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Sample records for junctional complex molecular

  1. Molecular electronic junction transport

    DEFF Research Database (Denmark)

    Solomon, Gemma C.; Herrmann, Carmen; Ratner, Mark

    2012-01-01

    Whenasinglemolecule,oracollectionofmolecules,isplacedbetween two electrodes and voltage is applied, one has a molecular transport junction. We discuss such junctions, their properties, their description, and some of their applications. The discussion is qualitative rather than quantitative, and f...

  2. Peltier cooling in molecular junctions

    Science.gov (United States)

    Cui, Longji; Miao, Ruijiao; Wang, Kun; Thompson, Dakotah; Zotti, Linda Angela; Cuevas, Juan Carlos; Meyhofer, Edgar; Reddy, Pramod

    2018-02-01

    The study of thermoelectricity in molecular junctions is of fundamental interest for the development of various technologies including cooling (refrigeration) and heat-to-electricity conversion1-4. Recent experimental progress in probing the thermopower (Seebeck effect) of molecular junctions5-9 has enabled studies of the relationship between thermoelectricity and molecular structure10,11. However, observations of Peltier cooling in molecular junctions—a critical step for establishing molecular-based refrigeration—have remained inaccessible. Here, we report direct experimental observations of Peltier cooling in molecular junctions. By integrating conducting-probe atomic force microscopy12,13 with custom-fabricated picowatt-resolution calorimetric microdevices, we created an experimental platform that enables the unified characterization of electrical, thermoelectric and energy dissipation characteristics of molecular junctions. Using this platform, we studied gold junctions with prototypical molecules (Au-biphenyl-4,4'-dithiol-Au, Au-terphenyl-4,4''-dithiol-Au and Au-4,4'-bipyridine-Au) and revealed the relationship between heating or cooling and charge transmission characteristics. Our experimental conclusions are supported by self-energy-corrected density functional theory calculations. We expect these advances to stimulate studies of both thermal and thermoelectric transport in molecular junctions where the possibility of extraordinarily efficient energy conversion has been theoretically predicted2-4,14.

  3. Transport properties of molecular junctions

    CERN Document Server

    Zimbovskaya, Natalya A

    2013-01-01

    A comprehensive overview of the physical mechanisms that control electron transport and the characteristics of metal-molecule-metal (MMM) junctions is presented. As far as possible, methods and formalisms presented elsewhere to analyze electron transport through molecules are avoided. This title introduces basic concepts—a description of the electron transport through molecular junctions—and briefly describes relevant experimental methods. Theoretical methods commonly used to analyze the electron transport through molecules are presented. Various effects that manifest in the electron transport through MMMs, as well as the basics of density-functional theory and its applications to electronic structure calculations in molecules are presented. Nanoelectronic applications of molecular junctions and similar systems are discussed as well. Molecular electronics is a diverse and rapidly growing field. Transport Properties of Molecular Junctions presents an up-to-date survey of the field suitable for researchers ...

  4. Stability of large-area molecular junctions

    NARCIS (Netherlands)

    Akkerman, Hylke B.; Kronemeijer, Auke J.; Harkema, Jan; van Hal, Paul A.; Smits, Edsger C. P.; de Leeuw, Dago M.; Blom, Paul W. M.

    The stability of molecular junctions is crucial for any application of molecular electronics. Degradation of molecular junctions when exposed to ambient conditions is regularly observed. In this report the stability of large-area molecular junctions under ambient conditions for more than two years

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

    Science.gov (United States)

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

    2017-09-25

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

  6. Molecular series-tunneling junctions.

    Science.gov (United States)

    Liao, Kung-Ching; Hsu, Liang-Yan; Bowers, Carleen M; Rabitz, Herschel; Whitesides, George M

    2015-05-13

    Charge transport through junctions consisting of insulating molecular units is a quantum phenomenon that cannot be described adequately by classical circuit laws. This paper explores tunneling current densities in self-assembled monolayer (SAM)-based junctions with the structure Ag(TS)/O2C-R1-R2-H//Ga2O3/EGaIn, where Ag(TS) is template-stripped silver and EGaIn is the eutectic alloy of gallium and indium; R1 and R2 refer to two classes of insulating molecular units-(CH2)n and (C6H4)m-that are connected in series and have different tunneling decay constants in the Simmons equation. These junctions can be analyzed as a form of series-tunneling junctions based on the observation that permuting the order of R1 and R2 in the junction does not alter the overall rate of charge transport. By using the Ag/O2C interface, this system decouples the highest occupied molecular orbital (HOMO, which is localized on the carboxylate group) from strong interactions with the R1 and R2 units. The differences in rates of tunneling are thus determined by the electronic structure of the groups R1 and R2; these differences are not influenced by the order of R1 and R2 in the SAM. In an electrical potential model that rationalizes this observation, R1 and R2 contribute independently to the height of the barrier. This model explicitly assumes that contributions to rates of tunneling from the Ag(TS)/O2C and H//Ga2O3 interfaces are constant across the series examined. The current density of these series-tunneling junctions can be described by J(V) = J0(V) exp(-β1d1 - β2d2), where J(V) is the current density (A/cm(2)) at applied voltage V and βi and di are the parameters describing the attenuation of the tunneling current through a rectangular tunneling barrier, with width d and a height related to the attenuation factor β.

  7. Molecular Diffusion through Cyanobacterial Septal Junctions.

    Science.gov (United States)

    Nieves-Morión, Mercedes; Mullineaux, Conrad W; Flores, Enrique

    2017-01-03

    Heterocyst-forming cyanobacteria grow as filaments in which intercellular molecular exchange takes place. During the differentiation of N 2 -fixing heterocysts, regulators are transferred between cells. In the diazotrophic filament, vegetative cells that fix CO 2 through oxygenic photosynthesis provide the heterocysts with reduced carbon and heterocysts provide the vegetative cells with fixed nitrogen. Intercellular molecular transfer has been traced with fluorescent markers, including calcein, 5-carboxyfluorescein, and the sucrose analogue esculin, which are observed to move down their concentration gradient. In this work, we used fluorescence recovery after photobleaching (FRAP) assays in the model heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120 to measure the temperature dependence of intercellular transfer of fluorescent markers. We find that the transfer rate constants are directly proportional to the absolute temperature. This indicates that the "septal junctions" (formerly known as "microplasmodesmata") linking the cells in the filament allow molecular exchange by simple diffusion, without any activated intermediate state. This constitutes a novel mechanism for molecular transfer across the bacterial cytoplasmic membrane, in addition to previously characterized mechanisms for active transport and facilitated diffusion. Cyanobacterial septal junctions are functionally analogous to the gap junctions of metazoans. Although bacteria are frequently considered just as unicellular organisms, there are bacteria that behave as true multicellular organisms. The heterocyst-forming cyanobacteria grow as filaments in which cells communicate. Intercellular molecular exchange is thought to be mediated by septal junctions. Here, we show that intercellular transfer of fluorescent markers in the cyanobacterial filament has the physical properties of simple diffusion. Thus, cyanobacterial septal junctions are functionally analogous to metazoan gap junctions

  8. Improving transition voltage spectroscopy of molecular junctions

    DEFF Research Database (Denmark)

    Markussen, Troels; Chen, Jingzhe; Thygesen, Kristian Sommer

    2011-01-01

    Transition voltage spectroscopy (TVS) is a promising spectroscopic tool for molecular junctions. The principles in TVS is to find the minimum on a Fowler-Nordheim plot where ln(I/V2) is plotted against 1/V and relate the voltage at the minimum Vmin to the closest molecular level. Importantly, Vmin...

  9. Towards molecular electronics with large-area molecular junctions

    NARCIS (Netherlands)

    Akkerman, HB; Blom, PWM; de Leeuw, DM; de Boer, B

    2006-01-01

    Electronic transport through single molecules has been studied extensively by academic(1-8) and industrial(9,10) research groups. Discrete tunnel junctions, or molecular diodes, have been reported using scanning probes(11,12), break junctions(13,14), metallic crossbars(6) and nanopores(8,15). For

  10. Mechanically controllable break junctions for molecular electronics.

    Science.gov (United States)

    Xiang, Dong; Jeong, Hyunhak; Lee, Takhee; Mayer, Dirk

    2013-09-20

    A mechanically controllable break junction (MCBJ) represents a fundamental technique for the investigation of molecular electronic junctions, especially for the study of the electronic properties of single molecules. With unique advantages, the MCBJ technique has provided substantial insight into charge transport processes in molecules. In this review, the techniques for sample fabrication, operation and the various applications of MCBJs are introduced and the history, challenges and future of MCBJs are discussed. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Charge Transport Processes in Molecular Junctions

    Science.gov (United States)

    Smith, Christopher Eugene

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

  12. Charge Transport Phenomena in Peptide Molecular Junctions

    International Nuclear Information System (INIS)

    Luchini, A.; Petricoin, E.F.; Geho, D.H.; Liotta, L.A.; Long, D.P.; Vaisman, I.I.

    2008-01-01

    Inelastic electron tunneling spectroscopy (IETS) is a valuable in situ spectroscopic analysis technique that provides a direct portrait of the electron transport properties of a molecular species. In the past, IETS has been applied to small molecules. Using self-assembled nano electronic junctions, IETS was performed for the first time on a large polypeptide protein peptide in the phosphorylated and native form, yielding interpretable spectra. A reproducible 10-fold shift of the I/V characteristics of the peptide was observed upon phosphorylation. Phosphorylation can be utilized as a site-specific modification to alter peptide structure and thereby influence electron transport in peptide molecular junctions. It is envisioned that kinases and phosphatases may be used to create tunable systems for molecular electronics applications, such as biosensors and memory devices.

  13. Electron and Phonon Transport in Molecular Junctions

    DEFF Research Database (Denmark)

    Li, Qian

    Molecular electronics provide the possibility to investigate electron and phonon transport at the smallest imaginable scale, where quantum effects can be investigated and exploited directly in the design. In this thesis, we study both electron transport and phonon transport in molecular junctions....... The system we are interested in here are π-stacked molecules connected with two semi-infinite leads. π-stacked aromatic rings, connected via π-π electronic coupling, provides a rather soft mechanical bridge while maintaining high electronic conductivity. We investigate electron transport...... transmission at the Fermi energy. We propose and analyze a way of using π   stacking to design molecular junctions to control heat transport. We develop a simple model system to identify optimal parameter regimes and then use density functional theory (DFT) to extract model parameters for a number of specific...

  14. Electron transport in doped fullerene molecular junctions

    Science.gov (United States)

    Kaur, Milanpreet; Sawhney, Ravinder Singh; Engles, Derick

    The effect of doping on the electron transport of molecular junctions is analyzed in this paper. The doped fullerene molecules are stringed to two semi-infinite gold electrodes and analyzed at equilibrium and nonequilibrium conditions of these device configurations. The contemplation is done using nonequilibrium Green’s function (NEGF)-density functional theory (DFT) to evaluate its density of states (DOS), transmission coefficient, molecular orbitals, electron density, charge transfer, current, and conductance. We conclude from the elucidated results that Au-C16Li4-Au and Au-C16Ne4-Au devices behave as an ordinary p-n junction diode and a Zener diode, respectively. Moreover, these doped fullerene molecules do not lose their metallic nature when sandwiched between the pair of gold electrodes.

  15. Electron Transport through Porphyrin Molecular Junctions

    Science.gov (United States)

    Zhou, Qi

    The goal of this work is to study the properties that would affect the electron transport through a porphyrin molecular junction. This work contributes to the field of electron transport in molecular junctions in the following 3 aspects. First of all, by carrying out experiments comparing the conductance of the iron (III) porphyrin (protected) and the free base porphyrin (protected), it is confirmed that the molecular energy level broadening and shifting occurs for porphyrin molecules when coupled with the metal electrodes, and this level broadening and shifting plays an important role in the electron transport through molecular junctions. Secondly, by carrying out an in-situ deprotection of the acetyl-protected free base porphyrin molecules, it is found out that the presence of acetyl groups reduces the conductance. Thirdly, by incorporating the Matrix-assisted laser desorption/ionization (MALDI) spectrum and the in-situ deprotection prior to formation of molecular junctions, it allows a more precise understanding of the molecules involved in the formation of molecular junctions, and therefore allows an accurate analysis of the conductance histogram. The molecules are prepared by self-assembly and the junctions are formed using a Scanning Tunneling Microscopy (STM) molecular break junction technique. The porphyrin molecules are characterized by MALDI in solution before self-assembly to a gold/mica substrate. The self-assembled monolayers (SAMs) of porphyrins on gold are characterized by Ultraviolet-visible (UV-Vis) reflection spectroscopy to confirm that the molecules are attached to the substrate. The SAMs are then characterized by Angle-Resolved X-ray photoelectron spectroscopy (ARXPS) to determine the thickness and the average molecular orientation of the molecular layer. The electron transport is measured by conductance-displacement (G-S) experiments under a given bias (-0.4V). The conductance value of a single molecule is identified by a statistical analysis

  16. Molecular Diffusion through Cyanobacterial Septal Junctions

    Directory of Open Access Journals (Sweden)

    Mercedes Nieves-Morión

    2017-01-01

    Full Text Available Heterocyst-forming cyanobacteria grow as filaments in which intercellular molecular exchange takes place. During the differentiation of N2-fixing heterocysts, regulators are transferred between cells. In the diazotrophic filament, vegetative cells that fix CO2 through oxygenic photosynthesis provide the heterocysts with reduced carbon and heterocysts provide the vegetative cells with fixed nitrogen. Intercellular molecular transfer has been traced with fluorescent markers, including calcein, 5-carboxyfluorescein, and the sucrose analogue esculin, which are observed to move down their concentration gradient. In this work, we used fluorescence recovery after photobleaching (FRAP assays in the model heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120 to measure the temperature dependence of intercellular transfer of fluorescent markers. We find that the transfer rate constants are directly proportional to the absolute temperature. This indicates that the “septal junctions” (formerly known as “microplasmodesmata” linking the cells in the filament allow molecular exchange by simple diffusion, without any activated intermediate state. This constitutes a novel mechanism for molecular transfer across the bacterial cytoplasmic membrane, in addition to previously characterized mechanisms for active transport and facilitated diffusion. Cyanobacterial septal junctions are functionally analogous to the gap junctions of metazoans.

  17. Electronic transport properties of phenylacetylene molecular junctions

    International Nuclear Information System (INIS)

    Liu Wen; Cheng Jie; Yan Cui-Xia; Li Hai-Hong; Wang Yong-Juan; Liu De-Sheng

    2011-01-01

    Electronic transport properties of a kind of phenylacetylene compound— (4-mercaptophenyl)-phenylacetylene are calculated by the first-principles method in the framework of density functional theory and the nonequilibrium Green's function formalism. The molecular junction shows an obvious rectifying behaviour at a bias voltage larger than 1.0 V. The rectification effect is attributed to the asymmetry of the interface contacts. Moreover, at a bias voltage larger than 2.0 V, which is not referred to in a relevant experiment [Fang L, Park J Y, Ma H, Jen A K Y and Salmeron M 2007 Langmuir 23 11522], we find a negative differential resistance phenomenon. The negative differential resistance effect may originate from the change of the delocalization degree of the molecular orbitals induced by the bias. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  18. Surface-Enhanced Raman Scattering in Molecular Junctions.

    Science.gov (United States)

    Iwane, Madoka; Fujii, Shintaro; Kiguchi, Manabu

    2017-08-18

    Surface-enhanced Raman scattering (SERS) is a surface-sensitive vibrational spectroscopy that allows Raman spectroscopy on a single molecular scale. Here, we present a review of SERS from molecular junctions, in which a single molecule or molecules are made to have contact from the top to the bottom of metal surfaces. The molecular junctions are nice platforms for SERS as well as transport measurement. Electronic characterization based on the transport measurements of molecular junctions has been extensively studied for the development of miniaturized electronic devices. Simultaneous SERS and transport measurement of the molecular junctions allow both structural (geometrical) and electronic information on the single molecule scale. The improvement of SERS measurement on molecular junctions open the door toward new nanoscience and nanotechnology in molecular electronics.

  19. Breaking into the epithelial apical-junctional complex--news from pathogen hackers.

    Science.gov (United States)

    Vogelmann, Roger; Amieva, Manuel R; Falkow, Stanley; Nelson, W James

    2004-02-01

    The epithelial apical-junctional complex is a key regulator of cellular functions. In addition, it is an important target for microbial pathogens that manipulate the cell to survive, proliferate and sometimes persist within a host. Out of a myriad of potential molecular targets, some bacterial and viral pathogens have selected a subset of protein targets at the apical-junctional complex of epithelial cells. Studying how microbes use these targets also teaches us about the inherent physiological properties of host molecules in the context of normal junctional structure and function. Thus, we have learned that three recently uncovered components of the apical-junctional complex of the Ig superfamily--junctional adhesion molecule, Nectin and the coxsackievirus and adenovirus receptor--are important regulators of junction structure and function and represent critical targets of microbial virulence gene products.

  20. Breaking into the epithelial apical–junctional complex — news from pathogen hackers

    Science.gov (United States)

    Vogelmann, Roger; Amieva, Manuel R; Falkow, Stanley; Nelson, W James

    2012-01-01

    The epithelial apical–junctional complex is a key regulator of cellular functions. In addition, it is an important target for microbial pathogens that manipulate the cell to survive, proliferate and sometimes persist within a host. Out of a myriad of potential molecular targets, some bacterial and viral pathogens have selected a subset of protein targets at the apical–junctional complex of epithelial cells. Studying how microbes use these targets also teaches us about the inherent physiological properties of host molecules in the context of normal junctional structure and function. Thus, we have learned that three recently uncovered components of the apical–junctional complex of the Ig superfamily — junctional adhesion molecule, Nectin and the coxsackievirus and adenovirus receptor — are important regulators of junction structure and function and represent critical targets of microbial virulence gene products. PMID:15037310

  1. On simulation of local fluxes in molecular junctions

    Science.gov (United States)

    Cabra, Gabriel; Jensen, Anders; Galperin, Michael

    2018-05-01

    We present a pedagogical review of the current density simulation in molecular junction models indicating its advantages and deficiencies in analysis of local junction transport characteristics. In particular, we argue that current density is a universal tool which provides more information than traditionally simulated bond currents, especially when discussing inelastic processes. However, current density simulations are sensitive to the choice of basis and electronic structure method. We note that while discussing the local current conservation in junctions, one has to account for the source term caused by the open character of the system and intra-molecular interactions. Our considerations are illustrated with numerical simulations of a benzenedithiol molecular junction.

  2. Virus interaction with the apical junctional complex.

    Science.gov (United States)

    Gonzalez-Mariscal, Lorenza; Garay, Erika; Lechuga, Susana

    2009-01-01

    In order to infect pathogens must breach the epithelial barriers that separate the organism from the external environment or that cover the internal cavities and ducts of the body. Epithelia seal the passage through the paracellular pathway with the apical junctional complex integrated by tight and adherens junctions. In this review we describe how viruses like coxsackie, swine vesicular disease virus, adenovirus, reovirus, feline calcivirus, herpes viruses 1 and 2, pseudorabies, bovine herpes virus 1, poliovirus and hepatitis C use as cellular receptors integral proteins present at the AJC of epithelial cells. Interaction with these proteins contributes in a significant manner in defining the particular tropism of each virus. Besides these proteins, viruses exhibit a wide range of cellular co-receptors among which proteins present in the basolateral cell surface like integrins are often found. Therefore targeting proteins of the AJC constitutes a strategy that might allow viruses to bypass the physical barrier that blocks their access to receptors expressed on the basolateral surface of epithelial cells.

  3. Amorphous molecular junctions produced by ion irradiation on carbon nanotubes

    International Nuclear Information System (INIS)

    Wang Zhenxia; Yu Liping; Zhang Wei; Ding Yinfeng; Li Yulan; Han Jiaguang; Zhu Zhiyuan; Xu Hongjie; He Guowei; Chen Yi; Hu Gang

    2004-01-01

    Experiments and molecular dynamics have demonstrated that electron irradiation could create molecular junctions between crossed single-wall carbon nanotubes. Recently molecular dynamics computation predicted that ion irradiation could also join single-walled carbon nanotubes. Employing carbon ion irradiation on multi-walled carbon nanotubes, we find that these nanotubes evolve into amorphous carbon nanowires, more importantly, during the process of which various molecular junctions of amorphous nanowires are formed by welding from crossed carbon nanotubes. It demonstrates that ion-beam irradiation could be an effective way not only for the welding of nanotubes but also for the formation of nanowire junctions

  4. Molecular electronics: some views on transport junctions and beyond.

    Science.gov (United States)

    Joachim, Christian; Ratner, Mark A

    2005-06-21

    The field of molecular electronics comprises a fundamental set of issues concerning the electronic response of molecules as parts of a mesoscopic structure and a technology-facing area of science. We will overview some important aspects of these subfields. The most advanced ideas in the field involve the use of molecules as individual logic or memory units and are broadly based on using the quantum state space of the molecule. Current work in molecular electronics usually addresses molecular junction transport, where the molecule acts as a barrier for incoming electrons: This is the fundamental Landauer idea of "conduction as scattering" generalized to molecular junction structures. Another point of view in terms of superexchange as a guiding mechanism for coherent electron transfer through the molecular bridge is discussed. Molecules generally exhibit relatively strong vibronic coupling. The last section of this overview focuses on vibronic effects, including inelastic electron tunneling spectroscopy, hysteresis in junction charge transport, and negative differential resistance in molecular transport junctions.

  5. Charge transport in single photochromic molecular junctions

    Science.gov (United States)

    Kim, Youngsang; Pietsch, T.; Scheer, Elke; Hellmuth, T.; Pauly, F.; Sysoiev, D.; Huhn, T.; Exner, T.; Groth, U.; Steiner, U.; Erbe, A.

    2012-02-01

    Recently, photoswitchable molecules, i.e. diarylethene, gained significant interest due to their applicability in data storage media, as optical switches, and in novel logic circuits [1]. Diarylethene-derivative molecules are the most promising candidates to design electronic functional elements, because of their excellent thermal stability, high fatigue resistance, and negligible change upon switching [1]. Here, we present the preferential conductance of specifically designed sulfur-free diarylethene molecules [2] bridging the mechanically controlled break-junctions at low temperatures [3]. The molecular energy levels and electrode couplings are obtained by evaluating the current-voltage characteristics using the single-level model [4]. The charge transport mechanism of different types of diarylethene molecules is investigated, and the results are discussed within the framework of novel theoretical predictions. [4pt] [1] M. Del Valle etal., Nat Nanotechnol 2, 176 (2007) S. J. van der Molen etal., Nano. Lett. 9, 76 (2009).[0pt] [2] D. Sysoiev etal., Chem. Eur. J. 17, 6663 (2011).[0pt] [3] Y. Kim etal., Phys. Rev. Lett. 106, 196804 (2011).[0pt] [4] Y. Kim etal., Nano Lett. 11, 3734 (2011). L. Zotti etal., Small 6, 1529 (2010).

  6. Molecular anatomy of interendothelial junctions in human blood-brain barrier microvessels.

    Directory of Open Access Journals (Sweden)

    Andrzej W Vorbrodt

    2004-07-01

    Full Text Available Immunogold cytochemical procedure was used to study the localization at the ultrastructural level of interendothelial junction-associated protein molecules in the human brain blood microvessels, representing the anatomic site of the blood-brain barrier (BBB. Ultrathin sections of Lowicryl K4M-embedded biopsy specimens of human cerebral cortex obtained during surgical procedures were exposed to specific antibodies, followed by colloidal gold-labeled secondary antibodies. All tight junction-specific integral membrane (transmembrane proteins--occludin, junctional adhesion molecule (JAM-1, and claudin-5--as well as peripheral zonula occludens protein (ZO-1 were highly expressed. Immunoreactivity of the adherens junction-specific transmembrane protein VE-cadherin was of almost similar intensity. Immunolabeling of the adherens junction-associated peripheral proteins--alpha-catenin, beta-catenin, and p120 catenin--although positive, was evidently less intense. The expression of gamma-catenin (plakoglobin was considered questionable because solitary immunosignals (gold particles appeared in only a few microvascular profiles. Double labeling of some sections made possible to observe strict colocalization of the junctional molecules, such as occludin and ZO-1 or JAM-1 and VE-cadherin, in the interendothelial junctions. We found that in human brain microvessels, the interendothelial junctional complexes contain molecular components specific for both tight and adherens junctions. It is assumed that the data obtained can help us find the immunodetectable junctional molecules that can serve as sensitive markers of normal or abnormal function of the BBB.

  7. Quantitatively accurate calculations of conductance and thermopower of molecular junctions

    DEFF Research Database (Denmark)

    Markussen, Troels; Jin, Chengjun; Thygesen, Kristian Sommer

    2013-01-01

    Thermopower measurements of molecular junctions have recently gained interest as a characterization technique that supplements the more traditional conductance measurements. Here we investigate the electronic conductance and thermopower of benzenediamine (BDA) and benzenedicarbonitrile (BDCN...

  8. Short chain molecular junctions: Charge transport versus dipole moment

    International Nuclear Information System (INIS)

    Ikram, I. Mohamed; Rabinal, M.K.

    2015-01-01

    Graphical abstract: - Highlights: • The role of dipole moment of organic molecules on molecular junctions has been studied. • Molecular junctions constituted using propargyl molecules of different dipole moments. • The electronic properties of the molecules were calculated using Gaussian software. • Junctions show varying rectification due to their varying dipole moment and orientation. - Abstract: The investigation of the influence of dipole moment of short chain organic molecules having three carbon atoms varying in end group on silicon surface was carried on. Here, we use three different molecules of propargyl series varying in dipole moment and its orientation to constitute molecular junctions. The charge transport mechanism in metal–molecules–semiconductor (MMS) junction obtained from current–voltage (I–V) characteristics shows the rectification behavior for two junctions whereas the other junction shows a weak rectification. The electronic properties of the molecules were calculated using Gaussian software package. The observed rectification behavior of these junctions is examined and found to be accounted to the orientation of dipole moment and electron cloud density distribution inside the molecules

  9. Advance of Mechanically Controllable Break Junction for Molecular Electronics.

    Science.gov (United States)

    Wang, Lu; Wang, Ling; Zhang, Lei; Xiang, Dong

    2017-06-01

    Molecular electronics stands for the ultimate size of functional elements, keeping up with an unstoppable trend over the past few decades. As a vital component of molecular electronics, single molecular junctions have attracted significant attention from research groups all over the world. Due to its pronounced superiority, the mechanically controllable break junctions (MCBJ) technique has been widely applied to characterize the dynamic performance of single molecular junctions. This review presents a system analysis for single-molecule junctions and offers an overview of four test-beds for single-molecule junctions, thus offering more insight into the mechanisms of electron transport. We mainly focus on the development of state-of-the-art mechanically controlled break junctions. The three-terminal gated MCBJ approaches are introduced to manipulate the electron transport of molecules, and MCBJs are combined with characterization techniques. Additionally, applications of MCBJs and remarkable properties of single molecules are addressed. Finally, the challenges and perspective for the mechanically controllable break junctions technique are provided.

  10. Observation of molecular level behavior in molecular electronic junction device

    Science.gov (United States)

    Maitani, Masato

    In this dissertation, I utilize AFM based scanning probe measurement and surface enhanced Raman scattering based vibrational spectroscopic analysis to directly characterize topographic, electronic, and chemical properties of molecules confined in the local area of M3 junction to elucidate the molecular level behavior of molecular junction electronic devices. In the introduction, the characterization of molecular electronic devices with different types of metal-molecule-metal (M3) structures based upon self-assembled monolayers (SAMs) is reviewed. A background of the characterization methods I use in this dissertation, conducting probe atomic force microscopy (cp-AFM) and surface enhanced Raman spectroscopy (SERS), is provided in chapter 1. Several attempts are performed to create the ideal top metal contacts on SAMs by metal vapor phase deposition in order to prevent the metal penetration inducing critical defects of the molecular electronic devices. The scanning probe microscopy (SPM), such as cp-AFM, contact mode (c-) AFM and non-contact mode (nc-) AFM, in ultra high vacuum conditions are utilized to study the process of the metal-SAM interface construction in terms of the correlation between the morphological and electrical properties including the metal nucleation and filament generation as a function of the functionalization of long-chain alkane thiolate SAMs on Au. In chapter 2, the nascent condensation process of vapor phase Al deposition on inert and reactive SAMs are studied by SPM. The results of top deposition, penetration, and filament generation of deposited Al are discussed and compared to the results previously observed by spectroscopic measurements. Cp-AFM was shown to provide new insights into Al filament formation which has not been observed by conventional spectroscopic analysis. Additionally, the electronic characteristics of individual Al filaments are measured. Chapter 3 reveals SPM characterization of Au deposition onto --COOH terminated SAMs

  11. Quantifying transition voltage spectroscopy of molecular junctions: Ab initio calculations

    DEFF Research Database (Denmark)

    Chen, Jingzhe; Markussen, Troels; Thygesen, Kristian Sommer

    2010-01-01

    Transition voltage spectroscopy (TVS) has recently been introduced as a spectroscopic tool for molecular junctions where it offers the possibility to probe molecular level energies at relatively low bias voltages. In this work we perform extensive ab initio calculations of the nonlinear current...

  12. Fast, clash-free RNA conformational morphing using molecular junctions.

    Science.gov (United States)

    Héliou, Amélie; Budday, Dominik; Fonseca, Rasmus; van den Bedem, Henry

    2017-07-15

    Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. Despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groups of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation. The source code, binaries and data are available at https://simtk.org/home/kgs . amelie.heliou@polytechnique.edu or vdbedem@stanford.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  13. Unique cell type-specific junctional complexes in vascular endothelium of human and rat liver sinusoids.

    Directory of Open Access Journals (Sweden)

    Cyrill Géraud

    Full Text Available Liver sinusoidal endothelium is strategically positioned to control access of fluids, macromolecules and cells to the liver parenchyma and to serve clearance functions upstream of the hepatocytes. While clearance of macromolecular debris from the peripheral blood is performed by liver sinusoidal endothelial cells (LSECs using a delicate endocytic receptor system featuring stabilin-1 and -2, the mannose receptor and CD32b, vascular permeability and cell trafficking are controlled by transcellular pores, i.e. the fenestrae, and by intercellular junctional complexes. In contrast to blood vascular and lymphatic endothelial cells in other organs, the junctional complexes of LSECs have not yet been consistently characterized in molecular terms. In a comprehensive analysis, we here show that LSECs express the typical proteins found in endothelial adherens junctions (AJ, i.e. VE-cadherin as well as α-, β-, p120-catenin and plakoglobin. Tight junction (TJ transmembrane proteins typical of endothelial cells, i.e. claudin-5 and occludin, were not expressed by rat LSECs while heterogenous immunreactivity for claudin-5 was detected in human LSECs. In contrast, junctional molecules preferentially associating with TJ such as JAM-A, B and C and zonula occludens proteins ZO-1 and ZO-2 were readily detected in LSECs. Remarkably, among the JAMs JAM-C was considerably over-expressed in LSECs as compared to lung microvascular endothelial cells. In conclusion, we show here that LSECs form a special kind of mixed-type intercellular junctions characterized by co-occurrence of endothelial AJ proteins, and of ZO-1 and -2, and JAMs. The distinct molecular architecture of the intercellular junctional complexes of LSECs corroborates previous ultrastructural findings and provides the molecular basis for further analyses of the endothelial barrier function of liver sinusoids under pathologic conditions ranging from hepatic inflammation to formation of liver metastasis.

  14. Temperature effects on quantum interference in molecular junctions

    DEFF Research Database (Denmark)

    Markussen, Troels; Thygesen, Kristian Sommer

    2014-01-01

    A number of experiments have demonstrated that destructive quantum interference (QI) effects in molecular junctions lead to very low conductances even at room temperature. On the other hand, another recent experiment showed increasing conductance with temperature which was attributed to decoheren...

  15. Trichomonas vaginalis perturbs the junctional complex in epithelial cells

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Trichomonas vaginalis, a protist parasite of the urogenital tract in humans, is the causative agent of trichomonosis,which in recent years have been associated with the cervical cancer development. In the present study we analyzed the modifications at the junctional complex level of Caco-2 cells after interaction with two isolates of T. vaginalis and the influence of the iron concentration present in the parasite's culture medium on the interaction effects. Our results show that T. vaginalis adheres to the epithelial cell causing alterations in the junctional complex, such as: (a) a decrease in transepithelial electrical resistance; (b) alteration in the pattern of junctional complex proteins distribution as obseryed for E-cadherin, occludin and ZO-1; and (c) enlargement of the spaces between epithelial cells. These effects were dependent on (a) the degree of the parasite virulence isolate, (b) the iron concentration in the culture medium, and (c) the expression of adhesin proteins on the parasite surface.

  16. Spin nutation effects in molecular nanomagnet–superconductor tunnel junctions

    International Nuclear Information System (INIS)

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

    2013-01-01

    We study the spin nutation effects of a molecular nanomagnet on the Josephson current through a superconductor|molecular nanomagnet|superconductor tunnel junction. We explicitly demonstrate that, due to the spin nutation of the molecular nanomagnet, two oscillatory terms emerge in the ac Josephson current in addition to the conventional ac Josephson current. Some resonances occur in the junction due to the interactions of the transported quasiparticles with the bias voltage and molecular nanomagnet spin dynamics. Their appearance indicates that the energy exchanged during these interactions is in the range of the superconducting energy gap. We also show that the spin nutation is able to convert the ac Josephson current to a dc current, which is interesting for applications. (paper)

  17. Transition from direct to inverted charge transport Marcus regions in molecular junctions via molecular orbital gating

    Science.gov (United States)

    Yuan, Li; Wang, Lejia; Garrigues, Alvar R.; Jiang, Li; Annadata, Harshini Venkata; Anguera Antonana, Marta; Barco, Enrique; Nijhuis, Christian A.

    2018-04-01

    Solid-state molecular tunnel junctions are often assumed to operate in the Landauer regime, which describes essentially activationless coherent tunnelling processes. In solution, on the other hand, charge transfer is described by Marcus theory, which accounts for thermally activated processes. In practice, however, thermally activated transport phenomena are frequently observed also in solid-state molecular junctions but remain poorly understood. Here, we show experimentally the transition from the Marcus to the inverted Marcus region in a solid-state molecular tunnel junction by means of intra-molecular orbital gating that can be tuned via the chemical structure of the molecule and applied bias. In the inverted Marcus region, charge transport is incoherent, yet virtually independent of temperature. Our experimental results fit well to a theoretical model that combines Landauer and Marcus theories and may have implications for the interpretation of temperature-dependent charge transport measurements in molecular junctions.

  18. An EMMPRIN–γ-catenin–Nm23 complex drives ATP production and actomyosin contractility at endothelial junctions

    Science.gov (United States)

    Moreno, Vanessa; Gonzalo, Pilar; Gómez-Escudero, Jesús; Pollán, Ángela; Acín-Pérez, Rebeca; Breckenridge, Mark; Yáñez-Mó, María; Barreiro, Olga; Orsenigo, Fabrizio; Kadomatsu, Kenji; Chen, Christopher S.; Enríquez, José A.; Dejana, Elisabetta; Sánchez-Madrid, Francisco; Arroyo, Alicia G.

    2014-01-01

    ABSTRACT Cell–cell adhesions are important sites through which cells experience and resist forces. In endothelial cells, these forces regulate junction dynamics and determine endothelial barrier strength. We identify the Ig superfamily member EMMPRIN (also known as basigin) as a coordinator of forces at endothelial junctions. EMMPRIN localization at junctions correlates with endothelial junction strength in different mouse vascular beds. Accordingly, EMMPRIN-deficient mice show altered junctions and increased junction permeability. Lack of EMMPRIN alters the localization and function of VE-cadherin (also known as cadherin-5) by decreasing both actomyosin contractility and tugging forces at endothelial cell junctions. EMMPRIN ensures proper actomyosin-driven maturation of competent endothelial junctions by forming a molecular complex with γ-catenin (also known as junction plakoglobin) and Nm23 (also known as NME1), a nucleoside diphosphate kinase, thereby locally providing ATP to fuel the actomyosin machinery. These results provide a novel mechanism for the regulation of actomyosin contractility at endothelial junctions and might have broader implications in biological contexts such as angiogenesis, collective migration and tissue morphogenesis by coupling compartmentalized energy production to junction assembly. PMID:24994937

  19. An EMMPRIN-γ-catenin-Nm23 complex drives ATP production and actomyosin contractility at endothelial junctions.

    Science.gov (United States)

    Moreno, Vanessa; Gonzalo, Pilar; Gómez-Escudero, Jesús; Pollán, Ángela; Acín-Pérez, Rebeca; Breckenridge, Mark; Yáñez-Mó, María; Barreiro, Olga; Orsenigo, Fabrizio; Kadomatsu, Kenji; Chen, Christopher S; Enríquez, José A; Dejana, Elisabetta; Sánchez-Madrid, Francisco; Arroyo, Alicia G

    2014-09-01

    Cell-cell adhesions are important sites through which cells experience and resist forces. In endothelial cells, these forces regulate junction dynamics and determine endothelial barrier strength. We identify the Ig superfamily member EMMPRIN (also known as basigin) as a coordinator of forces at endothelial junctions. EMMPRIN localization at junctions correlates with endothelial junction strength in different mouse vascular beds. Accordingly, EMMPRIN-deficient mice show altered junctions and increased junction permeability. Lack of EMMPRIN alters the localization and function of VE-cadherin (also known as cadherin-5) by decreasing both actomyosin contractility and tugging forces at endothelial cell junctions. EMMPRIN ensures proper actomyosin-driven maturation of competent endothelial junctions by forming a molecular complex with γ-catenin (also known as junction plakoglobin) and Nm23 (also known as NME1), a nucleoside diphosphate kinase, thereby locally providing ATP to fuel the actomyosin machinery. These results provide a novel mechanism for the regulation of actomyosin contractility at endothelial junctions and might have broader implications in biological contexts such as angiogenesis, collective migration and tissue morphogenesis by coupling compartmentalized energy production to junction assembly. © 2014. Published by The Company of Biologists Ltd.

  20. Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions

    Czech Academy of Sciences Publication Activity Database

    Zobač, Vladimír; Lewis, J.P.; Jelínek, Pavel

    2016-01-01

    Roč. 27, č. 28 (2016), 1-8, č. článku 285202. ISSN 0957-4484 R&D Projects: GA ČR(CZ) GA14-02079S Institutional support: RVO:68378271 Keywords : non-adiabatic molecular dynamics * molecular junctions * molecular switches * DFT Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.440, year: 2016

  1. Spin polarized electron tunneling and magnetoresistance in molecular junctions.

    Science.gov (United States)

    Szulczewski, Greg

    2012-01-01

    This chapter reviews tunneling of spin-polarized electrons through molecules positioned between ferromagnetic electrodes, which gives rise to tunneling magnetoresistance. Such measurements yield important insight into the factors governing spin-polarized electron injection into organic semiconductors, thereby offering the possibility to manipulate the quantum-mechanical spin degrees of freedom for charge carriers in optical/electrical devices. In the first section of the chapter a brief description of the Jullière model of spin-dependent electron tunneling is reviewed. Next, a brief description of device fabrication and characterization is presented. The bulk of the review highlights experimental studies on spin-polarized electron tunneling and magnetoresistance in molecular junctions. In addition, some experiments describing spin-polarized scanning tunneling microscopy/spectroscopy on single molecules are mentioned. Finally, some general conclusions and prospectus on the impact of spin-polarized tunneling in molecular junctions are offered.

  2. Understanding the length dependence of molecular junction thermopower

    DEFF Research Database (Denmark)

    Karlström, Sven Olov Harald; Strange, Mikkel; Solomon, Gemma

    2014-01-01

    Thermopower of molecular junctions is sensitive to details in the junction and may increase, decrease, or saturate with increasing chain length, depending on the system. Using McConnell's theory for exponentially suppressed transport together with a simple and easily interpretable tight binding...... model, we show how these different behaviors depend on the molecular backbone and its binding to the contacts. We distinguish between resonances from binding groups or undercoordinated electrode atoms, and those from the periodic backbone. It is demonstrated that while the former gives a length......-independent contribution to the thermopower, possibly changing its sign, the latter determines its length dependence. This means that the question of which orbitals from the periodic chain that dominate the transport should not be inferred from the sign of the thermopower but from its length dependence. We find...

  3. Mechanical tuning of conductance and thermopower in helicene molecular junctions

    Czech Academy of Sciences Publication Activity Database

    Vacek, Jaroslav; Vacek Chocholoušová, Jana; Stará, Irena G.; Starý, Ivo; Dubi, Y.

    2015-01-01

    Roč. 7, č. 19 (2015), s. 8793-8802 ISSN 2040-3364 R&D Projects: GA ČR(CZ) GAP207/10/2207 Institutional support: RVO:61388963 Keywords : helicene molecular junctions * quantum interference * stereoselective syntheses * nonlinear optical properties Subject RIV: CC - Organic Chemistry Impact factor: 7.760, year: 2015 http://pubs.rsc.org/en/content/articlepdf/2015/nr/c5nr01297j

  4. Adsorbate-driven cooling of carbene-based molecular junctions

    Czech Academy of Sciences Publication Activity Database

    Foti, Giuseppe; Vázquez, Héctor

    2017-01-01

    Roč. 8, Oct (2017), s. 2060-2068 ISSN 2190-4286 R&D Projects: GA ČR GA15-19672S EU Projects: European Commission(XE) 702114 - HEATEXMOL Institutional support: RVO:68378271 Keywords : adsorbate * carbene * current-induced heating and cooling * molecular junction * vibrations Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 3.127, year: 2016

  5. Fabrication of tunnel junction-based molecular electronics and spintronics devices

    International Nuclear Information System (INIS)

    Tyagi, Pawan

    2012-01-01

    Tunnel junction-based molecular devices (TJMDs) are highly promising for realizing futuristic electronics and spintronics devices for advanced logic and memory operations. Under this approach, ∼2.5 nm molecular device elements bridge across the ∼2-nm thick insulator of a tunnel junction along the exposed side edge(s). This paper details the efforts and insights for producing a variety of TJMDs by resolving multiple device fabrication and characterization issues. This study specifically discusses (i) compatibility between tunnel junction test bed and molecular solutions, (ii) optimization of the exposed side edge profile and insulator thickness for enhancing the probability of molecular bridging, (iii) effect of fabrication process-induced mechanical stresses, and (iv) minimizing electrical bias-induced instability after the device fabrication. This research will benefit other researchers interested in producing TJMDs efficiently. TJMD approach offers an open platform to test virtually any combination of magnetic and nonmagnetic electrodes, and promising molecules such as single molecular magnets, porphyrin, DNA, and molecular complexes.

  6. Communication: Finding destructive interference features in molecular transport junctions

    Energy Technology Data Exchange (ETDEWEB)

    Reuter, Matthew G., E-mail: mgreuter@u.northwestern.edu [Department of Chemistry, Northwestern University, Evanston, Illinois 60208 (United States); Hansen, Thorsten [Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen, DK 2100 Copenhagen (Denmark)

    2014-11-14

    Associating molecular structure with quantum interference features in electrode-molecule-electrode transport junctions has been difficult because existing guidelines for understanding interferences only apply to conjugated hydrocarbons. Herein we use linear algebra and the Landauer-Büttiker theory for electron transport to derive a general rule for predicting the existence and locations of interference features. Our analysis illustrates that interferences can be directly determined from the molecular Hamiltonian and the molecule–electrode couplings, and we demonstrate its utility with several examples.

  7. Tuning the thermal conductance of molecular junctions with interference effects

    Science.gov (United States)

    Klöckner, J. C.; Cuevas, J. C.; Pauly, F.

    2017-12-01

    We present an ab initio study of the role of interference effects in the thermal conductance of single-molecule junctions. To be precise, using a first-principles transport method based on density functional theory, we analyze the coherent phonon transport in single-molecule junctions made of several benzene and oligo(phenylene ethynylene) derivatives. We show that the thermal conductance of these junctions can be tuned via the inclusion of substituents, which induces destructive interference effects and results in a decrease of the thermal conductance with respect to the unmodified molecules. In particular, we demonstrate that these interference effects manifest as antiresonances in the phonon transmission, whose energy positions can be tuned by varying the mass of the substituents. Our work provides clear strategies for the heat management in molecular junctions and, more generally, in nanostructured metal-organic hybrid systems, which are important to determine how these systems can function as efficient energy-conversion devices such as thermoelectric generators and refrigerators.

  8. Dynamical photo-induced electronic properties of molecular junctions

    Science.gov (United States)

    Beltako, K.; Michelini, F.; Cavassilas, N.; Raymond, L.

    2018-03-01

    Nanoscale molecular-electronic devices and machines are emerging as promising functional elements, naturally flexible and efficient, for next-generation technologies. A deeper understanding of carrier dynamics in molecular junctions is expected to benefit many fields of nanoelectronics and power devices. We determine time-resolved charge current flowing at the donor-acceptor interface in molecular junctions connected to metallic electrodes by means of quantum transport simulations. The current is induced by the interaction of the donor with a Gaussian-shape femtosecond laser pulse. Effects of the molecular internal coupling, metal-molecule tunneling, and light-donor coupling on photocurrent are discussed. We then define the time-resolved local density of states which is proposed as an efficient tool to describe the absorbing molecule in contact with metallic electrodes. Non-equilibrium reorganization of hybridized molecular orbitals through the light-donor interaction gives rise to two phenomena: the dynamical Rabi shift and the appearance of Floquet-like states. Such insights into the dynamical photoelectronic structure of molecules are of strong interest for ultrafast spectroscopy and open avenues toward the possibility of analyzing and controlling the internal properties of quantum nanodevices with pump-push photocurrent spectroscopy.

  9. Structural Molecular Components of Septate Junctions in Cnidarians Point to the Origin of Epithelial Junctions in Eukaryotes

    KAUST Repository

    Ganot, P.; Zoccola, D.; Tambutte, E.; Voolstra, Christian R.; Aranda, Manuel; Allemand, D.; Tambutte, S.

    2014-01-01

    Septate junctions (SJs) insure barrier properties and control paracellular diffusion of solutes across epithelia in invertebrates. However, the origin and evolution of their molecular constituents in Metazoa have not been firmly established. Here

  10. Characterization of the Tetraspan Junctional Complex (4JC) superfamily.

    Science.gov (United States)

    Chou, Amy; Lee, Andre; Hendargo, Kevin J; Reddy, Vamsee S; Shlykov, Maksim A; Kuppusamykrishnan, Harikrishnan; Medrano-Soto, Arturo; Saier, Milton H

    2017-03-01

    Connexins or innexins form gap junctions, while claudins and occludins form tight junctions. In this study, statistical data, derived using novel software, indicate that these four junctional protein families and eleven other families of channel and channel auxiliary proteins are related by common descent and comprise the Tetraspan (4 TMS) Junctional Complex (4JC) Superfamily. These proteins all share similar 4 transmembrane α-helical (TMS) topologies. Evidence is presented that they arose via an intragenic duplication event, whereby a 2 TMS-encoding genetic element duplicated tandemly to give 4 TMS proteins. In cases where high resolution structural data were available, the conclusion of homology was supported by conducting structural comparisons. Phylogenetic trees reveal the probable relationships of these 15 families to each other. Long homologues containing fusions to other recognizable domains as well as internally duplicated or fused domains are reported. Large "fusion" proteins containing 4JC domains proved to fall predominantly into family-specific patterns as follows: (1) the 4JC domain was N-terminal; (2) the 4JC domain was C-terminal; (3) the 4JC domain was duplicated or occasionally triplicated and (4) mixed fusion types were present. Our observations provide insight into the evolutionary origins and subfunctions of these proteins as well as guides concerning their structural and functional relationships. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Electrochemically assisted mechanically controllable break junction studies on the stacking configurations of oligo(phenylene ethynylene)s molecular junctions

    International Nuclear Information System (INIS)

    Zheng, Jue-Ting; Yan, Run-Wen; Tian, Jing-Hua; Liu, Jun-Yang; Pei, Lin-Qi; Wu, De-Yin; Dai, Ke; Yang, Yang; Jin, Shan

    2016-01-01

    Highlights: • I-V characteristics of a series of oligo(phenylene ethynylene)s molecular junctions were measured. • Conductance values were found to be dependent on molecular length and substituent group. • The measured low conductance values were explained by theoretical calculations. • EC-MCBJ is feasible to fabricate and characterize molecular junctions. - Abstract: We demonstrate an electrochemically assisted mechanically controllable break junction (EC-MCBJ) approach for current-voltage characteristic (I-V curve) measurements of metal/molecule/metal junctions. A series of oligo(phenylene ethynylene)s compounds (OPEs), including those involving electron withdrawing substituent group and different backbone lengths, had been successfully designed, synthesized, and placed onto the fabricated nanogap to form molecular junctions. The observed evolution in the measured conductances of OPEs indicates that there is a dependence of conductance on molecular length and substituent group. Compared with those extracted from conductance histogram construction, the conductances of OPEs measured from I-V curves are considerably lower. Based on the transmission spectra of OPEs that calculated by density functional theory (DFT) combined with non-equilibrium Green’s function (NEGF) method, this difference was attributed to our distinct experimental operation, which may give rise to a stacking configuration of two OPE molecules.

  12. Influence of functional groups on charge transport in molecular junctions

    DEFF Research Database (Denmark)

    Mowbray, Duncan; Jones, Glenn; Thygesen, Kristian Sommer

    2008-01-01

    Using density functional theory (DFT), we analyze the influence of five classes of functional groups, as exemplified by NO2, OCH3, CH3, CCl3, and I, on the transport properties of a 1,4-benzenedithiolate (BDT) and 1,4-benzenediamine (BDA) molecular junction with gold electrodes. Our analysis...... demonstrates how ideas from functional group chemistry may be used to engineer a molecule's transport properties, as was shown experimentally and using a semiempirical model for BDA [Nano Lett. 7, 502 (2007)]. In particular, we show that the qualitative change in conductance due to a given functional group can...... be predicted from its known electronic effect (whether it is sigma/pi donating/withdrawing). However, the influence of functional groups on a molecule's conductance is very weak, as was also found in the BDA experiments. The calculated DFT conductances for the BDA species are five times larger than...

  13. Charging and geometric effects on conduction through Anthracene molecular junctions

    Science.gov (United States)

    Kaur, Rupan Preet; Sawhney, Ravinder Singh; Engles, Derick

    We studied the geometric effects on the charge transfer through the anthracenedithiol (ADT) molecular junction using density functional theory combined with the non-equilibrium Green’s function approach. Two major geometric aspects, bond length and bond angle, were moderated to optimize the electrical conduction. From the results established in this paper, we found that the electrical conduction can be tuned from 0.2 G0 to 0.9 G0 by varying the Au-S bond length, whereas the moderation of bonding angle assayed a minor change from 0.37 G0 to 0.47 G0. We attributed this escalating zero bias conductance to the increasing charge on the terminal sulfur atom of the ADT molecule, which increased the energy of the HOMO orbital towards Fermi level and exhibited a semi-metallic behaviour. Therefore, geometry plays a critical role in deciding the charge transport through the metal/molecule interface.

  14. Selective interface transparency in graphene nanoribbon based molecular junctions.

    Science.gov (United States)

    Dou, K P; Kaun, C C; Zhang, R Q

    2018-03-08

    A clear understanding of electrode-molecule interfaces is a prerequisite for the rational engineering of future generations of nanodevices that will rely on single-molecule coupling between components. With a model system, we reveal a peculiar dependence on interfaces in all graphene nanoribbon-based carbon molecular junctions. The effect can be classified into two types depending on the intrinsic feature of the embedded core graphene nanoflake (GNF). For metallic GNFs with |N A - N B | = 1, good/poor contact transparency occurs when the core device aligns with the center/edge of the electrode. The situation is reversed when a semiconducting GNF is the device, where N A = N B . These results may shed light on the design of real connecting components in graphene-based nanocircuits.

  15. Resonant tunneling via a Ru–dye complex using a nanoparticle bridge junction

    Science.gov (United States)

    Nishijima, Satoshi; Otsuka, Yoichi; Ohoyama, Hiroshi; Kajimoto, Kentaro; Araki, Kento; Matsumoto, Takuya

    2018-06-01

    Nonlinear current–voltage (I–V) characteristics is an important property for the realization of information processing in molecular electronics. We studied the electrical conduction through a Ru–dye complex (N-719) on a 2-aminoethanethiol (2-AET) monolayer in a nanoparticle bridge junction system. The nonlinear I–V characteristics exhibited a threshold voltage at around 1.2 V and little temperature dependence. From the calculation of the molecular states using density functional theory and the energy alignment between the electrodes and molecules, the conduction mechanism in this system was considered to be resonant tunneling via the HOMO level of N-719. Our results indicate that the weak electronic coupling of electrodes and molecules is essential for obtaining nonlinear I–V characteristics with a clear threshold voltage that reflect the intrinsic molecular state.

  16. Hydration effect on the electronic transport properties of oligomeric phenylene ethynylene molecular junctions

    International Nuclear Information System (INIS)

    Zong-Liang, Li; Huai-Zhi, Li; Yong, Ma; Guang-Ping, Zhang; Chuan-Kui, Wang

    2010-01-01

    A first-principles computational method based on the hybrid density functional theory is developed to simulate the electronic transport properties of oligomeric phenylene ethynylene molecular junctions with H 2 O molecules accumulated in the vicinity as recently reported by Na et al. [Nanotechnology 18 424001 (2007)]. The numerical results show that the hydrogen bonds between the oxygen atoms of the oligomeric phenylene ethynylene molecule and H 2 O molecules result in the localisation of the molecular orbitals and lead to the lower transition peaks. The H 2 O molecular chains accumulated in the vicinity of the molecular junction can not only change the electronic structure of the molecular junctions, but also open additional electronic transport pathways. The obvious influence of H 2 O molecules on the electronic structure of the molecular junction and its electronic transport properties is thus demonstrated. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  17. Negative differential resistance observation in complex convoluted fullerene junctions

    Science.gov (United States)

    Kaur, Milanpreet; Sawhney, Ravinder Singh; Engles, Derick

    2018-04-01

    In this work, we simulated the smallest fullerene molecule, C20 in a two-probe device model with gold electrodes. The gold electrodes comprised of (011) miller planes were carved to construct the novel geometry based four unique shapes, which were strung to fullerene molecules through mechanically controlled break junction techniques. The organized devices were later scrutinized using non-equilibrium Green's function based on the density functional theory to calculate their molecular orbitals, energy levels, charge transfers, and electrical parameters. After intense scrutiny, we concluded that five-edged and six-edged devices have the lowest and highest current-conductance values, which result from their electrode-dominating and electrode-subsidiary effects, respectively. However, an interesting observation was that the three-edged and four-edged electrodes functioned as semi-metallic in nature, allowing the C20 molecule to demonstrate its performance with the complementary effect of these electrodes in the electron conduction process of a two-probe device.

  18. [Dermoepidermic junction: a selective, complex and vital barrier].

    Science.gov (United States)

    Frede, Silvia C; Dionisio de Cabalier, María E; Zaya, Alejandro; Hliba, Ernesto

    2004-01-01

    Dermoepidermic junction (DEJ) is a highly complex region, containing a great variety of cellular elements, which despite of having different embriogenesis, interact with each other, generating different substances that keep the function and homeostasis of the greatest organ of the human body. DEJ is regarded as a highly specialized basal lamina, which acts as a highly selective pathway for the migration of cells and macromolecules, inducing cellular differentiation and micro enviromental metabolism modifications. DEJ may be divided into three zones regarding the basal lamina 1--the nearest to epidermic zone, having tonofilaments and hemidesmosomes, which keep anchored basal cells. This region is limited by the lamina densa 2--the intermediate zone, represented exclusively by lamina densa and finally the lamina 3,--the third region--extends from lamina densa to the upper dermis and extracelullar matrix. Despite there is much to learn about DEJ, the knowledge about each molecule and function of every compartment will enable us to know more about the pathogenesis of several dermatologic diseases, with a great prevalence in the clinical practice.

  19. Transition voltages of vacuum-spaced and molecular junctions with Ag and Pt electrodes

    KAUST Repository

    Wu, Kunlin; Bai, Meilin; Sanvito, Stefano; Hou, Shimin

    2014-01-01

    The transition voltage of vacuum-spaced and molecular junctions constructed with Ag and Pt electrodes is investigated by non-equilibrium Green's function formalism combined with density functional theory. Our calculations show that, similarly

  20. Large resistance change on magnetic tunnel junction based molecular spintronics devices

    Science.gov (United States)

    Tyagi, Pawan; Friebe, Edward

    2018-05-01

    Molecular bridges covalently bonded to two ferromagnetic electrodes can transform ferromagnetic materials and produce intriguing spin transport characteristics. This paper discusses the impact of molecule induced strong coupling on the spin transport. To study molecular coupling effect the octametallic molecular cluster (OMC) was bridged between two ferromagnetic electrodes of a magnetic tunnel junction (Ta/Co/NiFe/AlOx/NiFe/Ta) along the exposed side edges. OMCs induced strong inter-ferromagnetic electrode coupling to yield drastic changes in transport properties of the magnetic tunnel junction testbed at the room temperature. These OMCs also transformed the magnetic properties of magnetic tunnel junctions. SQUID and ferromagnetic resonance studies provided insightful data to explain transport studies on the magnetic tunnel junction based molecular spintronics devices.

  1. Structural Origins of Conductance Fluctuations in Gold–Thiolate Molecular Transport Junctions

    KAUST Repository

    French, William R.

    2013-03-21

    We report detailed atomistic simulations combined with high-fidelity conductance calculations to probe the structural origins of conductance fluctuations in thermally evolving Au-benzene-1,4-dithiolate-Au junctions. We compare the behavior of structurally ideal junctions (where the electrodes are modeled as flat surfaces) to structurally realistic, experimentally representative junctions resulting from break-junction simulations. The enhanced mobility of metal atoms in structurally realistic junctions results in significant changes to the magnitude and origin of the conductance fluctuations. Fluctuations are larger by a factor of 2-3 in realistic junctions compared to ideal junctions. Moreover, in junctions with highly deformed electrodes, the conductance fluctuations arise primarily from changes in the Au geometry, in contrast to results for junctions with nondeformed electrodes, where the conductance fluctuations are dominated by changes in the molecule geometry. These results provide important guidance to experimentalists developing strategies to control molecular conductance, and also to theoreticians invoking simplified structural models of junctions to predict their behavior. © 2013 American Chemical Society.

  2. Structural Origins of Conductance Fluctuations in Gold–Thiolate Molecular Transport Junctions

    KAUST Repository

    French, William R.; Iacovella, Christopher R.; Rungger, Ivan; Souza, Amaury Melo; Sanvito, Stefano; Cummings, Peter T.

    2013-01-01

    We report detailed atomistic simulations combined with high-fidelity conductance calculations to probe the structural origins of conductance fluctuations in thermally evolving Au-benzene-1,4-dithiolate-Au junctions. We compare the behavior of structurally ideal junctions (where the electrodes are modeled as flat surfaces) to structurally realistic, experimentally representative junctions resulting from break-junction simulations. The enhanced mobility of metal atoms in structurally realistic junctions results in significant changes to the magnitude and origin of the conductance fluctuations. Fluctuations are larger by a factor of 2-3 in realistic junctions compared to ideal junctions. Moreover, in junctions with highly deformed electrodes, the conductance fluctuations arise primarily from changes in the Au geometry, in contrast to results for junctions with nondeformed electrodes, where the conductance fluctuations are dominated by changes in the molecule geometry. These results provide important guidance to experimentalists developing strategies to control molecular conductance, and also to theoreticians invoking simplified structural models of junctions to predict their behavior. © 2013 American Chemical Society.

  3. Isolation of Synaptosomes, Synaptic Plasma Membranes, and Synaptic Junctional Complexes.

    Science.gov (United States)

    Michaelis, Mary L; Jiang, Lei; Michaelis, Elias K

    2017-01-01

    Isolation of synaptic nerve terminals or synaptosomes provides an opportunity to study the process of neurotransmission at many levels and with a variety of approaches. For example, structural features of the synaptic terminals and the organelles within them, such as synaptic vesicles and mitochondria, have been elucidated with electron microscopy. The postsynaptic membranes are joined to the presynaptic "active zone" of transmitter release through cell adhesion molecules and remain attached throughout the isolation of synaptosomes. These "post synaptic densities" or "PSDs" contain the receptors for the transmitters released from the nerve terminals and can easily be seen with electron microscopy. Biochemical and cell biological studies with synaptosomes have revealed which proteins and lipids are most actively involved in synaptic release of neurotransmitters. The functional properties of the nerve terminals, such as responses to depolarization and the uptake or release of signaling molecules, have also been characterized through the use of fluorescent dyes, tagged transmitters, and transporter substrates. In addition, isolated synaptosomes can serve as the starting material for the isolation of relatively pure synaptic plasma membranes (SPMs) that are devoid of organelles from the internal environment of the nerve terminal, such as mitochondria and synaptic vesicles. The isolated SPMs can reseal and form vesicular structures in which transport of ions such as sodium and calcium, as well as solutes such as neurotransmitters can be studied. The PSDs also remain associated with the presynaptic membranes during isolation of SPM fractions, making it possible to isolate the synaptic junctional complexes (SJCs) devoid of the rest of the plasma membranes of the nerve terminals and postsynaptic membrane components. Isolated SJCs can be used to identify the proteins that constitute this highly specialized region of neurons. In this chapter, we describe the steps involved

  4. Musical molecules: the molecular junction as an active component in audio distortion circuits

    Science.gov (United States)

    Bergren, Adam Johan; Zeer-Wanklyn, Lucas; Semple, Mitchell; Pekas, Nikola; Szeto, Bryan; McCreery, Richard L.

    2016-03-01

    Molecular junctions that have a non-linear current-voltage characteristic consistent with quantum mechanical tunneling are demonstrated as analog audio clipping elements in overdrive circuits widely used in electronic music, particularly with electric guitars. The performance of large-area molecular junctions fabricated at the wafer level is compared to currently standard semiconductor diode clippers, showing a difference in the sound character. The harmonic distributions resulting from the use of traditional and molecular clipping elements are reported and discussed, and differences in performance are noted that result from the underlying physics that controls the electronic properties of each clipping component. In addition, the ability to tune the sound using the molecular junction is demonstrated. Finally, the hybrid circuit is compared to an overdriven tube amplifier, which has been the standard reference electric guitar clipped tone for over 60 years. In order to investigate the feasibility of manufacturing molecular junctions for use in commercial applications, devices are fabricated using a low-density format at the wafer level, where 38 dies per wafer, each containing two molecular junctions, are made with exceptional non-shorted yield (99.4%, representing 718 out of 722 tested devices) without requiring clean room facilities.

  5. Musical molecules: the molecular junction as an active component in audio distortion circuits

    International Nuclear Information System (INIS)

    Bergren, Adam Johan; Zeer-Wanklyn, Lucas; Pekas, Nikola; Szeto, Bryan; McCreery, Richard L; Semple, Mitchell

    2016-01-01

    Molecular junctions that have a non-linear current–voltage characteristic consistent with quantum mechanical tunneling are demonstrated as analog audio clipping elements in overdrive circuits widely used in electronic music, particularly with electric guitars. The performance of large-area molecular junctions fabricated at the wafer level is compared to currently standard semiconductor diode clippers, showing a difference in the sound character. The harmonic distributions resulting from the use of traditional and molecular clipping elements are reported and discussed, and differences in performance are noted that result from the underlying physics that controls the electronic properties of each clipping component. In addition, the ability to tune the sound using the molecular junction is demonstrated. Finally, the hybrid circuit is compared to an overdriven tube amplifier, which has been the standard reference electric guitar clipped tone for over 60 years. In order to investigate the feasibility of manufacturing molecular junctions for use in commercial applications, devices are fabricated using a low-density format at the wafer level, where 38 dies per wafer, each containing two molecular junctions, are made with exceptional non-shorted yield (99.4%, representing 718 out of 722 tested devices) without requiring clean room facilities. (paper)

  6. Conformations of cyclopentasilane stereoisomers control molecular junction conductance

    DEFF Research Database (Denmark)

    Li, Haixing; Garner, Marc Hamilton; Shangguan, Zhichun

    2016-01-01

    ,3-position with methylthiomethyl electrode binding groups using both the scanning tunneling microscope-based break junction technique and density functional theory based ab initio calculations. In contrast with the linear ones, these cyclic silanes yield lower conductance values; calculations reveal...

  7. Test-beds for molecular electronics: metal-molecules-metal junctions based on Hg electrodes.

    Science.gov (United States)

    Simeone, Felice Carlo; Rampi, Maria Anita

    2010-01-01

    Junctions based on mesoscopic Hg electrodes are used to characterize the electrical properties of the organic molecules organized in self-assembled monolayers (SAMs). The junctions M-SAM//SAM-Hg are formed by one electrode based on metals (M) such as Hg, Ag, Au, covered by a SAM, and by a second electrode always formed by a Hg drop carrying also a SAM. The electrodes, brought together by using a micromanipulator, sandwich SAMs of different nature at the contact area (approximately = 0.7 microm2). The high versatility of the system allows a series of both electrical and electrochemical junctions to be assembled and characterized: (i) The compliant nature of the Hg electrodes allows incorporation into the junction and measurement of the electrical behavior of a large number of molecular systems and correlation of their electronic structure to the electrical behavior; (ii) by functionalizing both electrodes with SAMs exposing different functional groups, X and Y, it is possible to compare the rate of electron transfer through different X...Y molecular interactions; (iii) when the junction incorporates one of the electrode formed by a semitransparent film of Au, it allows electrical measurements under irradiation of the sandwiched SAMs. In this case the junction behaves as a photoswitch; iv) incorporation of redox centres with low lying, easily reachable energy levels, provides electron stations as indicated by the hopping mechanism dominating the current flow; (v) electrochemical junctions incorporating redox centres by both covalent and electrostatic interactions permit control of the potential of the electrodes with respect to that of the redox state by means of an external reference electrode. Both these junctions show an electrical behavior similar to that of conventional diodes, even though the mechanism generating the current flow is different. These systems, demonstrating high mechanical stability and reproducibility, easy assembly, and a wide variety of

  8. Stretching of BDT-gold molecular junctions: Thiol or thiolate termination?

    KAUST Repository

    Souza, Amaury De Melo; Rungger, Ivan; Pontes, Renato Borges; Rocha, Alexandre Reily; Da Silva, Antô nio José Roque; Schwingenschlö gl, Udo; Sanvito, S.

    2014-01-01

    It is often assumed that the hydrogen atoms in the thiol groups of a benzene-1,4-dithiol dissociate when Au-benzene-1,4-dithiol-Au junctions are formed. We demonstrate, by stability and transport property calculations, that this assumption cannot be made. We show that the dissociative adsorption of methanethiol and benzene-1,4-dithiol molecules on a flat Au(111) surface is energetically unfavorable and that the activation barrier for this reaction is as high as 1 eV. For the molecule in the junction, our results show, for all electrode geometries studied, that the thiol junctions are energetically more stable than their thiolate counterparts. Due to the fact that density functional theory (DFT) within the local density approximation (LDA) underestimates the energy difference between the lowest unoccupied molecular orbital and the highest occupied molecular orbital by several electron-volts, and that it does not capture the renormalization of the energy levels due to the image charge effect, the conductance of the Au-benzene-1,4-dithiol-Au junctions is overestimated. After taking into account corrections due to image charge effects by means of constrained-DFT calculations and electrostatic classical models, we apply a scissor operator to correct the DFT energy level positions, and calculate the transport properties of the thiol and thiolate molecular junctions as a function of the electrode separation. For the thiol junctions, we show that the conductance decreases as the electrode separation increases, whereas the opposite trend is found for the thiolate junctions. Both behaviors have been observed in experiments, therefore pointing to the possible coexistence of both thiol and thiolate junctions. Moreover, the corrected conductance values, for both thiol and thiolate, are up to two orders of magnitude smaller than those calculated with DFT-LDA. This brings the theoretical results in quantitatively good agreement with experimental data.

  9. Probing flexible conformations in molecular junctions by inelastic electron tunneling spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Mingsen [Department of Physics, Guizhou University, Guiyang, 550025 (China); Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Institute of Applied Physics, Guizhou Normal College, Guiyang, 550018 (China); Ye, Gui; Jiang, Jun, E-mail: jiangj1@ustc.edu.cn [Department of Chemical Physics, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, 230026 (China); Cai, Shaohong, E-mail: caish@mail.gufe.edu.cn [Department of Physics, Guizhou University, Guiyang, 550025 (China); Guizhou Key Laboratory of Economic System Simulation, Guizhou University of Finance and Economics, Guiyang, 550004 (China); Sun, Guangyu [Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Institute of Applied Physics, Guizhou Normal College, Guiyang, 550018 (China)

    2015-01-15

    The probe of flexible molecular conformation is crucial for the electric application of molecular systems. We have developed a theoretical procedure to analyze the couplings of molecular local vibrations with the electron transportation process, which enables us to evaluate the structural fingerprints of some vibrational modes in the inelastic electron tunneling spectroscopy (IETS). Based on a model molecule of Bis-(4-mercaptophenyl)-ether with a flexible center angle, we have revealed and validated a simple mathematical relationship between IETS signals and molecular angles. Our results might open a route to quantitatively measure key geometrical parameters of molecular junctions, which helps to achieve precise control of molecular devices.

  10. Structural Molecular Components of Septate Junctions in Cnidarians Point to the Origin of Epithelial Junctions in Eukaryotes

    KAUST Repository

    Ganot, P.

    2014-09-21

    Septate junctions (SJs) insure barrier properties and control paracellular diffusion of solutes across epithelia in invertebrates. However, the origin and evolution of their molecular constituents in Metazoa have not been firmly established. Here, we investigated the genomes of early branching metazoan representatives to reconstruct the phylogeny of the molecular components of SJs. Although Claudins and SJ cytoplasmic adaptor components appeared successively throughout metazoan evolution, the structural components of SJs arose at the time of Placozoa/Cnidaria/Bilateria radiation. We also show that in the scleractinian coral Stylophora pistillata, the structural SJ component Neurexin IV colocalizes with the cortical actin network at the apical border of the cells, at the place of SJs. We propose a model for SJ components in Cnidaria. Moreover, our study reveals an unanticipated diversity of SJ structural component variants in cnidarians. This diversity correlates with gene-specific expression in calcifying and noncalcifying tissues, suggesting specific paracellular pathways across the cell layers of these diploblastic animals.

