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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. Creating complex molecular topologies by configuring DNA four-way junctions

    Science.gov (United States)

    Liu, Di; Chen, Gang; Akhter, Usman; Cronin, Timothy M.; Weizmann, Yossi

    2016-10-01

    The realization of complex topologies at the molecular level represents a grand challenge in chemistry. This necessitates the manipulation of molecular interactions with high precision. Here we show that single-stranded DNA (ssDNA) knots and links can be created by utilizing the inherent topological properties that pertain to the DNA four-way junction, at which the two helical strands form a node and can be configured conveniently and connected for complex topological construction. Using this strategy, we produced series of ssDNA topoisomers with the same sequences. By finely designing the curvature and torsion, double-stranded DNA knots were accessed by hybridizing and ligating the complementary strands with the knotted ssDNA templates. Furthermore, we demonstrate the use of a constructed ssDNA knot both to probe the topological conversion catalysed by DNA topoisomerase and to study the DNA replication under topological constraint.

  3. Soft versus hard junction formation for α-terthiophene molecular wires and their charge transfer complexes

    Science.gov (United States)

    Vezzoli, Andrea; Grace, Iain M.; Brooke, Carly; Nichols, Richard J.; Lambert, Colin J.; Higgins, Simon J.

    2017-03-01

    We used a range of scanning tunnelling microscopy (STM)-based methods to conduct a detailed study of single molecule junction conductance enhancement upon charge transfer complex formation, using bis(thiaalkyl)arene molecular wires as electron donors and tetracyanoethylene (TCNE) as an electron acceptor. Using the "hard" STM break junction (STM-BJ) method, in which a Au STM tip is pushed into a Au substrate and then withdrawn in the presence of molecules, we see a single, very broad, peak in the resulting conductance histogram when all data are used; the conductance enhancement is 25-fold for a terthiophene donor and 15-fold for a phenyl group. After rational data selection, in which only current-distance curves that contain a current plateau >0.2 nm long are used in the conductance histogram, three sharper peaks are resolved in the histograms for the charge transfer complexes; two substantially lower-conductance peaks are resolved for the uncomplexed molecules. Using the "soft" STM I(s) technique, in which initial contact between tip and substrate is avoided and the current limit is about an order of magnitude lower, we were able to resolve two peaks for the uncomplexed molecules depending upon the initial set point current (i.e., tip height), one at the same value as the lower of the two data-selected STM-BJ histogram peaks and an additional peak beyond the low-current limit for the STM-BJ experiment. For the terthiophene, the low, medium, and high conductance peaks for the TCNE complex are, respectively, ca. 70, 70, and 46 times higher in conductance than the corresponding peaks for the free molecule.

  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. Thermoelectric efficiency of molecular junctions

    Science.gov (United States)

    Perroni, C. A.; Ninno, D.; Cataudella, V.

    2016-09-01

    Focus of the review is on experimental set-ups and theoretical proposals aimed to enhance thermoelectric performances of molecular junctions. In addition to charge conductance, the thermoelectric parameter commonly measured in these systems is the thermopower, which is typically rather low. We review recent experimental outcomes relative to several junction configurations used to optimize the thermopower. On the other hand, theoretical calculations provide estimations of all the thermoelectric parameters in the linear and non-linear regime, in particular of the thermoelectric figure of merit and efficiency, completing our knowledge of molecular thermoelectricity. For this reason, the review will mainly focus on theoretical studies analyzing the role of not only electronic, but also of the vibrational degrees of freedom. Theoretical results about thermoelectric phenomena in the coherent regime are reviewed focusing on interference effects which play a significant role in enhancing the figure of merit. Moreover, we review theoretical studies including the effects of molecular many-body interactions, such as electron-vibration couplings, which typically tend to reduce the efficiency. Since a fine tuning of many parameters and coupling strengths is required to optimize the thermoelectric conversion in molecular junctions, new theoretically proposed set-ups are discussed in the conclusions.

  6. Seebeck effect in molecular junctions

    Science.gov (United States)

    Zimbovskaya, Natalya A.

    2016-05-01

    Advances in the fabrication and characterization of nanoscale systems presently allow for a better understanding of their thermoelectric properties. As is known, the building blocks of thermoelectricity are the Peltier and Seebeck effects. In the present work we review results of theoretical studies of the Seebeck effect in single-molecule junctions and similar systems. The behavior of thermovoltage and thermopower in these systems is controlled by several factors including the geometry of molecular bridges, the characteristics of contacts between the bridge and the electrodes, the strength of the Coulomb interactions between electrons on the bridge, and of electron-phonon interactions. We describe the impact of these factors on the thermopower. Also, we discuss a nonlinear Seebeck effect in molecular junctions.

  7. Electron transport in molecular junctions

    DEFF Research Database (Denmark)

    Jin, Chengjun

    This thesis addresses the electron transport in molecular junctions, focusing on the energy level alignment and correlation effects. Various levels of theory have been applied to study the structural and electronic effects in different molecular junctions, starting from the single particle density...... charge position are in quantitative agreement with the experiments, while pure DFT is not. This is the consequence of the accurate energy level alignment, where the DFT+∑ method corrects the self-interaction error in the standard DFT functional and uses a static image charge model to include the image...... charge effect on the energy level renormalization. Additionally, the gating of the 4,4’-bipyridine (44BP) molecule contacted to either Ni or Au electrodes has been investigated. Here it is found that the gating mechanism is conceptually different between two cases. In the case of Ni contacts where...

  8. Nano-Molecular Junctions on STM Tips

    Institute of Scientific and Technical Information of China (English)

    Chun Huang∗; Jianshu Yang

    2011-01-01

    We present a technique for building metal-organic-metal junctions, which contain ten or fewer conjugated molecules between each of such junction, and the investigations of the I-V response of these junctions. The junctions are made by self assembling thiolated molecules onto gold coated tips for use in scanning tunneling microscopy. We show that this easy technique probes the qualitative properties of the molecules. Current-voltage characteristics of a Tour wire and a new molecular rectifier are presented.

  9. Nano-Molecular Junctions on STM Tips

    Institute of Scientific and Technical Information of China (English)

    Chun Huang; Jianshu Yang

    2011-01-01

    We present a technique for building metal-organic-metal junctions, which contain ten or fewer conjugated molecules between each of such junction, and the investigations of the I-V response of these junctions.The junctions are made by self assembling thiolated molecules onto gold coated tips for use in scanning tunneling microscopy. We show that this easy technique probes the qualitative properties of the molecules. Currentvoltage characteristics of a Tour wire and a new molecular rectifier are presented.

  10. Molecular junctions: can pulling influence optical controllability?

    Science.gov (United States)

    Parker, Shane M; Smeu, Manuel; Franco, Ignacio; Ratner, Mark A; Seideman, Tamar

    2014-08-13

    We suggest the combination of single molecule pulling and optical control as a way to enhance control over the electron transport characteristics of a molecular junction. We demonstrate using a model junction consisting of biphenyl-dithiol coupled to gold contacts. The junction is pulled while optically manipulating the dihedral angle between the two rings. Quantum dynamics simulations show that molecular pulling enhances the degree of control over the dihedral angle and hence over the transport properties.

  11. Junction Plasmon-Induced Molecular Reorientation

    Energy Technology Data Exchange (ETDEWEB)

    El-Khoury, Patrick Z.; Hu, Dehong; Hess, Wayne P.

    2013-10-17

    Time and frequency dependent intensity variations in sequences of Raman spectra recorded at plasmonic junctions can be assigned to molecular reorientation. This is revealed through Raman trajectories recorded at a nanojunction formed between a silver AFM tip and a corrugated silver surface coated with biphenyl-4,4’-dithiol. Molecular motion is not observed when the tip is retracted and only surface enhancement is operative. In effect, junction plasmon induced molecular reorientation is tracked.

  12. Temperature dependence of thermopower in molecular junctions

    Science.gov (United States)

    Kim, Youngsang; Lenert, Andrej; Meyhofer, Edgar; Reddy, Pramod

    2016-07-01

    The thermoelectric properties of molecular junctions are of considerable interest due to their promise for efficient energy conversion. While the dependence of thermoelectric properties of junctions on molecular structure has been recently studied, their temperature dependence remains unexplored. Using a custom built variable temperature scanning tunneling microscope, we measured the thermopower and electrical conductance of individual benzenedithiol junctions over a range of temperatures (100 K-300 K). We find that while the electrical conductance is independent of temperature, the thermopower increases linearly with temperature, confirming the predictions of the Landauer theory.

  13. Molecular signatures in the transport properties of molecular wire junctions: what makes a junction "molecular"?

    Science.gov (United States)

    Troisi, Alessandro; Ratner, Mark A

    2006-02-01

    The simplest component of molecular electronics consists of a single-molecule transport junction: a molecule sandwiched between source and drain electrodes, with or without a third gate electrode. In this Concept article, we focus on how molecules control transport in metal-electrode molecular junctions, and where the molecular signatures are to be found. In the situation where the molecule is relatively short and the gap between injection energy and molecular eigenstates is large, transport occurs largely by elastic tunneling, stochastic switching is common, and the vibronic signature can be found using inelastic electron tunneling spectroscopy (IETS). As the energy gaps for injection become smaller, one begins to see stronger molecular signatures - these include Franck-Condon-like structures in the current/voltage characteristic and strong vibronic interactions, which can lead to hopping behavior at the polaron limit. Conformational changes induced by the strong electric field lead to another strong manifestation of the molecular nature of the junction. We overview some of this mechanistic landscape, focusing on significant effects of switching (both stochastic and controlled by the electric field) and of molecular vibronic coupling.

  14. All-carbon molecular tunnel junctions.

    Science.gov (United States)

    Yan, Haijun; Bergren, Adam Johan; McCreery, Richard L

    2011-11-30

    This Article explores the idea of using nonmetallic contacts for molecular electronics. Metal-free, all-carbon molecular electronic junctions were fabricated by orienting a layer of organic molecules between two carbon conductors with high yield (>90%) and good reproducibility (rsd of current density at 0.5 V carbon devices exhibit current density-voltage (J-V) behavior similar to those with metallic Cu top contacts. However, the all-carbon devices display enhanced stability to bias extremes and greatly improved thermal stability. Completed carbon/nitroazobenzene(NAB)/carbon junctions can sustain temperatures up to 300 °C in vacuum for 30 min and can be scanned at ±1 V for at least 1.2 × 10(9) cycles in air at 100 °C without a significant change in J-V characteristics. Furthermore, these all-carbon devices can withstand much higher voltages and current densities than can Cu-containing junctions, which fail upon oxidation and/or electromigration of the copper. The advantages of carbon contacts stem mainly from the strong covalent bonding in the disordered carbon materials, which resists electromigration or penetration into the molecular layer, and provides enhanced stability. These results highlight the significance of nonmetallic contacts for molecular electronics and the potential for integration of all-carbon molecular junctions with conventional microelectronics.

  15. Vibrational Heat Transport in Molecular Junctions

    Science.gov (United States)

    Segal, Dvira; Agarwalla, Bijay Kumar

    2016-05-01

    We review studies of vibrational energy transfer in a molecular junction geometry, consisting of a molecule bridging two heat reservoirs, solids or large chemical compounds. This setup is of interest for applications in molecular electronics, thermoelectrics, and nanophononics, and for addressing basic questions in the theory of classical and quantum transport. Calculations show that system size, disorder, structure, dimensionality, internal anharmonicities, contact interaction, and quantum coherent effects are factors that combine to determine the predominant mechanism (ballistic/diffusive), effectiveness (poor/good), and functionality (linear/nonlinear) of thermal conduction at the nanoscale. We review recent experiments and relevant calculations of quantum heat transfer in molecular junctions. We recount the Landauer approach, appropriate for the study of elastic (harmonic) phononic transport, and outline techniques that incorporate molecular anharmonicities. Theoretical methods are described along with examples illustrating the challenge of reaching control over vibrational heat conduction in molecules.

  16. 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...... is approximately half the voltage required to see a peak in the dI/dV curve. Information about the molecular level position can thus be obtained at relatively low voltages. In this work we show that the molecular level position can be determined at even lower voltages, Vmin(α), by finding the minimum of ln...

  17. Charge Transport Phenomena in Peptide Molecular Junctions

    Directory of Open Access Journals (Sweden)

    Alessandra Luchini

    2008-01-01

    Full Text Available 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 nanoelectronic 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.

  18. 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.

  19. Improving transition voltage spectroscopy of molecular junctions

    Science.gov (United States)

    Markussen, Troels; Chen, Jingzhe; Thygesen, Kristian S.

    2011-04-01

    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 is approximately half the voltage required to see a peak in the dI/dV curve. Information about the molecular level position can thus be obtained at relatively low voltages. In this work we show that the molecular level position can be determined at even lower voltages, Vmin(α), by finding the minimum of ln(I/Vα) with α<2. On the basis of a simple Lorentzian transmission model we analyze theoretical ab initio as well as experimental I-V curves and show that the voltage required to determine the molecular levels can be reduced by ~30% as compared to conventional TVS. As for conventional TVS, the symmetry/asymmetry of the molecular junction needs to be taken into account in order to gain quantitative information. We show that the degree of asymmetry may be estimated from a plot of Vmin(α) vs α.

  20. 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

  1. Molecular modeling of inelastic electron transport in molecular junctions

    Science.gov (United States)

    Jiang, Jun; Kula, Mathias; Luo, Yi

    2008-09-01

    A quantum chemical approach for the modeling of inelastic electron tunneling spectroscopy of molecular junctions based on scattering theory is presented. Within a harmonic approximation, the proposed method allows us to calculate the electron-vibration coupling strength analytically, which makes it applicable to many different systems. The calculated inelastic electron transport spectra are often in very good agreement with their experimental counterparts, allowing the revelation of detailed information about molecular conformations inside the junction, molecule-metal contact structures, and intermolecular interaction that is largely inaccessible experimentally.

  2. Molecular modeling of inelastic electron transport in molecular junctions

    Energy Technology Data Exchange (ETDEWEB)

    Jiang Jun; Kula, Mathias; Luo Yi [Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, S-106 91 Stockholm (Sweden)], E-mail: luo@kth.se

    2008-09-17

    A quantum chemical approach for the modeling of inelastic electron tunneling spectroscopy of molecular junctions based on scattering theory is presented. Within a harmonic approximation, the proposed method allows us to calculate the electron-vibration coupling strength analytically, which makes it applicable to many different systems. The calculated inelastic electron transport spectra are often in very good agreement with their experimental counterparts, allowing the revelation of detailed information about molecular conformations inside the junction, molecule-metal contact structures, and intermolecular interaction that is largely inaccessible experimentally.

  3. Electronic transport properties of phenylacetylene molecular junctions

    Institute of Scientific and Technical Information of China (English)

    Liu Wen; Cheng Jie; Yah 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,Jan 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 orbitais induced by the bias.

  4. Controlling local currents in molecular junctions

    CERN Document Server

    Yadalam, Hari Kumar

    2016-01-01

    The effect of non-equilibrium constraints and dephasing on the circulating currents in molecular junctions are analyzed. Circulating currents are manifestations of quantum effects and can be induced either by externally applied bias or an external magnetic field through the molecular system. In symmetric Aharonov-Bohm ring, bond currents have two contributions, bias driven and magnetic field driven. We analyze the competition between these two contributions and show that, as a consequence, current through one of the branches can be completely suppressed. We then study the effect of asymmetry (as a result of chemical substitution) on the current pathways inside the molecule and study asymmetry induced circulating currents (without magnetic field) by tuning the coupling strength of the substituent (at finite bias).

  5. Transient Dynamics in Molecular Junctions: Coherent Bichromophoric Molecular Electron Pumps

    CERN Document Server

    Volkovich, Roie

    2010-01-01

    The possibility of using single molecule junctions as electron pumps for energy conversion and storage is considered. It is argued that the small dimensions of these systems enable to make use of unique intra-molecular quantum coherences in order to pump electrons between two leads and to overcome relaxation processes which tend to suppress the pumping efficiency. In particular, we demonstrate that a selective transient excitation of one chromophore in a bi-chromophoric donor-bridge-acceptor molecular junction model yields currents which transfer charge (electron and holes) unevenly to the two leads in the absence of a bias potential. The utility of this mechanism for charge pumping in steady state conditions is proposed.

  6. The critical power to maintain thermally stable molecular junctions

    Science.gov (United States)

    Wang, Yanlei; Xu, Zhiping

    2014-07-01

    With the rise of atomic-scale devices such as molecular electronics and scanning probe microscopies, energy transport processes through molecular junctions have attracted notable research interest recently. In this work, heat dissipation and transport across diamond/benzene/diamond molecular junctions are explored by performing atomistic simulations. We identify the critical power Pcr to maintain thermal stability of the junction through efficient dissipation of local heat. We also find that the molecule-probe contact features a power-dependent interfacial thermal resistance RK in the order of 109 kW-1. Moreover, both Pcr and RK display explicit dependence on atomic structures of the junction, force and temperature. For instance, Pcr can be elevated in multiple-molecule junctions, and streching the junction enhances RK by a factor of 2. The applications of these findings in molecular electronics and scanning probing measurements are discussed, providing practical guidelines in their rational design.

  7. Transient Dynamics in Molecular Junctions: Coherent Bichromophoric Molecular Electron Pumps

    OpenAIRE

    2010-01-01

    The possibility of using single molecule junctions as electron pumps for energy conversion and storage is considered. It is argued that the small dimensions of these systems enable to make use of unique intra-molecular quantum coherences in order to pump electrons between two leads and to overcome relaxation processes which tend to suppress the pumping efficiency. In particular, we demonstrate that a selective transient excitation of one chromophore in a bi-chromophoric donor-bridge-acceptor ...

  8. Electron and Phonon Transport in Molecular Junctions

    DEFF Research Database (Denmark)

    Li, Qian

    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....... 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...... and the thermoelectric response of five representative π-stacked systems. We find that the transmission and power factor are both enhanced by increasing the conjugation length or adding substituent groups. The local transmission shows that several extra paths are added by cyano groups, which increases the total...

  9. 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.

  10. Molecular Models for Conductance in Junctions and Electrochemical Electron Transfer

    Science.gov (United States)

    Mazinani, Shobeir Khezr Seddigh

    This thesis develops molecular models for electron transport in molecular junctions and intra-molecular electron transfer. The goal is to identify molecular descriptors that afford a substantial simplification of these electronic processes. First, the connection between static molecular polarizability and the molecular conductance is examined. A correlation emerges whereby the measured conductance of a tunneling junction decreases as a function of the calculated molecular polarizability for several systems, a result consistent with the idea of a molecule as a polarizable dielectric. A model based on a macroscopic extension of the Clausius-Mossotti equation to the molecular domain and Simmon's tunneling model is developed to explain this correlation. Despite the simplicity of the theory, it paves the way for further experimental, conceptual and theoretical developments in the use of molecular descriptors to describe both conductance and electron transfer. Second, the conductance of several biologically relevant, weakly bonded, hydrogen-bonded systems is systematically investigated. While there is no correlation between hydrogen bond strength and conductance, the results indicate a relation between the conductance and atomic polarizability of the hydrogen bond acceptor atom. The relevance of these results to electron transfer in biological systems is discussed. Hydrogen production and oxidation using catalysts inspired by hydrogenases provides a more sustainable alternative to the use of precious metals. To understand electrochemical and spectroscopic properties of a collection of Fe and Ni mimics of hydrogenases, high-level density functional theory calculations are described. The results, based on a detailed analysis of the energies, charges and molecular orbitals of these metal complexes, indicate the importance of geometric constraints imposed by the ligand on molecular properties such as acidity and electrocatalytic activity. Based on model calculations of

  11. High electronic couplings of single mesitylene molecular junctions

    Directory of Open Access Journals (Sweden)

    Yuki Komoto

    2015-12-01

    Full Text Available We report on an experimental analysis of the charge transport properties of single mesitylene (1,3,5-trimethylbenzene molecular junctions. The electronic conductance and the current–voltage characteristics of mesitylene molecules wired into Au electrodes were measured by a scanning tunnelling microscopy-based break-junction method at room temperature in a liquid environment. We found the molecular junctions exhibited two distinct conductance states with high conductance values of ca. 10−1G0 and of more than 10−3G0 (G0 = 2e2/h in the electronic conductance measurements. We further performed a statistical analysis of the current–voltage characteristics of the molecular junctions in the two states. Within a single channel resonant tunnelling model, we obtained electronic couplings in the molecular junctions by fitting the current–voltage characteristics to the single channel model. The origin of the high conductance was attributed to experimentally obtained large electronic couplings of the direct π-bonded molecular junctions (ca. 0.15 eV. Based on analysis of the stretch length of the molecular junctions and the large electronic couplings obtained from the I–V analysis, we proposed two structural models, in which (i mesitylene binds to the Au electrode perpendicular to the charge transport direction and (ii mesitylene has tilted from the perpendicular orientation.

  12. High electronic couplings of single mesitylene molecular junctions.

    Science.gov (United States)

    Komoto, Yuki; Fujii, Shintaro; Nishino, Tomoaki; Kiguchi, Manabu

    2015-01-01

    We report on an experimental analysis of the charge transport properties of single mesitylene (1,3,5-trimethylbenzene) molecular junctions. The electronic conductance and the current-voltage characteristics of mesitylene molecules wired into Au electrodes were measured by a scanning tunnelling microscopy-based break-junction method at room temperature in a liquid environment. We found the molecular junctions exhibited two distinct conductance states with high conductance values of ca. 10(-1) G 0 and of more than 10(-3) G 0 (G 0 = 2e (2)/h) in the electronic conductance measurements. We further performed a statistical analysis of the current-voltage characteristics of the molecular junctions in the two states. Within a single channel resonant tunnelling model, we obtained electronic couplings in the molecular junctions by fitting the current-voltage characteristics to the single channel model. The origin of the high conductance was attributed to experimentally obtained large electronic couplings of the direct π-bonded molecular junctions (ca. 0.15 eV). Based on analysis of the stretch length of the molecular junctions and the large electronic couplings obtained from the I-V analysis, we proposed two structural models, in which (i) mesitylene binds to the Au electrode perpendicular to the charge transport direction and (ii) mesitylene has tilted from the perpendicular orientation.

  13. A Study of Electrocyclic Reactions in a Molecular Junction

    DEFF Research Database (Denmark)

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

    2017-01-01

    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......) 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...

  14. Raman Scattering at Plasmonic Junctions Shorted by Conductive Molecular Bridges

    Energy Technology Data Exchange (ETDEWEB)

    El-Khoury, Patrick Z.; Hu, Dehong; Apkarian, V. Ara; Hess, Wayne P.

    2013-04-10

    Intensity spikes in Raman scattering, accompanied by switching between line spectra and band spectra, can be assigned to shorting the junction plasmon through molecular conductive bridges. This is demonstrated through Raman trajectories recorded at a plasmonic junction formed by a gold AFM tip in contact with a silver surface coated either with biphenyl-4,4’-dithiol or biphenyl-4-thiol. The fluctuations are absent in the monothiol. In effect, the making and breaking of chemical bonds is tracked.

  15. Electronic Transport in Molecular Junction Based on C20 Cages

    Institute of Scientific and Technical Information of China (English)

    OUYANG Fang-Ping; XU Hui

    2007-01-01

    Choosing closed-ended armchair(5,5)single-wall carbon nanotubes(CCNTs)as electrodes,we investigate the electron transport properties across an all-carbon molecular junction consisting of C20 molecules suspended between two semi-infinite carbon nanotubes.It is shown that the conductances are quite sensitive to the number of C20 molecules between electrodes for both configuration CFl and double-bonded models:the conductances of C20 dimers are markedly smaller than those of monomers.The physics is that incident electrons easily pass the C20 molecules and are predominantly scattered at the C20-C20 junctions.Moreover,we study the doping effect of such molecular junction by doping nitrogen atoms substitutionally.The bonding property of the molecular junction with configuration CFl has been analysed by calculating the Mulliken atomic charges.Our results have revealed that the C atoms in N-doped junctions are more ionic than those in pure-carbon ones,leading to the fact that N-doped junctions have relatively large conductance.

  16. 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.

  17. Internal photoemission in molecular junctions: parameters for interfacial barrier determinations.

    Science.gov (United States)

    Fereiro, Jerry A; Kondratenko, Mykola; Bergren, Adam Johan; McCreery, Richard L

    2015-01-28

    The photocurrent spectra for large-area molecular junctions are reported, where partially transparent copper top contacts permit illumination by UV-vis light. The effect of variation of the molecular structure and thickness are discussed. Internal photoemission (IPE), a process involving optical excitation of hot carriers in the contacts followed by transport across internal system barriers, is dominant when the molecular component does not absorb light. The IPE spectrum contains information regarding energy level alignment within a complete, working molecular junction, with the photocurrent sign indicating transport through either the occupied or unoccupied molecular orbitals. At photon energies where the molecular layer absorbs, a secondary phenomenon is operative in addition to IPE. In order to distinguish IPE from this secondary mechanism, we show the effect of the source intensity as well as the thickness of the molecular layer on the observed photocurrent. Our results clearly show that the IPE mechanism can be differentiated from the secondary mechanism by the effects of variation of experimental parameters. We conclude that IPE can provide valuable information regarding interfacial energetics in intact, working molecular junctions, including clear discrimination of charge transport mediated by electrons through unoccupied system orbitals from that mediated by hole transport through occupied system orbitals.

  18. Assembling molecular electronic junctions one molecule at a time.

    Science.gov (United States)

    Bonifas, Andrew P; McCreery, Richard L

    2011-11-01

    Diffusion of metal atoms onto a molecular monolayer attached to a conducting surface permits electronic contact to the molecules with minimal heat transfer or structural disturbance. Surface-mediated metal deposition (SDMD) involves contact between "cold" diffusing metal atoms and molecules, due to shielding of the molecules from direct exposure to metal vapor. Measurement of the current through the molecular layer during metal diffusion permits observation of molecular conductance for junctions containing as few as one molecule. Discrete conductance steps were observed for 1-10 molecules within a monolayer during a single deposition run, corresponding to "recruitment" of additional molecules as the contact area between the diffusing Au layer and molecules increases. For alkane monolayers, the molecular conductance measured with SDMD exhibited an exponential dependence on molecular length with a decay constant (β) of 0.90 per CH(2) group, comparable to that observed by other techniques. Molecular conductance values were determined for three azobenzene molecules, and correlated with the offset between the molecular HOMO and the contact Fermi level, as expected for hole-mediated tunneling. Current-voltage curves were obtained during metal deposition showed no change in shape for junctions containing 1, 2, and 10 molecules, implying minimal intermolecular interactions as single molecule devices transitioned into several molecules devices. SDMD represents a "soft" metal deposition method capable of providing single molecule conductance values, then providing quantitative comparisons to molecular junctions containing 10(6) to 10(10) molecules.

  19. 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.

  20. Molecular beam epitaxy growth of germanium junctions for multi-junction solar cell applications

    Science.gov (United States)

    Masuda, T.; Faucher, J.; Lee, M. L.

    2016-11-01

    We report on the molecular beam epitaxy (MBE) growth and device characteristics of Ge solar cells. Integrating a Ge bottom cell beneath a lattice-matched triple junction stack grown by MBE could enable ultra-high efficiencies without metamorphic growth or wafer bonding. However, a diffused junction cannot be readily formed in Ge by MBE due to the low sticking coefficient of group-V molecules on Ge surfaces. We therefore realized Ge junctions by growth of homo-epitaxial n-Ge on p-Ge wafers within a standard III-V MBE system. We then fabricated Ge solar cells, finding growth temperature and post-growth annealing to be key factors for achieving high efficiency. Open-circuit voltage and fill factor values of ~0.175 V and ~0.59 without a window layer were obtained, both of which are comparable to diffused Ge junctions formed by metal-organic vapor phase epitaxy. We also demonstrate growth of high-quality, single-domain GaAs on the Ge junction, as needed for subsequent growth of III-V subcells, and that the surface passivation afforded by the GaAs layer slightly improves the Ge cell performance.

  1. Picosecond time resolved conductance measurements of redox molecular junctions

    Science.gov (United States)

    Arielly, Rani; Nachman, Nirit; Zelinskyy, Yaroslav; May, Volkhard; Selzer, Yoram

    2017-03-01

    Due to bandwidth limitations of state of the art electronics, the transient transport properties of molecular junctions are experimentally a terra incognita, which can only be explored if novel picosecond current-probing techniques are developed. Here we demonstrate one such approach: the laser pulse-pair sequence scheme. The method is used to monitor in picosecond resolution the oxidation state of a redox molecule, 6-ferrocenyl-1-hexanethiol, within a junction and to quantify its redox rate constant, which is found to be (80 ps)-1.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    ) connected to gold electrodes using first‐principles calculations. We find excellent agreement with experiments for both molecules when exchange–correlation effects are described by the many‐body GW approximation. In contrast, results from standard density functional theory (DFT) deviate from experiments......‐interaction errors and image charge effects. Finally, we show that the conductance and thermopower of the considered junctions are relatively insensitive to the metal–molecule bonding geometry. Our results demonstrate that electronic and thermoelectric properties of molecular junctions can be predicted from first‐principles...... calculations when exchange–correlation effects are taken properly into account....

  3. Perfect spin filtering by symmetry in molecular junctions

    Science.gov (United States)

    Li, Dongzhe; Dappe, Yannick J.; Smogunov, Alexander

    2016-05-01

    Obtaining highly spin-polarized currents in molecular junctions is crucial and important for nanoscale spintronics devices. Motivated by our recent symmetry-based theoretical argument for complete blocking of one spin conductance channel in model molecular junctions [A. Smogunov and Y. J. Dappe, Nano Lett. 15, 3552 (2015), 10.1021/acs.nanolett.5b01004], we explore the generality of the proposed mechanism and the degree of achieved spin-polarized current for realistic molecular junctions made of various ferromagnetic electrodes (Ni, Co, Fe) connected by different molecules (quaterthiophene or p -quaterphenyl). A simple analysis of the spin-resolved local density of states of a free electrode allowed us to identify the Fe(110) as the most optimal electrode, providing perfect spin filtering and high conductance at the same time. These results are confirmed by ab initio quantum transport calculations and are similar to those reported previously for model junctions. It is found, moreover, that the distortion of the p -quaterphenyl molecule plays an important role, reducing significantly the overall conductance.

  4. Molecular design of electron transport with orbital rule: toward conductance-decay free molecular junctions.

    Science.gov (United States)

    Tada, Tomofumi; Yoshizawa, Kazunari

    2015-12-28

    In this study, we report our viewpoint of single molecular conductance in terms of frontier orbitals. The orbital rule derived from orbital phase and amplitude is a powerful guideline for the qualitative understanding of molecular conductance in both theoretical and experimental studies. The essence of the orbital rule is the phase-related quantum interference, and on the basis of this rule a constructive or destructive pathway for electron transport is easily predicted. We have worked on the construction of the orbital rule for more than ten years and recently found from its application that π-stacked molecular junctions fabricated experimentally are in line with the concept for conductance-decay free junctions. We explain the orbital rule using benzene molecular junctions with the para-, meta- and ortho-connections and discuss linear π-conjugated chains and π-stacked molecular junctions with respect to their small decay factors in this manuscript.

  5. Molecular mechanisms of gap junction mutations in myelinating cells.

    Science.gov (United States)

    Sargiannidou, Irene; Markoullis, Kyriaki; Kleopa, Kleopas A

    2010-09-01

    There is an emerging group of neurological disorders that result from genetic mutations affecting gap junction proteins in myelinating cells. The X-linked form of Charcot Marie Tooth disease (CMT1X) is caused by numerous mutations in the GJB1 gene encoding the gap junction protein connexin32 (Cx32), which is expressed in both Schwann cells in the PNS and oligodendrocytes in the CNS. Patients with CMT1X present mainly with a progressive peripheral neuropathy, showing mixed axonal and demyelinating features. In many cases there is also clinical or subclinical involvement of the CNS with acute or chronic phenotypes of encephalopathy. Furthermore, mutations in the GJA12/GJC2 gene encoding the gap junction protein Cx47, which is expressed in oligodendrocytes, have been identified in families with progressive leukodystrophy, known as Pelizaeus-Merzbacher-like disease, as well as in patients with hereditary spastic paraplegia. Recent studies have provided insights into the pattern of gap junction protein expression and function in CNS and PNS myelinating cells. Furthermore, in vitro and in vivo disease models have clarified some of the molecular and cellular mechanisms underlying these disorders. Here we provide an overview of the clinical, genetic, and neurobiological aspects of gap junction disorders affecting the nervous system.

  6. Effect of asymmetric molecule-electrode coupling and molecular bias on rectification in molecular junctions

    Science.gov (United States)

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

    2016-12-01

    In this research work, we compare the rectification trends of two symmetrical and one asymmetrical molecular junction formed with gold and silver electrodes bridging benzenedithiol molecule. The origin of rectification is attributed to both molecular bias drop and asymmetric molecule-electrode coupling. The electronic transport properties are computed by using semi-empirical extended Huckel method combined with non-equilibrium Green's function framework. The results are fully rationalized by analysing the distribution of molecular orbitals with changing bias voltage, available density of states and area of transmission spectra spanned within bias window, transmission eigenstates and transmission pathways. We deduce through this work that the molecular rectification is not only the property of asymmetric molecule-metal coupling, but molecular bias also plays vital role in stemming asymmetric I- V characteristics. Our results suggest how to realize molecular rectification by using different electrode materials which act as Schottky barriers in molecular junctions that emulate p-n junction diode in semiconductor electronics.

  7. The Mesoscopic Electrochemistry of Molecular Junctions

    Science.gov (United States)

    Bueno, Paulo R.; Benites, Tiago A.; Davis, Jason J.

    2016-01-01

    Within the context of an electron dynamic (time-dependent) perspective and a voltage driving force acting to redistribute electrons between metallic and addressable molecular states, we define here the associated electron admittance and conductance. We specifically present a mesoscopic approach to resolving the electron transfer rate associated with the electrochemistry of a redox active film tethered to metallic leads and immersed in electrolyte. The methodology is centred on aligning the lifetime of the process of electron exchange with associated resistance and capacitance quantities. Notably, however, these are no longer those empirically known as charge transfer resistance and pseudo-capacitance, but are those derived instead from a consideration of the quantum states contained in molecular films and their accessibility through a scattering region existing between them and the metallic probe. The averaged lifetime (τr) associated with the redox site occupancy is specifically dependent on scattering associated with the quantum channels linking them to the underlying metallic continuum and associated with both a quantum resistance (Rq) and an electrochemical (redox) capacitance (Cr). These are related to electron transfer rate through k = 1/τr = (RqCr)‑1. The proposed mesoscopic approach is consistent with Marcus’s (electron transfer rate) theory and experimental measurements obtained by capacitance spectroscopy.

  8. Nonlinear thermoelectric properties of molecular junctions with vibrational coupling

    DEFF Research Database (Denmark)

    Leijnse, Martin Christian; Wegewijs, M. R.; Flensberg, Karsten

    2010-01-01

    We present a detailed study of the nonlinear thermoelectric properties of a molecular junction, represented by a dissipative Anderson-Holstein model. A single-orbital level with strong Coulomb interaction is coupled to a localized vibrational mode and we account for both electron and phonon...... exchange with both electrodes, investigating how these contribute to the heat and charge transports. We calculate the efficiency and power output of the device operated as a heat to electric power converter in the regime of weak tunnel coupling and phonon exchange rate and identify the optimal operating...... conditions, which are found to be qualitatively changed by the presence of the vibrational mode. Based on this study of a generic model system, we discuss the desirable properties of molecular junctions for thermoelectric applications....

  9. Transmission eigenvalue distributions in highly conductive molecular junctions

    Directory of Open Access Journals (Sweden)

    Justin P. Bergfield

    2012-01-01

    Full Text Available Background: The transport through a quantum-scale device may be uniquely characterized by its transmission eigenvalues τn. Recently, highly conductive single-molecule junctions (SMJ with multiple transport channels (i.e., several τn > 0 have been formed from benzene molecules between Pt electrodes. Transport through these multichannel SMJs is a probe of both the bonding properties at the lead–molecule interface and of the molecular symmetry.Results: We use a many-body theory that properly describes the complementary wave–particle nature of the electron to investigate transport in an ensemble of Pt–benzene–Pt junctions. We utilize an effective-field theory of interacting π-electrons to accurately model the electrostatic influence of the leads, and we develop an ab initio tunneling model to describe the details of the lead–molecule bonding over an ensemble of junction geometries. We also develop a simple decomposition of transmission eigenchannels into molecular resonances based on the isolated resonance approximation, which helps to illustrate the workings of our many-body theory, and facilitates unambiguous interpretation of transmission spectra.Conclusion: We confirm that Pt–benzene–Pt junctions have two dominant transmission channels, with only a small contribution from a third channel with τn << 1. In addition, we demonstrate that the isolated resonance approximation is extremely accurate and determine that transport occurs predominantly via the HOMO orbital in Pt–benzene–Pt junctions. Finally, we show that the transport occurs in a lead–molecule coupling regime where the charge carriers are both particle-like and wave-like simultaneously, requiring a many-body description.

  10. Thermopower of molecular junctions: Tunneling to hopping crossover in DNA

    Science.gov (United States)

    Korol, Roman; Kilgour, Michael; Segal, Dvira

    2016-12-01

    We study the electrical conductance G and the thermopower S of single-molecule junctions and reveal signatures of different transport mechanisms: off-resonant tunneling, on-resonant coherent (ballistic) motion, and multi-step hopping. These mechanisms are identified by studying the behavior of G and S while varying molecular length and temperature. Based on a simple one-dimensional model for molecular junctions, we derive approximate expressions for the thermopower in these different regimes. Analytical results are compared to numerical simulations, performed using a variant of Büttiker's probe technique, the so-called voltage-temperature probe, which allows us to phenomenologically introduce environmentally induced elastic and inelastic electron scattering effects, while applying both voltage and temperature biases across the junction. We further simulate the thermopower of GC-rich DNA sequences with mediating A:T blocks and manifest the tunneling-to-hopping crossover in both the electrical conductance and the thermopower, in accord with measurements by Li et al. [Nat. Commun. 7, 11294 (2016)].

  11. Orthogonally modulated molecular transport junctions for resettable electronic logic gates

    Science.gov (United States)

    Meng, Fanben; Hervault, Yves-Marie; Shao, Qi; Hu, Benhui; Norel, Lucie; Rigaut, Stéphane; Chen, Xiaodong

    2014-01-01

    Individual molecules have been demonstrated to exhibit promising applications as functional components in the fabrication of computing nanocircuits. Based on their advantage in chemical tailorability, many molecular devices with advanced electronic functions have been developed, which can be further modulated by the introduction of external stimuli. Here, orthogonally modulated molecular transport junctions are achieved via chemically fabricated nanogaps functionalized with dithienylethene units bearing organometallic ruthenium fragments. The addressable and stepwise control of molecular isomerization can be repeatedly and reversibly completed with a judicious use of the orthogonal optical and electrochemical stimuli to reach the controllable switching of conductivity between two distinct states. These photo-/electro-cooperative nanodevices can be applied as resettable electronic logic gates for Boolean computing, such as a two-input OR and a three-input AND-OR. The proof-of-concept of such logic gates demonstrates the possibility to develop multifunctional molecular devices by rational chemical design.

  12. Conformations of cyclopentasilane stereoisomers control molecular junction conductance

    DEFF Research Database (Denmark)

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

    2016-01-01

    Here we examine the impact of ring conformation on the charge transport characteristics of cyclic pentasilane structures bound to gold electrodes in single molecule junctions. We investigate the conductance properties of alkylated cyclopentasilane cis and trans stereoisomers substituted in the 1......,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...... that the constrained dihedral geometries occurring within the ring are suboptimal for σ-orbital delocalization, and therefore, conductance. Theoretical calculations reproduce the measured conductance trends for both cis and trans isomers and find several distinct conformations that are likely to form stable molecular...

  13. Thermoelectricity in molecular junctions with harmonic and anharmonic modes

    Directory of Open Access Journals (Sweden)

    Bijay Kumar Agarwalla

    2015-11-01

    Full Text Available We study charge and energy transfer in two-site molecular electronic junctions in which electron transport is assisted by a vibrational mode. To understand the role of mode harmonicity/anharmonicity in transport behavior, we consider two limiting situations: (i the mode is assumed harmonic, (ii we truncate the mode spectrum to include only two levels, to represent an anharmonic mode. Based on the cumulant generating functions of the models, we analyze the linear-response and nonlinear performance of these junctions and demonstrate that while the electrical and thermal conductances are sensitive to whether the mode is harmonic/anharmonic, the Seebeck coefficient, the thermoelectric figure-of-merit, and the thermoelectric efficiency beyond linear response, conceal this information.

  14. 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...

  15. Molecular targeted agents for gastric and gastroesophageal junction cancer.

    Science.gov (United States)

    Oshima, Takashi; Masuda, Munetaka

    2012-04-01

    Despite recent improvements in surgical techniques and chemotherapy, advanced cancers of the stomach and gastroesophageal junction (GEJ) continue to have poor clinical outcomes. However, molecules intimately related to cancer cell proliferation, invasion, and metastasis have been studied as candidates for molecular targeted agents. Target molecules, such as the epidermal growth factor receptor, vascular endothelial growth factor receptor, and P13k/Akt/mTor pathway, as well as the insulin-like growth factor receptor, c-Met pathways, fibroblast growth factor receptor, and other pathways are considered to be promising candidates for molecular targeted therapy for gastric and GEJ cancer. In this review we focus on the recent developments in targeting relevant pathways in these types of cancer.

  16. State Representation Approach for Atomistic Time-Dependent Transport Calculations in Molecular Junctions.

    Science.gov (United States)

    Zelovich, Tamar; Kronik, Leeor; Hod, Oded

    2014-08-12

    We propose a new method for simulating electron dynamics in open quantum systems out of equilibrium, using a finite atomistic model. The proposed method is motivated by the intuitive and practical nature of the driven Liouville-von-Neumann equation approach of Sánchez et al. [J. Chem. Phys. 2006, 124, 214708] and Subotnik et al. [J. Chem. Phys. 2009, 130, 144105]. A key ingredient of our approach is a transformation of the Hamiltonian matrix from an atomistic to a state representation of the molecular junction. This allows us to uniquely define the bias voltage across the system while maintaining a proper thermal electronic distribution within the finite lead models. Furthermore, it allows us to investigate complex molecular junctions, including multilead configurations. A heuristic derivation of our working equation leads to explicit expressions for the damping and driving terms, which serve as appropriate electron sources and sinks that effectively "open" the finite model system. Although the method does not forbid it, in practice we find neither violation of Pauli's exclusion principles nor deviation from density matrix positivity throughout our numerical simulations of various tight-binding model systems. We believe that the new approach offers a practical and physically sound route for performing atomistic time-dependent transport calculations in realistic molecular junction models.

  17. Conductance saturation in a series of highly transmitting molecular junctions

    Science.gov (United States)

    Yelin, T.; Korytár, R.; Sukenik, N.; Vardimon, R.; Kumar, B.; Nuckolls, C.; Evers, F.; Tal, O.

    2016-04-01

    Revealing the mechanisms of electronic transport through metal-molecule interfaces is of central importance for a variety of molecule-based devices. A key method for understanding these mechanisms is based on the study of conductance versus molecule length in molecular junctions. However, previous works focused on transport governed either by coherent tunnelling or hopping, both at low conductance. Here, we study the upper limit of conductance across metal-molecule-metal interfaces. Using highly conducting single-molecule junctions based on oligoacenes with increasing length, we find that the conductance saturates at an upper limit where it is independent of molecule length. With the aid of two prototype systems, in which the molecules are contacted by either Ag or Pt electrodes, we find two different possible origins for conductance saturation. The results are explained by an intuitive model, backed by ab initio calculations. Our findings shed light on the mechanisms that constrain the conductance of metal-molecule interfaces at the high-transmission limit.

  18. Bottom-Up Molecular Tunneling Junctions Formed by Self-Assembly

    NARCIS (Netherlands)

    Zhang, Yanxi; Zhao, Zhiyuan; Fracasso, Davide; Chiechi, Ryan C

    2014-01-01

    This Minireview focuses on bottom-up molecular tunneling junctions - a fundamental component of molecular electronics - that are formed by self-assembly. These junctions are part of devices that, in part, fabricate themselves, and therefore, are particularly dependent on the chemistry of the molecul

  19. Giant amplification of tunnel magnetoresistance in a molecular junction: Molecular spin-valve transistor

    Energy Technology Data Exchange (ETDEWEB)

    Dhungana, Kamal B.; Pati, Ranjit, E-mail: patir@mtu.edu [Department of Physics, Michigan Technological University, Houghton, Michigan 49931 (United States)

    2014-04-21

    Amplification of tunnel magnetoresistance by gate field in a molecular junction is the most important requirement for the development of a molecular spin valve transistor. Herein, we predict a giant amplification of tunnel magnetoresistance in a single molecular spin valve junction, which consists of Ru-bis-terpyridine molecule as a spacer between two ferromagnetic nickel contacts. Based on the first-principles quantum transport approach, we show that a modest change in the gate field that is experimentally accessible can lead to a substantial amplification (320%) of tunnel magnetoresistance. The origin of such large amplification is attributed to the spin dependent modification of orbitals at the molecule-lead interface and the resultant Stark effect induced shift in channel position with respect to the Fermi energy.

  20. Highly conductive single naphthalene and anthracene molecular junction with well-defined conductance

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Chenyang [Department of Chemistry, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1 W4-10, Ookayama, Meguro-ku, Tokyo 152-8551 (Japan); School of Materials Science and Engineering, Tsinghua University, Beijing 100084 (China); Kaneko, Satoshi; Komoto, Yuki; Fujii, Shintaro, E-mail: fujii.s.af@m.titech.ac.jp; Kiguchi, Manabu, E-mail: kiguti@chem.titech.ac.jp [Department of Chemistry, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1 W4-10, Ookayama, Meguro-ku, Tokyo 152-8551 (Japan)

    2015-03-09

    We performed electronic investigation on single acene molecular junctions bridging Au-electrodes in ultra-high vacuum conditions using mechanically controllable break junction technique. While the molecular junctions displayed various conductance values at 100 K, they exhibited well-defined high conductance values (∼0.3 G{sub 0}) at 300 K, which is close to that of metal atomic contact. Direct π-binding of the molecules to the Au-electrodes leads to the high conductivities at the metal-molecule interface. At the elevated temperature, single molecular junctions trapped in local metastable structures can be fallen into energetically preferential more stable state and thus we fabricated structurally well-defined molecular junctions.

  1. Microsolvation in molecular complexes

    Energy Technology Data Exchange (ETDEWEB)

    Pasquini, M; Schiccheri, N; Piani, G; Pietraperzia, G; Becucci, M; Castellucci, E [European Laboratory for Non-Linear Spectroscopy (LENS), Polo Scientifico e Tecnologico Universita di Firenze, Via Nello Carrara 1, 50019 Sesto Fiorentino (Italy)], E-mail: gianni.pietraperzia@unifi.it

    2008-11-15

    In this paper, we report the results of our study of the microsolvation process involving the anisole molecule. We are able to study bimolecular complexes of different compositions. Changing the second partner molecule bound to anisole, we observed complexes of different geometries, because of the large variety of interactions possible for the anisole. High-resolution electronic spectroscopy is the best tool to reveal the correct vibrationally (zero-point) averaged geometry of the complex. That is done by analysing the rovibronic structure of the electronic spectra, which are related to the equilibrium geometry of the complex as well as dynamical processes, both in the ground and in the excited state. The interpretation of the experimental results is supported by high-level quantum calculations.

  2. An introduction to adherens junctions: from molecular mechanisms to tissue development and disease.

    Science.gov (United States)

    Harris, Tony J C

    2012-01-01

    Adherens junctions (AJs) are fundamental for the development of animal tissues and organs. The core complex is formed from transmembrane cell-cell adhesion molecules, cadherins, and adaptor molecules, the catenins, that link to cytoskeletal and regulatory networks within the cell. This complex can be considered over a wide range of biological organization, from atoms to molecules, protein complexes, molecular networks, cells, tissues, and overall animal development. AJs have also been an integral part of animal evolution, and play central roles in cancer development and pathogen infection. This book addresses major questions encompassing these aspects of AJ biology. How did AJs evolve? How do the cadherins and catenins interact to assemble AJs and mediate adhesion? How do AJs interface with other cellular machinery to couple adhesion with the whole cell? How do AJs affect cell behaviour and multicellular development? How can abnormal AJ activity lead to disease?

  3. Short-time dynamics of molecular junctions after projective measurement

    Science.gov (United States)

    Tang, Gaomin; Xing, Yanxia; Wang, Jian

    2017-08-01

    In this work, we study the short-time dynamics of a molecular junction described by Anderson-Holstein model using full-counting statistics after projective measurement. The coupling between the central quantum dot (QD) and two leads was turned on at remote past and the system is evolved to steady state at time t =0 , when we perform the projective measurement in one of the lead. Generating function for the charge transfer is expressed as a Fredholm determinant in terms of Keldysh nonequilibrium Green's function in the time domain. It is found that the current is not constant at short times indicating that the measurement does perturb the system. We numerically compare the current behaviors after the projective measurement with those in the transient regime where the subsystems are connected at t =0 . The universal scaling for high-order cumulants is observed for the case with zero QD occupation due to the unidirectional transport at short times. The influences of electron-phonon interaction on short-time dynamics of electric current, shot noise, and differential conductance are analyzed.

  4. Electron transport in molecular junctions with graphene as protecting layer

    Energy Technology Data Exchange (ETDEWEB)

    Hüser, Falco; Solomon, Gemma C., E-mail: gsolomon@nano.ku.dk [Nano-Science Center and Department of Chemistry, University of Copenhagen, 2100 København Ø (Denmark)

    2015-12-07

    We present ab initio transport calculations for molecular junctions that include graphene as a protecting layer between a single molecule and gold electrodes. This vertical setup has recently gained significant interest in experiment for the design of particularly stable and reproducible devices. We observe that the signals from the molecule in the electronic transmission are overlayed by the signatures of the graphene sheet, thus raising the need for a reinterpretation of the transmission. On the other hand, we see that our results are stable with respect to various defects in the graphene. For weakly physiosorbed molecules, no signs of interaction with the graphene are evident, so the transport properties are determined by offresonant tunnelling between the gold leads across an extended structure that includes the molecule itself and the additional graphene layer. Compared with pure gold electrodes, calculated conductances are about one order of magnitude lower due to the increased tunnelling distance. Relative differences upon changing the end group and the length of the molecule on the other hand, are similar.

  5. Noncovalent Self-Assembled Monolayers on Graphene as a Highly Stable Platform for Molecular Tunnel Junctions.

    Science.gov (United States)

    Song, Peng; Sangeeth, C S Suchand; Thompson, Damien; Du, Wei; Loh, Kian Ping; Nijhuis, Christian A

    2016-01-27

    Monolayer graphene is used as the bottom electrode to fabricate stable and high-quality self-assembled monolayer (SAM)-based tunnel junctions. The SAMs are formed on graphene via noncovalent bonds without altering the structure of the graphene. This work paves the way to new types of molecular electronic junctions based on 2D materials.

