good toxicity profile is also confirmed for active molecules on different pathways, such as crizotinib.

  12. Genetic and molecular coordinates of neuroendocrine lung tumors, with emphasis on small-cell lung carcinomas.

    PubMed Central

    Koutsami, Marilena K.; Doussis-Anagnostopoulou, Ipatia; Papavassiliou, Athanasios G.; Gorgoulis, Vassilis G.

    2002-01-01

    The aim of this review is to present the advances in our understanding of the progression of tumorigenesis in neuroendocrine lung tumors. Current information on established and putative diagnostic and prognostic markers of neuroendocrine tumors are evaluated, with a special reference to small-cell lung carcinoma, due to its higher incidence and aggressive behavior. The genetic and molecular changes that accompany these neoplasms are highlighted, and factors that influence cell-cycle progression, apoptosis, drug resistance, and escape from immune surveillance are critically assessed. PMID:12435853

  13. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

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

    PubMed

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

    2016-04-07

    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

  16. 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

    2015-07-10

    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.

  17. Small Animal Imaging Center Design: The Facility at the UCLA Crump Institute for Molecular Imaging

    PubMed Central

    Stout, David B.; Chatziioannou, Arion F.; Lawson, Timothy P.; Silverman, Robert W.; Gambhir, Sanjiv S.; Phelps, Michael E.

    2010-01-01

    Purpose The growing number of mouse and rat experiments, coupled with advances in small-animal imaging systems such as microPET®, optical, microCAT™, microMR, ultrasound and microSPECT, has necessitated a common technical center for imaging small animals. Procedures At the UCLA Crump Institute for Molecular Imaging, we have designed and built a facility to support the research interests of a wide range of investigators from multiple disciplines. Requirements to satisfy both research and regulatory oversight have been critically examined. Support is provided for investigator training, study scheduling, data acquisition, archiving, image display, and analysis. Results The center has been in operation for more than 18 months, supporting more than 13,000 individual imaging procedures. Conclusions We have created a facility that maximizes our resource utilization while providing optimal investigator support, as well as the means to continually improve the quality and diversity of the science by integrating physical and biological sciences. PMID:16261425

  18. Multiplatform-based molecular subtypes of non-small-cell lung cancer.

    PubMed

    Chen, F; Zhang, Y; Parra, E; Rodriguez, J; Behrens, C; Akbani, R; Lu, Y; Kurie, J M; Gibbons, D L; Mills, G B; Wistuba, I I; Creighton, C J

    2017-03-01

    Non-small-cell lung cancer (NSCLC) demonstrates remarkable molecular diversity. With the completion of The Cancer Genome Atlas (TCGA), there is opportunity for systematic analyses of the entire TCGA NSCLC cohort, including comparisons and contrasts between different disease subsets. On the basis of multidimensional and comprehensive molecular characterization (including DNA methylation and copy, and RNA and protein expression), 1023 NSCLC cases-519 from TCGA adenocarcinoma (AD) project and 504 from TCGA squamous cell carcinoma (SQCC) project-were classified using a 'cluster-of-clusters' analytic approach. Patterns from TCGA NSCLC subsets were examined in independent external databases, including the PROSPECT (Profiling of Resistance patterns and Oncogenic Signaling Pathways in Evaluation of Cancers of the Thorax) NSCLC data set. Nine genomic subtypes of NSCLC were identified, three within SQCC and six within AD. SQCC subtypes were associated with transcriptional targets of SOX2 or p63. One predominately AD subtype (with a large proportion of SQCC) shared molecular features with neuroendocrine tumors. Two AD subtypes manifested a CpG island methylator phenotype. Three AD subtypes showed high p38 and mTOR pathway activation. AD subtypes associated with low differentiation showed relatively worse prognosis. SQCC subtypes and two of the AD subtypes expressed cancer testis antigen genes, whereas three AD subtypes expressed several immune checkpoint genes including PDL1 and PDL2, corresponding with patterns of greater immune cell infiltration. Subtype associations for several immune-related markers-including PD1, PDL1, CD3 and CD8-were confirmed in the PROSPECT cohort using immunohistochemistry. NSCLC molecular subtypes have therapeutic implications and lend support to a personalized approach to NSCLC management based on molecular characterization.

  19. 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

  20. 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

  1. Electron Impact Ionization and Fragmentation Dynamics of Small Atomic and Molecular Clusters

    NASA Astrophysics Data System (ADS)

    Dorn, Alexander

    2016-09-01

    New ionization and fragmentation reactions emerge if target atoms or molecules are embedded in an environment as it is the case in small clusters or in the condensed phase. These can be intermolecular energy and charge transfer processes or a completely modified fragmentation behavior of the molecular ions. Here we study low energy electron impact induced ionization with a multi-electron and ion imaging spectrometer (reaction microscope) and a supersonic gas jet target which can produce small clusters of various target species. Interatomic reactions are studied for the model system of weakly bound Ar2 dimers. Here, the coincident detection of three electrons and two ions gives detailed insight in interatomic Coulombic decay and radiative charge transfer processes. Such processes were also found in bio-relevant systems like water clusters. We studied pure and water-mixed clusters of tetrahydrofuran (C4H8O, THF) which is the simplest analog of deoxyribose in the DNA backbone. One observation is that ionization of the outermost valence orbital for the monomer leads to stable THF ions. In contrast if THF is bound to another THF or a water molecule the molecular ring breaks. In addition we identify intermolecular Coulombic decay induced by energy transfer from a water molecule ionized in the inner valence shell to the neighboring THF molecule.

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

    PubMed

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

    2014-01-01

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

  3. Progress of small molecular inhibitors in the development of anti-influenza virus agents

    PubMed Central

    Wu, Xiaoai; Wu, Xiuli; Sun, Qizheng; Zhang, Chunhui; Yang, Shengyong; Li, Lin; Jia, Zhiyun

    2017-01-01

    The influenza pandemic is a major threat to human health, and highly aggressive strains such as H1N1, H5N1 and H7N9 have emphasized the need for therapeutic strategies to combat these pathogens. Influenza anti-viral agents, especially active small molecular inhibitors play important roles in controlling pandemics while vaccines are developed. Currently, only a few drugs, which function as influenza neuraminidase (NA) inhibitors and M2 ion channel protein inhibitors, are approved in clinical. However, the acquired resistance against current anti-influenza drugs and the emerging mutations of influenza virus itself remain the major challenging unmet medical needs for influenza treatment. It is highly desirable to identify novel anti-influenza agents. This paper reviews the progress of small molecular inhibitors act as antiviral agents, which include hemagglutinin (HA) inhibitors, RNA-dependent RNA polymerase (RdRp) inhibitors, NA inhibitors and M2 ion channel protein inhibitors etc. Moreover, we also summarize new, recently reported potential targets and discuss strategies for the development of new anti-influenza virus drugs. PMID:28382157

  4. Validation and extraction of molecular-geometry information from small-molecule databases

    PubMed Central

    Long, Fei; Emsley, Paul; Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas

    2017-01-01

    A freely available small-molecule structure database, the Crystallography Open Database (COD), is used for the extraction of molecular-geometry information on small-molecule compounds. The results are used for the generation of new ligand descriptions, which are subsequently used by macromolecular model-building and structure-refinement software. To increase the reliability of the derived data, and therefore the new ligand descriptions, the entries from this database were subjected to very strict validation. The selection criteria made sure that the crystal structures used to derive atom types, bond and angle classes are of sufficiently high quality. Any suspicious entries at a crystal or molecular level were removed from further consideration. The selection criteria included (i) the resolution of the data used for refinement (entries solved at 0.84 Å resolution or higher) and (ii) the structure-solution method (structures must be from a single-crystal experiment and all atoms of generated molecules must have full occupancies), as well as basic sanity checks such as (iii) consistency between the valences and the number of connections between atoms, (iv) acceptable bond-length deviations from the expected values and (v) detection of atomic collisions. The derived atom types and bond classes were then validated using high-order moment-based statistical techniques. The results of the statistical analyses were fed back to fine-tune the atom typing. The developed procedure was repeated four times, resulting in fine-grained atom typing, bond and angle classes. The procedure will be repeated in the future as and when new entries are deposited in the COD. The whole procedure can also be applied to any source of small-molecule structures, including the Cambridge Structural Database and the ZINC database. PMID:28177306

  5. Molecular Dynamics Simulations of Dislocation Activity in Single-Crystal and Nanocrystalline Copper Doped with Antimony

    NASA Astrophysics Data System (ADS)

    Rajgarhia, Rahul K.; Spearot, Douglas E.; Saxena, Ashok

    2010-04-01

    Recent experimental and simulation results have indicated that high-temperature grain growth in nanocrystalline (NC) materials can be suppressed by introducing dopant atoms at the grain boundaries. However, the influence of grain boundary dopants on the mechanical behavior of stabilized NC materials is less clear. In this work, molecular dynamics (MD) simulations are used to study the impact of very low dopant concentrations (<1.0 at. pct Sb) on plastic deformation in single-crystal and NC Cu. A new interatomic potential for low Sb concentration Cu-Sb solid-solution alloys is used to model dopant/host and dopant/dopant interatomic interactions within the MD framework. In single-crystal models, the strained regions around the Sb atoms act as heterogeneous sources for partial dislocation nucleation; the stress associated with this process decreases with increasing Sb concentration. In NC models, MD simulations indicate that Sb dopants randomly dispersed at the grain boundaries cause an increase in the flow stress in NC Cu, implying that Sb atoms at the grain boundaries retard both grain boundary sliding and dislocation nucleation from grain boundary regions.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2006-05-01

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

  8. Enhancement of photoluminescence in various Eu x Re(1- x)TTA3Phen (Re = Y, Tb) complexes molecularly doped in PMMA

    NASA Astrophysics Data System (ADS)

    Thejo Kalyani, N.; Dhoble, S. J.; Pode, R. B.

    2012-07-01

    Europium β-diketonate complexes Eu x Re(1- x)(TTA)3Phen, (Re = Y/Tb, TTA: thenoyl trifluro acetone, Phen: 1-10 Phenanthroline; x = 0.5) have been molecularly doped in poly methyl methacrylate matrix to study the concentration effect on the optical properties such as optical absorption and photoluminescence spectra for four different amounts of weight % (10, 25, 50 and 60 %). All these doped complexes show strong absorption peaks at 334 and 280 nm attributed to n-π* and π-π* transitions of β-diketonate ligand TTA respectively. The close absorptivity of all the complexes is due to the same tris chelated core TTA. Among the three complexes doped in PMMA matrix Eu0.5Tb0.5(TTA)3Phen complex shows hyper chromic shift with enhancement in the luminescent intensity. Enhancement of red light emission have been observed with the increase in wt% of all pure and doped systems in the order of Eu(TTA)3Phen, < Eu0.5Y0.5(TTA)3Phen < Eu0.5Tb0.5(TTA)3Phen. It has been observed that their PL intensity increases in the order of 10 > 25 > 50-60 %. However the luminescence intensity of these blended films with 50 and 60 % of rare earth complexes shows nearly equal value, indicating that the optimal doping concentration is about 50 % under the chosen experimental conditions. Hence these complexes are best suitable in fabricating eco-friendly organic light-emitting devices and displays by solution techniques, which can be operated at very low voltage.

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

    NASA Technical Reports Server (NTRS)

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

    1988-01-01

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

  10. Non-adiabatic molecular dynamics investigation of photoionization state formation and lifetime in Mn²⁺-doped ZnO quantum dots.

    PubMed

    Fischer, Sean A; Lingerfelt, David B; May, Joseph W; Li, Xiaosong

    2014-09-07

    The unique electronic structure of Mn(2+)-doped ZnO quantum dots gives rise to photoionization states that can be used to manipulate the magnetic state of the material and to generate zero-reabsorption luminescence. Fast formation and long non-radiative decay of this photoionization state is a necessary requirement for these important applications. In this work, surface hopping based non-adiabatic molecular dynamics are used to demonstrate the fast formation of a metal-to-ligand charge transfer state in a Mn(2+)-doped ZnO quantum dot. The formation occurs on an ultrafast timescale and is aided by the large density of states and significant mixing of the dopant Mn(2+) 3dt2 levels with the valence-band levels of the ZnO lattice. The non-radiative lifetime of the photoionization states is also investigated.

  11. 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.

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

    PubMed

    Huang, Pei-Hsing

    2015-09-21

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

  13. 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.

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

    PubMed

    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 SO(4)(2-) 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.

  15. The small molecular mass antifungal protein of Penicillium chrysogenum--a mechanism of action oriented review.

    PubMed

    Hegedus, Nikoletta; Leiter, Eva; Kovács, Barbara; Tomori, Valéria; Kwon, Nak-Jung; Emri, Tamás; Marx, Florentine; Batta, Gyula; Csernoch, László; Haas, Hubertus; Yu, Jae-Hyuk; Pócsi, István

    2011-12-01

    The β-lactam producing filamentous fungus Penicillium chrysogenum secretes a 6.25 kDa small molecular mass antifungal protein, PAF, which has a highly stable, compact 3D structure and is effective against a wide spectrum of plant and zoo pathogenic fungi. Its precise physiological functions and mode of action need to be elucidated before considering possible biomedical, agricultural or food technological applications. According to some more recent experimental data, PAF plays an important role in the fine-tuning of conidiogenesis in Penicillium chrysogenum. PAF triggers apoptotic cell death in sensitive fungi, and cell death signaling may be transmitted through two-component systems, heterotrimeric G protein coupled signal transduction and regulatory networks as well as via alteration of the Ca(2+) -homeostasis of the cells. Possible biotechnological applications of PAF are also outlined in the review.

  16. 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

  17. 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.

  18. Low energy emission bands in a small molecular fluorene derivative for organic light-emitting diodes

    NASA Astrophysics Data System (ADS)

    Lou, S. L.; Yu, H. S.; Ma, W. M.; Jiang, Y.; Zhang, Q.

    2008-11-01

    6,6'-(9H-fluoren-9,9-diyl)bis(2,3-bis(9,9-dihexyl-9H-fluoren-2-yl)quinoxaline) (BFLBBFLYQ) was a novel small molecular fluorene material with fluorescence maxima at 450 nm in spin cast films. Compared to spin cast films, BFLBBFLYQ vacuum evaporated deposition films exhibited different photo-physical properties. The low energy emission bands from 530 to 570 nm were observed from the electroluminescence (EL) and photoluminescence (PL) spectra of BFLBBFLYQ films evaporated deposition in ultrahigh vacuum circumstance, and the origin of these emission features were investigated and discussed. Also, the emissive properties of BFLBBFLYQ spin cast films upon thermal annealing and under UV irradiation in air were characterized for the effect of thermal oxidization and photo-oxidization.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

  2. Acidolysis small molecular phenolic ether used as accelerator in photosensitive diazonaphthaquinone systems

    NASA Astrophysics Data System (ADS)

    Zhou, Haihua; Zou, Yingquan

    2006-03-01

    The photosensitive compounds in the photosensitive coatings of positive PS plates are the diazonaphthaquinone derivatives. Some acidolysis small molecular phenolic ethers, which were synthesized by some special polyhydroxyl phenols with vinyl ethyl ether, are added in the positive diazonaphthaquinone photosensitive composition to improve its sensitivity, composed with photo-acid-generators. The effects to the photosensitivity, anti-alkali property, anti-isopropyl alcohol property, dot resolution and line resolution of the coatings are studied with different additive percent of the special phenolic ethers. In the conventional photosensitive diazonaphthaquinone systems for positive PS plates, the photosensitivity is improved without negative effects to resolution, anti-alkali and anti-isopropyl alcohol properties when added about 5% of the special acidolysis phenolic ethers, EAAE or DPHE, composed with photo-acid-generators.

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

    PubMed

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

    2014-04-01

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

  4. Small-Animal Molecular Imaging for Preclinical Cancer Research: .μPET and μ.SPECT.

    PubMed

    Cuccurullo, Vincenzo; Di Stasio, Giuseppe D; Schillirò, Maria L; Mansi, Luigi

    2016-01-01

    Due to different sizes of humans and rodents, the performance of clinical imaging devices is not enough for a scientifically reliable evaluation in mice and rats; therefore dedicated small-animal systems with a much higher sensitivity and spatial resolution, compared to the ones used in humans, are required. Smallanimal imaging represents a cutting-edge research method able to approach an enormous variety of pathologies in which animal models of disease may be used to elucidate the mechanisms underlying the human condition and/or to allow a translational pharmacological (or other) evaluation of therapeutic tools. Molecular imaging, avoiding animal sacrifice, permits repetitive (i.e. longitudinal) studies on the same animal which becomes its own control. In this way also the over time evaluation of disease progression or of the treatment response is enabled. Many different rodent models have been applied to study almost all kind of human pathologies or to experiment a wide series of drugs and/or other therapeutic instruments. In particular, relevant information has been achieved in oncology by in vivo neoplastic phenotypes, obtained through procedures such as subcutaneous tumor grafts, surgical transplantation of solid tumor, orthotopic injection of tumor cells into specific organs/sites of interest, genetic modification of animals to promote tumor-genesis; in this way traditional or innovative treatments, also including gene therapy, of animals with a cancer induced by a known carcinogen may be experimented. Each model has its own disadvantage but, comparing different studies, it is possible to achieve a panoramic and therefore substantially reliable view on the specific subject. Small-animal molecular imaging has become an invaluable component of modern biomedical research that will gain probably an increasingly important role in the next few years.

  5. First molecular isolation of Mycoplasma ovis from small ruminants in North Africa.

    PubMed

    Rjeibi, Mohamed R; Darghouth, Mohamed A; Omri, Houda; Souidi, Khemaïs; Rekik, Mourad; Gharbi, Mohamed

    2015-06-08

    Eperythrozoonosis is a small ruminant disease caused by the bacterium Mycoplasma ovis (formerly known as Eperythrozoon ovis). Whilst acute infection in sheep may result in an anaemia and ill thrift syndrome, most animals do not develop clinical signs. Molecular methods were used to compare and evaluate the prevalence of infection with M. ovis in sheep and goats in Tunisia. A total of 739 whole blood samples from 573 sheep and 166 goats were tested for the M. ovis 16S rRNA gene using PCR. The overall prevalence was 6.28% ± 0.019 (36/573). Only sheep were infected with M. ovis (p < 0.001), and the prevalence was significantly higher in central Tunisia (29.2%) compared with other regions (p < 0.05). The prevalence revealed significant differences according to breed and bioclimatic zones (p < 0.001). Furthermore, the prevalence in young sheep (35/330; 10.6%) was higher than in adults (1/243; 0.41%) (p < 0.001). Only sheep of the Barbarine breed were infected, with a prevalence of 11.8% (p < 0.001). This is the first molecular study and genetic characterisation of M. ovis in North African sheep breeds.

  6. Molecular phylogeny of the small carpenter bees (Hymenoptera: Apidae: Ceratinini) indicates early and rapid global dispersal.

    PubMed

    Rehan, Sandra M; Chapman, Tom W; Craigie, Andrew I; Richards, Miriam H; Cooper, Steven J B; Schwarz, Michael P

    2010-06-01

    The small carpenter bees (tribe Ceratinini, family Apidae) are recorded from all continents except Antarctica. The Ceratinini have a near-global distribution which contrasts strongly with their sister tribe, the Allodapini which has a largely southern Old World distribution. The Ceratinini therefore provides an excellent group to understand the factors that help determine the biogeography and radiation of the bees. This is the first molecular study of ceratinine bees covering representatives from both northern and southern hemisphere Old and New World regions. We use two mitochondrial and one nuclear marker (totalling 2807 nucleotides) to examine the age, cladogenesis and historical biogeography of this tribe. Tree topology and molecular dating support an African origin at about 47 Mya with subsequent dispersal into Eurasia 44 Mya, and followed by an American invasion 32 Mya. Concentrated African and Malagasy sampling revealed there were two or three dispersals events into Madagascar ranging from 25 to 9 Mya. Lineage through time analyses suggest higher rates of cladogenesis close to the origin of the tribe, and this corresponds to both major dispersal events and divergences of lineages leading to extant subgenera. Ceratinini have potentially great importance for future studies to understand the relative roles of dispersal ability and time of origin in determining bee biogeography.

  7. 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.

  8. Structural and functional homology between periplasmic bacterial molecular chaperones and small heat shock proteins.

    PubMed

    Zav'yalov, V P; Zav'yalova, G A; Denesyuk, A I; Gaestel, M; Korpela, T

    1995-07-01

    The periplasmic Yersinia pestis molecular chaperone Caf1M belongs to a superfamily of bacterial proteins for one of which (PapD protein of Escherichia coli) the immunoglobulin-like fold was solved by X-ray analysis. The N-terminal domain of Caf1M was found to share a 20% amino acid sequence identity with an inclusion body-associated protein IbpB of Escherichia coli. One of the regions that was compared, was 32 amino acids long, and displayed more than 40% identity, probability of random coincidence was 1.2 x 10(-4). IbpB is involved in a superfamily of small heat shock proteins which fulfil the function of molecular chaperone. On the basis of the revealed homology, an immunoglobulin-like one-domain model of IbpB three-dimensional structure was designed which could be a prototype conformation of sHsp's. The structure suggested is in good agreement with the known experimental data obtained for different members of sHsp's superfamily.

  9. Advances in the Development of Molecularly Targeted Agents in Non-Small-Cell Lung Cancer.

    PubMed

    Dolly, Saoirse O; Collins, Dearbhaile C; Sundar, Raghav; Popat, Sanjay; Yap, Timothy A

    2017-04-04

    Non-small-cell lung cancer (NSCLC) remains a significant global health challenge and the leading cause of cancer-related mortality. The traditional 'one-size-fits-all' treatment approach has now evolved into one that involves personalized strategies based on histological and molecular subtypes. The molecular era has revolutionized the treatment of patients harboring epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK) and ROS1 gene aberrations. In the appropriately selected population, anti-tumor agents against these molecular targets can significantly improve progression-free survival. However, the emergence of acquired resistance is inevitable. Novel potent compounds with much improved and rational selectivity profiles, such as third-generation EGFR T790M resistance mutation-specific inhibitors, have been developed and added to the NSCLC armamentarium. To date, attempts to overcome resistance bypass pathways through downstream signaling blockade has had limited success. Furthermore, the majority of patients still do not harbor known driver genetic or epigenetic alterations and/or have no new available treatment options, with chemotherapy remaining their standard of care. Several potentially actionable driver aberrations have recently been identified, with the early clinical development of multiple inhibitors against these promising targets currently in progress. The advent of immune checkpoint inhibitors has led to significant benefit for advanced NSCLC patients with durable responses observed. Further interrogation of the underlying biology of NSCLC, coupled with modern clinical trial designs, is now required to develop novel targeted therapeutics rationally matched with predictive biomarkers of response, so as to further advance NSCLC therapeutics through the next decade.

  10. Molecular architecture of the 90S small subunit pre-ribosome

    PubMed Central

    Sun, Qi; Zhu, Xing; Qi, Jia; An, Weidong; Lan, Pengfei; Tan, Dan; Chen, Rongchang; Wang, Bing; Zheng, Sanduo; Zhang, Cheng; Chen, Xining; Zhang, Wei; Chen, Jing; Dong, Meng-Qiu; Ye, Keqiong

    2017-01-01

    Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of Saccharomyces cerevisiae 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors. DOI: http://dx.doi.org/10.7554/eLife.22086.001 PMID:28244370

  11. 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)

  12. Effectiveness of beads for tracking small-scale molecular motor dynamics

    NASA Astrophysics Data System (ADS)

    Lade, Steven J.; Craig, Erin M.; Linke, Heiner

    2011-08-01

    Investigations into molecular motor dynamics are increasingly focused on small-scale features of the motor’s motion. We define performance measures of a common type of single-molecule motility assay, the bead assay, for its ability to detect such features. Using numerical models, we explore the dependence of assay performance on a number of experimentally controllable parameters, including bead size, optical force, and the method of attaching the bead to the motor. We find that the best parameter choice depends on the objective of the experiments, and give a guide to parameter selection. Comparison of the models against experimental data from a recent bead assay of myosin V exemplifies how our methods can also be used to extract additional information from bead assays, particularly that related to small-scale features. By analyzing the experimental data we find evidence for previously undetected multiple waiting states of the bead-motor complex. Furthermore, from numerical simulations we find that equilibrium bead dynamics display features previously attributed to aborted motor steps, and that bead dynamics alone can produce multiple subphases during a step.

  13. 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

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

    PubMed

    Starko-Bowes, Ryan; Pramanik, Sandipan

    2013-06-18

    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

  15. 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.

  16. Donor and acceptor levels in ZnO homoepitaxial thin films grown by molecular beam epitaxy and doped with plasma-activated nitrogen

    SciTech Connect

    Muret, Pierre; Tainoff, Dimitri; Morhain, Christian; Chauveau, Jean-Michel

    2012-09-17

    Deep level transient spectroscopy of both majority and minority carrier traps is performed in a n-type, nitrogen doped homoepitaxial ZnO layer grown on a m-plane by molecular beam epitaxy. Deep levels, most of them being not detected in undoped ZnO, lie close to the band edges with ionization energies in the range 0.12-0.60 eV. The two hole traps with largest capture cross sections are likely acceptors, 0.19 and 0.48 eV from the valence band edge, able to be ionized below room temperature. These results are compared with theoretical predictions and other experimental data.

  17. Path integral molecular dynamics simulation of quasi-free rotational motion of CO doped in a large para-hydrogen cluster

    NASA Astrophysics Data System (ADS)

    Mizumoto, Yoshihiko; Ohtsuki, Yukiyoshi

    2011-01-01

    Path integral molecular dynamics simulation is used to study the rotational motion of a CO molecule doped in a large para-hydrogen (p-H2) cluster. The quasi-free rotational motion of CO in a p-H2 cluster with a reduced rotational constant is derived from the imaginary-time orientational correlation functions, and is in good agreement with recent experimental observations. We attribute the reduced rotational constant to the low-viscous fluid-like behavior of the host p-H2 cluster.

  18. Ab Initio Computational Study of Chromate Molecular Anion Adsorption on the Surfaces of Pristine and B- or N-Doped Carbon Nanotubes and Graphene.

    PubMed

    Hizhnyi, Yuriy; Nedilko, Sergii; Borysiuk, Viktor; Shyichuk, Andrii

    2017-12-01

    Density functional theory (DFT) computations of the electronic structures of undoped, B- and N-doped CNT(3,3), CNT(5,5) carbon nanotubes, and graphene with adsorbed chromate anions CrO4(2-) were performed within molecular cluster approach. Relaxed geometries, binding energies, charge differences of the adsorbed CrO4(2-) anions, and electronic wave function contour plots were calculated using B3LYP hybrid exchange-correlation functional. Oscillator strengths of electronic transitions of CrO4(2-) anions adsorbed on the surfaces of studied carbon nanostructures were calculated by the TD-DFT method. Calculations reveal covalent bonding between the anion and the adsorbents in all studied adsorption configurations. For all studied types of adsorbent structures, doping with N strengthens chemical bonding with CrO4(2-) anions, providing a ~2-eV increase in binding energies comparatively to adsorption of the anion on undoped adsorbents. Additional electronic transitions of CrO4(2-) anions appear in the orange-green spectral region when the anions are adsorbed on the N-doped low-diameter carbon nanotubes CNT(3,3) and CNT(5,5).