  11. Negative differential resistance and switch behavior of T-BxNy (x, y = 5, 6, 11) molecular junctions

    Science.gov (United States)

    Wang, Shi-Liang; Yang, Chuan-Lu; Wang, Mei-Shan; Ma, Xiao-Guang; Xin, Jian-Guo

    2017-05-01

    The electronic transport properties of T-BxNy (x, y = 5, 6, 11) molecular junction are investigated based on first-principle density functional theory and non-equilibrium Green's function method. Strong negative differential resistance (NDR) behavior is observed for T-B5N6 molecule under negative and positive bias voltages, with an obvious switch effect for T-B6N5. However, only small NDR is shown for the complex of the two molecules. The projected device density of states, the spatial distribution of molecular orbitals, and the effect of transmission spectra under various bias voltages on the electronic transport properties are analyzed. The obvious effect of bias voltage on the changes in the electronic distribution of frontier molecular orbitals is responsible for the NDR or switch behavior. Therefore, different functional molecular devices can be obtained with different structures of T-BxNy.

  12. Molecular dynamics study of Ar flow and He flow inside carbon nanotube junction as a molecular nozzle and diffuser

    Directory of Open Access Journals (Sweden)

    Itsuo Hanasaki, Akihiro Nakatani and Hiroshi Kitagawa

    2004-01-01

    Full Text Available A carbon nanotube junction consists of two connected nanotubes with different diameters. It has been extensively investigated as a molecular electronic device since carbon nanotubes can be metallic and semiconductive, depending on their structure. However, a carbon nanotube junction can also be viewed as a nanoscale nozzle andv diffuser. Here, we focus on the nanotube junction from the perspective of an intersection between machine, material and device. We have conducted a molecular dynamics simulation of the molecular flow inside a modeled (12,12–(8,8 nanotube junction. A strong gravitational field and a periodic boundary condition are applied in the flow direction. We investigated dense-Ar flows and dense-He flows while controlling the temperature of the nanotube junction. The results show that Ar atoms tend to be near to the wall and the density of the Ar is higher in the wide (12,12 nanotube than in the narrow (8,8 nanotube, while it is lower in the wide tube when no flow occurs. The streaming velocities of both the Ar and the He are higher in the narrow nanotube than in the wide nanotube, but the velocity of the Ar is higher than the velocity of the He and the temperature of the flowing Ar is higher than the temperature of the He when the same magnitude of gravitational field is applied.

  13. Tuning electron transport through a single molecular junction by bridge modification

    International Nuclear Information System (INIS)

    Li, Xiao-Fei; Qiu, Qi; Luo, Yi

    2014-01-01

    The possibility of controlling electron transport in a single molecular junction represents the ultimate goal of molecular electronics. Here, we report that the modification of bridging group makes it possible to improve the performance and obtain new functions in a single cross-conjugated molecular junction, designed from a recently synthesized bipolar molecule bithiophene naphthalene diimide. Our first principles results show that the bipolar characteristic remains after the molecule was modified and sandwiched between two metal electrodes. Rectifying is the intrinsic characteristic of the molecular junction and its performance can be enhanced by replacing the saturated bridging group with an unsaturated group. A further improvement of the rectifying and a robust negative differential resistance (NDR) behavior can be achieved by the modification of unsaturated bridge. It is revealed that the modification can induce a deviation angle about 4° between the donor and the acceptor π-conjugations, making it possible to enhance the communication between the two π systems. Meanwhile, the low energy frontier orbitals of the junction can move close to the Fermi level and encounter in energy at certain biases, thus a transport channel with a considerable transmission can be formed near the Fermi level only at a narrow bias regime, resulting in the improvement of rectifying and the robust NDR behavior. This finding could be useful for the design of single molecular devices.

  14. Robust conductance of dumbbell molecular junctions with fullerene anchoring groups

    DEFF Research Database (Denmark)

    Markussen, Troels; Settnes, Mikkel; Thygesen, Kristian Sommer

    2011-01-01

    The conductance of a molecular wire connected to metallic electrodes is known to be sensitive to the atomic structure of the molecule-metal contact. This contact is to a large extent determined by the anchoring group linking the molecular wire to the metal. It has been found experimentally that a...

  15. A Strategy to Suppress Phonon Transport in Molecular Junctions Using pi-Stacked Systems

    DEFF Research Database (Denmark)

    Li, Qian; Strange, Mikkel; Duchemin, Ivan

    2017-01-01

    to suppress phonon transport in graphene-based molecular junctions preserving high electronic power factor, using nonbonded pi-stackal systems. Using first-principles calculations, we find that the thermal conductance of pi-stacked systems can be reduced by about 95%, compared with that of a covalently bonded...

  16. Electron transport in dipyridazine and dipyridimine molecular junctions: a first-principles investigation

    Science.gov (United States)

    Parashar, Sweta

    2018-05-01

    We present density functional theory-nonequilibrium Green’s function method for electron transport of dipyridazine and dipyridimine molecular junctions with gold, copper and nickel electrodes. Our investigation reveals that the junctions formed with gold and copper electrodes bridging dipyridazine molecule through thiol anchoring group enhance current as compared to the junctions in which the molecule and electrode were coupled directly. Further, nickel electrode displays weak decrease of current with increase of voltage at about 1.2 V. The result is fully rationalized by means of the distribution of molecular orbitals as well as shift in molecular energy levels and HOMO-LUMO gap with applied bias voltage. Our findings are compared with theoretical and experimental results available for other molecular junctions. Present results predict potential avenues for changing the transport behavior by not only changing the electrodes, but also the position of nitrogen atom and type of anchoring-atom that connect molecule and electrodes, thus extending applications of dipyridazine and dipyridimine molecule in future integrated circuits.

  17. Transition voltages of vacuum-spaced and molecular junctions with Ag and Pt electrodes

    KAUST Repository

    Wu, Kunlin

    2014-07-07

    The transition voltage of vacuum-spaced and molecular junctions constructed with Ag and Pt electrodes is investigated by non-equilibrium Green\\'s function formalism combined with density functional theory. Our calculations show that, similarly to the case of Au-vacuum-Au previously studied, the transition voltages of Ag and Pt metal-vacuum-metal junctions with atomic protrusions on the electrode surface are determined by the local density of states of the p-type atomic orbitals of the protrusion. Since the energy position of the Pt 6p atomic orbitals is higher than that of the 5p/6p of Ag and Au, the transition voltage of Pt-vacuum-Pt junctions is larger than that of both Ag-vacuum-Ag and Au-vacuum-Au junctions. When one moves to analyzing asymmetric molecular junctions constructed with biphenyl thiol as central molecule, then the transition voltage is found to depend on the specific bonding site for the sulfur atom in the thiol group. In particular agreement with experiments, where the largest transition voltage is found for Ag and the smallest for Pt, is obtained when one assumes S binding at the hollow-bridge site on the Ag/Au(111) surface and at the adatom site on the Pt(111) one. This demonstrates the critical role played by the linker-electrode binding geometry in determining the transition voltage of devices made of conjugated thiol molecules. © 2014 AIP Publishing LLC.

  18. Impact of exchange-correlation effects on the IV characteristics of a molecular junction

    DEFF Research Database (Denmark)

    Thygesen, Kristian Sommer

    2008-01-01

    The role of exchange-correlation effects in nonequilibrium quantum transport through molecular junctions is assessed by analyzing the IV curve of a generic two-level model using self-consistent many-body perturbation theory (second Born and GW approximations) on the Keldysh contour. It is demonst...... of dynamic correlations introduces quasiparticle (QP) scattering which in turn broadens the molecular resonances. The broadening increases strongly with bias and can have a large impact on the calculated IV characteristic....

  19. Controlling single-molecule junction conductance by molecular interactions

    Science.gov (United States)

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

    2015-01-01

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

  20. Interfacial trap states in junctions of molecular semiconductors

    International Nuclear Information System (INIS)

    Schlettwein, D.; Oekermann, T.; Jaeger, N.; Armstrong, N.R.; Woehrle, D.

    2002-01-01

    Interfacial states that were established in contacts of molecular semiconductors with aqueous electrolytes or in contacts with another organic semiconductor as a solid film were analyzed by photoelectrochemical experiments and by photoelectron spectroscopy. A crucial role of such states was indicated in the interfacial charge transfer and recombination kinetics of light-induced charge carriers and also in the energetic alignment in the solid contacts. Unsubstituted zinc-phthalocyanine (PcZn) served as model compound. The role of chemical interactions in the establishment of these interfacial states was investigated by use of different reaction partners, i.e., different redox couples in the electrolyte contacts and molecular semiconductors of different ionization potential in the solid contacts. Implications of these results for the use of organic semiconductor thin films in devices of molecular electronics and of dye molecules in dye-sensitized solar cells were also discussed

  1. A Computational and Theoretical Study of Conductance in Hydrogen-bonded Molecular Junctions

    Science.gov (United States)

    Wimmer, Michael

    This thesis is devoted to the theoretical and computational study of electron transport in molecular junctions where one or more hydrogen bonds are involved in the process. While electron transport through covalent bonds has been extensively studied, in recent work the focus has been shifted towards hydrogen-bonded systems due to their ubiquitous presence in biological systems and their potential in forming nano-junctions between molecular electronic devices and biological systems. This analysis allows us to significantly expand our comprehension of the experimentally observed result that the inclusion of hydrogen bonding in a molecular junction significantly impacts its transport properties, a fact that has important implications for our understanding of transport through DNA, and nano-biological interfaces in general. In part of this work I have explored the implications of quasiresonant transport in short chains of weakly-bonded molecular junctions involving hydrogen bonds. I used theoretical and computational analysis to interpret recent experiments and explain the role of Fano resonances in the transmission properties of the junction. In a different direction, I have undertaken the study of the transversal conduction through nucleotide chains that involve a variable number of different hydrogen bonds, e.g. NH˙˙˙O, OH˙˙˙O, and NH˙˙˙N, which are the three most prevalent hydrogen bonds in biological systems and organic electronics. My effort here has focused on the analysis of electronic descriptors that allow a simplified conceptual and computational understanding of transport properties. Specifically, I have expanded our previous work where the molecular polarizability was used as a conductance descriptor to include the possibility of atomic and bond partitions of the molecular polarizability. This is important because it affords an alternative molecular description of conductance that is not based on the conventional view of molecular orbitals as

  2. Bottom-up, Robust Graphene Ribbon Electronics in All-Carbon Molecular Junctions.

    Science.gov (United States)

    Supur, Mustafa; Van Dyck, Colin; Bergren, Adam J; McCreery, Richard L

    2018-02-21

    Large-area molecular electronic junctions consisting of 5-carbon wide graphene ribbons (GR) with lengths of 2-12 nm between carbon electrodes were fabricated by electrochemical reduction of diazotized 1,8-diaminonaphthalene. Their conductance greatly exceeds that observed for other molecular junctions of similar thicknesses, by a factor of >1 × 10 4 compared to polyphenylenes and >1 × 10 7 compared to alkane chains. The remarkable increase of conductance of the GR nanolayer results from (i) uninterrupted planarity of fused-arene structure affording extensive π-electron delocalization and (ii) enhanced electronic coupling of molecular layer with the carbon bottom contact by two-point covalent bonding, in agreement with DFT-based simulations.

  3. Sidewall GaAs tunnel junctions fabricated using molecular layer epitaxy

    Directory of Open Access Journals (Sweden)

    Takeo Ohno and Yutaka Oyama

    2012-01-01

    Full Text Available In this article we review the fundamental properties and applications of sidewall GaAs tunnel junctions. Heavily impurity-doped GaAs epitaxial layers were prepared using molecular layer epitaxy (MLE, in which intermittent injections of precursors in ultrahigh vacuum were applied, and sidewall tunnel junctions were fabricated using a combination of device mesa wet etching of the GaAs MLE layer and low-temperature area-selective regrowth. The fabricated tunnel junctions on the GaAs sidewall with normal mesa orientation showed a record peak current density of 35 000 A cm-2. They can potentially be used as terahertz devices such as a tunnel injection transit time effect diode or an ideal static induction transistor.

  4. Preparation of large-area molecular junctions with metallic conducting Langmuir–Blodgett films

    Energy Technology Data Exchange (ETDEWEB)

    Mochizuki, Kengo [Division of Marine Technology, Tokyo University of Marine Science and Technology, 2-1-6 Etchujima Koto-ku, Tokyo 135-8533 (Japan); Ohnuki, Hitoshi, E-mail: ohnuki@kaiyodai.ac.jp [Division of Marine Technology, Tokyo University of Marine Science and Technology, 2-1-6 Etchujima Koto-ku, Tokyo 135-8533 (Japan); Shimizu, Daisuke [Division of Marine Technology, Tokyo University of Marine Science and Technology, 2-1-6 Etchujima Koto-ku, Tokyo 135-8533 (Japan); Imakubo, Tatsuro [Department of Materials and Technology, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 (Japan); Tsuya, Daiju [National Institute for Materials Science,1-2-1 Sengen, Tsukuba, Ibaraki 305-0047 (Japan); Izumi, Mitsuru [Division of Marine Technology, Tokyo University of Marine Science and Technology, 2-1-6 Etchujima Koto-ku, Tokyo 135-8533 (Japan)

    2014-03-03

    Metallic conducting Langmuir–Blodgett (LB) films were used as soft electrodes to fabricate molecular junctions with self-assembled monolayers (SAMs) of alkanethiols (CH{sub 3}(CH{sub 2}){sub n−1}SH) on an Au surface. Alkanethiols can form highly ordered, stable dielectric SAMs on metal surfaces over large areas. However, it is difficult to establish electrical contacts on such SAMs, which has limited their application. In this work, we used metallic conducting LB films composed of bis(ethylenedioxy)tetrathiafulvalene and stearic acid as a soft electrode onto alkanethiol SAMs (C{sub n}-SAM, n = 12, 14, 16, 18) to prepare Au/SAM/metal junctions of relatively large size (∼ 15.6 × 10{sup 3} μm{sup 2}). The current density–voltage (J–V) characteristics across the junctions exhibited rectifying behavior with a ratio R of ∼ 5 (R = |J(V)|/|J(− V)| at ± 1 V). The lower transfer rate corresponding to the electron transport from Au to the LB films exhibited nonlinear J–V characteristics, while the higher transfer rate of electrons from the LB film to Au showed linear J–V characteristics. Kelvin probe force microscopy revealed that the work function of the metallic LB films was smaller than that of Au. The observed rectification behavior is probably caused by different electron transport mechanisms between the two current directions. - Highlights: • Metallic Langmuir–Blodgett (LB) films were used as soft electrodes. • Molecular junctions of metal–alkanethiol–LB films were fabricated. • The current–voltage curve across the junctions exhibited rectifying behavior. • This is the first observation for alkanethiol monolayer junctions. • The work function difference between the electrodes induces the rectification.

  5. Molecular and cellular mechanisms of tight junction dysfunction in the irritable bowel syndrome.

    Science.gov (United States)

    Cheng, Peng; Yao, Jianning; Wang, Chunfeng; Zhang, Lianfeng; Kong, Wuming

    2015-09-01

    The pathophysiological mechanisms of the irritable bowel syndrome (IBS), one of the most prevalent gastrointestinal disorders, are complex and have not been fully elucidated. The present study aimed to investigate the molecular and cellular mechanisms of tight junction (TJ) dysfunction in IBS. Intestinal tissues of IBS and non‑IBS patients were examined to observe cellular changes by cell chemical tracer electron microscopy and transmission electron microscopy, and intestinal claudin‑1 protein was detected by immunohistochemistry, western blot analysis and fluorescence quantitative polymerase chain reaction. Compared with the control group, TJ broadening and the tracer extravasation phenomenon were observed in the diarrhea‑predominant IBS group, and a greater number of neuroendocrine cells and mast cells filled with high‑density particles in the endocrine package pulp as well as a certain extent of vacuolization were present. The expression of claudin‑1 in diarrhea‑predominant IBS patients was decreased, while it was increased in constipation‑predominant IBS patients. In conclusion, the results of the present study indicated that changes in cellular structure and claudin‑1 levels were associated with Tjs in IBS.

  6. Exploring the Tilt-Angle Dependence of electron tunneling across Molecular junction of Self-Assembled Alkanethiols

    DEFF Research Database (Denmark)

    Frederiksen, Thomas; Munuera, C.; Ocal, C.

    2009-01-01

    Electronic transport mechanisms in molecular junctions are investigated by a combination of first-principles calculations and current−voltage measurements of several well-characterized structures. We study self-assembled layers of alkanethiols grown on Au(111) and form tunnel junctions...... for the longer molecular chains. Our calculations confirm the observed trends and explain them as a result of two mechanisms, namely, a previously proposed intermolecular tunneling enhancement as well as a hitherto overlooked tilt-dependent molecular gate effect....

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

    International Nuclear Information System (INIS)

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

    2009-01-01

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

  8. A Study of Electrocyclic Reactions in a Molecular Junction

    DEFF Research Database (Denmark)

    Olsen, Stine Tetzschner; Nielsen, Mogens Brøndsted; Hansen, Thorsten

    2017-01-01

    must be in accordance to the orbital symmetry rules expressed by the Woodward-Hoffmann rules (when the electrodes do not significantly alter the molecular orbital appearances). We find these two requirements to be valid for the dianion of (1E,3Z,5E)-hexa-1,3,5-triene-1,6-diamine, and the Coulomb...... blockade diamonds were therefore modeled for this compound to elucidate how a dark photoswitching event would manifest itself in the stability plot. From this modeling of conductance as a function of gate and bias potentials, we predict a collapse in Coulomb diamond size, that is, a decrease in the height...

  9. Dynamical image-charge effect in molecular tunnel junctions

    DEFF Research Database (Denmark)

    Jin, Chengjun; Thygesen, Kristian Sommer

    2014-01-01

    the finite IC formation time affects charge transport through a molecule suspended between two electrodes. For a single-level model, an analytical treatment shows that the conductance is suppressed by a factor Z(2), where Z is the quasiparticle renormalization factor, compared to the static IC approximation...... that the dynamical corrections can reduce the conductance by more than a factor of two when compared to static GW or density functional theory where the molecular energy levels have been shifted to match the exact quasiparticle levels....

  10. Chemical/molecular structure of the dentin-enamel junction is dependent on the intratooth location.

    Science.gov (United States)

    Xu, Changqi; Yao, Xiaomei; Walker, Mary P; Wang, Yong

    2009-03-01

    The dentin-enamel junction (DEJ) plays an important role in preventing crack propagation from enamel into dentin. This function stems from its complex structure and materials properties that are different from either dentin or enamel. The molecular structural differences in both mineral and organic matrix across the DEJ zone were investigated by two-dimensional confocal Raman microspectroscopic mapping/imaging technique. The intensity ratios of 1450 (CH, matrix)/960 (P-O, mineral) decreased gradually to nearly zero across the DEJ. The width of this transition zone was dependent on the intratooth location, with 12.9 +/- 3.2 microm width at occlusal positions and 6.2 +/- 1.3 microm at cervical positions. The difference in width was significant (P < 0.001). Concurrently, spectral differences in both organic and inorganic matrices across the DEJ were also noted. For example, the ratios of 1243 (amide III)/1450 (CH) within the DEJ were lower than the values in dentin; however, the ratios of 1665 (amide I)/1450 (CH) within the DEJ were higher than those values in dentin. In addition, the ratios of 1070 (carbonate)/960 (phosphate) within the dentin were lower than the values in the DEJ. Raman images indicated that the distribution of the above ratios across the DEJ zone were also different at occlusal and cervical positions. The results suggest that the intratooth-location-dependent structure of the DEJ may be related to its function. Micro-Raman spectroscopic/imaging analysis of the DEJ provides a powerful means of identifying the functional width and molecular structural differences across the DEJ.

  11. Elucidating the principles of the molecular organization of heteropolymeric tight junction strands

    OpenAIRE

    Piontek, Jörg; Fritzsche, Susanne; Cording, Jimmi; Richter, Sandra; Hartwig, Jens; Walter, Maria; Yu, Dan; Turner, Jerrold R.; Gehring, Claudia; Rahn, Hans-Peter; Wolburg, Hartwig; Blasig, Ingolf E.

    2011-01-01

    Paracellular barrier properties of tissues are mainly determined by the composition of claudin hetero-polymers. To analyze the molecular organization of tight junctions (TJ), we investigated the ability of claudins (Cld) to form homo- and heteromers. Cld1, -2, -3, -5, and -12 expressed in cerebral barriers were investigated. TJ-strands were reconstituted by claudin-transfection of HEK293-cells. cis-Interactions and/or spatial proximity were analyzed by fluorescence resonance energy transfer i...

  12. Manipulating the spin states in a double molecular magnets tunneling junction

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Liang; Liu, Xi [National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093 (China); Zhang, Zhengzhong, E-mail: zeikeezhang@126.com [National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093 (China); Nano Science and Technology Institute, University of Science and Technology of China, Suzhou 215123 (China); Wang, Ruiqiang [Laboratory of Quantum Engineering and Quantum Materials, South China Normal University, Guangzhou 510006 (China)

    2014-01-17

    We theoretically explore the spin transport through nano-structures consisting of two serially coupled single-molecular magnets (SMM) sandwiched between two nonmagnetic electrodes. We find that the magnetization of SMM can be controlled by the spin transfer torque with respect to the bias voltage direction, and the electron current can be switched on/off in different magnetic structures. Such a manipulation is performed by full electrical manner, and needs neither external magnetic field nor ferromagnetic electrodes in the tunneling junction. The proposal device scheme can be realized with the use of the present technology and has potential applications in molecular spintronics or quantum information processing.

  13. Manipulating the spin states in a double molecular magnets tunneling junction

    Science.gov (United States)

    Jiang, Liang; Liu, Xi; Zhang, Zhengzhong; Wang, Ruiqiang

    2014-01-01

    We theoretically explore the spin transport through nano-structures consisting of two serially coupled single-molecular magnets (SMM) sandwiched between two nonmagnetic electrodes. We find that the magnetization of SMM can be controlled by the spin transfer torque with respect to the bias voltage direction, and the electron current can be switched on/off in different magnetic structures. Such a manipulation is performed by full electrical manner, and needs neither external magnetic field nor ferromagnetic electrodes in the tunneling junction. The proposal device scheme can be realized with the use of the present technology [6] and has potential applications in molecular spintronics or quantum information processing.

  14. Enhanced Magnetoresistance in Molecular Junctions by Geometrical Optimization of Spin-Selective Orbital Hybridization.

    Science.gov (United States)

    Rakhmilevitch, David; Sarkar, Soumyajit; Bitton, Ora; Kronik, Leeor; Tal, Oren

    2016-03-09

    Molecular junctions based on ferromagnetic electrodes allow the study of electronic spin transport near the limit of spintronics miniaturization. However, these junctions reveal moderate magnetoresistance that is sensitive to the orbital structure at their ferromagnet-molecule interfaces. The key structural parameters that should be controlled in order to gain high magnetoresistance have not been established, despite their importance for efficient manipulation of spin transport at the nanoscale. Here, we show that single-molecule junctions based on nickel electrodes and benzene molecules can yield a significant anisotropic magnetoresistance of up to ∼200% near the conductance quantum G0. The measured magnetoresistance is mechanically tuned by changing the distance between the electrodes, revealing a nonmonotonic response to junction elongation. These findings are ascribed with the aid of first-principles calculations to variations in the metal-molecule orientation that can be adjusted to obtain highly spin-selective orbital hybridization. Our results demonstrate the important role of geometrical considerations in determining the spin transport properties of metal-molecule interfaces.

  15. Evidence for differential changes of junctional complex proteins in murine neurocysticercosis dependent upon CNS vasculature.

    Science.gov (United States)

    Alvarez, Jorge I; Teale, Judy M

    2007-09-12

    The delicate balance required to maintain homeostasis of the central nervous system (CNS) is controlled by the blood-brain barrier (BBB). Upon injury, the BBB is disrupted compromising the CNS. BBB disruption has been represented as a uniform event. However, our group has shown in a murine model of neurocysticercosis (NCC) that BBB disruption varies depending upon the anatomical site/vascular bed analyzed. In this study further understanding of the mechanisms of BBB disruption was explored in blood vessels located in leptomeninges (pial vessels) and brain parenchyma (parenchymal vessels) by examining the expression of junctional complex proteins in murine brain infected with Mesocestoides corti. Both pial and parenchymal vessels from mock infected animals showed significant colocalization of junctional proteins and displayed an organized architecture. Upon infection, the patterned organization was disrupted and in some cases, particular tight junction and adherens junction proteins were undetectable or appeared to be undergoing proteolysis. The extent and timing of these changes differed between both types of vessels (pial vessel disruption within days versus weeks for parenchymal vessels). To approach potential mechanisms, the expression and activity of matrix metalloproteinase-9 (MMP-9) were evaluated by in situ zymography. The results indicated an increase in MMP-9 activity at sites of BBB disruption exhibiting leukocyte infiltration. Moreover, the timing of MMP activity in pial and parenchymal vessels correlated with the timing of permeability disruption. Thus, breakdown of the BBB is a mutable process despite the similar structure of the junctional complex between pial and parenchymal vessels and involvement of MMP activity.

  16. P-N junction solar cell grown by molecular beam epitaxy

    International Nuclear Information System (INIS)

    Hazrati Fard, M.

    2001-01-01

    Growth of GaAs epilayers by Molecular Beam Epitaxy was accomplished for the first time in Iran. The layers were grown on GaAs (001) substrates (p+ wafer) with Si impurity for p n junction solar cell fabrication at a rate of nearly one micron per hour and 0.25 micron per quarter. Crystalline quality of grown layers had been monitored during growth by Reflection High Energy Electron Diffraction system. Doping profile and layer thickness was assessed by electrochemical C-V profiling method. Then Hall measurements were conducted on small samples both in room temperature and liquid nitrogen temperature so giving average carrier concentration and compensation ratio. The results as like: V oc , I sc , F F, η were comparable with other laboratory reports. information for obtaining good and repeatable growths was collected. Therefore, the conditions of repeatable quality growth p n junction solar cells onto GaAs (001) substrates were determined

  17. Ultrathin reduced graphene oxide films as transparent top-contacts for light switchable solid-state molecular junctions

    DEFF Research Database (Denmark)

    Li, Tao; Jevric, Martyn; Hauptmann, Jonas Rahlf

    2013-01-01

    A new type of solid-state molecular junction is introduced, which employs reduced graphene oxide as a transparent top contact that permits a self-assembled molecular monolayer to be photoswitched in situ, while simultaneously enabling charge-transport measurements across the molecules. The electr......A new type of solid-state molecular junction is introduced, which employs reduced graphene oxide as a transparent top contact that permits a self-assembled molecular monolayer to be photoswitched in situ, while simultaneously enabling charge-transport measurements across the molecules...

  18. Theoretical study on mechanical and electron-transport properties of conjugated molecular junctions with carboxylic or methyl sulfide links

    Energy Technology Data Exchange (ETDEWEB)

    Bao, De-Liang; Liu, Ran [College of Physics and Electronics, Shandong Normal University, Jinan 250014 (China); Leng, Jian-Cai [College of Physics and Electronics, Shandong Normal University, Jinan 250014 (China); School of Science, Qilu University of Technology, Jinan 250353 (China); Zuo, Xi; Jiao, Yang [College of Physics and Electronics, Shandong Normal University, Jinan 250014 (China); Li, Zong-Liang, E-mail: lizongliang@sdnu.edu.cn [College of Physics and Electronics, Shandong Normal University, Jinan 250014 (China); Wang, Chuan-Kui [College of Physics and Electronics, Shandong Normal University, Jinan 250014 (China)

    2014-03-01

    The mechanical and electronic transport properties of 4-(methylthio)benzoic acid (M1), 1,4-bis(methylthio) benzene (M2) and methyl 4-(methylthio)benzoate (M3) molecular junctions are studied employing density functional theory and elastic scattering Green's function method. The numerical results show that the rupture force of M1 and M2 junctions are both about 0.6±0.1 nN as experiment probed, which is much smaller than the force to break COO{sup −}–Au bond. The COO{sup −} group strongly influenced on M1 molecular junction and further strengthened SMe–Au bond at the other end of the junction. The M3 junction is less stable because the CH{sub 3} group linked to COO group destroyed the mechanical stability of COO–Au connection. The conductance of M2 junction is about an order larger than that of M1 junction as the experiment probed. The less stable feature of M3 junction leads the absence of conductive peak.

  19. Quantitative interpretation of the transition voltages in gold-poly(phenylene) thiol-gold molecular junctions

    KAUST Repository

    Wu, Kunlin

    2013-01-01

    The transition voltage of three different asymmetric Au/poly(phenylene) thiol/Au molecular junctions in which the central molecule is either benzene thiol, biphenyl thiol, or terphenyl thiol is investigated by first-principles quantum transport simulations. For all the junctions, the calculated transition voltage at positive polarity is in quantitative agreement with the experimental values and shows weak dependence on alterations of the Au-phenyl contact. When compared to the strong coupling at the Au-S contact, which dominates the alignment of various molecular orbitals with respect to the electrode Fermi level, the coupling at the Au-phenyl contact produces only a weak perturbation. Therefore, variations of the Au-phenyl contact can only have a minor influence on the transition voltage. These findings not only provide an explanation to the uniformity in the transition voltages found for π-conjugated molecules measured with different experimental methods, but also demonstrate the advantage of transition voltage spectroscopy as a tool for determining the positions of molecular levels in molecular devices. © 2013 AIP Publishing LLC.

  20. Prediction of quantum interference in molecular junctions using a parabolic diagram: Understanding the origin of Fano and anti-resonances

    DEFF Research Database (Denmark)

    Nozaki, Daijiro; Avdoshenko, Stanislav M.; Sevincli, Haldun

    2013-01-01

    Recently the interest in quantum interference (QI) phenomena in molecular devices (molecular junctions) has been growing due to the unique features observed in the transmission spectra. In order to design single molecular devices exploiting QI effects as desired, it is necessary to provide simple...... rules for predicting the appearance of QI effects such as anti-resonances or Fano line shapes and for controlling them. In this study, we derive a transmission function of a generic molecular junction with a side group (T-shaped molecular junction) using a minimal toy model. We developed a simple method...... to predict the appearance of quantum interference, Fano resonances or anti- resonances, and its position in the conductance spectrum by introducing a simple graphical representation (parabolic model). Using it we can easily visualize the relation between the key electronic parameters and the positions...

  1. Molecular complexes of tungsten oxotetrachloride with azomethins

    International Nuclear Information System (INIS)

    Abramenko, Yu.V.; Garnovskij, A.D.; Abramenko, V.A.; Medvedeva, T.E.

    1992-01-01

    Series of new molecular complexes of tungsten oxotetrachloride with benza- and salicylalimines of equimolar compositions obtained. Substances are studied using element analysis, IR spectroscopy and conductometry. Octahedral structure of complexes with central atom coordination of benzalaniline molecules via azomethin nitrogen atom, and salicylalimines - via carbonyl oxygen atom of quinoid tantometric form of ligand is assumed

  2. Transient photocurrent in molecular junctions: singlet switching on and triplet blocking.

    Science.gov (United States)

    Petrov, E G; Leonov, V O; Snitsarev, V

    2013-05-14

    The kinetic approach adapted to describe charge transmission in molecular junctions, is used for the analysis of the photocurrent under conditions of moderate light intensity of the photochromic molecule. In the framework of the HOMO-LUMO model for the single electron molecular states, the analytic expressions describing the temporary behavior of the transient and steady state sequential (hopping) as well as direct (tunnel) current components have been derived. The conditions at which the current components achieve their maximal values are indicated. It is shown that if the rates of charge transmission in the unbiased molecular diode are much lower than the intramolecular singlet-singlet excitation/de-excitation rate, and the threefold degenerated triplet excited state of the molecule behaves like a trap blocking the charge transmission, a possibility of a large peak-like transient switch-on photocurrent arises.

  3. A parabolic model to control quantum interference in T-shaped molecular junctions

    DEFF Research Database (Denmark)

    Nozaki, Daijiro; Sevincli, Haldun; Avdoshenko, Stanislav M.

    2013-01-01

    Quantum interference (QI) effects in molecular devices have drawn increasing attention over the past years due to their unique features observed in the conductance spectrum. For the further development of single molecular devices exploiting QI effects, it is of great theoretical and practical...... interest to develop simple methods controlling the emergence and the positions of QI effects like anti-resonances or Fano line shapes in conductance spectra. In this work, starting from a well-known generic molecular junction with a side group (T-shaped molecule), we propose a simple graphical method...... to visualize the conditions for the appearance of quantum interference, Fano resonances or anti-resonances, in the conductance spectrum. By introducing a simple graphical representation (parabolic diagram), we can easily visualize the relation between the electronic parameters and the positions of normal...

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

    International Nuclear Information System (INIS)

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

    2008-01-01

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

  5. Site-Selection in Single-Molecule Junction for Highly Reproducible Molecular Electronics.

    Science.gov (United States)

    Kaneko, Satoshi; Murai, Daigo; Marqués-González, Santiago; Nakamura, Hisao; Komoto, Yuki; Fujii, Shintaro; Nishino, Tomoaki; Ikeda, Katsuyoshi; Tsukagoshi, Kazuhito; Kiguchi, Manabu

    2016-02-03

    Adsorption sites of molecules critically determine the electric/photonic properties and the stability of heterogeneous molecule-metal interfaces. Then, selectivity of adsorption site is essential for development of the fields including organic electronics, catalysis, and biology. However, due to current technical limitations, site-selectivity, i.e., precise determination of the molecular adsorption site, remains a major challenge because of difficulty in precise selection of meaningful one among the sites. We have succeeded the single site-selection at a single-molecule junction by performing newly developed hybrid technique: simultaneous characterization of surface enhanced Raman scattering (SERS) and current-voltage (I-V) measurements. The I-V response of 1,4-benzenedithiol junctions reveals the existence of three metastable states arising from different adsorption sites. Notably, correlated SERS measurements show selectivity toward one of the adsorption sites: "bridge sites". This site-selectivity represents an essential step toward the reliable integration of individual molecules on metallic surfaces. Furthermore, the hybrid spectro-electric technique reveals the dependence of the SERS intensity on the strength of the molecule-metal interaction, showing the interdependence between the optical and electronic properties in single-molecule junctions.

  6. Atomistic simulations of highly conductive molecular transport junctions under realistic conditions

    KAUST Repository

    French, William R.; Iacovella, Christopher R.; Rungger, Ivan; Souza, Amaury Melo; Sanvito, Stefano; Cummings, Peter T.

    2013-01-01

    We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices. © 2013 The Royal Society of Chemistry.

  7. Modeling Complex Workflow in Molecular Diagnostics

    Science.gov (United States)

    Gomah, Mohamed E.; Turley, James P.; Lu, Huimin; Jones, Dan

    2010-01-01

    One of the hurdles to achieving personalized medicine has been implementing the laboratory processes for performing and reporting complex molecular tests. The rapidly changing test rosters and complex analysis platforms in molecular diagnostics have meant that many clinical laboratories still use labor-intensive manual processing and testing without the level of automation seen in high-volume chemistry and hematology testing. We provide here a discussion of design requirements and the results of implementation of a suite of lab management tools that incorporate the many elements required for use of molecular diagnostics in personalized medicine, particularly in cancer. These applications provide the functionality required for sample accessioning and tracking, material generation, and testing that are particular to the evolving needs of individualized molecular diagnostics. On implementation, the applications described here resulted in improvements in the turn-around time for reporting of more complex molecular test sets, and significant changes in the workflow. Therefore, careful mapping of workflow can permit design of software applications that simplify even the complex demands of specialized molecular testing. By incorporating design features for order review, software tools can permit a more personalized approach to sample handling and test selection without compromising efficiency. PMID:20007844

  8. Molecular identification of the Sporothrix schenckii complex.

    Science.gov (United States)

    Oliveira, Manoel Marques Evangelista; Almeida-Paes, Rodrigo; Gutierrez-Galhardo, Maria Clara; Zancope-Oliveira, Rosely M

    2014-01-01

    Sporothrix schenckii, an ascomycetous dimorphic organism that for over a century was recognized as the sole agent of sporotrichosis, a subcutaneous mycosis with a worldwide distribution. However, it has been proposed, based on physiologic and molecular aspects, that S. schenckii is a complex of distinct species: Sporothrix brasiliensis, Sporothrix mexicana, Sporothrix globosa, S. schenckii sensu strictu, Sporothrix luriei, and Sporothrix albicans (formerly Sporothrix pallida). Human disease has a broad range of clinical manifestations and can be classified into fixed cutaneous, lymphocutaneous, disseminated cutaneous, and extracutaneous sporotrichosis. The gold standard for the diagnosis of sporotrichosis is the culture; however, serologic, histopathologic and molecular approaches have been recently adopted for the diagnosis of this mycosis. Few molecular methods have been applied to the diagnosis of sporotrichosis to detect S. schenckii DNA from clinical specimens, and to identify Sporothrix spp. in culture. Until now, Sporothrix is the unique clinically relevant dimorphic fungus without an elucidated genome sequence, thus limiting molecular knowledge about the cryptic species of this complex, and the sexual form of all S. schenckii complex species. In this review we shall focus on the current diagnosis of the sporotrichosis, and discuss the current molecular tools applied to the diagnosis and identification of the Sporothrix complex species. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

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

    International Nuclear Information System (INIS)

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

    2011-01-01

    Based on the non-equilibrium Green's function method and first-principles density functional theory calculations, we investigate the electronic transport properties of a nitrogen/boron-doped capped-single-walled carbon-nanotube-based molecular junction. Obvious rectifying behavior is observed and it is strongly dependent on the doping site. The best rectifying performance can be carried out when the nitrogen/boron atom dopes at a carbon site in the second layer. Moreover, the rectifying performance can be further improved by adjusting the distance between the C 60 nanotube caps. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  10. Light emission and finite-frequency shot noise in molecular junctions: from tunneling to contact

    DEFF Research Database (Denmark)

    Lu, Jing Tao; Christensen, Rasmus Bjerregaard; Brandbyge, Mads

    2013-01-01

    Scanning tunneling microscope induced light emission from an atomic or molecular junction has been probed from the tunneling to contact regime in recent experiments. There, the measured light emission yields suggest a strong correlation with the high-frequency current/charge fluctuations. We show...... that this is consistent with the established theory in the tunneling regime, by writing the finite-frequency shot noise as a sum of inelastic transitions between different electronic states. Based on this, we develop a practical scheme to perform calculations on realistic structures using nonequilibrium Green's functions...

  11. On the widths of Stokes lines in Raman scattering from molecules adsorbed at metal surfaces and in molecular conduction junctions

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Yi, E-mail: yig057@ucsd.edu; Galperin, Michael, E-mail: migalperin@ucsd.edu [Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093 (United States); Nitzan, Abraham, E-mail: nitzan@post.tau.ac.il [Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA and School of Chemistry, Tel Aviv University, Tel Aviv 69978 (Israel)

    2016-06-28

    Within a generic model we analyze the Stokes linewidth in surface enhanced Raman scattering (SERS) from molecules embedded as bridges in molecular junctions. We identify four main contributions to the off-resonant Stokes signal and show that under zero voltage bias (a situation pertaining also to standard SERS experiments) and at low bias junctions only one of these contributions is pronounced. The linewidth of this component is determined by the molecular vibrational relaxation rate, which is dominated by interactions with the essentially bosonic thermal environment when the relevant molecular electronic energy is far from the metal(s) Fermi energy(ies). It increases when the molecular electronic level is close to the metal Fermi level so that an additional vibrational relaxation channel due to electron-hole (eh) exciton in the molecule opens. Other contributions to the Raman signal, of considerably broader linewidths, can become important at larger junction bias.

  12. A tight-binding model of the transmission probability through a molecular junction; a single molecule vs. a molecular layer

    International Nuclear Information System (INIS)

    Landau, A.; Nitzan, A.

    2006-01-01

    Full Text: Molecular electronics, one of the major fields of the current effort in nano-science, may be de ed as the study of electronic behaviors, devices and applications that depend on the properties of matter at the molecular scale. If the miniaturization trend of microelectronic devices is to continue, elements such as transistors and contacts will soon shrink to single molecules. The promise of these new technological breakthroughs has been major driving force in this ld. Moreover, the consideration of molecular systems as electronic devices has raised new fundamental questions. In particular, while traditional quantum chemistry deals with electronically closed systems, we now face problems involving molecular systems that are open to their electronic environment, moreover, function in far from equilibrium situations. A generic molecular junction is made of two electrodes connected by a molecular spacer that takes the form of a molecular chain of varying length or a molecular layer of varying thickness. We use a simple nearest-neighbors tight-biding model with the non-equilibrium Green's function (NEGF) method to investigate and compare between a self-assembled monolayer (SAM), finite molecular layer (FML), and single molecule (SM) chemisorption to a surface of a metal substrate. In addition, we examine the difference in the transmission probability through a SAM, FML and SM sandwiched between two metallic electrodes. Dramatic differences are observed between the SM, FML and SAM density of electronic states and transmission functions. In addition, we analyze the effects of changing different physical parameters such as molecule-substrate interaction, molecule-molecule interactions, etc; interesting effects that pertain to the conduction properties of single molecules and molecular layers are observed. Intriguing results are attained when we investigate the commensurability of the SAM with the metallic surface

  13. Quinonoid metal complexes: toward molecular switches.

    Science.gov (United States)

    Dei, Andrea; Gatteschi, Dante; Sangregorio, Claudio; Sorace, Lorenzo

    2004-11-01

    The peculiar redox-active character of quinonoid metal complexes makes them extremely appealing to design materials of potential technological interest. We show here how the tuning of the properties of these systems can be pursued by using appropriate molecular synthetic techniques. In particular, we focus our attention on metal polyoxolene complexes exhibiting intramolecular electron transfer processes involving either the ligand and the metal ion or the two dioxolene moieties of a properly designed ligand thus inducing electronic bistability. The transition between the two metastable electronic states can be induced by different external stimuli such as temperature, pressure, light, or pH suggesting the use of these systems for molecular switches.

  14. Superluminescence from an optically pumped molecular tunneling junction by injection of plasmon induced hot electrons

    Directory of Open Access Journals (Sweden)

    Kai Braun

    2015-05-01

    Full Text Available Here, we demonstrate a bias-driven superluminescent point light-source based on an optically pumped molecular junction (gold substrate/self-assembled molecular monolayer/gold tip of a scanning tunneling microscope, operating at ambient conditions and providing almost three orders of magnitude higher electron-to-photon conversion efficiency than electroluminescence induced by inelastic tunneling without optical pumping. A positive, steadily increasing bias voltage induces a step-like rise of the Stokes shifted optical signal emitted from the junction. This emission is strongly attenuated by reversing the applied bias voltage. At high bias voltage, the emission intensity depends non-linearly on the optical pump power. The enhanced emission can be modelled by rate equations taking into account hole injection from the tip (anode into the highest occupied orbital of the closest substrate-bound molecule (lower level and radiative recombination with an electron from above the Fermi level (upper level, hence feeding photons back by stimulated emission resonant with the gap mode. The system reflects many essential features of a superluminescent light emitting diode.

  15. Large Magnetoresistance at Room Temperature in Organic Molecular Tunnel Junctions with Nonmagnetic Electrodes.

    Science.gov (United States)

    Xie, Zuoti; Shi, Sha; Liu, Feilong; Smith, Darryl L; Ruden, P Paul; Frisbie, C Daniel

    2016-09-27

    We report room-temperature resistance changes of up to 30% under weak magnetic fields (0.1 T) for molecular tunnel junctions composed of oligophenylene thiol molecules, 1-2 nm in length, sandwiched between gold contacts. The magnetoresistance (MR) is independent of field orientation and the length of the molecule; it appears to be an interface effect. Theoretical analysis suggests that the source of the MR is a two-carrier (two-hole) interaction at the interface, resulting in spin coupling between the tunneling hole and a localized hole at the Au/molecule contact. Such coupling leads to significantly different singlet and triplet transmission barriers at the interface. Even weak magnetic fields impede spin relaxation processes and thus modify the ratio of holes tunneling via the singlet state versus the triplet state, which leads to the large MR. Overall, the experiments and analysis suggest significant opportunities to explore large MR effects in molecular tunnel junctions based on widely available molecules.

  16. Carcinoembryonic antigen promotes colorectal cancer progression by targeting adherens junction complexes

    Energy Technology Data Exchange (ETDEWEB)

    Bajenova, Olga, E-mail: o.bazhenova@spbu.ru [Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199034 (Russian Federation); Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034 (Russian Federation); Department of Surgery and Biomedical Sciences, Creighton University, Omaha, NE 68178 (United States); Chaika, Nina [Department of Surgery and Biomedical Sciences, Creighton University, Omaha, NE 68178 (United States); Tolkunova, Elena; Davydov-Sinitsyn, Alexander [Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064 (Russian Federation); Gapon, Svetlana [Boston Children' s Hospital, Boston, MA 02115 (United States); Thomas, Peter [Department of Surgery and Biomedical Sciences, Creighton University, Omaha, NE 68178 (United States); O’Brien, Stephen [Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199034 (Russian Federation)

    2014-06-10

    Oncomarkers play important roles in the detection and management of human malignancies. Carcinoembryonic antigen (CEA, CEACAM5) and epithelial cadherin (E-cadherin) are considered as independent tumor markers in monitoring metastatic colorectal cancer. They are both expressed by cancer cells and can be detected in the blood serum. We investigated the effect of CEA production by MIP101 colorectal carcinoma cell lines on E-cadherin adherens junction (AJ) protein complexes. No direct interaction between E-cadherin and CEA was detected; however, the functional relationships between E-cadherin and its AJ partners: α-, β- and p120 catenins were impaired. We discovered a novel interaction between CEA and beta-catenin protein in the CEA producing cells. It is shown in the current study that CEA overexpression alters the splicing of p120 catenin and triggers the release of soluble E-cadherin. The influence of CEA production by colorectal cancer cells on the function of E-cadherin junction complexes may explain the link between the elevated levels of CEA and the increase in soluble E-cadherin during the progression of colorectal cancer. - Highlights: • Elevated level of CEA increases the release of soluble E-cadherin during the progression of colorectal cancer. • CEA over-expression alters the binding preferences between E-cadherin and its partners: α-, β- and p120 catenins in adherens junction complexes. • CEA produced by colorectal cancer cells interacts with beta-catenin protein. • CEA over-expression triggers the increase in nuclear beta-catenin. • CEA over-expression alters the splicing of p120 catenin protein.

  17. Carcinoembryonic antigen promotes colorectal cancer progression by targeting adherens junction complexes

    International Nuclear Information System (INIS)

    Bajenova, Olga; Chaika, Nina; Tolkunova, Elena; Davydov-Sinitsyn, Alexander; Gapon, Svetlana; Thomas, Peter; O’Brien, Stephen

    2014-01-01

    Oncomarkers play important roles in the detection and management of human malignancies. Carcinoembryonic antigen (CEA, CEACAM5) and epithelial cadherin (E-cadherin) are considered as independent tumor markers in monitoring metastatic colorectal cancer. They are both expressed by cancer cells and can be detected in the blood serum. We investigated the effect of CEA production by MIP101 colorectal carcinoma cell lines on E-cadherin adherens junction (AJ) protein complexes. No direct interaction between E-cadherin and CEA was detected; however, the functional relationships between E-cadherin and its AJ partners: α-, β- and p120 catenins were impaired. We discovered a novel interaction between CEA and beta-catenin protein in the CEA producing cells. It is shown in the current study that CEA overexpression alters the splicing of p120 catenin and triggers the release of soluble E-cadherin. The influence of CEA production by colorectal cancer cells on the function of E-cadherin junction complexes may explain the link between the elevated levels of CEA and the increase in soluble E-cadherin during the progression of colorectal cancer. - Highlights: • Elevated level of CEA increases the release of soluble E-cadherin during the progression of colorectal cancer. • CEA over-expression alters the binding preferences between E-cadherin and its partners: α-, β- and p120 catenins in adherens junction complexes. • CEA produced by colorectal cancer cells interacts with beta-catenin protein. • CEA over-expression triggers the increase in nuclear beta-catenin. • CEA over-expression alters the splicing of p120 catenin protein

  18. Models of charge transport and transfer in molecular switch tunnel junctions of bistable catenanes and rotaxanes

    International Nuclear Information System (INIS)

    Flood, Amar H.; Wong, Eric W.; Stoddart, J. Fraser

    2006-01-01

    The processes by which charge transfer can occur play a foundational role in molecular electronics. Here we consider simplified models of the transfer processes that could be present in bistable molecular switch tunnel junction (MSTJ) devices during one complete cycle of the device from its low- to high- and back to low-conductance state. The bistable molecular switches, which are composed of a monolayer of either switchable catenanes or rotaxanes, exist in either a ground-state co-conformation or a metastable one in which the conduction properties of the two co-conformations, when measured at small biases (+0.1 V), are significantly different irrespective of whether transport is dominated by tunneling or hopping. The voltage-driven generation (±2 V) of molecule-based redox states, which are sufficiently long-lived to allow the relative mechanical movements necessary to switch between the two co-conformations, rely upon unequal charge transfer rates on to and/or off of the molecules. Surface-enhanced Raman spectroscopy has been used to image the ground state of the bistable rotaxane in MSTJ-like devices. Consideration of these models provide new ways of looking at molecular electronic devices that rely, not only on nanoscale charge-transport, but also upon the bustling world of molecular motion in mechanically interlocked bistable molecules

  19. ProbeZT: Simulation of transport coefficients of molecular electronic junctions under environmental effects using Büttiker's probes

    Science.gov (United States)

    Korol, Roman; Kilgour, Michael; Segal, Dvira

    2018-03-01

    We present our in-house quantum transport package, ProbeZT. This program provides linear response coefficients: electrical and electronic thermal conductances, as well as the thermopower of molecular junctions in which electrons interact with the surrounding thermal environment. Calculations are performed based on the Büttiker probe method, which introduces decoherence, energy exchange and dissipation effects phenomenologically using virtual electrode terminals called probes. The program can realize different types of probes, each introducing various environmental effects, including elastic and inelastic scattering of electrons. The molecular system is described by an arbitrary tight-binding Hamiltonian, allowing the study of different geometries beyond simple one-dimensional wires. Applications of the program to study the thermoelectric performance of molecular junctions are illustrated. The program also has a built-in functionality to simulate electron transport in double-stranded DNA molecules based on a tight-binding (ladder) description of the junction.

  20. Interaction between molecular complexes in dispersive media

    International Nuclear Information System (INIS)

    Banagas, E.A.; Manykin, E.A.

    1987-01-01

    The interaction between molecular complexes in different dispersive media with local and nonlocal screening is investigated theoretically. On the basis of results of numerical analysis on a computer, the dependence of the coupled-system spectrum and the interaction energy of the polarized modes on the characteristic parameters of the dispersive media is considered

  1. Carbon Electrode-Molecule Junctions: A Reliable Platform for Molecular Electronics.

    Science.gov (United States)

    Jia, Chuancheng; Ma, Bangjun; Xin, Na; Guo, Xuefeng

    2015-09-15

    The development of reliable approaches to integrate individual or a small collection of molecules into electrical nanocircuits, often termed "molecular electronics", is currently a research focus because it can not only overcome the increasing difficulties and fundamental limitations of miniaturization of current silicon-based electronic devices, but can also enable us to probe and understand the intrinsic properties of materials at the atomic- and/or molecular-length scale. This development might also lead to direct observation of novel effects and fundamental discovery of physical phenomena that are not accessible by traditional materials or approaches. Therefore, researchers from a variety of backgrounds have been devoting great effort to this objective, which has started to move beyond simple descriptions of charge transport and branch out in different directions, reflecting the interdisciplinarity. This Account exemplifies our ongoing interest and great effort in developing efficient lithographic methodologies capable of creating molecular electronic devices through the combination of top-down micro/nanofabrication with bottom-up molecular assembly. These devices use nanogapped carbon nanomaterials (such as single-walled carbon nanotubes (SWCNTs) and graphene), with a particular focus on graphene, as point contacts formed by electron beam lithography and precise oxygen plasma etching. Through robust amide linkages, functional molecular bridges terminated with diamine moieties are covalently wired into the carboxylic acid-functionalized nanogaps to form stable carbon electrode-molecule junctions with desired functionalities. At the macroscopic level, to improve the contact interface between electrodes and organic semiconductors and lower Schottky barriers, we used SWCNTs and graphene as efficient electrodes to explore the intrinsic properties of organic thin films, and then build functional high-performance organic nanotransistors with ultrahigh responsivities

  2. Controlling the formation process and atomic structures of single pyrazine molecular junction by tuning the strength of the metal-molecule interaction.

    Science.gov (United States)

    Kaneko, Satoshi; Takahashi, Ryoji; Fujii, Shintaro; Nishino, Tomoaki; Kiguchi, Manabu

    2017-04-12

    The formation process and atomic structures were investigated for single pyrazine molecular junctions sandwiched by three different Au, Ag, and Cu electrodes using a mechanically controllable break junction technique in ultrahigh vacuum conditions at 300 K. We demonstrated that the formation process of the single-molecule junction crucially depended on the choice of the metal electrodes. While single-molecule junction showing two distinct conductance states were found for the Au electrodes, only the single conductance state was evident for the Ag electrodes, and there was no junction formation for the Cu electrodes. These results suggested that metal-molecule interaction dominates the formation process and probability of the single-molecule junction. In addition to the metal-molecule interaction, temperature affected the formation process of the single-molecule junction. The single pyrazine molecular junction formed between Au electrodes exhibited significant temperature dependence where the junction-formation probability was about 8% at 300 K, while there was no junction-formation at 100 K. Instead of the junction formation, an Au atomic wire was formed at the low temperature. This study provides insight into the tuning of the junction-forming process for single-molecule junctions, which is needed to construct device structures on a single molecule scale.

  3. Effects of Electrode Distances on Geometric Structure and Electronic Transport Properties of Molecular 4,4'-Bipyridine Junction

    International Nuclear Information System (INIS)

    Li Zongliang; Zou Bin; Wang Chuankui; Luo Yi

    2006-01-01

    Influences of electrode distances on geometric structure of molecule and on electronic transport properties of molecular junctions have been investigated by means of a generalized quantum chemical approach based on the elastic scattering Green's function method. Numerical results show that, for organic molecule 4,4'-bipyridine, the geometric structure of the molecule especially the dihedral angle between the two pyridine rings is sensitive to the distances between the two electrodes. The currents of the molecular junction are taken nonlinearly increase with the increase of the bias. Shortening the distance of the metallic electrodes will result in stronger coupling and larger conductance

  4. Interface-Engineered Charge-Transport Properties in Benzenedithiol Molecular Electronic Junctions via Chemically p-Doped Graphene Electrodes.

    Science.gov (United States)

    Jang, Yeonsik; Kwon, Sung-Joo; Shin, Jaeho; Jeong, Hyunhak; Hwang, Wang-Taek; Kim, Junwoo; Koo, Jeongmin; Ko, Taeg Yeoung; Ryu, Sunmin; Wang, Gunuk; Lee, Tae-Woo; Lee, Takhee

    2017-12-06

    In this study, we fabricated and characterized vertical molecular junctions consisting of self-assembled monolayers of benzenedithiol (BDT) with a p-doped multilayer graphene electrode. The p-type doping of a graphene film was performed by treating pristine graphene (work function of ∼4.40 eV) with trifluoromethanesulfonic (TFMS) acid, producing a significantly increased work function (∼5.23 eV). The p-doped graphene-electrode molecular junctions statistically showed an order of magnitude higher current density and a lower charge injection barrier height than those of the pristine graphene-electrode molecular junctions, as a result of interface engineering. This enhancement is due to the increased work function of the TFMS-treated p-doped graphene electrode in the highest occupied molecular orbital-mediated tunneling molecular junctions. The validity of these results was proven by a theoretical analysis based on a coherent transport model that considers asymmetric couplings at the electrode-molecule interfaces.

  5. Tuning the thickness of electrochemically grafted layers in large area molecular junctions

    Energy Technology Data Exchange (ETDEWEB)

    Fluteau, T.; Bessis, C.; Barraud, C., E-mail: clement.barraud@univ-paris-diderot.fr; Della Rocca, M. L.; Lafarge, P. [Université Paris Diderot, Sorbonne Paris Cité, MPQ, UMR 7162, CNRS, 75205 Paris Cedex 13 (France); Martin, P.; Lacroix, J.-C. [Université Paris Diderot, Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J.-A. de Baïf, 75205 Paris Cedex 13 (France)

    2014-09-21

    We have investigated the thickness, the surface roughness, and the transport properties of oligo(1-(2-bisthienyl)benzene) (BTB) thin films grafted on evaporated Au electrodes, thanks to a diazonium-based electro-reduction process. The thickness of the organic film is tuned by varying the number of electrochemical cycles during the growth process. Atomic force microscopy measurements reveal the evolution of the thickness in the range of 2–27 nm. Its variation displays a linear dependence with the number of cycles followed by a saturation attributed to the insulating behavior of the organic films. Both ultrathin (2 nm) and thin (12 and 27 nm) large area BTB-based junctions have then been fabricated using standard CMOS processes and finally electrically characterized. The electronic responses are fully consistent with a tunneling barrier in case of ultrathin BTB film whereas a pronounced rectifying behavior is reported for thicker molecular films.

  6. Molecular dynamic simulation on boron cluster implantation for shallow junction formation

    International Nuclear Information System (INIS)

    Yuan Li; Yu Min; Li Wei; Ji Huihui; Ren Liming; Zhan Kai; Huang Ru; Zhang Xing; Wang Yangyuan; Zhang Jinyu; Oka, Hideki

    2006-01-01

    Boron cluster ion implantation is a potential technology for shallow junction formation in integrated circuits manufacture. A molecular dynamic method for cluster implantation simulation, aiming at microelectronics application, is presented in this paper. Accurate geometric structures of boron clusters are described by the model, and the H atoms in clusters are included. A potential function taking the form of combining the ZBL and the SW potentials is presented here to model interaction among the atoms in the boron cluster. The impact of these models on cluster implantation simulation is investigated. There are notable impact on dopant distribution and amount of implantation defects with consideration of these models. The simulation on the distributions of B and H are verified by SIMS data

  7. Molecular-Beam Epitaxially Grown MgB2 Thin Films and Superconducting Tunnel Junctions

    Directory of Open Access Journals (Sweden)

    Jean-Baptiste Laloë

    2011-01-01

    Full Text Available Since the discovery of its superconducting properties in 2001, magnesium diboride has generated terrific scientific and engineering research interest around the world. With a of 39 K and two superconducting gaps, MgB2 has great promise from the fundamental point of view, as well as immediate applications. Several techniques for thin film deposition and heterojunction formation have been established, each with its own advantages and drawbacks. Here, we will present a brief overview of research based on MgB2 thin films grown by molecular beam epitaxy coevaporation of Mg and B. The films are smooth and highly crystalline, and the technique allows for virtually any heterostructure to be formed, including all-MgB2 tunnel junctions. Such devices have been characterized, with both quasiparticle and Josephson tunneling reported. MgB2 remains a material of great potential for a multitude of further characterization and exploration research projects and applications.

  8. Molecular dynamics investigation of carbon nanotube junctions in non-aqueous solutions

    KAUST Repository

    Gkionis, Konstantinos

    2014-07-23

    The properties of liquids in a confined environment are known to differ from those in the bulk. Extending this knowledge to geometries defined by two metallic layers in contact with the ends of a carbon nanotube is important for describing a large class of nanodevices that operate in non-aqueous environments. Here we report a series of classical molecular dynamics simulations for gold-electrode junctions in acetone, cyclohexane and N,N-dimethylformamide solutions and analyze the structure and the dynamics of the solvents in different regions of the nanojunction. The presence of the nanotube has little effect on the ordering of the solvents along its axis, while in the transversal direction deviations are observed. Importantly, the orientational dynamics of the solvents at the electrode-nanotube interface differ dramatically from that found when only the electrodes are present.

  9. Nano-fabrication of molecular electronic junctions by targeted modification of metal-molecule bonds

    Science.gov (United States)

    Jafri, S. Hassan M.; Löfås, Henrik; Blom, Tobias; Wallner, Andreas; Grigoriev, Anton; Ahuja, Rajeev; Ottosson, Henrik; Leifer, Klaus

    2015-09-01

    Reproducibility, stability and the coupling between electrical and molecular properties are central challenges in the field of molecular electronics. The field not only needs devices that fulfill these criteria but they also need to be up-scalable to application size. In this work, few-molecule based electronics devices with reproducible electrical characteristics are demonstrated. Our previously reported 5 nm gold nanoparticles (AuNP) coated with ω-triphenylmethyl (trityl) protected 1,8-octanedithiol molecules are trapped in between sub-20 nm gap spacing gold nanoelectrodes forming AuNP-molecule network. When the trityl groups are removed, reproducible devices and stable Au-thiol junctions are established on both ends of the alkane segment. The resistance of more than 50 devices is reduced by orders of magnitude as well as a reduction of the spread in the resistance histogram is observed. By density functional theory calculations the orders of magnitude decrease in resistance can be explained and supported by TEM observations thus indicating that the resistance changes and strongly improved resistance spread are related to the establishment of reproducible and stable metal-molecule bonds. The same experimental sequence is carried out using 1,6-hexanedithiol functionalized AuNPs. The average resistances as a function of molecular length, demonstrated herein, are comparable to the one found in single molecule devices.

  10. Molecular architecture of myelinated nerve fibers: leaky paranodal junctions and paranodal dysmyelination.

    Science.gov (United States)

    Rosenbluth, Jack; Mierzwa, Amanda; Shroff, Seema

    2013-12-01

    Myelinated nerve fibers have evolved to optimize signal propagation. Each myelin segment is attached to the axon by the unique paranodal axoglial junction (PNJ), a highly complex structure that serves to define axonal ion channel domains and to direct nodal action currents through adjacent nodes. Surprisingly, this junction does not entirely seal the paranodal myelin sheath to the axon and thus does not entirely isolate the perinodal space from the internodal periaxonal space. Rather the paranode is penetrated by extracellular pathways between the myelin sheath and the axolemma for movement of molecules and the flow of current to and from the internodal axon. This review summarizes past and current studies demonstrating these pathways and considers what functional roles they subserve. In addition, modern genetic engineering methods permit modification of individual PNJ constituents, which provides an opportunity to define their specific functions. One component in particular, the transverse bands, plays a key role in maintaining the structure and function of the PNJ. Loss of transverse bands results not in frank demyelination but rather in subtle dysmyelination, which causes significant functional impairment. The consequences of such subtle defects in the PNJ are considered along with the relevance of these studies to human diseases of myelin.

  11. Polaron effects on the dc- and ac-tunneling characteristics of molecular Josephson junctions

    Science.gov (United States)

    Wu, B. H.; Cao, J. C.; Timm, C.

    2012-07-01

    We study the interplay of polaronic effect and superconductivity in transport through molecular Josephson junctions. The tunneling rates of electrons are dominated by vibronic replicas of the superconducting gap, which show up as prominent features in the differential conductance for the dc and ac current. For relatively large molecule-lead coupling, a features that appears when the Josephson frequency matches the vibron frequency can be identified with an over-the-gap structure observed by Marchenkov [Nat. Nanotech. 1748-338710.1038/nnano.2007.2182, 481 (2007)]. However, we are more concerned with the weak-coupling limit, where resonant tunneling through the molecular level dominates. We find that certain features involving both Andreev reflection and vibron emission show an unusual shift of the bias voltage V at their maximum with the gate voltage Vg as V˜(2/3)Vg. Moreover, due to the polaronic effect, the ac Josephson current shows a phase shift of π when the bias eV is increased by one vibronic energy quantum ℏωv. This distinctive even-odd effect is explained in terms of the different sign of the coupling to vibrons of electrons and of Andreev-reflected holes.

  12. Effect of electron-vibration interactions on the thermoelectric efficiency of molecular junctions.

    Science.gov (United States)

    Hsu, Bailey C; Chiang, Chi-Wei; Chen, Yu-Chang

    2012-07-11

    From first-principles approaches, we investigate the thermoelectric efficiency of a molecular junction where a benzene molecule is connected directly to the platinum electrodes. We calculate the thermoelectric figure of merit ZT in the presence of electron-vibration interactions with and without local heating under two scenarios: linear response and finite bias regimes. In the linear response regime, ZT saturates around the electrode temperature T(e) = 25 K in the elastic case, while in the inelastic case we observe a non-saturated and a much larger ZT beyond T(e) = 25 K attributed to the tail of the Fermi-Dirac distribution. In the finite bias regime, the inelastic effects reveal the signatures of the molecular vibrations in the low-temperature regime. The normal modes exhibiting structures in the inelastic profile are characterized by large components of atomic vibrations along the current density direction on top of each individual atom. In all cases, the inclusion of local heating leads to a higher wire temperature T(w) and thus magnifies further the influence of the electron-vibration interactions due to the increased number of local phonons.

  13. Fatigue crack propagation path across the dentinoenamel junction complex in human teeth.

    Science.gov (United States)

    Dong, X D; Ruse, N D

    2003-07-01

    The human tooth structures should be understood clearly to improve clinically used restorative materials. The dentinoenamel junction (DEJ) plays a key role in resisting crack propagation in teeth. The aim of this study was to determine the fracture toughness of the enamel-DEJ-dentin complex and to investigate the influence of the DEJ on the fatigue crack propagation path across it by characterizing fatigue-fractured enamel-DEJ-dentin complexes using optical and scanning electron microscopy. The results of this study showed that the fracture toughness of the enamel-DEJ-dentin complex was 1.50 +/- 0.28 Mpa x m(1/2). Based on the results of this investigation, it was concluded that the DEJ complex played a critical role in resisting crack propagation from enamel into dentin. The DEJ complex is, approximately, a 100 to 150 microm broad region at the interface between enamel and dentin. The toughening mechanism of the DEJ complex may be explained by the fact that crack paths were deflected as cracks propagated across it. Understanding the mechanism of crack deflection could help in improving dentin-composite as well as ceramic-cement interfacial qualities with the aim to decrease the risk of clinical failure of restorations. Both can be viewed as being composed from a layer of material of high strength and hardness bonded to a softer but tougher substratum (dentin). The bonding agent or the luting cement layer may play the critical role of the DEJ in improving the strength of these restorations in clinical situations. Copyright 2003 Wiley Periodicals, Inc.

  14. On-wire lithography-generated molecule-based transport junctions: a new testbed for molecular electronics.

    Science.gov (United States)

    Chen, Xiaodong; Jeon, You-Moon; Jang, Jae-Won; Qin, Lidong; Huo, Fengwei; Wei, Wei; Mirkin, Chad A

    2008-07-02

    On-wire lithography (OWL) fabricated nanogaps are used as a new testbed to construct molecular transport junctions (MTJs) through the assembly of thiolated molecular wires across a nanogap formed between two Au electrodes. In addition, we show that one can use OWL to rapidly characterize a MTJ and optimize gap size for two molecular wires of different dimensions. Finally, we have used this new testbed to identify unusual temperature-dependent transport mechanisms for alpha,omega-dithiol terminated oligo(phenylene ethynylene).

  15. Haploinsufficiency for Core Exon Junction Complex Components Disrupts Embryonic Neurogenesis and Causes p53-Mediated Microcephaly.

    Directory of Open Access Journals (Sweden)

    Hanqian Mao

    2016-09-01

    Full Text Available The exon junction complex (EJC is an RNA binding complex comprised of the core components Magoh, Rbm8a, and Eif4a3. Human mutations in EJC components cause neurodevelopmental pathologies. Further, mice heterozygous for either Magoh or Rbm8a exhibit aberrant neurogenesis and microcephaly. Yet despite the requirement of these genes for neurodevelopment, the pathogenic mechanisms linking EJC dysfunction to microcephaly remain poorly understood. Here we employ mouse genetics, transcriptomic and proteomic analyses to demonstrate that haploinsufficiency for each of the 3 core EJC components causes microcephaly via converging regulation of p53 signaling. Using a new conditional allele, we first show that Eif4a3 haploinsufficiency phenocopies aberrant neurogenesis and microcephaly of Magoh and Rbm8a mutant mice. Transcriptomic and proteomic analyses of embryonic brains at the onset of neurogenesis identifies common pathways altered in each of the 3 EJC mutants, including ribosome, proteasome, and p53 signaling components. We further demonstrate all 3 mutants exhibit defective splicing of RNA regulatory proteins, implying an EJC dependent RNA regulatory network that fine-tunes gene expression. Finally, we show that genetic ablation of one downstream pathway, p53, significantly rescues microcephaly of all 3 EJC mutants. This implicates p53 activation as a major node of neurodevelopmental pathogenesis following EJC impairment. Altogether our study reveals new mechanisms to help explain how EJC mutations influence neurogenesis and underlie neurodevelopmental disease.

  16. Structural and functional insights into the malaria parasite moving junction complex.

    Directory of Open Access Journals (Sweden)

    Brigitte Vulliez-Le Normand

    Full Text Available Members of the phylum Apicomplexa, which include the malaria parasite Plasmodium, share many features in their invasion mechanism in spite of their diverse host cell specificities and life cycle characteristics. The formation of a moving junction (MJ between the membranes of the invading apicomplexan parasite and the host cell is common to these intracellular pathogens. The MJ contains two key parasite components: the surface protein Apical Membrane Antigen 1 (AMA1 and its receptor, the Rhoptry Neck Protein (RON complex, which is targeted to the host cell membrane during invasion. In particular, RON2, a transmembrane component of the RON complex, interacts directly with AMA1. Here, we report the crystal structure of AMA1 from Plasmodium falciparum in complex with a peptide derived from the extracellular region of PfRON2, highlighting clear specificities of the P. falciparum RON2-AMA1 interaction. The receptor-binding site of PfAMA1 comprises the hydrophobic groove and a region that becomes exposed by displacement of the flexible Domain II loop. Mutations of key contact residues of PfRON2 and PfAMA1 abrogate binding between the recombinant proteins. Although PfRON2 contacts some polymorphic residues, binding studies with PfAMA1 from different strains show that these have little effect on affinity. Moreover, we demonstrate that the PfRON2 peptide inhibits erythrocyte invasion by P. falciparum merozoites and that this strong inhibitory potency is not affected by AMA1 polymorphisms. In parallel, we have determined the crystal structure of PfAMA1 in complex with the invasion-inhibitory peptide R1 derived by phage display, revealing an unexpected structural mimicry of the PfRON2 peptide. These results identify the key residues governing the interactions between AMA1 and RON2 in P. falciparum and suggest novel approaches to antimalarial therapeutics.