  6. 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.

  7. 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

    Molecular junctions are promising candidates for thermoelectric devices due to the potential to tune the electronic and thermal transport properties. However, a high figure of merit is hard to achieve, without reducing the phononic contribution to thermal conductance. Here, we propose a strategy...... 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...... molecular junction. Phonon transmission of pi-stacked systems is largely attenuated in the whole frequency range, and the remaining transmission occurs mainly below 5 THz, where out-of-plane channels dominate. The figure of merit (ZT) of the pi-stacked molecular junction is dramatically enhanced because...

  8. Anisotropy induced Kondo splitting in a mechanically stretched molecular junction: A first-principles based study

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xiaoli; Hou, Dong, E-mail: houdong@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Zheng, Xiao, E-mail: xz58@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Institute of Applied Physics, Guizhou Normal College, Guiyang, Guizhou 550018 (China); Yan, YiJing [Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026 (China); Department of Chemistry, Hong Kong University of Science and Technology, Hong Kong (China)

    2016-01-21

    The magnetic anisotropy and Kondo phenomena in a mechanically stretched magnetic molecular junction are investigated by combining the density functional theory (DFT) and hierarchical equations of motion (HEOM) approach. The system is comprised of a magnetic complex Co(tpy–SH){sub 2} sandwiched between adjacent gold electrodes, which is mechanically stretched in experiments done by Parks et al. [Science 328, 1370 (2010)]. The electronic structure and mechanical property of the stretched system are investigated via the DFT calculations. The HEOM approach is then employed to characterize the Kondo resonance features, based on the Anderson impurity model parameterized from the DFT results. It is confirmed that the ground state prefers the S = 1 local spin state. The structural properties, the magnetic anisotropy, and corresponding Kondo peak splitting in the axial stretching process are systematically evaluated. The results reveal that the strong electron correlations and the local magnetic properties of the molecule magnet are very sensitive to structural distortion. This work demonstrates that the combined DFT+HEOM approach could be useful in understanding and designing mechanically controlled molecular junctions.

  9. Cyclic conductance switching in networks of redox-active molecular junctions.

    Science.gov (United States)

    Liao, Jianhui; Agustsson, Jon S; Wu, Songmei; Schönenberger, Christian; Calame, Michel; Leroux, Yann; Mayor, Marcel; Jeannin, Olivier; Ran, Ying-Fen; Liu, Shi-Xia; Decurtins, Silvio

    2010-03-10

    Redox-active dithiolated tetrathiafulvalene derivatives (TTFdT) were inserted in two-dimensional nanoparticle arrays to build interlinked networks of molecular junctions. Upon oxidation of the TTFdT to the dication state, we observed a conductance increase of the networks by up to 1 order of magnitude. Successive oxidation and reduction cycles demonstrated a clear switching behavior of the molecular junction conductance. These results show the potential of interlinked nanoparticle arrays as chemical sensors.

  10. End-group Influence on the Frontier Molecular Orbital Reorganization in Molecular Junctions -- Effect on Thermopower

    Science.gov (United States)

    Balachandran, Janakiraman; Reddy, Pramod; Dunietz, Barry; Gavini, Vikram

    2014-03-01

    The frontier molecular orbital (FMO) reorganization and in turn on the thermopower of the aromatic molecules trapped between metal electrodes (aka molecular junctions) depends on two effects namely (1) the stabilization effect - due to the physical presence of the metal electrode atoms and (2) change in e-e interactions - due to end-group mediated charge transfer. The stabilization effect always reduces the FMO energies. The charge transfer effect increases the FMO energies in charge-gaining molecules, which in turn opposes the stabilization effect resulting in a small overall shift. However, the charge transfer effect decreases the FMO energies in charge-losing molecules, which in turn complements the stabilization effect resulting in a large overall downward shift. This hypothesis is validated by delineating the shifts due to stabilization and charge-transfer effects independently. Further we also demonstrate the generality of the hypothesis by applying it on a wide range of aromatic molecules with different length and end-groups. Finally, we also present computationally efficient strategies, based on the proposed mechanism, to quantitatively compute the FMO reorganization which in turn has potential for high throughput analysis of molecular junctions.

  11. Charge transport and rectification in molecular junctions formed with carbon-based electrodes.

    Science.gov (United States)

    Kim, Taekyeong; Liu, Zhen-Fei; Lee, Chulho; Neaton, Jeffrey B; Venkataraman, Latha

    2014-07-29

    Molecular junctions formed using the scanning-tunneling-microscope-based break-junction technique (STM-BJ) have provided unique insight into charge transport at the nanoscale. In most prior work, the same metal, typically Au, Pt, or Ag, is used for both tip and substrate. For such noble metal electrodes, the density of electronic states is approximately constant within a narrow energy window relevant to charge transport. Here, we form molecular junctions using the STM-BJ technique, with an Au metal tip and a microfabricated graphite substrate, and measure the conductance of a series of graphite/amine-terminated oligophenyl/Au molecular junctions. The remarkable mechanical strength of graphite and the single-crystal properties of our substrates allow measurements over few thousand junctions without any change in the surface properties. We show that conductance decays exponentially with molecular backbone length with a decay constant that is essentially the same as that for measurements with two Au electrodes. More importantly, despite the inherent symmetry of the oligophenylamines, we observe rectification in these junctions. State-of-art ab initio conductance calculations are in good agreement with experiment, and explain the rectification. We show that the highly energy-dependent graphite density of states contributes variations in transmission that, when coupled with an asymmetric voltage drop across the junction, leads to the observed rectification. Together, our measurements and calculations show how functionality may emerge from hybrid molecular-scale devices purposefully designed with different electrodes beyond the so-called "wide band limit," opening up the possibility of assembling molecular junctions with dissimilar electrodes using layered 2D materials.

  12. Effects of hydrogen bonding on current-voltage characteristics of molecular junctions

    Science.gov (United States)

    Kula, Mathias; Jiang, Jun; Lu, Wei; Luo, Yi

    2006-11-01

    We present a first-principles study of hydrogen bonding effect on current-voltage characteristics of molecular junctions. Three model charge-transfer molecules, 2'-amino-4,4'-di(ethynylphenyl)-1-benzenethiolate (DEPBT-D), 4,4'-di(ethynylphenyl)-2'-nitro-1-benzenethiolate (DEPBT-A), and 2'-amino-4,4'-di(ethynylphenyl)-5'-nitro-1-benzenethiolate (DEPBT-DA), have been examined and compared with the corresponding hydrogen bonded complexes formed with different water molecules. Large differences in current-voltage characteristics are observed for DEPBT-D and DEPBT-A molecules with or without hydrogen bonded waters, while relatively small differences are found for DEPBT-DA. It is predicted that the presence of water clusters can drastically reduce the conductivities of the charge-transfer molecules. The underlying microscopic mechanism has been discussed.

  13. Electronic transport properties of molecular junctions based on the direct binding of aromatic ring to electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Lan, Tran Nguyen, E-mail: lantran@ims.ac.jp

    2014-01-15

    Highlights: • Transport properties of molecular junction having direct binding of aromatic ring to electrode have been investigated. • The conductance of junction with sp-type electrode is higher than that of junction with sd-type electrode. • The rectifying mechanism critically depends on the nature of benzene–electrode coupling. • The p–n junction-like can be obtained even without heteroatom doping. • The negative differential resistance effect was observed for the case of sp-type electrode. - Abstract: We have used the non-equilibrium Green’s function in combination with the density functional theory to investigate the quantum transport properties of the molecular junctions including a terminated benzene ring directly coupled to surface of metal electrodes (physisorption). The other side of molecule was connected to electrode via thiolate bond (chemisorption). Two different electrodes have been studied, namely Cu and Al. Rectification and negative differential resistance behavior have been observed. We found that the electron transport mechanism is affected by the nature of benzene–electrode coupling. In other words, the transport mechanism depends on the nature of metallic electrode. Changing from sp- to sd-metallic electrode, the molecular junction changes from the Schottky to p–n junction-like diode. The transmission spectra, projected density of state, molecular projected self-consistent Hamiltonian, transmission eigenchannel, and Muliken population have been analyzed for explanation of electronic transport properties. Understanding the transport mechanism in junction having direct coupling of π-conjugate to electrode will be useful to design the future molecular devices.

  14. 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

    2016-03-09

    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.

  15. 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.

  16. Direct optical determination of interfacial transport barriers in molecular tunnel junctions.

    Science.gov (United States)

    Fereiro, Jerry A; McCreery, Richard L; Bergren, Adam Johan

    2013-07-03

    Molecular electronics seeks to build circuitry using organic components with at least one dimension in the nanoscale domain. Progress in the field has been inhibited by the difficulty in determining the energy levels of molecules after being perturbed by interactions with the conducting contacts. We measured the photocurrent spectra for large-area aliphatic and aromatic molecular tunnel junctions with partially transparent copper top contacts. Where no molecular absorption takes place, the photocurrent is dominated by internal photoemission, which exhibits energy thresholds corresponding to interfacial transport barriers, enabling their direct measurement in a functioning junction.

  17. Motor effect in electron transport through a molecular junction with torsional vibrations

    OpenAIRE

    Pshenichnyuk, Ivan A.; Čížek, Martin

    2010-01-01

    We propose a model for a molecular junction with internal anharmonic torsional vibrations interacting with an electric current. The Wangsness-Bloch-Redfield master equation approach is used to determine the stationary reduced density matrix of the molecule. The dependence of the current, excitation energy and angular momentum of the junction on the applied voltage is studied. Negative differential conductance is observed in the current-voltage characteristics. It is shown that a model with vi...

  18. Ambient organic molecular passivation of Si yields near-ideal, Schottky-Mott limited, junctions

    Directory of Open Access Journals (Sweden)

    Rotem Har-Lavan

    2012-03-01

    Full Text Available We report near-perfect transfer of the electrical properties of oxide-free Si surface, modified by a molecular monolayer, to the interface of a junction made with that modified Si surface. Such behavior is highly unusual for a covalent, narrow bandgap semiconductor, such as Si. Short, ambient atmosphere, room temperature treatment of oxide-free Si(100 in hydroquinone (HQ/alkyl alcohol solutions, fully passivates the Si surface, while allowing controlled change of the resulting surface potential. The junctions formed, upon contacting such surfaces with Hg, a metal that does not chemically interact with Si, follow the Schottky-Mott model for metal-semiconductor junctions closer than ever for Si-based junctions. Two examples of such ideal behavior are demonstrated: a Tuning the molecular surface dipole over 400 mV, with only negligible band bending, by changing the alkyl chain length. Because of the excellent passivation this yields junctions with Hg with barrier heights that follow the change in the Si effective electron affinity nearly ideally. b HQ/ methanol passivation of Si is accompanied by a large surface dipole, which suffices, as interface dipole, to drive the Si into strong inversion as shown experimentally via its photovoltaic effect. With only ∼0.3 nm molecular interlayer between the metal and the Si, our results proves that it is passivation and prevention of metal-semiconductor interactions that allow ideal metal-semiconductor junction behavior, rather than an insulating transport barrier.

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

    KAUST Repository

    Souza, Amaury De Melo

    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.

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

    Directory of Open Access Journals (Sweden)

    Mingsen Deng

    2015-01-01

    Full Text Available 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.

  1. 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 int...... and the main conduction channel from measurements in the case of orthogonal basis. The results obtained within the parabolic model are validated using density-functional based quantum transport calculations in realistic T-shaped molecular junctions....

  2. 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.

  3. Avoiding self-repulsion in density functional description of biased molecular junctions

    Energy Technology Data Exchange (ETDEWEB)

    Baer, Roi [Department of Physical Chemistry and Lise Meitner Minerva-Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Jerusalem 91904 (Israel)], E-mail: roi.baer@huji.ac.il; Livshits, Ester [Department of Physical Chemistry and Lise Meitner Minerva-Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Jerusalem 91904 (Israel); Neuhauser, Daniel [Department of Physical Chemistry and Lise Meitner Minerva-Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Jerusalem 91904 (Israel)], E-mail: dxn@chem.ucla.edu

    2006-10-26

    We examine the effects of self-repulsion on the predictions of charge distribution in biased molecular junctions by the local density functional theory methods. This is done using a functional with explicit long-range exchange term effects [R. Baer, D. Neuhauser, Phys. Rev. Lett. 94 (2005) 043002]. We discuss in detail the new density functional, pointing out some of the remaining difficulties in the theory. We find that in weakly coupled junctions (the typical molecular electronics case) local-density functionals fail to describe correctly the charge distribution in the intermediate bias regime.

  4. Influence of thermalization on thermal conduction through molecular junctions: Computational study of PEG oligomers

    Science.gov (United States)

    Pandey, Hari Datt; Leitner, David M.

    2017-08-01

    Thermalization in molecular junctions and the extent to which it mediates thermal transport through the junction are explored and illustrated with computational modeling of polyethylene glycol (PEG) oligomer junctions. We calculate rates of thermalization in the PEG oligomers from 100 K to 600 K and thermal conduction through PEG oligomer interfaces between gold and other materials, including water, motivated in part by photothermal applications of gold nanoparticles capped by PEG oligomers in aqueous and cellular environments. Variation of thermalization rates over a range of oligomer lengths and temperatures reveals striking effects of thermalization on thermal conduction through the junction. The calculated thermalization rates help clarify the scope of applicability of approaches that can be used to predict thermal conduction, e.g., where Fourier's law breaks down and where a Landauer approach is suitable. The rates and nature of vibrational energy transport computed for PEG oligomers are compared with available experimental results.

  5. 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.

  6. Interface states, negative differential resistance, and rectification in molecular junctions with transition-metal contacts

    Science.gov (United States)

    Dalgleish, Hugh; Kirczenow, George

    2006-06-01

    We present a theory of nonlinear transport phenomena in molecular junctions where single thiolated organic molecules bridge transition metal nanocontacts whose densities of states have strong d orbital components near the Fermi level. At moderate bias, we find electron transmission between the contacts to be mediated by interface states within the molecular highest-occupied-molecular-orbital-lowest-unoccupied-molecular-orbital gap that arise from hybridization between the thiol-terminated ends of the molecules and the d orbitals of the transition metals. Because these interface states are localized mainly within the metal electrodes, we find their energies to accurately track the electrochemical potentials of the contacts when a variable bias is applied across the junction. We predict resonant enhancement and reduction of the interface state transmission as the applied bias is varied, resulting in negative differential resistance (NDR) in molecular junctions with Pd nanocontacts. We show that these nonlinear phenomena can be tailored by suitably choosing the nanocontact materials: If a Rh electrode is substituted for one Pd contact, we predict enhancement of these NDR effects. The same mechanism is also predicted to give rise to rectification in Pd/molecule/Au junctions. The dependences of the interface state resonances on the orientation of the metal interface, the adsorption site of the molecule, and the separation between the thiolated ends of the molecule and the metal contacts are also discussed.

  7. Efficient electronic coupling and improved stability with dithiocarbamate-based molecular junctions

    Science.gov (United States)

    von Wrochem, Florian; Gao, Deqing; Scholz, Frank; Nothofer, Heinz-Georg; Nelles, Gabriele; Wessels, Jurina M.

    2010-08-01

    Molecular electronic devices require stable and highly conductive contacts between the metal electrodes and molecules. Thiols and amines are widely used to attach molecules to metals, but they form poor electrical contacts and lack the robustness required for device applications. Here, we demonstrate that dithiocarbamates provide superior electrical contact and thermal stability when compared to thiols on metals. Ultraviolet photoelectron spectroscopy and density functional theory show the presence of electronic states at 0.6 eV below the Fermi level of Au, which effectively reduce the charge injection barrier across the metal-molecule interface. Charge transport measurements across oligophenylene monolayers reveal that the conductance of terphenyl-dithiocarbamate junctions is two orders of magnitude higher than that of terphenyl-thiolate junctions. The stability and low contact resistance of dithiocarbamate-based molecular junctions represent a significant step towards the development of robust, organic-based electronic circuits.

  8. Fullerene as alligator clips for electrical conduction through anthracene molecular junctions

    Indian Academy of Sciences (India)

    RUPAN PREET KAUR; RAVINDER SINGH SAWHNEY; DERICK ENGLES

    2017-05-01

    The conductance of a single molecule transport junction comprising anthracene molecular junction (AMJ) with fullerene as alligator clips was investigated using $\\it{ab-initio}$ density functional theory (DFT) in the Landauer–Imry regime of coherent tunnelling transport. In our previous research, we have already calculatedthe electrical transport properties of aromatic molecules with thiol, amine, hydroxyl and selenol end groups concluding the exceptional assistance in the formation of robust molecular junctions. In this article, we have presented the suitability of fullerene anchoring in coupling anthracene molecule with gold electrodes. AMJ with boron-20 (B-20) and C-20 alligator clips exhibited strongest conduction in contrast to nitrogen, oxygen, fluorine and neon alligator clips.

  9. Universal scaling of the charge transport in large-area molecular junctions

    NARCIS (Netherlands)

    Kronemeijer, A.J.; Katsouras, I.; Huisman, E.H.; Hal, P.A. van; Geuns, T.C.T.; Blom, P.W.M.; Leeuw, D.M. de

    2011-01-01

    Charge transport through alkanes and para-phenylene oligomers is investigated in large-area molecular junctions. The molecules are self-assembled in a monolayer and contacted with a top electrode consisting of poly(3,4-ethylenedioxythiophene)-poly(4-styrenesulfonic acid) (PEDOT:PSS). The complete se

  10. Impact of derivatization on electron transmission through dithienylethene-based photoswitches in molecular junctions

    NARCIS (Netherlands)

    Van Dyck, Colin; Geskin, Victor; Kronemeijer, Auke J.; de Leeuw, Dago M.; Cornil, Jerome; Cornil, Jérôme

    2013-01-01

    We report a combined Non-Equilibrium Green's Function - Density Functional Theory study of molecular junctions made of photochromic diarylethenes between gold electrodes. The impact of derivatization of the molecule on the transmission spectrum is assessed by introducing: (i) substituents on the dia

  11. Gate-controlled energy barrier at a graphene/molecular semiconductor junction

    Science.gov (United States)

    Parui, S.; Pietrobon, L.; Ciudad, D.; Velez, S.; Sun, X.; Stoliar, P.; Casanova, F.; Hueso, L. E.

    The formation of an energy barrier at a metal/molecular semiconductor junction is both a ubiquitous phenomenon as well as the subject of intense research in order to improve the performance of molecular semiconductor-based electronic and optoelectronic devices. For these devices, a junction with a large energy barrier provides rectification, leading to a diode behavior, whereas a relatively small energy barrier provides nearly-ohmic behavior, resulting in efficient carrier injection (extraction) into the molecular semiconductor. Typically, a specific metal/molecular semiconductor combination leads to a fixed energy barrier; therefore, the possibility of a gate-controlled energy barrier is very appealing for advanced applications. Here, we present a graphene/C60 junction-based vertical field-effect transistor in which we demonstrate control of the interfacial energy-barrier such that the junction switches from a highly rectifying diode at negative gate voltages to a nearly-ohmic behavior at positive gate voltages and at room temperature. We extract an energy-barrier modulation of up to 660 meV, a transconductance of up to five orders of magnitude and a gate-modulated photocurrent.

  12. 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...

  13. Transverse charge transport through DNA oligomers in large-area molecular junctions

    NARCIS (Netherlands)

    Katsouras, I.; Piliego, C.; Blom, P.W.M.; Leeuw, D.M. de

    2013-01-01

    We investigate the nature of charge transport in deoxyribonucleic acid (DNA) using self-assembled layers of DNA in large-area molecular junctions. A protocol was developed that yields dense monolayers where the DNA molecules are not standing upright, but are lying flat on the substrate. As a result

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

    DEFF Research Database (Denmark)

    Paulsson, Magnus; Krag, Casper; Frederiksen, Thomas;

    2009-01-01

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

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

    NARCIS (Netherlands)

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

    2007-01-01

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

  16. Electronic and transport properties of a molecular junction with asymmetric contacts

    Science.gov (United States)

    Tsai, M.-H.; Lu, T.-H.

    2010-02-01

    Asymmetric molecular junctions have been shown experimentally to exhibit a dual-conductance transport property with a pulse-like current-voltage characteristic, by Reed and co-workers. Using a recently developed first-principles integrated piecewise thermal equilibrium current calculation method and a gold-benzene-1-olate-4-thiolate-gold model molecular junction, this unusual transport property has been reproduced. Analysis of the electrostatics and the electronic structure reveals that the high-current state results from subtle bias induced charge transfer at the electrode-molecule contacts that raises molecular orbital energies and enhances the current-contributing molecular density of states and the probabilities of resonance tunneling of conduction electrons from one electrode to another.

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

    Science.gov (United States)

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

    2014-07-01

    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 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.

  19. Molecular Rheology of Complex Fluids

    DEFF Research Database (Denmark)

    Huang, Qian; Rasmussen, Henrik Koblitz

    The processing of polymer materials is highly governed by its rheology, and influences the properties of the final product. For example, a recurring problem is instability in extrusion that leads to imperfect plastic parts. The ability to predict and control the rheological behavior of polymer......–state viscosity between melts and solutions is still an open question. Branched polymer melts have more complex molecular structures. A stress maximum during the start–up of uniaxial extensional flow was reported in 1979 for a low–density polyethylene (LDPE) melt. Subsequently observations of a steady stress......) linear polystyrene melts and solutions; 2) the bidisperse and polydisperse linear polystyrene melts; 3) the NMMD branched polystyrene melts; and 4) the polydisperse branched polyethylene melts. The experimental results are also compared with some developing theoretical models. Finally, to ensure...

  20. Charge transport in molecular electronic junctions: Compression of the molecular tunnel barrier in the strong coupling regime

    OpenAIRE

    Sayed, Sayed Y.; Fereiro, Jerry A.; Yan, Haijun; Richard L. McCreery; Bergren, Adam Johan

    2012-01-01

    Molecular junctions are essentially modified electrodes familiar to electrochemists where the electrolyte is replaced by a conducting “contact.” It is generally hypothesized that changing molecular structure will alter system energy levels leading to a change in the transport barrier. Here, we show the conductance of seven different aromatic molecules covalently bonded to carbon implies a modest range ( 2 eV range). These results are explained by considering the effect of bonding the molecule...

  1. Photocleavable junctions in complex polymer architectures and photoetchable thermoplastics

    Science.gov (United States)

    Sterner, Elizabeth Surles

    Polymer materials have become important tools in nanomanufacturing due to their facile processing and ready attainment of the necessary feature sizes. The development of cleavable junctions has led to advances in the production of polymer nanotemplates. Photocleavage strategies have come to the forefront of the field because photons, as a cleavage stimulus, do not have the mass-transport limitations of chemical methods, and provide for targeted two- and three-dimensional feature control. This dissertation presents a method for producing photocleavable materials by one-pot copper-catalyzed azide-alkyne "click" chemistry (CuAAC), activator regenerated by electron transfer atom transfer radical polymerization (ARGET ATRP) and activated ester substitution methods that have each block labeled with a fluorescent dye, enabling exploration of the polymer physics of these systems by correlation fluorescence spectroscopy. It also introduces a novel photocleavable linker, the o-nitrobenzyl-1,2,3-triazole, its behavior on photocleavage, and a facile method for the production of the o-nitrobenzyl azides necessary for their synthesis. The synthesis and properties of a bulk photodegradable polytriazole are reported, as are proof of concept experiments demonstrating its potential as a directly photoetchable material. Lastly, this dissertation contains a perspective on possible avenues of new research on the topics presented.

  2. Electron transfer statistics and thermal fluctuations in molecular junctions.

    Science.gov (United States)

    Goswami, Himangshu Prabal; Harbola, Upendra

    2015-02-28

    We derive analytical expressions for probability distribution function (PDF) for electron transport in a simple model of quantum junction in presence of thermal fluctuations. Our approach is based on the large deviation theory combined with the generating function method. For large number of electrons transferred, the PDF is found to decay exponentially in the tails with different rates due to applied bias. This asymmetry in the PDF is related to the fluctuation theorem. Statistics of fluctuations are analyzed in terms of the Fano factor. Thermal fluctuations play a quantitative role in determining the statistics of electron transfer; they tend to suppress the average current while enhancing the fluctuations in particle transfer. This gives rise to both bunching and antibunching phenomena as determined by the Fano factor. The thermal fluctuations and shot noise compete with each other and determine the net (effective) statistics of particle transfer. Exact analytical expression is obtained for delay time distribution. The optimal values of the delay time between successive electron transfers can be lowered below the corresponding shot noise values by tuning the thermal effects.

  3. Probing electron-phonon excitations in molecular junctions by quantum interference.

    Science.gov (United States)

    Bessis, C; Della Rocca, M L; Barraud, C; Martin, P; Lacroix, J C; Markussen, T; Lafarge, P

    2016-02-11

    Electron-phonon coupling is a fundamental inelastic interaction in condensed matter and in molecules. Here we probe phonon excitations using quantum interference in electron transport occurring in short chains of anthraquinone based molecular junctions. By studying the dependence of molecular junction's conductance as a function of bias voltage and temperature, we show that inelastic scattering of electrons by phonons can be detected as features in conductance resulting from quenching of quantum interference. Our results are in agreement with density functional theory calculations and are well described by a generic two-site model in the framework of non-equilibrium Green's functions formalism. The importance of the observed inelastic contribution to the current opens up new ways for exploring coherent electron transport through molecular devices.

  4. 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.

  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. Dynamical image-charge effect in molecular tunnel junctions

    DEFF Research Database (Denmark)

    Jin, Chengjun; Thygesen, Kristian Sommer

    2014-01-01

    When an electron tunnels between two metal contacts it temporarily induces an image charge (IC) in the electrodes which acts back on the tunneling electron. It is usually assumed that the IC forms instantaneously such that a static model for the image potential applies. Here we investigate how th...... 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....

  7. Stretch or contraction induced inversion of rectification in diblock molecular junctions.

    Science.gov (United States)

    Zhang, Guang-Ping; Hu, Gui-Chao; Song, Yang; Xie, Zhen; Wang, Chuan-Kui

    2013-09-01

    Based on ab initio theory and nonequilibrium Green's function method, the effect of stretch or contraction on the rectification in diblock co-oligomer molecular diodes is investigated theoretically. Interestingly, an inversion of rectifying direction induced by stretching or contracting the molecular junctions, which is closely related to the number of the pyrimidinyl-phenyl units, is proposed. The analysis of the molecular projected self-consistent Hamiltonian and the evolution of the frontier molecular orbitals as well as transmission coefficients under external biases gives an inside view of the observed results. It reveals that the asymmetric molecular level shift and asymmetric evolution of orbital wave functions under biases are competitive mechanisms for rectification. The stretching or contracting induced inversion of the rectification is due to the conversion of the dominant mechanism. This work suggests a feasible technique to manipulate the rectification performance in molecular diodes by use of the mechanically controllable method.

  8. Important issues facing model-based approaches to tunneling transport in molecular junctions

    CERN Document Server

    Baldea, Ioan

    2015-01-01

    Extensive studies on thin films indicated a generic cubic current-voltage $I-V$ dependence as a salient feature of charge transport by tunneling. A quick glance at $I-V$ data for molecular junctions suggests a qualitatively similar behavior. This would render model-based studies almost irrelevant, since, whatever the model, its parameters can always be adjusted to fit symmetric (asymmetric) $I-V$ curves characterized by two (three) expansion coefficients. Here, we systematically examine popular models based on tunneling barrier or tight-binding pictures and demonstrate that, for a quantitative description at biases of interest ($V$ slightly higher than the transition voltage $V_t$), cubic expansions do not suffice. A detailed collection of analytical formulae as well as their conditions of applicability are presented to facilitate experimentalists colleagues to process and interpret their experimental data by obtained by measuring currents in molecular junctions. We discuss in detail the limits of applicabili...

  9. Connexin26 regulates assembly and maintenance of cochlear gap junction macromolecular complex for normal hearing

    Science.gov (United States)

    Kamiya, Kazusaku; Fukunaga, Ichiro; Hatakeyama, Kaori; Ikeda, Katsuhisa

    2015-12-01

    Hereditary deafness affects about 1 in 2000 children and GJB2 gene mutation is most frequent cause for this disease in the world. GJB2 encodes connexin26 (Cx26), a component in cochlear gap junction. Recently, we found macromolecular change of gap junction plaques with two different types of Cx26 mutation as major classification of clinical case, one is a model of dominant negative type, Cx26R75W+ and the other is conditional gene deficient mouse, Cx26f/fP0Cre as a model for insufficiency of gap junction protein [6]. Gap junction composed mainly of Cx26 and Cx30 in wild type mice formed large planar gap junction plaques (GJP). In contrast, Cx26R75W+ and Cx26f/fP0Cre showed fragmented small round GJPs around the cell border. In Cx26f/fP0Cre, some of the cells with Cx26 expression due to their cellular mosaicism showed normal large GJP with Cx26 and Cx30 only at the cell junction site between two Cx26 positive cells. These indicate that bilateral Cx26 expressions from both adjacent cells are essential for the formation of the cochlear linear GJP, and it is not compensated by other cochlear Connexins such as Connexin30. In the present study, we demonstrated a new molecular pathology in most common hereditary deafness with different types of Connexin26 mutations, and this machinery can be a new target for drag design of hereditary deafness.

  10. Waiting time distribution for electron transport in a molecular junction with electron-vibration interaction

    Science.gov (United States)

    Kosov, Daniel S.

    2017-02-01

    On the elementary level, electronic current consists of individual electron tunnelling events that are separated by random time intervals. The waiting time distribution is a probability to observe the electron transfer in the detector electrode at time t +τ given that an electron was detected in the same electrode at an earlier time t. We study waiting time distribution for quantum transport in a vibrating molecular junction. By treating the electron-vibration interaction exactly and molecule-electrode coupling perturbatively, we obtain the master equation and compute the distribution of waiting times for electron transport. The details of waiting time distributions are used to elucidate microscopic mechanism of electron transport and the role of electron-vibration interactions. We find that as nonequilibrium develops in the molecular junction, the skewness and dispersion of the waiting time distribution experience stepwise drops with the increase of the electric current. These steps are associated with the excitations of vibrational states by tunnelling electrons. In the strong electron-vibration coupling regime, the dispersion decrease dominates over all other changes in the waiting time distribution as the molecular junction departs far away from the equilibrium.

  11. Impaired astrocytic gap junction coupling and potassium buffering in a mouse model of tuberous sclerosis complex.

    Science.gov (United States)

    Xu, Lin; Zeng, Ling-Hui; Wong, Michael

    2009-05-01

    Abnormalities in astrocytes occur in the brains of patients with Tuberous Sclerosis Complex (TSC) and may contribute to the pathogenesis of neurological dysfunction in this disease. Here, we report that knock-out mice with Tsc1 gene inactivation in glia (Tsc1(GFAP)CKO mice) exhibit decreased expression of the astrocytic connexin protein, Cx43, and an associated impairment in gap junction coupling between astrocytes. Correspondingly, hippocampal slices from Tsc1(GFAP)CKO mice have increased extracellular potassium concentration in response to stimulation. This impaired potassium buffering can be attributed to abnormal gap junction coupling, as a gap junction inhibitor elicits an additional increase in potassium concentration in control, but not Tsc1(GFAP)CKO slices. Furthermore, treatment with a mammalian target of rapamycin inhibitor reverses the deficient Cx43 expression and impaired potassium buffering. These findings suggest that Tsc1 inactivation in astrocytes causes defects in astrocytic gap junction coupling and potassium clearance, which may contribute to epilepsy in Tsc1(GFAP)CKO mice.

  12. Paramagnetic molecule induced strong antiferromagnetic exchange coupling on a magnetic tunnel junction based molecular spintronics device.

    Science.gov (United States)

    Tyagi, Pawan; Baker, Collin; D'Angelo, Christopher

    2015-07-31

    This paper reports our Monte Carlo (MC) studies aiming to explain the experimentally observed paramagnetic molecule induced antiferromagnetic coupling between ferromagnetic (FM) electrodes. Recently developed magnetic tunnel junction based molecular spintronics devices (MTJMSDs) were prepared by chemically bonding the paramagnetic molecules between the FM electrodes along the tunnel junction's perimeter. These MTJMSDs exhibited molecule-induced strong antiferromagnetic coupling. We simulated the 3D atomic model analogous to the MTJMSD and studied the effect of molecule's magnetic couplings with the two FM electrodes. Simulations show that when a molecule established ferromagnetic coupling with one electrode and antiferromagnetic coupling with the other electrode, then theoretical results effectively explained the experimental findings. Our studies suggest that in order to align MTJMSDs' electrodes antiparallel to each other, the exchange coupling strength between a molecule and FM electrodes should be ∼50% of the interatomic exchange coupling for the FM electrodes.

  13. Control of Electronic Symmetry and Rectification through Energy Level Variations in Bilayer Molecular Junctions.

    Science.gov (United States)

    Bayat, Akhtar; Lacroix, Jean-Christophe; McCreery, Richard L

    2016-09-21

    Two layers of molecular oligomers were deposited on flat carbon electrode surfaces by electrochemical reduction of diazonium reagents, then a top contact applied to complete a solid-state molecular junction containing a molecular bilayer. The structures and energy levels of the molecular layers included donor molecules with relatively high energy occupied orbitals and acceptors with low energy unoccupied orbitals. When the energy levels of the two molecular layers were similar, the device had electronic characteristics similar to a thick layer of a single molecule, but if the energy levels differed, the current voltage behavior exhibited pronounced rectification. Higher current was observed when the acceptor molecule was biased negatively in eight different bilayer combinations, and the direction of rectification was reversed if the molecular layers were also reversed. Rectification persisted at very low temperature (7 K), and was activationless between 7 and 100 K. The results are a clear example of a "molecular signature" in which electronic behavior is directly affected by molecular structure and orbital energies. The rectification mechanism is discussed, and may provide a basis for rational design of electronic properties by variation of molecular structure.

  14. An Additive Definition of Molecular Complexity.

    Science.gov (United States)

    Böttcher, Thomas

    2016-03-28

    A framework for molecular complexity is established that is based on information theory and consistent with chemical knowledge. The resulting complexity index Cm is derived from abstracting the information content of a molecule by the degrees of freedom in the microenvironments on a per-atom basis, allowing the molecular complexity to be calculated in a simple and additive way. This index allows the complexity of any molecule to be universally assessed and is sensitive to stereochemistry, heteroatoms, and symmetry. The performance of this complexity index is evaluated and compared against the current state of the art. Its additive character gives consistent values also for very large molecules and supports direct comparisons of chemical reactions. Finally, this approach may provide a useful tool for medicinal chemistry in drug design and lead selection, as demonstrated by correlating molecular complexities of antibiotics with compound-specific parameters.

  15. 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.

  16. Activationless charge transport across 4.5 to 22 nm in molecular electronic junctions.

    Science.gov (United States)

    Yan, Haijun; Bergren, Adam Johan; McCreery, Richard; Della Rocca, Maria Luisa; Martin, Pascal; Lafarge, Philippe; Lacroix, Jean Christophe

    2013-04-01

    In this work, we bridge the gap between short-range tunneling in molecular junctions and activated hopping in bulk organic films, and greatly extend the distance range of charge transport in molecular electronic devices. Three distinct transport mechanisms were observed for 4.5-22-nm-thick oligo(thiophene) layers between carbon contacts, with tunneling operative when d  16 nm for high temperatures and low bias, and a third mechanism consistent with field-induced ionization of highest occupied molecular orbitals or interface states to generate charge carriers when d = 8-22 nm. Transport in the 8-22-nm range is weakly temperature dependent, with a field-dependent activation barrier that becomes negligible at moderate bias. We thus report here a unique, activationless transport mechanism, operative over 8-22-nm distances without involving hopping, which severely limits carrier mobility and device lifetime in organic semiconductors. Charge transport in molecular electronic junctions can thus be effective for transport distances significantly greater than the 1-5 nm associated with quantum-mechanical tunneling.

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

    Science.gov (United States)

    Nozaki, Daijiro; Sevinçli, Hâldun; Avdoshenko, Stanislav M; Gutierrez, Rafael; Cuniberti, Gianaurelio

    2013-09-07

    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 resonant peaks and anti-resonant peaks induced by quantum interference in the conductance spectrum. This parabolic model not only can predict the emergence and energetic position of quantum interference from a few electronic parameters but also can enable one to know the coupling between the side group and the main conduction channel from measurements in the case of orthogonal basis. The results obtained within the parabolic model are validated using density-functional based quantum transport calculations in realistic T-shaped molecular junctions.

  18. Molecular complexes of phenols with DDQ

    Indian Academy of Sciences (India)

    T Vinod Kumar; T Veeraiah; G Venkateshwarlu

    2000-04-01

    Molecular complexes of phenols with DDQ have been studied spectrophotometrically in the temperature range of 10-30°C in a solvent (CHCl3) of low polarity under low donor concentrations. All the complexes exhibit one CT band each in the wavelength region where acceptor and donor do not have any absorption. The complexes are inferred to be of the - type and have y configuration in which the donor molecular orbital encompasses the substituent. The ionization potentials of the donors, the stability constants and thermodynamic parameters of the complexes have been evaluated.

  19. The exon junction complex as a node of post-transcriptional networks.

    Science.gov (United States)

    Le Hir, Hervé; Saulière, Jérôme; Wang, Zhen

    2016-01-01

    The exon junction complex (EJC) is deposited onto mRNAs following splicing and adopts a unique structure, which can both stably bind to mRNAs and function as an anchor for diverse processing factors. Recent findings revealed that in addition to its established roles in nonsense-mediated mRNA decay, the EJC is involved in mRNA splicing, transport and translation. While structural studies have shed light on EJC assembly, transcriptome-wide analyses revealed differential EJC loading at spliced junctions. Thus, the EJC functions as a node of post-transcriptional gene expression networks, the importance of which is being revealed by the discovery of increasing numbers of EJC-related disorders.

  20. The effects of contact configurations on the rectification of dipyrimidinyl-diphenyl diblock molecular junctions

    Institute of Scientific and Technical Information of China (English)

    Zhang Guang-Ping; Hu Gui-Chao; Li Zong-Liang; Wang Chuan-Kui

    2011-01-01

    The transport properties of a conjugated dipyrimidinyl-diphenyl diblock oligomer sandwiched between two gold electrodes,as recently reported by [Díez-Pérez et al.Nature Chem.1 635 (2009)],are theoretically investigated using the fully self-consistent nonequilibrium Green's function method combined with density functional theory.Two kinds of symmetrical anchoring geometries are considered.Calculated current-voltage curves show that the contact structure has a strong effect on the rectification behaviour of the molecular diode.For the equilateral triangle configuration,pronounced rectification behaviour comparable to the experimental measurement is revealed,and the theoretical analysis indicates that the observed rectification characteristic results from the asymmetric shift of the perturbed molecular energy levels under bias voltage.While for the tetrahedron configuration,both rectification and negative differential conductivity behaviours are observed.The calculated results further prove the close dependence of the transporting characteristics of molecular junctions on contact configuration.

  1. Protonation effects on electron transport through diblock molecular junctions:A theoretical study

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Diblock oligomers are widely used in molecular electronics. Based on fully self-consistent nonequilib-rium Green’s function method and density functional theory, we study the electron transport properties of the molecular junction with a dipyrimidinyl-diphenyl (PMPH) diblock molecule sandwiched between two gold electrodes. Effects of different kinds of molecule-electrode anchoring geometry and protona-tion of the PMPH molecule are studied. Protonation leads to both conductance and rectification en-hancements. However, the experimentally observed rectifying direction inversion is not found in our calculation. The preferential current direction is always from the pyrimidinyl to the phenyl side. Our calculations indicate that the protonation of the molecular wire is not the only reason of the rectification inversion.

  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. Photoactive molecular junctions based on self-assembled monolayers of indoline dyes.

    Science.gov (United States)

    Caranzi, Lorenzo; Pace, Giuseppina; Guarnera, Simone; Canesi, Eleonora V; Brambilla, Luigi; Raavi, Sai S K; Petrozza, Annamaria; Caironi, Mario

    2014-11-26

    We demonstrate the feasibility of a photodetector based on an ensemble molecular junction, where a self-assembled monolayer of an organic donor-acceptor dye is directly sandwiched between two electrodes. In such a device, upon photoexcitation and generation of a charge-transfer state on the molecule, charges are dissociated and directly collected at the electrodes without the need of transport through a bulk phase, as in usual photodetectors. We show that the device can work in photovoltaic regime and the spectral response can be tuned by varying the light absorbing dye. Therefore, the electro-optical properties of the downscaled device can be unambiguously related to the physical-chemical properties of the molecules, a commonly difficult point to demonstrate in a molecular junction device, because of the uncertainties of the interplay between molecules and electrodes. The proposed device, which relies on a simple self-assembly process, has a strong potentiality for fast responding, downscaled detectors, ultimately limited by charge dissociation dynamics, and can be considered also as a useful tool to investigate fundamental electro-optical processes in molecular monolayers.

  4. Organic electrodes based on grafted oligothiophene units in ultrathin, large-area molecular junctions.

    Science.gov (United States)

    Martin, Pascal; Della Rocca, Maria Luisa; Anthore, Anne; Lafarge, Philippe; Lacroix, Jean-Christophe

    2012-01-11

    Molecular junctions were fabricated with the combined use of electrochemistry and conventional CMOS tools. They consist of a 5-10 nm thick layer of oligo(1-(2-bisthienyl)benzene) between two gold electrodes. The layer was grafted onto the bottom electrode using diazonium electroreduction, which yields a stable and robust gold-oligomer interface. The top contact was obtained by direct electron-beam evaporation on the molecular layers through masks defined by electron-beam lithography. Transport mechanisms across such easily p-dopable layers were investigated by analysis of current density-voltage (J-V) curves. Application of a tunneling model led to a transport parameter (thickness of ~2.4 nm) that was not consistent with the molecular thickness measured using AFM (~7 nm). Furthermore, for these layers with thicknesses of 5-10 nm, asymmetric J-V curves were observed, with current flowing more easily when the grafted electrode was positively polarized. In addition, J-V experiments at two temperatures (4 and 300 K) showed that thermal activation occurs for such polarization but is not observed when the bias is reversed. These results indicate that simple tunneling cannot describe the charge transport in these junctions. Finally, analysis of the experimental results in term of "organic electrode" and redox chemistry in the material is discussed.

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

    KAUST Repository

    French, William R.

    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.

  6. 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...

  7. A study on electrical contact at the PEDOT:PSS electrode/molecule interface in large-area molecular junctions

    Science.gov (United States)

    Jeong, Inho; Song, Hyunwook

    2017-08-01

    We have investigated the effect of the PEDOT:PSS electrode/molecule contact on the charge transport characteristics of large-area molecular junctions. We incorporated two different benzenethiolate molecules into the molecular junctions: 4-methylbenzenethiol (MBT) and benzene- 1,4-dithiol (BDT). They have an identical backbone structure but different top end-groups. From statistical analysis, we found that the tunneling transport behavior showed a significant difference between the two prototype conjugated molecules, which was attributed to their distinct electrical contacts at the PEDOT:PSS electrode/molecule interface. We also observed an enhancement of the junction conductance at elevated temperatures, which would be caused by the increased grain size of the conducting PEDOT-rich cores and the removal of residual solvents or water in the junctions.

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

    Science.gov (United States)

    Gao, Yi; Galperin, Michael; Nitzan, Abraham

    2016-06-01

    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.

  9. 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...

  10. 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.

  11. 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).

  12. 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.

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

    Science.gov (United States)

    Braun, Kai; Wang, Xiao; Kern, Andreas M; Adler, Hilmar; Peisert, Heiko; Chassé, Thomas; Zhang, Dai; Meixner, Alfred J

    2015-01-01

    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.

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

    Institute of Scientific and Technical Information of China (English)

    ZHAO Peng; LIU De-Sheng; ZHANG Ying; WANG Pei-Ji; ZHANG Zhong

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

  15. Molecular simulation and modeling of complex I.

    Science.gov (United States)

    Hummer, Gerhard; Wikström, Mårten

    2016-07-01

    Molecular modeling and molecular dynamics simulations play an important role in the functional characterization of complex I. With its large size and complicated function, linking quinone reduction to proton pumping across a membrane, complex I poses unique modeling challenges. Nonetheless, simulations have already helped in the identification of possible proton transfer pathways. Simulations have also shed light on the coupling between electron and proton transfer, thus pointing the way in the search for the mechanistic principles underlying the proton pump. In addition to reviewing what has already been achieved in complex I modeling, we aim here to identify pressing issues and to provide guidance for future research to harness the power of modeling in the functional characterization of complex I. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Crystal structure of RuvC resolvase in complex with Holliday junction substrate.

    Science.gov (United States)

    Górecka, Karolina M; Komorowska, Weronika; Nowotny, Marcin

    2013-11-01

    The key intermediate in genetic recombination is the Holliday junction (HJ), a four-way DNA structure. At the end of recombination, HJs are cleaved by specific nucleases called resolvases. In Gram-negative bacteria, this cleavage is performed by RuvC, a dimeric endonuclease that belongs to the retroviral integrase superfamily. Here, we report the first crystal structure of RuvC in complex with a synthetic HJ solved at 3.75 Å resolution. The junction in the complex is in an unfolded 2-fold symmetrical conformation, in which the four arms point toward the vertices of a tetrahedron. The two scissile phosphates are located one nucleotide from the strand exchange point, and RuvC approaches them from the minor groove side. The key protein-DNA contacts observed in the structure were verified using a thiol-based site-specific cross-linking approach. Compared with known complex structures of the phage resolvases endonuclease I and endonuclease VII, the RuvC structure exhibits striking differences in the mode of substrate binding and location of the cleavage site.

  17. Light amplification by stimulated emission from an optically pumped molecular junction in a scanning tunneling microscope

    CERN Document Server

    Braun, K; Wang, X; Adler, H; Peisert, H; Chasse, T; Zhang, D; Meixner, A J

    2013-01-01

    Here, we introduce and experimentally demonstrate optical amplification and stimulated emission from a single optically pumped molecular tunneling junction of a scanning tunneling microscope. The gap between a sharp gold tip and a flat gold substrate covered with a self-assembled monolayer of 5-chloro-2-mercaptobenzothiazole molecules forms an extremely small optical gain medium. When electrons tunnel from the molecules highest occupied molecular orbital to the tip, holes are left behind. These can be repopulated by hot electrons induced by the laser-driven plasmon oscillation on the metal surfaces enclosing the cavity. Solving the laser-rate equations for this system shows that the repopulation process can be efficiently stimulated by the gap modes near field, TERS scattering from neighboring molecules acting as an optical seed. Our results demonstrate how optical enhancement inside the plasmonic cavity can be further increased by a stronger localization via tunneling through molecules. We anticipate that st...

  18. Discriminating single-molecule sensing by crown-ether-based molecular junctions

    Science.gov (United States)

    Ismael, Ali K.; Al-Jobory, Alaa; Grace, Iain; Lambert, Colin J.

    2017-02-01

    Crown-ether molecules are well known to selectively bind alkali atoms, so by incorporating these within wires, any change in electrical conductance of the wire upon binding leads to discriminating sensing. Using a density functional theory-based approach to quantum transport, we investigate the potential sensing capabilities of single-molecule junctions formed from crown ethers attached to anthraquinone units, which are in turn attached to gold electrodes via alkyl chains. We calculate the change in electrical conductance for binding of three different alkali ions (lithium, sodium, and potassium). Depending on the nature of the ionic analyte, the conductance is enhanced by different amounts. This change in electrical conductance is due to charge transfer from the ion to molecular wire causing the molecular resonances to shift closer to the electrode Fermi energy.

  19. Molecular cloud complex associated with ON 1

    Energy Technology Data Exchange (ETDEWEB)

    Israel, F.P.; Wooten, H.A.

    1983-03-15

    Observations of CO with different resolutions near the compact H ii region/maser source ON 1 are presented, as well as new H/sub 2/CO and HCO/sup +/ observations. ON 1 is part of an extended molecular cloud complex with overall dimensions of 25 x 60 pc at a distance of 1.4 kpc; it appears to be the only site of star formation in at least the western part of the complex. ON 1 coincides with a compact and dense molecular cloud core (size 0.8 pc) that shows little sign of disruption indicating that ON 1 has only recently turned on. The isolation and apparent youth of ON 1 suggest that we observe here the very beginning of the star formation phase of a molecular cloud complex.

  20. Charge transport in molecular electronic junctions: compression of the molecular tunnel barrier in the strong coupling regime.

    Science.gov (United States)

    Sayed, Sayed Y; Fereiro, Jerry A; Yan, Haijun; McCreery, Richard L; Bergren, Adam Johan

    2012-07-17

    Molecular junctions are essentially modified electrodes familiar to electrochemists where the electrolyte is replaced by a conducting "contact." It is generally hypothesized that changing molecular structure will alter system energy levels leading to a change in the transport barrier. Here, we show the conductance of seven different aromatic molecules covalently bonded to carbon implies a modest range ( 2 eV range). These results are explained by considering the effect of bonding the molecule to the substrate. Upon bonding, electronic inductive effects modulate the energy levels of the system resulting in compression of the tunneling barrier. Modification of the molecule with donating or withdrawing groups modulate the molecular orbital energies and the contact energy level resulting in a leveling effect that compresses the tunneling barrier into a range much smaller than expected. Whereas the value of the tunneling barrier can be varied by using a different class of molecules (alkanes), using only aromatic structures results in a similar equilibrium value for the tunnel barrier for different structures resulting from partial charge transfer between the molecular layer and the substrate. Thus, the system does not obey the Schottky-Mott limit, and the interaction between the molecular layer and the substrate acts to influence the energy level alignment. These results indicate that the entire system must be considered to determine the impact of a variety of electronic factors that act to determine the tunnel barrier.

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

    Science.gov (United States)

    Nozaki, Daijiro; Avdoshenko, Stanislav M.; Sevinçli, Hâldun; Gutierrez, Rafael; Cuniberti, Gianaurelio

    2013-03-01

    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 of normal resonant peaks and anti-resonant peaks induced by quantum interference in the conductance spectrum. We also demonstrate Fano and anti-resonance in T-shaped molecular junctions using a simple tight-binding model. This parabolic model enables one to infer on-site energies of T-shaped molecules and the coupling between side group and main conduction channel from transmission spectra.

  2. Molecular rectification and conductance switching in carbon-based molecular junctions by structural rearrangement accompanying electron injection.