  19. Ab Initio Computational Study of Chromate Molecular Anion Adsorption on the Surfaces of Pristine and B- or N-Doped Carbon Nanotubes and Graphene

    NASA Astrophysics Data System (ADS)

    Hizhnyi, Yuriy; Nedilko, Sergii; Borysiuk, Viktor; Shyichuk, Andrii

    2017-01-01

    Density functional theory (DFT) computations of the electronic structures of undoped, B- and N-doped CNT(3,3), CNT(5,5) carbon nanotubes, and graphene with adsorbed chromate anions CrO4 2- were performed within molecular cluster approach. Relaxed geometries, binding energies, charge differences of the adsorbed CrO4 2- anions, and electronic wave function contour plots were calculated using B3LYP hybrid exchange-correlation functional. Oscillator strengths of electronic transitions of CrO4 2- anions adsorbed on the surfaces of studied carbon nanostructures were calculated by the TD-DFT method. Calculations reveal covalent bonding between the anion and the adsorbents in all studied adsorption configurations. For all studied types of adsorbent structures, doping with N strengthens chemical bonding with CrO4 2- anions, providing a 2-eV increase in binding energies comparatively to adsorption of the anion on undoped adsorbents. Additional electronic transitions of CrO4 2- anions appear in the orange-green spectral region when the anions are adsorbed on the N-doped low-diameter carbon nanotubes CNT(3,3) and CNT(5,5).

  20. 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.

  1. 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.

  2. Histopathological and molecular characterization of encephalitic listeriosis in small ruminants from northern Paraná, Brazil.

    PubMed

    Headley, Selwyn Arlington; Bodnar, Lívia; Fritzen, Juliana T T; Bronkhorst, Dalton Evert; Alfieri, Alice Fernandes; Okano, Werner; Alfieri, Amauri Alcindo

    2013-01-01

    Listeriosis is a disease primarily of ruminants caused by the Gram-positive bacterium Listeria monocytogenes. Ruminants either demonstrate manifestations of the encephalitic, septicemic, or reproductive form of listeriosis. The pathological and molecular findings with encephalitic listeriosis in a 5.5-month-old, male, mixed-breed goat and a 3-year-old Texel-crossed sheep from northern Paraná, Brazil are described. Clinically, the kid demonstrated circling, lateral protrusion of the tongue, head tilt, and convulsions; the ewe presented ataxia, motor incoordination, and lateral decumbency. Brainstem dysfunctions were diagnosed clinically and listeriosis was suspected. Necropsy performed on both animals did not reveal remarkable gross lesions; significant histopathological alterations were restricted to the brainstem (medulla oblongata; rhombencephalitis) and were characterized as meningoencephalitis that consisted of extensive mononuclear perivascular cuffings, neutrophilic and macrophagic microabscesses, and neuroparenchymal necrosis. PCR assay and direct sequencing, using genomic bacterial DNA derived from the brainstem of both animals, amplified the desired 174 base pairs length amplicon of the listeriolysin O gene of L. monocytogenes. Phylogenetic analyses demonstrated that the strains associated with rhombencephalitis during this study clustered with known strains of L. monocytogenes lineage I from diverse geographical locations and from cattle of the state of Paraná with encephalitic listeriosis. Consequently, these strains should be classified as L. monocytogenes lineage I. These results confirm the active participation of lineage I strains of L. monocytogenes in the etiopathogenesis of the brainstem dysfunctions observed during this study, probably represent the first characterization of small ruminant listeriosis by molecular techniques in Latin America, and suggest that ruminants within the state of Paraná were infected by the strains of the same lineage

  3. The physics and chemistry of small molecular clouds in the Galactic plane. 2: H2CO

    NASA Astrophysics Data System (ADS)

    Turner, B. E.

    1994-12-01

    We have made extensive observations of 2 and 6 cm H2CO in all 27 of the Clemens-Barvainis small molecular clouds for which several structural models including hydrostatic equilibrium polytropes were developed in an earlier paper based on C(18)O and (13)CO observations. We have observed the 211-110 line at 2.0 mm in 11 of the CB objects and in 10 of 11 cirrus cores earlier studied in C(18)O, (13)CO, and H2CO. As with the cirrus cores, the three H2CO lines in CB objects are all well fitted by both polytropic models and ad hoc n approximately r-1 models, using the external UV fields derived in the earlier papers. The reanalysis of the cirrus cores includes the 2 mm H2CO lines as well as treating the C-12/C-13 ratio as a variable, and yields approximately 40% higher fractional abundances than the earlier analysis, as well as giving equal preference to both centrally peaked and radially flat distributions of the H2CO fractional abundance. The same central H2CO abundances are found for the CB objects, but these objects favor radially flat abundance distributions, possibly because of beam dilution of the 6 cm lines speculated as unaccounted for in the detailed estimates made using maps of every source. As before, no clear preference is shown for polytropic or r-1 structures although r-1 is favored for a subset of 11 objects with 211-110 data. The large central abundances derived for both types of object (mean value 1.4 x 10-8 for ortho H2CO) are too large by a factor 104 to be compatible with gas-phase formation of H2CO. Grain formation is indicated, as concluded earlier for cirrus cores. It is argued that photocatalysis on grains is consistent with either peaked or flat H2CO abundance distributions, but this cannot be tested conclusively within the uncertainties of determining the structures or the abundance distributions. By including consistently the effects of UV radiation fields and electron excitation, our models fit accurately all four lines of C(18)O and (13)CO

  4. Molecular Markers as Prognostic Factors in DCIS and Small Invasive Breast Cancers.

    PubMed

    Sänger, N; Engels, K; Graf, A; Ruckhäberle, E; Effenberger, K E; Fehm, T; Holtrich, U; Becker, S; Karn, T

    2014-11-01

    Ductal carcinoma in situ (DCIS) accounts for up to half of screen-detected breast cancers and thus constitutes a major public health problem. Despite effective current treatment many patients with DCIS are either over- or undertreated because of the paucity of precise models to predict recurrence or progression. The combination of clinical and molecular factors as already applied for invasive disease may help to build such models also for DCIS. We compared 53 DCIS (36.6 %) and 92 (63.4 %) invasive breast cancer cases and found no significant differences in age, receptor status of ER, PR, and HER2, and the use of radiotherapy. Interestingly, the proportion of disseminated tumor cells (DTC) did also not significantly differ between DCIS and invasive cases (p = 0.57). A negative PR status was associated with the detection of DTCs (p = 0.026). We then compared relationships of clinical parameters and biomarkers with patients' prognosis in 43 DCIS and 40 small invasive tumors ≤ 5 mm (T1a). ER negativity was associated with shorter relapse free survival in the complete cohort (p = 0.004) and showed a trend in both subgroups (p = 0.053 for DCIS and p = 0.046 for T1a, respectively). In conclusion, we found markedly similar properties of both DCIS and small invasive breast cancers with respect to the distribution of several parameters as well as to the prognostic value of biomarkers. DCIS with a luminal phenotype seem to be characterized by a favourable prognosis.

  5. Stochastic dynamics of small ensembles of non-processive molecular motors: the parallel cluster model.

    PubMed

    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.

  6. 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.

  7. Emission from small dust particles in diffuse and molecular cloud medium

    NASA Technical Reports Server (NTRS)

    Bernard, J. P.; Desert, X.

    1990-01-01

    Infrared Astronomy Satellite (IRAS) observations of the whole galaxy has shown that long wavelength emission (100 and 60 micron bands) can be explained by thermal emission from big grains (approx 0.1 micron) radiating at their equilibrium temperature when heated by the InterStellar Radiation Field (ISRF). This conclusion has been confirmed by continuum sub-millimeter observations of the galactic plane made by the EMILIE experiment at 870 microns (Pajot et al. 1986). Nevertheless, shorter wavelength observations like 12 and 25 micron IRAS bands, show an emission from the galactic plane in excess with the long wavelength measurements which can only be explained by a much hotter particles population. Because dust at equilibrium cannot easily reach high temperatures required to explain this excess, this component is thought to be composed of very small dust grains or big molecules encompassing thermal fluctuations. Researchers present here a numerical model that computes emission, from Near Infrared Radiation (NIR) to Sub-mm wavelengths, from a non-homogeneous spherical cloud heated by the ISRF. This model fully takes into account the heating of dust by multi-photon processes and back-heating of dust in the Visual/Infrared Radiation (VIS-IR) so that it is likely to describe correctly emission from molecular clouds up to large A sub v and emission from dust experiencing temperature fluctuations. The dust is a three component mixture of polycyclic aromatic hydrocarbons, very small grains, and classical big grains with independent size distributions (cut-off and power law index) and abundances.

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

    SciTech Connect

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

    2013-11-07

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

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

    PubMed

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

    2012-09-18

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

  10. Doping-free white organic light-emitting diodes without blue molecular emitter: An unexplored approach to achieve high performance via exciplex emission

    NASA Astrophysics Data System (ADS)

    Luo, Dongxiang; Xiao, Ye; Hao, Mingming; Zhao, Yu; Yang, Yibin; Gao, Yuan; Liu, Baiquan

    2017-02-01

    Doping-free white organic light-emitting diodes (DF-WOLEDs) are promising for the low-cost commercialization because of their simplified device structures. However, DF-WOLEDs reported thus far in the literature are based on the use of blue single molecular emitters, whose processing can represent a crucial point in device manufacture. Herein, DF-WOLEDs without the blue single molecular emitter have been demonstrated by managing a blue exciplex system. For the single-molecular-emitter (orange or yellow emitter) DF-WOLEDs, (i) a color rendering index (CRI) of 81 at 1000 cd/m2 can be obtained, which is one of the highest for the single-molecular-emitter WOLEDs, or (ii) a high efficiency of 35.4 lm/W can be yielded. For the dual-molecular-emitter (yellow/red emitters) DF-WOLED, a high CRI of 85 and low correlated color temperature of 2376 K at 1000 cd/m2 have been simultaneously achieved, which has not been reported by previous DF-WOLEDs. Such presented findings may unlock an alternative avenue to the simplified but high-performance WOLEDs.

  11. Antidiabetic effects of pterosin A, a small-molecular-weight natural product, on diabetic mouse models.

    PubMed

    Hsu, Feng-Lin; Huang, Chun-Fa; Chen, Ya-Wen; Yen, Yuan-Peng; Wu, Cheng-Tien; Uang, Biing-Jiun; Yang, Rong-Sen; Liu, Shing-Hwa

    2013-02-01

    The therapeutic effect of pterosin A, a small-molecular-weight natural product, on diabetes was investigated. Pterosin A, administered orally for 4 weeks, effectively improved hyperglycemia and glucose intolerance in streptozotocin, high-fat diet-fed, and db/db diabetic mice. There were no adverse effects in normal or diabetic mice treated with pterosin A for 4 weeks. Pterosin A significantly reversed the increased serum insulin and insulin resistance (IR) in dexamethasone-IR mice and in db/db mice. Pterosin A significantly reversed the reduced muscle GLUT-4 translocation and the increased liver phosphoenolpyruvate carboxyl kinase (PEPCK) expression in diabetic mice. Pterosin A also significantly reversed the decreased phosphorylations of AMP-activated protein kinase (AMPK) and Akt in muscles of diabetic mice. The decreased AMPK phosphorylation and increased p38 phosphorylation in livers of db/db mice were effectively reversed by pterosin A. Pterosin A enhanced glucose uptake and AMPK phosphorylation in cultured human muscle cells. In cultured liver cells, pterosin A inhibited inducer-enhanced PEPCK expression, triggered the phosphorylations of AMPK, acetyl CoA carboxylase, and glycogen synthase kinase-3, decreased glycogen synthase phosphorylation, and increased the intracellular glycogen level. These findings indicate that pterosin A may be a potential therapeutic option for diabetes.

  12. Small molecule kinase inhibitors alleviate different molecular features of myotonic dystrophy type 1.

    PubMed

    Wojciechowska, Marzena; Taylor, Katarzyna; Sobczak, Krzysztof; Napierala, Marek; Krzyzosiak, Wlodzimierz J

    2014-01-01

    Expandable (CTG)n repeats in the 3' UTR of the DMPK gene are a cause of myotonic dystrophy type 1 (DM1), which leads to a toxic RNA gain-of-function disease. Mutant RNAs with expanded CUG repeats are retained in the nucleus and aggregate in discrete inclusions. These foci sequester splicing factors of the MBNL family and trigger upregulation of the CUGBP family of proteins resulting in the mis-splicing of their target transcripts. To date, many efforts to develop novel therapeutic strategies have been focused on disrupting the toxic nuclear foci and correcting aberrant alternative splicing via targeting mutant CUG repeats RNA; however, no effective treatment for DM1 is currently available. Herein, we present results of culturing of human DM1 myoblasts and fibroblasts with two small-molecule ATP-binding site-specific kinase inhibitors, C16 and C51, which resulted in the alleviation of the dominant-negative effects of CUG repeat expansion. Reversal of the DM1 molecular phenotype includes a reduction of the size and number of foci containing expanded CUG repeat transcripts, decreased steady-state levels of CUGBP1 protein, and consequent improvement of the aberrant alternative splicing of several pre-mRNAs misregulated in DM1.

  13. 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.

  14. Molecular Dynamics Study of Small PNA Molecules in Lipid-Water System

    PubMed Central

    Weroński, Paweł; Jiang, Yi; Rasmussen, Steen

    2007-01-01

    We present the results of molecular dynamics simulations of small peptide nucleic acid (PNA) molecules, synthetic analogs of DNA, at a lipid bilayer in water. At neutral pH, without any salt, and in the NPnγT ensemble, two similar PNA molecules (6-mers) with the same nucleic base sequence and different terminal groups are investigated at the interface between water and a 1-palmitoyl-2-oleoylphosphatidylcholine lipid bilayer. The results of our simulations suggest that at low ionic strength of the solution, both PNA molecules adsorb at the lipid-water interface. In the case where the PNA molecule has charged terminal groups, the main driving force of adsorption is the electrostatic attraction between the charged groups of PNA and the lipid heads. The main driving force of adsorption of the PNA molecule with neutral terminal groups is the hydrophobic interaction of the nonpolar groups. Our simulations suggest that the system free energy change associated with PNA adsorption at the lipid-water interface is on the order of several tens of kT per PNA molecule in both cases. PMID:17307825

  15. 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.

  16. 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

  17. Fabrication of Composite Films by Controlling Molecular Doping Processes between Polyaniline and Soluble Multiwalled Nanotubes and Their Optical Characteristics

    NASA Astrophysics Data System (ADS)

    Feng, Wei; Zhou, Feng; Wang, Xiaogong; Bai, Xiaodong; Liang, Ji; Yoshino, Katsumi

    2003-09-01

    An efficient approach to composite film fabrication that involves the control of doping processes between soluble multiwalled nanotubes (s-MWNTs) and polyaniline (PAN) molecules has been developed in this work. The s-MWNTs were prepared by introducing carboxylic acid and sulfonic acid groups to the surfaces of nanotubes. The s-MWNT was used as a dopant to react with the imine nitrogens of emeraldine PAN via the protonation doping process in a layer-by-layer manner. The resultant composite films on the quartz substrates were characterized by UV/Vis spectroscopy, photoluminescence, Fourier-transform infrared spectroscopy, scanning electron micrograph and X-ray diffraction. Results showed that s-MWNTs were doped into polyaniline layers, which caused changes in the composite film characteristics such as electrical properties, spectroscopic features and morphology. Unlike the already-used layer-by-layer process based on electrostatic attraction, our process is based on the acid-base reaction between emeraldine and s-MWNT. Owing to the protonation doping, the bond between the carboxyl group and the imine nitrogen group becomes covalent, which enhances the stability of the film.

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

    PubMed Central

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

    2014-01-01

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

  19. 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.

  20. Molecular geometry and polarizability of small cadmium selenide clusters from all-electron ab initio and Density Functional Theory calculations.

    PubMed

    Karamanis, Panaghiotis; Maroulis, George; Pouchan, Claude

    2006-02-21

    We have calculated molecular geometries and electric polarizabilities for small cadmium selenide clusters. Our calculations were performed with conventional ab initio and density functional theory methods and Gaussian-type basis sets especially designed for (CdSe)(n). We find that the dipole polarizability per atom converges rapidly to the bulk value.

  1. Thin-film growth and patterning techniques for small molecular organic compounds used in optoelectronic device applications.

    PubMed

    Biswas, Shaurjo; Shalev, Olga; Shtein, Max

    2013-01-01

    Rapid advances in research and development in organic electronics have resulted in many exciting discoveries and applications, including organic light-emitting devices for information display and illumination, solar cells, photodetectors, chemosensors, and logic. Organic optoelectronic materials are broadly classified as polymeric or small molecular. For the latter category, solvent-free deposition techniques are generally preferred to form well-defined interfaces and improve device performance. This article reviews several deposition and patterning methods for small molecular thin films and devices, including organic molecular beam deposition, vacuum thermal evaporation, organic vapor phase deposition, and organic vapor jet printing, and compares them to several other methods that have been proposed recently. We hope this review provides a compact but informative summary of the state of the art in organic device processing and addresses the various techniques' governing physical principles.

  2. Delta-doping of Semiconductors

    NASA Astrophysics Data System (ADS)

    Schubert, E. F.

    2005-08-01

    Part I: 1. Introduction E. F. Schubert; Part II: 2. Electronic structure of delta-doped semiconductors C. R. Proetto; Part III: 3. Recent progress in delta-like confinement of impurities in GaAs K. H. Ploog; 4. Flow-rate modulation epitaxy (FME) of III-V semiconductors T. Makimoto and Y. Horikoshi; 5. Gas source molecular beam epitaxy (MBE) of delta-doped III-V semiconductors D. Ritter; 6. Solid phase epitaxy for delta-doping in silicon I. Eisele; 7. Low temperature MBE of silicon H.-J. Gossmann; Part IV: 8. Secondary ion mass spectrometry of delta-doped semiconductors H. S. Luftmann; 9. Capacitance-voltage profiling E. F. Schubert; 10. Redistribution of impurities in III-V semiconductors E. F. Schubert; 11. Dopant diffusion and segregation in delta-doped silicon films H.-J. Gossmann; 12. Characterisation of silicon and delta-doped structures in GaAs R. C. Newman; 13. The DX-center in silicon delta-doped GaAs and AlxGa1-xAs P. M. Koenraad; Part V: 14. Luminescence and ellipsometry spectroscopy H. Yao and E. F. Schubert; 15. Photoluminescence and Raman spectroscopy of single delta-doped III-V semiconductor heterostructures J. Wagner and D. Richards; 16. Electron transport in delta-doped quantum wells W. T. Masselink; 17. Electron mobility in delta-doped layers P. M. Koenraad; 18. Hot electrons in delta-doped GaAs M. Asche; 19. Ordered delta-doping R. L. Headrick, L. C. Feldman and B. E. Weir; Part IV: 20. Delta-doped channel III-V field effect transistors (FETs) W.-P. Hong; 21. Selectively doped heterostructure devices E. F. Schubert; 22. Silicon atomic layer doping FET K. Nakagawa and K. Yamaguchi; 23. Planar doped barrier devices R. J. Malik; 24. Silicon interband and intersubband photodetectors I. Eisele; 25. Doping superlattice devices E. F. Schubert.

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

    PubMed

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

    2014-06-01

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

  4. Morphological and molecular analyses of larval taeniid species in small mammals from contrasting habitats in Denmark.

    PubMed

    Al-Sabi, M N S; Jensen, P M; Christensen, M U; Kapel, C M O

    2015-01-01

    Taeniid infections in intermediate hosts manifest themselves as extraintestinal larval stages which, in early development, lack species-specific characteristics. The inability to distinguish infections of zoonotic importance such as Echinococcus multilocularis from other taeniid infections that have mainly veterinary significance stimulated the development of species-specific molecular diagnostics. In this study, the prevalence of taeniid infections in potential intermediate hosts was evaluated using both morphological diagnosis and a newly described multiplex polymerase chain reaction (PCR) for species determination. Small mammals (N= 719) were trapped in three different types of habitats in north-east Zealand, Denmark. The sensitivity of the multiplex PCR (90.5%) exceeded that of morphological examination (57.9%) for identifying 95 taeniid infections. The use of the multiplex PCR resulted in higher prevalence rates due to improved detection of immature liver infections with Hydatigera taeniaeformis and Versteria mustelae, but did not affect the observed prevalence rates of peritoneal metacestodes of Taenia polyacantha. The prevalence of taeniid infections showed a significant difference according to habitat type, potentially identifying a 'sylvatic' transmission and an 'urban' transmission, with marked variation among different taeniid species. Versteria mustelae and T. polyacantha were more prevalent in rural forests, while infections with H. taeniaeformis were dominant in urban parks/forests and in residential and farm gardens. The multiplex PCR facilitated a better utilization of wildlife samples by yielding a higher number of definitive diagnoses of ambiguous taeniid infections in liver lesions, allowing for more accurate epidemiological data and, hence, a more accurate risk assessment.

  5. 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

  6. 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.

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

    PubMed

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

    2014-04-15

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

  8. 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.

  9. 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.

  10. Precipitation control and activation enhancement in boron-doped p{sup +}-BaSi{sub 2} films grown by molecular beam epitaxy

    SciTech Connect

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

    2014-06-23

    Precipitation free boron (B)-doped as-grown p{sup +}-BaSi{sub 2} layer is essential for the BaSi{sub 2} p-n junction solar cells. In this article, B-doped p-BaSi{sub 2} layers were grown by molecular beam epitaxy on Si(111) substrates, and the influence of substrate growth temperature (T{sub S}) and B temperature (T{sub B}) in the Knudsen cell crucible were investigated on the formation of B precipitates and the activation efficiency. The hole concentration, p, reached 1.0 × 10{sup 19 }cm{sup −3} at room temperature for T{sub S} = 600 and T{sub B} = 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 T{sub S} was raised to 650 °C and the T{sub B} was decreased to 1350 °C, the p reached 6.8 × 10{sup 19 }cm{sup −3}, and the activation rate increased to more than 20%. No precipitation of B was also confirmed by TEM.

  11. X-ray and molecular modelling in fragment-based design of three small quinoline scaffolds for HIV integrase inhibitors.

    PubMed

    Majerz-Maniecka, Katarzyna; Musiol, Robert; Skórska-Stania, Agnieszka; Tabak, Dominik; Mazur, Pawel; Oleksyn, Barbara J; Polanski, Jaroslaw

    2011-03-01

    Crystal structures of three small molecular scaffolds based on quinoline, 2-methylquinoline-5,8-dione, 5-hydroxy-quinaldine-6-carboxylic acid and 8-hydroxy-quinaldine-7-carboxylic acid, were characterised. 5-Hydroxy-quinaldine-6-carboxylic acid was co-crystallized with cobalt(II) chloride to form a model of divalent metal cation-ligand interactions for potential HIV integrase inhibitors. Molecular docking into active site of HIV IN was also performed on 1WKN PDB file. Selected ligand-protein interactions have been found specific for active compounds. Studied structures can be used as scaffolds in fragment-based design of new potent drugs.

  12. Alloy formation during molecular beam epitaxy growth of Si-doped InAs nanowires on GaAs[111]B.

    PubMed

    Davydok, Anton; Rieger, Torsten; Biermanns, Andreas; Saqib, Muhammad; Grap, Thomas; Lepsa, Mihail Ion; Pietsch, Ullrich

    2013-08-01

    Vertically aligned InAs nanowires (NWs) doped with Si were grown self-assisted by molecular beam epitaxy on GaAs[111]B substrates covered with a thin SiO x layer. Using out-of-plane X-ray diffraction, the influence of Si supply on the growth process and nanostructure formation was studied. It was found that the number of parasitic crystallites grown between the NWs increases with increasing Si flux. In addition, the formation of a Ga0.2In0.8As alloy was observed if the growth was performed on samples covered by a defective oxide layer. This alloy formation is observed within the crystallites and not within the nanowires. The Ga concentration is determined from the lattice mismatch of the crystallites relative to the InAs nanowires. No alloy formation is found for samples with faultless oxide layers.

  13. Alloy formation during molecular beam epitaxy growth of Si-doped InAs nanowires on GaAs[111]B

    PubMed Central

    Davydok, Anton; Rieger, Torsten; Biermanns, Andreas; Saqib, Muhammad; Grap, Thomas; Lepsa, Mihail Ion; Pietsch, Ullrich

    2013-01-01

    Vertically aligned InAs nanowires (NWs) doped with Si were grown self-assisted by molecular beam epitaxy on GaAs[111]B substrates covered with a thin SiOx layer. Using out-of-plane X-ray diffraction, the influence of Si supply on the growth process and nanostructure formation was studied. It was found that the number of parasitic crystallites grown between the NWs increases with increasing Si flux. In addition, the formation of a Ga0.2In0.8As alloy was observed if the growth was performed on samples covered by a defective oxide layer. This alloy formation is observed within the crystallites and not within the nanowires. The Ga concentration is determined from the lattice mismatch of the crystallites relative to the InAs nanowires. No alloy formation is found for samples with faultless oxide layers. PMID:24046494

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

    NASA Astrophysics Data System (ADS)

    Furtmayr, Florian; Vielemeyer, Martin; Stutzmann, Martin; Arbiol, Jordi; Estradé, Sònia; Peirò, Francesca; Morante, Joan Ramon; Eickhoff, Martin

    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.

  15. One-step ethanolysis of lignin into small-molecular aromatic hydrocarbons over nano-SiC catalyst.

    PubMed

    Chen, Yigang; Wang, Fang; Jia, Yingjie; Yang, Nan; Zhang, Xianming

    2017-02-01

    Catalytic depolymerization of lignin for preparation of aromatic hydrocarbons without external hydrogen was first carried out over nano-SiC catalyst in supercritical ethanol. Mixture of the catalyst and lignin was innovatively suspended in a closed reactor and small-molecular aromatic hydrocarbons were successfully achieved at 500°C. Results revealed that not only did conversion of lignin increase sharply under the nano-SiC catalyst, but also phenols were not detected. The increase of residence time under the Fe-SiC catalyst did not change distribution of the liquid products besides the yield improvement, suggesting that the catalyst was suitable and selective towards formation of small-molecular benzenes, especially C6-C8 benzenes. Preliminary studies found that lignin depolymerization and deoxygenation were successfully fulfilled during the reactions, which provided a very effective route to conversion of lignin into high added-value molecules as transportation fuel additives.

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

    PubMed

    Daniels, Joshua B

    2013-11-01

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

  17. Deformation of poly(methyl methacrylate)-poly(ethylene oxide) blends: a molecular characterization by small-angle neutron scattering

    SciTech Connect

    Lefebvre, J.M.R.; Porter, S.; Wignall, G.D.