  17. Molecular Dynamics Studies on Ballistic Thermal Resistance of Graphene Nano-Junctions

    International Nuclear Information System (INIS)

    Yao Wen-Jun; Cao Bing-Yang

    2015-01-01

    Ballistic thermal resistance of graphene nano-junctions is investigated using non-equilibrium molecular dynamics simulation. The simulation system is consisted of two symmetrical trapezoidal or rectangular graphene nano-ribbons (GNRs) and a connecting nanoscale constriction in between. From the simulated temperature profile, a big temperature jump resulted from the constriction is found, which is proportional to the heat current and corresponds to a local ballistic thermal resistance. Fixing the constriction width and the length of GNRs, this ballistic thermal resistance is independent of the width of the GNRs bottom layer, i.e., the convex angle. But interestingly, this thermal resistance has obvious size effect. It is inversely proportional to the constriction width and will disappear with the constriction being wider. Moreover, based on the phonon dynamics theory, a theoretical model of the ballistic thermal resistance in two-dimensional nano-systems is developed, which gives a good explanation on microcosmic level and agrees well with the simulation result quantitatively and qualitatively. (paper)

  18. Boosting spin-caloritronic effects by attractive correlations in molecular junctions.

    Science.gov (United States)

    Weymann, Ireneusz

    2016-01-25

    In nanoscopic systems quantum confinement and interference can lead to an enhancement of thermoelectric properties as compared to conventional bulk materials. For nanostructures, such as molecules or quantum dots coupled to external leads, the thermoelectric figure of merit can reach or even exceed unity. Moreover, in the presence of external magnetic field or when the leads are ferromagnetic, an applied temperature gradient can generate a spin voltage and an associated spin current flow in the system, which makes such nanostructures particularly interesting for future thermoelectric applications. In this study, by using the numerical renormalization group method, we examine the spin-dependent thermoelectric transport properties of a molecular junction involving an orbital level with attractive Coulomb correlations coupled to ferromagnetic leads. We analyze how attractive correlations affect the spin-resolved transport properties of the system and find a nontrivial dependence of the conductance and tunnel magnetoresistance on the strength and sign of those correlations. We also demonstrate that attractive correlations can lead to an enhancement of the spin thermopower and the figure of merit, which can be controlled by a gate voltage.

  19. Full-counting statistics of energy transport of molecular junctions in the polaronic regime

    International Nuclear Information System (INIS)

    Tang, Gaomin; Yu, Zhizhou; Wang, Jian

    2017-01-01

    We investigate the full-counting statistics (FCS) of energy transport carried by electrons in molecular junctions for the Anderson–Holstein model in the polaronic regime. Using the two-time quantum measurement scheme, the generating function (GF) for the energy transport is derived and expressed as a Fredholm determinant in terms of Keldysh nonequilibrium Green’s function in the time domain. Dressed tunneling approximation is used in decoupling the phonon cloud operator in the polaronic regime. This formalism enables us to analyze the time evolution of energy transport dynamics after a sudden switch-on of the coupling between the dot and the leads towards the stationary state. The steady state energy current cumulant GF in the long time limit is obtained in the energy domain as well. Universal relations for steady state energy current FCS are derived under a finite temperature gradient with zero bias and this enabled us to express the equilibrium energy current cumulant by a linear combination of lower order cumulants. The behaviors of energy current cumulants in steady state under temperature gradient and external bias are numerically studied and explained. The transient dynamics of energy current cumulants is numerically calculated and analyzed. Universal scaling of normalized transient energy cumulants is found under both temperature gradient and external bias. (paper)

  20. Creation of stable molecular junctions with a custom-designed scanning tunneling microscope.

    Science.gov (United States)

    Lee, Woochul; Reddy, Pramod

    2011-12-02

    The scanning tunneling microscope break junction (STMBJ) technique is a powerful approach for creating single-molecule junctions and studying electrical transport in them. However, junctions created using the STMBJ technique are usually mechanically stable for relatively short times (scanning tunneling microscope that enables the creation of metal-single molecule-metal junctions that are mechanically stable for more than 1 minute at room temperature. This stability is achieved by a design that minimizes thermal drift as well as the effect of environmental perturbations. The utility of this instrument is demonstrated by performing transition voltage spectroscopy-at the single-molecule level-on Au-hexanedithiol-Au, Au-octanedithiol-Au and Au-decanedithiol-Au junctions.

  1. Creation of stable molecular junctions with a custom-designed scanning tunneling microscope

    International Nuclear Information System (INIS)

    Lee, Woochul; Reddy, Pramod

    2011-01-01

    The scanning tunneling microscope break junction (STMBJ) technique is a powerful approach for creating single-molecule junctions and studying electrical transport in them. However, junctions created using the STMBJ technique are usually mechanically stable for relatively short times (<1 s), impeding detailed studies of their charge transport characteristics. Here, we report a custom-designed scanning tunneling microscope that enables the creation of metal–single molecule–metal junctions that are mechanically stable for more than 1 minute at room temperature. This stability is achieved by a design that minimizes thermal drift as well as the effect of environmental perturbations. The utility of this instrument is demonstrated by performing transition voltage spectroscopy—at the single-molecule level—on Au–hexanedithiol–Au, Au–octanedithiol–Au and Au–decanedithiol–Au junctions.

  2. The Use of Next Generation Sequencing and Junction Sequence Analysis Bioinformatics to Achieve Molecular Characterization of Crops Improved Through Modern Biotechnology

    Directory of Open Access Journals (Sweden)

    David Kovalic

    2012-11-01

    Full Text Available The assessment of genetically modified (GM crops for regulatory approval currently requires a detailed molecular characterization of the DNA sequence and integrity of the transgene locus. In addition, molecular characterization is a critical component of event selection and advancement during product development. Typically, molecular characterization has relied on Southern blot analysis to establish locus and copy number along with targeted sequencing of polymerase chain reaction products spanning any inserted DNA to complete the characterization process. Here we describe the use of next generation (NexGen sequencing and junction sequence analysis bioinformatics in a new method for achieving full molecular characterization of a GM event without the need for Southern blot analysis. In this study, we examine a typical GM soybean [ (L. Merr.] line and demonstrate that this new method provides molecular characterization equivalent to the current Southern blot-based method. We also examine an event containing in vivo DNA rearrangement of multiple transfer DNA inserts to demonstrate that the new method is effective at identifying complex cases. Next generation sequencing and bioinformatics offers certain advantages over current approaches, most notably the simplicity, efficiency, and consistency of the method, and provides a viable alternative for efficiently and robustly achieving molecular characterization of GM crops.

  3. A complex craniovertebral junction malformation in a patient with late onset glycogenosis 2

    Directory of Open Access Journals (Sweden)

    Mariasofia Cotelli

    2014-01-01

    Full Text Available Glycogenosis II (GSDII is an autosomal recessive lysosomal storage disorder resulting from deficiency of acid alpha-glucosidase and subsequent lysosomal accumulation of glycogen in skeletal, cardiac and smooth muscles. The late-onset form is characterized by wide variability of the phenotypical spectrum. Clinical findings may include muscle weakness, respiratory insufficiency, vascular abnormalities, low bone mineral density and higher risk of developing osteoporosis. Craniovertebral junction (CVJ malformations have never been described so far. We here report on a GSDII 43-year-old woman who harbored the mutations IVS1-13T>G and c.2237G>A in the acid alpha-glucosidase gene. She recurrently suffered from headache, neck pain and dizziness. Brain MRI and CT scan showed the presence of a very rare complex CVJ malformation composed of basilar invagination, basiocciput hypoplasia, partial C1 assimilation, C1 posterior arch aplasia and C1 lateral mass hypoplasia and offset. Although we cannot rule out their coincidental occurrence, the rarity of multiple CVJ malformations in the general population as well as the well-known GSDII multisystem involvement should suggest to study the CVJ in the diagnostic process of GSDII patients in order to assess the CVJ malformation frequency in GSDII population and verify a possible relationship between these two conditions.

  4. Humidity dependence of molecular tunnel junctions with an AlOx/COOH- interface

    Science.gov (United States)

    Zhang, Xiaohang; McGill, Stephen; Xiong, Peng

    2006-03-01

    We have studied the electron transport in planar tunneling junctions with aluminum oxide and an organic self-assembled monolayer (SAM) as the tunnel barrier. The structure of the junctions is Al/AlOx/SAM/(Au, Pb) with a junction area of ˜ 0.4mm^2. The organic molecules investigated include mercaptohexadecanoic acid (MHA), hexadecanoic acid (HDA), and octadecyltrichlorosilane (OTS); all of which form ordered SAMs on top of aluminum oxide. The use of a superconducting electrode (Al) enables us to determine unambiguously that these are high-quality tunnel junctions. For junctions incorporating MHA, the transport behavior is found to be strongly humidity dependent. The resistance of these junctions drops more than 50% when placed in dry nitrogen and recovers when returned into the ambient. The same drop also occurs when the sample is placed into a vacuum, and backfilling the vacuum with either dry N2 or O2 has negligible effect on the resistance. For comparison, junctions with HDA show the same humidity dependence, while OTS samples do not. Since both MHA and HDA have carboxylic groups and OTS does not, the results suggest that water molecules at the AlOx/COOH- interface play the central role in the observed behavior. Inelastic tunneling spectroscopy (IETS) has also been performed to understand the role of water. This work was supported by a FSU Research Foundation PEG grant.

  5. Gap Junctions

    Science.gov (United States)

    Nielsen, Morten Schak; Axelsen, Lene Nygaard; Sorgen, Paul L.; Verma, Vandana; Delmar, Mario; Holstein-Rathlou, Niels-Henrik

    2013-01-01

    Gap junctions are essential to the function of multicellular animals, which require a high degree of coordination between cells. In vertebrates, gap junctions comprise connexins and currently 21 connexins are known in humans. The functions of gap junctions are highly diverse and include exchange of metabolites and electrical signals between cells, as well as functions, which are apparently unrelated to intercellular communication. Given the diversity of gap junction physiology, regulation of gap junction activity is complex. The structure of the various connexins is known to some extent; and structural rearrangements and intramolecular interactions are important for regulation of channel function. Intercellular coupling is further regulated by the number and activity of channels present in gap junctional plaques. The number of connexins in cell-cell channels is regulated by controlling transcription, translation, trafficking, and degradation; and all of these processes are under strict control. Once in the membrane, channel activity is determined by the conductive properties of the connexin involved, which can be regulated by voltage and chemical gating, as well as a large number of posttranslational modifications. The aim of the present article is to review our current knowledge on the structure, regulation, function, and pharmacology of gap junctions. This will be supported by examples of how different connexins and their regulation act in concert to achieve appropriate physiological control, and how disturbances of connexin function can lead to disease. © 2012 American Physiological Society. Compr Physiol 2:1981-2035, 2012. PMID:23723031

  6. Quantitative interpretation of the transition voltages in gold-poly(phenylene) thiol-gold molecular junctions

    KAUST Repository

    Wu, Kunlin; Bai, Meilin; Sanvito, Stefano; Hou, Shimin

    2013-01-01

    simulations. For all the junctions, the calculated transition voltage at positive polarity is in quantitative agreement with the experimental values and shows weak dependence on alterations of the Au-phenyl contact. When compared to the strong coupling

  7. Azobenzenes as light-controlled molecular electronic switches in nanoscale metal-molecule-metal junctions.

    Science.gov (United States)

    Mativetsky, Jeffrey M; Pace, Giuseppina; Elbing, Mark; Rampi, Maria A; Mayor, Marcel; Samorì, Paolo

    2008-07-23

    Conductance switching associated with the photoisomerization of azobenzene-based (Azo) molecules was observed in nanoscopic metal-molecule-metal junctions. The junctions were formed by using a conducting atomic force microscope (C-AFM) approach, where a metallic AFM tip was used to electrically contact a gold-supported Azo self-assembled monolayer. The measured 30-fold increase in conductance is consistent with the expected decrease in tunneling barrier length resulting from the conformational change of the Azo molecule.

  8. Food-web complexity across hydrothermal vents on the Azores triple junction

    Science.gov (United States)

    Portail, Marie; Brandily, Christophe; Cathalot, Cécile; Colaço, Ana; Gélinas, Yves; Husson, Bérengère; Sarradin, Pierre-Marie; Sarrazin, Jozée

    2018-01-01

    The assessment and comparison of food webs across various hydrothermal vent sites can enhance our understanding of ecological processes involved in the structure and function of biodiversity. The Menez Gwen, Lucky Strike and Rainbow vent fields are located on the Azores triple junction of the Mid-Atlantic Ridge. These fields have distinct depths (from 850 to 2320 m) and geological contexts (basaltic and ultramafic), but share similar faunal assemblages defined by the presence of foundation species that include Bathymodiolus azoricus, alvinocarid shrimp and gastropods. We compared the food webs of 13 faunal assemblages at these three sites using carbon and nitrogen stable isotope analyses (SIA). Results showed that photosynthesis-derived organic matter is a negligible basal source for vent food webs, at all depths. The contribution of methanotrophy versus autotrophy based on Calvin-Benson-Bassham (CBB) or reductive tricarboxylic acid (rTCA) cycles varied between and within vent fields according to the concentrations of reduced compounds (e.g. CH4, H2S). Species that were common to vent fields showed high trophic flexibility, suggesting weak trophic links to the metabolism of chemosynthetic primary producers. At the community level, a comparison of SIA-derived metrics between mussel assemblages from two vent fields (Menez Gwen & Lucky Strike) showed that the functional structure of food webs was highly similar in terms of basal niche diversification, functional specialization and redundancy. Coupling SIA to functional trait approaches included more variability within the analyses, but the functional structures were still highly comparable. These results suggest that despite variable environmental conditions (physico-chemical factors and basal sources) and faunal community structure, functional complexity remained relatively constant among mussel assemblages. This functional similarity may be favoured by the propensity of species to adapt to fluid variations and

  9. Molecular dynamics simulation of self-diffusion processes in titanium in bulk material, on grain junctions and on surface.

    Science.gov (United States)

    Sushko, Gennady B; Verkhovtsev, Alexey V; Yakubovich, Alexander V; Schramm, Stefan; Solov'yov, Andrey V

    2014-08-21

    The process of self-diffusion of titanium atoms in a bulk material, on grain junctions and on surface is explored numerically in a broad temperature range by means of classical molecular dynamics simulation. The analysis is carried out for a nanoscale cylindrical sample consisting of three adjacent sectors and various junctions between nanocrystals. The calculated diffusion coefficient varies by several orders of magnitude for different regions of the sample. The calculated values of the bulk diffusion coefficient correspond reasonably well to the experimental data obtained for solid and molten states of titanium. Investigation of diffusion in the nanocrystalline titanium is of a significant importance because of its numerous technological applications. This paper aims to reduce the lack of data on diffusion in titanium and describe the processes occurring in bulk, at different interfaces and on surface of the crystalline titanium.

  10. Current-induced forces: a new mechanism to induce negative differential resistance and current-switching effect in molecular junctions

    Science.gov (United States)

    Gu, Lei; Fu, Hua-Hua

    2015-12-01

    Current-induced forces can excite molecules, polymers and other low-dimensional materials, which in turn leads to an effective gate voltage through Holstein interaction. Here, by taking a short asymmetric DNA junction as an example, and using the Langevin approach, we find that when suppression of charge transport by the effective gate voltage surpasses the current increase from an elevated voltage bias, the current-voltage (I-V) curves display strong negative differential resistance (NDR) and perfect current-switching characteristics. The asymmetric DNA chain differs in mechanical stability under inverse voltages and the I-V curve is asymmetric about inverse biases, which can be used to understand recent transport experiments on DNA chains, and meanwhile provides a new strategy to realize NDR in molecular junctions and other low-dimensional quantum systems.

  11. Current-induced forces: a new mechanism to induce negative differential resistance and current-switching effect in molecular junctions

    International Nuclear Information System (INIS)

    Gu, Lei; Fu, Hua-Hua

    2015-01-01

    Current-induced forces can excite molecules, polymers and other low-dimensional materials, which in turn leads to an effective gate voltage through Holstein interaction. Here, by taking a short asymmetric DNA junction as an example, and using the Langevin approach, we find that when suppression of charge transport by the effective gate voltage surpasses the current increase from an elevated voltage bias, the current-voltage (I–V) curves display strong negative differential resistance (NDR) and perfect current-switching characteristics. The asymmetric DNA chain differs in mechanical stability under inverse voltages and the I–V curve is asymmetric about inverse biases, which can be used to understand recent transport experiments on DNA chains, and meanwhile provides a new strategy to realize NDR in molecular junctions and other low-dimensional quantum systems. (paper)

  12. Communication: Electronic and transport properties of molecular junctions under a finite bias: A dual mean field approach

    International Nuclear Information System (INIS)

    Liu, Shuanglong; Feng, Yuan Ping; Zhang, Chun

    2013-01-01

    We show that when a molecular junction is under an external bias, its properties cannot be uniquely determined by the total electron density in the same manner as the density functional theory for ground state properties. In order to correctly incorporate bias-induced nonequilibrium effects, we present a dual mean field (DMF) approach. The key idea is that the total electron density together with the density of current-carrying electrons are sufficient to determine the properties of the system. Two mean fields, one for current-carrying electrons and the other one for equilibrium electrons can then be derived. Calculations for a graphene nanoribbon junction show that compared with the commonly used ab initio transport theory, the DMF approach could significantly reduce the electric current at low biases due to the non-equilibrium corrections to the mean field potential in the scattering region

  13. The enhanced spin-polarized transport behaviors through cobalt benzene-porphyrin-benzene molecular junctions: the effect of functional groups

    Science.gov (United States)

    Cheng, Jue-Fei; Zhou, Liping; Wen, Zhongqian; Yan, Qiang; Han, Qin; Gao, Lei

    2017-05-01

    The modification effects of the groups amino (NH2) and nitro (NO2) on the spin polarized transport properties of the cobalt benzene-porphyrin-benzene (Co-BPB) molecule coupled to gold (Au) nanowire electrodes are investigated by the nonequilibrium Green’s function method combined with the density functional theory. The calculation results show that functional groups can lead to the significant spin-filter effect, enhanced low-bias negative differential resistance (NDR) behavior and novel reverse rectifying effect in Co-BPB molecular junction. The locations and types of functional groups have distinct influences on spin-polarized transport performances. The configuration with NH2 group substituting H atom in central porphyrin ring has larger spin-down current compared to that with NO2 substitution. And Co-BPB molecule junction with NH2 group substituting H atom in side benzene ring shows reverse rectifying effect. Detailed analyses confirm that NH2 and NO2 group substitution change the spin-polarized transferred charge, which makes the highest occupied molecular orbitals (HOMO) of spin-down channel of Co-BPB closer to the Fermi level. And the shift of HOMO strengthens the spin-polarized coupling between the molecular orbitals and the electrodes, leading to the enhanced spin-polarized behavior. Our findings might be useful in the design of multi-functional molecular devices in the future.

  14. Development and application of a 2-electron reduced density matrix approach to electron transport via molecular junctions

    Science.gov (United States)

    Hoy, Erik P.; Mazziotti, David A.; Seideman, Tamar

    2017-11-01

    Can an electronic device be constructed using only a single molecule? Since this question was first asked by Aviram and Ratner in the 1970s [Chem. Phys. Lett. 29, 277 (1974)], the field of molecular electronics has exploded with significant experimental advancements in the understanding of the charge transport properties of single molecule devices. Efforts to explain the results of these experiments and identify promising new candidate molecules for molecular devices have led to the development of numerous new theoretical methods including the current standard theoretical approach for studying single molecule charge transport, i.e., the non-equilibrium Green's function formalism (NEGF). By pairing this formalism with density functional theory (DFT), a wide variety of transport problems in molecular junctions have been successfully treated. For some systems though, the conductance and current-voltage curves predicted by common DFT functionals can be several orders of magnitude above experimental results. In addition, since density functional theory relies on approximations to the exact exchange-correlation functional, the predicted transport properties can show significant variation depending on the functional chosen. As a first step to addressing this issue, the authors have replaced density functional theory in the NEGF formalism with a 2-electron reduced density matrix (2-RDM) method, creating a new approach known as the NEGF-RDM method. 2-RDM methods provide a more accurate description of electron correlation compared to density functional theory, and they have lower computational scaling compared to wavefunction based methods of similar accuracy. Additionally, 2-RDM methods are capable of capturing static electron correlation which is untreatable by existing NEGF-DFT methods. When studying dithiol alkane chains and dithiol benzene in model junctions, the authors found that the NEGF-RDM predicts conductances and currents that are 1-2 orders of magnitude below

  15. Intraoperative computed tomography with an integrated navigation system in stabilization surgery for complex craniovertebral junction malformation.

    Science.gov (United States)

    Yu, Xinguang; Li, Lianfeng; Wang, Peng; Yin, Yiheng; Bu, Bo; Zhou, Dingbiao

    2014-07-01

    This study was designed to report our preliminary experience with stabilization procedures for complex craniovertebral junction malformation (CVJM) using intraoperative computed tomography (iCT) with an integrated neuronavigation system (NNS). To evaluate the workflow, feasibility and clinical outcome of stabilization procedures using iCT image-guided navigation for complex CVJM. The stabilization procedures in CVJM are complex because of the area's intricate geometry and bony structures, its critical relationship to neurovascular structures and the intricate biomechanical issues involved. A sliding gantry 40-slice computed tomography scanner was installed in a preexisting operating room. The images were transferred directly from the scanner to the NNS using an automated registration system. On the basis of the analysis of intraoperative computed tomographic images, 23 cases (11 males, 12 females) with complicated CVJM underwent navigated stabilization procedures to allow more control over screw placement. The age of these patients were 19-52 years (mean: 33.5 y). We performed C1-C2 transarticular screw fixation in 6 patients to produce atlantoaxial arthrodesis with better reliability. Because of a high-riding transverse foramen on at least 1 side of the C2 vertebra and an anomalous vertebral artery position, 7 patients underwent C1 lateral mass and C2 pedicle screw fixation. Ten additional patients were treated with individualized occipitocervical fixation surgery from the hypoplasia of C1 or constraints due to C2 bone structure. In total, 108 screws were inserted into 23 patients using navigational assistance. The screws comprised 20 C1 lateral mass screws, 26 C2, 14 C3, or 4 C4 pedicle screws, 32 occipital screws, and 12 C1-C2 transarticular screws. There were no vascular or neural complications except for pedicle perforations that were detected in 2 (1.9%) patients and were corrected intraoperatively without any persistent nerves or vessel damage. The overall

  16. Positron annihilation studies of some charge transfer molecular complexes

    CERN Document Server

    El-Sayed, A; Boraei, A A A

    2000-01-01

    Positron annihilation lifetimes were measured for some solid charge transfer (CT) molecular complexes of quinoline compounds (2,6-dimethylquinoline, 6-methoxyquinoline, quinoline, 6-methylquinoline, 3-bromoquinoline and 2-chloro-4-methylquinoline) as electron donor and picric acid as an electron acceptor. The infrared spectra (IR) of the solid complexes clearly indicated the formation of the hydrogen-bonding CT-complexes. The annihilation spectra were analyzed into two lifetime components using PATFIT program. The values of the average and bulk lifetimes divide the complexes into two groups according to the non-bonding ionization potential of the donor (electron donating power) and the molecular weight of the complexes. Also, it is found that the ionization potential of the donors and molecular weight of the complexes have a conspicuous effect on the average and bulk lifetime values. The bulk lifetime values of the complexes are consistent with the formation of stable hydrogen-bonding CT-complexes as inferred...

  17. Effects of stretching and compression on conducting properties of an Au–alkanedithiol–Au molecular junction

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Fang; Zhang, Xiao-Jiao; Yu, Ji-Hai; Xu, Hua; Chu, Yu-Fang [Physics Science and Engineering Technology College, Yichun University, Yichun 336000 (China); Fan, Zhi-Qiang, E-mail: fan0221@163.com [School of Physics and Electronic Science, Changsha University of Science and Technology, Changsha 410004 (China)

    2016-03-01

    We have studied the effects of stretching and compression on the electronic properties of 7-alkanedithiol covalently linked to two Au electrodes. Results show a progressive increase in conductivity upon molecule compression and decrease with molecule stretching. The notable conductance increase at high compression is attributed to a significant modification of HOMO and LUMO orbitals of the junction, which enhances electron delocalization and promotes tunneling across the junction. More important, the current switching ratios between the various stages of compressed/extended geometries almost maintain the constant values on the bias region from 0 V to 2 V. In other word, the mechanically-induced conductance enhancement and weakening are stable within a large bias voltage range.

  18. Tunneling rates in electron transport through double-barrier molecular junctions in a scanning tunneling microscope.

    Science.gov (United States)

    Nazin, G V; Wu, S W; Ho, W

    2005-06-21

    The scanning tunneling microscope enables atomic-scale measurements of electron transport through individual molecules. Copper phthalocyanine and magnesium porphine molecules adsorbed on a thin oxide film grown on the NiAl(110) surface were probed. The single-molecule junctions contained two tunneling barriers, vacuum gap, and oxide film. Differential conductance spectroscopy shows that electron transport occurs via vibronic states of the molecules. The intensity of spectral peaks corresponding to the individual vibronic states depends on the relative electron tunneling rates through the two barriers of the junction, as found by varying the vacuum gap tunneling rate by changing the height of the scanning tunneling microscope tip above the molecule. A simple, sequential tunneling model explains the observed trends.

  19. Tunneling rates in electron transport through double-barrier molecular junctions in a scanning tunneling microscope

    OpenAIRE

    Nazin, G. V.; Wu, S. W.; Ho, W.

    2005-01-01

    The scanning tunneling microscope enables atomic-scale measurements of electron transport through individual molecules. Copper phthalocyanine and magnesium porphine molecules adsorbed on a thin oxide film grown on the NiAl(110) surface were probed. The single-molecule junctions contained two tunneling barriers, vacuum gap, and oxide film. Differential conductance spectroscopy shows that electron transport occurs via vibronic states of the molecules. The intensity of spectral peaks correspondi...

  20. A Study of Electrocyclic Reactions in a Molecular Junction: Mechanistic and Energetic Requirements for Switching in the Coulomb Blockade Regime.

    Science.gov (United States)

    Olsen, Stine T; Brøndsted Nielsen, Mogens; Hansen, Thorsten; Ratner, Mark A; Mikkelsen, Kurt V

    2017-06-20

    Molecular photoswitches incorporated in molecular junctions yield the possibility of light-controlled switching of conductance due to the electronic difference of the photoisomers. Another isomerization mechanism, dark photoswitching, promoted by a voltage stimulus rather than by light, can be operative in the Coulomb blockade regime for a specific charge state of the molecule. Here we elucidate theoretically the mechanistic and thermodynamic restrictions for this dark photoswitching for donor-acceptor substituted 4n and 4n+2 π-electron open-chain oligoenes (1,3-butadiene and 1,3,5-hexatriene) by considering the molecular energies and orbitals of the molecules placed in a junction. For an electrocyclic ring closure reaction to occur for these compounds, we put forward two requirements: a) the closed stereoisomer (cis or trans form) must be of lower energy than the open form, and b) the reaction pathway must be in accordance to the orbital symmetry rules expressed by the Woodward-Hoffmann rules (when the electrodes do not significantly alter the molecular orbital appearances). We find these two requirements to be valid for the dianion of (1E,3Z,5E)-hexa-1,3,5-triene-1,6-diamine, and the Coulomb blockade diamonds were therefore modeled for this compound to elucidate how a dark photoswitching event would manifest itself in the stability plot. From this modeling of conductance as a function of gate and bias potentials, we predict a collapse in Coulomb diamond size, that is, a decrease in the height of the island of zero conductance. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Managing the complexity of communication: regulation of gap junctions by post-translational modification

    DEFF Research Database (Denmark)

    Axelsen, Lene Nygaard; Callø, Kirstine; von Holstein-Rathlou, Niels-Henrik

    2013-01-01

    Gap junctions are comprised of connexins that form cell-to-cell channels which couple neighboring cells to accommodate the exchange of information. The need for communication does, however, change over time and therefore must be tightly controlled. Although the regulation of connexin protein...... probability, single channel conductance or selectivity. The most extensively investigated post translational modifications are phosphorylations, which have been documented in all mammalian connexins. Besides phosphorylations, some connexins are known to be ubiquitinated, SUMOylated, nitrosylated, hydroxylated...

  2. Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA

    DEFF Research Database (Denmark)

    Andersen, Christian Brix Folsted; Ballut, Lionel; Johansen, Jesper Sanderhoff

    2006-01-01

    exon junction core complex containing the DEAD-box adenosine triphosphatase (ATPase) eukaryotic initiation factor 4AIII (eIF4AIII) bound to an ATP analog, MAGOH, Y14, a fragment of MLN51, and a polyuracil mRNA mimic. eIF4AIII interacts with the phosphate-ribose backbone of six consecutive nucleotides...... and prevents part of the bound RNA from being double stranded. The MAGOH and Y14 subunits lock eIF4AIII in a prehydrolysis state, and activation of the ATPase probably requires only modest conformational changes in eIF4AIII motif I....

  3. First-principles study of the electronic transport properties in (GaAs)n (n=2–4) nanocluster-based molecular junctions

    International Nuclear Information System (INIS)

    Zhang, Daoli; Xu, Yuanlan; Zhang, Jianbing; Miao, Xiangshui

    2012-01-01

    In this program the geometric structures and electronic transport properties of a series of (GaAs) n (n=2,3,4) clusters are comparatively studied using non-equilibrium Green's function (NEGF) combined with density functional theory (DFT). It is find that all the GaAs nanocluster-based molecular junctions show metallic behavior at low biases ([−2 V,2 V]) while negative differential resistance (NDR) appears at a certain high bias range. Our calculation shows that the current of (GaAs) 3 nanocluster-based molecular junction is almost the smallest at any bias. The mechanisms of the current–voltage characteristics of all the three molecular junctions are proposed.

  4. Molecular Architecture of the Yeast Monopolin Complex

    Energy Technology Data Exchange (ETDEWEB)

    Corbett, Kevin D.; Harrison, Stephen C. (Harvard-Med); (UCSD)

    2012-07-30

    The Saccharomyces cerevisiae monopolin complex directs proper chromosome segregation in meiosis I by mediating co-orientation of sister kinetochores on the meiosis I spindle. The monopolin subunits Csm1 and Lrs4 form a V-shaped complex that may directly crosslink sister kinetochores. We report here biochemical characterization of the monopolin complex subunits Mam1 and Hrr25 and of the complete four-protein monopolin complex. By purifying monopolin subcomplexes with different subunit combinations, we have determined the stoichiometry and overall architecture of the full monopolin complex. We have determined the crystal structure of Csm1 bound to a Mam1 fragment, showing how Mam1 wraps around the Csm1 dimer and alters the stoichiometry of kinetochore-protein binding by Csm1. We further show that the kinase activity of Hrr25 is altered by Mam1 binding, and we identify Hrr25 phosphorylation sites on Mam1 that may affect monopolin complex stability and/or kinetochore binding in meiosis.

  5. Binary Molecular Complexes and the Nature of Molecular Association

    African Journals Online (AJOL)

    NJD

    2004-06-15

    Jun 15, 2004 ... their values in the non-interacting monomer.20 We have selected as examples of hydrogen-bonded complexes for study those formed between methanol as proton donor and trimethylamine, dimethyl ether, methyl fluoride, trimethyl phosphine, dimethyl sulphide and methyl chloride as proton acceptors.

  6. Transforming growth factor beta 1 modulates extracellular matrix organization and cell-cell junctional complex formation during in vitro angiogenesis.

    Science.gov (United States)

    Merwin, J R; Anderson, J M; Kocher, O; Van Itallie, C M; Madri, J A

    1990-01-01

    Transforming growth factor-beta 1 (TGF-beta 1) is angiogenic in vivo. In two-dimensional (2-D) culture systems microvascular endothelial cell proliferation is inhibited up to 80% by TGF-beta 1; however, in three-dimensional (3-D) collagen gels TGF-beta 1 is found to have no effect on proliferation while eliciting the formation of calcium and magnesium dependent tube-like structures mimicking angiogenesis. DNA analyses performed on 3-D cell cultures reveal no significant difference in the amount of DNA or cell number in control versus TGF-beta 1 treated cultures. In 2-D cultures TGF-beta 1 is known to increase cellular fibronectin accumulation; however, in 3-D cultures no difference is seen between control and TGF-beta 1 treated cells as established by ELISA testing for type IV collagen, fibronectin, and laminin. In 3-D cultures there is increased synthesis and secretion of type V collagen in both control and TGF-beta 1 treated cultures over 2-D cultures. Even though an equal amount of type V collagen is seen in both 3-D conditions, there is a reorganization of the protein with concentration along an organizing basal lamina in TGF-beta 1 treated cultures. EM morphological analyses on 3-D cultures illustrate quiescent, control cells lacking cell contacts. In contrast, TGF-beta 1 treated cells show increased pseudopod formation, cell-cell contact, and organized basal lamina-like material closely apposed to the "abluminal" plasma membranes. TGF-beta 1 treated cells also appear to form junctional complexes between adjoining cells. Immunofluorescence using specific antibodies to the tight junction protein ZO-1 results in staining at apparent cell-cell junctions in the 3-D cultures. Northern blots of freshly isolated microvascular endothelium, 2-D and 3-D cultures, using cDNA and cRNA probes specific for the ZO-1 tight junction protein, reveal the presence of the 7.8 kb mRNA. Western blots of rat epididymal fat pad endothelial cells (RFC) monolayer lysates probed with

  7. Complex molecular orbital method: open-shell theory

    International Nuclear Information System (INIS)

    Hendekovic, J.

    1976-01-01

    A singe-determinant open-shell formalism for complex molecular orbitals is developed. An iterative algorithm for solving the resulting secular equations is constructed. It is based on a sequence of similarity transformations and matrix triangularizations

  8. Deoxynivanelol and Fumonisin, Alone or in Combination, Induce Changes on Intestinal Junction Complexes and in E-Cadherin Expression

    Directory of Open Access Journals (Sweden)

    Karina Basso

    2013-11-01

    Full Text Available Fusariotoxins such as fumonisin B1 (FB1 and deoxynivalenol (DON cause deleterious effects on the intestine of pigs. The aim of this study was to evaluate the effect of these mycotoxins, alone and in combination, on jejunal explants from piglets, using histological, immunohistochemical and ultrastructural assays. Five 24-day old pigs were used for sampling the explants. Forty-eight explants were sampled from each animal. Explants were incubated for 4 hours in culture medium and medium containing FB1 (100 µM, DON (10 µM and both mycotoxins (100 µM FB1 plus 10 µM DON. Exposure to all treatments induced a significant decrease in the normal intestinal morphology and in the number of goblet cells, which were more severe in explants exposed to DON and both mycotoxins. A significant reduction in villus height occurred in groups treated with DON and with co-contamination. Expression of E-cadherin was significantly reduced in explants exposed to FB1 (40%, DON (93% and FB1 plus DON (100%. The ultrastructural assay showed increased intercellular spaces and no junction complexes on enterocytes exposed to mycotoxins. The present data indicate that FB1 and DON induce changes in cell junction complexes that could contribute to increase paracellular permeability. The ex vivo model was adequate for assessing intestinal toxicity induced by exposure of isolated or associated concentrations of 100 µM of FB1 and 10 µM of DON.

  9. CRIM1 complexes with ß-catenin and cadherins, stabilizes cell-cell junctions and is critical for neural morphogenesis.

    Directory of Open Access Journals (Sweden)

    Virgilio G Ponferrada

    Full Text Available In multicellular organisms, morphogenesis is a highly coordinated process that requires dynamically regulated adhesion between cells. An excellent example of cellular morphogenesis is the formation of the neural tube from the flattened epithelium of the neural plate. Cysteine-rich motor neuron protein 1 (CRIM1 is a single-pass (type 1 transmembrane protein that is expressed in neural structures beginning at the neural plate stage. In the frog Xenopus laevis, loss of function studies using CRIM1 antisense morpholino oligonucleotides resulted in a failure of neural development. The CRIM1 knockdown phenotype was, in some cases, mild and resulted in perturbed neural fold morphogenesis. In severely affected embryos there was a dramatic failure of cell adhesion in the neural plate and complete absence of neural structures subsequently. Investigation of the mechanism of CRIM1 function revealed that it can form complexes with ß-catenin and cadherins, albeit indirectly, via the cytosolic domain. Consistent with this, CRIM1 knockdown resulted in diminished levels of cadherins and ß-catenin in junctional complexes in the neural plate. We conclude that CRIM1 is critical for cell-cell adhesion during neural development because it is required for the function of cadherin-dependent junctions.

  10. Molecular architecture of the yeast Mediator complex

    Science.gov (United States)

    Robinson, Philip J; Trnka, Michael J; Pellarin, Riccardo; Greenberg, Charles H; Bushnell, David A; Davis, Ralph; Burlingame, Alma L; Sali, Andrej; Kornberg, Roger D

    2015-01-01

    The 21-subunit Mediator complex transduces regulatory information from enhancers to promoters, and performs an essential role in the initiation of transcription in all eukaryotes. Structural information on two-thirds of the complex has been limited to coarse subunit mapping onto 2-D images from electron micrographs. We have performed chemical cross-linking and mass spectrometry, and combined the results with information from X-ray crystallography, homology modeling, and cryo-electron microscopy by an integrative modeling approach to determine a 3-D model of the entire Mediator complex. The approach is validated by the use of X-ray crystal structures as internal controls and by consistency with previous results from electron microscopy and yeast two-hybrid screens. The model shows the locations and orientations of all Mediator subunits, as well as subunit interfaces and some secondary structural elements. Segments of 20–40 amino acid residues are placed with an average precision of 20 Å. The model reveals roles of individual subunits in the organization of the complex. DOI: http://dx.doi.org/10.7554/eLife.08719.001 PMID:26402457

  11. The tunneling magnetoresistance and spin-polarized optoelectronic properties of graphyne-based molecular magnetic tunnel junctions

    International Nuclear Information System (INIS)

    Yang, Zhi; Ouyang, Bin; Lan, Guoqing; Xu, Li-Chun; Liu, Ruiping; Liu, Xuguang

    2017-01-01

    Using density functional theory and the non-equilibrium Green’s function method, we investigate the spin-dependent transport and optoelectronic properties of the graphyne-based molecular magnetic tunnel junctions (MMTJs). We find that these MMTJs exhibit an outstanding tunneling magnetoresistance (TMR) effect. The TMR value is as high as 10 6 %. When the magnetization directions of two electrodes are antiparallel under positive or negative bias voltages, two kinds of pure spin currents can be obtained in the systems. Furthermore, under the irradiation of infrared, visible or ultraviolet light, spin-polarized photocurrents can be generated in the MMTJs, but the corresponding microscopic mechanisms are different. More importantly, if the magnetization directions of two electrodes are antiparallel, the photocurrents with different spins are spatially separated, appearing at different electrodes. This phenomenon provides a new way to simultaneously generate two spin currents. (paper)

  12. Correlation analysis of the Taurus molecular cloud complex

    International Nuclear Information System (INIS)

    Kleiner, S.C.

    1985-01-01

    Autocorrelation and power spectrum methods were applied to the analysis of the density and velocity structure of the Taurus Complex and Heiles Cloud 2 as traced out by 13 CO J = 1 → 0 molecular line observations obtained with the 14m antenna of the Five College Radio Astronomy Observatory. Statistically significant correlations in the spacing of density fluctuations within the Taurus Complex and Heiles 2 were uncovered. The length scales of the observed correlations correspond in magnitude to the Jeans wavelengths characterizing gravitational instabilities with (i) interstellar atomic hydrogen gas for the case of the Taurus complex, and (ii) molecular hydrogen for Heiles 2. The observed correlations may be the signatures of past and current gravitational instabilities frozen into the structure of the molecular gas. The appendices provide a comprehensive description of the analytical and numerical methods developed for the correlation analysis of molecular clouds

  13. Computer modeling of properties of complex molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Kulkova, E.Yu. [Moscow State University of Technology “STANKIN”, Vadkovsky per., 1, Moscow 101472 (Russian Federation); Khrenova, M.G.; Polyakov, I.V. [Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1/3, Moscow 119991 (Russian Federation); Nemukhin, A.V. [Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1/3, Moscow 119991 (Russian Federation); N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow 119334 (Russian Federation)

    2015-03-10

    Large molecular aggregates present important examples of strongly nonhomogeneous systems. We apply combined quantum mechanics / molecular mechanics approaches that assume treatment of a part of the system by quantum-based methods and the rest of the system with conventional force fields. Herein we illustrate these computational approaches by two different examples: (1) large-scale molecular systems mimicking natural photosynthetic centers, and (2) components of prospective solar cells containing titan dioxide and organic dye molecules. We demonstrate that modern computational tools are capable to predict structures and spectra of such complex molecular aggregates.

  14. Effect of torsion angle on electronic transport through different anchoring groups in molecular junction

    International Nuclear Information System (INIS)

    Xia Caijuan; Fang Changfeng; Zhao Peng; Xie Shijie; Liu Desheng

    2009-01-01

    By applying nonequilibrium Green's function formalism combined with first-principles density functional theory, we investigate effect of torsion angle on electronic transport properties of 4,4 ' -biphenyl molecule connected with different anchoring groups (dithiocarboxylate and thiol group) to Au(111) electrodes. The influence of the HOMO-LUMO gaps and the spatial distributions of molecular orbitals on the quantum transport through the molecular device are discussed. Theoretical results show that the torsion angle plays important role in conducting behavior of molecular devices. By changing the torsion angle between two phenyl rings, namely changing the magnitude of the intermolecular coupling effect, a different transport behavior can be observed in these two systems.

  15. Charge transport across metal/molecular (alkyl) monolayer-Si junctions is dominated by the LUMO level

    NARCIS (Netherlands)

    Yaffe, O.; Qi, Y.; Scheres, L.M.W.; Puniredd, S.R.; Segev, L.; Ely, T.; Haick, H.; Zuilhof, H.; Vilan, A.; Kronik, L.; Kahn, A.; Cahen, D.

    2012-01-01

    We compare the charge transport characteristics of heavy-doped p(++)- and n(++)-Si-alkyl chain/Hg junctions. Based on negative differential resistance in an analogous semiconductor-inorganic insulator/metal junction we suggest that for both p(++)- and n(++)-type junctions, the energy difference

  16. Density functional theory study on Herzberg-Teller contribution in Raman scattering from 4-aminothiophenol-metal complex and metal-4-aminothiophenol-metal junction

    Science.gov (United States)

    Liu, Shasha; Zhao, Xiuming; Li, Yuanzuo; Zhao, Xiaohong; Chen, Maodu

    2009-06-01

    Density functional theory (DFT) and time-dependent DFT calculations have been performed to investigate the Raman scattering spectra of metal-molecule complex and metal-molecule-metal junction architectures interconnected with 4-aminothiophenol (PATP) molecule. The simulated profiles of normal Raman scattering (NRS) spectra for the two complexes (Ag2-PATP and PATP-Au2) and the two junctions (Ag2-PATP-Au2 and Au2-PATP-Ag2) are similar to each other, but exhibit obviously different Raman intensities. Due to the lager static polarizabilities of the two junctions, which directly influence the ground state chemical enhancement in NRS spectra, the calculated normal Raman intensities of them are stronger than those of two complexes by the factor of 102. We calculate preresonance Raman scattering (RRS) spectra with incident light at 1064 nm, which is much lower than the S1 electronic transition energy of complexes and junctions. Ag2-PATP-Au2 and Au2-PATP-Ag2 junctions yield higher Raman intensities than those of Ag2-PATP and PATP-Au2 complexes, especially for b2 modes. This effect is mainly attributed to charge transfer (CT) between the metal gap and the PAPT molecule which results in the occurrence of CT resonance enhancement. The calculated pre-RRS spectra strongly depend on the electronic transition state produced by new structures. With excitation at 514.5 nm, the calculated pre-RRS spectra of two complexes and two junctions are stronger than those of with excitation at 1064 nm. A charge difference densities methodology has been used to visually describe chemical enhancement mechanism of RRS spectrum. This methodology aims at visualizing intermolecular CT which provides direct evidence of the Herzberg-Teller mechanism.

  17. Junction and circuit fabrication

    International Nuclear Information System (INIS)

    Jackel, L.D.

    1980-01-01

    Great strides have been made in Josephson junction fabrication in the four years since the first IC SQUID meeting. Advances in lithography have allowed the production of devices with planar dimensions as small as a few hundred angstroms. Improved technology has provided ultra-high sensitivity SQUIDS, high-efficiency low-noise mixers, and complex integrated circuits. This review highlights some of the new fabrication procedures. The review consists of three parts. Part 1 is a short summary of the requirements on junctions for various applications. Part 2 reviews intergrated circuit fabrication, including tunnel junction logic circuits made at IBM and Bell Labs, and microbridge radiation sources made at SUNY at Stony Brook. Part 3 describes new junction fabrication techniques, the major emphasis of this review. This part includes a discussion of small oxide-barrier tunnel junctions, semiconductor barrier junctions, and microbridge junctions. Part 3 concludes by considering very fine lithography and limitations to miniaturization. (orig.)

  18. The emergence of complex behaviours in molecular magnetic materials.

    Science.gov (United States)

    Goss, Karin; Gatteschi, Dante; Bogani, Lapo

    2014-09-14

    Molecular magnetism is considered an area where magnetic phenomena that are usually difficult to demonstrate can emerge with particular clarity. Over the years, however, less understandable systems have appeared in the literature of molecular magnetic materials, in some cases showing features that hint at the spontaneous emergence of global structures out of local interactions. This ingredient is typical of a wider class of problems, called complex behaviours, where the theory of complexity is currently being developed. In this perspective we wish to focus our attention on these systems and the underlying problematic that they highlight. We particularly highlight the emergence of the signatures of complexity in several molecular magnetic systems, which may provide unexplored opportunities for physical and chemical investigations.

  19. Study of guided wave transmission through complex junction in sodium cooled reactor

    International Nuclear Information System (INIS)

    Elie, Q.; Le Bourdais, F.; Jezzine, K.; Baronian, V.

    2015-01-01

    Ultrasonic guided wave techniques are seen as suitable candidates for the inspection of welded structures within sodium cooled fast reactors (SFR), as the long range propagation of guided waves without amplitude attenuation can overcome the accessibility problem due to the liquid sodium. In the context of the development of the Advanced Sodium Test Reactor for Industrial Demonstration (ASTRID), the French Atomic Commission (CEA) investigates non-destructive testing techniques based on guided wave propagation. In this work, guided wave NDT methods are applied to control the integrity of welds located in a junction-type structure welded to the main vessel. The method presented in this paper is based on the analysis of scattering matrices peculiar to each expected defect, and takes advantage of the multi-modal and dispersive characteristics of guided wave generation. In a simulation study, an algorithm developed using the CIVA software is presented. It permits selecting appropriate incident modes to optimize detection and identification of expected flawed configurations. In the second part of this paper, experimental results corresponding to a first validation step of the simulation results are presented. The goal of the experiments is to estimate the effectiveness of the incident mode selection in plates. The results show good agreement between experience and simulation. (authors)

  20. Fabrication of hybrid molecular devices using multi-layer graphene break junctions

    Science.gov (United States)

    Island, J. O.; Holovchenko, A.; Koole, M.; Alkemade, P. F. A.; Menelaou, M.; Aliaga-Alcalde, N.; Burzurí, E.; van der Zant, H. S. J.

    2014-11-01

    We report on the fabrication of hybrid molecular devices employing multi-layer graphene (MLG) flakes which are patterned with a constriction using a helium ion microscope or an oxygen plasma etch. The patterning step allows for the localization of a few-nanometer gap, created by electroburning, that can host single molecules or molecular ensembles. By controlling the width of the sculpted constriction, we regulate the critical power at which the electroburning process begins. We estimate the flake temperature given the critical power and find that at low powers it is possible to electroburn MLG with superconducting contacts in close proximity. Finally, we demonstrate the fabrication of hybrid devices with superconducting contacts and anthracene-functionalized copper curcuminoid molecules. This method is extendable to spintronic devices with ferromagnetic contacts and a first step towards molecular integrated circuits.

  1. Modeling inelastic phonon scattering in atomic- and molecular-wire junctions

    DEFF Research Database (Denmark)

    Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads

    2005-01-01

    Computationally inexpensive approximations describing electron-phonon scattering in molecular-scale conductors are derived from the nonequilibrium Green's function method. The accuracy is demonstrated with a first-principles calculation on an atomic gold wire. Quantitative agreement between the f...

  2. Adherent-invasive Escherichia coli, strain LF82 disrupts apical junctional complexes in polarized epithelia

    Directory of Open Access Journals (Sweden)

    Ossa Juan C

    2009-08-01

    Full Text Available Abstract Background Although bacteria are implicated in the pathogenesis of chronic inflammatory bowel diseases (IBD, mechanisms of intestinal injury and immune activation remain unclear. Identification of adherent-invasive Escherichia coli (AIEC strains in IBD patients offers an opportunity to characterize the pathogenesis of microbial-induced intestinal inflammation in IBD. Previous studies have focused on the invasive phenotype of AIEC and the ability to replicate and survive in phagocytes. However, the precise mechanisms by which these newly identified microbes penetrate the epithelial lining remain to be clarified. Therefore, the aim of this study was to delineate the effects of AIEC, strain LF82 (serotype O83:H1 on model polarized epithelial monolayers as a contributor to intestinal injury in IBD. Results Infection of T84 and Madin-Darby Canine Kidney-I polarized epithelial cell monolayers with AIEC, strain LF82 led to a reduction in transepithelial electrical resistance and increased macromolecular (10 kilodalton dextran flux. Basolateral AIEC infection resulted in more severe disruption of the epithelial barrier. Increased permeability was accompanied by a redistribution of the tight junction adaptor protein, zonula occludens-1, demonstrated by confocal microscopy and formation of gaps between cells, as shown by transmission electron microscopy. After 4 h of infection of intestine 407 cells, bacteria replicated in the cell cytoplasm and were enclosed in membrane-bound vesicles positive for the late endosomal marker, LAMP1. Conclusion These findings indicate that AIEC, strain LF82 disrupts the integrity of the polarized epithelial cell barrier. This disruption enables bacteria to penetrate into the epithelium and replicate in the host cell cytoplasm. These findings provide important links between microbes related to IBD, the intestinal epithelial cell barrier and disease pathogenesis.

  3. Protocol for classical molecular dynamics simulations of nano-junctions in solution

    KAUST Repository

    Gkionis, Konstantinos; Rungger, Ivan; Sanvito, Stefano; Schwingenschlö gl, Udo

    2012-01-01

    Modeling of nanoscale electronic devices in water requires the evaluation of the transport properties averaged over the possible configurations of the solvent. They can be obtained from classical molecular dynamics for water confined in the device. A series of classical molecular dynamics simulations is performed to establish a methodology for estimating the average number of water molecules N confined between two static and semi-infinite goldelectrodes. Variations in key parameters of the simulations, as well as simulations with non-static infinite goldsurfaces of constant area and with anisotropically fluctuating cell dimensions lead to less than 1% discrepancies in the calculated N. Our approach is then applied to a carbon nanotube placed between the goldelectrodes. The atomic density profile along the axis separating the slabs shows the typical pattern of confined liquids, irrespective of the presence of the nanotube, while parallel to the slabs the nanotube perturbs the obtained profile.

  4. Protocol for classical molecular dynamics simulations of nano-junctions in solution

    KAUST Repository

    Gkionis, Konstantinos

    2012-10-19

    Modeling of nanoscale electronic devices in water requires the evaluation of the transport properties averaged over the possible configurations of the solvent. They can be obtained from classical molecular dynamics for water confined in the device. A series of classical molecular dynamics simulations is performed to establish a methodology for estimating the average number of water molecules N confined between two static and semi-infinite goldelectrodes. Variations in key parameters of the simulations, as well as simulations with non-static infinite goldsurfaces of constant area and with anisotropically fluctuating cell dimensions lead to less than 1% discrepancies in the calculated N. Our approach is then applied to a carbon nanotube placed between the goldelectrodes. The atomic density profile along the axis separating the slabs shows the typical pattern of confined liquids, irrespective of the presence of the nanotube, while parallel to the slabs the nanotube perturbs the obtained profile.

  5. Viral-Cellular DNA Junctions as Molecular Markers for Assessing Intra-Tumor Heterogeneity in Cervical Cancer and for the Detection of Circulating Tumor DNA

    Directory of Open Access Journals (Sweden)

    Katrin Carow

    2017-09-01

    Full Text Available The development of cervical cancer is frequently accompanied by the integration of human papillomaviruses (HPV DNA into the host genome. Viral-cellular junction sequences, which arise in consequence, are highly tumor specific. By using these fragments as markers for tumor cell origin, we examined cervical cancer clonality in the context of intra-tumor heterogeneity. Moreover, we assessed the potential of these fragments as molecular tumor markers and analyzed their suitability for the detection of circulating tumor DNA in sera of cervical cancer patients. For intra-tumor heterogeneity analyses tumors of 8 patients with up to 5 integration sites per tumor were included. Tumor islands were micro-dissected from cryosections of several tissue blocks representing different regions of the tumor. Each micro-dissected tumor area served as template for a single junction-specific PCR. For the detection of circulating tumor-DNA (ctDNA junction-specific PCR-assays were applied to sera of 21 patients. Samples were collected preoperatively and during the course of disease. In 7 of 8 tumors the integration site(s were shown to be homogenously distributed throughout different tumor regions. Only one tumor displayed intra-tumor heterogeneity. In 5 of 21 analyzed preoperative serum samples we specifically detected junction fragments. Junction-based detection of ctDNA was significantly associated with reduced recurrence-free survival. Our study provides evidence that HPV-DNA integration is as an early step in cervical carcinogenesis. Clonality with respect to HPV integration opens new perspectives for the application of viral-cellular junction sites as molecular biomarkers in a clinical setting such as disease monitoring.

  6. A Point Mutation in the Exon Junction Complex Factor Y14 Disrupts Its Function in mRNA Cap Binding and Translation Enhancement.

    Science.gov (United States)

    Chuang, Tzu-Wei; Lee, Kuo-Ming; Lou, Yuan-Chao; Lu, Chia-Chen; Tarn, Woan-Yuh

    2016-04-15

    Eukaryotic mRNA biogenesis involves a series of interconnected steps mediated by RNA-binding proteins. The exon junction complex core protein Y14 is required for nonsense-mediated mRNA decay (NMD) and promotes translation. Moreover, Y14 binds the cap structure of mRNAs and inhibits the activity of the decapping enzyme Dcp2. In this report, we show that an evolutionarily conserved tryptophan residue (Trp-73) of Y14 is critical for its binding to the mRNA cap structure. A Trp-73 mutant (W73V) bound weakly to mRNAs and failed to protect them from degradation. However, this mutant could still interact with the NMD and mRNA degradation factors and retained partial NMD activity. In addition, we found that the W73V mutant could not interact with translation initiation factors. Overexpression of W73V suppressed reporter mRNA translation in vitro and in vivo and reduced the level of a set of nascent proteins. These results reveal a residue of Y14 that confers cap-binding activity and is essential for Y14-mediated enhancement of translation. Finally, we demonstrated that Y14 may selectively and differentially modulate protein biosynthesis. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. Export of a Toxoplasma gondii rhoptry neck protein complex at the host cell membrane to form the moving junction during invasion.

    Directory of Open Access Journals (Sweden)

    Sébastien Besteiro

    2009-02-01

    Full Text Available One of the most conserved features of the invasion process in Apicomplexa parasites is the formation of a moving junction (MJ between the apex of the parasite and the host cell membrane that moves along the parasite and serves as support to propel it inside the host cell. The MJ was, up to a recent period, completely unknown at the molecular level. Recently, proteins originated from two distinct post-Golgi specialised secretory organelles, the micronemes (for AMA1 and the neck of the rhoptries (for RON2/RON4/RON5 proteins, have been shown to form a complex. AMA1 and RON4 in particular, have been localised to the MJ during invasion. Using biochemical approaches, we have identified RON8 as an additional member of the complex. We also demonstrated that all RON proteins are present at the MJ during invasion. Using metabolic labelling and immunoprecipitation, we showed that RON2 and AMA1 were able to interact in the absence of the other members. We also discovered that all MJ proteins are subjected to proteolytic maturation during trafficking to their respective organelles and that they could associate as non-mature forms in vitro. Finally, whereas AMA1 has previously been shown to be inserted into the parasite membrane upon secretion, we demonstrated, using differential permeabilization and loading of RON-specific antibodies into the host cell, that the RON complex is targeted to the host cell membrane, where RON4/5/8 remain associated with the cytoplasmic face. Globally, these results point toward a model of MJ organization where the parasite would be secreting and inserting interacting components on either side of the MJ, both at the host and at its own plasma membranes.

  8. Self-consistent GW calculations of electronic transport in thiol- and amine-linked molecular junctions

    DEFF Research Database (Denmark)

    Strange, M.; Rostgaard, Carsten; Hakkinen, H.

    2011-01-01

    suggest that more complex gold-thiolate structures where the thiolate anchors are chemically passivated by Au adatoms are responsible for the measured conductance. Analysis of the energy level alignment obtained with DFT, Hartree-Fock, and GW reveals the importance of self-interaction corrections...

  9. Memory Synapses Are Defined by Distinct Molecular Complexes: A Proposal.

    Science.gov (United States)

    Sossin, Wayne S

    2018-01-01

    Synapses are diverse in form and function. While there are strong evidential and theoretical reasons for believing that memories are stored at synapses, the concept of a specialized "memory synapse" is rarely discussed. Here, we review the evidence that memories are stored at the synapse and consider the opposing possibilities. We argue that if memories are stored in an active fashion at synapses, then these memory synapses must have distinct molecular complexes that distinguish them from other synapses. In particular, examples from Aplysia sensory-motor neuron synapses and synapses on defined engram neurons in rodent models are discussed. Specific hypotheses for molecular complexes that define memory synapses are presented, including persistently active kinases, transmitter receptor complexes and trans-synaptic adhesion proteins.

  10. Towards a Molecular Understanding of the Fanconi Anemia Core Complex

    Directory of Open Access Journals (Sweden)

    Charlotte Hodson

    2012-01-01

    Full Text Available Fanconi Anemia (FA is a genetic disorder characterized by the inability of patient cells to repair DNA damage caused by interstrand crosslinking agents. There are currently 14 verified FA genes, where mutation of any single gene prevents repair of DNA interstrand crosslinks (ICLs. The accumulation of ICL damage results in genome instability and patients having a high predisposition to cancers. The key event of the FA pathway is dependent on an eight-protein core complex (CC, required for the monoubiquitination of each member of the FANCD2-FANCI complex. Interestingly, the majority of patient mutations reside in the CC. The molecular mechanisms underlying the requirement for such a large complex to carry out a monoubiquitination event remain a mystery. This paper documents the extensive efforts of researchers so far to understand the molecular roles of the CC proteins with regard to its main function in the FA pathway, the monoubiquitination of FANCD2 and FANCI.

  11. Towards a Molecular Understanding of the Fanconi Anemia Core Complex

    Science.gov (United States)

    Hodson, Charlotte; Walden, Helen

    2012-01-01

    Fanconi Anemia (FA) is a genetic disorder characterized by the inability of patient cells to repair DNA damage caused by interstrand crosslinking agents. There are currently 14 verified FA genes, where mutation of any single gene prevents repair of DNA interstrand crosslinks (ICLs). The accumulation of ICL damage results in genome instability and patients having a high predisposition to cancers. The key event of the FA pathway is dependent on an eight-protein core complex (CC), required for the monoubiquitination of each member of the FANCD2-FANCI complex. Interestingly, the majority of patient mutations reside in the CC. The molecular mechanisms underlying the requirement for such a large complex to carry out a monoubiquitination event remain a mystery. This paper documents the extensive efforts of researchers so far to understand the molecular roles of the CC proteins with regard to its main function in the FA pathway, the monoubiquitination of FANCD2 and FANCI. PMID:22675617

  12. Probing Interactions in Complex Molecular Systems through Ordered Assembly

    International Nuclear Information System (INIS)

    De Yoreo, J.J.; Bartelt, M.C.; Orme, C.A.; Villacampa, A.; Weeks, B.L.; Miller, A.E.

    2002-01-01

    Emerging from the machinery of epitaxial science and chemical synthesis, is a growing emphasis on development of self-organized systems of complex molecular species. The nature of self-organization in these systems spans the continuum from simple crystallization of large molecules such as dendrimers and proteins, to assembly into large organized networks of nanometer-scale structures such as quantum dots or nanoparticles. In truth, self-organization in complex molecular systems has always been a central feature of many scientific disciplines including fields as diverse as structural biology, polymer science and geochemistry. But over the past decade, changes in those fields have often been marked by the degree to which researchers are using molecular-scale approaches to understand the hierarchy of structures and processes driven by this ordered assembly. At the same time, physical scientists have begun to use their knowledge of simple atomic and molecular systems to fabricate synthetic self-organized systems. This increasing activity in the field of self-organization is testament to the success of the physical and chemical sciences in building a detailed understanding of crystallization and epitaxy in simple atomic and molecular systems, one that is soundly rooted in thermodynamics and chemical kinetics. One of the fundamental challenges of chemistry and materials science in the coming decades is to develop a similarly well-founded physical understanding of assembly processes in complex molecular systems. Over the past five years, we have successfully used in situ atomic force microscopy (AFM) to investigate the physical controls on single crystal epitaxy from solutions for a wide range of molecular species. More recently, we have combined this method with grazing incidence X-ray diffraction and kinetic Monte Carlo modeling in order to relate morphology to surface atomic structure and processes. The purpose of this proposal was to extend this approach to assemblies

  13. Addressing the challenges of using ferromagnetic electrodes in the magnetic tunnel junction-based molecular spintronics devices

    International Nuclear Information System (INIS)

    Tyagi, Pawan; Friebe, Edward; Baker, Collin

    2015-01-01

    Addressing the challenges of using high-Curie temperature ferromagnetic (FM) electrodes is critical for molecular spintronics devices (MSDs) research. Two FM electrodes simultaneously chemically bonded with a thiol-functionalized molecule can produce novel MSDs to exploring new quantum mechanical phenomenon and computer technologies. For developing a commercially viable MSD, it is crucial to developing a device fabrication scheme that carefully considers FM electrodes’ susceptibility to oxidation, chemical etching, and stress-induced deformations during fabrication and usage. This paper studies NiFe, an alloy extensively used in present-day memory devices and high-temperature engineering applications, as a candidate FM electrode for the fabrication of MSDs. Our spectroscopic reflectance studies show that NiFe oxidized aggressively after heating beyond ∼90 °C. The NiFe surfaces, aged for several months or heated for several minutes below ∼90 °C, exhibited remarkable electrochemical activity and were found suitable for chemical bonding with the thiol-functionalized molecular device elements. NiFe also demonstrated excellent etching resistance against commonly used solvents and lithography related chemicals. Additionally, NiFe mitigated the adverse effects of mechanical stress by subsiding the stress-induced deformities. A magnetic tunnel junction-based MSD approach was designed by carefully considering the merits and limitations of NiFe. The device fabrication protocol considers the safe temperature limit to avoiding irreversible surface oxidation, the effect of mechanical stresses, surface roughness, and chemical etching. This paper provides foundational experimental insights in realizing a versatile MSD allowing a wide range of transport and magnetic studies

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-01-15

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

  15. Production and sympathetic cooling of complex molecular ions

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Chaobo

    2008-06-24

    This thesis reports on experimental and theoretical studies of the sympathetic cooling of complex molecular ions demonstrating that this general method for cooling atomic and molecular ions is reliable and efficient. For this purpose, complex molecular ions and barium ions have been confined simultaneously in a linear Paul trap. The complex molecular ions are generated in an electrospray ionization system and transferred to the trap via a 2 m long octopole ion guide. These molecular ions are pre-cooled by room temperature helium buffer gas so that they can be captured by the trap. The atomic barium ions are loaded from a barium evaporator oven and are laser-cooled by a 493 nm cooling laser and a 650 nm repumping laser. Due to the mutual Coulomb interaction among these charged particles, the kinetic energy of the complex molecular ions can be reduced significantly. In our experiments we have demonstrated the sympathetic cooling of various molecules (CO{sub 2}, Alexa Fluor 350, glycyrrhetinic acid, cytochrome c) covering a wide mass range from a few tens to 13000 amu. In every case the molecular ions could be cooled down to millikelvin temperatures. Photo-chemical reactions of the {sup 138}Ba{sup +} ions in the ({sup 2}P{sub 1/2}) excited state with gases such as O{sub 2}, CO{sub 2}, or N{sub 2}O, could be observed. If the initial {sup 138}Ba{sup +} ion ensemble is cold, the produced {sup 138}BaO{sup +} ions are cold as well, with a similar temperature as the laser-cooled barium ions (a few tens of millikelvin). The back-reaction of {sup 138}BaO{sup +} ions with neutral CO to {sup 138}Ba{sup +} is possible and was observed in our experiments as well. A powerful molecular dynamics (MD) simulation program has been developed. With this program dynamic properties of ion ensembles, such as sympathetic interactions or heating effects, have been investigated and experimental results have been analyzed to obtain, for example, ion numbers and temperatures. Additionally, the

  16. High Molecular Weight Forms of Mammalian Respiratory Chain Complex II

    Czech Academy of Sciences Publication Activity Database

    Kovářová, Nikola; Mráček, Tomáš; Nůsková, Hana; Holzerová, Eliška; Vrbacký, Marek; Pecina, Petr; Hejzlarová, Kateřina; Klučková, Katarína; Rohlena, Jakub; Neužil, Jiří; Houštěk, Josef

    2013-01-01

    Roč. 8, č. 8 (2013), e71869 E-ISSN 1932-6203 R&D Projects: GA ČR(CZ) GPP303/10/P227; GA MŠk(CZ) LL1204; GA MZd(CZ) NT12370; GA ČR(CZ) GAP301/10/1937 Institutional research plan: CEZ:AV0Z50520701 Institutional support: RVO:67985823 Keywords : supercomplexes * high molecular weihgt forms of complex II * native electrophoretic systems Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.534, year: 2013

  17. Lattice dynamics and molecular dynamics simulation of complex materials

    International Nuclear Information System (INIS)

    Chaplot, S.L.

    1997-01-01

    In this article we briefly review the lattice dynamics and molecular dynamics simulation techniques, as used for complex ionic and molecular solids, and demonstrate a number of applications through examples of our work. These computational studies, along with experiments, have provided microscopic insight into the structure and dynamics, phase transitions and thermodynamical properties of a variety of materials including fullerene, high temperature superconducting oxides and geological minerals as a function of pressure and temperature. The computational techniques also allow the study of the structures and dynamics associated with disorder, defects, surfaces, interfaces etc. (author)

  18. Production and sympathetic cooling of complex molecular ions

    International Nuclear Information System (INIS)

    Zhang, Chaobo

    2008-01-01

    This thesis reports on experimental and theoretical studies of the sympathetic cooling of complex molecular ions demonstrating that this general method for cooling atomic and molecular ions is reliable and efficient. For this purpose, complex molecular ions and barium ions have been confined simultaneously in a linear Paul trap. The complex molecular ions are generated in an electrospray ionization system and transferred to the trap via a 2 m long octopole ion guide. These molecular ions are pre-cooled by room temperature helium buffer gas so that they can be captured by the trap. The atomic barium ions are loaded from a barium evaporator oven and are laser-cooled by a 493 nm cooling laser and a 650 nm repumping laser. Due to the mutual Coulomb interaction among these charged particles, the kinetic energy of the complex molecular ions can be reduced significantly. In our experiments we have demonstrated the sympathetic cooling of various molecules (CO 2 , Alexa Fluor 350, glycyrrhetinic acid, cytochrome c) covering a wide mass range from a few tens to 13000 amu. In every case the molecular ions could be cooled down to millikelvin temperatures. Photo-chemical reactions of the 138 Ba + ions in the ( 2 P 1/2 ) excited state with gases such as O 2 , CO 2 , or N 2 O, could be observed. If the initial 138 Ba + ion ensemble is cold, the produced 138 BaO + ions are cold as well, with a similar temperature as the laser-cooled barium ions (a few tens of millikelvin). The back-reaction of 138 BaO + ions with neutral CO to 138 Ba + is possible and was observed in our experiments as well. A powerful molecular dynamics (MD) simulation program has been developed. With this program dynamic properties of ion ensembles, such as sympathetic interactions or heating effects, have been investigated and experimental results have been analyzed to obtain, for example, ion numbers and temperatures. Additionally, the feasibility of nondestructive spectroscopy via an optical dipole excitation

  19. Heterocellular interaction enhances recruitment of α and β-catenins and ZO-2 into functional gap-junction complexes and induces gap junction-dependant differentiation of mammary epithelial cells

    International Nuclear Information System (INIS)

    Talhouk, Rabih S.; Mroue, Rana; Mokalled, Mayssa; Abi-Mosleh, Lina; Nehme, Ralda; Ismail, Ayman; Khalil, Antoine; Zaatari, Mira; El-Sabban, Marwan E.