    Science.gov (United States)

    McCreery, Richard; Dieringer, Jon; Solak, Ali Osman; Snyder, Brian; Nowak, Aletha M; McGovern, William R; DuVall, Stacy

    2003-09-01

    Molecular junctions were fabricated consisting of a 3.7 nm thick layer of nitroazobenzene (NAB) molecules between a pyrolyzed photoresist substrate (PPF) and a titanium top contact which was protected from oxidation by a layer of gold. Raman spectroscopy, XPS, and AFM revealed that the NAB layer was 2-3 molecules thick and was bonded to the two conducting contacts by C-C and N-Ti covalent bonds. The current/voltage behavior of the PPF/NAB(3.7)/Ti junctions showed strong and reproducible rectification, with the current at +2 V exceeding that at -2 V by a factor of 600. The observed current density at +3 V was 0.71 A/cm(2), or about 10(5) e(-)/s/molecule. The i/V response was strongly dependent on temperature and scan rate, with the rectification ratio decreasing for lower temperature and faster scans. Junction conductivity increased with time over several seconds at room temperature in response to positive voltage pulses, with the rate of increase larger for more positive potentials. Voltage pulses to positive potentials and back to zero volts revealed that electrons are injected from the Ti to the NAB, to the extent of about 0.1-1 e(-)/molecule for a +3 V pulse. These electrons cause an activated transition of the NAB into a more conductive quinoid state, which in turn causes an increase in conductivity. The transition to the quinoid state involves nuclear rearrangement which occurs on a submillisecond to several second time scale, depending on the voltage applied. The quinoid state is stable as long as the applied electric field is present, but reverts back to NAB within several minutes after the field is relaxed. The results are interpreted in terms of a thermally activated, potential dependent electron transfer into the 3.7 nm NAB layer, which brings about a conductivity increase of several orders of magnitude.

  3. 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

    In higher eukaryotes, a multiprotein exon junction complex is deposited on spliced messenger RNAs. The complex is organized around a stable core, which serves as a binding platform for numerous factors that influence messenger RNA function. Here, we present the crystal structure of a tetrameric e...

  4. Do Haptic Representations Help Complex Molecular Learning?

    Science.gov (United States)

    Bivall, Petter; Ainsworth, Shaaron; Tibell, Lena A. E.

    2011-01-01

    This study explored whether adding a haptic interface (that provides users with somatosensory information about virtual objects by force and tactile feedback) to a three-dimensional (3D) chemical model enhanced students' understanding of complex molecular interactions. Two modes of the model were compared in a between-groups pre- and posttest…

  5. Selective permeability of gap junction channels.

    Science.gov (United States)

    Goldberg, Gary S; Valiunas, Virginijus; Brink, Peter R

    2004-03-23

    Gap junctions mediate the transfer of small cytoplasmic molecules between adjacent cells. A family of gap junction proteins exist that form channels with unique properties, and differ in their ability to mediate the transfer of specific molecules. Mutations in a number of individual gap junction proteins, called connexins, cause specific human diseases. Therefore, it is important to understand how gap junctions selectively move molecules between cells. Rules that dictate the ability of a molecule to travel through gap junction channels are complex. In addition to molecular weight and size, the ability of a solute to transverse these channels depends on its net charge, shape, and interactions with specific connexins that constitute gap junctions in particular cells. This review presents some data and interpretations pertaining to mechanisms that govern the differential transfer of signals through gap junction channels.

  6. Unraveling the electrical conduction of C-40 quasi-fullerene molecular junction

    Science.gov (United States)

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

    2016-07-01

    In this paper, we present the state of art theoretical calculations of charge transport through quasi-fullerene molecule C40 coupled rigidly between two 3D gold electrodes by applying different electro-chemical potentials. The methodology we adopted has been based on density functional theory approach combined with Keldysh’s non-equilibrium Green’s function (NEGF) framework suggested for mesoscopic systems. The results exhibited by this molecular junction confirmed it to be highly metallic and showed prominent conduction of the order of twice of the quantum conductance, i.e., 2*G0 at zero bias. Our results are consistent with theoretical predictions in ab initiocalculations with some variants of quasi-fullerenes.

  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. 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.

  9. 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.

  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. Inelastic Tunneling Spectroscopy of Gold-Thiol and Gold-Thiolate Interfaces in Molecular Junctions: The Role of Hydrogen

    CERN Document Server

    Demir, Firuz

    2012-01-01

    It is widely believed that when a molecule with thiol (S-H) end groups bridges a pair of gold electrodes, the S atoms bond to the gold and the thiol H atoms detach from the molecule. However, little is known regarding the details of this process, its time scale, and whether molecules with and without thiol hydrogen atoms can coexist in molecular junctions. Here we explore theoretically how inelastic tunneling spectroscopy (IETS) can shed light on these issues. We present calculations of the geometries, low bias conductances and IETS of propanedithiol and propanedithiolate molecular junctions with gold electrodes. We show that IETS can distinguish between junctions with molecules having no, one or two thiol hydrogen atoms. We find that in most cases the single-molecule junctions in the IETS experiment of Hihath et al. [Nano Lett. 8, 1673 (2008)] had no thiol H atoms, but that a molecule with a single thiol H atom may have bridged their junction occasionally. We also consider the evolution of the IETS spectrum ...

  12. Two Distinct MUS81-EME1 Complexes from Arabidopsis Process Holliday Junctions1[W

    Science.gov (United States)

    Geuting, Verena; Kobbe, Daniela; Hartung, Frank; Dürr, Jasmin; Focke, Manfred; Puchta, Holger

    2009-01-01

    The MUS81 endonuclease complex has been shown to play an important role in the repair of stalled or blocked replication forks and in the processing of meiotic recombination intermediates from yeast to humans. This endonuclease is composed of two subunits, MUS81 and EME1. Surprisingly, unlike other organisms, Arabidopsis (Arabidopsis thaliana) has two EME1 homologs encoded in its genome. AtEME1A and AtEME1B show 63% identity on the protein level. We were able to demonstrate that, after expression in Escherichia coli, each EME1 protein can assemble with the unique AtMUS81 to form a functional endonuclease. Both complexes, AtMUS81-AtEME1A and AtMUS81-AtEME1B, are not only able to cleave 3′-flap structures and nicked Holliday junctions (HJs) but also, with reduced efficiency, intact HJs. While the complexes have the same cleavage patterns with both nicked DNA substrates, slight differences in the processing of intact HJs can be detected. Our results are in line with an involvement of both MUS81-EME1 endonuclease complexes in DNA recombination and repair processes in Arabidopsis. PMID:19339504

  13. Two distinct MUS81-EME1 complexes from Arabidopsis process Holliday junctions.

    Science.gov (United States)

    Geuting, Verena; Kobbe, Daniela; Hartung, Frank; Dürr, Jasmin; Focke, Manfred; Puchta, Holger

    2009-06-01

    The MUS81 endonuclease complex has been shown to play an important role in the repair of stalled or blocked replication forks and in the processing of meiotic recombination intermediates from yeast to humans. This endonuclease is composed of two subunits, MUS81 and EME1. Surprisingly, unlike other organisms, Arabidopsis (Arabidopsis thaliana) has two EME1 homologs encoded in its genome. AtEME1A and AtEME1B show 63% identity on the protein level. We were able to demonstrate that, after expression in Escherichia coli, each EME1 protein can assemble with the unique AtMUS81 to form a functional endonuclease. Both complexes, AtMUS81-AtEME1A and AtMUS81-AtEME1B, are not only able to cleave 3'-flap structures and nicked Holliday junctions (HJs) but also, with reduced efficiency, intact HJs. While the complexes have the same cleavage patterns with both nicked DNA substrates, slight differences in the processing of intact HJs can be detected. Our results are in line with an involvement of both MUS81-EME1 endonuclease complexes in DNA recombination and repair processes in Arabidopsis.

  14. Protein tyrosine phosphatase σ targets apical junction complex proteins in the intestine and regulates epithelial permeability.

    Science.gov (United States)

    Murchie, Ryan; Guo, Cong-Hui; Persaud, Avinash; Muise, Aleixo; Rotin, Daniela

    2014-01-14

    Protein tyrosine phosphatase (PTP)σ (PTPRS) was shown previously to be associated with susceptibility to inflammatory bowel disease (IBD). PTPσ(-/-) mice exhibit an IBD-like phenotype in the intestine and show increased susceptibility to acute models of murine colitis. However, the function of PTPσ in the intestine is uncharacterized. Here, we show an intestinal epithelial barrier defect in the PTPσ(-/-) mouse, demonstrated by a decrease in transepithelial resistance and a leaky intestinal epithelium that was determined by in vivo tracer analysis. Increased tyrosine phosphorylation was observed at the plasma membrane of epithelial cells lining the crypts of the small bowel and colon of the PTPσ(-/-) mouse, suggesting the presence of PTPσ substrates in these regions. Using mass spectrometry, we identified several putative PTPσ intestinal substrates that were hyper-tyrosine-phosphorylated in the PTPσ(-/-) mice relative to wild type. Among these were proteins that form or regulate the apical junction complex, including ezrin. We show that ezrin binds to and is dephosphorylated by PTPσ in vitro, suggesting it is a direct PTPσ substrate, and identified ezrin-Y353/Y145 as important sites targeted by PTPσ. Moreover, subcellular localization of the ezrin phosphomimetic Y353E or Y145 mutants were disrupted in colonic Caco-2 cells, similar to ezrin mislocalization in the colon of PTPσ(-/-) mice following induction of colitis. Our results suggest that PTPσ is a positive regulator of intestinal epithelial barrier, which mediates its effects by modulating epithelial cell adhesion through targeting of apical junction complex-associated proteins (including ezrin), a process impaired in IBD.

  15. Cluster-formation in the Rosette molecular cloud at the junctions of filaments

    CERN Document Server

    Schneider, N; Hennemann, M; Motte, F; Didelon, P; Federrath, C; Bontemps, S; Di Francesco, J; Arzoumanian, D; Minier, V; André, Ph; Hill, T; Zavagno, A; Nguyen-Luong, Q; Attard, M; Bernard, J -Ph; Elia, D; Fallscheer, C; Griffin, M; Kirk, J; Klessen, R; Könyves, V; Martin, P; Men'shchikov, A; Palmeirim, P; Peretto, N; Pestalozzi, M; Russeil, D; Sadavoy, S; Sousbie, T; Testi, L; Tremblin, P; Ward-Thompson, D; White, G

    2012-01-01

    For many years feedback processes generated by OB-stars in molecular clouds, including expanding ionization fronts, stellar winds, or UV-radiation, have been proposed to trigger subsequent star formation. However, hydrodynamic models including radiation and gravity show that UV-illumination has little or no impact on the global dynamical evolution of the cloud. The Rosette molecular cloud, irradiated by the NGC2244 cluster, is a template region for triggered star-formation, and we investigated its spatial and density structure by applying a curvelet analysis, a filament-tracing algorithm (DisPerSE), and probability density functions (PDFs) on Herschel column density maps, obtained within the HOBYS key program. The analysis reveals not only the filamentary structure of the cloud but also that all known infrared clusters except one lie at junctions of filaments, as predicted by turbulence simulations. The PDFs of sub-regions in the cloud show systematic differences. The two UV-exposed regions have a double-peak...

  16. Complex wireframe DNA origami nanostructures with multi-arm junction vertices.

    Science.gov (United States)

    Zhang, Fei; Jiang, Shuoxing; Wu, Siyu; Li, Yulin; Mao, Chengde; Liu, Yan; Yan, Hao

    2015-09-01

    Structural DNA nanotechnology and the DNA origami technique, in particular, have provided a range of spatially addressable two- and three-dimensional nanostructures. These structures are, however, typically formed of tightly packed parallel helices. The development of wireframe structures should allow the creation of novel designs with unique functionalities, but engineering complex wireframe architectures with arbitrarily designed connections between selected vertices in three-dimensional space remains a challenge. Here, we report a design strategy for fabricating finite-size wireframe DNA nanostructures with high complexity and programmability. In our approach, the vertices are represented by n × 4 multi-arm junctions (n = 2-10) with controlled angles, and the lines are represented by antiparallel DNA crossover tiles of variable lengths. Scaffold strands are used to integrate the vertices and lines into fully assembled structures displaying intricate architectures. To demonstrate the versatility of the technique, a series of two-dimensional designs including quasi-crystalline patterns and curvilinear arrays or variable curvatures, and three-dimensional designs including a complex snub cube and a reconfigurable Archimedean solid were constructed.

  17. The endogenous Mus81-Eme1 complex resolves Holliday junctions by a nick and counternick mechanism.

    Science.gov (United States)

    Gaillard, Pierre-Henri L; Noguchi, Eishi; Shanahan, Paul; Russell, Paul

    2003-09-01

    Functional studies strongly suggest that the Mus81-Eme1 complex resolves Holliday junctions (HJs) in fission yeast, but in vitro it preferentially cleaves flexible three-way branched structures that model replication forks or 3' flaps. Here we report that a nicked HJ is the preferred substrate of endogenous and recombinant Mus81-Eme1. Cleavage occurs specifically on the strand that opposes the nick, resulting in resolution of the structure into linear duplex products. Resolving cuts made by the endogenous Mus81-Eme1 complex on an intact HJ are quasi-simultaneous, indicating that Mus81-Eme1 resolves HJs by a nick and counternick mechanism, with a large rate enhancement of the second cut arising from the flexible nature of the nicked HJ intermediate. Recombinant Mus81-Eme1 is ineffective at making the first cut. We also report that HJs accumulate in a DNA polymerase alpha mutant that lacks Mus81, providing further evidence that the Mus81-Eme1 complex targets HJs in vivo.

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

    Science.gov (United States)

    Zobač, Vladmír; Lewis, James P.; Jelínek, Pavel

    2016-07-01

    We report non-adiabatic molecular dynamic simulations of the ring opening reaction of diarylethene (DAE) derivative molecules, both free standing and embedded between gold electrodes. Simulations are performed by the surface hopping method employing density functional theory. Typically, the free-standing molecules exhibit large quantum yields to open and close; however the process is quenched for the molecules embedded between electrodes. Our simulations reveal the importance of the DAE side chemical groups, which explain the efficiency of the quenching process. Namely, delocalization of the LUMO state contributes to electronic coupling between the molecule and electrodes, suppressing or enhancing the reaction process. The simulations indicate that a proper choice of the chemical side group, which provides the strong localization of the LUMO state, can substantially diminish the quenching mechanism. Additionally, we analyze a strong dependency of the quantum yield of the opening reaction coming from the mechanical strength of the molecules.

  19. 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.

  20. Implications and applications of current-induced dynamics in molecular junctions.

    Science.gov (United States)

    Jorn, Ryan; Seideman, Tamar

    2010-09-21

    Instances of strongly nonadiabatic electronic-vibrational energy transfer have been studied since the early days of quantum mechanics and remain a topic of fundamental interest. Often such transfers are associated with electronic resonances, temporary states where transient localization of charge on the molecule provides a mechanism for channeling electronic energy into vibrational excitation. Extensively studied in the gas phase, electron resonance scattering also occurs with surface adsorbed molecules, where it manifests itself in broadened cross sections and desorption of adsorbates from metal surfaces. In this Account, we focus on a related topic: the implications of nonadiabatic, resonance-mediated scattering to the exciting field of molecular electronics. In this context, researchers can induce directed nuclear dynamics and control these processes in single molecules in contact with metallic and semiconducting electrodes. We discuss a variety of consequences and applications of current-driven nuclear excitation in molecular devices, ranging from the design of new forms of molecular machines to surface chemistry at the single-molecule level and atom-resolved lithography. We highlight two specific examples of molecular nanomachines. In the first, a Au-C(60)-Au transistor, the current induces the oscillatory motion of the center-of-mass coordinate of the C(60). The second, a zwitterion-based rattle, demonstrates excitation of intramolecular motion as the positively charged moiety is threaded back and forth through the negatively charged carbon ring. Finally, we discuss the current-induced desorption of organic molecules from Si(100) both to suggest the potential for controlled surface nanochemistry and to develop guidelines for the design of stable molecular junctions. Modeling the exchange of energy between tunneling electrons and the vibrational degrees of freedom of a target molecule subject to bias voltage, open boundary conditions in the electronic subspace

  1. Quantitative Interpretation of the Low-Bias Conductance of Au-Mesitylene-Au Molecular Junctions Formed from Mesitylene Monolayers.

    Science.gov (United States)

    Wang, Hao; Jiang, Zhuoling; Wang, Yongfeng; Sanvito, Stefano; Hou, Shimin

    2016-07-18

    The atomic structure and electronic transport properties of Au-mesitylene-Au molecular junctions formed from a mesitylene monolayer without any anchoring groups are investigated by employing the non-equilibrium Green's function formalism combined with density functional theory. The intermolecular and adsorbate-substrate interactions are described by the non-local optB88 van der Waals functional. Two types of Au-mesitylene-Au molecular junctions are constructed, in which either an isolated mesitylene molecule or a mesitylene molecule embedded into a monolayer lying flat on one electrode surface is in contact with an atomic protrusion of the other electrode surface. The calculated low-bias conductance values of these two junctions are both in quantitative agreement with the reported experimental values [S. Afsari, Z. Li, and E. Borguet, Angew. Chem. Int. Ed. 2014, 53, 9771; Angew. Chem. 2014, 126, 9929]. This indicates that the measured conductance is intrinsic at the single-molecule Au-mesitylene-Au junction and that the intermolecular interactions in the mesitylene monolayer have little effect.

  2. Magnetotransport in MgO-based magnetic tunnel junctions grown by molecular beam epitaxy (invited)

    Energy Technology Data Exchange (ETDEWEB)

    Andrieu, S., E-mail: stephane.andrieu@univ-lorraine.fr; Bonell, F.; Hauet, T.; Montaigne, F. [Institut Jean Lamour, Nancy University/CNRS, Bd des Aiguillettes, BP239, 54506 Vandoeuvre-lès-Nancy (France); Calmels, L.; Snoeck, E. [CEMES, CNRS and Toulouse University, 29 rue Jeanne Marvig, 31055 Toulouse (France); Lefevre, P.; Bertran, F. [Synchrotron SOLEIL-CNRS, L' Orme des Merisiers, Saint-Aubin, BP48, 91192 Gif-sur-Yvette cedex (France)

    2014-05-07

    The strong impact of molecular beam epitaxy growth and Synchrotron Radiation characterization tools in the understanding of fundamental issues in nanomagnetism and spintronics is illustrated through the example of fully epitaxial MgO-based Magnetic Tunnel Junctions (MTJs). If ab initio calculations predict very high tunnel magnetoresistance (TMR) in such devices, some discrepancy between theory and experiments still exists. The influence of imperfections in real systems has thus to be considered like surface contaminations, structural defects, unexpected electronic states, etc. The influence of possible oxygen contamination at the Fe/MgO(001) interface is thus studied, and is shown to be not so detrimental to TMR as predicted by ab initio calculations. On the contrary, the decrease of dislocations density in the MgO barrier of MTJs using Fe{sub 1−x}V{sub x} electrodes is shown to significantly increase TMR. Finally, unexpected transport properties in Fe{sub 1−X}Co{sub x}/MgO/Fe{sub 1−X}Co{sub x} (001) are presented. With the help of spin and symmetry resolved photoemission and ab initio calculation, the TMR decrease for Co content higher than 25% is shown to come from the existence of an interface state and the shift of the empty Δ1 minority spin state towards the Fermi level.

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

    Science.gov (United States)

    Tang, Gaomin; Yu, Zhizhou; Wang, Jian

    2017-08-01

    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.

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

    Science.gov (United States)

    Yao, Wen-Jun; Cao, Bing-Yang

    2015-05-01

    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. Supported by the National Natural Science Foundation of China under Grant Nos. 51322603, 51136001, 51356001, Science Fund for Creative Research Groups (No. 51321002), the Program for New Century Excellent Talents in University, Tsinghua University Initiative Scientific Research Program, the Tsinghua National Laboratory for Information Science and Technology of China

  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. Gap junctions.

    Science.gov (United States)

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

    2012-07-01

    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 2:1853-1872, 2012.

  7. Disrupted Junctional Membrane Complexes and Hyperactive Ryanodine Receptors Following Acute Junctophilin Knockdown in Mice

    Science.gov (United States)

    van Oort, Ralph J.; Garbino, Alejandro; Wang, Wei; Dixit, Sayali S.; Landstrom, Andrew P.; Gaur, Namit; De Almeida, Angela C.; Skapura, Darlene G.; Rudy, Yoram; Burns, Alan R.; Ackerman, Michael J.; Wehrens, Xander H.T.

    2011-01-01

    Background Excitation-contraction coupling in striated muscle requires proper communication of plasmalemmal voltage-activated Ca2+ channels and Ca2+ release channels on sarcoplasmic reticulum (SR) within junctional membrane complexes (JMCs). Whereas previous studies revealed a loss of JMCs and embryonic lethality in germ-line junctophilin-2 (JPH2) knockout mice, it has remained unclear whether JPH2 plays an essential role in JMC formation and the Ca2+-induced Ca2+ release process in the heart. Our recent work demonstrated loss-of-function mutations in JPH2 in patients with hypertrophic cardiomyopathy. Methods and Results To elucidate the role of JPH2 in the heart, we developed a novel approach to conditionally reduce JPH2 protein levels using RNA interference. Cardiac-specific JPH2 knockdown resulted in impaired cardiac contractility, which caused heart failure and increased mortality. JPH2 deficiency resulted in loss of excitation-contraction coupling gain, precipitated by a reduction in the number of JMCs and increased variability in the plasmalemma-SR distance. Conclusions Loss of JPH2 had profound effects on Ca2+ release channel inactivation, suggesting a novel functional role for JPH2 in regulating intracellular Ca2+ release channels in cardiac myocytes. Thus, our novel approach of cardiac-specific shRNA-mediated knockdown of junctophilin-2 has uncovered a critical role for junctophilin in intracellular Ca2+ release in the heart. PMID:21339484

  8. 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.

  9. Inelastic tunneling spectroscopy of gold-thiol and gold-thiolate interfaces in molecular junctions: the role of hydrogen.

    Science.gov (United States)

    Demir, Firuz; Kirczenow, George

    2012-09-07

    It is widely believed that when a molecule with thiol (S-H) end groups bridges a pair of gold electrodes, the S atoms bond to the gold and the thiol H atoms detach from the molecule. However, little is known regarding the details of this process, its time scale, and whether molecules with and without thiol hydrogen atoms can coexist in molecular junctions. Here, we explore theoretically how inelastic tunneling spectroscopy (IETS) can shed light on these issues. We present calculations of the geometries, low bias conductances, and IETS of propanedithiol and propanedithiolate molecular junctions with gold electrodes. We show that IETS can distinguish between junctions with molecules having no, one, or two thiol hydrogen atoms. We find that in most cases, the single-molecule junctions in the IETS experiment of Hihath et al. [Nano Lett. 8, 1673 (2008)] had no thiol H atoms, but that a molecule with a single thiol H atom may have bridged their junction occasionally. We also consider the evolution of the IETS spectrum as a gold STM tip approaches the intact S-H group at the end of a molecule bound at its other end to a second electrode. We predict the frequency of a vibrational mode of the thiol H atom to increase by a factor ~2 as the gap between the tip and molecule narrows. Therefore, IETS should be able to track the approach of the tip towards the thiol group of the molecule and detect the detachment of the thiol H atom from the molecule when it occurs.

  10. Complex sarcolemmal invaginations mimicking myotendinous junctions in a case of Laing early-onset distal myopathy.

    Science.gov (United States)

    Reis, Gerald F; de la Motte, Grant; Gooding, Rebecca; Laing, Nigel G; Margeta, Marta

    2015-12-01

    Distal myopathies are a group of clinically and pathologically overlapping muscle diseases that are genetically complex and can represent a diagnostic challenge. Laing early-onset distal myopathy (MPD1) is a form of distal myopathy caused by mutations in the MYH7 gene, which encodes the beta myosin heavy chain protein expressed in type 1 skeletal muscle fibers and cardiac myocytes. Here, we present a case of genetically confirmed MPD1 with a typical clinical presentation but distinctive light microscopic and ultrastructural findings on muscle biopsy. A 39-year-old professional male cellist presented with a bilateral foot drop that developed by age 8; analysis of the family pedigree showed an autosomal dominant pattern of inheritance. The physical exam demonstrated bilateral weakness of ankle dorsiflexors, toe extensors and finger extensors; creatine kinase level was normal. Biopsy of the quadriceps femoris muscle showed predominance and hypotrophy of type 1 fibers, hybrid fibers with co-expression of slow and fast myosin proteins (both in highly atrophic and normal size range), moth-eaten fibers and mini-cores, lack of rimmed vacuoles and rare desmin-positive eosinophilic sarcoplasmic inclusions. In addition to these abnormalities often observed in MPD1, the biopsy demonstrated frequent clefted fibers with complex sarcolemmal invaginations; on ultrastructural examination, these structures closely mimicked myotendinous junctions but were present away from the tendon and were almost exclusively found in type 1 fibers. Sequencing analysis of the MYH7 gene in the index patient and other affected family members demonstrated a previously described heterozygous c.4522_4524delGAG (p.Glu1508del) mutation. This case widens the pathologic spectrum of MPD1 and highlights the pathologic and clinical variability that can accompany the same genetic mutation, suggesting a significant role for modifier genes in MPD1 pathogenesis. © 2015 Japanese Society of Neuropathology.

  11. Experimental and Theoretical Analysis of Nanotransport in Oligophenylene Dithiol Junctions as a Function of Molecular Length and Contact Work Function.

    Science.gov (United States)

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

    2015-08-25

    We report the results of an extensive investigation of metal-molecule-metal tunnel junctions based on oligophenylene dithiols (OPDs) bound to several types of electrodes (M1-S-(C6H4)n-S-M2, with 1 ≤ n ≤ 4 and M1,2 = Ag, Au, Pt) to examine the impact of molecular length (n) and metal work function (Φ) on junction properties. Our investigation includes (1) measurements by scanning Kelvin probe microscopy of electrode work function changes (ΔΦ = ΦSAM - Φ) caused by chemisorption of OPD self-assembled monolayers (SAMs), (2) measurements of junction current-voltage (I-V) characteristics by conducting probe atomic force microscopy in the linear and nonlinear bias ranges, and (3) direct quantitative analysis of the full I-V curves. Further, we employ transition voltage spectroscopy (TVS) to estimate the energetic alignment εh = EF - EHOMO of the dominant molecular orbital (HOMO) relative to the Fermi energy EF of the junction. Where photoelectron spectroscopy data are available, the εh values agree very well with those determined by TVS. Using a single-level model, which we justify via ab initio quantum chemical calculations at post-density functional theory level and additional UV-visible absorption measurements, we are able to quantitatively reproduce the I-V measurements in the whole bias range investigated (∼1.0-1.5 V) and to understand the behavior of εh and Γ (contact coupling strength) extracted from experiment. We find that Fermi level pinning induced by the strong dipole of the metal-S bond causes a significant shift of the HOMO energy of an adsorbed molecule, resulting in εh exhibiting a weak dependence with the work function Φ. Both of these parameters play a key role in determining the tunneling attenuation factor (β) and junction resistance (R). Correlation among Φ, ΔΦ, R, transition voltage (Vt), and εh and accurate simulation provide a remarkably complete picture of tunneling transport in these prototypical molecular junctions.

  12. Evolution and cell physiology. 4. Why invent yet another protein complex to build junctions in epithelial cells?

    Science.gov (United States)

    Le Bivic, André

    2013-12-15

    The formation of the first epithelium was an essential step for animal evolution, since it has allowed coordination of the behavior of a cell layer and creation of a selective barrier between the internal medium and the outside world. The possibility of coupling the cells in a single layer has allowed morphogenetic events, such as tube formation, or gastrulation, to form more complex animal morphologies. The invention of sealed junctions between cells has allowed, on the other hand, creation of an asymmetry of nutrients or salts between the apical and the basal side of the epithelial layer. Creation of an internal medium has led to homeostasis, allowing the evolution of more complex physiological functions and the emergence of sophisticated animal shapes. During evolution, the origins of the first animals coincided with the invention of several protein complexes, including true cadherins and the polarity protein complexes. How these complexes regulate formation of the apicolateral border and the adherens junctions is still not fully understood. This review focuses on the role of these apical polarity complexes and, in particular, the Crumbs complex, which is essential for proper organization of epithelial layers from Drosophila to humans.

  13. 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

    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...... of normal resonant peaks and anti-resonant peaks induced by quantum interference in the conductance spectrum. We also demonstrate Fano and anti-resonance in T-shaped molecular junctions using a simple tight-binding model. This parabolic model enables one to infer on-site energies of T-shaped molecules...

  14. Electrical conductivity of single molecular junctions assembled from Co- and Co3C-encapsulating carbon nanocapsules.

    Science.gov (United States)

    Matsuura, Daisuke; Kizuka, Tokushi

    2014-03-01

    Single molecular junctions (SMJs) were assembled from cobalt (Co)- and Co carbide (Co3C)-encapsulating carbon nanocapsules (CNCs) and two gold electrodes inside a high-resolution transmission electron microscope equipped with a specimen-piezomanipulation system. The structure and electrical transport properties of the SMJs were investigated in situ. The current density depended on the perimeter of the contact area between CNCs and the electrodes, showing that the current flowed not through the encapsulated region but rather along the graphene layers of CNCs. It was demonstrated that the properties of graphene can be applied to nanodevices using CNCs irrespective of the encapsulating materials.

  15. Comparison of DC and AC Transport in 1.5-7.5 nm Oligophenylene Imine Molecular Wires across Two Junction Platforms: Eutectic Ga-In versus Conducting Probe Atomic Force Microscope Junctions.

    Science.gov (United States)

    Sangeeth, C S Suchand; Demissie, Abel T; Yuan, Li; Wang, Tao; Frisbie, C Daniel; Nijhuis, Christian A

    2016-06-15

    We have utilized DC and AC transport measurements to measure the resistance and capacitance of thin films of conjugated oligophenyleneimine (OPI) molecules ranging from 1.5 to 7.5 nm in length. These films were synthesized on Au surfaces utilizing the imine condensation chemistry between terephthalaldehyde and 1,4-benzenediamine. Near edge X-ray absorption fine structure (NEXAFS) spectroscopy yielded molecular tilt angles of 33-43°. To probe DC and AC transport, we employed Au-S-OPI//GaOx/EGaIn junctions having contact areas of 9.6 × 10(2) μm(2) (10(9) nm(2)) and compared to previously reported DC results on the same OPI system obtained using Au-S-OPI//Au conducting probe atomic force microscopy (CP-AFM) junctions with 50 nm(2) areas. We found that intensive observables agreed very well across the two junction platforms. Specifically, the EGaIn-based junctions showed: (i) a crossover from tunneling to hopping transport at molecular lengths near 4 nm; (ii) activated transport for wires >4 nm in length with an activation energy of 0.245 ± 0.008 eV for OPI-7; (iii) exponential dependence of conductance with molecular length with a decay constant β = 2.84 ± 0.18 nm(-1) (DC) and 2.92 ± 0.13 nm(-1) (AC) in the tunneling regime, and an apparent β = 1.01 ± 0.08 nm(-1) (DC) and 0.99 ± 0.11 nm(-1) (AC) in the hopping regime; (iv) previously unreported dielectric constant of 4.3 ± 0.2 along the OPI wires. However, the absolute resistances of Au-S-OPI//GaOx/EGaIn junctions were approximately 100 times higher than the corresponding CP-AFM junctions due to differences in metal-molecule contact resistances between the two platforms.

  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. Molecular base of biochemical complex I deficiency.

    NARCIS (Netherlands)

    Hoefs, S.J.G.; Rodenburg, R.J.T.; Smeitink, J.A.M.; Heuvel, L.P.W.J. van den

    2012-01-01

    The oxidative phosphorylation (OXPHOS) system, consisting of five enzyme complexes (I-V) together with 2 electron carriers, has an important role in the energy metabolism of the cell. With 45 subunits, complex I is the first and largest complex of the respiratory chain. It is under bigenomic control

  18. Dual Interaction of JAM-C with JAM-B and αMβ2 Integrin: Function in Junctional Complexes and Leukocyte AdhesionD⃞

    OpenAIRE

    Lamagna, Chrystelle; Meda, Paolo; Mandicourt, Guillaume; Brown, James; Gilbert, Robert J C; Jones, E Yvonne; Kiefer, Friedemann; Ruga, Pilar; Imhof, Beat A.; Aurrand-Lions, Michel

    2005-01-01

    The junctional adhesion molecules (JAMs) have been recently described as interendothelial junctional molecules and as integrin ligands. Here we show that JAM-B and JAM-C undergo heterophilic interaction in cell-cell contacts and that JAM-C is recruited and stabilized in junctional complexes by JAM-B. In addition, soluble JAM-B dissociates soluble JAM-C homodimers to form JAM-B/JAM-C heterodimers. This suggests that the affinity of JAM-C monomers to form dimers is higher for JAM-B than for JAM...

  19. Self-assembled molecular p/n junctions for applications in dye-sensitized solar energy conversion.

    Science.gov (United States)

    Farnum, Byron H; Wee, Kyung-Ryang; Meyer, Thomas J

    2016-09-01

    The achievement of long-lived photoinduced redox separation lifetimes has long been a central goal of molecular-based solar energy conversion strategies. The longer the redox-separation lifetime, the more time available for useful work to be extracted from the absorbed photon energy. Here we describe a novel strategy for dye-sensitized solar energy applications in which redox-separated lifetimes on the order of milliseconds to seconds can be achieved based on a simple toolkit of molecular components. Specifically, molecular chromophores (C), electron acceptors (A) and electron donors (D) were self-assembled on the surfaces of mesoporous, transparent conducting indium tin oxide nanoparticle (nanoITO) electrodes to prepare both photoanode (nanoITO|-A-C-D) and photocathode (nanoITO|-D-C-A) assemblies. Nanosecond transient-absorption and steady-state photolysis measurements show that the electrodes function microscopically as molecular analogues of semiconductor p/n junctions. These results point to a new chemical strategy for dye-sensitized solar energy conversion based on molecular excited states and electron acceptors/donors on the surfaces of transparent conducting oxide nanoparticle electrodes.

  20. 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.

  1. First principles investigations of electronic structure and transport properties of graphitic structures and single molecular junctions

    Science.gov (United States)

    Owens, Jonathan R.

    properties of the IV curves of single molecule nano-junctions. Specifically, these systems consist of a zinc-porphyrin molecule coupled between two gold electrodes, i.e., a nano-gap. The first observation we want to explain is the asymmetric nature of the experimental IV curve for this porphyrin system, where the IV curve is skewed heavily to the negative bias region. Using a plane-wave DFT calculation, we present the density of states of the porphyrin molecule (both in the presence and absence of the electrodes) and indeed see highly delocalized states (as confirmed by site-projection of the DOS) only in the negative bias region, meaning that the channels with high transmission probability reside there, in agreement with experimental observation. The next problem studied pertains to observed switching in an experimentally-measured IV curve, this time of a longer zinc porphyrin molecule, still within a gold nano-gap. The switching behavior is observed only at 300K, not at 4.2K. The temperature-dependance of this problem renders our previous toolset of DFT calculations void; DFT is a ground-state theory. Instead, we employ a density functional-based tight-binding (DFTB) approach in a molecular dynamics simulation. Basically, the structural configuration evaluated at each time step is based on a tight-binding electronic structure calculation, instead of a typical MD force field. Trajectories are presented at varying temperatures and electric field strengths. Indeed, we observe a conformation of the porphyrin molecule between two configurations of the dihedral angle of the central nitrogen ring, ±15. {o} at 300K, but not 4.2K. These confirmations are equally likely, i.e., the structure assumes these configurations an equal number of teams, meaning the average structure has an angle of 0. {o}. After computing the DOS of all three aforementioned configurations (0. {text{o}} and ±15. {text{o}}), we indeed see a difference between the DOS curves at ±15. {text{o}} (which are

  2. 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.

  3. 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

    We present density-functional theory calculations for the geometry and conductance of 4,4-bipyridine (BPD) nanojunctions with Au and Pt electrodes. The fact that transport takes place via bipyridine's lowest unoccupied molecular orbital (LUMO) suggests that the Au-BPD junction should have larger...... 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.......02G(0) for the Au and Pt contacts, respectively (G(0)=2e(2)/h is the conductance quantum). The effect of coupling to the electrodes is investigated by means of the group orbital which makes precise the concept of the local band. The construction allows us to explain and rationalize the first...

  4. The Design of Molecular Hosts, Guests, and Their Complexes.

    Science.gov (United States)

    Cram, Donald J.

    1988-01-01

    Describes the origins, definitions, tools, and principles of host-guest chemistry. Gives examples of chiral recognition in complexation, of partial transacylase mimics, of caviplexes, and of a synthetic molecular cell. (Author/RT)

  5. Molecular Mechanism of V(D)J Recombination from Synaptic RAG1-RAG2 Complex Structures.

    Science.gov (United States)

    Ru, Heng; Chambers, Melissa G; Fu, Tian-Min; Tong, Alexander B; Liao, Maofu; Wu, Hao

    2015-11-19

    Diverse repertoires of antigen-receptor genes that result from combinatorial splicing of coding segments by V(D)J recombination are hallmarks of vertebrate immunity. The (RAG1-RAG2)2 recombinase (RAG) recognizes recombination signal sequences (RSSs) containing a heptamer, a spacer of 12 or 23 base pairs, and a nonamer (12-RSS or 23-RSS) and introduces precise breaks at RSS-coding segment junctions. RAG forms synaptic complexes only with one 12-RSS and one 23-RSS, a dogma known as the 12/23 rule that governs the recombination fidelity. We report cryo-electron microscopy structures of synaptic RAG complexes at up to 3.4 Å resolution, which reveal a closed conformation with base flipping and base-specific recognition of RSSs. Distortion at RSS-coding segment junctions and base flipping in coding segments uncover the two-metal-ion catalytic mechanism. Induced asymmetry involving tilting of the nonamer-binding domain dimer of RAG1 upon binding of HMGB1-bent 12-RSS or 23-RSS underlies the molecular mechanism for the 12/23 rule. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. The EhCPADH112 complex of Entamoeba histolytica interacts with tight junction proteins occludin and claudin-1 to produce epithelial damage.

    Directory of Open Access Journals (Sweden)

    Abigail Betanzos

    Full Text Available Entamoeba histolytica, the protozoan responsible for human amoebiasis, causes between 30,000 and 100,000 deaths per year worldwide. Amoebiasis is characterized by intestinal epithelial damage provoking severe diarrhea. However, the molecular mechanisms by which this protozoan causes epithelial damage are poorly understood. Here, we studied the initial molecular interactions between the E. histolytica EhCPADH112 virulence complex and epithelial MDCK and Caco-2 cells. By confocal microscopy, we discovered that after contact with trophozoites or trophozoite extracts (TE, EhCPADH112 and proteins forming this complex (EhCP112 and EhADH112 co-localize with occludin and claudin-1 at tight junctions (TJ. Immunoprecipitation assays revealed interaction between EhCPADH112 and occludin, claudin-1, ZO-1 and ZO-2. Overlay assays confirmed an interaction of EhCP112 and EhADH112 with occludin and claudin-1, whereas only EhADH112 interacted also with ZO-2. We observed degradation of all mentioned TJ proteins after incubation with TE. Importantly, inhibiting proteolytic activity or blocking the complex with a specific antibody not only prevented TJ protein degradation but also epithelial barrier disruption. Furthermore, we discovered that TE treatment induces autophagy and apoptosis in MDCK cells that could contribute to the observed barrier disruption. Our results suggest a model in which epithelial damage caused by E. histolytica is initiated by the interaction of EhCP112 and EhADH112 with TJ proteins followed by their degradation. Disruption of TJs then induces increased paracellular permeability, thus facilitating the entry of more proteases and other parasite molecules leading eventually to tissue destruction.

  7. 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

    expression by transcription and translation is of great importance, the trafficking, channel activity and degradation are also under tight control. The function of connexins can be regulated by several post translational modifications, which affect numerous parameters; including number of channels, open......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...

  8. Glutamine supplementation attenuates ethanol-induced disruption of apical junctional complexes in colonic epithelium and ameliorates gut barrier dysfunction and fatty liver in mice.

    Science.gov (United States)

    Chaudhry, Kamaljit K; Shukla, Pradeep K; Mir, Hina; Manda, Bhargavi; Gangwar, Ruchika; Yadav, Nikki; McMullen, Megan; Nagy, Laura E; Rao, RadhaKrishna

    2016-01-01

    Previous in vitro studies showed that glutamine (Gln) prevents acetaldehyde-induced disruption of tight junctions and adherens junctions in Caco-2 cell monolayers and human colonic mucosa. In the present study, we evaluated the effect of Gln supplementation on ethanol-induced gut barrier dysfunction and liver injury in mice in vivo. Ethanol feeding caused a significant increase in inulin permeability in distal colon. Elevated permeability was associated with a redistribution of tight junction and adherens junction proteins and depletion of detergent-insoluble fractions of these proteins, suggesting that ethanol disrupts apical junctional complexes in colonic epithelium and increases paracellular permeability. Ethanol-induced increase in colonic mucosal permeability and disruption of junctional complexes were most severe in mice fed Gln-free diet. Gln supplementation attenuated ethanol-induced mucosal permeability and disruption of tight junctions and adherens junctions in a dose-dependent manner, indicating the potential role of Gln in nutritional intervention to alcoholic tissue injury. Gln supplementation dose-dependently elevated reduced-protein thiols in colon without affecting the level of oxidized-protein thiols. Ethanol feeding depleted reduced protein thiols and elevated oxidized protein thiols. Ethanol-induced protein thiol oxidation was most severe in mice fed with Gln-free diet and absent in mice fed with Gln-supplemented diet, suggesting that antioxidant effect is one of the likely mechanisms involved in Gln-mediated amelioration of ethanol-induced gut barrier dysfunction. Ethanol feeding elevated plasma transaminase and liver triglyceride, which was accompanied by histopathologic lesions in the liver; ethanol-induced liver damage was attenuated by Gln supplementation. These results indicate that Gln supplementation ameliorates alcohol-induced gut and liver injury.

  9. 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.

  10. Molecularly imprinted Ru complex catalysts integrated on oxide surfaces.

    Science.gov (United States)

    Muratsugu, Satoshi; Tada, Mizuki

    2013-02-19

    Selective catalysis is critical for the development of green chemical processes, and natural enzymes that possess specialized three-dimensional reaction pockets with catalytically active sites represent the most sophisticated systems for selective catalysis. A reaction space in an enzyme consists of an active metal center, functional groups for molecular recognition (such as amino acids), and a surrounding protein matrix to prepare the reaction pocket. The artificial design of such an integrated catalytic unit in a non-enzymatic system remains challenging. Molecular imprinting of a supported metal complex provides a promising approach for shape-selective catalysis. In this process, an imprinted cavity with a shape matched to a template molecule is created in a polymer matrix with a catalytically active metal site. In this Account, we review our studies on molecularly imprinted metal complex catalysts, focusing on Ru complexes, on oxide surfaces for shape-selective catalysis. Oxide surface-attached transition metal complex catalysts not only improve thermal stability and catalyst dispersion but also provide unique catalytic performance not observed in homogeneous precursors. We designed molecularly imprinted Ru complexes by using surface-attached Ru complexes with template ligands and inorganic/organic surface matrix overlayers to control the chemical environment around the active metal complex catalysts on oxide surfaces. We prepared the designed, molecularly imprinted Ru complexes on SiO(2) surfaces in a step-by-step manner and characterized them with solid-state (SS) NMR, diffuse-reflectance (DR) UV-vis, X-ray photoelectron spectroscopy (XPS), Brunauer-Emmett-Teller isotherm (BET), X-ray fluorescence (XRF), and Ru K-edge extended X-ray absorption fine structure (EXAFS). The catalytic performances of these Ru complexes suggest that this process of molecular imprinting facilitates the artificial integration of catalytic functions at surfaces. Further advances such

  11. Development of a Symmetric Ring Junction as a Four-Port Reflectometer for Complex Reflection Coefficient Measurements

    Directory of Open Access Journals (Sweden)

    K.Y. Lee

    2015-12-01

    Full Text Available Six-port reflectometer is well-known for its ability to measure magnitude and phase-shift of microwave signal using four power detectors that perform magnitude-only measurements. This paper presents the development of an innovative symmetric ring junction as four-port reflectometer for complex reflection coefficient measurements. It reduces the number of required detectors to two. Design optimization, new calibration modeling and algorithm are discussed in details for this four-port reflectometer. The developed four-port reflectometer is compared to five-port reflectometer and vector network analyzer. It is found that the measured magnitude and phase-shift shows good performance in comparison with the commercial vector network analyzer and the five-port reflectometer.

  12. Tip-induced gating of molecular levels in carbene-based junctions

    Science.gov (United States)

    Foti, Giuseppe; Vázquez, Héctor

    2016-03-01

    We study the conductance of N-heterocyclic carbene-based (NHC) molecules on gold by means of first-principles calculations based on density-functional theory and non-equilibrium Green’s functions. We consider several tip structures and find a strong dependence of the position of the NHC molecular levels with the atomistic structure of the tip. The position of the lowest unoccupied molecular orbital (LUMO) can change by almost 0.8 eV with tip shape. Through an analysis of the net charge transfer, electron redistribution and work function for each tip structure, we rationalize the LUMO shifts in terms of the sum of the work function and the maximum electrostatic potential arising from charge rearrangement. These differences in the LUMO position, effectively gating the molecular levels, result in large conductance variations. These findings open the way to modulating the conductance of NHC-based molecular circuits through the controlled design of the tip atomistic structure.

  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. Endoplasmic reticulum-plasma membrane junctions: structure, function and dynamics.

    Science.gov (United States)

    Okeke, Emmanuel; Dingsdale, Hayley; Parker, Tony; Voronina, Svetlana; Tepikin, Alexei V

    2016-06-01

    Endoplasmic reticulum (ER)-plasma membrane (PM) junctions are contact sites between the ER and the PM; the distance between the two organelles in the junctions is below 40 nm and the membranes are connected by protein tethers. A number of molecular tools and technical approaches have been recently developed to visualise, modify and characterise properties of ER-PM junctions. The junctions serve as the platforms for lipid exchange between the organelles and for cell signalling, notably Ca(2+) and cAMP signalling. Vice versa, signalling events regulate the development and properties of the junctions. Two Ca(2+) -dependent mechanisms of de novo formation of ER-PM junctions have been recently described and characterised. The junction-forming proteins and lipids are currently the focus of vigorous investigation. Junctions can be relatively short-lived and simple structures, forming and dissolving on the time scale of a few minutes. However, complex, sophisticated and multifunctional ER-PM junctions, capable of attracting numerous protein residents and other cellular organelles, have been described in some cell types. The road from simplicity to complexity, i.e. the transformation from simple 'nascent' ER-PM junctions to advanced stable multiorganellar complexes, is likely to become an attractive research avenue for current and future junctologists. Another area of considerable research interest is the downstream cellular processes that can be activated by specific local signalling events in the ER-PM junctions. Studies of the cell physiology and indeed pathophysiology of ER-PM junctions have already produced some surprising discoveries, likely to expand with advances in our understanding of these remarkable organellar contact sites. © 2016 The Authors. The Journal of Physiology © 2016 The Physiological Society.

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

    Energy Technology Data Exchange (ETDEWEB)

    Elie, Q.; Le Bourdais, F.; Jezzine, K.; Baronian, V. [Non Destructive Testing Department at the French Atomic Energy Commission (CEA), Saclay, 91191 Gif sur Yvette CEDEX, (France)

    2015-07-01

    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)

  16. Non-equilibrium quantum transport of spin-polarized electrons and back action on molecular magnet tunnel-junction

    Science.gov (United States)

    Zhang, Chao; Yao, Hui; Nie, Yi-Hang; Liang, J.-Q.

    2016-11-01

    We investigate the non-equilibrium quantum transport through a single-molecule magnet embedded in a tunnel junction with ferromagnetic electrodes, which generate spin-polarized electrons. The lead magnetization direction is non-collinear with the uniaxial anisotropy easy-axis of molecule-magnet. Based on the Pauli rate-equation approach we demonstrate the magnetization reversion of molecule-magnet induced by the back action of spin-polarized current in the sequential tunnel regime. The asymptotic magnetization of molecular magnet and spin-polarization of transport current are obtained as functions of time by means of time-dependent solution of the rate equation. It is found that the antiparallel configuration of the ferromagnetic electrodes and molecular anisotropy easy-axis is an effective structure to reverse both the magnetization of molecule-magnet and spin-polarization of the transport current. Particularly the non-collinear angle dependence provides useful knowledge for the quantum manipulation of molecule-magnet and spin polarized electron-transport.

  17. Non-equilibrium quantum transport of spin-polarized electrons and back action on molecular magnet tunnel-junction

    Directory of Open Access Journals (Sweden)

    Chao Zhang

    2016-11-01

    Full Text Available We investigate the non-equilibrium quantum transport through a single-molecule magnet embedded in a tunnel junction with ferromagnetic electrodes, which generate spin-polarized electrons. The lead magnetization direction is non-collinear with the uniaxial anisotropy easy-axis of molecule-magnet. Based on the Pauli rate-equation approach we demonstrate the magnetization reversion of molecule-magnet induced by the back action of spin-polarized current in the sequential tunnel regime. The asymptotic magnetization of molecular magnet and spin-polarization of transport current are obtained as functions of time by means of time-dependent solution of the rate equation. It is found that the antiparallel configuration of the ferromagnetic electrodes and molecular anisotropy easy-axis is an effective structure to reverse both the magnetization of molecule-magnet and spin-polarization of the transport current. Particularly the non-collinear angle dependence provides useful knowledge for the quantum manipulation of molecule-magnet and spin polarized electron-transport.

  18. Charge transport in molecular junctions: From tunneling to hopping with the probe technique

    CERN Document Server

    Kilgour, Michael

    2015-01-01

    We demonstrate that a simple phenomenological approach can be used to simulate electronic conduction in molecular wires under thermal effects induced by the surrounding environment. This "Landauer-B\\"uttiker's probe technique" can properly replicate different transport mechanisms: phase coherent nonresonant tunneling, ballistic behavior, and hopping conduction, to provide results consistent with experiments. Specifically, our simulations with the probe method recover the following central characteristics of charge transfer in molecular wires: (i) The electrical conductance of short wires falls off exponentially with molecular length, a manifestation of the tunneling (superexchange) mechanism. Hopping dynamics overtakes superexchange in long wires demonstrating an ohmic-like behavior. (ii) In off-resonance situations, weak dephasing effects facilitate charge transfer. Under large dephasing the electrical conductance is suppressed. (iii) At high enough temperatures, $k_BT/\\epsilon_B>1/25$, with $\\epsilon_B$ as ...

  19. 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.

  20. Semiconducting III-V nanowires with nanogaps for molecular junctions: DFT transport simulations

    DEFF Research Database (Denmark)

    Kallesøe, Christian; Fürst, Joachim Alexander; Mølhave, Kristian;

    2009-01-01

    We consider here the possibility of using III–V heterostructure nanowires as electrodes for molecular electronics instead of metal point contacts. Using ab initio electronic structure and transport calculations, we study the effect on electronic properties of placing a small molecule with thiol l...

  1. Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome

    NARCIS (Netherlands)

    Albers, C.A.; Paul, D.S.; Schulze, H.; Freson, K.; Stephens, J.C.; Smethurst, P.A.; Jolley, J.D.; Cvejic, A.; Kostadima, M.; Bertone, P.; Breuning, M.H.; Debili, N.; Deloukas, P.; Favier, R.; Fiedler, J.; Hobbs, C.M.; Huang, N.; Hurles, M.E.; Kiddle, G.; Krapels, I.; Nurden, P.; Ruivenkamp, C.A.; Sambrook, J.G.; Smith, K.; Stemple, D.L.; Strauss, G.; Thys, C.; Geet, C. van; Newbury-Ecob, R.; Ouwehand, W.H.; Ghevaert, C.