    1986-01-01

    The deformation behavior of miscible amorphous/amorphous PMMA/PEO blends has been compared to that of pure PMMA. Small-angle neutron scattering experiments have been performed on labeled systems made of PEO + D-PMMA + H-PMMA. Characteristic molecular parameters such as radius of gyration R/sub g/, molecular weight M/sub w/ and interaction parameter X have been extracted from the coherent scattering cross sections. Molecular anisotropy is measured on the solid state coextruded samples and the observed drawing efficiency is compared to the results of shrinkage tests. In the case of PMMA/PEO blends, anomalous scattering behavior precludes any quantitative interpretation of the scattering patterns, but revealed important structural changes upon drawing, namely a deformation-induced phase separation.

  18. Conversion process of the dominant electroluminescence mechanism in a molecularly doped organic light-emitting device with only electron trapping

    NASA Astrophysics Data System (ADS)

    Zhou, Liang; Zhang, Hongjie; Deng, Ruiping; Li, Zhefeng; Yu, Jiangbo; Guo, Zhiyong

    2007-09-01

    In this work, the detailed conversion process of the dominant electroluminescence (EL) mechanism in a device with Eu(TTA)3phen (TTA =thenoyltrifluoroacetone, phen =1,10-phenanthroline) doped CBP (4,4'-N,N'-dicarbazole-biphenyl) film as the emitting layer was investigated by analyzing the evolution of carrier distribution on dye and host molecules with increasing voltage. Firstly, it was confirmed that only electrons can be trapped in Eu(TTA)3phen doped CBP. As a result, holes and electrons would be situated on CBP and Eu(TTA)3phen molecules, respectively, and thus creates an unbalanced carrier distribution on both dye and host molecules. With the help of EL and photoluminescence spectra, the distribution of holes and electrons on both Eu(TTA)3phen and CBP molecules was demonstrated to change gradually with increasing voltage. Therefore, the dominant EL mechanism in this device changes gradually from carrier trapping at relatively low voltage to Förster energy transfer at relatively high voltage.

  19. Advances in preclinical therapeutics development using small animal imaging and molecular analyses: the gastrointestinal stromal tumors model.

    PubMed

    Pantaleo, M A; Landuzzi, L; Nicoletti, G; Nanni, C; Boschi, S; Piazzi, G; Santini, D; Di Battista, M; Castellucci, P; Lodi, F; Fanti, S; Lollini, P-L; Biasco, G

    2009-09-01

    The large use of target therapies in the treatment of gastrointestinal stromal tumors (GISTs) highlighted the urgency to integrate new molecular imaging technologies, to develop new criteria for tumor response evaluation and to reach a more comprehensive definition of the molecular target. These aspects, which come from clinical experiences, are not considered enough in preclinical research studies which aim to evaluate the efficacy of new drugs or new combination of drugs with molecular target. We developed a xenograft animal model GIST882 using nude mice. We evaluated both the molecular and functional characterization of the tumor mass. The mutational analysis of KIT receptor of the GIST882 cell lines and tumor mass showed a mutation on exon 13 that was still present after in vivo cell growth. The glucose metabolism and cell proliferation was evaluated with a small animal PET using both FDG and FLT. The experimental development of new therapies for GIST treatment requires sophisticated animal models in order to represent the tumor molecular heterogeneity already demonstrated in the clinical setting and in order to evaluate the efficacy of the treatment also considering the inhibition of tumor metabolism, and not only considering the change in size of tumors. This approach of cancer research on GISTs is crucial and essential for innovative perspectives that could cross over to other types of cancer.

  20. 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.

  1. Toward molecular mechanism of xenon anesthesia: a link to studies of xenon complexes with small aromatic molecules.

    PubMed

    Andrijchenko, Natalya N; Ermilov, Alexander Yu; Khriachtchev, Leonid; Räsänen, Markku; Nemukhin, Alexander V

    2015-03-19

    The present study illustrates the steps toward understanding molecular mechanism of xenon anesthesia by focusing on a link to the structures and spectra of intermolecular complexes of xenon with small aromatic molecules. A primary cause of xenon anesthesia is attributed to inhibition of N-methyl-D-aspartate (NMDA) receptors by an unknown mechanism. Following the results of quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) calculations we report plausible xenon action sites in the ligand binding domain of the NMDA receptor, which are due to interaction of xenon atoms with aromatic amino-acid residues. We rely in these calculations on computational protocols adjusted in combined experimental and theoretical studies of intermolecular complexes of xenon with phenol. Successful reproduction of vibrational shifts in molecular species upon complexation with xenon measured in low-temperature matrices allowed us to select a proper functional form in density functional theory (DFT) approach for use in QM subsystems, as well as to calibrate force field parameters for MD simulations. The results of molecular modeling show that xenon atoms can compete with agonists for a place in the corresponding protein cavity, thus indicating their active role in anesthetic action.

  2. Targeting the molecular chaperone SlyD to inhibit bacterial growth with a small molecule

    PubMed Central

    Kumar, Amit; Balbach, Jochen

    2017-01-01

    Molecular chaperones are essential molecules for cell growth, whereby they maintain protein homeostasis. Because of their central cellular function, bacterial chaperones might be potential candidates for drug targets. Antimicrobial resistance is currently one of the greatest threats to human health, with gram-negative bacteria being of major concern. We found that a Cu2+ complex readily crosses the bacterial cell wall and inhibits SlyD, which is a molecular chaperone, cis/trans peptidyl prolyl isomerise (PPIase) and involved in various other metabolic pathways. The Cu2+ complex binds to the active sites of SlyD, which suppresses its PPIase and chaperone activities. Significant cell growth retardation could be observed for pathogenic bacteria (e.g., Staphylococcus aureus and Pseudomonas aeruginosa). We anticipate that rational development of drugs targeting molecular chaperones might help in future control of pathogenic bacterial growth, in an era of rapidly increasing antibiotic resistance. PMID:28176839

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

    PubMed

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

    2015-07-03

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

  5. 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

  6. 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.

  7. Treatment algorithm in 2014 for advanced non-small cell lung cancer: therapy selection by tumour histology and molecular biology.

    PubMed

    Manegold, Christian

    2014-09-01

    The availability of antineoplastic monoclonal antibodies, small molecules and newer cytotoxics such as pemetrexed, the EGFR-tyrosine kinase inhibitors erlotinib, gefitinib, afatinib as well as the anti-angiogenic bevacizumab and the ALK-inhibitor crizotinib has recently changes the treatment algorithm of advanced non-small cell lung cancer. Decision making in 2014 is characterized by customizing therapy, by selecting a specific therapeutic regimen based on the histotype and the genotype of the tumour. This refers to first-line induction therapy and maintenance therapy as well, but also to subsequent lines of therapy since anti-neoplastic drugs and regimens used upfront clinically influence the selection of agents/regimes considered for second-/third-line treatment. Consequently, therapy customization through tumour histology and molecular markers has significantly influenced the work of pathologists around the globe and the process of obtaining an extended therapeutically relevant tumour diagnosis. Not only histological sub-typing became standard but molecular information is also considered of increasing importance for treatment selection. Routine molecular testing in certified laboratories must be established, and the diagnostic process should ideally be performed under the guidance of evidence based recommendation. The process of investigating and implementing medical targeting in lung cancer therefore, requires advanced diagnostic techniques and expertise and because of its large dimension is costly and influenced by the limitation of financial and clinical resources.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  9. 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.

  10. Direct prediction of residual dipolar couplings of small molecules in a stretched gel by stochastic molecular dynamics simulations.

    PubMed

    Frank, Andreas O; Freudenberger, J Christoph; Shaytan, Alexey K; Kessler, Horst; Luy, Burkhard

    2015-03-01

    Residual dipolar couplings are highly useful NMR parameters for calculating and refining molecular structures, dynamics, and interactions. For some applications, however, it is inevitable that the preferred orientation of a molecule in an alignment medium is calculated a priori. Several methods have been developed to predict molecular orientations and residual dipolar couplings. Being beneficial for macromolecules and selected small-molecule applications, such approaches lack sufficient accuracy for a large number of organic compounds for which the fine structure and eventually the flexibility of all involved molecules have to be considered or are limited to specific, well-studied liquid crystals. We introduce a simplified model for detailed all-atom molecular dynamics calculations with a polymer strand lined up along the principal axis as a new approach to simulate the preferred orientation of small to medium-sized solutes in polymer-based, gel-type alignment media. As is shown by a first example of strychnine in a polystyrene/CDCl3 gel, the simulations potentially enable the accurate prediction of residual dipolar couplings taking into account structural details and dynamic averaging effects of both the polymer and the solute.

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

    SciTech Connect

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

    1993-09-01

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

  13. 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%.

  14. 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

  15. 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.

  16. Molecular analysis of lungworms from European bison (Bison bonasus) on the basis of small subunit ribosomal RNA gene (SSU).

    PubMed

    Pyziel, Anna M

    2014-03-01

    Dictyocaulosis (Nematoda: Trichostrongyloidea) is a widespread parasitosis of the European bison (Bison bonasus) inhabiting Bialowieza Primeval Forest. Bearing in mind the current coexistence of bison with wild cervids, and with domestic ruminants in the 19th and 20th century, the need arose for molecular identification of lungworm species. Molecular analysis was done on adult lungworms that were obtained from the respiratory track of four free-roaming bison euthanized as a part of the population health control program. As the result of the study four identical small subunit-ribosomal RNA gene sequences from the lungworms were obtained and deposited in GenBank as sequence, 1708 bp long (GenBank KC771250). Comparative analysis of the SSU rRNA sequences revealed the European bison to be a host for the bovine lungworm Dictyocaulus viviparus.

  17. 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

  18. Inhibitory monoclonal antibody against a (myristylated) small-molecular-weight antigen from Plasmodium falciparum associated with the parasitophorous vacuole membrane.

    PubMed

    Kara, U A; Stenzel, D J; Ingram, L T; Bushell, G R; Lopez, J A; Kidson, C

    1988-04-01

    A small-molecular-weight antigen that occurs in asexual blood stages in synchronized cultures of Plasmodium falciparum was detected by a monoclonal antibody which inhibits parasite growth in vitro. This antigen, QF116, showed a molecular weight of 15,000 in parasite strain FCR-3K+ from The Gambia and 19,000 in strain FCQ-27 from Papua New Guinea. The protein did not show significant glycosylation by galactose or glucosamine labeling but was found to be acylated by myristic acid. By using immunogold labeling and electron microscopy, the location of the antigen could be attributed to the parasitophorous vacuole membrane and to inclusions and vesicles residing within the cytoplasm of the erythrocyte host cell.

  19. 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.

  20. Molecular phylogeny of Stentor (Ciliophora: Heterotrichea) based on small subunit ribosomal RNA sequences.

    PubMed

    Gong, Ying-Chun; Yu, Yu-He; Zhu, Fei-Yun; Feng, Wei-Song

    2007-01-01

    To determine the phylogenetic position of Stentor within the Class Heterotrichea, the complete small subunit rRNA genes of three Stentor species, namely Stentor polymorphus, Stentor coeruleus, and Stentor roeseli, were sequenced and used to construct phylogenetic trees using the maximum parsimony, neighbor joining, and Bayesian analysis. With all phylogenetic methods, the genus Stentor was monophyletic, with S. roeseli branching basally.

  1. 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...

  2. CT-guided transthoracic core needle biopsy for small pulmonary lesions: diagnostic performance and adequacy for molecular testing

    PubMed Central

    Tian, Panwen; Wang, Ye; Li, Lei; Zhou, Yongzhao; Luo, Wenxin

    2017-01-01

    Background Computed tomography (CT)-guided transthoracic needle biopsy is a well-established, minimally invasive diagnostic tool for pulmonary lesions. Few large studies have been conducted on the diagnostic performance and adequacy for molecular testing of transthoracic core needle biopsy (TCNB) for small pulmonary lesions. Methods This study included CT-guided TCNB with 18-gauge cutting needles in 560 consecutive patients with small (≤3 cm) pulmonary lesions from January 2012 to January 2015. There were 323 males and 237 females, aged 51.8±12.7 years. The size of the pulmonary lesions was 1.8±0.6 cm. The sensitivity, specificity, accuracy and complications of the biopsies were investigated. The risk factors of diagnostic failure were assessed using univariate and multivariate analyses. The sample’s adequacy for molecular testing of non-small cell lung cancer (NSCLC) was analyzed. Results The overall sensitivity, specificity, and accuracy for diagnosis of malignancy were 92.0% (311/338), 98.6% (219/222), and 94.6% (530/560), respectively. The incidence of bleeding complications was 22.9% (128/560), and the incidence of pneumothorax was 10.4% (58/560). Logistic multivariate regression analysis showed that the independent risk factors for diagnostic failure were a lesion size ≤1 cm [odds ratio (OR), 3.95; P=0.007], lower lobe lesions (OR, 2.83; P=0.001), and pneumothorax (OR, 1.98; P=0.004). Genetic analysis was successfully performed on 95.45% (168/176) of specimens diagnosed as NSCLC. At least 96.8% of samples with two or more passes from a lesion were sufficient for molecular testing. Conclusions The diagnostic yield of small pulmonary lesions by CT-guided TCNB is high, and the procedure is relatively safe. A lesion size ≤1 cm, lower lobe lesions, and pneumothorax are independent risk factors for biopsy diagnostic failure. TCNB specimens could provide adequate tissues for molecular testing. PMID:28275482

  3. Electric field poled polymeric nonlinear optical systems: molecular dynamics simulations of poly(methyl methacrylate) doped with disperse red chromophores.

    PubMed

    Tu, Yaoquan; Zhang, Qiong; Agren, Hans

    2007-04-12

    We demonstrate a complete procedure for simulations of electric field poled polymeric nonlinear optical systems with the purpose to evaluate the macroscopic electro-optic coefficients. The simulations cover the electric field poling effects on the chromophore order at the liquid state, the cooling procedure from the liquid to the solid state in the presence of the poling field, and the back-relaxation of the system after the removal of the field. We use Disperse Red chromophore molecules doped in a poly(methyl methacrylate) matrix for a numerical demonstration of the total procedure. On the basis of the simulation results, the polymer mobility and the static properties of the dopant chromophores are derived. In the liquid state, the chromophore molecules are closer to the side chains than to the backbones of the polymer matrix, and after the simulated annealing, the polymer matrix tends to be closely packed, leading to a significant change in the polymer structure around the chromophore molecules. Besides predicting the absolute macroscopic electro-optic coefficient values, the results are used to derive the microscopic origin of these values in terms of geometric and electronic structure, loading, poling, and back-relaxation effects, thereby aiding to establish design principles for optimum guest-host configurations.

  4. Molecular-sized fluorescent nanodiamonds

    NASA Astrophysics Data System (ADS)

    Vlasov, Igor I.; Shiryaev, Andrey A.; Rendler, Torsten; Steinert, Steffen; Lee, Sang-Yun; Antonov, Denis; Vörös, Márton; Jelezko, Fedor; Fisenko, Anatolii V.; Semjonova, Lubov F.; Biskupek, Johannes; Kaiser, Ute; Lebedev, Oleg I.; Sildos, Ilmo; Hemmer, Philip. R.; Konov, Vitaly I.; Gali, Adam; Wrachtrup, Jörg

    2014-01-01

    Doping of carbon nanoparticles with impurity atoms is central to their application. However, doping has proven elusive for very small carbon nanoparticles because of their limited availability and a lack of fundamental understanding of impurity stability in such nanostructures. Here, we show that isolated diamond nanoparticles as small as 1.6 nm, comprising only ~400 carbon atoms, are capable of housing stable photoluminescent colour centres, namely the silicon vacancy (SiV). Surprisingly, fluorescence from SiVs is stable over time, and few or only single colour centres are found per nanocrystal. We also observe size-dependent SiV emission supported by quantum-chemical simulation of SiV energy levels in small nanodiamonds. Our work opens the way to investigating the physics and chemistry of molecular-sized cubic carbon clusters and promises the application of ultrasmall non-perturbative fluorescent nanoparticles as markers in microscopy and sensing.

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. Anti-localization caused by small doping of heavy-mass impurity-atoms in carbon nanotubes and a novel spintronics device

    NASA Astrophysics Data System (ADS)

    Haruyama, Junji; Takesue, Izumi; Hasegawa, Tetsuro

    2002-01-01

    Multi-walled carbon nanotubes (MWNTs), standing in nanoporous alumina membranes, are doped at one end by impurity atoms from electrode materials. Doping of the light-mass materials (carbon and aluminum) leads to weak localization in Altshuler-Aronov-Spivak oscillation, consistent with past reports. In contrast, we find that doping of heavy-mass materials (gold and platinum) at a volume ratio of only about 5% changes this weak localization to anti-localization. It is understood by a drastic change of the phase interference, caused by the polarized injection of spin-flipped electrons due to spin-orbit interaction in the diffusion region, in the bulk of the MWNTs. We also propose a novel spintronics (electron-wave phase switching) circuit using this effect.

  12. 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.

  13. 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

  14. 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.

  15. Photoluminescence of Ga-doped ZnO film grown on c-Al2O3 (0001) by plasma-assisted molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Park, H. C.; Byun, D.; Angadi, B.; Hee Park, D.; Choi, W. K.; Choi, J. W.; Jung, Y. S.

    2007-10-01

    High quality gallium doped ZnO (Ga:ZnO) thin films were grown on c-Al2O3(1000) by plasma-assisted molecular beam epitaxy, and Ga concentration NGa was controlled in the range of 1×1018-2.5×1020/cm3 by adjusting/changing the Ga cell temperature. From the low-temperature photoluminescence at 10K, the donor bound exciton I8 related to Ga impurity was clearly observed and confirmed by comparing the calculated activation energy of 16.8meV of the emission peak intensity with the known localization energy, 16.1meV. Observed asymmetric broadening with a long tail on the lower energy side in the photoluminescence (PL) emission line shape could be fitted by the Stark effect and the compensation ratio was approximately 14-17% at NGa⩾1×1020/cm3. The measured broadening of photoluminescence PL emission is in good agreement with the total thermal broadening and potential fluctuations caused by random distribution of impurity at NGa lower than the Mott critical density.

  16. 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.

  17. 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.

  18. 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".

  19. 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.

  20. Pick-up, transport and release of a molecular cargo using a small-molecule robotic arm.

    PubMed

    Kassem, Salma; Lee, Alan T L; Leigh, David A; Markevicius, Augustinas; Solà, Jordi

    2016-02-01

    Modern-day factory assembly lines often feature robots that pick up, reposition and connect components in a programmed manner. The idea of manipulating molecular fragments in a similar way has to date only been explored using biological building blocks (specifically DNA). Here, we report on a wholly artificial small-molecule robotic arm capable of selectively transporting a molecular cargo in either direction between two spatially distinct, chemically similar, sites on a molecular platform. The arm picks up/releases a 3-mercaptopropanehydrazide cargo by formation/breakage of a disulfide bond, while dynamic hydrazone chemistry controls the cargo binding to the platform. Transport is controlled by selectively inducing conformational and configurational changes within an embedded hydrazone rotary switch that steers the robotic arm. In a three-stage operation, 79-85% of 3-mercaptopropanehydrazide molecules are transported in either (chosen) direction between the two platform sites, without the cargo at any time fully dissociating from the machine nor exchanging with other molecules in the bulk.

  1. 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

  2. Biomolecular Crowding Arising from Small Molecules, Molecular Constraints, Surface Packing, and Nano-Confinement.

    PubMed

    Hilaire, Mary Rose; Abaskharon, Rachel M; Gai, Feng

    2015-07-02

    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 cosolvent 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.

  3. 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

  4. 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.

  5. Molecular theory for the phase equilibria and cluster distribution of associating fluids with small bond angles.

    PubMed

    Marshall, Bennett D; Chapman, Walter G

    2013-08-07

    We develop a new theory for associating fluids with multiple association sites. The theory accounts for small bond angle effects such as steric hindrance, ring formation, and double bonding. The theory is validated against Monte Carlo simulations for the case of a fluid of patchy colloid particles with three patches and is found to be very accurate. Once validated, the theory is applied to study the phase diagram of a fluid composed of three patch colloids. It is found that bond angle has a significant effect on the phase diagram and the very existence of a liquid-vapor transition.

  6. 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.

  7. Water activity and mobility in solutions of glycerol and small molecular weight sugars: Implication for cryo- and lyopreservation

    NASA Astrophysics Data System (ADS)

    He, Xiaoming; Fowler, Alex; Toner, Mehmet

    2006-10-01

    In this study, the free volume models, originally developed for large molecular weight polymer-solvent systems, were used to study the water activity and mobility in solutions of four small molecular weight cryo-/lyoprotectants, viz., glycerol, a monosaccharide (fructose), and two disaccharides (sucrose and trehalose). The free volume model parameters were determined by fitting the models to available experimental data using a nonlinear optimization procedure. It was found that free volume models could accurately predict the available experimental data, which suggests that the free volume models might be generally applicable to aqueous solutions of small molecular weight cryo-/lyoprotectants. Furthermore, several models for estimating the mutual diffusion coefficient were tested using available experimental data for aqueous solutions of glycerol and a better method to estimate the mutual diffusion coefficient was proposed. Free volume models were used to predict and analyze the water activity and mobility in solutions of four cryo-/lyoprotectants under conditions frequently encountered in cryo-/lyopreservation applications. It was found that the water mobility in the glassy state of the above four solutions is essentially negligible in the case of cryopreservation with storage temperature lower than -110°C. However, the water mobility in a glass at higher temperature (>-80°C) may be significant. As a result, a subcooling of up to 50°C may be necessary for the long-term cryo-/lyopreservation of biomaterials depending on the water content and the type of cryo-/lyoprotectants. It was further shown that trehalose might be the best of the four protectants studied for lyopreservation (water mass fraction ⩽0.1) when the storage temperature is above the room temperature. The results from this study might be useful for the development of more effective protocols for both cryopreservation and lyopreservation of living cells and other biomaterials.

  8. Stability of small molecular clusters modelled with stochastic and deterministic dynamics

    NASA Astrophysics Data System (ADS)

    Natarajan, Sukina

    This investigation concerns the transition pathway of the condensation phase transition. Under certain conditions condensation is initiated by nucleation events, which are driven by fluctuations or instabilities in the vapour phase. This involves the spontaneous formation of groups of particles, which we refer to as clusters. The clusters have a highly unstable nature and exist momentarily, before breaking up. This makes them difficult to study experimentally and model mathematically, in comparison to larger more stable systems. The aim of this study is to explore the stability of these tiny molecular clusters that exist momentarily within their environment, in terms of the time taken for the cluster to lose particles (decay). To do this we employ a microscopic cluster model of n-nonane molecules in which the cluster is treated in isolation from the vapour particles that would normally surround it. The interactions between cluster particles are modelled using empirical potentials. The cluster's dynamics is modelled using deterministic molecular dynamics simulations. The simulations generate a time evolved trajectory of all the positions, velocities and forces of all the atoms in the cluster. The process of cluster decay in n-nonane clusters is modelled using a Langevin interpretation of the decay mechanism. This treatment views cluster decay as a process of single particle escape from a confining potential of mean force, driven by a particle's interactions with the surrounding cluster particles. The motion of a cluster particle is modelled using a Langevin equation, which is parameterised using the MD generated data in order to extract the decay related parameters. The decay parameters are used to evaluate an Arrhenius type equation for the kinetic decay rate. This is used to calculate the mean timescale of cluster decay for n-nonane clusters, which we refer to as the mean cluster lifetime. We compare the dynamically generated lifetimes calculated from the model to

  9. Geometric isotope effects on small chloride ion water clusters with path integral molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Wang, Qi; Suzuki, Kimichi; Nagashima, Umpei; Tachikawa, Masanori; Yan, Shiwei

    2013-11-01

    The geometric isotope effects on the structures of hydrated chloride ionic hydrogen bonded clusters are explored by carrying out path integral molecular dynamics simulations. First, an outer shell coordinate is selected to display the rearrangement of single and multi hydration shell cluster structures. Next, to show the competition of intramolecular and intermolecular nuclear quantum effects, the intramolecular OH∗ stretching and intermolecular ion-water wagging motions are studied for single and multi shell structures, respectively. The results indicate that the intermolecular nuclear quantum effects stabilize the ionic hydrogen bonds in single shell structures, while they are destabilized through the competition with intramolecular nuclear quantum effects in multi shell structures. In addition, the correlations between ion-water stretching motion and other cluster vibrational coordinates are discussed. The results indicate that the intermolecular nuclear quantum effects on the cluster structures are strongly related to the cooperation of the water-water hydrogen bond interactions.

  10. 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.

  11. 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.

  12. 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

  13. Role of Molecular Flexibility and Colloidal Descriptions of Proteins in Crowded Environments from Small-Angle Scattering.

    PubMed

    Castellanos, Maria Monica; Clark, Nicholas J; Watson, Max C; Krueger, Susan; McAuley, Arnold; Curtis, Joseph E

    2016-12-15

    Small-angle scattering is a powerful technique to study molecular conformation and interactions of proteins in solution and in amorphous solids. We have investigated the role of multiple protein configurations in the interaction parameters derived from small-angle scattering for proteins in concentrated solutions. In order to account for the wide configurational space sampled by proteins, we generate ensembles of atomistic structures for lysozyme and monoclonal antibodies, representing globular and flexible proteins, respectively. While recent work has argued that a colloidal approach is inadequate to model proteins, because of the large configurational space that they sample in solution, we find a range of length scales where colloidal models can be used to describe solution scattering data while simultaneously accounting for structural flexibility. We provide insights to determine the length scales where isotropic colloidal models can be used, and find smoothly varying sets of interaction parameters that encompass ensembles of structures. This approach may play an important role in the definition of long-range interactions in coarse-grained models of flexible proteins with experimental scattering constraints. Additionally, we apply the decoupling approximation to ensembles of lysozyme structures with atomistic detail and observe remarkably different results when using geometric solids, such as ellipsoids. The insights from this study provide guidelines for the analysis of small-angle scattering profiles of proteins in crowded environments.

  14. Results from a 'small box' realtime molecular contamination monitor on STS-3

    NASA Technical Reports Server (NTRS)

    Triolo, J.; Kruger, R.; Mcintosh, R.; Maag, C.

    1983-01-01

    On the basis of early estimates of the Shuttle induced environment, Scialdone (1979) concluded that in the vicinity of the cargo, the cargo would have the largest influence on the environment. As a contamination control device, realtime monitors can indicate safe operational periods for sensitive attached payloads. It was, therefore, decided to develop the OSS-1/Contamination Monitor Package (CMP) experiment which was seen as a forerunner of an operational monitor. A description of the CMP is provided, taking into account four actively temperature controlled quartz crystal microbalances (TQCM). The TQCM temperatures could be varied from -60 C to +80 C. The sensor consisted of a matched pair of quartz crystals. The crystals were designated as a sensor and reference crystal. Results obtained during the STS-3 mission are discussed. These results show the feasibility and advantages of a small real-time contamination monitor.

  15. 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.

  16. 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

  17. One-step pyrolytic synthesis of nitrogen and sulfur dual-doped porous carbon with high catalytic activity and good accessibility to small biomolecules.