    2008-01-01

    Gap junctions (GJ) are required for mammary epithelial differentiation. Using epithelial (SCp2) and myoepithelial-like (SCg6) mouse-derived mammary cells, the role of heterocellular interaction in assembly of GJ complexes and functional differentiation (β-casein expression) was evaluated. Heterocellular interaction is critical for β-casein expression, independent of exogenous basement membrane or cell anchoring substrata. Functional differentiation of SCp2, co-cultured with SCg6, is more sensitive to GJ inhibition relative to homocellular SCp2 cultures differentiated by exogenous basement membrane. Connexin (Cx)32 and Cx43 levels were not regulated across culture conditions; however, GJ functionality was enhanced under differentiation-permissive conditions. Immunoprecipitation studies demonstrated association of junctional complex components (α-catenin, β-catenin and ZO-2) with Cx32 and Cx43, in differentiation conditions, and additionally with Cx30 in heterocellular cultures. Although β-catenin did not shuttle between cadherin and GJ complexes, increased association between connexins and β-catenin in heterocellular cultures was observed. This was concomitant with reduced nuclear β-catenin, suggesting that differentiation in heterocellular cultures involves sequestration of β-catenin in GJ complexes

  20. Counting constituents in molecular complexes by fluorescence photon antibunching

    Energy Technology Data Exchange (ETDEWEB)

    Fore, S; Laurence, T; Hollars, C; Huser, T

    2007-04-17

    Modern single molecule fluorescence microscopy offers new, highly quantitative ways of studying the systems biology of cells while keeping the cells healthy and alive in their natural environment. In this context, a quantum optical technique, photon antibunching, has found a small niche in the continuously growing applications of single molecule techniques to small molecular complexes. Here, we review some of the most recent applications of photon antibunching in biophotonics, and we provide a guide for how to conduct photon antibunching experiments at the single molecule level by applying techniques borrowed from time-correlated single photon counting. We provide a number of new examples for applications of photon antibunching to the study of multichromophoric molecules and small molecular complexes.

  1. Assembly, destruction and manipulation of atomic, molecular and complex systems

    International Nuclear Information System (INIS)

    Le Padellec, Arnaud Pierre Frederic

    2003-04-01

    In this report for Accreditation to Supervise Researches (HDR), the author first indicates his professional curriculum (diplomas, teaching activities, responsibilities in the field of education and research, publications), and then proposes a presentation of his scientific works and researches. He notably proposes an overview of the different experimental techniques he implemented: CRYRING storage ring, confluent beams, flow post-discharge with mass spectrometry and Langmuir probe, crossed beams, and so on. He reports works dealing with the manipulation and destruction of atomic, molecular and complex systems: detachment of atomic anions by electronic impact, detachment and dissociation of small carbon aggregates by electronic impact, dissociative recombination, dissociative ionisation and excitation, creation of pairs of ions, manipulation of sodium fluoride aggregates. He finally presents research projects regarding the assembly of molecular and complex systems

  2. Effects of Radiographic Contrast Media on the Micromorphology of the Junctional Complex of Erythrocytes Visualized by Immunocytology

    Science.gov (United States)

    Franke, Ralf-Peter; Krüger, Anne; Scharnweber, Tim; Wenzel, Folker; Jung, Friedrich

    2014-01-01

    Effects of radiographic contrast media (RCM) application were demonstrated in vitro and in vivo where the injection of RCM into the A. axillaris of patients with coronary artery disease was followed by a significant and RCM-dependent decrease of erythrocyte velocity in downstream skin capillaries. Another study in pigs revealed that the deceleration of erythrocytes coincided with a significant reduction of the oxygen partial pressure in the myocardium—supplied by the left coronary artery—after the administration of RCM into this artery. Further reports showed RCM dependent alterations of erythrocytes like echinocyte formation and exocytosis, sequestration of actin or band 3 and the buckling of endothelial cells coinciding with a formation of interendothelial fenestrations leading to areas devoid of endothelial cells. Key to morphological alterations of erythrocytes is the membrane cytoskeleton, which is linked to the band 3 in the erythrocyte membrane via the junctional complex. Fundamental observations regarding the cell biological and biochemical aspects of the structure and function of the cell membrane and the membrane cytoskeleton of erythrocytes have been reported. This review focuses on recent results gained, e.g., by advanced confocal laser scanning microscopy of different double-stained structural elements of the erythrocyte membrane cytoskeleton. PMID:25222553

  3. Molecular photoionization using the complex Kohn variational method

    International Nuclear Information System (INIS)

    Lynch, D.L.; Schneider, B.I.

    1992-01-01

    We have applied the complex Kohn variational method to the study of molecular-photoionization processes. This requires electron-ion scattering calculations enforcing incoming boundary conditions. The sensitivity of these results to the choice of the cutoff function in the Kohn method has been studied and we have demonstrated that a simple matching of the irregular function to a linear combination of regular functions produces accurate scattering phase shifts

  4. Electrical responses by effects of molecular adsorption on channel and junctions of carbon nanotube field effect transistors

    International Nuclear Information System (INIS)

    Kang, Donghun; Park, Wanjun

    2008-01-01

    We report the adsorption effect on the electrical transport of nanotube field effect transistors. The source-drain current is monitored separately for the nanotube channel and the metal-nanotube junction under different pressures of ambient air with a blocking passivation. The metal-nanotube junction shows a significant change from p-type to ambipolar upon vacuum pumping, while the nanotube channel changes modestly. The metal-nanotube junction is found to be far more sensitive to the environment than the nanotube channel. We suggest that the adsorption states underneath the blocking layer do not desorb, and thus the positive carriers would not be diluted upon the vacuum pumping. This result is interpreted as the formation of an i-p-i and p-i-p junction with charge transfer by oxygen molecules. (fast track communication)

  5. Characterization of GaN P-N Junction Grown on Si (111) Substrate by Plasma-assisted Molecular Beam Epitaxy

    International Nuclear Information System (INIS)

    Rosfariza Radzali; Rosfariza Radzali; Mohd Anas Ahmad; Zainuriah Hassan; Norzaini Zainal; Kwong, Y.F.; Woei, C.C.; Mohd Zaki Mohd Yusoff; Mohd Zaki Mohd Yusoff

    2011-01-01

    In this report, the growth of GaN pn junction on Si (111) substrate by plasma assisted molecular beam epitaxy (PAMBE) is presented. Doping of GaN p-n junction has been carried out using Si and Mg as n-type dopant and p-type dopants, respectively. The sample had been characterized by PL, Raman spectroscopy, HR-XRD and SEM. PL spectrum showed strong band edge emission of GaN at ∼364 nm, indicating good quality of the sample. The image of SEM cross section of the sample showed sharp interfaces. The presence of peak ∼657 cm -1 in Raman measurement exhibited successful doping of Mg in the sample. (author)

  6. Middle Miocene paleotemperature anomalies within the Franciscan Complex of northern California: Thermo-tectonic responses near the Mendocino triple junction

    Science.gov (United States)

    Underwood, M.B.; Shelton, K.L.; McLaughlin, R.J.; Laughland, M.M.; Solomon, R.M.

    1999-01-01

    This study documents three localities in the Franciscan accretionary complex of northern California, now adjacent to the San Andreas fault, that were overprinted thermally between 13.9 and 12.2 Ma: Point Delgada-Shelter Cove (King Range terrane); Bolinas Ridge (San Bruno Mountain terrane); and Mount San Bruno (San Bruno Mountain terrane). Vein assemblages of quartz, carbonate, sulfide minerals, and adularia were precipitated locally in highly fractured wall rock. Vitrinite reflectance (Rm) values and illite crystallinity decrease away from the zones of metalliferous veins, where peak wall-rock temperatures, as determined from Rm, were as high as 315??C. The ??18O values of quartz and calcite indicate that two separate types of fluid contributed to vein precipitation. Higher ??18O fluids produced widespread quartz and calcite veins that are typical of the regional paleothermal regime. The widespread veins are by-products of heat conduction and diffuse fluid flow during zeolite and prehnite-pumpellyite-grade metamorphism, and we interpret their paleofluids to have evolved through dehydration reactions and/or extensive isotopic exchange with accreted Franciscan rocks. Lower ??18O fluids, in contrast, evolved from relatively high temperature exchange between seawater (or meteoric water) and basaltic and/or sedimentary host rocks; focused flow of those fluids resulted in local deposition of the metalliferous veins. Heat sources for the three paleothermal anomalies remain uncertain and may have been unrelated to one another. Higher temperature metalliferous fluids in the King Range terrane could have advected either from a site of ridge-trench interaction north of the Mendocino fracture zone or from a "slabless window" in the wake of the northward migrating Mendocino triple junction. A separate paradox involves the amount of Quaternary offset of Franciscan basement rocks near Shelter Cove by on-land faults that some regard as the main active trace of the San Andreas

  7. Positronium formation studies in crystalline molecular complexes: Triphenylphosphine oxide - Acetanilide

    Science.gov (United States)

    Oliveira, F. C.; Denadai, A. M. L.; Guerra, L. D. L.; Fulgêncio, F. H.; Windmöller, D.; Santos, G. C.; Fernandes, N. G.; Yoshida, M. I.; Donnici, C. L.; Magalhães, W. F.; Machado, J. C.

    2013-04-01

    Hydrogen bond formation in the triphenylphosphine oxide (TPPO), acetanilide (ACN) supramolecular heterosynton system, named [TPPO0.5·ACN0.5], has been studied by Positron Annihilation Lifetime Spectroscopy (PALS) and supported by several analytical techniques. In toluene solution, Isothermal Titration Calorimetry (ITC) presented a 1:1 stoichiometry and indicated that the complexation process is driven by entropy, with low enthalpy contribution. X-ray structure determination showed the existence of a three-dimensional network of hydrogen bonds, allowing also the confirmation of the existence of a 1:1 crystalline molecular complex in solid state. The results of thermal analysis (TGA, DTA and DSC) and FTIR spectroscopy showed that the interactions in the complex are relatively weaker than those found in pure precursors, leading to a higher positronium formation probability at [TPPO0.5·ACN0.5]. These weak interactions in the complex enhance the possibility of the n- and π-electrons to interact with positrons and consequently, the probability of positronium formation is higher. Through the present work is shown that PALS is a sensible powerful tool to investigate intermolecular interactions in solid heterosynton supramolecular systems.

  8. Complex basis functions for molecular resonances: Methodology and applications

    Science.gov (United States)

    White, Alec; McCurdy, C. William; Head-Gordon, Martin

    The computation of positions and widths of metastable electronic states is a challenge for molecular electronic structure theory because, in addition to the difficulty of the many-body problem, such states obey scattering boundary conditions. These resonances cannot be addressed with naïve application of traditional bound state electronic structure theory. Non-Hermitian electronic structure methods employing complex basis functions is one way that we may rigorously treat resonances within the framework of traditional electronic structure theory. In this talk, I will discuss our recent work in this area including the methodological extension from single determinant SCF-based approaches to highly correlated levels of wavefunction-based theory such as equation of motion coupled cluster and many-body perturbation theory. These approaches provide a hierarchy of theoretical methods for the computation of positions and widths of molecular resonances. Within this framework, we may also examine properties of resonances including the dependence of these parameters on molecular geometry. Some applications of these methods to temporary anions and dianions will also be discussed.

  9. Solving structures of protein complexes by molecular replacement with Phaser

    International Nuclear Information System (INIS)

    McCoy, Airlie J.

    2006-01-01

    Four case studies in using maximum-likelihood molecular replacement, as implemented in the program Phaser, to solve structures of protein complexes are described. Molecular replacement (MR) generally becomes more difficult as the number of components in the asymmetric unit requiring separate MR models (i.e. the dimensionality of the search) increases. When the proportion of the total scattering contributed by each search component is small, the signal in the search for each component in isolation is weak or non-existent. Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components with a ‘tree search with pruning’ approach. This method, as implemented in the automated search procedure of the program Phaser, has been very successful in solving many previously intractable MR problems. However, there are a number of cases in which the automated search procedure of Phaser is suboptimal or encounters difficulties. These include cases where there are a large number of copies of the same component in the asymmetric unit or where the components of the asymmetric unit have greatly varying B factors. Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard ‘automated MR’ mode and two case studies are used to show how to modify the automated search strategy for problematic cases

  10. RNA three-way junctions can act as flexible RNA structural elements in large RNA molecules: a molecular simulation analysis

    Czech Academy of Sciences Publication Activity Database

    Beššeová, Ivana; Réblová, Kamila; Leontis, N.B.; Šponer, Jiří

    2009-01-01

    Roč. 26, č. 6 (2009), s. 830-831 ISSN 0739-1102. [The 17th Conversation . 16.06.2009-20.06.2009, Albany] Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : RNA three-way junctions * RNA Subject RIV: BO - Biophysics

  11. Work function and temperature dependence of electron tunneling through an N-type perylene diimide molecular junction with isocyanide surface linkers.

    Science.gov (United States)

    Smith, Christopher E; Xie, Zuoti; Bâldea, Ioan; Frisbie, C Daniel

    2018-01-18

    Conducting probe atomic force microscopy (CP-AFM) was employed to examine electron tunneling in self-assembled monolayer (SAM) junctions. A 2.3 nm long perylene tetracarboxylic acid diimide (PDI) acceptor molecule equipped with isocyanide linker groups was synthesized, adsorbed onto Ag, Au and Pt substrates, and the current-voltage (I-V) properties were measured by CP-AFM. The dependence of the low-bias resistance (R) on contact work function indicates that transport is LUMO-assisted ('n-type behavior'). A single-level tunneling model combined with transition voltage spectroscopy (TVS) was employed to analyze the experimental I-V curves and to extract the effective LUMO position ε l = E LUMO - E F and the effective electronic coupling (Γ) between the PDI redox core and the contacts. This analysis revealed a strong Fermi level (E F ) pinning effect in all the junctions, likely due to interface dipoles that significantly increased with increasing contact work function, as revealed by scanning Kelvin probe microscopy (SKPM). Furthermore, the temperature (T) dependence of R was found to be substantial. For Pt/Pt junctions, R varied more than two orders of magnitude in the range 248 K tunneling mechanism and allow independent determination of ε l , giving values compatible with estimates of ε l based on analysis of the full I-V data. Theoretical analysis revealed a general criterion to unambiguously rule out a two-step transport mechanism: namely, if measured resistance data exhibit a pronounced Arrhenius-type temperature dependence, a two-step electron transfer scenario should be excluded in cases where the activation energy depends on contact metallurgy. Overall, our results indicate (1) the generality of the Fermi level pinning phenomenon in molecular junctions, (2) the utility of employing the single level tunneling model for determining essential electronic structure parameters (ε l and Γ), and (3) the importance of changing the nature of the contacts to

  12. Dynamic coherence in excitonic molecular complexes under various excitation conditions

    Energy Technology Data Exchange (ETDEWEB)

    Chenu, Aurélia; Malý, Pavel; Mančal, Tomáš, E-mail: mancal@karlov.mff.cuni.cz

    2014-08-17

    Highlights: • Dynamic coherence does not improve energy transfer efficiency in natural conditions. • Photo-induced quantum jumps are discussed in classical context. • Natural time scale of a light excitation event is identified. • Coherence in FMO complex averages out under excitation by neighboring antenna. • This result is valid even in absence of dissipation. - Abstract: We investigate the relevance of dynamic quantum coherence in the energy transfer efficiency of molecular aggregates. We derive the time evolution of the density matrix for an open quantum system excited by light or by a neighboring antenna. Unlike in the classical case, the quantum description does not allow for a formal decomposition of the dynamics into sudden jumps in an observable quantity – an expectation value. Rather, there is a natural finite time-scale associated with the excitation process. We propose a simple experiment to test the influence of this time scale on the yield of photosynthesis. We demonstrate, using typical parameters of the Fenna–Matthews–Olson (FMO) complex and a typical energy transfer rate from the chlorosome baseplate, that dynamic coherences are averaged out in the complex even when the FMO model is completely free of all dissipation and dephasing.

  13. Solid State Pathways towards Molecular Complexity in Space

    Science.gov (United States)

    Linnartz, Harold; Bossa, Jean-Baptiste; Bouwman, Jordy; Cuppen, Herma M.; Cuylle, Steven H.; van Dishoeck, Ewine F.; Fayolle, Edith C.; Fedoseev, Gleb; Fuchs, Guido W.; Ioppolo, Sergio; Isokoski, Karoliina; Lamberts, Thanja; Öberg, Karin I.; Romanzin, Claire; Tenenbaum, Emily; Zhen, Junfeng

    2011-12-01

    It has been a long standing problem in astrochemistry to explain how molecules can form in a highly dilute environment such as the interstellar medium. In the last decennium more and more evidence has been found that the observed mix of small and complex, stable and highly transient species in space is the cumulative result of gas phase and solid state reactions as well as gas-grain interactions. Solid state reactions on icy dust grains are specifically found to play an important role in the formation of the more complex ``organic'' compounds. In order to investigate the underlying physical and chemical processes detailed laboratory based experiments are needed that simulate surface reactions triggered by processes as different as thermal heating, photon (UV) irradiation and particle (atom, cosmic ray, electron) bombardment of interstellar ice analogues. Here, some of the latest research performed in the Sackler Laboratory for Astrophysics in Leiden, the Netherlands is reviewed. The focus is on hydrogenation, i.e., H-atom addition reactions and vacuum ultraviolet irradiation of interstellar ice analogues at astronomically relevant temperatures. It is shown that solid state processes are crucial in the chemical evolution of the interstellar medium, providing pathways towards molecular complexity in space.

  14. MOLECULAR SIMULATION OF PHASE EQUILIBRIA FOR COMPLEX FLUIDS

    Energy Technology Data Exchange (ETDEWEB)

    Athanassios Z. Panagiotopoulos

    2009-09-09

    The general area of this project was the development and application of novel molecular simulation methods for prediction of thermodynamic and structural properties of complex polymeric, surfactant and ionic fluids. Over this project period, we have made considerable progress in developing novel algorithms to meet the computational challenges presented by the strong or long-range interactions in these systems and have generated data for well-defined mod-els that can be used to test theories and compare to experimental data. Overall, 42 archival papers and many invited and contributed presentations and lectures have been based on work supported by this project. 6 PhD, 1 M.S. and 2 postdoctoral students have been associated with this work, as listed in the body of the report.

  15. Molecular model for annihilation rates in positron complexes

    Energy Technology Data Exchange (ETDEWEB)

    Assafrao, Denise [Laboratorio de Atomos e Moleculas Especiais, Departamento de Fisica, ICEx, Universidade Federal de Minas Gerais, P.O. Box 702, 30123-970 Belo Horizonte, MG (Brazil); Department of Applied Mathematics and Theoretical Physics, Queen' s University of Belfast, Belfast BT7 1NN, Northern Ireland (United Kingdom); Walters, H.R. James [Department of Applied Mathematics and Theoretical Physics, Queen' s University of Belfast, Belfast BT7 1NN, Northern Ireland (United Kingdom); Mohallem, Jose R. [Laboratorio de Atomos e Moleculas Especiais, Departamento de Fisica, ICEx, Universidade Federal de Minas Gerais, P.O. Box 702, 30123-970 Belo Horizonte, MG (Brazil); Department of Applied Mathematics and Theoretical Physics, Queen' s University of Belfast, Belfast BT7 1NN, Northern Ireland (United Kingdom)], E-mail: rachid@fisica.ufmg.br

    2008-02-15

    The molecular approach for positron interaction with atoms is developed further. Potential energy curves for positron motion are obtained. Two procedures accounting for the nonadiabatic effective positron mass are introduced for calculating annihilation rate constants. The first one takes the bound-state energy eigenvalue as an input parameter. The second is a self-contained and self-consistent procedure. The methods are tested with quite different states of the small complexes HPs, e{sup +}He (electronic triplet) and e{sup +}Be (electronic singlet and triplet). For states yielding the positronium cluster, the annihilation rates are quite stable, irrespective of the accuracy in binding energies. For the e{sup +}Be states, annihilation rates are larger and more consistent with qualitative predictions than previously reported ones.

  16. Molecular Simulation Of Phase Equilibria For Complex Fluids

    International Nuclear Information System (INIS)

    Panagiotopoulos, Athanassios Z.

    2009-01-01

    The general area of this project was the development and application of novel molecular simulation methods for prediction of thermodynamic and structural properties of complex polymeric, surfactant and ionic fluids. Over this project period, we have made considerable progress in developing novel algorithms to meet the computational challenges presented by the strong or long-range interactions in these systems and have generated data for well-defined mod-els that can be used to test theories and compare to experimental data. Overall, 42 archival papers and many invited and contributed presentations and lectures have been based on work supported by this project. 6 PhD, 1 M.S. and 2 postdoctoral students have been associated with this work, as listed in the body of the report.

  17. Molecular model for annihilation rates in positron complexes

    International Nuclear Information System (INIS)

    Assafrao, Denise; Walters, H.R. James; Mohallem, Jose R.

    2008-01-01

    The molecular approach for positron interaction with atoms is developed further. Potential energy curves for positron motion are obtained. Two procedures accounting for the nonadiabatic effective positron mass are introduced for calculating annihilation rate constants. The first one takes the bound-state energy eigenvalue as an input parameter. The second is a self-contained and self-consistent procedure. The methods are tested with quite different states of the small complexes HPs, e + He (electronic triplet) and e + Be (electronic singlet and triplet). For states yielding the positronium cluster, the annihilation rates are quite stable, irrespective of the accuracy in binding energies. For the e + Be states, annihilation rates are larger and more consistent with qualitative predictions than previously reported ones

  18. Molecular recognition in complexes of TRF proteins with telomeric DNA.

    Directory of Open Access Journals (Sweden)

    Miłosz Wieczór

    Full Text Available Telomeres are specialized nucleoprotein assemblies that protect the ends of linear chromosomes. In humans and many other species, telomeres consist of tandem TTAGGG repeats bound by a protein complex known as shelterin that remodels telomeric DNA into a protective loop structure and regulates telomere homeostasis. Shelterin recognizes telomeric repeats through its two major components known as Telomere Repeat-Binding Factors, TRF1 and TRF2. These two homologous proteins are therefore essential for the formation and normal function of telomeres. Indeed, TRF1 and TRF2 are implicated in a plethora of different cellular functions and their depletion leads to telomere dysfunction with chromosomal fusions, followed by apoptotic cell death. More specifically, it was found that TRF1 acts as a negative regulator of telomere length, and TRF2 is involved in stabilizing the loop structure. Consequently, these proteins are of great interest, not only because of their key role in telomere maintenance and stability, but also as potential drug targets. In the current study, we investigated the molecular basis of telomeric sequence recognition by TRF1 and TRF2 and their DNA binding mechanism. We used molecular dynamics (MD to calculate the free energy profiles for binding of TRFs to telomeric DNA. We found that the predicted binding free energies were in good agreement with experimental data. Further, different molecular determinants of binding, such as binding enthalpies and entropies, the hydrogen bonding pattern and changes in surface area, were analyzed to decompose and examine the overall binding free energies at the structural level. With this approach, we were able to draw conclusions regarding the consecutive stages of sequence-specific association, and propose a novel aspartate-dependent mechanism of sequence recognition. Finally, our work demonstrates the applicability of computational MD-based methods to studying protein-DNA interactions.

  19. Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase.

    Science.gov (United States)

    Szefler, Beata; Diudea, Mircea V; Putz, Mihai V; Grudzinski, Ireneusz P

    2016-10-27

    Glucose oxidase (GOx) is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state) to form d-glucono-1,5-lactone, which hydrolyses spontaneously to produce gluconic acid. A coproduct of this enzymatic reaction is hydrogen peroxide (H₂O₂). GOx has found several commercial applications in chemical and pharmaceutical industries including novel biosensors that use the immobilized enzyme on different nanomaterials and/or polymers such as polyethylenimine (PEI). The problem of GOx immobilization on PEI is retaining the enzyme native activity despite its immobilization onto the polymer surface. Therefore, the molecular dynamic (MD) study of the PEI ligand (C14N8_07_B22) and the GOx enzyme (3QVR) was performed to examine the final complex PEI-GOx stabilization and the affinity of the PEI ligand to the docking sites of the GOx enzyme. The docking procedure showed two places/regions of major interaction of the protein with the polymer PEI: (LIG1) of -5.8 kcal/mol and (LIG2) of -4.5 kcal/mol located inside the enzyme and on its surface, respectively. The values of enthalpy for the PEI-enzyme complex, located inside of the protein (LIG1) and on its surface (LIG2) were computed. Docking also discovered domains of the GOx protein that exhibit no interactions with the ligand or have even repulsive characteristics. The structural data clearly indicate some differences in the ligand PEI behavior bound at the two places/regions of glucose oxidase.

  20. Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase

    Directory of Open Access Journals (Sweden)

    Beata Szefler

    2016-10-01

    Full Text Available Glucose oxidase (GOx is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state to form d-glucono-1,5-lactone, which hydrolyses spontaneously to produce gluconic acid. A coproduct of this enzymatic reaction is hydrogen peroxide (H2O2. GOx has found several commercial applications in chemical and pharmaceutical industries including novel biosensors that use the immobilized enzyme on different nanomaterials and/or polymers such as polyethylenimine (PEI. The problem of GOx immobilization on PEI is retaining the enzyme native activity despite its immobilization onto the polymer surface. Therefore, the molecular dynamic (MD study of the PEI ligand (C14N8_07_B22 and the GOx enzyme (3QVR was performed to examine the final complex PEI-GOx stabilization and the affinity of the PEI ligand to the docking sites of the GOx enzyme. The docking procedure showed two places/regions of major interaction of the protein with the polymer PEI: (LIG1 of −5.8 kcal/mol and (LIG2 of −4.5 kcal/mol located inside the enzyme and on its surface, respectively. The values of enthalpy for the PEI-enzyme complex, located inside of the protein (LIG1 and on its surface (LIG2 were computed. Docking also discovered domains of the GOx protein that exhibit no interactions with the ligand or have even repulsive characteristics. The structural data clearly indicate some differences in the ligand PEI behavior bound at the two places/regions of glucose oxidase.

  1. Molecular Genotype Identification of Different Chickens: Major Histocompatibility Complex

    Directory of Open Access Journals (Sweden)

    Hongzhi Wang

    2014-09-01

    Full Text Available Chicken is a main poultry in China. Molecular breeding for disease resistance plays an important role in the control of diseases, especially infectious diseases. Choice of genes for disease resistance is the key technology of molecular breeding. The major histocompatibility complex (MHC is of great interest to poultry breeding scientists for its extraordinary polymorphism and close relation with traits of resistance against infectious diseases. The MHC-B haplotype plays an important role in the study of disease resistance in chicken. The traditional chicken MHC-B haplotype is commonly defined by serologic reactions of erythrocytes and the majority of studies have been conducted in Leghorn and broiler but study about other chicken breeds is little. In this study, firstly, the microsatellite marker LEI0258 which is located within the MHC was sequenced by using target sequence capture assay in different chicken breeds, and then according to the number of repeated structures and polymorphic sequences in microsatellite, sequence information for the region defined by LEI0258 was obtained for different haplotypes. Afterwards, we identified the relation between MHC-B haplotypes and disease resistance. Collectively, these observed results provided the reference data for disease-resistant breeding association with blood type and for further study of MHC gene function in poultry.

  2. Using photoelectron diffraction to determine complex molecular adsorption structures

    International Nuclear Information System (INIS)

    Woodruff, D P

    2010-01-01

    Backscattering photoelectron diffraction, particularly in the energy-scan mode, is now an established technique for determining in a quantitative fashion the local structure of adsorbates on surfaces, and has been used successfully for ∼100 adsorbate phases. The elemental and chemical-state specificity afforded by the characteristic core level photoelectron binding energies means that it has particular advantages for molecular adsorbates, as the local geometry of inequivalent atoms in the molecule can be determined in a largely independent fashion. On the other hand, polyatomic molecules present a general problem for all methods of surface structure determination in that a mismatch of intramolecular distances with interatomic distances on the substrate surface means that the atoms in the adsorbed molecule are generally in low-symmetry sites. The quantities measured experimentally then represent an incoherent sum of the properties of each structural domain that is inequivalent with respect to the substrate point group symmetry. This typically leads to greater ambiguity or precision in the structural solutions. The basic principles of the method are described and illustrated with a simple example involving molecule/substrate bonding through only one constituent atom (TiO 2 -(110)/H 2 O). This example demonstrates the importance of obtaining quantitative local structural information. Further examples illustrate both the successes and the problems of this approach when applied to somewhat more complex molecular adsorbates.

  3. Molecular diagnostics for the sigatoka disease complex of banana.

    Science.gov (United States)

    Arzanlou, Mahdi; Abeln, Edwin C A; Kema, Gert H J; Waalwijk, Cees; Carlier, Jean; Vries, Ineke de; Guzmán, Mauricio; Crous, Pedro W

    2007-09-01

    ABSTRACT The Sigatoka disease complex of banana involves three related ascomycetous fungi, Mycosphaerella fijiensis, M. musicola, and M. eumusae. The exact distribution of these three species and their disease epidemiology remain unclear, because their symptoms and life cycles are rather similar. Disease diagnosis in the Mycosphaerella complex of banana is based on the presence of host symptoms and fungal fruiting structures, which hamper preventive management strategies. In the present study, we have developed rapid and robust species-specific molecular-based diagnostic tools for detection and quantification of M. fijiensis, M. musicola, and M. eumusae. Conventional species-specific polymerase chain reaction (PCR) primers were developed based on the actin gene that detected DNA at as little as 100, 1, and 10 pg/mul from M. fijiensis, M. musicola, and M. eumusae, respectively. Furthermore, TaqMan real-time quantitative PCR assays were developed based on the beta-tubulin gene and detected quantities of DNA as low as 1 pg/mul for each Mycosphaerella sp. from pure cultures and DNA at 1.6 pg/mul per milligram of dry leaf tissue for M. fijiensis that was validated using naturally infected banana leaves.

  4. Quantum conductance of 4,4-bipyridine molecular junctions: Role of electrode work function and local d band

    DEFF Research Database (Denmark)

    Rauba, J.M.C.; Strange, Mikkel; Thygesen, Kristian Sommer

    2008-01-01

    conductance than the Pt-BPD junction due to the smaller work function of Au as compared to Pt. On the other hand, coupling to the local d band is stronger in the case of Pt and this broadens the LUMO resonance. We find that these effects largely outbalance each other leading to conductances of 0.01G(0) and 0......-principles results within a simple single-level model....

  5. Defining the value of injection current and effective electrical contact area for EGaIn-based molecular tunneling junctions.

    Science.gov (United States)

    Simeone, Felice C; Yoon, Hyo Jae; Thuo, Martin M; Barber, Jabulani R; Smith, Barbara; Whitesides, George M

    2013-12-04

    Analysis of rates of tunneling across self-assembled monolayers (SAMs) of n-alkanethiolates SCn (with n = number of carbon atoms) incorporated in junctions having structure Ag(TS)-SAM//Ga2O3/EGaIn leads to a value for the injection tunnel current density J0 (i.e., the current flowing through an ideal junction with n = 0) of 10(3.6±0.3) A·cm(-2) (V = +0.5 V). This estimation of J0 does not involve an extrapolation in length, because it was possible to measure current densities across SAMs over the range of lengths n = 1-18. This value of J0 is estimated under the assumption that values of the geometrical contact area equal the values of the effective electrical contact area. Detailed experimental analysis, however, indicates that the roughness of the Ga2O3 layer, and that of the Ag(TS)-SAM, determine values of the effective electrical contact area that are ~10(-4) the corresponding values of the geometrical contact area. Conversion of the values of geometrical contact area into the corresponding values of effective electrical contact area results in J0(+0.5 V) = 10(7.6±0.8) A·cm(-2), which is compatible with values reported for junctions using top-electrodes of evaporated Au, and graphene, and also comparable with values of J0 estimated from tunneling through single molecules. For these EGaIn-based junctions, the value of the tunneling decay factor β (β = 0.75 ± 0.02 Å(-1); β = 0.92 ± 0.02 nC(-1)) falls within the consensus range across different types of junctions (β = 0.73-0.89 Å(-1); β = 0.9-1.1 nC(-1)). A comparison of the characteristics of conical Ga2O3/EGaIn tips with the characteristics of other top-electrodes suggests that the EGaIn-based electrodes provide a particularly attractive technology for physical-organic studies of charge transport across SAMs.

  6. Disassembled DJ-1 high molecular weight complex in cortex mitochondria from Parkinson's disease patients

    Directory of Open Access Journals (Sweden)

    Adler Charles

    2009-07-01

    Full Text Available Abstract Correction to Nural H, He P, Beach T, Sue L, Xia W, Shen Y. Disassembled DJ-1 high molecular weight complex in cortex mitochondria from Parkinson's disease patients Molecular Neurodegeneration 2009, 4:23.

  7. Humidity-insensitive water evaporation from molecular complex fluids.

    Science.gov (United States)

    Salmon, Jean-Baptiste; Doumenc, Frédéric; Guerrier, Béatrice

    2017-09-01

    We investigated theoretically water evaporation from concentrated supramolecular mixtures, such as solutions of polymers or amphiphilic molecules, using numerical resolutions of a one-dimensional model based on mass transport equations. Solvent evaporation leads to the formation of a concentrated solute layer at the drying interface, which slows down evaporation in a long-time-scale regime. In this regime, often referred to as the falling rate period, evaporation is dominated by diffusive mass transport within the solution, as already known. However, we demonstrate that, in this regime, the rate of evaporation does not also depend on the ambient humidity for many molecular complex fluids. Using analytical solutions in some limiting cases, we first demonstrate that a sharp decrease of the water chemical activity at high solute concentration leads to evaporation rates which depend weakly on the humidity, as the solute concentration at the drying interface slightly depends on the humidity. However, we also show that a strong decrease of the mutual diffusion coefficient of the solution enhances considerably this effect, leading to nearly independent evaporation rates over a wide range of humidity. The decrease of the mutual diffusion coefficient indeed induces strong concentration gradients at the drying interface, which shield the concentration profiles from humidity variations, except in a very thin region close to the drying interface.

  8. MOLECULAR DYNAMICS STUDY OF CYTOCHROME C – LIPID COMPLEXES

    Directory of Open Access Journals (Sweden)

    V. Trusova

    2017-10-01

    Full Text Available The interactions between a mitochondrial hemoprotein cytochrome c (cyt c and the model lipid membranes composed of zwitterionic lipid phosphatidylcholine (PC and anionic lipids phosphatidylglycerol (PG, phosphatidylserine (PS or cardiolipin (CL were studied using the method of molecular dynamics. It was found that cyt c structure remains virtually unchanged in the protein complexes with PC/PG or PC/PS bilayers. In turn, protein binding to PC/CL bilayer is followed by the rise in cyt c radius of gyration and root-mean-square fluctuations. The magnitude of these changes was demonstrated to increase with the anionic lipid content. The revealed effect was interpreted in terms of the partial unfolding of polypeptide chain in the region Ala15-Leu32, widening of the heme crevice and enhancement of the conformational fluctuations in the region Pro76-Asp93 upon increasing the CL molar fraction from 5 to 25%. The results obtained seem to be of utmost importance in the context of amyloidogenic propensity of cyt c.

  9. Synthesis of molecular complexes for small molecule activation

    International Nuclear Information System (INIS)

    Andrez, Julie

    2016-01-01

    The redox chemistry of f-elements is drawing the attention of inorganic chemists due to their unusual reaction pathways. Notably low-valent f-element complexes have been shown to be able to activate small molecules such as CO_2 and N_2 in mild conditions. Compared to d-block metals, f-elements present a coordination chemistry dominated by electrostatic interactions and steric constraints. Molecular complexes of f-elements could thus provide new catalytic routes to transform small molecules into valuable chemicals. However the redox chemistry of low valent f-elements is dominated by single-electron transfers while the reductions of CO_2 and N_2 require multi-electronic processes. Accordingly the first approach of this PhD work was the use of redox active ligands as electron reservoir to support f-element centres increasing the electron number available for reduction events. The coordination of uranium with tridentate Schiff base ligand was investigated and led to isolation of a dinuclear electron-rich species able to undertake up to eight-electron reduction combining the redox activity of the ligands and the uranium centres. In order to obtain electron-rich compounds potentially able to polarize the C=O bond of CO_2, the synthesis of hetero-bimetallic species supported by salophen Schiff base ligand was also studied. In a second approach we have used bulky ligands with strong donor-character to tune the reducing abilities of low valent f-elements. In this case a bimolecular electron-transfer process is often observed. The reactivity of the U(III) siloxid complex [U(OSi(OtBu)_3)_4K] was further investigated. Notably, reaction with Ph_3PS led to the formation of a terminal U(IV) sulfide complex with multiple U-S bond which was analysed by DFT studies to better understand the bonding nature. Preliminary studies on the role of the counter-cation (M) in the system [U(OSi(OtBu)_3)_4M] on the outcome of the reactivity with CS_2 and CO_2 have also been performed. The

  10. Molecular complexity from polyunsaturated substrates: the gold catalysis approach.

    Science.gov (United States)

    Fensterbank, Louis; Malacria, Max

    2014-03-18

    Over the last two decades, electrophilic catalysis relying on platinum(II), gold(I), and gold(III) salts has emerged as a remarkable synthetic methodology. Chemists have discovered a large variety of organic transformations that convert a great assortment of highly functionalized precursors into valuable final products. In many cases, these methodologies offer unique features, allowing access to unprecedented molecular architectures. Due to the mild reaction conditions and high function compatibility, scientists have successfully developed applications in total synthesis of natural products, as well as in asymmetric catalysis. In addition, all these developments have been accompanied by the invention of well-tailored catalysts, so that a palette of different electrophilic agents is now commercially available or readily synthesized at the bench. In some respects, researchers' interests in developing homogeneous gold catalysis can be compared with the Californian gold rush of the 19th century. It has attracted into its fervor thousands of scientists, providing a huge number of versatile and important reports. More notably, it is clear that the contribution to the art of organic synthesis is very valuable, though the quest is not over yet. Because they rely on the intervention of previously unknown types of intermediates, new retrosynthetic disconnections are now possible. In this Account, we discuss our efforts on the use of readily available polyunsaturated precursors, such as enynes, dienynes, allenynes, and allenenes to give access to highly original polycyclic structures in a single operation. These transformations transit via previously undescribed intermediates A, B, D, F, and H that will be encountered later on. All these intermediates have been determined by both ourselves and others by DFT calculations and in some cases have been confirmed on the basis of experimental data. In addition, dual gold activation can be at work in some of these transformations

  11. Post-annealing effects on shallow-junction characteristics caused by 20 keV BGe molecular ion implantation

    International Nuclear Information System (INIS)

    Liang, J.H.; Sang, Y.J.; Wang, C.-H.; Wang, T.W.; Hsu, J.Y.; Niu, H.; Tseng, M.S.

    2005-01-01

    This study examines the post-annealing-dependent behaviors of the shallow junction produced by implanting 10 15 cm -2 20 keV BGe ions into n-type silicon specimens. Post-annealing treatments consisted of one- and two-step annealing including both furnace annealing (FA) and rapid thermal annealing (RTA). Comparison of the one-step FA at 550 deg. C and the one-step RTA at 1050 deg. C revealed that boron depth profiles were slightly diffused in the former but exhibited considerable transient-enhanced diffusion (TED) in the latter. However, both the one-step FA- and RTA-annealed germanium depth profiles barely diffused, while the latter diffusing slightly deeper than the former. The optimum value of junction depth (x j ) times sheet resistance (R s ) was obtained with one-step FA at 550 deg. C for 1 h. The two-step annealing (FA at 550 deg. C and RTA at 1050 deg. C) results showed that the RTA-induced TED in the boron depth profiles could be effectively retarded only when FA took place for more than 3 h. Again, germanium depth profiles are also barely diffused while the corresponding TEDs were larger than those in one-step FA but smaller than those in one-step RTA. Furthermore, the two-step annealing of FA at 550 deg. C for 3 h followed by RTA at 1050 deg. C for 30 s is suggested when attempting to obtain an optimum value of x j R s

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

    Science.gov (United States)

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

    2014-10-20

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

  13. Molecular structure of the pyruvate dehydrogenase complex from Escherichia coli K-12.

    Science.gov (United States)

    Vogel, O; Hoehn, B; Henning, U

    1972-06-01

    The pyruvate dehydrogenase core complex from E. coli K-12, defined as the multienzyme complex that can be obtained with a unique polypeptide chain composition, has a molecular weight of 3.75 x 10(6). All results obtained agree with the following numerology. The core complex consists of 48 polypeptide chains. There are 16 chains (molecular weight = 100,000) of the pyruvate dehydrogenase component, 16 chains (molecular weight = 80,000) of the dihydrolipoamide dehydrogenase component, and 16 chains (molecular weight = 56,000) of the dihydrolipoamide dehydrogenase component. Usually, but not always, pyruvate dehydrogenase complex is produced in vivo containing at least 2-3 mol more of dimers of the pyruvate dehydrogenase component than the stoichiometric ratio with respect to the core complex. This "excess" component is bound differently than are the eight dimers in the core complex.

  14. Molecular computing towards a novel computing architecture for complex problem solving

    CERN Document Server

    Chang, Weng-Long

    2014-01-01

    This textbook introduces a concise approach to the design of molecular algorithms for students or researchers who are interested in dealing with complex problems. Through numerous examples and exercises, you will understand the main difference of molecular circuits and traditional digital circuits to manipulate the same problem and you will also learn how to design a molecular algorithm of solving any a problem from start to finish. The book starts with an introduction to computational aspects of digital computers and molecular computing, data representation of molecular computing, molecular operations of molecular computing and number representation of molecular computing, and provides many molecular algorithm to construct the parity generator and the parity checker of error-detection codes on digital communication, to encode integers of different formats, single precision and double precision of floating-point numbers, to implement addition and subtraction of unsigned integers, to construct logic operations...

  15. Molecular organization and dynamics of micellar phase of polyelectrolyte-surfactant complexes: ESR spin probe study

    Science.gov (United States)

    Wasserman, A. M.; Kasaikin, V. A.; Zakharova, Yu. A.; Aliev, I. I.; Baranovsky, V. Yu.; Doseva, V.; Yasina, L. L.

    2002-04-01

    Molecular dynamics and organization of the micellar phase of complexes of linear polyelectrolytes with ionogenic and non-ionogenic surfactants was studied by the ESR spin probe method. Complexes of polyacrylic acid (PAA) and sodium polystyrenesulfonate (PSS) with alkyltrimethylammonium bromides (ATAB), as well as complexes of poly- N, N'-dimethyldiallylammonium chloride (PDACL) with sodium dodecylsulfate (SDS) were studied. The micellar phase of such complexes is highly organized molecular system, molecular ordering of which near the polymeric chain is much higher than in the 'center' of the micelle, it depends on the polymer-detergent interaction, flexibility of polymeric chain and length of carbonic part of the detergent molecule. Complexes of polymethacrylic acid (PMAA) with non-ionic detergent (dodecyl-substituted polyethyleneglycol), show that the local mobility of surfactant in such complexes is significantly lower than in 'free' micelles and depends on the number of micellar particles participating in formation of complexes.

  16. From HAMLET to XAMLET: The molecular complex selectively ...

    African Journals Online (AJOL)

    HAMLET (human α-lactalbumin made lethal to tumor cells) is a complex consisting of decalcinated α-lactalbumin and oleic acid. It has been shown to induce massive cell death in various cancers without serious damage to normal tissues in both in vitro and in vivo experiments. The complexity of the mechanism in the ...

  17. Molecular beam epitaxy of InP single junction and InP/In0.53Ga0.47As monolithically integrated tandem solar cells using solid phosphorous source material

    International Nuclear Information System (INIS)

    Delaney, A.; Chin, K.; Street, S.; Newman, F.; Aguilar, L.; Ignatiev, A.; Monier, C.; Velela, M.; Freundlich, A.

    1998-01-01

    This work reports the first InP solar cells, InP/In 0.53 Ga 0.47 As tandem solar cells and InP tunnel junctions to be grown using a solid phosphorous source cracker cell in a molecular beam epitaxy system. High p-type doping achieved with this system allowed for the development of InP tunnel junctions. These junctions which allow for improved current matching in subsequent monolithically integrated tandem devices also do not absorb photons which can be utilized in the InGaAs structure. Photocurrent spectral responses compared favorably to devices previously grown in a chemical beam epitaxy system. High resolution x-ray scans demonstrated good lattice matching between constituent parts of the tandem cell. AM0 efficiencies of both InP and InP/InGaAs tandem cells are reported

  18. Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

    Energy Technology Data Exchange (ETDEWEB)

    Llave, Ezequiel de la; Herrera, Santiago E.; Adam, Catherine; Méndez De Leo, Lucila P.; Calvo, Ernesto J.; Williams, Federico J., E-mail: fwilliams@qi.fcen.uba.ar [INQUIMAE-CONICET, Departamento de Química Inorgánica, Analítica y Química-Física, Facultad Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EHA (Argentina)

    2015-11-14

    The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge.

  19. 'Special K' and a Loss of Cell-To-Cell Adhesion in Proximal Tubule-Derived Epithelial Cells: Modulation of the Adherens Junction Complex by Ketamine

    Science.gov (United States)

    Hills, Claire E.; Jin, Tianrong; Siamantouras, Eleftherios; Liu, Issac K-K; Jefferson, Kieran P.; Squires, Paul E.

    2013-01-01

    Ketamine, a mild hallucinogenic class C drug, is the fastest growing ‘party drug’ used by 16–24 year olds in the UK. As the recreational use of Ketamine increases we are beginning to see the signs of major renal and bladder complications. To date however, we know nothing of a role for Ketamine in modulating both structure and function of the human renal proximal tubule. In the current study we have used an established model cell line for human epithelial cells of the proximal tubule (HK2) to demonstrate that Ketamine evokes early changes in expression of proteins central to the adherens junction complex. Furthermore we use AFM single-cell force spectroscopy to assess if these changes functionally uncouple cells of the proximal tubule ahead of any overt loss in epithelial cell function. Our data suggests that Ketamine (24–48 hrs) produces gross changes in cell morphology and cytoskeletal architecture towards a fibrotic phenotype. These physical changes matched the concentration-dependent (0.1–1 mg/mL) cytotoxic effect of Ketamine and reflect a loss in expression of the key adherens junction proteins epithelial (E)- and neural (N)-cadherin and β-catenin. Down-regulation of protein expression does not involve the pro-fibrotic cytokine TGFβ, nor is it regulated by the usual increase in expression of Slug or Snail, the transcriptional regulators for E-cadherin. However, the loss in E-cadherin can be partially rescued pharmacologically by blocking p38 MAPK using SB203580. These data provide compelling evidence that Ketamine alters epithelial cell-to-cell adhesion and cell-coupling in the proximal kidney via a non-classical pro-fibrotic mechanism and the data provides the first indication that this illicit substance can have major implications on renal function. Understanding Ketamine-induced renal pathology may identify targets for future therapeutic intervention. PMID:24009666

  20. Molecular Composition and Ultrastructure of the Caveolar Coat Complex

    Science.gov (United States)

    Ludwig, Alexander; Howard, Gillian; Mendoza-Topaz, Carolina; Deerinck, Thomas; Mackey, Mason; Sandin, Sara; Ellisman, Mark H.; Nichols, Benjamin J.

    2013-01-01

    Caveolae are an abundant feature of the plasma membrane of many mammalian cell types, and have key roles in mechano-transduction, metabolic regulation, and vascular permeability. Caveolin and cavin proteins, as well as EHD2 and pacsin 2, are all present in caveolae. How these proteins assemble to form a protein interaction network for caveolar morphogenesis is not known. Using in vivo crosslinking, velocity gradient centrifugation, immuno-isolation, and tandem mass spectrometry, we determine that cavins and caveolins assemble into a homogenous 80S complex, which we term the caveolar coat complex. There are no further abundant components within this complex, and the complex excludes EHD2 and pacsin 2. Cavin 1 forms trimers and interacts with caveolin 1 with a molar ratio of about 1∶4. Cavins 2 and 3 compete for binding sites within the overall coat complex, and form distinct subcomplexes with cavin 1. The core interactions between caveolin 1 and cavin 1 are independent of cavin 2, cavin 3, and EHD2 expression, and the cavins themselves can still interact in the absence of caveolin 1. Using immuno-electron microscopy as well as a recently developed protein tag for electron microscopy (MiniSOG), we demonstrate that caveolar coat complexes form a distinct coat all around the caveolar bulb. In contrast, and consistent with our biochemical data, EHD2 defines a different domain at the caveolar neck. 3D electron tomograms of the caveolar coat, labeled using cavin-MiniSOG, show that the caveolar coat is composed of repeating units of a unitary caveolar coat complex. PMID:24013648

  1. A Complex Approach for Unravelling Musaceae Phylogeny at Molecular Level

    Czech Academy of Sciences Publication Activity Database

    Němcová, Pavla; Hřibová, Eva; Valárik, Miroslav; Doležel, Jaroslav

    2011-01-01

    Roč. 897, SEP 14 (2011), s. 139-142 ISSN 0567-7572. [INTERNATIONAL ISHS-PROMUSA SYMPOSIUM ON GLOBAL PERSPECTIVES ON ASIAN CHALLENGES. Guangzhou, 14.08.2009-16.08.2009] R&D Projects: GA AV ČR IAA600380703 Institutional support: RVO:61389030 Keywords : DArT * low-copy genes * molecular phylogenetics Subject RIV: EF - Botanics http://www.actahort.org/books/897/897_14.htm

  2. Translational regulation shapes the molecular landscape of complex disease phenotypes

    Czech Academy of Sciences Publication Activity Database

    Schafer, S.; Adami, E.; Heinig, M.; Rodrigues, K. E. C.; Kreuchwig, F.; Šilhavý, Jan; van Heesch, S.; Simaite, D.; Rajewsky, N.; Cuppen, E.; Pravenec, Michal; Vingron, M.; Cook, S. A.; Hubner, N.

    2015-01-01

    Roč. 6, May 2015 (2015), s. 7200 ISSN 2041-1723 R&D Projects: GA ČR(CZ) GB14-36804G; GA MŠk(CZ) LL1204; GA MŠk(CZ) 7E10067 Institutional support: RVO:67985823 Keywords : translational regulation * RNA sequencing * ribosome profiling * rat Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 11.329, year: 2015

  3. Water oxidation catalyzed by molecular di- and nonanuclear Fe complexes: importance of a proper ligand framework.

    Science.gov (United States)

    Das, Biswanath; Lee, Bao-Lin; Karlsson, Erik A; Åkermark, Torbjörn; Shatskiy, Andrey; Demeshko, Serhiy; Liao, Rong-Zhen; Laine, Tanja M; Haukka, Matti; Zeglio, Erica; Abdel-Magied, Ahmed F; Siegbahn, Per E M; Meyer, Franc; Kärkäs, Markus D; Johnston, Eric V; Nordlander, Ebbe; Åkermark, Björn

    2016-09-14

    The synthesis of two molecular iron complexes, a dinuclear iron(iii,iii) complex and a nonanuclear iron complex, based on the dinucleating ligand 2,2'-(2-hydroxy-5-methyl-1,3-phenylene)bis(1H-benzo[d]imidazole-4-carboxylic acid) is described. The two iron complexes were found to drive the oxidation of water by the one-electron oxidant [Ru(bpy)3](3+).

  4. Chemistry at molecular junctions: Rotation and dissociation of O2 on the Ag(110) surface induced by a scanning tunneling microscope.

    Science.gov (United States)

    Roy, Sharani; Mujica, Vladimiro; Ratner, Mark A

    2013-08-21

    The scanning tunneling microscope (STM) is a fascinating tool used to perform chemical processes at the single-molecule level, including bond formation, bond breaking, and even chemical reactions. Hahn and Ho [J. Chem. Phys. 123, 214702 (2005)] performed controlled rotations and dissociations of single O2 molecules chemisorbed on the Ag(110) surface at precise bias voltages using STM. These threshold voltages were dependent on the direction of the bias voltage and the initial orientation of the chemisorbed molecule. They also observed an interesting voltage-direction-dependent and orientation-dependent pathway selectivity suggestive of mode-selective chemistry at molecular junctions, such that in one case the molecule underwent direct dissociation, whereas in the other case it underwent rotation-mediated dissociation. We present a detailed, first-principles-based theoretical study to investigate the mechanism of the tunneling-induced O2 dynamics, including the origin of the observed threshold voltages, the pathway dependence, and the rate of O2 dissociation. Results show a direct correspondence between the observed threshold voltage for a process and the activation energy for that process. The pathway selectivity arises from a competition between the voltage-modified barrier heights for rotation and dissociation, and the coupling strength of the tunneling electrons to the rotational and vibrational modes of the adsorbed molecule. Finally, we explore the "dipole" and "resonance" mechanisms of inelastic electron tunneling to elucidate the energy transfer between the tunneling electrons and chemisorbed O2.

  5. Molecular tilt-dependent and tyrosine-enhanced electron transfer across ITO/SAM/[DPPC–Au NP–Tyrosine] Janus nanoparticle junction

    Energy Technology Data Exchange (ETDEWEB)

    Sarangi, Nirod Kumar; Patnaik, Archita, E-mail: archita59@yahoo.com [Indian Institute of Technology Madras, Department of Chemistry (India)

    2016-09-15

    Enhanced interfacial electron transfer (ET) across the otherwise insulating indium tin oxide/alkanethiol self-assembled monolayer (SAM)/redox molecule junction was accomplished when a Janus gold nanoparticle (JNP) protected by bioinspired phosphatidylcholine (DPPC) lipid and tyrosine amino acid ligands was anchored on it. In addition to the most theoretical and experimental investigations on the distance-dependent ET across Metal–Organic SAM–Nanoparticle (NP) architectures, the current results succinctly illustrate molecular tilt angle of the SAM and the characteristic of JNP as key factors in expediting the ET rate via electron tunneling. In the absence of JNP, electron tunneling with a tunneling factor β = 1.1 Å{sup −1} across the SAM was the rate-limiting step, evidenced from electrochemical impedance spectroscopy (EIS). The apparent electron transfer rate constant (k{sub app}{sup 0}) for anchored SAM was enhanced by at least one order of magnitude than the DPPC-only protected nanoparticle, suggesting the potential role of tyrosine towards the enhanced ET. The asymmetric and biogenic nature of the construct sheds light on a potential bioelectronic device for novel electronic attributes.Graphical abstractEntry of TOC .

  6. Molecular diagnostics for the Sigatoka disease complex of banana

    NARCIS (Netherlands)

    Arzanlou, M.; Abeln, E.C.A.; Kema, G.H.J.; Waalwijk, C.; Carlier, J.; Crous, P.W.

    2007-01-01

    The Sigatoka disease complex of banana involves three related ascomycetous fungi, Mycosphaerella fijiensis, M. musicola, and M. eumusae. The exact distribution of these three species and their disease epidemiology remain unclear, because their symptoms and life cycles are rather similar. Disease

  7. In silico simulations of tunneling barrier measurements for molecular orbital-mediated junctions: A molecular orbital theory approach to scanning tunneling microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Terryn, Raymond J.; Sriraman, Krishnan; Olson, Joel A., E-mail: jolson@fit.edu; Baum, J. Clayton, E-mail: cbaum@fit.edu [Department of Chemistry, Florida Institute of Technology, 150 West University Boulevard, Melbourne, Florida 32901 (United States); Novak, Mark J. [Department of Chemistry and Applied Biological Sciences, South Dakota School of Mines and Technology, 501 E. Saint Joseph Street, Rapid City, South Dakota 57701 (United States)

    2016-09-15

    A new simulator for scanning tunneling microscopy (STM) is presented based on the linear combination of atomic orbitals molecular orbital (LCAO-MO) approximation for the effective tunneling Hamiltonian, which leads to the convolution integral when applied to the tip interaction with the sample. This approach intrinsically includes the structure of the STM tip. Through this mechanical emulation and the tip-inclusive convolution model, dI/dz images for molecular orbitals (which are closely associated with apparent barrier height, ϕ{sub ap}) are reported for the first time. For molecular adsorbates whose experimental topographic images correspond well to isolated-molecule quantum chemistry calculations, the simulator makes accurate predictions, as illustrated by various cases. Distortions in these images due to the tip are shown to be in accord with those observed experimentally and predicted by other ab initio considerations of tip structure. Simulations of the tunneling current dI/dz images are in strong agreement with experiment. The theoretical framework provides a solid foundation which may be applied to LCAO cluster models of adsorbate–substrate systems, and is extendable to emulate several aspects of functional STM operation.

  8. In silico simulations of tunneling barrier measurements for molecular orbital-mediated junctions: A molecular orbital theory approach to scanning tunneling microscopy

    International Nuclear Information System (INIS)

    Terryn, Raymond J.; Sriraman, Krishnan; Olson, Joel A.; Baum, J. Clayton; Novak, Mark J.

    2016-01-01

    A new simulator for scanning tunneling microscopy (STM) is presented based on the linear combination of atomic orbitals molecular orbital (LCAO-MO) approximation for the effective tunneling Hamiltonian, which leads to the convolution integral when applied to the tip interaction with the sample. This approach intrinsically includes the structure of the STM tip. Through this mechanical emulation and the tip-inclusive convolution model, dI/dz images for molecular orbitals (which are closely associated with apparent barrier height, ϕ_a_p) are reported for the first time. For molecular adsorbates whose experimental topographic images correspond well to isolated-molecule quantum chemistry calculations, the simulator makes accurate predictions, as illustrated by various cases. Distortions in these images due to the tip are shown to be in accord with those observed experimentally and predicted by other ab initio considerations of tip structure. Simulations of the tunneling current dI/dz images are in strong agreement with experiment. The theoretical framework provides a solid foundation which may be applied to LCAO cluster models of adsorbate–substrate systems, and is extendable to emulate several aspects of functional STM operation.

  9. Library of molecular associations: curating the complex molecular basis of liver diseases

    Directory of Open Access Journals (Sweden)

    Maass Thorsten

    2010-03-01

    Full Text Available Abstract Background Systems biology approaches offer novel insights into the development of chronic liver diseases. Current genomic databases supporting systems biology analyses are mostly based on microarray data. Although these data often cover genome wide expression, the validity of single microarray experiments remains questionable. However, for systems biology approaches addressing the interactions of molecular networks comprehensive but also highly validated data are necessary. Results We have therefore generated the first comprehensive database for published molecular associations in human liver diseases. It is based on PubMed published abstracts and aimed to close the gap between genome wide coverage of low validity from microarray data and individual highly validated data from PubMed. After an initial text mining process, the extracted abstracts were all manually validated to confirm content and potential genetic associations and may therefore be highly trusted. All data were stored in a publicly available database, Library of Molecular Associations http://www.medicalgenomics.org/databases/loma/news, currently holding approximately 1260 confirmed molecular associations for chronic liver diseases such as HCC, CCC, liver fibrosis, NASH/fatty liver disease, AIH, PBC, and PSC. We furthermore transformed these data into a powerful resource for molecular liver research by connecting them to multiple biomedical information resources. Conclusion Together, this database is the first available database providing a comprehensive view and analysis options for published molecular associations on multiple liver diseases.

  10. Linker-dependent Junction Formation Probability in Single-Molecule Junctions

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Pil Sun; Kim, Taekyeong [HankukUniversity of Foreign Studies, Yongin (Korea, Republic of)

    2015-01-15

    We compare the junction formation probabilities of single-molecule junctions with different linker molecules by using a scanning tunneling microscope-based break-junction technique. We found that the junction formation probability varies as SH > SMe > NH2 for the benzene backbone molecule with different types of anchoring groups, through quantitative statistical analysis. These results are attributed to different bonding forces according to the linker groups formed with Au atoms in the electrodes, which is consistent with previous works. Our work allows a better understanding of the contact chemistry in the metal.molecule junction for future molecular electronic devices.

  11. Molecular complexes of tungsten oxotetrachloride with azomethins. Molekulyarnye kompleksy oksotetrakhlorida vol'frama s azometinami

    Energy Technology Data Exchange (ETDEWEB)

    Abramenko, Yu V; Garnovskij, A D; Abramenko, V A; Medvedeva, T E [Rostovskij-na-Donu Gosudarstvennyj Univ., Rostov-na-Donu (Russian Federation). Nauchno-Issledovatel' skij Inst. Fizicheskoj i Organicheskoj Khimii

    1992-09-01

    Series of new molecular complexes of tungsten oxotetrachloride with benza- and salicylalimines of equimolar compositions obtained. Substances are studied using element analysis, IR spectroscopy and conductometry. Octahedral structure of complexes with central atom coordination of benzalaniline molecules via azomethin nitrogen atom, and salicylalimines - via carbonyl oxygen atom of quinoid tantometric form of ligand is assumed.

  12. Confirmation of molecular formulas of metallic complexes through X-ray fluorescence quantitative analysis

    International Nuclear Information System (INIS)

    Filgueiras, C.A.L.; Marques, E.V.; Machado, R.M.

    1984-01-01

    X-ray fluorescence spectrophotometry was employed to determined the metal content in a series of five transition element complexes (Mn, Ti, Zn, V). The results confirmed the molecular formulas of these complexes, already proposed on the basis of elemental microanalysis, solution condutimetry and other analytical methods. (C.L.B.) [pt

  13. Cyclodextrin--piroxicam inclusion complexes: analyses by mass spectrometry and molecular modelling

    Science.gov (United States)

    Gallagher, Richard T.; Ball, Christopher P.; Gatehouse, Deborah R.; Gates, Paul J.; Lobell, Mario; Derrick, Peter J.

    1997-11-01

    Mass spectrometry has been used to investigate the natures of non-covalent complexes formed between the anti-inflammatory drug piroxicam and [alpha]-, [beta]- and [gamma]-cyclodextrins. Energies of these complexes have been calculated by means of molecular modelling. There is a correlation between peak intensities in the mass spectra and the calculated energies.

  14. Single Molecule Nanoelectrochemistry in Electrical Junctions.

    Science.gov (United States)

    Nichols, Richard J; Higgins, Simon J

    2016-11-15

    gating. This has been referred to as to a "single molecule transistor configuration" with the gate voltage being provided by the controllable potential achieved through the electrochemical double layer. It is shown how the electrolyte medium can control such gating, with ionic liquids providing more efficient gate coupling than aqueous electrolytes. Control of the conductance of viologen molecular wires can also be achieved by encapsulating the viologen redox moiety within a molecular cage, thereby controlling its immediate environment. Molecular conductance can also be gated through multiple redox states. This has been shown for the redox moiety pyrrolo-tetrathiafulvalene, which undergoes single molecule electrochemical transistor gating through three redox states in molecular junctions. Charge transport through this junction follows a two-step hopping mechanism, demonstrating the role of the redox center in electron transfer across the molecular bridge. Recent electrolyte gating studies of rigid, conjugated redox-active metal complexes with tailored terpyridine coordinating ligands and anchors are also presented. These aforementioned studies have all been performed with gold electrode contacts. The Account concludes with recent data showing that it is now possible to study single molecule electrochemical gating with nickel electrodes. This opens up new perspectives for studying interfacial charge transfer with a wide variety of other electrode materials including semiconductor electrodes and also points toward future opportunities for coupling molecular spintronics and nanoelectrochemistry.

  15. Measuring pair-wise molecular interactions in a complex mixture

    Science.gov (United States)

    Chakraborty, Krishnendu; Varma, Manoj M.; Venkatapathi, Murugesan

    2016-03-01

    Complex biological samples such as serum contain thousands of proteins and other molecules spanning up to 13 orders of magnitude in concentration. Present measurement techniques do not permit the analysis of all pair-wise interactions between the components of such a complex mixture to a given target molecule. In this work we explore the use of nanoparticle tags which encode the identity of the molecule to obtain the statistical distribution of pair-wise interactions using their Localized Surface Plasmon Resonance (LSPR) signals. The nanoparticle tags are chosen such that the binding between two molecules conjugated to the respective nanoparticle tags can be recognized by the coupling of their LSPR signals. This numerical simulation is done by DDA to investigate this approach using a reduced system consisting of three nanoparticles (a gold ellipsoid with aspect ratio 2.5 and short axis 16 nm, and two silver ellipsoids with aspect ratios 3 and 2 and short axes 8 nm and 10 nm respectively) and the set of all possible dimers formed between them. Incident light was circularly polarized and all possible particle and dimer orientations were considered. We observed that minimum peak separation between two spectra is 5 nm while maximum is 184nm.

  16. Phospho-regulated Drosophila adducin is a determinant of synaptic plasticity in a complex with Dlg and PIP2 at the larval neuromuscular junction

    Directory of Open Access Journals (Sweden)

    Simon Ji Hau Wang

    2014-11-01

    Full Text Available Adducin is a ubiquitously expressed actin- and spectrin-binding protein involved in cytoskeleton organization, and is regulated through phosphorylation of the myristoylated alanine-rich C-terminal kinase (MARCKS-homology domain by protein kinase C (PKC. We have previously shown that the Drosophila adducin, Hu-li tai shao (Hts, plays a role in larval neuromuscular junction (NMJ growth. Here, we find that the predominant isoforms of Hts at the NMJ contain the MARCKS-homology domain, which is important for interactions with Discs large (Dlg and phosphatidylinositol 4,5-bisphosphate (PIP2. Through the use of Proximity Ligation Assay (PLA, we show that the adducin-like Hts isoforms are in complexes with Dlg and PIP2 at the NMJ. We provide evidence that Hts promotes the phosphorylation and delocalization of Dlg at the NMJ through regulation of the transcript distribution of the PAR-1 and CaMKII kinases in the muscle. We also show that Hts interactions with Dlg and PIP2 are impeded through phosphorylation of the MARCKS-homology domain. These results are further evidence that Hts is a signaling-responsive regulator of synaptic plasticity in Drosophila.

  17. A Point Mutation in the Exon Junction Complex Factor Y14 Disrupts Its Function in mRNA Cap Binding and Translation Enhancement*

    Science.gov (United States)

    Chuang, Tzu-Wei; Lee, Kuo-Ming; Lou, Yuan-Chao; Lu, Chia-Chen; Tarn, Woan-Yuh

    2016-01-01

    Eukaryotic mRNA biogenesis involves a series of interconnected steps mediated by RNA-binding proteins. The exon junction complex core protein Y14 is required for nonsense-mediated mRNA decay (NMD) and promotes translation. Moreover, Y14 binds the cap structure of mRNAs and inhibits the activity of the decapping enzyme Dcp2. In this report, we show that an evolutionarily conserved tryptophan residue (Trp-73) of Y14 is critical for its binding to the mRNA cap structure. A Trp-73 mutant (W73V) bound weakly to mRNAs and failed to protect them from degradation. However, this mutant could still interact with the NMD and mRNA degradation factors and retained partial NMD activity. In addition, we found that the W73V mutant could not interact with translation initiation factors. Overexpression of W73V suppressed reporter mRNA translation in vitro and in vivo and reduced the level of a set of nascent proteins. These results reveal a residue of Y14 that confers cap-binding activity and is essential for Y14-mediated enhancement of translation. Finally, we demonstrated that Y14 may selectively and differentially modulate protein biosynthesis. PMID:26887951

  18. Increase in Complexity and Information through Molecular Evolution

    Directory of Open Access Journals (Sweden)

    Peter Schuster

    2016-11-01

    Full Text Available Biological evolution progresses by essentially three different mechanisms: (I optimization of properties through natural selection in a population of competitors; (II development of new capabilities through cooperation of competitors caused by catalyzed reproduction; and (III variation of genetic information through mutation or recombination. Simplified evolutionary processes combine two out of the three mechanisms: Darwinian evolution combines competition (I and variation (III and is represented by the quasispecies model, major transitions involve cooperation (II of competitors (I, and the third combination, cooperation (II and variation (III provides new insights in the role of mutations in evolution. A minimal kinetic model based on simple molecular mechanisms for reproduction, catalyzed reproduction and mutation is introduced, cast into ordinary differential equations (ODEs, and analyzed mathematically in form of its implementation in a flow reactor. Stochastic aspects are investigated through computer simulation of trajectories of the corresponding chemical master equations. The competition-cooperation model, mechanisms (I and (II, gives rise to selection at low levels of resources and leads to symbiontic cooperation in case the material required is abundant. Accordingly, it provides a kind of minimal system that can undergo a (major transition. Stochastic effects leading to extinction of the population through self-enhancing oscillations destabilize symbioses of four or more partners. Mutations (III are not only the basis of change in phenotypic properties but can also prevent extinction provided the mutation rates are sufficiently large. Threshold phenomena are observed for all three combinations: The quasispecies model leads to an error threshold, the competition-cooperation model allows for an identification of a resource-triggered bifurcation with the transition, and for the cooperation-mutation model a kind of stochastic threshold for

  19. Flexible 2D layered material junctions

    Science.gov (United States)

    Balabai, R.; Solomenko, A.

    2018-03-01

    Within the framework of the methods of the electron density functional and the ab initio pseudopotential, we have obtained the valence electron density spatial distribution, the densities of electron states, the widths of band gaps, the charges on combined regions, and the Coulomb potentials for graphene-based flexible 2D layered junctions, using author program complex. It is determined that the bending of the 2D layered junctions on the angle α leads to changes in the electronic properties of these junctions. In the graphene/graphane junction, there is clear charge redistribution with different signs in the regions of junctions. The presence in the heterojunctions of charge regions with different signs leads to the formation of potential barriers. The greatest potential jump is in the graphene/fluorographene junction. The greatest value of the band gap width is in the graphene/graphane junction.

  20. Identifying Slow Molecular Motions in Complex Chemical Reactions.

    Science.gov (United States)

    Piccini, GiovanniMaria; Polino, Daniela; Parrinello, Michele

    2017-09-07

    We have studied the cyclization reaction of deprotonated 4-chloro-1-butanethiol to tetrahydrothiophene by means of well-tempered metadynamics. To properly select the collective variables, we used the recently proposed variational approach to conformational dynamics within the framework of metadyanmics. This allowed us to select the appropriate linear combinations from a set of collective variables representing the slow degrees of freedom that best describe the slow modes of the reaction. We performed our calculations at three different temperatures, namely, 300, 350, and 400 K. We show that the choice of such collective variables allows one to easily interpret the complex free-energy surface of such a reaction by univocal identification of the conformers belonging to reactants and product states playing a fundamental role in the reaction mechanism.