    2012-01-01

    The exon-junction complex (EJC) performs essential RNA processing tasks. Here, we describe the first human disorder, thrombocytopenia with absent radii (TAR), caused by deficiency in one of the four EJC subunits. Compound inheritance of a rare null allele and one of two low-frequency SNPs in the reg

  2. Evolution of photoelectron-vibrational coupling with molecular complexity

    Energy Technology Data Exchange (ETDEWEB)

    Poliakoff, E D [Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803 (United States); Lucchese, R R [Department of Chemistry, Texas A and M University, College Station, TX 77843 (United States)

    2006-11-15

    We review how electronic and vibrational degrees of freedom become coupled in molecular photoionization, and describe effects that emerge as the molecular complexity increases. Molecular photoionization is frequently influenced by the temporary trapping of the continuum electron in the field of the target molecules, which is referred to as a shape resonance, as it depends on the shape of the potential experienced by the exiting photoelectron. Such resonances couple electronic and vibrational motion, and the nature of the coupling can vary widely for polyatomic molecules. We show how vibrationally resolved photoelectron spectra acquired as a function of energy can be used to elucidate such coupling. The experiments are analysed using physically realistic and computationally tractable Schwinger variational theory, and the systems studied to date can be well understood using an independent-particle, adiabatic nuclei framework. As a result, simple and intuitive pictures emerge, even when dealing with scattering phenomena involving complex molecular targets and potentials.

  3. 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.

  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. Molecular genetics of the R complex of maize. Final technical report DE-FG02-86ER13627

    Energy Technology Data Exchange (ETDEWEB)

    Dellaporta, Stephen

    2000-10-01

    A molecular genetic characterization of the maize R-r complex of maize was completed during the period of support. The complex was shown to consist of two main regions: the P region, containing the r-p gene which controlled pigmentation of plant parts, and the S subcomplex, containing two rl-s genes in head-to-head orientation and a nonfunctional component termed rl-q. By examining the DNA sequences at the junction of the rl genes, the complex was shown to be derived by a series of abortive transposition events. The transposable element involved in the gene duplication and rearrangements was characterized and called doppia. Meiotic instability of the R-r complex was also characterized. Loss of P or S function was associated with several structural changes including intrachromosomal recombination and excision of a novel transposable element that appears to show instability only during meiosis.

  6. The Smc5-Smc6 complex is required to remove chromosome junctions in meiosis.

    Directory of Open Access Journals (Sweden)

    Sarah Farmer

    Full Text Available Meiosis, a specialized cell division with a single cycle of DNA replication round and two consecutive rounds of nuclear segregation, allows for the exchange of genetic material between parental chromosomes and the formation of haploid gametes. The structural maintenance of chromosome (SMC proteins aid manipulation of chromosome structures inside cells. Eukaryotic SMC complexes include cohesin, condensin and the Smc5-Smc6 complex. Meiotic roles have been discovered for cohesin and condensin. However, although Smc5-Smc6 is known to be required for successful meiotic divisions, the meiotic functions of the complex are not well understood. Here we show that the Smc5-Smc6 complex localizes to specific chromosome regions during meiotic prophase I. We report that meiotic cells lacking Smc5-Smc6 undergo catastrophic meiotic divisions as a consequence of unresolved linkages between chromosomes. Surprisingly, meiotic segregation defects are not rescued by abrogation of Spo11-induced meiotic recombination, indicating that at least some chromosome linkages in smc5-smc6 mutants originate from other cellular processes. These results demonstrate that, as in mitosis, Smc5-Smc6 is required to ensure proper chromosome segregation during meiosis by preventing aberrant recombination intermediates between homologous chromosomes.

  7. 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 full nonequilibrium Green's function calculation and the newly derived expressions is obtained while simplifying the computational burden by several orders of magnitude. In addition, analytical models provide intuitive understanding of the conductance including nonequilibrium heating and provide...... a convenient way of parameterizing the physics. This is exemplified by fitting the expressions to the experimentally observed conductances through both an atomic gold wire and a hydrogen molecule....

  8. Crystalline molecular complexes and compounds structures and principles

    CERN Document Server

    Herbstein, Frank H

    2005-01-01

    This book provides an account of the structure and properties of crystalline binary adducts. Such crystals are perhaps better known as molecular compounds and complexes and are estimated to make up one quarter of the world's crystals. More than 600 figures, 200 tables and 3500 references are included in the book.

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

    Science.gov (United States)

    Tyagi, Pawan; Friebe, Edward; Baker, Collin

    2015-11-01

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Tyagi, Pawan, E-mail: ptyagi@udc.edu; Friebe, Edward; Baker, Collin [University of the District of Columbia, Department of Mechanical Engineering (United States)

    2015-11-15

    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.

  11. 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.

  12. Experimental and numerical study of a complex cross-junction microchannel

    Science.gov (United States)

    Nowak, Emilia; Simmons, Mark; Kahouadji, Lyes; Craster, Richard; Matar, Omar; Juric, Damir; Chergui, Jalel; Shin, Seungwon

    2016-11-01

    Microfluidic devices occur in various fields such as inkjet printing, DNA chips, lab-on-a-chip technology, micro-propulsion and droplet-based microfluidics. Here, we examine drop and plug formation of immiscible liquids in a cross-shaped microchannel via high-speed imaging, shadowgraphy and PIV that allows interface topology and flow field tracking. We also present comparisons with direct numerical simulations using the new solver, BLUE, for massively parallel simulations of fully three-dimensional multiphase flows in complex solid geometries. EPSRC UK Programme Grant MEMPHIS (EP/K003976/1).

  13. 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

    The electronic conductance of a benzene molecule connected to gold electrodes via thiol, thiolate, or amino anchoring groups is calculated using nonequilibrium Green functions in combination with the fully self-consistent GW approximation for exchange and correlation. The calculated conductance...... 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...

  14. A quantum chemical study from a molecular perspective: ionization and electron attachment energies for species often used to fabricate single-molecule junctions

    CERN Document Server

    Baldea, Ioan

    2015-01-01

    The accurate determination of the lowest electron attachment ($EA$) and ionization ($IP$) energies for molecules embedded in molecular junctions is important for correctly estimating, \\emph{e.g.}, the magnitude of the currents ($I$) or the biases ($V$) where an $I-V$-curve exhibits a significant non-Ohmic behavior. Benchmark calculations for the lowest electron attachment and ionization energies of several typical molecules utilized to fabricate single-molecule junctions characterized by n-type conduction (4,4'-bipyridine, 1,4-dicyanobenzene, and 4,4'-dicyano-1,1'-biphenyl) and p-type conduction (benzenedithiol, biphenyldithiol, hexanemonothiol, and hexanedithiol] based on the EOM-CCSD (equation-of-motion coupled-cluster singles and doubles) state-of-the-art method of quantum chemistry are presented. They indicate significant differences from the results obtained within current approaches to molecular transport. The present study emphasizes that, in addition to a reliable quantum chemical method, basis sets m...

  15. Structural assembly of molecular complexes based on residual dipolar couplings.

    Science.gov (United States)

    Berlin, Konstantin; O'Leary, Dianne P; Fushman, David

    2010-07-07

    We present and evaluate a rigid-body molecular docking method, called PATIDOCK, that relies solely on the three-dimensional structure of the individual components and the experimentally derived residual dipolar couplings (RDCs) for the complex. We show that, given an accurate ab initio predictor of the alignment tensor from a protein structure, it is possible to accurately assemble a protein-protein complex by utilizing the RDCs' sensitivity to molecular shape to guide the docking. The proposed docking method is robust against experimental errors in the RDCs and computationally efficient. We analyze the accuracy and efficiency of this method using experimental or synthetic RDC data for several proteins, as well as synthetic data for a large variety of protein-protein complexes. We also test our method on two protein systems for which the structure of the complex and steric-alignment data are available (Lys48-linked diubiquitin and a complex of ubiquitin and a ubiquitin-associated domain) and analyze the effect of flexible unstructured tails on the outcome of docking. The results demonstrate that it is fundamentally possible to assemble a protein-protein complex solely on the basis of experimental RDC data and the prediction of the alignment tensor from 3D structures. Thus, despite the purely angular nature of RDCs, they can be converted into intermolecular distance/translational constraints. Additionally, we show a method for combining RDCs with other experimental data, such as ambiguous constraints from interface mapping, to further improve structure characterization of protein complexes.

  16. 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.

  17. Molecular Split-Ring Resonators Based on Metal String Complexes

    CERN Document Server

    Shen, Yao; Ai, Qing; Peng, Shie-Ming; Jin, Bih-Yaw

    2014-01-01

    Metal string complexes or extended metal atom chains (EMACs) belong to a family of molecules that consist of a linear chain of directly bonded metal atoms embraced helically by four multidentate organic ligands. These four organic ligands are usually made up of repeating pyridyl units, single-nitrogen-substituted heterocyclic annulenes, bridged by independent amido groups. Here, in this paper, we show that these heterocyclic annulenes are actually nanoscale molecular split-ring resonators (SRRs) that can exhibit simultaneous negative electric permittivity and magnetic permeability in the UV-Vis region. Moreover, a monolayer of self-assembled EMACs is a periodic array of molecular SRRs which can be considered as a negative refractive index material. In the molecular scale, where the quantum-size effect is significant, we apply the tight-binding method to obtain the frequency-dependent permittivity and permeability of these molecular SRRs with their tensorial properties carefully considered.

  18. Solvation of complex surfaces via molecular density functional theory

    CERN Document Server

    Levesque, Maximilien; Rotenberg, Benjamin; Jeanmairet, Guillaume; Vuilleumier, Rodolphe; Borgis, Daniel

    2012-01-01

    We show that classical molecular density functional theory (MDFT), here in the homogeneous reference fluid approximation in which the functional is inferred from the properties of the bulk solvent, is a powerful new tool to study, at a fully molecular level, the solvation of complex surfaces and interfaces by polar solvents. This implicit solvent method allows for the determination of structural, orientational and energetic solvation properties that are on a par with all-atom molecular simulations performed for the same system, while reducing the computer time by two orders of magnitude. This is illustrated by the study of an atomistically-resolved clay surface composed of over a thousand atoms wetted by a molecular dipolar solvent. The high numerical efficiency of the method is exploited to carry a systematic analysis of the electrostatic and non-electrostatic components of the surface-solvent interaction within the popular CLAYFF force field. Solvent energetics and structure are found to depend weakly upon ...

  19. Dynamical image-charge effect in molecular tunnel junctions: Beyond energy level alignment

    Science.gov (United States)

    Jin, Chengjun; Thygesen, Kristian S.

    2014-01-01

    When an electron tunnels between two metal contacts it temporarily induces an image charge (IC) in the electrodes which acts back on the tunneling electron. It is usually assumed that the IC forms instantaneously such that a static model for the image potential applies. Here we investigate how 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 Z2, where Z is the quasiparticle renormalization factor, compared to the static IC approximation. We show that Z can be expressed either in terms of the plasma frequency of the electrode or as the overlap between electrode wave functions corresponding to an empty and filled level, respectively. First-principles GW calculations for benzene-diamine connected to gold electrodes show 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.

  20. Bacterial interference with host epithelial junctional complexes: Probiotic bacteria vs. A/E lesion-forming Escherichia coli

    Directory of Open Access Journals (Sweden)

    TANIA TOPOUZOVA-HRISTOVA

    2012-01-01

    Full Text Available During colonization, enteropathogenic (EPEC and enterohaemorrhagic (EHEC Escherichia coli are capable to manipulate host cytoskeleton and colonize gut epithelia by a specific mode of attachment known as the attaching and effacing lesion (A/E lesion. While actin rearrangements during A/E lesion formation have been extensively investigated, the possible alterations of other cytoskeletal elements like those comprising the intercellular junctional complexes (JC of polarized cells during infection have only lately attracted attention. The present mini-review addresses the opposite effects of two groups of bacteria, A/E lesion-forming pathogenic E. coli and probiotic bacterial strains, on JC. JC are important in maintaining gut barrier functions. EPEC and EHEC can disrupt JC which as a consequence leads to reduction in the transepitelial electrical resistance (TER and an increase of the permeability to macromolecules. Probiotic bacteria on the other hand stabilize JC thus increasing TER and reducing permeability to macromolecular markers. Probiotic strains can protect JC integrity of polarized cells from the damage caused by EPEC or EHEC. Together with the promise of these results, of concern is the fact that the outcome of the studies can differ dependent on experimental protocols. Studies with living bacteria and different strain combinations have also put forward strain specific effects. Therefore, an important practical item for future studies is the identification of the molecules synthesized by probiotic bacteria that may be active on JC stability.

  1. 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

    2014-09-12

    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.

  2. Knock and Drill Technique: A Simple Tips for the Instrumentation in Complex Craniovertebral Junction Anomalies without using Fluoroscopy

    Science.gov (United States)

    Srivastava, Arun; Sardhara, Jayesh; Behari, Sanjay; Pavaman, Sindgikar; Joseph, Jeena; Das, Kuntal; Mehrotra, Anant; Jaiswal, Awadhesh K.; Bhaishora, Kamlesh

    2017-01-01

    Context: Existence of complex variable bony and vertebral artery (VA) anomalies at craniovertebral junction (CVJ) in subset of complex CVJ anomalies demands individualized instrumentation policy and placing screws in each bone requires strategic preoperative planning and intraoperative skills. Aim: To evaluate the clinical accuracy of knock and drill (K and D) technique for the screw placement in complex CVJ anomalies. Settings and Design: Prospective study and operative technical note. Materials and Methods: Totally 36 consecutive patients (16 - pediatrics, 20 - adult patients) of complex CVJ: Complete/partial occipitalized C1 vertebra; at least one hypoplastic (C1/C2) articular mass, rotational component, and variations in the third part of VA were included in this study. Preoperative detail computed tomography (CT) CT CVJ with three-dimensional reconstruction was done for the assessment of CVJ anatomy and facet joint orientation. The accuracy of novel technique was assessed with postoperative CT to evaluate cortical breach in between 5th and 7th postoperative day in all the patients. All patients were underwent clinico-radiological evaluation at 6-month follow-up. Results: Totally 144 screws were placed using K and D technique (pediatric group - 64 screws, adult patients - 80 screws). Total of 12 screws were placed in C1 lateral mass in both age group without any bony cortical breach and complication. Sixteen C2 pedicle screws and 12 C2 pars screw in pediatrics and 18 C2 pedicle screws in adult patients were placed without any bony breach or VA injury. Out of thirty subaxial lateral mass screws in pediatric group, the bony breach was encountered with one screw (3.3%). Total of 38 C2 pars screws was placed in adult group in which bony breach along with VA injury was encounter with 1screw (2.6%). Conclusion: A simple technique of K and D for placing a screw increases the accuracy and spectrum of bony purchase and has the potential to reduce the complication in

  3. Probing Interactions in Complex Molecular Systems through Ordered Assembly

    Energy Technology Data Exchange (ETDEWEB)

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

    2002-01-31

    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

  4. Models for the Binary Complex of Bacteriophage T4 Gp59 Helicase Loading Protein. GP32 Single-Stranded DNA-Binding Protein and Ternary Complex with Pseudo-Y Junction DNA

    Energy Technology Data Exchange (ETDEWEB)

    Hinerman, Jennifer M. [Univ. of Toledo, OH (United States); Dignam, J. David [Univ. of Toledo, OH (United States); Mueser, Timothy C. [Univ. of Toledo, OH (United States)

    2012-04-05

    The bacteriophage T4 gp59 helicase assembly protein (gp59) is required for loading of gp41 replicative helicase onto DNA protected by gp32 single-stranded DNA-binding protein. The gp59 protein recognizes branched DNA structures found at replication and recombination sites. Binding of gp32 protein (full-length and deletion constructs) to gp59 protein measured by isothermal titration calorimetry demonstrates that the gp32 protein C-terminal A-domain is essential for protein-protein interaction in the absence of DNA. Sedimentation velocity experiments with gp59 protein and gp32ΔB protein (an N-terminal B-domain deletion) show that these proteins are monomers but form a 1:1 complex with a dissociation constant comparable with that determined by isothermal titration calorimetry. Small angle x-ray scattering (SAXS) studies indicate that the gp59 protein is a prolate monomer, consistent with the crystal structure and hydrodynamic properties determined from sedimentation velocity experiments. SAXS experiments also demonstrate that gp32ΔB protein is a prolate monomer with an elongated A-domain protruding from the core. Moreover, fitting structures of gp59 protein and the gp32 core into the SAXS-derived molecular envelope supports a model for the gp59 protein-gp32ΔB protein complex. Our earlier work demonstrated that gp59 protein attracts full-length gp32 protein to pseudo-Y junctions. A model of the gp59 protein-DNA complex, modified to accommodate new SAXS data for the binary complex together with mutational analysis of gp59 protein, is presented in the accompanying article (Dolezal, D., Jones, C. E., Lai, X., Brister, J. R., Mueser, T. C., Nossal, N. G., and Hinton, D. M. (2012) J. Biol. Chem. 287, 18596–18607).

  5. Molecular Signatures of Membrane Protein Complexes Underlying Muscular Dystrophy*

    Science.gov (United States)

    Turk, Rolf; Hsiao, Jordy J.; Smits, Melinda M.; Ng, Brandon H.; Pospisil, Tyler C.; Jones, Kayla S.; Campbell, Kevin P.; Wright, Michael E.

    2016-01-01

    Mutations in genes encoding components of the sarcolemmal dystrophin-glycoprotein complex (DGC) are responsible for a large number of muscular dystrophies. As such, molecular dissection of the DGC is expected to both reveal pathological mechanisms, and provides a biological framework for validating new DGC components. Establishment of the molecular composition of plasma-membrane protein complexes has been hampered by a lack of suitable biochemical approaches. Here we present an analytical workflow based upon the principles of protein correlation profiling that has enabled us to model the molecular composition of the DGC in mouse skeletal muscle. We also report our analysis of protein complexes in mice harboring mutations in DGC components. Bioinformatic analyses suggested that cell-adhesion pathways were under the transcriptional control of NFκB in DGC mutant mice, which is a finding that is supported by previous studies that showed NFκB-regulated pathways underlie the pathophysiology of DGC-related muscular dystrophies. Moreover, the bioinformatic analyses suggested that inflammatory and compensatory mechanisms were activated in skeletal muscle of DGC mutant mice. Additionally, this proteomic study provides a molecular framework to refine our understanding of the DGC, identification of protein biomarkers of neuromuscular disease, and pharmacological interrogation of the DGC in adult skeletal muscle https://www.mda.org/disease/congenital-muscular-dystrophy/research. PMID:27099343

  6. W43: the closest molecular complex of the Galactic Bar?

    CERN Document Server

    Long, Q Nguyen; Schuller, F; Schneider, N; Bontemps, S; Schilke, P; Menten, K M; Heitsch, F; Wyrowski, F; Carlhoff, P; Bronfman, L; Henning, T

    2011-01-01

    We used a large database extracted from Galaxy-wide surveys of H {\\scriptsize I}, $^{13}$CO 1-0, $8 \\micron$ and $870 \\micron$ continuum to trace diffuse atomic gas, low- to medium-density molecular gas, high-density molecular gas, and star formation activity which we complemented by dedicated $^{12}$CO 2--1, 3--2 observations of the W43 region. From the detailed 3D (space-space-velocity) analysis of the molecular and atomic cloud tracers through the region and despite its wide velocity range (\\emph{FWHM}$\\sim22.3 \\kms$ around $\\vlsr\\sim 95.9 \\kms$), we identified W43 as a large (equivalent diameter $\\sim 140$ pc) and coherent complex of molecular clouds which is surrounded by an atomic gas envelope (equivalent diameter $\\sim 290$ pc). We measured the total mass of this newly-identified molecular complex ($M_{{\\tiny total}}\\sim 7.1 \\times 10^6 \\msun$), the mass contained in dense $870 \\micron$ clumps ($<5$ pc dense cloud structures, $M_{{\\tiny clumps}}\\sim 8.4 \\times 10^5 \\msun$) and conclude that W43 is p...

  7. 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

  8. Complex molecular assemblies at hand via interactive simulations.

    Science.gov (United States)

    Delalande, Olivier; Férey, Nicolas; Grasseau, Gilles; Baaden, Marc

    2009-11-30

    Studying complex molecular assemblies interactively is becoming an increasingly appealing approach to molecular modeling. Here we focus on interactive molecular dynamics (IMD) as a textbook example for interactive simulation methods. Such simulations can be useful in exploring and generating hypotheses about the structural and mechanical aspects of biomolecular interactions. For the first time, we carry out low-resolution coarse-grain IMD simulations. Such simplified modeling methods currently appear to be more suitable for interactive experiments and represent a well-balanced compromise between an important gain in computational speed versus a moderate loss in modeling accuracy compared to higher resolution all-atom simulations. This is particularly useful for initial exploration and hypothesis development for rare molecular interaction events. We evaluate which applications are currently feasible using molecular assemblies from 1900 to over 300,000 particles. Three biochemical systems are discussed: the guanylate kinase (GK) enzyme, the outer membrane protease T and the soluble N-ethylmaleimide-sensitive factor attachment protein receptors complex involved in membrane fusion. We induce large conformational changes, carry out interactive docking experiments, probe lipid-protein interactions and are able to sense the mechanical properties of a molecular model. Furthermore, such interactive simulations facilitate exploration of modeling parameters for method improvement. For the purpose of these simulations, we have developed a freely available software library called MDDriver. It uses the IMD protocol from NAMD and facilitates the implementation and application of interactive simulations. With MDDriver it becomes very easy to render any particle-based molecular simulation engine interactive. Here we use its implementation in the Gromacs software as an example.

  9. Molecular electrostatic potential analysis of non-covalent complexes

    Indian Academy of Sciences (India)

    PADINJARE VEETIL BIJINA; CHERUMUTTATHU H SURESH

    2016-10-01

    Ab initio MP4/Aug-cc-pvDZ//MP2/6-311++g(d,p) level interaction energy (Eint) and molecular electrostatic potential analysis (MESP) of a large variety of non-covalent intermolecular complexes, viz. tetrel, chalcogen, pnicogen, halogen, hydrogen, dihydrogen and lithium bonded complexes have been reported. The electronic changes associated with the non-covalent complex formation is monitored in terms of MESP minimum (Vmin) in the free and complexed states of the donor and acceptor molecules as well as in terms ofMESP at the donor and acceptor atoms (Vn) of the free monomers and complexes. The change in Vmin or Vn on the donor molecule (ΔVmin(D) or ΔVn(D)) during complex formation is proportional to its electron donating ability while such a change on the acceptor molecule (ΔVmin(A) or ΔVn(A)) is proportional to its electron accepting ability. Further, the quantities ΔΔVmin = ΔVmin(D) −ΔVmin(A) and ΔΔVn = ΔVn(D) −ΔVn(A) have shown strong linear correlations with Eint of the complex (Eint values fall in the range 0.7 to 46.2 kcal/mol for 54 complexes) and suggest that the intermolecular non-covalent interactions in a wide variety of systems can be monitored and assessed in terms of change in MESP due to complex formation in the gas phase. With the incorporation of solvent effect in the calculation, charged systems showed significant deviations from the linear correlation. The MESP based analysis proposes that the large variety of intermolecular non-covalent complexes considered in this study can be grouped under the general category of electron donor-acceptor (eDA) complexes

  10. 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.

  11. Molecular methods for genotyping complex copy number polymorphisms.

    Science.gov (United States)

    Cantsilieris, Stuart; Baird, Paul N; White, Stefan J

    2013-02-01

    Genome structural variation shows remarkable complexity with respect to copy number, sequence content and distribution. While the discovery of copy number polymorphisms (CNP) has increased exponentially in recent years, the transition from discovery to genotyping has proved challenging, particularly for CNPs embedded in complex regions of the genome. CNPs that are collectively common in the population and possess a dynamic range of copy numbers have proved the most difficult to genotype in association studies. This is in some part due to technical limitations of genotyping assays and the sequence properties of the genomic region being analyzed. Here we describe in detail the basis of a number of molecular techniques used to genotype complex CNPs, compare and contrast these approaches for determination of multi-allelic copy number, and discuss the potential application of these techniques in genetic studies.

  12. Catalytic Hydrogenation over Palladium Complex of Molecular Complex of Poly(4-vinylpyridine) with Acetic Acid

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The palladium complex of the molecular complex of poly(4-vinylpyridine) with acetic acid(PVP/HAc-Pd) was prepared. Its catalytic activity for the hydrogenation of nitrobenzene was found much higher than that of the corresponding palladium complex of poly(4-vinylpyridine). In the presence of a strong inorganic alkali, especially potassium hydroxide, the catalytic activity is greatly improved. The suitable hydrogenation condition for PVP/HAc-Pd is to use 0.1 mol/L ethanol solution of potassium hydroxide as the hydrogenation medium and the hydrogenation is carried out at 45 ℃.

  13. The Drosophila larval neuromuscular junction as a model for scaffold complexes at glutamatergic synapses: benefits and limitations.

    Science.gov (United States)

    Thomas, Ulrich; Kobler, Oliver; Gundelfinger, Eckart D

    2010-09-01

    Based on unbeatable genetic accessibility and relative simplicity, the Drosophila larval neuromuscular junction has become a widely used model system for studying functional and structural aspects of excitatory glutamatergic synapses. Membrane-associated guanylate kinase-like proteins (MAGUKs) are first-order scaffolding molecules enriched at many cellular junctions, including synapses, where they coordinate multiple binding partners, including cell adhesion molecules and ion channels. The enrichment of the prototypic MAGUK Discs-Large at larval NMJs apparently parallels the high abundance of its homologs at excitatory synapses in the mammalian central nervous system. Here, the authors review selected aspects of the long-standing work on Dlg at fly neuromuscular junctions, thereby scrutinizing its subcellular localization, function, and regulation with regard to corresponding aspects of MAGUKs in vertebrate neurons.

  14. Solvation of complex surfaces via molecular density functional theory.

    Science.gov (United States)

    Levesque, Maximilien; Marry, Virginie; Rotenberg, Benjamin; Jeanmairet, Guillaume; Vuilleumier, Rodolphe; Borgis, Daniel

    2012-12-14

    We show that classical molecular density functional theory, here in the homogeneous reference fluid approximation in which the functional is inferred from the properties of the bulk solvent, is a powerful new tool to study, at a fully molecular level, the solvation of complex surfaces and interfaces by polar solvents. This implicit solvent method allows for the determination of structural, orientational, and energetic solvation properties that are on a par with all-atom molecular simulations performed for the same system, while reducing the computer time by two orders of magnitude. This is illustrated by the study of an atomistically-resolved clay surface composed of over a thousand atoms wetted by a molecular dipolar solvent. The high numerical efficiency of the method is exploited to carry a systematic analysis of the electrostatic and non-electrostatic components of the surface-solvent interaction within the popular Clay Force Field (CLAYFF). Solvent energetics and structure are found to depend weakly upon the atomic charges distribution of the clay surface, even for a rather polar solvent. We conclude on the consequences of such findings for force-field development.

  15. The stardust family protein MPP7 forms a tripartite complex with LIN7 and DLG1 that regulates the stability and localization of DLG1 to cell junctions.

    Science.gov (United States)

    Bohl, Joanna; Brimer, Nicole; Lyons, Charles; Vande Pol, Scott B

    2007-03-30

    MPP7, a previously uncharacterized member of the p55 Stardust family of membrane-associated guanylate kinase (MAGUK) proteins, was found in a tripartite complex with DLG1 and LIN7A or LIN7C. MPP7 dimerizes with all three LIN7 family members (LIN7A, -B, and -C) through interaction of the single L27 domain of LIN7 with the carboxyl-terminal L27 domain of MPP7, thereby stabilizing both proteins. The dimer of MPP7 with LIN7A or LIN7C associates with DLG1 through an interaction requiring the amino-terminal L27 domain of MPP7. The amino-terminal L27 domain of MPP7 is not sufficient for interaction with DLG1 but interacts efficiently only if MPP7 is in a complex with LIN7A or -C. Thus the specificity of interaction of DLG1 with the LIN7-MPP7 complex is determined by L27 interactions with both MPP7 and LIN7. The tripartite complex forms in a ratio of 1:1:1 and localizes to epithelial adherens junctions in a manner dependent upon MPP7. Expression of MPP7 stabilizes DLG1 in an insoluble compartment. Expression of MPP7 deleted of the PDZ or Src homology 3 domain redistributes MPP7, DLG1, and LIN7 out of adherens junctions and into the soluble cytoplasmic fraction without changing the localization of E-cadherin. Thus, the stability and localization of DLG1 to cell-cell junctions are complex functions determined by the expression and association of particular Stardust family members together with particular LIN7 family members.

  16. Direct experimental determination of spectral densities of molecular complexes

    Energy Technology Data Exchange (ETDEWEB)

    Pachón, Leonardo A. [Grupo de Física Atómica y Molecular, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia); Chemical Physics Theory Group, Department of Chemistry and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6 (Canada); Brumer, Paul [Chemical Physics Theory Group, Department of Chemistry and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6 (Canada)

    2014-11-07

    Determining the spectral density of a molecular system immersed in a proteomic scaffold and in contact to a solvent is a fundamental challenge in the coarse-grained description of, e.g., electron and energy transfer dynamics. Once the spectral density is characterized, all the time scales are captured and no artificial separation between fast and slow processes need to be invoked. Based on the fluorescence Stokes shift function, we utilize a simple and robust strategy to extract the spectral density of a number of molecular complexes from available experimental data. Specifically, we show that experimental data for dye molecules in several solvents, amino acid proteins in water, and some photochemical systems (e.g., rhodopsin and green fluorescence proteins), are well described by a three-parameter family of sub-Ohmic spectral densities that are characterized by a fast initial Gaussian-like decay followed by a slow algebraic-like decay rate at long times.

  17. Astrochemistry: the issue of molecular complexity in astrophysical environments

    CERN Document Server

    De Becker, M

    2013-01-01

    Astrochemistry aims at studying chemical processes in astronomical environments. This discipline -- located at the crossroad between astrophysics and chemistry -- is rapidly evolving and explores the issue of the formation of molecules of increasing complexity in particular physical conditions that deviate significantly from those frequently encountered in chemistry laboratories. The main goal of this paper is to provide an overview of this discipline. So far, about 170 molecules have been identified in the interstellar medium (ISM). The presence of this molecular diversity constitutes a firm evidence that efficient formation processes are at work in the interstellar medium. This paper aims at summarizing most of present ideas that are explored by astrochemists to investigate the chemistry taking place in various astronomical environments, with emphasis on the particular conditions which are met in space (including radiation fields, cosmic-rays, low densities...). The more ambitious question of the molecular ...

  18. Direct Experimental Determination of Spectral Densities of Molecular Complexes

    CERN Document Server

    Pachon, Leonardo A

    2014-01-01

    Determining the spectral density of a molecular system immersed in a proteomic scaffold and in contact to a solvent is a fundamental challenge in the coarse-grained description of, e.g., electron and energy transfer dynamics. Once the spectral density is characterized, all the time scales are captured and no artificial separation between fast and slow processes need be invoked. Based on the fluorescence Stokes shift function, we utilize a simple and robust strategy to extract the spectral density of a number of molecular complexes from available experimental data. Specifically, we show that experimental data for dye molecules in several solvents, amino acid proteins in water, and some photochemical systems (e.g., rhodopsin and green fluorescence proteins), are well described by a three-parameter family of sub-Ohmic spectral densities that are characterized by a fast initial Gaussian-like decay followed by a slow algebraic-like decay rate at long times.

  19. An important impact of the molecule-electrode couplings asymmetry on the efficiency of bias-driven redox processes in molecular junctions

    CERN Document Server

    Baldea, Ioan

    2015-01-01

    Two recent experimental (Li, J.~\\emphj{et al}, \\emph{Proc.\\ Natl.\\ Acad.\\ Sci.\\ U.~S.~A.} {\\bf 2014}, 111, 1282-1287) and theoretical studies (B\\^aldea, I, \\emph{Phys.\\ Chem.\\ Chem.\\ Phys.}\\ {\\bf 2014}, 16, 25942-25949) have addressed the problem of tuning molecular charge and vibrational properties of single molecules embedded in nanojunctions. These are molecular characteristics escaping so far to an efficient experimental control in broad ranges. Here, we present a general argument demonstrating why, out of various experimental platforms possible, those wherein active molecules are asymmetrically coupled to electrodes are to be preferred to those symmetrically coupled for achieving a(n almost) complete redox process, and why electrochemical environment has advantages over "dry" setups. This study aims at helping to nanofabricate molecular junctions using the most appropriate platforms enabling the broadest possible bias-driven control of the redox state and vibrational modes of single molecules linked to e...

  20. Computational molecular basis for improved silica surface complexation models

    Energy Technology Data Exchange (ETDEWEB)

    Sahai, Nita; Rosso, Kevin M.

    2006-06-06

    The acidity and reactivity of surface sites on amorphous and crystalline polymorphs of silica and other oxides control their thermodynamic stability and kinetic reactivity towards reactants in surface-controlled processes of environmental, industrial, biomedical and technological relevance. Recent advances in computational methodologies such as CPMD and increasing computer power combined with spectroscopic measurements are now making it possible to link, with an impressive degree of accuracy, the molecular-level description of these processes to phenomenological, surface complexation models The future challenge now lies in linking mesoscale properties at the nanometer scale to phenomenological models that will afford a more intuitive understanding of the systems under consideration.

  1. Molecular complexity in astrophysical environments: From astrochemistry to "astrobiology"?

    Science.gov (United States)

    Le Sergeant D'Hendecourt, L.

    2011-01-01

    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 statement. However, the

  2. Complex molecular gas structure in the Medusa merger

    CERN Document Server

    Aalto, S

    2000-01-01

    High resolution OVRO aperture synthesis maps of the 12CO 1-0 emission in the `Medusa' galaxy merger (NGC4194) reveal the molecular emission being surprisingly extended. It is distributed on a total scale of 25$''$ (4.7 kpc) - despite the apparent advanced stage of the merger. The complex, striking CO morphology occupies mainly the center and the north-eastern part of the main optical body. The extended 12CO flux is tracing two prominent dust lanes: one which is crossing the central region at right angle and a second which curves to the north-east and then into the beginning of the northern tidal tail. The bulk of the 12CO emission (67%) can be found in a complex starburst region encompassing the central 2kpc. The molecular gas is distributed in five major emission regions of typical size 300pc. About 15% of the total 12CO flux is found in a bright region 1.5'' south of the radio continuum nucleus. We suggest that this region together with the kpc sized central starburst is being fueled by gas flows along the ...

  3. Molecular assembly and organic film growth on complex intermetallic surfaces

    Science.gov (United States)

    Al-Mahboob, Abdullah; Sharma, Hem Raj; Sadowski, Jerzy T.; Ledieu, Julian; Fournée, Vincent; McGrath, Ronan

    We extensively studied the role of molecular symmetry and symmetry/structures of wide ranges of substrate-surfaces from non-periodic to periodic to quasi-crystalline in nucleation, growth and phase transition in films made of organic molecular materials. Recently, most interest in quasicrystals is due to the generalization of aperiodic ordering to several classes of systems. Compared to periodic materials, these provide a closer approximation to an isotropic first Brillouin zone, which is of great importance to the design of new functional materials. Here, we present results obtained from our ongoing study of interface mediated molecular assembly extended on complex intermetallic surfaces with specific examples of C60 and Zn-phthalocyanine on quasicrystalline and approximant surfaces. We employed in-situ real-time low-energy electron microscopy (LEEM) for investigation of the processes in assembly and film growth and post-growth STM study and DFT calculations to understand structural details and growth mechanism. Research were carried out in part at the Center for Functional Nanomaterials, Brookhaven National Lab, USA; partly at Institut Jean Lamour, Université de Lorraine, France; and partly at the Surface Science Research Centre, University of Liverpool, UK.

  4. Molecular environments of 51 Planck cold clumps in Orion complex

    CERN Document Server

    Liu, Tie; Zhang, Huawei

    2012-01-01

    A mapping survey towards 51 Planck cold clumps projected on Orion complex was performed with J=1-0 lines of $^{12}$CO and $^{13}$CO at the 13.7 m telescope of Purple Mountain Observatory. The mean column densities of the Planck gas clumps range from 0.5 to 9.5$\\times10^{21}$ cm$^{-2}$, with an average value of (2.9$\\pm$1.9)$\\times10^{21}$ cm$^{-2}$. While the mean excitation temperatures of these clumps range from 7.4 to 21.1 K, with an average value of 12.1$\\pm$3.0 K. The averaged three-dimensional velocity dispersion $\\sigma_{3D}$ in these molecular clumps is 0.66$\\pm$0.24 km s$^{-1}$. Most of the clumps have $\\sigma_{NT}$ larger than or comparable with $\\sigma_{Therm}$. 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. Through analyzing the distributions of the physical parameters, we suggest turbulent flows can shape the clump structure and dominate their density distribution in large scale, but not affect ...

  5. Large scale molecular dynamics study of polymer-surfactant complex

    Science.gov (United States)

    Goswami, Monojoy; Sumpter, Bobby

    2012-02-01

    In this work, we study the self-assembly of cationic polyelectrolytes mediated by anionic surfactants in dilute or semi-dilute and gel states. The understanding of the dilute system is a requirement for the understanding of gel states. The importance of polyelectrolyte with oppositely charged colloidal particles can be found in biological systems, such as immobilization of enzymes in polyelectrolyte complexes or nonspecific association of DNA with protein. With the same understanding, interaction of surfactants with polyelectrolytes shows intriguing phenomena that are important for both in academic research as well as industrial applications. Many useful properties of PE surfactant complexes come from the highly ordered structures of surfactant self-assembly inside the PE aggregate. We do large scale molecular dynamics simulation using LAMMPS to understand the structure and dynamics of PE-surfactant systems. Our investigation shows highly ordered ring-string structures that have been observed experimentally in biological systems. We will investigate many different properties of PE-surfactant complexation which will be helpful for pharmaceutical, engineering and biological applications.

  6. Mapping the Orion Molecular Cloud Complex in Radio Frequencies

    Science.gov (United States)

    Castelaz, Michael W.; Lemly, C.

    2013-01-01

    The purpose of this research project was to create a large-scale intensity map of the Orion Molecular Cloud Complex at a radio frequency of 1420 MHz. A mapping frequency of 1420 MHz was chosen because neutral hydrogen, which is the primary component of the Orion Molecular Complex, naturally emits radio waves at this frequency. The radio spectral data for this project were gathered using a 4.6-m radio telescope whose spectrometer was tuned to 1420 MHz and whose beam width was 2.7 degrees. The map created for this project consisted of an eight-by-eight grid centered on M42 spanning 21.6 degrees per side. The grid consisted of 64 individual squares spanning 2.7 degrees per side (corresponding to the beam width of the telescope). Radio spectra were recorded for each of these individual squares at an IF gain of 18. Each spectrum consisted of intensity on an arbitrary scale from 0 to 10 plotted as a function frequencies ranging from -400 kHz to +100 kHz around the origin of 1420 MHz. The data from all 64 radio spectra were imported into Wolfram Alpha, which was used to fit Gaussian functions to the data. The peak intensity and the frequency at which this peak intensity occurs could then be extracted from the Gaussian functions. Other helpful quantities that could be calculated from the Gaussian functions include flux (integral of Gaussian function over frequency range), average value of intensity (flux integral divided by frequency range), and half maximum of intensity. Because all of the radio spectra were redshifted, the velocities of the hydrogen gas clouds of the Orion Molecular Cloud Complex could be calculated using the Doppler equation. The data extracted from the Gaussian functions were then imported into Mathcad to create 2D grayscale maps with right ascension (RA) on the x-axis, declination on the y-axis, and intensity (or flux, etc.) represented on a scale from black to white (with white representing the highest intensities). These 2D maps were then imported

  7. A metallocene molecular complex as visible-light absorber for high-voltage organic-inorganic hybrid photovoltaic cells.

    Science.gov (United States)

    Ishii, Ayumi; Miyasaka, Tsutomu

    2014-04-14

    A thin solid-state dye-sensitized photovoltaic cell is fabricated by composing organic and inorganic heterojunctions in which the visible-light sensitizers are cyclopentadiene derivatives (Cp*) coordinated to a metal oxide, typically TiO2. The coordination bonds of the metallocene molecular complex (Ti-Cp*) create a new LMCT (ligand-to-metal charge transfer) absorption band and induce a rectified charge transfer from the organic ligands to TiO2, leading to photocurrent generation. Photovoltaic junctions are completed by coating crystalline organic molecules (perylene) as a hole-transport layer on the Cp*-coordinated TiO2 surface by using the vapor deposition method. The molecular plane of Cp* on the TiO2 surfaces seems to help the hole-transport layer to form ordered structures, which effectively improve carrier conductivities and minimize interfacial resistance. The organic-inorganic hybrid thin-film photocell with metallocene molecular complexes is capable of generating high open-circuit voltages exceeding 1.2 V. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Porcine lactoferrin-derived peptide LFP-20 protects intestinal barrier by maintaining tight junction complex and modulating inflammatory response.

    Science.gov (United States)

    Zong, Xin; Hu, Wangyang; Song, Deguang; Li, Zhi; Du, Huahua; Lu, Zeqing; Wang, Yizhen

    2016-03-15

    LFP-20, a 20-amino acid antimicrobial peptide in the N terminus of porcine lactoferrin, has antimicrobial and immunomodulatory activities. This study assessed the protective effects of LFP-20 on LPS-induced intestinal damage in a LPS-induced mouse model and in vitro, using intestinal porcine epithelial cell line 1 (IPEC-1) cells. LFP-20 prevented LPS-induced impairment in colon epithelium tissues, infiltration of macrophages or leukocytes, histological evidence of inflammation and increased levels of TNF-a, IL-6 and IFN-γ. LFP-20 increased the expression of zonula occludens-1, occludin and claudin-1 and reduced permeability as well as apoptosis of the colon in LPS-treated mice. In IPEC-1 cells, LFP-20 increased transepithelial electrical resistance and tight junction expression. Moreover, we found LFP-20 decreased the MyD88 and AKT levels to affect the NF-κB signaling pathway, to modulate inflammation response and tight junction networks in the processing of LPS stimulation. In summary, LFP-20 prevents the inflammatory response and disruption of tight junction structure induced by LPS, suggesting the potential use of LFP-20 as a prophylactic agent to protect intestinal barrier function.

  9. 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.

  10. 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.

  11. Mechanistic modeling confronts the complexity of molecular cell biology.

    Science.gov (United States)

    Phair, Robert D

    2014-11-05

    Mechanistic modeling has the potential to transform how cell biologists contend with the inescapable complexity of modern biology. I am a physiologist-electrical engineer-systems biologist who has been working at the level of cell biology for the past 24 years. This perspective aims 1) to convey why we build models, 2) to enumerate the major approaches to modeling and their philosophical differences, 3) to address some recurrent concerns raised by experimentalists, and then 4) to imagine a future in which teams of experimentalists and modelers build-and subject to exhaustive experimental tests-models covering the entire spectrum from molecular cell biology to human pathophysiology. There is, in my view, no technical obstacle to this future, but it will require some plasticity in the biological research mind-set.

  12. Molecular Weight and Charge Density Asymmetry in Polyelectrolyte Complexation

    Science.gov (United States)

    Audus, Debra; Fredrickson, Glenn; Duechs, Dominik

    2009-03-01

    We investigate the phase diagram of oppositely charged polymers in a good solvent using a field-theoretic model. Mean-field solutions fail to predict the experimentally observed macroscopic phase separation into a solvent-rich phase and a dense liquid aggregate of polymers - a ``complex coacervate.'' We therefore study the model within a one-loop approximation, which accounts for Gaussian fluctuations in electrostatic and chemical potentials. Our particular focus is the effect of molecular weight, ionic strength, and charge asymmetry on the phase envelope. A set of dimensionless parameters is identified that dictate the size and shape of the two-phase region. Our results should be helpful in guiding experimental studies of coacervation.

  13. Conserved Molecular Mechanisms Underlying Homeostasis of the Golgi Complex

    Directory of Open Access Journals (Sweden)

    Cathal Wilson

    2010-01-01

    Full Text Available The Golgi complex performs a central function in the secretory pathway in the sorting and sequential processing of a large number of proteins destined for other endomembrane organelles, the plasma membrane, or secretion from the cell, in addition to lipid metabolism and signaling. The Golgi apparatus can be regarded as a self-organizing system that maintains a relatively stable morphofunctional organization in the face of an enormous flux of lipids and proteins. A large number of the molecular players that operate in these processes have been identified, their functions and interactions defined, but there is still debate about many aspects that regulate protein trafficking and, in particular, the maintenance of these highly dynamic structures and processes. Here, we consider how an evolutionarily conserved underlying mechanism based on retrograde trafficking that uses lipids, COPI, SNAREs, and tethers could maintain such a homeodynamic system.

  14. 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.

  15. 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.

    2016-01-01

    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. PMID:27801788

  16. 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.

  17. Molecular paleontology and complexity in the last eukaryotic common ancestor.

    Science.gov (United States)

    Koumandou, V Lila; Wickstead, Bill; Ginger, Michael L; van der Giezen, Mark; Dacks, Joel B; Field, Mark C

    2013-01-01

    Eukaryogenesis, the origin of the eukaryotic cell, represents one of the fundamental evolutionary transitions in the history of life on earth. This event, which is estimated to have occurred over one billion years ago, remains rather poorly understood. While some well-validated examples of fossil microbial eukaryotes for this time frame have been described, these can provide only basic morphology and the molecular machinery present in these organisms has remained unknown. Complete and partial genomic information has begun to fill this gap, and is being used to trace proteins and cellular traits to their roots and to provide unprecedented levels of resolution of structures, metabolic pathways and capabilities of organisms at these earliest points within the eukaryotic lineage. This is essentially allowing a molecular paleontology. What has emerged from these studies is spectacular cellular complexity prior to expansion of the eukaryotic lineages. Multiple reconstructed cellular systems indicate a very sophisticated biology, which by implication arose following the initial eukaryogenesis event but prior to eukaryotic radiation and provides a challenge in terms of explaining how these early eukaryotes arose and in understanding how they lived. Here, we provide brief overviews of several cellular systems and the major emerging conclusions, together with predictions for subsequent directions in evolution leading to extant taxa. We also consider what these reconstructions suggest about the life styles and capabilities of these earliest eukaryotes and the period of evolution between the radiation of eukaryotes and the eukaryogenesis event itself.

  18. 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.

  19. Rotational Spectroscopy of the NH3-H2 Molecular Complex

    Science.gov (United States)

    Surin, L. A.; Tarabukin, I. V.; Schlemmer, S.; Breier, A. A.; Giesen, T. F.; McCarthy, M. C.; van der Avoird, A.

    2017-03-01

    We report the first high resolution spectroscopic study of the NH3–H2 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 NH3–H2 in the wide frequency range from 39 to 230 GHz. Two nuclear spin species, (o)-NH3–(o)-H2 and (p)-NH3–(o)-H2, 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 NH3–H2 PES, which is a key issue for reliable computations of the collisional excitation and de-excitation of ammonia in the dense interstellar medium.

  20. Molecular paleontology and complexity in the last eukaryotic common ancestor

    Science.gov (United States)

    Koumandou, V. Lila; Wickstead, Bill; Ginger, Michael L.; van der Giezen, Mark; Dacks, Joel B.

    2013-01-01

    Eukaryogenesis, the origin of the eukaryotic cell, represents one of the fundamental evolutionary transitions in the history of life on earth. This event, which is estimated to have occurred over one billion years ago, remains rather poorly understood. While some well-validated examples of fossil microbial eukaryotes for this time frame have been described, these can provide only basic morphology and the molecular machinery present in these organisms has remained unknown. Complete and partial genomic information has begun to fill this gap, and is being used to trace proteins and cellular traits to their roots and to provide unprecedented levels of resolution of structures, metabolic pathways and capabilities of organisms at these earliest points within the eukaryotic lineage. This is essentially allowing a molecular paleontology. What has emerged from these studies is spectacular cellular complexity prior to expansion of the eukaryotic lineages. Multiple reconstructed cellular systems indicate a very sophisticated biology, which by implication arose following the initial eukaryogenesis event but prior to eukaryotic radiation and provides a challenge in terms of explaining how these early eukaryotes arose and in understanding how they lived. Here, we provide brief overviews of several cellular systems and the major emerging conclusions, together with predictions for subsequent directions in evolution leading to extant taxa. We also consider what these reconstructions suggest about the life styles and capabilities of these earliest eukaryotes and the period of evolution between the radiation of eukaryotes and the eukaryogenesis event itself. PMID:23895660

  1. Molecular dynamics simulations of a membrane protein/amphipol complex.

    Science.gov (United States)

    Perlmutter, Jason D; Popot, Jean-Luc; Sachs, Jonathan N

    2014-10-01

    Amphipathic polymers known as "amphipols" provide a highly stabilizing environment for handling membrane proteins in aqueous solutions. A8-35, an amphipol with a polyacrylate backbone and hydrophobic grafts, has been extensively characterized and widely employed for structural and functional studies of membrane proteins using biochemical and biophysical approaches. Given the sensitivity of membrane proteins to their environment, it is important to examine what effects amphipols may have on the structure and dynamics of the proteins they complex. Here we present the first molecular dynamics study of an amphipol-stabilized membrane protein, using Escherichia coli OmpX as a model. We begin by describing the structure of the complexes formed by supplementing OmpX with increasing amounts of A8-35, in order to determine how the amphipol interacts with the transmembrane and extramembrane surfaces of the protein. We then compare the dynamics of the protein in either A8-35, a detergent, or a lipid bilayer. We find that protein dynamics on all accessible length scales is restrained by A8-35, which provides a basis to understanding some of the stabilizing and functional effects of amphipols that have been experimentally observed.

  2. Lifetimes and stabilities of familiar explosives molecular adduct complexes during ion mobility measurements

    Science.gov (United States)

    McKenzie, Alan; DeBord, John Daniel; Ridgeway, Mark; Park, Melvin; Eiceman, Gary; Fernandez-Lima, Francisco

    2015-01-01

    Trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) was utilized for the separation and identification of familiar explosives in complex mixtures. For the first time, molecular adduct complex lifetimes, relative stability, binding energies and candidate structures are reported for familiar explosives. Experimental and theoretical results showed that the adduct size and reactivity, complex binding energy and the explosive structure tailors the stability of the molecular adduct complex. TIMS flexibility to adapt the mobility separation as a function of the molecular adduct complex stability (i.e., short or long IMS experiments / low or high IMS resolution) permits targeted measurements of explosives in complex mixtures with higher confidence levels. PMID:26153567

  3. 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.