    PubMed

    Gao, Weiwei; Feng, Xun; Zhang, Tianyi; Huang, Hao; Li, Jin; Song, Wenbo

    2014-01-01

    As one of promising catalysts that contain high density of active sites, N doped carbons have been extensively researched, while the reports for N, S dual-doped carbon materials are far less exhaustive. Herein, devoid of activation process and template, N, S dual-doped porous carbon (N-S-PC) was prepared for the first time via one-step pyrolysis of sodium citrate and cysteine. Possessing unique porous structure and large pore volume as well as good accessibility, N-S-PC demonstrates significantly improved electrocatalytic activity toward oxidation of ascorbic acid (AA), dopamine (DA), and uric acid (UA). In the coexisting system, the peak potential separation between AA and DA is up to 251 mV, which is much larger than for most of the other carbons. On the basis of large potential separation and high current response, selective and sensitive simultaneous determination of AA, DA, and UA was successfully accomplished by differential pulse voltammetry, displaying a linear response from 50 to 2000 μM, from 0.1 to 50 μM, and from 0.1 to 50 μM with a detection limit (S/N = 3) of 0.78, 0.02, and 0.06 μM. This work highlights the importance of N, S dual doping and hierarchical porous carbons for efficient catalysis.

  18. Stable and controlled amphoteric doping by encapsulation of organic molecules inside carbon nanotubes.

    PubMed

    Takenobu, Taishi; Takano, Takumi; Shiraishi, Masashi; Murakami, Yousuke; Ata, Masafumi; Kataura, Hiromichi; Achiba, Yohji; Iwasa, Yoshihiro

    2003-10-01

    Single-walled carbon nanotubes (SWNTs) have strong potential for molecular electronics, owing to their unique structural and electronic properties. However, various outstanding issues still need to be resolved before SWNT-based devices can be made. In particular, large-scale, air-stable and controlled doping is highly desirable. Here we present a method for integrating organic molecules into SWNTs that promises to push the performance limit of these materials for molecular electronics. Reaction of SWNTs with molecules having large electron affinity and small ionization energy achieved p- and n-type doping, respectively. Optical characterization revealed that charge transfer between SWNTs and molecules starts at certain critical energies. X-ray diffraction experiments revealed that molecules are predominantly encapsulated inside SWNTs, resulting in an improved stability in air. The simplicity of the synthetic process offers a viable route for the large-scale production of SWNTs with controlled doping states.

  19. 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.

  20. Direct optical carbon dioxide sensing based on a polymeric film doped with a selective molecular tweezer-type ionophore.

    PubMed

    Xie, Xiaojiang; Pawlak, Marcin; Tercier-Waeber, Mary-Lou; Bakker, Eric

    2012-04-03

    A novel optical method for the determination of CO(2) concentration in aqueous and gaseous samples of plasticized PVC film is presented. The detection principle makes use of a direct molecular recognition of the carbonate ion by a molecular tweezer-type ionophore, which has previously been demonstrated to exhibit excellent carbonate selectivity. The carbonate ion is extracted together with hydrogen ions into a polymeric film that contains the anion exchanger tridodecylmethylammonium chloride, a lipophilic, electrically charged, and highly basic pH indicator, which is used for the readout in absorbance mode, in addition to the lipophilic carbonate ionophore. According to known bulk optode principles, such an optical sensor responds to the product of the carbonate ion activity and the square of hydrogen ion activity. This quantity is thermodynamically linked to the activity of carbon dioxide. This allows one to realize a direct carbon dioxide sensor that does not make use of the traditional Severinghaus sensing principle of measuring a pH change upon CO(2) equilibration across a membrane. A selectivity analysis shows that common ions such as chloride are sufficiently suppressed for direct PCO(2) measurements in freshwater samples at pH 8. Chloride interference, however, is too severe for direct seawater measurements at the same pH. This may be overcome by placing a gas-permeable membrane over the optode sensing film. This is conceptually confirmed by establishing that the sensor is equally useful for gas-phase PCO(2) measurements. As expected, humid air samples are required for proper sensor functioning, as dry CO(2) gas will not cause any signal change. The sensor showed acceptable response times and good reproducibility under both conditions.

  1. 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

  2. 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.

  3. Giardia intestinalis escapes oxidative stress by colonizing the small intestine: A molecular hypothesis.

    PubMed

    Mastronicola, Daniela; Giuffrè, Alessandro; Testa, Fabrizio; Mura, Antonella; Forte, Elena; Bordi, Eugenio; Pucillo, Leopoldo Paolo; Fiori, Pier Luigi; Sarti, Paolo

    2011-01-01

    Giardia intestinalis is the microaerophilic protozoon causing giardiasis, a common infectious intestinal disease. Giardia possesses an O(2) -scavenging activity likely essential for survival in the host. We report that Giardia trophozoites express the O(2) -detoxifying flavodiiron protein (FDP), detected by immunoblotting, and are able to reduce O(2) to H(2) O rapidly (∼3 μM O(2) × min × 10(6) cells at 37 °C) and with high affinity (C(50) = 3.4 ± 0.7 μM O(2)). Following a short-term (minutes) exposure to H(2) O(2) ≥ 100 μM, the O(2) consumption by the parasites is irreversibly impaired, and the FDP undergoes a degradation, prevented by the proteasome-inhibitor MG132. Instead, H(2) O(2) does not cause degradation or inactivation of the isolated FDP. On the basis of the elevated susceptibility of Giardia to oxidative stress, we hypothesize that the parasite preferentially colonizes the small intestine since, compared with colon, it is characterized by a greater capacity for redox buffering and a lower propensity to oxidative stress.

  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. 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.

  6. Small molecular, macromolecular, and cellular chloramines react with thiocyanate to give the human defense factor hypothiocyanite.

    PubMed

    Xulu, Bheki A; Ashby, Michael T

    2010-03-09

    Thiocyanate reacts noncatalytically with myeloperoxidase-derived HOCl to produce hypothiocyanite (OSCN(-)), thereby potentially limiting the propensity of HOCl to inflict host tissue damage that can lead to inflammatory diseases. However, the efficiency with which SCN(-) captures HOCl in vivo depends on the concentration of SCN(-) relative to other chemical targets. In blood plasma, where the concentration of SCN(-) is relatively low, proteins may be the principal initial targets of HOCl, and chloramines are a significant product. Chloramines eventually decompose to irreversibly damage proteins. In the present study, we demonstrate that SCN(-) reacts efficiently with chloramines in small molecules, in proteins, and in Escherichia coli cells to give OSCN(-) and the parent amine. Remarkably, OSCN(-) reacts faster than SCN(-) with chloramines. These reactions of SCN(-) and OSCN(-) with chloramines may repair some of the damage that is inflicted on protein amines by HOCl. Our observations are further evidence for the importance of secondary reactions during the redox cascades that are associated with oxidative stress by hypohalous acids.

  7. High molecular weight RNAs and small interfering RNAs induce systemic posttranscriptional gene silencing in plants

    PubMed Central

    Klahre, Ulrich; Crété, Patrice; Leuenberger, Sabrina A.; Iglesias, Victor A.; Meins, Frederick

    2002-01-01

    Posttranscriptional gene silencing (PTGS) in transgenic plants is an epigenetic form of RNA degradation related to PTGS and RNA interference (RNAi) in fungi and animals. Evidence suggests that transgene loci and RNA viruses can generate double-stranded RNAs similar in sequence to the transcribed region of target genes, which then undergo endonucleolytic cleavage to generate small interfering RNAs (siRNA) that promote degradation of cognate RNAs. The silent state in transgenic plants and in Caenorhabditis elegans can spread systemically, implying that mobile silencing signals exist. Neither the chemical nature of these signals nor their exact source in the PTGS pathway is known. Here, we use a positive marker system and real-time monitoring of green fluorescent protein expression to show that large sense, antisense, and double-stranded RNAs as well as double-stranded siRNAs delivered biolistically into plant cells trigger silencing capable of spreading locally and systemically. Systemically silenced leaves show greatly reduced levels of target RNA and accumulate siRNAs, confirming that RNA can induce systemic PTGS. The induced siRNAs represent parts of the target RNA that are outside of the region of homology with the triggering siRNA. Our results imply that siRNAs themselves or intermediates induced by siRNAs could comprise silencing signals and that these signals induce self-amplifying production of siRNAs. PMID:12181491

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

    PubMed Central

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

    2009-01-01

    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. PMID:19405660

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

    PubMed Central

    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 β-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. 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.

  11. Molecular Survey of Zoonotic Agents in Rodents and Other Small Mammals in Croatia

    PubMed Central

    Tadin, Ante; Tokarz, Rafal; Markotić, Alemka; Margaletić, Josip; Turk, Nenad; Habuš, Josipa; Svoboda, Petra; Vucelja, Marko; Desai, Aaloki; Jain, Komal; Ian Lipkin, W.

    2016-01-01

    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

  12. Aptamer-Based Molecular Recognition of Lysergamine, Metergoline and Small Ergot Alkaloids

    PubMed Central

    Rouah-Martin, Elsa; Mehta, Jaytry; van Dorst, Bieke; de Saeger, Sarah; Dubruel, Peter; Maes, Bert U. W.; Lemiere, Filip; Goormaghtigh, Erik; Daems, Devin; Herrebout, Wouter; van Hove, François; Blust, Ronny; Robbens, Johan

    2012-01-01

    Ergot alkaloids are mycotoxins produced by fungi of the genus Claviceps, which infect cereal crops and grasses. The uptake of ergot alkaloid contaminated cereal products can be lethal to humans and animals. For food safety assessment, analytical techniques are currently used to determine the presence of ergot alkaloids in food and feed samples. However, the number of samples which can be analyzed is limited, due to the cost of the equipment and the need for skilled personnel. In order to compensate for the lack of rapid tests for the detection of ergot alkaloids, the aim of this study was to develop a specific recognition element for ergot alkaloids, which could be further applied to produce a colorimetric reaction in the presence of these toxins. As recognition elements, single-stranded DNA ligands were selected by using an iterative selection procedure named SELEX, i.e., Systematic Evolution of Ligands by EXponential enrichment. After several selection cycles, the resulting aptamers were cloned and sequenced. A surface plasmon resonance analysis enabled determination of the dissociation constants of the complexes of aptamers and lysergamine. Dissociation constants in the nanomolar range were obtained with three selected aptamers. One of the selected aptamers, having a dissociation constant of 44 nM, was linked to gold nanoparticles and it was possible to produce a colorimetric reaction in the presence of lysergamine. This system could also be applied to small ergot alkaloids in an ergot contaminated flour sample. PMID:23242153

  13. 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.

  14. Insights on the structural dynamics of Leishmania braziliensis Hsp90 molecular chaperone by small angle X-ray scattering.

    PubMed

    Seraphim, Thiago V; Silva, Kelly P; Dores-Silva, Paulo R; Barbosa, Leandro R S; Borges, Júlio C

    2017-04-01

    Heat shock protein of 90kDa (Hsp90) is an essential molecular chaperone involved in a plethora of cellular activities which modulate protein homeostasis. During the Hsp90 mechanochemical cycle, it undergoes large conformational changes, oscillating between open and closed states. Although structural and conformational equilibria of prokaryotic and some eukaryotic Hsp90s are known, some protozoa Hsp90 structures and dynamics are poorly understood. In this study, we report the solution structure and conformational dynamics of Leishmania braziliensis Hsp90 (LbHsp90) investigated by small angle X-ray scattering (SAXS). The results indicate that LbHsp90 coexists in open and closed conformations in solution and that the linkers between domains are not randomly distributed. These findings noted interesting features of the LbHsp90 system, opening doors for further conformational studies of other protozoa chaperones.

  15. 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.

  16. Molecular Phylogeny of the Small Ermine Moth Genus Yponomeuta (Lepidoptera, Yponomeutidae) in the Palaearctic

    PubMed Central

    Turner, Hubert; Lieshout, Niek; Van Ginkel, Wil E.; Menken, Steph B. J.

    2010-01-01

    Background The small ermine moth genus Yponomeuta (Lepidoptera, Yponomeutidae) contains 76 species that are specialist feeders on hosts from Celastraceae, Rosaceae, Salicaceae, and several other plant families. The genus is a model for studies in the evolution of phytophagous insects and their host-plant associations. Here, we reconstruct the phylogeny to provide a solid framework for these studies, and to obtain insight into the history of host-plant use and the biogeography of the genus. Methodology/Principal Findings DNA sequences from an internal transcribed spacer region (ITS-1) and from the 16S rDNA (16S) and cytochrome oxidase (COII) mitochondrial genes were collected from 20–23 (depending on gene) species and two outgroup taxa to reconstruct the phylogeny of the Palaearctic members of this genus. Sequences were analysed using three different phylogenetic methods (parsimony, likelihood, and Bayesian inference). Conclusions/Significance Roughly the same patterns are retrieved irrespective of the method used, and they are similar among the three genes. Monophyly is well supported for a clade consisting of the Japanese (but not the Dutch) population of Yponomeuta sedellus and Y. yanagawanus, a Y. kanaiellus–polystictus clade, and a Rosaceae-feeding, western Palaearctic clade (Y. cagnagellus–irrorellus clade). Within these clades, relationships are less well supported, and the patterns between the different gene trees are not so similar. The position of the remaining taxa is also variable among the gene trees and rather weakly supported. The phylogenetic information was used to elucidate patterns of biogeography and resource use. In the Palaearctic, the genus most likely originated in the Far East, feeding on Celastraceae, dispersing to the West concomitant with a shift to Rosaceae and further to Salicaceae. The association of Y. cagnagellus with Euonymus europaeus (Celastraceae), however, is a reversal. The only oligophagous species, Y. padellus, belongs

  17. 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

  18. 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.

  19. 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.

  20. Preclinical molecular imaging: development of instrumentation for translational research with small laboratory animals

    PubMed Central

    Mejia, Jorge; Miranda, Ana Claudia Camargo; Durante, Ana Claudia Ranucci; de Oliveira, Larissa Rolim; de Barboza, Marycel Rosa Felisa Figols; Rosell, Katerin Taboada; Jardim, Daniele Pereira; Campos, Alexandre Holthausen; dos Reis, Marilia Alves; Catanoso, Marcela Forli; Galvis-Alonso, Orfa Yineth; Cabral, Francisco Romero

    2016-01-01

    ABSTRACT Objective: To present the result of upgrading a clinical gamma-camera to be used to obtain in vivo tomographic images of small animal organs, and its application to register cardiac, renal and neurological images. Methods: An updated version of the miniSPECT upgrading device was built, which is composed of mechanical, electronic and software subsystems. The device was attached to a Discovery VH (General Electric Healthcare) gamma-camera, which was retired from the clinical service and installed at the Centro de Imagem Pré-Clínica of the Hospital Israelita Albert Einstein. The combined system was characterized, determining operational parameters, such as spatial resolution, magnification, maximum acceptable target size, number of projections, and acquisition and reconstruction times. Results: Images were obtained with 0.5mm spatial resolution, with acquisition and reconstruction times between 30 and 45 minutes, using iterative reconstruction with 10 to 20 iterations and 4 projection subsets. The system was validated acquiring in vivo tomographic images of the heart, kidneys and brain of normal animals (mice and adult rats), using the radiopharmaceuticals technetium-labeled hexakis-2-methoxy-isobutyl isonitrile (99mTc-Sestamibi), technetium-labeled dimercaptosuccinic acid (99mTc-DMSA) and technetium-labeled hexamethyl propyleneamine oxime (99mTc-HMPAO). Conclusion: This kind of application, which consists in the adaptation for an alternative objective of already existing instrumentation, resulted in a low-cost infrastructure option, allowing to carry out large scale in vivo studies with enhanced quality in several areas, such as neurology, nephrology, cardiology, among others. PMID:27759832

  1. Molecular Evolution of the Small Subunit of Ribulose Bisphosphate Carboxylase: Nucleotide Substitution and Gene Conversion

    PubMed Central

    Meagher, R. B.; Berry-Lowe, S.; Rice, K.

    1989-01-01

    The nucleotide sequences encoding the mature portion of 31 ribulose 1,5-bisphosphate carboxylase small subunit (SSU) genes from 17 genera of plants, green algae and cyanobacteria were examined. Among the 465 pairwise sequence comparisons, SSU multigene family members within the same species were more similar to each other in nonsynonymous or replacement nucleotide substitutions (RNS) than they were to SSU sequences in any other organism. The concerted evolution of independent SSU gene lineages within closely related plant species suggests that homogenization of RNS positions has occurred at least once in the life of each genus. The rate of expected RNS among mature SSU sequences was calculated to be 1.25 X 10(-9)/site/yr for the first 70 million years (MY) of divergence with a significant slowing to 0.13 X 10(-9)/site/yr for the next 1,400 MY. The data suggest that mature SSU sequences do not accumulate more than 20% differences in the RNS positions without compensatory changes in other components of this enzyme system. During the first 70 MY of divergence between species, the rate of expected synonymous or silent nucleotide substitutions (SNS) is ~6.6 X 10(-9)/site/yr. This is five times the RNS rate and is similar to the silent rate observed in animals. In striking contrast, SNS and RNS do not show this correlation among SSU gene family members within a species. A mechanism involving gene conversion within the exons followed by selection for biased gene conversion products with conservation of RNS positions and divergence of SNS positions is discussed. A SSU gene tree based on corrected RNS for 31 SSU sequences is presented and agrees well with a species tree based on morphological and cytogenetic traits for the 17 genera examined. SSU gene comparisons may be useful in predicting phylogenetic relationships and in some cases divergence times of various plant, algal and cyanobacterial species. PMID:2515110

  2. 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.

  3. INFRARED AND RADIO OBSERVATIONS OF A SMALL GROUP OF PROTOSTELLAR OBJECTS IN THE MOLECULAR CORE, L1251-C

    SciTech Connect

    Kim, Jungha; Lee, Jeong-Eun; Choi, Minho; Kang, Miju; Bourke, Tyler L.; II, Neal J. Evans; Francesco, James Di; Cieza, Lucas A.; Dunham, Michael M.

    2015-05-15

    We present a multi-wavelength observational study of a low-mass star-forming region, L1251-C, with observational results at wavelengths from the near-infrared to the millimeter. Spitzer Space Telescope observations confirmed that IRAS 22343+7501 is a small group of protostellar objects. The extended emission in the east–west direction with its intensity peak at the center of L1251A has been detected at 350 and 850 μm with the Caltech Submillimeter Observatory and James Clerk Maxwell telescopes, tracing dense envelope material around L1251A. The single-dish data from the Korean VLBI Network and TRAO telescopes show inconsistencies between the intensity peaks of several molecular emission lines and that of the continuum emission, suggesting complex distributions of molecular abundances around L1251A. The Submillimeter Array interferometer data, however, show intensity peaks of CO 2–1 and {sup 13}CO 2–1 located at the position of IRS 1, which is both the brightest source in the Infrared Array Camera image and the weakest source in the 1.3 mm dust-continuum map. IRS 1 is the strongest candidate for the driving source of the newly detected compact CO 2–1 outflow. Over the entire region (14′ × 14′) of L125l-C, 3 Class I and 16 Class II sources have been detected, including three young stellar objects (YSOs) in L1251A. A comparison between the average projected distance among the 19 YSOs in L1251-C and that among the 3 YSOs in L1251A suggests that L1251-C is an example of low-mass cluster formation where protostellar objects form in a small group.

  4. 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.

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

    PubMed

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

    2016-04-05

    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.

  6. Surface treatment by binary solvents induces the crystallization of a small molecular donor for enhanced photovoltaic performance.

    PubMed

    Zhou, Weihua; Xie, Yuanpeng; Hu, Xiaotian; Zhang, Lin; Meng, Xiangchuan; Zhang, Yong; Ma, Wei; Chen, Yiwang

    2016-01-14

    The surface treatment of the active layer with binary solvents composed of methanol (MeOH) and 1-chloronaphthalene (CN), was demonstrated to effectively improve the power conversion efficiency (PCE) from 2.4% to 6.5% for p-DTS(FBTTh2)2:PC71BM based small molecular solar cells. The optical properties and morphology of the p-DTS(FBTTh2)2:PC71BM films were carefully investigated. The results indicate that treatment with MeOH:CN binary solvents could significantly enhance the absorption of the active layer, due to the formation of more p-DTS(FBTTh2)2 nanofibrils associated with higher crystallinity as revealed by atomic force microscopy (AFM) and transmission electron microscopy (TEM). The two-dimensional grazing incidence wide-angle X-ray scattering (GIWAXS) results further demonstrate that the molecular packing of p-DTS(FBTTh2)2 molecules could be strongly enhanced after treatment with the binary solvents. In contrast, pristine methanol shows no significant influence on the crystalline structure, phase separation or the photovoltaic properties of the p-DTS(FBTTh2)2:PC71BM system, showing that the CN solvent plays the main role in inducing the crystallization of p-DTS(FBTTh2)2 molecules.

  7. 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.

  8. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches

    DOE PAGES

    Huang, Jing; Mei, Ye; König, Gerhard; ...

    2017-01-24

    Here in this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PADmore » energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other eleven solute molecules, while the PAD model has a much better performance with R2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. Lastly, this suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.« less

  9. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

    PubMed

    Huang, Jing; Mei, Ye; König, Gerhard; Simmonett, Andrew C; Pickard, Frank C; Wu, Qin; Wang, Lee-Ping; MacKerell, Alexander D; Brooks, Bernard R; Shao, Yihan

    2017-02-14

    In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R(2) value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R(2) values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

  10. 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.

  11. Study of Gd-doped Bi{sub 2}Te{sub 3} thin films: Molecular beam epitaxy growth and magnetic properties

    SciTech Connect

    Harrison, S. E.; Huo, Y.; Harris, J. S.; Collins-McIntyre, L. J.; Hesjedal, T.; Li, S.; Baker, A. A.; Shelford, L. R.; Laan, G. van der; Pushp, A.; Parkin, S. S. P.; Arenholz, E.

    2014-01-14

    Incorporation of magnetic dopants into topological insulators to break time-reversal symmetry is a prerequisite for observing the quantum anomalous Hall (QAHE) effect and other novel magnetoelectric phenomena. GdBiTe{sub 3} with a Gd:Bi ratio of 1:1 is a proposed QAHE system, however, the reported solubility limit for Gd doping into Bi{sub 2}Te{sub 3} bulk crystals is between ∼0.01 and 0.05. We present a magnetic study of molecular beam epitaxy grown (Gd{sub x}Bi{sub 1–x}){sub 2}Te{sub 3} thin films with a high Gd concentration, up to x ≈ 0.3. Magnetometry reveals that the films are paramagnetic down to 1.5 K. X-ray magnetic circular dichroism at the Gd M{sub 4,5} edge at 1.5 K reveals a saturation field of ∼6 T, and a slow decay of the magnetic moment with temperature up to 200 K. The Gd{sup 3+} ions, which are substitutional on Bi sites in the Bi{sub 2}Te{sub 3} lattice, exhibit a large atomic moment of ∼7 μ{sub B}, as determined by bulk-sensitive superconducting quantum interference device magnetometry. Surface oxidation and the formation of Gd{sub 2}O{sub 3} lead to a reduced moment of ∼4 μ{sub B} as determined by surface-sensitive x-ray magnetic circular dichroism. Their large atomic moment makes these films suitable for incorporation into heterostructures, where interface polarization effects can lead to the formation of magnetic order within the topological insulators.

  12. Sec62 bridges the gap from 3q amplification to molecular cell biology in non-small cell lung cancer.

    PubMed

    Linxweiler, Maximilian; Linxweiler, Johannes; Barth, Monika; Benedix, Julia; Jung, Volker; Kim, Yoo-Jin; Bohle, Rainer M; Zimmermann, Richard; Greiner, Markus

    2012-02-01

    The molecular carcinogenesis of lung cancer has yet to be clearly elucidated. We investigated the possible oncogenic function of SEC62 in lung cancer, which was predicted based on our previous findings that lung and thyroid cancer tissue samples exhibited increased Sec62 protein levels. The SEC62 gene locus is at 3q26.2, and 3q amplification is reportedly the most common genomic alteration in non-small cell lung cancer. We analyzed SEC62 mRNA and protein levels in tissue samples from lung cancer patients by real-time quantitative PCR, Western blot, and IHC and found significantly increased SEC62 mRNA and protein levels in tumors compared with tumor-free tissue samples from the same patients. Correlation analyses revealed significantly higher Sec62 levels in tumors with lymph node metastases compared with nonmetastatic tumors, as well as in poorly compared with moderately differentiated tumors. On the basis of these promising results, we examined the role of Sec62 in cancer cell biology in vitro. Cell migration assays with lung and thyroid cancer cells showed distinct stimulation of migration in SEC62-overexpressing cells and inhibition of migration in Sec62-depleted cells. Moreover, we found that SEC62 silencing sensitized the cells to thapsigargin-induced endoplasmic reticulum stress. Thus, our results indicate that SEC62 represents a potential candidate oncogene in the amplified 3q region in cases of non-small cell lung cancer and harbors various functions in cancer cell biology.

  13. Array Formatting of the Heat-Transfer Method (HTM) for the Detection of Small Organic Molecules by Molecularly Imprinted Polymers

    PubMed Central

    Wackers, Gideon; Vandenryt, Thijs; Cornelis, Peter; Kellens, Evelien; Thoelen, Ronald; De Ceuninck, Ward; Losada-Pérez, Patricia; van Grinsven, Bart; Peeters, Marloes; Wagner, Patrick

    2014-01-01

    In this work we present the first steps towards a molecularly imprinted polymer (MIP)-based biomimetic sensor array for the detection of small organic molecules via the heat-transfer method (HTM). HTM relies on the change in thermal resistance upon binding of the target molecule to the MIP-type receptor. A flow-through sensor cell was developed, which is segmented into four quadrants with a volume of 2.5 μL each, allowing four measurements to be done simultaneously on a single substrate. Verification measurements were conducted, in which all quadrants received a uniform treatment and all four channels exhibited a similar response. Subsequently, measurements were performed in quadrants, which were functionalized with different MIP particles. Each of these quadrants was exposed to the same buffer solution, spiked with different molecules, according to the MIP under analysis. With the flow cell design we could discriminate between similar small organic molecules and observed no significant cross-selectivity. Therefore, the MIP array sensor platform with HTM as a readout technique, has the potential to become a low-cost analysis tool for bioanalytical applications. PMID:24955945

  14. Array formatting of the heat-transfer method (HTM) for the detection of small organic molecules by molecularly imprinted polymers.

    PubMed

    Wackers, Gideon; Vandenryt, Thijs; Cornelis, Peter; Kellens, Evelien; Thoelen, Ronald; De Ceuninck, Ward; Losada-Pérez, Patricia; van Grinsven, Bart; Peeters, Marloes; Wagner, Patrick

    2014-06-20

    In this work we present the first steps towards a molecularly imprinted polymer (MIP)-based biomimetic sensor array for the detection of small organic molecules via the heat-transfer method (HTM). HTM relies on the change in thermal resistance upon binding of the target molecule to the MIP-type receptor. A flow-through sensor cell was developed, which is segmented into four quadrants with a volume of 2.5 μL each, allowing four measurements to be done simultaneously on a single substrate. Verification measurements were conducted, in which all quadrants received a uniform treatment and all four channels exhibited a similar response. Subsequently, measurements were performed in quadrants, which were functionalized with different MIP particles. Each of these quadrants was exposed to the same buffer solution, spiked with different molecules, according to the MIP under analysis. With the flow cell design we could discriminate between similar small organic molecules and observed no significant cross-selectivity. Therefore, the MIP array sensor platform with HTM as a readout technique, has the potential to become a low-cost analysis tool for bioanalytical applications.