  1. Alkynes as a versatile platform for construction of chemical molecular complexity and realization of molecular 3D printing

    International Nuclear Information System (INIS)

    Galkin, K I; Ananikov, V P

    2016-01-01

    The current level of scientific and technological development requires the formation of general tools and techniques. One of the most versatile technologies is 3D printing, which allows fast and efficient creation of materials and biological objects of desired shape and composition. Today, methods have been developed for 3D printing of macro- and nano-sized objects and for production of films and deposited materials with molecular precision but the most promising technology is printing at the molecular level (molecular 3D printing) for the purpose of direct construction of molecular complexity. This process is currently at the initial stage concerning selection of simple molecules to be used as building blocks possessing flexibility, availability and ease of modification. In this review, we examine the possible versatile synthons suitable for preparation of the main types of organic compounds using molecular 3D printing. The surveyed data strongly indicate that alkyne molecules may be used as a building material in a molecular 3D printer working on hydrocarbons. The bibliography includes 428 references

  2. Seroepidemiology and molecular diversity of Leishmania donovani complex in Georgia.

    Science.gov (United States)

    Babuadze, Giorgi; Farlow, Jason; de Koning, Harry P; Carrillo, Eugenia; Chakhunashvili, Giorgi; Murskvaladze, Mari; Kekelidze, Merab; Karseladze, Irakli; Kokaia, Nora; Kalandadze, Irine; Tsereteli, David; Markhvashvili, Ivane; Sidamonidze, Ketevan; Chanturia, Gvantsa; Adeishvili, Ekaterine; Imnadze, Paata

    2016-05-13

    Leishmaniasis includes multiple clinical syndromes, most notably visceral, cutaneous, and mucosal forms. Visceral leishmaniasis (VL), also known as kala-azar, is a potentially fatal disease endemic to large parts of Africa and Asia, and in South-Eastern Europe (Greece, Turkey, Georgia). Visceral leishmaniasis is a parasitic zoonosis caused by species of the L. donovani complex. In the classical epidemiological model the main reservoir for VL are canines. The study included a cohort of 513 individuals of both genders (190 males and 323 females) from the ages of 1 to 70 years that were screened in ten villages across two districts in Kakheti using the Kalazar Detect™ rK39 rapid diagnostic test. The phylogenetic diversity patterns of local strains, based on the rDNA internal transcribed spacer (ITS) sequences, were assessed for samples obtained from patients with suspected L. donovani infection, from canine reservoirs and from Phlebotomus sand flies obtained from different geographical areas of Georgia and from Azerbaijan. Out of a total of 600 domestic dog blood samples 95 (15.8 %) were positive by rK39 rapid diagnostic tests. For symptomatic domestic dogs, the testing of conjunctival swabs or bone marrow aspirates revealed a higher VL incidence in Kvareli District (Kvareli; 19.4 %, n = 329) compared with that observed for Sagarejo District (Sagarejo; 11.4 %, n = 271). A total of 231 sand flies of both genders were collected during the 2-month period; of the 114 females, 1.75 % were PCR positive for the presence of Leishmania spp. VL infection rates remain high in both canines and humans in Georgia, with disease in several known natural foci. The genetic relationships derived from rDNA internal transcribed spacer (ITS) sequence comparisons identified genetic subgroups, revealing preliminary insights into the genetic structure of L. donovani complex members currently circulating in the South Caucasus and demonstrates the utility of ITS-based genotyping

  3. MOLECULAR COMPLEXES OF SULPHUR DIOXIDE WITH N,O-CONTAINING ORGANIC BASES (REVIEW

    Directory of Open Access Journals (Sweden)

    R. E. Khoma

    2016-10-01

    Full Text Available The literature data on the synthesis, stoichiometry, structure and relative stability of molecular  complexes of sulphur dioxide with N,O-containing organic bases have been systematized and  generalized. It was shown that the yield of the reaction product of sulfur dioxide with organic  bases (such as amines are strongly influenced by the conditions of synthesis: the nature of  the solvent (basicity, polarity, the temperature and SO2:L ratio in the reaction medium. The stoichiometry of SO2*nL molecular complexes depends on ligand denticity, as well as its  ability to H-bonding. The reaction of the sulfur oxide (IV with organic bases can give S←N and S←O complexes. With the increase of the value of base proton affinity the decrease ΔrSN values has been marked. Characteristic parameter Δr SN = r SN – a1(rS+ rN (where rSNis the S←N donor-acceptor bond length has been determined by microwave spectroscopy and X-ray analysis, rSand rNwere the tabulated values of the homopolar covalent radii of sulphur and nitrogen heteroatoms. The dependence of formation enthalpy of molecular complexes of basic amines and spectral characteristics has been noted; enthalpy-entropy compensation for S←N and S←O complex-es has been stated. Despite the limited experimental data on the thermodynamics of complex formation and the lengths of donor-acceptor bonds for the same compounds it has been found bond S←N strength in SO2 molecular complexes to depend on the intrinsic value of ΔrSN. The contribution of van der Waals forces and charge transfer forces to the formation of molecular complexes of sulphur dioxide has been stated.

  4. The Dissolution of Double Holliday Junctions

    DEFF Research Database (Denmark)

    Bizard, Anna H; Hickson, Ian D

    2014-01-01

    as "double Holliday junction dissolution." This reaction requires the cooperative action of a so-called "dissolvasome" comprising a Holliday junction branch migration enzyme (Sgs1/BLM RecQ helicase) and a type IA topoisomerase (Top3/TopoIIIα) in complex with its OB (oligonucleotide/oligosaccharide binding......Double Holliday junctions (dHJS) are important intermediates of homologous recombination. The separate junctions can each be cleaved by DNA structure-selective endonucleases known as Holliday junction resolvases. Alternatively, double Holliday junctions can be processed by a reaction known......) fold containing accessory factor (Rmi1). This review details our current knowledge of the dissolution process and the players involved in catalyzing this mechanistically complex means of completing homologous recombination reactions....

  5. Evidence for a hopping mechanism in metal|single molecule|metal junctions involving conjugated metal–terpyridyl complexes; potential-dependent conductances of complexes [M(pyterpy)2]2+(M = Co and Fe; pyterpy = 4′-(pyridin-4-yl)-2,2′:6′,2′′-terpyridine) in ionic liquid

    DEFF Research Database (Denmark)

    Chappell, Sarah; Brooke, Carly; Nichols, Richard John

    2016-01-01

    Extensive studies of various families of conjugated molecules in metal|molecule|metal junctions suggest that the mechanism of conductance is usually tunnelling for molecular lengths < ca. 4 nm, and that for longer molecules, coherence is lost as a hopping element becomes more significant. In this...

  6. Carbon Nanotubes: Molecular Electronic Components

    Science.gov (United States)

    Srivastava, Deepak; Saini, Subhash; Menon, Madhu

    1997-01-01

    The carbon Nanotube junctions have recently emerged as excellent candidates for use as the building blocks in the formation of nanoscale molecular electronic networks. While the simple joint of two dissimilar tubes can be generated by the introduction of a pair of heptagon-pentagon defects in an otherwise perfect hexagonal graphene sheet, more complex joints require other mechanisms. In this work we explore structural characteristics of complex 3-point junctions of carbon nanotubes using a generalized tight-binding molecular-dynamics scheme. The study of pi-electron local densities of states (LDOS) of these junctions reveal many interesting features, most prominent among them being the defect-induced states in the gap.

  7. Complexation and molecular modeling studies of europium(III)-gallic acid-amino acid complexes.

    Science.gov (United States)

    Taha, Mohamed; Khan, Imran; Coutinho, João A P

    2016-04-01

    With many metal-based drugs extensively used today in the treatment of cancer, attention has focused on the development of new coordination compounds with antitumor activity with europium(III) complexes recently introduced as novel anticancer drugs. The aim of this work is to design new Eu(III) complexes with gallic acid, an antioxida'nt phenolic compound. Gallic acid was chosen because it shows anticancer activity without harming health cells. As antioxidant, it helps to protect human cells against oxidative damage that implicated in DNA damage, cancer, and accelerated cell aging. In this work, the formation of binary and ternary complexes of Eu(III) with gallic acid, primary ligand, and amino acids alanine, leucine, isoleucine, and tryptophan was studied by glass electrode potentiometry in aqueous solution containing 0.1M NaNO3 at (298.2 ± 0.1) K. Their overall stability constants were evaluated and the concentration distributions of the complex species in solution were calculated. The protonation constants of gallic acid and amino acids were also determined at our experimental conditions and compared with those predicted by using conductor-like screening model for realistic solvation (COSMO-RS) model. The geometries of Eu(III)-gallic acid complexes were characterized by the density functional theory (DFT). The spectroscopic UV-visible and photoluminescence measurements are carried out to confirm the formation of Eu(III)-gallic acid complexes in aqueous solutions. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Vibrationally coupled electron transport through single-molecule junctions

    Energy Technology Data Exchange (ETDEWEB)

    Haertle, Rainer

    2012-04-26

    vibrational effects have a profound influence on the transport characteristics of a single-molecule contact and play therefore a fundamental role in this transport problem. Our findings demonstrate that vibrationally coupled electron transport through a molecular junction involves two types of processes: (i) transport processes, where an electron tunnels through the molecular bridge from one lead to the other, and (ii) electron-hole pair creation processes, where an electron tunnels from one of the leads onto the molecular bridge and back to the same lead again. Transport processes directly contribute to the electrical current flowing through a molecular contact and involve both excitation and deexcitation processes of the vibrational modes of the junction. Electron-hole pair creation processes do not directly contribute to the electrical current and typically involve only deexcitation processes. Nevertheless, they constitute a cooling mechanism for the vibrational modes of a single-molecule junction that is as important as cooling by transport processes. As the level of vibrational excitation determines the efficiency of electron transport processes, they have an indirect influence on the electrical current flowing through the junction. As we show, however, this influence can be substantial, in particular, if the molecule is coupled asymmetrically to the leads. Accounting for all these processes and their complex interrelationship, we analyze a number of intriguing transport phenomena, including rectification, negative differential resistance, anomalous peak broadening, mode-selective vibrational excitation and vibrationally induced decoherence. Moreover, we show that higher levels of vibrational excitation are obtained for weaker electronic-vibrational coupling. Thus, based on physical grounds, we establish a relation between the weak electronic-vibrational coupling limit and the limit of large bias voltages, where the level of vibrational excitation in a molecular junction

  9. Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes

    Directory of Open Access Journals (Sweden)

    Le Novère Nicolas

    2010-03-01

    Full Text Available Abstract Background Most cellular signal transduction mechanisms depend on a few molecular partners whose roles depend on their position and movement in relation to the input signal. This movement can follow various rules and take place in different compartments. Additionally, the molecules can form transient complexes. Complexation and signal transduction depend on the specific states partners and complexes adopt. Several spatial simulator have been developed to date, but none are able to model reaction-diffusion of realistic multi-state transient complexes. Results Meredys allows for the simulation of multi-component, multi-feature state molecular species in two and three dimensions. Several compartments can be defined with different diffusion and boundary properties. The software employs a Brownian dynamics engine to simulate reaction-diffusion systems at the reactive particle level, based on compartment properties, complex structure, and hydro-dynamic radii. Zeroth-, first-, and second order reactions are supported. The molecular complexes have realistic geometries. Reactive species can contain user-defined feature states which can modify reaction rates and outcome. Models are defined in a versatile NeuroML input file. The simulation volume can be split in subvolumes to speed up run-time. Conclusions Meredys provides a powerful and versatile way to run accurate simulations of molecular and sub-cellular systems, that complement existing multi-agent simulation systems. Meredys is a Free Software and the source code is available at http://meredys.sourceforge.net/.

  10. Prediction of complexes of uranyl and organic substances by molecular orbital calculation

    International Nuclear Information System (INIS)

    Nagasaki, S.; Tsushima, S.; Todoriki, M.; Tanaka, S.; Suzuki, A.

    1999-01-01

    Structure of UO 2 2+ complexes with salicylic acid was optimized by using molecular orbital calculation (ab initio method). The bond distances between U and O atoms (O eq ) of carboxyl group and phenyl group in salicylic acid were evaluated and compared with those measured experimentally by Denecke et al. The calculated distance relatively agrees with the experimental one. The frontier electron densities in the complexes were also calculated. Strong localization of frontier electron density in the complexes was not observed, suggesting that the complexes are subject to only weak interactions with rocks, minerals and other compounds in the geosphere. (author)

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

    Science.gov (United States)

    Yang, Xiaozhou; Li, Yanxiao

    2016-01-15

    This paper reported a diamine ligand and its Re(I) complex for potential application in oxygen sensing. The novelty of this diamine ligand localized at its increased conjugation chain which had a typical electron-withdrawing group of 1,3,4-oxadiazole. Electronic distribution of excited electrons and their lifetime were supposed to be increased, favoring oxygen sensing collision. This hypothesis was confirmed by single crystal analysis, theoretical calculation and photophysical measurement. It was found that this Re(I) complex had a long-lived emission peaking at 545 nm, favoring sensing application. By doping this complex into a silica matrix MCM-41, oxygen sensing performance and mechanism of the resulting composites were discussed in detail. Non-linear Stern-Volmer working curves were observed with maximum sensitivity of 5.54 and short response time of ~6 s. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Fullerene Derived Molecular Electronic Devices

    Science.gov (United States)

    Menon, Madhu; Srivastava, Deepak; Saini, Subbash

    1998-01-01

    The carbon Nanotube junctions have recently emerged as excellent candidates for use as the building blocks in the formation of nanoscale electronic devices. While the simple joint of two dissimilar tubes can be generated by the introduction of a pair of heptagon-pentagon defects in an otherwise perfect hexagonal grapheme sheet, more complex joints require other mechanisms. In this work we explore structural and electronic properties of complex 3-point junctions of carbon nanotubes using a generalized tight-binding molecular-dynamics scheme.

  13. Low-Frequency Carbon Recombination Lines in the Orion Molecular Cloud Complex

    Science.gov (United States)

    Tremblay, Chenoa D.; Jordan, Christopher H.; Cunningham, Maria; Jones, Paul A.; Hurley-Walker, Natasha

    2018-05-01

    We detail tentative detections of low-frequency carbon radio recombination lines from within the Orion molecular cloud complex observed at 99-129 MHz. These tentative detections include one alpha transition and one beta transition over three locations and are located within the diffuse regions of dust observed in the infrared at 100 μm, the Hα emission detected in the optical, and the synchrotron radiation observed in the radio. With these observations, we are able to study the radiation mechanism transition from collisionally pumped to radiatively pumped within the H ii regions within the Orion molecular cloud complex.

  14. Inclusion Complexes of Sunscreen Agents with β-Cyclodextrin: Spectroscopic and Molecular Modeling Studies

    Directory of Open Access Journals (Sweden)

    Nathir A. F. Al-Rawashdeh

    2013-01-01

    Full Text Available The inclusion complexes of selected sunscreen agents, namely, oxybenzone (Oxy, octocrylene (Oct, and ethylhexyl-methoxycinnamate (Cin with β-cyclodextrin (β-CD were studied by UV-Vis spectroscopy, differential scanning calorimetry (DSC, 13C NMR techniques, and molecular mechanics (MM calculations and modeling. Molecular modeling (MM study of the entire process of the formation of 1 : 1 stoichiometry sunscreen agent/β-cyclodextrin structures has been used to contribute to the understanding and rationalization of the experimental results. Molecular mechanics calculations, together with 13C NMR measurements, for the complex with β-CD have been used to describe details of the structural, energetic, and dynamic features of host-guest complex. Accurate structures of CD inclusion complexes have been derived from molecular mechanics (MM calculations and modeling. The photodegradation reaction of the sunscreen agents' molecules in lotion was explored using UV-Vis spectroscopy. It has been demonstrated that the photostability of these selected sunscreen agents has been enhanced upon forming inclusion complexes with β-CD in lotion. The results of this study demonstrate that β-CD can be utilized as photostabilizer additive for enhancing the photostability of the selected sunscreen agents' molecules.

  15. Electron transport in molecular junctions

    DEFF Research Database (Denmark)

    Jin, Chengjun

    on the benzene-diamine (BDA) molecule has furthermore been studied and it is found that the correct energy level alignment for the BDA molecule in Au contacts is only captured by the GW approach. Consequently, the GW approach provides an accurate description for the conductance change resulting from the side...... groups. The failure of the DFT based description is due to the strong energy level pinning when the BDA molecule is in contact with Au contacts. The effect of contact geometries on the conductance and the thermopower has also been addressed. It is found that both GW and the DFT+∑ with a certain image...

  16. The Ly6 protein coiled is required for septate junction and blood brain barrier organisation in Drosophila.

    Directory of Open Access Journals (Sweden)

    Assia Hijazi

    Full Text Available BACKGROUND: Genetic analysis of the Drosophila septate junctions has greatly contributed to our understanding of the mechanisms controlling the assembly of these adhesion structures, which bear strong similarities with the vertebrate tight junctions and the paranodal septate junctions. These adhesion complexes share conserved molecular components and have a common function: the formation of paracellular barriers restraining the diffusion of solutes through epithelial and glial envelopes. METHODOLOGY/PRINCIPAL FINDINGS: In this work we characterise the function of the Drosophila cold gene, that codes for a protein belonging to the Ly6 superfamily of extracellular ligands. Analysis of cold mutants shows that this gene is specifically required for the organisation of the septate junctions in epithelial tissues and in the nervous system, where its contribution is essential for the maintenance of the blood-brain barrier. We show that cold acts in a cell autonomous way, and we present evidence indicating that this protein could act as a septate junction component. CONCLUSION/SIGNIFICANCE: We discuss the specific roles of cold and three other Drosophila members of the Ly6 superfamily that have been shown to participate in a non-redundant way in the process of septate junction assembly. We propose that vertebrate Ly6 proteins could fulfill analogous roles in tight junctions and/or paranodal septate junctions.

  17. The Ly6 protein coiled is required for septate junction and blood brain barrier organisation in Drosophila.

    Science.gov (United States)

    Hijazi, Assia; Haenlin, Marc; Waltzer, Lucas; Roch, Fernando

    2011-03-15

    Genetic analysis of the Drosophila septate junctions has greatly contributed to our understanding of the mechanisms controlling the assembly of these adhesion structures, which bear strong similarities with the vertebrate tight junctions and the paranodal septate junctions. These adhesion complexes share conserved molecular components and have a common function: the formation of paracellular barriers restraining the diffusion of solutes through epithelial and glial envelopes. In this work we characterise the function of the Drosophila cold gene, that codes for a protein belonging to the Ly6 superfamily of extracellular ligands. Analysis of cold mutants shows that this gene is specifically required for the organisation of the septate junctions in epithelial tissues and in the nervous system, where its contribution is essential for the maintenance of the blood-brain barrier. We show that cold acts in a cell autonomous way, and we present evidence indicating that this protein could act as a septate junction component. We discuss the specific roles of cold and three other Drosophila members of the Ly6 superfamily that have been shown to participate in a non-redundant way in the process of septate junction assembly. We propose that vertebrate Ly6 proteins could fulfill analogous roles in tight junctions and/or paranodal septate junctions.

  18. Identification of MarvelD3 as a tight junction-associated transmembrane protein of the occludin family

    Directory of Open Access Journals (Sweden)

    Balda Maria S

    2009-12-01

    Full Text Available Abstract Background Tight junctions are an intercellular adhesion complex of epithelial and endothelial cells, and form a paracellular barrier that restricts the diffusion of solutes on the basis of size and charge. Tight junctions are formed by multiprotein complexes containing cytosolic and transmembrane proteins. How these components work together to form functional tight junctions is still not well understood and will require a complete understanding of the molecular composition of the junction. Results Here we identify a new transmembrane component of tight junctions: MarvelD3, a four-span transmembrane protein. Its predicted transmembrane helices form a Marvel (MAL and related proteins for vesicle traffic and membrane link domain, a structural motif originally discovered in proteins involved in membrane apposition and fusion events, such as the tight junction proteins occludin and tricellulin. In mammals, MarvelD3 is expressed as two alternatively spliced isoforms. Both isoforms exhibit a broad tissue distribution and are expressed by different types of epithelial as well as endothelial cells. MarvelD3 co-localises with occludin at tight junctions in intestinal and corneal epithelial cells. RNA interference experiments in Caco-2 cells indicate that normal MarvelD3 expression is not required for the formation of functional tight junctions but depletion results in monolayers with increased transepithelial electrical resistance. Conclusions Our data indicate that MarvelD3 is a third member of the tight junction-associated occludin family of transmembrane proteins. Similar to occludin, normal expression of MarvelD3 is not essential for the formation of functional tight junctions. However, MarvelD3 functions as a determinant of epithelial paracellular permeability properties.

  19. Magnetic resonance and fluorescence studies on pyruvate dehydrogenase complexes and their small molecular weight constituents

    NARCIS (Netherlands)

    Grande, H.J.

    1976-01-01

    The articles presented in this thesis do not describe at first glance one well-defined subject. They are, however, in fact connected by one central theme: the study of large enzyme aggregates by molecular physical methods. Chosen was the pyruvate dehydrogenase complex (PDC) because of its

  20. Molecular details of ovalbumin-pectin complexes at the air/water interface: A spectroscopic study

    NARCIS (Netherlands)

    Kudryashova, E.V.; Visser, A.J.W.G.; Hoek, A. van; Jongh, H.H.J. de

    2007-01-01

    To stabilize air-water interfaces, as in foams, the adsorption of surface-active components is a prerequisite. An approach to controlling the surface activity of proteins is noncovalent complex formation with a polyelectrolyte in the bulk phase. The molecular properties of egg white ovalbumin in a

  1. Molecular details of ovalbumin-pectin complexes at the air/water interface: a spectroscopic study.

    NARCIS (Netherlands)

    Kudryashova, E.V.; Visser, A.J.W.G.; Hoek, van A.; Jongh, de H.H.J.

    2007-01-01

    To stabilize air-water interfaces, as in foams, the adsorption of surface-active components is a prerequisite. An approach to controlling the surface activity of proteins is noncovalent complex formation with a polyelectrolyte in the bulk phase. The molecular properties of egg white ovalbumin in a

  2. Exploring Fluorescence Antibunching in Solution To Determine the Stoichiometry of Molecular Complexes

    Czech Academy of Sciences Publication Activity Database

    Sýkora, Jan; Kaiser, K.; Gregor, I.; Bönigk, W.; Schmalzing, G.; Enderlain, J.

    2007-01-01

    Roč. 79, - (2007), s. 4040-4049 ISSN 0003-2700 R&D Projects: GA MŠk(CZ) LC06063 Institutional research plan: CEZ:AV0Z40400503 Keywords : exploring fluorescence antibunching * molecular complex es * biophysical methods Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.287, year: 2007

  3. Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer

    DEFF Research Database (Denmark)

    Solov'yov, Ilia A.; Korol, Andrei V.; Solov'yov, Andrey V.

    This book introduces readers to MesoBioNano (MBN) Explorer - a multi-purpose software package designed to model molecular systems at various levels of size and complexity. In addition, it presents a specially designed multi-task toolkit and interface - the MBN Studio - which enables the set-up of...

  4. Low Molecular Weight Chitosan–Insulin Polyelectrolyte Complex: Characterization and Stability Studies

    Directory of Open Access Journals (Sweden)

    Zakieh I. Al-Kurdi

    2015-03-01

    Full Text Available The aim of the work reported herein was to investigate the effect of various low molecular weight chitosans (LMWCs on the stability of insulin using USP HPLC methods. Insulin was found to be stable in a polyelectrolyte complex (PEC consisting of insulin and LMWC in the presence of a Tris-buffer at pH 6.5. In the presence of LMWC, the stability of insulin increased with decreasing molecular weight of LMWC; 13 kDa LMWC was the most efficient molecular weight for enhancing the physical and chemical stability of insulin. Solubilization of insulin-LMWC polyelectrolyte complex (I-LMWC PEC in a reverse micelle (RM system, administered to diabetic rats, results in an oral delivery system for insulin with acceptable bioactivity.

  5. Molecular Gas toward the Gemini OB1 Molecular Cloud Complex. II. CO Outflow Candidates with Possible WISE Associations

    Science.gov (United States)

    Li, Yingjie; Li, Fa-Cheng; Xu, Ye; Wang, Chen; Du, Xin-Yu; Yang, Wenjin; Yang, Ji

    2018-03-01

    We present a large-scale survey of CO outflows in the Gem OB1 molecular cloud complex and its surroundings, using the Purple Mountain Observatory Delingha 13.7 m telescope. A total of 198 outflow candidates were identified over a large area (∼58.5 square degrees), of which 193 are newly detected. Approximately 68% (134/198) are associated with the Gem OB1 molecular cloud complex, including clouds GGMC 1, GGMC 2, BFS 52, GGMC 3, and GGMC 4. Other regions studied are: the Local arm (Local Lynds, West Front), Swallow, Horn, and Remote cloud. Outflow candidates in GGMC 1, BFS 52, and Swallow are mainly located at ring-like or filamentary structures. To avoid excessive uncertainty in distant regions (≳3.8 kpc), we only estimated the physical parameters for clouds in the Gem OB1 molecular cloud complex and in the Local arm. In those clouds, the total kinetic energy and the energy injection rate of the identified outflow candidates are ≲1% and ≲3% of the turbulent energy and the turbulent dissipation rate of each cloud, indicating that the identified outflow candidates cannot provide enough energy to balance turbulence of their host cloud at the scale of the entire cloud (several to dozens of parsecs). The gravitational binding energy of each cloud is ≳135 times the total kinetic energy of the identified outflow candidates within the corresponding cloud, indicating that the identified outflow candidates cannot cause major disruptions to the integrity of their host cloud at the scale of the entire cloud.

  6. CO observations of a molecular cloud complex associated with the bright rim near VY Canis Majoris

    International Nuclear Information System (INIS)

    Lada, C.J.; Reid, M.J.

    1978-01-01

    Extensive CO observations of a large molecular cloud complex (approx. 15 pc) associated with a bright rim near the peculiar star VY CMa are presented. CO emission peaks in a region along and adjacent to the bright rim which forms the western border of the cloud complex. This emission abruptly decreases across the bright rim, and this decrease suggests a physical association of the rim with the cloud. The molecular complex is found to consist of two clouds which have different radial velocities and physical properties. The possibility that these two clouds may be in near-collision is discussed. The physical association of the bright rim with the cloud complex indicates that the clouds are at the same distance, 1.5 kpc, as the stars which excite the rim. Since VY CMa appears to be located at the tip of the bright rim and has a velocity similar to that of the molecular cloud complex and the stars of the cluster NGC 2362, it is concluded that VY CMa is also at the same distance. The resulting luminosity of VY CMa (5 x 10 5 L sub solar) indicates that the star is very massive, and places constraints on interpretation of its evolutionary state. 5 figures, 2 tables

  7. The psychostimulant modafinil enhances gap junctional communication in cortical astrocytes.

    Science.gov (United States)

    Liu, Xinhe; Petit, Jean-Marie; Ezan, Pascal; Gyger, Joël; Magistretti, Pierre; Giaume, Christian

    2013-12-01

    Sleep-wake cycle is characterized by changes in neuronal network activity. However, for the last decade there is increasing evidence that neuroglial interaction may play a role in the modulation of sleep homeostasis and that astrocytes have a critical impact in this process. Interestingly, astrocytes are organized into communicating networks based on their high expression of connexins, which are the molecular constituents of gap junction channels. Thus, neuroglial interactions should also be considered as the result of the interplay between neuronal and astroglial networks. Here, we investigate the effect of modafinil, a wakefulness-promoting agent, on astrocyte gap junctional communication. We report that in the cortex modafinil injection increases the expression of mRNA and protein of connexin 30 but not those of connexin 43, the other major astroglial connexin. These increases are correlated with an enhancement of intercellular dye coupling in cortical astrocytes, which is abolished when neuronal activity is silenced by tetrodotoxin. Moreover, gamma-hydroxybutyric acid, which at a millimolar concentration induces sleep, has an opposite effect on astroglial gap junctions in an activity-independent manner. These results support the proposition that astroglia may play an important role in complex physiological brain functions, such as sleep regulation, and that neuroglial networking interaction is modified during sleep-wake cycle. This article is part of the Special Issue Section entitled 'Current Pharmacology of Gap Junction Channels and Hemichannels'. Copyright © 2013. Published by Elsevier Ltd.

  8. Implementation of exterior complex scaling in B-splines to solve atomic and molecular collision problems

    International Nuclear Information System (INIS)

    McCurdy, C William; MartIn, Fernando

    2004-01-01

    B-spline methods are now well established as widely applicable tools for the evaluation of atomic and molecular continuum states. The mathematical technique of exterior complex scaling has been shown, in a variety of other implementations, to be a powerful method with which to solve atomic and molecular scattering problems, because it allows the correct imposition of continuum boundary conditions without their explicit analytic application. In this paper, an implementation of exterior complex scaling in B-splines is described that can bring the well-developed technology of B-splines to bear on new problems, including multiple ionization and breakup problems, in a straightforward way. The approach is demonstrated for examples involving the continuum motion of nuclei in diatomic molecules as well as electronic continua. For problems involving electrons, a method based on Poisson's equation is presented for computing two-electron integrals over B-splines under exterior complex scaling

  9. Molecular Modeling and Physicochemical Properties of Supramolecular Complexes of Limonene with α- and β-Cyclodextrins.

    Science.gov (United States)

    Dos Passos Menezes, Paula; Dos Santos, Polliana Barbosa Pereira; Dória, Grace Anne Azevedo; de Sousa, Bruna Maria Hipólito; Serafini, Mairim Russo; Nunes, Paula Santos; Quintans-Júnior, Lucindo José; de Matos, Iara Lisboa; Alves, Péricles Barreto; Bezerra, Daniel Pereira; Mendonça Júnior, Francisco Jaime Bezerra; da Silva, Gabriel Francisco; de Aquino, Thiago Mendonça; de Souza Bento, Edson; Scotti, Marcus Tullius; Scotti, Luciana; de Souza Araujo, Adriano Antunes

    2017-02-01

    This study evaluated three different methods for the formation of an inclusion complex between alpha- and beta-cyclodextrin (α- and β-CD) and limonene (LIM) with the goal of improving the physicochemical properties of limonene. The study samples were prepared through physical mixing (PM), paste complexation (PC), and slurry complexation (SC) methods in the molar ratio of 1:1 (cyclodextrin:limonene). The complexes prepared were evaluated with thermogravimetry/derivate thermogravimetry, infrared spectroscopy, X-ray diffraction, complexation efficiency through gas chromatography/mass spectrometry analyses, molecular modeling, and nuclear magnetic resonance. The results showed that the physical mixing procedure did not produce complexation, but the paste and slurry methods produced inclusion complexes, which demonstrated interactions outside of the cavity of the CDs. However, the paste obtained with β-cyclodextrin did not demonstrate complexation in the gas chromatographic technique because, after extraction, most of the limonene was either surface-adsorbed by β-cyclodextrin or volatilized during the procedure. We conclude that paste complexation and slurry complexation are effective and economic methods to improve the physicochemical character of limonene and could have important applications in pharmacological activities in terms of an increase in solubility.

  10. Synthesis of Fe–Li–Cr Multinuclear Complexes as Molecular Magnet Materials

    Directory of Open Access Journals (Sweden)

    Iis Siti Jahro

    2008-03-01

    Full Text Available Multinuclear complexes have received considerable interest as molecular magnet materials. Up to now, several complex compounds based on bidentate ligand 2,2’ bipyridine have been synthesized. In this research, the Fe-Li-Cr multinuclear complexes with derivative 2’2- bipyridine ligands: 2-(2’-pyridylquinoline(pq, 2,2’-Pyridil(pdl have been synthesized. The oxalate (ox ligand has also been used as a bridging ligand in these multinuclear complexes. The chemical formula of Li[FeCr(ox2(pq(BF42(H2O2] and [Fe(pdln][LiCr(ox3] complexes have been verified using metal and C, H, N elemental analysis data. The IR spectra in 350 – 4000 cm-1 range exhibit characteristic absorptions, which support the proposed structure of complex. The plausible structure of the compounds has been drawn based on complex formation mechanism. The magnetic susceptibility at room temperature of the pq-complex is about 5.7 BM and of the pdl- complexes are 4.8 and 5.5 BM. These indicated that both spin states of iron(II exist in the multinuclear complexes.

  11. al junctions

    African Journals Online (AJOL)

    Preferred Customer

    Capacitance per unit area as well as the width of the depletion layer are obtained from the complex impedance analysis. ... Thermo ionic emission theory is applied to extract the parameters. .... limit is usually obtained by extrapolation. The.

  12. Comparative study of anchoring groups for molecular electronics: structure and conductance of Au-S-Au and Au-NH2-Au junctions

    DEFF Research Database (Denmark)

    Kristensen, Iben Sig; Mowbray, Duncan; Thygesen, Kristian Sommer

    2008-01-01

    The electrical properties of single-molecule junctions, consisting of an organic molecule coupled to metal electrodes, are sensitive to the detailed atomic structure of the molecule-metal contact. This, in turn, is determined by the anchoring group linking the molecule to the metal. With the aim ...

  13. Theoretical Study of Copper Complexes: Molecular Structure, Properties, and Its Application to Solar Cells

    Directory of Open Access Journals (Sweden)

    Jesus Baldenebro-Lopez

    2013-01-01

    Full Text Available We present a theoretical investigation of copper complexes with potential applications as sensitizers for solar cells. The density functional theory (DFT and time-dependent DFT were utilized, using the M06 hybrid meta-GGA functional with the LANL2DZ (D95V on first row and DZVP basis sets. This level of calculation was used to find the optimized molecular structure, the absorption spectra, the molecular orbitals energies, and the chemical reactivity parameters that arise from conceptual DFT. Solvent effects have been taken into account by an implicit approach, namely, the polarizable continuum model (PCM, using the nonequilibrium version of the IEF-PCM model.

  14. Morphological and molecular characterization of Cladosporium cladosporioides species complex causing pecan tree leaf spot.

    Science.gov (United States)

    Walker, C; Muniz, M F B; Rolim, J M; Martins, R R O; Rosenthal, V C; Maciel, C G; Mezzomo, R; Reiniger, L R S

    2016-09-16

    The objective of this study was to characterize species of the Cladosporium cladosporioides complex isolated from pecan trees (Carya illinoinensis) with symptoms of leaf spot, based on morphological and molecular approaches. Morphological attributes were assessed using monosporic cultures on potato dextrose agar medium, which were examined for mycelial growth, sporulation, color, and conidia and ramoconidia size. Molecular characterization comprised isolation of DNA and subsequent amplification of the translation elongation factor 1α (TEF-1α) region. Three species of the C. cladosporioides complex were identified: C. cladosporioides, Cladosporium pseudocladosporioides, and Cladosporium subuliforme. Sporulation was the most important characteristic differentiating species of this genus. However, morphological features must be considered together with molecular analysis, as certain characters are indistinguishable between species. TEF-1αcan be effectively used to identify and group isolates belonging to the C. cladosporioides complex. The present study provides an important example of a methodology to ascertain similarity between isolates of this complex causing leaf spot in pecan trees, which should facilitate future pathogenicity studies.

  15. Atomic level insights into realistic molecular models of dendrimer-drug complexes through MD simulations

    Science.gov (United States)

    Jain, Vaibhav; Maiti, Prabal K.; Bharatam, Prasad V.

    2016-09-01

    Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details. For this purpose, possible inclusion complexes of model drug Nateglinide (Ntg) (antidiabetic, belongs to Biopharmaceutics Classification System class II) with amine- and acetyl-terminated G4 poly(amidoamine) (G4 PAMAM(NH2) and G4 PAMAM(Ac)) dendrimers at neutral and low pH conditions are explored in this work. MD simulation analysis on dendrimer-drug complexes revealed that the drug encapsulation efficiency of G4 PAMAM(NH2) and G4 PAMAM(Ac) dendrimers at neutral pH was 6 and 5, respectively, while at low pH it was 12 and 13, respectively. Center-of-mass distance analysis showed that most of the drug molecules are located in the interior hydrophobic pockets of G4 PAMAM(NH2) at both the pH; while in the case of G4 PAMAM(Ac), most of them are distributed near to the surface at neutral pH and in the interior hydrophobic pockets at low pH. Structural properties such as radius of gyration, shape, radial density distribution, and solvent accessible surface area of dendrimer-drug complexes were also assessed and compared with that of the drug unloaded dendrimers. Further, binding energy calculations using molecular mechanics Poisson-Boltzmann surface area approach revealed that the location of drug molecules in the dendrimer is not the decisive factor for the higher and lower binding affinity of the complex, but the charged state of dendrimer and drug, intermolecular interactions, pH-induced conformational changes, and surface groups of dendrimer do play an

  16. Carbon Nanotube Based Molecular Electronics

    Science.gov (United States)

    Srivastava, Deepak; Saini, Subhash; Menon, Madhu

    1998-01-01

    Carbon nanotubes and the nanotube heterojunctions have recently emerged as excellent candidates for nanoscale molecular electronic device components. Experimental measurements on the conductivity, rectifying behavior and conductivity-chirality correlation have also been made. While quasi-one dimensional simple heterojunctions between nanotubes with different electronic behavior can be generated by introduction of a pair of heptagon-pentagon defects in an otherwise all hexagon graphene sheet. Other complex 3- and 4-point junctions may require other mechanisms. Structural stability as well as local electronic density of states of various nanotube junctions are investigated using a generalized tight-binding molecular dynamics (GDBMD) scheme that incorporates non-orthogonality of the orbitals. The junctions investigated include straight and small angle heterojunctions of various chiralities and diameters; as well as more complex 'T' and 'Y' junctions which do not always obey the usual pentagon-heptagon pair rule. The study of local density of states (LDOS) reveal many interesting features, most prominent among them being the defect-induced states in the gap. The proposed three and four pointjunctions are one of the smallest possible tunnel junctions made entirely of carbon atoms. Furthermore the electronic behavior of the nanotube based device components can be taylored by doping with group III-V elements such as B and N, and BN nanotubes as a wide band gap semiconductor has also been realized in experiments. Structural properties of heteroatomic nanotubes comprising C, B and N will be discussed.

  17. Geodynamical simulation of the RRF triple junction

    Science.gov (United States)

    Wang, Z.; Wei, D.; Liu, M.; Shi, Y.; Wang, S.

    2017-12-01

    Triple junction is the point at which three plate boundaries meet. Three plates at the triple junction form a complex geological tectonics, which is a natural laboratory to study the interactions of plates. This work studies a special triple junction, the oceanic transform fault intersects the collinear ridges with different-spreading rates, which is free of influence of ridge-transform faults and nearby hotspots. First, we build 3-D numerical model of this triple junction used to calculate the stead-state velocity and temperature fields resulting from advective and conductive heat transfer. We discuss in detail the influence of the velocity and temperature fields of the triple junction from viscosity, spreading rate of the ridge. The two sides of the oceanic transform fault are different sensitivities to the two factors. And, the influence of the velocity mainly occurs within 200km of the triple junction. Then, we modify the model by adding a ridge-transform fault to above model and directly use the velocity structure of the Macquarie triple junction. The simulation results show that the temperature at both sides of the oceanic transform fault decreases gradually from the triple junction, but the temperature difference between the two sides is a constant about 200°. And, there is little effect of upwelling velocity away from the triple junction 100km. The model results are compared with observational data. The heat flux and thermal topography along the oceanic transform fault of this model are consistent with the observed data of the Macquarie triple junction. The earthquakes are strike slip distributed along the oceanic transform fault. Their depths are also consistent with the zone of maximum shear stress. This work can help us to understand the interactions of plates of triple junctions and help us with the foundation for the future study of triple junctions.

  18. N2 Reduction and Hydrogenation to Ammonia by a Molecular Iron-Potassium Complex

    Science.gov (United States)

    Rodriguez, Meghan M.; Bill, Eckhard; Brennessel, William W.; Holland, Patrick L.

    2011-01-01

    The most common catalyst in the Haber-Bosch process for the hydrogenation of dinitrogen (N2) to ammonia is an iron surface promoted with K+, but soluble iron complexes have neither reduced the N-N bond of N2 to nitride nor produced large amounts of NH3 from N2. We report a molecular iron complex that reacts with N2 and a potassium reductant to give a complex with two nitrides, which are bound to iron and potassium cations. The product has a Fe3N2 core, implying that three iron atoms cooperate to break the N-N triple bond through a six-electron reduction. The nitride complex reacts with acid and with H2 to give substantial yields of N2-derived ammonia. These reactions, though not yet catalytic, give structural and spectroscopic insight into N2 cleavage and N-H bond-forming reactions of iron. PMID:22076372

  19. N₂reduction and hydrogenation to ammonia by a molecular iron-potassium complex.

    Science.gov (United States)

    Rodriguez, Meghan M; Bill, Eckhard; Brennessel, William W; Holland, Patrick L

    2011-11-11

    The most common catalyst in the Haber-Bosch process for the hydrogenation of dinitrogen (N(2)) to ammonia (NH(3)) is an iron surface promoted with potassium cations (K(+)), but soluble iron complexes have neither reduced the N-N bond of N(2) to nitride (N(3-)) nor produced large amounts of NH(3) from N(2). We report a molecular iron complex that reacts with N(2) and a potassium reductant to give a complex with two nitrides, which are bound to iron and potassium cations. The product has a Fe(3)N(2) core, implying that three iron atoms cooperate to break the N-N triple bond through a six-electron reduction. The nitride complex reacts with acid and with H(2) to give substantial yields of N(2)-derived ammonia. These reactions, although not yet catalytic, give structural and spectroscopic insight into N(2) cleavage and N-H bond-forming reactions of iron.

  20. Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement

    International Nuclear Information System (INIS)

    Makino, Debora Lika; Conti, Elena

    2013-01-01

    The crystallographic steps towards the structure determination of a complete eukaryotic exosome complex bound to RNA are presented. Phasing of this 11-protein subunit complex was carried out via molecular replacement. The RNA exosome is an evolutionarily conserved multi-protein complex involved in the 3′ degradation of a variety of RNA transcripts. In the nucleus, the exosome participates in the maturation of structured RNAs, in the surveillance of pre-mRNAs and in the decay of a variety of noncoding transcripts. In the cytoplasm, the exosome degrades mRNAs in constitutive and regulated turnover pathways. Several structures of subcomplexes of eukaryotic exosomes or related prokaryotic exosome-like complexes are known, but how the complete assembly is organized to fulfil processive RNA degradation has been unclear. An atomic snapshot of a Saccharomyces cerevisiae 420 kDa exosome complex bound to an RNA substrate in the pre-cleavage state of a hydrolytic reaction has been determined. Here, the crystallographic steps towards the structural elucidation, which was carried out by molecular replacement, are presented

  1. Computational Molecular Nanoscience Study of the Properties of Copper Complexes for Dye-Sensitized Solar Cells

    Science.gov (United States)

    Baldenebro-López, Jesús; Castorena-González, José; Flores-Holguín, Norma; Almaral-Sánchez, Jorge; Glossman-Mitnik, Daniel

    2012-01-01

    In this work, we studied a copper complex-based dye, which is proposed for potential photovoltaic applications and is named Cu (I) biquinoline dye. Results of electron affinities and ionization potentials have been used for the correlation between different levels of calculation used in this study, which are based on The Density Functional Theory (DFT) and time-dependent (TD) DFT. Further, the maximum absorption wavelengths of our theoretical calculations were compared with the experimental data. It was found that the M06/LANL2DZ + DZVP level of calculation provides the best approximation. This level of calculation was used to find the optimized molecular structure and to predict the main molecular vibrations, the molecular orbitals energies, dipole moment, isotropic polarizability and the chemical reactivity parameters that arise from Conceptual DFT. PMID:23443107

  2. PhytoAuthent: Molecular authentication of complex herbal food supplements for safety and efficacy

    Directory of Open Access Journals (Sweden)

    Mihael Ichim

    2017-10-01

    Full Text Available The PhytoAuthent project was structured to gather, test, develop and apply, in real life case scenarios, molecular techniques, such as biochemical fingerprinting and DNA sequence-based methods, for plant identification of constituents in complex herbal products. The project had a strong focus on applied aspects like protecting consumers from health risks associated with product substitution and contamination of herbal products.

  3. A computer program for external modes in complex ionic crystals (the rigid molecular-ion model)

    International Nuclear Information System (INIS)

    Chaplot, S.L.

    1978-01-01

    A computer program DISPR has been developed to calculate the external mode phonon dispersion relation in the harmonic approximation for complex ionic crystals using the rigid molecular ion model. A description of the program, the flow diagram and the required input information are given. A sample calculation for α-KNO 3 is presented. The program can handle any type of crystal lattice with any number of atoms and molecules per unit cell with suitable changes in dimension statements. (M.G.B.)

  4. Venom Resistance as a Model for Understanding the Molecular Basis of Complex Coevolutionary Adaptations.

    Science.gov (United States)

    Holding, Matthew L; Drabeck, Danielle H; Jansa, Sharon A; Gibbs, H Lisle

    2016-11-01

    SynopsisVenom and venom resistance are molecular phenotypes widely considered to have diversified through coevolution between predators and prey. However, while evolutionary and functional studies on venom have been extensive, little is known about the molecular basis, variation, and complexity of venom resistance. We review known mechanisms of venom resistance and relate these mechanisms to their predicted impact on coevolutionary dynamics with venomous enemies. We then describe two conceptual approaches which can be used to examine venom/resistance systems. At the intraspecific level, tests of local adaptation in venom and resistance phenotypes can identify the functional mechanisms governing the outcomes of coevolution. At deeper evolutionary timescales, the combination of phylogenetically informed analyses of protein evolution coupled with studies of protein function promise to elucidate the mode and tempo of evolutionary change on potentially coevolving genes. We highlight case studies that use each approach to extend our knowledge of these systems as well as address larger questions about coevolutionary dynamics. We argue that resistance and venom are phenotypic traits which hold exceptional promise for investigating the mechanisms, dynamics, and outcomes of coevolution at the molecular level. Furthermore, extending the understanding of single gene-for-gene interactions to the whole resistance and venom phenotypes may provide a model system for examining the molecular and evolutionary dynamics of complex multi-gene interactions. © The Author 2016. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

  5. C sub 6 sub 0 fullerene and its molecular complexes under axial and shear deformation

    CERN Document Server

    Spitsina, N G; Bashkin, I V; Meletov, K P

    2002-01-01

    We have studied the pristine C sub 6 sub 0 and its molecular complexes with the organic donors bis(ethylenedithio) tetrathiafulvalene (BEDT-TTF or ET) and tetramethyltetraselenafulvalene (TMTSF) by means of ESR and Raman spectroscopy at high pressure. The important changes in the ESR signal of C sub 6 sub 0 were observed under axial pressure combined with shear deformation. It is shown that the treatment at a anisotropic pressure of 4 GPa results in a reduction in the symmetry of the C sub 6 sub 0 molecule and the formation of radicals. Treatment of the molecular complex of (ET) sub 2 centre dot C sub 6 sub 0 at a pressure of approx 4.5 GPa and a temperature of 150 deg. C leads to the formation of C sub 6 sub 0 dimers. The Raman spectra of the molecular complex C sub 6 sub 0 centre dot TMTSF centre dot 2(CS sub 2) were measured in situ at ambient temperature and pressures up to 9.5 GPa. The pressure behaviour of the Raman peaks reveals singularity at 5.0 +- 0.5 GPa related to the softening and splitting of so...

  6. Fibroblast growth factor signaling potentiates VE-cadherin stability at adherens junctions by regulating SHP2.

    Directory of Open Access Journals (Sweden)

    Kunihiko Hatanaka

    Full Text Available The fibroblast growth factor (FGF system plays a critical role in the maintenance of vascular integrity via enhancing the stability of VE-cadherin at adherens junctions. However, the precise molecular mechanism is not well understood. In the present study, we aimed to investigate the detailed mechanism of FGF regulation of VE-cadherin function that leads to endothelial junction stabilization.In vitro studies demonstrated that the loss of FGF signaling disrupts the VE-cadherin-catenin complex at adherens junctions by increasing tyrosine phosphorylation levels of VE-cadherin. Among protein tyrosine phosphatases (PTPs known to be involved in the maintenance of the VE-cadherin complex, suppression of FGF signaling reduces SHP2 expression levels and SHP2/VE-cadherin interaction due to accelerated SHP2 protein degradation. Increased endothelial permeability caused by FGF signaling inhibition was rescued by SHP2 overexpression, indicating the critical role of SHP2 in the maintenance of endothelial junction integrity.These results identify FGF-dependent maintenance of SHP2 as an important new mechanism controlling the extent of VE-cadherin tyrosine phosphorylation, thereby regulating its presence in adherens junctions and endothelial permeability.

  7. Delimitating cryptic species in the Gracilaria domingensis complex (Gracilariaceae, Rhodophyta) using molecular and morphological data.

    Science.gov (United States)

    Lyra, Goia de M; Gurgel, C Frederico D; Costa, Emmanuelle da S; de Jesus, Priscila B; Oliveira, Mariana C; Oliveira, Eurico C; Davis, Charles C; Nunes, José Marcos de Castro

    2016-12-01

    Species in the genus Gracilaria that display conspicuously flattened vegetative morphologies are a taxonomically challenging group of marine benthic red algae. This is a result of their species richness, morphological similarity, and broad phenotypic plasticity. Within this group, the Gracilaria domingensis complex is one of the most common, conspicuous, and morphologically variable species along the tropical western Atlantic Ocean. Previous research has identified that members of this complex belong to two distantly related clades. However, despite this increased phylogentic resolution, species delimitations within each of these clades remain unclear. Our study assessed the species diversity within this difficult complex using morphological and molecular data from three genetic markers (cox1, UPA, and rbcL). We additionally applied six single-marker species delimitation methods (SDM: ABGD, GMYCs, GMYCm, SPN, bPTP, and PTP) to rbcL, which were largely in agreement regarding species delimitation. These results, combined with our analysis of morphology, indicate that the G. domingensis complex includes seven distinct species, each of which are not all most closely related: G. cervicornis; a ressurected G. ferox; G. apiculata subsp. apiculata; a new species, Gracilaria baiana sp. nov.; G. intermedia subsp. intermedia; G. venezuelensis; and G. domingensis sensu stricto, which includes the later heterotypic synonym, G. yoneshigueana. Our study demonstrates the value of multipronged strategies, including the use of both molecular and morphological approaches, to decipher cryptic species of red algae. © 2016 Phycological Society of America.

  8. Enhancing the magnetic anisotropy of maghemite nanoparticles via the surface coordination of molecular complexes

    Science.gov (United States)

    Prado, Yoann; Daffé, Niéli; Michel, Aude; Georgelin, Thomas; Yaacoub, Nader; Grenèche, Jean-Marc; Choueikani, Fadi; Otero, Edwige; Ohresser, Philippe; Arrio, Marie-Anne; Cartier-dit-Moulin, Christophe; Sainctavit, Philippe; Fleury, Benoit; Dupuis, Vincent; Lisnard, Laurent; Fresnais, Jérôme

    2015-01-01

    Superparamagnetic nanoparticles are promising objects for data storage or medical applications. In the smallest—and more attractive—systems, the properties are governed by the magnetic anisotropy. Here we report a molecule-based synthetic strategy to enhance this anisotropy in sub-10-nm nanoparticles. It consists of the fabrication of composite materials where anisotropic molecular complexes are coordinated to the surface of the nanoparticles. Reacting 5 nm γ-Fe2O3 nanoparticles with the [CoII(TPMA)Cl2] complex (TPMA: tris(2-pyridylmethyl)amine) leads to the desired composite materials and the characterization of the functionalized nanoparticles evidences the successful coordination—without nanoparticle aggregation and without complex dissociation—of the molecular complexes to the nanoparticles surface. Magnetic measurements indicate the significant enhancement of the anisotropy in the final objects. Indeed, the functionalized nanoparticles show a threefold increase of the blocking temperature and a coercive field increased by one order of magnitude. PMID:26634987

  9. A mononuclear zinc(II) complex with piroxicam: Crystal structure, DNA- and BSA-binding studies; in vitro cell cytotoxicity and molecular modeling of oxicam complexes

    Science.gov (United States)

    Jannesari, Zahra; Hadadzadeh, Hassan; Amirghofran, Zahra; Simpson, Jim; Khayamian, Taghi; Maleki, Batool

    2015-02-01

    A new mononuclear Zn(II) complex, trans-[Zn(Pir)2(DMSO)2], where Pir- is 4-hydroxy-2-methyl-N-2-pyridyl-2H-1,2-benzothiazine-3-carboxamide-1,1-dioxide (piroxicam), has been synthesized and characterized. The crystal structure of the complex was obtained by the single crystal X-ray diffraction technique. The interaction of the complex with DNA and BSA was investigated. The complex interacts with FS-DNA by two binding modes, viz., electrostatic and groove binding (major and minor). The microenvironment and the secondary structure of BSA are changed in the presence of the complex. The anticancer effects of the seven complexes of oxicam family were also determined on the human K562 cell lines and the results showed reasonable cytotoxicities. The interactions of the oxicam complexes with BSA and DNA were modeled by molecular docking and molecular dynamic simulation methods.

  10. Supramolecular chemistry: from molecular information towards self-organization and complex matter

    International Nuclear Information System (INIS)

    Lehn, Jean-Marie

    2004-01-01

    Molecular chemistry has developed a wide range of very powerful procedures for constructing ever more sophisticated molecules from atoms linked by covalent bonds. Beyond molecular chemistry lies supramolecular chemistry, which aims at developing highly complex chemical systems from components interacting via non-covalent intermolecular forces. By the appropriate manipulation of these interactions, supramolecular chemistry became progressively the chemistry of molecular information, involving the storage of information at the molecular level, in the structural features, and its retrieval, transfer, and processing at the supramolecular level, through molecular recognition processes operating via specific interactional algorithms. This has paved the way towards apprehending chemistry also as an information science. Numerous receptors capable of recognizing, i.e. selectively binding, specific substrates have been developed, based on the molecular information stored in the interacting species. Suitably functionalized receptors may perform supramolecular catalysis and selective transport processes. In combination with polymolecular organization, recognition opens ways towards the design of molecular and supramolecular devices based on functional (photoactive, electroactive, ionoactive, etc) components. A step beyond preorganization consists in the design of systems undergoing self-organization, i.e. systems capable of spontaneously generating well-defined supramolecular architectures by self-assembly from their components. Self-organization processes, directed by the molecular information stored in the components and read out at the supramolecular level through specific interactions, represent the operation of programmed chemical systems. They have been implemented for the generation of a variety of discrete functional architectures of either organic or inorganic nature. Self-organization processes also give access to advanced supramolecular materials, such as

  11. Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory

    International Nuclear Information System (INIS)

    Mrugalla, Florian; Kast, Stefan M

    2016-01-01

    Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute–solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute–solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems. (paper)

  12. Ab initio molecular orbital calculations on the associated complexes of lithium cyanide with ammonia

    International Nuclear Information System (INIS)

    Mohandas, P.; Shivaglal, M.C.; Chandrasekhar, J.

    1995-01-01

    Ab initio molecular orbital (MO) calculations with the 3-21G and 6-31G basis sets are carried out on a series of complexes of NH 3 with Li + , C triple-bond N - , LiCN, and its isomer LiNC. The BSSE-corrected interaction energies, geometrical parameters, internal force constants, and harmonic vibrational frequencies are evaluated for 15 species. Complexes with trifurcated (C 3v ) structures are calculated to be saddle points on the potential energy surfaces and have one imaginary frequency each. Calculated energies, geometrical parameters, internal force constants, and harmonic vibrational frequencies of the various species considered are discussed in terms of the nature of association of LiCN with ammonia. The vibrational frequencies of the relevant complexed species are compared with the experimental frequencies reported earlier for solutions of lithium cyanide in liquid ammonia. 40 refs., 1 fig., 4 tabs

  13. AMMOS2: a web server for protein–ligand–water complexes refinement via molecular mechanics

    Science.gov (United States)

    Labbé, Céline M.; Pencheva, Tania; Jereva, Dessislava; Desvillechabrol, Dimitri; Becot, Jérôme; Villoutreix, Bruno O.; Pajeva, Ilza

    2017-01-01

    Abstract AMMOS2 is an interactive web server for efficient computational refinement of protein–small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein–ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein–ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein–ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein–ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein–ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein–ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php. PMID:28486703

  14. AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics.

    Science.gov (United States)

    Labbé, Céline M; Pencheva, Tania; Jereva, Dessislava; Desvillechabrol, Dimitri; Becot, Jérôme; Villoutreix, Bruno O; Pajeva, Ilza; Miteva, Maria A

    2017-07-03

    AMMOS2 is an interactive web server for efficient computational refinement of protein-small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein-ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein-ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein-ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein-ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein-ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein-ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. The Seasonality and Ecology of the Anopheles gambiae complex (Dipetra: Culicidae) in Liberia Using Molecular Identification.

    Science.gov (United States)

    Fahmy, N T; Villinski, J T; Bolay, F; Stoops, C A; Tageldin, R A; Fakoli, L; Okasha, O; Obenauer, P J; Diclaro, J W

    2015-05-01

    Members of the Anopheles gambiae sensu lato (Giles) complex define a group of seven morphologically indistinguishable species, including the principal malaria vectors in Sub-Saharan Africa. Members of this complex differ in behavior and ability to transmit malaria; hence, precise identification of member species is critical to monitoring and evaluating malaria threat levels. We collected mosquitoes from five counties in Liberia every other month from May 2011 until May 2012, using various trapping techniques. A. gambiae complex members were identified using molecular techniques based on differences in the ribosomal DNA (rDNA) region between species and the molecular forms (S and M) of A. gambiae sensu stricto (s.s) specimens. In total, 1,696 A. gambiae mosquitoes were collected and identified. DNA was extracted from legs of each specimen with species identification determined by multiplex polymerase chain reaction using specific primers. The molecular forms (M or S) of A. gambiae s.s were determined by restriction fragment length polymorphism. Bivariate and multivariate logistic regression models identified environmental variables associated with genomic differentiation. Our results indicate widespread occurrence of A. gambiae s.s., the principal malaria vector in the complex, although two Anopheles melas Theobald/A. merus Donitz mosquitoes were detected. We found 72.6, 25.5, and 1.9% of A. gambiae s.s specimens were S, M, and hybrid forms, respectively. Statistical analysis indicates that the S form was more likely to be found in rural areas during rainy seasons and indoor catchments. This information will enhance vector control efforts in Liberia. Published by Oxford University Press on behalf of Entomological Society of America 2015. This work is written by US Government employees and is in the public domain in the US.

  16. Gap junctional communication modulates gene transcription by altering the recruitment of Sp1 and Sp3 to connexin-response elements in osteoblast promoters

    Science.gov (United States)

    Stains, Joseph P.; Lecanda, Fernando; Screen, Joanne; Towler, Dwight A.; Civitelli, Roberto

    2003-01-01

    Loss-of-function mutations of gap junction proteins, connexins, represent a mechanism of disease in a variety of tissues. We have shown that recessive (gene deletion) or dominant (connexin45 overexpression) disruption of connexin43 function results in osteoblast dysfunction and abnormal expression of osteoblast genes, including down-regulation of osteocalcin transcription. To elucidate the molecular mechanisms of gap junction-sensitive transcriptional regulation, we systematically analyzed the rat osteocalcin promoter for sensitivity to gap junctional intercellular communication. We identified an Sp1/Sp3 containing complex that assembles on a minimal element in the -70 to -57 region of the osteocalcin promoter in a gap junction-dependent manner. This CT-rich connexin-response element is necessary and sufficient to confer gap junction sensitivity to the osteocalcin proximal promoter. Repression of osteocalcin transcription occurs as a result of displacement of the stimulatory Sp1 by the inhibitory Sp3 on the promoter when gap junctional communication is perturbed. Modulation of Sp1/Sp3 recruitment also occurs on the collagen Ialpha1 promoter and translates into gap junction-sensitive transcriptional control of collagen Ialpha1 gene expression. Thus, regulation of Sp1/Sp3 recruitment to the promoter may represent a potential general mechanism for transcriptional control of target genes by signals passing through gap junctions.

  17. Characterization of pioglitazone cyclodextrin complexes: Molecular modeling to in vivo evaluation

    Directory of Open Access Journals (Sweden)

    Dinesh M Bramhane

    2016-01-01

    Full Text Available Aims: The objective of present study was to study the influence of different β-cyclodextrin derivatives and different methods of complexation on aqueous solubility and consequent translation in in vivo performance of Pioglitazone (PE. Material and Methods: Three cyclodextrins: β-cyclodextrin (BCD, hydroxypropyl-β-cyclodextrin (HPBCD and Sulfobutylether-7-β-cyclodextrin (SBEBCD were employed in preparation of 1:1 Pioglitazone complexes by three methods viz. co-grinding, kneading and co-evaporation. Complexation was confirmed by phase solubility, proton NMR, Fourier Transform Infrared spectroscopy, Differential Scanning Calorimetry (DSC and X-Ray diffraction (XRD. Mode of complexation was investigated by molecular dynamic studies. Pharmacodynamic study of blood glucose lowering activity of PE complexes was performed in Alloxan induced diabetic rat model. Results: Aqueous solubility of PE was significantly improved in presence of cyclodextrin. Apparent solubility constants were observed to be 254.33 M–1 for BCD-PE, 737.48 M–1 for HPBCD-PE and 5959.06 M–1 for SBEBCD-PE. The in silico predictions of mode of inclusion were in close agreement with the experimental proton NMR observation. DSC and XRD demonstrated complete amorphization of crystalline PE upon inclusion. All complexes exhibited >95% dissolution within 10 min compared to drug powder that showed <40% at the same time. Marked lowering of blood glucose was recorded for all complexes. Conclusion: Complexation of PE with different BCD significantly influenced its aqueous solubility, improved in vitro dissolution and consequently translated into enhanced pharmacodynamic activity in rats

  18. Multiscale modeling of complex molecular structure and dynamics with MBN Explorer

    CERN Document Server

    Solov’yov, Ilia A; Solov’yov, Andrey V

    2017-01-01

    This book introduces readers to MesoBioNano (MBN) Explorer – a multi-purpose software package designed to model molecular systems at various levels of size and complexity. In addition, it presents a specially designed multi-task toolkit and interface – the MBN Studio – which enables the set-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science, and guides readers through its applications in numerous areas of research in bio- and chemical physics and material science – ranging from the nano- to the meso-scale. MBN Explorer is particularly suited to computing the system’s energy, to optimizing molecular structure, and to exploring the various facets of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potenti...

  19. Molecular typing of Burkholderia cepacia complex isolated from patients attending an Italian Cystic Fibrosis Centre.

    Science.gov (United States)

    Teri, Antonio; Sottotetti, Samantha; Biffi, Arianna; Girelli, Daniela; D'Accico, Monica; Arghittu, Milena; Colombo, Carla; Corti, Fabiola; Pizzamiglio, Giovanna; Cariani, Lisa

    2018-04-01

    Bacteria from the Burkholderia cepacia complex (Bcc) are capable of causing severe infections in patients with cystic fibrosis (CF). Bcc infection is often extremely difficult to treat due to its intrinsic resistance to multiple antibiotics. In addition, it seems to speed up the decline of lung function and is considered a contraindication for lung transplantation in CF. This study investigates the species of the Bcc strains recovered from chronically infected CF subjects by means of: isolation, identification methods and complete recA nucleotide sequences of 151 samples. Molecular typing showed that B. cenocepacia III is the dominant strain found in the group of subjects being treated at the Milan CF Centre (Italy) and that the infection is chronically maintained by the same species. Defining species by means of molecular analysis yields important information for the clinician in order to establish the most appropriate therapy and implement correct measures for prevention of transmission among CF subjects.

  20. AB INITIO molecular orbital studies of some high temperature metal halide complexes

    International Nuclear Information System (INIS)

    Curtiss, L.A.

    1978-01-01

    The use of ab initio molecular orbital calculations to aid in the characterization, i.e., structures and energies, of metal halide complexes present in high temperature salt vapors has been investigated. Standard LCAO-SCF methods were used and calculations were carried out using the minimal STO-3G basis set. The complexes included in this study were Al 2 F 6 , Al 2 Cl 6 , AlF 3 NH 3 , AlCl 3 NH 3 , and AlF 3 N 2 . The Al 2 X 6 complexes are found to have D/sub 2h/ symmetry in agreement with most experimental results. A planar form was found to be considerably higher in energy. The AlX 3 NH 3 complexes are found to have C/sub 3v/ symmetry with a small barrier to rotation about the Al-N axis. The AlF 3 N 2 complex is found to be weakly bound together with a binding energy of -8.2 kcal/mole at the STO-3G level

  1. Consequences of intramolecular dityrosine formation on a DNA-protein complex: a molecular modeling study

    International Nuclear Information System (INIS)

    Gras, Julien; Sy, Denise; Eon, Severine; Charlier, Michel; Spotheim-Maurizot, Melanie

    2005-01-01

    Irradiation of the free lac repressor with γ-rays abolishes protein's ability to specifically bind operator DNA. A possible radiation-induced protein damage is a dityrosine (DTyr) formed by two spatially close radiation-induced tyrosyl radicals. We performed the molecular modeling of complexes between operator DNA and DTyr-bearing parts (headpieces) of the repressor. The presence of DTyr affects the structure and the interactions between partners. A detailed analysis allows to conclude this damage can partially account for the loss of repressor ability to bind DNA

  2. Isotope effects in complex scattering lengths for He collisions with molecular hydrogen

    International Nuclear Information System (INIS)

    Nolte, J. L.; Yang, B. H.; Stancil, P. C.; Lee, Teck-Ghee; Balakrishnan, N.; Forrey, R. C.; Dalgarno, A.

    2010-01-01

    We examine the effect of theoretically varying the collision-system reduced mass in collisions of He with vibrationally excited molecular hydrogen and observe zero-energy resonances for select atomic 'hydrogen' masses less than 1 u or a 'helium' mass of 1.95 u. Complex scattering lengths, state-to-state vibrational quenching cross sections, and a low-energy elastic scattering resonance are all studied as a function of collision-system reduced mass. Experimental observations of these phenomena in the cold and ultracold regimes for collisions of 3 He and 4 He with H 2 , HD, HT, and DT should be feasible in the near future.

  3. Molecular complexity in astrophysical environments: From astrochemistry to “astrobiology”?

    Directory of Open Access Journals (Sweden)

    d’Hendecourt L. Le Sergeant

    2012-01-01

    Full Text Available I present in this paper my own view about the intricate problem between the evolution of molecular complexity as observed from an astrophysicist point of view and its possible relation to the problem of the origin of life as we know it on Earth. Using arguments from observational astrophysics, I propose that life cannot really be based on other elements that the ones organizing our own so that other life forms based on totally different elemental and molecular processes are highly improbable. As a consequence terrestrial-type environments are probably the most favorable ones to life’s “emergence” and subsequent evolution. Discussing molecular (organic complexity, I show where this molecular complexity is located in astrophysical environments, mostly within inter/circumstellar solid state materials known as “grains” which, at least partly, end up in comets and asteroids and finally on planetary surfaces as meteorites. Considerations based on non directed laboratory simulations experiments, recent results regarding chiral asymmetry in potentially prebiotic matter and the possible explanation to the determinism about the choice of the L sign of the enantiomeric excesses in meteoritic amino acids, following a plausible astrophysical scenario, lead to the idea that the origin of life on Earth was indeed the result of a rather deterministic phenomenon, albeit difficult if not impossible to apprehend in its intimate mechanisms via a complete understanding of all the processes involved. Finally, the crucial point in supporting the idea of life’s ubiquity and wide distribution in our Galaxy (or universe? lies in the fact that planetary evolution, another astrophysical argument, is a major and very strong constraint for the development of life above its “minimal definition”. Life, particularly the complex and evolved one, could be indeed very rare in our Galaxy, although the very large number of exoplanets may be a counter-argument to this

  4. Construction of tunable peptide nucleic acid junctions.

    Science.gov (United States)

    Duan, Tanghui; He, Liu; Tokura, Yu; Liu, Xin; Wu, Yuzhou; Shi, Zhengshuang

    2018-03-15

    We report here the construction of 3-way and 4-way peptide nucleic acid (PNA) junctions as basic structural units for PNA nanostructuring. The incorporation of amino acid residues into PNA chains makes PNA nanostructures with more structural complexity and architectural flexibility possible, as exemplified by building 3-way PNA junctions with tunable nanopores. Given that PNA nanostructures have good thermal and enzymatic stabilities, they are expected to have broad potential applications in biosensing, drug delivery and bioengineering.

  5. Spinal Gap Junction Channels in Neuropathic Pain

    OpenAIRE

    Jeon, Young Hoon; Youn, Dong Ho

    2015-01-01

    Damage to peripheral nerves or the spinal cord is often accompanied by neuropathic pain, which is a complex, chronic pain state. Increasing evidence indicates that alterations in the expression and activity of gap junction channels in the spinal cord are involved in the development of neuropathic pain. Thus, this review briefly summarizes evidence that regulation of the expression, coupling, and activity of spinal gap junction channels modulates pain signals in neuropathic pain states induced...

  6. Synthesis, solid and solution studies of paraquat dichloride calixarene complexes. Molecular modelling

    International Nuclear Information System (INIS)

    Garcia S, I.; Ramirez, F. M.