  4. Molecular mechanisms for interaction of glycine betaine with supra-molecular phycobiliprotein complexes

    Institute of Scientific and Technical Information of China (English)

    XU XiuLing; LI Heng; XIE Jie; ZHAO JingQuan

    2009-01-01

    Glycine betaine (GB) is a biologically important small molecule protecting cells,proteins and enzymes in vivo and in vitro under environmental stresses.Recently,it was found that GB could also relax the structure and inactivate the function of phycobiliproteins and phycobilisome (PBS),a kind of supramolecular complexes,in cyanobacterial cells.The molecular mechanisms for the opposite phenomena are quite ambiguous.Taking PBS and a trimeric or monomeric C-phycocyanin (C-PC) as models,the molecular mechanism for the interaction of GB with supra-molecular complexes or nuclear proteins was investigated.The energetic decoupling of PBS components induced by GB suggests that the PBS core-membrane linking polypeptide was the most sensitive site while the rod-core linker was the next.Biochemistry analysis proves that PBS structure was loosened but not dissociated into the components.On the basis of the results and structure knowledge,it was proposed that GB screened the electrostatic attraction of the opposite charges on a linker and a protein leading to a much looser structure.It was observed that GB induced a spectral blue shift for trimeric C-PC but a red shift for s monomeric C-PC (a nuclear protein),which were ascribed to GB's screening of the electrostatic attraction of a linker to a protein and strengthening of the hydrophobic interaction between C-PC monomers.The trimers and monomers' forming of the same products under high concentration of GB was ascribed to a compromise of the opposite interaction forces.

  5. Molecular mechanisms for interaction of glycine betaine with supra-molecular phycobiliprotein complexes

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Glycine betaine(GB) is a biologically important small molecule protecting cells,proteins and enzymes in vivo and in vitro under environmental stresses.Recently,it was found that GB could also relax the structure and inactivate the function of phycobiliproteins and phycobilisome(PBS),a kind of supramolecular complexes,in cyanobacterial cells.The molecular mechanisms for the opposite phenomena are quite ambiguous.Taking PBS and a trimeric or monomeric C-phycocyanin(C-PC) as models,the molecular mechanism for the interaction of GB with supra-molecular complexes or nuclear proteins was investigated.The energetic decoupling of PBS components induced by GB suggests that the PBS core-membrane linking polypeptide was the most sensitive site while the rod-core linker was the next.Biochemistry analysis proves that PBS structure was loosened but not dissociated into the components.On the basis of the results and structure knowledge,it was proposed that GB screened the electrostatic attraction of the opposite charges on a linker and a protein leading to a much looser structure.It was observed that GB induced a spectral blue shift for trimeric C-PC but a red shift for a monomeric C-PC(a nuclear protein),which were ascribed to GB’s screening of the electrostatic attraction of a linker to a protein and strengthening of the hydrophobic interaction between C-PC monomers.The trimers and monomers’ forming of the same products under high concentration of GB was ascribed to a compromise of the opposite interaction forces.

  6. Sporothrix schenckii complex in Iran: Molecular identification and antifungal susceptibility.

    Science.gov (United States)

    Mahmoudi, Shahram; Zaini, Farideh; Kordbacheh, Parivash; Safara, Mahin; Heidari, Mansour

    2016-08-01

    Sporotrichosis is a global subcutaneous fungal infection caused by the Sporothrix schenckii complex. Sporotrichosis is an uncommon infection in Iran, and there have been no phenotypic, molecular typing or antifungal susceptibility studies of Sporothrix species. This study aimed to identify nine Iranian isolates of the S. schenckii complex to the species level using colony morphology, carbohydrate assimilation tests, and PCR-sequencing of the calmodulin gene. The antifungal susceptibilities of these Sporothrix isolates to five antifungal agents (amphotericin B (AMB), voriconazole (VRC), itraconazole (ITC), fluconazole (FLC), and terbinafine (TRB)) were also evaluated according to the M27-A3 and M38-A2 protocols of the Clinical and Laboratory Standards Institute for yeast and mycelial phases, respectively. Five of seven clinical isolates were identified as S. schenckii, and two clinical and two environmental isolates were identified as S. globosa. This is the first report of S. globosa in Iran. There was significant agreement (73%) between the results of the phenotypic and genotypic identification methods. TRB and ITC were the most effective antifungals against the Sporothrix isolates. The minimum inhibitory concentration (MIC) values of TRB for the yeast and mycelial phases of S. schenckii differed significantly. There was also a significant difference in the minimum fungicidal concentration (MFC) values of AMB and TRB for the two phases. Considering the low efficacy of VRC and FLC and the wide MIC ranges of AMB (1-16 μg/ml and 1-8 μg/ml for yeast and mycelial forms, respectively) observed in the present study, in vitro antifungal susceptibility testing should be performed to determine appropriate therapeutic regimens.

  7. 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

    by contacting the molecular layers with the tip of a conductive force microscope. Measurements done under low-load conditions permit us to obtain reliable tilt-angle and molecular length dependencies of the low-bias conductance through the alkanethiol layers. The observed dependence on tilt-angle is stronger...... 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....

  8. The Fractal Dimension of the ρ Ophiucus Molecular Cloud Complex

    Science.gov (United States)

    Lee, Yongung; Yi, Di; Kim, Y. S.; Jung, J. H.; Kang, H. W.; Lee, C. H.; Yim, I. S.; Kim, H. G.

    2016-12-01

    We estimate the fractal dimension of the ρ Ophiuchus Molecular Cloud Complex, associated with star forming regions. We selected a cube (v, l, b) database, obtained with J=1-0 transition lines of \\coand tco at a resolution of 22'' using a multibeam receiver system on the 14-m telescope of the Five College Radio Astronomy Observatory. Using a code developed within IRAF, we identified slice-clouds with two threshold temperatures to estimate the fractal dimension. With threshold temperatures of 2.25 K (3σ) and 3.75 K (5σ), the fractal dimension of the target cloud is estimated to be D = 1.52-1.54, where P ∝ A^{D/2} , which is larger than previous results. We suggest that the sampling rate (spatial resolution) of observed data must be an important parameter when estimating the fractal dimension, and that narrower or wider dispersion around an arbitrary fit line and the intercepts at NP = 100 should be checked whether they relate to rms noise level or characteristic structure of the target cloud. This issue could be investigated by analysing several high resolution databases with different quality (low or moderate sensitivity).

  9. Protein corona – from molecular adsorption to physiological complexity

    Directory of Open Access Journals (Sweden)

    Lennart Treuel

    2015-03-01

    Full Text Available In biological environments, nanoparticles are enshrouded by a layer of biomolecules, predominantly proteins, mediating its subsequent interactions with cells. Detecting this protein corona, understanding its formation with regards to nanoparticle (NP and protein properties, and elucidating its biological implications were central aims of bio-related nano-research throughout the past years. Here, we discuss the mechanistic parameters that are involved in the protein corona formation and the consequences of this corona formation for both, the particle, and the protein. We review consequences of corona formation for colloidal stability and discuss the role of functional groups and NP surface functionalities in shaping NP–protein interactions. We also elaborate the recent advances demonstrating the strong involvement of Coulomb-type interactions between NPs and charged patches on the protein surface. Moreover, we discuss novel aspects related to the complexity of the protein corona forming under physiological conditions in full serum. Specifically, we address the relation between particle size and corona composition and the latest findings that help to shed light on temporal evolution of the full serum corona for the first time. Finally, we discuss the most recent advances regarding the molecular-scale mechanistic role of the protein corona in cellular uptake of NPs.

  10. Massive Stars in the W33 Giant Molecular Complex

    CERN Document Server

    Messineo, Maria; Figer, Donald F; Kudritzki, Rolf-Peter; Najarro, Francisco; Rich, R Michael; Menten, Karl M; Ivanov, Valentin D; Valenti, Elena; Trombley, Christine; Chen, C -H Rosie; Davies, Ben

    2015-01-01

    Rich in HII regions, giant molecular clouds are natural laboratories to study massive stars and sequential star formation. The Galactic star forming complex W33 is located at l=~12.8deg and at a distance of 2.4 kpc, has a size of ~10 pc and a total mass of (~0.8 - ~8.0) X 10^5 Msun. The integrated radio and IR luminosity of W33 - when combined with the direct detection of methanol masers, the protostellar object W33A, and protocluster embedded within the radio source W33 main - mark the region out as a site of vigorous ongoing star formation. In order to assess the long term star formation history, we performed an infrared spectroscopic search for massive stars, detecting for the first time fourteen early-type stars, including one WN6 star and four O4-7 stars. The distribution of spectral types suggests that this population formed during the last ~2-4 Myr, while the absence of red supergiants precludes extensive star formation at ages 6-30 Myr. This activity appears distributed throughout the region and does ...

  11. Reaction Ensemble Monte Carlo Simulation of Complex Molecular Systems.

    Science.gov (United States)

    Rosch, Thomas W; Maginn, Edward J

    2011-02-08

    Acceptance rules for reaction ensemble Monte Carlo (RxMC) simulations containing classically modeled atomistic degrees of freedom are derived for complex molecular systems where insertions and deletions are achieved gradually by utilizing the continuous fractional component (CFC) method. A self-consistent manner in which to utilize statistical mechanical data contained in ideal gas free energy parameters during RxMC moves is presented. The method is tested by applying it to two previously studied systems containing intramolecular degrees of freedom: the propene metathesis reaction and methyl-tert-butyl-ether (MTBE) synthesis. Quantitative agreement is found between the current results and those of Keil et al. (J. Chem. Phys. 2005, 122, 164705) for the propene metathesis reaction. Differences are observed between the equilibrium concentrations of the present study and those of Lísal et al. (AIChE J. 2000, 46, 866-875) for the MTBE reaction. It is shown that most of this difference can be attributed to an incorrect formulation of the Monte Carlo acceptance rule. Efficiency gains using CFC MC as opposed to single stage molecule insertions are presented.

  12. Protein corona - from molecular adsorption to physiological complexity.

    Science.gov (United States)

    Treuel, Lennart; Docter, Dominic; Maskos, Michael; Stauber, Roland H

    2015-01-01

    In biological environments, nanoparticles are enshrouded by a layer of biomolecules, predominantly proteins, mediating its subsequent interactions with cells. Detecting this protein corona, understanding its formation with regards to nanoparticle (NP) and protein properties, and elucidating its biological implications were central aims of bio-related nano-research throughout the past years. Here, we discuss the mechanistic parameters that are involved in the protein corona formation and the consequences of this corona formation for both, the particle, and the protein. We review consequences of corona formation for colloidal stability and discuss the role of functional groups and NP surface functionalities in shaping NP-protein interactions. We also elaborate the recent advances demonstrating the strong involvement of Coulomb-type interactions between NPs and charged patches on the protein surface. Moreover, we discuss novel aspects related to the complexity of the protein corona forming under physiological conditions in full serum. Specifically, we address the relation between particle size and corona composition and the latest findings that help to shed light on temporal evolution of the full serum corona for the first time. Finally, we discuss the most recent advances regarding the molecular-scale mechanistic role of the protein corona in cellular uptake of NPs.

  13. The Exon Junction Complex Controls the Efficient and Faithful Splicing of a Subset of Transcripts Involved in Mitotic Cell-Cycle Progression

    Directory of Open Access Journals (Sweden)

    Kazuhiro Fukumura

    2016-08-01

    Full Text Available The exon junction complex (EJC that is deposited onto spliced mRNAs upstream of exon–exon junctions plays important roles in multiple post-splicing gene expression events, such as mRNA export, surveillance, localization, and translation. However, a direct role for the human EJC in pre-mRNA splicing has not been fully understood. Using HeLa cells, we depleted one of the EJC core components, Y14, and the resulting transcriptome was analyzed by deep sequencing (RNA-Seq and confirmed by RT–PCR. We found that Y14 is required for efficient and faithful splicing of a group of transcripts that is enriched in short intron-containing genes involved in mitotic cell-cycle progression. Tethering of EJC core components (Y14, eIF4AIII or MAGOH to a model reporter pre-mRNA harboring a short intron showed that these core components are prerequisites for the splicing activation. Taken together, we conclude that the EJC core assembled on pre-mRNA is critical for efficient and faithful splicing of a specific subset of short introns in mitotic cell cycle-related genes.

  14. Exon Junction Complexes Show a Distributional Bias toward Alternatively Spliced mRNAs and against mRNAs Coding for Ribosomal Proteins

    Directory of Open Access Journals (Sweden)

    Christian Hauer

    2016-08-01

    Full Text Available The exon junction complex (EJC connects spliced mRNAs to posttranscriptional processes including RNA localization, transport, and regulated degradation. Here, we provide a comprehensive analysis of bona fide EJC binding sites across the transcriptome including all four RNA binding EJC components eIF4A3, BTZ, UPF3B, and RNPS1. Integration of these data sets permits definition of high-confidence EJC deposition sites as well as assessment of whether EJC heterogeneity drives alternative nonsense-mediated mRNA decay pathways. Notably, BTZ (MLN51 or CASC3 emerges as the EJC subunit that is almost exclusively bound to sites 20–24 nucleotides upstream of exon-exon junctions, hence defining EJC positions. By contrast, eIF4A3, UPF3B, and RNPS1 display additional RNA binding sites suggesting accompanying non-EJC functions. Finally, our data show that EJCs are largely distributed across spliced RNAs in an orthodox fashion, with two notable exceptions: an EJC deposition bias in favor of alternatively spliced transcripts and against the mRNAs that encode ribosomal proteins.

  15. The EhCPADH112 Complex of Entamoeba histolytica Interacts with Tight Junction Proteins Occludin and Claudin-1 to Produce Epithelial Damage

    OpenAIRE

    Abigail Betanzos; Rosario Javier-Reyna; Guillermina García-Rivera; Cecilia Bañuelos; Lorenza González-Mariscal; Michael Schnoor; Esther Orozco

    2013-01-01

    Entamoeba histolytica, the protozoan responsible for human amoebiasis, causes between 30,000 and 100,000 deaths per year worldwide. Amoebiasis is characterized by intestinal epithelial damage provoking severe diarrhea. However, the molecular mechanisms by which this protozoan causes epithelial damage are poorly understood. Here, we studied the initial molecular interactions between the E. histolytica EhCPADH112 virulence complex and epithelial MDCK and Caco-2 cells. By confocal microscopy, we...

  16. GEN1/Yen1 and the SLX4 complex: solutions to the problem of Holliday junction resolution

    Science.gov (United States)

    Svendsen, Jennifer M.; Harper, J. Wade

    2010-01-01

    Chromosomal double-strand breaks (DSBs) are considered to be among the most deleterious DNA lesions found in eukaryotic cells due to their propensity to promote genome instability. DSBs occur as a result of exogenous or endogenous DNA damage, and also occur during meiotic recombination. DSBs are often repaired through a process called homologous recombination (HR), which employs the sister chromatid in mitotic cells or the homologous chromosome in meiotic cells, as a template for repair. HR frequently involves the formation and resolution of four-way DNA structures referred to as the Holliday junction (HJ). Despite extensive study, the machinery and mechanisms used to process these structures in eukaryotes have remained poorly understood. Recent work has identified XPG and UvrC/GIY domain-containing structure-specific endonucleases that can symmetrically cleave HJs in vitro in a manner that allows for religation without additional processing, properties that are reminiscent of the classical RuvC HJ resolvase in bacteria. Genetic studies reveal potential roles for these HJ resolvases in repair after DNA damage and during meiosis. The stage is now set for a more comprehensive understanding of the specific roles these enzymes play in the response of cells to DSBs, collapsed replication forks, telomere dysfunction, and meiotic recombination. PMID:20203129

  17. An asymmetric A-B-A' metallo-supramolecular triblock copolymer linked by Ni(2+)-bis-terpyridine complexes at one junction.

    Science.gov (United States)

    Li, Haixia; Wei, Wei; Xiong, Huiming

    2016-02-01

    A metallo-supramolecular triblock copolymer polystyrene-b-polyisoprene-[Ni(2+)]-polystyrene (SI-[Ni(2+)]-S') has been efficiently prepared using a one-pot, two-step procedure, where the blocks are held by bis-terpyridine complexes at the junction of SI-S'. This specific metallo-supramolecular chemistry is demonstrated to be a robust approach to potentially broaden the diversity of block copolymers. The location of the metal-ligand complexes has a profound influence on the phase separation of the triblock copolymer in the bulk, which results in a distinctive phase segregation between the end blocks and leads to an unexpected asymmetry of the triblock copolymer. The metal-ligand complexes are found to be preferentially located on the adjacent spherical domain and form a core-shell structure. The resulting multiphase material exhibits distinct elastomeric properties with significant toughness and creep recovery behavior. This type of triblock copolymer is anticipated to be a novel class of hybrid thermo-plastic elastomeric material with wide tunability and functionality.

  18. '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

  19. Molecular mechanism underlying RAG1/RAG2 synaptic complex formation.

    Science.gov (United States)

    Shlyakhtenko, Luda S; Gilmore, Jamie; Kriatchko, Aleksei N; Kumar, Sushil; Swanson, Patrick C; Lyubchenko, Yuri L

    2009-07-31

    Two lymphoid cell-specific proteins, RAG1 and RAG2 (RAG), initiate V(D)J recombination by assembling a synaptic complex with recombination signal sequences (RSSs) abutting two different antigen receptor gene coding segments, and then introducing a DNA double strand break at the end of each RSS. Despite the biological importance of this system, the structure of the synaptic complex, and the RAG protein stoichiometry and arrangement of DNA within the synaptosome, remains poorly understood. Here we applied atomic force microscopy to directly visualize and characterize RAG synaptic complexes. We report that the pre-cleavage RAG synaptic complex contains about twice the protein content as a RAG complex bound to a single RSS, with a calculated mass consistent with a pair of RAG heterotetramers. In the synaptic complex, the RSSs are predominantly oriented in a side-by-side configuration with no DNA strand crossover. The mass of the synaptic complex, and the conditions under which it is formed in vitro, favors an association model of assembly in which isolated RAG-RSS complexes undergo synapsis mediated by RAG protein-protein interactions. The replacement of Mg2+ cations with Ca2+ leads to a dramatic change in protein stoichiometry for all RAG-RSS complexes, suggesting that the cation composition profoundly influences the type of complex assembled.

  20. Molecular Mechanism Underlying RAG1/RAG2 Synaptic Complex Formation*

    Science.gov (United States)

    Shlyakhtenko, Luda S.; Gilmore, Jamie; Kriatchko, Aleksei N.; Kumar, Sushil; Swanson, Patrick C.; Lyubchenko, Yuri L.

    2009-01-01

    Two lymphoid cell-specific proteins, RAG1 and RAG2 (RAG), initiate V(D)J recombination by assembling a synaptic complex with recombination signal sequences (RSSs) abutting two different antigen receptor gene coding segments, and then introducing a DNA double strand break at the end of each RSS. Despite the biological importance of this system, the structure of the synaptic complex, and the RAG protein stoichiometry and arrangement of DNA within the synaptosome, remains poorly understood. Here we applied atomic force microscopy to directly visualize and characterize RAG synaptic complexes. We report that the pre-cleavage RAG synaptic complex contains about twice the protein content as a RAG complex bound to a single RSS, with a calculated mass consistent with a pair of RAG heterotetramers. In the synaptic complex, the RSSs are predominantly oriented in a side-by-side configuration with no DNA strand crossover. The mass of the synaptic complex, and the conditions under which it is formed in vitro, favors an association model of assembly in which isolated RAG-RSS complexes undergo synapsis mediated by RAG protein-protein interactions. The replacement of Mg2+ cations with Ca2+ leads to a dramatic change in protein stoichiometry for all RAG-RSS complexes, suggesting that the cation composition profoundly influences the type of complex assembled. PMID:19502597

  1. (Molecular cloning and structural characteristics of the R complex of maize)

    Energy Technology Data Exchange (ETDEWEB)

    1992-01-01

    Studies on the R complex in Maize continued Progress is discussed in the following areas: Establishing identity of R components and cloning of R components; CO allele origin; molecular organization of R-r complex; NCO allele origin; genetic analysis of R-r complex; studies of the Sn locus and reverse paramutation.

  2. [Molecular cloning and structural characteristics of the R complex of maize]. Annual progress report

    Energy Technology Data Exchange (ETDEWEB)

    1992-07-01

    Studies on the R complex in Maize continued Progress is discussed in the following areas: Establishing identity of R components and cloning of R components; CO allele origin; molecular organization of R-r complex; NCO allele origin; genetic analysis of R-r complex; studies of the Sn locus and reverse paramutation.

  3. 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...

  4. 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.

  5. Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations.

    Science.gov (United States)

    Chen, Alan A; García, Angel E

    2012-06-12

    An RNA kissing loop from the Moloney murine leukemia virus (MMLV) exhibits unusual mechanical stability despite having only two intermolecular base pairs. Mutations at this junction have been shown to destabilize genome dimerization, with concomitant reductions in viral packaging efficiency and infectivity. Optical tweezers experiments have shown that it requires as much force to break the MMLV kissing-loop complex as is required to unfold an 11-bp RNA hairpin [Li PTX, Bustamante C, Tinoco I (2006) Proc Natl Acad Sci USA 103:15847-15852]. Using nonequilibrium all-atom molecular dynamics simulations, we have developed a detailed model for the kinetic intermediates of the force-induced dissociation of the MMLV dimerization initiation site kissing loop. Two hundred and eight dissociation events were simulated (approximately 16 μs total simulation time) under conditions of constant applied external force, which we use to construct a Markov state model for kissing-loop dissociation. We find that the complex undergoes a conformational rearrangement, which allows for equal distribution of the applied force among all of the intermolecular hydrogen bonds, which is intrinsically more stable than the sequential unzipping of an ordinary hairpin. Stacking interactions with adjacent, unpaired loop adenines further stabilize the complex by increasing the repair rate of partially broken H-bonds. These stacking interactions are prominently featured in the transition state, which requires additional coordinates orthogonal to the end-to-end extension to be uniquely identified. We propose that these stabilizing features explain the unusual stability of other retroviral kissing-loop complexes such as the HIV dimerization site.

  6. Lifetimes and stabilities of familiar explosive molecular adduct complexes during ion mobility measurements.

    Science.gov (United States)

    McKenzie-Coe, Alan; DeBord, John Daniel; Ridgeway, Mark; Park, Melvin; Eiceman, Gary; Fernandez-Lima, Francisco

    2015-08-21

    Trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) was utilized for the separation and identification of familiar explosives in complex mixtures. For the first time, molecular adduct complex lifetimes, relative stability, binding energies and candidate structures are reported for familiar explosives. Experimental and theoretical results showed that the adduct size and reactivity, complex binding energy and the explosive structure tailor the stability of the molecular adduct complex. The flexibility of TIMS to adapt the mobility separation as a function of the molecular adduct complex stability (i.e., short or long IMS experiments/low or high IMS resolution) permits targeted measurements of explosives in complex mixtures with high confidence levels.

  7. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    Energy Technology Data Exchange (ETDEWEB)

    Nagaoka, Masataka [Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601 (Japan); Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Honmachi, Kawaguchi 332-0012 (Japan); ESICB, Kyoto University, Kyodai Katsura, Nishikyo-ku, Kyoto 615-8520 (Japan)

    2015-12-31

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

  8. Mre11-Rad50 complex crystals suggest molecular calisthenics

    NARCIS (Netherlands)

    C. Wyman (Claire); J.H.G. Lebbink (Joyce); R. Kanaar (Roland)

    2011-01-01

    textabstractRecently published crystal structures of different Mre11 and Rad50 complexes show the arrangement of these proteins and imply dramatic ligand-induced rearrangements with important functional consequences.

  9. Thermodynamic stability and crystallization behavior of molecular complexes with TEP host

    Science.gov (United States)

    Fijiwara, Atsushi; Kitamura, Mitsutaka

    2013-06-01

    In the crystallization of molecular complex (co-crystal, clathrate complex), polymorphism in regard to the host structure frequently appears. Previously, we studied the release process of the biocide, CMI (5-chloro-2-methyl-4-isothiazolin-3-one) from the molecular complex with TEP (1,1,2,2-tetrakis(4-hydroxyphenyl)ethane) (TEP·2CMI) in methanol-water mixed solvents. It was clear that the release process of the biocide (CMI) is composed of the transformation from the TEP·2CMI crystal to a more stable molecular complex crystal with solvent. In this work, the crystallization was performed in the methanol solutions including TEP and CMI at constant temperature (298 K and 308 K). It appeared that two kinds of TEP molecular complexes (TEP·2CMI and TEP·2MeOH) crystallize competitively. The crystallization zone of each molecular complex was shown in the map using the coordinates of initial concentrations of TEP and CMI. In the boundary zone both molecular complexes appeared and the transformation from TEP·2CMI to TEP·2MeOH was observed, indicating that the stable form is TEP·2MeOH. Without the boundary zone the corresponding stable form crystallized in each zone. The value of the initial concentration ratio of CMI/TEP for the selective crystallization of TEP·2CMI was higher at 298 K (1.54) than that (1.36) at 308 K. The equilibrium concentrations of TEP and CMI in the presence of two molecular complexes were expressed using the dissociation constants of the molecular complexes and it was indicated that the dissociation of TEP·2CMI highly increases with temperature

  10. Magnesium Lowers the Incidence of Postoperative Junctional Ectopic Tachycardia in Congenital Heart Surgical Patients: Is There a Relationship to Surgical Procedure Complexity?

    Science.gov (United States)

    He, Dingchao; Sznycer-Taub, Nathaniel; Cheng, Yao; McCarter, Robert; Jonas, Richard A; Hanumanthaiah, Sridhar; Moak, Jeffrey P

    2015-08-01

    Magnesium sulfate was given to pediatric cardiac surgical patients during cardiopulmonary bypass period in an attempt to reduce the occurrence of postoperative junctional ectopic tachycardia (PO JET). We reviewed our data to evaluate the effect of magnesium on the occurrence of JET and assess a possible relationship between PO JET and procedure complexity. A total of 1088 congenital heart surgeries (CHS), performed from 2005 to 2010, were reviewed. A total of 750 cases did not receive magnesium, and 338 cases received magnesium (25 mg/kg). All procedures were classified according to Aristotle score from 1 to 4. Overall, there was a statistically significant decrease in PO JET occurrence between the two groups regardless of the Aristotle score, 15.3 % (115/750) in non-magnesium group versus 7.1 % (24/338) in magnesium group, P < 0.001. In the absence of magnesium, the risk of JET increased with increasing Aristotle score, P = 0.01. Following magnesium administration and controlling for body weight, surgical and aortic cross-clamp times in the analyses, reduction in adjusted risk of JET was significantly greater with increasing Aristotle level of complexity (JET in non-magnesium vs. magnesium group, Aristotle level 1: 9.8 vs. 14.3 %, level 4: 11.5 vs. 3.2 %; odds ratio 0.54, 95 % CI 0.31-0.94, P = 0.028). Our data confirmed that intra-operative usage of magnesium reduced the occurrence of PO JET in a larger number and more diverse group of CHS patients than has previously been reported. Further, our data suggest that magnesium's effect on PO JET occurrence seemed more effective in CHS with higher levels of Aristotle complexity.

  11. Molecular composition and ultrastructure of the caveolar coat complex.

    Directory of Open Access Journals (Sweden)

    Alexander Ludwig

    Full Text Available 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.

  12. Comparison of single junction AlGaInP and GaInP solar cells grown by molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Masuda, T; Tomasulo, S; Lang, JR; Lee, ML

    2015-03-07

    We have investigated similar to 2.0 eV (AlxGa1-x)(0.51)In0.49P and similar to 1.9 eV Ga0.51In0.49P single junction solar cells grown on both on-axis and misoriented GaAs substrates by molecular beam epitaxy (MBE). Although lattice-matched (AlxGa1-x)(0.51)In0.49P solar cells are highly attractive for space and concentrator photovoltaics, there have been few reports on the MBE growth of such cells. In this work, we demonstrate open circuit voltages (V-oc) ranging from 1.29 to 1.30 V for Ga0.51In0.49P cells, and 1.35-1.37 V for (AlxGa1-x)(0.51)In0.49P cells. Growth on misoriented substrates enabled the bandgap-voltage offset (W-oc = E-g/q - V-oc) of Ga0.51In0.49P cells to decrease from similar to 575 mV to similar to 565 mV, while that of (AlxGa1-x)(0.51)In0.49P cells remained nearly constant at 620 mV. The constant Woc as a function of substrate offcut for (AlxGa1-x)(0.51)In0.49P implies greater losses from non-radiative recombination compared with the Ga0.51In0.49P devices. In addition to larger Woc values, the (AlxGa1-x)(0.51)In0.49P cells exhibited significantly lower internal quantum efficiency (IQE) values than Ga0.51In0.49P cells due to recombination at the emitter/window layer interface. A thin emitter design is experimentally shown to be highly effective in improving IQE, particularly at short wavelengths. Our work shows that with further optimization of both cell structure and growth conditions, MBE-grown (AlxGa1-x)(0.51)In0.49P will be a promising wide-bandgap candidate material for high-efficiency, lattice-matched multi-junction solar cells. (C) 2015 AIP Publishing LLC.

  13. Luminescent molecular rods - transition-metal alkynyl complexes.

    Science.gov (United States)

    Yam, Vivian Wing-Wah; Wong, Keith Man-Chung

    2005-01-01

    A number of transition-metal complexes have been reported to exhibit rich luminescence, usually originating from phosphorescence. Such luminescence properties of the triplet excited state with a large Stoke's shift, long lifetime, high luminescence quantum yield as well as lower excitation energy, are envisaged to serve as an ideal candidate in the area of potential applications for chemosensors, dye-sensitized solar cells, flat panel displays, optics, new materials and biological sciences. Organic alkynes (poly-ynes), with extended or conjugatedπ-systems and rigid structure with linear geometry, have become a significant research area due to their novel electronic and physical properties and their potential applications in nanotechnology. Owing to the presence of unsaturated sp-hybridized carbon atoms, the alkynyl unit can serve as a versatile building block in the construction of alkynyl transition-metal complexes, not only throughσ-bonding but also viaπ-bonding interactions. By incorporation of linear alkynyl groups into luminescent transition-metal complexes, the alkynyl moiety with goodσ-donor,π-donor andπ-acceptor abilities is envisaged to tune or perturb the emission behaviors, including emission energy (color), intensity and lifetime by its role as an auxiliary ligand as well as to govern the emission origin from its direct involvement. This review summarizes recent efforts on the synthesis of luminescent rod-like alkynyl complexes with different classes of transition metals and details the effects of the introduction of alkynyl groups on the luminescence properties of the complexes.

  14. Molecular Recognition by Q-BISDIEN and Its Dinuclear Complexes

    Science.gov (United States)

    1992-01-30

    KR12 . The first binuclear (u-hydroxo) complex forms a malonato bridged species in contrast to the observations of the dicopper phosphate system...O-BISDIEN/Co(II) malonato adducts discussed in this section. A different p[H] profile is obtained for the O-BISDIEN, Co(ll)-malonate system when it...Figure 6, the dioxygen complexes are plainly obvious, especially the non-hydroxo-bridged Co 2 BdMal(0 2) 2 + , 6, where apparently the malonato bridge

  15. Complex reaction noise in a molecular quasispecies model

    Science.gov (United States)

    Hochberg, David; Zorzano, María-Paz; Morán, Federico

    2006-05-01

    We have derived exact Langevin equations for a model of quasispecies dynamics. The inherent multiplicative reaction noise is complex and its statistical properties are specified completely. The numerical simulation of the complex Langevin equations is carried out using the Cholesky decomposition for the noise covariance matrix. This internal noise, which is due to diffusion-limited reactions, produces unavoidable spatio-temporal density fluctuations about the mean field value. In two dimensions, this noise strictly vanishes only in the perfectly mixed limit, a situation difficult to attain in practice.

  16. Polarized Emission of Molecular Film With Lanthanide (Ⅲ) Complex

    Institute of Scientific and Technical Information of China (English)

    M.Hasegawa

    2007-01-01

    1 Results In the coordination system by using complexation with organic ligand, the ff emission of lanthanide(Ⅲ) (Ln(Ⅲ)) is induced the excitation energy transfer form the organic chromophore under the light-irradiation. However, there are not so much number of reports to discuss the energy relaxation mechanism in such complexes with Ln(Ⅲ). Recently, we succeeded firstly to estimate the rate constant of the energy transfer between the ligand and Ln(Ⅲ) in Pr(Ⅲ)-phenanthroline analogs[1]. Here, we will di...

  17. THE BIMODAL MOLECULAR WEIGHT DISTRIBUTION OF cis-POLYBUTADIENE POLYMERIZED WITH LANTHANIDE COMPLEX CATALYSTS

    Institute of Scientific and Technical Information of China (English)

    CHENG Rongshi; HU Huizhen; JIANG Liansheng

    1987-01-01

    The variation of the molecular weight and molecular weight distribution of cis-polybutadiene in the course of polymerization catalyzed by lanthanide complex composed of triisobutyl aluminium or diisobutyl aluminium hydride was investigated by osmometry, viscometry and size exclusion chromatography. By analyzing the experimental data, the reasons of the appearance of bimodal molecular weight distribution were elucidated and the possible mechanisms of polymerization were discussed.

  18. Resonant Scattering of Muonic Hydrogen Atoms and Dynamics of Muonic Molecular Complex

    CERN Document Server

    Fujiwara, M C; Bailey, J M; Beer, G A; Beveridge, J L; Faifman, M P; Huber, T M; Kammel, P; Kim, S K; Knowles, P E; Kunselman, A R; Maier, M; Markushin, V E; Marshall, G M; Martoff, C J; Mason, G R; Mulhauser, F; Olin, A; Petitjean, C; Porcelli, T A; Wozniak, J; Zmeskal, J

    2001-01-01

    Resonant scattering of muonic hydrogen atoms via back decay of molecular complex, a key process in the understanding of epithermal muonic molecular formation, is analyzed. The limitations of the effective rate approximation are discussed and the importance of the explicit treatment of the back decay is stressed. An expression of the energy distribution for the back-decayed atoms is given.

  19. First-principles study of the variation of electron transport in a single molecular junction with the length of the molecular wire

    Science.gov (United States)

    Pal, Partha Pratim; Pati, Ranjit

    2010-07-01

    We report a first-principles study of quantum transport in a prototype two-terminal device consisting of a molecular nanowire acting as an inter-connect between two gold electrodes. The wire is composed of a series of bicyclo[1.1.1]pentane (BCP) cage-units. The length of the wire (L) is increased by sequentially increasing the number of BCP cage units in the wire from 1 to 3. A two terminal model device is made out of each of the three wires. A parameter free, nonequilibrium Green’s function approach, in which the bias effect is explicitly included within a many body framework, is used to calculate the current-voltage characteristics of each of the devices. In the low bias regime that is considered in our study, the molecular devices are found to exhibit Ohmic behavior with resistances of 0.12, 1.4, and 6.5μΩ for the wires containing one, two, and three cages respectively. Thus the conductance value, Gc , which is the reciprocal of resistance, decreases as e-βL with a decay constant (β) of 0.59Å-1 . This observed variation of conductance with the length of the wire is in excellent agreement with the earlier reported exponential decay feature of the electron transfer rate predicted from the electron transfer coupling matrix values obtained using the two-state Marcus-Hush model and the Koopman’s theorem approximation. The downright suppression of the computed electrical current for a bias up to 0.4 V in the longest wire can be exploited in designing a three terminal molecular transistor; this molecular wire could potentially be used as a throttle to avoid leakage gate current.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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 dia

  5. Correlative super-resolution fluorescence and electron microscopy of the nuclear pore complex with molecular resolution.

    Science.gov (United States)

    Löschberger, Anna; Franke, Christian; Krohne, Georg; van de Linde, Sebastian; Sauer, Markus

    2014-10-15

    Here, we combine super-resolution fluorescence localization microscopy with scanning electron microscopy to map the position of proteins of nuclear pore complexes in isolated Xenopus laevis oocyte nuclear envelopes with molecular resolution in both imaging modes. We use the periodic molecular structure of the nuclear pore complex to superimpose direct stochastic optical reconstruction microscopy images with a precision of <20 nm on electron micrographs. The correlative images demonstrate quantitative molecular labeling and localization of nuclear pore complex proteins by standard immunocytochemistry with primary and secondary antibodies and reveal that the nuclear pore complex is composed of eight gp210 (also known as NUP210) protein homodimers. In addition, we find subpopulations of nuclear pore complexes with ninefold symmetry, which are found occasionally among the more typical eightfold symmetrical structures.

  6. Optical and transport properties of complex molecular systems

    OpenAIRE

    2009-01-01

    Esta Tesis presenta el estudio de las propiedades ópticas y de transporte de sistemas de baja dimensionalidad a través de modelos de enlace fuerte. Nuestro trabajo se centra en dos tipos de sistemas: agregados moleculares lineales y moléculas de ADN.En los Capítulos 2, 3 y 4 se estudian las propiedades de localización de un Hamiltoniano de Frenkel desordenado unidimensional. El desorden se introduce en las energías de sitio y es correlacionado de largo alcance. Para correlaciones fuertes, se ...

  7. Synthesis, molecular spectroscopy and thermal analysis of some cefepime complexes

    Science.gov (United States)

    Masoud, Mamdouh S.; Ali, Alaa E.; Ghareeb, Doaa A.; Nasr, Nessma M.

    2016-03-01

    The metal complexes of cefepime with Cr (III), Mn (II), Fe (III), Co (II), Cu (II), Zn (II), Cd (II), Hg (II) and mixed metals (Fe, Ni) or (Cu, Fe) were synthesized, the suggested structures of the complexes are based on the results of the elemental analysis, infrared, UV-visible, mass and HNMR spectra, effective magnetic moment as well as the thermal analysis (DTA, TGA & DSC) and characterized by energy dispersive x-ray (EDX) and scanning electron microscopy (SEM). The results obtained suggested that cefepime reacted with metal ions as bidentate ligand through the nitrogen of the β-lactone thiozolidine ring and carboxylate ion forming a five membered ring. The kinetic thermodynamic parameters were estimated from the DTA curves.

  8. Molecular complexities of patched signaling in cancer development

    OpenAIRE

    2004-01-01

    Basal Cell Cancer (BCC) is the most common cancer in the Western world. Although BCCs hardly ever metastasize, invasive growth may cause considerable local tissue destruction. BCCs mainly occur as sporadic tumors but can also be found in a hereditary form in the Nevoid Basal Cell Carcinoma Syndrome (NBCCS). The gene underlying the NBCCS is Patched1 (PTCH1), a tumor suppressor gene that is mutated or deleted in these patients. This thesis is focusing in deciphering complex...

  9. Molecular architecture of the preinitiation complex in adenovirus DNA replication

    OpenAIRE

    Mysiak, Monika Elzbieta

    2004-01-01

    After infection of a host cell, adenovirus (Ad) aims for generation of progeny viruses, and thus it rapidly replicates its genomic DNA. The replication process starts with the assembly of the preinitiation complex (PIC) on the origin DNA. The PIC consists of three viral proteins, DNA polymerase (pol), precursor terminal protein (pTP), DNA binding protein (DBP) and two transcription factors of the host cell, Nuclear Factor I (NFI) and Octamer binding protein (Oct-1). Both transcription factors...

  10. 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.

  11. Streching of (DNA/functional molecules) complex between electrodes towards DNA molecular wire

    Science.gov (United States)

    Kobayashi, Norihisa; Nishizawa, Makoto; Inoue, Shintarou; Nakamura, Kazuki

    2009-08-01

    DNA/functional molecules such as (Ru(bpy)32+ complex, conducting polymer etc.) complex was prepared to study molecular structure and I-V characteristics towards DNA molecular wire. For example, Ru(bpy)32+ was associated with duplex of DNA by not only electrostatic interaction but also intercalation in the aqueous solution. Singlemolecular structure of DNA/Ru(bpy)32+ complex was analyzed with AFM. We found a network structure of DNA/Ru(bpy)32+ complex on the mica substrate, which is similar to native DNA. The height of DNA/Ru(bpy)32+ complex on the mica substrate was ranging from 0.8 to 1.6 nm, which was higher than the naked DNA (0.5-1.0 nm). This indicates that single-molecular DNA/Ru(bpy)32+ complex also connects to each other to form network structure on a mica substrate. In order to stretch DNA complex between electrodes, we employed high frequency and high electric field stretching method proposed by Washizu et al. We stretched and immobilized DNA single molecules between a pair of electrodes and its structures were analyzed with AFM technique. The I-V characteristics of DNA single molecules between electrodes were improved by the association of functional molecules with DNA. The molecular structure and I-V characteristics of DNA complex were discussed.

  12. Nanoporous carbon sorbent for molecular-sieve chromatography of lipoprotein complex

    Science.gov (United States)

    Kerimkulova, A. R.; Mansurova, B. B.; Gil'manov, M. K.; Mansurov, Z. A.

    2012-06-01

    The physicochemical characteristics of carbon sorbents are investigated. Electron microscopy data for the sorbent and separated lipoprotein complex are presented. It is found that the obtained carbon sorbent possess high porosity. Nanoporous carbon sorbents for the chromatography of molecular-sieve markers are obtained and tested. The applicability of nanoporous carbon sorbents for separation of lipoprotein complexes (LPC) is investigated.

  13. On the masses of giant molecular cloud complexes

    Science.gov (United States)

    Stark, A. A.; Blitz, L.

    1978-01-01

    A method of mass estimation for molecular clouds is presented which is based on approximate balance in the outer cloud layers between the cloud's gravitation, the galactic tide, and internal pressure. The largest observed clouds, which have greatest linear extents of 100 pc, are found to have masses of at least 200,000 solar masses. The cloud masses cannot exceed this lower limit by more than a factor of 3, or the velocity distributions of disk stars would be more relaxed than is actually observed. This implied upper limit to cloud masses combined with the galactic tide may be related to the absence of clouds at galactocentric radii less than 4 kpc. If Sagittarius B2 is bound, its mass must be more than 50 million solar masses.

  14. 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

  15. Visualization of complex processes in lipid systems using computer simulations and molecular graphics.

    Science.gov (United States)

    Telenius, Jelena; Vattulainen, Ilpo; Monticelli, Luca

    2009-01-01

    Computer simulation has become an increasingly popular tool in the study of lipid membranes, complementing experimental techniques by providing information on structure and dynamics at high spatial and temporal resolution. Molecular visualization is the most powerful way to represent the results of molecular simulations, and can be used to illustrate complex transformations of lipid aggregates more easily and more effectively than written text. In this chapter, we review some basic aspects of simulation methodologies commonly employed in the study of lipid membranes and we describe a few examples of complex phenomena that have been recently investigated using molecular simulations. We then explain how molecular visualization provides added value to computational work in the field of biological membranes, and we conclude by listing a few molecular graphics packages widely used in scientific publications.

  16. 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.

  17. A taco complex derived from a bis-crown ether capable of executing molecular logic operation through reversible complexation.

    Science.gov (United States)

    Mandal, Amal Kumar; Das, Priyadip; Mahato, Prasenjit; Acharya, Suhash; Das, Amitava

    2012-08-17

    As learned from natural systems, self-assembly and self-sorting help in interconnecting different molecular logic gates and thus achieve high-level logic functions. In this context, demonstration of important logic operations using changes in optical responses due to the formation of molecular assemblies is even more desirable for the construction of a molecular computer. Synthesis of an appropriate divalent as well as a luminescent crown ether based host 1 and paraquat derivatives, 2(PF(6))(2) and 3(PF(6))(2), as guests helped in demonstrating a reversible [3](taco complex) (1·{2(PF(6))(2)}(2) or 1·{3(PF(6))(2)}(2)) formation in nonpolar solvent. Detailed (1)H NMR studies revealed that two paraquat units were bound cooperatively by the two crown units in 1. Because of preorganization, the flexible host molecule 1 adopts a folded conformation, where each of two paraquat units remain sandwiched between the two aromatic units of each folded crown ether moiety in 1. Disassembly of the "taco" complex in the presence of KPF(6) and reassembly on subsequent addition of DB18C6 was initially demonstrated by (1)H NMR spectral studies, which were subsequently corroborated through luminescence spectral studies. Further, luminescence spectral responses as output signals with appropriate and two independent molecular inputs could be correlated to demonstrate basic logic operation like OR and YES gates, while the results of the three molecular inputs could be utilized to demonstrate important logic operation like an INHIBIT gate.

  18. CD Spectroscopic Study on the Molecular Recognition of Chiral Salen-Metal Complexes

    Institute of Scientific and Technical Information of China (English)

    刘涛; 阮文娟; 南晶; 朱志昂

    2003-01-01

    The molecular recognition behavior of the chiral salen-metal complexes towards guest molecules, such as imidazole derivatives and amino-acid ester, was systematically investigated by means of circular dichroism (CD) spectra. The coordination numbers of the host-guest complexes as well as the recognition capability of the salen-metal complexes were explained by character and intensity analyses of the CD spectra.

  19. 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...

  20. Structure Stability of Ⅰ-Type Carbon Nanotube Junctions

    Institute of Scientific and Technical Information of China (English)

    夏丹; 袁喆; 李家明

    2002-01-01

    Carbon nanotubes with junctions may play an important role in future ‘nanoelectronics' and future ‘nano devices'.In particular, junctions constructed with metal and semiconducting nanotubes have potential applications. Basedon the orthogonal tight-binding molecular dynamics method, we present our study of the structure stability ofI-type carbon nanotube junctions.

  1. 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

  2. Rectification in tunneling junctions: 2,2'-bipyridyl-terminated n-alkanethiolates.

    Science.gov (United States)

    Yoon, Hyo Jae; Liao, Kung-Ching; Lockett, Matthew R; Kwok, Sen Wai; Baghbanzadeh, Mostafa; Whitesides, George M

    2014-12-10

    Molecular rectification is a particularly attractive phenomenon to examine in studying structure-property relationships in charge transport across molecular junctions, since the tunneling currents across the same molecular junction are measured, with only a change in the sign of the bias, with the same electrodes, molecule(s), and contacts. This type of experiment minimizes the complexities arising from measurements of current densities at one polarity using replicate junctions. This paper describes a new organic molecular rectifier: a junction having the structure Ag(TS)/S(CH2)11-4-methyl-2,2'-bipyridyl//Ga2O3/EGaIn (Ag(TS): template-stripped silver substrate; EGaIn: eutectic gallium-indium alloy) which shows reproducible rectification with a mean r(+) = |J(+1.0 V)|/|J(-1.0 V)| = 85 ± 2. This system is important because rectification occurs at a polarity opposite to that of the analogous but much more extensively studied systems based on ferrocene. It establishes (again) that rectification is due to the SAM, and not to redox reactions involving the Ga2O3 film, and confirms that rectification is not related to the polarity in the junction. Comparisons among SAM-based junctions incorporating the Ga2O3/EGaIn top electrode and a variety of heterocyclic terminal groups indicate that the metal-free bipyridyl group, not other features of the junction, is responsible for the rectification. The paper also describes a structural and mechanistic hypothesis that suggests a partial rationalization of values of rectification available in the literature.

  3. 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.

  4. Dynamic Coherence in Excitonic Molecular Complexes under Various Excitation Conditions

    CERN Document Server

    Chenu, Aurélia; Mancal, Tomáš

    2013-01-01

    In this paper, we investigate the relevance of dynamic electronic coherence under conditions natural to light-harvesting systems. We formulate the results of a quantum mechanical treatment of a weak light-matter interaction in terms of experimental observable, such as the incident light spectrum and the absorption spectrum of the material, and we derive the description of the incoherent F\\"orster type energy transfer fully from the wave function formalism. We demonstrate that excitation of a coherent superposition of electronic eigenstates of natural light-harvesting complexes by sunlight or by excitation transfer from a neighboring antenna is unlikely and that dynamical coherence therefore cannot play any significant role in natural photosynthesis, regardless of their life time. Dynamical coherence as a transient phenomenon must be strictly distinguished from the effect of excited state delocalization (also termed quantum coherence in the literature) which is established by interaction between the pigments a...

  5. Molecular complexity of primary open angle glaucoma: current concepts

    Indian Academy of Sciences (India)

    Kunal Ray; Suddhasil Mookherjee

    2009-12-01

    Glaucoma is a group of heterogeneous optic neuropathies with complex genetic basis. Among the three principle subtypes of glaucoma, primary open angle glaucoma (POAG) occurs most frequently. Till date, 25 loci have been found to be linked to POAG. However, only three underlying genes (Myocilin, Optineurin and WDR36) have been identified. In addition, at least 30 other genes have been reported to be associated with POAG. Despite strong genetic influence in POAG pathogenesis, only a small part of the disease can be explained in terms of genetic aberration. Current concepts of glaucoma pathogenesis suggest it to be a neurodegenerative disorder which is triggered by different factors including mechanical stress due to intra-ocular pressure, reduced blood flow to retina, reperfusion injury, oxidative stress, glutamate excitotoxicity, and aberrant immune response. Here we present a mechanistic overview of potential pathways and crosstalk between them operating in POAG pathogenesis.

  6. Molecular test to assign individuals within the Cacopsylla pruni complex.

    Directory of Open Access Journals (Sweden)

    Jean Peccoud

    Full Text Available Crop protection requires the accurate identification of disease vectors, a task that can be made difficult when these vectors encompass cryptic species. Here we developed a rapid molecular diagnostic test to identify individuals of Cacopsyllapruni (Scopoli, 1763 (Hemiptera: Psyllidae, the main vector of the European stone fruit yellows phytoplasma. This psyllid encompasses two highly divergent genetic groups that are morphologically similar and that are characterized by genotyping several microsatellite markers, a costly and time-consuming protocol. With the aim of developing species-specific PCR primers, we sequenced the Internal Transcribed Spacer 2 (ITS2 on a collection of C. pruni samples from France and other European countries. ITS2 sequences showed that the two genetic groups represent two highly divergent clades. This enabled us to develop specific primers for the assignment of individuals to either genetic group in a single PCR, based on ITS2 amplicon size. All previously assigned individuals yielded bands of expected sizes, and the PCR proved efficient on a larger sample of 799 individuals. Because none appeared heterozygous at the ITS2 locus (i.e., none produced two bands, we inferred that the genetic groups of C. pruni, whose distribution is partly sympatric, constitute biological species that have not exchanged genes for an extended period of time. Other psyllid species (Cacopsylla, Psylla, Triozidae and Aphalaridae failed to yield any amplicon. These primers are therefore unlikely to produce false positives and allow rapid assignment of C. pruni individuals to either cryptic species.

  7. Quantum Chemistry Meets Rotational Spectroscopy for Astrochemistry: Increasing Molecular Complexity

    Science.gov (United States)

    Puzzarini, Cristina

    2016-06-01

    For many years, scientists suspected that the interstellar medium was too hostile for organic species and that only a few simple molecules could be formed under such extreme conditions. However, the detection of approximately 180 molecules in interstellar or circumstellar environments in recent decades has changed this view dramatically. A rich chemistry has emerged, and relatively complex molecules such as C60 and C70 are formed. Recently, researchers have also detected complex organic and potentially prebiotic molecules, such as amino acids, in meteorites and in other space environments. Those discoveries have further stimulated the debate on the origin of the building blocks of life in the universe. Rotational spectroscopy plays a crucial role in the investigation of planetary atmosphere and the interstellar medium. Increasingly these astrochemical investigations are assisted by quantum-mechanical calculations of structures as well as spectroscopic and thermodynamic properties to guide and support observations, line assignments, and data analysis in these new and chemically complicated situations. However, it has proved challenging to extend accurate quantum-chemical computational approaches to larger systems because of the unfavorable scaling with the number of degrees of freedom (both electronic and nuclear). In this contribution, it is demonstrated that it is now possible to compute physicochemical properties of building blocks of biomolecules with an accuracy rivaling that of the most sophisticated experimental techniques. We analyze the spectroscopic properties of representative building blocks of DNA bases (uracil and thiouracil), of proteins (glycine and glycine dipeptide analogue), and also of PAH (phenalenyl radical and cation). V. Barone, M. Biczysko, C. Puzzarini 2015, Acc. Chem. Res., 48, 1413

  8. 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.