  15. Ultrafast laser irradiation of spherical nanoparticles: molecular-dynamics results on fragmentation and small-angle scattering

    NASA Astrophysics Data System (ADS)

    Fahdiran, Riser; Urbassek, Herbert M.

    2015-02-01

    Using molecular dynamics simulation we study the response of a spherical nanoparticle to a sudden homogeneous energization, such as effected by ultrashort pulse laser irradiation. We consider a Lennard-Jones model system and two different values of the energization. For the smaller one, the sphere expands while a multitude of voids are created inside; the sphere develops finally into an external shell filled with gas and small clusters. For the higher energization, the sphere expands uniformly and no shell structure is formed. An analysis of the pressure generated confirms that in the latter case the pressure is compressive throughout the sphere expansion, while it is temporarily tensile for the lower energization leading to void formation. The final state of both systems shows the fragmentation of the sphere into a multitude of clusters. With increasing fragmentation the cluster distribution becomes shifted to smaller sizes. Simulated small-angle scattering functions of the exploding NP are presented. The distribution of minima allows for an easy determination of the particle size during expansion.

  16. The reaction enthalpy of hydrogen dissociation calculated with the Small System Method from simulation of molecular fluctuations.

    PubMed

    Skorpa, Ragnhild; Simon, Jean-Marc; Bedeaux, Dick; Kjelstrup, Signe

    2014-09-28

    We show how we can find the enthalpy of a chemical reaction under non-ideal conditions using the Small System Method to sample molecular dynamics simulation data for fluctuating variables. This method, created with Hill's thermodynamic analysis, is used to find properties in the thermodynamic limit, such as thermodynamic correction factors, partial enthalpies, volumes, heat capacities and compressibility. The values in the thermodynamic limit at (T,V, μj) are then easily transformed into other ensembles, (T,V,Nj) and (T,P,Nj), where the last ensemble gives the partial molar properties which are of interest to chemists. The dissociation of hydrogen from molecules to atoms was used as a convenient model system. Molecular dynamics simulations were performed with three densities; ρ = 0.0052 g cm(-3) (gas), ρ = 0.0191 g cm(-3) (compressed gas) and ρ = 0.0695 g cm(-3) (liquid), and temperatures in the range; T = 3640-20,800 K. The enthalpy of reaction was observed to follow a quadratic trend as a function of temperature for all densities. The enthalpy of reaction was observed to only have a small pressure dependence. With a reference point close to an ideal state (T = 3640 K and ρ = 0.0052 g cm(-3)), we were able to calculate the thermodynamic equilibrium constant, and thus the deviation from ideal conditions for the lowest density. We found the thermodynamic equilibrium constant to increase with increasing temperature, and to have a negligible pressure dependence. Taking the enthalpy variation into account in the calculation of the thermodynamic equilibrium constant, we found the ratio of activity coefficients to be in the order of 0.7-1.0 for the lowest density, indicating repulsive forces between H and H2. This study shows that the compressed gas- and liquid density values at higher temperatures are far from those calculated under ideal conditions. It is important to have a method that can give access to partial molar properties, independent of the ideality of

  17. 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

  18. [The analysis of the low and medium molecular weight substances for differential diagnostics of deaths from acute small-focal myocardial infarction and other forms of cardiac pathology].

    PubMed

    Edelev, N S; Obuhova, L M; Edelev, I S; Katirkina, A A

    2017-01-01

    The objective of the present study was to analyze the possibilities for the use of the low and medium molecular weight substances for differential diagnostics of deaths from acute small-focal myocardial infarction and other forms of cardiac pathology. We determined the amount of the low and medium molecular weight substances in the urine obtained from the subjects who had died as a result of chronic coronary heart disease, acute myocardial infarction, and alcoholic cardiomyopathy. The levels of the low and medium molecular weight substances in the urine were measured by the method of N.Ya. Malakhov in the modification of T.V. Kopytova [5]. The study has demonstrated the appearance of the products of cardiomyocyte degradation (giving rise to a peak at a wavelength of 278 nm) in the fraction of the low and medium molecular weight substances of the urine from the patients suffering from acute small-focal myocardial infarction and some other forms of cardiac pathology.

  19. 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.

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

    PubMed

    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

    2015-08-19

    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.

  1. Molecular and quantitative trait variation within and among small fragmented populations of the endangered plant species Psilopeganum sinense

    PubMed Central

    Ye, Qigang; Tang, Feiyan; Wei, Na; Yao, Xiaohong

    2014-01-01

    Background and Aims Natural selection and genetic drift are important evolutionary forces in determining genetic and phenotypic differentiation in plant populations. The extent to which these two distinct evolutionary forces affect locally adaptive quantitative traits has been well studied in common plant and animal species. However, we know less about how quantitative traits respond to selection pressures and drift in endangered species that have small population sizes and fragmented distributions. To address this question, this study assessed the relative strengths of selection and genetic drift in shaping population differentiation of phenotypic traits in Psilopeganum sinense, a naturally rare and recently endangered plant species. Methods Population differentiation at five quantitative traits (QST) obtained from a common garden experiment was compared with differentiation at putatively neutral microsatellite markers (FST) in seven populations of P. sinense. QST estimates were derived using a Bayesian hierarchical variance component method. Key Results Trait-specific QST values were equal to or lower than FST. Neutral genetic diversity was not correlated with quantitative genetic variation within the populations of P. sinense. Conclusions Despite the prevalent empirical evidence for QST > FST, the results instead suggest a definitive role of stabilizing selection and drift leading to phenotypic differentiation among small populations. Three traits exhibited a significantly lower QST relative to FST, suggesting that populations of P. sinense might have experienced stabilizing selection for the same optimal phenotypes despite large geographical distances between populations and habitat fragmentation. For the other two traits, QST estimates were of the same magnitude as FST, indicating that divergence in these traits could have been achieved by genetic drift alone. The lack of correlation between molecular marker and quantitative genetic variation suggests that

  2. 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

  3. WE-H-206-02: Recent Advances in Multi-Modality Molecular Imaging of Small Animals.

    PubMed

    Tsui, B

    2016-06-01

    Lihong V. Wang: Photoacoustic tomography (PAT), combining non-ionizing optical and ultrasonic waves via the photoacoustic effect, provides in vivo multiscale functional, metabolic, and molecular imaging. Broad applications include imaging of the breast, brain, skin, esophagus, colon, vascular system, and lymphatic system in humans or animals. Light offers rich contrast but does not penetrate biological tissue in straight paths as x-rays do. Consequently, high-resolution pure optical imaging (e.g., confocal microscopy, two-photon microscopy, and optical coherence tomography) is limited to penetration within the optical diffusion limit (∼1 mm in the skin). Ultrasonic imaging, on the contrary, provides fine spatial resolution but suffers from both poor contrast in early-stage tumors and strong speckle artifacts. In PAT, pulsed laser light penetrates tissue and generates a small but rapid temperature rise, which induces emission of ultrasonic waves due to thermoelastic expansion. The ultrasonic waves, orders of magnitude less scattering than optical waves, are then detected to form high-resolution images of optical absorption at depths up to 7 cm, conquering the optical diffusion limit. PAT is the only modality capable of imaging across the length scales of organelles, cells, tissues, and organs (up to whole-body small animals) with consistent contrast. This rapidly growing technology promises to enable multiscale biological research and accelerate translation from microscopic laboratory discoveries to macroscopic clinical practice. PAT may also hold the key to label-free early detection of cancer by in vivo quantification of hypermetabolism, the quintessential hallmark of malignancy.

  4. 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

  5. The effect of nitrogen doping on mercury oxidation/chemical adsorption on the CuCo2O4(110) surface: a molecular-level description.

    PubMed

    Mei, Zhijian; Fan, Maohong; Zhang, Ruiqing; Shen, Zhemin; Wang, Wenhua

    2014-07-14

    Based on density functional theory (DFT) calculations, the detailed mercury oxidation/chemical adsorption mechanisms on the N-doped CuCo2O4(110) surface are studied. The DFT calculations show that Ow (bonded with one Cu(2+) ion and one Co(3+) ion) is far more active than Os (bonded with three Co(3+) ions) and the mercury oxidation/chemical adsorption activation energy (Ea) on the virgin CuCo2O4(110) surface involving Ow is 0.85 eV. The physically adsorbed mercury overcomes the Ea and enters the energy well that plays an important role in mercury oxidation/chemical adsorption. Nitrogen doping can greatly increase the activity of Ow and decrease the activity of Os at the same time, which greatly affect the mercury oxidation/chemical adsorption abilities on the CuCo2O4(110) surface, and the Ea variation of mercury oxidation/chemical adsorption is as follows: 0.85 eV (virgin CuCo2O4(110)) → 0.76 eV (one N-doped CuCo2O4(110)) → 0.69 eV (two N-doped CuCo2O4(110)) → 0.48 eV (three N-doped CuCo2O4(110)). In addition, N-doping can decrease the adsorption energy of mercury and mercuric oxide. The effect of N-doping on the bonding mechanism of mercury adsorption on the CuCo2O4(110) surface is analyzed by the local density of state (LDOS) and the natural bonding orbital (NBO). The calculation results correspond well to the experimental data.

  6. Evaluation of the absolute photoluminescence quantum yields of molecularly doped organic composite films and the electroluminescence efficiencies of molecular light-emitting devices containing oligoheterocycles as efficient emission centers

    NASA Astrophysics Data System (ADS)

    Kushto, Gary P.; Hill, Ian G.; Mitschke, Ullrich; Baeuerle, Peter; Kafafi, Zakya H.

    2001-02-01

    The absolute photoluminescence quantum yields ((Phi) PL) of three end-capped oligothiophene derivatives dispersed in N,N'-((alpha) -naphthyl)-N,N'-diphenyl-1,1'-biphenyl ((alpha) -NPD) have been evaluated and the most efficient of the emitters was used as a dopant in molecular organic LEDs. Composite films of 2,5-bis [5-(4,5,6,7- tetrahydrobenzo[b]thien-2-yl) thien-2-yl]-furan (EC5FUR); 2,5-bis [5-(4,5,6,7- tetrahydrobenzo[b]thien-2-yl) thien-2-yl]-oxazole (EC5OXZ) and 2,5-bis [5-(4,5,6,7- tetrahydrobenzo[b]thien-2-yl)thien-2-yl]-1,3,4- oxadiazole (EC5OXD) doped into (alpha) -NPD were found to have (Phi) PL values of 78, 62 and 28%, respectively. MOLED devices were fabricated using an EC5FUR/(alpha) -NPD composite as the emitting layer and the external quantum efficiencies ((eta) EL) of these devices were evaluated. The results of the device characterization show that the inclusion of EC5FUR in the NPD hole transport layer increases the device (eta) EL to 1.45% at a current density of 10 mA/cm2. In addition, the concentration dependence of the (eta) EL on the EC5FUR dopant in certain device structures when considered in conjunction with the current results of ultraviolet photoemission spectroscopic experiments suggests that this dopant species may be acting as both a hole and electron trap in the (alpha) -NPD host.

  7. 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

  8. Centromeric association of small supernumerary marker chromosomes with their sister-chromosomes detected by three dimensional molecular cytogenetics

    PubMed Central

    2012-01-01

    Background Small supernumerary marker chromosomes (sSMC) are detected in 0.043% of general population and can be characterized for their chromosomal origin, genetic content and shape by molecular cytogenetic approaches. Even though recently progress was achieved towards genotype-phenotype-correlations of sSMC, nothing is known on the influence that an additional derivative extra chromosome has on the nuclear architecture. Results Here we present the first three-dimensional interphase fluorescence in situ hybridization (FISH) studies for the nuclear architecture of sSMC. It could be shown that sSMC derived from chromosomes 15, 16 or 18 preferentially colocalized with one of their corresponding sister chromosomes. This was true in B- and T-lymphocytes as well as in skin fibroblasts. Additionally, a case with a complex sSMC with a karyotype 47,XY,+der(18)t(8;18)(8p23.2 ~ 23.1;18q11.1) was studied. Here the sSMC co-localized with one homologous chromosome 8 instead of 18. Conclusion Overall, there is a kind of "attraction" between an sSMC and one of its homologous sister chromosomes. This seems to be transmitted by the euchromatic part of the sSMC rather than its heterochromatic one. PMID:22413994

  9. 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.

  10. Therapeutic potential of brain-derived neurotrophic factor (BDNF) and a small molecular mimics of BDNF for traumatic brain injury

    PubMed Central

    Wurzelmann, Mary; Romeika, Jennifer; Sun, Dong

    2017-01-01

    Traumatic brain injury (TBI) is a major health problem worldwide. Following primary mechanical insults, a cascade of secondary injuries often leads to further neural tissue loss. Thus far there is no cure to rescue the damaged neural tissue. Current therapeutic strategies primarily target the secondary injuries focusing on neuroprotection and neuroregeneration. The neurotrophin brain-derived neurotrophic factor (BDNF) has significant effect in both aspects, promoting neuronal survival, synaptic plasticity and neurogenesis. Recently, the flavonoid 7,8-dihydroxyflavone (7,8-DHF), a small TrkB agonist that mimics BDNF function, has shown similar effects as BDNF in promoting neuronal survival and regeneration following TBI. Compared to BDNF, 7,8-DHF has a longer half-life and much smaller molecular size, capable of penetrating the blood-brain barrier, which makes it possible for non-invasive clinical application. In this review, we summarize functions of the BDNF/TrkB signaling pathway and studies examining the potential of BDNF and 7,8-DHF as a therapy for TBI. PMID:28250730

  11. 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

  12. Investigating the significance of zero-point motion in small molecular clusters of sulphuric acid and water.

    PubMed

    Stinson, Jake L; Kathmann, Shawn M; Ford, Ian J

    2014-01-14

    The nucleation of particles from trace gases in the atmosphere is an important source of cloud condensation nuclei, and these are vital for the formation of clouds in view of the high supersaturations required for homogeneous water droplet nucleation. The methods of quantum chemistry have increasingly been employed to model nucleation due to their high accuracy and efficiency in calculating configurational energies; and nucleation rates can be obtained from the associated free energies of particle formation. However, even in such advanced approaches, it is typically assumed that the nuclei have a classical nature, which is questionable for some systems. The importance of zero-point motion (also known as quantum nuclear dynamics) in modelling small clusters of sulphuric acid and water is tested here using the path integral molecular dynamics method at the density functional level of theory. The general effect of zero-point motion is to distort the mean structure slightly, and to promote the extent of proton transfer with respect to classical behaviour. In a particular configuration of one sulphuric acid molecule with three waters, the range of positions explored by a proton between a sulphuric acid and a water molecule at 300 K (a broad range in contrast to the confinement suggested by geometry optimisation at 0 K) is clearly affected by the inclusion of zero point motion, and similar effects are observed for other configurations.

  13. Molecular mechanism of mRNA repression in trans by a ProQ-dependent small RNA.

    PubMed

    Smirnov, Alexandre; Wang, Chuan; Drewry, Lisa L; Vogel, Jörg

    2017-04-13

    Research into post-transcriptional control of mRNAs by small noncoding RNAs (sRNAs) in the model bacteria Escherichia coli and Salmonella enterica has mainly focused on sRNAs that associate with the RNA chaperone Hfq. However, the recent discovery of the protein ProQ as a common binding partner that stabilizes a distinct large class of structured sRNAs suggests that additional RNA regulons exist in these organisms. The cellular functions and molecular mechanisms of these new ProQ-dependent sRNAs are largely unknown. Here, we report in Salmonella Typhimurium the mode-of-action of RaiZ, a ProQ-dependent sRNA that is made from the 3' end of the mRNA encoding ribosome-inactivating protein RaiA. We show that RaiZ is a base-pairing sRNA that represses in trans the mRNA of histone-like protein HU-α. RaiZ forms an RNA duplex with the ribosome-binding site of hupA mRNA, facilitated by ProQ, to prevent 30S ribosome loading and protein synthesis of HU-α. Similarities and differences between ProQ- and Hfq-mediated regulation will be discussed.

  14. Body Composition and Circulating High-Molecular-Weight Adiponectin and IGF-I in Infants Born Small for Gestational Age

    PubMed Central

    de Zegher, Francis; Sebastiani, Giorgia; Diaz, Marta; Sánchez-Infantes, David; Lopez-Bermejo, Abel; Ibáñez, Lourdes

    2012-01-01

    Prenatal growth restraint, if followed by postnatal overweight, confers risk for adult disease including diabetes. The mechanisms whereby neonatal nutrition may modulate such risk are poorly understood. We studied the effects of nutrition (breast-feeding [BRF] vs. formula-feeding [FOF]) on weight partitioning and endocrine state (as judged by high-molecular-weight [HMW] adiponectin and IGF-I) of infants born small for gestational age (SGA). Body composition (by absorptiometry), HMW adiponectin, and IGF-I were assessed at birth and 4 months in BRF infants born appropriate for gestational age (AGA; n = 72) and SGA infants receiving BRF (n = 46) or FOF (n = 56), the latter being randomized to receive a standard (FOF1) or protein-rich formula (FOF2). Compared with AGA-BRF infants, the catchup growth of SGA infants was confined to lean mass, independently of nutrition. Compared with AGA-BRF infants, SGA-BRF infants had normal HMW adiponectin and IGF-I levels at 4 months, whereas SGA-FOF infants had elevated levels of HMW adiponectin (particularly SGA-FOF1) and IGF-I (particularly SGA-FOF2). In conclusion, neonatal nutrition seems to influence endocrinology more readily than body composition of SGA infants. Follow-up will disclose whether the endocrine abnormalities in SGA-FOF infants can serve as early markers of an unfavorable metabolic course and whether they may contribute to design early interventions that prevent subsequent disease, including diabetes. PMID:22648385

  15. 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.

  16. Antibiotic discovery throughout the Small World Initiative: A molecular strategy to identify biosynthetic gene clusters involved in antagonistic activity.

    PubMed

    Davis, Elizabeth; Sloan, Tyler; Aurelius, Krista; Barbour, Angela; Bodey, Elijah; Clark, Brigette; Dennis, Celeste; Drown, Rachel; Fleming, Megan; Humbert, Allison; Glasgo, Elizabeth; Kerns, Trent; Lingro, Kelly; McMillin, MacKenzie; Meyer, Aaron; Pope, Breanna; Stalevicz, April; Steffen, Brittney; Steindl, Austin; Williams, Carolyn; Wimberley, Carmen; Zenas, Robert; Butela, Kristen; Wildschutte, Hans

    2017-01-22

    The emergence of bacterial pathogens resistant to all known antibiotics is a global health crisis. Adding to this problem is that major pharmaceutical companies have shifted away from antibiotic discovery due to low profitability. As a result, the pipeline of new antibiotics is essentially dry and many bacteria now resist the effects of most commonly used drugs. To address this global health concern, citizen science through the Small World Initiative (SWI) was formed in 2012. As part of SWI, students isolate bacteria from their local environments, characterize the strains, and assay for antibiotic production. During the 2015 fall semester at Bowling Green State University, students isolated 77 soil-derived bacteria and genetically characterized strains using the 16S rRNA gene, identified strains exhibiting antagonistic activity, and performed an expanded SWI workflow using transposon mutagenesis to identify a biosynthetic gene cluster involved in toxigenic compound production. We identified one mutant with loss of antagonistic activity and through subsequent whole-genome sequencing and linker-mediated PCR identified a 24.9 kb biosynthetic gene locus likely involved in inhibitory activity in that mutant. Further assessment against human pathogens demonstrated the inhibition of Bacillus cereus, Listeria monocytogenes, and methicillin-resistant Staphylococcus aureus in the presence of this compound, thus supporting our molecular strategy as an effective research pipeline for SWI antibiotic discovery and genetic characterization.

  17. Therapeutic potential of brain-derived neurotrophic factor (BDNF) and a small molecular mimics of BDNF for traumatic brain injury.

    PubMed

    Wurzelmann, Mary; Romeika, Jennifer; Sun, Dong

    2017-01-01

    Traumatic brain injury (TBI) is a major health problem worldwide. Following primary mechanical insults, a cascade of secondary injuries often leads to further neural tissue loss. Thus far there is no cure to rescue the damaged neural tissue. Current therapeutic strategies primarily target the secondary injuries focusing on neuroprotection and neuroregeneration. The neurotrophin brain-derived neurotrophic factor (BDNF) has significant effect in both aspects, promoting neuronal survival, synaptic plasticity and neurogenesis. Recently, the flavonoid 7,8-dihydroxyflavone (7,8-DHF), a small TrkB agonist that mimics BDNF function, has shown similar effects as BDNF in promoting neuronal survival and regeneration following TBI. Compared to BDNF, 7,8-DHF has a longer half-life and much smaller molecular size, capable of penetrating the blood-brain barrier, which makes it possible for non-invasive clinical application. In this review, we summarize functions of the BDNF/TrkB signaling pathway and studies examining the potential of BDNF and 7,8-DHF as a therapy for TBI.

  18. 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.

  19. Pronounced Effects of a Triazine Core on Photovoltaic Performance-Efficient Organic Solar Cells Enabled by a PDI Trimer-Based Small Molecular Acceptor.

    PubMed

    Duan, Yuwei; Xu, Xiaopeng; Yan, He; Wu, Wenlin; Li, Zuojia; Peng, Qiang

    2017-02-01

    A novel-small molecular acceptor with electron-deficient 1,3,5-triazine as the core and perylene diimides as the arms is developed as the acceptor material for efficient bulk heterojunction organic solar cells with an efficiency of 9.15%.

  20. Effect of isovalent doping with phosphorus on the cluster formation in gallium arsenide grown by molecular-beam epitaxy at a relatively low temperature

    SciTech Connect

    Boitsov, A. V. Bert, N. A.; Musikhin, Yu. G.; Chaldyshev, V. V.; Yagovkina, M. A.; Preobrazhenskii, V. V.; Putyato, M. A.; Semyagin, B. R.

    2006-07-15

    Transmitting electron microscopy and X-ray diffractometry are used to study the GaAs layers undoped or doped uniformly with phosphorus (2.3 mol %) and grown at a temperature of 250 deg. C and then annealed isochronously at 400, 500, 600, or 700 deg. C. It is ascertained that doping with phosphorus reduces the amount of excess arsenic captured in the layer in the course of growth and also brings about a retardation of precipitation during subsequent annealing. The concentration of excess arsenic in undoped samples amounted to {approx}0.2 at %; clusters were observed after annealing at a temperature of 500 deg. C. The concentration of excess arsenic amounted to 0.1 at % in the samples containing phosphorus; in this case, the clusters were observed only after a heat treatment at 600 deg. C. The average size of clusters in doped samples is smaller than that in undoped samples at the same heat-treatment temperatures.

  1. Thermoelectrics in an array of molecular junctions.

    PubMed

    Müller, K-H

    2008-07-28

    The room temperature thermoelectric properties of a three-dimensional array of molecular junctions are calculated. The array is composed of n-doped silicon nanoparticles where the surfaces are partially covered with polar molecules and the nanoparticles are bridged by trans-polyacetylene molecules. The role of the polar molecules is to reduce the band bending in the n-doped silicon nanoparticles and to shift the electronic resonances of the bridging molecules to the nanoparticle conduction band edges where the molecular resonances act as electron energy filters. The transmission coefficients of the bridging molecules that appear in the formulas for the Seebeck coefficient, the electrical conductance, and the electronic thermal conductance, are calculated using the nonequilibrium Green's function technique. A simple tight-binding Hamiltonian is used to describe the bridging molecules, and the self-energy term is calculated using the parabolic conduction band approximation. The dependencies of the thermoelectric properties of the molecular junctions on the silicon doping concentration and on the molecule-nanoparticle coupling are discussed. The maximal achievable thermoelectric figure of merit ZT of the array is estimated as a function of the phononic thermal conductance of the bridging molecules and the doping of the nanoparticles. The power factor of the array is also calculated. For sufficiently small phononic thermal conductances of the bridging molecules, very high ZT values are predicted.

  2. 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.

  3. 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.

  4. 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.

  5. Molecular Cloning and Induced Expression of Six Small Heat Shock Proteins Mediating Cold-Hardiness in Harmonia axyridis (Coleoptera: Coccinellidae).

    PubMed

    Wang, Hui-Juan; Shi, Zuo-Kun; Shen, Qi-Da; Xu, Cai-Di; Wang, Bing; Meng, Zhao-Jun; Wang, Shi-Gui; Tang, Bin; Wang, Su

    2017-01-01

    The main function of small heat shock proteins (sHSPs) as molecular chaperones is to protect proteins from denaturation under adverse conditions. Molecular and physiological data were used to examine the sHSPs underlying cold-hardiness in Harmonia axyridis. Complementary DNA sequences were obtained for six H. axyridis sHSPs based on its transcriptome, and the expression of the genes coding for these sHSPs was evaluated by quantitative real-time PCR (qRT-PCR) in several developmental stages, under short-term cooling or heating conditions, and in black and yellow females of experimental and overwintering populations under low-temperature storage. In addition, we measured water content and the super cooling and freezing points (SCP and FP, respectively) of H. axyridis individuals from experimental and overwintering populations. The average water content was not significantly different between adults of both populations, but the SCP and FP of the overwintering population were significantly lower than that of the experimental population. Overall, the six sHSPs genes showed different expression patterns among developmental stages. In the short-term cooling treatment, Hsp16.25 and Hsp21.00 expressions first increased and then decreased, while Hsp10.87 and Hsp21.56 expressions increased during the entire process. Under short-term heating, the expressions of Hsp21.00, Hsp21.62, Hsp10.87, and Hsp16.25 showed an increasing trend, whereas Hsp36.77 first decreased and then increased. Under low-temperature storage conditions, the expression of Hsp36.77 decreased, while the expressions of Hsp21.00 and Hsp21.62 were higher than that of the control group in the experimental population. The expression of Hsp36.77 first increased and then decreased, whereas Hsp21.56 expression was always higher than that of the control group in the overwintering population. Thus, differences in sHSPs gene expression were correlated with the H. axyridis forms, suggesting that the mechanism of cold

  6. Molecular Cloning and Induced Expression of Six Small Heat Shock Proteins Mediating Cold-Hardiness in Harmonia axyridis (Coleoptera: Coccinellidae)

    PubMed Central

    Wang, Hui-Juan; Shi, Zuo-Kun; Shen, Qi-Da; Xu, Cai-Di; Wang, Bing; Meng, Zhao-Jun; Wang, Shi-Gui; Tang, Bin; Wang, Su

    2017-01-01

    The main function of small heat shock proteins (sHSPs) as molecular chaperones is to protect proteins from denaturation under adverse conditions. Molecular and physiological data were used to examine the sHSPs underlying cold-hardiness in Harmonia axyridis. Complementary DNA sequences were obtained for six H. axyridis sHSPs based on its transcriptome, and the expression of the genes coding for these sHSPs was evaluated by quantitative real-time PCR (qRT-PCR) in several developmental stages, under short-term cooling or heating conditions, and in black and yellow females of experimental and overwintering populations under low-temperature storage. In addition, we measured water content and the super cooling and freezing points (SCP and FP, respectively) of H. axyridis individuals from experimental and overwintering populations. The average water content was not significantly different between adults of both populations, but the SCP and FP of the overwintering population were significantly lower than that of the experimental population. Overall, the six sHSPs genes showed different expression patterns among developmental stages. In the short-term cooling treatment, Hsp16.25 and Hsp21.00 expressions first increased and then decreased, while Hsp10.87 and Hsp21.56 expressions increased during the entire process. Under short-term heating, the expressions of Hsp21.00, Hsp21.62, Hsp10.87, and Hsp16.25 showed an increasing trend, whereas Hsp36.77 first decreased and then increased. Under low-temperature storage conditions, the expression of Hsp36.77 decreased, while the expressions of Hsp21.00 and Hsp21.62 were higher than that of the control group in the experimental population. The expression of Hsp36.77 first increased and then decreased, whereas Hsp21.56 expression was always higher than that of the control group in the overwintering population. Thus, differences in sHSPs gene expression were correlated with the H. axyridis forms, suggesting that the mechanism of cold

  7. 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

  8. 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

  9. 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.