    2010-01-01

    The interaction of the herbicide paraquat dichloride (P Q, substrate) with p-tert-butylcalix arenas (L, receptor) was investigated in both the solution and solid states. The isolated paraquat calixarene complexes were characterised by UV-visible, 1 H NMR, ESI-Ms, Luminescence and IR spectroscopies and elemental analysis. The stoichiometry of complexes 1 and 2 was 1:1 (1 herbicide: 1 calixarene) and both revealed a biexponential luminescence decay with lifetimes depending on the size and the conformational particularity of the calixarenes. Molecular modelling suggested that both calixarenes interact with the herbicide through cation-π interaction. P Q in included in the p-tert butylcalix a rene cavity, a situation favoured by its pinched conformation in polar solvent while it is partially included in the p-tert butylcalix a rene cavity because of its in-out cone conformation. The theoretical results, in particular using Mopac procedures, were in agreement with the experimental findings. (Author)

  7. Synthesis, solid and solution studies of paraquat dichloride calixarene complexes. Molecular modelling

    Energy Technology Data Exchange (ETDEWEB)

    Garcia S, I.; Ramirez, F. M., E-mail: flor.ramirez@inin.gob.m [ININ, Departamento de Quimica, Carretera Mexico-Toluca s/n, 52750 Ocoyoacac, Estado de Mexico (Mexico)

    2010-07-01

    The interaction of the herbicide paraquat dichloride (P Q, substrate) with p-tert-butylcalix arenas (L, receptor) was investigated in both the solution and solid states. The isolated paraquat calixarene complexes were characterised by UV-visible, {sup 1}H NMR, ESI-Ms, Luminescence and IR spectroscopies and elemental analysis. The stoichiometry of complexes 1 and 2 was 1:1 (1 herbicide: 1 calixarene) and both revealed a biexponential luminescence decay with lifetimes depending on the size and the conformational particularity of the calixarenes. Molecular modelling suggested that both calixarenes interact with the herbicide through cation-{pi} interaction. P Q in included in the p-tert butylcalix a rene cavity, a situation favoured by its pinched conformation in polar solvent while it is partially included in the p-tert butylcalix a rene cavity because of its in-out cone conformation. The theoretical results, in particular using Mopac procedures, were in agreement with the experimental findings. (Author)

  8. A molecular mechanics (MM3(96)) force field for metal-amide complexes

    International Nuclear Information System (INIS)

    Hay, B.P.; Clement, O.; Sandrone, G.; Dixon, D.A.

    1998-01-01

    A molecular mechanics (MM3(96)) force field is reported for modeling metal complexes of amides in which the amide is coordinated through oxygen. This model uses a points-on-a-sphere approach which involves the parameterization of the Msingle bondO stretch, the Msingle bondO double-bond C bend, and the Msingle bondO double-bond Csingle bondX (X = C, H, N) torsion interactions. Relationships between force field parameters and metal ion properties (charge, ionic radius, and electronegativity) are presented that allow the application of this model to a wide range of metal ions. The model satisfactorily reproduces the structures of over fifty amide complexes with the alkaline earths, transition metals, lanthanides, and actinides

  9. Molecular beam epitaxial growth of Bi2Te3 and Sb2Te3 topological insulators on GaAs (111 substrates: a potential route to fabricate topological insulator p-n junction

    Directory of Open Access Journals (Sweden)

    Zhaoquan Zeng

    2013-07-01

    Full Text Available High quality Bi2Te3 and Sb2Te3 topological insulators films were epitaxially grown on GaAs (111 substrate using solid source molecular beam epitaxy. Their growth and behavior on both vicinal and non-vicinal GaAs (111 substrates were investigated by reflection high-energy electron diffraction, atomic force microscopy, X-ray diffraction, and high resolution transmission electron microscopy. It is found that non-vicinal GaAs (111 substrate is better than a vicinal substrate to provide high quality Bi2Te3 and Sb2Te3 films. Hall and magnetoresistance measurements indicate that p type Sb2Te3 and n type Bi2Te3 topological insulator films can be directly grown on a GaAs (111 substrate, which may pave a way to fabricate topological insulator p-n junction on the same substrate, compatible with the fabrication process of present semiconductor optoelectronic devices.

  10. Dissecting the molecular assembly of the Toxoplasma gondii MyoA motility complex.

    Science.gov (United States)

    Powell, Cameron J; Jenkins, Meredith L; Parker, Michelle L; Ramaswamy, Raghavendran; Kelsen, Anne; Warshaw, David M; Ward, Gary E; Burke, John E; Boulanger, Martin J

    2017-11-24

    Apicomplexan parasites such as Toxoplasma gondii rely on a unique form of locomotion known as gliding motility. Generating the mechanical forces to support motility are divergent class XIV myosins (MyoA) coordinated by accessory proteins known as light chains. Although the importance of the MyoA-light chain complex is well-established, the detailed mechanisms governing its assembly and regulation are relatively unknown. To establish a molecular blueprint of this dynamic complex, we first mapped the adjacent binding sites of light chains MLC1 and ELC1 on the MyoA neck (residues 775-818) using a combination of hydrogen-deuterium exchange mass spectrometry and isothermal titration calorimetry. We then determined the 1.85 Å resolution crystal structure of MLC1 in complex with its cognate MyoA peptide. Structural analysis revealed a bilobed architecture with MLC1 clamping tightly around the helical MyoA peptide, consistent with the stable 10 nm K d measured by isothermal titration calorimetry. We next showed that coordination of calcium by an EF-hand in ELC1 and prebinding of MLC1 to the MyoA neck enhanced the affinity of ELC1 for the MyoA neck 7- and 8-fold, respectively. When combined, these factors enhanced ELC1 binding 49-fold (to a K d of 12 nm). Using the full-length MyoA motor (residues 1-831), we then showed that, in addition to coordinating the neck region, ELC1 appears to engage the MyoA converter subdomain, which couples the motor domain to the neck. These data support an assembly model where staged binding events cooperate to yield high-affinity complexes that are able to maximize force transduction. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Exploring molecular complexity with ALMA (EMoCA): Deuterated complex organic molecules in Sagittarius B2(N2)

    Science.gov (United States)

    Belloche, A.; Müller, H. S. P.; Garrod, R. T.; Menten, K. M.

    2016-03-01

    Context. Deuteration is a powerful tracer of the history of the cold prestellar phase in star-forming regions. Apart from methanol, little is known about deuterium fractionation of complex organic molecules in the interstellar medium, especially in regions forming high-mass stars. Aims: Our goal is to detect deuterated complex organic molecules toward the high mass star-forming region Sagittarius B2 (Sgr B2) and derive the level of deuteration for these molecules. Methods: We use a complete 3-mm spectral line survey performed with the Atacama Large Millimeter/submillimeter Array (ALMA) to search for deuterated complex organic molecules toward the hot molecular core Sgr B2(N2). We constructed population diagrams and integrated intensity maps to fit rotational temperatures and emission sizes for each molecule. Column densities are derived by modeling the full spectrum under the assumption of local thermodynamic equilibrium. We compare the results to predictions of two astrochemical models that treat the deuteration process. Results: We report the detection of CH2DCN toward Sgr B2(N2) with a deuteration level of 0.4%, and tentative detections of CH2DOH, CH2DCH2CN, the chiral molecule CH3CHDCN, and DC3N with levels in the range 0.05%-0.12%. A stringent deuteration upper limit is obtained for CH3OD (cyanide, the four deuterated species of ethanol, and CH2DOCHO. Ethyl cyanide is less deuterated than methyl cyanide by at least a factor five. The [CH2DOH]/[CH3OD] abundance ratio is higher than 1.8. It may still be consistent with the value obtained in Orion KL. Except for methyl cyanide, the measured deuteration levels lie at least a factor four below the predictions of current astrochemical models. The deuteration levels in Sgr B2(N2) are also lower than in Orion KL by a factor of a few up to a factor ten. Conclusions: The discrepancy between the deuteration levels of Sgr B2(N2) and the predictions of chemical models, and the difference between Sgr B2(N2) and Orion KL may

  12. Thermodynamics of formation for the 18-crown-6-triglycine molecular complex in water-dimethylsulfoxide solvents

    Science.gov (United States)

    Usacheva, T. R.; Lan, Pham Thi; Sharnin, V. A.

    2014-06-01

    The effect of a water-dimethylsulfoxide (DMSO) solvent on the formation of a molecular complex of 18-crown-6 (18C6) with triglycine (diglycylglycine, 3Gly) is studied via calorimetric titration. It is found that switching from water to an H2O-DMSO mixture with DMSO mole fraction of 0.30 is accompanied by a monotonic increase in the stability of [3Gly18C6] complex, from log K ∘ = 1.10 to log K ∘ = 2.44, and an increase in the exothermicity of the reaction of its formation, from -5.9 to -16.9 kJ/mol. It is shown that the [3Gly18C6] complex exhibits enthalpy stabilization with negative values of enthalpy and entropy over the investigated range of H2O-DMSO solvents. Analysis of the reagents' solvation characteristics reveals that the increase in the reaction's exothermicity of transfer is due to differences in the solvation of [3Gly18C6] and 18C6 with a small solvation contribution from 3Gly. It is concluded that the change in the Gibbs energy of the reaction 3Glysolv + 18C6solv ↔ [3Gly18C6]solv is due to differences in the change in the solvation state of the complex and the peptide (Δtr G ∘([3Gly18C6])-Δtr G ∘(3Gly)).

  13. Controlled molecular self-assembly of complex three-dimensional structures in soft materials.

    Science.gov (United States)

    Huang, Changjin; Quinn, David; Suresh, Subra; Hsia, K Jimmy

    2018-01-02

    Many applications in tissue engineering, flexible electronics, and soft robotics call for approaches that are capable of producing complex 3D architectures in soft materials. Here we present a method using molecular self-assembly to generate hydrogel-based 3D architectures that resembles the appealing features of the bottom-up process in morphogenesis of living tissues. Our strategy effectively utilizes the three essential components dictating living tissue morphogenesis to produce complex 3D architectures: modulation of local chemistry, material transport, and mechanics, which can be engineered by controlling the local distribution of polymerization inhibitor (i.e., oxygen), diffusion of monomers/cross-linkers through the porous structures of cross-linked polymer network, and mechanical constraints, respectively. We show that oxygen plays a role in hydrogel polymerization which is mechanistically similar to the role of growth factors in tissue growth, and the continued growth of hydrogel enabled by diffusion of monomers/cross-linkers into the porous hydrogel similar to the mechanisms of tissue growth enabled by material transport. The capability and versatility of our strategy are demonstrated through biomimetics of tissue morphogenesis for both plants and animals, and its application to generate other complex 3D architectures. Our technique opens avenues to studying many growth phenomena found in nature and generating complex 3D structures to benefit diverse applications. Copyright © 2017 the Author(s). Published by PNAS.

  14. Reversible photocontrol of molecular assemblies of metal complex containing azo-amphiphiles

    International Nuclear Information System (INIS)

    Einaga, Yasuaki; Mikami, Rie; Akitsu, Takashiro; Li, Guangming

    2005-01-01

    Photo-controllable molecular systems, [M(en) 2 ][Pt(en) 2 Cl 2 ](1) 4 (M 2+ =Pt 2+ , Pd 2+ and en=ethylenediamine), have been designed by the self-assembly of chloride-bridged platinum/palladium complexes and photochromic amphiphiles of the azobenzene derivative, 4-[4-(N-methyl-N-n-dodecylamino)phenylazo]benzene sulfonic acid (designated as compound 1). Reversible structural changes caused by cis-trans photoisomerization of azo groups in compound 1 were observed by alternating illumination of UV and visible light. Visible illumination resulted in the formation of the plate-like structures, whereas UV illumination resulted in fragmentation of the assembling structures. Reversible changes were observed in the electronic states of the chloride-bridged platinum/palladium complexes; the plate-like structures exhibited charge transfer absorption of chloride-bridged platinum complexes and delocalized Pt(II)/Pt(IV) states, while the fragments of the separated complexes exhibited no charge transfer bands. As a consequence, we have discovered that the reversible structural changes in this system could be controlled by photoillumination

  15. Molecular identification of Mycobacterium tuberculosis complex isolates from Kermanshah Province, Iran

    Directory of Open Access Journals (Sweden)

    Roghieh Moghaddam

    2016-01-01

    Full Text Available Tuberculosis is one of the most important zoonotic diseases in the world. Rapid diagnosis of the disease and identification of species is extremely important for proper treatment of the disease as some species of the complex are resistant to the first-line of tuberculosis drugs. The aim of present study was molecular identification of Mycobacterium tuberculosis (MTB complex isolates from Kermanshah Province, Iran, which were submitted to the Tuberculosis Reference Laboratory at Razi Vaccine and Serum Research Institute (Tehran, Iran. To identify the genus Mycobacterium, all isolates were subjected to 16S rRNA polymerase chain reaction (PCR, and PCR-IS6110 was subsequently used to confirm that the isolates belonged to MTB complex. Finally, region of difference (RD typing was used to identify the species in the complex. The results of 16S rRNA and IS6110 PCR analysis showed the presence of 543-bp and 245-bp bands, respectively. Furthermore, 146bp, 172bp, 235bp, and 369bp at RD1, RD4, RD9, and RD12, respectively, were observed during RD typing. Thus, based on the results, all isolates were identified as MTB. It is worth mentioning that most tuberculosis cases are identified on the basis of acid-fast bacilli detection, and antibiotic therapy is immediately initiated subsequently. Moreover, it should be noted that some of these acid-fast positive cases might not be of genus Mycobacterium, and thus, the antibiotics prescribed might threaten the health of the patients. Additionally, if the identified bacilli are not within MTB complex, the drug therapy would differ. However, Mycobacterium bovis, which is a member of MTB complex and is resistant to pyrazinamide, requires exact strain identification. Based on the findings, individual isolates should be identified by RD typing methods, which could clearly discriminate the species from each other.

  16. Discovery of Multiseeded Multimode Formation of Embedded Clusters in the Rosette Molecular Complex

    Science.gov (United States)

    Li, Jin Zeng; Smith, Michael D.

    2005-02-01

    An investigation based on data from the spatially complete Two Micron All Sky Survey (2MASS) reveals that a remarkable burst of clustered star formation is taking place throughout the southeast quadrant of the Rosette Molecular Cloud. Compact clusters are forming in a multiseeded mode, in parallel and at various places. In addition, sparse aggregates of embedded young stars are extensively distributed. In this study we report the primary results and implications for high-mass and clustered star formation in giant molecular clouds. In particular, we incorporate for the first time the birth of medium- to low-mass stars into the scenario of sequential formation of OB clusters. Following the emergence of the young OB cluster NGC 2244, a variety of manifestations of forming clusters of medium to high mass appears in the vicinity of the swept-up layer of the H II region as well as farther into the molecular cloud. The embedded clusters appear to form in a structured manner, which suggests they follow tracks laid out by the decay of macroturbulence. We address the possible origins of the turbulence. This leads us to propose a tree model to interpret the neat spatial distribution of clusters within a large section of the Rosette complex. Prominent new-generation OB clusters are identified at the root of the tree pattern.

  17. LARGE-SCALE CO MAPS OF THE LUPUS MOLECULAR CLOUD COMPLEX

    International Nuclear Information System (INIS)

    Tothill, N. F. H.; Loehr, A.; Stark, A. A.; Lane, A. P.; Harnett, J. I.; Bourke, T. L.; Myers, P. C.; Parshley, S. C.; Wright, G. A.; Walker, C. K.

    2009-01-01

    Fully sampled degree-scale maps of the 13 CO 2-1 and CO 4-3 transitions toward three members of the Lupus Molecular Cloud Complex-Lupus I, III, and IV-trace the column density and temperature of the molecular gas. Comparison with IR extinction maps from the c2d project requires most of the gas to have a temperature of 8-10 K. Estimates of the cloud mass from 13 CO emission are roughly consistent with most previous estimates, while the line widths are higher, around 2 km s -1 . CO 4-3 emission is found throughout Lupus I, indicating widespread dense gas, and toward Lupus III and IV. Enhanced line widths at the NW end and along the edge of the B 228 ridge in Lupus I, and a coherent velocity gradient across the ridge, are consistent with interaction between the molecular cloud and an expanding H I shell from the Upper-Scorpius subgroup of the Sco-Cen OB Association. Lupus III is dominated by the effects of two HAe/Be stars, and shows no sign of external influence. Slightly warmer gas around the core of Lupus IV and a low line width suggest heating by the Upper-Centaurus-Lupus subgroup of Sco-Cen, without the effects of an H I shell.

  18. Molecular epidemiology is becoming complex under the dynamic HIV prevalence: The perspective from Harbin, China.

    Science.gov (United States)

    Shao, Bing; Song, Bo; Cao, Lijun; Du, Juan; Sun, Dongying; Lin, Yuanlong; Wang, Binyou; Wang, Fuxiang; Wang, Sunran

    2016-05-01

    Unlike most areas of China, HIV transmission via men who have sex with men (MSM) is increasing rapidly, and has become the main route of HIV transmission in Harbin city. The purpose of the current study was to elaborate the molecular epidemiologic characteristics of the new HIV epidemic. Eighty-one HIV-1 gag gene sequences (HXB2:806-1861) from local HIV infections were isolated; CRF01_AE predominated among HIV infections (71.6%), followed by subtype B (16.5%), CRF07_BC (6.2%), and unique recombinant strains (URFs; 6.2%). URFs were most often identified in the MSM population, which consisted of a recombination of CRF01_AE with subtype B or CRF07_BC. Six clusters were formed in this analysis; clusters I and II mainly circulated in southwest China. Clusters III and IV mainly circulated in southwest, southeast, and central China. Clusters V and VI mainly circulated in north and northeast China. Clusters III and IV may facilitate the transmission of the CRF01_AE strain from the southwest to the north and northeast regions of China. HIV subtypes are becoming diverse with the persistent epidemic in this geographic region. In brief, our results indicate that the molecular epidemiology of HIV is trending to be more complex. Thus, timely molecular epidemiologic supervision of HIV is necessary, especially for the MSM population. © 2015 Wiley Periodicals, Inc.

  19. Discovery of Paragonimus westermani in Vietnam and its molecular phylogenetic status in P. westermani complex.

    Science.gov (United States)

    Doanh, Pham Ngoc; Shinohara, Akio; Horii, Yoichiro; Habe, Shigehisa; Nawa, Yukifumi

    2009-04-01

    Paragonimus westermani is the most well-known species among the genus Paragonimus. It is widely distributed in Asia with considerable genetic diversity to form P. westermani species complex. While P. westermani distributed in Japan, Korea, China, and Taiwan are genetically homogeneous to form the East Asia group, those found in other geographic areas are heterogeneous and would be divided into several groups. Recent discoveries of P. westermani in India and Sri Lanka highlighted new insights on molecular phylogenetic relationship of geographic isolates of this species complex. Since Vietnam is located at the east end of Southeast Asia, the intermediate position between South and East Asia, it is of interest to see whether P. westermani is distributed in this country. Here, we report that P. westermani metacercariae were found in mountainous crabs, Potamiscus sp., collected in Quangtri province in the central Vietnam. Adult worms were successfully obtained by experimental infection in cats. Molecular phylogenetic analyses revealed that P. westermani of Vietnamese isolates have high similarities with those of East Asia group.

  20. Josephson junction arrays

    International Nuclear Information System (INIS)

    Bindslev Hansen, J.; Lindelof, P.E.

    1985-01-01

    In this review we intend to cover recent work involving arrays of Josephson junctions. The work on such arrays falls naturally into three main areas of interest: 1. Technical applications of Josephson junction arrays for high-frequency devices. 2. Experimental studies of 2-D model systems (Kosterlitz-Thouless phase transition, commensurate-incommensurate transition in frustrated (flux) lattices). 3. Investigations of phenomena associated with non-equilibrium superconductivity in and around Josephson junctions (with high current density). (orig./BUD)

  1. Hybrid artificial photosynthetic systems comprising semiconductors as light harvesters and biomimetic complexes as molecular cocatalysts.

    Science.gov (United States)

    Wen, Fuyu; Li, Can

    2013-11-19

    Solar fuel production through artificial photosynthesis may be a key to generating abundant and clean energy, thus addressing the high energy needs of the world's expanding population. As the crucial components of photosynthesis, the artificial photosynthetic system should be composed of a light harvester (e.g., semiconductor or molecular dye), a reduction cocatalyst (e.g., hydrogenase mimic, noble metal), and an oxidation cocatalyst (e.g., photosystem II mimic for oxygen evolution from water oxidation). Solar fuel production catalyzed by an artificial photosynthetic system starts from the absorption of sunlight by the light harvester, where charge separation takes place, followed by a charge transfer to the reduction and oxidation cocatalysts, where redox reaction processes occur. One of the most challenging problems is to develop an artificial photosynthetic solar fuel production system that is both highly efficient and stable. The assembly of cocatalysts on the semiconductor (light harvester) not only can facilitate the charge separation, but also can lower the activation energy or overpotential for the reactions. An efficient light harvester loaded with suitable reduction and oxidation cocatalysts is the key for high efficiency of artificial photosynthetic systems. In this Account, we describe our strategy of hybrid photocatalysts using semiconductors as light harvesters with biomimetic complexes as molecular cocatalysts to construct efficient and stable artificial photosynthetic systems. We chose semiconductor nanoparticles as light harvesters because of their broad spectral absorption and relatively robust properties compared with a natural photosynthesis system. Using biomimetic complexes as cocatalysts can significantly facilitate charge separation via fast charge transfer from the semiconductor to the molecular cocatalysts and also catalyze the chemical reactions of solar fuel production. The hybrid photocatalysts supply us with a platform to study the

  2. Equivalent Josephson junctions

    International Nuclear Information System (INIS)

    Boyadzhiev, T.L.; ); Semerdzhieva, E.G.; Shukrinov, Yu.M.; Fiziko-Tekhnicheskij Inst., Dushanbe

    2008-01-01

    The magnetic field dependences of critical current are numerically constructed for a long Josephson junction with a shunt- or resistor-type microscopic inhomogeneities and compared to the critical curve of a junction with exponentially varying width. The numerical results show that it is possible to replace the distributed inhomogeneity of a long Josephson junction by an inhomogeneity localized at one of its ends, which has certain technological advantages. It is also shown that the critical curves of junctions with exponentially varying width and inhomogeneities localized at the ends are unaffected by the mixed fluxon-antifluxon distributions of the magnetic flux [ru

  3. Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics.

    Science.gov (United States)

    Yang, Qian; Sing-Long, Carlos A; Reed, Evan J

    2017-08-01

    We propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. In contrast, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our method on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. The framework described in this work paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates.

  4. A molecular perspective on a complex polymorphic inversion system with cytological evidence of multiply reused breakpoints.

    Science.gov (United States)

    Orengo, D J; Puerma, E; Papaceit, M; Segarra, C; Aguadé, M

    2015-06-01

    Genome sequence comparison across the Drosophila genus revealed that some fixed inversion breakpoints had been multiply reused at this long timescale. Cytological studies of Drosophila inversion polymorphism had previously shown that, also at this shorter timescale, some breakpoints had been multiply reused. The paucity of molecularly characterized polymorphic inversion breakpoints has so far precluded contrasting whether cytologically shared breakpoints of these relatively young inversions are actually reused at the molecular level. The E chromosome of Drosophila subobscura stands out because it presents several inversion complexes. This is the case of the E1+2+9+3 arrangement that originated from the ancestral Est arrangement through the sequential accumulation of four inversions (E1, E2, E9 and E3) sharing some breakpoints. We recently identified the breakpoints of inversions E1 and E2, which allowed establishing reuse at the molecular level of the cytologically shared breakpoint of these inversions. Here, we identified and sequenced the breakpoints of inversions E9 and E3, because they share breakpoints at sections 58D and 64C with those of inversions E1 and E2. This has allowed establishing that E9 and E3 originated through the staggered-break mechanism. Most importantly, sequence comparison has revealed the multiple reuse at the molecular level of the proximal breakpoint (section 58D), which would have been used at least by inversions E2, E9 and E3. In contrast, the distal breakpoint (section 64C) might have been only reused once by inversions E1 and E2, because the distal E3 breakpoint is displaced >70 kb from the other breakpoint limits.

  5. Iterative Calibration: A Novel Approach for Calibrating the Molecular Clock Using Complex Geological Events.

    Science.gov (United States)

    Loeza-Quintana, Tzitziki; Adamowicz, Sarah J

    2018-02-01

    During the past 50 years, the molecular clock has become one of the main tools for providing a time scale for the history of life. In the era of robust molecular evolutionary analysis, clock calibration is still one of the most basic steps needing attention. When fossil records are limited, well-dated geological events are the main resource for calibration. However, biogeographic calibrations have often been used in a simplistic manner, for example assuming simultaneous vicariant divergence of multiple sister lineages. Here, we propose a novel iterative calibration approach to define the most appropriate calibration date by seeking congruence between the dates assigned to multiple allopatric divergences and the geological history. Exploring patterns of molecular divergence in 16 trans-Bering sister clades of echinoderms, we demonstrate that the iterative calibration is predominantly advantageous when using complex geological or climatological events-such as the opening/reclosure of the Bering Strait-providing a powerful tool for clock dating that can be applied to other biogeographic calibration systems and further taxa. Using Bayesian analysis, we observed that evolutionary rate variability in the COI-5P gene is generally distributed in a clock-like fashion for Northern echinoderms. The results reveal a large range of genetic divergences, consistent with multiple pulses of trans-Bering migrations. A resulting rate of 2.8% pairwise Kimura-2-parameter sequence divergence per million years is suggested for the COI-5P gene in Northern echinoderms. Given that molecular rates may vary across latitudes and taxa, this study provides a new context for dating the evolutionary history of Arctic marine life.

  6. Large scale IRAM 30 m CO-observations in the giant molecular cloud complex W43

    Science.gov (United States)

    Carlhoff, P.; Nguyen Luong, Q.; Schilke, P.; Motte, F.; Schneider, N.; Beuther, H.; Bontemps, S.; Heitsch, F.; Hill, T.; Kramer, C.; Ossenkopf, V.; Schuller, F.; Simon, R.; Wyrowski, F.

    2013-12-01

    We aim to fully describe the distribution and location of dense molecular clouds in the giant molecular cloud complex W43. It was previously identified as one of the most massive star-forming regions in our Galaxy. To trace the moderately dense molecular clouds in the W43 region, we initiated W43-HERO, a large program using the IRAM 30 m telescope, which covers a wide dynamic range of scales from 0.3 to 140 pc. We obtained on-the-fly-maps in 13CO (2-1) and C18O (2-1) with a high spectral resolution of 0.1 km s-1 and a spatial resolution of 12''. These maps cover an area of ~1.5 square degrees and include the two main clouds of W43 and the lower density gas surrounding them. A comparison to Galactic models and previous distance calculations confirms the location of W43 near the tangential point of the Scutum arm at approximately 6 kpc from the Sun. The resulting intensity cubes of the observed region are separated into subcubes, which are centered on single clouds and then analyzed in detail. The optical depth, excitation temperature, and H2 column density maps are derived out of the 13CO and C18O data. These results are then compared to those derived from Herschel dust maps. The mass of a typical cloud is several 104 M⊙ while the total mass in the dense molecular gas (>102 cm-3) in W43 is found to be ~1.9 × 106 M⊙. Probability distribution functions obtained from column density maps derived from molecular line data and Herschel imaging show a log-normal distribution for low column densities and a power-law tail for high densities. A flatter slope for the molecular line data probability distribution function may imply that those selectively show the gravitationally collapsing gas. Appendices are available in electronic form at http://www.aanda.orgThe final datacubes (13CO and C18O) for the entire survey are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/560/A24

  7. Molecular diagnostic development for begomovirus-betasatellite complexes undergoing diversification: A case study.

    Science.gov (United States)

    Brown, Judith K; Ur-Rehman, Muhammad Zia; Avelar, Sofia; Chingandu, N; Hameed, Usman; Haider, Saleem; Ilyas, Muhammad

    2017-09-15

    At least five begomoviral species that cause leaf curl disease of cotton have emerged recently in Asia and Africa, reducing fiber quality and yield. The potential for the spread of these viruses to other cotton-vegetable growing regions throughout the world is extensive, owing to routine, global transport of alternative hosts of the leaf curl viruses, especially ornamentals. The research reported here describes the design and validation of polymerase chain reaction (PCR) primers undertaken to facilitate molecular detection of the two most-prevalent leaf curl-associated begomovirus-betasatellite complexes in the Indian Subcontinent and Africa, the Cotton leaf curl Kokhran virus-Burewala strain and Cotton leaf curl Gezira virus, endemic to Asia and Africa, respectively. Ongoing genomic diversification of these begomoviral-satellite complexes was evident based on nucleotide sequence alignments, and analysis of single nucleotide polymorphisms, both factors that created new challenges for primer design. The additional requirement for species and strain-specific, and betasatellite-specific primer design, imposes further constraints on primer design and validation due to the large number of related species and strains extant in 'core leaf curl virus complex', now with expanded distribution in south Asia, the Pacific region, and Africa-Arabian Peninsula that have relatively highly conserved coding and non-coding regions, which precludes much of the genome-betasatellite sequence when selecting primer 'targets'. Here, PCR primers were successfully designed and validated for detection of cloned viral genomes and betasatellites for representative 'core leaf curl' strains and species, distant relatives, and total DNA isolated from selected plant species. The application of molecular diagnostics to screen plant imports prior to export or release from ports of entry is expected to greatly reduce the likelihood of exotic leaf curl virus introductions that could dramatically affect

  8. Molecular systematics reveals increased diversity within the South African Laurencia complex (Rhodomelaceae, Rhodophyta).

    Science.gov (United States)

    Francis, Caitlynne; Bolton, John J; Mattio, Lydiane; Mandiwana-Neudani, Tshifhiwa G; Anderson, Robert J

    2017-08-01

    Previous publications list ten species in the Laurencia complex from South Africa with all ascribed to the genus Laurencia sensu stricto. However, the diversity of the complex in South Africa has not yet been re-assessed following the numerous recent taxonomic changes. This study investigated the phylogenetic relationships and taxonomy of this group in South Africa using recent collections. Methods included molecular phylogenetic analyses of plastid rbcL gene sequences (a total of 146; including eleven outgroup taxa) using Maximum Likelihood and Bayesian Inference, and the examination of morphological and anatomical characters, including the number of corps en cerise when present. The seven genera of the Laurencia complex formed monophyletic clades with high posterior probabilities. Seventeen morphotypes were identified: 14 in the genus Laurencia sensu stricto, among which eight corresponded to Laurencia species currently recognized from South Africa and one each to species of Palisada, Chondrophycus, and Laurenciella. The six remaining morphotypes in Laurencia sensu stricto did not match any descriptions and are described here as five new species: Laurencia alfredensis sp. nov., Laurencia dichotoma sp. nov., Laurencia digitata sp. nov., Laurencia multiclavata sp. nov. and Laurencia sodwaniensis sp. nov. and a new variety: Laurencia pumila var. dehoopiensis var. nov. Laurencia stegengae nom. nov. is established to replace Laurencia peninsularis Stegenga, Bolton and Anderson nom. illeg. The diversity is likely greater, with six additional unidentified specimens found in this molecular investigation. These findings place South Africa alongside Australia in having one of the most diverse floras of this group in the world. © 2017 Phycological Society of America.

  9. Experimental, molecular docking investigations and bioavailability study on the inclusion complexes of finasteride and cyclodextrins

    Directory of Open Access Journals (Sweden)

    Mady FM

    2017-06-01

    Full Text Available Fatma M Mady,1,2 Usama Farghaly Aly2 1Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Taibah University, Medina, Saudi Arabia; 2Department of Pharmaceutics, Faculty of Pharmacy, Minia University, Minia, Egypt Abstract: Finasteride (FIN is a Class II candidate of the Biopharmaceutics Classification System (BCS. The lipophilic cavity of cyclodextrins (CyDs enables it to construct a non-covalent inclusion complex with different insoluble drugs. Only β-cyclodextrin (β-CyD and hydroxypropyl-β-CyD (HP-β-CyD have been previously examined with FIN. This study aimed to investigate the consistence of FIN with different kinds of β-CyDs, including dimethyl-β-cyclodextrin (DM-β-CyD, carboxymethyl-β-cyclodextrin (CM-β-CyD, HP-β-CyD, sulfobutyl ether-β-cyclodextrin (SBE-β-CyD, and β-CyD, by the coprecipitation method. The resultant inclusion systems were characterized by differential scanning calorimetry, infrared spectroscopy, X-ray diffractometry, and dissolution studies. Moreover, molecular docking for the selected inclusion systems was carried out to explore the suitable arrangements of FIN in the cavity of β-CyD or its derivatives. The results suggested that the DM-β-CyD inclusion system gave the higher complexation efficiency for improvement in solubility of FIN and hence enhancement of its bioavailability. Pharmacokinetic parameters displayed a higher absorption rate and higher area under the curve of the FIN/DM-β-CyD inclusion complex when compared with the drug alone, which indicates an improvement in the absorption and bioavailability of FIN in the DM-β-CyD inclusion system. Keywords: finasteride, cyclodextrins, molecular docking, pharmacokinetics, bioavailability

  10. Molecular Phylogeny and Zoogeography of the Capoeta damascina Species Complex (Pisces: Teleostei: Cyprinidae.

    Directory of Open Access Journals (Sweden)

    Nisreen Alwan

    Full Text Available Capoeta damascina was earlier considered by many authors as one of the most common freshwater fish species found throughout the Levant, Mesopotamia, Turkey, and Iran. However, owing to a high variation in morphological characters among and within its various populations, 17 nominal species were described, several of which were regarded as valid by subsequent revising authors. Capoeta damascina proved to be a complex of closely related species, which had been poorly studied. The current study aims at defining C. damascina and the C. damascina species complex. It investigates phylogenetic relationships among the various members of the C. damascina complex, based on mitochondrial and nuclear DNA sequences. Phylogenetic relationships were projected against paleogeographical events to interpret the geographic distribution of the taxa under consideration in relation to the area's geological history. Samples were obtained from throughout the geographic range and were subjected to genetic analyses, using two molecular markers targeting the mitochondrial cytochrome oxidase I (n = 103 and the two adjacent divergence regions (D1-D2 of the nuclear 28S rRNA genes (n = 65. Six closely related species were recognized within the C. damascina complex, constituting two main lineages: A western lineage represented by C. caelestis, C. damascina, and C. umbla and an eastern lineage represented by C. buhsei, C. coadi, and C. saadii. The results indicate that speciation of these taxa is rather a recent event. Dispersal occurred during the Pleistocene, resulting in present-day distribution patterns. A coherent picture of the phylogenetic relationships and evolutionary history of the C. damascina species complex is drawn, explaining the current patterns of distribution as a result of paleogeographic events and ecological adaptations.

  11. Molecular Phylogeny and Zoogeography of the Capoeta damascina Species Complex (Pisces: Teleostei: Cyprinidae).

    Science.gov (United States)

    Alwan, Nisreen; Esmaeili, Hamid-Reza; Krupp, Friedhelm

    2016-01-01

    Capoeta damascina was earlier considered by many authors as one of the most common freshwater fish species found throughout the Levant, Mesopotamia, Turkey, and Iran. However, owing to a high variation in morphological characters among and within its various populations, 17 nominal species were described, several of which were regarded as valid by subsequent revising authors. Capoeta damascina proved to be a complex of closely related species, which had been poorly studied. The current study aims at defining C. damascina and the C. damascina species complex. It investigates phylogenetic relationships among the various members of the C. damascina complex, based on mitochondrial and nuclear DNA sequences. Phylogenetic relationships were projected against paleogeographical events to interpret the geographic distribution of the taxa under consideration in relation to the area's geological history. Samples were obtained from throughout the geographic range and were subjected to genetic analyses, using two molecular markers targeting the mitochondrial cytochrome oxidase I (n = 103) and the two adjacent divergence regions (D1-D2) of the nuclear 28S rRNA genes (n = 65). Six closely related species were recognized within the C. damascina complex, constituting two main lineages: A western lineage represented by C. caelestis, C. damascina, and C. umbla and an eastern lineage represented by C. buhsei, C. coadi, and C. saadii. The results indicate that speciation of these taxa is rather a recent event. Dispersal occurred during the Pleistocene, resulting in present-day distribution patterns. A coherent picture of the phylogenetic relationships and evolutionary history of the C. damascina species complex is drawn, explaining the current patterns of distribution as a result of paleogeographic events and ecological adaptations.

  12. Junctional transfer in cultured vascular endothelium: II. Dye and nucleotide transfer

    International Nuclear Information System (INIS)

    Larson, D.M.; Sheridan, J.D.

    1985-01-01

    Vascular endothelial cultures, derived from large vessels, retain many of the characteristics of their in vivo counterparts. However, the observed reduction in size and complexity of intercellular gap and tight junctions in these cultured cells suggests that important functions, thought to be mediated by these structures, may be altered in vitro. In continuing studies on intercellular communication in vessel wall cells, the authors have quantitated the extent of junctional transfer of small molecular tracers (the fluorescent dye Lucifer Yellow CH and tritiated uridine nucleotides) in confluent cultures of calf aortic (BAEC) and umbilical vein (BVEC) endothelium. Both BAEC and BVEC show extensive (and quantitatively equivalent) dye and nucleotide transfer. As an analogue of intimal endothelium, the authors have also tested dye transfer in freshly isolated sheets of endothelium. Transfer in BAEC and BVEC sheets was more rapid, extensive and homogeneous than in the cultured cells, implying a reduction in molecular coupling as endothelium adapts to culture conditions. In addition, they have documented heterocellular nucleotide transfer between cultured endothelium and vascular smooth muscle cells, of particular interest considering the prevalence of ''myo-endothelial'' junctions in vivo. These data yield further information on junctional transfer in cultured vascular endothelium and have broad implications for the functional integration of the vessel wall in the physiology and pathophysiology of the vasculature

  13. The role of apical cell-cell junctions and associated cytoskeleton in mechanotransduction.

    Science.gov (United States)

    Sluysmans, Sophie; Vasileva, Ekaterina; Spadaro, Domenica; Shah, Jimit; Rouaud, Florian; Citi, Sandra

    2017-04-01

    Tissues of multicellular organisms are characterised by several types of specialised cell-cell junctions. In vertebrate epithelia and endothelia, tight and adherens junctions (AJ) play critical roles in barrier and adhesion functions, and are connected to the actin and microtubule cytoskeletons. The interaction between junctions and the cytoskeleton is crucial for tissue development and physiology, and is involved in the molecular mechanisms governing cell shape, motility, growth and signalling. The machineries which functionally connect tight and AJ to the cytoskeleton comprise proteins which either bind directly to cytoskeletal filaments, or function as adaptors for regulators of the assembly and function of the cytoskeleton. In the last two decades, specific cytoskeleton-associated junctional molecules have been implicated in mechanotransduction, revealing the existence of multimolecular complexes that can sense mechanical cues and translate them into adaptation to tensile forces and biochemical signals. Here, we summarise the current knowledge about the machineries that link tight and AJ to actin filaments and microtubules, and the molecular basis for mechanotransduction at epithelial and endothelial AJ. © 2017 Société Française des Microscopies and Société de Biologie Cellulaire de France. Published by John Wiley & Sons Ltd.

  14. Speciation in ancient cryptic species complexes: evidence from the molecular phylogeny of Brachionus plicatilis (Rotifera).

    Science.gov (United States)

    Gómez, Africa; Serra, Manuel; Carvalho, Gary R; Lunt, David H

    2002-07-01

    Continental lake-dwelling zooplanktonic organisms have long been considered cosmopolitan species with little geographic variation in spite of the isolation of their habitats. Evidence of morphological cohesiveness and high dispersal capabilities support this interpretation. However, this view has been challenged recently as many such species have been shown either to comprise cryptic species complexes or to exhibit marked population genetic differentiation and strong phylogeographic structuring at a regional scale. Here we investigate the molecular phylogeny of the cosmopolitan passively dispersing rotifer Brachionus plicatilis (Rotifera: Monogononta) species complex using nucleotide sequence variation from both nuclear (ribosomal internal transcribed spacer 1, ITS1) and mitochondrial (cytochrome c oxidase subunit I, COI) genes. Analysis of rotifer resting eggs from 27 salt lakes in the Iberian Peninsula plus lakes from four continents revealed nine genetically divergent lineages. The high level of sequence divergence, absence of hybridization, and extensive sympatry observed support the specific status of these lineages. Sequence divergence estimates indicate that the B. plicatilis complex began diversifying many millions of years ago, yet has showed relatively high levels of morphological stasis. We discuss these results in relation to the ecology and genetics of aquatic invertebrates possessing dispersive resting propagules and address the apparent contradiction between zooplanktonic population structure and their morphological stasis.

  15. A heteromeric molecular complex regulates the migration of lung alveolar epithelial cells during wound healing.

    Science.gov (United States)

    Ghosh, Manik C; Makena, Patrudu S; Kennedy, Joseph; Teng, Bin; Luellen, Charlean; Sinclair, Scott E; Waters, Christopher M

    2017-05-19

    Alveolar type II epithelial cells (ATII) are instrumental in early wound healing in response to lung injury, restoring epithelial integrity through spreading and migration. We previously reported in separate studies that focal adhesion kinase-1 (FAK) and the chemokine receptor CXCR4 promote epithelial repair mechanisms. However, potential interactions between these two pathways were not previously considered. In the present study, we found that wounding of rat ATII cells promoted increased association between FAK and CXCR4. In addition, protein phosphatase-5 (PP5) increased its association with this heteromeric complex, while apoptosis signal regulating kinase-1 (ASK1) dissociated from the complex. Cell migration following wounding was decreased when PP5 expression was decreased using shRNA, but migration was increased in ATII cells isolated from ASK1 knockout mice. Interactions between FAK and CXCR4 were increased upon depletion of ASK1 using shRNA in MLE-12 cells, but unaffected when PP5 was depleted. Furthermore, we found that wounded rat ATII cells exhibited decreased ASK1 phosphorylation at Serine-966, decreased serine phosphorylation of FAK, and decreased association of phosphorylated ASK1 with FAK. These changes in phosphorylation were dependent upon expression of PP5. These results demonstrate a unique molecular complex comprising CXCR4, FAK, ASK1, and PP5 in ATII cells during wound healing.

  16. Parameterization of the prosthetic redox centers of the bacterial cytochrome bc(1) complex for atomistic molecular dynamics simulations

    DEFF Research Database (Denmark)

    Kaszuba, K.; Postila, P. A.; Cramariuc, O.

    2013-01-01

    studied in large-scale classical molecular dynamics (MD) simulations. In part, this is due to lack of suitable force field parameters, centered atomic point charges in particular, for the complex's prosthetic redox centers. Accurate redox center charges are needed to depict realistically the inter-molecular...... interactions at different redox stages of the cyt bc(1) complex. Accordingly, here we present high-precision atomic point charges for the metal centers of the cyt bc(1) complex of Rhodobacter capsulatus derived from extensive density functional theory calculations, fitted using the restrained electrostatic...

  17. Anomalies in the equilibrium and nonequilibrium properties of correlated ions in complex molecular environments

    Science.gov (United States)

    Mahakrishnan, Sathiya; Chakraborty, Subrata; Vijay, Amrendra

    2017-11-01

    Emergent statistical attributes, and therefore the equations of state, of an assembly of interacting charge carriers embedded within a complex molecular environment frequently exhibit a variety of anomalies, particularly in the high-density (equivalently, the concentration) regime, which are not well understood, because they do not fall under the low-concentration phenomenologies of Debye-Hückel-Onsager and Poisson-Nernst-Planck, including their variants. To go beyond, we here use physical concepts and mathematical tools from quantum scattering theory, transport theory with the Stosszahlansatz of Boltzmann, and classical electrodynamics (Lorentz gauge) and obtain analytical expressions both for the average and the frequency-wave vector-dependent longitudinal and transverse current densities, diffusion coefficient, and the charge density, and therefore the analytical expressions for (a) the chemical potential, activity coefficient, and the equivalent conductivity for strong electrolytes and (b) the current-voltage characteristics for ion-transport processes in complex molecular environments. Using a method analogous to the notion of Debye length and thence the electrical double layer, we here identify a pair of characteristic length scales (longitudinal and the transverse), which, being wave vector and frequency dependent, manifestly exhibit nontrivial fluctuations in space-time. As a unifying theme, we advance a quantity (inverse length dimension), gscat(a ), which embodies all dynamical interactions, through various quantum scattering lengths, relevant to molecular species a, and the analytical behavior which helps us to rationalize the properties of strong electrolytes, including anomalies, in all concentration regimes. As an example, the behavior of gscat(a ) in the high-concentration regime explains the anomalous increase of the Debye length with concentration, as seen in a recent experiment on electrolyte solutions. We also put forth an extension of the

  18. Understanding charge transport in molecular electronics.

    Science.gov (United States)

    Kushmerick, J J; Pollack, S K; Yang, J C; Naciri, J; Holt, D B; Ratner, M A; Shashidhar, R

    2003-12-01

    For molecular electronics to become a viable technology the factors that control charge transport across a metal-molecule-metal junction need to be elucidated. We use an experimentally simple crossed-wire tunnel junction to interrogate how factors such as metal-molecule coupling, molecular structure, and the choice of metal electrode influence the current-voltage characteristics of a molecular junction.

  19. Supramolecular tunneling junctions

    NARCIS (Netherlands)

    Wimbush, K.S.

    2012-01-01

    In this study a variety of supramolecular tunneling junctions were created. The basis of these junctions was a self-assembled monolayer of heptathioether functionalized ß-cyclodextrin (ßCD) formed on an ultra-flat Au surface, i.e., the bottom electrode. This gave a well-defined hexagonally packed

  20. Supramolecular Systems and Chemical Reactions in Single-Molecule Break Junctions.

    Science.gov (United States)

    Li, Xiaohui; Hu, Duan; Tan, Zhibing; Bai, Jie; Xiao, Zongyuan; Yang, Yang; Shi, Jia; Hong, Wenjing

    2017-04-01

    The major challenges of molecular electronics are the understanding and manipulation of the electron transport through the single-molecule junction. With the single-molecule break junction techniques, including scanning tunneling microscope break junction technique and mechanically controllable break junction technique, the charge transport through various single-molecule and supramolecular junctions has been studied during the dynamic fabrication and continuous characterization of molecular junctions. This review starts from the charge transport characterization of supramolecular junctions through a variety of noncovalent interactions, such as hydrogen bond, π-π interaction, and electrostatic force. We further review the recent progress in constructing highly conductive molecular junctions via chemical reactions, the response of molecular junctions to external stimuli, as well as the application of break junction techniques in controlling and monitoring chemical reactions in situ. We suggest that beyond the measurement of single molecular conductance, the single-molecule break junction techniques provide a promising access to study molecular assembly and chemical reactions at the single-molecule scale.

  1. Intestinal epithelial barrier function and tight junction proteins with heat and exercise

    DEFF Research Database (Denmark)

    Dokladny, Karol; Zuhl, Micah N; Moseley, Pope L

    2016-01-01

    A single layer of enterocytes and tight junctions (intercellular multiprotein complexes) form the intestinal epithelial barrier that controls transport of molecules through transcellular and paracellular pathways. A dysfunctional or "leaky" intestinal tight junction barrier allows augmented perme...

  2. Computation of Collision-Induced Absorption by Simple Molecular Complexes, for Astrophysical Applications

    Science.gov (United States)

    Abel, Martin; Frommhold, Lothar; Li, Xiaoping; Hunt, Katharine L. C.

    2012-06-01

    The interaction-induced absorption by collisional pairs of H{_2} molecules is an important opacity source in the atmospheres of various types of planets and cool stars, such as late stars, low-mass stars, brown dwarfs, cool white dwarf stars, the ambers of the smaller, burnt out main sequence stars, exoplanets, etc., and therefore of special astronomical interest The emission spectra of cool white dwarf stars differ significantly in the infrared from the expected blackbody spectra of their cores, which is largely due to absorption by collisional H{_2}-H{_2}, H{_2}-He, and H{_2}-H complexes in the stellar atmospheres. Using quantum-chemical methods we compute the atmospheric absorption from hundreds to thousands of kelvin. Laboratory measurements of interaction-induced absorption spectra by H{_2} pairs exist only at room temperature and below. We show that our results reproduce these measurements closely, so that our computational data permit reliable modeling of stellar atmosphere opacities even for the higher temperatures. First results for H_2-He complexes have already been applied to astrophysical models have shown great improvements in these models. L. Frommhold, Collision-Induced Absorption in Gases, Cambridge University Press, Cambridge, New York, 1993 and 2006 X. Li, K. L. C. Hunt, F. Wang, M. Abel, and L. Frommhold, Collision-Induced Infrared Absorption by Molecular Hydrogen Pairs at Thousands of Kelvin, Int. J. of Spect., vol. 2010, Article ID 371201, 11 pages, 2010. doi: 10.1155/2010/371201 M. Abel, L. Frommhold, X. Li, and K. L. C. Hunt, Collision-induced absorption by H{_2} pairs: From hundreds to thousands of Kelvin, J. Phys. Chem. A, 115, 6805-6812, 2011} L. Frommhold, M. Abel, F. Wang, M. Gustafsson, X. Li, and K. L. C. Hunt, "Infrared atmospheric emission and absorption by simple molecular complexes, from first principles", Mol. Phys. 108, 2265, 2010 M. Abel, L. Frommhold, X. Li, and K. L. C. Hunt, Infrared absorption by collisional H_2-He complexes

  3. Molecular nanomagnets: Syntheses and characterization of high nuclearity transition metal complexes

    Science.gov (United States)

    Foguet-Albiol, Maria D.

    2006-12-01

    High nuclearity transition metal complexes have attracted a lot of attention because of their aesthetically pleasant structures and/or their potential applications. The fusion of the world of magnetism with the exciting research in physics and chemistry led to the realization of interesting types of materials that can function as nanoscale magnetic particles. The study of the magnetism of inorganic complexes and especially the study of these molecular nanomagnets (or single-molecule magnets, SMMs) is a field that has generated intense interest in the scientific community. Interest in these molecular nanomagnets arises as part of a broader investigation of nanomagnetism (and nanotechnology), as these represent the ultimate step in device miniaturization. The primary purpose of this dissertation is the development of new synthetic methods intended for the preparation of novel single-molecule magnets (SMMs). The definition of the "bottom-up approach" is to increase the size of molecules by adding new magnetic centers; this is attractive but does not actually reflect how the chemistry takes place. Various strategies have been employed in developing the aforementioned synthetic methods which include the use of mononuclear as well as preformed clusters as starting materials; and the introduction of new alcohol based ligands as N-methyldiethanolamine (mdaH2) and triethanolamine (teaH3), since currently only a few alcohol based ligands have been used by different research groups. Many of these efforts have led to the isolation of new polynuclear Mn clusters with nuclearities ranging all the way from four to thirty-one. Additionally, a family of related Fe7 complexes has been synthesized. The transition metal cluster chemistry has also been extended to nickel-containing species. Many of these polynulear transition metal complexes function as single-molecule magnets. An additional research direction discussed herein is the study of the exchange-coupled dimer of single

  4. A molecular timescale of eukaryote evolution and the rise of complex multicellular life

    Science.gov (United States)

    Hedges, S. Blair; Blair, Jaime E.; Venturi, Maria L.; Shoe, Jason L.

    2004-01-01

    BACKGROUND: The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time. RESULTS: Our phylogenetic analyses revealed that (i) animals are more closely related to fungi than to plants, (ii) red algae are closer to plants than to animals or fungi, (iii) choanoflagellates are closer to animals than to fungi or plants, (iv) diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v) diplomonads are basal to other eukaryotes (including alveolates and euglenozoans). Divergence times were estimated from global and local clock methods using 20-188 proteins per node, with data treated separately (multigene) and concatenated (supergene). Different time estimation methods yielded similar results (within 5%): vertebrate-arthropod (964 million years ago, Ma), Cnidaria-Bilateria (1,298 Ma), Porifera-Eumetozoa (1,351 Ma), Pyrenomycetes-Plectomycetes (551 Ma), Candida-Saccharomyces (723 Ma), Hemiascomycetes-filamentous Ascomycota (982 Ma), Basidiomycota-Ascomycota (968 Ma), Mucorales-Basidiomycota (947 Ma), Fungi-Animalia (1,513 Ma), mosses-vascular plants (707 Ma), Chlorophyta-Tracheophyta (968 Ma), Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma), Plantae-Animalia (1,609 Ma), Alveolata-plants+animals+fungi (1,973 Ma), Euglenozoa-plants+animals+fungi (1,961 Ma), and Giardia-plants+animals+fungi (2,309 Ma). By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to

  5. A molecular timescale of eukaryote evolution and the rise of complex multicellular life

    Directory of Open Access Journals (Sweden)

    Venturi Maria L

    2004-01-01

    Full Text Available Abstract Background The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time. Results Our phylogenetic analyses revealed that (i animals are more closely related to fungi than to plants, (ii red algae are closer to plants than to animals or fungi, (iii choanoflagellates are closer to animals than to fungi or plants, (iv diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v diplomonads are basal to other eukaryotes (including alveolates and euglenozoans. Divergence times were estimated from global and local clock methods using 20–188 proteins per node, with data treated separately (multigene and concatenated (supergene. Different time estimation methods yielded similar results (within 5%: vertebrate-arthropod (964 million years ago, Ma, Cnidaria-Bilateria (1,298 Ma, Porifera-Eumetozoa (1,351 Ma, Pyrenomycetes-Plectomycetes (551 Ma, Candida-Saccharomyces (723 Ma, Hemiascomycetes-filamentous Ascomycota (982 Ma, Basidiomycota-Ascomycota (968 Ma, Mucorales-Basidiomycota (947 Ma, Fungi-Animalia (1,513 Ma, mosses-vascular plants (707 Ma, Chlorophyta-Tracheophyta (968 Ma, Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma, Plantae-Animalia (1,609 Ma, Alveolata-plants+animals+fungi (1,973 Ma, Euglenozoa-plants+animals+fungi (1,961 Ma, and Giardia-plants+animals+fungi (2,309 Ma. By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to ~10

  6. Cloud fluid compression and softening in spiral arms and the formation of giant molecular cloud complexes

    International Nuclear Information System (INIS)

    Cowie, L.L.

    1981-01-01

    In this, the second paper of a series on the galactodynamics of the cloudy interstellar medium, we consider the response of such a gas to a forcing potential in the tight-winding density wave theory. The cloud fluid is treated in the hydrodynamic limit with an equation of state which softens at high densities. It is shown that in the inner regions of the galaxy, cooling of the cloud fluid in the arms can result in gravitational instability and the formation of large bound complexes of clouds which we identify with the giant molecular clouds (GMCs). Masses dimensions, distributions, and scale heights of the GMCs are predicted by the theory. It is suggested that the interstellar gas density in the disk is regulated by the gravitational instability mechanism in the arms which siphons material into star formation. Implications for the evolution of individual GMCs and for galactic morphology are discussed

  7. A direct ab initio molecular dynamics (MD) study on the benzophenone-water 1 : 1 complex.

    Science.gov (United States)

    Tachikawa, Hiroto; Iyama, Tetsuji; Kato, Kohichi

    2009-07-28

    Direct ab initio molecular dynamics (MD) method has been applied to a benzophenone-water 1 : 1 complex Bp(H(2)O) and free benzophenone (Bp) to elucidate the effects of zero-point energy (ZPE) vibration and temperature on the absorption spectra of Bp(H(2)O). The n-pi transition of free-Bp (S(1) state) was blue-shifted by the interaction with a water molecule, whereas three pi-pi transitions (S(2), S(3) and S(4)) were red-shifted. The effects of the ZPE vibration and temperature of Bp(H(2)O) increased the intensity of the n-pi transition of Bp(H(2)O) and caused broadening of the pi-pi transitions. In case of the temperature effect, the intensity of n-pi transition increases with increasing temperature. The electronic states of Bp(H(2)O) were discussed on the basis of the theoretical results.

  8. Molecular Complex of Lumiflavin and 2-Aminobenzoic Acid : Crystal Structure, Crystal Spectra, and Solution Properties

    OpenAIRE

    Shieh, Huey-Sheng; Ghisla, Sandro; Hanson, Louise Karle; Ludwig, Martha L.; Nordman, Christer E.

    1981-01-01

    The molecular complex lumiflavin-2-aminobenzoic acid monohydrate (C13H12N402●C7H7N02●H2O)crystallizes from aqueous solution as red triclinic prisms. The space group is P1 with cell dimensions a = 9.660 A, b = 14.866 Å, c = 7.045 Å, α = 95.44°, β = 95.86°, and γ = 105.66°. The crystal structure was solved by direct methods and refined by block-diagonal least-squares procedures to an R value of 0.050 on the basis of 1338 observed reflections. The structure is composed of stacks of alternating l...

  9. Programming molecular self-assembly of intrinsically disordered proteins containing sequences of low complexity

    Science.gov (United States)

    Simon, Joseph R.; Carroll, Nick J.; Rubinstein, Michael; Chilkoti, Ashutosh; López, Gabriel P.

    2017-06-01

    Dynamic protein-rich intracellular structures that contain phase-separated intrinsically disordered proteins (IDPs) composed of sequences of low complexity (SLC) have been shown to serve a variety of important cellular functions, which include signalling, compartmentalization and stabilization. However, our understanding of these structures and our ability to synthesize models of them have been limited. We present design rules for IDPs possessing SLCs that phase separate into diverse assemblies within droplet microenvironments. Using theoretical analyses, we interpret the phase behaviour of archetypal IDP sequences and demonstrate the rational design of a vast library of multicomponent protein-rich structures that ranges from uniform nano-, meso- and microscale puncta (distinct protein droplets) to multilayered orthogonally phase-separated granular structures. The ability to predict and program IDP-rich assemblies in this fashion offers new insights into (1) genetic-to-molecular-to-macroscale relationships that encode hierarchical IDP assemblies, (2) design rules of such assemblies in cell biology and (3) molecular-level engineering of self-assembled recombinant IDP-rich materials.

  10. Molecular variation and distribution of Anopheles fluviatilis (Diptera: Culicidae) complex in Iran.

    Science.gov (United States)

    Naddaf, Saied Reza; Razavi, Mohammad Reza; Bahramali, Golnaz

    2010-09-01

    Anopheles fluviatilis James (Diptera: Culicidae) is one of the known malaria vectors in south and southeastern Iran. Earlier ITS2 sequences analysis of specimens from Iran demonstrated only a single genotype that was identical to species Y in India, which is also the same as species T. We identified 2 haplotypes in the An. fluviatilis populations of Iran based on differences in nucleotide sequences of D3 domain of the 28S locus of ribosomal DNA (rDNA). Comparison of sequence data from 44 Iranian specimens with those publicly available in the Genbank database showed that all of the 28S-D3 sequences from Kazeroun and Khesht regions in Fars Province were identical to the database entry representing species U in India. In other regions, all the individuals showed heterozygosity at the single nucleotide position, which identifies species U and T. It is argued that the 2 species may co-occur in some regions and hybridize; however, the heterozygosity in the 28S-D3 locus was not reflected in ITS2 sequences and this locus for all individuals was identical to species T. This study shows that in a newly diverged species, like members of An. fluviatilis complex, a single molecular marker may not be sufficiently discriminatory to identify all the taxa over a vast geographical area. In addition, other molecular markers may provide more reliable information for species discrimination.

  11. Rotational Spectroscopy of the NH{sub 3}–H{sub 2} Molecular Complex

    Energy Technology Data Exchange (ETDEWEB)

    Surin, L. A.; Schlemmer, S. [I. Physikalisches Institut, University of Cologne, Zülpicher Str. 77, D-50937 Cologne (Germany); Tarabukin, I. V. [Institute of Spectroscopy of Russian Academy of Sciences, Fizicheskaya Str. 5, 108840 Troitsk, Moscow, Russia (Russian Federation); Breier, A. A.; Giesen, T. F. [Institute of Physics, University of Kassel, Heinrich-Plett-Str. 40, D-34132 Kassel (Germany); McCarthy, M. C. [Harvard-Smithsonian Center for Astrophysics, Cambridge, MA 02138 (United States); Avoird, A. van der, E-mail: surin@ph1.uni-koeln.de, E-mail: A.vanderAvoird@theochem.ru.nl [Theoretical Chemistry, Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands)

    2017-03-20

    We report the first high resolution spectroscopic study of the NH{sub 3}–H{sub 2} van der Waals molecular complex. Three different experimental techniques, a molecular beam Fourier transform microwave spectrometer, a millimeter-wave intracavity jet OROTRON spectrometer, and a submillimeter-wave jet spectrometer with multipass cell, were used to detect pure rotational transitions of NH{sub 3}–H{sub 2} in the wide frequency range from 39 to 230 GHz. Two nuclear spin species, ( o )-NH{sub 3}–( o )-H{sub 2} and ( p )-NH{sub 3}–( o )-H{sub 2}, have been assigned as carriers of the observed lines on the basis of accompanying rovibrational calculations performed using the ab initio intermolecular potential energy surface (PES) of Maret et al. The experimental spectra were compared with the theoretical bound state results, thus providing a critical test of the quality of the NH{sub 3}–H{sub 2} PES, which is a key issue for reliable computations of the collisional excitation and de-excitation of ammonia in the dense interstellar medium.

  12. Epigenetics and Shared Molecular Processes in the Regeneration of Complex Structures

    Directory of Open Access Journals (Sweden)

    Labib Rouhana

    2016-01-01

    Full Text Available The ability to regenerate complex structures is broadly represented in both plant and animal kingdoms. Although regenerative abilities vary significantly amongst metazoans, cumulative studies have identified cellular events that are broadly observed during regenerative events. For example, structural damage is recognized and wound healing initiated upon injury, which is followed by programmed cell death in the vicinity of damaged tissue and a burst in proliferation of progenitor cells. Sustained proliferation and localization of progenitor cells to site of injury give rise to an assembly of differentiating cells known as the regeneration blastema, which fosters the development of new tissue. Finally, preexisting tissue rearranges and integrates with newly differentiated cells to restore proportionality and function. While heterogeneity exists in the basic processes displayed during regenerative events in different species—most notably the cellular source contributing to formation of new tissue—activation of conserved molecular pathways is imperative for proper regulation of cells during regeneration. Perhaps the most fundamental of such molecular processes entails chromatin rearrangements, which prime large changes in gene expression required for differentiation and/or dedifferentiation of progenitor cells. This review provides an overview of known contributions to regenerative processes by noncoding RNAs and chromatin-modifying enzymes involved in epigenetic regulation.

  13. Molecular dynamics of conformation-specific dopamine transporter-inhibitor complexes.

    Science.gov (United States)

    Jean, Bernandie; Surratt, Christopher K; Madura, Jeffry D

    2017-09-01

    The recreational psychostimulant cocaine inhibits dopamine reuptake from the synapse, resulting in excessive stimulation of postsynaptic dopamine receptors in brain areas associated with reward and addiction. Cocaine binds to and stabilizes the outward- (extracellular-) facing conformation of the dopamine transporter (DAT) protein, while the low abuse potential DAT inhibitor benztropine prefers the inward- (cytoplasmic-) facing conformation. A correlation has been previously postulated between psychostimulant abuse potential and preference for the outward-facing DAT conformation. The 3β-aryltropane cocaine analogs LX10 and LX11, however, differ only in stereochemistry and share a preference for the outward-facing DAT, yet are reported to vary widely in abuse potential in an animal model. In search of the molecular basis for DAT conformation preference, complexes of cocaine, benztropine, LX10 or LX11 bound to each DAT conformation were subjected to 100ns of all-atom molecular dynamics simulation. Results were consistent with previous findings from cysteine accessibility assays used to assess an inhibitor's DAT conformation preference. The respective 2β- and 2α-substituted phenyltropanes of LX10 and LX11 interacted with hydrophobic regions of the DAT S1 binding site that were inaccessible to cocaine. Solvent accessibility measurements also revealed subtle differences in inhibitor positioning within a given DAT conformation. This work serves to advance our understanding of the conformational selectivity of DAT inhibitors and suggests that MD may be useful in antipsychostimulant therapeutic design. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Molecular chaperone complexes with antagonizing activities regulate stability and activity of the tumor suppressor LKB1.

    Science.gov (United States)

    Gaude, H; Aznar, N; Delay, A; Bres, A; Buchet-Poyau, K; Caillat, C; Vigouroux, A; Rogon, C; Woods, A; Vanacker, J-M; Höhfeld, J; Perret, C; Meyer, P; Billaud, M; Forcet, C

    2012-03-22

    LKB1 is a tumor suppressor that is constitutionally mutated in a cancer-prone condition, called Peutz-Jeghers syndrome, as well as somatically inactivated in a sizeable fraction of lung and cervical neoplasms. The LKB1 gene encodes a serine/threonine kinase that associates with the pseudokinase STRAD (STE-20-related pseudokinase) and the scaffolding protein MO25, the formation of this heterotrimeric complex promotes allosteric activation of LKB1. We have previously reported that the molecular chaperone heat shock protein 90 (Hsp90) binds to and stabilizes LKB1. Combining pharmacological studies and RNA interference approaches, we now provide evidence that the co-chaperone Cdc37 participates to the regulation of LKB1 stability. It is known that the Hsp90-Cdc37 complex recognizes a surface within the N-terminal catalytic lobe of client protein kinases. In agreement with this finding, we found that the chaperones Hsp90 and Cdc37 interact with an LKB1 isoform that differs in the C-terminal region, but not with a novel LKB1 variant that lacks a portion of the kinase N-terminal lobe domain. Reconstitution of the two complexes LKB1-STRAD and LKB1-Hsp90-Cdc37 with recombinant proteins revealed that the former is catalytically active whereas the latter is inactive. Furthermore, consistent with a documented repressor function of Hsp90, LKB1 kinase activity was transiently stimulated upon dissociation of Hsp90. Finally, disruption of the LKB1-Hsp90 complex favors the recruitment of both Hsp/Hsc70 and the U-box dependent E3 ubiquitin ligase CHIP (carboxyl terminus of Hsc70-interacting protein) that triggers LKB1 degradation. Taken together, our results establish that the Hsp90-Cdc37 complex controls both the stability and activity of the LKB1 kinase. This study further shows that two chaperone complexes with antagonizing activities, Hsp90-Cdc37 and Hsp/Hsc70-CHIP, finely control the cellular level of LKB1 protein.

  15. Molecular cloning, functional expression, and tissue distribution of a novel human gap junction-forming protein, connexin-31.9. Interaction with zona occludens protein-1

    NARCIS (Netherlands)

    Nielsen, Peter A; Beahm, Derek L; Giepmans, Ben N G; Baruch, Amos; Hall, James E; Kumar, Nalin M

    2002-01-01

    A novel human connexin gene (GJA11) was cloned from a genomic library. The open reading frame encoded a hypothetical protein of 294 amino acid residues with a predicted molecular mass of 31,933, hence referred to as connexin-31.9 (Cx31.9) or alpha 11 connexin. A clone in GenBank containing the

  16. Photoresponsive Molecular Memory Films Composed of Sequentially Assembled Heterolayers Containing Ruthenium Complexes.

    Science.gov (United States)

    Nagashima, Takumi; Ozawa, Hiroaki; Suzuki, Takashi; Nakabayashi, Takuya; Kanaizuka, Katsuhiko; Haga, Masa-Aki

    2016-01-26

    Photoresponsive molecular memory films were fabricated by a layer-by-layer (LbL) assembling of two dinuclear Ru complexes with tetrapodal phosphonate anchors, containing either 2,3,5,6-tetra(2-pyridyl)pyrazine or 1,2,4,5-tetra(2-pyridyl)benzene as a bridging ligand (Ru-NP and Ru-CP, respectively), using zirconium phosphonate to link the layers. Various types of multilayer homo- and heterostructures were constructed. In the multilayer heterofilms such as ITO||(Ru-NP)m |(Ru-CP)n , the difference in redox potentials between Ru-NP and Ru-CP layers was approximately 0.7 V, which induced a potential gradient determined by the sequence of the layers. In the ITO||(Ru-NP)m |(Ru-CP)n multilayer heterofilms, the direct electron transfer (ET) from the outer Ru-CP layers to the ITO were observed to be blocked for m>2, and charge trapping in the outer Ru-CP layers became evident from the appearance of an intervalence charge transfer (IVCT) band at 1140 nm from the formation of the mixed-valent state of Ru-CP units, resulting from the reductive ET mediation of the inner Ru-NP layers. Therefore, the charging/discharging ("1"and "0") states in the outer Ru-CP layers could be addressed and interconverted by applying potential pulses between -0.5 and +0.7 V. The two states could be read out by the direction of the photocurrent (anodic or cathodic). The molecular heterolayer films thus represent a typical example of a photoresponsive memory device; that is, the writing process may be achieved by the applied potential (-0.5 or +0.7 V), while the readout process is achieved by measuring the direction of the photocurrent (anodic or cathodic). Sequence-sensitive multilayer heterofilms, using redox-active complexes as building blocks, thus demonstrate great potential for the design of molecular functional devices. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Molecular phylogeny of Glossodoris (Ehrenberg, 1831) nudibranchs and related genera reveals cryptic and pseudocryptic species complexes

    KAUST Repository

    Matsuda, Shayle B.; Gosliner, Terrence M.

    2017-01-01

    Chromodorid nudibranchs (Chromodorididae) are brightly coloured sea slugs that live in some of the most biodiverse and threatened coral reefs on the planet. However, the evolutionary relationships within this family have not been well understood, especially in the genus Glossodoris. Members of Glossodoris have experienced large-scale taxonomic instability over the last century and have been the subject of repeated taxonomic changes, in part due to morphological characters being the sole traditional taxonomic sources of data. Changing concepts of traditional generic boundaries based on morphology also have contributed to this instability. Despite recent advances in molecular systematics, many aspects of chromodorid taxonomy remain poorly understood, particularly at the traditional species and generic levels. In this study, 77 individuals comprising 32 previously defined species were used to build the most robust phylogenetic tree of Glossodoris and related genera using mitochondrial genes cytochrome c oxidase subunit I and 16S, and the nuclear gene 28S. Bayesian inference, maximum likelihood, and maximum parsimony analyses verify the most recent hypothesized evolutionary relationships within Glossodoris. Additionally, a pseudocryptic and cryptic species complex within Glossodoris cincta and a pseudocryptic complex within Glossodoris pallida emerged, and three new species of Doriprismatica are identified.

  18. Molecular Self-Assembly of Group 11 Pyrazolate Complexes as Phosphorescent Chemosensors for Detection of Benzene

    Science.gov (United States)

    Ghazalli, N. F.; Yuliati, L.; Lintang, H. O.