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

    Science.gov (United States)

    Galkin, K. I.; Ananikov, V. P.

    2016-03-01

    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.

  10. Transcriptional mechanisms coordinating tight junction assembly during epithelial differentiation.

    Science.gov (United States)

    Boivin, Felix J; Schmidt-Ott, Kai M

    2017-06-01

    Epithelial tissues form a selective barrier via direct cell-cell interactions to separate and establish concentration gradients between the different compartments of the body. Proper function and formation of this barrier rely on the establishment of distinct intercellular junction complexes. These complexes include tight junctions, adherens junctions, desmosomes, and gap junctions. The tight junction is by far the most diverse junctional complex in the epithelial barrier. Its composition varies greatly across different epithelial tissues to confer various barrier properties. Thus, epithelial cells rely on tightly regulated transcriptional mechanisms to ensure proper formation of the epithelial barrier and to achieve tight junction diversity. Here, we review different transcriptional mechanisms utilized during embryogenesis and disease development to promote tight junction assembly and maintenance of intercellular barrier integrity. We focus particularly on the Grainyhead-like transcription factors and ligand-activated nuclear hormone receptors, two central families of proteins in epithelialization. © 2017 New York Academy of Sciences.

  11. Comparison of single junction AlGaInP and GaInP solar cells grown by molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Masuda, Taizo, E-mail: taizo.masuda@yale.edu; Tomasulo, Stephanie; Lang, Jordan R.; Lee, Minjoo Larry [Department of Electrical Engineering, Yale University, New Haven, Connecticut 06511 (United States)

    2015-03-07

    We have investigated ∼2.0 eV (Al{sub x}Ga{sub 1−x}){sub 0.51}In{sub 0.49}P and ∼1.9 eV Ga{sub 0.51}In{sub 0.49}P single junction solar cells grown on both on-axis and misoriented GaAs substrates by molecular beam epitaxy (MBE). Although lattice-matched (Al{sub x}Ga{sub 1−x}){sub 0.51}In{sub 0.49}P solar cells are highly attractive for space and concentrator photovoltaics, there have been few reports on the MBE growth of such cells. In this work, we demonstrate open circuit voltages (V{sub oc}) ranging from 1.29 to 1.30 V for Ga{sub 0.51}In{sub 0.49}P cells, and 1.35–1.37 V for (Al{sub x}Ga{sub 1−x}){sub 0.51}In{sub 0.49}P cells. Growth on misoriented substrates enabled the bandgap-voltage offset (W{sub oc} = E{sub g}/q − V{sub oc}) of Ga{sub 0.51}In{sub 0.49}P cells to decrease from ∼575 mV to ∼565 mV, while that of (Al{sub x}Ga{sub 1−x}){sub 0.51}In{sub 0.49}P cells remained nearly constant at 620 mV. The constant W{sub oc} as a function of substrate offcut for (Al{sub x}Ga{sub 1−x}){sub 0.51}In{sub 0.49}P implies greater losses from non-radiative recombination compared with the Ga{sub 0.51}In{sub 0.49}P devices. In addition to larger W{sub oc} values, the (Al{sub x}Ga{sub 1−x}){sub 0.51}In{sub 0.49}P cells exhibited significantly lower internal quantum efficiency (IQE) values than Ga{sub 0.51}In{sub 0.49}P cells due to recombination at the emitter/window layer interface. A thin emitter design is experimentally shown to be highly effective in improving IQE, particularly at short wavelengths. Our work shows that with further optimization of both cell structure and growth conditions, MBE-grown (Al{sub x}Ga{sub 1−x}){sub 0.51}In{sub 0.49}P will be a promising wide-bandgap candidate material for high-efficiency, lattice-matched multi-junction solar cells.

  12. 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.

  13. 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/.

  14. 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.

  15. Highlighting Kathleen Green and Mario Delmar, guest editors of special issue (part 2): junctional targets of skin and heart disease.

    Science.gov (United States)

    Cowin, Pamela

    2014-06-01

    Cell Communication and Adhesion has been fortunate to enlist two pioneers of epidermal and cardiac cell junctions, Kathleen Green and Mario Delmar, as Guest Editors of a two part series on junctional targets of skin and heart disease. Part 2 of this series begins with an overview from Dipal Patel and Kathy Green comparing epidermal desmosomes to cardiac area composita junctions, and surveying the pathogenic mechanisms resulting from mutations in their components in heart disease. This is followed by a review from David Kelsell on the role of desmosomal mutation in inherited syndromes involving skin fragility. Agnieszka Kobeliak discusses how structural deficits in the epidermal barrier intersect with the NFkB signaling pathway to induce inflammatory diseases such as psoriasis and atopic dermatitis. Farah Sheikh reviews the specialized junctional components in cardiomyocytes of the cardiac conduction system and Robert Gourdie discusses how molecular complexes between sodium channels and gap junction proteins within the perijunctional microdomains within the intercalated disc facilitate conduction. Glenn Radice evaluates the role of N-cadherin in heart. Andre Kleber and Chris Chen explore new approaches to study junctional mechanotransduction in vitro with a focus on the effects of connexin ablation and the role of cadherins, respectively. To complement this series of reviews, we have interviewed Werner Franke, whose systematic documentation the tissue-specific complexity of desmosome composition and pioneering discovery of the cardiac area composita junction greatly facilitated elucidation of the role of desmosomal components in the pathophysiology of human heart disease.

  16. Proteomic and bioinformatic analysis of epithelial tight junction reveals an unexpected cluster of synaptic molecules

    Directory of Open Access Journals (Sweden)

    Tang Vivian W

    2006-12-01

    Full Text Available Abstract Background Zonula occludens, also known as the tight junction, is a specialized cell-cell interaction characterized by membrane "kisses" between epithelial cells. A cytoplasmic plaque of ~100 nm corresponding to a meshwork of densely packed proteins underlies the tight junction membrane domain. Due to its enormous size and difficulties in obtaining a biochemically pure fraction, the molecular composition of the tight junction remains largely unknown. Results A novel biochemical purification protocol has been developed to isolate tight junction protein complexes from cultured human epithelial cells. After identification of proteins by mass spectroscopy and fingerprint analysis, candidate proteins are scored and assessed individually. A simple algorithm has been devised to incorporate transmembrane domains and protein modification sites for scoring membrane proteins. Using this new scoring system, a total of 912 proteins have been identified. These 912 hits are analyzed using a bioinformatics approach to bin the hits in 4 categories: configuration, molecular function, cellular function, and specialized process. Prominent clusters of proteins related to the cytoskeleton, cell adhesion, and vesicular traffic have been identified. Weaker clusters of proteins associated with cell growth, cell migration, translation, and transcription are also found. However, the strongest clusters belong to synaptic proteins and signaling molecules. Localization studies of key components of synaptic transmission have confirmed the presence of both presynaptic and postsynaptic proteins at the tight junction domain. To correlate proteomics data with structure, the tight junction has been examined using electron microscopy. This has revealed many novel structures including end-on cytoskeletal attachments, vesicles fusing/budding at the tight junction membrane domain, secreted substances encased between the tight junction kisses, endocytosis of tight junction

  17. Antipyrine-gamma cyclodextrin inclusion complex: Molecular modeling, preparation, characterization and cytotoxicity studies

    Science.gov (United States)

    Gannimani, Ramesh; Perumal, Amanda; Ramesh, Muthusamy; Pillay, Karen; Soliman, Mahmoud E.; Govender, Patrick

    2015-06-01

    Molecular docking, semi-empirical and molecular dynamics studies were conducted for α, β and γ-cyclodextrin-associated inclusion complexes of antipyrine. The results of molecular modeling were systematically analyzed to determine the stability of inclusion complexes. In preliminary computational screening, β and γ-cyclodextrin inclusion complexes of antipyrine were found to be more stable as compared to α-cyclodextrin based on docking score and binding free energies. Further, inclusion complex of antipyrine with γ-cyclodextrin was prepared by freeze drying method. Formation of the inclusion complex was investigated by solid state characterization techniques such as thermogravimetric analysis, differential scanning calorimetry, X-ray diffraction, Fourier transform infrared spectroscopy and scanning electron microscopy. The changes observed in decomposition temperature, diffractogram, vibrational frequencies and morphological appearance confirmed the formation of inclusion complex. In addition, results from 1H NMR and 2D NOESY studies supported the inclusion phenomenon. The results obtained from computational studies were found to be in consistent with experimental data to ascertain the encapsulation of antipyrine into γ-cyclodextrin. The inclusion complex was found to be non-toxic toward MDCK-1 cell lines. Thus, this approach may be helpful in the formulation of drug molecules using cyclodextrins.

  18. Integrated genomics and molecular breeding approaches for dissecting the complex quantitative traits in crop plants.

    Science.gov (United States)

    Kujur, Alice; Saxena, Maneesha S; Bajaj, Deepak; Laxmi; Parida, Swarup K

    2013-12-01

    The enormous population growth, climate change and global warming are now considered major threats to agriculture and world's food security. To improve the productivity and sustainability of agriculture, the development of highyielding and durable abiotic and biotic stress-tolerant cultivars and/climate resilient crops is essential. Henceforth, understanding the molecular mechanism and dissection of complex quantitative yield and stress tolerance traits is the prime objective in current agricultural biotechnology research. In recent years, tremendous progress has been made in plant genomics and molecular breeding research pertaining to conventional and next-generation whole genome, transcriptome and epigenome sequencing efforts, generation of huge genomic, transcriptomic and epigenomic resources and development of modern genomics-assisted breeding approaches in diverse crop genotypes with contrasting yield and abiotic stress tolerance traits. Unfortunately, the detailed molecular mechanism and gene regulatory networks controlling such complex quantitative traits is not yet well understood in crop plants. Therefore, we propose an integrated strategies involving available enormous and diverse traditional and modern -omics (structural, functional, comparative and epigenomics) approaches/resources and genomics-assisted breeding methods which agricultural biotechnologist can adopt/utilize to dissect and decode the molecular and gene regulatory networks involved in the complex quantitative yield and stress tolerance traits in crop plants. This would provide clues and much needed inputs for rapid selection of novel functionally relevant molecular tags regulating such complex traits to expedite traditional and modern marker-assisted genetic enhancement studies in target crop species for developing high-yielding stress-tolerant varieties.

  19. Model Building to Facilitate Understanding of Holliday Junction and Heteroduplex Formation, and Holliday Junction Resolution

    Science.gov (United States)

    Selvarajah, Geeta; Selvarajah, Susila

    2016-01-01

    Students frequently expressed difficulty in understanding the molecular mechanisms involved in chromosomal recombination. Therefore, we explored alternative methods for presenting the two concepts of the double-strand break model: Holliday junction and heteroduplex formation, and Holliday junction resolution. In addition to a lecture and…

  20. Spectroscopic study of molecular structure, antioxidant activity and biological effects of metal hydroxyflavonol complexes

    Science.gov (United States)

    Samsonowicz, Mariola; Regulska, Ewa

    2017-02-01

    Flavonols with varied hydroxyl substitution can act as strong antioxidants. Thanks to their ability to chelate metals as well as to donate hydrogen atoms they have capacity to scavenge free radicals. Their metal complexes are often more active in comparison with free ligands. They exhibit interesting biological properties, e.g. anticancer, antiphlogistic and antibacterial. The relationship between molecular structure and their biological properties was intensively studied using spectroscopic methods (UV-Vis, IR, Raman, NMR, ESI-MS). The aim of this paper is review on spectroscopic analyses of molecular structure and biological activity of hydroxyflavonol metal complexes.

  1. Identification and subcellular localization of molecular complexes of Gq/11α protein in HEK293 cells.

    Science.gov (United States)

    Drastichova, Zdenka; Novotny, Jiri

    2012-08-01

    Heterotrimeric G-proteins localized in the plasma membrane convey the signals from G-protein-coupled receptors (GPCRs) to different effectors. At least some types of G-protein α subunits have been shown to be partly released from plasma membranes and to move into the cytosol after receptor activation by the agonists. However, the mechanism underlying subcellular redistribution of trimeric G-proteins is not well understood and no definitive conclusions have been reached regarding the translocation of Gα subunits between membranes and cytosol. Here we used subcellular fractionation and clear-native polyacrylamide gel electrophoresis to identify molecular complexes of G(q/11)α protein and to determine their localization in isolated fractions and stability in naïve and thyrotropin-releasing hormone (TRH)-treated HEK293 cells expressing high levels of TRH receptor and G(11)α protein. We identified two high-molecular-weight complexes of 300 and 140 kDa in size comprising the G(q/11) protein, which were found to be membrane-bound. Both of these complexes dissociated after prolonged treatment with TRH. Still other G(q/11)α protein complexes of lower molecular weight were determined in the cytosol. These 70 kDa protein complexes were barely detectable under control conditions but their levels markedly increased after prolonged (4-16 h) hormone treatment. These results support the notion that a portion of G(q/11)α can undergo translocation from the membrane fraction into soluble fraction after a long-term activation of TRH receptor. At the same time, these findings indicate that the redistribution of G(q/11)α is brought about by the dissociation of high-molecular-weight complexes and concomitant formation of low-molecular-weight complexes containing the G(q/11)α protein.

  2. Identification and subcellular localization of molecular complexes of Gq/11α protein in HEK293 cells

    Institute of Scientific and Technical Information of China (English)

    Zdenka Drastichova; Jiri Novotny

    2012-01-01

    Heterotrimeric G-proteins localized in the plasma membrane convey the signals from G-protein-coupled receptors (GPCRs) to different effectors.At least some types of Gprotein o subunits have been shown to be partly released from plasma membranes and to move into the cytosol after receptor activation by the agonists.However,the mechanism underlying subcellular redistribution of trimeric G-proteins is not well understood and no definitive conclusions have been reached regarding the translocation of Gα subunits between membranes and cytosol.Here we used subcellular fractionation and clear-native polyacrylamide gel electrophoresis to identify molecular complexes of Gq/1 1α protein and to determine their localization in isolated fractions and stability in naive and thyrotropin-releasing hormone (TRH)-treated HEK293 cells expressing high levels of TRH receptor and G11α protein.We identified two high-molecular-weight complexes of 300 and 140 kDa in size comprising the Gq/11 protein,which were found to be membrane-bound.Both of these complexes dissociated after prolonged treatment with TRH.Still other Gq/11α protein complexes of lower molecular weight were determined in the cytosol.These 70 kDa protein complexes were barely detectable under control conditions but their levels markedly increased after prolonged (4-16 h)hormone treatment.These results support the notion that a portion of Gq/11α can undergo translocation from the membrane fraction into soluble fraction after a long-term activation of TRH receptor.At the same time,these findings indicate that the redistribution of Gq/11α is broughtabout by the dissociation of high-molecular-weight complexes and concomitant formation of low-molecular-weight complexes containing the Gq/11α protein.

  3. 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...... of identifying and comparing the intrinsic properties of two commonly used anchoring groups, namely thiol and amine groups, we have calculated the atomic structure and conductance traces of different Au-S-Au and Au-NH2-Au nanojunctions using density functional theory (DFT). Whereas NH2 shows a strong structural...... selectivity towards atop-gold configurations, S shows large variability in its bonding geometries. As a result, the conductance of the Au-NH2-Au junction is less sensitive to the structure of the gold contacts than the Au-S-Au junction. These findings support recent experiments which show that amine...

  4. Molecular characterisation of the nucleocapsid protein gene, glycoprotein gene and gene junctions of rhabdovirus 903/87, a novel fish pathogenic rhabdovirus

    DEFF Research Database (Denmark)

    Johansson, Tove; Nylund, S.; Olesen, Niels Jørgen

    2001-01-01

    The sequences of the nucleocapsid and glycoprotein genes and the gene junctions of the fish pathogenic rhabdovirus 903/87 were determined from cDNA and PCR clones. The mRNA of the nucleocapsid is most likely 1492 nucleotides long and encodes a protein of 426 amino acids, whereas the mRNA of the g......The sequences of the nucleocapsid and glycoprotein genes and the gene junctions of the fish pathogenic rhabdovirus 903/87 were determined from cDNA and PCR clones. The mRNA of the nucleocapsid is most likely 1492 nucleotides long and encodes a protein of 426 amino acids, whereas the m...

  5. DMPD: Molecular mechanisms of macrophage activation and deactivation bylipopolysaccharide: roles of the receptor complex. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 14609719 Molecular mechanisms of macrophage activation and deactivation bylipopolysaccharide: role...ivation and deactivation bylipopolysaccharide: roles of the receptor complex. Pub...medID 14609719 Title Molecular mechanisms of macrophage activation and deactivation bylipopolysaccharide: role

  6. [Mass spectrometry of triterpene glycosides molecular complexation with purine bases of nucleic acids].

    Science.gov (United States)

    Lekar', A V; Vetrova, E V; Borisenko, N I; Iakovishin, L A; Grishkovets, V I

    2011-01-01

    The molecular complexation of adenine and guanine with hederagenin 3-O-alpha-L-rhamnopyranosyl-(1-->2)-O-alpha-L-arabinopyranoside (alpha-hederin) and its 28-O-alpha-L-rhamnopyranosyl-(1-->4)-O-beta-D-glucopyranosyl-(1-->6)-O-beta-D-glucopyranosyl ester (hederasaponin C) was investigated for the first time using the method of electrospray ionization mass spectrometry. Guanine forms complexes more diverse in composition than adenine.

  7. Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems

    Science.gov (United States)

    Marchi, Massimo; Ballone, Pietro

    1999-02-01

    This study deals with a novel molecular simulation technique, named adiabatic bias molecular dynamics (MD), which provides a simple and reasonably inexpensive route to generate MD trajectories joining points in conformational space separated by activation barriers. Because of the judicious way the biasing potential is updated during the MD runs, the technique allows with some additional effort the computation of the free energy change experienced during the trajectory. The adiabatic bias method has been applied to a nontrivial problem: The unfolding of an atomistic model of lysozyme. Here, the radius of gyration (Rg) was used as a convenient reaction coordinate. For changes in Rg between 19.7 and 28 Å, we observe a net loss of the native tertiary structure of lysozyme. At the same time, secondary structure elements such as α-helices are retained although some of the original order is diminished. The calculated free energy profile for the unfolding transition shows a monotonous increase with Rg and depends crucially on the nonbonded cutoff used in the potential model.

  8. Classical molecular simulations of complex industrially-important systems on the Intel Paragon

    Energy Technology Data Exchange (ETDEWEB)

    Cochran, H.D.; LoCascio, P.F.; Cummings, P.T. [Univ. of Tennessee, Knoxville, TN (United States)

    1996-06-01

    Advances in parallel supercomputing now make possible molecular-based engineering and science calculations that will soon revolutionize many technologies, such as those involving polymers and those involving aqueous electrolytes. We have developed a suite of message-passing codes for classical molecular simulation of such complex fluids and amorphous materials and have completed a number of demonstration calculations of problems of scientific and technological importance with each. In this overview paper we will outline the techniques for classical molecular simulation of these industrially-important systems on the Inter Paragon and we will summarize some of the important scientific and technical results of the varied applications, including the following: (1) Parallel codes for quatemion dynamics using techniques for handling long-range Coulombic forces allow study of ion pairing in supercritical aqueous electrolyte solutions. Ion pairing lies at the heart of technological problems with corrosion and solids deposition in industrial processes utilizing high temperature water. (2) Non-equilibrium, multiple time step molecular dynamics lets us investigate the rheology of molecular fluids. Such calculations enable the molecular-based design of new synthetic lubricants of importance in the automotive engines of the future. (3) Chain molecule Monte Carlo simulations in the Gibbs ensemble now permit calculation of phase equilibrium of long-chain molecular systems. With complementary equilibrium molecular dynamics (with multiple time steps) we have been able to gain fundamental insight into the technologically-important problem of liquid-liquid phase separation in polymer blends.

  9. Charge transfer complexes of fullerene[60] with porphyrins as molecular rectifiers. A theoretical study.

    Science.gov (United States)

    Montiel, Filiberto; Fomina, Lioudmila; Fomine, Serguei

    2015-01-01

    Molecular diodes based on charge transfer complexes of fullerene[60] with different metalloporphyrins have been modeled. Their current-voltage characteristics and the rectification ratios (RR) were calculated using direct ab initio method at PBE/def2-SVP level of theory with D3 dispersion correction, for voltages ranging from -2 to +2 V. The highest RR of 32.5 was determined for the complex of fullerene[60] with zinc tetraphenylporphyrin at 0.8 V. Other molecular diodes possessed lower RR, however, all complexes showed RR higher than 1 at all bias voltages. The asymmetric evolutions and alignment of the molecular orbitals with the applied bias were found to be essential for generating the molecular diode rectification behavior. Metal nature of metalloporphyrins and the interaction porphyrin-electrode significantly affect RR of molecular diode. Large metal ions like Cd(2+) and Ag(2+) in metalloporphyrins disfavor rectification creating conducting channels in two directions, while smaller ions Zn(2+) and Cu(2+) favor rectification increasing the interaction between gold electrode and porphyrin macrocycle.

  10. Dissection of neuronal gap junction circuits that regulate social behavior in Caenorhabditis elegans

    Science.gov (United States)

    Jang, Heeun; Levy, Sagi; Flavell, Steven W.; Mende, Fanny; Latham, Richard; Zimmer, Manuel; Bargmann, Cornelia I.

    2017-01-01

    A hub-and-spoke circuit of neurons connected by gap junctions controls aggregation behavior and related behavioral responses to oxygen, pheromones, and food in Caenorhabditis elegans. The molecular composition of the gap junctions connecting RMG hub neurons with sensory spoke neurons is unknown. We show here that the innexin gene unc-9 is required in RMG hub neurons to drive aggregation and related behaviors, indicating that UNC-9–containing gap junctions mediate RMG signaling. To dissect the circuit in detail, we developed methods to inhibit unc-9–based gap junctions with dominant-negative unc-1 transgenes. unc-1(dn) alters a stomatin-like protein that regulates unc-9 electrical signaling; its disruptive effects can be rescued by a constitutively active UNC-9::GFP protein, demonstrating specificity. Expression of unc-1(dn) in RMG hub neurons, ADL or ASK pheromone-sensing neurons, or URX oxygen-sensing neurons disrupts specific elements of aggregation-related behaviors. In ADL, unc-1(dn) has effects opposite to those of tetanus toxin light chain, separating the roles of ADL electrical and chemical synapses. These results reveal roles of gap junctions in a complex behavior at cellular resolution and provide a tool for similar exploration of other gap junction circuits. PMID:28143932

  11. Molecular simulation of N-acetylneuraminic acid analogs and molecular dynamics studies of cholera toxin-Neu5Gc complex.

    Science.gov (United States)

    Blessy, J Jino; Sharmila, D Jeya Sundara

    2015-01-01

    Cholera toxin (CT) is an AB5 protein complex secreted by the pathogen Vibrio cholera, which is responsible for cholera infection. N-acetylneuraminic acid (NeuNAc) is a derivative of neuraminic acid with nine-carbon backbone. NeuNAc is distributed on the cell surface mainly located in the terminal components of glycoconjugates, and also plays an important role in cell-cell interaction. In our current study, molecular docking and molecular dynamic (MD) simulations were implemented to identify the potent NeuNAc analogs with high-inhibitory activity against CT protein. Thirty-four NeuNAc analogs, modified in different positions C-1/C-2/C-4/C-5/C-7/C-8/C-9, were modeled and docked against the active site of CT protein. Among the 34 NeuNAc analogs, the analog Neu5Gc shows the least extra precision glide score of -9.52 and glide energy of -44.71 kcal/mol. NeuNAc analogs block the CT active site residues HIS:13, ASN:90, LYS:91, GLN:56, GLN:61, and TRP:88 through intermolecular hydrogen bonding. The MD simulation for CT-Neu5Gc docking complex was performed using Desmond. MD simulation of CT-Neu5Gc complex reveals the stable nature of docking interaction.

  12. 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

  13. 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

  14. MOLECULAR CHARACTERIZATION OF A RECURRING COMPLEX CHROMOSOMAL TRANSLOCATION IN 2 HUMAN EXTRAGONADAL GERM-CELL TUMORS

    NARCIS (Netherlands)

    SINKE, RJ; WEGHUIS, DO; SUIJKERBUIJK, RF; TANIGAMI, A; NAKAMURA, Y; LARSSON, C; WEBER, G; DEJONG, B; OOSTERHUIS, JW; MOLENAAR, WM; VANKESSEL, AG

    1994-01-01

    The molecular characterization of a recurring complex chromosomal translocation involving 6p21, 6p22, 6p23, and 11q13 in two independent bur similar extragonadal human germ cell rumors was initiated using fluorescence in situ hybridization (FISH) and pulse field gel electrophoresis (PFGE) techniques

  15. Molecular characterization of a recurring complex chromosomal translocation in two human extragonadal germ cell tumors.

    NARCIS (Netherlands)

    Sinke, R J; Weghuis, D O; Suijkerbuijk, R F; Tanigami, A; Nakamura, Y; Larsson, C; Weber, G; Jong, B de; Oosterhuis, J W; Molenaar, W M

    1994-01-01

    The molecular characterization of a recurring complex chromosomal translocation involving 6p21, 6p22, 6q23, and 11q13 in two independent but similar extragonadal human germ cell tumors was initiated using fluorescence in situ hybridization (FISH) and pulse field gel electrophoresis (PFGE) techniques

  16. MOLECULAR CHARACTERIZATION OF A RECURRING COMPLEX CHROMOSOMAL TRANSLOCATION IN 2 HUMAN EXTRAGONADAL GERM-CELL TUMORS

    NARCIS (Netherlands)

    SINKE, RJ; WEGHUIS, DO; SUIJKERBUIJK, RF; TANIGAMI, A; NAKAMURA, Y; LARSSON, C; WEBER, G; DEJONG, B; OOSTERHUIS, JW; MOLENAAR, WM; VANKESSEL, AG

    1994-01-01

    The molecular characterization of a recurring complex chromosomal translocation involving 6p21, 6p22, 6p23, and 11q13 in two independent bur similar extragonadal human germ cell rumors was initiated using fluorescence in situ hybridization (FISH) and pulse field gel electrophoresis (PFGE) techniques

  17. Magnetic resonance and fluorescence studies on pyruvate hydrogenase 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 physiologi

  18. 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 c

  19. Host-guest chemistry of Cu2+/Histidine complexes in molecular sieves

    NARCIS (Netherlands)

    Mesu, Jan Gijsbert

    2005-01-01

    The high activity and selectivity of enzymes have inspired many scientists to study the structure and working mechanism of bio-molecular complexes. Also in the catalysis community this subject is of topical interest, as it may provide inspiration for the development of a new generation of bio-inspir

  20. 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...

  1. Molecular Diagnostics for Complex Pest and Disease Resistance and Tuber Quality Traits: Concept, Achievements and Perspectives

    NARCIS (Netherlands)

    Gebhardt, C.; Urbany, C.; Li, L.; Stich, B.; Caldas Paulo, M.J.; Draffehn, A.; Ballvora, A.

    2011-01-01

    We summarize the concept of molecular diagnostic of complex traits related to pest and disease resistance and to tuber quality of potato, and describe recent achievements and perspectives. Many potato characteristics are controlled by multiple genetic and environmental factors. Knowing the genes and

  2. 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......) 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....

  3. A holistic molecular docking approach for predicting protein-protein complex structure

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A holistic protein-protein molecular docking approach,HoDock,was established,composed of such steps as binding site prediction,initial complex structure sampling,refined complex structure sampling,structure clustering,scoring and final structure selection.This article explains the detailed steps and applications for CAPRI Target 39.The CAPRI result showed that three predicted binding site residues,A191HIS,B512ARG and B531ARG,were correct,and there were five submitted structures with a high fraction of correct receptor-ligand interface residues,indicating that this docking approach may improve prediction accuracy for protein-protein complex structures.

  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 genetics of the swine major histocompatibility complex, the SLA complex.

    Science.gov (United States)

    Lunney, Joan K; Ho, Chak-Sum; Wysocki, Michal; Smith, Douglas M

    2009-03-01

    The swine major histocompatibility complex (MHC) or swine leukocyte antigen (SLA) complex is one of the most gene-dense regions in the swine genome. It consists of three major gene clusters, the SLA class I, class III and class II regions, that span approximately 1.1, 0.7 and 0.5Mb, respectively, making the swine MHC the smallest among mammalian MHC so far examined and the only one known to span the centromere. This review summarizes recent updates to the Immuno Polymorphism Database-MHC (IPD-MHC) website (http://www.ebi.ac.uk/ipd/mhc/sla/) which serves as the repository for maintaining a list of all SLA recognized genes and their allelic sequences. It reviews the expression of SLA proteins on cell subsets and their role in antigen presentation and regulating immune responses. It concludes by discussing the role of SLA genes in swine models of transplantation, xenotransplantation, cancer and allergy and in swine production traits and responses to infectious disease and vaccines.

  6. 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.

  7. Emergence of hydrogen bonds from molecular dynamics simulation of substituted N-phenylthiourea-catechol oxidase complex.

    Science.gov (United States)

    Park, Kyung-Lae

    2017-01-01

    A series of N-phenylthiourea derivatives was built starting from the X-ray structure in the molecular mechanics framework and the interaction profile in the complex with the catechol oxidase was traced using molecular dynamics simulation. The results showed that the geometry and interactions between ligand and receptor were highly related to the position of the substituted side chains of phenyl moiety. At the end of molecular dynamics run, a concentrated multicenter hydrogen bond was created between the substituted ligand and receptor. The conformation of the ligand itself were also restricted in the receptor pocket. Furthermore, the simulation time of 50 ns were found to be long enough to explore the relevant conformational space and the stationary behavior of the molecular dynamic could be observed.

  8. 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.

    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......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...

  9. 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 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...

  10. Inclusion complexes of pyrimethamine in 2-hydroxypropyl-beta-cyclodextrin: characterization, phase solubility and molecular modelling.

    Science.gov (United States)

    de Araújo, Márcia Valéria Gaspar; Vieira, Elze Kelly Barbosa; Lázaro, Gilderman Silva; de Souza Conegero, Leila; Ferreira, Odair Pastor; Almeida, Lui S Eduardo; Barreto, Ledjane Silva; da Costa, Nivan Bezerra; Gimenez, Iara F

    2007-09-01

    The inclusion complexation of pyrimethamine in 2-hydroxypropyl-beta-cyclodextrin has been investigated by 2D (1)H NMR, FTIR and UV/visible spectroscopy and also by molecular modelling methods (AM1, PM3, MM3). From the phase-solubility diagram a linear increase was observed in pyrimethamine aqueous solubility in the presence of 2-hydroxypropyl-beta-cyclodextrin, evidencing the formation of a soluble inclusion complex. According to the continuous variation method (Job's plot) applied to fluorescence measurements, a 1:1 stoichiometry has been proposed for the complex. Concerning the structure of the complex, a Cl-in orientation of pyrimethamine in the 2-hydroxypropyl-beta-cyclodextrin cavity has been proposed from the theoretical calculations, being confirmed by two-dimensional (1)H NMR spectroscopy (ROESY). The thermal behaviour has also been studied, providing complementary evidences of complex formation.

  11. First principles molecular dynamics study of nitrogen vacancy complexes in boronitrene.

    Science.gov (United States)

    Ukpong, A M; Chetty, N

    2012-07-04

    We present the results of first principles molecular dynamics simulations of nitrogen vacancy complexes in monolayer hexagonal boron nitride. The threshold for local structure reconstruction is found to be sensitive to the presence of a substitutional carbon impurity. We show that activated nitrogen dynamics triggers the annihilation of defects in the layer through formation of Stone-Wales-type structures. The lowest energy state of nitrogen vacancy complexes is negatively charged and spin polarized. Using the divacancy complex, we show that their formation induces spontaneous magnetic moments, which is tunable by electron or hole injection. The Fermi level s-resonant defect state is identified as a unique signature of the ground state of the divacancy complex. Due to their ability to enhance structural cohesion, only the divacancy and the nitrogen vacancy carbon-antisite complexes are able to suppress the Fermi level resonant defect state to open a gap between the conduction and valence bands.

  12. Loss of αT-catenin alters the hybrid adhering junctions in the heart and leads to dilated cardiomyopathy and ventricular arrhythmia following acute ischemia.

    Science.gov (United States)

    Li, Jifen; Goossens, Steven; van Hengel, Jolanda; Gao, Erhe; Cheng, Lan; Tyberghein, Koen; Shang, Xiying; De Rycke, Riet; van Roy, Frans; Radice, Glenn L

    2012-02-15

    It is generally accepted that the intercalated disc (ICD) required for mechano-electrical coupling in the heart consists of three distinct junctional complexes: adherens junctions, desmosomes and gap junctions. However, recent morphological and molecular data indicate a mixing of adherens junctional and desmosomal components, resulting in a 'hybrid adhering junction' or 'area composita'. The α-catenin family member αT-catenin, part of the N-cadherin-catenin adhesion complex in the heart, is the only α-catenin that interacts with the desmosomal protein plakophilin-2 (PKP2). Thus, it has been postulated that αT-catenin might serve as a molecular integrator of the two adhesion complexes in the area composita. To investigate the role of αT-catenin in the heart, gene targeting technology was used to delete the Ctnna3 gene, encoding αT-catenin, in the mouse. The αT-catenin-null mice are viable and fertile; however, the animals exhibit progressive cardiomyopathy. Adherens junctional and desmosomal proteins were unaffected by loss of αT-catenin, with the exception of the desmosomal protein PKP2. Immunogold labeling at the ICD demonstrated in the αT-catenin-null heart a preferential reduction of PKP2 at the area composita compared with the desmosome. Furthermore, gap junction protein Cx43 was reduced at the ICD, including its colocalization with N-cadherin. Gap junction remodeling in αT-catenin-knockout hearts was associated with an increased incidence of ventricular arrhythmias after acute ischemia. This novel animal model demonstrates for the first time how perturbation in αT-catenin can affect both PKP2 and Cx43 and thereby highlights the importance of understanding the crosstalk between the junctional proteins of the ICD and its implications for arrhythmogenic cardiomyopathy.

  13. 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.

  14. Structural analysis of the human SYCE2-TEX12 complex provides molecular insights into synaptonemal complex assembly.

    Science.gov (United States)

    Davies, Owen R; Maman, Joseph D; Pellegrini, Luca

    2012-07-01

    The successful completion of meiosis is essential for all sexually reproducing organisms. The synaptonemal complex (SC) is a large proteinaceous structure that holds together homologous chromosomes during meiosis, providing the structural framework for meiotic recombination and crossover formation. Errors in SC formation are associated with infertility, recurrent miscarriage and aneuploidy. The current lack of molecular information about the dynamic process of SC assembly severely restricts our understanding of its function in meiosis. Here, we provide the first biochemical and structural analysis of an SC protein component and propose a structural basis for its function in SC assembly. We show that human SC proteins SYCE2 and TEX12 form a highly stable, constitutive complex, and define the regions responsible for their homotypic and heterotypic interactions. Biophysical analysis reveals that the SYCE2-TEX12 complex is an equimolar hetero-octamer, formed from the association of an SYCE2 tetramer and two TEX12 dimers. Electron microscopy shows that biochemically reconstituted SYCE2-TEX12 complexes assemble spontaneously into filamentous structures that resemble the known physical features of the SC central element (CE). Our findings can be combined with existing biological data in a model of chromosome synapsis driven by growth of SYCE2-TEX12 higher-order structures within the CE of the SC.

  15. Preparation, characterization and molecular modeling studies of the inclusion complex of Caffeine with Beta-cyclodextrin

    Science.gov (United States)

    Prabu, Samikannu; Swaminathan, Meenakshisundaram; Sivakumar, Krishnamoorthy; Rajamohan, Rajaram

    2015-11-01

    The formation through supramolecular interaction of a host-guest inclusion complex of caffeine (CA) with nano-hydrophobic cavity beta-cyclodextrin (β-CD) is achieved by a physical mixture, a kneading method and a co-precipitation method. The formation of the inclusion complex of CA with β-CD in solution state is confirmed by UV-visible spectrophotometer, fluorescence spectrophotometer and time-resolved fluorescence spectrophotometer. The stoichiometry of the inclusion complex is 1:1; the imidazole ring and pyrimidine ring of caffeine is deeply entrapped in the beta-cyclodextrin as confirmed by spectral shifts. The Benesi-Hildebrand plot is used to calculate the binding constant of the inclusion complex of CA with β-CD at room temperature. The Gibbs free energy change of the inclusion complex process is calculated and the process is found to be spontaneous. The thermal stability of the inclusion complex of CA with β-CD is analyzed using differential scanning calorimetry. The crystal structure modification of a solid inclusion complex is confirmed by scanning electron microscopy image analysis. The formation of the inclusion complex of CA with β-CD in the solid phase is also confirmed by FT-IR and XRD. The formation of the inclusion complex between CA and β-CD, as confirmed by molecular docking studies, is in good relationship with the results obtained through different experimental methods.

  16. MOLECULAR MODEL OF CYTOTOXIN-1 FROM NAJA MOSSAMBICA MOSSAMBICA VENOM IN COMPLEX WITH CHYMOTRYPSIN.

    Science.gov (United States)

    Munawar, Aisha; Akrem, Ahmed; Hussain, Ashiq; Spencer, Patrick; Betzel, Christian

    2015-01-01

    Snake venom is a myriad of biologically active proteins and peptides. Three finger toxins are highly conserved in their molecular structure, but interestingly possess diverse biological functions. During the course of evolution the introduction of subtle mutations in loop regions and slight variations in the three dimensional structure, has resulted in their functional versatility. Cytotoxin-1 (UniProt ID: P01467), isolated from Naja mossambica mossambica, showed the potential to inhibit chymotrypsin and the chymotryptic activity of the 20S proteasome. In the present work we describe a molecular model of cytotoxin-1 in complex with chymotrypsin, prepared by the online server ClusPro. Analysis of the molecular model shows that Cytotoxin-1 (P01467) binds to chymotrypsin through its loop I located near the N-terminus. The concave side of loop I of the toxin fits well in the substrate binding pocket of the protease. We propose Phe10 as the dedicated P1 site of the ligand. Being a potent inhibitor of the 20S proteasome, cytotoxin-1 (P01467) can serve as a potential antitumor agent. Already snake venom cytotoxins have been investigated for their ability as an anticancer agent. The molecular model of cytotoxin-1 in complex with chymotrypsin provides important information towards understanding the complex formation.

  17. Molecular modeling of zinc paddlewheel molecular complexes and the pores of a flexible metal organic framework.

    Science.gov (United States)

    Alzahrani, Khalid A H; Deeth, Robert J

    2016-04-01

    A new all-atom first-principles force field (FF) is constructed for the bimetallic, four-bladed zinc paddlewheel (ZPW) motif. Zinc-ligand interactions are described via Morse functions and the angular geometry at the metal centers is modeled with a pure ligand-ligand repulsion term. The ZPW-FF is principally based on 15 DFT-optimized model systems of general formula ZnPR.nL, where ZnP is the base Zn2(O2CR)4 unit, R = H, CH3 or CF3, L = NH3 or pyridine, and n = 0, 1 or 2. It correctly generates the distorted tetrahedral coordination of the uncapped [Zn2(O2CR)4] species in their ground states as well as giving reasonable structures and energies for the higher symmetry D4h transition state conformations. The zinc-ligand Morse function reference distance, r 0 , is further refined against 30 complexes located in the Cambridge Structural Database and this FF is applied to pore models of the flexible metal-organic framework (MOF) [Zn(bdc)2(dabco)]n (bdc = 1,4-benzendicarboxylate; dabco = 1,4-diazabicyclo(2.2.2)octane). A single pore model reproduces the unit cell of the evacuated MOF system while a 3×3 grid model is necessary to provide good agreement with the observed pronounced structural changes upon adsorption of either dimethylformamide or benzene.

  18. 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 BACKGROUND: 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. METHODS AND FINDINGS: 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. CONCLUSIONS: 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.

  19. Molecular Assembly of Clostridium botulinum progenitor M complex of type E.

    Science.gov (United States)

    Eswaramoorthy, Subramaniam; Sun, Jingchuan; Li, Huilin; Singh, Bal Ram; Swaminathan, Subramanyam

    2015-12-07

    Clostridium botulinum neurotoxin (BoNT) is released as a progenitor complex, in association with a non-toxic-non-hemagglutinin protein (NTNH) and other associated proteins. We have determined the crystal structure of M type Progenitor complex of botulinum neurotoxin E [PTC-E(M)], a heterodimer of BoNT and NTNH. The crystal structure reveals that the complex exists as a tight, interlocked heterodimer of BoNT and NTNH. The crystal structure explains the mechanism of molecular assembly of the complex and reveals several acidic clusters at the interface responsible for association at low acidic pH and disassociation at basic/neutral pH. The similarity of the general architecture between the PTC-E(M) and the previously determined PTC-A(M) strongly suggests that the progenitor M complexes of all botulinum serotypes may have similar molecular arrangement, although the neurotoxins apparently can take very different conformation when they are released from the M complex.

  20. Integrated genomics and molecular breeding approaches for dissecting the complex quantitative traits in crop plants

    Indian Academy of Sciences (India)

    Alice Kujur; Maneesha S Saxena; Deepak Bajaj; Laxmi; Swarup K Parida

    2013-12-01

    The enormous population growth, climate change and global warming are now considered major threats to agriculture and world’s food security. To improve the productivity and sustainability of agriculture, the development of high-yielding and durable abiotic and biotic stress-tolerant cultivars and/climate resilient crops is essential. Henceforth, understanding the molecular mechanism and dissection of complex quantitative yield and stress tolerance traits is the prime objective in current agricultural biotechnology research. In recent years, tremendous progress has been made in plant genomics and molecular breeding research pertaining to conventional and next-generation whole genome, transcriptome and epigenome sequencing efforts, generation of huge genomic, transcriptomic and epigenomic resources and development of modern genomics-assisted breeding approaches in diverse crop genotypes with contrasting yield and abiotic stress tolerance traits. Unfortunately, the detailed molecular mechanism and gene regulatory networks controlling such complex quantitative traits is not yet well understood in crop plants. Therefore, we propose an integrated strategies involving available enormous and diverse traditional and modern –omics (structural, functional, comparative and epigenomics) approaches/resources and genomics-assisted breeding methods which agricultural biotechnologist can adopt/utilize to dissect and decode the molecular and gene regulatory networks involved in the complex quantitative yield and stress tolerance traits in crop plants. This would provide clues and much needed inputs for rapid selection of novel functionally relevant molecular tags regulating such complex traits to expedite traditional and modern marker-assisted genetic enhancement studies in target crop species for developing high-yielding stress-tolerant varieties.

  1. High-Resolution Imaging of Molecular Gas and Dust in the Antennae (NGC 4038/39) Super Giant Molecular Complexes

    CERN Document Server

    Wilson, C D; Madden, S C; Charmandaris, V

    2000-01-01

    We present new aperture synthesis CO maps of the Antennae (NGC 4038/39) obtained with the Caltech Millimeter Array. These sensitive images show molecular emission associated with the two nuclei and a partial ring of star formation to the west of NGC 4038, as well as revealing the large extent of the extra-nuclear region of star formation (the ``overlap region''), which dominates the CO emission from this system. The largest molecular complexes have masses of 3-6x10^8 M_sun, typically an order of magnitude larger than the largest structures seen to date in more quiescent galaxy disks. The extremely red luminous star clusters identified previously with HST are well-correlated with the CO emission, which supports the conclusion that they are highly embedded young objects rather than old globular clusters. There is an excellent correlation between the CO emission and the 15 micron emission seen with ISO, particularly for the brightest regions. The most massive complexes in the overlap region have similar [NeIII]/...

  2. Molecular characterization of Mycobacterium tuberculosis complex isolates from wild ungulates in south-central Spain.

    Science.gov (United States)

    Gortazar, Christian; Vicente, Joaquín; Samper, Sofia; Garrido, Joseba M; Fernández-De-Mera, Isabel G; Gavín, Patricia; Juste, Ramón A; Martín, Carlos; Acevedo, Pelayo; De La Puente, Manuel; Höfle, Ursula

    2005-01-01

    The role of European wild ungulates in the epidemiology of tuberculosis (TB) is still under discussion. This study describes the geographical distribution and molecular typing of 77 Mycobacterium tuberculosis complex isolates belonging either to M. bovis or to M. caprae, cultivated from hunter harvested red deer (Cervus elaphus) and European wild boar (Sus scrofa) in 24 Spanish localities, and compares them with spoligotypes detected previously in humans, livestock or wild animals, as described in the literature. The distribution of the molecular type patterns suggests that the population of M. tuberculosis complex strains isolated from Spanish wild ungulates is spatially structured despite the lack of important geographical barriers and despite the increasingly frequent wildlife translocations. Red deer and the European wild boar can share the same molecular types in localities in which the M. tuberculosis complex was isolated from both species. Strains of bovine and caprine origin do circulate in the same local wildlife populations. Six out of 11 spoligotypes were similar to types described in human cases. The isolation of TB strains in fenced estates from wild animals that have not had contact with domestic livestock for at least the past two decades, strongly suggests that the M. tuberculosis complex is able to survive in these populations. Therefore, wildlife including cervids and the wild boar need to be considered in the epidemiology and control of tuberculosis.

  3. 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.

  4. 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

  5. SchiffBase Dinuclear Complex Catalyst for Oxidation of Cyclohexene with Molecular Oxygen

    Institute of Scientific and Technical Information of China (English)

    SHAO; DongXu

    2001-01-01

    In the past decades, the oxidation of hydrocarbons by transition metal complexes has been studied extensively. The current progress of the research on synthetic quasiporphyrin catalysts has led to the development of several systems that are able to reproduce the hene-enzyme mediated oxygenation and oxidation reactions[1]. In our group[2,51, the mononuclear complexes of amino acid Schiff base have been synthesized and their catalytic oxidation has been studied. In this paper, two dinuclear complexes, such as Salicylidence-β-alanine-Co(II)-Cu(II) and Salicylidence-β-alanine-Co(II)Mn(II), were prepared with amino acid Schiff bases and metal ions. In the presence of these dinuclear complexes, cyclohexene was effectively oxidized under 1 atm of molecular oxygen without any coreductants. The allylic hydroperoxide was obtained as an important product, which suggested a clear allylic pathway of oxidation of cyclohexene.  ……

  6. Atomic and molecular complex resonances from real eigenvalues using standard (hermitian) electronic structure calculations

    CERN Document Server

    Landau, Arie; Kaprálová-Žďánská, Petra Ruth; Moiseyev, Nimrod

    2015-01-01

    Complex eigenvalues, resonances, play an important role in large variety of fields in physics and chemistry. For example, in cold molecular collision experiments and electron scattering experiments, autoionizing and pre-dissociative metastable resonances are generated. However, the computation of complex resonance eigenvalues is difficult, since it requires severe modifications of standard electronic structure codes and methods. Here we show how resonance eigenvalues, positions and widths, can be calculated using the standard, widely used, electronic-structure packages. Our method enables the calculations of the complex resonance eigenvalues by using analytical continuation procedures (such as Pad\\'{e}). The key point in our approach is the existence of narrow analytical passages from the real axis to the complex energy plane. In fact, the existence of these analytical passages relies on using finite basis sets. These passages become narrower as the basis set becomes more complete, whereas in the exact limit,...

  7. Including Quantum Effects in the Dynamics of Complex (i.e., Large)Molecular Systems

    Energy Technology Data Exchange (ETDEWEB)

    Miller, William H.

    2006-04-27

    The development in the 1950's and 60's of crossed molecular beam methods for studying chemical reactions at the single-collision molecular level stimulated the need and desire for theoretical methods to describe these and other dynamical processes in molecular systems. Chemical dynamics theory has made great strides in the ensuing decades, so that methods are now available for treating the quantum dynamics of small molecular systems essentially completely. For the large molecular systems that are of so much interest nowadays (e.g. chemical reactions in solution, in clusters, in nano-structures, in biological systems, etc.), however, the only generally available theoretical approach is classical molecular dynamics (MD) simulations. Much effort is currently being devoted to the development of approaches for describing the quantum dynamics of these complex systems. This paper reviews some of these approaches, especially the use of semiclassical approximations for adding quantum effects to classical MD simulations, also showing some new versions that should make these semiclassical approaches even more practical and accurate.

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

    Energy Technology Data Exchange (ETDEWEB)

    Makino, Debora Lika, E-mail: dmakino@biochem.mpg.de; Conti, Elena [Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried (Germany)

    2013-11-01

    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.

  9. 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.

  10. On the origin of the Orion and Monoceros molecular cloud complexes

    Science.gov (United States)

    Franco, J.; Tenorio-Tagle, G.; Bodenheimer, P.; Rozyczka, M.; Mirabel, I. F.

    1988-01-01

    A detailed model for the origin of the Orion and Monoceros cloud complexes is presented, showing that a single high-velocity H I cloud-galaxy collision can explain their main observed features. The collision generates massive shocked layers, and self-gravity can then provide the conditions for the transformation of these layers into molecular clouds. The clouds formed by the collision maintain the motion of their parental shocked gas and reach positions located far away from the plane. According to this model, both the Orion and Monoceros complexes were formed some 60 million yr ago, when the original shocked layer was fragmented by Galactic tidal forces.

  11. A trinuclear ruthenium complex as a highly efficient molecular catalyst for water oxidation.

    Science.gov (United States)

    Zhang, L L; Gao, Y; Liu, Z; Ding, X; Yu, Z; Sun, L C

    2016-03-01

    A trinuclear ruthenium complex, 3, was designed and synthesized with the ligand 2,2'-bipyridine-6,6'-dicarboxylic acid (bda) and we found that this complex could function as a highly efficient molecular catalyst for water oxidation in homogeneous systems. This trinuclear molecular water oxidation catalyst, 3, displayed much higher efficiencies in terms of turnover numbers and initial oxygen evolution rate than its counterparts, a binuclear catalyst, 2, and a mononuclear catalyst, 1, in both chemically driven and photochemically driven water oxidation based on either the whole catalytic molecules or just the active Ru centers. The reasons for the superior performance of catalyst 3 were discussed and we believe that multiple Ru centers in a single molecule are indeed beneficial for increasing the probability of the formation of O-O bonds through an intramolecular radical coupling pathway.

  12. Complex Reaction Environments and Competing Reaction Mechanisms in Zeolite Catalysis: Insights from Advanced Molecular Dynamics.