  10. Molecular characterization of two small heat shock protein genes in rice: their expression patterns, localizations, networks, and heterogeneous overexpressions.

    PubMed

    Ham, Deok-Jae; Moon, Jun-Chul; Hwang, Sun-Goo; Jang, Cheol Seong

    2013-09-28

    Heat stress is an example of a severe abiotic stress that plants can suffer in the field, causing a significant detrimental effect on their growth and productivity. Understanding the mechanism of plant response to heat stress is important for improving the productivity of crop plants under global warming. We used a microarray dataset that is deposited in the public database to evaluate plant responses to heat stress, and we selected the top 10 genes that are highly expressed under heat stress in rice. Two genes, OsSHSP1 (Os03g16030) and OsSHSP2 (Os01g04380), were selected for further study. These genes were highly induced in response to salt and drought but not in response to cold. In addition, OsSHSP1 and OsSHSP2 gene transcripts were induced under abscisic acid and salicylic acid but not under jasmonic acid and ethylene. Subcellular localization of proteins of 35S::OsSHSP1 were associated with the cytosol, whereas those of and 35S::OsSHSP2 were associated with the cytosol and nucleus. Heterogeneous overexpression of both genes exhibited higher germination rates than those of wild-type plants under the salt treatment, but not under heat or drought stress, supporting a hypothesis regarding functional specialization of members of small heat-shock protein family over evolutionary time. The network of both genes harboring nine sHSPs as well as at least 13 other chaperone genes might support the idea of a role for sHSPs in the chaperone network. Our findings might provide clues to shed light on the molecular functions of OsSHSP1 and OsSHSP2 in response to abiotic stresses, especially heat stress.

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

    PubMed

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

    2014-01-01

    Small conductance Ca(2+)-sensitive potassium (SK2) channels are voltage-independent, Ca(2+)-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 Ca(2+) 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 Ca(2+) and Ca(2+)-bound calmodulin differentially regulate their protein interactions. Our findings suggest that the SK2 isoforms may be distinctly modulated by activity-induced Ca(2+) influx. Alternative splicing of SK2 may serve as a novel mechanism to differentially regulate the maturation and function of olivocochlear and neuronal synapses.

  12. 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

  13. Sensitivity and bias of molecular marker-based aerosol source apportionment models to small conltibutions of coal combustion soot.

    PubMed

    Rutter, Andrew P; Snyder, David C; Schauer, James J; DeMinter, Jeff; Shelton, Brandon

    2009-10-15

    Carbonaceous atmospheric particulate matter (PM25) collected in the midwestern United States revealed that soot emissions from incomplete coal combustion were important sources of several organic molecular markers used in source apportionment studies. Despite not constituting a major source of organic carbon in the PM25, coal soot was an important source of polyaromatic hydrocarbons, hopanes, and elemental carbon. These marker compounds are becoming widely used for source apportionment of atmospheric organic PM, meaning that significant emissions of these marker compounds from unaccounted sources such as coal soot could bias apportionment results. This concept was demonstrated using measurements of atmospheric PM collected on a 1-in-6 day schedule at three monitoring sites in Ohio: Mingo Junction (near Steubenville), Cincinnati, and Cleveland. Impacts of coal sootwere measured to be significant at Mingo Junction and small at Cleveland and Cincinnati. As a result, biases in apportionment results were substantial at Mingo Junction and insignificant at Cleveland and Cincinnati. Misapportionments of organic carbon mass at Mingo Junction were significant when coal soot was detected in the particulate samples as identified bythe presence of picene, but when coal soot was not included in the model: gasoline engines (+8% to +58% of OC), smoking engines (0% to -17% of OC), biomass combustion (+1% to +11% of OC), diesel engines (-1% to -2% of OC), natural gas combustion (0% to -2% of OC), and unapportioned OC (0% to -47% of OC). These results suggest that the role of coal soot in source apportionment studies needs to be better examined in many parts of the United States and other parts of the world.

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

    PubMed

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

    2015-05-07

    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.

  15. Small angle X-ray scattering of wheat seed-storage proteins: alpha-, gamma- and omega-gliadins and the high molecular weight (HMW) subunits of glutenin.

    PubMed

    Thomson, N H; Miles, M J; Popineau, Y; Harries, J; Shewry, P; Tatham, A S

    1999-03-19

    Small angle X-ray scattering in solution was performed on seed-storage proteins from wheat. Three different groups of gliadins (alpha-, gamma- and omega-) and a high molecular weight (HMW) subunit of glutenin (1Bx20) were studied to determine molecular size parameters. All the gliadins could be modelled as prolate ellipsoids with extended conformations. The HMW subunit existed as a highly extended rod-like particle in solution with a length of about 69 nm and a diameter of about 6.4 nm. Specific aggregation effects were observed which may reflect mechanisms of self-assembly that contribute to the unique viscoelastic properties of wheat dough.

  16. 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

  17. Direct label-free measurement of the distribution of small molecular weight compound inside thick biological tissue using coherent Raman microspectroscopy.

    PubMed

    Kawagishi, Masahiko; Obara, Yuki; Suzuki, Takayuki; Hayashi, Masumi; Misawa, Kazuhiko; Terada, Sumio

    2015-09-10

    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.

  18. 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

  19. The Influence of Fluorination on Nano-Scale Phase Separation and Photovoltaic Performance of Small Molecular/PC71BM Blends

    PubMed Central

    Lu, Zhen; Liu, Wen; Li, Jingjing; Fang, Tao; Li, Wanning; Zhang, Jicheng; Feng, Feng; Li, Wenhua

    2016-01-01

    To investigate the fluorination influence on the photovoltaic performance of small molecular based organic solar cells (OSCs), six small molecules based on 2,1,3-benzothiadiazole (BT), and diketopyrrolopyrrole (DPP) as core and fluorinated phenyl (DFP) and triphenyl amine (TPA) as different terminal units (DFP-BT-DFP, DFP-BT-TPA, TPA-BT-TPA, DFP-DPP-DFP, DFP-DPP-TPA, and TPA-DPP-TPA) were synthesized. With one or two fluorinated phenyl as the end group(s), HOMO level of BT and DPP based small molecular donors were gradually decreased, inducing high open circuit voltage for fluorinated phenyl based OSCs. DFP-BT-TPA and DFP-DPP-TPA based blend films both displayed stronger nano-scale aggregation in comparison to TPA-BT-TPA and TPA-DPP-TPA, respectively, which would also lead to higher hole motilities in devices. Ultimately, improved power conversion efficiency (PCE) of 2.17% and 1.22% was acquired for DFP-BT-TPA and DFP-DPP-TPA based devices, respectively. These results demonstrated that the nano-scale aggregation size of small molecules in photovoltaic devices could be significantly enhanced by introducing a fluorine atom at the donor unit of small molecules, which will provide understanding about the relationship of chemical structure and nano-scale phase separation in OSCs.

  20. Role of the pulmonologist in ordering post-procedure molecular markers in non-small-cell lung cancer: implications for personalized medicine.

    PubMed

    Murgu, Septimiu; Colt, Henri

    2013-11-01

    In the growing era of personalized medicine for the treatment of non-small-cell lung cancer (NSCLC), it is becoming increasingly important that sufficient quality and quantity of tumor tissue are available for morphologic diagnosis and molecular analysis. As new treatment options emerge that might require more frequent and possibly higher volume biopsies, the role of the pulmonologist will expand, and it will be important for pulmonologists to work within a multidisciplinary team to provide optimal therapeutic management for patients with NSCLC. In this review, we discuss the rationale for individualized treatment decisions for patients with NSCLC, molecular pathways and specific molecular predictors relevant to personalized NSCLC therapy, assay technologies for molecular marker analysis, and specifics regarding tumor specimen selection, acquisition, and handling. Moreover, we briefly address issues regarding racial and socioeconomic disparities as they relate to molecular testing and treatment decisions, and cost considerations for molecular testing and targeted therapies in NSCLC. We also propose a model for an institution-based multidisciplinary team, including oncologists, pathologists, pulmonologists, interventional radiologists, and thoracic surgeons, to ensure adequate material is available for cytological and histological studies and to standardize methods of tumor specimen handling and processing in an effort to provide beneficial, individualized therapy for patients with NSCLC.

  1. 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.

  2. Probing the emitter site of Renilla luciferase using small organic molecules; an attempt to understand the molecular architecture of the emitter site.

    PubMed

    Salehi, Farajollah; Emamzadeh, Rahman; Nazari, Mahboobeh; Rasa, Seyed Mohammad Mahdi

    2016-12-01

    Renilla luciferase is a sensitive enzyme and has wide applications in biotechnology such as drug screening. Previous studies have tried to show the catalytic residues, nevertheless, the accurate architecture and molecular behavior of its emitter site remains uncharacterized. In this study, the activity of Renilla luciferase, in the presence of two small organic molecules including dimethyl sulfoxide (DMSO) and isopropanol was considered and the structure was studied by circular dichroism (CD) and fluorescence spectroscopy. Moreover, the interaction of small organic molecules with the Renilla luciferase was studied using molecular dynamics simulations. Kinetics studies showed that at low concentration of DMSO (16.6-66mM) and isopropanol (19.3-76mM) the Km changed and a competitive inhibition pattern was observed. Moreover, spectroscopy studies reveled that the changes of activity of Renilla luciferase in the presence of low concentrations of small organic molecules was not associated with structural collapse or severe changes in the enzyme conformation. Molecular dynamics simulations indicated that DMSO and isopropanol, as probing molecules, were both able to bind to the emitter site and remained with the residues of the emitter site. Based on the probing data, the architecture of the emitter site in the "non-binding" model was proposed.

  3. Highly doped silicon nanowires by monolayer doping.

    PubMed

    Veerbeek, Janneke; Ye, Liang; Vijselaar, Wouter; Kudernac, Tibor; van der Wiel, Wilfred G; Huskens, Jurriaan

    2017-02-23

    Controlling the doping concentration of silicon nanostructures is challenging. Here, we investigated three different monolayer doping techniques to obtain silicon nanowires with a high doping dose. These routes were based on conventional monolayer doping, starting from covalently bound dopant-containing molecules, or on monolayer contact doping, in which a source substrate coated with a monolayer of a carborane silane was the dopant source. As a third route, both techniques were combined to retain the benefits of conformal monolayer formation and the use of an external capping layer. These routes were used for doping fragile porous nanowires fabricated by metal-assisted chemical etching. Differences in porosity were used to tune the total doping dose inside the nanowires, as measured by X-ray photoelectron spectroscopy and secondary ion mass spectrometry measurements. The higher the porosity, the higher was the surface available for dopant-containing molecules, which in turn led to a higher doping dose. Slightly porous nanowires could be doped via all three routes, which resulted in highly doped nanowires with (projected areal) doping doses of 10(14)-10(15) boron atoms per cm(2) compared to 10(12) atoms per cm(2) for a non-porous planar sample. Highly porous nanowires were not compatible with the conventional monolayer doping technique, but monolayer contact doping and the combined route resulted for these highly porous nanowires in tremendously high doping doses up to 10(17) boron atoms per cm(2).

  4. Measuring the molecular dimensions of wine tannins: comparison of small-angle X-ray scattering, gel-permeation chromatography and mean degree of polymerization.

    PubMed

    McRae, Jacqui M; Kirby, Nigel; Mertens, Haydyn D T; Kassara, Stella; Smith, Paul A

    2014-07-23

    The molecular size of wine tannins can influence astringency, and yet it has been unclear as to whether the standard methods for determining average tannin molecular weight (MW), including gel-permeation chromatography (GPC) and depolymerization reactions, are actually related to the size of the tannin in wine-like conditions. Small-angle X-ray scattering (SAXS) was therefore used to determine the molecular sizes and corresponding MWs of wine tannin samples from 3 and 7 year old Cabernet Sauvignon wine in a variety of wine-like matrixes: 5-15% and 100% ethanol; 0-200 mM NaCl and pH 3.0-4.0, and compared to those measured using the standard methods. The SAXS results indicated that the tannin samples from the older wine were larger than those of the younger wine and that wine composition did not greatly impact on tannin molecular size. The average tannin MWs as determined by GPC correlated strongly with the SAXS results, suggesting that this method does give a good indication of tannin molecular size in wine-like conditions. The MW as determined from the depolymerization reactions did not correlate as strongly with the SAXS results. To our knowledge, SAXS measurements have not previously been attempted for wine tannins.

  5. 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.

  6. Heteroatom-Containing Porous Carbons Derived from Ionic Liquid-Doped Alkali Organic Salts for Supercapacitors.

    PubMed

    Zhu, Jingyue; Xu, Dan; Qian, Wenjing; Zhang, Jinyu; Yan, Feng

    2016-04-13

    A simple strategy for the synthesis of heteroatom-doped porous carbon materials (CMs) via using ionic liquid (IL)-doped alkali organic salts as small molecular precursors is developed. Doping of alkali organic salts (such as sodium glutamate, sodium tartrate, and sodium citrate) with heteroatoms containing ILs (including 1-butyl-3-methylimidazolium chlorine and 3-butyl-4-methythiazolebromination) not only incorporates the heteroatoms into the carbon frameworks but also highly improves the carbonization yield, as compared with that of either alkali organic salts or ILs as precursors. The porous structure of CMs can be tuned by adjusting the feed ratio of ILs. The porous CMs derived from 1-butyl-3-methylimidazolium chlorine-doped sodium glutamate exhibit high charge storage capacity with a specific capacitance of 287 F g(-1) and good stability over 5000 cycles in 6 m KOH at a current density of 1 A g(-1) for supercapacitors. This strategy opens a simple and efficient method for the synthesis of heteroatom-doped porous CMs.

  7. 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.

  8. Molecular alterations in non-small-cell lung cancer: perspective for targeted therapy and specimen management for the bronchoscopist.

    PubMed

    Czarnecka-Kujawa, Kasia; Yasufuku, Kazuhiro

    2014-11-01

    Major advances have occurred over the past decade in our understanding of lung cancer pathobiology. Increasing knowledge of molecular aberrations in lung cancer, specifically the discovery of two driver genes in pharmacologically targetable tyrosine kinases involved in growth factor receptor signalling, epidermal growth factor receptor and anaplastic lymphoma kinase, has been of major therapeutic and prognostic importance. This discovery has allowed for new, personalized approach to the management of lung cancer. Recognizing the importance of molecular signatures of lung cancer, the College of American Pathologists, International Association for the Study of Lung Cancer and Association for Molecular Pathology released the first guidelines for molecular testing in lung cancer. The introduction of minimally invasive needle techniques for the evaluation of lung cancer patients, such as endobronchial ultrasound transbronchial needle aspiration and oesophageal ultrasound-fine-needle aspiration, has revolutionized the way lung cancer patients are assessed. Samples obtained using the minimally invasive needle approaches have been shown to be sufficient not only for routine molecular testing but also for multigenic analysis. This allows bronchoscopist to assume an increasingly important role in the diagnostic workup of patients with lung cancer at all stages of the disease and contribute to personalizing the care of lung cancer patients.

  9. Gene doping.

    PubMed

    Azzazy, Hassan M E

    2010-01-01

    Gene doping abuses the legitimate approach of gene therapy. While gene therapy aims to correct genetic disorders by introducing a foreign gene to replace an existing faulty one or by manipulating existing gene(s) to achieve a therapeutic benefit, gene doping employs the same concepts to bestow performance advantages on athletes over their competitors. Recent developments in genetic engineering have contributed significantly to the progress of gene therapy research and currently numerous clinical trials are underway. Some athletes and their staff are probably watching this progress closely. Any gene that plays a role in muscle development, oxygen delivery to tissues, neuromuscular coordination, or even pain control is considered a candidate for gene dopers. Unfortunately, detecting gene doping is technically very difficult because the transgenic proteins expressed by the introduced genes are similar to their endogenous counterparts. Researchers today are racing the clock because assuring the continued integrity of sports competition depends on their ability to develop effective detection strategies in preparation for the 2012 Olympics, which may mark the appearance of genetically modified athletes.

  10. 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.

  11. Continuously adjustable, molecular-sieving “gate” on 5A zeolite for distinguishing small organic molecules by size

    SciTech Connect

    Song, Zhuonan; Huang, Yi; Xu, Weiwei L.; Wang, Lei; Bao, Yu; Li, Shiguang; Yu, Miao

    2015-09-11

    Zeolites/molecular sieves with uniform, molecular-sized pores are important for many adsorption-based separation processes. Pore size gaps, however, exist in the current zeolite family. This leads to a great challenge of separating molecules with size differences at ~0.01 nm level. Here, we report a novel concept, pore misalignment, to form a continuously adjustable, molecular-sieving “gate” at the 5A zeolite pore entrance without sacrificing the internal capacity. Misalignment of the micropores of the alumina coating with the 5A zeolite pores was related with and facilely adjusted by the coating thickness. For the first time, organic molecules with sub-0.01 nm size differences were effectively distinguished via appropriate misalignment. Lastly, this novel concept may have great potential to fill the pore size gaps of the zeolite family and realize size-selective adsorption separation.

  12. 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

  13. Continuously adjustable, molecular-sieving “gate” on 5A zeolite for distinguishing small organic molecules by size

    DOE PAGES

    Song, Zhuonan; Huang, Yi; Xu, Weiwei L.; ...

    2015-09-11

    Zeolites/molecular sieves with uniform, molecular-sized pores are important for many adsorption-based separation processes. Pore size gaps, however, exist in the current zeolite family. This leads to a great challenge of separating molecules with size differences at ~0.01 nm level. Here, we report a novel concept, pore misalignment, to form a continuously adjustable, molecular-sieving “gate” at the 5A zeolite pore entrance without sacrificing the internal capacity. Misalignment of the micropores of the alumina coating with the 5A zeolite pores was related with and facilely adjusted by the coating thickness. For the first time, organic molecules with sub-0.01 nm size differences weremore » effectively distinguished via appropriate misalignment. Lastly, this novel concept may have great potential to fill the pore size gaps of the zeolite family and realize size-selective adsorption separation.« less

  14. Global and local reactivity indexes applied to understand the chemistry of graphene oxide and doped graphene.

    PubMed

    Cortés Arriagada, Diego

    2013-02-01

    At the density functional theory level, the electronic reactivity of oxidized and doped (with N, B, and P) graphene (G) has been analyzed. Molecular hardness and electrophilicity were used as global reactivity descriptors, while those at the local level, Fukui functions, Mulliken charges and molecular electrostatic potential were used in the order to characterize the intramolecular and intermolecular reactivity. These descriptors show that in GO, the global and local reactivity of the basal plane is improved mainly by hydroxyl groups, which improve besides the physisorption of small molecules, while, the active carbon atoms around the functional group would allow enhancement of the consecutively chemisorption. Furthermore, epoxide, carbonyl and carboxyl groups allow mainly enhancement of intermolecular non-covalent interactions. On the other hand, doping with N and B atoms increases the electrophilic character and the reactivity in the bulk. Specifically, in N-doped G, N and around carbon atoms would be able to serve as active sites of detection by frontier-controlled processes, explaining the improvement in electrochemical sensing; in addition, electron-deficient carbon atoms around N enhance the physisorption. Respecting the B-doped G, dopant and carbon atoms adjacent to B act as donor sites, suggesting that adsorption of cations on B-doped G is a frontier-controlled process; moreover, positively-charged B atoms enhance charge-controlled interactions with polarized molecules, and consecutively, in a frontier-controlled step, chemisorption is possible. Finally, P-doping increases the electrophilic reactivity in the bulk; also, P atoms enhance the physisorption of chemical species with negatively-charged centers or lone-pair electrons, and consecutively, chemisorption on P is possible.

  15. Quasiequilibrium unfolding thermodynamics of a small protein studied by molecular dynamics simulation with an explicit water model.

    PubMed

    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.

  16. Inner salt-shaped small molecular photosensitizer with extremely enhanced two-photon absorption for mitochondrial-targeted photodynamic therapy.

    PubMed

    Hu, Wenbo; He, Tingchao; Jiang, Rongcui; Yin, Jun; Li, Lin; Lu, Xiaomei; Zhao, Hui; Zhang, Lei; Huang, Ling; Sun, Handong; Huang, Wei; Fan, Quli

    2017-02-04

    Herein, we experimentally and theoretically demonstrate an unprecedentedly enhanced two-photon absorption in a small organic molecule by a simple introduction of an inner salt-shaped structure. Moreover, such an inner salt-shaped small molecule also exhibits superior singlet oxygen quantum yield and fascinating structure-inherent mitochondrial-targeting ability for highly efficient two-photon photodynamic therapy via a mitochondrial apoptosis pathway.

  17. 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,...

  18. 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

  19. Efficient organic photovoltaic diodes based on doped pentacene.

    PubMed

    Schon, J H; Kloc, C; Bucher, E; Batlogg, B

    2000-01-27

    Recent work on solar cells based on interpenetrating polymer networks and solid-state dye-sensitized devices shows that efficient solar-energy conversion is possible using organic materials. Further, it has been demonstrated that the performance of photovoltaic devices based on small molecules can be effectively enhanced by doping the organic material with electron-accepting molecules. But as inorganic solar cells show much higher efficiencies, well above 15 per cent, the practical utility of organic-based cells will require their fabrication by lower-cost techniques, ideally on flexible substrates. Here we demonstrate efficiency enhancement by molecular doping in Schottky-type photovoltaic diodes based on pentacene--an organic semiconductor that has received much attention as a promising material for organic thin-film transistors, but relatively little attention for use in photovoltaic devices. The incorporation of the dopant improves the internal quantum efficiency by more than five orders of magnitude and yields an external energy conversion efficiency as high as 2.4 per cent for a standard solar spectrum. Thin-film devices based on doped pentacene therefore appear promising for the production of efficient 'plastic' solar cells.

  20. Molecular mechanisms for the regulation of insulin-stimulated glucose uptake by small guanosine triphosphatases in skeletal muscle and adipocytes.

    PubMed

    Satoh, Takaya

    2014-10-16

    Insulin is a hormone that regulates the blood glucose level by stimulating various physiological responses in its target tissues. In skeletal muscle and adipose tissue, insulin promotes membrane trafficking of the glucose transporter GLUT4 from GLUT4 storage vesicles to the plasma membrane, thereby facilitating the uptake of glucose from the circulation. Detailed mechanisms underlying insulin-dependent intracellular signal transduction for glucose uptake remain largely unknown. In this article, I give an overview on the recently identified signaling network involving Rab, Ras, and Rho family small guanosine triphosphatases (GTPases) that regulates glucose uptake in insulin-responsive tissues. In particular, the regulatory mechanisms for these small GTPases and the cross-talk between protein kinase and small GTPase cascades are highlighted.

  1. Molecular modeling of the inhibition of protein-protein interactions with small molecules: The IL2-IL2Rα case

    NASA Astrophysics Data System (ADS)

    Pieraccini, Stefano; De Gonda, Riccardo; Sironi, Maurizio

    2011-12-01

    Developing drug like molecules targeting protein-protein interactions is one of the main goals of current medicinal chemistry. To drive the design process it is fundamental to locate those sites on the protein-protein contact surface that are more critical for protein binding, which are the most eligible targets to affect the protein complex formation. In this work we show how computational alanine scanning can be used to identify such critical sites and evaluate their interactions with small molecules designed to inhibit the complex formation. Complex of protein IL2 with IL2Rα and with some small molecule inhibitors are used as an example.

  2. A bio-inspired two-layer sensing structure of polypeptide and multiple-walled carbon nanotube to sense small molecular gases.

    PubMed

    Wang, Li-Chun; Su, Tseng-Hsiung; Ho, Cheng-Long; Yang, Shang-Ren; Chiu, Shih-Wen; Kuo, Han-Wen; Tang, Kea-Tiong

    2015-03-05

    In this paper, we propose a bio-inspired, two-layer, multiple-walled carbon nanotube (MWCNT)-polypeptide composite sensing device. The MWCNT serves as a responsive and conductive layer, and the nonselective polypeptide (40 mer) coating the top of the MWCNT acts as a filter into which small molecular gases pass. Instead of using selective peptides to sense specific odorants, we propose using nonselective, peptide-based sensors to monitor various types of volatile organic compounds. In this study, depending on gas interaction and molecular sizes, the randomly selected polypeptide enabled the recognition of certain polar volatile chemical vapors, such as amines, and the improved discernment of low-concentration gases. The results of our investigation demonstrated that the polypeptide-coated sensors can detect ammonia at a level of several hundred ppm and barely responded to triethylamine.

  3. Spectral-luminescent properties of silver molecular clusters and nanoparticles formed by ion exchange in antimony-doped photo-thermo-refractive glasses

    NASA Astrophysics Data System (ADS)

    Sgibnev, E. M.; Nikonorov, N. V.; Ignat'ev, A. I.

    2017-01-01

    The formation of silver molecular clusters and nanoparticles in photo-thermo-refractive (PTR) glasses with different antimony contents has been investigated using ion exchange with subsequent thermal treatment. The influence of the antimony oxide (Sb2O3) concentration and treatment temperature on the spectral-luminescent properties of silver molecular clusters and nanoparticles in glass has been investigated. It is shown that silver molecular clusters in PTR glasses are characterized by strong broadband luminescence in the visible and near-IR ranges and that the formation of silver nanoparticles leads to luminescence quenching.

  4. A Delicate Balance When Substituting a Small Hydrophobe onto Low Molecular Weight Polyethylenimine to Improve Its Nucleic Acid Delivery Efficiency.