    2018-01-01

    We highlight the systematic study on vapochromic sensing of aromatic vapors such as benzene using phosphorescent trinuclear pyrazolate complexes (2) with supramolecular assembly of a weak intermolecular metal-metal interaction consisting of 4-(3,5-dimethoxybenzyl)-3,5-dimethyl pyrazole ligand (1) and group 11 metal ions (Cu(I), Ag(I), Au(I)). The resulting chemosensor 2(Cu) revealed positive response to benzene vapors in 5 mins by blue-shifting its emission band in 44 nm (from 616 to 572 nm) and emitted bright orange to green, where this change cannot be recovered even with external stimuli. Comparing to 2(Ag) with longer metal-metal distance (473 nm) with same sensing time and quenching in 37%, 2(Au) gave quenching in 81% from its original intensity at 612 nm with reusability in 82% without external stimuli and emitted less emissive of red-orange from its original color. The shifting phenomenon in 2(Cu) suggests diffusion of benzene vapors to inside molecules for formation of intermolecular interaction with Cu(I)-Cu(I) interaction while quenching phenomenon in 2(Au) suggests diffusion of benzene vapors to between the Au(I)-Au(I) interaction. These results indicate that suitable molecular structure of ligand and metal ion in pyrazolate complex is important for designing chemosensor in the detection of benzene vapors.

  19. Lipid clustering correlates with membrane curvature as revealed by molecular simulations of complex lipid bilayers.

    Directory of Open Access Journals (Sweden)

    Heidi Koldsø

    2014-10-01

    Full Text Available Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP2, in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP2, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins.

  20. 20(S-Protopanaxadiol Phospholipid Complex: Process Optimization, Characterization, In Vitro Dissolution and Molecular Docking Studies

    Directory of Open Access Journals (Sweden)

    Yiqiong Pu

    2016-10-01

    Full Text Available 20(S-Protopanaxadiol (PPD, a bioactive compound extracted from ginseng, possesses cardioprotective, neuroprotective, anti-inflammatory, antiestrogenic, anticancer and anxiolytic effects. However, the clinical application of PPD is limited by its weak aqueous solubility. In this study, we optimized an efficient method of preparing its phospholipid complex (PPD-PLC using a central composite design and response surface analysis. The prepared PPD-PLC was characterized by differential scanning calorimetric, powder X-ray diffraction, Fourier-transformed infrared spectroscopy and nuclear magnetic resonance analyses associated with molecular docking calculation. The equilibrium solubility of PPD-PLC in water and n-octanol increased 6.53- and 1.53-times, respectively. Afterwards, using PPD-PLC as the intermediate, the PPD-PLC-loaded dry suspension (PPD-PLC-SU was prepared with our previous method. In vitro evaluations were conducted on PPD-PLC and PPD-PLC-SU, including dissolution behaviors and stability properties under different conditions. Results of in vitro dissolution behavior revealed the improved dissolution extents and rates of PPD-PLC and PPD-PLC-SU (p < 0.05. Results of the formulation stability investigation also exposed the better stability of PPD-PLC-SU compared with free PPD. Therefore, phospholipid complex technology is a useful formulation strategy for BCS II drugs, as it could effectively improve their hydrophilicity and lipophilicity.

  1. Molecular phylogeny of Glossodoris (Ehrenberg, 1831) nudibranchs and related genera reveals cryptic and pseudocryptic species complexes

    KAUST Repository

    Matsuda, Shayle B.

    2017-03-01

    Chromodorid nudibranchs (Chromodorididae) are brightly coloured sea slugs that live in some of the most biodiverse and threatened coral reefs on the planet. However, the evolutionary relationships within this family have not been well understood, especially in the genus Glossodoris. Members of Glossodoris have experienced large-scale taxonomic instability over the last century and have been the subject of repeated taxonomic changes, in part due to morphological characters being the sole traditional taxonomic sources of data. Changing concepts of traditional generic boundaries based on morphology also have contributed to this instability. Despite recent advances in molecular systematics, many aspects of chromodorid taxonomy remain poorly understood, particularly at the traditional species and generic levels. In this study, 77 individuals comprising 32 previously defined species were used to build the most robust phylogenetic tree of Glossodoris and related genera using mitochondrial genes cytochrome c oxidase subunit I and 16S, and the nuclear gene 28S. Bayesian inference, maximum likelihood, and maximum parsimony analyses verify the most recent hypothesized evolutionary relationships within Glossodoris. Additionally, a pseudocryptic and cryptic species complex within Glossodoris cincta and a pseudocryptic complex within Glossodoris pallida emerged, and three new species of Doriprismatica are identified.

  2. Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems

    Directory of Open Access Journals (Sweden)

    Josh Fass

    2018-04-01

    Full Text Available While Langevin integrators are popular in the study of equilibrium properties of complex systems, it is challenging to estimate the timestep-induced discretization error: the degree to which the sampled phase-space or configuration-space probability density departs from the desired target density due to the use of a finite integration timestep. Sivak et al., introduced a convenient approach to approximating a natural measure of error between the sampled density and the target equilibrium density, the Kullback-Leibler (KL divergence, in phase space, but did not specifically address the issue of configuration-space properties, which are much more commonly of interest in molecular simulations. Here, we introduce a variant of this near-equilibrium estimator capable of measuring the error in the configuration-space marginal density, validating it against a complex but exact nested Monte Carlo estimator to show that it reproduces the KL divergence with high fidelity. To illustrate its utility, we employ this new near-equilibrium estimator to assess a claim that a recently proposed Langevin integrator introduces extremely small configuration-space density errors up to the stability limit at no extra computational expense. Finally, we show how this approach to quantifying sampling bias can be applied to a wide variety of stochastic integrators by following a straightforward procedure to compute the appropriate shadow work, and describe how it can be extended to quantify the error in arbitrary marginal or conditional distributions of interest.

  3. Benchmarking of London Dispersion-Accounting Density Functional Theory Methods on Very Large Molecular Complexes.

    Science.gov (United States)

    Risthaus, Tobias; Grimme, Stefan

    2013-03-12

    A new test set (S12L) containing 12 supramolecular noncovalently bound complexes is presented and used to evaluate seven different methods to account for dispersion in DFT (DFT-D3, DFT-D2, DFT-NL, XDM, dDsC, TS-vdW, M06-L) at different basis set levels against experimental, back-corrected reference energies. This allows conclusions about the performance of each method in an explorative research setting on "real-life" problems. Most DFT methods show satisfactory performance but, due to the largeness of the complexes, almost always require an explicit correction for the nonadditive Axilrod-Teller-Muto three-body dispersion interaction to get accurate results. The necessity of using a method capable of accounting for dispersion is clearly demonstrated in that the two-body dispersion contributions are on the order of 20-150% of the total interaction energy. MP2 and some variants thereof are shown to be insufficient for this while a few tested D3-corrected semiempirical MO methods perform reasonably well. Overall, we suggest the use of this benchmark set as a "sanity check" against overfitting to too small molecular cases.

  4. MILKY WAY STAR-FORMING COMPLEXES AND THE TURBULENT MOTION OF THE GALAXY'S MOLECULAR GAS

    International Nuclear Information System (INIS)

    Lee, Eve J.; Rahman, Mubdi; Murray, Norman

    2012-01-01

    We analyze Spitzer GLIMPSE, Midcourse Space Experiment (MSX), and Wilkinson Microwave Anisotropy Probe (WMAP) images of the Milky Way to identify 8 μm and free-free sources in the Galaxy. Seventy-two of the 88 WMAP sources have coverage in the GLIMPSE and MSX surveys suitable for identifying massive star-forming complexes (SFCs). We measure the ionizing luminosity functions of the SFCs and study their role in the turbulent motion of the Galaxy's molecular gas. We find a total Galactic free-free flux f ν = 46,177.6 Jy; the 72 WMAP sources with full 8 μm coverage account for 34,263.5 Jy (∼75%), with both measurements made at ν = 94 GHz (W band). We find a total of 280 SFCs, of which 168 have unique kinematic distances and free-free luminosities. We use a simple model for the radial distribution of star formation to estimate the free-free and ionizing luminosity for the sources lacking distance determinations. The total dust-corrected ionizing luminosity is Q = (2.9 ± 0.5) × 10 53 photons s –1 , which implies a Galactic star formation rate of M-dot * = 1.2±0.2 M ☉ yr -1 . We present the (ionizing) luminosity function of the SFCs and show that 24 sources emit half the ionizing luminosity of the Galaxy. The SFCs appear as bubbles in GLIMPSE or MSX images; the radial velocities associated with the bubble walls allow us to infer the expansion velocity of the bubbles. We calculate the kinetic luminosity of the bubble expansion and compare it to the turbulent luminosity of the inner molecular disk. SFCs emitting 80% of the total Galactic free-free luminosity produce a kinetic luminosity equal to 65% of the turbulent luminosity in the inner molecular disk. This suggests that the expansion of the bubbles is a major driver of the turbulent motion of the inner Milky Way molecular gas.

  5. MOLECULAR ENVIRONMENTS OF 51 PLANCK COLD CLUMPS IN THE ORION COMPLEX

    Energy Technology Data Exchange (ETDEWEB)

    Liu Tie; Wu Yuefang; Zhang Huawei, E-mail: liutiepku@gmail.com, E-mail: ywu@pku.edu.cn [Department of Astronomy, Peking University, 100871 Beijing (China)

    2012-09-15

    A mapping survey of 51 Planck cold clumps projected on the Orion complex was performed with J = 1-0 lines of {sup 12}CO and {sup 13}CO with the 13.7 m telescope at the Purple Mountain Observatory. The mean column densities of the Planck gas clumps range from 0.5 to 9.5 Multiplication-Sign 10{sup 21} cm{sup -2}, with an average value of (2.9 {+-} 1.9) Multiplication-Sign 10{sup 21} cm{sup -2}. The mean excitation temperatures of these clumps range from 7.4 to 21.1 K, with an average value of 12.1 {+-} 3.0 K and the average three-dimensional velocity dispersion {sigma}{sub 3D} in these molecular clumps is 0.66 {+-} 0.24 km s{sup -1}. Most of the clumps have {sigma}{sub NT} larger than or comparable to {sigma}{sub Therm}. The H{sub 2} column density of the molecular clumps calculated from molecular lines correlates with the aperture flux at 857 GHz of the dust emission. By analyzing the distributions of the physical parameters, we suggest that turbulent flows can shape the clump structure and dominate their density distribution on large scales, but not function on small scales due to local fluctuations. Eighty-two dense cores are identified in the molecular clumps. The dense cores have an average radius and local thermal equilibrium (LTE) mass of 0.34 {+-} 0.14 pc and 38{sup +5}{sub -30} M{sub Sun }, respectively. The structures of low column density cores are more affected by turbulence, while the structures of high column density cores are more affected by other factors, especially by gravity. The correlation of velocity dispersion versus core size is very weak for the dense cores. The dense cores are found to be most likely gravitationally bounded rather than pressure confined. The relationship between M{sub vir} and M{sub LTE} can be well fitted with a power law. The core mass function here is much flatter than the stellar initial mass function. The lognormal behavior of the core mass distribution is most likely determined by internal turbulence.

  6. MOLECULAR ENVIRONMENTS OF 51 PLANCK COLD CLUMPS IN THE ORION COMPLEX

    International Nuclear Information System (INIS)

    Liu Tie; Wu Yuefang; Zhang Huawei

    2012-01-01

    A mapping survey of 51 Planck cold clumps projected on the Orion complex was performed with J = 1–0 lines of 12 CO and 13 CO with the 13.7 m telescope at the Purple Mountain Observatory. The mean column densities of the Planck gas clumps range from 0.5 to 9.5 × 10 21 cm –2 , with an average value of (2.9 ± 1.9) × 10 21 cm –2 . The mean excitation temperatures of these clumps range from 7.4 to 21.1 K, with an average value of 12.1 ± 3.0 K and the average three-dimensional velocity dispersion σ 3D in these molecular clumps is 0.66 ± 0.24 km s –1 . Most of the clumps have σ NT larger than or comparable to σ Therm . The H 2 column density of the molecular clumps calculated from molecular lines correlates with the aperture flux at 857 GHz of the dust emission. By analyzing the distributions of the physical parameters, we suggest that turbulent flows can shape the clump structure and dominate their density distribution on large scales, but not function on small scales due to local fluctuations. Eighty-two dense cores are identified in the molecular clumps. The dense cores have an average radius and local thermal equilibrium (LTE) mass of 0.34 ± 0.14 pc and 38 +5 –30 M ☉ , respectively. The structures of low column density cores are more affected by turbulence, while the structures of high column density cores are more affected by other factors, especially by gravity. The correlation of velocity dispersion versus core size is very weak for the dense cores. The dense cores are found to be most likely gravitationally bounded rather than pressure confined. The relationship between M vir and M LTE can be well fitted with a power law. The core mass function here is much flatter than the stellar initial mass function. The lognormal behavior of the core mass distribution is most likely determined by internal turbulence.

  7. Synthesis and Self-Assembly of Chiral Cylindrical Molecular Complexes: Functional Heterogeneous Liquid-Solid Materials Formed by Helicene Oligomers

    Directory of Open Access Journals (Sweden)

    Nozomi Saito

    2018-01-01

    Full Text Available Chiral cylindrical molecular complexes of homo- and hetero-double-helices derived from helicene oligomers self-assemble in solution, providing functional heterogeneous liquid-solid materials. Gels and liotropic liquid crystals are formed by fibril self-assembly in solution; molecular monolayers and fibril films are formed by self-assembly on solid surfaces; gels containing gold nanoparticles emit light; silica nanoparticles aggregate and adsorb double-helices. Notable dynamics appears during self-assembly, including multistep self-assembly, solid surface catalyzed double-helix formation, sigmoidal and stairwise kinetics, molecular recognition of nanoparticles, discontinuous self-assembly, materials clocking, chiral symmetry breaking and homogeneous-heterogeneous transitions. These phenomena are derived from strong intercomplex interactions of chiral cylindrical molecular complexes.

  8. Visualizing molecular juggling within a B[subscript 12]-dependent methyltransferase complex

    Energy Technology Data Exchange (ETDEWEB)

    Kung, Yan; Ando, Nozomi; Doukov, Tzanko I.; Blasiak, Leah C.; Bender, Güne; #351; ; Seravalli, Javier; Ragsdale, Stephen W.; Drennan, Catherine L. (MIT); (Michigan); (UNL)

    2013-04-08

    Derivatives of vitamin B{sub 12} are used in methyl group transfer in biological processes as diverse as methionine synthesis in humans and CO{sub 2} fixation in acetogenic bacteria. This seemingly straightforward reaction requires large, multimodular enzyme complexes that adopt multiple conformations to alternately activate, protect and perform catalysis on the reactive B{sub 12} cofactor. Crystal structures determined thus far have provided structural information for only fragments of these complexes, inspiring speculation about the overall protein assembly and conformational movements inherent to activity. Here we present X-ray crystal structures of a complete 220 kDa complex that contains all enzymes responsible for B{sub 12}-dependent methyl transfer, namely the corrinoid iron-sulphur protein and its methyltransferase from the model acetogen Moorella thermoacetica. These structures provide the first three-dimensional depiction of all protein modules required for the activation, protection and catalytic steps of B{sub 12}-dependent methyl transfer. In addition, the structures capture B{sub 12} at multiple locations between its 'resting' and catalytic positions, allowing visualization of the dramatic protein rearrangements that enable methyl transfer and identification of the trajectory for B{sub 12} movement within the large enzyme scaffold. The structures are also presented alongside in crystallo spectroscopic data, which confirm enzymatic activity within crystals and demonstrate the largest known conformational movements of proteins in a crystalline state. Taken together, this work provides a model for the molecular juggling that accompanies turnover and helps explain why such an elaborate protein framework is required for such a simple, yet biologically essential reaction.

  9. Biological Activity and Molecular Structures of Bis(benzimidazole and Trithiocyanurate Complexes

    Directory of Open Access Journals (Sweden)

    Pavel Kopel

    2015-06-01

    Full Text Available 1-(1H-Benzimidazol-2-yl-N-(1H-benzimidazol-2-ylmethylmethanamine (abb and 2-(1H-benzimidazol-2-ylmethylsulfanylmethyl-1H-benzimidazole (tbb have been prepared and characterized by elemental analysis. These bis(benzimidazoles have been further used in combination with trithiocyanuric acid for the preparation of complexes. The crystal and molecular structures of two of them have been solved. Each nickel atom in the structure of trinuclear complex [Ni3(abb3(H2O3(μ-ttc](ClO43·3H2O·EtOH (1, where ttcH3 = trithiocyanuric acid, is coordinated with three N atoms of abb, the N,S donor set of ttc anion and an oxygen of a water molecule. The crystal of [(tbbH2(ttcH22(ttcH3(H2O] (2 is composed of a protonated bis(benzimidazole, two ttcH2 anions, ttcH3 and water. The structure is stabilized by a network of hydrogen bonds. These compounds were primarily synthesized for their potential antimicrobial activity and hence their possible use in the treatment of infections caused by bacteria or yeasts (fungi. The antimicrobial and antifungal activity of the prepared compounds have been evaluated on a wide spectrum of bacterial and yeast strains and clinical specimens isolated from patients with infectious wounds and the best antimicrobial properties were observed in strains after the use of ligand abb and complex 1, when at least 80% growth inhibition was achieved.

  10. Molecular phylogenetics and historical biogeography of the west-palearctic common toads (Bufo bufo species complex).

    Science.gov (United States)

    Garcia-Porta, J; Litvinchuk, S N; Crochet, P A; Romano, A; Geniez, P H; Lo-Valvo, M; Lymberakis, P; Carranza, S

    2012-04-01

    In most pan-Eurasiatic species complexes, two phenomena have been traditionally considered key processes of their cladogenesis and biogeography. First, it is hypothesized that the origin and development of the Central Asian Deserts generated a biogeographic barrier that fragmented past continuous distributions in Eastern and Western domains. Second, Pleistocene glaciations have been proposed as the main process driving the regional diversification within each of these domains. The European common toad and its closest relatives provide an interesting opportunity to examine the relative contributions of these paleogeographic and paleoclimatic events to the phylogeny and biogeography of a widespread Eurasiatic group. We investigate this issue by applying a multiproxy approach combining information from molecular phylogenies, a multiple correspondence analysis of allozyme data and species distribution models. Our study includes 304 specimens from 164 populations, covering most of the distributional range of the Bufo bufo species complex in the Western Palearctic. The phylogenies (ML and Bayesian analyses) were based on a total of 1988 bp of mitochondrial DNA encompassing three genes (tRNAval, 16S and ND1). A dataset with 173 species of the family Bufonidae was assembled to estimate the separation of the two pan-Eurasiatic species complexes of Bufo and to date the main biogeographic events within the Bufo bufo species complex. The allozyme study included sixteen protein systems, corresponding to 21 presumptive loci. Finally, the distribution models were based on maximum entropy. Our distribution models show that Eastern and Western species complexes are greatly isolated by the Central Asian Deserts, and our dating estimates place this divergence during the Middle Miocene, a moment in which different sources of evidence document a major upturn of the aridification rate of Central Asia. This climate-driven process likely separated the Eastern and Western species. At the

  11. D2+ Molecular complex in non-uniform height quantum ribbon under crossed electric and magnetic fields

    Science.gov (United States)

    Suaza, Y. A.; Laroze, D.; Fulla, M. R.; Marín, J. H.

    2018-05-01

    The D2+ molecular complex fundamental properties in a uniform and multi-hilled semiconductor quantum ribbon under orthogonal electric and magnetic fields are theoretically studied. The energy structure is calculated by using adiabatic approximation combined with diagonalization procedure. The D2+ energy structure is more strongly controlled by the geometrical structural hills than the Coulomb interaction. The formation of vibrational and rotational states is discussed. Aharanov-Bohm oscillation patterns linked to rotational states as well as the D2+ molecular complex stability are highly sensitive to the number of hills while electric field breaks the electron rotational symmetry and removes the energy degeneration between low-lying states.

  12. Measurement and control of detailed electronic properties in a single molecule break junction.

    Science.gov (United States)

    Wang, Kun; Hamill, Joseph; Zhou, Jianfeng; Guo, Cunlan; Xu, Bingqian

    2014-01-01

    The lack of detailed experimental controls has been one of the major obstacles hindering progress in molecular electronics. While large fluctuations have been occurring in the experimental data, specific details, related mechanisms, and data analysis techniques are in high demand to promote our physical understanding at the single-molecule level. A series of modulations we recently developed, based on traditional scanning probe microscopy break junctions (SPMBJs), have helped to discover significant properties in detail which are hidden in the contact interfaces of a single-molecule break junction (SMBJ). For example, in the past we have shown that the correlated force and conductance changes under the saw tooth modulation and stretch-hold mode of PZT movement revealed inherent differences in the contact geometries of a molecular junction. In this paper, using a bias-modulated SPMBJ and utilizing emerging data analysis techniques, we report on the measurement of the altered alignment of the HOMO of benzene molecules with changing the anchoring group which coupled the molecule to metal electrodes. Further calculations based on Landauer fitting and transition voltage spectroscopy (TVS) demonstrated the effects of modulated bias on the location of the frontier molecular orbitals. Understanding the alignment of the molecular orbitals with the Fermi level of the electrodes is essential for understanding the behaviour of SMBJs and for the future design of more complex devices. With these modulations and analysis techniques, fruitful information has been found about the nature of the metal-molecule junction, providing us insightful clues towards the next step for in-depth study.

  13. Primary Tunnel Junction Thermometry

    International Nuclear Information System (INIS)

    Pekola, Jukka P.; Holmqvist, Tommy; Meschke, Matthias

    2008-01-01

    We describe the concept and experimental demonstration of primary thermometry based on a four-probe measurement of a single tunnel junction embedded within four arrays of junctions. We show that in this configuration random sample specific and environment-related errors can be avoided. This method relates temperature directly to Boltzmann constant, which will form the basis of the definition of temperature and realization of official temperature scales in the future

  14. Quantum Junction Solar Cells

    KAUST Repository

    Tang, Jiang

    2012-09-12

    Colloidal quantum dot solids combine convenient solution-processing with quantum size effect tuning, offering avenues to high-efficiency multijunction cells based on a single materials synthesis and processing platform. The highest-performing colloidal quantum dot rectifying devices reported to date have relied on a junction between a quantum-tuned absorber and a bulk material (e.g., TiO 2); however, quantum tuning of the absorber then requires complete redesign of the bulk acceptor, compromising the benefits of facile quantum tuning. Here we report rectifying junctions constructed entirely using inherently band-aligned quantum-tuned materials. Realizing these quantum junction diodes relied upon the creation of an n-type quantum dot solid having a clean bandgap. We combine stable, chemically compatible, high-performance n-type and p-type materials to create the first quantum junction solar cells. We present a family of photovoltaic devices having widely tuned bandgaps of 0.6-1.6 eV that excel where conventional quantum-to-bulk devices fail to perform. Devices having optimal single-junction bandgaps exhibit certified AM1.5 solar power conversion efficiencies of 5.4%. Control over doping in quantum solids, and the successful integration of these materials to form stable quantum junctions, offers a powerful new degree of freedom to colloidal quantum dot optoelectronics. © 2012 American Chemical Society.

  15. Automated builder and database of protein/membrane complexes for molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Sunhwan Jo

    2007-09-01

    Full Text Available Molecular dynamics simulations of membrane proteins have provided deeper insights into their functions and interactions with surrounding environments at the atomic level. However, compared to solvation of globular proteins, building a realistic protein/membrane complex is still challenging and requires considerable experience with simulation software. Membrane Builder in the CHARMM-GUI website (http://www.charmm-gui.org helps users to build such a complex system using a web browser with a graphical user interface. Through a generalized and automated building process including system size determination as well as generation of lipid bilayer, pore water, bulk water, and ions, a realistic membrane system with virtually any kinds and shapes of membrane proteins can be generated in 5 minutes to 2 hours depending on the system size. Default values that were elaborated and tested extensively are given in each step to provide reasonable options and starting points for both non-expert and expert users. The efficacy of Membrane Builder is illustrated by its applications to 12 transmembrane and 3 interfacial membrane proteins, whose fully equilibrated systems with three different types of lipid molecules (DMPC, DPPC, and POPC and two types of system shapes (rectangular and hexagonal are freely available on the CHARMM-GUI website. One of the most significant advantages of using the web environment is that, if a problem is found, users can go back and re-generate the whole system again before quitting the browser. Therefore, Membrane Builder provides the intuitive and easy way to build and simulate the biologically important membrane system.

  16. Structure and dynamics of a [1:1] drug-DNA complex: Analysis of 2D NMR data using molecular mechanics and molecular dynamics calculations

    International Nuclear Information System (INIS)

    Sarma, R.H.; Sarma, M.H.; Umemoto, K.

    1990-01-01

    1D/2D NMR studies are reported for a [1:1] complex of d(GA 4 T 4 C) 2 and Dst2 (an analogue of distamycin A). Full- Matrix NOESY Simulations, Molecular Mechanics and Molecular Dynamics Calculations are performed to analyze the NMR data. Results show that drug-DNA complex formation is driven by static features like H-bonding and steric interactions in the minor-groove of DNA. As a consequence of drug binding, a non-linear oscillatory mode is activated. In this mode the molecule samples equilibrium structural states of difference degrees of bending. It is noted that these structures belong to three distinctly different energy wells that satisfy the same NMR data. 14 refs., 4 figs., 2 tabs

  17. Investigation of the complex reaction coordinate of acid catalyzed amide hydrolysis from molecular dynamics simulations

    International Nuclear Information System (INIS)

    Zahn, Dirk

    2004-01-01

    The rate-determining step of acid catalyzed peptide hydrolysis is the nucleophilic attack of a water molecule to the carbon atom of the amide group. Therein the addition of the hydroxyl group to the amide carbon atom involves the association of a water molecule transferring one of its protons to an adjacent water molecule. The protonation of the amide nitrogen atom follows as a separate reaction step. Since the nucleophilic attack involves the breaking and formation of several bonds, the underlying reaction coordinate is rather complex. We investigate this reaction step from path sampling Car-Parrinello molecular dynamics simulations. This approach does not require the predefinition of reaction coordinates and is thus particularly suited for investigating reaction mechanisms. From our simulations the most relevant components of the reaction coordinate are elaborated. Though the C···O distance of the oxygen atom of the water molecule performing the nucleophilic attack and the corresponding amide carbon atom is a descriptor of the reaction progress, a complete picture of the reaction coordinate must include all three molecules taking part in the reaction. Moreover, the proton transfer is found to depend on favorable solvent configurations. Thus, also the arrangement of non-reacting, i.e. solvent water molecules needs to be considered in the reaction coordinate

  18. Mapping of Drug-like Chemical Universe with Reduced Complexity Molecular Frameworks.

    Science.gov (United States)

    Kontijevskis, Aleksejs

    2017-04-24

    The emergence of the DNA-encoded chemical libraries (DEL) field in the past decade has attracted the attention of the pharmaceutical industry as a powerful mechanism for the discovery of novel drug-like hits for various biological targets. Nuevolution Chemetics technology enables DNA-encoded synthesis of billions of chemically diverse drug-like small molecule compounds, and the efficient screening and optimization of these, facilitating effective identification of drug candidates at an unprecedented speed and scale. Although many approaches have been developed by the cheminformatics community for the analysis and visualization of drug-like chemical space, most of them are restricted to the analysis of a maximum of a few millions of compounds and cannot handle collections of 10 8 -10 12 compounds typical for DELs. To address this big chemical data challenge, we developed the Reduced Complexity Molecular Frameworks (RCMF) methodology as an abstract and very general way of representing chemical structures. By further introducing RCMF descriptors, we constructed a global framework map of drug-like chemical space and demonstrated how chemical space occupied by multi-million-member drug-like Chemetics DNA-encoded libraries and virtual combinatorial libraries with >10 12 members could be analyzed and mapped without a need for library enumeration. We further validate the approach by performing RCMF-based searches in a drug-like chemical universe and mapping Chemetics library selection outputs for LSD1 targets on a global framework chemical space map.

  19. Soliton analysis in complex molecular systems: A zig-zag chain

    International Nuclear Information System (INIS)

    Christiansen, P.L.; Savin, A.V.; Zolotaryuk, A.V.

    1997-01-01

    A simple numerical method for seeking solitary wave solutions of a permanent profile in molecular systems of big complexity is presented. The method is essentially based on the minimization of a finite-dimensional function which is chosen under an appropriate discretization of time derivatives in equations of motion. In the present paper, it is applied to a zig-zag chain backbone of coupled particles, each of which has two degrees of freedom (longitudinal and transverse). Both topological and nontopological soliton solutions are treated for this chain when it is (i) subjected to a two-dimensional periodic substrate potential or (ii) considered as an isolated object, respectively. In the first case, which may be considered as a zig-zag generalization of the Frenkel-Kontorova chain model, two types of kink solutions with different topological charges, describing vacancies of one or two atoms (I- or II-kinks) and defects with excess one or two atoms in the chain (I- or II-antikinks), have been found. The second case (isolated chain) is a generalization of the well-known Fermi-Pasta-Ulam chain model, which takes into account transverse degrees of freedom of the chain molecules. Two types of stable nontopological soliton solutions which describe either (i) a supersonic solitary wave of longitudinal stretching accompanied by transverse slandering or supersonic pulses of longitudinal compression propagating together with localized transverse thickening (bulge) have been obtained. 32 refs., 11 figs

  20. Soliton Analysis in Complex Molecular Systems: A Zig-Zag Chain

    Science.gov (United States)

    Christiansen, P. L.; Savin, A. V.; Zolotaryuk, A. V.

    1997-06-01

    A simple numerical method for seeking solitary wavesolutions of a permanent profile in molecular systems of big complexity is presented. The method is essentially based on the minimization of a finite-dimensional function which is chosen under an appropriate discretization of time derivatives in equations of motion. In the present paper, it is applied to a zig-zag chain backbone of coupled particles, each of which has twodegrees of freedom (longitudinal and transverse). Both topological and nontopological soliton solutions are treated for this chain when it is (i) subjected to a two-dimensional periodic substrate potential or (ii) considered as an isolated object, respectively. In the first case, which may be considered as a zig-zag generalization of the Frenkel-Kontorova chain model, two types of kink solutions with different topological charges, describing vacancies of one or two atoms (I- or II-kinks) and defects with excess one or two atoms in the chain (I- or II-antikinks), have been found. The second case (isolated chain) is a generalization of the well-known Fermi-Pasta-Ulam chain model, which takes into account transverse degrees of freedom of the chain molecules. Two types of stable nontopological soliton solutions which describe either (i) a supersonic solitary wave of longitudinal stretching accompanied by transverse slendering or (ii) supersonic pulses of longitudinal compression propagating together with localized transverse thickening (bulge) have been obtained.

  1. Design of a multi-purpose fragment screening library using molecular complexity and orthogonal diversity metrics

    Science.gov (United States)

    Lau, Wan F.; Withka, Jane M.; Hepworth, David; Magee, Thomas V.; Du, Yuhua J.; Bakken, Gregory A.; Miller, Michael D.; Hendsch, Zachary S.; Thanabal, Venkataraman; Kolodziej, Steve A.; Xing, Li; Hu, Qiyue; Narasimhan, Lakshmi S.; Love, Robert; Charlton, Maura E.; Hughes, Samantha; van Hoorn, Willem P.; Mills, James E.

    2011-07-01

    Fragment Based Drug Discovery (FBDD) continues to advance as an efficient and alternative screening paradigm for the identification and optimization of novel chemical matter. To enable FBDD across a wide range of pharmaceutical targets, a fragment screening library is required to be chemically diverse and synthetically expandable to enable critical decision making for chemical follow-up and assessing new target druggability. In this manuscript, the Pfizer fragment library design strategy which utilized multiple and orthogonal metrics to incorporate structure, pharmacophore and pharmacological space diversity is described. Appropriate measures of molecular complexity were also employed to maximize the probability of detection of fragment hits using a variety of biophysical and biochemical screening methods. In addition, structural integrity, purity, solubility, fragment and analog availability as well as cost were important considerations in the selection process. Preliminary analysis of primary screening results for 13 targets using NMR Saturation Transfer Difference (STD) indicates the identification of uM-mM hits and the uniqueness of hits at weak binding affinities for these targets.

  2. Molecular Identification and Echinocandin Susceptibility of Candida parapsilosis Complex Bloodstream Isolates in Italy, 2007-2014.

    Directory of Open Access Journals (Sweden)

    Grazia Lovero

    Full Text Available The Candida parapsilosis group encompasses three species: C. parapsilosis, C. orthopsilosis, and C. metapsilosis. Here, we describe the incidence and echinocandin susceptibility profile of bloodstream isolates of these three species collected from patients admitted to an Italian university hospital from 2007 to 2014. Molecular identification of cryptic species of the C. parapsilosis complex was performed using polymerase chain reaction amplification of the gene encoding secondary alcohol dehydrogenase, followed by digestion with the restriction enzyme BanI. Minimum inhibitory concentrations were determined using the broth microdilution method according to European Committee for Antimicrobial Susceptibility Testing (EUCAST EDef 7.2 and Clinical Laboratory Standards Institute (CLSI M27-A3 guidelines, and the results were compared with those obtained using the E-test and Sensititre methods. Of the 163 C. parapsilosis complex isolates, 136 (83.4% were identified as C. parapsilosis, and 27 (16.6% as C. orthopsilosis. The species-specific incidences were 2.9/10,000 admissions for C. parapsilosis and 0.6/10,000 admissions for C. orthopsilosis. No resistance to echinocandins was detected with any of the methods. The percent essential agreement (EA between the EUCAST and E-test/Sensititre methods for anidulafungin, caspofungin, and micafungin susceptibility was, respectively, as follows: C. parapsilosis, 95.6/97.8, 98.5/88.2, and 93.4/96.3; C. orthopsilosis, 92.6/92.6, 96.3/77.8, and 63.0/66.7. The EA between the CLSI and E-test/Sensititre methods was, respectively, as follows: C. parapsilosis, 99.3/100, 98.5/89.0, and 96.3/98.5; C. orthopsilosis, 96.3/92.6, 100/81.5, and 92.6/88.9. Only minor discrepancies, ranging from 16.9% (C. parapsilosis to 11.1% (C. orthopsilosis, were observed between the CLSI and E-test/Sensititre methods. In conclusion, this epidemiologic study shows a typical C. parapsilosis complex species distribution, no echinocandin

  3. Structural elucidation of dendritic host-guest complexes by X-ray crystallography and molecular dynamics simulations

    NARCIS (Netherlands)

    Chang, T.; Pieterse, K.; Broeren, M.A.C.; Kooijman, H.; Spek, A.L.; Hilbers, P.A.J.; Meijer, E.W.

    2007-01-01

    The multiple monovalent binding of adamantyl-urea poly(propyleneimine) dendrimers with carboxylic acid-urea guests was investigated using molecular dynamics simulations and X-ray crystallography to better understand the structure and behavior of the dynamic multivalent complex in solution. The

  4. Studies of the charge instabilities in the complex nano-objects: clusters and bio-molecular systems

    International Nuclear Information System (INIS)

    Manil, B.

    2007-11-01

    For the last 6 years, my main research works focused on i) the Coulomb instabilities and the fragmentation processes of fullerenes and clusters of fullerenes ii) the stability and the reactivity of complex bio-molecular systems. Concerning the clusters of fullerenes, which are van der Waals type clusters, we have shown that the multiply charged species, obtained in collisions with slow highly charged ions, keep their structural properties but become very good electric conductor. In another hand, with the aim to understand the role of the biologic environment at the molecular scale in the irradiation damage of complex biomolecules, we have studied the charge stabilities of clusters of small biomolecules and the dissociation processes of larger nano-hydrated biomolecules. Theses studies have shown that first, specific molecular recognition mechanisms continue to exist in gas phase and secondly, a small and very simple biochemical environment is enough to change the dynamics of instabilities. (author)

  5. Molecular dynamics simulations of ter-pyridine, BTP, and their complexes with La3+, Eu3+ and Lu3+

    International Nuclear Information System (INIS)

    Guilbaud, P.; Dognon, J.P.

    2000-01-01

    This poster presents molecular dynamics simulations performed to study ter-pyridine and bis-triazinyl-pyridine with lanthanide cations for the gas phase and for water solution. Different counter-ions have been tested in order to assess their influence on complexes structures and stabilities in both phases. For stable complexes, Gibbs free energy calculations have been achieved to estimate the selectivity of these complexes towards the lanthanide cations. Finally, some tests have been done adding a polarization term in the potential energy in order to have a more precise description of interaction energies. (authors)

  6. Phase solubility, 1H NMR and molecular modelling studies of bupivacaine hydrochloride complexation with different cyclodextrin derivates

    Science.gov (United States)

    Jug, Mario; Mennini, Natascia; Melani, Fabrizio; Maestrelli, Francesca; Mura, Paola

    2010-11-01

    A novel method, which simultaneously exploits experimental (NMR) and theoretically calculated data obtained by a molecular modelling technique, was proposed, to obtain deeper insight into inclusion geometry and possible stereoselective binding of bupivacaine hydrochloride with selected cyclodextrin derivatives. Sulphobuthylether-β-cyclodextrin and water soluble polymeric β-cyclodextrin demonstrated to be the best complexing agents for the drug, resulting in formation of the most stable inclusion complexes with the highest increase in aqueous drug solubility. The drug-carrier binding modes with these cyclodextrins and phenomena which may be directly related to the higher stability and better aqueous solubility of complexes formed were discussed in details.

  7. Behavior of tight-junction, adherens-junction and cell polarity proteins during HNF-4α-induced epithelial polarization

    International Nuclear Information System (INIS)

    Satohisa, Seiro; Chiba, Hideki; Osanai, Makoto; Ohno, Shigeo; Kojima, Takashi; Saito, Tsuyoshi; Sawada, Norimasa

    2005-01-01

    We previously reported that expression of tight-junction molecules occludin, claudin-6 and claudin-7, as well as establishment of epithelial polarity, was triggered in mouse F9 cells expressing hepatocyte nuclear factor (HNF)-4α [H. Chiba, T. Gotoh, T. Kojima, S. Satohisa, K. Kikuchi, M. Osanai, N. Sawada. Hepatocyte nuclear factor (HNF)-4α triggers formation of functional tight junctions and establishment of polarized epithelial morphology in F9 embryonal carcinoma cells, Exp. Cell Res. 286 (2003) 288-297]. Using these cells, we examined in the present study behavior of tight-junction, adherens-junction and cell polarity proteins and elucidated the molecular mechanism behind HNF-4α-initiated junction formation and epithelial polarization. We herein show that not only ZO-1 and ZO-2, but also ZO-3, junctional adhesion molecule (JAM)-B, JAM-C and cell polarity proteins PAR-3, PAR-6 and atypical protein kinase C (aPKC) accumulate at primordial adherens junctions in undifferentiated F9 cells. In contrast, CRB3, Pals1 and PATJ appeared to exhibit distinct subcellular localization in immature cells. Induced expression of HNF-4α led to translocation of these tight-junction and cell polarity proteins to beltlike tight junctions, where occludin, claudin-6 and claudin-7 were assembled, in differentiated cells. Interestingly, PAR-6, aPKC, CRB3 and Pals1, but not PAR-3 or PATJ, were also concentrated on the apical membranes in differentiated cells. These findings indicate that HNF-4α provokes not only expression of tight-junction adhesion molecules, but also modulation of subcellular distribution of junction and cell polarity proteins, resulting in junction formation and epithelial polarization

  8. Binding of molecular oxygen by an artificial heme analogue: investigation on the formation of an Fe–tetracarbene superoxo complex

    KAUST Repository

    Anneser, Markus R.

    2016-02-26

    The dioxygen reactivity of a cyclic iron(II) tetra–NHC-complex (NHC: N-heterocyclic carbene) is investigated. Divergent oxidation behavior is observed depending on the choice of the solvent (acetonitrile or acetone). In the first case, exposure to molecular oxygen leads to an oxygen free Fe(III) whereas in the latter case an oxide bridged Fe(III) dimer is formed. In acetone, an Fe(III)-superoxide can be trapped, isolated and characterized as intermediate at low temperatures. An Fe(III)–O–Fe(III) dimer is formed from the Fe(III) superoxide in acetone upon warming and the molecular structure has been revealed by single crystal X-ray diffraction. It is shown that the oxidation of the Fe(II) complex in both solvents is a reversible process. For the regeneration of the initial Fe(II) complex both organic and inorganic reducing agents can be used.

  9. Direct characterization of the energy level alignments and molecular components in an organic hetero-junction by integrated photoemission spectroscopy and reflection electron energy loss spectroscopy analysis.

    Science.gov (United States)

    Yun, Dong-Jin; Shin, Weon-Ho; Bulliard, Xavier; Park, Jong Hwan; Kim, Seyun; Chung, Jae Gwan; Kim, Yongsu; Heo, Sung; Kim, Seong Heon

    2016-08-26

    A novel, direct method for the characterization of the energy level alignments at bulk-heterojunction (BHJ)/electrode interfaces on the basis of electronic spectroscopy measurements is proposed. The home-made in situ photoemission system is used to perform x-ray/ultraviolet photoemission spectroscopy (XPS/UPS), reflection electron energy loss spectroscopy (REELS) and inverse photoemission spectroscopy of organic-semiconductors (OSCs) deposited onto a Au substrate. Through this analysis system, we are able to obtain the electronic structures of a boron subphthalocyanine chloride:fullerene (SubPC:C60) BHJ and those of the separate OSC/electrode structures (SubPC/Au and C60/Au). Morphology and chemical composition analyses confirm that the original SubPC and C60 electronic structures remain unchanged in the electrodes prepared. Using this technique, we ascertain that the position and area of the nearest peak to the Fermi energy (EF = 0 eV) in the UPS (REELS) spectra of SubPC:C60 BHJ provide information on the highest occupied molecular orbital level (optical band gap) and combination ratio of the materials, respectively. Thus, extracting the adjusted spectrum from the corresponding SubPC:C60 BHJ UPS (REELS) spectrum reveals its electronic structure, equivalent to that of the C60 materials. This novel analytical approach allows complete energy-level determination for each combination ratio by separating its electronic structure information from the BHJ spectrum.

  10. Delimiting Species Boundaries within a Paraphyletic Species Complex: Insights from Morphological, Genetic, and Molecular Data on Paramecium sonneborni (Paramecium aurelia species complex, Ciliophora, Protozoa).

    Science.gov (United States)

    Przyboś, Ewa; Tarcz, Sebastian; Rautian, Maria; Sawka, Natalia

    2015-09-01

    The demarcation of boundaries between protist species is often problematic because of the absence of a uniform species definition, the abundance of cryptic diversity, and the occurrence of convergent morphology. The ciliates belonging to the Paramecium aurelia complex, consisting of 15 species, are a good model for such systematic and evolutionary studies. One member of the complex is P. sonneborni, previously known only from one stand in Texas (USA), but recently found in two new sampling sites in Cyprus (creeks running to Salt Lake and Oroklini Lake near Larnaca). The studied Paramecium sonneborni strains (from the USA and Cyprus) reveal low viability in the F1 and F2 generations of interstrain hybrids and may be an example of ongoing allopatric speciation. Despite its molecular distinctiveness, we postulate that P. sonneborni should remain in the P. aurelia complex, making it a paraphyletic taxon. Morphological studies have revealed that some features of the nuclear apparatus of P. sonneborni correspond to the P. aurelia spp. complex, while others are similar to P. jenningsi and P. schewiakoffi. The observed discordance indicates rapid splitting of the P. aurelia-P. jenningsi-P. schewiakoffi group, in which genetic, morphological, and molecular boundaries between species are not congruent. Copyright © 2015 Elsevier GmbH. All rights reserved.

  11. Evolution of complex organic molecules in hot molecular cores. Synthetic spectra at (sub-)mm wavebands

    Science.gov (United States)

    Choudhury, R.; Schilke, P.; Stéphan, G.; Bergin, E.; Möller, T.; Schmiedeke, A.; Zernickel, A.

    2015-03-01

    Context. Hot molecular cores (HMCs) are intermediate stages of high-mass star formation and are also known for their rich chemical reservoirs and emission line spectra at (sub-)mm wavebands. Complex organic molecules (COMs) such as methanol (CH3OH), ethanol (C2H5OH), dimethyl ether (CH3OCH3), and methyl formate (HCOOCH3) produce most of these observed lines. The observed spectral feature of HMCs such as total number of emission lines and associated line intensities are also found to vary with evolutionary stages. Aims: We aim to investigate the spectral evolution of these COMs to explore the initial evolutionary stages of high-mass star formation including HMCs. Methods: We developed various 3D models for HMCs guided by the evolutionary scenarios proposed by recent empirical and modeling studies. We then investigated the spatio-temporal variation of temperature and molecular abundances in HMCs by consistently coupling gas-grain chemical evolution with radiative transfer calculations. We explored the effects of varying physical conditions on molecular abundances including density distribution and luminosity evolution of the central protostar(s) among other parameters. Finally, we simulated the synthetic spectra for these models at different evolutionary timescales to compare with observations. Results: Temperature has a profound effect on the formation of COMs through the depletion and diffusion on grain surface to desorption and further gas-phase processing. The time-dependent temperature structure of the hot core models provides a realistic framework for investigating the spatial variation of ice mantle evaporation as a function of evolutionary timescales. We find that a slightly higher value (15 K) than the canonical dark cloud temperature (10 K) provides a more productive environment for COM formation on grain surface. With increasing protostellar luminosity, the water ice evaporation font (~100 K) expands and the spatial distribution of gas phase abundances of

  12. NEAR-INFRARED POLARIMETRY OF A NORMAL SPIRAL GALAXY VIEWED THROUGH THE TAURUS MOLECULAR CLOUD COMPLEX

    International Nuclear Information System (INIS)

    Clemens, Dan P.; Cashman, L. R.; Pavel, M. D.

    2013-01-01

    Few normal galaxies have been probed using near-infrared polarimetry, even though it reveals magnetic fields in the cool interstellar medium better than either optical or radio polarimetry. Deep H-band (1.6 μm) linear imaging polarimetry toward Taurus serendipitously included the galaxy 2MASX J04412715+2433110 with adequate sensitivity and resolution to map polarization across nearly its full extent. The observations revealed the galaxy to be a steeply inclined (∼75°) disk type with a diameter, encompassing 90% of the Petrosian flux, of 4.2 kpc at a distance of 53 Mpc. Because the sight line passes through the Taurus Molecular Cloud complex, the foreground polarization needed to be measured and removed. The foreground extinction A V of 2.00 ± 0.10 mag and reddening E(H – K) of 0.125 ± 0.009 mag were also assessed and removed, based on analysis of Two Micron All Sky Survey, UKIRT Infrared Deep Sky Survey, Spitzer, and Wide-field Infrared Survey Explorer photometry using the Near-Infrared Color Excess, NICE-Revisited, and Rayleigh-Jeans Color Excess methods. Corrected for the polarized foreground, the galaxy polarization values range from 0% to 3%. The polarizations are dominated by a disk-parallel magnetic field geometry, especially to the northeast, while either a vertical field or single scattering of bulge light produces disk-normal polarizations to the southwest. The multi-kiloparsec coherence of the magnetic field revealed by the infrared polarimetry is in close agreement with short-wavelength radio synchrotron observations of edge-on galaxies, indicating that both cool and warm interstellar media of disk galaxies may be threaded by common magnetic fields.

  13. Molecular variation in the Paragonimus heterotremus complex in Thailand and Myanmar.

    Science.gov (United States)

    Sanpool, Oranuch; Intapan, Pewpan M; Thanchomnang, Tongjit; Janwan, Penchom; Nawa, Yukifumi; Blair, David; Maleewong, Wanchai

    2013-12-01

    Paragonimiasis is an important food-borne parasitic zoonosis caused by infection with lung flukes of the genus Paragonimus. Of the 7 members of the genus known in Thailand until recently, only P. heterotremus has been confirmed as causing human disease. An 8th species, P. pseudoheterotremus, has recently been proposed from Thailand, and has been found in humans. Molecular data place this species as a sister species to P. heterotremus, and it is likely that P. pseudoheterotremus is not specifically distinct from P. heterotremus. In this study, we collected metacercariae of both nominal species (identification based on metacercarial morphology) from freshwater crabs from Phetchabun Province in northern Thailand, Saraburi Province in central Thailand, and Surat Thani Province in southern Thailand. In addition, we purchased freshwater crabs imported from Myanmar at Myawaddy Province, western Thailand, close to the Myanmar-Thailand border. The DNAs extracted from excysted metacercariae were PCR-amplified and sequenced for ITS2 and cox1 genes. The ITS2 sequences were nearly identical among all samples (99-100%). Phylogenies inferred from all available partial cox1 sequences contained several clusters. Sequences from Indian P. heterotremus formed a sister group to sequences from P. pseudoheterotremus-type metacercariae. Sequences of P. heterotremus from Thailand, Vietnam, and China formed a separate distinct clade. One metacercaria from Phitsanulok Province was distinct from all others. There is clearly considerable genetic variation in the P. heterotremus complex in Thailand and the form referred to as P. pseudoheterotremus is widely distributed in Thailand and the Thai-Myanmar border region.

  14. Auricularia auricular polysaccharide-low molecular weight chitosan polyelectrolyte complex nanoparticles: Preparation and characterization

    Directory of Open Access Journals (Sweden)

    Wei Xiong

    2016-06-01

    Full Text Available Novel polyelectrolyte complex nanoparticles (AAP/LCS NPs were prepared in this study and these were produced by mixing negatively charged auricularia auricular polysaccharide (AAP with positively charged low molecular weight chitosan (LCS in an aqueous medium. The AAP was extracted and purified from auricularia auricular, and then characterized by micrOTOF-Q mass spectrometry, UV/Vis spectrophotometry, moisture analyzer and SEM. The yield, moisture, and total sugar content of the AAP were 4.5%, 6.2% and 90.12% (w/w, respectively. The AAP sample was water-soluble and exhibited white flocculence. The characteristics of AAP/LCS NPs, such as the particle size, zeta potential, morphology, FT-IR spectra, DSC were investigated. The results obtained revealed that the AAP/LCS NPs had a spherical shape with a diameter of 223 nm and a smooth surface, and the results of the FT-IR spectra and DSC investigations indicated that there was an electrostatic interaction between the two polyelectrolyte polymers. Bovine serum albumin (BSA, pI = 4.8 and bovine hemoglobin (BHb, pI = 6.8 were used as model drugs to investigate the loading and release features of the AAP/LCS NPs. The results obtained showed that the AAP/LCS NPs had a higher entrapment efficiency (92.6% for BHb than for BSA (81.5%. The cumulative release of BSA and BHb from AAP/LCS NPs after 24 h in vitro was 95.4% and 91.9%, respectively. The in vitro release demonstrated that AAP/LCS NPs provided a sustained release matrix suitable for the delivery of protein drugs. These studies demonstrate that AAP/LCS NPs have a very promising potential as a delivery system for protein drugs.

  15. Four-junction superconducting circuit

    Science.gov (United States)

    Qiu, Yueyin; Xiong, Wei; He, Xiao-Ling; Li, Tie-Fu; You, J. Q.

    2016-01-01

    We develop a theory for the quantum circuit consisting of a superconducting loop interrupted by four Josephson junctions and pierced by a magnetic flux (either static or time-dependent). In addition to the similarity with the typical three-junction flux qubit in the double-well regime, we demonstrate the difference of the four-junction circuit from its three-junction analogue, including its advantages over the latter. Moreover, the four-junction circuit in the single-well regime is also investigated. Our theory provides a tool to explore the physical properties of this four-junction superconducting circuit. PMID:27356619

  16. Tunable Nitride Josephson Junctions.

    Energy Technology Data Exchange (ETDEWEB)

    Missert, Nancy A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Henry, Michael David [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Lewis, Rupert M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Howell, Stephen W. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Wolfley, Steven L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Brunke, Lyle Brent [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Wolak, Matthaeus [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-12-01

    We have developed an ambient temperature, SiO2/Si wafer - scale process for Josephson junctions based on Nb electrodes and Ta x N barriers with tunable electronic properties. The films are fabricated by magnetron sputtering. The electronic properties of the TaxN barriers are controlled by adjusting the nitrogen flow during sputtering. This technology offers a scalable alternative to the more traditional junctions based on AlOx barriers for low - power, high - performance computing.

  17. Fabrication and characterization of graphene/molecule/graphene vertical junctions with aryl alkane monolayers

    Science.gov (United States)

    Jeong, Inho; Song, Hyunwook

    2017-11-01

    In this study, we fabricated and characterized graphene/molecule/graphene (GMG) vertical junctions with aryl alkane monolayers. The constituent molecules were chemically self-assembled via electrophilic diazonium reactions into a monolayer on the graphene bottom electrode, while the other end physically contacted the graphene top electrode. A full understanding of the transport properties of molecular junctions is a key step in the realization of molecular-scale electronic devices and requires detailed microscopic characterization of the junction's active region. Using a multiprobe approach combining a variety of transport techniques, we elucidated the transport mechanisms and electronic structure of the GMG junctions, including temperature- and length-variable transport measurements, and transition voltage spectroscopy. These results provide criteria to establish a valid molecular junction and to determine the most probable transport characteristics of the GMG junctions.

  18. Temporal correlations and structural memory effects in break junction measurements

    DEFF Research Database (Denmark)

    Magyarkuti, A.; Lauritzen, Kasper Primdal; Balogh, Zoltan Imre

    2017-01-01

    that correlations between the opening and subsequent closing traces may indicate structural memory effects in atomic-sized metallic and molecular junctions. Applying these methods on measured and simulated gold metallic contacts as a test system, we show that the surface diffusion induced flattening of the broken......-molecule junctions, we demonstrate pronounced contact memory effects and recovery of the molecule for junctions breaking before atomic chains are formed. However, if chains are pulled the random relaxation of the chain and molecule after rupture prevents opening-closing correlations....

  19. No junctional communication between epithelial cells in hydra

    DEFF Research Database (Denmark)

    de Laat, S W; Tertoolen, L G; Grimmelikhuijzen, C J

    1980-01-01

    junctions between epithelial cells of hydra. However, until now, there has been no report published on whether these junctions enable the epithelial cells to exchange molecules of small molecular weight, as has been described in other organisms. Therefore we decided to investigate the communicative...... properties of the junctional membranes by electrophysiological methods and by intracellular-dye iontophoresis. We report here that no electrotonic coupling is detectable between epithelial cells of Hydra attenuata in: (1) intact animals, (2) head-regenerating animals, (3) cell re-aggregates, and (4) hydra...

  20. Quantum Junction Solar Cells

    KAUST Repository

    Tang, Jiang; Liu, Huan; Zhitomirsky, David; Hoogland, Sjoerd; Wang, Xihua; Furukawa, Melissa; Levina, Larissa; Sargent, Edward H.

    2012-01-01

    -performing colloidal quantum dot rectifying devices reported to date have relied on a junction between a quantum-tuned absorber and a bulk material (e.g., TiO 2); however, quantum tuning of the absorber then requires complete redesign of the bulk acceptor, compromising

  1. The low molecular weight protein PsaI stabilizes the light-harvesting complex II docking site of photosystem I

    DEFF Research Database (Denmark)

    Plöchinger, Magdalena; Torabi, Salar; Rantala, Marjaana

    2016-01-01

    PsaI represents one of three low molecular weight peptides of PSI. Targeted inactivation of the plastid PsaI gene in Nicotiana tabacum has no measurable effect on photosynthetic electron transport around PSI or on accumulation of proteins involved in photosynthesis. Instead, the lack of Psa......I destabilizes the association of PsaL and PsaH to PSI, both forming the light-harvesting complex (LHC)II docking site of PSI. These alterations at the LHCII binding site surprisingly did not prevent state transition but led to an increased incidence of PSI-LHCII complexes, coinciding with an elevated...

  2. L-lysine-L-tartaric acid: New molecular complex with nonlinear optical properties. Structure, vibrational spectra and phase transitions

    International Nuclear Information System (INIS)

    Debrus, S.; Marchewka, M.K.; Baran, J.; Drozd, M.; Czopnik, R.; Pietraszko, A.; Ratajczak, H.

    2005-01-01

    The first X-ray diffraction and vibrational spectroscopic analysis of a novel complex between L-lysine and L-tartaric acid is reported. The structure was solved in two temperatures (320 and 260 K) showing incommensurate phase between them. Room-temperature powder infrared and Raman measurements for the L-lysine-L-tartaric acid molecular complex (1:1) were carried out. DSC measurements on powder samples indicate two phase transitions points at about 295, 300 and 293, 300 K, for heating and cooling, respectively, with noticeable temperature interval between them. Second harmonic generation efficiency d eff =0.35 d eff (KDP)

  3. Molecular orbital calculations of the unpaired electron distribution and electric field gradients in divalent paramagnetic Ir complexes

    International Nuclear Information System (INIS)

    Nogueira, S.R.; Vugman, N.V.; Guenzburger, D.

    1988-01-01

    Semi-empirical Molecular Orbital calculations were performed for the paramagnetic complex ions [Ir(CN) 5 ] 3- , [Ir(CN) 5 Cl] 4- and [Ir(CN) 4 Cl 2 ] 4- . Energy levels schemes and Mulliken-type populations were obtained. The distribution of the unpaired spin over the atoms in the complexes was derived, and compared to data obtained from Electron Paramagnetic Resonance spectra with the aid of a Ligand Field model. The electric field gradients at the Ir nucleus were calculated and compared to experiment. The results are discussed in terms of the chemical bonds formed by Ir and the ligands. (author) [pt

  4. Molecular modeling of human acidic mammalian chitinase in complex with the natural-product cyclopentapeptide chitinase inhibitor argifin.

    Science.gov (United States)

    Gouda, Hiroaki; Terashima, Shinichi; Iguchi, Kanami; Sugawara, Akihiro; Saito, Yoshifumi; Yamamoto, Tsuyoshi; Hirose, Tomoyasu; Shiomi, Kazuro; Sunazuka, Toshiaki; Omura, Satoshi; Hirono, Shuichi

    2009-09-01

    Human acidic mammalian chitinase (hAMCase) is an attractive target for developing anti-asthma medications. We used a variety of computational methods to investigate the interaction between hAMCase and the natural-product cyclopentapeptide chitinase inhibitor argifin. The three-dimensional structure of hAMCase was first constructed using homology modeling. The interaction mode and binding free energy between argifin and hAMCase were then examined by the molecular-docking calculation and the molecular mechanics Poisson-Boltzmann surface area method combined with molecular dynamics simulation, respectively. The results suggested that argifin binds to hAMCase in a similar fashion to the interaction mode observed in the crystal structure of argifin-human chitotriosidase complex, and possesses inhibitory activity against hAMCase in the micromolar range. We further designed argifin derivatives expected to be selective for hAMCase.

  5. Excitation energy transfer in molecular complexes: transport processes, optical properties and effects of nearby placed metal nano-particles

    Science.gov (United States)

    May, Volkhard; Megow, Jörg; Zelinskyi, Iaroslav

    2012-04-01

    Excitation energy transfer (EET) in molecular systems is studied theoretically. Chromophore complexes are considered which are formed by a butanediamine dendrimer with four pheophorbide-a molecules. To achieve a description with an atomic resolution and to account for the effect of an ethanol solvent a mixed quantum classical methodology is utilized. Details of the EET and spectra of transient anisotropy showing signatures of EET are presented. A particular control of intermolecular EET is achieved by surface plasmons of nearby placed metal nanoparticles (MNP). To attain a quantum description of the molecule-MNP system a microscopic theory is introduced. As a particular application surface plasmon affected absorption spectra of molecular complexes placed in the proximity of a spherical MNP are discussed.

  6. Interaction of Cosup(III) complexes with radiation on 'in vitro' mammalian cells and on molecular systems

    International Nuclear Information System (INIS)

    Alvarez, M.V.; Cabildo, P.; Lopez Zumel, M.C.

    1978-01-01

    Cosup(III) complexes could be considered as potential radiosensitizers in dependence of the electronic configuration of the metal. Due to the high redox state that causes its powerful electrophilia they possibly act through electron-affinic mechanisms. In this paper the effect of [Co(NH 3 ) 5 Cl]Cl 2 on TC.SV-40 hamster cells is reported, in aerobic and hypoxic conditions, and its action, at a non-toxic concentration, in a combined treatment with X-rays. Results show the small protection induced by the product in the survival curves. As a contribution to the knowledge of its possible mechanism of action some molecular proofs and the interaction test with -SHNP cellular groups are made. A high degree of reaction is observed as is the case with good radiosensitizers but at molecular level the behaviour of the complex formed between DNA and the product reveals mutual protection due to their corresponding radiodegradation. (orig.) [de

  7. Redox-switched complexation/decomplexation of K(+) and Cs(+) by molecular cyanometalate boxes.

    Science.gov (United States)

    Boyer, Julie L; Ramesh, Maya; Yao, Haijun; Rauchfuss, Thomas B; Wilson, Scott R

    2007-02-21

    The reaction of [N(PPh(3))(2)][CpCo(CN)(3)] and [Cb*Co(NCMe)(3)]PF(6) (Cb* = C(4)Me(4)) in the presence of K(+) afforded {K subset[CpCo(CN)(3)](4)[Cb*Co](4)}PF(6), [KCo(8)]PF(6). IR, NMR, ESI-MS indicate that [KCo(8)]PF(6) is a high-symmetry molecular box containing a potassium ion at its interior. The analogous heterometallic cage {K subset[Cp*Rh(CN)(3)](4)[Cb*Co](4)}PF(6) ([KRh(4)Co(4)]PF(6)) was prepared similarly via the condensation of K[Cp*Rh(CN)(3)] and [Cb*Co(NCMe)(3)]PF(6). Crystallographic analysis confirmed the structure of [KCo(8)]PF(6). The cyanide ligands are ordered, implying that no Co-CN bonds are broken upon cage formation and ion complexation. Eight Co-CN-Co edges of the box bow inward toward the encapsulated K(+), and the remaining four mu-CN ligands bow outward. MeCN solutions of [KCo(8)](+) and [KRh(4)Co(4)](+) were found to undergo ion exchange with Cs(+) to give [CsCo(8)](+) and [CsRh(4)Co(4)](+), both in quantitative yields. Labeling experiments involving [(MeC5H4)Co(CN)(3)]- demonstrated that Cs(+)-for-K(+) ion exchange is accompanied by significant fragmentation. Ion exchange of NH(4+) with [KCo(8)](+) proceeds to completion in THF solution, but in MeCN solution, the exclusive products were [Cb*Co(NCMe)(3)]PF(6) and the poorly soluble salt NH(4)CpCo(CN)(3). The lability of the NH(4+)-containing cage was also indicated by the rapid exchange of the acidic protons in [NH(4)Co(8)](+). Oxidation of [MCo(8)](+) with 4 equiv of FcPF(6) produced paramagnetic (S = 4/2) [Co(8)](4+), releasing Cs(+) or K(+). The oxidation-induced dissociation of M(+) from the cages is chemically reversed by treatment of [Co(8)](4+) and CsOTf with 4 equiv of Cp(2)Co. Cation recognition by [Co(8)] and [Rh(4)Co(4)] cages was investigated. Electrochemical measurements indicated that E(1/2)(Cs(+))--E(1/2)(K(+)) approximately 0.08 V for [MCo(8)](+).

  8. Adaptive molecular evolution of the Major Histocompatibility Complex genes, DRA and DQA, in the genus Equus.

    Science.gov (United States)

    Kamath, Pauline L; Getz, Wayne M

    2011-05-18

    Major Histocompatibility Complex (MHC) genes are central to vertebrate immune response and are believed to be under balancing selection by pathogens. This hypothesis has been supported by observations of extremely high polymorphism, elevated nonsynonymous to synonymous base pair substitution rates and trans-species polymorphisms at these loci. In equids, the organization and variability of this gene family has been described, however the full extent of diversity and selection is unknown. As selection is not expected to act uniformly on a functional gene, maximum likelihood codon-based models of selection that allow heterogeneity in selection across codon positions can be valuable for examining MHC gene evolution and the molecular basis for species adaptations. We investigated the evolution of two class II MHC genes of the Equine Lymphocyte Antigen (ELA), DRA and DQA, in the genus Equus with the addition of novel alleles identified in plains zebra (E. quagga, formerly E. burchelli). We found that both genes exhibited a high degree of polymorphism and inter-specific sharing of allele lineages. To our knowledge, DRA allelic diversity was discovered to be higher than has ever been observed in vertebrates. Evidence was also found to support a duplication of the DQA locus. Selection analyses, evaluated in terms of relative rates of nonsynonymous to synonymous mutations (dN/dS) averaged over the gene region, indicated that the majority of codon sites were conserved and under purifying selection (dN

  9. Adaptive molecular evolution of the Major Histocompatibility Complex genes, DRA and DQA, in the genus Equus

    Directory of Open Access Journals (Sweden)

    Getz Wayne M

    2011-05-01

    Full Text Available Abstract Background Major Histocompatibility Complex (MHC genes are central to vertebrate immune response and are believed to be under balancing selection by pathogens. This hypothesis has been supported by observations of extremely high polymorphism, elevated nonsynonymous to synonymous base pair substitution rates and trans-species polymorphisms at these loci. In equids, the organization and variability of this gene family has been described, however the full extent of diversity and selection is unknown. As selection is not expected to act uniformly on a functional gene, maximum likelihood codon-based models of selection that allow heterogeneity in selection across codon positions can be valuable for examining MHC gene evolution and the molecular basis for species adaptations. Results We investigated the evolution of two class II MHC genes of the Equine Lymphocyte Antigen (ELA, DRA and DQA, in the genus Equus with the addition of novel alleles identified in plains zebra (E. quagga, formerly E. burchelli. We found that both genes exhibited a high degree of polymorphism and inter-specific sharing of allele lineages. To our knowledge, DRA allelic diversity was discovered to be higher than has ever been observed in vertebrates. Evidence was also found to support a duplication of the DQA locus. Selection analyses, evaluated in terms of relative rates of nonsynonymous to synonymous mutations (dN/dS averaged over the gene region, indicated that the majority of codon sites were conserved and under purifying selection (dN dS. However, the most likely evolutionary codon models allowed for variable rates of selection across codon sites at both loci and, at the DQA, supported the hypothesis of positive selection acting on specific sites. Conclusions Observations of elevated genetic diversity and trans-species polymorphisms supported the conclusion that balancing selection may be acting on these loci. Furthermore, at the DQA, positive selection was

  10. Molecular complex of lumiflavin and 2-aminobenzoic acid: crystal structure, crystal spectra, and solution properties.

    Science.gov (United States)

    Shieh, H S; Ghisla, S; Hanson, L K; Ludwig, M L; Nordman, C E

    1981-08-04

    The molecular complex lumiflavin-2-aminobenzoic acid monohydrate (C13H12N4O2.C7H7NO2.H2O) crystallizes from from aqueous solution as red triclinic prisms. The space group is P1 with cell dimensions a = 9.660 A, b = 14.866 A, c = 7.045 A, alpha = 95.44 degrees , beta = 95.86 degrees, and gamma = 105.66 degrees . The crystal structure was solved by direct methods and refined by block-diagonal least-squares procedures to an R value of 0.050 on the basis of 1338 observed reflections. The structure is composed of stacks of alternating lumiflavin adn un-ionized (neutral) 2-aminobenzoic acid molecules. Two different modes of stacking interaction are observed. In one, 2-aminobenzoic acid overlaps all three of the isoalloxazine rings, at a mean distance of 3.36 A; in the other, 2-aminobenzoic acid interacts distance of 3.36 A; in the other, 2-aminobenzoic acid interacts with the pyrazine and dimethylbenzene moieties, at a distance of 3.42 A. Perpendicular to the stacking direction, the molecules form a continuous sheet. Each flavin is hydrogen bonded via O(2) and NH(3) to two symmetrically related aminobenzoates; the water of crystallization forms three hydrogen bonds, bridging two flavins, via O(4) and N(5), and one aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid molecules. Measurements of the polarized optical absorption spectra of crystals show that the transition moment direction for the long wavelength absorbance (beyond 530 nm) contains an out-of-plane component which can only arise from a charge-transfer interaction. Since the amino N does not make exceptionally close interactions with isoalloxazine atoms in either stacking mode (minimum interatomic distance 3.52 A), the charge transfer is presumed to involve pi orbitals of the 2-aminobenzoic acid donor.

  11. Synthesis, molecular structure, biological properties and molecular docking studies on Mn(II), Co(II) and Zn(II) complexes containing bipyridine-azide ligands.

    Science.gov (United States)

    Thamilarasan, Vijayan; Jayamani, Arumugam; Sengottuvelan, Nallathambi

    2015-01-07

    Metal complexes of the type Mn(bpy)2(N3)2 (1), Co(bpy)2(N3)2·3H2O (2) and Zn2(bpy)2(N3)4 (3) (Where bpy = 2,2-bipyridine) have been synthesized and characterized by elemental analysis and spectral (FT-IR, UV-vis) studies. The structure of complexes (1-3) have been determined by single crystal X-ray diffraction studies and the configuration of ligand-coordinated metal(II) ion was well described as distorted octahedral coordination geometry for Mn(II), Co(II) and distorted square pyramidal geometry for Zn(II) complexes. DNA binding interaction of these complexes (1-3) were investigated by UV-vis absorption, fluorescence circular dichroism spectral and molecular docking studies. The intrinsic binding constants Kb of complexes 1, 2 and 3 with CT-DNA obtained from UV-vis absorption studies were 8.37 × 10(4), 2.23 × 10(5) and 5.52 × 10(4) M(-1) respectively. The results indicated that the three complexes are able to bind to DNA with different binding affinity, in the order 2 > 1 > 3. Complexes (1-3) exhibit a good binding propensity to bovine serum albumin (BSA) proteins having relatively high binding constant values. Gel electrophoresis assay demonstrated the ability of the complexes 1-3 promote the cleavage ability of the pBR322 plasmid DNA in the presence of the reducing agent 3-mercaptopropionic acid (MPA) but with different cleavage mechanisms: the complex 3 cleaves DNA via hydrolytic pathway (T4 DNA ligase assay), while the DNA cleavage by complexes 1 and 2 follows oxidative pathway. The chemical nuclease activity follows the order: 2 > 1 > 3. The effects of various activators were also investigated and the nuclease activity efficacy followed the order MPA > GSH > H2O2 > Asc. The cytotoxicity studies of complexes 1-3 were tested in vitro on breast cancer cell line (MCF-7) and they found to be active. Copyright © 2014. Published by Elsevier Masson SAS.