    Science.gov (United States)

    De Wispelaere, Kristof; Ensing, Bernd; Ghysels, An; Meijer, Evert Jan; Van Speybroeck, Veronique

    2015-06-22

    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 principle molecular dynamics techniques to capture this complexity is shown by means of two case studies. Firstly, the adsorption behavior of methanol and water in H-SAPO-34 at 350 °C is investigated. Hereby an important degree of framework flexibility and proton mobility was observed. Secondly, the methylation of benzene by methanol through a competitive direct and stepwise pathway in the AFI topology was studied. Both case studies clearly show that a first-principle molecular dynamics approach enables unprecedented insights into zeolite-catalyzed reactions at the nanometer scale to be obtained.

  13. Molecular Weight and Proposed Structure of the Angelica sinensis Polysaccharide-iron Complex

    Institute of Scientific and Technical Information of China (English)

    WANG,Kai-Ping; CHEN,Zhi-Xiang; ZHANG,Yu; WANG,Pei-Pei; WANG,Ji-Hong; DAI,Li-Quan

    2008-01-01

    The molecular weight and the proposed structure of the Angelica sinensis polysaccharide-iron complex (APIC) were studied.Fourier transform infrared spectroscopy,X-ray powder diffraction,differential scanning calorimetry,transmission electron microscopy,electron paramagnetic resonance,thermogravimetric analysis,atomic force microscopy,and gel filtration chromatography were used to characterize APIC,which is a macromolecule complex composed of Angelica sinensis polysaccharide (ASP) and iron.The structure of APIC was proposed to be a polynuclear ferrihydrite core chelated firmly by an encircling framework of ASP chains,forming a core molecule,which is surrounded by a removable outer protective sheath of colloidal ASP.And the molecular formula of APIC was proposed to be { [(Fe2O3·2.2H2O)1043(ASP)32](ASP)12 },with MW=270000 Da.

  14. Geant4 Applications for Modeling Molecular Transport in Complex Vacuum Geometries

    CERN Document Server

    Singal, J; Schindler, R

    2013-01-01

    This letter discusses a novel use of the Geant4 simulation toolkit to model molecular transport in a vacuum environment, in the molecular flow regime. The Geant4 toolkit was originally developed by the high energy physics community to simulate the interactions of elementary particles within complex detector systems. Here its capabilities are utilized to model molecular vacuum transport in geometries where other techniques are impractical. The techniques are verified with an application representing a simple vacuum geometry that has been studied previously both analytically and by basic Monte Carlo simulation. We discuss the use of an application with a very complicated geometry, that of the Large Synoptic Survey Telescope camera cryostat, to determine probabilities of transport of contaminant molecules to optical surfaces where control of contamination is crucial.

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

    Directory of Open Access Journals (Sweden)

    Jorge Almaral-Sánchez

    2012-11-01

    Full Text Available 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.

  16. A Molecular Artisans Guide to Supramolecular Coordination Complexes and Metal Organic Frameworks

    Science.gov (United States)

    Wu, Xialu; Young, David J.; Hor, T. S. Andy

    2015-10-01

    As molecular synthesis advances, we are beginning to learn control of not only the chemical reactivity (and function) of molecules, but also of their interactions with other molecules. It is this basic idea that has led to the current explosion of supramolecular science and engineering. Parallel to this development, chemists have been actively pursuing the design of very large molecules using basic molecular building blocks. Herein, we review the general development of supramolecular chemistry and particularly of two new branches: supramolecular coordination complexes (SCCs) and metal organic frameworks (MOFs). These two fields are discussed in detail with typical examples to illustrate what is now possible and what challenges lie ahead for tomorrow's molecular artisans.

  17. 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

    2012-11-28

    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.

  18. Some aspects of radical chemistry in the assembly of complex molecular architectures

    Directory of Open Access Journals (Sweden)

    Béatrice Quiclet-Sire

    2013-03-01

    Full Text Available This review article describes briefly some of the radical processes developed in the authors’ laboratory as they pertain to the concise assembly of complex molecular scaffolds. The emphasis is placed on the use of nitrogen-centred radicals, on the degenerate addition–transfer of xanthates, especially on its potential for intermolecular carbon–carbon bond formation, and on the generation and capture of radicals through electron transfer processes.

  19. Vertical Distribution of Galactic Disc Stars and Gas Constrained by a Molecular Cloud Complex

    CERN Document Server

    Jog, C J; Jog, Chanda J.; Narayan, Chaitra A.

    2001-01-01

    We investigate the dynamical effects of a molecular cloud complex with a mass of about 10**7 M_sun and a size of a few 100 pc on the vertical distribution of stars and atomic hydrogen gas in a spiral galactic disc. Such massive complexes have now been observed in a number of spiral galaxies. The extended mass distribution in a complex, with an average mass density 6 times higher than the Oort limit, is shown to dominate the local gravitational field. This results in a significant redistribution of the surrounding disc components towards the mid-plane, with a resulting decrease in their vertical scaleheights. A surprising result is the large radial distance of about 500 pc from the complex centre over which the complex influences the disc. The complex has a comparable effect on the vertical distribution of HI in the galactic disc. This `pinching' or constraining effect should be detectable in the nearby spiral galaxies. Thus the gravitational field of a complex results in local corrugations of the stellar and ...

  20. 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...

  1. Cationic complexation with dissolved organic matter: Insights from molecular dynamics computer simulations and NMR spectroscopy

    Science.gov (United States)

    Kalinichev, A. G.; Xu, X.; Kirkpatrick, R.

    2006-12-01

    Dissolved organic matter (DOM) is ubiquitous in soil and surface water and plays many important geochemical and environmental roles acting as a proton donor/acceptor and pH buffer and interacting with metal ions, minerals and organic species to form water-soluble and water-insoluble complexes of widely differing chemical and biological stabilities. There are strong correlations among the concentration of DOM and the speciation, solubility and toxicity of many trace metals in soil and water due to metal-DOM interaction. DOM can also significantly negatively affect the performance of nanofiltration and reverse osmosis membranes used industrially for water purification and desalination, being one of the major causes of a so-called `membrane bio- fouling'. The molecular scale mechanisms and dynamics of the DOM interactions with metals and membranes are, however, quite poorly understood. Methods of computational molecular modeling, combined with element- specific nuclear magnetic resonance (NMR) spectroscopy, can serve as highly effective tools to probe and quantify on a fundamental molecular level the DOM interactions with metal cations in aqueous solutions, and to develop predictive models of the molecular mechanisms responsible for the metal-DOM complexation in the environment. This paper presents the results of molecular dynamics (MD) computer simulations of the interaction of DOM with dissolved Na+, Cs+, Mg2+, and Ca2+. Na+ forms only very weak outer-sphere complexes with DOM. These results and the results of other recent molecular modeling efforts (e.g., Sutton et al., Environmental Toxicology and Chemistry, 24, 1902-1911, 2005), clearly indicate that both the structural and dynamic aspects of the cation-DOM complexation follow a simple trend in terms of the charge/size ratio for the ions. Due to the competition between ion hydration in bulk aqueous solution and adsorption of these cations by the negatively charged DOM functional groups (primarily carboxylate

  2. A molecular model for positron complexes: long-range effects on 2{gamma} pair-annihilation rates

    Energy Technology Data Exchange (ETDEWEB)

    Mohallem, Jose R; Rolim, Flavia; Goncalves, Cristina P [Laboratorio de Atomos e Moleculas Especiais, Departamento de FIsica, ICEx, Universidade Federal de Minas Gerais, PO Box 702, 30123-970, Belo Horizonte, MG (Brazil)

    2004-03-14

    A molecular model for positron complexes is developed and used to study the effects of the nucleus-positron distance long-range regime on the 2{gamma} annihilation rates ({gamma}) of atomic complexes. The available data for {gamma} of some systems are then rationalized on its basis and some predictions are made. The model is shown to be capable of generating information on positron positioning and of making predictions of values of {gamma} in molecular complexes as well.

  3. 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

    2015-02-05

    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.

  4. 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.

  5. 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.

  6. POLYMER BOUND TRANSITION METAL COMPLEXES FOR CATALYTIC OXIDATION OF CYCLOHEXENE WITH MOLECULAR OXYGEN

    Institute of Scientific and Technical Information of China (English)

    HAO Chengjun; ZhAO Ganqing

    2007-01-01

    Polymer-bound Schiff-base ligand (PS-Sal-Cys) was prepared from the polystyrene-bound salicylaldehyde and L-cysteine, its complex (PS-Sal-Cys-Mn) was also synthesized. The polymer ligand and its complex were characterized by infrared spectra (IR), small area X-ray photoelectron spectroscopy (XPS), and inductively coupled plasma-atomic emission spectro (ICP-AES). In the presence of complex, cyclohexane can be effectively oxidized by molecular oxygen without a reductant. The major products of the reaction are 2-cyclohexen-1-ol, 2-cyclohexen-1-one, and 2-cyclohexen-1-hydroperoxide, which is different from the typical oxidation of cyclohexene. The mechanism of cyclohexene oxidation is also discussed.

  7. Shear zone junctions: Of zippers and freeways

    Science.gov (United States)

    Passchier, Cees W.; Platt, John P.

    2017-02-01

    Ductile shear zones are commonly treated as straight high-strain domains with uniform shear sense and characteristic curved foliation trails, bounded by non-deforming wall rock. Many shear zones, however, are branched, and if movement on such branches is contemporaneous, the resulting shape can be complicated and lead to unusual shear sense arrangement and foliation geometries in the wall rock. For Y-shaped shear zone triple junctions with three joining branches and transport direction at a high angle to the branchline, only eight basic types of junction are thought to be stable and to produce significant displacement. The simplest type, called freeway junctions, have similar shear sense in all three branches. The other types show joining or separating behaviour of shear zone branches similar to the action of a zipper. Such junctions may have shear zone branches that join to form a single branch (closing zipper junction), or a single shear zone that splits to form two branches, (opening zipper junction). All categories of shear zone junctions show characteristic foliation patterns and deflection of markers in the wall rock. Closing zipper junctions are unusual, since they form a non-active zone with opposite deflection of foliations in the wall rock known as an extraction fault or wake. Shear zipper junctions can form domains of overprinting shear sense along their flanks. A small and large field example are given from NE Spain and Eastern Anatolia. The geometry of more complex, 3D shear zone junctions with slip parallel and oblique to the branchline is briefly discussed.

  8. Gene knockout using transcription activator-like effector nucleases (TALENs) reveals that human NDUFA9 protein is essential for stabilizing the junction between membrane and matrix arms of complex I.

    Science.gov (United States)

    Stroud, David A; Formosa, Luke E; Wijeyeratne, Xiaonan W; Nguyen, Thanh N; Ryan, Michael T

    2013-01-18

    Transcription activator-like effector nucleases (TALENs) represent a promising approach for targeted knock-out of genes in cultured human cells. We used TALEN-technology to knock out the nuclear gene encoding NDUFA9, a subunit of mitochondrial respiratory chain complex I in HEK293T cells. Screening for the knock-out revealed a mixture of NDUFA9 cell clones that harbored partial deletions of the mitochondrial N-terminal targeting signal but were still capable of import. A cell line lacking functional copies of both NDUFA9 alleles resulted in a loss of NDUFA9 protein expression, impaired assembly of complex I, and cells incapable of growth in galactose medium. Cells lacking NDUFA9 contained a complex I subcomplex consisting of membrane arm subunits but not marker subunits of the matrix arm. Re-expression of NDUFA9 restored the defects in complex I assembly. We conclude that NDUFA9 is involved in stabilizing the junction between membrane and matrix arms of complex I, a late assembly step critical for complex I biogenesis and activity.

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

    Science.gov (United States)

    Mrugalla, Florian; Kast, Stefan M.

    2016-09-01

    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.

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

    Science.gov (United States)

    Mrugalla, Florian; Kast, Stefan M

    2016-09-01

    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.

  11. The topology and dynamics of protein complexes: insights from intra- molecular network theory.

    Science.gov (United States)

    Hu, Guang; Zhou, Jianhong; Yan, Wenying; Chen, Jiajia; Shen, Bairong

    2013-03-01

    Intra-molecular interactions within complex systems play a pivotal role in the biological function. They form a major challenge to computational structural proteomics. The network paradigm treats any system as a set of nodes linked by edges corresponding to the relations existing between the nodes. It offers a computationally efficient tool to meet this challenge. Here, we review the recent advances in the use of network theory to study the topology and dynamics of protein- ligand and protein-nucleic acid complexes. The study of protein complexes networks not only involves the topological classification in term of network parameters, but also reveals the consistent picture of intrinsic functional dynamics. Current dynamical analysis focuses on a plethora of functional phenomena: the process of allosteric communication, the binding induced conformational changes, prediction and identification of binding sites of protein complexes, which will give insights into intra-protein complexes interactions. Furthermore, such computational results may elucidate a variety of known biological processes and experimental data, and thereby demonstrate a huge potential for applications such as drug design and functional genomics. Finally we describe some web-based resources for protein complexes, as well as protein network servers and related bioinformatics tools.

  12. Molecular assembly of the ternary granulocyte-macrophage colony-stimulating factor receptor complex.

    Science.gov (United States)

    McClure, Barbara J; Hercus, Timothy R; Cambareri, Bronwyn A; Woodcock, Joanna M; Bagley, Christopher J; Howlett, Geoff J; Lopez, Angel F

    2003-02-15

    Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a hematopoietic cytokine that stimulates the production and functional activity of granulocytes and macrophages, properties that have encouraged its clinical use in bone marrow transplantation and in certain infectious diseases. Despite the importance of GM-CSF in regulating myeloid cell numbers and function, little is known about the exact composition and mechanism of assembly of the GM-CSF receptor complex. We have now produced soluble forms of the GM-CSF receptor alpha chain (sGMRalpha) and beta chain (sbetac) and utilized GM-CSF, the GM-CSF antagonist E21R (Glu21Arg), and the betac-blocking monoclonal antibody BION-1 to define the molecular assembly of the GM-CSF receptor complex. We found that GM-CSF and E21R were able to form low-affinity, binary complexes with sGMRalpha, each having a stoichiometry of 1:1. Importantly, GM-CSF but not E21R formed a ternary complex with sGMRalpha and sbetac, and this complex could be disrupted by E21R. Significantly, size-exclusion chromatography, analytical ultracentrifugation, and radioactive tracer experiments indicated that the ternary complex is composed of one sbetac dimer with a single molecule each of sGMRalpha and of GM-CSF. In addition, a hitherto unrecognized direct interaction between betac and GM-CSF was detected that was absent with E21R and was abolished by BION-1. These results demonstrate a novel mechanism of cytokine receptor assembly likely to apply also to interleukin-3 (IL-3) and IL-5 and have implications for our molecular understanding and potential manipulation of GM-CSF activation of its receptor.

  13. Exploring Molecular Complexity with ALMA (EMoCA): Deuterated complex organic molecules in Sagittarius B2(N2)

    CERN Document Server

    Belloche, A; Garrod, R T; Menten, K M

    2015-01-01

    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 high mass star forming regions. We use a spectral line survey performed with ALMA to search for deuterated complex organic molecules toward the hot molecular core Sgr B2(N2). Population diagrams and integrated intensity maps are constructed to fit rotational temperatures and emission sizes for each molecule. Column densities are derived by modelling the full spectrum under the LTE assumption. The results are compared to predictions of two astrochemical models that treat the deuteration process. 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 (<0.07%). Upp...

  14. A superconducting tunnel junction receiver for submillimeter astronomy, and analysis of observations of post-AGB star molecular envelopes. [AGB (asymptotic giant branch)

    Energy Technology Data Exchange (ETDEWEB)

    Jaminet, P.A.

    1992-01-01

    A heterodyne receiver designed for astronomical use between 450 and 520 GHz has been constructed. Very low capacitance (C [approximately] 5-10 fF) Superconductor-Insulator-Superconductor (SIS) junctions have been fabricated as the detectors; these junctions lie on the edges of niobium thin films and form Nb-Al-Al[sub 2]O[sub 3]-Al-Nb sandwiches. The double sideband (DSB) receiver noise temperature is between 400 K and 800 K throughout the 70 GHz band. In addition, detailed modelling and analysis of astronomical observations of two post-AGB (Asymptotic Giant Branch) stars was performed. The observations were made with an SIS receiver designed for 345 GHz. CO observations and modelling of the young planetary nebula NGC 7027 provided the best determination yet of its AGB mass loss rate, the first direct evidence for bipolarity in its AGB mass loss, evidence for close hydrodynamic coupling between the planetary nebula and the relic AGB wind, and evidence for evolution in the metallicity of the stellar wind. Observations of the proto-planetary nebula CRL 2688 found evidence for spatially extended fast wind emission with a non-bipolar morphology, and evidence for evolution is elemental abundances in the stellar wind.

  15. Early diagnosis of complex diseases by molecular biomarkers, network biomarkers, and dynamical network biomarkers.

    Science.gov (United States)

    Liu, Rui; Wang, Xiangdong; Aihara, Kazuyuki; Chen, Luonan

    2014-05-01

    Many studies have been carried out for early diagnosis of complex diseases by finding accurate and robust biomarkers specific to respective diseases. In particular, recent rapid advance of high-throughput technologies provides unprecedented rich information to characterize various disease genotypes and phenotypes in a global and also dynamical manner, which significantly accelerates the study of biomarkers from both theoretical and clinical perspectives. Traditionally, molecular biomarkers that distinguish disease samples from normal samples are widely adopted in clinical practices due to their ease of data measurement. However, many of them suffer from low coverage and high false-positive rates or high false-negative rates, which seriously limit their further clinical applications. To overcome those difficulties, network biomarkers (or module biomarkers) attract much attention and also achieve better performance because a network (or subnetwork) is considered to be a more robust form to characterize diseases than individual molecules. But, both molecular biomarkers and network biomarkers mainly distinguish disease samples from normal samples, and they generally cannot ensure to identify predisease samples due to their static nature, thereby lacking ability to early diagnosis. Based on nonlinear dynamical theory and complex network theory, a new concept of dynamical network biomarkers (DNBs, or a dynamical network of biomarkers) has been developed, which is different from traditional static approaches, and the DNB is able to distinguish a predisease state from normal and disease states by even a small number of samples, and therefore has great potential to achieve "real" early diagnosis of complex diseases. In this paper, we comprehensively review the recent advances and developments on molecular biomarkers, network biomarkers, and DNBs in particular, focusing on the biomarkers for early diagnosis of complex diseases considering a small number of samples and high

  16. Spectroscopic, docking and molecular dynamics simulation studies on the interaction of two Schiff base complexes with human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Fani, N. [Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111 (Iran, Islamic Republic of); Bordbar, A.K., E-mail: bordbar@chem.ui.ac.ir [Department of Chemistry, University of Isfahan, Isfahan 81746-73441 (Iran, Islamic Republic of); Ghayeb, Y. [Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111 (Iran, Islamic Republic of)

    2013-09-15

    This study was designed to examine the interaction of two Schiff base complexes with human serum albumin (HSA), by different kinds of spectroscopic and molecular modeling techniques. Fluorescence quenching and absorption spectra were investigated in order to estimate the binding parameters. The analysis of absorption data at different temperatures were done in order to estimate the thermodynamics parameters of interactions between Schiff base complexes and HSA. The experimental data suggested that both complexes demonstrated a significant binding affinity to HSA and the process is enthalpy driven. Molecular docking study indicated that both Schiff base complexes bind to polar and apolar residues located in the subdomain IB of HSA. Molecular dynamics (MD) simulations were also performed with the GROMACS program package to study the characters of HSA in binding states. Molecular dynamics results suggested that both Schiff base complexes can interact with HSA, without affecting the secondary structure of HSA but probably with a slight modification of its tertiary structure. All the molecular docking and molecular dynamics results kept in good consistence with experimental data. -- Highlights: • The fluorescence of HSA quenched due to reacting with Schiff base complexes. • The absorbance of Schiff base complexes in the presence of HSA changed. • Binding parameters and the pose of the molecules in the binding site were estimated. • Both complexes can interact with HSA, without affecting the secondary structure. • Simulation results predicted slight compactness of tertiary structure for HSA.

  17. Spectroscopic studies and molecular orbital calculations of charge transfer complexation between 3,5-dimethylpyrazole with DDQ in acetonitrile.

    Science.gov (United States)

    Habeeb, Moustafa M; Al-Attas, Amirah S; Al-Raimi, Doaa S

    2015-05-05

    Charge transfer (CT) interaction between 3,5-dimethylpyrazole (DMP) with the π-acceptor 2,3-dichloro-5,6-dicyano-p-benzoquinon (DDQ) has been investigated spectrophotometrically in acetonitrile (AN). Simultaneous reddish brown color has been observed upon mixing donor with acceptor solutions attributing to CT complex formation. The electronic spectra of the formed complex exhibited multi-charge transfer bands at 429, 447, 506, 542 and 589nm, respectively. Job(')s method of continuous variations and spectrophotometric titration methods confirmed the formation of the studied complex in 1:2 ratio between DMP and DDQ. Benesi-Hildebrand equation has been applied to calculate the stability constant of the formed complex where it recorded high value supporting formation of stable complex. Molecular orbital calculations using MM2 method and GAMESS (General Atomic and Molecular Electronic Structure System) interface computations as a package of ChemBio3D Ultra12 software were carried out for more analysis of the formed complex in the gas phase. The computational analysis included energy minimisation, stabilisation energy, molecular geometry, Mullikan charges, molecular electrostatic potential (MEP) surfaces of reactants and complex as well as characterization of the higher occupied molecular orbitals (HOMO) and lower unoccupied molecular orbitals (LUMO) surfaces of the complex. A good consistency between experimental and theoretical results has been recorded.

  18. 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 (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 both be due to the higher kinetic temperatures that characterize the Galactic center region compared to nearby clouds. Alternatively, they may result from a lower overall abundance of deuterium itself in the Galactic center region by up to a factor ten.

  19. Pseudo-symmetry analysis of the d-block molecular orbitals in four-coordinate complexes.

    Science.gov (United States)

    Falceto, Andrés; Casanova, David; Alemany, Pere; Alvarez, Santiago

    2013-06-03

    A rigorous definition of the concept of pseudo-symmetry, which is as important to chemistry as the concepts of symmetry implemented through group theory, should allow us to apply those group theoretical tools to molecules that are significantly distorted from those ideal symmetries best known and understood by the chemical community. In this paper, we consider four-coordinate transition-metal complexes with geometries along the interconversion path between the square and the tetrahedron and show how their molecular orbitals can be expressed in terms of either the tetrahedral or tetragonal symmetry groups. Furthermore, we analyze how the intensity of a d-d absorption band can be related to the degree of symmetry loss of the d-block molecular orbitals by means of their decomposition in terms of contributions from different pseudo-symmetry representations. As a final example, we also show how the substitution of a single ligand in a square planar complex affects the symmetry of the molecular orbitals and the absorption intensity associated to an electronic transition.

  20. Molecular typing of clinical isolates of Cryptococcus neoformans/Cryptococcus gattii species complex from Northeast Mexico.

    Science.gov (United States)

    González, Gloria M; Casillas-Vega, Néstor; Garza-González, Elvira; Hernández-Bello, Romel; Rivera, Gildardo; Rodríguez, Jesús Ancer; Bocanegra-Garcia, Virgilio

    2016-01-01

    Cryptococcosis is caused by members of the Cryptococcus neoformans/Cryptococcus gattii species complex. Based on molecular identification, these two species have been further differentiated into molecular types. The aim of this work was to characterize clinical cryptococcal isolates recovered from six hospitals in Northeast Mexico from 1995 to 2011. One hundred and sixty-six isolates, which were characterized by biochemical tests and in vitro susceptibility to amphotericin B, fluconazole, and voriconazole, and M13 PCR fingerprinting, were included in this study. Utilizing phenotypic tests, 153 isolates (92.16 %) were identified as C. neoformans and 13 (7.83 %) as C. gattii. All isolates were susceptible to all antifungals tested. Employing M13 PCR fingerprinting, eight molecular types were detected. VNI was the most common genotype (124 cases; 74.6 %), followed by VNII (15 cases; 9 %), VNIII (8 cases; 4.8 %), VNIV (6 cases; 3.6 %), VGI (6 cases; 3.6 %), VGII (3 cases; 1.8 %), and VGIII and VGIV (2 cases, 1.2 % each). We confirm the presence of C. gattii in clinical isolates in Northeast Mexico, and a high clonal diversity in the studied strains of C. neoformans/C. gattii species complex.

  1. The Structure of a Low-Metallicity Giant Molecular Cloud Complex

    CERN Document Server

    Leroy, A K; Bot, C; Engelbracht, C W; Gordon, K; Israel, F P; Rubio, M; Sandstrom, K; Stanimirović, S

    2009-01-01

    To understand the impact of low metallicities on giant molecular cloud (GMC) structure, we compare far infrared dust emission, CO emission, and dynamics in the star-forming complex N83 in the Wing of the Small Magellanic Cloud. Dust emission (measured by Spitzer as part of the S3MC and SAGE-SMC surveys) probes the total gas column independent of molecular line emission and traces shielding from photodissociating radiation. We calibrate a method to estimate the dust column using only the high-resolution Spitzer data and verify that dust traces the ISM in the HI-dominated region around N83. This allows us to resolve the relative structures of H2, dust, and CO within a giant molecular cloud complex, one of the first times such a measurement has been made in a low-metallicity galaxy. Our results support the hypothesis that CO is photodissociated while H2 self-shields in the outer parts of low-metallicity GMCs, so that dust/self shielding is the primary factor determining the distribution of CO emission. Four piec...

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

    Science.gov (United States)

    Bramhane, Dinesh M.; Kulkarni, Preethi A.; Martis, Elvis A. F.; Pissurlenkar, Raghuvir R. S.; Coutinho, Evans C.; Nagarsenker, Mangal S.

    2016-01-01

    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 PMID:27134470

  3. 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

  4. 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.

  5. Coordination mode of nitrate in uranyl(VI) complexes: a first-principles molecular dynamics study.

    Science.gov (United States)

    Bühl, Michael; Diss, Romain; Wipff, Georges

    2007-06-25

    According to Car-Parrinello molecular dynamics simulations for [UO(2)(NO(3))(3)](-), [UO(2)(NO(3))(4)](2-), and [UO(2)(OH(2))(4-)(NO(3))](+) complexes in the gas phase and in aqueous solution, the nitrate coordination mode to uranyl depends on the interplay between ligand-metal attractions, interligand repulsions, and solvation. In the trinitrate, the eta(2)-coordination is clearly favored in water and in the gas phase, leading to a coordination number (CN) of 6. According to pointwise thermodynamic integration involving constrained molecular dynamics simulations, a change in free energy of +6 kcal/mol is predicted for eta(2)- to eta(1)-transition of one of the three nitrate ligands in the gas phase. In the gas phase, the mononitrate-hydrate complex also prefers a eta(2)-binding mode but with a CN of 5, one H(2)O molecule being in the second shell. This contrasts with the aqueous solution where the nitrate binds in a eta(1)-fashion and uranyl coordinates to four H2O ligands. A driving force of ca. -3 kcal/mol is predicted for the eta(2)- to eta(1)- transition in water. This structural preference is interpreted in terms of steric arguments and differential solvation of terminal vs uranyl-coordinated O atoms of the nitrate ligands. The [UO(2)(NO(3))(4)](2-) complex with two eta(2)- and two eta(1)- coordinated nitrates, observed in the solid state, is stable for 1-2 ps in the gas phase and in solution. In the studied series, the modulation of uranyl-ligand distances upon immersion of the complex in water is found to depend on the nature of the ligand and the composition of the complex.

  6. 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...

  7. Molecular basis for the dissociation dynamics of protein A-immunoglobulin G1 complex.

    Directory of Open Access Journals (Sweden)

    Fu-Feng Liu

    Full Text Available Staphylococcus aureus protein A (SpA is the most popular affinity ligand for immunoglobulin G1 (IgG1. However, the molecular basis for the dissociation dynamics of SpA-IgG1 complex is unclear. Herein, coarse-grained (CG molecular dynamics (MD simulations with the Martini force field were used to study the dissociation dynamics of the complex. The CG-MD simulations were first verified by the agreement in the structural and interactional properties of SpA and human IgG1 (hIgG1 in the association process between the CG-MD and all-atom MD at different NaCl concentrations. Then, the CG-MD simulation studies focused on the molecular insight into the dissociation dynamics of SpA-hIgG1 complex at pH 3.0. It is found that there are four steps in the dissociation process of the complex. First, there is a slight conformational adjustment of helix II in SpA. This is followed by the phenomena that the electrostatic interactions provided by the three hot spots (Glu143, Arg146 and Lys154 of helix II of SpA break up, leading to the dissociation of helix II from the binding site of hIgG1. Subsequently, breakup of the hydrophobic interactions between helix I (Phe132, Tyr133 and His137 in SpA and hIgG1 occurs, resulting in the disengagement of helix I from its binding site of hIgG1. Finally, the non-specific interactions between SpA and hIgG1 decrease slowly till disappearance, leading to the complete dissociation of the SpA-hIgG1 complex. This work has revealed that CG-MD coupled with the Martini force field is an effective method for studying the dissociation dynamics of protein-protein complex.

  8. Luminescence of Nanosized Supramolecular Material of Mesoporous Molecular Sieve and Samarium (Ⅲ) Complex

    Institute of Scientific and Technical Information of China (English)

    YIN Wei; ZHANG Mai-sheng

    2003-01-01

    The solutions of rare earth complexes Sm(Phen)2(TTA)(Bipy)(NO3)3 and Sm(L)x(TTA)4-x(NO3)3[L=Phen(1,10-phenanthroline) or Bipy(2,2′-bipyridine), x=4, 3, 2, 1, 0; TTA is 2-thenoyltrifluoacetone] in EtOH(1×10-3 mol/L) were prepared. The coefficients of antenna effect are 31.5, 18.2 and 5.6 for Phen, Bipy and TTA, respectively, when the electron configuration of the excited state of the samarium atom in the complexes is 4D1/2. The fluorescent intensity and the lifetime of the supramolecular encapsulation products of (CH3)3Si-MCM-41 and Sm3+ complexes are stronger and longer than those of the encapsulation products of MCM-41 and Sm3+ complexes respectively. The results show that the host with lipophilic channels is more favourable to the fluorescence of the rare earth complexes than the hydrophilic mesoporous molecular sieve. The fluorescent intensity of (CH3)3Si-MCM-41-Sm(Phen)3(TTA)(NO3)3 is the strongest amongthe encapsulation series of Sm3+ complexes, which is assumed to result from the greatly reduction of SiO-H vibration relaxation in host (CH3)3Si-MCM-41 and the presence of the discrete strong luminescent centres of the guest molecules associated with the nanosized material′s structure. The luminescent decay halftime of the supramolecular materials is much shorter than that of the powder of the samarium complexes. The result shows that the ligand transferring energy from the triplet state to the singlet state of Sm3+(T1→S, intersystem crossing) becomes higher. The fluorescent experimental results indicate that the interaction between the host and the guest influences the luminescent properties of the nanostructured supramolecular materials.

  9. Investigation of molecular interactions in the complex formation of tartaric acid derivatives with di(2-ethylhexyl) phosphoric acid

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The molecular interactions in the complex formation of two tartaric acid derivatives with di(2-ethylhexyl) phosphoric acid are investigated. The complex formation with a 1:1 stoichiometry between tartaric acid derivatives and D2EHPA can be obtained through UV-Vis titration, NMR chemical shifts and molecular dynamic simulations. Furthermore, the differences of the two complexes on the binding constants and strength of hydrogen bonds can also be determined. Such research will ideally provide insight into ways of regulating the complex forming properties of tartaric acid derivatives for composing or syn- thesizing new chiral resolving agents.

  10. Investigation of molecular interactions in the complex formation of tartaric acid derivatives with di(2-ethylhexyl) phosphoric acid

    Institute of Scientific and Technical Information of China (English)

    TAN Bin; ZHAI Zheng; LUO GuangSheng; WANG JiaDing

    2008-01-01

    The molecular interactions in the complex formation of two tartaric acid derivatives with di(2-ethylhexyl) phosphoric acid are investigated. The complex formation with a 1:1 stoichiometry between tartaric acid derivatives and D2EHPA can be obtained through UV-Vis titration, NMR chemical shifts and molecular dynamic simulations. Furthermore, the differences of the two complexes on the binding constants and strength of hydrogen bonds can also be determined. Such research will ideally provide insight into ways of regulating the complex forming properties of tartaric acid derivatives for composing or syn-thesizing new chiral resolving agents.

  11. Morphogenesis of rat myotendinous junction.

    Science.gov (United States)

    Curzi, Davide; Ambrogini, Patrizia; Falcieri, Elisabetta; Burattini, Sabrina

    2013-10-01

    Myotendinous junction (MTJ) is the highly specialized complex which connects the skeletal muscle to the tendon for transmitting the contractile force between the two tissues. The purpose of this study was to investigate the MTJ development and rat EDL was chosen as a model. 1, 15, 30 day animals were considered and the junctions were analyzed by light and electron microscopy. The MTJ interface architecture increased during the development, extending the interaction between muscle and tendon. 1-day-old rats showed disorganized myofibril bundles, spread cytosol and incomplete rough endoplasmic reticulum, features partially improved in 15-day-old rats, and completely developed in 30-day-old animals. These findings indicate that muscle-tendon interface displays, during rat lifetime, numerically increased and longer tendon interdigitations, correlated with an improved organization of both tissues and with a progressive acquirement of full functionality.

  12. Co-assembly of tetrapeptides into complex pH-responsive molecular hydrogel networks

    OpenAIRE

    Tena Solsona, Marta; Alonso de Castro, S.; Miravet Celades, Juan Felipe; Escuder Gil, Beatriu

    2014-01-01

    Here we prepare pH-responsive complex molecular hydrogels from oppositely charged tetrapeptidic components that can be pH-tuned resulting in interconversion between different networks. Two different systems are described based on tetrapeptides with an alternating sequence of non-polar (F) and polar (D or K) residues. Co-aggregated hydrogels are easily formed in situ at neutral pH whereas one-component networks are maintained after changing into acidic or basic pH. These systems have been appl...

  13. 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

  14. Complex materials for molecular spintronics applications: cobalt bis(dioxolene) valence tautomers, from molecules to polymers.

    Science.gov (United States)

    Calzolari, Arrigo; Chen, Yifeng; Lewis, Geoffrey F; Dougherty, Daniel B; Shultz, David; Nardelli, Marco Buongiorno

    2012-11-01

    Using first principles calculations, we predict a complex multifunctional behavior in cobalt bis(dioxolene) valence tautomeric compounds. Molecular spin-state switching is shown to dramatically alter electronic properties and corresponding transport properties. This spin state dependence has been demonstrated for technologically relevant coordination polymers of valence tautomers as well as for novel conjugated polymers with valence tautomeric functionalization. As a result, these materials are proposed as promising candidates for spintronic devices that can couple magnetic bistability with novel electrical and spin conduction properties. Our findings pave the way to the fundamental understanding and future design of active multifunctional organic materials for spintronics applications.

  15. 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)

  16. Molecular Components of the Sporothrix schenckii Complex that Induce Immune Response.

    Science.gov (United States)

    Alba-Fierro, Carlos A; Pérez-Torres, Armando; Toriello, Conchita; Romo-Lozano, Yolanda; López-Romero, Everardo; Ruiz-Baca, Estela

    2016-08-01

    Sporotrichosis is a fungal disease caused by the Sporothrix schenckii complex that includes species such as S. brasiliensis, S. schenckii sensu stricto, S. globosa, S. luriei, S. mexicana, and S. pallida, which exhibit different potentially antigenic molecular components. The immune response of susceptible hosts to control infection and disease caused by these fungi has been little studied. Besides, the fungus-host interaction induces the activation of different types of immune response. This mini-review analyzes and discusses existing reports on the identification and functional characterization of molecules from species of the S. schenckii complex with clinical relevance, and the mechanisms that mediate the type and magnitude of the immune response in experimental models in vivo and in vitro. This knowledge is expected to contribute to the development of protective and therapeutic strategies against sporotrichosis and other mycoses.

  17. Microwave Spectrum and Molecular Structure of the ARGON-CIS-1,2-DICHLOROETHYLENE Complex

    Science.gov (United States)

    Marshall, Mark D.; Leung, Helen O.; Nelson, Craig J.; Yoon, Leonard H.

    2016-06-01

    The non-planar molecular structure of the complex formed between the argon atom and cis-1,2-dichloroethylene is determined via analysis of its microwave spectrum. Spectra of the 35Cl and 37Cl isotopologues are observed in natural abundance and the nuclear quadrupole splitting due to the two chlorine nuclei is fully resolved. In addition, the complete quadrupole coupling tensor for the cis-1,2-dichloroethylene molecule, including the single non-zero off-diagonal element, has been determined. Unlike the argon-cis-1,2-difluoroethylene and the argon-vinyl chloride complexes, tunneling between the two equivalent non-planar configurations of argon-cis-1,2-dichloroethylene is not observed.

  18. Inclusion complexation of sulfapyridine with α- and β-cyclodextrins: Spectral and molecular modeling study

    Science.gov (United States)

    Rajendiran, N.; Siva, S.; Saravanan, J.

    2013-12-01

    The inclusion complexes of sulfapyridine (SFP) with α-CD and β-CD were investigated by absorption, fluorescence, time-resolved fluorescence, FTIR, DSC, XRD, 1H NMR, SEM, TEM and molecular modeling methods. The normal fluorescence takes place from locally excited (LE) state while twisted intramolecular charge transfer (TICT) is responsible for highly Stokes shifted fluorescence. The enhancement of TICT emission in both CDs suggesting that the inclusion process plays the major role in this emission. The spectral shifts revealed that part of pyridine ring of SFP is entrapped in the CDs cavities. TEM images confirmed round shaped nanoparticles with the average size about 20-50 nm were observed in SFP with α-CD and β-CD inclusion complexes. PM3 calculations have suggested that the large stabilization of excited singlet state of SFP with twisted conformation occurring at the amide SN bond between the electron donor group (aniline ring) and the electron acceptor group (pyridine ring).

  19. An efficient tool to calculate two-dimensional optical spectra for photoactive molecular complexes

    CERN Document Server

    Duan, Hong-Guang; Nalbach, Peter; Thorwart, Michael

    2015-01-01

    We combine the coherent modified Redfield theory (CMRT) with the equation of motion-phase matching approach (PMA) to calculate two-dimensional photon echo spectra for photoactive molecular complexes with an intermediate strength of the coupling to their environment. Both techniques are highly efficient, yet they involve approximations at different levels. By explicitly comparing with the numerically exact quasi-adiabatic path integral approach, we show for the Fenna-Matthews-Olson complex that the CMRT describes the decay rates in the population dynamics well, but final stationary populations and the oscillation frequencies differ slightly. In addition, we use the combined CMRT+PMA to calculate two-dimensional photon-echo spectra for a simple dimer model. We find excellent agreement with the exact path integral calculations at short waiting times where the dynamics is still coherent. For long waiting times, differences occur due to different final stationary states, specifically for strong system-bath couplin...

  20. Short-range interactions within molecular complexes formed in supersonic beams: structural effects and chiral discrimination

    Science.gov (United States)

    Latini; Satta; Guidoni; Piccirillo; Speranza

    2000-03-17

    One- and two-color, mass-selected R2PI spectra of the S13-pentanol, were recorded after a supersonic molecular beam expansion. Spectral analysis, coupled with theoretical calculations, indicate that several hydrogen-bonded [R.solv] conformers are present in the beam. The R2PI excitation spectra of [R.solv] are characterized by significant shifts of their band origin relative to that of bare R. The extent and direction of these spectral shifts depend on the structure and configuration of solv and are attributed to different short-range interactions in the ground and excited [R.solv] complexes. Measurement of the binding energies of [R.solv] in their neutral and ionic states points to a subtle balance between attractive (electrostatic and dispersive) and repulsive (steric) forces, which control the spectral features of the complexes and allow enantiomeric discrimination of chiral solv molecules.

  1. π-Bonded dithiolene complexes: synthesis, molecular structures, electrochemical behavior, and density functional theory calculations.

    Science.gov (United States)

    Damas, Aurélie; Chamoreau, Lise-Marie; Cooksy, Andrew L; Jutand, Anny; Amouri, Hani

    2013-02-04

    The synthesis and X-ray molecular structure of the first metal-stabilized o-dithiobenzoquinone [Cp*Ir-o-(η(4)-C(6)H(4)S(2))] (2) are described. The presence of the metal stabilizes this elusive intermediate by π coordination and increases the nucleophilic character of the sulfur atoms. Indeed, the π-bonded dithiolene complex 2 was found to react with the organometallic solvated species [Cp*M(acetone)(3)][OTf](2) (M = Rh, Ir) to give a unique class of binuclear dithiolene compounds [Cp*Ir(C(6)H(4)S(2))MCp*][OTf](2) [M = Rh (3), Ir (4)] in which the elusive dithiolene η-C(6)H(4)S(2) acts as a bridging ligand toward the two Cp*M moieties. The electrochemical behavior of all complexes was investigated and provided us with valuable information about their redox properties. Density functional theory (DFT) calculations on the π-bonded dithiobenzoquinone ligand and related bimetallic systems show that the presence of Cp*M at the arene system of the dithiolene ligand increases the stability compared to the known monomeric species [Cp*Ir-o-(C(6)H(4)S(2)-κ(2)-S,S)] and enables these complexes Cp*Ir(C(6)H(4)S(2))MCp*][OTf](2) (3 and 4) to act as electron reservoirs. Time-dependent DFT calculations also predict the qualitative trends in the experimental UV-vis spectra and indicate that the strongest transitions arise from ligand-metal charge transfer involving primarily the HOMO-1 and LUMO. All of these compounds were fully characterized and identified by single-crystal X-ray crystallography. These results illustrate the first examples describing the coordination chemistry of the elusive o-dithiobenzoquinone to yield bimetallic complexes with an o-benzodithiolene ligand. These compounds might have important applications in the area of molecular materials.

  2. Molecular orbital studies of gas-phase interactions between complex molecules.

    Science.gov (United States)

    Gaudreault, Roger; Whitehead, M A; van de Ven, Theo G M

    2006-03-16

    Describing interactions among large molecules theoretically is a challenging task. As an example, we investigated gas-phase interactions between a linear nonionic oligomer and various model compounds (cofactors), which have been reported to associate experimentally, using PM3 semiempirical molecular orbital theory. As oligomer, we studied the hexamer of poly(ethylene oxide) (PEO), and as cofactors, we studied corilagin and related compounds containing phenolic groups (R-OH). These systems are of interest because they are models for PEO/cofactor flocculation systems, used in industrial applications. The PM3 delocalized molecular orbitals (DLMO) describe the bonding between (PEO)6 and cofactors, and some of them cover the complete complex. The DLMOs which cover the traditionally considered hydrogen bonds R-OH...O or R-CH...O show a distinct "pinch", a decrease of the electron density, between the H...O atoms. Calculations of Gibbs free energy, entropy, and enthalpy show that the PEO/cofactor complexes do not form at room temperature, because the loss of entropy exceeds the increase in enthalpy. The change in enthalpy is linearly related to the change in entropy for the different complexes. Even though bond lengths, bond angles, DLMOs, and electron densities for the PEO/cofactor complexes are consistent with the definition of hydrogen bonds, the number of intermolecular R-OH...O and R-CH...O bonds does not correlate with the enthalpy of association, indicating that the bonding mechanism for these systems is the sum of many small contributions of many delocalized orbitals.

  3. Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease.

    Science.gov (United States)

    Estarellas, Carolina; Otyepka, Michal; Koča, Jaroslav; Banáš, Pavel; Krepl, Miroslav; Šponer, Jiří

    2015-05-01

    Many prokaryotic genomes comprise Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) offering defense against foreign nucleic acids. These immune systems are conditioned by the production of small CRISPR-derived RNAs matured from long RNA precursors. This often requires a Csy4 endoribonuclease cleaving the RNA 3'-end. We report extended explicit solvent molecular dynamic (MD) simulations of Csy4/RNA complex in precursor and product states, based on X-ray structures of product and inactivated precursor (55 simulations; ~3.7μs in total). The simulations identify double-protonated His29 and deprotonated terminal phosphate as the likely dominant protonation states consistent with the product structure. We revealed potential substates consistent with Ser148 and His29 acting as the general base and acid, respectively. The Ser148 could be straightforwardly deprotonated through solvent and could without further structural rearrangements deprotonate the nucleophile, contrasting similar studies investigating the general base role of nucleobases in ribozymes. We could not locate geometries consistent with His29 acting as general base. However, we caution that the X-ray structures do not always capture the catalytically active geometries and then the reactive structures may be unreachable by the simulation technique. We identified potential catalytic arrangement of the Csy4/RNA complex but we also report limitations of the simulation technique. Even for the dominant protonation state we could not achieve full agreement between the simulations and the structural data. Potential catalytic arrangement of the Csy4/RNA complex is found. Further, we provide unique insights into limitations of simulations of protein/RNA complexes, namely, the influence of the starting experimental structures and force field limitations. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. Magnetic tunnel junctions (MTJs)

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    We review the giant tunnel magnetoresistance (TMR) in ferromagnetic-insulator-ferromagnetic junctions discovered in recent years, which is the magnetoresistance (MR) associated with the spin-dependent tunneling between two ferromagnetic metal films separated by an insulating thin tunnel barrier. The theoretical and experimental results including junction conductance, magnetoresistance and their temperature and bias dependences are described.

  5. Stacked Josephson Junctions

    DEFF Research Database (Denmark)

    Madsen, Søren Find; Pedersen, Niels Falsig; Christiansen, Peter Leth

    2010-01-01

    Long Josephson junctions have for some time been considered as a source of THz radiation. Solitons moving coherently in the junctions is a possible source for this radiation. Analytical computations of the bunched state and bunching-inducing methods are reviewed. Experiments showing THz radiation...

  6. Wing geometric morphometrics and molecular assessment of members in the Albitarsis Complex from Colombia.

    Science.gov (United States)

    Gómez, G; Jaramillo, L; Correa, M M

    2013-11-01

    Malaria parasites are transmitted to humans by female mosquitoes of the genus Anopheles. The Albitarsis Complex harbours at least eight species not readily differentiable by morphology. This complicates the determination of those species involved in malaria transmission and the implementation of targeted and effective vector control strategies. In Colombia, there is little information about the identity and distribution of the Albitarsis Complex members. In this work, COI DNA barcoding was used to assign specimens Anopheles albitarsis s.l. to any of the previously designated species of the Albitarsis Complex. Two molecular operational taxonomic units (MOTUs), differentially distributed in Colombia, were detected, A. albitarsis I in the NW and NE, and A. albitarsis F, E and NE Colombia. In contrast, nuclear white gene and ITS2 sequence analyses did not allow differentiating between the MOTUs. Wing landmark-based geometric morphometrics applied to explore intertaxa phenotypic heterogeneity showed a subtle but significant difference in size, while shape did not allow the separation of the MOTUs. In general, the multiple marker analysis was not supportive of the existence in Colombia of more than one species of the Albitarsis Complex.

  7. The tomato Prf complex is a molecular trap for bacterial effectors based on Pto transphosphorylation.

    Science.gov (United States)

    Ntoukakis, Vardis; Balmuth, Alexi L; Mucyn, Tatiana S; Gutierrez, Jose R; Jones, Alexandra M E; Rathjen, John P

    2013-01-01

    The major virulence strategy of phytopathogenic bacteria is to secrete effector proteins into the host cell to target the immune machinery. AvrPto and AvrPtoB are two such effectors from Pseudomonas syringae, which disable an overlapping range of kinases in Arabidopsis and Tomato. Both effectors target surface-localized receptor-kinases to avoid bacterial recognition. In turn, tomato has evolved an intracellular effector-recognition complex composed of the NB-LRR protein Prf and the Pto kinase. Structural analyses have shown that the most important interaction surface for AvrPto and AvrPtoB is the Pto P+1 loop. AvrPto is an inhibitor of Pto kinase activity, but paradoxically, this kinase activity is a prerequisite for defense activation by AvrPto. Here using biochemical approaches we show that disruption of Pto P+1 loop stimulates phosphorylation in trans, which is possible because the Pto/Prf complex is oligomeric. Both P+1 loop disruption and transphosphorylation are necessary for signalling. Thus, effector perturbation of one kinase molecule in the complex activates another. Hence, the Pto/Prf complex is a sophisticated molecular trap for effectors that target protein kinases, an essential aspect of the pathogen's virulence strategy. The data presented here give a clear view of why bacterial virulence and host recognition mechanisms are so often related and how the slowly evolving host is able to keep pace with the faster-evolving pathogen.

  8. The tomato Prf complex is a molecular trap for bacterial effectors based on Pto transphosphorylation.

    Directory of Open Access Journals (Sweden)

    Vardis Ntoukakis

    2013-01-01

    Full Text Available The major virulence strategy of phytopathogenic bacteria is to secrete effector proteins into the host cell to target the immune machinery. AvrPto and AvrPtoB are two such effectors from Pseudomonas syringae, which disable an overlapping range of kinases in Arabidopsis and Tomato. Both effectors target surface-localized receptor-kinases to avoid bacterial recognition. In turn, tomato has evolved an intracellular effector-recognition complex composed of the NB-LRR protein Prf and the Pto kinase. Structural analyses have shown that the most important interaction surface for AvrPto and AvrPtoB is the Pto P+1 loop. AvrPto is an inhibitor of Pto kinase activity, but paradoxically, this kinase activity is a prerequisite for defense activation by AvrPto. Here using biochemical approaches we show that disruption of Pto P+1 loop stimulates phosphorylation in trans, which is possible because the Pto/Prf complex is oligomeric. Both P+1 loop disruption and transphosphorylation are necessary for signalling. Thus, effector perturbation of one kinase molecule in the complex activates another. Hence, the Pto/Prf complex is a sophisticated molecular trap for effectors that target protein kinases, an essential aspect of the pathogen's virulence strategy. The data presented here give a clear view of why bacterial virulence and host recognition mechanisms are so often related and how the slowly evolving host is able to keep pace with the faster-evolving pathogen.

  9. Molecular karyotype analysis and mapping of housekeeping genes to chromosomes of selected species complexes of Leishmania

    Directory of Open Access Journals (Sweden)

    Celso Cruz Tavares

    1992-12-01

    Full Text Available The molecular karyotypes for 20 reference strais of species complexes of Leishmania were determined by contour-clamped homogeneous eletric field (CHEF electrosphoresis. Determination of number/position of chromosome-sized bands and chromosomal DNA locations of house-keeping genes were the two criteria used for differentiating and classifying the Leishmania species. We have established two gel running conditions of optimal separation of chromosomes, wich resolved DNA molecules as large as 2,500 kilobase pairs (kb. Chromosomes were polymorphic in number (22-30 and size (200-2,500 kb of bands among members of five complexes of Leishmania. Although each stock had a distinct karyotype, in general the differences found between strains and/or species within each complex were not clear enough for parasite identification. However, each group showed a specific number of size-concordant DNA molecules, wich allowed distinction among the Leishmania complex parasites. Clear differences between the Old and New world groups of parasites or among some New World Leishmania species were also apparent in relation to the chromosome locations of beta-tubulin genes. Based on these results as well as data from other published studies the potencial of using DNA karyotype for identifying and classifying leishmanial field isolates is discussed.