    PubMed

    Meneksedag-Erol, Deniz; KC, Remant Bahadur; Tang, Tian; Uludağ, Hasan

    2015-11-11

    High molecular weight (HMW) polyethylenimine (PEI) is one of the most versatile nonviral gene vectors that was extensively investigated over the past two decades. The cytotoxic profile of HMW PEI, however, encouraged a search for safer alternatives. Because of lack of cytotoxicity of low molecular weight (LMW) PEI, enhancing its performance via hydrophobic modifications has been pursued to this end. Since the performance of modified PEIs depends on the nature and extent of substituents, we systematically investigated the effect of hydrophobic modification of LMW (1.2 kDa) PEI with a short propionic acid (PrA). Moderate enhancements in PEI hydrophobicity resulted in enhanced cellular uptake of polyplexes and siRNA-induced silencing efficacy, whereas further increase in PrA substitution abolished the uptake as well as the silencing. We performed all-atom molecular dynamics simulations to elucidate the mechanistic details behind these observations. A new assembly mechanism was observed by the presence of hydrophobic PrA moieties, where PrA migrated to core of the polyplex. This phenomenon caused higher surface hydrophobicity and surface charge density at low substitutions, and it caused deleterious effects on surface hydrophobicity and cationic charge at higher substitutions. It is evident that an optimal balance of hydrophobicity/hydrophilicity is needed to achieve the desired polyplex properties for an efficient siRNA delivery, and our mechanistic findings should provide valuable insights for the design of improved substituents on nonviral carriers.

  5. Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations

    DOE PAGES

    Pan, Jianjun; Cheng, Xiaolin; Sharp, Melissa; ...

    2014-10-29

    We report that the detailed structural and mechanical properties of a tetraoleoyl cardiolipin (TOCL) bilayer were determined using neutron spin echo (NSE) spectroscopy, small angle neutron and X-ray scattering (SANS and SAXS, respectively), and molecular dynamics (MD) simulations. We used MD simulations to develop a scattering density profile (SDP) model, which was then utilized to jointly refine SANS and SAXS data. In addition to commonly reported lipid bilayer structural parameters, component distributions were obtained, including the volume probability, electron density and neutron scattering length density.

  6. Molecular weight-gyration radius relation of globular proteins: a comparison of light scattering, small-angle X-ray scattering and structure-based data.

    PubMed

    Smilgies, Detlef-M; Folta-Stogniew, Ewa

    2015-10-01

    The molecular weight-gyration radius relation for a number of globular proteins based on experimental light scattering data is compared with small-angle X-ray scattering data recently published by Mylonas & Svergun [J. Appl. Cryst. (2007 ▸), 40, s245-s249]. In addition, other recent experimental data and theoretical calculations are reviewed. It is found that the MW-Rg relation for the globular proteins is well represented by a power law with an exponent of 0.37 (2).

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

    NASA Astrophysics Data System (ADS)

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

    2010-04-01

    The parameters of fullerene C60 dissolved in carbon disulfide CS2 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 C60 (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 C60 in CS2 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 C60 dimers (comprising 10% of the total particle number density) in the solution.

  8. 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

  9. Small Atomic Orbital Basis Set First-Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources.

    PubMed

    Sure, Rebecca; Brandenburg, Jan Gerit; Grimme, Stefan

    2016-04-01

    In quantum chemical computations the combination of Hartree-Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double-zeta quality is still widely used, for example, in the popular B3LYP/6-31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean-field methods.

  10. Chlorine Incorporation in the CH3NH3PbI3 Perovskite: Small Concentration, Big Effect.

    PubMed

    Quarti, Claudio; Mosconi, Edoardo; Umari, Paolo; De Angelis, Filippo

    2017-01-03

    The role of chlorine doping in CH3NH3PbI3 represents an important open issue in the use of hybrid perovskites for photovoltaic applications. In particular, even if a positive role of chlorine doping on perovskite film formation and on material morphology has been demonstrated, an inherent positive effect on the electronic and photovoltaic properties cannot be excluded. Here we carried out periodic density functional theory and Car-Parrinello molecular dynamics simulations, going down to ∼1% doping, to investigate the effect of chlorine on CH3NH3PbI3. We found that such a small doping has important effects on the dynamics of the crystalline structure, both with respect to the inorganic framework and with respect to the cation libration motion. Together, we observe a dynamic spatial localization of the valence and conduction states in separated spatial material regions, which takes place in the 10(-1) ps time scale and which could be the key to ease of exciton dissociation and, likely, to small charge recombination in hybrid perovskites. Moreover, such localization is enhanced by chlorine doping, demonstrating an inherent positive role of chlorine doping on the electronic properties of this class of materials.

  11. Ferromagnetism in doped or undoped spintronics nanomaterials

    NASA Astrophysics Data System (ADS)

    Qiang, You

    2010-10-01

    Much interest has been sparked by the discovery of ferromagnetism in a range of oxide doped and undoped semiconductors. The development of ferromagnetic oxide semiconductor materials with giant magnetoresistance (GMR) offers many advantages in spintronics devices for future miniaturization of computers. Among them, TM-doped ZnO is an extensively studied n-type wide-band-gap (3.36 eV) semiconductor with a tremendous interest as future mini-computer, blue light emitting, and solar cells. In this talk, Co-doped ZnO and Co-doped Cu2O semiconductor nanoclusters are successfully synthesized by a third generation sputtering-gas-aggregation cluster technique. The Co-doped nanoclusters are ferromagnetic with Curie temperature above room temperature. Both of Co-doped nanoclusters show positive magnetoresistance (PMR) at low temperature, but the amplitude of the PMRs shows an anomalous difference. For similar Co doping concentration at 5 K, PMR is greater than 800% for Co-doped ZnO but only 5% for Co-doped Cu2O nanoclusters. Giant PMR in Co-doped ZnO which is attributed to large Zeeman splitting effect has a linear dependence on applied magnetic field with very high sensitivity, which makes it convenient for the future spintronics applications. The small PMR in Co-doped Cu2O is related to its vanishing density of states at Fermi level. Undoped Zn/ZnO core-shell nanoparticle gives high ferromagnetic properties above room temperature due to the defect induced magnetization at the interface.

  12. Growth kinetics and electronic properties of unintentionally doped semi-insulating GaN on SiC and high-resistivity GaN on sapphire grown by ammonia molecular-beam epitaxy

    NASA Astrophysics Data System (ADS)

    Tang, H.; Fang, Z. Q.; Rolfe, S.; Bardwell, J. A.; Raymond, S.

    2010-05-01

    Growth of unintentionally doped (UID) semi-insulating GaN on SiC and highly resistive GaN on sapphire using the ammonia molecular-beam epitaxy technique is reported. The semi-insulating UID GaN on SiC shows room temperature (RT) resistivity of 1011 Ω cm and well defined activation energy of 1.0 eV. The balance of compensation of unintentional donors and acceptors is such that the Fermi level is lowered to midgap, and controlled by a 1.0 eV deep level defect, which is thought to be related to the nitrogen antisite NGa, similar to the "EL2" center (arsenic antisite) in unintentionally doped semi-insulating GaAs. The highly resistive GaN on sapphire shows RT resistivity in range of 106-109 Ω cm and activation energy varying from 0.25 to 0.9 eV. In this case, the compensation of shallow donors is incomplete, and the Fermi level is controlled by levels shallower than the 1.0 eV deep centers. The growth mechanisms for the resistive UID GaN materials were investigated by experimental studies of the surface kinetics during growth. The required growth regime involves a moderate growth temperature range of 740-780 °C, and a high ammonia flux (beam equivalent pressure of 1×10-4 Torr), which ensures supersaturated coverage of surface adsorption sites with NHx radicals. Such highly nitrogen rich growth conditions lead to two-dimensional layer by layer growth and reduced oxygen incorporation.

  13. Growth kinetics and electronic properties of unintentionally doped semi-insulating GaN on SiC and high-resistivity GaN on sapphire grown by ammonia molecular-beam epitaxy

    SciTech Connect

    Tang, H.; Rolfe, S.; Bardwell, J. A.; Raymond, S.; Fang, Z. Q.

    2010-05-15

    Growth of unintentionally doped (UID) semi-insulating GaN on SiC and highly resistive GaN on sapphire using the ammonia molecular-beam epitaxy technique is reported. The semi-insulating UID GaN on SiC shows room temperature (RT) resistivity of 10{sup 11} {Omega} cm and well defined activation energy of 1.0 eV. The balance of compensation of unintentional donors and acceptors is such that the Fermi level is lowered to midgap, and controlled by a 1.0 eV deep level defect, which is thought to be related to the nitrogen antisite N{sub Ga}, similar to the ''EL2'' center (arsenic antisite) in unintentionally doped semi-insulating GaAs. The highly resistive GaN on sapphire shows RT resistivity in range of 10{sup 6}-10{sup 9} {Omega} cm and activation energy varying from 0.25 to 0.9 eV. In this case, the compensation of shallow donors is incomplete, and the Fermi level is controlled by levels shallower than the 1.0 eV deep centers. The growth mechanisms for the resistive UID GaN materials were investigated by experimental studies of the surface kinetics during growth. The required growth regime involves a moderate growth temperature range of 740-780 deg. C, and a high ammonia flux (beam equivalent pressure of 1x10{sup -4} Torr), which ensures supersaturated coverage of surface adsorption sites with NH{sub x} radicals. Such highly nitrogen rich growth conditions lead to two-dimensional layer by layer growth and reduced oxygen incorporation.

  14. Effect of free-carrier concentration and optical injection on carrier lifetimes in undoped and iodine doped CdMgTe/CdSeTe double heterostructures grown by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Sohal, S.; Edirisooriya, M.; Ogedengbe, O. S.; Petersen, J. E.; Swartz, C. H.; LeBlanc, E. G.; Myers, T. H.; Li, J. V.; Holtz, M.

    2016-12-01

    Time-resolved and time integrated photoluminescence (PL) studies are reported for undoped and doped CdMgTe/CdSeTe double heterostructures (DHs) grown by molecular beam epitaxy. Undoped DHs are studied with absorber layer thickness varying from 0.5 to 2.5 µm. The n-type free-carrier concentration is varied ~7  ×  1015, 8.4  ×  1016, and 8.4  ×  1017 cm-3 using iodine as a dopant in different absorber layer thicknesses (0.25-2.0 µm). Optical injection is varied from 1  ×  1010 to 3  ×  1011 photons/pulse/cm2, corresponding to the initial injection of photo-carriers up to ~8  ×  1015 cm-3, to examine the effects of excess carrier concentration on the PL lifetimes. Undoped DHs exhibit an initial rapid decay followed by a slower dependence with carrier lifetimes up to ~485 ns. The dependence of carrier lifetimes on the thickness of the absorber layers (0.5-2.5 µm) suggests interface recombination velocities ({{v}\\operatorname{int}}~ ) ~ 1288 and 238 cm s-1 in the initial and later decay times, respectively, corresponding to high and low photo-carrier concentrations. The Shockley-Read-Hall model is used to describe the results in which variations are observed in {{v}\\operatorname{int}}~ for undoped DHs. The lifetimes of doped DHs show a consistent trend with thickness. The {{v}\\operatorname{int}}~ ~ 80-200 cm s-1 is estimated for doping n ~ 7  ×  1015 cm-3 and 240-410 cm s-1 for n ~ 8.4  ×  1016 cm-3. The observed decrease in carrier lifetimes with increasing n is consistent with growing importance of the radiative recombination rate due to the excess carrier concentration. The effect of carrier concentration on the PL spectrum is also discussed.

  15. Metal-doped organic foam

    DOEpatents

    Rinde, James A.

    1982-01-01

    Organic foams having a low density and very small cell size and method for producing same in either a metal-loaded or unloaded (nonmetal loaded) form are described. Metal-doped foams are produced by soaking a polymer gel in an aqueous solution of desired metal salt, soaking the gel successively in a solvent series of decreasing polarity to remove water from the gel and replace it with a solvent of lower polarity with each successive solvent in the series being miscible with the solvents on each side and being saturated with the desired metal salt, and removing the last of the solvents from the gel to produce the desired metal-doped foam having desired density cell size, and metal loading. The unloaded or metal-doped foams can be utilized in a variety of applications requiring low density, small cell size foam. For example, rubidium-doped foam made in accordance with the invention has utility in special applications, such as in x-ray lasers.

  16. Carbon dioxide and methane transport in DDR zeolite: insights from molecular simulations into carbon dioxide separations in small pore zeolites

    NASA Astrophysics Data System (ADS)

    Jee, Sang Eun; Sholl, David

    2009-03-01

    Zeolites are good candidates as a membranes for chemical separations because of their excellent chemical and thermal stability. Cage type zeolites are promising materials for gas separation since their narrow windows are expected to control molecular transport. DDR is one of the strongest candidates for light gas separations because of its narrow 8MR window. In our study, we examined the separation selectivity of DDR for CO2/CH4 separation using atomistic simulation methods. We introduced new force fields which can reproduce experimental single component adsorption and diffusion data for this material for the first time. Previously interatomic potentials that have been applied to DDR overestimate experimental diffusivities at least one order of magnitude. We characterized single-component and binary adsorption using Grand Canonical Monte Carlo, and single-component. diffusion using a combination of Molecular Dynamics and Transition State Theory. The most important observation from our calculation is that CO2/CH4 diffusion in DDR is very different from the usual situation in nanoporous materials, where the presence of a slowly diffusing species retards transport rates of a more rapidly diffusing species. In DDR, we show that CO2 diffusion rates are only weakly affected by the presence of CH4, despite the very slow diffusion of the latter species. The physical origins of this unusual behavior are explained by analyzing the adsorption sites and diffusion mechanism for each species.

  17. Carbon dioxide and methane transport in DDR zeolite: insights from molecular simulations into carbon dioxide separations in small pore zeolites.

    PubMed

    Jee, Sang Eun; Sholl, David S

    2009-06-10

    The silica zeolite DDR is a strong candidate for separations of CO(2)/CH(4) because of the narrow windows that control molecular transport inside the material's pores. We have used molecular simulations to describe diffusion of CO(2) and CH(4) inside DDR pores. Our simulations introduce a new force-field for this system that for the first time gives results that are consistent with experimental measurements of single-component adsorption and diffusion. Diffusivities obtained from previous simulations greatly overestimated the transport rates of CH(4) and, to a lesser extent, CO(2). Because CH(4) diffuses extremely slowly in DDR, we applied a transition state theory-based kinetic Monte Carlo scheme to accurately describe this diffusion. The most important observation from our calculations is that the characteristics of CO(2)/CH(4) diffusion in DDR are very different from the usual situation in nanoporous materials, where the presence of a slowly diffusing species retards transport rates of a more rapidly diffusing species. In DDR, we show that CO(2) diffusion rates are only weakly affected by the presence of CH(4), despite the very slow diffusion of the latter molecules. The physical origins of this unusual behavior are explained by analyzing the adsorption sites and diffusion mechanism for each species. Our finding suggests DDR membranes are favorable for CO(2)/CH(4) separations and that similar properties may exist for other 8MR zeolites.

  18. Doping of graphene induced by boron/silicon substrate.

    PubMed

    Dianat, Arezoo; Liao, Zhongquan; Gall, Martin; Zhang, Tao; Gutierrez, Rafael; Zschech, Ehrenfried; Cuniberti, Gianaurelio

    2017-04-12

    In this work, we show the doping of graphene most likely from heteroatoms induced by the substrate using Raman spectrum, X-ray photoelectron spectroscopy (XPS), energy dispersive X-ray spectroscopy (EDX) and ab initio molecular dynamics simulations. The doping of graphene on a highly boron-doped silicon substrate was achieved by an annealing at 400 K for about 3 hours in an oven with air flow. With the same annealing, only the Raman features similar to that from the pristine graphene were observed in the freestanding graphene and the graphene on a typical Si/SiO2 wafer. Ab initio molecular dynamics (MD) simulations were performed for defected graphene on boron-doped silicon substrate at several temperatures. All vacancy sites in the graphene are occupied either with B atoms or Si atoms resulting in the mixed boron-silicon doping of the graphene. The MD simulations validated the experimetal finding of graphene doped behaviour observed by Raman spectrum. The electronic structure analysis indicated the p-type nature of doped graphene. The observed doping by the possible incorporation of heteroatoms into the graphene, simply only using 400 K annealing the boron-doped Si substrate, could provide a new approach to synthesize doped graphene in a more economic way.

  19. 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

  20. 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.

  1. Disassembly of amphiphilic small molecular prodrug with fluorescence switch induced by pH and folic acid receptors for targeted delivery and controlled release.

    PubMed

    Xu, Zhigang; Shi, Xiaoxiao; Hou, Meili; Xue, Peng; Gao, Yong-E; Liu, Shiying; Kang, Yuejun

    2017-02-01

    We develop a new type of pH-responsive amphiphilic small molecular prodrug by conjugating folic acid with anti-tumour doxorubicin via a hydrazone bond. This prodrug is featured by high and precise drug loading (55.4wt%), which can self-assemble into micellar nanoparticles in neutral environment while disassemble in the presence of tumour cells expressing folic acid receptors or the acidic tumoral endosomal environment. The prodrug nanoparticles can effectively improve anticancer efficacy due to the features of pH-triggered drug release and targeted delivery. Moreover, in vitro cell study further indicated that the resulting prodrug nanoparticles had enhanced cytotoxicity for folic-acid-positive cells (HeLa) compared to folic-acid-negative cells (MCF-7). More importantly, the induced disassembly of prodrug nanoparticles can "switch on" the inherent fluorescence of the internalized doxorubicin drug in the tumour microenvironment, which can be used for the detection of tumour cells. We believe that this strategy can pave a new way for designing small molecular drug delivery systems and facilitate tumour diagnosis and treatment simultaneously.

  2. 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.

  3. Strong Photo-Amplification Effects in Flexible Organic Capacitors with Small Molecular Solid-State Electrolyte Layers Sandwiched between Photo-Sensitive Conjugated Polymer Nanolayers.

    PubMed

    Lee, Hyena; Kim, Jungnam; Kim, Hwajeong; Kim, Youngkyoo

    2016-02-05

    We demonstrate strong photo-amplification effects in flexible organic capacitors which consist of small molecular solid-state electrolyte layers sandwiched between light-sensitive conjugated polymer nanolayers. The small molecular electrolyte layers were prepared from aqueous solutions of tris(8-hydroxyquinoline-5-sulfonic acid) aluminum (ALQSA3), while poly(3-hexylthiophene) (P3HT) was employed as the light-sensitive polymer nanolayer that is spin-coated on the indium-tin oxide (ITO)-coated poly(ethylene terephthalate) (PET) film substrates. The resulting capacitors feature a multilayer device structure of PET/ITO/P3HT/ALQSA3/P3HT/ITO/PET, which were mechanically robust due to good adhesion between the ALQSA3 layers and the P3HT nanolayers. Results showed that the specific capacitance was increased by ca. 3-fold when a white light was illuminated to the flexible organic multilayer capacitors. In particular, the capacity of charge storage was remarkably (ca. 250-fold) enhanced by a white light illumination in the potentiostatic charge/discharge operation, and the photo-amplification functions were well maintained even after bending for 300 times at a bending angle of 180(°).

  4. The Role of PET/CT Molecular Imaging in the Diagnosis of Recurrence and Surveillance of Patients Treated for Non-Small Cell Lung Cancer

    PubMed Central

    Jiménez-Bonilla, Julio Francisco; Quirce, Remedios; Martínez-Rodríguez, I.; De Arcocha-Torres, María; Carril, José Manuel; Banzo, Ignacio

    2016-01-01

    Non-small cell lung cancer (NSCLC) is the leading cause of cancer mortality worldwide and its prognosis remains poor. Molecular imaging with 18F-FDG PET/CT can metabolically characterize the nature of lesions as benign or malignant, allowing a better staging at the diagnosis of this kind of patient. This advantage can also be applied in the re-staging due to the suspicion of recurrent disease. Many patients have a recurrence of the disease, including surgically treated patients. In the current context, with new personalized oncological treatments, the surveillance for recurrence and its accurate diagnosis are crucial to improve their survival. In this paper, we revise the current knowledge about the clinical and molecular factors related to the recurrent disease. In the context of new, promising, available personalized treatments, the role of molecular imaging with PET/CT and 18F-FDG and non-18F-FDG radiotracers in the follow-up of NSCLC-treated patients is especially attractive and interesting. PMID:27706025

  5. 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.

  6. Molecular Profiling of Circulating Tumour Cells Identifies Notch1 as a Principal Regulator in Advanced Non-Small Cell Lung Cancer

    PubMed Central

    Mariscal, Javier; Alonso-Nocelo, Marta; Muinelo-Romay, Laura; Barbazan, Jorge; Vieito, Maria; Abalo, Alicia; Gomez-Tato, Antonio; Maria de los Angeles, Casares de Cal; Garcia-Caballero, Tomas; Rodriguez, Carmela; Brozos, Elena; Baron, Francisco; Lopez-Lopez, Rafael; Abal, Miguel

    2016-01-01

    Knowledge on the molecular mechanisms underlying metastasis colonization in Non-Small Cell Lung Cancer (NSCLC) remains incomplete. A complete overview integrating driver mutations, primary tumour heterogeneity and overt metastasis lacks the dynamic contribution of disseminating metastatic cells due to the inaccessibility to the molecular profiling of Circulating Tumour Cells (CTCs). By combining immunoisolation and whole genome amplification, we performed a global gene expression analysis of EpCAM positive CTCs from advanced NSCLC patients. We identified an EpCAM+ CTC-specific expression profile in NSCLC patients mostly associated with cellular movement, cell adhesion and cell-to-cell signalling mediated by PI3K/AKT, ERK1/2 and NF-kB pathways. NOTCH1 emerged as a driver connecting active signalling pathways, with a reduced number of related candidate genes (NOTCH1, PTP4A3, LGALS3 and ITGB3) being further validated by RT-qPCR on an independent cohort of NSCLC patients. In addition, these markers demonstrated high prognostic value for Progression-Free Survival (PFS). In conclusion, molecular characterization of EpCAM+ CTCs from advanced NSCLC patients provided with highly specific biomarkers with potential applicability as a “liquid biopsy” for monitoring of NSCLC patients and confirmed NOTCH1 as a potential therapeutic target to block lung cancer dissemination. PMID:27901069

  7. 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

  8. Three slow skeletal muscle troponin genes in small-tailed Han sheep (Ovis aries): molecular cloning, characterization and expression analysis.

    PubMed

    Sun, Yan; Wang, Guizhi; Ji, Zhibin; Chao, Tianle; Liu, Zhaohua; Wang, Xiaolong; Liu, Guanqing; Wu, Changhao; Wang, Jianmin

    2016-09-01

    To explore the basic characteristics and expressing profile of the three slow skeletal muscle troponin genes TNNC1 (Troponin C type 1), TNNI1 (troponin I type 1) and TNNT1 (troponin T type 1). Three purebred Dorper sheep and another three purebred small-tailed Han sheep were selected. The sequence of the genes from the small-tailed Han sheep was cloned using rapid amplification of cDNA ends and reverse transcription-polymerase chain reaction; The characteristics of the predicted amino acids sequences were analyzed using bioinformatics analysis software; Gene expression analyses were performed using quantitative reverse transcription PCR. The full-length cDNA sequences of the genes were 707, 898, and 1001 bp, respectively, and were submitted to GenBank under accession numbers KR153938, KT218688 and KT218690. The three predicted proteins were predicted to be hydrophilic, non-secretory proteins and contain several phosphorylation sites. Multiple alignments and phylogenetic tree analyses showed that the predicted proteins were relatively conserved in mammals. The expression results of the three genes in eight tissues of Dorper and small-tailed Han sheep revealed that the three genes had a similar mRNA expression pattern, whereas distinct differences were observed among the eight tissues of the two sheep species. We cloned the full-length cDNA of the three genes, analyzed the amino acid sequences, and determined the expression levels of the genes. These results might play important roles in facilitating the future research of the three genes.

  9. Molecular epidemiology of the SH (small hydrophobic) gene of human respiratory syncytial virus (HRSV), over 2 consecutive years.

    PubMed

    Lima, Hildenêr Nogueira; Botosso, Viviane Fongaro; Oliveira, Danielle Bruna Leal; Campos, Angélica Cristine de Almeida; Leal, Andrea Lima; Silva, Tereza Souza; Bosso, Patrícia Alves Ramos; Moraes, Claudia Trigo Pedroso; Filho, Claudionor Gomes da Silva; Vieira, Sandra Elisabete; Gilio, Alfredo Elias; Stewien, Klaus Eberhard; Durigon, Edison Luiz

    2012-01-01

    Human respiratory syncytial virus (HRSV) strains were isolated from nasopharyngeal aspirates collected from 965 children between 2004 and 2005, yielding 424 positive samples. We sequenced the small hydrophobic protein (SH) gene of 117 strains and compared them with other viruses identified worldwide. Phylogenetic analysis showed a low genetic variability among the isolates but allowed us to classify the viruses into different genotypes for both groups, HRSVA and HRSVB. It is also shown that the novel BA-like genotype was well segregated from the others, indicating that the mutations are not limited to the G gene.

  10. Recent Advances in the Development of Small-Molecular Inhibitors Target HIV Integrase-LEDGF/p75 Interaction.

    PubMed

    Zhao, Yu; Luo, Zaigang

    2015-01-01

    Lens epithelium-derived growth factor (LEDGF/p75) plays an essential role in the HIV-1 replication. It acts by tethering integrase (IN) into the host cellular chromatin. Due to its significance of the IN-LEDGF/p75 interaction affords a novel therapeutic approach for the design of new classes of antiretroviral agents. To date, many small molecules have been found to be the inhibitors of INLEDGF/ p75 interaction. This review summarizes recent advances in the development of potential structure-based IN-LEDGF/p75 interaction inhibitors. The work will be helpful to shed light on the antiretroviral drug development pipeline in the next future.

  11. A comparison of the performance of molecularly imprinted polymer nanoparticles for small molecule targets and antibodies in the ELISA format

    NASA Astrophysics Data System (ADS)

    Smolinska-Kempisty, Katarzyna; Guerreiro, Antonio; Canfarotta, Francesco; Cáceres, César; Whitcombe, Michael J.; Piletsky, Sergey

    2016-11-01

    Here we show that molecularly imprinted polymer nanoparticles, prepared in aqueous media by solid phase synthesis with immobilised L-thyroxine, glucosamine, fumonisin B2 or biotin as template, can demonstrate comparable or better performance to commercially produced antibodies in enzyme-linked competitive assays. Imprinted nanoparticles-based assays showed detection limits in the pM range and polymer-coated microplates are stable to storage at room temperature for at least 1 month. No response to analyte was detected in control experiments with nanoparticles imprinted with an unrelated template (trypsin) but prepared with the same polymer composition. The ease of preparation, high affinity of solid-phase synthesised imprinted nanoparticles and the lack of requirement for cold chain logistics make them an attractive alternative to traditional antibodies for use in immunoassays.

  12. Recent advances in small molecular, non-polymeric organic hole transporting materials for solid-state DSSC

    NASA Astrophysics Data System (ADS)

    Bui, Thanh-Tuan; Goubard, Fabrice

    2013-10-01

    Issue from thin-film technologies, dye-sensitized solar cells have become one of the most promising technologies in the field of renewable energies. Their success is not only due to their low weight, the possibility of making large flexible surfaces, but also to their photovoltaic efficiency which are found to be more and more significant (>12% with a liquid electrolyte, >7% with a solid organic hole conductor). This short review highlights recent advances in the characteristics and use of low-molecular-weight glass-forming organic materials as hole transporters in all solid-state dye-sensitized solar cells. These materials must feature specific physical and chemical properties that will ensure both the operation of a photovoltaic cell and the easy implementation. This review is an english extended version based on our recent article published in Matériaux & Techniques 101, 102 (2013).