  12. Spectroscopic mapping and selective electronic tuning of molecular orbitals in phosphorescent organometallic complexes – a new strategy for OLED materials

    Directory of Open Access Journals (Sweden)

    Pascal R. Ewen

    2014-11-01

    Full Text Available The improvement of molecular electronic devices such as organic light-emitting diodes requires fundamental knowledge about the structural and electronic properties of the employed molecules as well as their interactions with neighboring molecules or interfaces. We show that highly resolved scanning tunneling microscopy (STM and spectroscopy (STS are powerful tools to correlate the electronic properties of phosphorescent complexes (i.e., triplet emitters with their molecular structure as well as the local environment around a single molecule. We used spectroscopic mapping to visualize several occupied and unoccupied molecular frontier orbitals of Pt(II complexes adsorbed on Au(111. The analysis showed that the molecules exhibit a peculiar localized strong hybridization that leads to partial depopulation of a dz² orbital, while the ligand orbitals are almost unchanged. We further found that substitution of functional groups at well-defined positions can alter specific molecular orbitals without influencing the others. The results open a path toward the tailored design of electronic and optical properties of triplet emitters by smart ligand substitution, which may improve the performance of future OLED devices.

  13. Nonlinear gap junctions enable long-distance propagation of pulsating calcium waves in astrocyte networks.

    Directory of Open Access Journals (Sweden)

    Mati Goldberg

    Full Text Available A new paradigm has recently emerged in brain science whereby communications between glial cells and neuron-glia interactions should be considered together with neurons and their networks to understand higher brain functions. In particular, astrocytes, the main type of glial cells in the cortex, have been shown to communicate with neurons and with each other. They are thought to form a gap-junction-coupled syncytium supporting cell-cell communication via propagating Ca(2+ waves. An identified mode of propagation is based on cytoplasm-to-cytoplasm transport of inositol trisphosphate (IP(3 through gap junctions that locally trigger Ca(2+ pulses via IP(3-dependent Ca(2+-induced Ca(2+ release. It is, however, currently unknown whether this intracellular route is able to support the propagation of long-distance regenerative Ca(2+ waves or is restricted to short-distance signaling. Furthermore, the influence of the intracellular signaling dynamics on intercellular propagation remains to be understood. In this work, we propose a model of the gap-junctional route for intercellular Ca(2+ wave propagation in astrocytes. Our model yields two major predictions. First, we show that long-distance regenerative signaling requires nonlinear coupling in the gap junctions. Second, we show that even with nonlinear gap junctions, long-distance regenerative signaling is favored when the internal Ca(2+ dynamics implements frequency modulation-encoding oscillations with pulsating dynamics, while amplitude modulation-encoding dynamics tends to restrict the propagation range. As a result, spatially heterogeneous molecular properties and/or weak couplings are shown to give rise to rich spatiotemporal dynamics that support complex propagation behaviors. These results shed new light on the mechanisms implicated in the propagation of Ca(2+ waves across astrocytes and the precise conditions under which glial cells may participate in information processing in the brain.

  14. Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer

    DEFF Research Database (Denmark)

    Solov'yov, Ilia A.; Korol, Andrei V.; Solov'yov, Andrey V.

    -up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science...... of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potentials and can, e.g., be configured to select any subset of a molecular system as rigid fragments, whenever a significant reduction in the number of dynamical degrees of freedom is required for computational...... practicalities. MBN Studio enables users to easily construct initial geometries for the molecular, liquid, crystalline, gaseous and hybrid systems that serve as input for the subsequent simulations of their physical and chemical properties using MBN Explorer. Despite its universality, the computational...

  15. Inclusion complexes of cefuroxime axetil with β-cyclodextrin: Physicochemical characterization, molecular modeling and effect of l-arginine on complexation

    Directory of Open Access Journals (Sweden)

    Sarika Sapte

    2016-10-01

    Full Text Available The inclusion complexes of poorly water-soluble cephalosporin, cefuroxime axetil (CFA, were prepared with β-cyclodextrin (βCD with or without addition of l-arginine (ARG to improve its physicochemical properties. We also investigated the effect of ARG on complexation efficiency (CE of βCD towards CFA in an aqueous medium through phase solubility behaviour according to Higuchi and Connors. Although phase solubility studies showed AL (linear type of solubility curve in presence and absence of ARG, the CE and association constant (Ks of βCD towards CFA were significantly promoted in presence of ARG, justifying its use as a ternary component. The solid systems of CFA with βCD were obtained by spray drying technique with or without incorporation of ARG and characterized by differential scanning calorimetry (DSC, X-ray powder diffractometry (XRPD, scanning electron microscopy (SEM, and saturation solubility and dissolution studies. The molecular modeling studies provided a better insight into geometry and inclusion mode of CFA inside βCD cavity. The solubility and dissolution rate of CFA were significantly improved upon complexation with βCD as compared to CFA alone. However, ternary system incorporated with ARG performed better than binary system in physicochemical evaluation. In conclusion, ARG could be exploited as a ternary component to improve the physicochemical properties of CFA via βCD complexation.

  16. The critical current of point symmetric Josephson tunnel junctions

    International Nuclear Information System (INIS)

    Monaco, Roberto

    2016-01-01

    Highlights: • We disclose some geometrical properties of the critical current field dependence that apply to a large class of Josephson junctions characterized by a point symmetric shape. • The developed theory is valid for any orientation of the applied magnetic field, therefore it allows the determine the consequences of field misalignment in the experimental setups. • We also address that the threshold curves of Josephson tunnel junctions with complex shapes can be expressed as a linear combination of the threshold curves of junctions with simpler point symmetric shapes. - Abstract: The physics of Josephson tunnel junctions drastically depends on their geometrical configurations. The shape of the junction determines the specific form of the magnetic-field dependence of its Josephson current. Here we address the magnetic diffraction patterns of specially shaped planar Josephson tunnel junctions in the presence of an in-plane magnetic field of arbitrary orientations. We focus on a wide ensemble of junctions whose shape is invariant under point reflection. We analyze the implications of this type of isometry and derive the threshold curves of junctions whose shape is the union or the relative complement of two point symmetric plane figures.

  17. Chemical complexity induced by efficient ice evaporation in the Barnard 5 molecular cloud

    OpenAIRE

    Taquet, Vianney; Wirström, Eva; Charnley, Steven B.; Faure, Alexandre; López-Sepulcre, Ana; Persson, Carina M.

    2017-01-01

    Cold gas-phase water has recently been detected in a cold dark cloud, Barnard 5 located in the Perseus complex, by targeting methanol peaks as signposts for ice mantle evaporation. Observed morphology and abundances of methanol and water are consistent with a transient non-thermal evaporation process only affecting the outermost ice mantle layers, possibly triggering a more complex chemistry. We present the detection of the Complex Organic Molecules (COMs) acetaldehyde and methyl formate as w...

  18. Synthesis and molecular structure of YbI(bipy)(DME)2 complex

    International Nuclear Information System (INIS)

    Petrovskaya, T.V.; Fedyushkin, I.L.; Nevodchikov, V.I.; Bochkarev, M.N.; Borodina, N.V.; Eremenko, I.L.; Nefedov, S.E.

    1998-01-01

    The reaction of the ytterbium naphthaline complex [Yb(DME) 2 ] 2 (μ-C 10 H 8 ) with 2,2 ' -bipyridine in DME is found to lead to the formation of the complex with the Yb 2+ atom, YbI(bipy)(DME) 2 (1) containing 2,2 ' -bipyridine radical anion. Complex 1 is characterized by IR and UV spectroscopy, magnetic methods and X-ray analysis [ru

  19. [Molecular dynamics of immune complex of photoadduct-containing DNA with Fab-Anti-DNA antibody fragment].

    Science.gov (United States)

    Akberova, N I; Zhmurov, A A; Nevzorova, T A; Litvinov, R I

    2016-01-01

    Antibodies to DNA play an important role in the pathogenesis of autoimmune diseases. The elucidation of structural mechanisms of both the antigen recognition and the interaction of anti-DNA antibodies with DNA will help to understand the role of DNA-containing immune complexes in various pathologies and can provide a basis for new treatment modalities. Moreover, the DNA-antibody complex is an analog of specific intracellular DNA-protein interactions. In this work, we used in silico molecular dynamic simulations of bimolecular complexes of the dsDNA segment containing the Fab fragment of an anti-DNA antibody to obtain the detailed thermodynamic and structural characteristics of dynamic intermolecular interactions. Using computationally modified crystal structure of the Fab-DNA complex (PDB ID: 3VW3), we studied the equilibrium molecular dynamics of the 64M-5 antibody Fab fragment associated with the dsDNA fragment containing the thymine dimer, the product of DNA photodamage. Amino acid residues that constitute paratopes and the complementary nucleotide epitopes for the Fab-DNA construct were identified. Stacking and electrostatic interactions were found to play the main role in mediating the most specific antibody-dsDNA contacts, while hydrogen bonds were less significant. These findings may shed light on the formation and properties of pathogenic anti-DNA antibodies in autoimmune diseases, such as systemic lupus erythematosus associated with skin photosensitivity and DNA photodamage.

  20. Molecular Cloning Designer Simulator (MCDS: All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects

    Directory of Open Access Journals (Sweden)

    Zhenyu Shi

    2016-12-01

    Full Text Available Molecular Cloning Designer Simulator (MCDS is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1 it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2 it can perform a user-defined workflow of cloning steps in a single execution of the software; (3 it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4 it includes experimental information to conveniently guide wet lab work; and (5 it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com. Keywords: BioCAD, Genetic engineering software, Molecular cloning software, Synthetic biology, Workflow simulation and management

  1. 3D Architecture of the Trypanosoma brucei Flagella Connector, a Mobile Transmembrane Junction.

    Directory of Open Access Journals (Sweden)

    Johanna L Höög

    2016-01-01

    Full Text Available Cellular junctions are crucial for the formation of multicellular organisms, where they anchor cells to each other and/or supportive tissue and enable cell-to-cell communication. Some unicellular organisms, such as the parasitic protist Trypanosoma brucei, also have complex cellular junctions. The flagella connector (FC is a three-layered transmembrane junction that moves with the growing tip of a new flagellum and attaches it to the side of the old flagellum. The FC moves via an unknown molecular mechanism, independent of new flagellum growth. Here we describe the detailed 3D architecture of the FC suggesting explanations for how it functions and its mechanism of motility.We have used a combination of electron tomography and cryo-electron tomography to reveal the 3D architecture of the FC. Cryo-electron tomography revealed layers of repetitive filamentous electron densities between the two flagella in the interstitial zone. Though the FC does not change in length and width during the growth of the new flagellum, the interstitial zone thickness decreases as the FC matures. This investigation also shows interactions between the FC layers and the axonemes of the new and old flagellum, sufficiently strong to displace the axoneme in the old flagellum. We describe a novel filament, the flagella connector fibre, found between the FC and the axoneme in the old flagellum.The FC is similar to other cellular junctions in that filamentous proteins bridge the extracellular space and are anchored to underlying cytoskeletal structures; however, it is built between different portions of the same cell and is unique because of its intrinsic motility. The detailed description of its structure will be an important tool to use in attributing structure / function relationships as its molecular components are discovered in the future. The FC is involved in the inheritance of cell shape, which is important for the life cycle of this human parasite.

  2. Electrocatalytic oxidation of organic substrates with molecular oxygen using tetradentate ruthenium(III)-Schiff base complexes as catalysts

    International Nuclear Information System (INIS)

    Ourari, Ali; Khelafi, Mostefa; Aggoun, Djouhra; Jutand, Anny; Amatore, Christian

    2012-01-01

    Three complexes Ru(III)ClL n involving different tetradentate Schiff base ligands L n (see L 1 , L 2 and L 3 in ) were used as catalysts in the oxidation of cyclooctene and tetraline in the presence of molecular dioxygen associated with benzoic anhydride. The efficiency of this oxidation reaction was tested in the presence of two apical bases: 1- or 2-methylimidazole. All complexes exhibit a quasi-reversible redox system. The electrolysis experiments were carried out at controlled potential for each complex, using different substrates such as cyclooctene and tetraline. The oxidized products are cyclooctene oxide (turnover 6.7), a mixture of 1-tetralol and 1-tetralone (turnover 7.6) respectively.

  3. MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories

    KAUST Repository

    Abdel-Azeim, Safwat

    2014-05-06

    Background: Molecular Dynamics ( MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface. Results: On these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between different snapshots. A "consensus contact map" is also provided, where the conservation of the different contacts is drawn in a grey scale. Finally, the interface area of the complex is monitored during the simulations. To show its utility, we used this novel approach to study two protein-protein complexes with interfaces of comparable size and both dominated by hydrophilic interactions, but having binding affinities at the extremes of the experimental range. MDcons is demonstrated to be extremely useful to analyse the MD trajectories of the investigated complexes, adding important insight into the dynamic behavior of their biological interface. Conclusions: MDcons specifically allows the user to highlight and characterize the dynamics of the interface in protein complexes and can thus be used as a complementary tool for the analysis of MD simulations of both experimental and predicted structures of protein complexes.

  4. Molecular complexation of curcumin with pH sensitive cationic copolymer enhances the aqueous solubility, stability and bioavailability of curcumin.

    Science.gov (United States)

    Kumar, Sunny; Kesharwani, Siddharth S; Mathur, Himanshi; Tyagi, Mohit; Bhat, G Jayarama; Tummala, Hemachand

    2016-01-20

    Curcumin is a natural dietary compound with demonstrated potential in preventing/treating several chronic diseases in animal models. However, this success is yet to be translated to humans mainly because of its poor oral bioavailability caused by extremely low water solubility. This manuscript demonstrates that water insoluble curcumin (~1μg/ml) forms highly aqueous soluble complexes (>2mg/ml) with a safe pH sensitive polymer, poly(butyl-methacrylate-co-(2-dimethylaminoethyl) methacrylate-co-methyl-methacrylate) when precipitated together in water. The complexation process was optimized to enhance curcumin loading by varying several formulation factors. Acetone as a solvent and polyvinyl alcohol as a stabilizer with 1:2 ratio of drug to polymer yielded complexes with relatively high loading (~280μg/ml) and enhanced solubility (>2mg/ml). The complexes were amorphous in solid and were soluble only in buffers with pHs less than 5.0. Hydrogen bond formation and hydrophobic interactions between curcumin and the polymer were recorded by infrared spectroscopy and nuclear magnetic resonance spectroscopy, respectively. Molecular complexes of curcumin were more stable at various pHs compared to unformulated curcumin. In mice, these complexes increased peak plasma concentration of curcumin by 6 times and oral bioavailability by ~20 times. This is a simple, economic and safer strategy of enhancing the oral bioavailability of curcumin. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Spectroscopic and molecular docking studies on the interaction of human serum albumin with copper(II) complexes

    Science.gov (United States)

    Guhathakurta, Bhargab; Pradhan, Ankur Bikash; Das, Suman; Bandyopadhyay, Nirmalya; Lu, Liping; Zhu, Miaoli; Naskar, Jnan Prakash

    2017-02-01

    Two osazone based ligands, butane-2,3-dione bis(2‧-pyridylhydrazone) (BDBPH) and hexane-3,4-dione bis(2‧-pyridylhydrazone) (HDBPH), were synthesized out of the 2:1 M Schiff base condensation of 2-hydrazino pyridine respectively with 2,3-butanedione and 3,4-hexanedione. The X-ray crystal structures of both the ligands have been determined. The copper(II) complex of HDBPH has also been synthesized and structurally characterized. HDBPH and its copper(II) complex have thoroughly been characterized through various spectroscopic and analytical techniques. The X-ray crystal structure of the copper complex of HDBPH shows that it is a monomeric Cu(II) complex having 'N4O2' co-ordination chromophore. Interaction of human serum albumin (HSA) with these ligands and their monomeric copper(II) complexes have been studied by various spectroscopic means. The experimental findings show that the ligands as well as their copper complexes are good HSA binders. Molecular docking investigations have also been done to unravel the mode of binding of the species with HSA.

  6. Molecular Recognition in the Oxidation of Catechols by Dicobalt-BISDIEN Dioxygen Complexes

    Science.gov (United States)

    1992-01-30

    Recognition in the Oxidation of Catechols by Dicobalt-RISDIEN Dioxygen Complexes Lizete F S Cezar and Bruno Szpoganicz Departamento de Quimica ...bridged bi- nuclear Co(II)-BISDIEN dioxygen complexes; Co20 2 LCat2 + is the bivalent form, and Co20 2 (OH)LCat + and Co 20 2 (OH)2 Cat° are hydroxo

  7. Synthesis of sp3-rich scaffolds for molecular libraries through complexity-generating cascade reactions

    DEFF Research Database (Denmark)

    Flagstad, Thomas; Min, Geanna; Bonnet, K.

    2016-01-01

    An efficient strategy for the synthesis of complex small molecules from simple building blocks is presented. Key steps of the strategy include tandem Petasis and Diels–Alder reactions, and divergent complexity-generating cyclization cascades from a key dialdehyde intermediate. The methodology...

  8. MOLECULAR BIOLOGICAL AND RADIOLOGICAL TECHNOLOGIES IN THE COMPLEX DIAGNOSIS OF AUXILLARY PATHOLOGY

    Directory of Open Access Journals (Sweden)

    N. I. Rozhkova

    2009-01-01

    Full Text Available Introduction. A diversity of axillary pathologies was a prerequisite for the development of a new differential approach to diagnosing such conditions. There are new technologies (pre- and intraoperative radionuclide studies, molecular genetic techniques, that have shown themselves, along with classical methods (physical examination, mammography, X-ray and ultrasound studies.Materials and methods. The subject of the analysis is the results of a comprehensive examination of 502 women aged 22 to 84 years. Different groups were comprehensively examined using both X-ray, ultrasound, radionuclide, and molecular genetic (polymerase chain reaction studies.Results. The molecular genetic and cytological studies could provide the actual results in 95 and 84% of cases, respectively; but a com- prehensive clinical study and X-ray ultrasound computed tomography could yield them in marginal metastases in only 65.3%. Conclusion. The authors have proposed the optimal diagnostic algorithm for examination in the ambulatory-outpatient network and specialized institutions.

  9. Josephson junctions array resonators

    Energy Technology Data Exchange (ETDEWEB)

    Gargiulo, Oscar; Muppalla, Phani; Mirzaei, Iman; Kirchmair, Gerhard [Institute for Quantum Optics and Quantum Information, Innsbruck (Austria)

    2016-07-01

    We present an experimental analysis of the self- and cross-Kerr effect of extended plasma resonances in Josephson junction chains. The chain consists of 1600 individual junctions and we can measure quality factors in excess of 10000. The Kerr effect manifests itself as a frequency shift that depends linearly on the number of photons in a resonant mode. By changing the input power we are able to measure this frequency shift on a single mode (self-kerr). By changing the input power on another mode while measuring the same one, we are able to evaluate the cross-kerr effect. We can measure the cross-Kerr effect by probing the resonance frequency of one mode while exciting another mode of the array with a microwave drive.

  10. Curved Josephson junction

    International Nuclear Information System (INIS)

    Dobrowolski, Tomasz

    2012-01-01

    The constant curvature one and quasi-one dimensional Josephson junction is considered. On the base of Maxwell equations, the sine–Gordon equation that describes an influence of curvature on the kink motion was obtained. It is showed that the method of geometrical reduction of the sine–Gordon model from three to lower dimensional manifold leads to an identical form of the sine–Gordon equation. - Highlights: ► The research on dynamics of the phase in a curved Josephson junction is performed. ► The geometrical reduction is applied to the sine–Gordon model. ► The results of geometrical reduction and the fundamental research are compared.

  11. Discovery of Novel Complex Metal Hydrides for Hydrogen Storage through Molecular Modeling and Combinatorial Methods

    Energy Technology Data Exchange (ETDEWEB)

    Lesch, David A; Adriaan Sachtler, J.W. J.; Low, John J; Jensen, Craig M; Ozolins, Vidvuds; Siegel, Don; Harmon, Laurel

    2011-02-14

    UOP LLC, a Honeywell Company, Ford Motor Company, and Striatus, Inc., collaborated with Professor Craig Jensen of the University of Hawaii and Professor Vidvuds Ozolins of University of California, Los Angeles on a multi-year cost-shared program to discover novel complex metal hydrides for hydrogen storage. This innovative program combined sophisticated molecular modeling with high throughput combinatorial experiments to maximize the probability of identifying commercially relevant, economical hydrogen storage materials with broad application. A set of tools was developed to pursue the medium throughput (MT) and high throughput (HT) combinatorial exploratory investigation of novel complex metal hydrides for hydrogen storage. The assay programs consisted of monitoring hydrogen evolution as a function of temperature. This project also incorporated theoretical methods to help select candidate materials families for testing. The Virtual High Throughput Screening served as a virtual laboratory, calculating structures and their properties. First Principles calculations were applied to various systems to examine hydrogen storage reaction pathways and the associated thermodynamics. The experimental program began with the validation of the MT assay tool with NaAlH4/0.02 mole Ti, the state of the art hydrogen storage system given by decomposition of sodium alanate to sodium hydride, aluminum metal, and hydrogen. Once certified, a combinatorial 21-point study of the NaAlH4 LiAlH4Mg(AlH4)2 phase diagram was investigated with the MT assay. Stability proved to be a problem as many of the materials decomposed during synthesis, altering the expected assay results. This resulted in repeating the entire experiment with a mild milling approach, which only temporarily increased capacity. NaAlH4 was the best performer in both studies and no new mixed alanates were observed, a result consistent with the VHTS. Powder XRD suggested that the reverse reaction, the regeneration of the

  12. Syntheses, spectroscopic properties and molecular structure of silver phytate complexes - IR, UV-VIS studies and DFT calculations

    Science.gov (United States)

    Zając, A.; Dymińska, L.; Lorenc, J.; Ptak, M.; Hanuza, J.

    2018-03-01

    Silver phytate IP6, IP6Ag, IP6Ag2 and IP6Ag3 complexes in the solid state have been synthesized changing the phosphate to metal mole ratio. The obtained products have been characterized by means of chemical and spectroscopic studies. Attenuated total reflection Fourier transform infrared technique and Raman microscope were used in the measurements. These results were discussed in terms of DFT (Density Functional Theory) quantum chemical calculations using the B3LYP/6-31G(d,p) approach. The molecular structures of these compounds have been proposed on the basis of group theory and geometry optimization taking into account the shape and the number of the observed bands corresponding to the stretching and bending vibrations of the phosphate group and metal-oxygen polyhedron. The role of inter- and intra-hydrogen bonds in stabilization of the structure has been discussed. It was found that three types of hydrogen bonds appear in the studied compounds: terminal, and those engaged in the inter- and intra-molecular interactions. The Fermi resonance as a result of the strong intra-molecular Osbnd H⋯O hydrogen bonds was discovered. Electron absorption spectra have been measured to characterize the electron properties of the studied complexes and their local symmetry.

  13. Controlling formation of single-molecule junctions by electrochemical reduction of diazonium terminal groups.

    Science.gov (United States)

    Hines, Thomas; Díez-Pérez, Ismael; Nakamura, Hisao; Shimazaki, Tomomi; Asai, Yoshihiro; Tao, Nongjian

    2013-03-06

    We report controlling the formation of single-molecule junctions by means of electrochemically reducing two axialdiazonium terminal groups on a molecule, thereby producing direct Au-C covalent bonds in situ between the molecule and gold electrodes. We report a yield enhancement in molecular junction formation as the electrochemical potential of both junction electrodes approach the reduction potential of the diazonium terminal groups. Step length analysis shows that the molecular junction is significantly more stable, and can be pulled over a longer distance than a comparable junction created with amine anchoring bonds. The stability of the junction is explained by the calculated lower binding energy associated with the direct Au-C bond compared with the Au-N bond.

  14. Single-molecule detection of dihydroazulene photo-thermal reaction using break junction technique

    Science.gov (United States)

    Huang, Cancan; Jevric, Martyn; Borges, Anders; Olsen, Stine T.; Hamill, Joseph M.; Zheng, Jue-Ting; Yang, Yang; Rudnev, Alexander; Baghernejad, Masoud; Broekmann, Peter; Petersen, Anne Ugleholdt; Wandlowski, Thomas; Mikkelsen, Kurt V.; Solomon, Gemma C.; Brøndsted Nielsen, Mogens; Hong, Wenjing

    2017-05-01

    Charge transport by tunnelling is one of the most ubiquitous elementary processes in nature. Small structural changes in a molecular junction can lead to significant difference in the single-molecule electronic properties, offering a tremendous opportunity to examine a reaction on the single-molecule scale by monitoring the conductance changes. Here, we explore the potential of the single-molecule break junction technique in the detection of photo-thermal reaction processes of a photochromic dihydroazulene/vinylheptafulvene system. Statistical analysis of the break junction experiments provides a quantitative approach for probing the reaction kinetics and reversibility, including the occurrence of isomerization during the reaction. The product ratios observed when switching the system in the junction does not follow those observed in solution studies (both experiment and theory), suggesting that the junction environment was perturbing the process significantly. This study opens the possibility of using nano-structured environments like molecular junctions to tailor product ratios in chemical reactions.

  15. Tunable Complex Stability in Surface Molecular Recognition Mediated by Self-Complementary Quadruple Hydrogen Bonds

    NARCIS (Netherlands)

    Zou, S(han); Zhang, Zhihong; Forch, Renate; Knoll, Wolfgang; Schönherr, Holger; Vancso, Gyula J.

    2003-01-01

    We show that surfaces modified with asymmetric 2-ureido-4[1H]-pyrimidinone-hydroxyalkane disulfide adsorbates exhibit efficient and controllable self-complementary molecular recognition of the pyrimidinone moieties. Two novel asymmetric 2-ureido-4[1H]-pyrimidinone-hydroxyalkane disulfide adsorbates,

  16. Molecular assessment of complex microbial communities degrading long chain fatty acids (LCFA) in methanogenic bioreactors

    NARCIS (Netherlands)

    Sousa, D.Z.; Pereira, M.A.; Smidt, H.; Stams, A.J.M.; Alves, M.M.

    2007-01-01

    Microbial diversity of anaerobic sludge after extended contact with long chain fatty acids (LCFA) was studied using molecular approaches. Samples containing high amounts of accumulated LCFA were obtained after continuous loading of two bioreactors with oleate or with palmitate. These sludge samples

  17. An approach towards understanding the structure of complex molecular systems: the case of lower aliphatic alcohols

    Energy Technology Data Exchange (ETDEWEB)

    Vrhovsek, Aleksander; Gereben, Orsolya; Pothoczki, Szilvia; Pusztai, Laszlo [Research Institute for Solid State Physics and Optics, Hungarian Academy of Sciences, H-1525 Budapest, PO Box 49 (Hungary); Tomsic, Matija; Jamnik, Andrej [Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, SI-1001 Ljubljana (Slovenia); Kohara, Shinji, E-mail: aleksander.vrhovsek@gmail.co [Research and Utilization Division, Japan Synchrotron Radiation Research Institute (JASRI, SPring-8), 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan)

    2010-10-13

    An extensive study of liquid aliphatic alcohols methanol, ethanol, and propanol, applying reverse Monte Carlo modelling as a method of interpretation of diffraction data, is presented. The emphasis is on the evaluation of several computational strategies in view of their suitability to obtain high quality molecular models via the reverse Monte Carlo procedure. A consistent set of distances of closest approach and fixed neighbour constraints applicable to all three investigated systems was developed. An all-atom description is compared with a united-atom approach. The potentialities of employment of neutron diffraction data of completely deuterated and isotopically substituted samples, x-ray diffraction data, and results of either molecular dynamics or Monte Carlo calculations were investigated. Results show that parallel application of x-ray and neutron diffraction data, the latter being from completely deuterated samples, within an all-atom reverse Monte Carlo procedure is the most successful strategy towards attaining reliable, detailed, and well-structured molecular models, especially if the models are subsequently refined with the results of molecular dynamics simulations.

  18. Molecular Mechanisms Underlying the Epileptogenesis and Seizure Progression in Tuberous Sclerosis Complex 1 Deficient Mouse Models

    Science.gov (United States)

    2016-10-01

    dysregulation in epileptogenesis in the developing brain? 2) What are the molecular mechanisms downstream of mTOR hyperactivation that trigger epileptogenesis...underlying epilepsy. Hopefully, a knowledge of these mechanisms will aid in a rational development of therapies. KEYWORDS Tuberous Sclerosis, Epilepsy

  19. Ultrafast studies of dynamic & complex systems: Understanding molecular and ionization dynamics

    OpenAIRE

    Hockett, Paul

    2016-01-01

    Presentation given at the ITAMP workshop "Ultrafast atomic and molecular physics with cutting-edge light sources: New opportunities and challenges", held at Kansas State University, Nov. 2013.  A video of the presentation can be found on the ITAMP Youtube channel, https://www.youtube.com/watch?v=x8RWWDWZJpk

  20. Molecular Fluoride-Bridged 3d-4f Complexes and Their Magnetic Properties

    DEFF Research Database (Denmark)

    Pedersen, K. S.; Bendix, J.

    2016-01-01

    trifluorides with very high lattice enthalpies, building block approaches are not limited to robust systems and use of labile transition metal fluoride complexes has met with unexpected success. The physical properties of fluoride-bridged 3d-4f systems are crucially dependent on coordination geometries, which...... be utilized efficiently in tailored synthesis of polynuclear complexes and extended structures. In particular, the strong affinity of the lanthanides for fluoride makes it a good choice for directed synthesis of mixed lanthanide-transition metal complexes. Despite the competition from formation of lanthanide...

  1. Molecular Basis of Natural Killer Cell Tumor Target Recognition: The NKr/MHC Class I Complex

    National Research Council Canada - National Science Library

    Hasemann, Charles

    1999-01-01

    .... We have pursued this via the heterologous expression of wild type and mutant NK receptors for the purpose of the determination of the atomic structure of an NK receptor/ class I MHC complex via X-ray crystallography...

  2. Coarse-grained molecular dynamics simulation of transport through the nuclear pore complex

    NARCIS (Netherlands)

    Ghavami, Ali

    2014-01-01

    Dit proefschrift is gewijd aan het mechanisme van Nucleo - cytoplasmatisch transport openbaren door grofkorrelige moleculaire dynamica simulaties van ontvouwen eiwitten in de nucleaire porie complex (NPC) . NPC's zijn zeer selectief poorten, die alle transporten over nucleaire envelop controleren .

  3. Molecular Diagnostics in the Mycosphaerella Leaf Spot Disease Complex of Banana and for Radopholus similis

    NARCIS (Netherlands)

    Arzanlou, M.; Kema, G.H.J.; Waalwijk, C.; Carlier, I.; Vries, de P.M.; Guzmán, M.; Araya Vargas, M.; Helder, J.; Crous, P.W.

    2009-01-01

    Mycosphaerella leaf spots and nematodes threaten banana cultivation worldwide. The Mycosphaerella disease complex involves three related ascomycetous fungi: Mycosphaerella fijiensis, M. musicola and M. eumusae. The exact distribution of these three species and their disease epidemiology remain

  4. High spin-filter efficiency and Seebeck effect through spin-crossover iron–benzene complex

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Qiang; Zhou, Liping, E-mail: zhoulp@suda.edu.cn; Cheng, Jue-Fei; Wen, Zhongqian; Han, Qin; Wang, Xue-Feng [College of Physics, Optoelectronics and Energy and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou 215006 (China)

    2016-04-21

    Electronic structures and coherent quantum transport properties are explored for spin-crossover molecule iron-benzene Fe(Bz){sub 2} using density functional theory combined with non-equilibrium Green’s function. High- and low-spin states are investigated for two different lead-molecule junctions. It is found that the asymmetrical T-shaped contact junction in the high-spin state behaves as an efficient spin filter while it has a smaller conductivity than that in the low-spin state. Large spin Seebeck effect is also observed in asymmetrical T-shaped junction. Spin-polarized properties are absent in the symmetrical H-shaped junction. These findings strongly suggest that both the electronic and contact configurations play significant roles in molecular devices and metal-benzene complexes are promising materials for spintronics and thermo-spintronics.

  5. Evaluation of molecular species of prostate-specific antigen complexed with immunoglobulin M in prostate cancer and benign prostatic hyperplasia.

    Science.gov (United States)

    Goč, Sanja; Janković, Miroslava

    2013-01-01

    This study was aimed at defining molecular species of prostate-specific antigen (PSA) in immune complexes with immunoglobulin M (IgM). Having in mind the oligoreactivity of IgM and its preference for carbohydrate antigens, there is the possibility that it can selectively recognize known PSA glycoisoforms. PSA-IgM complexes and free PSA fractions were separated from the sera of subjects with prostate cancer (PCa) and benign prostatic hyperplasia (BPH) by gel filtration and subjected to on-chip immunoaffinity and ion-exchange chromatography. PSA-immunoreactive species were detected using surface-enhanced laser desorption/ionization time of flight mass spectrometry. The obtained spectra were analyzed for protein and glycan composition. The general pattern of the molecular species of PCa PSA and BPH PSA found in complexes with IgM was similar. It comprised major peaks at 17 kDa and minor peaks at 28 kDa, corresponding to the entire mature glycosylated PSA. The main difference was the presence of incompletely glycosylated 26.8 kDa species, having putative paucimannosidic structures, observed in PCa PSA-IgM, but not in BPH PSA-IgM. Characteristic PCa PSA-IgM glycoforms pose the question of the possible role of glycosylation as a framework for immune surveillance and may be of interest in light of recent data indicating mannose-containing glycans as cancer biomarker.

  6. Evaluation of Molecular Species of Prostate-Specific Antigen Complexed with Immunoglobulin M in Prostate Cancer and Benign Prostatic Hyperplasia

    Directory of Open Access Journals (Sweden)

    Sanja Goč

    2013-01-01

    Full Text Available This study was aimed at defining molecular species of prostate-specific antigen (PSA in immune complexes with immunoglobulin M (IgM. Having in mind the oligoreactivity of IgM and its preference for carbohydrate antigens, there is the possibility that it can selectively recognize known PSA glycoisoforms. PSA-IgM complexes and free PSA fractions were separated from the sera of subjects with prostate cancer (PCa and benign prostatic hyperplasia (BPH by gel filtration and subjected to on-chip immunoaffinity and ion-exchange chromatography. PSA-immunoreactive species were detected using surface-enhanced laser desorption/ionization time of flight mass spectrometry. The obtained spectra were analyzed for protein and glycan composition. The general pattern of the molecular species of PCa PSA and BPH PSA found in complexes with IgM was similar. It comprised major peaks at 17 kDa and minor peaks at 28 kDa, corresponding to the entire mature glycosylated PSA. The main difference was the presence of incompletely glycosylated 26.8 kDa species, having putative paucimannosidic structures, observed in PCa PSA-IgM, but not in BPH PSA-IgM. Characteristic PCa PSA-IgM glycoforms pose the question of the possible role of glycosylation as a framework for immune surveillance and may be of interest in light of recent data indicating mannose-containing glycans as cancer biomarker.

  7. Molecular modeling and molecular dynamics simulation study of archaeal leucyl-tRNA synthetase in complex with different mischarged tRNA in editing conformation.

    Science.gov (United States)

    Rayevsky, A V; Sharifi, M; Tukalo, M A

    2017-09-01

    Aminoacyl-tRNA synthetases (aaRSs) play important roles in maintaining the accuracy of protein synthesis. Some aaRSs accomplish this via editing mechanisms, among which leucyl-tRNA synthetase (LeuRS) edits non-cognate amino acid norvaline mainly by post-transfer editing. However, the molecular basis for this pathway for eukaryotic and archaeal LeuRS remain unclear. In this study, a complex of archaeal P. horikoshii LeuRS (PhLeuRS) with misacylated tRNA Leu was modeled wherever tRNA's acceptor stem was oriented directly into the editing site. To understand the distinctive features of organization we reconstructed a complex of PhLeuRS with tRNA and visualize post-transfer editing interactions mode by performing molecular dynamics (MD) simulation studies. To study molecular basis for substrate selectivity by PhLeuRS's editing site we utilized MD simulation of the entire LeuRS complexes using a diverse charged form of tRNAs, namely norvalyl-tRNA Leu and isoleucyl-tRNA Leu . In general, the editing site organization of LeuRS from P.horikoshii has much in common with bacterial LeuRS. The MD simulation results revealed that the post-transfer editing substrate norvalyl-A76, binds more strongly than isoleucyl-A76. Moreover, the branched side chain of isoleucine prevents water molecules from being closer and hence the hydrolysis reaction slows significantly. To investigate a possible mechanism of the post-transfer editing reaction, by PhLeuRS we have determined that two water molecules (the attacking and assisting water molecules) are localized near the carbonyl group of the amino acid to be cleaved off. These water molecules approach the substrate from the opposite side to that observed for Thermus thermophilus LeuRS (TtLeuRS). Based on the results obtained, it was suggested that the post-transfer editing mechanism of PhLeuRS differs from that of prokaryotic TtLeuRS. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Molecular interactions in the complexes of toluene with butyronitrile: A DFT approach

    Science.gov (United States)

    Karthick, N. K.; Arivazhagan, G.

    2018-04-01

    Density Functional Theory (DFT) has been employed to investigate the self association of butyronitrile and the heterointeractions in the 1:2 (toluene: butyronitrile) and 1:1 complexes of toluene with butyronitrile. For this investigation the B3LYP functional with Grimme's dispersion correction (D3) term and ωB97XD functionals were used. The theoretical frequency analysis shows the unsuitability of B3LYP with D3 for the present investigation. Therefore, Natural Bonding Orbital analysis was done at the functional ωB97XD. It is found through this work that only the methylene hydrogens of butyronitrile are responsible for the self association among the butyronitrile molecules. In 1:1 complex, the red shift in the butyronitrile methyl asymmetric stretching mode is not due to the active participation of this group in heterointeractions and it is solely due to the other interactions happening in its vicinity. Only the interaction (TOL) C - H ⋯ N(BN) is present in the complex. In 1:2 complex the butyronitrile methyl/methylene hydrogens interact with the delocalized electron cloud of toluene and the toluene hydrogens interact with the butyronitrile nitrogen. Comparison of interaction energies shows that the stability of 1:2 complex is more than that of butyronitrile dimer and 1:1 complex.

  9. Molecular, crystal, and electronic structure of the cobalt(II) complex with 10-(2-benzothiazolylazo)-9-phenanthrol

    Energy Technology Data Exchange (ETDEWEB)

    Linko, R. V., E-mail: rlinko@mail.ru [Peoples' Friendship University of Russia (Russian Federation); Sokol, V. I. [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation); Polyanskaya, N. A.; Ryabov, M. A.; Strashnov, P. V.; Davydov, V. V. [Peoples' Friendship University of Russia (Russian Federation); Sergienko, V. S. [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation)

    2013-05-15

    The reaction of 10-(2-benzothiazolylazo)-9-phenanthrol (HL) with cobalt(II) acetate gives the coordination compound [CoL{sub 2}] {center_dot} CHCl{sub 3} (I). The molecular and crystal structure of I is determined by X-ray diffraction. The coordination polyhedron of the Co atom in complex I is an octahedron. The anion L acts as a tridentate chelating ligand and is coordinated to the Co atom through the phenanthrenequinone O1 atom and the benzothiazole N1 atom of the moieties L and the N3 atom of the azo group to form two five-membered metallocycles. The molecular and electronic structures of the compounds HL, L, and CoL{sub 2} are studied at the density functional theory level. The results of the quantum-chemical calculations are in good agreement with the values determined by X-ray diffraction.

  10. Molecular, crystal, and electronic structure of the cobalt(II) complex with 10-(2-benzothiazolylazo)-9-phenanthrol

    International Nuclear Information System (INIS)

    Linko, R. V.; Sokol, V. I.; Polyanskaya, N. A.; Ryabov, M. A.; Strashnov, P. V.; Davydov, V. V.; Sergienko, V. S.

    2013-01-01

    The reaction of 10-(2-benzothiazolylazo)-9-phenanthrol (HL) with cobalt(II) acetate gives the coordination compound [CoL 2 ] · CHCl 3 (I). The molecular and crystal structure of I is determined by X-ray diffraction. The coordination polyhedron of the Co atom in complex I is an octahedron. The anion L acts as a tridentate chelating ligand and is coordinated to the Co atom through the phenanthrenequinone O1 atom and the benzothiazole N1 atom of the moieties L and the N3 atom of the azo group to form two five-membered metallocycles. The molecular and electronic structures of the compounds HL, L, and CoL 2 are studied at the density functional theory level. The results of the quantum-chemical calculations are in good agreement with the values determined by X-ray diffraction.

  11. Exploring the science of thinking independently together: Faraday Discussion Volume 204 - Complex Molecular Surfaces and Interfaces, Sheffield, UK, July 2017.

    Science.gov (United States)

    Samperi, M; Hirsch, B E; Diaz Fernandez, Y A

    2017-11-23

    The 2017 Faraday Discussion on Complex Molecular Surfaces and Interfaces brought together theoreticians and experimentalists from both physical and chemical backgrounds to discuss the relevant applied and fundamental research topics within the broader field of chemical surface analysis and characterization. Main discussion topics from the meeting included the importance of "disordered" two-dimensional (2D) molecular structures and the utility of kinetically trapped states. An emerging need for new experimental tools to address dynamics and kinetic pathways involved in self-assembled systems, as well as the future prospects and current limitations of in silico studies were also discussed. The following article provides a brief overview of the work presented and the challenges discussed during the meeting.

  12. Mechanical break junctions: enormous information in a nanoscale package.

    Science.gov (United States)

    Natelson, Douglas

    2012-04-24

    Mechanical break junctions, particularly those in which a metal tip is repeatedly moved in and out of contact with a metal film, have provided many insights into electronic conduction at the atomic and molecular scale, most often by averaging over many possible junction configurations. This averaging throws away a great deal of information, and Makk et al. in this issue of ACS Nano demonstrate that, with both simulated and real experimental data, more sophisticated two-dimensional analysis methods can reveal information otherwise obscured in simple histograms. As additional measured quantities come into play in break junction experiments, including thermopower, noise, and optical response, these more sophisticated analytic approaches are likely to become even more powerful. While break junctions are not directly practical for useful electronic devices, they are incredibly valuable tools for unraveling the electronic transport physics relevant for ultrascaled nanoelectronics.

  13. Experimental and theoretical investigation of topological and energetic characteristics of Sb complexes reversibly binding molecular oxygen.

    Science.gov (United States)

    Fukin, Georgy K; Baranov, Evgenii V; Jelsch, Christian; Guillot, Benoît; Poddel'sky, Andrey I; Cherkasov, Vladimir K; Abakumov, Gleb A

    2011-07-28

    The experimental distribution of electron density in Ph(3)(4,5-OMe-3,6-Bu(t)-Cat)Sb·MeCN (1*) and Ph(3)(4,5-N(2)C(4)H(6)-3,6-Bu(t)-Cat)Sb·MeOH (2*) complexes was studied. According to atoms in molecules theory, the Sb-C(Ph), Sb-O(catecholate), and Sb···N(O) bonds are intermediate, whereas the O-C and C-C bonds are covalent, respectively. The energy of the Sb···N(MeCN) and Sb···O(MeOH) bonds are 7.0 and 11.3 kcal/mol according to the Espinosa equation. Density functional theory and Hartree-Fock calculations were carried out for a series of catecholate and amidophenolate complexes of antimony(V). It was shown that such calculations reliably reproduce geometrical and topological parameters and therefore can be used for a criterion search of dioxygen reversible binding by the catecholate and amidophenolate complexes of antimony(V). It was found that the "critical" value of the HOMO energy vary in the range from -5.197 to -5.061 eV for reversible binding of dioxygen complexes. This can serve as a thermodynamic criterion to predict the possibility of the dioxygen reversible binding by the catecholate and amidophenolate complexes of Sb(V). The HOMO energies correlate with the conversion of the catecholate and amidophenolate complexes in corresponding spiroendoperoxide derivatives as well. The contribution of the atom orbitals of the carbon atoms in the five-membered metallocycle to HOMO in complexes with different substitutes in the 4- and 5-positions of the catecholate ligand allows predicting the place of dioxygen addition. © 2011 American Chemical Society

  14. Molecular epidemiology of Mycobacterium tuberculosis complex in Brussels, 2010-2013.

    Directory of Open Access Journals (Sweden)

    Christelle Vluggen

    Full Text Available The tuberculosis (TB incidence rate in Brussels-Capital Region is 3-fold higher than in Belgium as a whole. Eight years after the realization of initial prospective population-based molecular epidemiology investigations in this Region, a similar study over the period 2010-2013 was conducted. TB strains isolated from 945 patients were submitted to genotyping by standardized 24-locus-MIRU-VNTR typing and spoligotyping. The phylogenetic analysis showed that the LAM (16.7% and Haarlem (15.7% branches are the two most prevalent TB lineages circulating in Brussels. Analysis of the MDR subgroup showed an association with Beijing strains (39.9% and patients native of Eastern Europe (40.7%. Genotyping detected 113 clusters involving 321 patients, giving a recent transmission index of 22.9%. Molecular-guided epidemiological investigations and routine surveillance activities revealed family transmission or social contact for patients distributed over 34 clusters. Most of the patients were foreign-born (75.7%. However, cluster analysis revealed only limited trans-national transmission. Comparison with the previous study shows a stable epidemiological situation except for the mean age difference between Belgian-born and foreign-born patients which has disappeared. This study confirms that molecular epidemiology has become an important determinant for TB control programs. However, sufficient financial means need to be available to perform all required epidemiological investigations.

  15. The nearly neutral and selection theories of molecular evolution under the fisher geometrical framework: substitution rate, population size, and complexity.

    Science.gov (United States)

    Razeto-Barry, Pablo; Díaz, Javier; Vásquez, Rodrigo A

    2012-06-01

    The general theories of molecular evolution depend on relatively arbitrary assumptions about the relative distribution and rate of advantageous, deleterious, neutral, and nearly neutral mutations. The Fisher geometrical model (FGM) has been used to make distributions of mutations biologically interpretable. We explored an FGM-based molecular model to represent molecular evolutionary processes typically studied by nearly neutral and selection models, but in which distributions and relative rates of mutations with different selection coefficients are a consequence of biologically interpretable parameters, such as the average size of the phenotypic effect of mutations and the number of traits (complexity) of organisms. A variant of the FGM-based model that we called the static regime (SR) represents evolution as a nearly neutral process in which substitution rates are determined by a dynamic substitution process in which the population's phenotype remains around a suboptimum equilibrium fitness produced by a balance between slightly deleterious and slightly advantageous compensatory substitutions. As in previous nearly neutral models, the SR predicts a negative relationship between molecular evolutionary rate and population size; however, SR does not have the unrealistic properties of previous nearly neutral models such as the narrow window of selection strengths in which they work. In addition, the SR suggests that compensatory mutations cannot explain the high rate of fixations driven by positive selection currently found in DNA sequences, contrary to what has been previously suggested. We also developed a generalization of SR in which the optimum phenotype can change stochastically due to environmental or physiological shifts, which we called the variable regime (VR). VR models evolution as an interplay between adaptive processes and nearly neutral steady-state processes. When strong environmental fluctuations are incorporated, the process becomes a selection model

  16. Platinum(II)-gadolinium(III) complexes as potential single-molecular theranostic agents for cancer treatment.

    Science.gov (United States)

    Zhu, Zhenzhu; Wang, Xiaoyong; Li, Tuanjie; Aime, Silvio; Sadler, Peter J; Guo, Zijian

    2014-11-24

    Theranostic agents are emerging multifunctional molecules capable of simultaneous therapy and diagnosis of diseases. We found that platinum(II)-gadolinium(III) complexes with the formula [{Pt(NH3)2Cl}2GdL](NO3)2 possess such properties. The Gd center is stable in solution and the cytoplasm, whereas the Pt centers undergo ligand substitution in cancer cells. The Pt units interact with DNA and significantly promote the cellular uptake of Gd complexes. The cytotoxicity of the Pt-Gd complexes is comparable to that of cisplatin at high concentrations (≥0.1 mM), and their proton relaxivity is higher than that of the commercial magnetic resonance imaging (MRI) contrast agent Gd-DTPA. T1-weighted MRI on B6 mice demonstrated that these complexes can reveal the accumulation of platinum drugs in vivo. Their cytotoxicity and imaging capabilities make the Pt-Gd complexes promising theranostic agents for cancer treatment. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Molecular Speciation of Trace Metal Organic Complexes in the Pacific Ocean

    Science.gov (United States)

    Repeta, D.; Boiteau, R. M.; Bundy, R. M.; Babcock-Adams, L.

    2017-12-01

    Microbial production across approximately one third of the surface ocean is limited by extraordinarily low (picomolar) concentrations of dissolved iron, essentially all of which is complexed to strong organic ligands of unknown composition. Other biologically important trace metals (cobalt, copper, zinc, nickel) are also complexed to strong organic ligands, which again have not been extensively characterized. Nevertheless, organic ligands exert a strong influence on metal bioavailability and toxicity. For example, amendment experiments using commercially available siderophores, organic compounds synthesized by microbes to facilitate iron uptake, show these ligands can both facilitate or impede iron uptake depending on the siderophore composition and available uptake pathways. Over the past few years we have developed analytical techniques using high pressure liquid chromatography interfaced with inductively coupled plasma and electrospray ionization mass spectrometry to identify and quantify trace metal organic complexes in laboratory cultures of marine microbes and in seawater. We found siderophores to be widely distributed in the ocean, particularly in regions characterized by low iron concentrations. We also find chemically distinct complexes of copper, zinc, colbalt and nickel that we have yet to fully characterize. We will discuss some of our recent work on trace metal organic speciation in seawater and laboratory cultures, and outline future efforts to better understand the microbial cycling of trace metal organic complexes in the sea.

  18. Molecular study of the dentin-pulp complex responses to caries progression

    Directory of Open Access Journals (Sweden)

    Yani Corvianindya Rahayu

    2007-03-01

    Full Text Available The dentin-pulp complex exhibits various responses to caries, including events of injury, defense, and repair. The overall responses dependent on pulp cell activity and the signaling processes, which regulate the behavior of these cells. The signals for tissue repair are thought to be mediated by dentin-bound growth factors released during caries progression. Growth factors are a key of molecules responsible for signaling a variety of cellular process following dental injury. The endogenous proteolytic enzymes (Matrix metalloproteinases, MMPs present in dentin matrix might also participate in releasing bioactive molecule. Several members of the MMP family are found in the soft and hard tissue compartment of dentin-pulp complex. Their presumed role in many physiological process during the development and maintenance of the dentin-pulp complex, they may also contribute to the pathogenesis of dentin caries and the responses elicited by caries.

  19. Molecular characterization of covalent complexes between tissue transglutaminase and gliadin peptides

    DEFF Research Database (Denmark)

    Fleckenstein, Burkhard; Qiao, Shuo-Wang; Larsen, Martin Røssel

    2004-01-01

    recognized by intestinal T cells from patients. Incubation of TG2 with gliadin peptides also results in the formation of covalent TG2-peptide complexes. Here we report the characterization of complexes between TG2 and two immunodominant gliadin peptides. Two types of covalent complexes were found......; the peptides are either linked via a thioester bond to the active site cysteine of TG2 or via isopeptide bonds to particular lysine residues of the enzyme. We quantified the number of gliadin peptides bound to TG2 under different conditions. After 30 min of incubation of TG2 at 1 microm with an equimolar ratio...... of peptides to TG2, approximately equal amounts of peptides were bound by thioester and isopeptide linkage. At higher peptide to TG2 ratios, more than one peptide was linked to TG2, and isopeptide bond formation dominated. The lysine residues in TG2 that act as acyl acceptors were identified by matrix...

  20. A Comparison of Molecular Typing Methods Applied to Enterobacter cloacae complex: hsp60 Sequencing, Rep-PCR, and MLST

    Directory of Open Access Journals (Sweden)

    Roberto Viau

    2017-02-01

    Full Text Available Molecular typing using repetitive sequenced-based PCR (rep-PCR and hsp60 sequencing were applied to a collection of diverse Enterobacter cloacae complex isolates. To determine the most practical method for reference laboratories, we analyzed 71 E. cloacae complex isolates from sporadic and outbreak occurrences originating from 4 geographic areas. While rep-PCR was more discriminating, hsp60 sequencing provided a broader and a more objective geographical tracking method similar to multilocus sequence typing (MLST. In addition, we suggest that MLST may have higher discriminative power compared to hsp60 sequencing, although rep-PCR remains the most discriminative method for local outbreak investigations. In addition, rep-PCR can be an effective and inexpensive method for local outbreak investigation.

  1. Complex Formation of Selected Radionuclides with Ligands Commonly Found in Ground Water: Low Molecular Organic Acids

    DEFF Research Database (Denmark)

    Jensen, Bror Skytte; Jensen, H.

    1985-01-01

    A general approach to the analysis of potentiometric data on complex formation between cations and polybasic amphoteric acids is described. The method is used for the characterisation of complex formation between Cs+, Sr2+, Co2+, La 3+, and Eu3+ with a α-hydroxy acids, tartaric acid and citric ac......, and with the α-amino acids, aspartic acid and L-cysteine. The cations have been chosen as typical components of reactor waste, and the acids because they are often found as products of microbial activity in pits or wherever organic material decays...

  2. The human myotendinous junction

    DEFF Research Database (Denmark)

    Knudsen, A B; Larsen, M; Mackey, Abigail

    2015-01-01

    The myotendinous junction (MTJ) is a specialized structure in the musculotendinous system, where force is transmitted from muscle to tendon. Animal models have shown that the MTJ takes form of tendon finger-like processes merging with muscle tissue. The human MTJ is largely unknown and has never...... been described in three dimensions (3D). The aim of this study was to describe the ultrastructure of the human MTJ and render 3D reconstructions. Fourteen subjects (age 25 ± 3 years) with isolated injury of the anterior cruciate ligament (ACL), scheduled for reconstruction with a semitendinosus...

  3. Tight junctions and human diseases.

    Science.gov (United States)

    Sawada, Norimasa; Murata, Masaki; Kikuchi, Keisuke; Osanai, Makoto; Tobioka, Hirotoshi; Kojima, Takashi; Chiba, Hideki

    2003-09-01

    Tight junctions are intercellular junctions adjacent to the apical end of the lateral membrane surface. They have two functions, the barrier (or gate) function and the fence function. The barrier function of tight junctions regulates the passage of ions, water, and various macromolecules, even of cancer cells, through paracellular spaces. The barrier function is thus relevant to edema, jaundice, diarrhea, and blood-borne metastasis. On the other hand, the fence function maintains cell polarity. In other words, tight junctions work as a fence to prevent intermixing of molecules in the apical membrane with those in the lateral membrane. This function is deeply involved in cancer cell biology, in terms of loss of cell polarity. Of the proteins comprising tight junctions, integral membrane proteins occludin, claudins, and JAMs have been recently discovered. Of these molecules, claudins are exclusively responsible for the formation of tight-junction strands and are connected with the actin cytoskeleton mediated by ZO-1. Thus, both functions of tight junctions are dependent on the integrity of the actin cytoskeleton as well as ATP. Mutations in the claudin14 and the claudin16 genes result in hereditary deafness and hereditary hypomagnesemia, respectively. Some pathogenic bacteria and viruses target and affect the tight-junction function, leading to diseases. In this review, the relationship between tight junctions and human diseases is summarized.

  4. Gap junctions and motor behavior

    DEFF Research Database (Denmark)

    Kiehn, Ole; Tresch, Matthew C.

    2002-01-01

    The production of any motor behavior requires coordinated activity in motor neurons and premotor networks. In vertebrates, this coordination is often assumed to take place through chemical synapses. Here we review recent data suggesting that electrical gap-junction coupling plays an important role...... in coordinating and generating motor outputs in embryonic and early postnatal life. Considering the recent demonstration of a prevalent expression of gap-junction proteins and gap-junction structures in the adult mammalian spinal cord, we suggest that neuronal gap-junction coupling might also contribute...... to the production of motor behavior in adult mammals....

  5. Synthesis, Cytotoxicity and Molecular Docking Study of Complexes Containing Thiazole Moiety

    Directory of Open Access Journals (Sweden)

    Mohammed Shafeeulla

    2017-07-01

    Full Text Available The ligand 5-methyl-2-phenyl-4-[(E-1,3-thiazol-2-yldiazenyl]-2,4-dihydro-3H-pyrazol-3-one (Dy has been synthesized by diazo coupling reactions of 5-methyl-2-phenyl- 2,4-dihydro-3H-pyrazol-3-one with 2-aminothiazole and ferric hydrogen sulfate (FHS, as a catalyst, under solvent-free conditions. A series of complexes of the ligand with Co(II, Ni(II, Cu(II, and Zn(II ions are synthesized and structurally characterized by 1H NMR, FTIR, and UV–Visible spectral techniques. The cytotoxic activity of the complexes and the uncoordinated ligand against human breast cancer (MCF-7 and chronic myelogenous leukemia cell line (human erythroleukemia (K-562 cell lines exhibits good viability in the range of 50.16–55.16% at a concentration of >100-110 µg/mL as compared to the inhibition in the untreated cells. Further, the metal complexes and ligand were screened against antibacterial strains of S. typhi, S. aureus, and E. coli. Both the cytotoxicity and antioxidant studies are correlated with computational docking analysis and powder XRD studies reviles that all complexes are in crystalline nature.

  6. Synthesis of molecular hexatechnetium clusters by means of dimensional reduction of their polymeric complexes

    International Nuclear Information System (INIS)

    Ikai, T.; Yoshimura, T.; Shinohara, A.; Takayama, T.; Sekine, T.

    2006-01-01

    Selenide capping hexatechnetium cluster complex [Tc 6 (μ 3 -Se) 8 CN 6 ] 4- (1) was prepared by the reactions of one-dimensional polymer complex [Tc 6 (μ 3 -Se) 8 Br 4 ] 2- and cyanides at high temperature. Similar reaction of sulfide capping hexatechnetium cluster complex, [Tc 6 (μ 3 -S) 8 Br 6 ] 4- with cyanide gave the terminal substituted complex [Tc 6 (μ 3 -S) 8 CN 6 ] 4- (2). The single-crystal X-ray analysis of 1 and 2, showed that the Tc-Tc bond lengths become longer with lager ionic radius of the face capping ligands in the order S -1 , and that of 2 showed it at 2119 cm -1 . Each of cyclic voltammogram of 1 and 2 showed a reversible one electron redox wave assignable to the Tc 6 III /Tc 5 III Tc IV process. These redox potentials shift to the positive about 0.4V compared to those of the Re cluster analogs. (author)

  7. Studies on cluster, salt and molecular complex of zinc-quinolinate

    Indian Academy of Sciences (India)

    Reactions of zinc halides with 8-hydroxyquinoline (hydroxQ) in equimolar ratio were carried out in different solvents. ... determination of surface area. We prepared a ..... resulted in the formation of de-solvated complex, which on standing at ...

  8. Molecular dynamic simulation of complex NS2B-NS3 DENV2 ...

    African Journals Online (AJOL)

    Several vaccines have been developed against the disease, but they only ... a two component NS2B-NS3 protease that cleaves viral precursor proteins, and ... The results provide conformational changes of enzyme-inhibitor complex that is ...

  9. Molecular and electronic structure of chromium(V) nitrido complexes with azide and isothiocyanate ligands

    DEFF Research Database (Denmark)

    Bendix, Jesper; Birk, Torben; Weyhermüller, Thomas

    2005-01-01

    . This absorption provides the spectrochemical series for the equatorial ligands, which is found to be numerically almost identical to that determined for chromium(III). DFT calculations reproduce the observed structures and corroborate the ligand field picture of the electronic structure of these complexes....

  10. Finding the molecular basis of complex genetic variation in humans and mice

    OpenAIRE

    Mott, Richard

    2006-01-01

    I survey the state of the art in complex trait analysis, including the use of new experimental and computational technologies and resources becoming available, and the challenges facing us. I also discuss how the prospects of rodent model systems compare with association mapping in humans.

  11. The influence of molecular complexity on expanding flows of ideal and dense gases

    NARCIS (Netherlands)

    Harinck, J.; Guardone, A.; Colonna, P.

    2009-01-01

    This paper presents an investigation about the effect of the complexity of a fluid molecule on the fluid dynamic quantities sound speed, velocity, and Mach number in isentropic expansions. Ideal-gas and dense-gas expansions are analyzed, using the polytropic ideal gas and Van der Waals thermodynamic

  12. Complex Reaction Environments and Competing Reaction Mechanisms in Zeolite Catalysis: Insights from Advanced Molecular Dynamics

    NARCIS (Netherlands)

    De Wispelaere, K.; Ensing, B.; Ghysels, A.; Meijer, E.J.; van Van Speybroeck, V.

    2015-01-01

    The methanol-to-olefin process is a showcase example of complex zeolite-catalyzed chemistry. At real operating conditions, many factors affect the reactivity, such as framework flexibility, adsorption of various guest molecules, and competitive reaction pathways. In this study, the strength of first

  13. Detection of Molecular Chirality by Induced Resonance Raman Optical Activity in Europium Complexes

    Czech Academy of Sciences Publication Activity Database

    Yamamoto, Shigeki; Bouř, Petr

    2012-01-01

    Roč. 51, č. 44 (2012), s. 11058-11061 ISSN 1433-7851 R&D Projects: GA MŠk(CZ) LH11033; GA ČR GAP208/11/0105 Institutional support: RVO:61388963 Keywords : europium * complexes * raman optical activity * resonance Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 13.734, year: 2012

  14. Silver(I) complexes with hydantoins and allantoin: synthesis, crystal and molecular structure, cytotoxicity and pharmacokinetics.

    Science.gov (United States)

    Puszyńska-Tuszkanow, Mariola; Grabowski, Tomasz; Daszkiewicz, Marek; Wietrzyk, Joanna; Filip, Beata; Maciejewska, Gabriela; Cieślak-Golonka, Maria

    2011-01-01

    Coordination polymers [Ag(L(1,3))](n) (L(1)=hydantoin, L(3)=5,5-dimethylhydantoin), {[Ag(L(2))](.)0.5H(2)O}(n) (L(2)=1-methylhydantoin) and [Ag(NH(3))(L(4))](n) (L(4)=allantoin) were prepared and characterized by elemental analysis, spectroscopic (IR, FTIR and NMR), thermal and mass spectrometry methods. The crystal structure of {[Ag(1-methylhydantoin)]·0,5H(2)O}(n) was determined and analyzed. Three 1-methylhydantoinate ligands create a T-shape (CN=3) coordination sphere around the Ag(+) ion. Additionally, a short Ag⋯Ag distance of 2.997Å was found in the structure resulting in the expanded [3+2] environment of a distorted square shape. The [Ag(L(2))] entities are bound to each other by the bridging organic ligands. Thus a two-dimensional coordination polymer is created with water molecules located between the layers. In contrast to hydantoins, the allantoin complex contains an additional ammonia molecule in the coordination sphere. Moreover, in the Ag-alla complex the M-organic ligand binding site is shifted to the N-atom of the ureid chain. Free ligands are cytotoxically inactive against human MCF-7 and A549 cancer cell lines and mouse fibroblasts Balb/3T3. The silver hydantoin complexes exhibit a very strong activity against these lines. (The introduction of the methyl groups to the ring slightly increases resistance only against the A549 cell line.) In contrast, the silver complex of allantoin shows only a weak activity which may be related to the presence of the cytotoxic ammonia group in the composition of the compound and/or the different binding site of the ligand. Calculated in silico physiochemical parameters are promising for the future application of the complexes as drugs. Copyright © 2010 Elsevier Inc. All rights reserved.

  15. Targeted association mapping demonstrating the complex molecular genetics of fatty acid formation in soybean.

    Science.gov (United States)

    Li, Ying-hui; Reif, Jochen C; Ma, Yan-song; Hong, Hui-long; Liu, Zhang-xiong; Chang, Ru-zhen; Qiu, Li-juan

    2015-10-23

    The relative abundance of five dominant fatty acids (FAs) (palmitic, stearic, oleic, linoleic and linolenic acids) is a major factor determining seed quality in soybean. To clarify the currently poorly understood genetic architecture of FAs in soybean, targeted association analysis was conducted in 421 diverse accessions phenotyped in three environments and genotyped using 1536 pre-selected SNPs. The population of 421 soybean accessions displayed significant genetic variation for each FA. Analysis of the molecular data revealed three subpopulations, which reflected a trend depending on latitude of cultivation. A total of 37 significant (p seed quality of soybean with benefits for human health and for food processing.

  16. Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics

    Czech Academy of Sciences Publication Activity Database

    Réblová, Kamila; Fadrná, E.; Sarzynska, J.; Kulinski, T.; Kulhánek, P.; Ennifar, E.; Koča, J.; Šponer, Jiří

    2007-01-01

    Roč. 93, č. 11 (2007), s. 3932-3949 ISSN 0006-3495 R&D Projects: GA MŠk(CZ) LC06030; GA ČR(CZ) GA203/05/0009; GA ČR(CZ) GA203/05/0388; GA AV ČR(CZ) 1QS500040581 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : molecular dynamics * RNA * virus Subject RIV: BO - Biophysics Impact factor: 4.627, year: 2007

  17. Molecular dynamic simulation of the self-assembly of DAP12-NKG2C activating immunoreceptor complex.

    Directory of Open Access Journals (Sweden)

    Peng Wei

    Full Text Available The DAP12-NKG2C activating immunoreceptor complex is one of the multisubunit transmembrane protein complexes in which ligand-binding receptor chains assemble with dimeric signal-transducing modules through non-covalent associations in their transmembrane (TM domains. In this work, both coarse grained and atomistic molecular dynamic simulation methods were applied to investigate the self-assembly dynamics of the transmembrane domains of the DAP12-NKG2C activating immunoreceptor complex. Through simulating the dynamics of DAP12-NKG2C TM heterotrimer and point mutations, we demonstrated that a five-polar-residue motif including: 2 Asps and 2 Thrs in DAP12 dimer, as well as 1 Lys in NKG2C TM plays an important role in the assembly structure of the DAP12-NKG2C TM heterotrimer. Furthermore, we provided clear evidences to exclude the possibility that another NKG2C could stably associate with the DAP12-NKG2C heterotrimer. Based on the simulation results, we proposed a revised model for the self-assembly of DAP12-NKG2C activating immunoreceptor complex, along with a plausible explanation for the association of only one NKG2C with a DAP12 dimer.

  18. Crystal and Molecular Structure of Bis(2,2-diphenyl-N-(di-n-propylcarbamothioyl acetamidocopper(II Complex

    Directory of Open Access Journals (Sweden)

    Hakan Arslan

    2011-01-01

    Full Text Available Bis(2,2-diphenyl-N-(di-n-propylcarbamothioyl acetamidocopper(II complex has been synthesized and characterized by elemental analysis and FT-IR spectroscopy. The crystal and molecular structure of the title compound has been determined from single crystal X-ray diffraction data. It crystallizes in the triclinic space group P-1, with a = 13.046(2 Å, b = 13.135(2 Å, c = 13.179(2 Å, α= 67.083(4°, β= 67.968(4°, γ = 84.756(4° and Dcalc =1.330 g/cm3 for Z = 2. The crystal structure confirms that the complex is a mononuclear copper(II complex and the 2,2-diphenyl-N-(di-n-propyl-carbamothioylacetamide ligand is a bidentate chelating ligand, coordinating to the copper atom through the thiocarbonyl and carbonyl groups. This coordination has a slightly distorted square-planar geometry (O1-Cu1-O2: 86.48(11°, O1-Cu1-S1: 93.85(9°, O2-Cu1-S2: 94.20(9° and S1-Cu1-S2: 91.21(4°. The title molecule shows a cis-arrangement and C–O, C–S and C–N bond lengths of the complex suggest considerable electronic delocalization in the chelate rings.

  19. Molecular Cloning Designer Simulator (MCDS): All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects.

    Science.gov (United States)

    Shi, Zhenyu; Vickers, Claudia E

    2016-12-01

    Molecular Cloning Designer Simulator (MCDS) is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1) it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2) it can perform a user-defined workflow of cloning steps in a single execution of the software; (3) it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4) it includes experimental information to conveniently guide wet lab work; and (5) it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com.

  20. Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons.

    Science.gov (United States)

    Popa, Vlad; Trecroce, Danielle A; McAllister, Robert G; Konermann, Lars

    2016-06-16

    Electrospray ionization mass spectrometry (ESI-MS) has become an indispensable technique for examining noncovalent protein complexes. Collision-induced dissociation (CID) of these multiply protonated gaseous ions usually culminates in ejection of a single subunit with a disproportionately large amount of charge. Experiments suggest that this process involves subunit unfolding prior to separation from the residual complex, as well as H(+) migration onto the unravelling chain. Molecular dynamics (MD) simulations are a promising avenue for gaining detailed insights into these CID events. Unfortunately, typical MD algorithms do not allow for mobile protons. Here we address this limitation by implementing a strategy that combines atomistic force fields (such as OPLS/AA and CHARMM36) with a proton hopping algorithm, focusing on the tetrameric complexes transthyretin and streptavidin. Protons are redistributed over all acidic and basic sites in 20 ps intervals, subject to an energy function that reflects electrostatic interactions and proton affinities. Our simulations predict that nativelike conformers at the onset of collisional heating contain multiple salt bridges. Collisional heating initially causes subtle structural changes that lead to a gradual decline of these zwitterionic patterns. Many of the MD runs show gradual unfolding of a single subunit in conjunction with H(+) migration, culminating in subunit separation from the complex. However, there are also instances where two or more chains start to unfold simultaneously, giving rise to charge competition. The scission point where the "winning" subunit separates from the complex can be attained for different degrees of unfolding, giving rise to product ions in various charge states. The simulated product ion distributions are in close agreement with experimental CID data. Proton enrichment in the departing subunit is driven by charge-charge repulsion, but the combination of salt bridge depletion, charge migration