  10. The Apaf-1*procaspase-9 apoptosome complex functions as a proteolytic-based molecular timer.

    Science.gov (United States)

    Malladi, Srinivas; Challa-Malladi, Madhavi; Fearnhead, Howard O; Bratton, Shawn B

    2009-07-08

    During stress-induced apoptosis, the initiator caspase-9 is activated by the Apaf-1 apoptosome and must remain bound to retain significant catalytic activity. Nevertheless, in apoptotic cells the vast majority of processed caspase-9 is paradoxically observed outside the complex. We show herein that apoptosome-mediated cleavage of procaspase-9 occurs exclusively through a CARD-displacement mechanism, so that unlike the effector procaspase-3, procaspase-9 cannot be processed by the apoptosome as a typical substrate. Indeed, procaspase-9 possessed higher affinity for the apoptosome and could displace the processed caspase-9 from the complex, thereby facilitating a continuous cycle of procaspase-9 recruitment/activation, processing, and release from the complex. Owing to its rapid autocatalytic cleavage, however, procaspase-9 per se contributed little to the activation of procaspase-3. Thus, the Apaf-1 apoptosome functions as a proteolytic-based 'molecular timer', wherein the intracellular concentration of procaspase-9 sets the overall duration of the timer, procaspase-9 autoprocessing activates the timer, and the rate at which the processed caspase-9 dissociates from the complex (and thus loses its capacity to activate procaspase-3) dictates how fast the timer 'ticks' over.

  11. Designing metal hydride complexes for water splitting reactions: a molecular electrostatic potential approach.

    Science.gov (United States)

    Sandhya, K S; Suresh, Cherumuttathu H

    2014-08-28

    The hydridic character of octahedral metal hydride complexes of groups VI, VII and VIII has been systematically studied using molecular electrostatic potential (MESP) topography. The absolute minimum of MESP at the hydride ligand (Vmin) and the MESP value at the hydride nucleus (VH) are found to be very good measures of the hydridic character of the hydride ligand. The increasing/decreasing electron donating feature of the ligand environment is clearly reflected in the increasing/decreasing negative character of Vmin and VH. The formation of an outer sphere metal hydride-water complex showing the HH dihydrogen interaction is supported by the location and the value of Vmin near the hydride ligand. A higher negative MESP suggested lower activation energy for H2 elimination. Thus, MESP features provided a way to fine-tune the ligand environment of a metal-hydride complex to achieve high hydridicity for the hydride ligand. The applicability of an MESP based hydridic descriptor in designing water splitting reactions is tested for group VI metal hydride model complexes of tungsten.

  12. Molecular identification of Mycobacterium tuberculosis complex isolates from Kermanshah Province, Iran.

    Science.gov (United States)

    Moghaddam, Roghieh; Mosavari, Nader; Mahalati, Ardeshir Hesampoor

    2016-12-01

    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. Copyright © 2016.

  13. Energetics, molecular electronic structure, and spectroscopy of forming Group IIA dihalide complexes

    Science.gov (United States)

    Devore, T. C.; Gole, J. L.

    1999-02-01

    Multiple-collision relaxed (helium) chemiluminescence and laser-induced fluorescent spectroscopy have been used to demonstrate the highly efficient collisional stabilization of electronically excited Group IIA dihalide collision complexes formed in M (Ca,Sr)+X 2 (XY) (Cl 2, Br 2, ICl, IBr, I 2) reactive encounters. The first discrete emission spectra for the CaCl 2, CaBr 2, SrCl 2, SrBr 2, and SrICl dihalides are observed and evaluated; however, the low-pressure `continuous' chemiluminescent emission observed for forming barium dihalide (BaX 2) complexes is quenched under these experimental conditions. The reactions of the Group IIA metals with molecular fluorine do not readily produce the corresponding dihalide. While the lowest-lying observed dihalide visible transition is, as predicted, found to result in an extended progression in a dihalide complex bending mode (SrCl 2), the observed progression suggests the presence of a residual halogen (Cl-Cl) bond. Two higher-lying transitions are dominated by a vibrational mode structure corresponding to progressions in the symmetric stretching mode or, for nominally forbidden electronic transitions, odd quanta of the asymmetric stretching mode. Some evidence for sequence structure associated with the dihalide bending mode is also obtained. These observations are consistent with complex formation as it is coupled with a modified valence electron structure (correlation diagram) associated with the highly ionic nature of the dihalides. The bonding in the Group IIA dihalides (and their complexes), whose atomization energies are more than twice the metal monohalide bond energy, strongly influences the evaluation of energetics and the determination of monohalide bond energies from chemiluminescent processes. Discrepancies between those bond strengths determined by mass spectrometry and chemiluminescence are discussed with a focus on energy partitioning in dihalide complex formation and its influence on chemical vapor

  14. 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.

  15. Beyond 'furballs' and 'dumpling soups' - towards a molecular architecture of signaling complexes and networks.

    Science.gov (United States)

    Lewitzky, Marc; Simister, Philip C; Feller, Stephan M

    2012-08-14

    The molecular architectures of intracellular signaling networks are largely unknown. Understanding their design principles and mechanisms of processing information is essential to grasp the molecular basis of virtually all biological processes. This is particularly challenging for human pathologies like cancers, as essentially each tumor is a unique disease with vastly deranged signaling networks. However, even in normal cells we know almost nothing. A few 'signalosomes', like the COP9 and the TCR signaling complexes have been described, but detailed structural information on their architectures is largely lacking. Similarly, many growth factor receptors, for example EGF receptor, insulin receptor and c-Met, signal via huge protein complexes built on large platform proteins (Gab, Irs/Dok, p130Cas[BCAR1], Frs families etc.), which are structurally not well understood. Subsequent higher order processing events remain even more enigmatic. We discuss here methods that can be employed to study signaling architectures, and the importance of too often neglected features like macromolecular crowding, intrinsic disorder in proteins and the sophisticated cellular infrastructures, which need to be carefully considered in order to develop a more mature understanding of cellular signal processing.

  16. Gap junction intercellular communication and benzene toxicity.

    Science.gov (United States)

    Rivedal, Edgar; Witz, Gisela; Leithe, Edward

    2010-03-19

    Aberrant regulation of gap junction intercellular communication (GJIC) has been linked to several human diseases, including cancer and abnormal hematopoietic development. Benzene exposure has been shown to cause hematotoxicity and leukemia, but the underlying mechanisms involved remain unclear. We have observed that several metabolites of benzene have the ability to block gap junction intercellular communication. The ring-opened trans,trans-muconaldehyde (MUC) was found to be the most potent inhibitor of gap junction channels. MUC was found to induce cross-linking of the gap junction protein connexin43, which seemed to be responsible for the induced inhibition of GJIC. Glutaraldehyde, which has a similar molecular structure as MUC, was found to possess similar effects on gap junctions as MUC, while the mono-aldehyde formaldehyde shows lower potency, both as a connexin cross-linker, and as an inhibitor of GJIC. Both glutaraldehyde and formaldehyde have previously been associated with induction of leukemia and disturbance of hematopoiesis. Taken together, the data support a possible link between the effect of MUC on gap junctions, and the toxic effects of benzene. Copyright (c) 2009 Elsevier Ireland Ltd. All rights reserved.

  17. 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.

  18. Molecular architecture of the yeast Elongator complex reveals an unexpected asymmetric subunit arrangement.

    Science.gov (United States)

    Setiaputra, Dheva T; Cheng, Derrick Th; Lu, Shan; Hansen, Jesse M; Dalwadi, Udit; Lam, Cindy Hy; To, Jeffrey L; Dong, Meng-Qiu; Yip, Calvin K

    2017-02-01

    Elongator is a ~850 kDa protein complex involved in multiple processes from transcription to tRNA modification. Conserved from yeast to humans, Elongator is assembled from two copies of six unique subunits (Elp1 to Elp6). Despite the wealth of structural data on the individual subunits, the overall architecture and subunit organization of the full Elongator and the molecular mechanisms of how it exerts its multiple activities remain unclear. Using single-particle electron microscopy (EM), we revealed that yeast Elongator adopts a bilobal architecture and an unexpected asymmetric subunit arrangement resulting from the hexameric Elp456 subassembly anchored to one of the two Elp123 lobes that form the structural scaffold. By integrating the EM data with available subunit crystal structures and restraints generated from cross-linking coupled to mass spectrometry, we constructed a multiscale molecular model that showed the two Elp3, the main catalytic subunit, are located in two distinct environments. This work provides the first structural insights into Elongator and a framework to understand the molecular basis of its multifunctionality.

  19. Molecular architecture of the human sperm IZUMO1 and egg JUNO fertilization complex.

    Science.gov (United States)

    Aydin, Halil; Sultana, Azmiri; Li, Sheng; Thavalingam, Annoj; Lee, Jeffrey E

    2016-06-23

    Fertilization is an essential biological process in sexual reproduction and comprises a series of molecular interactions between the sperm and egg. The fusion of the haploid spermatozoon and oocyte is the culminating event in mammalian fertilization, enabling the creation of a new, genetically distinct diploid organism. The merger of two gametes is achieved through a two-step mechanism in which the sperm protein IZUMO1 on the equatorial segment of the acrosome-reacted sperm recognizes its receptor, JUNO, on the egg surface. This recognition is followed by the fusion of the two plasma membranes. IZUMO1 and JUNO proteins are indispensable for fertilization, as constitutive knockdown of either protein results in mice that are healthy but infertile. Despite their central importance in reproductive medicine, the molecular architectures of these proteins and the details of their functional roles in fertilization are not known. Here we present the crystal structures of human IZUMO1 and JUNO in unbound and bound conformations. The human IZUMO1 structure exhibits a distinct boomerang shape and provides structural insights into the IZUMO family of proteins. Human IZUMO1 forms a high-affinity complex with JUNO and undergoes a major conformational change within its N-terminal domain upon binding to the egg-surface receptor. Our results provide insights into the molecular basis of sperm-egg recognition, cross-species fertilization, and the barrier to polyspermy, thereby promising benefits for the rational development of non-hormonal contraceptives and fertility treatments for humans and other mammals.

  20. Large-Scale CO Maps of the Lupus Molecular Cloud Complex

    CERN Document Server

    Tothill, N F H; Parshley, S C; Stark, A A; Lane, A P; Harnett, J I; Wright, G A; Walker, C K; Bourke, T L; Myers, P C

    2009-01-01

    Fully sampled degree-scale maps of the 13CO 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 13CO emission are roughly consistent with most previous estimates, while the line widths are higher, around 2 km/s. 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 B228 ridge in Lupus I, and a coherent velocity gradient across the ridge, are consistent with interaction between the molecular cloud and an expanding HI 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 ...

  1. 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.

  2. Understanding the complex etiologies of developmental disorders: behavioral and molecular genetic approaches.

    Science.gov (United States)

    Willcutt, Erik G; Pennington, Bruce F; Duncan, Laramie; Smith, Shelley D; Keenan, Janice M; Wadsworth, Sally; Defries, John C; Olson, Richard K

    2010-09-01

    This article has 2 primary goals. First, a brief tutorial on behavioral and molecular genetic methods is provided for readers without extensive training in these areas. To illustrate the application of these approaches to developmental disorders, etiologically informative studies of reading disability (RD), math disability (MD), and attention-deficit hyperactivity disorder (ADHD) are then reviewed. Implications of the results for these specific disorders and for developmental disabilities as a whole are discussed, and novel directions for future research are highlighted. Previous family and twin studies of RD, MD, and ADHD are reviewed systematically, and the extensive molecular genetic literatures on each disorder are summarized. To illustrate 4 novel extensions of these etiologically informative approaches, new data are presented from the Colorado Learning Disabilities Research Center, an ongoing twin study of the etiology of RD, ADHD, MD, and related disorders. RD, MD, and ADHD are familial and heritable, and co-occur more frequently than expected by chance. Molecular genetic studies suggest that all 3 disorders have complex etiologies, with multiple genetic and environmental risk factors each contributing to overall risk for each disorder. Neuropsychological analyses indicate that the 3 disorders are each associated with multiple neuropsychological weaknesses, and initial evidence suggests that comorbidity between the 3 disorders is due to common genetic risk factors that lead to slow processing speed.

  3. Differential proteomic profiling unveils new molecular mechanisms associated with mitochondrial complex III deficiency.

    Science.gov (United States)

    Marín-Buera, Lorena; García-Bartolomé, Alberto; Morán, María; López-Bernardo, Elia; Cadenas, Susana; Hidalgo, Beatriz; Sánchez, Ricardo; Seneca, Sara; Arenas, Joaquín; Martín, Miguel A; Ugalde, Cristina

    2015-01-15

    We have analyzed the cellular pathways and metabolic adaptations that take place in primary skin fibroblasts from patients with mutations in BCS1L, a major genetic cause of mitochondrial complex III enzyme deficiency. Mutant fibroblasts exhibited low oxygen consumption rates and intracellular ATP levels, indicating that the main altered molecular event probably is a limited respiration-coupled ATP production through the OXPHOS system. Two-dimensional DIGE and MALDI-TOF/TOF mass spectrometry analyses unambiguously identified 39 proteins whose expression was significantly altered in complex III-deficient fibroblasts. Extensive statistical and cluster analyses revealed a protein profile characteristic for the BCS1L mutant fibroblasts that included alterations in energy metabolism, cell signaling and gene expression regulation, cytoskeleton formation and maintenance, and intracellular stress responses. The physiological validation of the predicted functional adaptations of human cultured fibroblasts to complex III deficiency confirmed the up-regulation of glycolytic enzyme activities and the accumulation of branched-chain among other amino acids, suggesting the activation of anaerobic glycolysis and cellular catabolic states, in particular protein catabolism, together with autophagy as adaptive responses to mitochondrial respiratory chain dysfunction and ATP deficiency. Our data point to an overall metabolic and genetic reprogramming that could contribute to explain the clinical manifestations of complex III deficiency in patients. Despite considerable knowledge about their genetic origins, the pathophysiological mechanisms that contribute to the clinical manifestations of mitochondrial disorders remain poorly understood. We have investigated the molecular pathways and metabolic adaptations that take place in primary skin fibroblasts from patients with mutations in the BCS1L gene, a primary cause of mitochondrial complex III enzyme deficiency. Two-dimensional DIGE

  4. 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

  5. Identification of low molecular weight nuclear complexes containing integrase during the early stages of HIV-1 infection.

    Science.gov (United States)

    Gérard, Annabelle; Soler, Nicolas; Ségéral, Emmanuel; Belshan, Michael; Emiliani, Stéphane

    2013-02-01

    HIV-1 replication requires integration of its reverse transcribed viral cDNA into a host cell chromosome. The DNA cutting and joining reactions associated to this key step are catalyzed by the viral protein integrase (IN). In infected cells, IN binds the viral cDNA, together with viral and cellular proteins, to form large nucleoprotein complexes. However, the dynamics of IN complexes formation is still poorly understood. Here, we characterized IN complexes during the early stages of T-lymphocyte infection. We found that following viral entry into the host cell, IN was rapidly targeted to proteasome-mediated degradation. Interactions between IN and cellular cofactors LEDGF/p75 and TNPO3 were detected as early as 6 h post-infection. Size exclusion chromatography of infected cell extracts revealed distinct IN complexes in vivo. While at 2 h post-infection the majority of IN eluted within a high molecular weight complex competent for integration (IN complex I), IN was also detected in a low molecular weight complex devoid of full-length viral cDNA (IN complex II, ~440 KDa). At 6 h post-infection the relative proportion of IN complex II increased. Inhibition of reverse transcription or integration did not alter the elution profile of IN complex II in infected cells. However, in cells depleted for LEDGF/p75 IN complex II shifted to a lower molecular weight complex (IN complex III, ~150 KDa) containing multimers of IN. Notably, cell fractionation experiments indicated that both IN complex II and III were exclusively nuclear. Finally, IN complex II was not detected in cells infected with a virus harboring a mutated IN defective for LEDGF/p75 interaction and tetramerization. Our findings indicate that, shortly after viral entry, a significant portion of DNA-free IN that is distinct from active pre-integration complexes accumulates in the nucleus.

  6. Identification of low molecular weight nuclear complexes containing integrase during the early stages of HIV-1 infection

    Directory of Open Access Journals (Sweden)

    Gérard Annabelle

    2013-02-01

    Full Text Available Abstract Background HIV-1 replication requires integration of its reverse transcribed viral cDNA into a host cell chromosome. The DNA cutting and joining reactions associated to this key step are catalyzed by the viral protein integrase (IN. In infected cells, IN binds the viral cDNA, together with viral and cellular proteins, to form large nucleoprotein complexes. However, the dynamics of IN complexes formation is still poorly understood. Results Here, we characterized IN complexes during the early stages of T-lymphocyte infection. We found that following viral entry into the host cell, IN was rapidly targeted to proteasome-mediated degradation. Interactions between IN and cellular cofactors LEDGF/p75 and TNPO3 were detected as early as 6 h post-infection. Size exclusion chromatography of infected cell extracts revealed distinct IN complexes in vivo. While at 2 h post-infection the majority of IN eluted within a high molecular weight complex competent for integration (IN complex I, IN was also detected in a low molecular weight complex devoid of full-length viral cDNA (IN complex II, ~440 KDa. At 6 h post-infection the relative proportion of IN complex II increased. Inhibition of reverse transcription or integration did not alter the elution profile of IN complex II in infected cells. However, in cells depleted for LEDGF/p75 IN complex II shifted to a lower molecular weight complex (IN complex III, ~150 KDa containing multimers of IN. Notably, cell fractionation experiments indicated that both IN complex II and III were exclusively nuclear. Finally, IN complex II was not detected in cells infected with a virus harboring a mutated IN defective for LEDGF/p75 interaction and tetramerization. Conclusions Our findings indicate that, shortly after viral entry, a significant portion of DNA–free IN that is distinct from active pre-integration complexes accumulates in the nucleus.

  7. Molecular typing of environmental Cryptococcus neoformans/C. gattii species complex isolates from Manaus, Amazonas, Brazil.

    Science.gov (United States)

    Alves, Gleica Soyan Barbosa; Freire, Ana Karla Lima; Bentes, Amaury Dos Santos; Pinheiro, José Felipe de Souza; de Souza, João Vicente Braga; Wanke, Bodo; Matsuura, Takeshi; Jackisch-Matsuura, Ani Beatriz

    2016-08-01

    Cryptococcus neoformans and Cryptococcus gattii are the main causative agents of cryptococcosis, a systemic fungal disease that affects internal organs and skin, and which is acquired by inhalation of spores or encapsulated yeasts. It is currently known that the C. neoformans/C. gattii species complex has a worldwide distribution, however, some molecular types seem to prevail in certain regions. Few environmental studies of Cryptococcus have been conducted in the Brazilian Amazon. This is the first ecological study of the pathogenic fungi C. neoformans/C. gattii species complex in the urban area of Manaus, Amazonas, Brazil. A total of 506 samples from pigeon droppings (n = 191), captive bird droppings (n = 60) and tree hollows (n = 255) were collected from June 2012 to January 2014 at schools and public buildings, squares, pet shops, households, the zoo and the bus station. Samples were plated on niger seed agar (NSA) medium supplemented with chloramphenicol and incubated at 25°C for 5 days. Dark-brown colonies were isolated and tested for thermotolerance at 37°C, cycloheximide resistance and growth on canavanine-glycine-bromothymol blue agar. Molecular typing was done by PCR-RFLP. Susceptibility to the antifungal drugs amphotericin B, fluconazole, itraconazole and ketoconazole was tested using Etest(®) strips. In total, 13 positive samples were obtained: one tree hollow (C. gattiiVGII), nine pigeon droppings (C. neoformansVNI) and three captive bird droppings (C. neoformansVNI). The environmental cryptococcal isolates found in this study were of the same molecular types as those responsible for infections in Manaus. © 2016 Blackwell Verlag GmbH.

  8. Spontaneous Binding of Molecular Oxygen at the Qo-Site of the bc1 Complex Could Stimulate Superoxide Formation

    DEFF Research Database (Denmark)

    Husen, Peter; Solov'yov, Ilia A

    2016-01-01

    to drive ATP synthesis. This molecular machinery, however, is suspected to be a source of superoxide, which is toxic to the cell, even in minuscular quantities, and believed to be a factor in aging. Through molecular dynamics simulations, we investigate here the migration of molecular oxygen in the bc1...... complex in order to identify possible reaction sites that could lead to superoxide formation. It is found, in particular, that oxygen penetrates spontaneously the Qo binding site of the bc1 complex in the presence of an intermediate semiquinone radical, thus making the Qo-site a strong candidate for being...... a center of superoxide production....

  9. Identification of neuronal and angiogenic growth factors in an in vitro blood-brain barrier model system: Relevance in barrier integrity and tight junction formation and complexity.

    Science.gov (United States)

    Freese, Christian; Hanada, Sanshiro; Fallier-Becker, Petra; Kirkpatrick, C James; Unger, Ronald E

    2017-05-01

    We previously demonstrated that the co-cultivation of endothelial cells with neural cells resulted in an improved integrity of the in vitro blood-brain barrier (BBB), and that this model could be useful to evaluate the transport properties of potential central nervous system disease drugs through the microvascular brain endothelial. In this study we have used real-time PCR, fluorescent microscopy, protein arrays and enzyme-linked immunosorbent assays to determine which neural- and endothelial cell-derived factors are produced in the co-culture and improve the integrity of the BBB. In addition, a further improvement of the BBB integrity was achieved by adjusting serum concentrations and growth factors or by the addition of brain pericytes. Under specific conditions expression of angiogenic, angiostatic and neurotrophic factors such as endostatin, pigment epithelium derived factor (PEDF/serpins-F1), tissue inhibitor of metalloproteinases (TIMP-1), and vascular endothelial cell growth factor (VEGF) closely mimicked the in vivo situation. Freeze-fracture analysis of these cultures demonstrated the quality and organization of the endothelial tight junction structures and their association to the two different lipidic leaflets of the membrane. Finally, a multi-cell culture model of the BBB with a transendothelial electrical resistance up to 371 (±15) Ω×cm(2) was developed, which may be useful for preliminary screening of drug transport across the BBB and to evaluate cellular crosstalk of cells involved in the neurovascular unit.

  10. Improved surface plasmon enhanced photodetection at an Au-GaAs Schottky junction using a novel molecular beam epitaxy grown Otto coupling structure

    Energy Technology Data Exchange (ETDEWEB)

    Daboo, C.; Baird, M.J.; Hughes, H.P. (PCS Group, Cavendish Lab., Cambridge (UK)); Apsley, N.; Emeny, M.T. (Royal Signals and Radar Establishment, Great Malvern (UK))

    1991-06-05

    Measurements of reflectivity and photocurrent as a function of angle of incidence and wavelength have been made for a GaAs-AlAs-GaAs-Au Schottky structure based on an Otto coupling geometry which allows incident p-polarized radiation to couple to the surface plasmon (SP) mode at the Au-GaAs interface. At resonance, E fields associated with the SP excitation are concentrated at the GaAs-Au Schottky interface itself, enabling strong enhancement of the internal photoemission photocurrent across the Schottky barrier. Enhancement factors of the order of 20 have been achieved. A direct comparison between the resonant effects of exciting the SP at the GaAs-Au Schottky junction itself and at the outer Au-air interface has been made. A simple model for the photocurrent in the device indicates that the excited photocarriers created in the gold film have a very short scattering length {delta}{approx equal}10 nm, which emphasizes the importance of exciting the SP at the Schottky interface. (orig.).

  11. The dynamical complexity of work-hardening: a large-scale molecular dynamics simulation

    Institute of Scientific and Technical Information of China (English)

    Markus J. Buehler; Alexander Hartmaier; Mark A. Duchaineau; Farid F. Abraham; Huajian Gao

    2005-01-01

    We analyze a large-scale molecular dynamics simulation of work hardening in a model system of a ductile solid.With tensile loading, we observe emission of thousands of dislocations from two sharp cracks. The dislocations interact in a complex way, revealing three fundamental mechanisms of work-hardening in this ductile material. These are (1) dislocation cutting processes, jog formation and generation of trails of point defects; (2) activation of secondary slip systems by Frank-Read and cross-slip mechanisms; and (3) formation of sessile dislocations such as Lomer-Cottrell locks.We report the discovery of a new class of point defects referred to as trail of partial point defects, which could play an important role in situations when partial dislocations dominate plasticity. Another important result of the present work is the rediscovery of the Fleischer-mechanism of cross-slip of partial dislocations that was theoretically proposed more than 50 years ago, and is now, for the first time, confirmed by atomistic simulation. On the typical time scale of molecular dynamics simulations, the dislocations self-organize into a complex sessile defect topology. Our analysis illustrates numerous mechanisms formerly only conjectured in textbooks and observed indirectly in experiments. It is the first time that such a rich set of fundamental phenomena have been revealed in a single computer simulation, and its dynamical evolution has been studied. The present study exemplifies the simulation and analysis of the complex nonlinear dynamics of a many-particle system during failure using ultra-large scale computing.

  12. 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

    2017-04-22

    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

  13. Pulsed supersonic molecular beam for characterization of chemically active metal-organic complexes at surfaces

    Science.gov (United States)

    Lear, Amanda M.

    Metal-organic coordination networks (MOCNs) at surfaces consist of a complex of organic ligands bound to an atomic metal center. The MOCNs, when chosen appropriately, can form highly-ordered arrays at surfaces. Ultra-high vacuum surface studies allow control of surface composition and provide 2D growth restrictions, which lead to under-coordinated metal centers. These systems provide an opportunity to tailor the chemical function of the metal centers due to the steric restrictions imposed by the surface. Tuning the adsorption/desorption energy at a metal center and developing a cooperative environment for catalysis are the key scientific questions that motivate the construction of a molecular beam surface analysis system. Characterization of the created systems can be performed utilizing a pulsed supersonic molecular beam (PSMB) in unison with a quadrupole mass spectrometer. A PSMB allows for the highly controlled delivery of reactants with well-defined energy to a given platform making it possible to elucidate detailed chemical tuning information. In this thesis, a summary of prior theoretical molecular beam derivations is provided. Design considerations and an overview of the construction procedure for the current molecular beam apparatus, including initial characterization experiments, are presented. By impinging an Ar beam on a Ag(111) surface, the location of the specular angle (˜65°) and rough sample perimeter coordinates were determined. Additionally, surface analysis experiments, mainly Auger Electron Spectroscopy (AES), were performed to investigate the oxidation of epitaxial graphene on the SiC(0001) surface utilizing an oxygen cracking method. The AES experiments are described in detail and highlight the challenges that were faced when several different graphene samples were used for the oxygen adsorption/desorption experiments.

  14. Studies on cluster, salt and molecular complex of zinc-quinolinate

    Indian Academy of Sciences (India)

    Prithiviraj Khakhlary; Jubaraj B Baruah

    2015-02-01

    Reactions of zinc halides with 8-hydroxyquinoline (hydroxQ) in equimolar ratio were carried out in different solvents. Respective solvates of tetranuclear clusters, namely [Zn4(oxyQ)6X2].(solvent)2, (when X=Cl, Solvent=dimethylformamide (1), dimethylacetamide (2) and dimethysulphoxide (3); X = Br, solvent = dimethylformamide (4), oxyQ=quinolinate anion) were obtained. Bond parameters of these isostructural clusteres 1–4 are compared from their single crystal structures. Anhydrous form of the cluster have porous packing and is thermally stable below 250° C. Surface area of the clusters 1 and 4 are 8.933 and 6.172 m2/g, respectively. Complexes 1 and 4 can be reversibly hydrated, which is reflected in colour changes. The reaction of zinc chloride with 8-hydroxyquinoline in equimolar ratio followed by crystallization from water gave salt (HhydroxQ)2 [ZnCl4] (5) and a similar reaction followed by crystallization from 3-methylpyridine (3mepy) resulted in the molecular complex [Zn(oxyQ)2(3mepy)]. [Zn(oxyQ)2(3mepy)2].3H2O (6). Complex 5 is formed from a hydrolytic equilibrium of water with zinc chloride yielding tetrachloro zinc anion and zinc hydroxide. Taking advantage of this reaction, a composite material of ZnO@complex 5 exhibiting dual fluorescence at 450 and 575 nm on excitation at 390 nm was prepared. Fluorescence emission properties of all the complexes in solid state are compared with fluorescence emission of the ligand

  15. 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.

  16. Phenol-benzene complexation dynamics: quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy.

    Science.gov (United States)

    Kwac, Kijeong; Lee, Chewook; Jung, Yousung; Han, Jaebeom; Kwak, Kyungwon; Zheng, Junrong; Fayer, M D; Cho, Minhaeng

    2006-12-28

    Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.

  17. Very stable high molecular mass multiprotein complex with DNase and amylase activities in human milk.

    Science.gov (United States)

    Soboleva, Svetlana E; Dmitrenok, Pavel S; Verkhovod, Timofey D; Buneva, Valentina N; Sedykh, Sergey E; Nevinsky, Georgy A

    2015-01-01

    For breastfed infants, human milk is more than a source of nutrients; it furnishes a wide array of proteins, peptides, antibodies, and other components promoting neonatal growth and protecting infants from viral and bacterial infection. It has been proposed that most biological processes are performed by protein complexes. Therefore, identification and characterization of human milk components including protein complexes is important for understanding the function of milk. Using gel filtration, we have purified a stable high molecular mass (~1000 kDa) multiprotein complex (SPC) from 15 preparations of human milk. Light scattering and gel filtration showed that the SPC was stable in the presence of high concentrations of NaCl and MgCl2 but dissociated efficiently under the conditions that destroy immunocomplexes (2 M MgCl2 , 0.5 M NaCl, and 10 mM DTT). Such a stable complex is unlikely to be a casual associate of different proteins. The relative content of the individual SPCs varied from 6% to 25% of the total milk protein. According to electrophoretic and mass spectrometry analysis, all 15 SPCs contained lactoferrin (LF) and α-lactalbumin as major proteins, whereas human milk albumin and β-casein were present in moderate or minor amounts; a different content of IgGs and sIgAs was observed. All SPCs efficiently hydrolyzed Plasmid supercoiled DNA and maltoheptaose. Some freshly prepared SPC preparations contained not only intact LF but also small amounts of its fragments, which appeared in all SPCs during their prolonged storage; the fragments, similar to intact LF, possessed DNase and amylase activities. LF is found in human epithelial secretions, barrier body fluids, and in the secondary granules of leukocytes. LF is a protein of the acute phase response and nonspecific defense against different types of microbial and viral infections. Therefore, LF complexes with other proteins may be important for its functions not only in human milk.

  18. MesoBioNano Explorer-A Universal Program for Multiscale Computer Simulations of Complex Molecular Structure and Dynamics

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Yakubovich, Alexander V.; Nikolaev, Pavel V.;

    2012-01-01

    We present a multipurpose computer code MesoBioNano Explorer (MBN Explorer). The package allows to model molecular systems of varied level of complexity. In particular, MBN Explorer is suited to compute system's energy, to optimize molecular structure as well as to consider the molecular and random...... walk dynamics. MBN Explorer allows to use a broad variety of interatomic potentials, to model different molecular systems, such as atomic clusters, fullerenes, nanotubes, polypeptides, proteins, DNA, composite systems, nanofractals, and so on. A distinct feature of the program, which makes...

  19. Maghemite (hematite) core (shell) nanorods via thermolysis of a molecular solid of Fe-complex.

    Science.gov (United States)

    Chaudhari, N S; Warule, S S; Muduli, S; Kale, B B; Jouen, S; Lefez, B; Hannoyer, B; Ogale, S B

    2011-08-21

    An Fe-metal complex with 2'-hydroxy chalcone (2'-HC) ligands [Fe(III) (2'-hydroxy chalcone)(3)] is synthesized by a chemical route and is subjected to different thermal treatments. Upon thermolysis in air at 450 °C for 3 h the complex yields maghemite (γ-Fe(2)O(3)) nanorods with a thin hematite (α-Fe(2)O(3)) shell. X-Ray diffraction (XRD), Mössbauer spectroscopy, diffuse reflectance spectroscopy (UV-DRS), high resolution transmission electron microscopy (HR-TEM), field emission scanning electron microscopy (FE-SEM) and vibrating sample magnetometry (VSM) are used to characterize the samples. The stability of the ligand and the Fe-complex is further examined by using thermogravimmetric/differential thermal analysis (TGA/DTA). We suggest a residual ligand controlled mechanism for the formation of an anisotropic nanostructure in a crumbling molecular solid undergoing ligand decomposition. Since the band gap of iron oxide is in the visible range, we explored the use of our core shell nano-rod sample for photocatalytic activity for H(2) generation by H(2)S splitting under solar light. We observed high photocatalytic activity for hydrogen generation (75 ml h(-1)). This journal is © The Royal Society of Chemistry 2011

  20. All-atom molecular dynamics simulation of a photosystem I/detergent complex

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Bradley J. [Univ. of Tennessee, Knoxville, TN (United States); Cheng, Xiaolin [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Frymier, Paul [Univ. of Tennessee, Knoxville, TN (United States)

    2014-09-18

    All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Moreover, we find that the docking of soluble electron mediators such as cytochrome c6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.

  1. Self-assembly of ball-shaped molecular complexes in water.

    Science.gov (United States)

    Grawe, Thomas; Schrader, Thomas; Zadmard, Reza; Kraft, Arno

    2002-05-31

    We present a simple and versatile access to spheroidal molecular assemblies with pronounced stability in highly polar solvents. These complexes are composed of doubly and triply charged complementary building blocks based on ammonium or amidinium cations and phosphonate anions. Their high thermodynamic stability is best explained by the formation of a cyclic array of alternating positive and negative charges interconnected by a regular network of hydrogen bonds. Association constants reach 10(6) M(-1) in methanol and often surpass 10(3) M(-1) in water. The broad range of binding energies correlates well with the varying degree of preorganization of both complex partners. As a byproduct of these investigations, new recognition motifs for histidine and arginine esters and the unsubstituted guanidinium ion are proposed. The additional introduction of methyl groups in the 2-, 4-, and 6-positions of the central benzene ring in either cations or anions causes a marked drop in the corresponding K(a) values of 1 order of magnitude; the related rotational barriers were estimated at 0.3-2.1 kcal/mol. Spontaneous formation of defined 2:1 complexes from three components has also been observed.

  2. Water oxidation with molecularly defined iridium complexes: insights into homogeneous versus heterogeneous catalysis.

    Science.gov (United States)

    Junge, Henrik; Marquet, Nicolas; Kammer, Anja; Denurra, Stefania; Bauer, Matthias; Wohlrab, Sebastian; Gärtner, Felix; Pohl, Marga-Martina; Spannenberg, Anke; Gladiali, Serafino; Beller, Matthias

    2012-10-01

    Molecularly defined Ir complexes and different samples of supported IrO(2) nanoparticles have been tested and compared in the catalytic water oxidation with cerium ammonium nitrate (CAN) as the oxidant. By comparing the activity of nano-scaled supported IrO(2) particles to the one of organometallic complexes it is shown that the overall activity of the homogeneous Ir precursors is defined by both the formation of the homogeneous active species and its conversion to Ir(IV)-oxo nanoparticles. In the first phase of the reaction the activity is dominated by the homogeneous active species. With increasing reaction time, the influence of nano-sized Ir-oxo particles becomes more evident. Notably, the different conversion rates of the homogeneous precursor into the active species as well as the conversion into Ir-oxo nanoparticles and the different particle sizes have a significant influence on the overall activity. In addition to the homogeneous systems, IrO(2)@MCM-41 has also been synthesized, which contains stabilized nanoparticles of between 1 and 3 nm in size. This latter system shows a similar activity to IrCl(3)⋅xH(2)O and complexes 4 and 5. Mechanistic insights were obtained by in situ X-ray absorption spectroscopy and scanning transmission electron microscopy.

  3. A CO Survey of the Most Extensive Translucent Molecular Cloud Complex, MBM 53-55

    Science.gov (United States)

    Aguti, E. D.; Dame, T. M.; Thaddeus, P.; Masheder, M. R. W.

    2004-12-01

    We present a new, sensitive CO J=1rightarrow 0 survey of the large translucent molecular cloud complex, MBM 53-55 using the CfA 1.2 m millimeter-wave telescope. A region extending from (l) = 84° to 97° and (b) = -44° to -30° was observed every 1/4 °--roughly every other beamwidth--to an rms noise of 0.15 K per 0.65 km s(-1) channel, for a total of 2968 spectra. Detected at velocities ranging from -15 to 0 km s(-1), CO is concentrated in an arc-shaped structure over 10° long. Comparison with HI data suggests that this complex coincides with the edge of an expanding HI shell, as previously noted by Gir, Blitz, & Magnani (1994). This complex is also seen in IRAS 100 μm observations. We derive an integrated mass of 1.3× 103 Msun assuming a distance of 150 pc (Welty et al 1989). An atomic mass of (3.3 × 103) Msun) was similarly derived from the HI emission integrated over the velocity range -15 to 0 km s(-1).

  4. Exploring molecular complexity with ALMA (EMoCA): Alkanethiols and alkanols in Sagittarius B2(N2)

    CERN Document Server

    Müller, H S P; Xu, L -H; Lees, R M; Garrod, R T; Walters, A; van Wijngaarden, J; Lewen, F; Schlemmer, S; Menten, K M

    2015-01-01

    Over the past five decades, radio astronomy has shown that molecular complexity is a natural outcome of interstellar chemistry, in particular in star forming regions. However, the pathways that lead to the formation of complex molecules are not completely understood and the depth of chemical complexity has not been entirely revealed. In addition, the sulfur chemistry in the dense interstellar medium is not well understood. We want to know the relative abundances of alkanethiols and alkanols in the Galactic Center source Sagittarius B2(N2), the northern hot molecular core in Sgr B2(N), whose relatively small line widths are favorable for studying the molecular complexity in space. We investigated spectroscopic parameter sets that were able to reproduce published laboratory rotational spectra of ethanethiol and studied effects that modify intensities in the predicted rotational spectrum of ethanol. We used the Atacama Large Millimeter Array (ALMA) in its Cycles~0 and 1 for a spectral line survey of Sagittarius ...

  5. Molecular identification of collagen 17a1 as a major genetic modifier of laminin gamma 2 mutation-induced junctional epidermolysis bullosa in mice.

    Directory of Open Access Journals (Sweden)

    Thomas J Sproule

    2014-02-01

    Full Text Available Epidermolysis Bullosa (EB encompasses a spectrum of mechanobullous disorders caused by rare mutations that result in structural weakening of the skin and mucous membranes. While gene mutated and types of mutations present are broadly predictive of the range of disease to be expected, a remarkable amount of phenotypic variability remains unaccounted for in all but the most deleterious cases. This unexplained variance raises the possibility of genetic modifier effects. We tested this hypothesis using a mouse model that recapitulates a non-Herlitz form of junctional EB (JEB owing to the hypomorphic jeb allele of laminin gamma 2 (Lamc2. By varying normally asymptomatic background genetics, we document the potent impact of genetic modifiers on the strength of dermal-epidermal adhesion and on the clinical severity of JEB in the context of the Lamc2(jeb mutation. Through an unbiased genetic approach involving a combination of QTL mapping and positional cloning, we demonstrate that Col17a1 is a strong genetic modifier of the non-Herlitz JEB that develops in Lamc2(jeb mice. This modifier is defined by variations in 1-3 neighboring amino acids in the non-collagenous 4 domain of the collagen XVII protein. These allelic variants alter the strength of dermal-epidermal adhesion in the context of the Lamc2(jeb mutation and, consequentially, broadly impact the clinical severity of JEB. Overall the results provide an explanation for how normally innocuous allelic variants can act epistatically with a disease causing mutation to impact the severity of a rare, heritable mechanobullous disorder.

  6. Molecular identification of collagen 17a1 as a major genetic modifier of laminin gamma 2 mutation-induced junctional epidermolysis bullosa in mice.

    Science.gov (United States)

    Sproule, Thomas J; Bubier, Jason A; Grandi, Fiorella C; Sun, Victor Z; Philip, Vivek M; McPhee, Caroline G; Adkins, Elisabeth B; Sundberg, John P; Roopenian, Derry C

    2014-02-01

    Epidermolysis Bullosa (EB) encompasses a spectrum of mechanobullous disorders caused by rare mutations that result in structural weakening of the skin and mucous membranes. While gene mutated and types of mutations present are broadly predictive of the range of disease to be expected, a remarkable amount of phenotypic variability remains unaccounted for in all but the most deleterious cases. This unexplained variance raises the possibility of genetic modifier effects. We tested this hypothesis using a mouse model that recapitulates a non-Herlitz form of junctional EB (JEB) owing to the hypomorphic jeb allele of laminin gamma 2 (Lamc2). By varying normally asymptomatic background genetics, we document the potent impact of genetic modifiers on the strength of dermal-epidermal adhesion and on the clinical severity of JEB in the context of the Lamc2(jeb) mutation. Through an unbiased genetic approach involving a combination of QTL mapping and positional cloning, we demonstrate that Col17a1 is a strong genetic modifier of the non-Herlitz JEB that develops in Lamc2(jeb) mice. This modifier is defined by variations in 1-3 neighboring amino acids in the non-collagenous 4 domain of the collagen XVII protein. These allelic variants alter the strength of dermal-epidermal adhesion in the context of the Lamc2(jeb) mutation and, consequentially, broadly impact the clinical severity of JEB. Overall the results provide an explanation for how normally innocuous allelic variants can act epistatically with a disease causing mutation to impact the severity of a rare, heritable mechanobullous disorder.

  7. 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 Cx31.

  8. 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 Cx31.

  9. F-Theory Description of 3-String Junction

    Institute of Scientific and Technical Information of China (English)

    YANGFu-Zhong

    2003-01-01

    The geometrical description of BPS 3-string junction in the F-theory background is given by lifting a string junction in lib into F-theory and constructing a holomorphic curve in K3 with respect to a special complex structure of K3. The holomorphic curve is fibration of 1-cycles of the elliptic fiber over the geodesic string junction. The F-theory picture in this paper provides a unifying description of both string and string junction, and is advantageous over their M-theory picture.

  10. F-Theory Description of 3-String Junction

    Institute of Scientific and Technical Information of China (English)

    YANG Fu-Zhong

    2003-01-01

    The geometrical description of BPS 3-string junction in the F-theory background is given by lifting a string junction in IIB into F-theory and constructing a holomorphic curve in K3 with respect to a special complex structure of K3. The holomorphic curve is fibration of 1-cycles of the elliptic fiber over the geodesic string junction. The F-theory picture in this paper provides a unifying description of both string and string junction, and is advantageous over their M-theory picture.

  11. 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

  12. 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

  13. 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

  14. Equivalent Josephson junctions

    Science.gov (United States)

    Boyadjiev, T. L.; Semerdjieva, E. G.; Shukrinov, Yu. M.

    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 adequate 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 flow. This fact may explain the improvement of the spectra of microwave radiation noted in the literature.

  15. The molecular evolution of four anti-malarial immune genes in the Anopheles gambiae species complex

    Directory of Open Access Journals (Sweden)

    Simard Frederic

    2008-03-01

    Full Text Available Abstract Background If the insect innate immune system is to be used as a potential blocking step in transmission of malaria, then it will require targeting one or a few genes with highest relevance and ease of manipulation. The problem is to identify and manipulate those of most importance to malaria infection without the risk of decreasing the mosquito's ability to stave off infections by microbes in general. Molecular evolution methodologies and concepts can help identify such genes. Within the setting of a comparative molecular population genetic and phylogenetic framework, involving six species of the Anopheles gambiae complex, we investigated whether a set of four pre-selected immunity genes (gambicin, NOS, Rel2 and FBN9 might have evolved under selection pressure imposed by the malaria parasite. Results We document varying levels of polymorphism within and divergence between the species, in all four genes. Introgression and the sharing of ancestral polymorphisms, two processes that have been documented in the past, were verified in this study in all four studied genes. These processes appear to affect each gene in different ways and to different degrees. However, there is no evidence of positive selection acting on these genes. Conclusion Considering the results presented here in concert with previous studies, genes that interact directly with the Plasmodium parasite, and play little or no role in defense against other microbes, are probably the most likely candidates for a specific adaptive response against P. falciparum. Furthermore, since it is hard to establish direct evidence linking the adaptation of any candidate gene to P. falciparum infection, a comparative framework allowing at least an indirect link should be provided. Such a framework could be achieved, if a similar approach like the one involved here, was applied to all other anopheline complexes that transmit P. falciparum malaria.

  16. Structure-Property Relationships in Atomic-Scale Junctions: Histograms and Beyond.

    Science.gov (United States)

    Hybertsen, Mark S; Venkataraman, Latha

    2016-03-15

    Over the past 10 years, there has been tremendous progress in the measurement, modeling and understanding of structure-function relationships in single molecule junctions. Numerous research groups have addressed significant scientific questions, directed both to conductance phenomena at the single molecule level and to the fundamental chemistry that controls junction functionality. Many different functionalities have been demonstrated, including single-molecule diodes, optically and mechanically activated switches, and, significantly, physical phenomena with no classical analogues, such as those based on quantum interference effects. Experimental techniques for reliable and reproducible single molecule junction formation and characterization have led to this progress. In particular, the scanning tunneling microscope based break-junction (STM-BJ) technique has enabled rapid, sequential measurement of large numbers of nanoscale junctions allowing a statistical analysis to readily distinguish reproducible characteristics. Harnessing fundamental link chemistry has provided the necessary chemical control over junction formation, enabling measurements that revealed clear relationships between molecular structure and conductance characteristics. Such link groups (amines, methylsuflides, pyridines, etc.) maintain a stable lone pair configuration that selectively bonds to specific, undercoordinated transition metal atoms available following rupture of a metal point contact in the STM-BJ experiments. This basic chemical principle rationalizes the observation of highly reproducible conductance signatures. Subsequently, the method has been extended to probe a variety of physical phenomena ranging from basic I-V characteristics to more complex properties such as thermopower and electrochemical response. By adapting the technique to a conducting cantilever atomic force microscope (AFM-BJ), simultaneous measurement of the mechanical characteristics of nanoscale junctions as they

  17. Evolution of a single gene highlights the complexity underlying molecular descriptions of fitness

    Science.gov (United States)

    Peña, Matthew I.; Van Itallie, Elizabeth; Bennett, Matthew R.; Shamoo, Yousif

    2010-06-01

    Evolution by natural selection is the driving force behind the endless variation we see in nature, yet our understanding of how changes at the molecular level give rise to different phenotypes and altered fitness at the population level remains inadequate. The reproductive fitness of an organism is the most basic metric that describes the chance that an organism will succeed or fail in its environment and it depends upon a complex network of inter- and intramolecular interactions. A deeper understanding of the quantitative relationships relating molecular evolution to adaptation, and consequently fitness, can guide our understanding of important issues in biomedicine such as drug resistance and the engineering of new organisms with applications to biotechnology. We have developed the "weak link" approach to determine how changes in molecular structure and function can relate to fitness and evolutionary outcomes. By replacing adenylate kinase (AK), an essential gene, in a thermophile with a homologous AK from a mesophile we have created a maladapted weak link that produces a temperature-sensitive phenotype. The recombinant strain adapts to nonpermissive temperatures through point mutations to the weak link that increase both stability and activity of the enzyme AK at higher temperatures. Here, we propose a fitness function relating enzyme activity to growth rate and use it to create a dynamic model of a population of bacterial cells. Using metabolic control analysis we show that the growth rate exhibits thresholdlike behavior, saturating at high enzyme activity as other reactions in the energy metabolism pathway become rate limiting. The dynamic model accurately recapitulates observed evolutionary outcomes. These findings suggest that in vitro enzyme kinetic data, in combination with metabolic network analysis, can be used to create fitness functions and dynamic models of evolution within simple metabolic systems.

  18. Multiscale molecular dynamics simulations of lipid interactions with P-glycoprotein in a complex membrane.

    Science.gov (United States)

    Domicevica, Laura; Koldsø, Heidi; Biggin, Philip C

    2017-09-02

    P-glycoprotein (P-gp) can transport a wide range of very different hydrophobic organic molecules across the membrane. Its ability to extrude molecules from the cell creates delivery problems for drugs that target proteins in the central nervous system (CNS) and also causes drug-resistance in many forms of cancer. Whether a drug will be susceptible to export by P-gp is difficult to predict and currently this is usually assessed with empirical and/or animal models. Thus, there is a need to better understand how P-gp works at the molecular level in order to fulfil the 3Rs: Refinement, reduction and replacement of animals in research. As structural information increasingly becomes available, our understanding at the molecular level improves. Proteins like P-gp are however very dynamic entities and thus one of the most appropriate ways to study them is with molecular dynamics simulations, especially as this can capture the influence of the surrounding environment. Recent parameterization developments have meant that it is now possible to simulate lipid bilayers that more closely resemble in vivo membranes in terms of their composition. In this report we construct a complex lipid bilayer that mimics the composition of brain epithelial cells and examine the interactions of it with P-gp. We find that the negatively charged phosphatidylserine lipids in the inner leaflet of the membrane tend to form an annulus around P-gp. We also observed the interaction of cholesterol with three distinct areas of the P-gp. Potential of mean force (PMF) calculations suggest that a crevice between transmembrane helices 10 and 12 has particularly favourable interaction energy for cholesterol. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  19. Molecular dynamics simulations of the cardiac troponin complex performed with FRET distances as restraints.

    Directory of Open Access Journals (Sweden)

    Jayant James Jayasundar

    Full Text Available Cardiac troponin (cTn is the Ca(2+-sensitive molecular switch that controls cardiac muscle activation and relaxation. However, the molecular detail of the switching mechanism and how the Ca(2+ signal received at cardiac troponin C (cTnC is communicated to cardiac troponin I (cTnI are still elusive. To unravel the structural details of troponin switching, we performed ensemble Förster resonance energy transfer (FRET measurements and molecular dynamic (MD simulations of the cardiac troponin core domain complex. The distance distributions of forty five inter-residue pairs were obtained under Ca(2+-free and saturating Ca(2+ conditions from time-resolved FRET measurements. These distances were incorporated as restraints during the MD simulations of the cardiac troponin core domain. Compared to the Ca(2+-saturated structure, the absence of regulatory Ca(2+ perturbed the cTnC N-domain hydrophobic pocket which assumed a closed conformation. This event partially unfolded the cTnI regulatory region/switch. The absence of Ca(2+, induced flexibility to the D/E linker and the cTnI inhibitory region, and rotated the cTnC N-domain with respect to rest of the troponin core domain. In the presence of saturating Ca(2+ the above said phenomenon were absent. We postulate that the secondary structure perturbations experienced by the cTnI regulatory region held within the cTnC N-domain hydrophobic pocket, coupled with the rotation of the cTnC N-domain would control the cTnI mobile domain interaction with actin. Concomitantly the rotation of the cTnC N-domain and perturbation of the D/E linker rigidity would control the cTnI inhibitory region interaction with actin to effect muscle relaxation.

  20. 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.