  13. A comparison of the performance of molecularly imprinted polymer nanoparticles for small molecule targets and antibodies in the ELISA format.

    PubMed

    Smolinska-Kempisty, Katarzyna; Guerreiro, Antonio; Canfarotta, Francesco; Cáceres, César; Whitcombe, Michael J; Piletsky, Sergey

    2016-11-24

    Here we show that molecularly imprinted polymer nanoparticles, prepared in aqueous media by solid phase synthesis with immobilised L-thyroxine, glucosamine, fumonisin B2 or biotin as template, can demonstrate comparable or better performance to commercially produced antibodies in enzyme-linked competitive assays. Imprinted nanoparticles-based assays showed detection limits in the pM range and polymer-coated microplates are stable to storage at room temperature for at least 1 month. No response to analyte was detected in control experiments with nanoparticles imprinted with an unrelated template (trypsin) but prepared with the same polymer composition. The ease of preparation, high affinity of solid-phase synthesised imprinted nanoparticles and the lack of requirement for cold chain logistics make them an attractive alternative to traditional antibodies for use in immunoassays.

  14. A comparison of the performance of molecularly imprinted polymer nanoparticles for small molecule targets and antibodies in the ELISA format

    PubMed Central

    Smolinska-Kempisty, Katarzyna; Guerreiro, Antonio; Canfarotta, Francesco; Cáceres, César; Whitcombe, Michael J.; Piletsky, Sergey

    2016-01-01

    Here we show that molecularly imprinted polymer nanoparticles, prepared in aqueous media by solid phase synthesis with immobilised L-thyroxine, glucosamine, fumonisin B2 or biotin as template, can demonstrate comparable or better performance to commercially produced antibodies in enzyme-linked competitive assays. Imprinted nanoparticles-based assays showed detection limits in the pM range and polymer-coated microplates are stable to storage at room temperature for at least 1 month. No response to analyte was detected in control experiments with nanoparticles imprinted with an unrelated template (trypsin) but prepared with the same polymer composition. The ease of preparation, high affinity of solid-phase synthesised imprinted nanoparticles and the lack of requirement for cold chain logistics make them an attractive alternative to traditional antibodies for use in immunoassays. PMID:27883023

  15. 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.

  16. Proton irradiation effects on deep level states in Mg-doped p-type GaN grown by ammonia-based molecular beam epitaxy

    SciTech Connect

    Zhang, Z.; Arehart, A. R.; Ringel, S. A.; Kyle, E. C. H.; Speck, J. S.; Chen, J.; Zhang, E. X.; Fleetwood, D. M.; Schrimpf, R. D.

    2015-01-12

    The impact of proton irradiation on the deep level states throughout the Mg-doped p-type GaN bandgap is investigated using deep level transient and optical spectroscopies. Exposure to 1.8 MeV protons of 1 × 10{sup 13 }cm{sup −2} and 3 × 10{sup 13 }cm{sup −2} fluences not only introduces a trap with an E{sub V} + 1.02 eV activation energy but also brings monotonic increases in concentration for as-grown deep states at E{sub V} + 0.48 eV, E{sub V} + 2.42 eV, E{sub V} + 3.00 eV, and E{sub V} + 3.28 eV. The non-uniform sensitivities for individual states suggest different physical sources and/or defect generation mechanisms. Comparing with prior theoretical calculations reveals that several traps are consistent with associations to nitrogen vacancy, nitrogen interstitial, and gallium vacancy origins, and thus are likely generated through displacing nitrogen and gallium atoms from the crystal lattice in proton irradiation environment.

  17. The Structure of Human Apolipoprotein A-IV as Revealed by Stable Isotope-assisted Cross-linking, Molecular Dynamics, and Small Angle X-ray Scattering*

    PubMed Central

    Walker, Ryan G.; Deng, Xiaodi; Melchior, John T.; Morris, Jamie; Tso, Patrick; Jones, Martin K.; Segrest, Jere P.; Thompson, Thomas B.; Davidson, W. Sean

    2014-01-01

    Apolipoprotein (apo)A-IV plays important roles in dietary lipid and glucose metabolism, and knowledge of its structure is required to fully understand the molecular basis of these functions. However, typical of the entire class of exchangeable apolipoproteins, its dynamic nature and affinity for lipid has posed challenges to traditional high resolution structural approaches. We previously reported an x-ray crystal structure of a dimeric truncation mutant of apoA-IV, which showed a unique helix-swapping molecular interface. Unfortunately, the structures of the N and C termini that are important for lipid binding were not visualized. To build a more complete model, we used chemical cross-linking to derive distance constraints across the full-length protein. The approach was enhanced with stable isotope labeling to overcome ambiguities in determining molecular span of the cross-links given the remarkable similarities in the monomeric and dimeric apoA-IV structures. Using 51 distance constraints, we created a starting model for full-length monomeric apoA-IV and then subjected it to two modeling approaches: (i) molecular dynamics simulations and (ii) fitting to small angle x-ray scattering data. This resulted in the most detailed models yet for lipid-free monomeric or dimeric apoA-IV. Importantly, these models were of sufficient detail to direct the experimental identification of new functional residues that participate in a “clasp” mechanism to modulate apoA-IV lipid affinity. The isotope-assisted cross-linking approach should prove useful for further study of this family of apolipoproteins in both the lipid-free and -bound states. PMID:24425874

  18. Molecular Phenotyping Small (Asian) versus Large (Western) Plaque Psoriasis Shows Common Activation of IL-17 Pathway Genes but Different Regulatory Gene Sets.

    PubMed

    Kim, Jaehwan; Oh, Chil-Hwan; Jeon, Jiehyun; Baek, Yoosang; Ahn, Jaewoo; Kim, Dong Joo; Lee, Hyun-Soo; Correa da Rosa, Joel; Suárez-Fariñas, Mayte; Lowes, Michelle A; Krueger, James G

    2016-01-01

    Psoriasis is present in all racial groups, but in varying frequencies and severity. Considering that small plaque psoriasis is specific to the Asian population and severe psoriasis is more predominant in the Western population, we defined Asian small and intermediate plaque psoriasis as psoriasis subtypes and compared their molecular signatures with the classic subtype of Western large plaque psoriasis. Two different characteristics of psoriatic spreading-vertical growth and radial expansion-were contrasted between subtypes, and genomic data were correlated to histologic and clinical measurements. Compared with Western large plaque psoriasis, Asian small plaque psoriasis revealed limited psoriasis spreading, but IL-17A and IL-17-regulated proinflammatory cytokines were highly expressed. Paradoxically, IL-17A and IL-17-regulated proinflammatory cytokines were lower in Western large plaque psoriasis, whereas T cells and dendritic cells in total psoriatic skin area were exponentially increased. Negative immune regulators, such as CD69 and FAS, were decreased in both Western large plaque psoriasis and psoriasis with accompanying arthritis or obesity, and their expression was correlated with psoriasis severity index. Based on the disease subtype comparisons, we propose that dysregulation of T-cell expansion enabled by downregulation of immune negative regulators is the main mechanism for development of large plaque psoriasis subtypes.

  19. Molecular cloning of Xenopus fibrillarin, a conserved U3 small nuclear ribonucleoprotein recognized by antisera from humans with autoimmune disease.

    PubMed Central

    Lapeyre, B; Mariottini, P; Mathieu, C; Ferrer, P; Amaldi, F; Amalric, F; Caizergues-Ferrer, M

    1990-01-01

    Autoantibodies against U3 small nuclear ribonucleoprotein are associated with scleroderma autoimmune disease. They were shown to react with fibrillarin, a 34- to 36-kilodalton protein that has been detected in all eukaryotes tested from humans to yeasts. We isolated a 1.6-kilobase cDNA encoding fibrillarin from a Xenopus laevis cDNA library. The protein contains a 79-residue-long Gly-Arg-rich domain in its N-terminal region and a putative RNA-binding domain with ribonucleoprotein consensus sequence in its central portion. This is the first report of cloning of fibrillarin, and the deduced protein sequence is in agreement with the involvement of the protein in a ribonucleoprotein particle. Images PMID:2136767

  20. The cryptic Y-autosome translocation in the small Indian mongoose, Herpestes auropunctatus, revealed by molecular cytogenetic approaches.

    PubMed

    Murata, Chie; Sawaya, Hirohito; Nakata, Katsushi; Yamada, Fumio; Imoto, Issei; Kuroiwa, Asato

    2016-09-01

    In initial studies of the eutherian small Indian mongoose (Herpestes auropunctatus), the Y chromosome could not be identified in somatic cells. The male chromosome number is uniquely odd, 2n = 35, whereas that of females is 2n = 36. Previous reports indicated that this unique karyotype resulted from a translocation of the ancestral Y chromosome to an autosome. However, it has been difficult to identify the chromosomes that harbor the translocated Y chromosomal segment because it is an extremely small euchromatic region. Using a Southern blot analysis, we detected four conserved Y-linked genes, SRY, EIF2S3Y, KDM5D, and ZFY, in the male genome. We cloned homologues of these genes and determined their sequences, which showed high homology to genes in two carnivore species, cat and dog. To unambiguously identify the Y-bearing autosome, we performed immunostaining of pachytene spermatocytes using antibodies against SYCP3, γH2AX, and the centromere. We observed trivalent chromosomes, and the associations between the distal ends of the chromosomes were consistent with those of Y and X1 chromosomes. The centromere of the Y chromosome was located on the ancestral Y chromosomal segment. We mapped the complementary DNA (cDNA) clones of these genes to the male chromosomes using fluorescence in situ hybridization (FISH), and the linear localization of all genes was confirmed by two-colored FISH. These Y-linked genes were localized to the proximal region of the long arm of a single telomeric chromosome, and we successfully identified the chromosome harboring the ancestral Y chromosomal segment.

  1. Molecular characterization of peste des petits ruminants viruses from outbreaks caused by unrestricted movements of small ruminants in pakistan.

    PubMed

    Munir, M; Saeed, A; Abubakar, M; Kanwal, S; Berg, M

    2015-02-01

    Peste des petits ruminants (PPR) is an endemic disease of small ruminants, and vaccination has been the method of control but outbreaks are continuously occurring in Pakistan. The following study presents a detailed investigation of an outbreak, suspected to be PPR, probably introduced by PPRV-infected sheep and goats from Sindh Province (north-west) to Punjab Province (central) of Pakistan during the flood relief campaign in 2011. A total of 70 serum samples from 28 different flocks were tested with competitive ELISA (H antibodies), which detected 24 (34.2%) samples positive for PPRV antibodies. Nasal swabs and faeces were tested with immunocapture ELISA (N antigen), which detected 18 (25.7%) samples positive for PPRV antigen. The RNA detected positive (n = 28, 40%) using real-time PCR was subjected to conventional PCR for the amplification of the fusion and nucleoprotein genes. Sequencing of both genes and subsequent phylogenetic analysis indicated the grouping of all the sequences to be in lineage IV along with other Asian isolates of PPRV. However, sequences of both genes were divided into two groups within lineage IV. One group of viruses clustered with previously characterized Pakistani isolates, whereas the other group was distinctly clustered with isolates from the Middle East or India. The sequence identity indicated the introduction of at least one population of PPRV from a different source and circulation in the local flocks of small ruminants, which emphasized the need to obtain health clearance certificate before movement of animals. The results of this study provide baseline data for the genetic characterization of different PPRV populations in Pakistan.

  2. Hormones as doping in sports.

    PubMed

    Duntas, Leonidas H; Popovic, Vera

    2013-04-01

    Though we may still sing today, as did Pindar in his eighth Olympian Victory Ode, "… of no contest greater than Olympia, Mother of Games, gold-wreathed Olympia…", we must sadly admit that today, besides blatant over-commercialization, there is no more ominous threat to the Olympic games than doping. Drug-use methods are steadily becoming more sophisticated and ever harder to detect, increasingly demanding the use of complex analytical procedures of biotechnology and molecular medicine. Special emphasis is thus given to anabolic androgenic steroids, recombinant growth hormone and erythropoietin as well as to gene doping, the newly developed mode of hormones abuse which, for its detection, necessitates high-tech methodology but also multidisciplinary individual measures incorporating educational and psychological methods. In this Olympic year, the present review offers an update on the current technologically advanced endocrine methods of doping while outlining the latest procedures applied-including both the successes and pitfalls of proteomics and metabolomics-to detect doping while contributing to combating this scourge.

  3. How a Small Change in Retinal Leads to G-Protein Activation: Initial Events Suggested by Molecular Dynamics Calculations

    PubMed Central

    Crozier, Paul S.; Stevens, Mark J.; Woolf, Thomas B.

    2010-01-01

    Rhodopsin is the prototypical G-protein coupled receptor, coupling light activation with high efficiency to signaling molecules. The dark-state X-ray structures of the protein provide a starting point for consideration of the relaxation from initial light activation to conformational changes that may lead to signaling. In this study we create an energetically unstable retinal in the light activated state and then use molecular dynamics simulations to examine the types of compensation, relaxation, and conformational changes that occur following the cis–trans light activation. The results suggest that changes occur throughout the protein, with changes in the orientation of Helices 5 and 6, a closer interaction between Ala 169 on Helix 4 and retinal, and a shift in the Schiff base counterion that also reflects changes in sidechain interactions with the retinal. Taken together, the simulation is suggestive of the types of changes that lead from local conformational change to light-activated signaling in this prototypical system. PMID:17109408

  4. Small molecular antioxidants effectively protect from PUVA-induced oxidative stress responses underlying fibroblast senescence and photoaging.

    PubMed

    Briganti, Stefania; Wlaschek, Meinhard; Hinrichs, Christina; Bellei, Barbara; Flori, Enrica; Treiber, Nicolai; Iben, Sebastian; Picardo, Mauro; Scharffetter-Kochanek, Karin

    2008-09-01

    Exposure of human fibroblasts to 8-methoxypsoralen plus ultraviolet-A irradiation (PUVA) results in stress-induced cellular senescence in fibroblasts. We here studied the role of the antioxidant defense system in the accumulation of reactive oxygen species (ROS) and the effect of the antioxidants alpha-tocopherol, N-acetylcysteine, and alpha-lipoic acid on PUVA-induced cellular senescence. PUVA treatment induced an immediate and increasing generation of intracellular ROS. Supplementation of PUVA-treated fibroblasts with alpha-tocopherol (alpha-Toc), N-acetylcysteine (NAC), or alpha-lipoic acid (alpha-LA) abrogated the increased ROS generation and rescued fibroblasts from the ROS-dependent changes into the cellular senescence phenotype, such as cytoplasmic enlargement, enhanced expression of senescence-associated-beta-galactosidase and matrix-metalloproteinase-1, hallmarks of photoaging and intrinsic aging. PUVA treatment disrupted the integrity of cellular membranes and impaired homeostasis and function of the cellular antioxidant system with a significant decrease in glutathione and hydrogen peroxide-detoxifying enzymes activities. Supplementation with NAC, alpha-LA, and alpha-Toc counteracted these changes. Our data provide causal evidence that (i) oxidative stress due to an imbalance in the overall cellular antioxidant capacity contributes to the induction and maintenance of the PUVA-induced fibroblast senescence and that (ii) low molecular antioxidants protect effectively against these deleterious alterations.

  5. Probing the interaction mechanism of small molecule inhibitors with matriptase based on molecular dynamics simulation and free energy calculations.

    PubMed

    Sun, Dong-Ru; Zheng, Qing-Chuan; Zhang, Hong-Xing

    2017-03-01

    Matriptase is a serine protease associated with a wide variety of human tumors and carcinoma progression. Up to now, many promising anti-cancer drugs have been developed. However, the detailed structure-function relationship between inhibitors and matriptase remains elusive. In this work, molecular dynamics simulation and binding free energy studies were performed to investigate the biochemistry behaviors of two class inhibitors binding to matriptase. The binding free energies predicted by MM/GBSA methods are in good agreement with the experimental bioactivities, and the analysis of the individual energy terms suggests that the van der Waals interaction is the major driving force for ligand binding. The key residues responsible for achieving strong binding have been identified by the MM/GBSA free energy decomposition analysis. Especially, Trp215 and Phe99 had an important impact on active site architecture and ligand binding. The results clearly identify the two class inhibitors exist different binding modes. Through summarizing the two different modes, we have mastered some important and favorable interaction patterns between matriptase and inhibitors. Our findings would be helpful for understanding the interaction mechanism between the inhibitor and matriptase and afford important guidance for the rational design of potent matriptase inhibitors.

  6. A molecular dynamics-based algorithm for evaluating the glycosaminoglycan mimicking potential of synthetic, homogenous, sulfated small molecules

    PubMed Central

    Nagarajan, Balaji; Sankaranarayanan, Nehru Viji; Patel, Bhaumik B.

    2017-01-01

    Glycosaminoglycans (GAGs) are key natural biopolymers that exhibit a range of biological functions including growth and differentiation. Despite this multiplicity of function, natural GAG sequences have not yielded drugs because of problems of heterogeneity and synthesis. Recently, several homogenous non-saccharide glycosaminoglycan mimetics (NSGMs) have been reported as agents displaying major therapeutic promise. Yet, it remains unclear whether sulfated NSGMs structurally mimic sulfated GAGs. To address this, we developed a three-step molecular dynamics (MD)-based algorithm to compare sulfated NSGMs with GAGs. In the first step of this algorithm, parameters related to the range of conformations sampled by the two highly sulfated molecules as free entities in water were compared. The second step compared identity of binding site geometries and the final step evaluated comparable dynamics and interactions in the protein-bound state. Using a test case of interactions with fibroblast growth factor-related proteins, we show that this three-step algorithm effectively predicts the GAG structure mimicking property of NSGMs. Specifically, we show that two unique dimeric NSGMs mimic hexameric GAG sequences in the protein-bound state. In contrast, closely related monomeric and trimeric NSGMs do not mimic GAG in either the free or bound states. These results correspond well with the functional properties of NSGMs. The results show for the first time that appropriately designed sulfated NSGMs can be good structural mimetics of GAGs and the incorporation of a MD-based strategy at the NSGM library screening stage can identify promising mimetics of targeted GAG sequences. PMID:28182755

  7. Small-molecule interferon inducers. Toward the comprehension of the molecular determinants through ligand-based approaches.

    PubMed

    Musmuca, Ira; Simeoni, Silvia; Caroli, Antonia; Ragno, Rino

    2009-07-01

    Hepatitis C is becoming an increasingly common cause of mortality especially in the HIV-coinfected group. Due to the efficacy of interferon (IFN) based therapy in the treatment of hepatitis C, various compounds possessing IFN-inducing activity have been hitherto reported. In the present study, we describe how steric, electrostatic, hydrophobic, and hydrogen-bonding interactions might influence the biological activity of a published set of IFN inducers, using a three-dimensional quantitative structure-activity relationship (3-D QSAR) approach. Analyses were conducted evaluating different series of compounds structurally related to 8-hydroxyadenines and 1H-imidazo[4,5-c]quinolines. A ligand-based alignment protocol in combination with the GRID/GOLPE approach was applied: 62 3-D QSAR models were derived using different GRID probes and several training sets. Performed 3-D QSAR investigations proved to be of good statistical value displaying r2, q2CV-LOO, and cross-validated SDEP values of 0.73, 0.61, 0.61 and 0.89, 0.64, 0.58 using the OH or the DRY probe, respectively. Additionally, the predictive performance was evaluated using an external test set of 20 compounds. Analyses of the resulting models led to the definition of a pharmacophore model that can be of interest to explain the observed affinities of known compounds as well as to design novel low molecular weight IFN inducers (IFNIs). To the best of our knowledge, this is the first 3-D QSAR application on IFN-inducing agents.

  8. Refinement of causative genes in monosomy 1p36 through clinical and molecular cytogenetic characterization of small interstitial deletions.

    PubMed

    Rosenfeld, Jill A; Crolla, John A; Tomkins, Susan; Bader, Patricia; Morrow, Bernice; Gorski, Jerome; Troxell, Robin; Forster-Gibson, Cynthia; Cilliers, Deirdre; Hislop, R Gordon; Lamb, Allen; Torchia, Beth; Ballif, Blake C; Shaffer, Lisa G

    2010-08-01

    Monosomy 1p36 is the most common terminal deletion syndrome seen in humans, occurring in approximately 1 in 5,000 live births. Common features include mental retardation, characteristic dysmorphic features, hypotonia, seizures, hearing loss, heart defects, cardiomyopathy, and behavior abnormalities. Similar phenotypes are seen among patients with a variety of deletion sizes, including terminal and interstitial deletions, complex rearrangements, and unbalanced translocations. Consequently, critical regions harboring causative genes for each of these features have been difficult to identify. Here we report on five individuals with 200-823 kb overlapping deletions of proximal 1p36.33, four of which are apparently de novo. They present with features of monosomy 1p36, including developmental delay and mental retardation, dysmorphic features, hypotonia, behavioral abnormalities including hyperphagia, and seizures. The smallest region of deletion overlap is 174 kb and contains five genes; these genes are likely candidates for some of the phenotypic features in monosomy 1p36. Other genes deleted in a subset of the patients likely play a contributory role in the phenotypes, including GABRD and seizures, PRKCZ and neurologic features, and SKI and dysmorphic and neurologic features. Characterization of small deletions is important for narrowing critical intervals and for the identification of causative or candidate genes for features of monosomy 1p36 syndrome.

  9. Surgical molecular navigation with a Ratiometric Activatable Cell Penetrating Peptide improves intraoperative identification and resection of small salivary gland cancers

    PubMed Central

    Hussain, Timon; Savariar, Elamprakash N.; Diaz-Perez, Julio A.; Messer, Karen; Pu, Minya; Tsien, Roger Y.; Nguyen, Quyen T.

    2015-01-01

    Background We evaluated the use of intraoperative fluorescence guidance by enzymatically cleavable ratiometric activatable cell-penetrating peptide (RACPPPLGC(Me)AG) containing Cy5 as a fluorescent donor and Cy7 as a fluorescent acceptor for salivary gland cancer surgery in a mouse model. Methods Surgical resection of small parotid gland cancers in mice was performed with fluorescence guidance or white light (WL) imaging alone. Tumor identification accuracy, operating time and tumor free survival were compared. Results RACPP guidance aided tumor detection (positive histology in 90% (27/30) vs. 48% (15/31) for WL, p<0.001). A ~25% ratiometric signal increase as the threshold to distinguish between tumor and adjacent tissue, yielded >90% detection sensitivity and specificity. Operating time was reduced by 54% (p<0.001), tumor free survival was increased with RACPP guidance (p=0.025). Conclusions RACPP provides real-time intraoperative guidance leading to improved survival. Ratiometric signal thresholds can be set according to desired detection accuracy levels for future RACPP applications. PMID:25521629

  10. Efficient Differentiation of TBX18(+)/WT1(+) Epicardial-Like Cells from Human Pluripotent Stem Cells Using Small Molecular Compounds.

    PubMed

    Zhao, Jianmin; Cao, Henghua; Tian, Luyang; Huo, Weibang; Zhai, Kui; Wang, Pei; Ji, Guangju; Ma, Yue

    2017-04-01

    The epicardium promotes neovascularization and cardiomyocyte regeneration by generating vascular smooth muscle cells (SMCs) and producing regenerative factors after adult heart infarction. It is therefore a potential cell resource for repair of the injured heart. However, the epicardium also participates in fibrosis and scarring of the injured heart, complicating its use in regenerative medicine. In this study, we report coexpression of TBX18 and WT1 in the majority of epicardial cells during mouse embryonic epicardial development. Furthermore, we describe a convenient chemically defined, immunogen-free, small molecule-based method for generating TBX18(+)/WT1(+) epicardial-like cell populations with 80% homogeneity from human pluripotent stem cells by modulation of the WNT and retinoic acid signaling pathways. These epicardial-like cells exhibited characteristic epicardial cell morphology following passaging and differentiation into functional SMCs or cardiac fibroblast-like cells. Our findings add to existing understanding of human epicardial development and provide an efficient and stable method for generating both human epicardial-like cells and SMCs.

  11. A molecular phylogeny of the marine red algae (Rhodophyta) based on the nuclear small-subunit rRNA gene.

    PubMed Central

    Ragan, M A; Bird, C J; Rice, E L; Gutell, R R; Murphy, C A; Singh, R K

    1994-01-01

    A phylogeny of marine Rhodophyta has been inferred by a number of methods from nucleotide sequences of nuclear genes encoding small subunit rRNA from 39 species in 15 orders. Sequence divergences are relatively large, especially among bangiophytes and even among congeners in this group. Subclass Bangiophycidae appears polyphyletic, encompassing at least three lineages, with Porphyridiales distributed between two of these. Subclass Florideophycidae is monophyletic, with Hildenbrandiales, Corallinales, Ahnfeltiales, and a close association of Nemaliales, Acrochaetiales, and Palmariales forming the four deepest branches. Cermiales may represent a convergence of vegetative and reproductive morphologies, as family Ceramiaceae is at best weakly related to the rest of the order, and one of its members appears to be allied to Gelidiales. Except for Gigartinales, for which more data are required, the other florideophyte orders appear distinct and taxonomically justified. A good correlation was observed with taxonomy based on pit-plug ultrastructure. Tests under maximum-likelihood and parsimony of alternative phylogenies based on structure and chemistry refuted suggestions that Acrochaetiales is the most primitive florideophyte order and that Gelidiales and Hildenbrandiales are sister groups. PMID:8041780

  12. Second-Line Treatment of Non-Small Cell Lung Cancer: Clinical, Pathological, and Molecular Aspects of Nintedanib

    PubMed Central

    Corrales, Luis; Nogueira, Amanda; Passiglia, Francesco; Listi, Angela; Caglevic, Christian; Giallombardo, Marco; Raez, Luis; Santos, Edgardo; Rolfo, Christian

    2017-01-01

    Lung carcinoma is the leading cause of death by cancer in the world. Nowadays, most patients will experience disease progression during or after first-line chemotherapy demonstrating the need for new, effective second-line treatments. The only approved second-line therapies for patients without targetable oncogenic drivers are docetaxel, gemcitabine, pemetrexed, and erlotinib and for patients with target-specific oncogenes afatinib, osimertinib, crizotinib, alectinib, and ceritinib. In recent years, evidence on the role of antiangiogenic agents have been established as important and effective therapeutic targets in non-small cell lung cancer (NSCLC). Nintedanib is a tyrosine kinase inhibitor targeting three angiogenesis-related transmembrane receptors (vascular endothelial growth factor, fibroblast growth factor, and platelet-derived growth factor). Several preclinical and clinical studies have proven the usefulness of nintedanib as an anticancer agent for NSCLC. The most important study was the phase III LUME-Lung 1 trial, which investigated the combination of nintedanib with docetaxel for second-line treatment in advanced NSCLC patients. The significant improvement in overall survival and the manageable safety profile led to the approval of this new treatment in Europe. This review focuses on the preclinical and clinical studies with nintedanib in NSCLC. PMID:28293555